Ljung, Karin - Root Development and Shoot-Root Communication

@article{kokla_long-distance_2025,
	title = {A long-distance inhibitory system regulates haustoria numbers in parasitic plants},
	volume = {122},
	url = {https://www.pnas.org/doi/10.1073/pnas.2424557122},
	doi = {10.1073/pnas.2424557122},
	abstract = {The ability of parasitic plants to withdraw nutrients from their hosts depends on the formation of an infective structure known as the haustorium. How parasites regulate their haustoria numbers is poorly understood, and here, we uncovered that existing haustoria in the facultative parasitic plants Phtheirospermum japonicum and Parentucellia viscosa suppressed the formation of new haustoria located on distant roots. Using Phtheirospermum, we found that this effect depended on the formation of mature haustoria and could be induced through the application of external nutrients. To understand the molecular basis of this root plasticity, we analyzed hormone response and found that existing infections upregulated cytokinin-responsive genes first at the haustoria and then more distantly in Phtheirospermum shoots. We observed that infections increased endogenous cytokinin levels in Phtheirospermum roots and shoots, and this increase appeared relevant since local treatments with exogenous cytokinins blocked the formation of both locally and distantly formed haustoria. In addition, local overexpression of a cytokinin-degrading enzyme in Phtheirospermum prevented this systemic interhaustoria repression and increased haustoria numbers locally. We propose that a long-distance signal produced by haustoria negatively regulates future haustoria, and in Phtheirospermum, such a signaling system is mediated by a local increase in cytokinin to regulate haustoria numbers and balance nutrient acquisition.},
	number = {8},
	urldate = {2025-02-21},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Kokla, Anna and Leso, Martina and Šimura, Jan and Wärdig, Cecilia and Hayashi, Marina and Nishii, Naoshi and Tsuchiya, Yuichiro and Ljung, Karin and Melnyk, Charles W.},
	month = feb,
	year = {2025},
	note = {Publisher: Proceedings of the National Academy of Sciences},
	pages = {e2424557122},
}

The ability of parasitic plants to withdraw nutrients from their hosts depends on the formation of an infective structure known as the haustorium. How parasites regulate their haustoria numbers is poorly understood, and here, we uncovered that existing haustoria in the facultative parasitic plants Phtheirospermum japonicum and Parentucellia viscosa suppressed the formation of new haustoria located on distant roots. Using Phtheirospermum, we found that this effect depended on the formation of mature haustoria and could be induced through the application of external nutrients. To understand the molecular basis of this root plasticity, we analyzed hormone response and found that existing infections upregulated cytokinin-responsive genes first at the haustoria and then more distantly in Phtheirospermum shoots. We observed that infections increased endogenous cytokinin levels in Phtheirospermum roots and shoots, and this increase appeared relevant since local treatments with exogenous cytokinins blocked the formation of both locally and distantly formed haustoria. In addition, local overexpression of a cytokinin-degrading enzyme in Phtheirospermum prevented this systemic interhaustoria repression and increased haustoria numbers locally. We propose that a long-distance signal produced by haustoria negatively regulates future haustoria, and in Phtheirospermum, such a signaling system is mediated by a local increase in cytokinin to regulate haustoria numbers and balance nutrient acquisition.

@article{casanova-saez_suitable_2025,
	title = {A suitable strategy to find {IAA} metabolism mutants},
	volume = {177},
	copyright = {© 2025 The Author(s). Physiologia Plantarum published by John Wiley \& Sons Ltd on behalf of Scandinavian Plant Physiology Society.},
	issn = {1399-3054},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/ppl.70166},
	doi = {10.1111/ppl.70166},
	abstract = {Indole-3-acetic acid (IAA), the most common form of auxin, is involved in a great range of plant physiological processes. IAA is synthesized from the amino acid tryptophan and can be transported and inactivated in a myriad of ways. Despite intense research efforts, there are still dark corners in our comprehension of IAA metabolism and its interplays with other pathways. Genetic screens are a powerful tool for unbiasedly looking for new players in a given biological process. However, pleiotropism of auxin-related phenotypes and indirect effects make it necessary to incorporate additional screening steps to specifically find mutants affected in IAA homeostasis. We previously developed and validated a high-throughput methodology to simultaneously quantify IAA, key precursors, and inactive forms from as little as 10 mg of fresh tissue. We have carried out a genetic screening to identify mutants involved in IAA metabolism. Auxin reporters DR5pro:VENUS and 35Spro:DII-VENUS were EMS-mutagenized and subjected to a parallel morphological and reporter-signal pre-screen. We then obtained the auxin metabolite profile of 325 M3 selected lines and used multivariate data analysis to identify potential IAA-metabolism mutants. To test the screening design, we identified the causal mutations in three of the candidate lines by mapping-by-sequencing: dii365.3, dii571.1 and dr693. These carry new alleles of CYP83A1, MIAO, and SUPERROOT2, respectively, all of which have been previously involved in auxin homeostasis. Our results support the suitability of this approach to find new genes involved in IAA metabolism.},
	language = {en},
	number = {2},
	urldate = {2025-04-04},
	journal = {Physiologia Plantarum},
	author = {Casanova-Sáez, Rubén and Pěnčík, Aleš and Muñoz-Viana, Rafael and Brunoni, Federica and Pinto, Rui and Novák, Ondřej and Ljung, Karin and Mateo-Bonmatí, Eduardo},
	year = {2025},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/ppl.70166},
	pages = {e70166},
}

Indole-3-acetic acid (IAA), the most common form of auxin, is involved in a great range of plant physiological processes. IAA is synthesized from the amino acid tryptophan and can be transported and inactivated in a myriad of ways. Despite intense research efforts, there are still dark corners in our comprehension of IAA metabolism and its interplays with other pathways. Genetic screens are a powerful tool for unbiasedly looking for new players in a given biological process. However, pleiotropism of auxin-related phenotypes and indirect effects make it necessary to incorporate additional screening steps to specifically find mutants affected in IAA homeostasis. We previously developed and validated a high-throughput methodology to simultaneously quantify IAA, key precursors, and inactive forms from as little as 10 mg of fresh tissue. We have carried out a genetic screening to identify mutants involved in IAA metabolism. Auxin reporters DR5pro:VENUS and 35Spro:DII-VENUS were EMS-mutagenized and subjected to a parallel morphological and reporter-signal pre-screen. We then obtained the auxin metabolite profile of 325 M3 selected lines and used multivariate data analysis to identify potential IAA-metabolism mutants. To test the screening design, we identified the causal mutations in three of the candidate lines by mapping-by-sequencing: dii365.3, dii571.1 and dr693. These carry new alleles of CYP83A1, MIAO, and SUPERROOT2, respectively, all of which have been previously involved in auxin homeostasis. Our results support the suitability of this approach to find new genes involved in IAA metabolism.

@article{xiao_protein_2025,
	title = {The protein kinases {KIPK} and {KIPK}-{LIKE1} suppress overbending during negative hypocotyl gravitropic growth in {Arabidopsis}},
	volume = {37},
	issn = {1040-4651},
	url = {https://doi.org/10.1093/plcell/koaf056},
	doi = {10.1093/plcell/koaf056},
	abstract = {Plants use environmental cues to orient organ and plant growth, such as the direction of gravity or the direction, quantity, and quality of light. During the germination of Arabidopsis thaliana seeds in soil, negative gravitropism responses direct hypocotyl elongation such that the seedling can reach the light for photosynthesis and autotrophic growth. Similarly, hypocotyl elongation in the soil also requires mechanisms to efficiently grow around obstacles such as soil particles. Here, we identify KIPK (KINESIN-LIKE CALMODULIN-BINDING PROTEIN-INTERACTING PROTEIN KINASE) and the paralogous KIPKL1 (KIPK-LIKE1) as genetically redundant regulators of gravitropic hypocotyl bending. Moreover, we demonstrate that the homologous KIPKL2 (KIPK-LIKE2), which shows strong sequence similarity, must be functionally distinct. KIPK and KIPKL1 are polarly localized plasma membrane-associated proteins that can activate PIN-FORMED auxin transporters. KIPK and KIPKL1 are required to efficiently align hypocotyl growth with the gravity vector when seedling hypocotyls are grown on media plates or in soil, where contact with soil particles and obstacle avoidance impede direct negative gravitropic growth. Therefore, the polar KIPK and KIPKL1 kinases have different biological functions from the related AGC1 family kinases D6PK (D6 PROTEIN KINASE) or PAX (PROTEIN KINASE ASSOCIATED WITH BRX).},
	number = {4},
	urldate = {2025-04-25},
	journal = {The Plant Cell},
	author = {Xiao, Yao and Zourelidou, Melina and Bassukas, Alkistis E Lanassa and Weller, Benjamin and Janacek, Dorina P and Šimura, Jan and Ljung, Karin and Hammes, Ulrich Z and Li, Jia and Schwechheimer, Claus},
	month = apr,
	year = {2025},
	pages = {koaf056},
}

Plants use environmental cues to orient organ and plant growth, such as the direction of gravity or the direction, quantity, and quality of light. During the germination of Arabidopsis thaliana seeds in soil, negative gravitropism responses direct hypocotyl elongation such that the seedling can reach the light for photosynthesis and autotrophic growth. Similarly, hypocotyl elongation in the soil also requires mechanisms to efficiently grow around obstacles such as soil particles. Here, we identify KIPK (KINESIN-LIKE CALMODULIN-BINDING PROTEIN-INTERACTING PROTEIN KINASE) and the paralogous KIPKL1 (KIPK-LIKE1) as genetically redundant regulators of gravitropic hypocotyl bending. Moreover, we demonstrate that the homologous KIPKL2 (KIPK-LIKE2), which shows strong sequence similarity, must be functionally distinct. KIPK and KIPKL1 are polarly localized plasma membrane-associated proteins that can activate PIN-FORMED auxin transporters. KIPK and KIPKL1 are required to efficiently align hypocotyl growth with the gravity vector when seedling hypocotyls are grown on media plates or in soil, where contact with soil particles and obstacle avoidance impede direct negative gravitropic growth. Therefore, the polar KIPK and KIPKL1 kinases have different biological functions from the related AGC1 family kinases D6PK (D6 PROTEIN KINASE) or PAX (PROTEIN KINASE ASSOCIATED WITH BRX).

@article{mishra_adventitious_2024,
	title = {Adventitious rooting in response to long-term cold: a possible mechanism of clonal growth in alpine perennials},
	volume = {15},
	issn = {1664-462X},
	shorttitle = {Adventitious rooting in response to long-term cold},
	url = {https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2024.1352830/full},
	doi = {10.3389/fpls.2024.1352830},
	abstract = {{\textless}p{\textgreater}Arctic alpine species experience extended periods of cold and unpredictable conditions during flowering. Thus, often, alpine plants use both sexual and asexual means of reproduction to maximize fitness and ensure reproductive success. We used the arctic alpine perennial {\textless}italic{\textgreater}Arabis alpina{\textless}/italic{\textgreater} to explore the role of prolonged cold exposure on adventitious rooting. We exposed plants to 4°C for different durations and scored the presence of adventitious roots on the main stem and axillary branches. Our physiological studies demonstrated the presence of adventitious roots after 21 weeks at 4°C saturating the effect of cold on this process. Notably, adventitious roots on the main stem developing in specific internodes allowed us to identify the gene regulatory network involved in the formation of adventitious roots in cold using transcriptomics. These data and histological studies indicated that adventitious roots in {\textless}italic{\textgreater}A. alpina{\textless}/italic{\textgreater} stems initiate during cold exposure and emerge after plants experience growth promoting conditions. While the initiation of adventitious root was not associated with changes of {\textless}italic{\textgreater}DR5{\textless}/italic{\textgreater} auxin response and free endogenous auxin level in the stems, the emergence of the adventitious root primordia was. Using the transcriptomic data, we discerned the sequential hormone responses occurring in various stages of adventitious root formation and identified supplementary pathways putatively involved in adventitious root emergence, such as glucosinolate metabolism. Together, our results highlight the role of low temperature during clonal growth in alpine plants and provide insights on the molecular mechanisms involved at distinct stages of adventitious rooting.{\textless}/p{\textgreater}},
	language = {English},
	urldate = {2024-05-03},
	journal = {Frontiers in Plant Science},
	author = {Mishra, Priyanka and Roggen, Adrian and Ljung, Karin and Albani, Maria C. and Vayssières, Alice},
	month = apr,
	year = {2024},
	note = {Publisher: Frontiers},
	keywords = {Adventitious root, Arabis alpina, Clonal propagation, Transcriptome, alpine, extended cold exposure, phytohormones},
}

\textlessp\textgreaterArctic alpine species experience extended periods of cold and unpredictable conditions during flowering. Thus, often, alpine plants use both sexual and asexual means of reproduction to maximize fitness and ensure reproductive success. We used the arctic alpine perennial \textlessitalic\textgreaterArabis alpina\textless/italic\textgreater to explore the role of prolonged cold exposure on adventitious rooting. We exposed plants to 4°C for different durations and scored the presence of adventitious roots on the main stem and axillary branches. Our physiological studies demonstrated the presence of adventitious roots after 21 weeks at 4°C saturating the effect of cold on this process. Notably, adventitious roots on the main stem developing in specific internodes allowed us to identify the gene regulatory network involved in the formation of adventitious roots in cold using transcriptomics. These data and histological studies indicated that adventitious roots in \textlessitalic\textgreaterA. alpina\textless/italic\textgreater stems initiate during cold exposure and emerge after plants experience growth promoting conditions. While the initiation of adventitious root was not associated with changes of \textlessitalic\textgreaterDR5\textless/italic\textgreater auxin response and free endogenous auxin level in the stems, the emergence of the adventitious root primordia was. Using the transcriptomic data, we discerned the sequential hormone responses occurring in various stages of adventitious root formation and identified supplementary pathways putatively involved in adventitious root emergence, such as glucosinolate metabolism. Together, our results highlight the role of low temperature during clonal growth in alpine plants and provide insights on the molecular mechanisms involved at distinct stages of adventitious rooting.\textless/p\textgreater

@article{blume-werry_situ_2024,
	title = {In situ seasonal patterns of root auxin concentrations and meristem length in an arctic sedge},
	copyright = {© 2024 The Authors. New Phytologist © 2024 New Phytologist Foundation},
	issn = {1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/nph.19616},
	doi = {10.1111/nph.19616},
	abstract = {Seasonal dynamics of root growth play an important role in large-scale ecosystem processes; they are largely governed by growth regulatory compounds and influenced by environmental conditions. Yet, our knowledge about physiological drivers of root growth is mostly limited to laboratory-based studies on model plant species. We sampled root tips of Eriophorum vaginatum and analyzed their auxin concentrations and meristem lengths biweekly over a growing season in situ in a subarctic peatland, both in surface soil and at the permafrost thawfront. Auxin concentrations were almost five times higher in surface than in thawfront soils and increased over the season, especially at the thawfront. Surprisingly, meristem length showed an opposite pattern and was almost double in thawfront compared with surface soils. Meristem length increased from peak to late season in the surface soils but decreased at the thawfront. Our study of in situ seasonal dynamics in root physiological parameters illustrates the potential for physiological methods to be applied in ecological studies and emphasizes the importance of in situ measurements. The strong effect of root location and the unexpected opposite patterns of meristem length and auxin concentrations likely show that auxin actively governs root growth to ensure a high potential for nutrient uptake at the thawfront.},
	language = {en},
	urldate = {2024-02-23},
	journal = {New Phytologist},
	author = {Blume-Werry, Gesche and Semenchuk, Philipp and Ljung, Karin and Milbau, Ann and Novak, Ondrej and Olofsson, Johan and Brunoni, Federica},
	month = feb,
	year = {2024},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/nph.19616},
	keywords = {Eriophorum vaginatum, auxin, meristem length, permafrost, root growth, root phenology},
}

Seasonal dynamics of root growth play an important role in large-scale ecosystem processes; they are largely governed by growth regulatory compounds and influenced by environmental conditions. Yet, our knowledge about physiological drivers of root growth is mostly limited to laboratory-based studies on model plant species. We sampled root tips of Eriophorum vaginatum and analyzed their auxin concentrations and meristem lengths biweekly over a growing season in situ in a subarctic peatland, both in surface soil and at the permafrost thawfront. Auxin concentrations were almost five times higher in surface than in thawfront soils and increased over the season, especially at the thawfront. Surprisingly, meristem length showed an opposite pattern and was almost double in thawfront compared with surface soils. Meristem length increased from peak to late season in the surface soils but decreased at the thawfront. Our study of in situ seasonal dynamics in root physiological parameters illustrates the potential for physiological methods to be applied in ecological studies and emphasizes the importance of in situ measurements. The strong effect of root location and the unexpected opposite patterns of meristem length and auxin concentrations likely show that auxin actively governs root growth to ensure a high potential for nutrient uptake at the thawfront.

@article{karady_profiling_2024,
	title = {Profiling of 1-aminocyclopropane-1-carboxylic acid and selected phytohormones in {Arabidopsis} using liquid chromatography-tandem mass spectrometry},
	volume = {20},
	issn = {1746-4811},
	url = {https://doi.org/10.1186/s13007-024-01165-8},
	doi = {10.1186/s13007-024-01165-8},
	abstract = {Gaseous phytohormone ethylene levels are directly influenced by the production of its immediate non-volatile precursor 1-aminocyclopropane-1-carboxylic acid (ACC). Owing to the strongly acidic character of the ACC molecule, its quantification has been difficult to perform. Here, we present a simple and straightforward validated method for accurate quantification of not only ACC levels, but also major members of other important phytohormonal classes – auxins, cytokinins, jasmonic acid, abscisic acid and salicylic acid from the same biological sample.},
	number = {1},
	urldate = {2024-03-22},
	journal = {Plant Methods},
	author = {Karady, Michal and Hladík, Pavel and Cermanová, Kateřina and Jiroutová, Petra and Antoniadi, Ioanna and Casanova-Sáez, Rubén and Ljung, Karin and Novák, Ondřej},
	month = mar,
	year = {2024},
	keywords = {1-aminocyclopropane-1-carboxylic acid, ACC, Abscisic acid, Arabidopsis, Auxin, Cytokinin, Ethylene, Jasmonic acid, Liquid chromatography, Mass spectrometry, Plant hormones, Salicylic acid},
	pages = {41},
}

Gaseous phytohormone ethylene levels are directly influenced by the production of its immediate non-volatile precursor 1-aminocyclopropane-1-carboxylic acid (ACC). Owing to the strongly acidic character of the ACC molecule, its quantification has been difficult to perform. Here, we present a simple and straightforward validated method for accurate quantification of not only ACC levels, but also major members of other important phytohormonal classes – auxins, cytokinins, jasmonic acid, abscisic acid and salicylic acid from the same biological sample.

@article{el_arbi_arabidopsis_2024,
	title = {The {Arabidopsis} splicing factor {PORCUPINE}/{SmE1} orchestrates temperature-dependent root development via auxin homeostasis maintenance},
	volume = {244},
	copyright = {© 2024 The Author(s). New Phytologist © 2024 New Phytologist Foundation.},
	issn = {1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/nph.20153},
	doi = {10.1111/nph.20153},
	abstract = {Appropriate abiotic stress response is pivotal for plant survival and makes use of multiple signaling molecules and phytohormones to achieve specific and fast molecular adjustments. A multitude of studies has highlighted the role of alternative splicing in response to abiotic stress, including temperature, emphasizing the role of transcriptional regulation for stress response. Here we investigated the role of the core-splicing factor PORCUPINE (PCP) on temperature-dependent root development. We used marker lines and transcriptomic analyses to study the expression profiles of meristematic regulators and mitotic markers, and chemical treatments, as well as root hormone profiling to assess the effect of auxin signaling. The loss of PCP significantly alters RAM architecture in a temperature-dependent manner. Our results indicate that PCP modulates the expression of central meristematic regulators and is required to maintain appropriate levels of auxin in the RAM. We conclude that alternative pre-mRNA splicing is sensitive to moderate temperature fluctuations and contributes to root meristem maintenance, possibly through the regulation of phytohormone homeostasis and meristematic activity.},
	language = {en},
	number = {4},
	urldate = {2024-10-25},
	journal = {New Phytologist},
	author = {El Arbi, Nabila and Nardeli, Sarah Muniz and Šimura, Jan and Ljung, Karin and Schmid, Markus},
	year = {2024},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/nph.20153},
	keywords = {Arabidopsis thaliana, SmE, alternative RNA splicing, auxin signaling, root apical meristem, root development, temperature signaling},
	pages = {1408--1421},
}

Appropriate abiotic stress response is pivotal for plant survival and makes use of multiple signaling molecules and phytohormones to achieve specific and fast molecular adjustments. A multitude of studies has highlighted the role of alternative splicing in response to abiotic stress, including temperature, emphasizing the role of transcriptional regulation for stress response. Here we investigated the role of the core-splicing factor PORCUPINE (PCP) on temperature-dependent root development. We used marker lines and transcriptomic analyses to study the expression profiles of meristematic regulators and mitotic markers, and chemical treatments, as well as root hormone profiling to assess the effect of auxin signaling. The loss of PCP significantly alters RAM architecture in a temperature-dependent manner. Our results indicate that PCP modulates the expression of central meristematic regulators and is required to maintain appropriate levels of auxin in the RAM. We conclude that alternative pre-mRNA splicing is sensitive to moderate temperature fluctuations and contributes to root meristem maintenance, possibly through the regulation of phytohormone homeostasis and meristematic activity.

@article{tognacca_unveiling_2024,
	title = {Unveiling {Molecular} {Signatures} in {Light}-{Induced} {Seed} {Germination}: {Insights} from {PIN3}, {PIN7}, and {AUX1} in {Arabidopsis} thaliana},
	volume = {13},
	copyright = {http://creativecommons.org/licenses/by/3.0/},
	issn = {2223-7747},
	shorttitle = {Unveiling {Molecular} {Signatures} in {Light}-{Induced} {Seed} {Germination}},
	url = {https://www.mdpi.com/2223-7747/13/3/408},
	doi = {10.3390/plants13030408},
	abstract = {Light provides seeds with information that is essential for the adjustment of their germination to the conditions that are most favorable for the successful establishment of the future seedling. The promotion of germination depends mainly on environmental factors, like temperature and light, as well as internal factors associated with the hormonal balance between gibberellins (GA) and abscisic acid (ABA), although other hormones such as auxins may act secondarily. While transcriptomic studies of light-germinating Arabidopsis thaliana seeds suggest that auxins and auxin transporters are necessary, there are still no functional studies connecting the activity of the auxin transporters in light-induced seed germination. In this study, we investigated the roles of two auxin efflux carrier (PIN3 and PIN7) proteins and one auxin influx (AUX1) carrier protein during Arabidopsis thaliana seed germination. By using next-generation sequencing (RNAseq), gene expression analyses, hormonal sensitivity assays, and the quantification of indole-3-acetic acid (IAA) levels, we assessed the functional roles of PIN3, PIN7, and AUX1 during light-induced seed germination. We showed that auxin levels are increased 24 h after a red-pulse (Rp). Additionally, we evaluated the germination responses of pin3, pin7, and aux1 mutant seeds and showed that PIN3, PIN7, and AUX1 auxin carriers are important players in the regulation of seed germination. By using gene expression analysis in water, fluridone (F), and ABA+F treated seeds, we confirmed that Rp-induced seed germination is associated with auxin transport, and ABA controls the function of PIN3, PIN7, and AUX1 during this process. Overall, our results highlight the relevant and positive role of auxin transporters in germinating the seeds of Arabidopsis thaliana.},
	language = {en},
	number = {3},
	urldate = {2024-02-16},
	journal = {Plants},
	author = {Tognacca, Rocío Soledad and Ljung, Karin and Botto, Javier Francisco},
	month = jan,
	year = {2024},
	note = {Number: 3
Publisher: Multidisciplinary Digital Publishing Institute},
	keywords = {\textit{Arabidopsis thaliana}, ABA, AUX1, PIN3, PIN7, auxin, hormonal crosstalk, molecular regulation, seed germination},
	pages = {408},
}

Light provides seeds with information that is essential for the adjustment of their germination to the conditions that are most favorable for the successful establishment of the future seedling. The promotion of germination depends mainly on environmental factors, like temperature and light, as well as internal factors associated with the hormonal balance between gibberellins (GA) and abscisic acid (ABA), although other hormones such as auxins may act secondarily. While transcriptomic studies of light-germinating Arabidopsis thaliana seeds suggest that auxins and auxin transporters are necessary, there are still no functional studies connecting the activity of the auxin transporters in light-induced seed germination. In this study, we investigated the roles of two auxin efflux carrier (PIN3 and PIN7) proteins and one auxin influx (AUX1) carrier protein during Arabidopsis thaliana seed germination. By using next-generation sequencing (RNAseq), gene expression analyses, hormonal sensitivity assays, and the quantification of indole-3-acetic acid (IAA) levels, we assessed the functional roles of PIN3, PIN7, and AUX1 during light-induced seed germination. We showed that auxin levels are increased 24 h after a red-pulse (Rp). Additionally, we evaluated the germination responses of pin3, pin7, and aux1 mutant seeds and showed that PIN3, PIN7, and AUX1 auxin carriers are important players in the regulation of seed germination. By using gene expression analysis in water, fluridone (F), and ABA+F treated seeds, we confirmed that Rp-induced seed germination is associated with auxin transport, and ABA controls the function of PIN3, PIN7, and AUX1 during this process. Overall, our results highlight the relevant and positive role of auxin transporters in germinating the seeds of Arabidopsis thaliana.

@article{dash_changes_2023,
	title = {Changes in cell wall composition due to a pectin biosynthesis enzyme {GAUT10} impact root growth},
	volume = {193},
	issn = {0032-0889},
	url = {https://doi.org/10.1093/plphys/kiad465},
	doi = {10.1093/plphys/kiad465},
	abstract = {Arabidopsis (Arabidopsis thaliana) root development is regulated by multiple dynamic growth cues that require central metabolism pathways such as β-oxidation and auxin. Loss of the pectin biosynthesizing enzyme GALACTURONOSYLTRANSFERASE 10 (GAUT10) leads to a short-root phenotype under sucrose-limited conditions. The present study focused on determining the specific contributions of GAUT10 to pectin composition in primary roots and the underlying defects associated with gaut10 roots. Using live-cell microscopy, we determined reduced root growth in gaut10 is due to a reduction in both root apical meristem size and epidermal cell elongation. In addition, GAUT10 was required for normal pectin and hemicellulose composition in primary Arabidopsis roots. Specifically, loss of GAUT10 led to a reduction in galacturonic acid and xylose in root cell walls and altered the presence of rhamnogalacturonan-I (RG-I) and homogalacturonan (HG) polymers in the root. Transcriptomic analysis of gaut10 roots compared to wild type uncovered hundreds of genes differentially expressed in the mutant, including genes related to auxin metabolism and peroxisome function. Consistent with these results, both auxin signaling and metabolism were modified in gaut10 roots. The sucrose-dependent short-root phenotype in gaut10 was linked to β-oxidation based on hypersensitivity to indole-3-butyric acid (IBA) and an epistatic interaction with TRANSPORTER OF IBA1 (TOB1). Altogether, these data support a growing body of evidence suggesting that pectin composition may influence auxin pathways and peroxisome activity.},
	number = {4},
	urldate = {2023-11-24},
	journal = {Plant Physiology},
	author = {Dash, Linkan and Swaminathan, Sivakumar and Šimura, Jan and Gonzales, Caitlin Leigh P and Montes, Christian and Solanki, Neel and Mejia, Ludvin and Ljung, Karin and Zabotina, Olga A and Kelley, Dior R},
	month = dec,
	year = {2023},
	pages = {2480--2497},
}

Arabidopsis (Arabidopsis thaliana) root development is regulated by multiple dynamic growth cues that require central metabolism pathways such as β-oxidation and auxin. Loss of the pectin biosynthesizing enzyme GALACTURONOSYLTRANSFERASE 10 (GAUT10) leads to a short-root phenotype under sucrose-limited conditions. The present study focused on determining the specific contributions of GAUT10 to pectin composition in primary roots and the underlying defects associated with gaut10 roots. Using live-cell microscopy, we determined reduced root growth in gaut10 is due to a reduction in both root apical meristem size and epidermal cell elongation. In addition, GAUT10 was required for normal pectin and hemicellulose composition in primary Arabidopsis roots. Specifically, loss of GAUT10 led to a reduction in galacturonic acid and xylose in root cell walls and altered the presence of rhamnogalacturonan-I (RG-I) and homogalacturonan (HG) polymers in the root. Transcriptomic analysis of gaut10 roots compared to wild type uncovered hundreds of genes differentially expressed in the mutant, including genes related to auxin metabolism and peroxisome function. Consistent with these results, both auxin signaling and metabolism were modified in gaut10 roots. The sucrose-dependent short-root phenotype in gaut10 was linked to β-oxidation based on hypersensitivity to indole-3-butyric acid (IBA) and an epistatic interaction with TRANSPORTER OF IBA1 (TOB1). Altogether, these data support a growing body of evidence suggesting that pectin composition may influence auxin pathways and peroxisome activity.

@article{walker_cytokinin_2023,
	title = {Cytokinin signaling regulates two-stage inflorescence arrest in {Arabidopsis}},
	volume = {191},
	issn = {0032-0889},
	url = {https://doi.org/10.1093/plphys/kiac514},
	doi = {10.1093/plphys/kiac514},
	abstract = {To maximize reproductive success, flowering plants must correctly time entry and exit from the reproductive phase. While much is known about mechanisms that regulate initiation of flowering, end-of-flowering remains largely uncharacterized. End-of-flowering in Arabidopsis (Arabidopsis thaliana) consists of quasi-synchronous arrest of inflorescences, but it is unclear how arrest is correctly timed with respect to environmental stimuli and reproductive success. Here, we showed that Arabidopsis inflorescence arrest is a complex developmental phenomenon, which includes the arrest of the inflorescence meristem (IM), coupled with a separable “floral arrest” of all unopened floral primordia; these events occur well before visible inflorescence arrest. We showed that global inflorescence removal delays both IM and floral arrest, but that local fruit removal only delays floral arrest, emphasizing their separability. We tested whether cytokinin regulates inflorescence arrest, and found that cytokinin signaling dynamics mirror IM activity, while cytokinin treatment can delay both IM and floral arrest. We further showed that gain-of-function cytokinin receptor mutants can delay IM and floral arrest; conversely, loss-of-function mutants prevented the extension of flowering in response to inflorescence removal. Collectively, our data suggest that the dilution of cytokinin among an increasing number of sink organs leads to end-of-flowering in Arabidopsis by triggering IM and floral arrest.},
	number = {1},
	urldate = {2023-01-09},
	journal = {Plant Physiology},
	author = {Walker, Catriona H and Ware, Alexander and Šimura, Jan and Ljung, Karin and Wilson, Zoe and Bennett, Tom},
	month = jan,
	year = {2023},
	pages = {479--495},
}

To maximize reproductive success, flowering plants must correctly time entry and exit from the reproductive phase. While much is known about mechanisms that regulate initiation of flowering, end-of-flowering remains largely uncharacterized. End-of-flowering in Arabidopsis (Arabidopsis thaliana) consists of quasi-synchronous arrest of inflorescences, but it is unclear how arrest is correctly timed with respect to environmental stimuli and reproductive success. Here, we showed that Arabidopsis inflorescence arrest is a complex developmental phenomenon, which includes the arrest of the inflorescence meristem (IM), coupled with a separable “floral arrest” of all unopened floral primordia; these events occur well before visible inflorescence arrest. We showed that global inflorescence removal delays both IM and floral arrest, but that local fruit removal only delays floral arrest, emphasizing their separability. We tested whether cytokinin regulates inflorescence arrest, and found that cytokinin signaling dynamics mirror IM activity, while cytokinin treatment can delay both IM and floral arrest. We further showed that gain-of-function cytokinin receptor mutants can delay IM and floral arrest; conversely, loss-of-function mutants prevented the extension of flowering in response to inflorescence removal. Collectively, our data suggest that the dilution of cytokinin among an increasing number of sink organs leads to end-of-flowering in Arabidopsis by triggering IM and floral arrest.

@article{bernacka-wojcik_flexible_2023,
	title = {Flexible {Organic} {Electronic} {Ion} {Pump} for {Flow}-{Free} {Phytohormone} {Delivery} into {Vasculature} of {Intact} {Plants}},
	volume = {10},
	issn = {2198-3844},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/advs.202206409},
	doi = {10.1002/advs.202206409},
	abstract = {Plant vasculature transports molecules that play a crucial role in plant signaling including systemic responses and acclimation to diverse environmental conditions. Targeted controlled delivery of molecules to the vascular tissue can be a biomimetic way to induce long distance responses, providing a new tool for the fundamental studies and engineering of stress-tolerant plants. Here, a flexible organic electronic ion pump, an electrophoretic delivery device, for controlled delivery of phytohormones directly in plant vascular tissue is developed. The c-OEIP is based on polyimide-coated glass capillaries that significantly enhance the mechanical robustness of these microscale devices while being minimally disruptive for the plant. The polyelectrolyte channel is based on low-cost and commercially available precursors that can be photocured with blue light, establishing much cheaper and safer system than the state-of-the-art. To trigger OEIP-induced plant response, the phytohormone abscisic acid (ABA) in the petiole of intact Arabidopsis plants is delivered. ABA is one of the main phytohormones involved in plant stress responses and induces stomata closure under drought conditions to reduce water loss and prevent wilting. The OEIP-mediated ABA delivery triggered fast and long-lasting stomata closure far away from the delivery point demonstrating systemic vascular transport of the delivered ABA, verified delivering deuterium-labeled ABA.},
	language = {en},
	number = {14},
	urldate = {2023-05-26},
	journal = {Advanced Science},
	author = {Bernacka-Wojcik, Iwona and Talide, Loïc and Abdel Aziz, Ilaria and Simura, Jan and Oikonomou, Vasileios K. and Rossi, Stefano and Mohammadi, Mohsen and Dar, Abdul Manan and Seitanidou, Maria and Berggren, Magnus and Simon, Daniel T. and Tybrandt, Klas and Jonsson, Magnus P. and Ljung, Karin and Niittylä, Totte and Stavrinidou, Eleni},
	month = may,
	year = {2023},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/advs.202206409},
	keywords = {bioelectronic devices, drug delivery, photo-crosslinking, plants vasculature, polyelectrolytes},
	pages = {2206409},
}

Plant vasculature transports molecules that play a crucial role in plant signaling including systemic responses and acclimation to diverse environmental conditions. Targeted controlled delivery of molecules to the vascular tissue can be a biomimetic way to induce long distance responses, providing a new tool for the fundamental studies and engineering of stress-tolerant plants. Here, a flexible organic electronic ion pump, an electrophoretic delivery device, for controlled delivery of phytohormones directly in plant vascular tissue is developed. The c-OEIP is based on polyimide-coated glass capillaries that significantly enhance the mechanical robustness of these microscale devices while being minimally disruptive for the plant. The polyelectrolyte channel is based on low-cost and commercially available precursors that can be photocured with blue light, establishing much cheaper and safer system than the state-of-the-art. To trigger OEIP-induced plant response, the phytohormone abscisic acid (ABA) in the petiole of intact Arabidopsis plants is delivered. ABA is one of the main phytohormones involved in plant stress responses and induces stomata closure under drought conditions to reduce water loss and prevent wilting. The OEIP-mediated ABA delivery triggered fast and long-lasting stomata closure far away from the delivery point demonstrating systemic vascular transport of the delivered ABA, verified delivering deuterium-labeled ABA.

@article{urbancsok_flexure_2023,
	title = {Flexure wood formation via growth reprogramming in hybrid aspen involves jasmonates and polyamines and transcriptional changes resembling tension wood development},
	copyright = {New Phytologist© 2023 The Authors New Phytologist © 2023 New Phytologist Foundation},
	issn = {1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/nph.19307},
	doi = {10.1111/nph.19307},
	abstract = {Stem bending in trees induces flexure wood but its properties and development are poorly understood. Here, we investigated the effects of low-intensity multidirectional stem flexing on growth and wood properties of hybrid aspen, and on its transcriptomic and hormonal responses. Glasshouse-grown trees were either kept stationary or subjected to several daily shakes for 5 wk, after which the transcriptomes and hormones were analyzed in the cambial region and developing wood tissues, and the wood properties were analyzed by physical, chemical and microscopy techniques. Shaking increased primary and secondary growth and altered wood differentiation by stimulating gelatinous-fiber formation, reducing secondary wall thickness, changing matrix polysaccharides and increasing cellulose, G- and H-lignin contents, cell wall porosity and saccharification yields. Wood-forming tissues exhibited elevated jasmonate, polyamine, ethylene and brassinosteroids and reduced abscisic acid and gibberellin signaling. Transcriptional responses resembled those during tension wood formation but not opposite wood formation and revealed several thigmomorphogenesis-related genes as well as novel gene networks including FLA and XTH genes encoding plasma membrane-bound proteins. Low-intensity stem flexing stimulates growth and induces wood having improved biorefinery properties through molecular and hormonal pathways similar to thigmomorphogenesis in herbaceous plants and largely overlapping with the tension wood program of hardwoods.},
	language = {en},
	urldate = {2023-10-20},
	journal = {New Phytologist},
	author = {Urbancsok, János and Donev, Evgeniy N. and Sivan, Pramod and van Zalen, Elena and Barbut, Félix R. and Derba-Maceluch, Marta and Šimura, Jan and Yassin, Zakiya and Gandla, Madhavi L. and Karady, Michal and Ljung, Karin and Winestrand, Sandra and Jönsson, Leif J. and Scheepers, Gerhard and Delhomme, Nicolas and Street, Nathaniel R. and Mellerowicz, Ewa J.},
	month = oct,
	year = {2023},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/nph.19307},
	keywords = {Populus tremula × tremuloides, flexure wood, jasmonic acid signaling, mechanostimulation, polyamines, saccharification, thigmomorphogenesis, wood development},
}

Stem bending in trees induces flexure wood but its properties and development are poorly understood. Here, we investigated the effects of low-intensity multidirectional stem flexing on growth and wood properties of hybrid aspen, and on its transcriptomic and hormonal responses. Glasshouse-grown trees were either kept stationary or subjected to several daily shakes for 5 wk, after which the transcriptomes and hormones were analyzed in the cambial region and developing wood tissues, and the wood properties were analyzed by physical, chemical and microscopy techniques. Shaking increased primary and secondary growth and altered wood differentiation by stimulating gelatinous-fiber formation, reducing secondary wall thickness, changing matrix polysaccharides and increasing cellulose, G- and H-lignin contents, cell wall porosity and saccharification yields. Wood-forming tissues exhibited elevated jasmonate, polyamine, ethylene and brassinosteroids and reduced abscisic acid and gibberellin signaling. Transcriptional responses resembled those during tension wood formation but not opposite wood formation and revealed several thigmomorphogenesis-related genes as well as novel gene networks including FLA and XTH genes encoding plasma membrane-bound proteins. Low-intensity stem flexing stimulates growth and induces wood having improved biorefinery properties through molecular and hormonal pathways similar to thigmomorphogenesis in herbaceous plants and largely overlapping with the tension wood program of hardwoods.

@article{skalicky_fluorescence-activated_2023,
	title = {Fluorescence-activated multi-organelle mapping of subcellular plant hormone distribution},
	volume = {116},
	copyright = {© 2023 The Authors. The Plant Journal published by Society for Experimental Biology and John Wiley \& Sons Ltd.},
	issn = {1365-313X},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/tpj.16456},
	doi = {10.1111/tpj.16456},
	abstract = {Auxins and cytokinins are two major families of phytohormones that control most aspects of plant growth, development and plasticity. Their distribution in plants has been described, but the importance of cell- and subcellular-type specific phytohormone homeostasis remains undefined. Herein, we revealed auxin and cytokinin distribution maps showing their different organelle-specific allocations within the Arabidopsis plant cell. To do so, we have developed Fluorescence-Activated multi-Organelle Sorting (FAmOS), an innovative subcellular fractionation technique based on flow cytometric principles. FAmOS allows the simultaneous sorting of four differently labelled organelles based on their individual light scatter and fluorescence parameters while ensuring hormone metabolic stability. Our data showed different subcellular distribution of auxin and cytokinins, revealing the formation of phytohormone gradients that have been suggested by the subcellular localization of auxin and cytokinin transporters, receptors and metabolic enzymes. Both hormones showed enrichment in vacuoles, while cytokinins were also accumulated in the endoplasmic reticulum.},
	language = {en},
	number = {6},
	urldate = {2023-12-22},
	journal = {The Plant Journal},
	author = {Skalický, Vladimír and Antoniadi, Ioanna and Pěnčík, Aleš and Chamrád, Ivo and Lenobel, René and Kubeš, Martin F. and Zatloukal, Marek and Žukauskaitė, Asta and Strnad, Miroslav and Ljung, Karin and Novák, Ondřej},
	month = sep,
	year = {2023},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/tpj.16456},
	keywords = {Arabidopsis thaliana, Auxin, LC–MS/MS, cytokinin, flow cytometry, subcellular fractionation, subcellular homeostasis, technical advances},
	pages = {1825--1841},
}

Auxins and cytokinins are two major families of phytohormones that control most aspects of plant growth, development and plasticity. Their distribution in plants has been described, but the importance of cell- and subcellular-type specific phytohormone homeostasis remains undefined. Herein, we revealed auxin and cytokinin distribution maps showing their different organelle-specific allocations within the Arabidopsis plant cell. To do so, we have developed Fluorescence-Activated multi-Organelle Sorting (FAmOS), an innovative subcellular fractionation technique based on flow cytometric principles. FAmOS allows the simultaneous sorting of four differently labelled organelles based on their individual light scatter and fluorescence parameters while ensuring hormone metabolic stability. Our data showed different subcellular distribution of auxin and cytokinins, revealing the formation of phytohormone gradients that have been suggested by the subcellular localization of auxin and cytokinin transporters, receptors and metabolic enzymes. Both hormones showed enrichment in vacuoles, while cytokinins were also accumulated in the endoplasmic reticulum.

@article{jourquin_golven_2023,
	title = {{GOLVEN} peptides regulate lateral root spacing as part of a negative feedback loop on the establishment of auxin maxima},
	volume = {74},
	issn = {0022-0957},
	url = {https://doi.org/10.1093/jxb/erad123},
	doi = {10.1093/jxb/erad123},
	abstract = {Lateral root initiation requires the accumulation of auxin in lateral root founder cells, yielding a local auxin maximum. The positioning of auxin maxima along the primary root determines the density and spacing of lateral roots. The GOLVEN6 (GLV6) and GLV10 signaling peptides and their receptors have been established as regulators of lateral root spacing via their inhibitory effect on lateral root initiation in Arabidopsis. However, it was unclear how these GLV peptides interfere with auxin signaling or homeostasis. Here, we show that GLV6/10 signaling regulates the expression of a subset of auxin response genes, downstream of the canonical auxin signaling pathway, while simultaneously inhibiting the establishment of auxin maxima within xylem-pole pericycle cells that neighbor lateral root initiation sites. We present genetic evidence that this inhibitory effect relies on the activity of the PIN3 and PIN7 auxin export proteins. Furthermore, GLV6/10 peptide signaling was found to enhance PIN7 abundance in the plasma membranes of xylem-pole pericycle cells, which likely stimulates auxin efflux from these cells. Based on these findings, we propose a model in which the GLV6/10 signaling pathway serves as a negative feedback mechanism that contributes to the robust patterning of auxin maxima along the primary root.},
	number = {14},
	urldate = {2023-08-31},
	journal = {Journal of Experimental Botany},
	author = {Jourquin, Joris and Fernandez, Ana Ibis and Wang, Qing and Xu, Ke and Chen, Jian and Šimura, Jan and Ljung, Karin and Vanneste, Steffen and Beeckman, Tom},
	month = aug,
	year = {2023},
	pages = {4031--4049},
}

Lateral root initiation requires the accumulation of auxin in lateral root founder cells, yielding a local auxin maximum. The positioning of auxin maxima along the primary root determines the density and spacing of lateral roots. The GOLVEN6 (GLV6) and GLV10 signaling peptides and their receptors have been established as regulators of lateral root spacing via their inhibitory effect on lateral root initiation in Arabidopsis. However, it was unclear how these GLV peptides interfere with auxin signaling or homeostasis. Here, we show that GLV6/10 signaling regulates the expression of a subset of auxin response genes, downstream of the canonical auxin signaling pathway, while simultaneously inhibiting the establishment of auxin maxima within xylem-pole pericycle cells that neighbor lateral root initiation sites. We present genetic evidence that this inhibitory effect relies on the activity of the PIN3 and PIN7 auxin export proteins. Furthermore, GLV6/10 peptide signaling was found to enhance PIN7 abundance in the plasma membranes of xylem-pole pericycle cells, which likely stimulates auxin efflux from these cells. Based on these findings, we propose a model in which the GLV6/10 signaling pathway serves as a negative feedback mechanism that contributes to the robust patterning of auxin maxima along the primary root.

@article{grenzi_long-distance_2023,
	title = {Long-distance turgor pressure changes induce local activation of plant glutamate receptor-like channels},
	issn = {0960-9822},
	url = {https://www.sciencedirect.com/science/article/pii/S0960982223000763},
	doi = {10.1016/j.cub.2023.01.042},
	abstract = {In Arabidopsis thaliana, local wounding and herbivore feeding provoke leaf-to-leaf propagating Ca2+ waves that are dependent on the activity of members of the glutamate receptor-like channels (GLRs). In systemic tissues, GLRs are needed to sustain the synthesis of jasmonic acid (JA) with the subsequent activation of JA-dependent signaling response required for the plant acclimation to the perceived stress. Even though the role of GLRs is well established, the mechanism through which they are activated remains unclear. Here, we report that in vivo, the amino-acid-dependent activation of the AtGLR3.3 channel and systemic responses require a functional ligand-binding domain. By combining imaging and genetics, we show that leaf mechanical injury, such as wounds and burns, as well as hypo-osmotic stress in root cells, induces the systemic apoplastic increase of L-glutamate (L-Glu), which is largely independent of AtGLR3.3 that is instead required for systemic cytosolic Ca2+ elevation. Moreover, by using a bioelectronic approach, we show that the local release of minute concentrations of L-Glu in the leaf lamina fails to induce any long-distance Ca2+ waves.},
	language = {en},
	urldate = {2023-03-23},
	journal = {Current Biology},
	author = {Grenzi, Matteo and Buratti, Stefano and Parmagnani, Ambra Selene and Abdel Aziz, Ilaria and Bernacka-Wojcik, Iwona and Resentini, Francesca and Šimura, Jan and Doccula, Fabrizio Gandolfo and Alfieri, Andrea and Luoni, Laura and Ljung, Karin and Bonza, Maria Cristina and Stavrinidou, Eleni and Costa, Alex},
	month = feb,
	year = {2023},
	keywords = {glutamate receptor-like channels, implantable bioelectronic device, ligand-binding domain, long-distance Ca signaling},
}

In Arabidopsis thaliana, local wounding and herbivore feeding provoke leaf-to-leaf propagating Ca2+ waves that are dependent on the activity of members of the glutamate receptor-like channels (GLRs). In systemic tissues, GLRs are needed to sustain the synthesis of jasmonic acid (JA) with the subsequent activation of JA-dependent signaling response required for the plant acclimation to the perceived stress. Even though the role of GLRs is well established, the mechanism through which they are activated remains unclear. Here, we report that in vivo, the amino-acid-dependent activation of the AtGLR3.3 channel and systemic responses require a functional ligand-binding domain. By combining imaging and genetics, we show that leaf mechanical injury, such as wounds and burns, as well as hypo-osmotic stress in root cells, induces the systemic apoplastic increase of L-glutamate (L-Glu), which is largely independent of AtGLR3.3 that is instead required for systemic cytosolic Ca2+ elevation. Moreover, by using a bioelectronic approach, we show that the local release of minute concentrations of L-Glu in the leaf lamina fails to induce any long-distance Ca2+ waves.

@article{israeli_modulating_2023,
	title = {Modulating auxin response stabilizes tomato fruit set},
	volume = {192},
	issn = {0032-0889},
	url = {https://doi.org/10.1093/plphys/kiad205},
	doi = {10.1093/plphys/kiad205},
	abstract = {Fruit formation depends on successful fertilization and is highly sensitive to weather fluctuations that affect pollination. Auxin promotes fruit initiation and growth following fertilization. Class A auxin response factors (Class A ARFs) repress transcription in the absence of auxin and activate transcription in its presence. Here we explore how multiple members of the ARF family regulate fruit set and fruit growth in tomato (Solanum lycopersicum) and Arabidopsis thaliana, and test whether reduction of SlARF activity improves yield stability in fluctuating temperatures. We found that several tomato Slarf mutant combinations produced seedless parthenocarpic fruits, most notably mutants deficient in SlARF8A and SlARF8B genes. Arabidopsis Atarf8 mutants deficient in the orthologous gene had less complete parthenocarpy than did tomato Slarf8a Slarf8b mutants. Conversely, Atarf6 Atarf8 double mutants had reduced fruit growth after fertilization. AtARF6 and AtARF8 likely switch from repression to activation of fruit growth in response to a fertilization-induced auxin increase in gynoecia. Tomato plants with reduced SlARF8A and SlARF8B gene dosage had substantially higher yield than the wild type under controlled or ambient hot and cold growth conditions. In field trials, partial reduction in the SlARF8 dose increased yield under extreme temperature with minimal pleiotropic effects. The stable yield of the mutant plants resulted from a combination of early onset of fruit set, more fruit-bearing branches and more flowers setting fruits. Thus, ARF8 proteins mediate the control of fruit set, and relieving this control with Slarf8 mutations may be utilized in breeding to increase yield stability in tomato and other crops.},
	number = {3},
	urldate = {2023-04-14},
	journal = {Plant Physiology},
	author = {Israeli, Alon and Schubert, Ramona and Man, Nave and Teboul, Naama and Serrani Yarce, Juan Carlos and Rosowski, Emily E and Wu, Miin-Feng and Levy, Matan and Efroni, Idan and Ljung, Karin and Hause, Bettina and Reed, Jason W and Ori, Naomi},
	month = jul,
	year = {2023},
	pages = {2336--2355},
}

Fruit formation depends on successful fertilization and is highly sensitive to weather fluctuations that affect pollination. Auxin promotes fruit initiation and growth following fertilization. Class A auxin response factors (Class A ARFs) repress transcription in the absence of auxin and activate transcription in its presence. Here we explore how multiple members of the ARF family regulate fruit set and fruit growth in tomato (Solanum lycopersicum) and Arabidopsis thaliana, and test whether reduction of SlARF activity improves yield stability in fluctuating temperatures. We found that several tomato Slarf mutant combinations produced seedless parthenocarpic fruits, most notably mutants deficient in SlARF8A and SlARF8B genes. Arabidopsis Atarf8 mutants deficient in the orthologous gene had less complete parthenocarpy than did tomato Slarf8a Slarf8b mutants. Conversely, Atarf6 Atarf8 double mutants had reduced fruit growth after fertilization. AtARF6 and AtARF8 likely switch from repression to activation of fruit growth in response to a fertilization-induced auxin increase in gynoecia. Tomato plants with reduced SlARF8A and SlARF8B gene dosage had substantially higher yield than the wild type under controlled or ambient hot and cold growth conditions. In field trials, partial reduction in the SlARF8 dose increased yield under extreme temperature with minimal pleiotropic effects. The stable yield of the mutant plants resulted from a combination of early onset of fruit set, more fruit-bearing branches and more flowers setting fruits. Thus, ARF8 proteins mediate the control of fruit set, and relieving this control with Slarf8 mutations may be utilized in breeding to increase yield stability in tomato and other crops.

@article{ntefidou_physcomitrium_2023,
	title = {Physcomitrium patens {PpRIC}, an ancestral {CRIB}-domain {ROP} effector, inhibits auxin-induced differentiation of apical initial cells},
	volume = {42},
	issn = {2211-1247},
	url = {https://www.cell.com/cell-reports/abstract/S2211-1247(23)00141-9},
	doi = {10.1016/j.celrep.2023.112130},
	abstract = {RHO guanosine triphosphatases are important eukaryotic regulators of cell differentiation and behavior. Plant ROP (RHO of plant) family members activate specific, incompletely characterized downstream signaling. The structurally simple land plant Physcomitrium patens is missing homologs of key animal and flowering plant RHO effectors but contains a single CRIB (CDC42/RAC interactive binding)-domain-containing RIC (ROP-interacting CRIB-containing) protein (PpRIC). Protonemal P. patens filaments elongate based on regular division and PpROP-dependent tip growth of apical initial cells, which upon stimulation by the hormone auxin differentiate caulonemal characteristics. PpRIC interacts with active PpROP1, co-localizes with this protein at the plasma membrane at the tip of apical initial cells, and accumulates in the nucleus. Remarkably, PpRIC is not required for tip growth but is targeted to the nucleus to block caulonema differentiation downstream of auxin-controlled gene expression. These observations establish functions of PpRIC in mediating crosstalk between ROP and auxin signaling, which contributes to the maintenance of apical initial cell identity.},
	language = {English},
	number = {2},
	urldate = {2023-02-23},
	journal = {Cell Reports},
	author = {Ntefidou, Maria and Eklund, D. Magnus and Bail, Aude Le and Schulmeister, Sylwia and Scherbel, Franziska and Brandl, Lisa and Dörfler, Wolfgang and Eichstädt, Chantal and Bannmüller, Anna and Ljung, Karin and Kost, Benedikt},
	month = feb,
	year = {2023},
	pmid = {36790931},
	note = {Publisher: Elsevier},
	keywords = {CP: Developmental biology, CP: Plants, CRIB domain, Physcomitrium patens, RHO/ROP GTPases, RHO/ROP effectors, auxin, cell differentiation, initial cells, land plant evolution, nuclear targeting, tip growth},
}

RHO guanosine triphosphatases are important eukaryotic regulators of cell differentiation and behavior. Plant ROP (RHO of plant) family members activate specific, incompletely characterized downstream signaling. The structurally simple land plant Physcomitrium patens is missing homologs of key animal and flowering plant RHO effectors but contains a single CRIB (CDC42/RAC interactive binding)-domain-containing RIC (ROP-interacting CRIB-containing) protein (PpRIC). Protonemal P. patens filaments elongate based on regular division and PpROP-dependent tip growth of apical initial cells, which upon stimulation by the hormone auxin differentiate caulonemal characteristics. PpRIC interacts with active PpROP1, co-localizes with this protein at the plasma membrane at the tip of apical initial cells, and accumulates in the nucleus. Remarkably, PpRIC is not required for tip growth but is targeted to the nucleus to block caulonema differentiation downstream of auxin-controlled gene expression. These observations establish functions of PpRIC in mediating crosstalk between ROP and auxin signaling, which contributes to the maintenance of apical initial cell identity.

@article{lihavainen_salicylic_2023,
	title = {Salicylic acid metabolism and signalling coordinate senescence initiation in aspen in nature},
	volume = {14},
	copyright = {2023 The Author(s)},
	issn = {2041-1723},
	url = {https://www.nature.com/articles/s41467-023-39564-5},
	doi = {10.1038/s41467-023-39564-5},
	abstract = {Deciduous trees exhibit a spectacular phenomenon of autumn senescence driven by the seasonality of their growth environment, yet there is no consensus which external or internal cues trigger it. Senescence starts at different times in European aspen (Populus tremula L.) genotypes grown in same location. By integrating omics studies, we demonstrate that aspen genotypes utilize similar transcriptional cascades and metabolic cues to initiate senescence, but at different times during autumn. The timing of autumn senescence initiation appeared to be controlled by two consecutive “switches”; 1) first the environmental variation induced the rewiring of the transcriptional network, stress signalling pathways and metabolic perturbations and 2) the start of senescence process was defined by the ability of the genotype to activate and sustain stress tolerance mechanisms mediated by salicylic acid. We propose that salicylic acid represses the onset of leaf senescence in stressful natural conditions, rather than promoting it as often observed in annual plants.},
	language = {en},
	number = {1},
	urldate = {2023-07-21},
	journal = {Nature Communications},
	author = {Lihavainen, Jenna and Šimura, Jan and Bag, Pushan and Fataftah, Nazeer and Robinson, Kathryn Megan and Delhomme, Nicolas and Novák, Ondřej and Ljung, Karin and Jansson, Stefan},
	month = jul,
	year = {2023},
	note = {Number: 1
Publisher: Nature Publishing Group},
	keywords = {Metabolomics, Plant physiology, Regulatory networks, Senescence},
	pages = {4288},
}

Deciduous trees exhibit a spectacular phenomenon of autumn senescence driven by the seasonality of their growth environment, yet there is no consensus which external or internal cues trigger it. Senescence starts at different times in European aspen (Populus tremula L.) genotypes grown in same location. By integrating omics studies, we demonstrate that aspen genotypes utilize similar transcriptional cascades and metabolic cues to initiate senescence, but at different times during autumn. The timing of autumn senescence initiation appeared to be controlled by two consecutive “switches”; 1) first the environmental variation induced the rewiring of the transcriptional network, stress signalling pathways and metabolic perturbations and 2) the start of senescence process was defined by the ability of the genotype to activate and sustain stress tolerance mechanisms mediated by salicylic acid. We propose that salicylic acid represses the onset of leaf senescence in stressful natural conditions, rather than promoting it as often observed in annual plants.

@article{su_tree_2023,
	title = {Tree architecture: {A} strigolactone-deficient mutant reveals a connection between branching order and auxin gradient along the tree stem},
	volume = {120},
	shorttitle = {Tree architecture},
	url = {https://www.pnas.org/doi/10.1073/pnas.2308587120},
	doi = {10.1073/pnas.2308587120},
	abstract = {Due to their long lifespan, trees and bushes develop higher order of branches in a perennial manner. In contrast to a tall tree, with a clearly defined main stem and branching order, a bush is shorter and has a less apparent main stem and branching pattern. To address the developmental basis of these two forms, we studied several naturally occurring architectural variants in silver birch (Betula pendula). Using a candidate gene approach, we identified a bushy kanttarelli variant with a loss-of-function mutation in the BpMAX1 gene required for strigolactone (SL) biosynthesis. While kanttarelli is shorter than the wild type (WT), it has the same number of primary branches, whereas the number of secondary branches is increased, contributing to its bush-like phenotype. To confirm that the identified mutation was responsible for the phenotype, we phenocopied kanttarelli in transgenic BpMAX1::RNAi birch lines. SL profiling confirmed that both kanttarelli and the transgenic lines produced very limited amounts of SL. Interestingly, the auxin (IAA) distribution along the main stem differed between WT and BpMAX1::RNAi. In the WT, the auxin concentration formed a gradient, being higher in the uppermost internodes and decreasing toward the basal part of the stem, whereas in the transgenic line, this gradient was not observed. Through modeling, we showed that the different IAA distribution patterns may result from the difference in the number of higher-order branches and plant height. Future studies will determine whether the IAA gradient itself regulates aspects of plant architecture.},
	number = {48},
	urldate = {2023-11-24},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Su, Chang and Kokosza, Andrzej and Xie, Xiaonan and Pěnčík, Aleš and Zhang, Youjun and Raumonen, Pasi and Shi, Xueping and Muranen, Sampo and Topcu, Melis Kucukoglu and Immanen, Juha and Hagqvist, Risto and Safronov, Omid and Alonso-Serra, Juan and Eswaran, Gugan and Venegas, Mirko Pavicic and Ljung, Karin and Ward, Sally and Mähönen, Ari Pekka and Himanen, Kristiina and Salojärvi, Jarkko and Fernie, Alisdair R. and Novák, Ondřej and Leyser, Ottoline and Pałubicki, Wojtek and Helariutta, Ykä and Nieminen, Kaisa},
	month = nov,
	year = {2023},
	note = {Publisher: Proceedings of the National Academy of Sciences},
	pages = {e2308587120},
}

Due to their long lifespan, trees and bushes develop higher order of branches in a perennial manner. In contrast to a tall tree, with a clearly defined main stem and branching order, a bush is shorter and has a less apparent main stem and branching pattern. To address the developmental basis of these two forms, we studied several naturally occurring architectural variants in silver birch (Betula pendula). Using a candidate gene approach, we identified a bushy kanttarelli variant with a loss-of-function mutation in the BpMAX1 gene required for strigolactone (SL) biosynthesis. While kanttarelli is shorter than the wild type (WT), it has the same number of primary branches, whereas the number of secondary branches is increased, contributing to its bush-like phenotype. To confirm that the identified mutation was responsible for the phenotype, we phenocopied kanttarelli in transgenic BpMAX1::RNAi birch lines. SL profiling confirmed that both kanttarelli and the transgenic lines produced very limited amounts of SL. Interestingly, the auxin (IAA) distribution along the main stem differed between WT and BpMAX1::RNAi. In the WT, the auxin concentration formed a gradient, being higher in the uppermost internodes and decreasing toward the basal part of the stem, whereas in the transgenic line, this gradient was not observed. Through modeling, we showed that the different IAA distribution patterns may result from the difference in the number of higher-order branches and plant height. Future studies will determine whether the IAA gradient itself regulates aspects of plant architecture.

@article{amanda_auxin_2022,
	title = {Auxin boosts energy generation pathways to fuel pollen maturation in barley},
	volume = {32},
	issn = {0960-9822},
	url = {https://www.sciencedirect.com/science/article/pii/S0960982222003438},
	doi = {10.1016/j.cub.2022.02.073},
	abstract = {Pollen grains become increasingly independent of the mother plant as they reach maturity through poorly understood developmental programs. We report that the hormone auxin is essential during barley pollen maturation to boost the expression of genes encoding almost every step of heterotrophic energy production pathways. Accordingly, auxin is necessary for the flux of sucrose and hexoses into glycolysis and to increase the levels of pyruvate and two tricarboxylic (TCA) cycle metabolites (citrate and succinate). Moreover, bioactive auxin is synthesized by the pollen-localized enzyme HvYUCCA4, supporting that pollen grains autonomously produce auxin to stimulate a specific cellular output, energy generation, that fuels maturation processes such as starch accumulation. Our results demonstrate that auxin can shift central carbon metabolism to drive plant cell development, which suggests a direct mechanism for auxin’s ability to promote growth and differentiation.},
	language = {en},
	number = {8},
	urldate = {2022-05-06},
	journal = {Current Biology},
	author = {Amanda, Dhika and Frey, Felix P. and Neumann, Ulla and Przybyl, Marine and Šimura, Jan and Zhang, Youjun and Chen, Zongliang and Gallavotti, Andrea and Fernie, Alisdair R. and Ljung, Karin and Acosta, Iván F.},
	month = apr,
	year = {2022},
	keywords = {anther, auxin, barley, metabolism, plant male fertility, pollen, stamen maturation, starch},
	pages = {1798--1811.e8},
}

Pollen grains become increasingly independent of the mother plant as they reach maturity through poorly understood developmental programs. We report that the hormone auxin is essential during barley pollen maturation to boost the expression of genes encoding almost every step of heterotrophic energy production pathways. Accordingly, auxin is necessary for the flux of sucrose and hexoses into glycolysis and to increase the levels of pyruvate and two tricarboxylic (TCA) cycle metabolites (citrate and succinate). Moreover, bioactive auxin is synthesized by the pollen-localized enzyme HvYUCCA4, supporting that pollen grains autonomously produce auxin to stimulate a specific cellular output, energy generation, that fuels maturation processes such as starch accumulation. Our results demonstrate that auxin can shift central carbon metabolism to drive plant cell development, which suggests a direct mechanism for auxin’s ability to promote growth and differentiation.

@article{antoniadi_fluorescence_2022,
	title = {Fluorescence activated cell sorting—{A} selective tool for plant cell isolation and analysis},
	volume = {101},
	issn = {1552-4930},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/cyto.a.24461},
	doi = {10.1002/cyto.a.24461},
	abstract = {Instrumentation for flow cytometry and sorting is designed around the assumption that samples are single-cell suspensions. However, with few exceptions, higher plants comprise complex multicellular tissues and organs, in which the individual cells are held together by shared cell walls. Single-cell suspensions can be obtained through digestion of the cells walls and release of the so-called protoplasts (plants without their cell wall). Here we describe best practices for protoplast preparation, and for analysis through flow cytometry and cell sorting. Finally, the numerous downstream applications involving sorted protoplasts are discussed.},
	language = {en},
	number = {9},
	urldate = {2022-09-16},
	journal = {Cytometry Part A},
	author = {Antoniadi, Ioanna and Skalický, Vladimír and Sun, Guiling and Ma, Wen and Galbraith, David W. and Novák, Ondřej and Ljung, Karin},
	month = may,
	year = {2022},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/cyto.a.24461},
	keywords = {autofluorescence, best practices, plant flow cytometry and sorting, protoplasts, viability and integrity},
	pages = {725--736},
}

Instrumentation for flow cytometry and sorting is designed around the assumption that samples are single-cell suspensions. However, with few exceptions, higher plants comprise complex multicellular tissues and organs, in which the individual cells are held together by shared cell walls. Single-cell suspensions can be obtained through digestion of the cells walls and release of the so-called protoplasts (plants without their cell wall). Here we describe best practices for protoplast preparation, and for analysis through flow cytometry and cell sorting. Finally, the numerous downstream applications involving sorted protoplasts are discussed.

@article{antoniadi_ipt9_2022,
	title = {{IPT9}, a cis-zeatin cytokinin biosynthesis gene, promotes root growth},
	volume = {13},
	issn = {1664-462X},
	url = {https://www.frontiersin.org/articles/10.3389/fpls.2022.932008},
	abstract = {Cytokinin and auxin are plant hormones that coordinate many aspects of plant development. Their interactions in plant underground growth are well established, occurring at the levels of metabolism, signaling, and transport. Unlike many plant hormone classes, cytokinins are represented by more than one active molecule. Multiple mutant lines, blocking specific parts of cytokinin biosynthetic pathways, have enabled research in plants with deficiencies in specific cytokinin-types. While most of these mutants have confirmed the impeding effect of cytokinin on root growth, the ipt29 double mutant instead surprisingly exhibits reduced primary root length compared to the wild type. This mutant is impaired in cis-zeatin (cZ) production, a cytokinin-type that had been considered inactive in the past. Here we have further investigated the intriguing ipt29 root phenotype, opposite to known cytokinin functions, and the (bio)activity of cZ. Our data suggest that despite the ipt29 short-root phenotype, cZ application has a negative impact on primary root growth and can activate a cytokinin response in the stele. Grafting experiments revealed that the root phenotype of ipt29 depends mainly on local signaling which does not relate directly to cytokinin levels. Notably, ipt29 displayed increased auxin levels in the root tissue. Moreover, analyses of the differential contributions of ipt2 and ipt9 to the ipt29 short-root phenotype demonstrated that, despite its deficiency on cZ levels, ipt2 does not show any root phenotype or auxin homeostasis variation, while ipt9 mutants were indistinguishable from ipt29. We conclude that IPT9 functions may go beyond cZ biosynthesis, directly or indirectly, implicating effects on auxin homeostasis and therefore influencing plant growth.},
	urldate = {2022-10-19},
	journal = {Frontiers in Plant Science},
	author = {Antoniadi, Ioanna and Mateo-Bonmatí, Eduardo and Pernisová, Markéta and Brunoni, Federica and Antoniadi, Mariana and Villalonga, Mauricio Garcia-Atance and Ament, Anita and Karády, Michal and Turnbull, Colin and Doležal, Karel and Pěnčík, Aleš and Ljung, Karin and Novák, Ondřej},
	month = oct,
	year = {2022},
	keywords = {⛔ No DOI found},
}

Cytokinin and auxin are plant hormones that coordinate many aspects of plant development. Their interactions in plant underground growth are well established, occurring at the levels of metabolism, signaling, and transport. Unlike many plant hormone classes, cytokinins are represented by more than one active molecule. Multiple mutant lines, blocking specific parts of cytokinin biosynthetic pathways, have enabled research in plants with deficiencies in specific cytokinin-types. While most of these mutants have confirmed the impeding effect of cytokinin on root growth, the ipt29 double mutant instead surprisingly exhibits reduced primary root length compared to the wild type. This mutant is impaired in cis-zeatin (cZ) production, a cytokinin-type that had been considered inactive in the past. Here we have further investigated the intriguing ipt29 root phenotype, opposite to known cytokinin functions, and the (bio)activity of cZ. Our data suggest that despite the ipt29 short-root phenotype, cZ application has a negative impact on primary root growth and can activate a cytokinin response in the stele. Grafting experiments revealed that the root phenotype of ipt29 depends mainly on local signaling which does not relate directly to cytokinin levels. Notably, ipt29 displayed increased auxin levels in the root tissue. Moreover, analyses of the differential contributions of ipt2 and ipt9 to the ipt29 short-root phenotype demonstrated that, despite its deficiency on cZ levels, ipt2 does not show any root phenotype or auxin homeostasis variation, while ipt9 mutants were indistinguishable from ipt29. We conclude that IPT9 functions may go beyond cZ biosynthesis, directly or indirectly, implicating effects on auxin homeostasis and therefore influencing plant growth.

@article{casanova-saez_inactivation_2022,
	title = {Inactivation of the entire {Arabidopsis} group {II} {GH3s} confers tolerance to salinity and water deficit},
	volume = {235},
	issn = {1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/nph.18114},
	doi = {10.1111/nph.18114},
	abstract = {Indole-3-acetic acid (IAA) controls a plethora of developmental processes. Thus, regulation of its concentration is of great relevance for plant performance. Cellular IAA concentration depends on its transport, biosynthesis and the various pathways for IAA inactivation, including oxidation and conjugation. Group II members of the GRETCHEN HAGEN 3 (GH3) gene family code for acyl acid amido synthetases catalysing the conjugation of IAA to amino acids. However, the high degree of functional redundancy among them has hampered thorough analysis of their roles in plant development. In this work, we generated an Arabidopsis gh3.1,2,3,4,5,6,9,17 (gh3oct) mutant to knock out the group II GH3 pathway. The gh3oct plants had an elaborated root architecture, showed an increased tolerance to different osmotic stresses, including an IAA-dependent tolerance to salinity, and were more tolerant to water deficit. Indole-3-acetic acid metabolite quantification in gh3oct plants suggested the existence of additional GH3-like enzymes in IAA metabolism. Moreover, our data suggested that 2-oxindole-3-acetic acid production depends, at least in part, on the GH3 pathway. Targeted stress-hormone analysis further suggested involvement of abscisic acid in the differential response to salinity of gh3oct plants. Taken together, our data provide new insights into the roles of group II GH3s in IAA metabolism and hormone-regulated plant development.},
	language = {en},
	number = {1},
	urldate = {2022-06-09},
	journal = {New Phytologist},
	author = {Casanova-Sáez, Rubén and Mateo-Bonmatí, Eduardo and Šimura, Jan and Pěnčík, Aleš and Novák, Ondřej and Ljung, Karin},
	year = {2022},
	keywords = {Arabidopsis, GH3, auxin, drought, salinity, stress tolerance},
	pages = {263--275},
}

Indole-3-acetic acid (IAA) controls a plethora of developmental processes. Thus, regulation of its concentration is of great relevance for plant performance. Cellular IAA concentration depends on its transport, biosynthesis and the various pathways for IAA inactivation, including oxidation and conjugation. Group II members of the GRETCHEN HAGEN 3 (GH3) gene family code for acyl acid amido synthetases catalysing the conjugation of IAA to amino acids. However, the high degree of functional redundancy among them has hampered thorough analysis of their roles in plant development. In this work, we generated an Arabidopsis gh3.1,2,3,4,5,6,9,17 (gh3oct) mutant to knock out the group II GH3 pathway. The gh3oct plants had an elaborated root architecture, showed an increased tolerance to different osmotic stresses, including an IAA-dependent tolerance to salinity, and were more tolerant to water deficit. Indole-3-acetic acid metabolite quantification in gh3oct plants suggested the existence of additional GH3-like enzymes in IAA metabolism. Moreover, our data suggested that 2-oxindole-3-acetic acid production depends, at least in part, on the GH3 pathway. Targeted stress-hormone analysis further suggested involvement of abscisic acid in the differential response to salinity of gh3oct plants. Taken together, our data provide new insights into the roles of group II GH3s in IAA metabolism and hormone-regulated plant development.

@article{hamon-josse_kai2_2022,
	title = {{KAI2} regulates seedling development by mediating light-induced remodelling of auxin transport},
	volume = {235},
	issn = {1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/nph.18110},
	doi = {10.1111/nph.18110},
	abstract = {Photomorphogenic remodelling of seedling growth is a key developmental transition in the plant life cycle. The α/β-hydrolase signalling protein KARRIKIN-INSENSITIVE2 (KAI2), a close homologue of the strigolactone receptor DWARF14 (D14), is involved in this process, but it is unclear how the effects of KAI2 on development are mediated. Here, using a combination of physiological, pharmacological, genetic and imaging approaches in Arabidopsis thaliana (Heynh.) we show that kai2 phenotypes arise because of a failure to downregulate auxin transport from the seedling shoot apex towards the root system, rather than a failure to respond to light per se. We demonstrate that KAI2 controls the light-induced remodelling of the PIN-mediated auxin transport system in seedlings, promoting a reduction in PIN7 abundance in older tissues, and an increase of PIN1/PIN2 abundance in the root meristem. We show that removing PIN3, PIN4 and PIN7 from kai2 mutants, or pharmacological inhibition of auxin transport and synthesis, is sufficient to suppress most kai2 seedling phenotypes. We conclude that KAI2 regulates seedling morphogenesis by its effects on the auxin transport system. We propose that KAI2 is not required for the light-mediated changes in PIN gene expression but is required for the appropriate changes in PIN protein abundance within cells.},
	language = {en},
	number = {1},
	urldate = {2022-06-09},
	journal = {New Phytologist},
	author = {Hamon-Josse, Maxime and Villaécija-Aguilar, José Antonio and Ljung, Karin and Leyser, Ottoline and Gutjahr, Caroline and Bennett, Tom},
	year = {2022},
	keywords = {Arabidopsis, KAI2 signalling, PIN proteins, auxin, auxin transport, light signalling, seedling development},
	pages = {126--140},
}

Photomorphogenic remodelling of seedling growth is a key developmental transition in the plant life cycle. The α/β-hydrolase signalling protein KARRIKIN-INSENSITIVE2 (KAI2), a close homologue of the strigolactone receptor DWARF14 (D14), is involved in this process, but it is unclear how the effects of KAI2 on development are mediated. Here, using a combination of physiological, pharmacological, genetic and imaging approaches in Arabidopsis thaliana (Heynh.) we show that kai2 phenotypes arise because of a failure to downregulate auxin transport from the seedling shoot apex towards the root system, rather than a failure to respond to light per se. We demonstrate that KAI2 controls the light-induced remodelling of the PIN-mediated auxin transport system in seedlings, promoting a reduction in PIN7 abundance in older tissues, and an increase of PIN1/PIN2 abundance in the root meristem. We show that removing PIN3, PIN4 and PIN7 from kai2 mutants, or pharmacological inhibition of auxin transport and synthesis, is sufficient to suppress most kai2 seedling phenotypes. We conclude that KAI2 regulates seedling morphogenesis by its effects on the auxin transport system. We propose that KAI2 is not required for the light-mediated changes in PIN gene expression but is required for the appropriate changes in PIN protein abundance within cells.

@article{kokla_nitrogen_2022,
	title = {Nitrogen represses haustoria formation through abscisic acid in the parasitic plant {Phtheirospermum} japonicum},
	volume = {13},
	copyright = {2022 The Author(s)},
	issn = {2041-1723},
	url = {https://www.nature.com/articles/s41467-022-30550-x},
	doi = {10.1038/s41467-022-30550-x},
	abstract = {Parasitic plants are globally prevalent pathogens that withdraw nutrients from their host plants using an organ known as the haustorium. The external environment including nutrient availability affects the extent of parasitism and to understand this phenomenon, we investigated the role of nutrients and found that nitrogen is sufficient to repress haustoria formation in the root parasite Phtheirospermum japonicum. Nitrogen increases levels of abscisic acid (ABA) in P. japonicum and prevents the activation of hundreds of genes including cell cycle and xylem development genes. Blocking ABA signaling overcomes nitrogen’s inhibitory effects indicating that nitrogen represses haustoria formation by increasing ABA. The effect of nitrogen appears more widespread since nitrogen also inhibits haustoria in the obligate root parasite Striga hermonthica. Together, our data show that nitrogen acts as a haustoria repressing factor and suggests a mechanism whereby parasitic plants use nitrogen availability in the external environment to regulate the extent of parasitism.},
	language = {en},
	number = {1},
	urldate = {2022-06-02},
	journal = {Nature Communications},
	author = {Kokla, Anna and Leso, Martina and Zhang, Xiang and Simura, Jan and Serivichyaswat, Phanu T. and Cui, Songkui and Ljung, Karin and Yoshida, Satoko and Melnyk, Charles W.},
	month = may,
	year = {2022},
	keywords = {Parasitism, Plant hormones, Plant physiology},
	pages = {2976},
}

Parasitic plants are globally prevalent pathogens that withdraw nutrients from their host plants using an organ known as the haustorium. The external environment including nutrient availability affects the extent of parasitism and to understand this phenomenon, we investigated the role of nutrients and found that nitrogen is sufficient to repress haustoria formation in the root parasite Phtheirospermum japonicum. Nitrogen increases levels of abscisic acid (ABA) in P. japonicum and prevents the activation of hundreds of genes including cell cycle and xylem development genes. Blocking ABA signaling overcomes nitrogen’s inhibitory effects indicating that nitrogen represses haustoria formation by increasing ABA. The effect of nitrogen appears more widespread since nitrogen also inhibits haustoria in the obligate root parasite Striga hermonthica. Together, our data show that nitrogen acts as a haustoria repressing factor and suggests a mechanism whereby parasitic plants use nitrogen availability in the external environment to regulate the extent of parasitism.

@article{burko_pif7_2022,
	title = {{PIF7} is a master regulator of thermomorphogenesis in shade},
	volume = {13},
	copyright = {2022 The Author(s)},
	issn = {2041-1723},
	url = {https://www.nature.com/articles/s41467-022-32585-6},
	doi = {10.1038/s41467-022-32585-6},
	abstract = {The size of plant organs is highly responsive to environmental conditions. The plant’s embryonic stem, or hypocotyl, displays phenotypic plasticity, in response to light and temperature. The hypocotyl of shade avoiding species elongates to outcompete neighboring plants and secure access to sunlight. Similar elongation occurs in high temperature. However, it is poorly understood how environmental light and temperature cues interact to effect plant growth. We found that shade combined with warm temperature produces a synergistic hypocotyl growth response that dependent on PHYTOCHROME-INTERACTING FACTOR 7 (PIF7) and auxin. This unique but agriculturally relevant scenario was almost totally independent on PIF4 activity. We show that warm temperature is sufficient to promote PIF7 DNA binding but not transcriptional activation and we demonstrate that additional, unknown factor/s must be working downstream of the phyB-PIF-auxin module. Our findings will improve the predictions of how plants will respond to increased ambient temperatures when grown at high density.},
	language = {en},
	number = {1},
	urldate = {2022-09-01},
	journal = {Nature Communications},
	author = {Burko, Yogev and Willige, Björn Christopher and Seluzicki, Adam and Novák, Ondřej and Ljung, Karin and Chory, Joanne},
	month = aug,
	year = {2022},
	note = {Number: 1
Publisher: Nature Publishing Group},
	keywords = {Light responses, Plant development, Plant signalling},
	pages = {4942},
}

The size of plant organs is highly responsive to environmental conditions. The plant’s embryonic stem, or hypocotyl, displays phenotypic plasticity, in response to light and temperature. The hypocotyl of shade avoiding species elongates to outcompete neighboring plants and secure access to sunlight. Similar elongation occurs in high temperature. However, it is poorly understood how environmental light and temperature cues interact to effect plant growth. We found that shade combined with warm temperature produces a synergistic hypocotyl growth response that dependent on PHYTOCHROME-INTERACTING FACTOR 7 (PIF7) and auxin. This unique but agriculturally relevant scenario was almost totally independent on PIF4 activity. We show that warm temperature is sufficient to promote PIF7 DNA binding but not transcriptional activation and we demonstrate that additional, unknown factor/s must be working downstream of the phyB-PIF-auxin module. Our findings will improve the predictions of how plants will respond to increased ambient temperatures when grown at high density.

@article{templalexis_potassium_2022,
	title = {Potassium transporter {TRH1}/{KUP4} contributes to distinct auxin-mediated root system architecture responses},
	volume = {188},
	issn = {0032-0889},
	url = {https://doi.org/10.1093/plphys/kiab472},
	doi = {10.1093/plphys/kiab472},
	abstract = {In plants, auxin transport and development are tightly coupled, just as hormone and growth responses are intimately linked in multicellular systems. Here we provide insights into uncoupling this tight control by specifically targeting the expression of TINY ROOT HAIR 1 (TRH1), a member of plant high-affinity potassium (K+)/K+ uptake/K+ transporter (HAK/KUP/KT) transporters that facilitate K+ uptake by co-transporting protons, in Arabidopsis root cell files. Use of this system pinpointed specific root developmental responses to acropetal versus basipetal auxin transport. Loss of TRH1 function shows TRHs and defective root gravitropism, associated with auxin imbalance in the root apex. Cell file-specific expression of TRH1 in the central cylinder rescued trh1 root agravitropism, whereas positional TRH1 expression in peripheral cell layers, including epidermis and cortex, restored trh1 defects. Applying a system-level approach, the role of RAP2.11 and ROOT HAIR DEFECTIVE-LIKE 5 transcription factors (TFs) in root hair development was verified. Furthermore, ERF53 and WRKY51 TFs were overrepresented upon restoration of root gravitropism supporting involvement in gravitropic control. Auxin has a central role in shaping root system architecture by regulating multiple developmental processes. We reveal that TRH1 jointly modulates intracellular ionic gradients and cell-to-cell polar auxin transport to drive root epidermal cell differentiation and gravitropic response. Our results indicate the developmental importance of HAK/KUP/KT proton-coupled K+ transporters.},
	number = {2},
	urldate = {2022-03-24},
	journal = {Plant Physiology},
	author = {Templalexis, Dimitris and Tsitsekian, Dikran and Liu, Chen and Daras, Gerasimos and Šimura, Jan and Moschou, Panagiotis and Ljung, Karin and Hatzopoulos, Polydefkis and Rigas, Stamatis},
	month = feb,
	year = {2022},
	pages = {1043--1060},
}

In plants, auxin transport and development are tightly coupled, just as hormone and growth responses are intimately linked in multicellular systems. Here we provide insights into uncoupling this tight control by specifically targeting the expression of TINY ROOT HAIR 1 (TRH1), a member of plant high-affinity potassium (K+)/K+ uptake/K+ transporter (HAK/KUP/KT) transporters that facilitate K+ uptake by co-transporting protons, in Arabidopsis root cell files. Use of this system pinpointed specific root developmental responses to acropetal versus basipetal auxin transport. Loss of TRH1 function shows TRHs and defective root gravitropism, associated with auxin imbalance in the root apex. Cell file-specific expression of TRH1 in the central cylinder rescued trh1 root agravitropism, whereas positional TRH1 expression in peripheral cell layers, including epidermis and cortex, restored trh1 defects. Applying a system-level approach, the role of RAP2.11 and ROOT HAIR DEFECTIVE-LIKE 5 transcription factors (TFs) in root hair development was verified. Furthermore, ERF53 and WRKY51 TFs were overrepresented upon restoration of root gravitropism supporting involvement in gravitropic control. Auxin has a central role in shaping root system architecture by regulating multiple developmental processes. We reveal that TRH1 jointly modulates intracellular ionic gradients and cell-to-cell polar auxin transport to drive root epidermal cell differentiation and gravitropic response. Our results indicate the developmental importance of HAK/KUP/KT proton-coupled K+ transporters.

@article{navarro-quiles_arabidopsis_2022,
	title = {The {Arabidopsis} {ATP}-{Binding} {Cassette} {E} protein {ABCE2} is a conserved component of the translation machinery},
	volume = {13},
	issn = {1664-462X},
	url = {https://www.frontiersin.org/articles/10.3389/fpls.2022.1009895},
	abstract = {ATP-Binding Cassette E (ABCE) proteins dissociate cytoplasmic ribosomes after translation terminates, and contribute to ribosome recycling, thus linking translation termination to initiation. This function has been demonstrated to be essential in animals, fungi, and archaea, but remains unexplored in plants. In most species, ABCE is encoded by a single-copy gene; by contrast, Arabidopsis thaliana has two ABCE paralogs, of which ABCE2 seems to conserve the ancestral function. We isolated apiculata7-1 (api7-1), the first viable, hypomorphic allele of ABCE2, which has a pleiotropic morphological phenotype reminiscent of mutations affecting ribosome biogenesis factors and ribosomal proteins. We also studied api7-2, a null, recessive lethal allele of ABCE2. Co-immunoprecipitation experiments showed that ABCE2 physically interacts with components of the translation machinery. An RNA-seq study of the api7-1 mutant showed increased responses to iron and sulfur starvation. We also found increased transcript levels of genes related to auxin signaling and metabolism. Our results support for the first time a conserved role for ABCE proteins in translation in plants, as previously shown for the animal, fungal, and archaeal lineages. In Arabidopsis, the ABCE2 protein seems important for general growth and vascular development, likely due to an indirect effect through auxin metabolism.},
	urldate = {2022-11-10},
	journal = {Frontiers in Plant Science},
	author = {Navarro-Quiles, Carla and Mateo-Bonmatí, Eduardo and Candela, Héctor and Robles, Pedro and Martínez-Laborda, Antonio and Fernández, Yolanda and Šimura, Jan and Ljung, Karin and Rubio, Vicente and Ponce, María Rosa and Micol, José Luis},
	month = oct,
	year = {2022},
	keywords = {⛔ No DOI found},
}

ATP-Binding Cassette E (ABCE) proteins dissociate cytoplasmic ribosomes after translation terminates, and contribute to ribosome recycling, thus linking translation termination to initiation. This function has been demonstrated to be essential in animals, fungi, and archaea, but remains unexplored in plants. In most species, ABCE is encoded by a single-copy gene; by contrast, Arabidopsis thaliana has two ABCE paralogs, of which ABCE2 seems to conserve the ancestral function. We isolated apiculata7-1 (api7-1), the first viable, hypomorphic allele of ABCE2, which has a pleiotropic morphological phenotype reminiscent of mutations affecting ribosome biogenesis factors and ribosomal proteins. We also studied api7-2, a null, recessive lethal allele of ABCE2. Co-immunoprecipitation experiments showed that ABCE2 physically interacts with components of the translation machinery. An RNA-seq study of the api7-1 mutant showed increased responses to iron and sulfur starvation. We also found increased transcript levels of genes related to auxin signaling and metabolism. Our results support for the first time a conserved role for ABCE proteins in translation in plants, as previously shown for the animal, fungal, and archaeal lineages. In Arabidopsis, the ABCE2 protein seems important for general growth and vascular development, likely due to an indirect effect through auxin metabolism.

@article{boussardon_rpn12a_2022,
	title = {The {RPN12a} proteasome subunit is essential for the multiple hormonal homeostasis controlling the progression of leaf senescence},
	volume = {5},
	copyright = {2022 The Author(s)},
	issn = {2399-3642},
	url = {https://www.nature.com/articles/s42003-022-03998-2},
	doi = {10.1038/s42003-022-03998-2},
	abstract = {The 26S proteasome is a conserved multi-subunit machinery in eukaryotes. It selectively degrades ubiquitinated proteins, which in turn provides an efficient molecular mechanism to regulate numerous cellular functions and developmental processes. Here, we studied a new loss-of-function allele of RPN12a, a plant ortholog of the yeast and human structural component of the 19S proteasome RPN12. Combining a set of biochemical and molecular approaches, we confirmed that a rpn12a knock-out had exacerbated 20S and impaired 26S activities. The altered proteasomal activity led to a pleiotropic phenotype affecting both the vegetative growth and reproductive phase of the plant, including a striking repression of leaf senescence associate cell-death. Further investigation demonstrated that RPN12a is involved in the regulation of several conjugates associated with the auxin, cytokinin, ethylene and jasmonic acid homeostasis. Such enhanced aptitude of plant cells for survival in rpn12a contrasts with reports on animals, where 26S proteasome mutants generally show an accelerated cell death phenotype.},
	language = {en},
	number = {1},
	urldate = {2022-10-03},
	journal = {Communications Biology},
	author = {Boussardon, Clément and Bag, Pushan and Juvany, Marta and Šimura, Jan and Ljung, Karin and Jansson, Stefan and Keech, Olivier},
	month = sep,
	year = {2022},
	keywords = {Leaf development, Senescence},
	pages = {1--14},
}

The 26S proteasome is a conserved multi-subunit machinery in eukaryotes. It selectively degrades ubiquitinated proteins, which in turn provides an efficient molecular mechanism to regulate numerous cellular functions and developmental processes. Here, we studied a new loss-of-function allele of RPN12a, a plant ortholog of the yeast and human structural component of the 19S proteasome RPN12. Combining a set of biochemical and molecular approaches, we confirmed that a rpn12a knock-out had exacerbated 20S and impaired 26S activities. The altered proteasomal activity led to a pleiotropic phenotype affecting both the vegetative growth and reproductive phase of the plant, including a striking repression of leaf senescence associate cell-death. Further investigation demonstrated that RPN12a is involved in the regulation of several conjugates associated with the auxin, cytokinin, ethylene and jasmonic acid homeostasis. Such enhanced aptitude of plant cells for survival in rpn12a contrasts with reports on animals, where 26S proteasome mutants generally show an accelerated cell death phenotype.

@article{parizkova_ip_2022,
	title = {{iP} \& {OEIP} – {Cytokinin} {Micro} {Application} {Modulates} {Root} {Development} with {High} {Spatial} {Resolution}},
	issn = {2365-709X},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/admt.202101664},
	doi = {10.1002/admt.202101664},
	abstract = {State-of-the-art technology based on organic electronics can be used as a flow-free delivery method for organic substances with high spatial resolution. Such highly targeted drug micro applications can be used in plant research for the regulation of physiological processes on tissue and cellular levels. Here, for the first time, an organic electronic ion pump (OEIP) is reported that can transport an isoprenoid-type cytokinin, N6-isopentenyladenine (iP), to intact plants. Cytokinins (CKs) are plant hormones involved in many essential physiological processes, including primary root (PR) and lateral root (LR) development. Using the Arabidopsis thaliana root as a model system, efficient iP delivery is demonstrated with a biological output – cytokinin-related PR and LR growth inhibition. The spatial resolution of iP delivery, defined for the first time for an organic compound, is shown to be less than 1 mm, exclusively affecting the OEIP-targeted LR. Results from the application of the high-resolution OIEP treatment method confirm previously published findings showing that the influence of CKs may vary at different stages of LR development. Thus, OEIP-based technologies offer a novel, electronically controlled method for phytohormone delivery that could contribute to unraveling cytokinin functions during different developmental processes with high specificity.},
	language = {en},
	urldate = {2022-04-29},
	journal = {Advanced Materials Technologies},
	author = {Pařízková, Barbora and Antoniadi, Ioanna and Poxson, David J. and Karady, Michal and Simon, Daniel T. and Zatloukal, Marek and Strnad, Miroslav and Doležal, Karel and Novák, Ondřej and Ljung, Karin},
	month = apr,
	year = {2022},
	keywords = {arabidopsis, cytokinin, hormone delivery, lateral root, organic bioelectronics, root development, spatial resolution},
	pages = {2101664},
}

State-of-the-art technology based on organic electronics can be used as a flow-free delivery method for organic substances with high spatial resolution. Such highly targeted drug micro applications can be used in plant research for the regulation of physiological processes on tissue and cellular levels. Here, for the first time, an organic electronic ion pump (OEIP) is reported that can transport an isoprenoid-type cytokinin, N6-isopentenyladenine (iP), to intact plants. Cytokinins (CKs) are plant hormones involved in many essential physiological processes, including primary root (PR) and lateral root (LR) development. Using the Arabidopsis thaliana root as a model system, efficient iP delivery is demonstrated with a biological output – cytokinin-related PR and LR growth inhibition. The spatial resolution of iP delivery, defined for the first time for an organic compound, is shown to be less than 1 mm, exclusively affecting the OEIP-targeted LR. Results from the application of the high-resolution OIEP treatment method confirm previously published findings showing that the influence of CKs may vary at different stages of LR development. Thus, OEIP-based technologies offer a novel, electronically controlled method for phytohormone delivery that could contribute to unraveling cytokinin functions during different developmental processes with high specificity.

@article{takahashi_alterations_2021,
	title = {Alterations in hormonal signals spatially coordinate distinct responses to {DNA} double-strand breaks in {Arabidopsis} roots},
	volume = {7},
	issn = {2375-2548},
	doi = {10/gkzft9},
	abstract = {Plants have a high ability to cope with changing environments and grow continuously throughout life. However, the mechanisms by which plants strike a balance between stress response and organ growth remain elusive. Here, we found that DNA double-strand breaks enhance the accumulation of cytokinin hormones through the DNA damage signaling pathway in the Arabidopsis root tip. Our data showed that activation of cytokinin signaling suppresses the expression of some of the PIN-FORMED genes that encode efflux carriers of another hormone, auxin, thereby decreasing the auxin signals in the root tip and causing cell cycle arrest at G2 phase and stem cell death. Elevated cytokinin signaling also promotes an early transition from cell division to endoreplication in the basal part of the root apex. We propose that plant hormones spatially coordinate differential DNA damage responses, thereby maintaining genome integrity and minimizing cell death to ensure continuous root growth.},
	language = {eng},
	number = {25},
	journal = {Science Advances},
	author = {Takahashi, Naoki and Inagaki, Soichi and Nishimura, Kohei and Sakakibara, Hitoshi and Antoniadi, Ioanna and Karady, Michal and Ljung, Karin and Umeda, Masaaki},
	month = jun,
	year = {2021},
	pages = {eabg0993},
}

Plants have a high ability to cope with changing environments and grow continuously throughout life. However, the mechanisms by which plants strike a balance between stress response and organ growth remain elusive. Here, we found that DNA double-strand breaks enhance the accumulation of cytokinin hormones through the DNA damage signaling pathway in the Arabidopsis root tip. Our data showed that activation of cytokinin signaling suppresses the expression of some of the PIN-FORMED genes that encode efflux carriers of another hormone, auxin, thereby decreasing the auxin signals in the root tip and causing cell cycle arrest at G2 phase and stem cell death. Elevated cytokinin signaling also promotes an early transition from cell division to endoreplication in the basal part of the root apex. We propose that plant hormones spatially coordinate differential DNA damage responses, thereby maintaining genome integrity and minimizing cell death to ensure continuous root growth.

@article{casanova-saez_auxin_2021,
	title = {Auxin {Metabolism} in {Plants}},
	volume = {13},
	issn = {1943-0264},
	url = {http://cshperspectives.cshlp.org/lookup/doi/10.1101/cshperspect.a039867},
	doi = {10/gkcr6m},
	abstract = {The major natural auxin in plants, indole-3-acetic acid (IAA), orchestrates a plethora of developmental responses that largely depend on the formation of auxin concentration gradients within plant tissues. Together with inter- and intracellular transport, IAA metabolism—which comprises biosynthesis, conjugation, and degradation—modulates auxin gradients and is therefore critical for plant growth. It is now very well established that IAA is mainly produced from Trp and that the IPyA pathway is a major and universally conserved biosynthetic route in plants, while other redundant pathways operate in parallel. Recent findings have shown that metabolic inactivation of IAA is also redundantly performed by oxidation and conjugation processes. An exquisite spatiotemporal expression of the genes for auxin synthesis and inactivation have been shown to drive several plant developmental processes. Moreover, a group of transcription factors and epigenetic regulators controlling the expression of auxin metabolic genes have been identified in past years, which are illuminating the road to understanding the molecular mechanisms behind the coordinated responses of local auxin metabolism to specific cues. Besides transcriptional regulation, subcellular compartmentalization of the IAA metabolism and posttranslational modifications of the metabolic enzymes are emerging as important contributors to IAA homeostasis. In this review, we summarize the current knowledge on (1) the pathways for IAA biosynthesis and inactivation in plants, (2) the influence of spatiotemporally regulated IAA metabolism on auxin-mediated responses, and (3) the regulatory mechanisms that modulate IAA levels in response to external and internal cues during plant development.},
	language = {en},
	number = {3},
	urldate = {2021-06-03},
	journal = {Cold Spring Harbor Perspectives in Biology},
	author = {Casanova-Sáez, Rubén and Mateo-Bonmatí, Eduardo and Ljung, Karin},
	month = mar,
	year = {2021},
	pages = {a039867},
}

The major natural auxin in plants, indole-3-acetic acid (IAA), orchestrates a plethora of developmental responses that largely depend on the formation of auxin concentration gradients within plant tissues. Together with inter- and intracellular transport, IAA metabolism—which comprises biosynthesis, conjugation, and degradation—modulates auxin gradients and is therefore critical for plant growth. It is now very well established that IAA is mainly produced from Trp and that the IPyA pathway is a major and universally conserved biosynthetic route in plants, while other redundant pathways operate in parallel. Recent findings have shown that metabolic inactivation of IAA is also redundantly performed by oxidation and conjugation processes. An exquisite spatiotemporal expression of the genes for auxin synthesis and inactivation have been shown to drive several plant developmental processes. Moreover, a group of transcription factors and epigenetic regulators controlling the expression of auxin metabolic genes have been identified in past years, which are illuminating the road to understanding the molecular mechanisms behind the coordinated responses of local auxin metabolism to specific cues. Besides transcriptional regulation, subcellular compartmentalization of the IAA metabolism and posttranslational modifications of the metabolic enzymes are emerging as important contributors to IAA homeostasis. In this review, we summarize the current knowledge on (1) the pathways for IAA biosynthesis and inactivation in plants, (2) the influence of spatiotemporally regulated IAA metabolism on auxin-mediated responses, and (3) the regulatory mechanisms that modulate IAA levels in response to external and internal cues during plant development.

@article{galbraith_best_2021,
	title = {Best practices in plant cytometry},
	volume = {99},
	issn = {1552-4922, 1552-4930},
	url = {https://onlinelibrary.wiley.com/doi/10.1002/cyto.a.24295},
	doi = {10/gkcr59},
	language = {en},
	number = {4},
	urldate = {2021-06-03},
	journal = {Cytometry Part A},
	author = {Galbraith, David and Loureiro, João and Antoniadi, Ioanna and Bainard, Jillian and Bureš, Petr and Cápal, Petr and Castro, Mariana and Castro, Sílvia and Čertner, Martin and Čertnerová, Dora and Chumová, Zuzana and Doležel, Jaroslav and Giorgi, Debora and Husband, Brian C. and Kolář, Filip and Koutecký, Petr and Kron, Paul and Leitch, Ilia J. and Ljung, Karin and Lopes, Sara and Lučanová, Magdalena and Lucretti, Sergio and Ma, Wen and Melzer, Susanne and Molnár, István and Novák, Ondřej and Poulton, Nicole and Skalický, Vladimír and Sliwinska, Elwira and Šmarda, Petr and Smith, Tyler W. and Sun, Guiling and Talhinhas, Pedro and Tárnok, Attila and Temsch, Eva M. and Trávníček, Pavel and Urfus, Tomáš},
	month = apr,
	year = {2021},
	pages = {311--317},
}

@article{mateo-bonmati_broadening_2021,
	title = {Broadening the roles of {UDP}-glycosyltransferases in auxin homeostasis and plant development},
	issn = {1469-8137},
	doi = {10/gmhq7j},
	abstract = {The levels of the important plant growth regulator indole-3-acetic acid (IAA) are tightly controlled within plant tissues to spatiotemporally orchestrate concentration gradients that drive plant growth and development. Metabolic inactivation of bioactive IAA is known to participate in the modulation of IAA maxima and minima. IAA can be irreversibly inactivated by oxidation and conjugation to aspartate and glutamate. Usually overlooked because of its reversible nature, the most abundant inactive IAA form is the IAA-glucose (IAA-glc) conjugate. Glycosylation of IAA in Arabidopsis thaliana is reported to be carried out by UDP-glycosyltransferase 84B1 (UGT84B1), while UGT74D1 has been implicated in the glycosylation of the irreversibly formed IAA catabolite oxIAA. Here we demonstrated that both UGT84B1 and UGT74D1 modulate IAA levels throughout plant development by dual IAA and oxIAA glycosylation. Moreover, we identified a novel UGT subfamily whose members redundantly mediate the glycosylation of oxIAA and modulate skotomorphogenic growth.},
	language = {eng},
	journal = {The New Phytologist},
	author = {Mateo-Bonmatí, Eduardo and Casanova-Sáez, Rubén and Šimura, Jan and Ljung, Karin},
	month = jul,
	year = {2021},
	keywords = {Arabidopsis, IAA-glucose, UDP-glycosyltransferases (UGT), auxin, indole-3-acetic acid (IAA), oxIAA-glucose},
}

The levels of the important plant growth regulator indole-3-acetic acid (IAA) are tightly controlled within plant tissues to spatiotemporally orchestrate concentration gradients that drive plant growth and development. Metabolic inactivation of bioactive IAA is known to participate in the modulation of IAA maxima and minima. IAA can be irreversibly inactivated by oxidation and conjugation to aspartate and glutamate. Usually overlooked because of its reversible nature, the most abundant inactive IAA form is the IAA-glucose (IAA-glc) conjugate. Glycosylation of IAA in Arabidopsis thaliana is reported to be carried out by UDP-glycosyltransferase 84B1 (UGT84B1), while UGT74D1 has been implicated in the glycosylation of the irreversibly formed IAA catabolite oxIAA. Here we demonstrated that both UGT84B1 and UGT74D1 modulate IAA levels throughout plant development by dual IAA and oxIAA glycosylation. Moreover, we identified a novel UGT subfamily whose members redundantly mediate the glycosylation of oxIAA and modulate skotomorphogenic growth.

@article{mboene_noah_dynamics_2021,
	title = {Dynamics of {Auxin} and {Cytokinin} {Metabolism} during {Early} {Root} and {Hypocotyl} {Growth} in {Theobroma} cacao},
	volume = {10},
	issn = {2223-7747},
	url = {https://www.mdpi.com/2223-7747/10/5/967},
	doi = {10/gkcr5m},
	abstract = {The spatial location and timing of plant developmental events are largely regulated by the well balanced effects of auxin and cytokinin phytohormone interplay. Together with transport, localized metabolism regulates the concentration gradients of their bioactive forms, ultimately eliciting growth responses. In order to explore the dynamics of auxin and cytokinin metabolism during early seedling growth in Theobroma cacao (cacao), we have performed auxin and cytokinin metabolite profiling in hypocotyls and root developmental sections at different times by using ultra-high-performance liquid chromatography-electrospray tandem mass spectrometry (UHPLC-MS/MS). Our work provides quantitative characterization of auxin and cytokinin metabolites throughout early root and hypocotyl development and identifies common and distinctive features of auxin and cytokinin metabolism during cacao seedling development.},
	language = {en},
	number = {5},
	urldate = {2021-06-03},
	journal = {Plants},
	author = {Mboene Noah, Alexandre and Casanova-Sáez, Rubén and Makondy Ango, Rolande Eugenie and Antoniadi, Ioanna and Karady, Michal and Novák, Ondřej and Niemenak, Nicolas and Ljung, Karin},
	month = may,
	year = {2021},
	pages = {967},
}

The spatial location and timing of plant developmental events are largely regulated by the well balanced effects of auxin and cytokinin phytohormone interplay. Together with transport, localized metabolism regulates the concentration gradients of their bioactive forms, ultimately eliciting growth responses. In order to explore the dynamics of auxin and cytokinin metabolism during early seedling growth in Theobroma cacao (cacao), we have performed auxin and cytokinin metabolite profiling in hypocotyls and root developmental sections at different times by using ultra-high-performance liquid chromatography-electrospray tandem mass spectrometry (UHPLC-MS/MS). Our work provides quantitative characterization of auxin and cytokinin metabolites throughout early root and hypocotyl development and identifies common and distinctive features of auxin and cytokinin metabolism during cacao seedling development.

@article{vaughanhirsch_function_2021,
	title = {Function of the pseudo phosphotransfer proteins has diverged between rice and {Arabidopsis}},
	volume = {106},
	issn = {0960-7412, 1365-313X},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/tpj.15156},
	doi = {10/gkcr6p},
	language = {en},
	number = {1},
	urldate = {2021-06-03},
	journal = {The Plant Journal},
	author = {Vaughan‐Hirsch, John and Tallerday, Emily J. and Burr, Christian A. and Hodgens, Charlie and Boeshore, Samantha L. and Beaver, Kevin and Melling, Allison and Sari, Kartika and Kerr, Ian D. and Šimura, Jan and Ljung, Karin and Xu, Dawei and Liang, Wanqi and Bhosale, Rahul and Schaller, G. Eric and Bishopp, Anthony and Kieber, Joseph J.},
	month = apr,
	year = {2021},
	pages = {159--173},
}

@article{bai_modulation_2021,
	title = {Modulation of {Arabidopsis} root growth by specialized triterpenes},
	volume = {230},
	issn = {0028-646X, 1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/nph.17144},
	doi = {10.1111/nph.17144},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {New Phytologist},
	author = {Bai, Yuechen and Fernández‐Calvo, Patricia and Ritter, Andrés and Huang, Ancheng C. and Morales‐Herrera, Stefania and Bicalho, Keylla U. and Karady, Michal and Pauwels, Laurens and Buyst, Dieter and Njo, Maria and Ljung, Karen and Martins, José C. and Vanneste, Steffen and Beeckman, Tom and Osbourn, Anne and Goossens, Alain and Pollier, Jacob},
	month = apr,
	year = {2021},
	pages = {228--243},
}

@article{pandey_plant_2021,
	title = {Plant roots sense soil compaction through restricted ethylene diffusion},
	volume = {371},
	issn = {0036-8075, 1095-9203},
	url = {https://www.sciencemag.org/lookup/doi/10.1126/science.abf3013},
	doi = {10/ghtf3b},
	abstract = {Soil compaction represents a major challenge for modern agriculture. Compaction is intuitively thought to reduce root growth by limiting the ability of roots to penetrate harder soils. We report that root growth in compacted soil is instead actively suppressed by the volatile hormone ethylene. We found that mutant
              Arabidopsis
              and rice roots that were insensitive to ethylene penetrated compacted soil more effectively than did wild-type roots. Our results indicate that soil compaction lowers gas diffusion through a reduction in air-filled pores, thereby causing ethylene to accumulate in root tissues and trigger hormone responses that restrict growth. We propose that ethylene acts as an early warning signal for roots to avoid compacted soils, which would be relevant to research into the breeding of crops resilient to soil compaction.},
	language = {en},
	number = {6526},
	urldate = {2021-06-04},
	journal = {Science},
	author = {Pandey, Bipin K. and Huang, Guoqiang and Bhosale, Rahul and Hartman, Sjon and Sturrock, Craig J. and Jose, Lottie and Martin, Olivier C. and Karady, Michal and Voesenek, Laurentius A. C. J. and Ljung, Karin and Lynch, Jonathan P. and Brown, Kathleen M. and Whalley, William R. and Mooney, Sacha J. and Zhang, Dabing and Bennett, Malcolm J.},
	month = jan,
	year = {2021},
	pages = {276--280},
}

Soil compaction represents a major challenge for modern agriculture. Compaction is intuitively thought to reduce root growth by limiting the ability of roots to penetrate harder soils. We report that root growth in compacted soil is instead actively suppressed by the volatile hormone ethylene. We found that mutant Arabidopsis and rice roots that were insensitive to ethylene penetrated compacted soil more effectively than did wild-type roots. Our results indicate that soil compaction lowers gas diffusion through a reduction in air-filled pores, thereby causing ethylene to accumulate in root tissues and trigger hormone responses that restrict growth. We propose that ethylene acts as an early warning signal for roots to avoid compacted soils, which would be relevant to research into the breeding of crops resilient to soil compaction.

@article{landberg_studies_2021,
	title = {Studies of moss reproductive development indicate that auxin biosynthesis in apical stem cells may constitute an ancestral function for focal growth control},
	volume = {229},
	issn = {0028-646X, 1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/nph.16914},
	doi = {10.1111/nph.16914},
	language = {en},
	number = {2},
	urldate = {2021-06-07},
	journal = {New Phytologist},
	author = {Landberg, Katarina and Šimura, Jan and Ljung, Karin and Sundberg, Eva and Thelander, Mattias},
	month = jan,
	year = {2021},
	pages = {845--860},
}

@article{woude_chemical_2021,
	title = {The chemical compound ‘{Heatin}’ stimulates hypocotyl elongation and interferes with the {Arabidopsis} {NIT1}‐subfamily of nitrilases},
	issn = {0960-7412, 1365-313X},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/tpj.15250},
	doi = {10/gkcr8m},
	language = {en},
	urldate = {2021-06-03},
	journal = {The Plant Journal},
	author = {Woude, Lennard and Piotrowski, Markus and Klaasse, Gruson and Paulus, Judith K. and Krahn, Daniel and Ninck, Sabrina and Kaschani, Farnusch and Kaiser, Markus and Novák, Ondřej and Ljung, Karin and Bulder, Suzanne and Verk, Marcel and Snoek, Basten L. and Fiers, Martijn and Martin, Nathaniel I. and Hoorn, Renier A. L. and Robert, Stéphanie and Smeekens, Sjef and Zanten, Martijn},
	month = may,
	year = {2021},
	pages = {tpj.15250},
}

@article{zhang_woxauxin_2020,
	title = {A {WOX}/{Auxin} {Biosynthesis} {Module} {Controls} {Growth} to {Shape} {Leaf} {Form}},
	volume = {30},
	issn = {09609822},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0960982220313683},
	doi = {10.1016/j.cub.2020.09.037},
	language = {en},
	number = {24},
	urldate = {2021-06-07},
	journal = {Current Biology},
	author = {Zhang, Zhongjuan and Runions, Adam and Mentink, Remco A. and Kierzkowski, Daniel and Karady, Michal and Hashemi, Babak and Huijser, Peter and Strauss, Sören and Gan, Xiangchao and Ljung, Karin and Tsiantis, Miltos},
	month = dec,
	year = {2020},
	pages = {4857--4868.e6},
}

@article{ware_auxin_2020,
	title = {Auxin export from proximal fruits drives arrest in temporally competent inflorescences},
	volume = {6},
	issn = {2055-0278},
	url = {http://www.nature.com/articles/s41477-020-0661-z},
	doi = {10.1038/s41477-020-0661-z},
	language = {en},
	number = {6},
	urldate = {2021-06-07},
	journal = {Nature Plants},
	author = {Ware, Alexander and Walker, Catriona H. and Šimura, Jan and González-Suárez, Pablo and Ljung, Karin and Bishopp, Anthony and Wilson, Zoe A. and Bennett, Tom},
	month = jun,
	year = {2020},
	pages = {699--707},
}

@article{antoniadi_cell-surface_2020,
	title = {Cell-surface receptors enable perception of extracellular cytokinins},
	volume = {11},
	issn = {2041-1723},
	url = {http://www.nature.com/articles/s41467-020-17700-9},
	doi = {10.1038/s41467-020-17700-9},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Nature Communications},
	author = {Antoniadi, Ioanna and Novák, Ondřej and Gelová, Zuzana and Johnson, Alexander and Plíhal, Ondřej and Simerský, Radim and Mik, Václav and Vain, Thomas and Mateo-Bonmatí, Eduardo and Karady, Michal and Pernisová, Markéta and Plačková, Lenka and Opassathian, Korawit and Hejátko, Jan and Robert, Stéphanie and Friml, Jiří and Doležal, Karel and Ljung, Karin and Turnbull, Colin},
	month = dec,
	year = {2020},
	pages = {4284},
}

@article{brunoni_conifers_2020,
	title = {Conifers exhibit a characteristic inactivation of auxin to maintain tissue homeostasis},
	volume = {226},
	issn = {0028-646X, 1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/nph.16463},
	doi = {10.1111/nph.16463},
	language = {en},
	number = {6},
	urldate = {2021-06-07},
	journal = {New Phytologist},
	author = {Brunoni, Federica and Collani, Silvio and Casanova‐Sáez, Rubén and Šimura, Jan and Karady, Michal and Schmid, Markus and Ljung, Karin and Bellini, Catherine},
	month = jun,
	year = {2020},
	pages = {1753--1765},
}

@article{dong_heartbreak_2020,
	title = {{HEARTBREAK} {Controls} {Post}-translational {Modification} of {INDEHISCENT} to {Regulate} {Fruit} {Morphology} in {Capsella}},
	volume = {30},
	issn = {09609822},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0960982220310800},
	doi = {10.1016/j.cub.2020.07.055},
	language = {en},
	number = {19},
	urldate = {2021-06-07},
	journal = {Current Biology},
	author = {Dong, Yang and Majda, Mateusz and Šimura, Jan and Horvath, Robert and Srivastava, Anjil K. and Łangowski, Łukasz and Eldridge, Tilly and Stacey, Nicola and Slotte, Tanja and Sadanandom, Ari and Ljung, Karin and Smith, Richard S. and Østergaard, Lars},
	month = oct,
	year = {2020},
	pages = {3880--3888.e5},
}

@article{gaillochet_hy5_2020,
	title = {{HY5} and phytochrome activity modulate shoot to root coordination during thermomorphogenesis},
	issn = {1477-9129, 0950-1991},
	url = {https://journals.biologists.com/dev/article/doi/10.1242/dev.192625/267053/HY5-and-phytochrome-activity-modulate-shoot-to},
	doi = {10/gjcxk6},
	abstract = {Temperature is one of the most impactful environmental factors to which plants adjust their growth and development. While the regulation of temperature signaling has been extensively investigated for the aerial part of plants, much less is known and understood about how roots sense and modulate their growth in response to fluctuating temperatures. Here we found that shoot and root growth responses to high ambient temperature are coordinated during early seedling development. A shoot signaling module that includes HY5, the phytochromes and the PIFs exerts a central function in coupling these growth responses and maintain auxin levels in the root. In addition to the HY5/PIF-dependent shoot module, a regulatory axis composed of auxin biosynthesis and auxin perception factors controls root responses to high ambient temperature. Together, our findings show that shoot and root developmental responses to temperature are tightly coupled during thermomorphogenesis and suggest that roots integrate energy signals with local hormonal inputs.},
	language = {en},
	urldate = {2021-06-07},
	journal = {Development},
	author = {Gaillochet, Christophe and Burko, Yogev and Platre, Matthieu Pierre and Zhang, Ling and Simura, Jan and Willige, Björn C. and Kumar, S. Vinod and Ljung, Karin and Chory, Joanne and Busch, Wolfgang},
	month = jan,
	year = {2020},
	pages = {dev.192625},
}

Temperature is one of the most impactful environmental factors to which plants adjust their growth and development. While the regulation of temperature signaling has been extensively investigated for the aerial part of plants, much less is known and understood about how roots sense and modulate their growth in response to fluctuating temperatures. Here we found that shoot and root growth responses to high ambient temperature are coordinated during early seedling development. A shoot signaling module that includes HY5, the phytochromes and the PIFs exerts a central function in coupling these growth responses and maintain auxin levels in the root. In addition to the HY5/PIF-dependent shoot module, a regulatory axis composed of auxin biosynthesis and auxin perception factors controls root responses to high ambient temperature. Together, our findings show that shoot and root developmental responses to temperature are tightly coupled during thermomorphogenesis and suggest that roots integrate energy signals with local hormonal inputs.

@article{mishra_natural_2020,
	title = {Natural {Variation} in {Adventitious} {Rooting} in the {Alpine} {Perennial} {Arabis} alpina},
	volume = {9},
	issn = {2223-7747},
	url = {https://www.mdpi.com/2223-7747/9/2/184},
	doi = {10.3390/plants9020184},
	abstract = {Arctic alpine species follow a mixed clonal-sexual reproductive strategy based on the environmental conditions at flowering. Here, we explored the natural variation for adventitious root formation among genotypes of the alpine perennial Arabis alpina that show differences in flowering habit. We scored the presence of adventitious roots on the hypocotyl, main stem and axillary branches on plants growing in a long-day greenhouse. We also assessed natural variation for adventitious rooting in response to foliar auxin spray. In both experimental approaches, we did not detect a correlation between adventitious rooting and flowering habit. In the greenhouse, and without the application of synthetic auxin, the accession Wca showed higher propensity to produce adventitious roots on the main stem compared to the other accessions. The transcript accumulation of the A. alpina homologue of the auxin inducible GH3.3 gene (AaGH3.3) on stems correlated with the adventitious rooting phenotype of Wca. Synthetic auxin, 1-Naphthaleneacetic acid (1-NAA), enhanced the number of plants with adventitious roots on the main stem and axillary branches. A. alpina plants showed an age-, dosage- and genotype-dependent response to 1-NAA. Among the genotypes tested, the accession Dor was insensitive to auxin and Wca responded to auxin on axillary branches.},
	language = {en},
	number = {2},
	urldate = {2021-06-07},
	journal = {Plants},
	author = {Mishra, Priyanka and Roggen, Adrian and Ljung, Karin and Albani, Maria C.},
	month = feb,
	year = {2020},
	pages = {184},
}

Arctic alpine species follow a mixed clonal-sexual reproductive strategy based on the environmental conditions at flowering. Here, we explored the natural variation for adventitious root formation among genotypes of the alpine perennial Arabis alpina that show differences in flowering habit. We scored the presence of adventitious roots on the hypocotyl, main stem and axillary branches on plants growing in a long-day greenhouse. We also assessed natural variation for adventitious rooting in response to foliar auxin spray. In both experimental approaches, we did not detect a correlation between adventitious rooting and flowering habit. In the greenhouse, and without the application of synthetic auxin, the accession Wca showed higher propensity to produce adventitious roots on the main stem compared to the other accessions. The transcript accumulation of the A. alpina homologue of the auxin inducible GH3.3 gene (AaGH3.3) on stems correlated with the adventitious rooting phenotype of Wca. Synthetic auxin, 1-Naphthaleneacetic acid (1-NAA), enhanced the number of plants with adventitious roots on the main stem and axillary branches. A. alpina plants showed an age-, dosage- and genotype-dependent response to 1-NAA. Among the genotypes tested, the accession Dor was insensitive to auxin and Wca responded to auxin on axillary branches.

@article{lagercrantz_nyctinastic_2020,
	title = {Nyctinastic thallus movement in the liverwort {Marchantia} polymorpha is regulated by a circadian clock},
	volume = {10},
	issn = {2045-2322},
	url = {http://www.nature.com/articles/s41598-020-65372-8},
	doi = {10.1038/s41598-020-65372-8},
	abstract = {Abstract
            
              The circadian clock coordinates an organism’s growth, development and physiology with environmental factors. One illuminating example is the rhythmic growth of hypocotyls and cotyledons in
              Arabidopsis thaliana
              . Such daily oscillations in leaf position are often referred to as sleep movements or nyctinasty. Here, we report that plantlets of the liverwort
              Marchantia polymorpha
              show analogous rhythmic movements of thallus lobes, and that the circadian clock controls this rhythm, with auxin a likely output pathway affecting these movements. The mechanisms of this circadian clock are partly conserved as compared to angiosperms, with homologs to the core clock genes
              PRR
              ,
              RVE
              and
              TOC1
              forming a core transcriptional feedback loop also in
              M. polymorpha
              .},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Scientific Reports},
	author = {Lagercrantz, Ulf and Billhardt, Anja and Rousku, Sabine N. and Ljung, Karin and Eklund, D. Magnus},
	month = dec,
	year = {2020},
	pages = {8658},
}

Abstract The circadian clock coordinates an organism’s growth, development and physiology with environmental factors. One illuminating example is the rhythmic growth of hypocotyls and cotyledons in Arabidopsis thaliana . Such daily oscillations in leaf position are often referred to as sleep movements or nyctinasty. Here, we report that plantlets of the liverwort Marchantia polymorpha show analogous rhythmic movements of thallus lobes, and that the circadian clock controls this rhythm, with auxin a likely output pathway affecting these movements. The mechanisms of this circadian clock are partly conserved as compared to angiosperms, with homologs to the core clock genes PRR , RVE and TOC1 forming a core transcriptional feedback loop also in M. polymorpha .

@article{de_zio_reaction_2020,
	title = {Reaction {Wood} {Anatomical} {Traits} and {Hormonal} {Profiles} in {Poplar} {Bent} {Stem} and {Root}},
	volume = {11},
	issn = {1664-462X},
	url = {https://www.frontiersin.org/articles/10.3389/fpls.2020.590985/full},
	doi = {10.3389/fpls.2020.590985},
	abstract = {Reaction wood (RW) formation is an innate physiological response of woody plants to counteract mechanical constraints in nature, reinforce structure and redirect growth toward the vertical direction. Differences and/or similarities between stem and root response to mechanical constraints remain almost unknown especially in relation to phytohormones distribution and RW characteristics. Thus,
              Populus nigra
              stem and root subjected to static non-destructive mid-term bending treatment were analyzed. The distribution of tension and compression forces was firstly modeled along the main bent stem and root axis; then, anatomical features, chemical composition, and a complete auxin and cytokinin metabolite profiles of the stretched convex and compressed concave side of three different bent stem and root sectors were analyzed. The results showed that in bent stems RW was produced on the upper stretched convex side whereas in bent roots it was produced on the lower compressed concave side. Anatomical features and chemical analysis showed that bent stem RW was characterized by a low number of vessel, poor lignification, and high carbohydrate, and thus gelatinous layer in fiber cell wall. Conversely, in bent root, RW was characterized by high vessel number and area, without any significant variation in carbohydrate and lignin content. An antagonistic interaction of auxins and different cytokinin forms/conjugates seems to regulate critical aspects of RW formation/development in stem and root to facilitate upward/downward organ bending. The observed differences between the response stem and root to bending highlight how hormonal signaling is highly organ-dependent.},
	urldate = {2021-06-07},
	journal = {Frontiers in Plant Science},
	author = {De Zio, Elena and Montagnoli, Antonio and Karady, Michal and Terzaghi, Mattia and Sferra, Gabriella and Antoniadi, Ioanna and Scippa, Gabriella S. and Ljung, Karin and Chiatante, Donato and Trupiano, Dalila},
	month = dec,
	year = {2020},
	pages = {590985},
}

Reaction wood (RW) formation is an innate physiological response of woody plants to counteract mechanical constraints in nature, reinforce structure and redirect growth toward the vertical direction. Differences and/or similarities between stem and root response to mechanical constraints remain almost unknown especially in relation to phytohormones distribution and RW characteristics. Thus, Populus nigra stem and root subjected to static non-destructive mid-term bending treatment were analyzed. The distribution of tension and compression forces was firstly modeled along the main bent stem and root axis; then, anatomical features, chemical composition, and a complete auxin and cytokinin metabolite profiles of the stretched convex and compressed concave side of three different bent stem and root sectors were analyzed. The results showed that in bent stems RW was produced on the upper stretched convex side whereas in bent roots it was produced on the lower compressed concave side. Anatomical features and chemical analysis showed that bent stem RW was characterized by a low number of vessel, poor lignification, and high carbohydrate, and thus gelatinous layer in fiber cell wall. Conversely, in bent root, RW was characterized by high vessel number and area, without any significant variation in carbohydrate and lignin content. An antagonistic interaction of auxins and different cytokinin forms/conjugates seems to regulate critical aspects of RW formation/development in stem and root to facilitate upward/downward organ bending. The observed differences between the response stem and root to bending highlight how hormonal signaling is highly organ-dependent.

@article{smith_cep5_2020,
	title = {The {CEP5} {Peptide} {Promotes} {Abiotic} {Stress} {Tolerance}, {As} {Revealed} by {Quantitative} {Proteomics}, and {Attenuates} the {AUX}/{IAA} {Equilibrium} in {Arabidopsis}},
	volume = {19},
	issn = {15359476},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S1535947620349604},
	doi = {10.1074/mcp.RA119.001826},
	language = {en},
	number = {8},
	urldate = {2021-06-07},
	journal = {Molecular \& Cellular Proteomics},
	author = {Smith, Stephanie and Zhu, Shanshuo and Joos, Lisa and Roberts, Ianto and Nikonorova, Natalia and Vu, Lam Dai and Stes, Elisabeth and Cho, Hyunwoo and Larrieu, Antoine and Xuan, Wei and Goodall, Benjamin and van de Cotte, Brigitte and Waite, Jessic Marie and Rigal, Adeline and Ramans Harborough, Sigurd and Persiau, Geert and Vanneste, Steffen and Kirschner, Gwendolyn K. and Vandermarliere, Elien and Martens, Lennart and Stahl, Yvonne and Audenaert, Dominique and Friml, Jirí and Felix, Georg and Simon, Rüdiger and Bennett, Malcolm J. and Bishopp, Anthony and De Jaeger, Geert and Ljung, Karin and Kepinski, Stefan and Robert, Stephanie and Nemhauser, Jennifer and Hwang, Ildoo and Gevaert, Kris and Beeckman, Tom and De Smet, Ive},
	month = aug,
	year = {2020},
	pages = {1248--1262},
}

@article{vayssieres_vernalization_2020,
	title = {Vernalization shapes shoot architecture and ensures the maintenance of dormant buds in the perennial \textit{{Arabis} alpina}},
	volume = {227},
	issn = {0028-646X, 1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/nph.16470},
	doi = {10.1111/nph.16470},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {New Phytologist},
	author = {Vayssières, Alice and Mishra, Priyanka and Roggen, Adrian and Neumann, Ulla and Ljung, Karin and Albani, Maria C.},
	month = jul,
	year = {2020},
	pages = {99--115},
}

@article{van_moerkercke_myc2myc3myc4-dependent_2019,
	title = {A {MYC2}/{MYC3}/{MYC4}-dependent transcription factor network regulates water spray-responsive gene expression and jasmonate levels},
	volume = {116},
	issn = {0027-8424, 1091-6490},
	url = {http://www.pnas.org/lookup/doi/10.1073/pnas.1911758116},
	doi = {10.1073/pnas.1911758116},
	abstract = {Mechanical stimuli, such as wind, rain, and touch affect plant development, growth, pest resistance, and ultimately reproductive success. Using water spray to simulate rain, we demonstrate that jasmonic acid (JA) signaling plays a key role in early gene-expression changes, well before it leads to developmental changes in flowering and plant architecture. The JA-activated transcription factors MYC2/MYC3/MYC4 modulate transiently induced expression of 266 genes, most of which peak within 30 min, and control 52\% of genes induced {\textgreater}100-fold. Chromatin immunoprecipitation-sequencing analysis indicates that MYC2 dynamically binds {\textgreater}1,300 promoters and
              trans
              -activation assays show that MYC2 activates these promoters. By mining our multiomic datasets, we identified a core MYC2/MYC3/MYC4-dependent “regulon” of 82 genes containing many previously unknown MYC2 targets, including transcription factors
              bHLH19
              and
              ERF109
              . bHLH19 can in turn directly activate the
              ORA47
              promoter, indicating that MYC2/MYC3/MYC4 initiate a hierarchical network of downstream transcription factors. Finally, we also reveal that rapid water spray-induced accumulation of JA and JA-isoleucine is directly controlled by MYC2/MYC3/MYC4 through a positive amplification loop that regulates JA-biosynthesis genes.},
	language = {en},
	number = {46},
	urldate = {2021-06-07},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Van Moerkercke, Alex and Duncan, Owen and Zander, Mark and Šimura, Jan and Broda, Martyna and Vanden Bossche, Robin and Lewsey, Mathew G. and Lama, Sbatie and Singh, Karam B. and Ljung, Karin and Ecker, Joseph R. and Goossens, Alain and Millar, A. Harvey and Van Aken, Olivier},
	month = nov,
	year = {2019},
	pages = {23345--23356},
}

Mechanical stimuli, such as wind, rain, and touch affect plant development, growth, pest resistance, and ultimately reproductive success. Using water spray to simulate rain, we demonstrate that jasmonic acid (JA) signaling plays a key role in early gene-expression changes, well before it leads to developmental changes in flowering and plant architecture. The JA-activated transcription factors MYC2/MYC3/MYC4 modulate transiently induced expression of 266 genes, most of which peak within 30 min, and control 52% of genes induced \textgreater100-fold. Chromatin immunoprecipitation-sequencing analysis indicates that MYC2 dynamically binds \textgreater1,300 promoters and trans -activation assays show that MYC2 activates these promoters. By mining our multiomic datasets, we identified a core MYC2/MYC3/MYC4-dependent “regulon” of 82 genes containing many previously unknown MYC2 targets, including transcription factors bHLH19 and ERF109 . bHLH19 can in turn directly activate the ORA47 promoter, indicating that MYC2/MYC3/MYC4 initiate a hierarchical network of downstream transcription factors. Finally, we also reveal that rapid water spray-induced accumulation of JA and JA-isoleucine is directly controlled by MYC2/MYC3/MYC4 through a positive amplification loop that regulates JA-biosynthesis genes.

@article{brunoni_bacterial_2019,
	title = {A bacterial assay for rapid screening of {IAA} catabolic enzymes},
	volume = {15},
	issn = {1746-4811},
	url = {https://plantmethods.biomedcentral.com/articles/10.1186/s13007-019-0509-6},
	doi = {10.1186/s13007-019-0509-6},
	abstract = {Abstract
            
              Background
              
                Plants rely on concentration gradients of the native auxin, indole-3-acetic acid (IAA), to modulate plant growth and development. Both metabolic and transport processes participate in the dynamic regulation of IAA homeostasis. Free IAA levels can be reduced by inactivation mechanisms, such as conjugation and degradation. IAA can be conjugated via ester linkage to glucose, or via amide linkage to amino acids, and degraded via oxidation. Members of the UDP glucosyl transferase (UGT) family catalyze the conversion of IAA to indole-3-acetyl-1-glucosyl ester (IAGlc); by contrast, IAA is irreversibly converted to indole-3-acetyl-
                l
                -aspartic acid (IAAsp) and indole-3-acetyl glutamic acid (IAGlu) by Group II of the GRETCHEN HAGEN3 (GH3) family of acyl amido synthetases. Dioxygenase for auxin oxidation (DAO) irreversibly oxidizes IAA to oxindole-3-acetic acid (oxIAA) and, in turn, oxIAA can be further glucosylated to oxindole-3-acetyl-1-glucosyl ester (oxIAGlc) by UGTs. These metabolic pathways have been identified based on mutant analyses, in vitro activity measurements, and
                in planta
                feeding assays. In vitro assays for studying protein activity are based on producing Arabidopsis enzymes in a recombinant form in bacteria or yeast followed by recombinant protein purification. However, the need to extract and purify the recombinant proteins represents a major obstacle when performing in vitro assays.
              
            
            
              Results
              In this work we report a rapid, reproducible and cheap method to screen the enzymatic activity of recombinant proteins that are known to inactivate IAA. The enzymatic reactions are carried out directly in bacteria that produce the recombinant protein. The enzymatic products can be measured by direct injection of a small supernatant fraction from the bacterial culture on ultrahigh-performance liquid chromatography coupled to electrospray ionization tandem spectrometry (UHPLC–ESI-MS/MS). Experimental procedures were optimized for testing the activity of different classes of IAA-modifying enzymes without the need to purify recombinant protein.
            
            
              Conclusions
              This new method represents an alternative to existing in vitro assays. It can be applied to the analysis of IAA metabolites that are produced upon supplementation of substrate to engineered bacterial cultures and can be used for a rapid screening of orthologous candidate genes from non-model species.},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Plant Methods},
	author = {Brunoni, Federica and Collani, Silvio and Šimura, Jan and Schmid, Markus and Bellini, Catherine and Ljung, Karin},
	month = dec,
	year = {2019},
	pages = {126},
}

Abstract Background Plants rely on concentration gradients of the native auxin, indole-3-acetic acid (IAA), to modulate plant growth and development. Both metabolic and transport processes participate in the dynamic regulation of IAA homeostasis. Free IAA levels can be reduced by inactivation mechanisms, such as conjugation and degradation. IAA can be conjugated via ester linkage to glucose, or via amide linkage to amino acids, and degraded via oxidation. Members of the UDP glucosyl transferase (UGT) family catalyze the conversion of IAA to indole-3-acetyl-1-glucosyl ester (IAGlc); by contrast, IAA is irreversibly converted to indole-3-acetyl- l -aspartic acid (IAAsp) and indole-3-acetyl glutamic acid (IAGlu) by Group II of the GRETCHEN HAGEN3 (GH3) family of acyl amido synthetases. Dioxygenase for auxin oxidation (DAO) irreversibly oxidizes IAA to oxindole-3-acetic acid (oxIAA) and, in turn, oxIAA can be further glucosylated to oxindole-3-acetyl-1-glucosyl ester (oxIAGlc) by UGTs. These metabolic pathways have been identified based on mutant analyses, in vitro activity measurements, and in planta feeding assays. In vitro assays for studying protein activity are based on producing Arabidopsis enzymes in a recombinant form in bacteria or yeast followed by recombinant protein purification. However, the need to extract and purify the recombinant proteins represents a major obstacle when performing in vitro assays. Results In this work we report a rapid, reproducible and cheap method to screen the enzymatic activity of recombinant proteins that are known to inactivate IAA. The enzymatic reactions are carried out directly in bacteria that produce the recombinant protein. The enzymatic products can be measured by direct injection of a small supernatant fraction from the bacterial culture on ultrahigh-performance liquid chromatography coupled to electrospray ionization tandem spectrometry (UHPLC–ESI-MS/MS). Experimental procedures were optimized for testing the activity of different classes of IAA-modifying enzymes without the need to purify recombinant protein. Conclusions This new method represents an alternative to existing in vitro assays. It can be applied to the analysis of IAA metabolites that are produced upon supplementation of substrate to engineered bacterial cultures and can be used for a rapid screening of orthologous candidate genes from non-model species.

@article{doyle_role_2019,
	title = {A role for the auxin precursor anthranilic acid in root gravitropism via regulation of {PIN}-{FORMED} protein polarity and relocalisation in {Arabidopsis}},
	volume = {223},
	issn = {0028-646X, 1469-8137},
	shorttitle = {A role for the auxin precursor anthranilic acid in root gravitropism via regulation of {PIN}-{FORMED} protein polarity and relocalisation in {Arabidopsis}},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/nph.15877},
	doi = {10.1111/nph.15877},
	language = {en},
	number = {3},
	urldate = {2021-06-07},
	journal = {New Phytologist},
	author = {Doyle, Siamsa M. and Rigal, Adeline and Grones, Peter and Karady, Michal and Barange, Deepak K. and Majda, Mateusz and Pařízková, Barbora and Karampelias, Michael and Zwiewka, Marta and Pěnčík, Aleš and Almqvist, Fredrik and Ljung, Karin and Novák, Ondřej and Robert, Stéphanie},
	month = aug,
	year = {2019},
	pages = {1420--1432},
}

@article{hajheidari_autoregulation_2019,
	title = {Autoregulation of {RCO} by {Low}-{Affinity} {Binding} {Modulates} {Cytokinin} {Action} and {Shapes} {Leaf} {Diversity}},
	volume = {29},
	issn = {09609822},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0960982219313806},
	doi = {10.1016/j.cub.2019.10.040},
	language = {en},
	number = {24},
	urldate = {2021-06-07},
	journal = {Current Biology},
	author = {Hajheidari, Mohsen and Wang, Yi and Bhatia, Neha and Vuolo, Francesco and Franco-Zorrilla, José Manuel and Karady, Michal and Mentink, Remco A. and Wu, Anhui and Oluwatobi, Bello Rilwan and Müller, Bruno and Dello Ioio, Raffaele and Laurent, Stefan and Ljung, Karin and Huijser, Peter and Gan, Xiangchao and Tsiantis, Miltos},
	month = dec,
	year = {2019},
	pages = {4183--4192.e6},
}

@article{bogaert_auxin_2019,
	title = {Auxin {Function} in the {Brown} {Alga} \textit{{Dictyota} dichotoma}},
	volume = {179},
	issn = {0032-0889, 1532-2548},
	url = {https://academic.oup.com/plphys/article/179/1/280-299/6116458},
	doi = {10/gjcrcp},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Plant Physiology},
	author = {Bogaert, Kenny A. and Blommaert, Lander and Ljung, Karin and Beeckman, Tom and De Clerck, Olivier},
	month = jan,
	year = {2019},
	pages = {280--299},
}

@article{brunoni_control_2019,
	title = {Control of root meristem establishment in conifers},
	volume = {165},
	issn = {00319317},
	url = {http://doi.wiley.com/10.1111/ppl.12783},
	doi = {10.1111/ppl.12783},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Physiologia Plantarum},
	author = {Brunoni, Federica and Ljung, Karin and Bellini, Catherine},
	month = jan,
	year = {2019},
	pages = {81--89},
}

@article{mateo-bonmati_epigenetic_2019,
	title = {Epigenetic {Regulation} of {Auxin} {Homeostasis}},
	volume = {9},
	issn = {2218-273X},
	url = {https://www.mdpi.com/2218-273X/9/10/623},
	doi = {10.3390/biom9100623},
	abstract = {Epigenetic regulation involves a myriad of mechanisms that regulate the expression of loci without altering the DNA sequence. These different mechanisms primarily result in modifications of the chromatin topology or DNA chemical structure that can be heritable or transient as a dynamic response to environmental cues. The phytohormone auxin plays an important role in almost every aspect of plant life via gradient formation. Auxin maxima/minima result from a complex balance of metabolism, transport, and signaling. Although epigenetic regulation of gene expression during development has been known for decades, the specific mechanisms behind the spatiotemporal dynamics of auxin levels in plants are only just being elucidated. In this review, we gather current knowledge on the epigenetic mechanisms regulating the expression of genes for indole-3-acetic acid (IAA) metabolism and transport in Arabidopsis and discuss future perspectives of this emerging field.},
	language = {en},
	number = {10},
	urldate = {2021-06-07},
	journal = {Biomolecules},
	author = {Mateo-Bonmatí, Eduardo and Casanova-Sáez, Rubén and Ljung, Karin},
	month = oct,
	year = {2019},
	pages = {623},
}

Epigenetic regulation involves a myriad of mechanisms that regulate the expression of loci without altering the DNA sequence. These different mechanisms primarily result in modifications of the chromatin topology or DNA chemical structure that can be heritable or transient as a dynamic response to environmental cues. The phytohormone auxin plays an important role in almost every aspect of plant life via gradient formation. Auxin maxima/minima result from a complex balance of metabolism, transport, and signaling. Although epigenetic regulation of gene expression during development has been known for decades, the specific mechanisms behind the spatiotemporal dynamics of auxin levels in plants are only just being elucidated. In this review, we gather current knowledge on the epigenetic mechanisms regulating the expression of genes for indole-3-acetic acid (IAA) metabolism and transport in Arabidopsis and discuss future perspectives of this emerging field.

@article{van_der_woude_histone_2019,
	title = {{HISTONE} {DEACETYLASE} 9 stimulates auxin-dependent thermomorphogenesis in \textit{{Arabidopsis} thaliana} by mediating {H2A}.{Z} depletion},
	volume = {116},
	issn = {0027-8424, 1091-6490},
	url = {http://www.pnas.org/lookup/doi/10.1073/pnas.1911694116},
	doi = {10.1073/pnas.1911694116},
	abstract = {Many plant species respond to unfavorable high ambient temperatures by adjusting their vegetative body plan to facilitate cooling. This process is known as thermomorphogenesis and is induced by the phytohormone auxin. Here, we demonstrate that the chromatin-modifying enzyme HISTONE DEACETYLASE 9 (HDA9) mediates thermomorphogenesis but does not interfere with hypocotyl elongation during shade avoidance. HDA9 is stabilized in response to high temperature and mediates histone deacetylation at the
              YUCCA8
              locus, a rate-limiting enzyme in auxin biosynthesis, at warm temperatures. We show that HDA9 permits net eviction of the H2A.Z histone variant from nucleosomes associated with
              YUCCA8
              , allowing binding and transcriptional activation by PHYTOCHROME INTERACTING FACTOR 4, followed by auxin accumulation and thermomorphogenesis.},
	language = {en},
	number = {50},
	urldate = {2021-06-07},
	journal = {Proceedings of the National Academy of Sciences},
	author = {van der Woude, Lennard C. and Perrella, Giorgio and Snoek, Basten L. and van Hoogdalem, Mark and Novák, Ondřej and van Verk, Marcel C. and van Kooten, Heleen N. and Zorn, Lennert E. and Tonckens, Rolf and Dongus, Joram A. and Praat, Myrthe and Stouten, Evelien A. and Proveniers, Marcel C. G. and Vellutini, Elisa and Patitaki, Eirini and Shapulatov, Umidjon and Kohlen, Wouter and Balasubramanian, Sureshkumar and Ljung, Karin and van der Krol, Alexander R. and Smeekens, Sjef and Kaiserli, Eirini and van Zanten, Martijn},
	month = dec,
	year = {2019},
	pages = {25343--25354},
}

Many plant species respond to unfavorable high ambient temperatures by adjusting their vegetative body plan to facilitate cooling. This process is known as thermomorphogenesis and is induced by the phytohormone auxin. Here, we demonstrate that the chromatin-modifying enzyme HISTONE DEACETYLASE 9 (HDA9) mediates thermomorphogenesis but does not interfere with hypocotyl elongation during shade avoidance. HDA9 is stabilized in response to high temperature and mediates histone deacetylation at the YUCCA8 locus, a rate-limiting enzyme in auxin biosynthesis, at warm temperatures. We show that HDA9 permits net eviction of the H2A.Z histone variant from nucleosomes associated with YUCCA8 , allowing binding and transcriptional activation by PHYTOCHROME INTERACTING FACTOR 4, followed by auxin accumulation and thermomorphogenesis.

@article{bernackawojcik_implantable_2019,
	title = {Implantable {Organic} {Electronic} {Ion} {Pump} {Enables} {ABA} {Hormone} {Delivery} for {Control} of {Stomata} in an {Intact} {Tobacco} {Plant}},
	volume = {15},
	issn = {1613-6810, 1613-6829},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/smll.201902189},
	doi = {10/gjbhcp},
	language = {en},
	number = {43},
	urldate = {2021-06-07},
	journal = {Small},
	author = {Bernacka‐Wojcik, Iwona and Huerta, Miriam and Tybrandt, Klas and Karady, Michal and Mulla, Mohammad Yusuf and Poxson, David J. and Gabrielsson, Erik O. and Ljung, Karin and Simon, Daniel T. and Berggren, Magnus and Stavrinidou, Eleni},
	month = oct,
	year = {2019},
	pages = {1902189},
}

@article{skokan_pin-driven_2019,
	title = {{PIN}-driven auxin transport emerged early in streptophyte evolution},
	volume = {5},
	issn = {2055-0278},
	url = {http://www.nature.com/articles/s41477-019-0542-5},
	doi = {10.1038/s41477-019-0542-5},
	language = {en},
	number = {11},
	urldate = {2021-06-07},
	journal = {Nature Plants},
	author = {Skokan, Roman and Medvecká, Eva and Viaene, Tom and Vosolsobě, Stanislav and Zwiewka, Marta and Müller, Karel and Skůpa, Petr and Karady, Michal and Zhang, Yuzhou and Janacek, Dorina P. and Hammes, Ulrich Z. and Ljung, Karin and Nodzyński, Tomasz and Petrášek, Jan and Friml, Jiří},
	month = nov,
	year = {2019},
	pages = {1114--1119},
}

@article{dong_regulatory_2019,
	title = {Regulatory {Diversification} of {INDEHISCENT} in the {Capsella} {Genus} {Directs} {Variation} in {Fruit} {Morphology}},
	volume = {29},
	issn = {09609822},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0960982219300867},
	doi = {10/gfv5z4},
	language = {en},
	number = {6},
	urldate = {2021-06-07},
	journal = {Current Biology},
	author = {Dong, Yang and Jantzen, Friederike and Stacey, Nicola and Łangowski, Łukasz and Moubayidin, Laila and Šimura, Jan and Ljung, Karin and Østergaard, Lars},
	month = mar,
	year = {2019},
	pages = {1038--1046.e4},
}

@article{vain_selective_2019,
	title = {Selective auxin agonists induce specific {AUX}/{IAA} protein degradation to modulate plant development},
	volume = {116},
	issn = {0027-8424, 1091-6490},
	url = {http://www.pnas.org/lookup/doi/10.1073/pnas.1809037116},
	doi = {10/gfxjp6},
	abstract = {Auxin phytohormones control most aspects of plant development through a complex and interconnected signaling network. In the presence of auxin, AUXIN/INDOLE-3-ACETIC ACID (AUX/IAA) transcriptional repressors are targeted for degradation by the SKP1-CULLIN1-F-BOX (SCF) ubiquitin-protein ligases containing TRANSPORT INHIBITOR RESISTANT 1/AUXIN SIGNALING F-BOX (TIR1/AFB). CULLIN1-neddylation is required for SCF
              TIR1/AFB
              functionality, as exemplified by mutants deficient in the NEDD8-activating enzyme subunit AUXIN-RESISTANT 1 (AXR1). Here, we report a chemical biology screen that identifies small molecules requiring AXR1 to modulate plant development. We selected four molecules of interest, RubNeddin 1 to 4 (RN1 to -4), among which RN3 and RN4 trigger selective auxin responses at transcriptional, biochemical, and morphological levels. This selective activity is explained by their ability to consistently promote the interaction between TIR1 and a specific subset of AUX/IAA proteins, stimulating the degradation of particular AUX/IAA combinations. Finally, we performed a genetic screen using RN4, the RN with the greatest potential for dissecting auxin perception, which revealed that the chromatin remodeling ATPase BRAHMA is implicated in auxin-mediated apical hook development. These results demonstrate the power of selective auxin agonists to dissect auxin perception for plant developmental functions, as well as offering opportunities to discover new molecular players involved in auxin responses.},
	language = {en},
	number = {13},
	urldate = {2021-06-07},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Vain, Thomas and Raggi, Sara and Ferro, Noel and Barange, Deepak Kumar and Kieffer, Martin and Ma, Qian and Doyle, Siamsa M. and Thelander, Mattias and Pařízková, Barbora and Novák, Ondřej and Ismail, Alexandre and Enquist, Per-Anders and Rigal, Adeline and Łangowska, Małgorzata and Ramans Harborough, Sigurd and Zhang, Yi and Ljung, Karin and Callis, Judy and Almqvist, Fredrik and Kepinski, Stefan and Estelle, Mark and Pauwels, Laurens and Robert, Stéphanie},
	month = mar,
	year = {2019},
	pages = {6463--6472},
}

Auxin phytohormones control most aspects of plant development through a complex and interconnected signaling network. In the presence of auxin, AUXIN/INDOLE-3-ACETIC ACID (AUX/IAA) transcriptional repressors are targeted for degradation by the SKP1-CULLIN1-F-BOX (SCF) ubiquitin-protein ligases containing TRANSPORT INHIBITOR RESISTANT 1/AUXIN SIGNALING F-BOX (TIR1/AFB). CULLIN1-neddylation is required for SCF TIR1/AFB functionality, as exemplified by mutants deficient in the NEDD8-activating enzyme subunit AUXIN-RESISTANT 1 (AXR1). Here, we report a chemical biology screen that identifies small molecules requiring AXR1 to modulate plant development. We selected four molecules of interest, RubNeddin 1 to 4 (RN1 to -4), among which RN3 and RN4 trigger selective auxin responses at transcriptional, biochemical, and morphological levels. This selective activity is explained by their ability to consistently promote the interaction between TIR1 and a specific subset of AUX/IAA proteins, stimulating the degradation of particular AUX/IAA combinations. Finally, we performed a genetic screen using RN4, the RN with the greatest potential for dissecting auxin perception, which revealed that the chromatin remodeling ATPase BRAHMA is implicated in auxin-mediated apical hook development. These results demonstrate the power of selective auxin agonists to dissect auxin perception for plant developmental functions, as well as offering opportunities to discover new molecular players involved in auxin responses.

@article{wang_surveillance_2019,
	title = {Surveillance of cell wall diffusion barrier integrity modulates water and solute transport in plants},
	volume = {9},
	issn = {2045-2322},
	url = {http://www.nature.com/articles/s41598-019-40588-5},
	doi = {10/gjcrr9},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Scientific Reports},
	author = {Wang, Peng and Calvo-Polanco, Monica and Reyt, Guilhem and Barberon, Marie and Champeyroux, Chloe and Santoni, Véronique and Maurel, Christophe and Franke, Rochus B. and Ljung, Karin and Novak, Ondrej and Geldner, Niko and Boursiac, Yann and Salt, David E.},
	month = dec,
	year = {2019},
	pages = {4227},
}

@article{de_zio_tissue-specific_2019,
	title = {Tissue-specific hormone profiles from woody poplar roots under bending stress},
	volume = {165},
	issn = {00319317},
	url = {http://doi.wiley.com/10.1111/ppl.12830},
	doi = {10.1111/ppl.12830},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Physiologia Plantarum},
	author = {De Zio, Elena and Trupiano, Dalila and Karady, Michal and Antoniadi, Ioanna and Montagnoli, Antonio and Terzaghi, Mattia and Chiatante, Donato and Ljung, Karin and Scippa, Gabriella S.},
	month = jan,
	year = {2019},
	pages = {101--113},
}

@article{bhosale_mechanistic_2018,
	title = {A mechanistic framework for auxin dependent {Arabidopsis} root hair elongation to low external phosphate},
	volume = {9},
	issn = {2041-1723},
	url = {http://www.nature.com/articles/s41467-018-03851-3},
	doi = {10/gdfv4v},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Nature Communications},
	author = {Bhosale, Rahul and Giri, Jitender and Pandey, Bipin K. and Giehl, Ricardo F. H. and Hartmann, Anja and Traini, Richard and Truskina, Jekaterina and Leftley, Nicola and Hanlon, Meredith and Swarup, Kamal and Rashed, Afaf and Voß, Ute and Alonso, Jose and Stepanova, Anna and Yun, Jeonga and Ljung, Karin and Brown, Kathleen M. and Lynch, Jonathan P. and Dolan, Liam and Vernoux, Teva and Bishopp, Anthony and Wells, Darren and von Wirén, Nicolaus and Bennett, Malcolm J. and Swarup, Ranjan},
	month = dec,
	year = {2018},
	pages = {1409},
}

@article{van_der_schuren_broad_2018,
	title = {Broad spectrum developmental role of {Brachypodium} {AUX1}},
	volume = {219},
	issn = {0028646X},
	url = {http://doi.wiley.com/10.1111/nph.15332},
	doi = {10/gd3g53},
	language = {en},
	number = {4},
	urldate = {2021-06-07},
	journal = {New Phytologist},
	author = {van der Schuren, Alja and Voiniciuc, Catalin and Bragg, Jennifer and Ljung, Karin and Vogel, John and Pauly, Markus and Hardtke, Christian S.},
	month = sep,
	year = {2018},
	pages = {1216--1223},
}

@article{edwards_circadian_2018,
	title = {Circadian clock components control daily growth activities by modulating cytokinin levels and cell division-associated gene expression in \textit{{Populus}} trees: {Control} of growth in {Populus}.},
	volume = {41},
	issn = {01407791},
	shorttitle = {Circadian clock components control daily growth activities by modulating cytokinin levels and cell division-associated gene expression in \textit{{Populus}} trees},
	url = {http://doi.wiley.com/10.1111/pce.13185},
	doi = {10/gd8xdq},
	language = {en},
	number = {6},
	urldate = {2021-06-07},
	journal = {Plant, Cell \& Environment},
	author = {Edwards, Kieron D. and Takata, Naoki and Johansson, Mikael and Jurca, Manuela and Novák, Ondřej and Hényková, Eva and Liverani, Silvia and Kozarewa, Iwanka and Strnad, Miroslav and Millar, Andrew J. and Ljung, Karin and Eriksson, Maria E.},
	month = jun,
	year = {2018},
	pages = {1468--1482},
}

@article{bai_combined_2018,
	title = {Combined transcriptome and translatome analyses reveal a role for tryptophan-dependent auxin biosynthesis in the control of \textit{{DOG1}} -dependent seed dormancy},
	volume = {217},
	issn = {0028646X},
	url = {http://doi.wiley.com/10.1111/nph.14885},
	doi = {10/gcwrgv},
	language = {en},
	number = {3},
	urldate = {2021-06-07},
	journal = {New Phytologist},
	author = {Bai, Bing and Novák, Ondřej and Ljung, Karin and Hanson, Johannes and Bentsink, Leónie},
	month = feb,
	year = {2018},
	pages = {1077--1085},
}

@article{simura_plant_2018,
	title = {Plant {Hormonomics}: {Multiple} {Phytohormone} {Profiling} by {Targeted} {Metabolomics}},
	volume = {177},
	issn = {1532-2548},
	shorttitle = {Plant {Hormonomics}},
	url = {https://academic.oup.com/plphys/article/177/2/476/6117035},
	doi = {10/gdrpsw},
	abstract = {Abstract
            Phytohormones are physiologically important small molecules that play essential roles in intricate signaling networks that regulate diverse processes in plants. We present a method for the simultaneous targeted profiling of 101 phytohormone-related analytes from minute amounts of fresh plant material (less than 20 mg). Rapid and nonselective extraction, fast one-step sample purification, and extremely sensitive ultra-high-performance liquid chromatography-tandem mass spectrometry enable concurrent quantification of the main phytohormone classes: cytokinins, auxins, brassinosteroids, gibberellins, jasmonates, salicylates, and abscisates. We validated this hormonomic approach in salt-stressed and control Arabidopsis (Arabidopsis thaliana) seedlings, quantifying a total of 43 endogenous compounds in both root and shoot samples. Subsequent multivariate statistical data processing and cross-validation with transcriptomic data highlighted the main hormone metabolites involved in plant adaptation to salt stress.},
	language = {en},
	number = {2},
	urldate = {2021-06-07},
	journal = {Plant Physiology},
	author = {Šimura, Jan and Antoniadi, Ioanna and Široká, Jitka and Tarkowská, Danu¡e and Strnad, Miroslav and Ljung, Karin and Novák, Ondřej},
	month = jun,
	year = {2018},
	pages = {476--489},
}

Abstract Phytohormones are physiologically important small molecules that play essential roles in intricate signaling networks that regulate diverse processes in plants. We present a method for the simultaneous targeted profiling of 101 phytohormone-related analytes from minute amounts of fresh plant material (less than 20 mg). Rapid and nonselective extraction, fast one-step sample purification, and extremely sensitive ultra-high-performance liquid chromatography-tandem mass spectrometry enable concurrent quantification of the main phytohormone classes: cytokinins, auxins, brassinosteroids, gibberellins, jasmonates, salicylates, and abscisates. We validated this hormonomic approach in salt-stressed and control Arabidopsis (Arabidopsis thaliana) seedlings, quantifying a total of 43 endogenous compounds in both root and shoot samples. Subsequent multivariate statistical data processing and cross-validation with transcriptomic data highlighted the main hormone metabolites involved in plant adaptation to salt stress.

@article{giri_rice_2018,
	title = {Rice auxin influx carrier {OsAUX1} facilitates root hair elongation in response to low external phosphate},
	volume = {9},
	issn = {2041-1723},
	url = {http://www.nature.com/articles/s41467-018-03850-4},
	doi = {10.1038/s41467-018-03850-4},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Nature Communications},
	author = {Giri, Jitender and Bhosale, Rahul and Huang, Guoqiang and Pandey, Bipin K. and Parker, Helen and Zappala, Susan and Yang, Jing and Dievart, Anne and Bureau, Charlotte and Ljung, Karin and Price, Adam and Rose, Terry and Larrieu, Antoine and Mairhofer, Stefan and Sturrock, Craig J. and White, Philip and Dupuy, Lionel and Hawkesford, Malcolm and Perin, Christophe and Liang, Wanqi and Peret, Benjamin and Hodgman, Charlie T. and Lynch, Jonathan and Wissuwa, Matthias and Zhang, Dabing and Pridmore, Tony and Mooney, Sacha J. and Guiderdoni, Emmanuel and Swarup, Ranjan and Bennett, Malcolm J.},
	month = dec,
	year = {2018},
	pages = {1408},
}

@article{orman-ligeza_xerobranching_2018,
	title = {The {Xerobranching} {Response} {Represses} {Lateral} {Root} {Formation} {When} {Roots} {Are} {Not} in {Contact} with {Water}},
	volume = {28},
	issn = {09609822},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0960982218310042},
	doi = {10.1016/j.cub.2018.07.074},
	language = {en},
	number = {19},
	urldate = {2021-06-07},
	journal = {Current Biology},
	author = {Orman-Ligeza, Beata and Morris, Emily C. and Parizot, Boris and Lavigne, Tristan and Babé, Aurelie and Ligeza, Aleksander and Klein, Stephanie and Sturrock, Craig and Xuan, Wei and Novák, Ondřey and Ljung, Karin and Fernandez, Maria A. and Rodriguez, Pedro L. and Dodd, Ian C. and De Smet, Ive and Chaumont, Francois and Batoko, Henri and Périlleux, Claire and Lynch, Jonathan P. and Bennett, Malcolm J. and Beeckman, Tom and Draye, Xavier},
	month = oct,
	year = {2018},
	pages = {3165--3173.e5},
}

@article{minina_transcriptional_2018,
	title = {Transcriptional stimulation of rate-limiting components of the autophagic pathway improves plant fitness},
	volume = {69},
	issn = {0022-0957, 1460-2431},
	url = {https://academic.oup.com/jxb/article/69/6/1415/4818325},
	doi = {10.1093/jxb/ery010},
	language = {en},
	number = {6},
	urldate = {2021-06-07},
	journal = {Journal of Experimental Botany},
	author = {Minina, Elena A and Moschou, Panagiotis N and Vetukuri, Ramesh R and Sanchez-Vera, Victoria and Cardoso, Catarina and Liu, Qinsong and Elander, Pernilla H and Dalman, Kerstin and Beganovic, Mirela and Lindberg Yilmaz, Jenny and Marmon, Sofia and Shabala, Lana and Suarez, Maria F and Ljung, Karin and Novák, Ondřej and Shabala, Sergey and Stymne, Sten and Hofius, Daniel and Bozhkov, Peter V},
	editor = {Raines, Christine},
	month = mar,
	year = {2018},
	pages = {1415--1432},
}

@article{pencik_ultra-rapid_2018,
	title = {Ultra-rapid auxin metabolite profiling for high-throughput mutant screening in {Arabidopsis}},
	volume = {69},
	issn = {0022-0957, 1460-2431},
	url = {https://academic.oup.com/jxb/article/69/10/2569/4919650},
	doi = {10.1093/jxb/ery084},
	language = {en},
	number = {10},
	urldate = {2021-06-07},
	journal = {Journal of Experimental Botany},
	author = {Pěnčík, Aleš and Casanova-Sáez, Rubén and Pilařová, Veronika and Žukauskaitė, Asta and Pinto, Rui and Micol, José Luis and Ljung, Karin and Novák, Ondřej},
	month = apr,
	year = {2018},
	pages = {2569--2579},
}

@article{sun_altered_2017,
	title = {Altered expression of maize {PLASTOCHRON1} enhances biomass and seed yield by extending cell division duration},
	volume = {8},
	issn = {2041-1723},
	url = {http://www.nature.com/articles/ncomms14752},
	doi = {10.1038/ncomms14752},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Nature Communications},
	author = {Sun, Xiaohuan and Cahill, James and Van Hautegem, Tom and Feys, Kim and Whipple, Clinton and Novák, Ondrej and Delbare, Sofie and Versteele, Charlot and Demuynck, Kirin and De Block, Jolien and Storme, Veronique and Claeys, Hannes and Van Lijsebettens, Mieke and Coussens, Griet and Ljung, Karin and De Vliegher, Alex and Muszynski, Michael and Inzé, Dirk and Nelissen, Hilde},
	month = apr,
	year = {2017},
	pages = {14752},
}

@article{di_mambro_auxin_2017,
	title = {Auxin minimum triggers the developmental switch from cell division to cell differentiation in the \textit{{Arabidopsis}} root},
	volume = {114},
	issn = {0027-8424, 1091-6490},
	url = {http://www.pnas.org/lookup/doi/10.1073/pnas.1705833114},
	doi = {10/gbwhtt},
	abstract = {In multicellular organisms, a stringent control of the transition between cell division and differentiation is crucial for correct tissue and organ development. In the
              Arabidopsis
              root, the boundary between dividing and differentiating cells is positioned by the antagonistic interaction of the hormones auxin and cytokinin. Cytokinin affects polar auxin transport, but how this impacts the positional information required to establish this tissue boundary, is still unknown. By combining computational modeling with molecular genetics, we show that boundary formation is dependent on cytokinin’s control on auxin polar transport and degradation. The regulation of both processes shapes the auxin profile in a well-defined auxin minimum. This auxin minimum positions the boundary between dividing and differentiating cells, acting as a trigger for this developmental transition, thus controlling meristem size.},
	language = {en},
	number = {36},
	urldate = {2021-06-07},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Di Mambro, Riccardo and De Ruvo, Micol and Pacifici, Elena and Salvi, Elena and Sozzani, Rosangela and Benfey, Philip N. and Busch, Wolfgang and Novak, Ondrej and Ljung, Karin and Di Paola, Luisa and Marée, Athanasius F. M. and Costantino, Paolo and Grieneisen, Verônica A. and Sabatini, Sabrina},
	month = sep,
	year = {2017},
	pages = {E7641--E7649},
}

In multicellular organisms, a stringent control of the transition between cell division and differentiation is crucial for correct tissue and organ development. In the Arabidopsis root, the boundary between dividing and differentiating cells is positioned by the antagonistic interaction of the hormones auxin and cytokinin. Cytokinin affects polar auxin transport, but how this impacts the positional information required to establish this tissue boundary, is still unknown. By combining computational modeling with molecular genetics, we show that boundary formation is dependent on cytokinin’s control on auxin polar transport and degradation. The regulation of both processes shapes the auxin profile in a well-defined auxin minimum. This auxin minimum positions the boundary between dividing and differentiating cells, acting as a trigger for this developmental transition, thus controlling meristem size.

@article{martins_brassinosteroid_2017,
	title = {Brassinosteroid signaling-dependent root responses to prolonged elevated ambient temperature},
	volume = {8},
	issn = {2041-1723},
	url = {http://www.nature.com/articles/s41467-017-00355-4},
	doi = {10/gbttbb},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Nature Communications},
	author = {Martins, Sara and Montiel-Jorda, Alvaro and Cayrel, Anne and Huguet, Stéphanie and Roux, Christine Paysant-Le and Ljung, Karin and Vert, Grégory},
	month = dec,
	year = {2017},
	pages = {309},
}

@article{edlund_contrasting_2017,
	title = {Contrasting patterns of cytokinins between years in senescing aspen leaves},
	volume = {40},
	issn = {0140-7791, 1365-3040},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/pce.12899},
	doi = {10.1111/pce.12899},
	language = {en},
	number = {5},
	urldate = {2021-06-07},
	journal = {Plant, Cell \& Environment},
	author = {Edlund, Erik and Novak, Ondrej and Karady, Michal and Ljung, Karin and Jansson, Stefan},
	month = may,
	year = {2017},
	pages = {622--634},
}

@article{adolfsson_enhanced_2017,
	title = {Enhanced {Secondary}- and {Hormone} {Metabolism} in {Leaves} of {Arbuscular} {Mycorrhizal} \textit{{Medicago} truncatula}},
	volume = {175},
	issn = {0032-0889, 1532-2548},
	url = {https://academic.oup.com/plphys/article/175/1/392-411/6117013},
	doi = {10/gbvxq8},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Plant Physiology},
	author = {Adolfsson, Lisa and Nziengui, Hugues and Abreu, Ilka N and Šimura, Jan and Beebo, Azeez and Herdean, Andrei and Aboalizadeh, Jila and Široká, Jitka and Moritz, Thomas and Novák, Ondřej and Ljung, Karin and Schoefs, Benoît and Spetea, Cornelia},
	month = sep,
	year = {2017},
	pages = {392--411},
}

@incollection{kleine-vehn_high-resolution_2017,
	address = {New York, NY},
	title = {High-{Resolution} {Cell}-{Type} {Specific} {Analysis} of {Cytokinins} in {Sorted} {Root} {Cell} {Populations} of {Arabidopsis} thaliana},
	volume = {1497},
	isbn = {978-1-4939-6467-3 978-1-4939-6469-7},
	url = {http://link.springer.com/10.1007/978-1-4939-6469-7_19},
	language = {en},
	urldate = {2021-06-07},
	booktitle = {Plant {Hormones}},
	publisher = {Springer New York},
	author = {Novák, Ondřej and Antoniadi, Ioanna and Ljung, Karin},
	editor = {Kleine-Vehn, Jürgen and Sauer, Michael},
	year = {2017},
	doi = {10.1007/978-1-4939-6469-7_19},
	note = {Series Title: Methods in Molecular Biology},
	pages = {231--248},
}

@article{poxson_regulating_2017,
	title = {Regulating plant physiology with organic electronics},
	volume = {114},
	issn = {0027-8424, 1091-6490},
	url = {http://www.pnas.org/lookup/doi/10.1073/pnas.1617758114},
	doi = {10.1073/pnas.1617758114},
	abstract = {The organic electronic ion pump (OEIP) provides flow-free and accurate delivery of small signaling compounds at high spatiotemporal resolution. To date, the application of OEIPs has been limited to delivery of nonaromatic molecules to mammalian systems, particularly for neuroscience applications. However, many long-standing questions in plant biology remain unanswered due to a lack of technology that precisely delivers plant hormones, based on cyclic alkanes or aromatic structures, to regulate plant physiology. Here, we report the employment of OEIPs for the delivery of the plant hormone auxin to induce differential concentration gradients and modulate plant physiology. We fabricated OEIP devices based on a synthesized dendritic polyelectrolyte that enables electrophoretic transport of aromatic substances. Delivery of auxin to transgenic
              Arabidopsis thaliana
              seedlings in vivo was monitored in real time via dynamic fluorescent auxin-response reporters and induced physiological responses in roots. Our results provide a starting point for technologies enabling direct, rapid, and dynamic electronic interaction with the biochemical regulation systems of plants.},
	language = {en},
	number = {18},
	urldate = {2021-06-07},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Poxson, David J. and Karady, Michal and Gabrielsson, Roger and Alkattan, Aziz Y. and Gustavsson, Anna and Doyle, Siamsa M. and Robert, Stéphanie and Ljung, Karin and Grebe, Markus and Simon, Daniel T. and Berggren, Magnus},
	month = may,
	year = {2017},
	pages = {4597--4602},
}

The organic electronic ion pump (OEIP) provides flow-free and accurate delivery of small signaling compounds at high spatiotemporal resolution. To date, the application of OEIPs has been limited to delivery of nonaromatic molecules to mammalian systems, particularly for neuroscience applications. However, many long-standing questions in plant biology remain unanswered due to a lack of technology that precisely delivers plant hormones, based on cyclic alkanes or aromatic structures, to regulate plant physiology. Here, we report the employment of OEIPs for the delivery of the plant hormone auxin to induce differential concentration gradients and modulate plant physiology. We fabricated OEIP devices based on a synthesized dendritic polyelectrolyte that enables electrophoretic transport of aromatic substances. Delivery of auxin to transgenic Arabidopsis thaliana seedlings in vivo was monitored in real time via dynamic fluorescent auxin-response reporters and induced physiological responses in roots. Our results provide a starting point for technologies enabling direct, rapid, and dynamic electronic interaction with the biochemical regulation systems of plants.

@article{ge_shade_2017,
	title = {{SHADE} {AVOIDANCE} 4 {Is} {Required} for {Proper} {Auxin} {Distribution} in the {Hypocotyl}},
	volume = {173},
	issn = {0032-0889, 1532-2548},
	url = {https://academic.oup.com/plphys/article/173/1/788-800/6116141},
	doi = {10.1104/pp.16.01491},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Plant Physiology},
	author = {Ge, Yanhua and Yan, Fenglian and Zourelidou, Melina and Wang, Meiling and Ljung, Karin and Fastner, Astrid and Hammes, Ulrich Z. and Di Donato, Martin and Geisler, Markus and Schwechheimer, Claus and Tao, Yi},
	month = jan,
	year = {2017},
	pages = {788--800},
}

@article{weiste_arabidopsis_2017,
	title = {The {Arabidopsis} {bZIP11} transcription factor links low-energy signalling to auxin-mediated control of primary root growth},
	volume = {13},
	issn = {1553-7404},
	url = {https://dx.plos.org/10.1371/journal.pgen.1006607},
	doi = {10.1371/journal.pgen.1006607},
	language = {en},
	number = {2},
	urldate = {2021-06-07},
	journal = {PLOS Genetics},
	author = {Weiste, Christoph and Pedrotti, Lorenzo and Selvanayagam, Jebasingh and Muralidhara, Prathibha and Fröschel, Christian and Novák, Ondřej and Ljung, Karin and Hanson, Johannes and Dröge-Laser, Wolfgang},
	editor = {Reed, Jason},
	month = feb,
	year = {2017},
	pages = {e1006607},
}

@article{yan_type_2017,
	title = {Type {B} {Response} {Regulators} {Act} {As} {Central} {Integrators} in {Transcriptional} {Control} of the {Auxin} {Biosynthesis} {Enzyme} {TAA1}},
	volume = {175},
	issn = {0032-0889, 1532-2548},
	url = {https://academic.oup.com/plphys/article/175/3/1438-1454/6117004},
	doi = {10/gckj69},
	language = {en},
	number = {3},
	urldate = {2021-06-07},
	journal = {Plant Physiology},
	author = {Yan, Zhenwei and Liu, Xin and Ljung, Karin and Li, Shuning and Zhao, Wanying and Yang, Fan and Wang, Meiling and Tao, Yi},
	month = nov,
	year = {2017},
	pages = {1438--1454},
}

@article{novak_zooming_2017,
	title = {Zooming {In} on {Plant} {Hormone} {Analysis}: {Tissue}- and {Cell}-{Specific} {Approaches}},
	volume = {68},
	issn = {1543-5008, 1545-2123},
	shorttitle = {Zooming {In} on {Plant} {Hormone} {Analysis}},
	url = {http://www.annualreviews.org/doi/10.1146/annurev-arplant-042916-040812},
	doi = {10.1146/annurev-arplant-042916-040812},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Annual Review of Plant Biology},
	author = {Novák, Ondřej and Napier, Richard and Ljung, Karin},
	month = apr,
	year = {2017},
	pages = {323--348},
}

@article{steenackers_cis-cinnamic_2017,
	title = {cis-{Cinnamic} {Acid} {Is} a {Novel}, {Natural} {Auxin} {Efflux} {Inhibitor} {That} {Promotes} {Lateral} {Root} {Formation}},
	volume = {173},
	issn = {0032-0889, 1532-2548},
	url = {https://academic.oup.com/plphys/article/173/1/552-565/6116022},
	doi = {10.1104/pp.16.00943},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Plant Physiology},
	author = {Steenackers, Ward and Klíma, Petr and Quareshy, Mussa and Cesarino, Igor and Kumpf, Robert P. and Corneillie, Sander and Araújo, Pedro and Viaene, Tom and Goeminne, Geert and Nowack, Moritz K. and Ljung, Karin and Friml, Jiří and Blakeslee, Joshua J. and Novák, Ondřej and Zažímalová, Eva and Napier, Richard and Boerjan, Wout and Vanholme, Bartel},
	month = jan,
	year = {2017},
	pages = {552--565},
}

@article{bennett_connective_2016,
	title = {Connective {Auxin} {Transport} in the {Shoot} {Facilitates} {Communication} between {Shoot} {Apices}},
	volume = {14},
	issn = {1545-7885},
	url = {https://dx.plos.org/10.1371/journal.pbio.1002446},
	doi = {10/f3t29d},
	language = {en},
	number = {4},
	urldate = {2021-06-07},
	journal = {PLOS Biology},
	author = {Bennett, Tom and Hines, Geneviève and van Rongen, Martin and Waldie, Tanya and Sawchuk, Megan G. and Scarpella, Enrico and Ljung, Karin and Leyser, Ottoline},
	editor = {Reed, Jason},
	month = apr,
	year = {2016},
	pages = {e1002446},
}

@article{pedmale_cryptochromes_2016,
	title = {Cryptochromes {Interact} {Directly} with {PIFs} to {Control} {Plant} {Growth} in {Limiting} {Blue} {Light}},
	volume = {164},
	issn = {00928674},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0092867415016426},
	doi = {10.1016/j.cell.2015.12.018},
	language = {en},
	number = {1-2},
	urldate = {2021-06-07},
	journal = {Cell},
	author = {Pedmale, Ullas V. and Huang, Shao-shan Carol and Zander, Mark and Cole, Benjamin J. and Hetzel, Jonathan and Ljung, Karin and Reis, Pedro A.B. and Sridevi, Priya and Nito, Kazumasa and Nery, Joseph R. and Ecker, Joseph R. and Chory, Joanne},
	month = jan,
	year = {2016},
	pages = {233--245},
}

@article{porco_dioxygenase-encoding_2016,
	title = {Dioxygenase-encoding \textit{{AtDAO1}} gene controls {IAA} oxidation and homeostasis in \textit{{Arabidopsis}}},
	volume = {113},
	issn = {0027-8424, 1091-6490},
	url = {http://www.pnas.org/lookup/doi/10.1073/pnas.1604375113},
	doi = {10/f3t58q},
	abstract = {Auxin represents a key signal in plants, regulating almost every aspect of their growth and development. Major breakthroughs have been made dissecting the molecular basis of auxin transport, perception, and response. In contrast, how plants control the metabolism and homeostasis of the major form of auxin in plants, indole-3-acetic acid (IAA), remains unclear. In this paper, we initially describe the function of the
              Arabidopsis thaliana
              gene
              DIOXYGENASE FOR AUXIN OXIDATION 1
              (
              AtDAO1
              ). Transcriptional and translational reporter lines revealed that
              AtDAO1
              encodes a highly root-expressed, cytoplasmically localized IAA oxidase. Stable isotope-labeled IAA feeding studies of loss and gain of function
              AtDAO1
              lines showed that this oxidase represents the major regulator of auxin degradation to 2-oxoindole-3-acetic acid (oxIAA) in
              Arabidopsis
              . Surprisingly,
              AtDAO1
              loss and gain of function lines exhibited relatively subtle auxin-related phenotypes, such as altered root hair length. Metabolite profiling of mutant lines revealed that disrupting
              AtDAO1
              regulation resulted in major changes in steady-state levels of oxIAA and IAA conjugates but not IAA. Hence, IAA conjugation and catabolism seem to regulate auxin levels in
              Arabidopsis
              in a highly redundant manner. We observed that transcripts of
              AtDOA1
              IAA oxidase and
              GH3
              IAA-conjugating enzymes are auxin-inducible, providing a molecular basis for their observed functional redundancy. We conclude that the
              AtDAO1
              gene plays a key role regulating auxin homeostasis in
              Arabidopsis
              , acting in concert with
              GH3
              genes, to maintain auxin concentration at optimal levels for plant growth and development.},
	language = {en},
	number = {39},
	urldate = {2021-06-07},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Porco, Silvana and Pěnčík, Aleš and Rashed, Afaf and Voß, Ute and Casanova-Sáez, Rubén and Bishopp, Anthony and Golebiowska, Agata and Bhosale, Rahul and Swarup, Ranjan and Swarup, Kamal and Peňáková, Pavlína and Novák, Ondřej and Staswick, Paul and Hedden, Peter and Phillips, Andrew L. and Vissenberg, Kris and Bennett, Malcolm J. and Ljung, Karin},
	month = sep,
	year = {2016},
	pages = {11016--11021},
}

Auxin represents a key signal in plants, regulating almost every aspect of their growth and development. Major breakthroughs have been made dissecting the molecular basis of auxin transport, perception, and response. In contrast, how plants control the metabolism and homeostasis of the major form of auxin in plants, indole-3-acetic acid (IAA), remains unclear. In this paper, we initially describe the function of the Arabidopsis thaliana gene DIOXYGENASE FOR AUXIN OXIDATION 1 ( AtDAO1 ). Transcriptional and translational reporter lines revealed that AtDAO1 encodes a highly root-expressed, cytoplasmically localized IAA oxidase. Stable isotope-labeled IAA feeding studies of loss and gain of function AtDAO1 lines showed that this oxidase represents the major regulator of auxin degradation to 2-oxoindole-3-acetic acid (oxIAA) in Arabidopsis . Surprisingly, AtDAO1 loss and gain of function lines exhibited relatively subtle auxin-related phenotypes, such as altered root hair length. Metabolite profiling of mutant lines revealed that disrupting AtDAO1 regulation resulted in major changes in steady-state levels of oxIAA and IAA conjugates but not IAA. Hence, IAA conjugation and catabolism seem to regulate auxin levels in Arabidopsis in a highly redundant manner. We observed that transcripts of AtDOA1 IAA oxidase and GH3 IAA-conjugating enzymes are auxin-inducible, providing a molecular basis for their observed functional redundancy. We conclude that the AtDAO1 gene plays a key role regulating auxin homeostasis in Arabidopsis , acting in concert with GH3 genes, to maintain auxin concentration at optimal levels for plant growth and development.

@article{mellor_dynamic_2016,
	title = {Dynamic regulation of auxin oxidase and conjugating enzymes \textit{{AtDAO1}} and \textit{{GH3}} modulates auxin homeostasis},
	volume = {113},
	issn = {0027-8424, 1091-6490},
	url = {http://www.pnas.org/lookup/doi/10.1073/pnas.1604458113},
	doi = {10/f3t6ch},
	abstract = {The hormone auxin is a key regulator of plant growth and development, and great progress has been made understanding auxin transport and signaling. Here, we show that auxin metabolism and homeostasis are also regulated in a complex manner. The principal auxin degradation pathways in
              Arabidopsis
              include oxidation by
              Arabidopsis thaliana
              gene
              DIOXYGENASE FOR AUXIN OXIDATION 1/2
              (AtDAO1/2) and conjugation by Gretchen Hagen3s (GH3s). Metabolic profiling of
              dao1-1
              root tissues revealed a 50\% decrease in the oxidation product 2-oxoindole-3-acetic acid (oxIAA) and increases in the conjugated forms indole-3-acetic acid aspartic acid (IAA-Asp) and indole-3-acetic acid glutamic acid (IAA-Glu) of 438- and 240-fold, respectively, whereas auxin remains close to the WT. By fitting parameter values to a mathematical model of these metabolic pathways, we show that, in addition to reduced oxidation, both auxin biosynthesis and conjugation are increased in
              dao1-1
              . Transcripts of
              AtDAO1
              and
              GH3
              genes increase in response to auxin over different timescales and concentration ranges. Including this regulation of
              AtDAO1
              and
              GH3
              in an extended model reveals that auxin oxidation is more important for auxin homoeostasis at lower hormone concentrations, whereas auxin conjugation is most significant at high auxin levels. Finally, embedding our homeostasis model in a multicellular simulation to assess the spatial effect of the
              dao1-1
              mutant shows that auxin increases in outer root tissues in agreement with the
              dao1-1
              mutant root hair phenotype. We conclude that auxin homeostasis is dependent on
              AtDAO1
              , acting in concert with
              GH3
              , to maintain auxin at optimal levels for plant growth and development.},
	language = {en},
	number = {39},
	urldate = {2021-06-07},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Mellor, Nathan and Band, Leah R. and Pěnčík, Aleš and Novák, Ondřej and Rashed, Afaf and Holman, Tara and Wilson, Michael H. and Voß, Ute and Bishopp, Anthony and King, John R. and Ljung, Karin and Bennett, Malcolm J. and Owen, Markus R.},
	month = sep,
	year = {2016},
	pages = {11022--11027},
}

The hormone auxin is a key regulator of plant growth and development, and great progress has been made understanding auxin transport and signaling. Here, we show that auxin metabolism and homeostasis are also regulated in a complex manner. The principal auxin degradation pathways in Arabidopsis include oxidation by Arabidopsis thaliana gene DIOXYGENASE FOR AUXIN OXIDATION 1/2 (AtDAO1/2) and conjugation by Gretchen Hagen3s (GH3s). Metabolic profiling of dao1-1 root tissues revealed a 50% decrease in the oxidation product 2-oxoindole-3-acetic acid (oxIAA) and increases in the conjugated forms indole-3-acetic acid aspartic acid (IAA-Asp) and indole-3-acetic acid glutamic acid (IAA-Glu) of 438- and 240-fold, respectively, whereas auxin remains close to the WT. By fitting parameter values to a mathematical model of these metabolic pathways, we show that, in addition to reduced oxidation, both auxin biosynthesis and conjugation are increased in dao1-1 . Transcripts of AtDAO1 and GH3 genes increase in response to auxin over different timescales and concentration ranges. Including this regulation of AtDAO1 and GH3 in an extended model reveals that auxin oxidation is more important for auxin homoeostasis at lower hormone concentrations, whereas auxin conjugation is most significant at high auxin levels. Finally, embedding our homeostasis model in a multicellular simulation to assess the spatial effect of the dao1-1 mutant shows that auxin increases in outer root tissues in agreement with the dao1-1 mutant root hair phenotype. We conclude that auxin homeostasis is dependent on AtDAO1 , acting in concert with GH3 , to maintain auxin at optimal levels for plant growth and development.

@article{zheng_local_2016,
	title = {Local auxin metabolism regulates environment-induced hypocotyl elongation},
	volume = {2},
	issn = {2055-0278},
	url = {http://www.nature.com/articles/nplants201625},
	doi = {10/f3t37r},
	language = {en},
	number = {4},
	urldate = {2021-06-07},
	journal = {Nature Plants},
	author = {Zheng, Zuyu and Guo, Yongxia and Novák, Ondřej and Chen, William and Ljung, Karin and Noel, Joseph P. and Chory, Joanne},
	month = apr,
	year = {2016},
	pages = {16025},
}

@article{pacheco-villalobos_effects_2016,
	title = {The {Effects} of {High} {Steady} {State} {Auxin} {Levels} on {Root} {Cell} {Elongation} in {Brachypodium}},
	volume = {28},
	issn = {1040-4651, 1532-298X},
	url = {https://academic.oup.com/plcell/article/28/5/1009-1024/6098461},
	doi = {10/bhng},
	language = {en},
	number = {5},
	urldate = {2021-06-07},
	journal = {The Plant Cell},
	author = {Pacheco-Villalobos, David and Díaz-Moreno, Sara M. and van der Schuren, Alja and Tamaki, Takayuki and Kang, Yeon Hee and Gujas, Bojan and Novak, Ondrej and Jaspert, Nina and Li, Zhenni and Wolf, Sebastian and Oecking, Claudia and Ljung, Karin and Bulone, Vincent and Hardtke, Christian S.},
	month = may,
	year = {2016},
	pages = {1009--1024},
}

@article{santuari_plethora_2016,
	title = {The {PLETHORA} {Gene} {Regulatory} {Network} {Guides} {Growth} and {Cell} {Differentiation} in {Arabidopsis} {Roots}},
	volume = {28},
	issn = {1040-4651, 1532-298X},
	url = {https://academic.oup.com/plcell/article/28/12/2937-2951/6098272},
	doi = {10.1105/tpc.16.00656},
	language = {en},
	number = {12},
	urldate = {2021-06-07},
	journal = {The Plant Cell},
	author = {Santuari, Luca and Sanchez-Perez, Gabino F. and Luijten, Marijn and Rutjens, Bas and Terpstra, Inez and Berke, Lidija and Gorte, Maartje and Prasad, Kalika and Bao, Dongping and Timmermans-Hereijgers, Johanna L.P.M. and Maeo, Kenichiro and Nakamura, Kenzo and Shimotohno, Akie and Pencik, Ales and Novak, Ondrej and Ljung, Karin and van Heesch, Sebastiaan and de Bruijn, Ewart and Cuppen, Edwin and Willemsen, Viola and Mähönen, Ari Pekka and Lukowitz, Wolfgang and Snel, Berend and de Ridder, Dick and Scheres, Ben and Heidstra, Renze},
	month = dec,
	year = {2016},
	pages = {2937--2951},
}

@article{steenackers_allelochemical_2016,
	title = {The allelochemical {MDCA} inhibits lignification and affects auxin homeostasis},
	issn = {0032-0889, 1532-2548},
	url = {https://academic.oup.com/plphys/article/172/2/874-888/6115977},
	doi = {10.1104/pp.15.01972},
	language = {en},
	urldate = {2021-06-07},
	journal = {Plant Physiology},
	author = {Steenackers, Ward Jan and Cesarino, Igor and Klíma, Petr and Quareshy, Mussa and Vanholme, Ruben and Corneillie, Sander and Kumpf, Robert P. and Van de Wouwer, Dorien and Ljung, Karin and Goeminne, Geert and Novak, Ondrej and Zažímalová, Eva and Napier, Richard M. and Boerjan, Wout A and Vanholme, Bartel},
	month = aug,
	year = {2016},
	pages = {pp.01972.2015},
}

@article{procko_epidermis_2016,
	title = {The epidermis coordinates auxin-induced stem growth in response to shade},
	volume = {30},
	issn = {0890-9369, 1549-5477},
	url = {http://genesdev.cshlp.org/lookup/doi/10.1101/gad.283234.116},
	doi = {10/f3t2tn},
	language = {en},
	number = {13},
	urldate = {2021-06-07},
	journal = {Genes \& Development},
	author = {Procko, Carl and Burko, Yogev and Jaillais, Yvon and Ljung, Karin and Long, Jeff A. and Chory, Joanne},
	month = jul,
	year = {2016},
	pages = {1529--1541},
}

@article{zhang_intrinsic_2015,
	title = {An intrinsic {microRNA} timer regulates progressive decline in shoot regenerative capacity in plants},
	volume = {27},
	issn = {1532-298X (Electronic) 1040-4651 (Linking)},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/25649435},
	doi = {10.1105/tpc.114.135186},
	abstract = {Plant cells are totipotent and competent to regenerate from differentiated organs. It has been shown that two phytohormones, auxin and cytokinin, play critical roles within this process. As in animals, the regenerative capacity declines with age in plants, but the molecular basis for this phenomenon remains elusive. Here, we demonstrate that an age-regulated microRNA, miR156, regulates shoot regenerative capacity. As a plant ages, the gradual increase in miR156-targeted SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) transcription factors leads to the progressive decline in shoot regenerative capacity. In old plants, SPL reduces shoot regenerative capacity by attenuating the cytokinin response through binding with the B-type ARABIDOPSIS RESPONSE REGULATORs, which encode the transcriptional activators in the cytokinin signaling pathway. Consistently, the increased amount of exogenous cytokinin complements the reduced shoot regenerative capacity in old plants. Therefore, the recruitment of age cues in response to cytokinin contributes to shoot regenerative competence.},
	language = {en},
	number = {2},
	urldate = {2021-06-07},
	journal = {Plant Cell},
	author = {Zhang, T. Q. and Lian, H. and Tang, H. and Dolezal, K. and Zhou, C. M. and Yu, S. and Chen, J. H. and Chen, Q. and Liu, H. and Ljung, K. and Wang, J. W.},
	month = feb,
	year = {2015},
	note = {Edition: 2015/02/05},
	keywords = {Arabidopsis/genetics/*physiology, Cytokinins/pharmacology, Genes, Plant, MicroRNAs/genetics/*metabolism, Plant Proteins/metabolism, Plant Shoots/*genetics/*physiology, Regeneration/*genetics, Tobacco/genetics/*physiology},
	pages = {349--60},
}

Plant cells are totipotent and competent to regenerate from differentiated organs. It has been shown that two phytohormones, auxin and cytokinin, play critical roles within this process. As in animals, the regenerative capacity declines with age in plants, but the molecular basis for this phenomenon remains elusive. Here, we demonstrate that an age-regulated microRNA, miR156, regulates shoot regenerative capacity. As a plant ages, the gradual increase in miR156-targeted SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) transcription factors leads to the progressive decline in shoot regenerative capacity. In old plants, SPL reduces shoot regenerative capacity by attenuating the cytokinin response through binding with the B-type ARABIDOPSIS RESPONSE REGULATORs, which encode the transcriptional activators in the cytokinin signaling pathway. Consistently, the increased amount of exogenous cytokinin complements the reduced shoot regenerative capacity in old plants. Therefore, the recruitment of age cues in response to cytokinin contributes to shoot regenerative competence.

@article{antoniadi_cell-type-specific_2015,
	title = {Cell-{Type}-{Specific} {Cytokinin} {Distribution} within the {Arabidopsis} {Primary} {Root} {Apex}},
	volume = {27},
	issn = {1532-298X (Electronic) 1040-4651 (Linking)},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/26152699},
	doi = {10.1105/tpc.15.00176},
	abstract = {Cytokinins (CKs) play a crucial role in many physiological and developmental processes at the levels of individual plant components (cells, tissues, and organs) and by coordinating activities across these parts. High-resolution measurements of intracellular CKs in different plant tissues can therefore provide insights into their metabolism and mode of action. Here, we applied fluorescence-activated cell sorting of green fluorescent protein (GFP)-marked cell types, combined with solid-phase microextraction and an ultra-high-sensitivity mass spectrometry (MS) method for analysis of CK biosynthesis and homeostasis at cellular resolution. This method was validated by series of control experiments, establishing that protoplast isolation and cell sorting procedures did not greatly alter endogenous CK levels. The MS-based method facilitated the quantification of all the well known CK isoprenoid metabolites in four different transgenic Arabidopsis thaliana lines expressing GFP in specific cell populations within the primary root apex. Our results revealed the presence of a CK gradient within the Arabidopsis root tip, with a concentration maximum in the lateral root cap, columella, columella initials, and quiescent center cells. This distribution, when compared with previously published auxin gradients, implies that the well known antagonistic interactions between the two hormone groups are cell type specific.},
	language = {en},
	number = {7},
	urldate = {2021-06-07},
	journal = {Plant Cell},
	author = {Antoniadi, I. and Plackova, L. and Simonovik, B. and Dolezal, K. and Turnbull, C. and Ljung, K. and Novak, O.},
	month = jul,
	year = {2015},
	note = {Edition: 2015/07/15},
	keywords = {Arabidopsis/cytology/*metabolism, Biological Transport, Cell Separation, Cytokinins/*metabolism, Flow Cytometry, Green Fluorescent Proteins/metabolism, Indoleacetic Acids/metabolism, Meristem/metabolism, Metabolome, Miniaturization, Organ Specificity, Plant Roots/cytology/*metabolism, Protoplasts/metabolism, Solid Phase Extraction},
	pages = {1955--67},
}

Cytokinins (CKs) play a crucial role in many physiological and developmental processes at the levels of individual plant components (cells, tissues, and organs) and by coordinating activities across these parts. High-resolution measurements of intracellular CKs in different plant tissues can therefore provide insights into their metabolism and mode of action. Here, we applied fluorescence-activated cell sorting of green fluorescent protein (GFP)-marked cell types, combined with solid-phase microextraction and an ultra-high-sensitivity mass spectrometry (MS) method for analysis of CK biosynthesis and homeostasis at cellular resolution. This method was validated by series of control experiments, establishing that protoplast isolation and cell sorting procedures did not greatly alter endogenous CK levels. The MS-based method facilitated the quantification of all the well known CK isoprenoid metabolites in four different transgenic Arabidopsis thaliana lines expressing GFP in specific cell populations within the primary root apex. Our results revealed the presence of a CK gradient within the Arabidopsis root tip, with a concentration maximum in the lateral root cap, columella, columella initials, and quiescent center cells. This distribution, when compared with previously published auxin gradients, implies that the well known antagonistic interactions between the two hormone groups are cell type specific.

@article{petersson_cell-type_2015,
	title = {Cell-type specific metabolic profiling of {Arabidopsis} thaliana protoplasts as a tool for plant systems biology},
	volume = {11},
	issn = {1573-3882 (Print) 1573-3882 (Linking)},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/26491421},
	doi = {10.1007/s11306-015-0814-7},
	abstract = {Flow cytometry combined with cell sorting of protoplasts has previously been used successfully for transcript profiling of the Arabidopsis thaliana root. We have developed the technique further, and in this paper we present a robust and reliable method for metabolite profiling in specific cell types isolated from Arabidopsis roots. The method uses a combination of fluorescence-activated cell sorting and gas chromatography-time of flight-mass spectrometry analysis. Cortical and endodermal cells from the green fluorescent protein (GFP)-expressing enhancer trap line J0571 were analysed and compared with non-GFP-expressing cells and intact root tissue. Of the metabolites identified, several showed significant differences in concentration between cell types. Multivariate statistical analysis was used to compare metabolite patterns between cell and tissue types, showing that the patterns differed substantially. Isolation of specific cell populations combined with highly sensitive MS-analysis will be a powerful tool for future studies of plant metabolism, and can also be combined with transcript and protein profiling for in-depth analyses of cellular processes.},
	language = {en},
	number = {6},
	urldate = {2021-06-07},
	journal = {Metabolomics},
	author = {Petersson, S. V. and Linden, P. and Moritz, T. and Ljung, K.},
	month = dec,
	year = {2015},
	note = {Edition: 2015/10/23},
	keywords = {Arabidopsis thaliana, Flow cytometry, Gas chromatography-mass spectrometry, Metabolite profiling, Multivariate statistical analysis, Untargeted metabolomics},
	pages = {1679--1689},
}

Flow cytometry combined with cell sorting of protoplasts has previously been used successfully for transcript profiling of the Arabidopsis thaliana root. We have developed the technique further, and in this paper we present a robust and reliable method for metabolite profiling in specific cell types isolated from Arabidopsis roots. The method uses a combination of fluorescence-activated cell sorting and gas chromatography-time of flight-mass spectrometry analysis. Cortical and endodermal cells from the green fluorescent protein (GFP)-expressing enhancer trap line J0571 were analysed and compared with non-GFP-expressing cells and intact root tissue. Of the metabolites identified, several showed significant differences in concentration between cell types. Multivariate statistical analysis was used to compare metabolite patterns between cell and tissue types, showing that the patterns differed substantially. Isolation of specific cell populations combined with highly sensitive MS-analysis will be a powerful tool for future studies of plant metabolism, and can also be combined with transcript and protein profiling for in-depth analyses of cellular processes.

@article{de_wit_contrasting_2015,
	title = {Contrasting growth responses in lamina and petiole during neighbor detection depend on differential auxin responsiveness rather than different auxin levels},
	volume = {208},
	issn = {1469-8137 (Electronic) 0028-646X (Linking)},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/25963518},
	doi = {10.1111/nph.13449},
	abstract = {Foliar shade triggers rapid growth of specific structures that facilitate access of the plant to direct sunlight. In leaves of many plant species, this growth response is complex because, although shade triggers the elongation of petioles, it reduces the growth of the lamina. How the same external cue leads to these contrasting growth responses in different parts of the leaf is not understood. Using mutant analysis, pharmacological treatment and gene expression analyses, we investigated the role of PHYTOCHROME INTERACTING FACTOR7 (PIF7) and the growth-promoting hormone auxin in these contrasting leaf growth responses. Both petiole elongation and lamina growth reduction are dependent on PIF7. The induction of auxin production is both necessary and sufficient to induce opposite growth responses in petioles vs lamina. However, these contrasting growth responses are not caused by different auxin concentrations in the two leaf parts. Our work suggests that a transient increase in auxin levels triggers tissue-specific growth responses in different leaf parts. We provide evidence suggesting that this may be caused by the different sensitivity to auxin in the petiole vs the blade and by tissue-specific gene expression.},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {New Phytol},
	author = {de Wit, M. and Ljung, K. and Fankhauser, C.},
	month = oct,
	year = {2015},
	note = {Edition: 2015/05/13},
	keywords = {*Light, Arabidopsis Proteins/*metabolism, Arabidopsis/growth \& development/metabolism/*physiology, DNA-Binding Proteins/*metabolism, Darkness, Gene Expression, Indoleacetic Acids/*metabolism, Phytochrome interacting factor (pif), Plant Leaves/growth \& development/metabolism/*physiology, Xyloglucan endotransglucosylase/hydrolase (xth), auxin, leaf growth, neighbor detection, shade avoidance response},
	pages = {198--209},
}

Foliar shade triggers rapid growth of specific structures that facilitate access of the plant to direct sunlight. In leaves of many plant species, this growth response is complex because, although shade triggers the elongation of petioles, it reduces the growth of the lamina. How the same external cue leads to these contrasting growth responses in different parts of the leaf is not understood. Using mutant analysis, pharmacological treatment and gene expression analyses, we investigated the role of PHYTOCHROME INTERACTING FACTOR7 (PIF7) and the growth-promoting hormone auxin in these contrasting leaf growth responses. Both petiole elongation and lamina growth reduction are dependent on PIF7. The induction of auxin production is both necessary and sufficient to induce opposite growth responses in petioles vs lamina. However, these contrasting growth responses are not caused by different auxin concentrations in the two leaf parts. Our work suggests that a transient increase in auxin levels triggers tissue-specific growth responses in different leaf parts. We provide evidence suggesting that this may be caused by the different sensitivity to auxin in the petiole vs the blade and by tissue-specific gene expression.

@article{vayssieres_development_2015,
	title = {Development of the {Poplar}-{Laccaria} bicolor {Ectomycorrhiza} {Modifies} {Root} {Auxin} {Metabolism}, {Signaling}, and {Response}},
	volume = {169},
	issn = {1532-2548 (Electronic) 0032-0889 (Linking)},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/26084921},
	doi = {10.1104/pp.114.255620},
	abstract = {Root systems of host trees are known to establish ectomycorrhizae (ECM) interactions with rhizospheric fungi. This mutualistic association leads to dramatic developmental modifications in root architecture, with the formation of numerous short and swollen lateral roots ensheathed by a fungal mantle. Knowing that auxin plays a crucial role in root development, we investigated how auxin metabolism, signaling, and response are affected in poplar (Populus spp.)-Laccaria bicolor ECM roots. The plant-fungus interaction leads to the arrest of lateral root growth with simultaneous attenuation of the synthetic auxin response element DR5. Measurement of auxin-related metabolites in the free-living partners revealed that the mycelium of L. bicolor produces high concentrations of the auxin indole-3-acetic acid (IAA). Metabolic profiling showed an accumulation of IAA and changes in the indol-3-pyruvic acid-dependent IAA biosynthesis and IAA conjugation and degradation pathways during ECM formation. The global analysis of auxin response gene expression and the regulation of AUXIN SIGNALING F-BOX PROTEIN5, AUXIN/IAA, and AUXIN RESPONSE FACTOR expression in ECM roots suggested that symbiosis-dependent auxin signaling is activated during the colonization by L. bicolor. Taking all this evidence into account, we propose a model in which auxin signaling plays a crucial role in the modification of root growth during ECM formation.},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Plant Physiol},
	author = {Vayssieres, A. and Pencik, A. and Felten, J. and Kohler, A. and Ljung, K. and Martin, F. and Legue, V.},
	month = sep,
	year = {2015},
	note = {Edition: 2015/06/19},
	keywords = {*Signal Transduction/drug effects, Gene Expression Regulation, Plant/drug effects, Indoleacetic Acids/*metabolism/pharmacology, Laccaria/drug effects/*physiology, Metabolome/drug effects, Models, Biological, Multivariate Analysis, Mycorrhizae/drug effects/*physiology, Plant Proteins/metabolism, Plant Roots/drug effects/growth \& development/*metabolism/*microbiology, Populus/drug effects/*microbiology},
	pages = {890--902},
}

Root systems of host trees are known to establish ectomycorrhizae (ECM) interactions with rhizospheric fungi. This mutualistic association leads to dramatic developmental modifications in root architecture, with the formation of numerous short and swollen lateral roots ensheathed by a fungal mantle. Knowing that auxin plays a crucial role in root development, we investigated how auxin metabolism, signaling, and response are affected in poplar (Populus spp.)-Laccaria bicolor ECM roots. The plant-fungus interaction leads to the arrest of lateral root growth with simultaneous attenuation of the synthetic auxin response element DR5. Measurement of auxin-related metabolites in the free-living partners revealed that the mycelium of L. bicolor produces high concentrations of the auxin indole-3-acetic acid (IAA). Metabolic profiling showed an accumulation of IAA and changes in the indol-3-pyruvic acid-dependent IAA biosynthesis and IAA conjugation and degradation pathways during ECM formation. The global analysis of auxin response gene expression and the regulation of AUXIN SIGNALING F-BOX PROTEIN5, AUXIN/IAA, and AUXIN RESPONSE FACTOR expression in ECM roots suggested that symbiosis-dependent auxin signaling is activated during the colonization by L. bicolor. Taking all this evidence into account, we propose a model in which auxin signaling plays a crucial role in the modification of root growth during ECM formation.

@article{mellor_modelling_2015,
	title = {Modelling of {Arabidopsis} {LAX3} expression suggests auxin homeostasis},
	volume = {366},
	issn = {00225193},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0022519314006353},
	doi = {10/f3pwnp},
	language = {en},
	urldate = {2021-06-08},
	journal = {Journal of Theoretical Biology},
	author = {Mellor, Nathan and Péret, Benjamin and Porco, Silvana and Sairanen, Ilkka and Ljung, Karin and Bennett, Malcolm and King, John},
	month = feb,
	year = {2015},
	pages = {57--70},
}

@article{ljung_new_2015,
	title = {New mechanistic links between sugar and hormone signalling networks},
	volume = {25},
	issn = {1879-0356 (Electronic) 1369-5266 (Linking)},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/26037392},
	doi = {10.1016/j.pbi.2015.05.022},
	abstract = {Plant growth and development must be coordinated with metabolism, notably with the efficiency of photosynthesis and the uptake of nutrients. This coordination requires local connections between hormonal response and metabolic state, as well as long-distance connections between shoot and root tissues. Recently, several molecular mechanisms have been proposed to explain the integration of sugar signalling with hormone pathways. In this work, DELLA and PIF proteins have emerged as hubs in sugar-hormone cross-regulation networks.},
	language = {en},
	urldate = {2021-06-07},
	journal = {Curr Opin Plant Biol},
	author = {Ljung, K. and Nemhauser, J. L. and Perata, P.},
	month = jun,
	year = {2015},
	note = {Edition: 2015/06/04},
	keywords = {*Plant Physiological Phenomena, *Signal Transduction, Biological Transport, Brassinosteroids/metabolism, Carbohydrate Metabolism, Carbohydrates, Gibberellins/metabolism, Indoleacetic Acids/metabolism, Photosynthesis, Plant Development, Plant Growth Regulators/*metabolism, Plant Roots/growth \& development/metabolism, Plants/*metabolism},
	pages = {130--7},
}

Plant growth and development must be coordinated with metabolism, notably with the efficiency of photosynthesis and the uptake of nutrients. This coordination requires local connections between hormonal response and metabolic state, as well as long-distance connections between shoot and root tissues. Recently, several molecular mechanisms have been proposed to explain the integration of sugar signalling with hormone pathways. In this work, DELLA and PIF proteins have emerged as hubs in sugar-hormone cross-regulation networks.

@article{voss_circadian_2015,
	title = {The circadian clock rephases during lateral root organ initiation in {Arabidopsis} thaliana},
	volume = {6},
	issn = {2041-1723 (Electronic) 2041-1723 (Linking)},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/26144255},
	doi = {10.1038/ncomms8641},
	abstract = {The endogenous circadian clock enables organisms to adapt their growth and development to environmental changes. Here we describe how the circadian clock is employed to coordinate responses to the key signal auxin during lateral root (LR) emergence. In the model plant, Arabidopsis thaliana, LRs originate from a group of stem cells deep within the root, necessitating that new organs emerge through overlying root tissues. We report that the circadian clock is rephased during LR development. Metabolite and transcript profiling revealed that the circadian clock controls the levels of auxin and auxin-related genes including the auxin response repressor IAA14 and auxin oxidase AtDAO2. Plants lacking or overexpressing core clock components exhibit LR emergence defects. We conclude that the circadian clock acts to gate auxin signalling during LR development to facilitate organ emergence.},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Nat Commun},
	author = {Voss, U. and Wilson, M. H. and Kenobi, K. and Gould, P. D. and Robertson, F. C. and Peer, W. A. and Lucas, M. and Swarup, K. and Casimiro, I. and Holman, T. J. and Wells, D. M. and Peret, B. and Goh, T. and Fukaki, H. and Hodgman, T. C. and Laplaze, L. and Halliday, K. J. and Ljung, K. and Murphy, A. S. and Hall, A. J. and Webb, A. A. and Bennett, M. J.},
	month = jul,
	year = {2015},
	note = {Edition: 2015/07/07},
	keywords = {Arabidopsis Proteins/genetics/metabolism, Arabidopsis/*growth \& development, Circadian Clocks/*physiology, Gene Expression Regulation, Plant/*physiology, Gravitropism, Indoleacetic Acids/metabolism, Mutation, Oxidoreductases/genetics/metabolism, Plant Roots/*physiology, Time Factors, Transcription Factors/genetics/metabolism, Transcriptome},
	pages = {7641},
}

The endogenous circadian clock enables organisms to adapt their growth and development to environmental changes. Here we describe how the circadian clock is employed to coordinate responses to the key signal auxin during lateral root (LR) emergence. In the model plant, Arabidopsis thaliana, LRs originate from a group of stem cells deep within the root, necessitating that new organs emerge through overlying root tissues. We report that the circadian clock is rephased during LR development. Metabolite and transcript profiling revealed that the circadian clock controls the levels of auxin and auxin-related genes including the auxin response repressor IAA14 and auxin oxidase AtDAO2. Plants lacking or overexpressing core clock components exhibit LR emergence defects. We conclude that the circadian clock acts to gate auxin signalling during LR development to facilitate organ emergence.

@article{coudert_three_2015,
	title = {Three ancient hormonal cues co-ordinate shoot branching in a moss},
	volume = {4},
	issn = {2050-084X (Electronic) 2050-084X (Linking)},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/25806686},
	doi = {10.7554/eLife.06808},
	abstract = {Shoot branching is a primary contributor to plant architecture, evolving independently in flowering plant sporophytes and moss gametophytes. Mechanistic understanding of branching is largely limited to flowering plants such as Arabidopsis, which have a recent evolutionary origin. We show that in gametophytic shoots of Physcomitrella, lateral branches arise by re-specification of epidermal cells into branch initials. A simple model co-ordinating the activity of leafy shoot tips can account for branching patterns, and three known and ancient hormonal regulators of sporophytic branching interact to generate the branching pattern- auxin, cytokinin and strigolactone. The mode of auxin transport required in branch patterning is a key divergence point from known sporophytic pathways. Although PIN-mediated basipetal auxin transport regulates branching patterns in flowering plants, this is not so in Physcomitrella, where bi-directional transport is required to generate realistic branching patterns. Experiments with callose synthesis inhibitors suggest plasmodesmal connectivity as a potential mechanism for transport.},
	language = {en},
	urldate = {2021-06-07},
	journal = {Elife},
	author = {Coudert, Y. and Palubicki, W. and Ljung, K. and Novak, O. and Leyser, O. and Harrison, C. J.},
	month = mar,
	year = {2015},
	note = {Edition: 2015/03/26},
	keywords = {Biological Transport/drug effects, Body Patterning/drug effects, Bryopsida/drug effects/*growth \& development, Cytokinins/biosynthesis, Gene Expression Regulation, Plant/drug effects, Indoleacetic Acids/metabolism/pharmacology, Lactones/pharmacology, Models, Biological, Morphogenesis/*drug effects, Mutation/genetics, Physcomitrella, Plant Epidermis/cytology/growth \& development, Plant Growth Regulators/*pharmacology, Plant Proteins/metabolism, Plant Shoots/drug effects/*growth \& development, Plants, Genetically Modified, apical dominance, branching, developmental biology, gametophyte, plant biology, stem cells},
	pages = {e06808},
}

Shoot branching is a primary contributor to plant architecture, evolving independently in flowering plant sporophytes and moss gametophytes. Mechanistic understanding of branching is largely limited to flowering plants such as Arabidopsis, which have a recent evolutionary origin. We show that in gametophytic shoots of Physcomitrella, lateral branches arise by re-specification of epidermal cells into branch initials. A simple model co-ordinating the activity of leafy shoot tips can account for branching patterns, and three known and ancient hormonal regulators of sporophytic branching interact to generate the branching pattern- auxin, cytokinin and strigolactone. The mode of auxin transport required in branch patterning is a key divergence point from known sporophytic pathways. Although PIN-mediated basipetal auxin transport regulates branching patterns in flowering plants, this is not so in Physcomitrella, where bi-directional transport is required to generate realistic branching patterns. Experiments with callose synthesis inhibitors suggest plasmodesmal connectivity as a potential mechanism for transport.

@article{li_adp1_2014,
	title = {{ADP1} {Affects} {Plant} {Architecture} by {Regulating} {Local} {Auxin} {Biosynthesis}},
	volume = {10},
	issn = {1553-7404},
	url = {https://dx.plos.org/10.1371/journal.pgen.1003954},
	doi = {10/f3p7dr},
	language = {en},
	number = {1},
	urldate = {2021-06-08},
	journal = {PLoS Genetics},
	author = {Li, Ruixi and Li, Jieru and Li, Shibai and Qin, Genji and Novák, Ondřej and Pěnčík, Aleš and Ljung, Karin and Aoyama, Takashi and Liu, Jingjing and Murphy, Angus and Gu, Hongya and Tsuge, Tomohiko and Qu, Li-Jia},
	editor = {Copenhaver, Gregory P.},
	month = jan,
	year = {2014},
	pages = {e1003954},
}

@article{disante_alleviation_2014,
	title = {Alleviation of {Zn} toxicity by low water availability},
	volume = {150},
	issn = {00319317},
	url = {http://doi.wiley.com/10.1111/ppl.12095},
	doi = {10/f25dnq},
	language = {en},
	number = {3},
	urldate = {2021-06-08},
	journal = {Physiologia Plantarum},
	author = {Disante, Karen B. and Cortina, Jordi and Vilagrosa, Alberto and Fuentes, David and Hernández, Encarni I. and Ljung, Karin},
	month = mar,
	year = {2014},
	pages = {412--424},
}

@article{maharjan_arabidopsis_2014,
	title = {Arabidopsis \textit{gulliver1/superroot2‐7} identifies a metabolic basis for auxin and brassinosteroid synergy},
	volume = {80},
	issn = {0960-7412, 1365-313X},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/tpj.12678},
	doi = {10/f3m3r2},
	language = {en},
	number = {5},
	urldate = {2021-06-08},
	journal = {The Plant Journal},
	author = {Maharjan, Puna M. and Dilkes, Brian P. and Fujioka, Shozo and Pěnčík, Aleš and Ljung, Karin and Burow, Meike and Halkier, Barbara A. and Choe, Sunghwa},
	month = dec,
	year = {2014},
	pages = {797--808},
}

@article{de_jong_auxin_2014,
	title = {Auxin and {Strigolactone} {Signaling} {Are} {Required} for {Modulation} of {Arabidopsis} {Shoot} {Branching} by {Nitrogen} {Supply}},
	volume = {166},
	issn = {1532-2548},
	url = {https://academic.oup.com/plphys/article/166/1/384/6113280},
	doi = {10/f3p27f},
	abstract = {Abstract
            The degree of shoot branching is strongly affected by environmental conditions, such as nutrient availability. Here we demonstrate that nitrate limitation reduces shoot branching in Arabidopsis (Arabidopsis thaliana) both by delaying axillary bud activation and by attenuating the basipetal sequence of bud activation that is triggered following floral transition. Ammonium supply has similar effects, suggesting that they are caused by plant nitrogen (N) status, rather than direct nitrate signaling. We identify increased auxin export from active shoot apices, resulting in increased auxin in the polar auxin transport stream of the main stem, as a likely cause for the suppression of basal branches. Consistent with this idea, in the auxin response mutant axr1 and the strigolactone biosynthesis mutant more axillary growth1, increased retention of basal branches on low N is associated with a failure to increase auxin in the main stem. The complex interactions between the hormones that regulate branching make it difficult to rule out other mechanisms of N action, such as up-regulation of strigolactone synthesis. However, the proposed increase in auxin export from active buds can also explain how reduced shoot branching is achieved without compromising root growth, leading to the characteristic shift in relative biomass allocation to the root when N is limiting.},
	language = {en},
	number = {1},
	urldate = {2021-06-08},
	journal = {Plant Physiology},
	author = {de Jong, Maaike and George, Gilu and Ongaro, Veronica and Williamson, Lisa and Willetts, Barbara and Ljung, Karin and McCulloch, Hayley and Leyser, Ottoline},
	month = aug,
	year = {2014},
	pages = {384--395},
}

Abstract The degree of shoot branching is strongly affected by environmental conditions, such as nutrient availability. Here we demonstrate that nitrate limitation reduces shoot branching in Arabidopsis (Arabidopsis thaliana) both by delaying axillary bud activation and by attenuating the basipetal sequence of bud activation that is triggered following floral transition. Ammonium supply has similar effects, suggesting that they are caused by plant nitrogen (N) status, rather than direct nitrate signaling. We identify increased auxin export from active shoot apices, resulting in increased auxin in the polar auxin transport stream of the main stem, as a likely cause for the suppression of basal branches. Consistent with this idea, in the auxin response mutant axr1 and the strigolactone biosynthesis mutant more axillary growth1, increased retention of basal branches on low N is associated with a failure to increase auxin in the main stem. The complex interactions between the hormones that regulate branching make it difficult to rule out other mechanisms of N action, such as up-regulation of strigolactone synthesis. However, the proposed increase in auxin export from active buds can also explain how reduced shoot branching is achieved without compromising root growth, leading to the characteristic shift in relative biomass allocation to the root when N is limiting.

@article{mounier_auxin-mediated_2014,
	title = {Auxin-mediated nitrate signalling by {NRT1}.1 participates in the adaptive response of \textit{{Arabidopsis}} root architecture to the spatial heterogeneity of nitrate availability: {Nitrate} signalling by {NRT1}.1},
	volume = {37},
	issn = {01407791},
	shorttitle = {Auxin-mediated nitrate signalling by {NRT1}.1 participates in the adaptive response of \textit{{Arabidopsis}} root architecture to the spatial heterogeneity of nitrate availability},
	url = {http://doi.wiley.com/10.1111/pce.12143},
	doi = {10/f24x7s},
	language = {en},
	number = {1},
	urldate = {2021-06-08},
	journal = {Plant, Cell \& Environment},
	author = {Mounier, Emmanuelle and Pervent, Marjorie and Ljung, Karin and Gojon, Alain and Nacry, Philippe},
	month = jan,
	year = {2014},
	pages = {162--174},
}

@article{procko_cotyledon-generated_2014,
	title = {Cotyledon-{Generated} {Auxin} {Is} {Required} for {Shade}-{Induced} {Hypocotyl} {Growth} in \textit{{Brassica} rapa}},
	volume = {165},
	issn = {1532-2548},
	url = {https://academic.oup.com/plphys/article/165/3/1285/6113202},
	doi = {10/f3p44r},
	abstract = {Abstract
            Plant architecture is optimized for the local light environment. In response to foliar shade or neighbor proximity (low red to far-red light), some plant species exhibit shade-avoiding phenotypes, including increased stem and hypocotyl growth, which increases the likelihood of outgrowing competitor plants. If shade persists, early flowering and the reallocation of growth resources to stem elongation ultimately affect the yield of harvestable tissues in crop species. Previous studies have shown that hypocotyl growth in low red to far-red shade is largely dependent on the photoreceptor phytochrome B and the phytohormone auxin. However, where shade is perceived in the plant and how auxin regulates growth spatially are less well understood. Using the oilseed and vegetable crop species Brassica rapa, we show that the perception of low red to far-red shade by the cotyledons triggers hypocotyl cell elongation and auxin target gene expression. Furthermore, we find that following shade perception, elevated auxin levels occur in a basipetal gradient away from the cotyledons and that this is coincident with a gradient of auxin target gene induction. These results show that cotyledon-generated auxin regulates hypocotyl elongation. In addition, we find in mature B. rapa plants that simulated shade does not affect seed oil composition but may affect seed yield. This suggests that in field settings where mutual shading between plants may occur, a balance between plant density and seed yield per plant needs to be achieved for maximum oil yield, while oil composition might remain constant.},
	language = {en},
	number = {3},
	urldate = {2021-06-08},
	journal = {Plant Physiology},
	author = {Procko, Carl and Crenshaw, Charisse Michelle and Ljung, Karin and Noel, Joseph Patrick and Chory, Joanne},
	month = jun,
	year = {2014},
	pages = {1285--1301},
}

Abstract Plant architecture is optimized for the local light environment. In response to foliar shade or neighbor proximity (low red to far-red light), some plant species exhibit shade-avoiding phenotypes, including increased stem and hypocotyl growth, which increases the likelihood of outgrowing competitor plants. If shade persists, early flowering and the reallocation of growth resources to stem elongation ultimately affect the yield of harvestable tissues in crop species. Previous studies have shown that hypocotyl growth in low red to far-red shade is largely dependent on the photoreceptor phytochrome B and the phytohormone auxin. However, where shade is perceived in the plant and how auxin regulates growth spatially are less well understood. Using the oilseed and vegetable crop species Brassica rapa, we show that the perception of low red to far-red shade by the cotyledons triggers hypocotyl cell elongation and auxin target gene expression. Furthermore, we find that following shade perception, elevated auxin levels occur in a basipetal gradient away from the cotyledons and that this is coincident with a gradient of auxin target gene induction. These results show that cotyledon-generated auxin regulates hypocotyl elongation. In addition, we find in mature B. rapa plants that simulated shade does not affect seed oil composition but may affect seed yield. This suggests that in field settings where mutual shading between plants may occur, a balance between plant density and seed yield per plant needs to be achieved for maximum oil yield, while oil composition might remain constant.

@article{viaene_directional_2014,
	title = {Directional {Auxin} {Transport} {Mechanisms} in {Early} {Diverging} {Land} {Plants}},
	volume = {24},
	issn = {09609822},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0960982214012196},
	doi = {10/f3pxg8},
	language = {en},
	number = {23},
	urldate = {2021-06-08},
	journal = {Current Biology},
	author = {Viaene, Tom and Landberg, Katarina and Thelander, Mattias and Medvecka, Eva and Pederson, Eric and Feraru, Elena and Cooper, Endymion D. and Karimi, Mansour and Delwiche, Charles F. and Ljung, Karin and Geisler, Markus and Sundberg, Eva and Friml, Jiří},
	month = dec,
	year = {2014},
	pages = {2786--2791},
}

@article{stirk_effect_2014,
	title = {Effect of light on growth and endogenous hormones in {Chlorella} minutissima ({Trebouxiophyceae})},
	volume = {79},
	issn = {09819428},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0981942814000837},
	doi = {10/f3p3qd},
	language = {en},
	urldate = {2021-06-08},
	journal = {Plant Physiology and Biochemistry},
	author = {Stirk, W.A. and Bálint, P. and Tarkowská, D. and Novák, O. and Maróti, G. and Ljung, K. and Turečková, V. and Strnad, M. and Ördög, V. and van Staden, J.},
	month = jun,
	year = {2014},
	pages = {66--76},
}

@article{pacurar_identification_2014,
	title = {Identification of new adventitious rooting mutants amongst suppressors of the {Arabidopsis} thaliana superroot2 mutation},
	volume = {65},
	issn = {0022-0957},
	url = {https://doi.org/10.1093/jxb/eru026},
	doi = {10/f23rss},
	abstract = {The plant hormone auxin plays a central role in adventitious rooting and is routinely used with many economically important, vegetatively propagated plant species to promote adventitious root initiation and development on cuttings. Nevertheless the molecular mechanisms through which it acts are only starting to emerge. The Arabidopsis superroot2-1 (sur2-1) mutant overproduces auxin and, as a consequence, develops excessive adventitious roots in the hypocotyl. In order to increase the knowledge of adventitious rooting and of auxin signalling pathways and crosstalk, this study performed a screen for suppressors of superroot2-1 phenotype. These suppressors provide a new resource for discovery of genetic players involved in auxin signalling pathways or at the crosstalk of auxin and other hormones or environmental signals. This study reports the identification and characterization of 26 sur2-1 suppressor mutants, several of which were identified as mutations in candidate genes involved in either auxin biosynthesis or signalling. In addition to confirming the role of auxin as a central regulator of adventitious rooting, superroot2 suppressors indicated possible crosstalk with ethylene signalling in this process.},
	number = {6},
	urldate = {2021-06-08},
	journal = {Journal of Experimental Botany},
	author = {Pacurar, Daniel Ioan and Pacurar, Monica Lacramioara and Bussell, John Desmond and Schwambach, Joseli and Pop, Tiberia Ioana and Kowalczyk, Mariusz and Gutierrez, Laurent and Cavel, Emilie and Chaabouni, Salma and Ljung, Karin and Fett-Neto, Arthur Germano and Pamfil, Doru and Bellini, Catherine},
	month = apr,
	year = {2014},
	pages = {1605--1618},
}

The plant hormone auxin plays a central role in adventitious rooting and is routinely used with many economically important, vegetatively propagated plant species to promote adventitious root initiation and development on cuttings. Nevertheless the molecular mechanisms through which it acts are only starting to emerge. The Arabidopsis superroot2-1 (sur2-1) mutant overproduces auxin and, as a consequence, develops excessive adventitious roots in the hypocotyl. In order to increase the knowledge of adventitious rooting and of auxin signalling pathways and crosstalk, this study performed a screen for suppressors of superroot2-1 phenotype. These suppressors provide a new resource for discovery of genetic players involved in auxin signalling pathways or at the crosstalk of auxin and other hormones or environmental signals. This study reports the identification and characterization of 26 sur2-1 suppressor mutants, several of which were identified as mutations in candidate genes involved in either auxin biosynthesis or signalling. In addition to confirming the role of auxin as a central regulator of adventitious rooting, superroot2 suppressors indicated possible crosstalk with ethylene signalling in this process.

@article{de_rybel_integration_2014,
	title = {Integration of growth and patterning during vascular tissue formation in \textit{{Arabidopsis}}},
	volume = {345},
	issn = {0036-8075, 1095-9203},
	url = {https://www.sciencemag.org/lookup/doi/10.1126/science.1255215},
	doi = {10/f3p69f},
	abstract = {Coordination of cell division and pattern formation is central to tissue and organ development, particularly in plants where walls prevent cell migration. Auxin and cytokinin are both critical for division and patterning, but it is unknown how these hormones converge upon tissue development. We identify a genetic network that reinforces an early embryonic bias in auxin distribution to create a local, nonresponding cytokinin source within the root vascular tissue. Experimental and theoretical evidence shows that these cells act as a tissue organizer by positioning the domain of oriented cell divisions. We further demonstrate that the auxin-cytokinin interaction acts as a spatial incoherent feed-forward loop, which is essential to generate distinct hormonal response zones, thus establishing a stable pattern within a growing vascular tissue.},
	language = {en},
	number = {6197},
	urldate = {2021-06-08},
	journal = {Science},
	author = {De Rybel, Bert and Adibi, Milad and Breda, Alice S. and Wendrich, Jos R. and Smit, Margot E. and Novák, Ondřej and Yamaguchi, Nobutoshi and Yoshida, Saiko and Van Isterdael, Gert and Palovaara, Joakim and Nijsse, Bart and Boekschoten, Mark V. and Hooiveld, Guido and Beeckman, Tom and Wagner, Doris and Ljung, Karin and Fleck, Christian and Weijers, Dolf},
	month = aug,
	year = {2014},
	pages = {1255215},
}

Coordination of cell division and pattern formation is central to tissue and organ development, particularly in plants where walls prevent cell migration. Auxin and cytokinin are both critical for division and patterning, but it is unknown how these hormones converge upon tissue development. We identify a genetic network that reinforces an early embryonic bias in auxin distribution to create a local, nonresponding cytokinin source within the root vascular tissue. Experimental and theoretical evidence shows that these cells act as a tissue organizer by positioning the domain of oriented cell divisions. We further demonstrate that the auxin-cytokinin interaction acts as a spatial incoherent feed-forward loop, which is essential to generate distinct hormonal response zones, thus establishing a stable pattern within a growing vascular tissue.

@article{hersch_light_2014,
	title = {Light intensity modulates the regulatory network of the shade avoidance response in {Arabidopsis}},
	volume = {111},
	issn = {0027-8424, 1091-6490},
	url = {http://www.pnas.org/cgi/doi/10.1073/pnas.1320355111},
	doi = {10/f3p63k},
	language = {en},
	number = {17},
	urldate = {2021-06-08},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Hersch, M. and Lorrain, S. and de Wit, M. and Trevisan, M. and Ljung, K. and Bergmann, S. and Fankhauser, C.},
	month = apr,
	year = {2014},
	pages = {6515--6520},
}

@article{kami_reduced_2014,
	title = {Reduced phototropism in \textit{pks} mutants may be due to altered auxin-regulated gene expression or reduced lateral auxin transport},
	volume = {77},
	issn = {09607412},
	url = {http://doi.wiley.com/10.1111/tpj.12395},
	doi = {10/f25d98},
	language = {en},
	number = {3},
	urldate = {2021-06-08},
	journal = {The Plant Journal},
	author = {Kami, Chitose and Allenbach, Laure and Zourelidou, Melina and Ljung, Karin and Schütz, Frédéric and Isono, Erika and Watahiki, Masaaki K. and Yamamoto, Kotaro T. and Schwechheimer, Claus and Fankhauser, Christian},
	month = feb,
	year = {2014},
	pages = {393--403},
}

@article{ranocha_arabidopsis_2013,
	title = {Arabidopsis {WAT1} is a vacuolar auxin transport facilitator required for auxin homoeostasis},
	volume = {4},
	issn = {2041-1723},
	url = {http://www.nature.com/articles/ncomms3625},
	doi = {10/f23w2p},
	language = {en},
	number = {1},
	urldate = {2021-06-08},
	journal = {Nature Communications},
	author = {Ranocha, Philippe and Dima, Oana and Nagy, Réka and Felten, Judith and Corratgé-Faillie, Claire and Novák, Ondřej and Morreel, Kris and Lacombe, Benoît and Martinez, Yves and Pfrunder, Stephanie and Jin, Xu and Renou, Jean-Pierre and Thibaud, Jean-Baptiste and Ljung, Karin and Fischer, Urs and Martinoia, Enrico and Boerjan, Wout and Goffner, Deborah},
	month = dec,
	year = {2013},
	pages = {2625},
}

@article{cecchetti_auxin_2013,
	title = {Auxin controls {Arabidopsis} anther dehiscence by regulating endothecium lignification and jasmonic acid biosynthesis},
	volume = {74},
	issn = {09607412},
	url = {http://doi.wiley.com/10.1111/tpj.12130},
	doi = {10/f23td7},
	language = {en},
	number = {3},
	urldate = {2021-06-08},
	journal = {The Plant Journal},
	author = {Cecchetti, Valentina and Altamura, Maria Maddalena and Brunetti, Patrizia and Petrocelli, Valentina and Falasca, Giuseppina and Ljung, Karin and Costantino, Paolo and Cardarelli, Maura},
	month = may,
	year = {2013},
	pages = {411--422},
}

@article{ljung_auxin_2013,
	title = {Auxin metabolism and homeostasis during plant development},
	volume = {140},
	issn = {1477-9129, 0950-1991},
	url = {https://journals.biologists.com/dev/article/140/5/943/45952/Auxin-metabolism-and-homeostasis-during-plant},
	doi = {10/f23cpj},
	abstract = {Auxin plays important roles during the entire life span of a plant. This small organic acid influences cell division, cell elongation and cell differentiation, and has great impact on the final shape and function of cells and tissues in all higher plants. Auxin metabolism is not well understood but recent discoveries, reviewed here, have started to shed light on the processes that regulate the synthesis and degradation of this important plant hormone.},
	language = {en},
	number = {5},
	urldate = {2021-06-08},
	journal = {Development},
	author = {Ljung, Karin},
	month = mar,
	year = {2013},
	pages = {943--950},
}

Auxin plays important roles during the entire life span of a plant. This small organic acid influences cell division, cell elongation and cell differentiation, and has great impact on the final shape and function of cells and tissues in all higher plants. Auxin metabolism is not well understood but recent discoveries, reviewed here, have started to shed light on the processes that regulate the synthesis and degradation of this important plant hormone.

@article{zheng_coordination_2013,
	title = {Coordination of auxin and ethylene biosynthesis by the aminotransferase {VAS1}},
	volume = {9},
	issn = {1552-4450, 1552-4469},
	url = {http://www.nature.com/articles/nchembio.1178},
	doi = {10/f234vk},
	language = {en},
	number = {4},
	urldate = {2021-06-08},
	journal = {Nature Chemical Biology},
	author = {Zheng, Zuyu and Guo, Yongxia and Novák, Ondřej and Dai, Xinhua and Zhao, Yunde and Ljung, Karin and Noel, Joseph P and Chory, Joanne},
	month = apr,
	year = {2013},
	pages = {244--246},
}

@article{pacheco-villalobos_disturbed_2013,
	title = {Disturbed {Local} {Auxin} {Homeostasis} {Enhances} {Cellular} {Anisotropy} and {Reveals} {Alternative} {Wiring} of {Auxin}-ethylene {Crosstalk} in {Brachypodium} distachyon {Seminal} {Roots}},
	volume = {9},
	issn = {1553-7404},
	url = {https://dx.plos.org/10.1371/journal.pgen.1003564},
	doi = {10/f236vj},
	language = {en},
	number = {6},
	urldate = {2021-06-08},
	journal = {PLoS Genetics},
	author = {Pacheco-Villalobos, David and Sankar, Martial and Ljung, Karin and Hardtke, Christian S.},
	editor = {Yu, Hao},
	month = jun,
	year = {2013},
	pages = {e1003564},
}

@article{tiwari_physiological_2013,
	title = {Physiological and morphological changes during early and later stages of fruit growth in \textit{{Capsicum} annuum}},
	volume = {147},
	issn = {00319317},
	url = {http://doi.wiley.com/10.1111/j.1399-3054.2012.01673.x},
	doi = {10/f23jvb},
	language = {en},
	number = {3},
	urldate = {2021-06-08},
	journal = {Physiologia Plantarum},
	author = {Tiwari, Aparna and Vivian-Smith, Adam and Ljung, Karin and Offringa, Remko and Heuvelink, Ep},
	month = mar,
	year = {2013},
	pages = {396--406},
}

@article{pencik_regulation_2013,
	title = {Regulation of {Auxin} {Homeostasis} and {Gradients} in \textit{{Arabidopsis}} {Roots} through the {Formation} of the {Indole}-3-{Acetic} {Acid} {Catabolite} 2-{Oxindole}-3-{Acetic} {Acid}},
	volume = {25},
	issn = {1040-4651, 1532-298X},
	url = {https://academic.oup.com/plcell/article/25/10/3858-3870/6099549},
	doi = {10/f2zn6c},
	language = {en},
	number = {10},
	urldate = {2021-06-08},
	journal = {The Plant Cell},
	author = {Pěnčík, Aleš and Simonovik, Biljana and Petersson, Sara V. and Henyková, Eva and Simon, Sibu and Greenham, Kathleen and Zhang, Yi and Kowalczyk, Mariusz and Estelle, Mark and Zažímalová, Eva and Novák, Ondřej and Sandberg, Göran and Ljung, Karin},
	month = oct,
	year = {2013},
	pages = {3858--3870},
}

@article{rigas_root_2013,
	title = {Root gravitropism and root hair development constitute coupled developmental responses regulated by auxin homeostasis in the \textit{{Arabidopsis}} root apex},
	volume = {197},
	issn = {0028-646X, 1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/nph.12092},
	doi = {10/f22m5k},
	language = {en},
	number = {4},
	urldate = {2021-06-08},
	journal = {New Phytologist},
	author = {Rigas, Stamatis and Ditengou, Franck Anicet and Ljung, Karin and Daras, Gerasimos and Tietz, Olaf and Palme, Klaus and Hatzopoulos, Polydefkis},
	month = mar,
	year = {2013},
	pages = {1130--1141},
}

@article{peret_sequential_2013,
	title = {Sequential induction of auxin efflux and influx carriers regulates lateral root emergence},
	volume = {9},
	issn = {1744-4292, 1744-4292},
	url = {https://onlinelibrary.wiley.com/doi/10.1038/msb.2013.43},
	doi = {10/f2pc8d},
	language = {en},
	number = {1},
	urldate = {2021-06-08},
	journal = {Molecular Systems Biology},
	author = {Péret, Benjamin and Middleton, Alistair M and French, Andrew P and Larrieu, Antoine and Bishopp, Anthony and Njo, Maria and Wells, Darren M and Porco, Silvana and Mellor, Nathan and Band, Leah R and Casimiro, Ilda and Kleine‐Vehn, Jürgen and Vanneste, Steffen and Sairanen, Ilkka and Mallet, Romain and Sandberg, Göran and Ljung, Karin and Beeckman, Tom and Benkova, Eva and Friml, Jiří and Kramer, Eric and King, John R and De Smet, Ive and Pridmore, Tony and Owen, Markus and Bennett, Malcolm J},
	month = jan,
	year = {2013},
	pages = {699},
}

@article{sairanen_soluble_2013,
	title = {Soluble {Carbohydrates} {Regulate} {Auxin} {Biosynthesis} via {PIF} {Proteins} in \textit{{Arabidopsis}}},
	volume = {24},
	issn = {1532-298X, 1040-4651},
	url = {https://academic.oup.com/plcell/article/24/12/4907/6098068},
	doi = {10/f2z2pm},
	abstract = {Abstract
            Plants are necessarily highly competitive and have finely tuned mechanisms to adjust growth and development in accordance with opportunities and limitations in their environment. Sugars from photosynthesis form an integral part of this growth control process, acting as both an energy source and as signaling molecules in areas targeted for growth. The plant hormone auxin similarly functions as a signaling molecule and a driver of growth and developmental processes. Here, we show that not only do the two act in concert but that auxin metabolism is itself regulated by the availability of free sugars. The regulation of the biosynthesis and degradation of the main auxin, indole-3-acetic acid (IAA), by sugars requires changes in the expression of multiple genes and metabolites linked to several IAA biosynthetic pathways. The induction also involves members of the recently described central regulator PHYTOCHROME-INTERACTING FACTOR transcription factor family. Linking these three known regulators of growth provides a model for the dynamic coordination of responses to a changing environment.},
	language = {en},
	number = {12},
	urldate = {2021-06-08},
	journal = {The Plant Cell},
	author = {Sairanen, Ilkka and Novák, Ondřej and Pěnčík, Aleš and Ikeda, Yoshihisa and Jones, Brian and Sandberg, Göran and Ljung, Karin},
	month = jan,
	year = {2013},
	pages = {4907--4916},
}

Abstract Plants are necessarily highly competitive and have finely tuned mechanisms to adjust growth and development in accordance with opportunities and limitations in their environment. Sugars from photosynthesis form an integral part of this growth control process, acting as both an energy source and as signaling molecules in areas targeted for growth. The plant hormone auxin similarly functions as a signaling molecule and a driver of growth and developmental processes. Here, we show that not only do the two act in concert but that auxin metabolism is itself regulated by the availability of free sugars. The regulation of the biosynthesis and degradation of the main auxin, indole-3-acetic acid (IAA), by sugars requires changes in the expression of multiple genes and metabolites linked to several IAA biosynthetic pathways. The induction also involves members of the recently described central regulator PHYTOCHROME-INTERACTING FACTOR transcription factor family. Linking these three known regulators of growth provides a model for the dynamic coordination of responses to a changing environment.

@article{moubayidin_spatial_2013,
	title = {Spatial {Coordination} between {Stem} {Cell} {Activity} and {Cell} {Differentiation} in the {Root} {Meristem}},
	volume = {26},
	issn = {15345807},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S1534580713003882},
	doi = {10/f23ftm},
	language = {en},
	number = {4},
	urldate = {2021-06-08},
	journal = {Developmental Cell},
	author = {Moubayidin, Laila and Di Mambro, Riccardo and Sozzani, Rosangela and Pacifici, Elena and Salvi, Elena and Terpstra, Inez and Bao, Dongping and van Dijken, Anja and Dello Ioio, Raffaele and Perilli, Serena and Ljung, Karin and Benfey, Philip N. and Heidstra, Renze and Costantino, Paolo and Sabatini, Sabrina},
	month = aug,
	year = {2013},
	pages = {405--415},
}

@article{milhinhos_thermospermine_2013,
	title = {Thermospermine levels are controlled by an auxin-dependent feedback loop mechanism in \textit{{Populus}} xylem},
	volume = {75},
	issn = {09607412},
	url = {http://doi.wiley.com/10.1111/tpj.12231},
	doi = {10/f22nbr},
	language = {en},
	number = {4},
	urldate = {2021-06-08},
	journal = {The Plant Journal},
	author = {Milhinhos, Ana and Prestele, Jakob and Bollhöner, Benjamin and Matos, Andreia and Vera-Sirera, Francisco and Rambla, José L. and Ljung, Karin and Carbonell, Juan and Blázquez, Miguel A. and Tuominen, Hannele and Miguel, Célia M.},
	month = aug,
	year = {2013},
	pages = {685--698},
}

@article{lilley_endogenous_2012,
	title = {An {Endogenous} {Carbon}-{Sensing} {Pathway} {Triggers} {Increased} {Auxin} {Flux} and {Hypocotyl} {Elongation}},
	volume = {160},
	issn = {1532-2548},
	url = {https://academic.oup.com/plphys/article/160/4/2261/6109644},
	doi = {10/f22bb5},
	abstract = {Abstract
            The local environment has a substantial impact on early seedling development. Applying excess carbon in the form of sucrose is known to alter both the timing and duration of seedling growth. Here, we show that sucrose changes growth patterns by increasing auxin levels and rootward auxin transport in Arabidopsis (Arabidopsis thaliana). Sucrose likely interacts with an endogenous carbon-sensing pathway via the PHYTOCHROME-INTERACTING FACTOR (PIF) family of transcription factors, as plants grown in elevated carbon dioxide showed the same PIF-dependent growth promotion. Overexpression of PIF5 was sufficient to suppress photosynthetic rate, enhance response to elevated carbon dioxide, and prolong seedling survival in nitrogen-limiting conditions. Thus, PIF transcription factors integrate growth with metabolic demands and thereby facilitate functional equilibrium during photomorphogenesis.},
	language = {en},
	number = {4},
	urldate = {2021-06-08},
	journal = {Plant Physiology},
	author = {Lilley, Jodi L. Stewart and Gee, Christopher W. and Sairanen, Ilkka and Ljung, Karin and Nemhauser, Jennifer L.},
	month = dec,
	year = {2012},
	pages = {2261--2270},
}

Abstract The local environment has a substantial impact on early seedling development. Applying excess carbon in the form of sucrose is known to alter both the timing and duration of seedling growth. Here, we show that sucrose changes growth patterns by increasing auxin levels and rootward auxin transport in Arabidopsis (Arabidopsis thaliana). Sucrose likely interacts with an endogenous carbon-sensing pathway via the PHYTOCHROME-INTERACTING FACTOR (PIF) family of transcription factors, as plants grown in elevated carbon dioxide showed the same PIF-dependent growth promotion. Overexpression of PIF5 was sufficient to suppress photosynthetic rate, enhance response to elevated carbon dioxide, and prolong seedling survival in nitrogen-limiting conditions. Thus, PIF transcription factors integrate growth with metabolic demands and thereby facilitate functional equilibrium during photomorphogenesis.

@article{fuentes_fruit_2012,
	title = {Fruit {Growth} in \textit{{Arabidopsis}} {Occurs} via {DELLA}-{Dependent} and {DELLA}-{Independent} {Gibberellin} {Responses}},
	volume = {24},
	issn = {1040-4651, 1532-298X},
	url = {https://academic.oup.com/plcell/article/24/10/3982-3996/6101547},
	doi = {10/f22dj7},
	language = {en},
	number = {10},
	urldate = {2021-06-08},
	journal = {The Plant Cell},
	author = {Fuentes, Sara and Ljung, Karin and Sorefan, Karim and Alvey, Elizabeth and Harberd, Nicholas P. and Østergaard, Lars},
	month = oct,
	year = {2012},
	pages = {3982--3996},
}

@article{li_linking_2012,
	title = {Linking photoreceptor excitation to changes in plant architecture},
	volume = {26},
	issn = {0890-9369},
	url = {http://genesdev.cshlp.org/cgi/doi/10.1101/gad.187849.112},
	doi = {10/f2zrkq},
	language = {en},
	number = {8},
	urldate = {2021-06-08},
	journal = {Genes \& Development},
	author = {Li, L. and Ljung, K. and Breton, G. and Schmitz, R. J. and Pruneda-Paz, J. and Cowing-Zitron, C. and Cole, B. J. and Ivans, L. J. and Pedmale, U. V. and Jung, H.-S. and Ecker, J. R. and Kay, S. A. and Chory, J.},
	month = apr,
	year = {2012},
	pages = {785--790},
}

@article{hornitschek_phytochrome_2012,
	title = {Phytochrome interacting factors 4 and 5 control seedling growth in changing light conditions by directly controlling auxin signaling: {PIF4} and {PIF5} control auxin signaling},
	volume = {71},
	issn = {09607412},
	shorttitle = {Phytochrome interacting factors 4 and 5 control seedling growth in changing light conditions by directly controlling auxin signaling},
	url = {http://doi.wiley.com/10.1111/j.1365-313X.2012.05033.x},
	doi = {10/f233dh},
	language = {en},
	number = {5},
	urldate = {2021-06-08},
	journal = {The Plant Journal},
	author = {Hornitschek, Patricia and Kohnen, Markus V. and Lorrain, Séverine and Rougemont, Jacques and Ljung, Karin and López-Vidriero, Irene and Franco-Zorrilla, José M. and Solano, Roberto and Trevisan, Martine and Pradervand, Sylvain and Xenarios, Ioannis and Fankhauser, Christian},
	month = sep,
	year = {2012},
	pages = {699--711},
}

@article{band_root_2012,
	title = {Root gravitropism is regulated by a transient lateral auxin gradient controlled by a tipping-point mechanism},
	volume = {109},
	issn = {0027-8424, 1091-6490},
	url = {https://www.pnas.org/content/109/12/4668},
	doi = {10/f2392k},
	abstract = {Gravity profoundly influences plant growth and development. Plants respond to changes in orientation by using gravitropic responses to modify their growth. Cholodny and Went hypothesized over 80 years ago that plants bend in response to a gravity stimulus by generating a lateral gradient of a growth regulator at an organ's apex, later found to be auxin. Auxin regulates root growth by targeting Aux/IAA repressor proteins for degradation. We used an Aux/IAA-based reporter, domain II (DII)-VENUS, in conjunction with a mathematical model to quantify auxin redistribution following a gravity stimulus. Our multidisciplinary approach revealed that auxin is rapidly redistributed to the lower side of the root within minutes of a 90° gravity stimulus. Unexpectedly, auxin asymmetry was rapidly lost as bending root tips reached an angle of 40° to the horizontal. We hypothesize roots use a “tipping point” mechanism that operates to reverse the asymmetric auxin flow at the midpoint of root bending. These mechanistic insights illustrate the scientific value of developing quantitative reporters such as DII-VENUS in conjunction with parameterized mathematical models to provide high-resolution kinetics of hormone redistribution.},
	language = {en},
	number = {12},
	urldate = {2021-06-08},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Band, Leah R. and Wells, Darren M. and Larrieu, Antoine and Sun, Jianyong and Middleton, Alistair M. and French, Andrew P. and Brunoud, Géraldine and Sato, Ethel Mendocilla and Wilson, Michael H. and Péret, Benjamin and Oliva, Marina and Swarup, Ranjan and Sairanen, Ilkka and Parry, Geraint and Ljung, Karin and Beeckman, Tom and Garibaldi, Jonathan M. and Estelle, Mark and Owen, Markus R. and Vissenberg, Kris and Hodgman, T. Charlie and Pridmore, Tony P. and King, John R. and Vernoux, Teva and Bennett, Malcolm J.},
	month = mar,
	year = {2012},
	pmid = {22393022},
	note = {Publisher: National Academy of Sciences
Section: Biological Sciences},
	keywords = {environmental sensing, systems biology},
	pages = {4668--4673},
}

Gravity profoundly influences plant growth and development. Plants respond to changes in orientation by using gravitropic responses to modify their growth. Cholodny and Went hypothesized over 80 years ago that plants bend in response to a gravity stimulus by generating a lateral gradient of a growth regulator at an organ's apex, later found to be auxin. Auxin regulates root growth by targeting Aux/IAA repressor proteins for degradation. We used an Aux/IAA-based reporter, domain II (DII)-VENUS, in conjunction with a mathematical model to quantify auxin redistribution following a gravity stimulus. Our multidisciplinary approach revealed that auxin is rapidly redistributed to the lower side of the root within minutes of a 90° gravity stimulus. Unexpectedly, auxin asymmetry was rapidly lost as bending root tips reached an angle of 40° to the horizontal. We hypothesize roots use a “tipping point” mechanism that operates to reverse the asymmetric auxin flow at the midpoint of root bending. These mechanistic insights illustrate the scientific value of developing quantitative reporters such as DII-VENUS in conjunction with parameterized mathematical models to provide high-resolution kinetics of hormone redistribution.

@article{jones_subterranean_2012,
	title = {Subterranean space exploration: the development of root system architecture},
	volume = {15},
	issn = {13695266},
	shorttitle = {Subterranean space exploration},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S1369526611001646},
	doi = {10/frcjbh},
	language = {en},
	number = {1},
	urldate = {2021-06-08},
	journal = {Current Opinion in Plant Biology},
	author = {Jones, Brian and Ljung, Karin},
	month = feb,
	year = {2012},
	pages = {97--102},
}

@article{staldal_arabidopsis_2012,
	title = {The {Arabidopsis} thaliana transcriptional activator {STYLISH1} regulates genes affecting stamen development, cell expansion and timing of flowering},
	volume = {78},
	issn = {0167-4412, 1573-5028},
	url = {http://link.springer.com/10.1007/s11103-012-9888-z},
	doi = {10/f24hk4},
	language = {en},
	number = {6},
	urldate = {2021-06-08},
	journal = {Plant Molecular Biology},
	author = {Ståldal, Veronika and Cierlik, Izabela and Chen, Song and Landberg, Katarina and Baylis, Tammy and Myrenås, Mattias and Sundström, Jens F. and Eklund, D. Magnus and Ljung, Karin and Sundberg, Eva},
	month = apr,
	year = {2012},
	pages = {545--559},
}

@article{novak_tissue-specific_2012,
	title = {Tissue-specific profiling of the \textit{{Arabidopsis} thaliana} auxin metabolome: \textit{{Auxin} metabolite profiling in} {Arabidopsis}},
	volume = {72},
	issn = {09607412},
	shorttitle = {Tissue-specific profiling of the \textit{{Arabidopsis} thaliana} auxin metabolome},
	url = {http://doi.wiley.com/10.1111/j.1365-313X.2012.05085.x},
	doi = {10/f23drs},
	language = {en},
	number = {3},
	urldate = {2021-06-08},
	journal = {The Plant Journal},
	author = {Novák, Ondřej and Hényková, Eva and Sairanen, Ilkka and Kowalczyk, Mariusz and Pospíšil, Tomáš and Ljung, Karin},
	month = nov,
	year = {2012},
	pages = {523--536},
}

@article{jones_auxin_2011,
	title = {Auxin and cytokinin regulate each other’s levels via a metabolic feedback loop},
	volume = {6},
	issn = {1559-2324},
	url = {http://www.tandfonline.com/doi/abs/10.4161/psb.6.6.15323},
	doi = {10/bdn8kg},
	language = {en},
	number = {6},
	urldate = {2021-06-08},
	journal = {Plant Signaling \& Behavior},
	author = {Jones, Brian and Ljung, Karin},
	month = jun,
	year = {2011},
	pages = {901--904},
}

@article{greenham_retracted_2011,
	title = {{RETRACTED}: {The} {AFB4} {Auxin} {Receptor} {Is} a {Negative} {Regulator} of {Auxin} {Signaling} in {Seedlings}},
	volume = {21},
	issn = {09609822},
	shorttitle = {{RETRACTED}},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S096098221100220X},
	doi = {10/fd497k},
	language = {en},
	number = {6},
	urldate = {2021-06-08},
	journal = {Current Biology},
	author = {Greenham, Katie and Santner, Aaron and Castillejo, Cristina and Mooney, Sutton and Sairanen, Ilkka and Ljung, Karin and Estelle, Mark},
	month = mar,
	year = {2011},
	pages = {520--525},
}

@article{lucas_short-root_2011,
	title = {{SHORT}-{ROOT} {Regulates} {Primary}, {Lateral}, and {Adventitious} {Root} {Development} in {Arabidopsis}},
	volume = {155},
	issn = {1532-2548},
	url = {https://academic.oup.com/plphys/article/155/1/384/6111549},
	doi = {10/c9mbrr},
	abstract = {Abstract
            SHORT-ROOT (SHR) is a well-characterized regulator of radial patterning and indeterminacy of the Arabidopsis (Arabidopsis thaliana) primary root. However, its role during the elaboration of root system architecture remains unclear. We report that the indeterminate wild-type Arabidopsis root system was transformed into a determinate root system in the shr mutant when growing in soil or agar. The root growth behavior of the shr mutant results from its primary root apical meristem failing to initiate cell division following germination. The inability of shr to reactivate mitotic activity in the root apical meristem is associated with the progressive reduction in the abundance of auxin efflux carriers, PIN-FORMED1 (PIN1), PIN2, PIN3, PIN4, and PIN7. The loss of primary root growth in shr is compensated by the activation of anchor root primordia, whose tissues are radially patterned like the wild type. However, SHR function is not restricted to the primary root but is also required for the initiation and patterning of lateral root primordia. In addition, SHR is necessary to maintain the indeterminate growth of lateral and anchor roots. We conclude that SHR regulates a wide array of Arabidopsis root-related developmental processes.},
	language = {en},
	number = {1},
	urldate = {2021-06-08},
	journal = {Plant Physiology},
	author = {Lucas, Mikaël and Swarup, Ranjan and Paponov, Ivan A. and Swarup, Kamal and Casimiro, Ilda and Lake, David and Peret, Benjamin and Zappala, Susan and Mairhofer, Stefan and Whitworth, Morag and Wang, Jiehua and Ljung, Karin and Marchant, Alan and Sandberg, Goran and Holdsworth, Michael J. and Palme, Klaus and Pridmore, Tony and Mooney, Sacha and Bennett, Malcolm J.},
	month = jan,
	year = {2011},
	pages = {384--398},
}

Abstract SHORT-ROOT (SHR) is a well-characterized regulator of radial patterning and indeterminacy of the Arabidopsis (Arabidopsis thaliana) primary root. However, its role during the elaboration of root system architecture remains unclear. We report that the indeterminate wild-type Arabidopsis root system was transformed into a determinate root system in the shr mutant when growing in soil or agar. The root growth behavior of the shr mutant results from its primary root apical meristem failing to initiate cell division following germination. The inability of shr to reactivate mitotic activity in the root apical meristem is associated with the progressive reduction in the abundance of auxin efflux carriers, PIN-FORMED1 (PIN1), PIN2, PIN3, PIN4, and PIN7. The loss of primary root growth in shr is compensated by the activation of anchor root primordia, whose tissues are radially patterned like the wild type. However, SHR function is not restricted to the primary root but is also required for the initiation and patterning of lateral root primordia. In addition, SHR is necessary to maintain the indeterminate growth of lateral and anchor roots. We conclude that SHR regulates a wide array of Arabidopsis root-related developmental processes.

@article{agusti_strigolactone_2011,
	title = {Strigolactone signaling is required for auxin-dependent stimulation of secondary growth in plants},
	volume = {108},
	issn = {0027-8424, 1091-6490},
	url = {https://www.pnas.org/content/108/50/20242},
	doi = {10/fhvk7k},
	abstract = {Long distance cell-to-cell communication is critical for the development of multicellular organisms. In this respect, plants are especially demanding as they constantly integrate environmental inputs to adjust growth processes to different conditions. One example is thickening of shoots and roots, also designated as secondary growth. Secondary growth is mediated by the vascular cambium, a stem cell-like tissue whose cell-proliferating activity is regulated over a long distance by the plant hormone auxin. How auxin signaling is integrated at the level of cambium cells and how cambium activity is coordinated with other growth processes are largely unknown. Here, we provide physiological, genetic, and pharmacological evidence that strigolactones (SLs), a group of plant hormones recently described to be involved in the repression of shoot branching, positively regulate cambial activity and that this function is conserved among species. We show that SL signaling in the vascular cambium itself is sufficient for cambium stimulation and that it interacts strongly with the auxin signaling pathway. Our results provide a model of how auxin-based long-distance signaling is translated into cambium activity and suggest that SLs act as general modulators of plant growth forms linking the control of shoot branching with the thickening of stems and roots.},
	language = {en},
	number = {50},
	urldate = {2021-06-08},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Agusti, Javier and Herold, Silvia and Schwarz, Martina and Sanchez, Pablo and Ljung, Karin and Dun, Elizabeth A. and Brewer, Philip B. and Beveridge, Christine A. and Sieberer, Tobias and Sehr, Eva M. and Greb, Thomas},
	month = dec,
	year = {2011},
	pmid = {22123958},
	note = {Publisher: National Academy of Sciences
Section: Biological Sciences},
	keywords = {MORE AXILLARY BRANCHES, meristem, wood production},
	pages = {20242--20247},
}

Long distance cell-to-cell communication is critical for the development of multicellular organisms. In this respect, plants are especially demanding as they constantly integrate environmental inputs to adjust growth processes to different conditions. One example is thickening of shoots and roots, also designated as secondary growth. Secondary growth is mediated by the vascular cambium, a stem cell-like tissue whose cell-proliferating activity is regulated over a long distance by the plant hormone auxin. How auxin signaling is integrated at the level of cambium cells and how cambium activity is coordinated with other growth processes are largely unknown. Here, we provide physiological, genetic, and pharmacological evidence that strigolactones (SLs), a group of plant hormones recently described to be involved in the repression of shoot branching, positively regulate cambial activity and that this function is conserved among species. We show that SL signaling in the vascular cambium itself is sufficient for cambium stimulation and that it interacts strongly with the auxin signaling pathway. Our results provide a model of how auxin-based long-distance signaling is translated into cambium activity and suggest that SLs act as general modulators of plant growth forms linking the control of shoot branching with the thickening of stems and roots.

@article{rizzardi_tfl2lhp1_2011,
	title = {{TFL2}/{LHP1} is involved in auxin biosynthesis through positive regulation of {YUCCA} genes: {Positive} regulation of {YUCCA} genes by {TFL2}},
	volume = {65},
	issn = {09607412},
	shorttitle = {{TFL2}/{LHP1} is involved in auxin biosynthesis through positive regulation of {YUCCA} genes},
	url = {http://doi.wiley.com/10.1111/j.1365-313X.2010.04470.x},
	doi = {10/dr4w6d},
	language = {en},
	number = {6},
	urldate = {2021-06-08},
	journal = {The Plant Journal},
	author = {Rizzardi, Kristina and Landberg, Katarina and Nilsson, Lars and Ljung, Karin and Sundås-Larsson, Annika},
	month = mar,
	year = {2011},
	pages = {897--906},
}

@article{stepanova_arabidopsis_2011,
	title = {The {Arabidopsis} {YUCCA1} {Flavin} {Monooxygenase} {Functions} in the {Indole}-3-{Pyruvic} {Acid} {Branch} of {Auxin} {Biosynthesis}},
	volume = {23},
	issn = {1532-298X, 1040-4651},
	url = {https://academic.oup.com/plcell/article/23/11/3961/6097553},
	doi = {10/fpsm3j},
	abstract = {Abstract
            The effects of auxins on plant growth and development have been known for more than 100 years, yet our understanding of how plants synthesize this essential plant hormone is still fragmentary at best. Gene loss- and gain-of-function studies have conclusively implicated three gene families, CYTOCHROME P450 79B2/B3 (CYP79B2/B3), YUCCA (YUC), and TRYPTOPHAN AMINOTRANSFERASE OF ARABIDOPSIS1/TRYPTOPHAN AMINOTRANSFERASE-RELATED (TAA1/TAR), in the production of this hormone in the reference plant Arabidopsis thaliana. Each of these three gene families is believed to represent independent routes of auxin biosynthesis. Using a combination of pharmacological, genetic, and biochemical approaches, we examined the possible relationships between the auxin biosynthetic pathways defined by these three gene families. Our findings clearly indicate that TAA1/TARs and YUCs function in a common linear biosynthetic pathway that is genetically distinct from the CYP79B2/B3 route. In the redefined TAA1-YUC auxin biosynthetic pathway, TAA1/TARs are required for the production of indole-3-pyruvic acid (IPyA) from Trp, whereas YUCs are likely to function downstream. These results, together with the extensive genetic analysis of four pyruvate decarboxylases, the putative downstream components of the TAA1 pathway, strongly suggest that the enzymatic reactions involved in indole-3-acetic acid (IAA) production via IPyA are different than those previously postulated, and a new and testable model for how IAA is produced in plants is needed.},
	language = {en},
	number = {11},
	urldate = {2021-06-08},
	journal = {The Plant Cell},
	author = {Stepanova, Anna N. and Yun, Jeonga and Robles, Linda M. and Novak, Ondrej and He, Wenrong and Guo, Hongwei and Ljung, Karin and Alonso, Jose M.},
	month = nov,
	year = {2011},
	pages = {3961--3973},
}

Abstract The effects of auxins on plant growth and development have been known for more than 100 years, yet our understanding of how plants synthesize this essential plant hormone is still fragmentary at best. Gene loss- and gain-of-function studies have conclusively implicated three gene families, CYTOCHROME P450 79B2/B3 (CYP79B2/B3), YUCCA (YUC), and TRYPTOPHAN AMINOTRANSFERASE OF ARABIDOPSIS1/TRYPTOPHAN AMINOTRANSFERASE-RELATED (TAA1/TAR), in the production of this hormone in the reference plant Arabidopsis thaliana. Each of these three gene families is believed to represent independent routes of auxin biosynthesis. Using a combination of pharmacological, genetic, and biochemical approaches, we examined the possible relationships between the auxin biosynthetic pathways defined by these three gene families. Our findings clearly indicate that TAA1/TARs and YUCs function in a common linear biosynthetic pathway that is genetically distinct from the CYP79B2/B3 route. In the redefined TAA1-YUC auxin biosynthetic pathway, TAA1/TARs are required for the production of indole-3-pyruvic acid (IPyA) from Trp, whereas YUCs are likely to function downstream. These results, together with the extensive genetic analysis of four pyruvate decarboxylases, the putative downstream components of the TAA1 pathway, strongly suggest that the enzymatic reactions involved in indole-3-acetic acid (IAA) production via IPyA are different than those previously postulated, and a new and testable model for how IAA is produced in plants is needed.

@article{wu_role_2010,
	title = {A role for {ABCB19}-mediated polar auxin transport in seedling photomorphogenesis mediated by cryptochrome 1 and phytochrome {B}: {ABCB19} and the photocontrol of hypocotyl growth},
	volume = {62},
	issn = {09607412},
	shorttitle = {A role for {ABCB19}-mediated polar auxin transport in seedling photomorphogenesis mediated by cryptochrome 1 and phytochrome {B}},
	url = {http://doi.wiley.com/10.1111/j.1365-313X.2010.04137.x},
	doi = {10/cp6ptv},
	language = {en},
	number = {2},
	urldate = {2021-06-08},
	journal = {The Plant Journal},
	author = {Wu, Guosheng and Cameron, John N. and Ljung, Karin and Spalding, Edgar P.},
	month = jan,
	year = {2010},
	pages = {179--191},
}

@article{le_bail_auxin_2010,
	title = {Auxin {Metabolism} and {Function} in the {Multicellular} {Brown} {Alga} \textit{{Ectocarpus} siliculosus}},
	volume = {153},
	issn = {1532-2548},
	url = {https://academic.oup.com/plphys/article/153/1/128/6108337},
	doi = {10/dsq4bg},
	abstract = {Abstract
            Ectocarpus siliculosus is a small brown alga that has recently been developed as a genetic model. Its thallus is filamentous, initially organized as a main primary filament composed of elongated cells and round cells, from which branches differentiate. Modeling of its early development suggests the involvement of very local positional information mediated by cell-cell recognition. However, this model also indicates that an additional mechanism is required to ensure proper organization of the branching pattern. In this paper, we show that auxin indole-3-acetic acid (IAA) is detectable in mature E. siliculosus organisms and that it is present mainly at the apices of the filaments in the early stages of development. An in silico survey of auxin biosynthesis, conjugation, response, and transport genes showed that mainly IAA biosynthesis genes from land plants have homologs in the E. siliculosus genome. In addition, application of exogenous auxins and 2,3,5-triiodobenzoic acid had different effects depending on the developmental stage of the organism, and we propose a model in which auxin is involved in the negative control of progression in the developmental program. Furthermore, we identified an auxin-inducible gene called EsGRP1 from a small-scale microarray experiment and showed that its expression in a series of morphogenetic mutants was positively correlated with both their elongated-to-round cell ratio and their progression in the developmental program. Altogether, these data suggest that IAA is used by the brown alga Ectocarpus to relay cell-cell positional information and induces a signaling pathway different from that known in land plants.},
	language = {en},
	number = {1},
	urldate = {2021-06-08},
	journal = {Plant Physiology},
	author = {Le Bail, Aude and Billoud, Bernard and Kowalczyk, Nathalie and Kowalczyk, Mariusz and Gicquel, Morgane and Le Panse, Sophie and Stewart, Sarah and Scornet, Delphine and Cock, Jeremy Mark and Ljung, Karin and Charrier, Bénédicte},
	month = may,
	year = {2010},
	pages = {128--144},
}

Abstract Ectocarpus siliculosus is a small brown alga that has recently been developed as a genetic model. Its thallus is filamentous, initially organized as a main primary filament composed of elongated cells and round cells, from which branches differentiate. Modeling of its early development suggests the involvement of very local positional information mediated by cell-cell recognition. However, this model also indicates that an additional mechanism is required to ensure proper organization of the branching pattern. In this paper, we show that auxin indole-3-acetic acid (IAA) is detectable in mature E. siliculosus organisms and that it is present mainly at the apices of the filaments in the early stages of development. An in silico survey of auxin biosynthesis, conjugation, response, and transport genes showed that mainly IAA biosynthesis genes from land plants have homologs in the E. siliculosus genome. In addition, application of exogenous auxins and 2,3,5-triiodobenzoic acid had different effects depending on the developmental stage of the organism, and we propose a model in which auxin is involved in the negative control of progression in the developmental program. Furthermore, we identified an auxin-inducible gene called EsGRP1 from a small-scale microarray experiment and showed that its expression in a series of morphogenetic mutants was positively correlated with both their elongated-to-round cell ratio and their progression in the developmental program. Altogether, these data suggest that IAA is used by the brown alga Ectocarpus to relay cell-cell positional information and induces a signaling pathway different from that known in land plants.

@article{jones_cytokinin_2010,
	title = {Cytokinin {Regulation} of {Auxin} {Synthesis} in \textit{{Arabidopsis}} {Involves} a {Homeostatic} {Feedback} {Loop} {Regulated} via {Auxin} and {Cytokinin} {Signal} {Transduction}},
	volume = {22},
	issn = {1532-298X, 1040-4651},
	url = {https://academic.oup.com/plcell/article/22/9/2956/6096141},
	doi = {10/dszfmr},
	abstract = {Abstract
            Together, auxin and cytokinin regulate many of the processes that are critical to plant growth, development, and environmental responsiveness. We have previously shown that exogenous auxin regulates cytokinin biosynthesis in Arabidopsis thaliana. In this work, we show that, conversely, the application or induced ectopic biosynthesis of cytokinin leads to a rapid increase in auxin biosynthesis in young, developing root and shoot tissues. We also show that reducing endogenous cytokinin levels, either through the induction of CYTOKININ OXIDASE expression or the mutation of one or more of the cytokinin biosynthetic ISOPENTENYLTRANSFERASE genes leads to a reduction in auxin biosynthesis. Cytokinin modifies the abundance of transcripts for several putative auxin biosynthetic genes, suggesting a direct induction of auxin biosynthesis by cytokinin. Our data indicate that cytokinin is essential, not only to maintain basal levels of auxin biosynthesis in developing root and shoot tissues but also for the dynamic regulation of auxin biosynthesis in response to changing developmental or environmental conditions. In combination with our previous work, the data suggest that a homeostatic feedback regulatory loop involving both auxin and cytokinin signaling acts to maintain appropriate auxin and cytokinin concentrations in developing root and shoot tissues.},
	language = {en},
	number = {9},
	urldate = {2021-06-08},
	journal = {The Plant Cell},
	author = {Jones, Brian and Gunnerås, Sara Andersson and Petersson, Sara V. and Tarkowski, Petr and Graham, Neil and May, Sean and Dolezal, Karel and Sandberg, Göran and Ljung, Karin},
	month = oct,
	year = {2010},
	pages = {2956--2969},
}

Abstract Together, auxin and cytokinin regulate many of the processes that are critical to plant growth, development, and environmental responsiveness. We have previously shown that exogenous auxin regulates cytokinin biosynthesis in Arabidopsis thaliana. In this work, we show that, conversely, the application or induced ectopic biosynthesis of cytokinin leads to a rapid increase in auxin biosynthesis in young, developing root and shoot tissues. We also show that reducing endogenous cytokinin levels, either through the induction of CYTOKININ OXIDASE expression or the mutation of one or more of the cytokinin biosynthetic ISOPENTENYLTRANSFERASE genes leads to a reduction in auxin biosynthesis. Cytokinin modifies the abundance of transcripts for several putative auxin biosynthetic genes, suggesting a direct induction of auxin biosynthesis by cytokinin. Our data indicate that cytokinin is essential, not only to maintain basal levels of auxin biosynthesis in developing root and shoot tissues but also for the dynamic regulation of auxin biosynthesis in response to changing developmental or environmental conditions. In combination with our previous work, the data suggest that a homeostatic feedback regulatory loop involving both auxin and cytokinin signaling acts to maintain appropriate auxin and cytokinin concentrations in developing root and shoot tissues.

@article{eklund_homologues_2010,
	title = {Homologues of the \textit{{Arabidopsis} thaliana {SHI}/{STY}/{LRP1}} genes control auxin biosynthesis and affect growth and development in the moss \textit{{Physcomitrella} patens}},
	volume = {137},
	issn = {1477-9129, 0950-1991},
	url = {https://journals.biologists.com/dev/article/137/8/1275/44242/Homologues-of-the-Arabidopsis-thaliana-SHI-STY},
	doi = {10/fgs5s3},
	abstract = {The plant hormone auxin plays fundamental roles in vascular plants. Although exogenous auxin also stimulates developmental transitions and growth in non-vascular plants, the effects of manipulating endogenous auxin levels have thus far not been reported. Here, we have altered the levels and sites of auxin production and accumulation in the moss Physcomitrella patens by changing the expression level of homologues of the Arabidopsis SHI/STY family proteins, which are positive regulators of auxin biosynthesis genes. Constitutive expression of PpSHI1 resulted in elevated auxin levels, increased and ectopic expression of the auxin response reporter GmGH3pro:GUS, and in an increased caulonema/chloronema ratio, an effect also induced by exogenous auxin application. In addition, we observed premature ageing and necrosis in cells ectopically expressing PpSHI1. Knockout of either of the two PpSHI genes resulted in reduced auxin levels and auxin biosynthesis rates in leafy shoots, reduced internode elongation, delayed ageing, a decreased caulonema/chloronema ratio and an increased number of axillary hairs, which constitute potential auxin biosynthesis sites. Some of the identified auxin functions appear to be analogous in vascular and non-vascular plants. Furthermore, the spatiotemporal expression of the PpSHI genes and GmGH3pro:GUS strongly overlap, suggesting that local auxin biosynthesis is important for the regulation of auxin peak formation in non-vascular plants.},
	language = {en},
	number = {8},
	urldate = {2021-06-08},
	journal = {Development},
	author = {Eklund, D. Magnus and Thelander, Mattias and Landberg, Katarina and Ståldal, Veronika and Nilsson, Anders and Johansson, Monika and Valsecchi, Isabel and Pederson, Eric R. A. and Kowalczyk, Mariusz and Ljung, Karin and Ronne, Hans and Sundberg, Eva},
	month = apr,
	year = {2010},
	pages = {1275--1284},
}

The plant hormone auxin plays fundamental roles in vascular plants. Although exogenous auxin also stimulates developmental transitions and growth in non-vascular plants, the effects of manipulating endogenous auxin levels have thus far not been reported. Here, we have altered the levels and sites of auxin production and accumulation in the moss Physcomitrella patens by changing the expression level of homologues of the Arabidopsis SHI/STY family proteins, which are positive regulators of auxin biosynthesis genes. Constitutive expression of PpSHI1 resulted in elevated auxin levels, increased and ectopic expression of the auxin response reporter GmGH3pro:GUS, and in an increased caulonema/chloronema ratio, an effect also induced by exogenous auxin application. In addition, we observed premature ageing and necrosis in cells ectopically expressing PpSHI1. Knockout of either of the two PpSHI genes resulted in reduced auxin levels and auxin biosynthesis rates in leafy shoots, reduced internode elongation, delayed ageing, a decreased caulonema/chloronema ratio and an increased number of axillary hairs, which constitute potential auxin biosynthesis sites. Some of the identified auxin functions appear to be analogous in vascular and non-vascular plants. Furthermore, the spatiotemporal expression of the PpSHI genes and GmGH3pro:GUS strongly overlap, suggesting that local auxin biosynthesis is important for the regulation of auxin peak formation in non-vascular plants.

@article{zhao_hormonal_2010,
	title = {Hormonal control of the shoot stem-cell niche},
	volume = {465},
	issn = {0028-0836, 1476-4687},
	url = {http://www.nature.com/articles/nature09126},
	doi = {10/bq25jx},
	language = {en},
	number = {7301},
	urldate = {2021-06-08},
	journal = {Nature},
	author = {Zhao, Zhong and Andersen, Stig U. and Ljung, Karin and Dolezal, Karel and Miotk, Andrej and Schultheiss, Sebastian J. and Lohmann, Jan U.},
	month = jun,
	year = {2010},
	pages = {1089--1092},
}

@article{bashandy_interplay_2010,
	title = {Interplay between the {NADP}-{Linked} {Thioredoxin} and {Glutathione} {Systems} in \textit{{Arabidopsis}} {Auxin} {Signaling}},
	volume = {22},
	issn = {1532-298X, 1040-4651},
	url = {https://academic.oup.com/plcell/article/22/2/376/6095921},
	doi = {10/cmkrm9},
	abstract = {Abstract
            Intracellular redox status is a critical parameter determining plant development in response to biotic and abiotic stress. Thioredoxin (TRX) and glutathione are key regulators of redox homeostasis, and the TRX and glutathione pathways are essential for postembryonic meristematic activities. Here, we show by associating TRX reductases (ntra ntrb) and glutathione biosynthesis (cad2) mutations that these two thiol reduction pathways interfere with developmental processes through modulation of auxin signaling. The triple ntra ntrb cad2 mutant develops normally at the rosette stage, undergoes the floral transition, but produces almost naked stems, reminiscent of the phenotype of several mutants affected in auxin transport or biosynthesis. In addition, the ntra ntrb cad2 mutant shows a loss of apical dominance, vasculature defects, and reduced secondary root production, several phenotypes tightly regulated by auxin. We further show that auxin transport capacities and auxin levels are perturbed in the mutant, suggesting that the NTR-glutathione pathways alter both auxin transport and metabolism. Analysis of ntr and glutathione biosynthesis mutants suggests that glutathione homeostasis plays a major role in auxin transport as both NTR and glutathione pathways are involved in auxin homeostasis.},
	language = {en},
	number = {2},
	urldate = {2021-06-08},
	journal = {The Plant Cell},
	author = {Bashandy, Talaat and Guilleminot, Jocelyne and Vernoux, Teva and Caparros-Ruiz, David and Ljung, Karin and Meyer, Yves and Reichheld, Jean-Philippe},
	month = mar,
	year = {2010},
	pages = {376--391},
}

Abstract Intracellular redox status is a critical parameter determining plant development in response to biotic and abiotic stress. Thioredoxin (TRX) and glutathione are key regulators of redox homeostasis, and the TRX and glutathione pathways are essential for postembryonic meristematic activities. Here, we show by associating TRX reductases (ntra ntrb) and glutathione biosynthesis (cad2) mutations that these two thiol reduction pathways interfere with developmental processes through modulation of auxin signaling. The triple ntra ntrb cad2 mutant develops normally at the rosette stage, undergoes the floral transition, but produces almost naked stems, reminiscent of the phenotype of several mutants affected in auxin transport or biosynthesis. In addition, the ntra ntrb cad2 mutant shows a loss of apical dominance, vasculature defects, and reduced secondary root production, several phenotypes tightly regulated by auxin. We further show that auxin transport capacities and auxin levels are perturbed in the mutant, suggesting that the NTR-glutathione pathways alter both auxin transport and metabolism. Analysis of ntr and glutathione biosynthesis mutants suggests that glutathione homeostasis plays a major role in auxin transport as both NTR and glutathione pathways are involved in auxin homeostasis.

@article{krouk_nitrate-regulated_2010,
	title = {Nitrate-{Regulated} {Auxin} {Transport} by {NRT1}.1 {Defines} a {Mechanism} for {Nutrient} {Sensing} in {Plants}},
	volume = {18},
	issn = {15345807},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S1534580710002169},
	doi = {10/dq3gjd},
	language = {en},
	number = {6},
	urldate = {2021-06-08},
	journal = {Developmental Cell},
	author = {Krouk, Gabriel and Lacombe, Benoît and Bielach, Agnieszka and Perrine-Walker, Francine and Malinska, Katerina and Mounier, Emmanuelle and Hoyerova, Klara and Tillard, Pascal and Leon, Sarah and Ljung, Karin and Zazimalova, Eva and Benkova, Eva and Nacry, Philippe and Gojon, Alain},
	month = jun,
	year = {2010},
	pages = {927--937},
}

@article{vera-sirera_role_2010,
	title = {Role of polyamines in plant vascular development},
	volume = {48},
	issn = {09819428},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0981942810000173},
	doi = {10/c429rn},
	language = {en},
	number = {7},
	urldate = {2021-06-08},
	journal = {Plant Physiology and Biochemistry},
	author = {Vera-Sirera, Francisco and Minguet, Eugenio G. and Singh, Sunil Kumar and Ljung, Karin and Tuominen, Hannele and Blázquez, Miguel A. and Carbonell, Juan},
	month = jul,
	year = {2010},
	pages = {534--539},
}

@article{sorefan_regulated_2009,
	title = {A regulated auxin minimum is required for seed dispersal in {Arabidopsis}},
	volume = {459},
	issn = {0028-0836, 1476-4687},
	url = {http://www.nature.com/articles/nature07875},
	doi = {10/dwbb4c},
	language = {en},
	number = {7246},
	urldate = {2021-06-08},
	journal = {Nature},
	author = {Sorefan, Karim and Girin, Thomas and Liljegren, Sarah J. and Ljung, Karin and Robles, Pedro and Galván-Ampudia, Carlos S. and Offringa, Remko and Friml, Jiří and Yanofsky, Martin F. and Østergaard, Lars},
	month = may,
	year = {2009},
	pages = {583--586},
}

@article{petersson_auxin_2009,
	title = {An {Auxin} {Gradient} and {Maximum} in the \textit{{Arabidopsis}} {Root} {Apex} {Shown} by {High}-{Resolution} {Cell}-{Specific} {Analysis} of {IAA} {Distribution} and {Synthesis}},
	volume = {21},
	issn = {1532-298X, 1040-4651},
	url = {https://academic.oup.com/plcell/article/21/6/1659/6095411},
	doi = {10/ddgn83},
	abstract = {Abstract
            Local concentration gradients of the plant growth regulator auxin (indole-3-acetic acid [IAA]) are thought to instruct the positioning of organ primordia and stem cell niches and to direct cell division, expansion, and differentiation. High-resolution measurements of endogenous IAA concentrations in support of the gradient hypothesis are required to substantiate this hypothesis. Here, we introduce fluorescence-activated cell sorting of green fluorescent protein–marked cell types combined with highly sensitive mass spectrometry methods as a novel means for analyses of IAA distribution and metabolism at cellular resolution. Our results reveal the presence of IAA concentration gradients within the Arabidopsis thaliana root tip with a distinct maximum in the organizing quiescent center of the root apex. We also demonstrate that the root apex provides an important source of IAA and that cells of all types display a high synthesis capacity, suggesting a substantial contribution of local biosynthesis to auxin homeostasis in the root tip. Our results indicate that local biosynthesis and polar transport combine to produce auxin gradients and maxima in the root tip.},
	language = {en},
	number = {6},
	urldate = {2021-06-08},
	journal = {The Plant Cell},
	author = {Petersson, Sara V. and Johansson, Annika I. and Kowalczyk, Mariusz and Makoveychuk, Alexander and Wang, Jean Y. and Moritz, Thomas and Grebe, Markus and Benfey, Philip N. and Sandberg, Göran and Ljung, Karin},
	month = aug,
	year = {2009},
	pages = {1659--1668},
}

Abstract Local concentration gradients of the plant growth regulator auxin (indole-3-acetic acid [IAA]) are thought to instruct the positioning of organ primordia and stem cell niches and to direct cell division, expansion, and differentiation. High-resolution measurements of endogenous IAA concentrations in support of the gradient hypothesis are required to substantiate this hypothesis. Here, we introduce fluorescence-activated cell sorting of green fluorescent protein–marked cell types combined with highly sensitive mass spectrometry methods as a novel means for analyses of IAA distribution and metabolism at cellular resolution. Our results reveal the presence of IAA concentration gradients within the Arabidopsis thaliana root tip with a distinct maximum in the organizing quiescent center of the root apex. We also demonstrate that the root apex provides an important source of IAA and that cells of all types display a high synthesis capacity, suggesting a substantial contribution of local biosynthesis to auxin homeostasis in the root tip. Our results indicate that local biosynthesis and polar transport combine to produce auxin gradients and maxima in the root tip.

@article{ali_auxin_2009,
	title = {Auxin production by plant associated bacteria: impact on endogenous {IAA} content and growth of \textit{{Triticum} aestivum} {L}.},
	volume = {48},
	issn = {02668254, 1472765X},
	shorttitle = {Auxin production by plant associated bacteria},
	url = {http://doi.wiley.com/10.1111/j.1472-765X.2009.02565.x},
	doi = {10/djz756},
	language = {en},
	number = {5},
	urldate = {2021-06-08},
	journal = {Letters in Applied Microbiology},
	author = {Ali, B. and Sabri, A.N. and Ljung, K. and Hasnain, S.},
	month = may,
	year = {2009},
	pages = {542--547},
}

@article{lewis_auxin_2009,
	title = {Auxin transport into cotyledons and cotyledon growth depend similarly on the {ABCB19} {Multidrug} {Resistance}-like transporter},
	volume = {60},
	issn = {09607412, 1365313X},
	url = {http://doi.wiley.com/10.1111/j.1365-313X.2009.03941.x},
	doi = {10/bf6r5r},
	language = {en},
	number = {1},
	urldate = {2021-06-08},
	journal = {The Plant Journal},
	author = {Lewis, Daniel R. and Wu, Guosheng and Ljung, Karin and Spalding, Edgar P.},
	month = oct,
	year = {2009},
	pages = {91--101},
}

@article{prusinkiewicz_control_2009,
	title = {Control of bud activation by an auxin transport switch},
	volume = {106},
	issn = {0027-8424, 1091-6490},
	url = {http://www.pnas.org/cgi/doi/10.1073/pnas.0906696106},
	doi = {10/d5w9ft},
	language = {en},
	number = {41},
	urldate = {2021-06-08},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Prusinkiewicz, P. and Crawford, S. and Smith, R. S. and Ljung, K. and Bennett, T. and Ongaro, V. and Leyser, O.},
	month = oct,
	year = {2009},
	pages = {17431--17436},
}

@article{ikeda_local_2009,
	title = {Local auxin biosynthesis modulates gradient-directed planar polarity in {Arabidopsis}},
	volume = {11},
	issn = {1465-7392, 1476-4679},
	url = {http://www.nature.com/articles/ncb1879},
	doi = {10/bdkdmx},
	language = {en},
	number = {6},
	urldate = {2021-06-08},
	journal = {Nature Cell Biology},
	author = {Ikeda, Yoshihisa and Men, Shuzhen and Fischer, Urs and Stepanova, Anna N. and Alonso, José M. and Ljung, Karin and Grebe, Markus},
	month = jun,
	year = {2009},
	pages = {731--738},
}

@article{ali_quantification_2009,
	title = {Quantification of indole-3-acetic acid from plant associated {Bacillus} spp. and their phytostimulatory effect on {Vigna} radiata ({L}.)},
	volume = {25},
	issn = {0959-3993, 1573-0972},
	url = {http://link.springer.com/10.1007/s11274-008-9918-9},
	doi = {10/fjqgq7},
	language = {en},
	number = {3},
	urldate = {2021-06-08},
	journal = {World Journal of Microbiology and Biotechnology},
	author = {Ali, Basharat and Sabri, Anjum Nasim and Ljung, Karin and Hasnain, Shahida},
	month = mar,
	year = {2009},
	pages = {519--526},
}

@article{rawat_reveille1_2009,
	title = {{REVEILLE1}, a {Myb}-like transcription factor, integrates the circadian clock and auxin pathways},
	volume = {106},
	issn = {0027-8424, 1091-6490},
	url = {http://www.pnas.org/cgi/doi/10.1073/pnas.0813035106},
	doi = {10/bwffw9},
	language = {en},
	number = {39},
	urldate = {2021-06-08},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Rawat, R. and Schwartz, J. and Jones, M. A. and Sairanen, I. and Cheng, Y. and Andersson, C. R. and Zhao, Y. and Ljung, K. and Harmer, S. L.},
	month = sep,
	year = {2009},
	pages = {16883--16888},
}

@article{tromas_auxin_2009,
	title = {The {AUXIN} {BINDING} {PROTEIN} 1 {Is} {Required} for {Differential} {Auxin} {Responses} {Mediating} {Root} {Growth}},
	volume = {4},
	issn = {1932-6203},
	url = {https://dx.plos.org/10.1371/journal.pone.0006648},
	doi = {10/drhr8k},
	language = {en},
	number = {9},
	urldate = {2021-06-08},
	journal = {PLoS ONE},
	author = {Tromas, Alexandre and Braun, Nils and Muller, Philippe and Khodus, Tatyana and Paponov, Ivan A. and Palme, Klaus and Ljung, Karin and Lee, Ji-Young and Benfey, Philip and Murray, James A. H. and Scheres, Ben and Perrot-Rechenmann, Catherine},
	editor = {Newbigin, Edward},
	month = sep,
	year = {2009},
	pages = {e6648},
}

@article{staldal_auxin_2008,
	title = {Auxin can act independently of \textit{{CRC}} , \textit{{LUG}} , \textit{{SEU}} , \textit{{SPT}} and \textit{{STY1}} in style development but not apical-basal patterning of the \textit{{Arabidopsis}} gynoecium},
	volume = {180},
	issn = {0028646X, 14698137},
	url = {http://doi.wiley.com/10.1111/j.1469-8137.2008.02625.x},
	doi = {10/dbpq5p},
	language = {en},
	number = {4},
	urldate = {2021-06-10},
	journal = {New Phytologist},
	author = {Ståldal, Veronika and Sohlberg, Joel J. and Eklund, D. Magnus and Ljung, Karin and Sundberg, Eva},
	month = dec,
	year = {2008},
	pages = {798--808},
}

@article{nieminen_cytokinin_2008,
	title = {Cytokinin signaling regulates cambial development in poplar},
	volume = {105},
	issn = {0027-8424, 1091-6490},
	url = {http://www.pnas.org/cgi/doi/10.1073/pnas.0805617106},
	doi = {10/cv6jmj},
	language = {en},
	number = {50},
	urldate = {2021-06-10},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Nieminen, K. and Immanen, J. and Laxell, M. and Kauppinen, L. and Tarkowski, P. and Dolezal, K. and Tahtiharju, S. and Elo, A. and Decourteix, M. and Ljung, K. and Bhalerao, Rishikesh P. and Keinonen, K. and Albert, V. A. and Helariutta, Y.},
	month = dec,
	year = {2008},
	pages = {20032--20037},
}

@article{stone_disruptions_2008,
	title = {Disruptions in {AUX1}-{Dependent} {Auxin} {Influx} {Alter} {Hypocotyl} {Phototropism} in {Arabidopsis}},
	volume = {1},
	issn = {16742052},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S1674205214603324},
	doi = {10/d6wcw6},
	language = {en},
	number = {1},
	urldate = {2021-06-10},
	journal = {Molecular Plant},
	author = {Stone, Bethany B. and Stowe-Evans, Emily L. and Harper, Reneé M. and Celaya, R. Brandon and Ljung, Karin and Sandberg, Göran and Liscum, Emmanuel},
	month = jan,
	year = {2008},
	pages = {129--144},
}

@article{larsson_inhibited_2008,
	title = {Inhibited polar auxin transport results in aberrant embryo development in {Norway} spruce},
	volume = {177},
	issn = {0028-646X, 1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/j.1469-8137.2007.02289.x},
	doi = {10/fcmjzj},
	language = {en},
	number = {2},
	urldate = {2021-06-10},
	journal = {New Phytologist},
	author = {Larsson, Emma and Sitbon, Folke and Ljung, Karin and Von Arnold, Sara},
	month = jan,
	year = {2008},
	pages = {356--366},
}

@article{tao_rapid_2008,
	title = {Rapid {Synthesis} of {Auxin} via a {New} {Tryptophan}-{Dependent} {Pathway} {Is} {Required} for {Shade} {Avoidance} in {Plants}},
	volume = {133},
	issn = {00928674},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0092867408002146},
	doi = {10/frnv64},
	language = {en},
	number = {1},
	urldate = {2021-06-10},
	journal = {Cell},
	author = {Tao, Yi and Ferrer, Jean-Luc and Ljung, Karin and Pojer, Florence and Hong, Fangxin and Long, Jeff A. and Li, Lin and Moreno, Javier E. and Bowman, Marianne E. and Ivans, Lauren J. and Cheng, Youfa and Lim, Jason and Zhao, Yunde and Ballaré, Carlos L. and Sandberg, Göran and Noel, Joseph P. and Chory, Joanne},
	month = apr,
	year = {2008},
	pages = {164--176},
}

@article{andersen_requirement_2008,
	title = {Requirement of {B2}-{Type} \textit{{Cyclin}-{Dependent} {Kinases}} for {Meristem} {Integrity} in \textit{{Arabidopsis} thaliana}},
	volume = {20},
	issn = {1532-298X},
	url = {https://academic.oup.com/plcell/article/20/1/88/6091364},
	doi = {10/djf5gv},
	abstract = {Abstract
            To maintain proper meristem function, cell division and differentiation must be coordinately regulated in distinct subdomains of the meristem. Although a number of regulators necessary for the correct organization of the shoot apical meristem (SAM) have been identified, it is still largely unknown how their function is integrated with the cell cycle machinery to translate domain identity into correct cellular behavior. We show here that the cyclin-dependent kinases CDKB2;1 and CDKB2;2 are required both for normal cell cycle progression and for meristem organization. Consistently, the CDKB2 genes are highly expressed in the SAM in a cell cycle–dependent fashion, and disruption of CDKB2 function leads to severe meristematic defects. In addition, strong alterations in hormone signaling both at the level of active hormones and with respect to transcriptional and physiological outputs were observed in plants with disturbed CDKB2 activity.},
	language = {en},
	number = {1},
	urldate = {2021-06-10},
	journal = {The Plant Cell},
	author = {Andersen, Stig Uggerhøj and Buechel, Sabine and Zhao, Zhong and Ljung, Karin and Novák, Ondřej and Busch, Wolfgang and Schuster, Christoph and Lohmann, Jan U.},
	month = feb,
	year = {2008},
	pages = {88--100},
}

Abstract To maintain proper meristem function, cell division and differentiation must be coordinately regulated in distinct subdomains of the meristem. Although a number of regulators necessary for the correct organization of the shoot apical meristem (SAM) have been identified, it is still largely unknown how their function is integrated with the cell cycle machinery to translate domain identity into correct cellular behavior. We show here that the cyclin-dependent kinases CDKB2;1 and CDKB2;2 are required both for normal cell cycle progression and for meristem organization. Consistently, the CDKB2 genes are highly expressed in the SAM in a cell cycle–dependent fashion, and disruption of CDKB2 function leads to severe meristematic defects. In addition, strong alterations in hormone signaling both at the level of active hormones and with respect to transcriptional and physiological outputs were observed in plants with disturbed CDKB2 activity.

@article{swarup_auxin_2008,
	title = {The auxin influx carrier {LAX3} promotes lateral root emergence},
	volume = {10},
	issn = {1465-7392, 1476-4679},
	url = {http://www.nature.com/articles/ncb1754},
	doi = {10/cc9bgf},
	language = {en},
	number = {8},
	urldate = {2021-06-10},
	journal = {Nature Cell Biology},
	author = {Swarup, Kamal and Benková, Eva and Swarup, Ranjan and Casimiro, Ilda and Péret, Benjamin and Yang, Yaodong and Parry, Geraint and Nielsen, Erik and De Smet, Ive and Vanneste, Steffen and Levesque, Mitch P. and Carrier, David and James, Nicholas and Calvo, Vanessa and Ljung, Karin and Kramer, Eric and Roberts, Rebecca and Graham, Neil and Marillonnet, Sylvestre and Patel, Kanu and Jones, Jonathan D.G. and Taylor, Christopher G. and Schachtman, Daniel P. and May, Sean and Sandberg, Goran and Benfey, Philip and Friml, Jiri and Kerr, Ian and Beeckman, Tom and Laplaze, Laurent and Bennett, Malcolm J.},
	month = aug,
	year = {2008},
	pages = {946--954},
}

@article{ruzicka_ethylene_2007,
	title = {Ethylene {Regulates} {Root} {Growth} through {Effects} on {Auxin} {Biosynthesis} and {Transport}-{Dependent} {Auxin} {Distribution}},
	volume = {19},
	issn = {1532-298X},
	url = {https://academic.oup.com/plcell/article/19/7/2197/6092111},
	doi = {10/c2w5xb},
	abstract = {Abstract
            In plants, each developmental process integrates a network of signaling events that are regulated by different phytohormones, and interactions among hormonal pathways are essential to modulate their effect. Continuous growth of roots results from the postembryonic activity of cells within the root meristem that is controlled by the coordinated action of several phytohormones, including auxin and ethylene. Although their interaction has been studied intensively, the molecular and cellular mechanisms underlying this interplay are unknown. We show that the effect of ethylene on root growth is largely mediated by the regulation of the auxin biosynthesis and transport-dependent local auxin distribution. Ethylene stimulates auxin biosynthesis and basipetal auxin transport toward the elongation zone, where it activates a local auxin response leading to inhibition of cell elongation. Consistently, in mutants affected in auxin perception or basipetal auxin transport, ethylene cannot activate the auxin response nor regulate the root growth. In addition, ethylene modulates the transcription of several components of the auxin transport machinery. Thus, ethylene achieves a local activation of the auxin signaling pathway and regulates root growth by both stimulating the auxin biosynthesis and by modulating the auxin transport machinery.},
	language = {en},
	number = {7},
	urldate = {2021-06-10},
	journal = {The Plant Cell},
	author = {Růžička, Kamil and Ljung, Karin and Vanneste, Steffen and Podhorská, Radka and Beeckman, Tom and Friml, Jiří and Benková, Eva},
	month = aug,
	year = {2007},
	pages = {2197--2212},
}

Abstract In plants, each developmental process integrates a network of signaling events that are regulated by different phytohormones, and interactions among hormonal pathways are essential to modulate their effect. Continuous growth of roots results from the postembryonic activity of cells within the root meristem that is controlled by the coordinated action of several phytohormones, including auxin and ethylene. Although their interaction has been studied intensively, the molecular and cellular mechanisms underlying this interplay are unknown. We show that the effect of ethylene on root growth is largely mediated by the regulation of the auxin biosynthesis and transport-dependent local auxin distribution. Ethylene stimulates auxin biosynthesis and basipetal auxin transport toward the elongation zone, where it activates a local auxin response leading to inhibition of cell elongation. Consistently, in mutants affected in auxin perception or basipetal auxin transport, ethylene cannot activate the auxin response nor regulate the root growth. In addition, ethylene modulates the transcription of several components of the auxin transport machinery. Thus, ethylene achieves a local activation of the auxin signaling pathway and regulates root growth by both stimulating the auxin biosynthesis and by modulating the auxin transport machinery.

@article{swarup_ethylene_2007,
	title = {Ethylene {Upregulates} {Auxin} {Biosynthesis} in \textit{{Arabidopsis}} {Seedlings} to {Enhance} {Inhibition} of {Root} {Cell} {Elongation}},
	volume = {19},
	issn = {1532-298X},
	url = {https://academic.oup.com/plcell/article/19/7/2186/6092109},
	doi = {10/cd3mq3},
	abstract = {Abstract
            Ethylene represents an important regulatory signal for root development. Genetic studies in Arabidopsis thaliana have demonstrated that ethylene inhibition of root growth involves another hormone signal, auxin. This study investigated why auxin was required by ethylene to regulate root growth. We initially observed that ethylene positively controls auxin biosynthesis in the root apex. We subsequently demonstrated that ethylene-regulated root growth is dependent on (1) the transport of auxin from the root apex via the lateral root cap and (2) auxin responses occurring in multiple elongation zone tissues. Detailed growth studies revealed that the ability of the ethylene precursor 1-aminocyclopropane-1-carboxylic acid to inhibit root cell elongation was significantly enhanced in the presence of auxin. We conclude that by upregulating auxin biosynthesis, ethylene facilitates its ability to inhibit root cell expansion.},
	language = {en},
	number = {7},
	urldate = {2021-06-10},
	journal = {The Plant Cell},
	author = {Swarup, Ranjan and Perry, Paula and Hagenbeek, Dik and Van Der Straeten, Dominique and Beemster, Gerrit T.S. and Sandberg, Göran and Bhalerao, Rishikesh P. and Ljung, Karin and Bennett, Malcolm J.},
	month = aug,
	year = {2007},
	pages = {2186--2196},
}

Abstract Ethylene represents an important regulatory signal for root development. Genetic studies in Arabidopsis thaliana have demonstrated that ethylene inhibition of root growth involves another hormone signal, auxin. This study investigated why auxin was required by ethylene to regulate root growth. We initially observed that ethylene positively controls auxin biosynthesis in the root apex. We subsequently demonstrated that ethylene-regulated root growth is dependent on (1) the transport of auxin from the root apex via the lateral root cap and (2) auxin responses occurring in multiple elongation zone tissues. Detailed growth studies revealed that the ability of the ethylene precursor 1-aminocyclopropane-1-carboxylic acid to inhibit root cell elongation was significantly enhanced in the presence of auxin. We conclude that by upregulating auxin biosynthesis, ethylene facilitates its ability to inhibit root cell expansion.

@article{yin_ubiquitin_2007,
	title = {Ubiquitin {Lysine} 63 {Chain}–{Forming} {Ligases} {Regulate} {Apical} {Dominance} in \textit{{Arabidopsis}}},
	volume = {19},
	issn = {1532-298X},
	url = {https://academic.oup.com/plcell/article/19/6/1898/6092124},
	doi = {10/cwwcnr},
	abstract = {Abstract
            Lys-63–linked multiubiquitin chains play important roles in signal transduction in yeast and in mammals, but the functions for this type of chain in plants remain to be defined. The RING domain protein RGLG2 (for RING domain Ligase2) from Arabidopsis thaliana can be N-terminally myristoylated and localizes to the plasma membrane. It can form Lys-63–linked multiubiquitin chains in an in vitro reaction. RGLG2 has overlapping functions with its closest sequelog, RGLG1, and single mutants in either gene are inconspicuous. rglg1 rglg2 double mutant plants exhibit loss of apical dominance and altered phyllotaxy, two traits critically influenced by the plant hormone auxin. Auxin and cytokinin levels are changed, and the plants show a decreased response to exogenously added auxin. Changes in the abundance of PIN family auxin transport proteins and synthetic lethality with a mutation in the auxin transport regulator BIG suggest that the directional flow of auxin is modulated by RGLG activity. Modification of proteins by Lys-63–linked multiubiquitin chains is thus important for hormone-regulated, basic plant architecture.},
	language = {en},
	number = {6},
	urldate = {2021-06-10},
	journal = {The Plant Cell},
	author = {Yin, Xiao-Jun and Volk, Sara and Ljung, Karin and Mehlmer, Norbert and Dolezal, Karel and Ditengou, Franck and Hanano, Shigeru and Davis, Seth J. and Schmelzer, Elmon and Sandberg, Göran and Teige, Markus and Palme, Klaus and Pickart, Cecile and Bachmair, Andreas},
	month = jul,
	year = {2007},
	pages = {1898--1911},
}

Abstract Lys-63–linked multiubiquitin chains play important roles in signal transduction in yeast and in mammals, but the functions for this type of chain in plants remain to be defined. The RING domain protein RGLG2 (for RING domain Ligase2) from Arabidopsis thaliana can be N-terminally myristoylated and localizes to the plasma membrane. It can form Lys-63–linked multiubiquitin chains in an in vitro reaction. RGLG2 has overlapping functions with its closest sequelog, RGLG1, and single mutants in either gene are inconspicuous. rglg1 rglg2 double mutant plants exhibit loss of apical dominance and altered phyllotaxy, two traits critically influenced by the plant hormone auxin. Auxin and cytokinin levels are changed, and the plants show a decreased response to exogenously added auxin. Changes in the abundance of PIN family auxin transport proteins and synthetic lethality with a mutation in the auxin transport regulator BIG suggest that the directional flow of auxin is modulated by RGLG activity. Modification of proteins by Lys-63–linked multiubiquitin chains is thus important for hormone-regulated, basic plant architecture.

@article{esmon_gradient_2006,
	title = {A gradient of auxin and auxin-dependent transcription precedes tropic growth responses},
	volume = {103},
	copyright = {Copyright © 2006, The National Academy of Sciences},
	issn = {0027-8424, 1091-6490},
	url = {https://www.pnas.org/content/103/1/236},
	doi = {10.1073/pnas.0507127103},
	abstract = {Plants, although sessile, can reorient growth axes in response to changing environmental conditions. Phototropism and gravitropism represent adaptive growth responses induced by changes in light direction and growth axis orientation relative to gravitational direction, respectively. The nearly 80-year-old Cholodny–Went theory [Went, F. W. \& Thimann, K. V. (1937) Phytohormones (Macmillan, New York)] predicts that formation of a gradient of the plant morphogen auxin is central to the establishment of tropic curvature. Loss of tropic responses in seedling stems of Arabidopsis thaliana mutants lacking the auxin-regulated transcriptional activator NPH4/ARF7 has further suggested that a gradient of gene expression represents an essential output from the auxin gradient. Yet the molecular identities of such output components, which are likely to encode proteins directly involved in growth control, have remained elusive. Here we report the discovery of a suite of tropic stimulus-induced genes in Brassica oleracea that are responsive to an auxin gradient and exhibit morphologically graded expression concomitant with, or before, observable curvature responses. These results provide compelling molecular support for the Cholodny–Went theory and suggest that morphologically graded transcription represents an important mechanism for interpreting tropically stimulated gradients of auxin. Intriguingly, two of the tropic stimulus-induced genes, EXPA1 and EXPA8, encode enzymes involved in cell wall extension, a response prerequisite for differential growth leading to curvatures, and are up-regulated before curvature in the flank that will elongate. This observation suggests that morphologically graded transcription likely leads to the graded expression of proteins whose activities can directly regulate the establishment and modulation of tropic curvatures.},
	language = {en},
	number = {1},
	urldate = {2021-06-11},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Esmon, C. Alex and Tinsley, Amanda G. and Ljung, Karin and Sandberg, Goran and Hearne, Leonard B. and Liscum, Emmanuel},
	month = jan,
	year = {2006},
	pmid = {16371470},
	note = {Publisher: National Academy of Sciences
Section: Biological Sciences},
	keywords = {NPH4/ARF7, gravitropism, phototropism},
	pages = {236--241},
}

Plants, although sessile, can reorient growth axes in response to changing environmental conditions. Phototropism and gravitropism represent adaptive growth responses induced by changes in light direction and growth axis orientation relative to gravitational direction, respectively. The nearly 80-year-old Cholodny–Went theory [Went, F. W. & Thimann, K. V. (1937) Phytohormones (Macmillan, New York)] predicts that formation of a gradient of the plant morphogen auxin is central to the establishment of tropic curvature. Loss of tropic responses in seedling stems of Arabidopsis thaliana mutants lacking the auxin-regulated transcriptional activator NPH4/ARF7 has further suggested that a gradient of gene expression represents an essential output from the auxin gradient. Yet the molecular identities of such output components, which are likely to encode proteins directly involved in growth control, have remained elusive. Here we report the discovery of a suite of tropic stimulus-induced genes in Brassica oleracea that are responsive to an auxin gradient and exhibit morphologically graded expression concomitant with, or before, observable curvature responses. These results provide compelling molecular support for the Cholodny–Went theory and suggest that morphologically graded transcription represents an important mechanism for interpreting tropically stimulated gradients of auxin. Intriguingly, two of the tropic stimulus-induced genes, EXPA1 and EXPA8, encode enzymes involved in cell wall extension, a response prerequisite for differential growth leading to curvatures, and are up-regulated before curvature in the flank that will elongate. This observation suggests that morphologically graded transcription likely leads to the graded expression of proteins whose activities can directly regulate the establishment and modulation of tropic curvatures.

@article{reuille_computer_2006,
	title = {Computer simulations reveal properties of the cell-cell signaling network at the shoot apex in {Arabidopsis}},
	volume = {103},
	copyright = {Copyright © 2006, The National Academy of Sciences},
	issn = {0027-8424, 1091-6490},
	url = {https://www.pnas.org/content/103/5/1627},
	doi = {10/dc72k6},
	abstract = {The active transport of the plant hormone auxin plays a major role in the initiation of organs at the shoot apex. Polar localized membrane proteins of the PIN1 family facilitate this transport, and recent observations suggest that auxin maxima created by these proteins are at the basis of organ initiation. This hypothesis is based on the visual, qualitative characterization of the complex distribution patterns of the PIN1 protein in Arabidopsis. To take these analyses further, we investigated the properties of the patterns using computational modeling. The simulations reveal previously undescribed properties of PIN1 distribution. In particular, they suggest an important role for the meristem summit in the distribution of auxin. We confirm these predictions by further experimentation and propose a detailed model for the dynamics of auxin fluxes at the shoot apex.},
	language = {en},
	number = {5},
	urldate = {2021-06-11},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Reuille, Pierre Barbier de and Bohn-Courseau, Isabelle and Ljung, Karin and Morin, Halima and Carraro, Nicola and Godin, Christophe and Traas, Jan},
	month = jan,
	year = {2006},
	pmid = {16432202},
	note = {Publisher: National Academy of Sciences
Section: Biological Sciences},
	keywords = {auxin, modeling, shoot meristem},
	pages = {1627--1632},
}

The active transport of the plant hormone auxin plays a major role in the initiation of organs at the shoot apex. Polar localized membrane proteins of the PIN1 family facilitate this transport, and recent observations suggest that auxin maxima created by these proteins are at the basis of organ initiation. This hypothesis is based on the visual, qualitative characterization of the complex distribution patterns of the PIN1 protein in Arabidopsis. To take these analyses further, we investigated the properties of the patterns using computational modeling. The simulations reveal previously undescribed properties of PIN1 distribution. In particular, they suggest an important role for the meristem summit in the distribution of auxin. We confirm these predictions by further experimentation and propose a detailed model for the dynamics of auxin fluxes at the shoot apex.

@article{fischer_vectorial_2006,
	title = {Vectorial {Information} for {Arabidopsis} {Planar} {Polarity} {Is} {Mediated} by {Combined} {AUX1}, {EIN2}, and {GNOM} {Activity}},
	volume = {16},
	issn = {0960-9822},
	url = {https://www.sciencedirect.com/science/article/pii/S0960982206022044},
	doi = {10.1016/j.cub.2006.08.091},
	abstract = {Cell polarity is commonly coordinated within the plane of a single tissue layer (planar polarity), and hair positioning has been exploited as a simple marker for planar polarization of animal epithelia [1]. The root epidermis of the plant Arabidopsis similarly reveals planar polarity of hair localization close to root tip-oriented (basal) ends of hair-forming cells 2, 3, 4. Hair position is directed toward a concentration maximum of the hormone auxin in the root tip 4, 5, but mechanisms driving this plant-specific planar polarity remain elusive. Here, we report that combinatorial action of the auxin influx carrier AUX16, 7, ETHYLENE-INSENSITIVE2 (EIN2) [8], and GNOM[9] genes mediates the vector for coordinate hair positioning. In aux1;ein2;gnomeb triple mutant roots, hairs display axial (apical or basal) instead of coordinate polar (basal) position, and recruitment of Rho-of-Plant (ROP) GTPases to the hair initiation site 10, 11 reveals the same polar-to-axial switch. The auxin concentration gradient is virtually abolished in aux1;ein2;gnomeb roots, where locally applied auxin can coordinate hair positioning. Moreover, auxin overproduction in sectors of wild-type roots enhances planar ROP and hair polarity over long and short distances. Hence, auxin may provide vectorial information for planar polarity that requires combinatorial AUX1, EIN2, and GNOM activity upstream of ROP positioning.},
	language = {en},
	number = {21},
	urldate = {2021-06-11},
	journal = {Current Biology},
	author = {Fischer, Urs and Ikeda, Yoshihisa and Ljung, Karin and Serralbo, Olivier and Singh, Manoj and Heidstra, Renze and Palme, Klaus and Scheres, Ben and Grebe, Markus},
	month = nov,
	year = {2006},
	keywords = {DEVBIO},
	pages = {2143--2149},
}

Cell polarity is commonly coordinated within the plane of a single tissue layer (planar polarity), and hair positioning has been exploited as a simple marker for planar polarization of animal epithelia [1]. The root epidermis of the plant Arabidopsis similarly reveals planar polarity of hair localization close to root tip-oriented (basal) ends of hair-forming cells 2, 3, 4. Hair position is directed toward a concentration maximum of the hormone auxin in the root tip 4, 5, but mechanisms driving this plant-specific planar polarity remain elusive. Here, we report that combinatorial action of the auxin influx carrier AUX16, 7, ETHYLENE-INSENSITIVE2 (EIN2) [8], and GNOM[9] genes mediates the vector for coordinate hair positioning. In aux1;ein2;gnomeb triple mutant roots, hairs display axial (apical or basal) instead of coordinate polar (basal) position, and recruitment of Rho-of-Plant (ROP) GTPases to the hair initiation site 10, 11 reveals the same polar-to-axial switch. The auxin concentration gradient is virtually abolished in aux1;ein2;gnomeb roots, where locally applied auxin can coordinate hair positioning. Moreover, auxin overproduction in sectors of wild-type roots enhances planar ROP and hair polarity over long and short distances. Hence, auxin may provide vectorial information for planar polarity that requires combinatorial AUX1, EIN2, and GNOM activity upstream of ROP positioning.

@article{sorin_auxin_2005,
	title = {Auxin and {Light} {Control} of {Adventitious} {Rooting} in {Arabidopsis} {Require} {ARGONAUTE1}},
	volume = {17},
	issn = {1040-4651},
	url = {https://doi.org/10.1105/tpc.105.031625},
	doi = {10/bsmnt5},
	abstract = {Adventitious rooting is a quantitative genetic trait regulated by both environmental and endogenous factors. To better understand the physiological and molecular basis of adventitious rooting, we took advantage of two classes of Arabidopsis thaliana mutants altered in adventitious root formation: the superroot mutants, which spontaneously make adventitious roots, and the argonaute1 (ago1) mutants, which unlike superroot are barely able to form adventitious roots. The defect in adventitious rooting observed in ago1 correlated with light hypersensitivity and the deregulation of auxin homeostasis specifically in the apical part of the seedlings. In particular, a clear reduction in endogenous levels of free indoleacetic acid (IAA) and IAA conjugates was shown. This was correlated with a downregulation of the expression of several auxin-inducible GH3 genes in the hypocotyl of the ago1-3 mutant. We also found that the Auxin Response Factor17 (ARF17) gene, a potential repressor of auxin-inducible genes, was overexpressed in ago1-3 hypocotyls. The characterization of an ARF17-overexpressing line showed that it produced fewer adventitious roots than the wild type and retained a lower expression of GH3 genes. Thus, we suggest that ARF17 negatively regulates adventitious root formation in ago1 mutants by repressing GH3 genes and therefore perturbing auxin homeostasis in a light-dependent manner. These results suggest that ARF17 could be a major regulator of adventitious rooting in Arabidopsis.},
	number = {5},
	urldate = {2021-06-11},
	journal = {The Plant Cell},
	author = {Sorin, Céline and Bussell, John D. and Camus, Isabelle and Ljung, Karin and Kowalczyk, Mariusz and Geiss, Gaia and McKhann, Heather and Garcion, Christophe and Vaucheret, Hervé and Sandberg, Göran and Bellini, Catherine},
	month = may,
	year = {2005},
	pages = {1343--1359},
}

Adventitious rooting is a quantitative genetic trait regulated by both environmental and endogenous factors. To better understand the physiological and molecular basis of adventitious rooting, we took advantage of two classes of Arabidopsis thaliana mutants altered in adventitious root formation: the superroot mutants, which spontaneously make adventitious roots, and the argonaute1 (ago1) mutants, which unlike superroot are barely able to form adventitious roots. The defect in adventitious rooting observed in ago1 correlated with light hypersensitivity and the deregulation of auxin homeostasis specifically in the apical part of the seedlings. In particular, a clear reduction in endogenous levels of free indoleacetic acid (IAA) and IAA conjugates was shown. This was correlated with a downregulation of the expression of several auxin-inducible GH3 genes in the hypocotyl of the ago1-3 mutant. We also found that the Auxin Response Factor17 (ARF17) gene, a potential repressor of auxin-inducible genes, was overexpressed in ago1-3 hypocotyls. The characterization of an ARF17-overexpressing line showed that it produced fewer adventitious roots than the wild type and retained a lower expression of GH3 genes. Thus, we suggest that ARF17 negatively regulates adventitious root formation in ago1 mutants by repressing GH3 genes and therefore perturbing auxin homeostasis in a light-dependent manner. These results suggest that ARF17 could be a major regulator of adventitious rooting in Arabidopsis.

@article{vanneste_cell_2005,
	title = {Cell cycle progression in the pericycle is not sufficient for {SOLITARY} {ROOT}/{IAA14}-mediated lateral root initiation in {Arabidopsis} thaliana},
	volume = {17},
	issn = {1040-4651},
	doi = {10/dwzcgw},
	abstract = {To study the mechanisms behind auxin-induced cell division, lateral root initiation was used as a model system. By means of microarray analysis, genome-wide transcriptional changes were monitored during the early steps of lateral root initiation. Inclusion of the dominant auxin signaling mutant solitary root1 (slr1) identified genes involved in lateral root initiation that act downstream of the auxin/indole-3-acetic acid (AUX/IAA) signaling pathway. Interestingly, key components of the cell cycle machinery were strongly defective in slr1, suggesting a direct link between AUX/IAA signaling and core cell cycle regulation. However, induction of the cell cycle in the mutant background by overexpression of the D-type cyclin (CYCD3;1) was able to trigger complete rounds of cell division in the pericycle that did not result in lateral root formation. Therefore, lateral root initiation can only take place when cell cycle activation is accompanied by cell fate respecification of pericycle cells. The microarray data also yielded evidence for the existence of both negative and positive feedback mechanisms that regulate auxin homeostasis and signal transduction in the pericycle, thereby fine-tuning the process of lateral root initiation.},
	language = {English},
	number = {11},
	journal = {Plant Cell},
	author = {Vanneste, S. and De Rybel, B. and Beemster, G. T. S. and Ljung, K. and De Smet, I. and Van Isterdael, G. and Naudts, M. and Iida, R. and Gruissem, W. and Tasaka, M. and Inze, D. and Fukaki, H. and Beeckman, T.},
	month = nov,
	year = {2005},
	note = {Place: Rockville
Publisher: Amer Soc Plant Biologists
WOS:000232991700017},
	keywords = {amino-acids, aux/iaa   proteins, box protein tir1, dependent kinase, domain-ii, family, gene-expression, microarray, plant development, polar auxin transport},
	pages = {3035--3050},
}

To study the mechanisms behind auxin-induced cell division, lateral root initiation was used as a model system. By means of microarray analysis, genome-wide transcriptional changes were monitored during the early steps of lateral root initiation. Inclusion of the dominant auxin signaling mutant solitary root1 (slr1) identified genes involved in lateral root initiation that act downstream of the auxin/indole-3-acetic acid (AUX/IAA) signaling pathway. Interestingly, key components of the cell cycle machinery were strongly defective in slr1, suggesting a direct link between AUX/IAA signaling and core cell cycle regulation. However, induction of the cell cycle in the mutant background by overexpression of the D-type cyclin (CYCD3;1) was able to trigger complete rounds of cell division in the pericycle that did not result in lateral root formation. Therefore, lateral root initiation can only take place when cell cycle activation is accompanied by cell fate respecification of pericycle cells. The microarray data also yielded evidence for the existence of both negative and positive feedback mechanisms that regulate auxin homeostasis and signal transduction in the pericycle, thereby fine-tuning the process of lateral root initiation.

@article{weijers_maintenance_2005,
	title = {Maintenance of {Embryonic} {Auxin} {Distribution} for {Apical}-{Basal} {Patterning} by {PIN}-{FORMED}–{Dependent} {Auxin} {Transport} in {Arabidopsis}},
	volume = {17},
	issn = {1040-4651},
	url = {https://doi.org/10.1105/tpc.105.034637},
	doi = {10/b3g9nd},
	abstract = {Molecular mechanisms of pattern formation in the plant embryo are not well understood. Recent molecular and cellular studies, in conjunction with earlier microsurgical, physiological, and genetic work, are now starting to define the outlines of a model where gradients of the signaling molecule auxin play a central role in embryo patterning. It is relatively clear how these gradients are established and interpreted, but how they are maintained is still unresolved. Here, we have studied the contributions of auxin biosynthesis, conjugation, and transport pathways to the maintenance of embryonic auxin gradients. Auxin homeostasis in the embryo was manipulated by region-specific conditional expression of indoleacetic acid-tryptophan monooxygenase or indoleacetic acid-lysine synthetase, bacterial enzymes for auxin biosynthesis or conjugation. Neither manipulation of auxin biosynthesis nor of auxin conjugation interfered with auxin gradients and patterning in the embryo. This result suggests a compensatory mechanism for buffering auxin gradients in the embryo. Chemical and genetic inhibition revealed that auxin transport activity, in particular that of the PIN-FORMED1 (PIN1) and PIN4 proteins, is a major factor in the maintenance of these gradients.},
	number = {9},
	urldate = {2021-06-11},
	journal = {The Plant Cell},
	author = {Weijers, Dolf and Sauer, Michael and Meurette, Olivier and Friml, Jiří and Ljung, Karin and Sandberg, Göran and Hooykaas, Paul and Offringa, Remko},
	month = sep,
	year = {2005},
	pages = {2517--2526},
}

Molecular mechanisms of pattern formation in the plant embryo are not well understood. Recent molecular and cellular studies, in conjunction with earlier microsurgical, physiological, and genetic work, are now starting to define the outlines of a model where gradients of the signaling molecule auxin play a central role in embryo patterning. It is relatively clear how these gradients are established and interpreted, but how they are maintained is still unresolved. Here, we have studied the contributions of auxin biosynthesis, conjugation, and transport pathways to the maintenance of embryonic auxin gradients. Auxin homeostasis in the embryo was manipulated by region-specific conditional expression of indoleacetic acid-tryptophan monooxygenase or indoleacetic acid-lysine synthetase, bacterial enzymes for auxin biosynthesis or conjugation. Neither manipulation of auxin biosynthesis nor of auxin conjugation interfered with auxin gradients and patterning in the embryo. This result suggests a compensatory mechanism for buffering auxin gradients in the embryo. Chemical and genetic inhibition revealed that auxin transport activity, in particular that of the PIN-FORMED1 (PIN1) and PIN4 proteins, is a major factor in the maintenance of these gradients.

@article{ljung_sites_2005,
	title = {Sites and {Regulation} of {Auxin} {Biosynthesis} in {Arabidopsis} {Roots}},
	volume = {17},
	issn = {1040-4651},
	url = {https://doi.org/10.1105/tpc.104.029272},
	doi = {10/bccfh4},
	abstract = {Auxin has been shown to be important for many aspects of root development, including initiation and emergence of lateral roots, patterning of the root apical meristem, gravitropism, and root elongation. Auxin biosynthesis occurs in both aerial portions of the plant and in roots; thus, the auxin required for root development could come from either source, or both. To monitor putative internal sites of auxin synthesis in the root, a method for measuring indole-3-acetic acid (IAA) biosynthesis with tissue resolution was developed. We monitored IAA synthesis in 0.5- to 2-mm sections of Arabidopsis thaliana roots and were able to identify an important auxin source in the meristematic region of the primary root tip as well as in the tips of emerged lateral roots. Lower but significant synthesis capacity was observed in tissues upward from the tip, showing that the root contains multiple auxin sources. Root-localized IAA synthesis was diminished in a cyp79B2 cyp79B3 double knockout, suggesting an important role for Trp-dependent IAA synthesis pathways in the root. We present a model for how the primary root is supplied with auxin during early seedling development.},
	number = {4},
	urldate = {2021-06-11},
	journal = {The Plant Cell},
	author = {Ljung, Karin and Hull, Anna K. and Celenza, John and Yamada, Masashi and Estelle, Mark and Normanly, Jennifer and Sandberg, Göran},
	month = apr,
	year = {2005},
	pages = {1090--1104},
}

Auxin has been shown to be important for many aspects of root development, including initiation and emergence of lateral roots, patterning of the root apical meristem, gravitropism, and root elongation. Auxin biosynthesis occurs in both aerial portions of the plant and in roots; thus, the auxin required for root development could come from either source, or both. To monitor putative internal sites of auxin synthesis in the root, a method for measuring indole-3-acetic acid (IAA) biosynthesis with tissue resolution was developed. We monitored IAA synthesis in 0.5- to 2-mm sections of Arabidopsis thaliana roots and were able to identify an important auxin source in the meristematic region of the primary root tip as well as in the tips of emerged lateral roots. Lower but significant synthesis capacity was observed in tissues upward from the tip, showing that the root contains multiple auxin sources. Root-localized IAA synthesis was diminished in a cyp79B2 cyp79B3 double knockout, suggesting an important role for Trp-dependent IAA synthesis pathways in the root. We present a model for how the primary root is supplied with auxin during early seedling development.

@article{rampey_family_2004,
	title = {A {Family} of {Auxin}-{Conjugate} {Hydrolases} {That} {Contributes} to {Free} {Indole}-3-{Acetic} {Acid} {Levels} during {Arabidopsis} {Germination}},
	volume = {135},
	issn = {0032-0889},
	url = {https://doi.org/10.1104/pp.104.039677},
	doi = {10/cxw94f},
	abstract = {Auxins are hormones important for numerous processes throughout plant growth and development. Plants use several mechanisms to regulate levels of the auxin indole-3-acetic acid (IAA), including the formation and hydrolysis of amide-linked conjugates that act as storage or inactivation forms of the hormone. Certain members of an Arabidopsis amidohydrolase family hydrolyze these conjugates to free IAA in vitro. We examined amidohydrolase gene expression using northern and promoter-β-glucuronidase analyses and found overlapping but distinct patterns of expression. To examine the in vivo importance of auxin-conjugate hydrolysis, we generated a triple hydrolase mutant, ilr1 iar3 ill2, which is deficient in three of these hydrolases. We compared root and hypocotyl growth of the single, double, and triple hydrolase mutants on IAA-Ala, IAA-Leu, and IAA-Phe. The hydrolase mutant phenotypic profiles on different conjugates reveal the in vivo activities and relative importance of ILR1, IAR3, and ILL2 in IAA-conjugate hydrolysis. In addition to defective responses to exogenous conjugates, ilr1 iar3 ill2 roots are slightly less responsive to exogenous IAA. The triple mutant also has a shorter hypocotyl and fewer lateral roots than wild type on unsupplemented medium. As suggested by the mutant phenotypes, ilr1 iar3 ill2 imbibed seeds and seedlings have lower IAA levels than wild type and accumulate IAA-Ala and IAA-Leu, conjugates that are substrates of the absent hydrolases. These results indicate that amidohydrolases contribute free IAA to the auxin pool during germination in Arabidopsis.},
	number = {2},
	urldate = {2021-06-15},
	journal = {Plant Physiology},
	author = {Rampey, Rebekah A. and LeClere, Sherry and Kowalczyk, Mariusz and Ljung, Karin and Sandberg, Göran and Bartel, Bonnie},
	month = jun,
	year = {2004},
	pages = {978--988},
}

Auxins are hormones important for numerous processes throughout plant growth and development. Plants use several mechanisms to regulate levels of the auxin indole-3-acetic acid (IAA), including the formation and hydrolysis of amide-linked conjugates that act as storage or inactivation forms of the hormone. Certain members of an Arabidopsis amidohydrolase family hydrolyze these conjugates to free IAA in vitro. We examined amidohydrolase gene expression using northern and promoter-β-glucuronidase analyses and found overlapping but distinct patterns of expression. To examine the in vivo importance of auxin-conjugate hydrolysis, we generated a triple hydrolase mutant, ilr1 iar3 ill2, which is deficient in three of these hydrolases. We compared root and hypocotyl growth of the single, double, and triple hydrolase mutants on IAA-Ala, IAA-Leu, and IAA-Phe. The hydrolase mutant phenotypic profiles on different conjugates reveal the in vivo activities and relative importance of ILR1, IAR3, and ILL2 in IAA-conjugate hydrolysis. In addition to defective responses to exogenous conjugates, ilr1 iar3 ill2 roots are slightly less responsive to exogenous IAA. The triple mutant also has a shorter hypocotyl and fewer lateral roots than wild type on unsupplemented medium. As suggested by the mutant phenotypes, ilr1 iar3 ill2 imbibed seeds and seedlings have lower IAA levels than wild type and accumulate IAA-Ala and IAA-Leu, conjugates that are substrates of the absent hydrolases. These results indicate that amidohydrolases contribute free IAA to the auxin pool during germination in Arabidopsis.

@article{friml_pinoid-dependent_2004,
	title = {A {PINOID}-{Dependent} {Binary} {Switch} in {Apical}-{Basal} {PIN} {Polar} {Targeting} {Directs} {Auxin} {Efflux}},
	volume = {306},
	url = {https://www.science.org/doi/10.1126/science.1100618},
	doi = {10.1126/science.1100618},
	number = {5697},
	urldate = {2021-10-14},
	journal = {Science},
	author = {Friml, Jiří and Yang, Xiong and Michniewicz, Marta and Weijers, Dolf and Quint, Ab and Tietz, Olaf and Benjamins, René and Ouwerkerk, Pieter B. F. and Ljung, Karin and Sandberg, Göran and Hooykaas, Paul J. J. and Palme, Klaus and Offringa, Remko},
	month = oct,
	year = {2004},
	pages = {862--865},
}

@article{friml_atpin4_2002,
	title = {{AtPIN4} {Mediates} {Sink}-{Driven} {Auxin} {Gradients} and {Root} {Patterning} in {Arabidopsis}},
	volume = {108},
	issn = {0092-8674},
	url = {https://www.sciencedirect.com/science/article/pii/S0092867402006566},
	doi = {10.1016/S0092-8674(02)00656-6},
	abstract = {In contrast to animals, little is known about pattern formation in plants. Physiological and genetic data suggest the involvement of the phytohormone auxin in this process. Here, we characterize a novel member of the PIN family of putative auxin efflux carriers, Arabidopsis PIN4, that is localized in developing and mature root meristems. Atpin4 mutants are defective in establishment and maintenance of endogenous auxin gradients, fail to canalize externally applied auxin, and display various patterning defects in both embryonic and seedling roots. We propose a role for AtPIN4 in generating a sink for auxin below the quiescent center of the root meristem that is essential for auxin distribution and patterning.},
	language = {en},
	number = {5},
	urldate = {2021-10-19},
	journal = {Cell},
	author = {Friml, Jiřı́ and Benková, Eva and Blilou, Ikram and Wisniewska, Justyna and Hamann, Thorsten and Ljung, Karin and Woody, Scott and Sandberg, Goran and Scheres, Ben and Jürgens, Gerd and Palme, Klaus},
	month = mar,
	year = {2002},
	pages = {661--673},
}

In contrast to animals, little is known about pattern formation in plants. Physiological and genetic data suggest the involvement of the phytohormone auxin in this process. Here, we characterize a novel member of the PIN family of putative auxin efflux carriers, Arabidopsis PIN4, that is localized in developing and mature root meristems. Atpin4 mutants are defective in establishment and maintenance of endogenous auxin gradients, fail to canalize externally applied auxin, and display various patterning defects in both embryonic and seedling roots. We propose a role for AtPIN4 in generating a sink for auxin below the quiescent center of the root meristem that is essential for auxin distribution and patterning.

@article{ljung_biosynthesis_2002,
	title = {Biosynthesis, conjugation, catabolism and homeostasis of indole-3-acetic acid in {Arabidopsis} thaliana},
	volume = {49},
	issn = {1573-5028},
	url = {https://doi.org/10.1023/A:1015298812300},
	doi = {10/bws57n},
	language = {en},
	number = {3},
	urldate = {2021-10-19},
	journal = {Plant Molecular Biology},
	author = {Ljung, Karin and Hull, Anna K. and Kowalczyk, Mariusz and Marchant, Alan and Celenza, John and Cohen, Jerry D. and Sandberg, Göran},
	month = jun,
	year = {2002},
	pages = {249--272},
}

@article{grebe_cell_2002,
	title = {Cell {Polarity} {Signaling} in {Arabidopsis} {Involves} a {BFA}-{Sensitive} {Auxin} {Influx} {Pathway}},
	volume = {12},
	issn = {0960-9822},
	url = {https://www.sciencedirect.com/science/article/pii/S0960982202006541},
	doi = {10.1016/S0960-9822(02)00654-1},
	abstract = {Coordination of cell and tissue polarity commonly involves directional signaling [1]. In the Arabidopsis root epidermis, cell polarity is revealed by basal, root tip-oriented, hair outgrowth from hair-forming cells (trichoblasts) [2]. The plant hormone auxin displays polar movements 1, 3 and accumulates at maximum concentration in the root tip 4, 5. The application of polar auxin transport inhibitors [3] evokes changes in trichoblast polarity only at high concentrations and after long-term application 2, 4. Thus, it remains open whether components of the auxin transport machinery mediate establishment of trichoblast polarity. Here we report that the presumptive auxin influx carrier AUX1 6, 7 contributes to apical-basal hair cell polarity. AUX1 function is required for polarity changes induced by exogenous application of the auxin 2,4-D, a preferential influx carrier substrate. Similar to aux1 mutants, the vesicle trafficking inhibitor brefeldin A (BFA) interferes with polar hair initiation, and AUX1 function is required for BFA-mediated polarity changes. Consistently, BFA inhibits membrane trafficking of AUX1, trichoblast hyperpolarization induced by 2,4-D, and alters the distal auxin maximum. Our results identify AUX1 as one component of a novel BFA-sensitive auxin transport pathway polarizing cells toward a hormone maximum.},
	language = {en},
	number = {4},
	urldate = {2021-10-19},
	journal = {Current Biology},
	author = {Grebe, Markus and Friml, Jiří and Swarup, Ranjan and Ljung, Karin and Sandberg, Göran and Terlou, Maarten and Palme, Klaus and Bennett, Malcolm J. and Scheres, Ben},
	month = feb,
	year = {2002},
	pages = {329--334},
}

Coordination of cell and tissue polarity commonly involves directional signaling [1]. In the Arabidopsis root epidermis, cell polarity is revealed by basal, root tip-oriented, hair outgrowth from hair-forming cells (trichoblasts) [2]. The plant hormone auxin displays polar movements 1, 3 and accumulates at maximum concentration in the root tip 4, 5. The application of polar auxin transport inhibitors [3] evokes changes in trichoblast polarity only at high concentrations and after long-term application 2, 4. Thus, it remains open whether components of the auxin transport machinery mediate establishment of trichoblast polarity. Here we report that the presumptive auxin influx carrier AUX1 6, 7 contributes to apical-basal hair cell polarity. AUX1 function is required for polarity changes induced by exogenous application of the auxin 2,4-D, a preferential influx carrier substrate. Similar to aux1 mutants, the vesicle trafficking inhibitor brefeldin A (BFA) interferes with polar hair initiation, and AUX1 function is required for BFA-mediated polarity changes. Consistently, BFA inhibits membrane trafficking of AUX1, trichoblast hyperpolarization induced by 2,4-D, and alters the distal auxin maximum. Our results identify AUX1 as one component of a novel BFA-sensitive auxin transport pathway polarizing cells toward a hormone maximum.

@article{tobena-santamaria_floozy_2002,
	title = {{FLOOZY} of petunia is a flavin mono-oxygenase-like protein required for the specification of leaf and flower architecture},
	volume = {16},
	issn = {0890-9369, 1549-5477},
	url = {http://genesdev.cshlp.org/content/16/6/753},
	doi = {10/d6fq3h},
	abstract = {The mechanisms that determine the relative positions of floral organs, and thereby their numbers, is a poorly understood aspect of flower development. We isolated a petunia mutant, floozy(fzy), in which the formation of floral organ primordia in the outermost three floral whorls and one of the two bracts at the base of the flower is blocked at an early stage. In addition, fzymutants fail to generate secondary veins in leaves and bracts and display a decreased apical dominance in the inflorescence. FZYencodes an enzyme with homology to flavin mono-oxygenases and appears to be the ortholog of YUCCA genes of Arabidopsis. FZY is expressed in young leafs and bracts and in developing flowers. In young floral meristems FZY is expressed in the center of the meristem dome and, later, expression becomes localized on the flanks of the initiating petal and stamen primordia and at several sites in maturing anthers and carpels. These findings indicate that FZY is involved in synthesizing a signaling compound that is required for floral organ initiation and specification of the vascularization pattern in leaves. Although fzy mutants contain normal auxin levels, ectopic expression of FZY results in excessive auxin accumulation, suggesting that the signaling compound is auxin.},
	language = {en},
	number = {6},
	urldate = {2021-10-19},
	journal = {Genes \& Development},
	author = {Tobeña-Santamaria, Rafael and Bliek, Mattijs and Ljung, Karin and Sandberg, Göran and Mol, Joseph N. M. and Souer, Erik and Koes, Ronald},
	month = mar,
	year = {2002},
	pmid = {11914280},
	note = {Company: Cold Spring Harbor Laboratory Press
Distributor: Cold Spring Harbor Laboratory Press
Institution: Cold Spring Harbor Laboratory Press
Label: Cold Spring Harbor Laboratory Press
Publisher: Cold Spring Harbor Lab},
	keywords = {Flavin mono-oxygenase, flower development, leaf development, meristem initiation, transposon tagging, vascularization},
	pages = {753--763},
}

The mechanisms that determine the relative positions of floral organs, and thereby their numbers, is a poorly understood aspect of flower development. We isolated a petunia mutant, floozy(fzy), in which the formation of floral organ primordia in the outermost three floral whorls and one of the two bracts at the base of the flower is blocked at an early stage. In addition, fzymutants fail to generate secondary veins in leaves and bracts and display a decreased apical dominance in the inflorescence. FZYencodes an enzyme with homology to flavin mono-oxygenases and appears to be the ortholog of YUCCA genes of Arabidopsis. FZY is expressed in young leafs and bracts and in developing flowers. In young floral meristems FZY is expressed in the center of the meristem dome and, later, expression becomes localized on the flanks of the initiating petal and stamen primordia and at several sites in maturing anthers and carpels. These findings indicate that FZY is involved in synthesizing a signaling compound that is required for floral organ initiation and specification of the vascularization pattern in leaves. Although fzy mutants contain normal auxin levels, ectopic expression of FZY results in excessive auxin accumulation, suggesting that the signaling compound is auxin.

@article{bhalerao_shoot-derived_2002,
	title = {Shoot-derived auxin is essential for early lateral root emergence in {Arabidopsis} seedlings},
	volume = {29},
	issn = {1365-313X},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1046/j.0960-7412.2001.01217.x},
	doi = {10/cjt66p},
	abstract = {Lateral root formation is profoundly affected by auxins. Here we present data which indicate that light influences the formation of indole-3-acetic acid (IAA) in germinating Arabidopsis seedlings. IAA transported from the developing leaves to the root system is detectable as a short-lived pulse in the roots and is required for the emergence of the lateral root primordia (LRP) during early seedling development. LRP emergence is inhibited by the removal of apical tissues prior to detection of the IAA pulse in the root, but this treatment has minimal effects on LRP initiation. Our results identify the first developing true leaves as the most likely source for the IAA required for the first emergence of the LRP, as removal of cotyledons has only a minor effect on LRP emergence in contrast to removal of the leaves. A basipetal IAA concentration gradient with high levels of IAA in the root tip appears to control LRP initiation, in contrast to their emergence. A significant increase in the ability of the root system to synthesize IAA is observed 10 days after germination, and this in turn is reflected in the reduced dependence of the lateral root emergence on aerial tissue-derived auxin at this stage. We propose a model for lateral root formation during early seedling development that can be divided into two phases: (i) an LRP initiation phase dependent on a root tip-localized IAA source, and (ii) an LRP emergence phase dependent on leaf-derived IAA up to 10 days after germination.},
	language = {en},
	number = {3},
	urldate = {2021-10-19},
	journal = {The Plant Journal},
	author = {Bhalerao, Rishikesh P. and Eklöf, Jan and Ljung, Karin and Marchant, Alan and Bennett, Malcolm and Sandberg, Göran},
	year = {2002},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1046/j.0960-7412.2001.01217.x},
	keywords = {Arabidopsis thaliana, IAA, auxin, lateral root},
	pages = {325--332},
}

Lateral root formation is profoundly affected by auxins. Here we present data which indicate that light influences the formation of indole-3-acetic acid (IAA) in germinating Arabidopsis seedlings. IAA transported from the developing leaves to the root system is detectable as a short-lived pulse in the roots and is required for the emergence of the lateral root primordia (LRP) during early seedling development. LRP emergence is inhibited by the removal of apical tissues prior to detection of the IAA pulse in the root, but this treatment has minimal effects on LRP initiation. Our results identify the first developing true leaves as the most likely source for the IAA required for the first emergence of the LRP, as removal of cotyledons has only a minor effect on LRP emergence in contrast to removal of the leaves. A basipetal IAA concentration gradient with high levels of IAA in the root tip appears to control LRP initiation, in contrast to their emergence. A significant increase in the ability of the root system to synthesize IAA is observed 10 days after germination, and this in turn is reflected in the reduced dependence of the lateral root emergence on aerial tissue-derived auxin at this stage. We propose a model for lateral root formation during early seedling development that can be divided into two phases: (i) an LRP initiation phase dependent on a root tip-localized IAA source, and (ii) an LRP emergence phase dependent on leaf-derived IAA up to 10 days after germination.

@article{tantikanjana_control_2001,
	title = {Control of axillary bud initiation and shoot architecture in {Arabidopsis} through the {SUPERSHOOT} gene},
	volume = {15},
	issn = {0890-9369, 1549-5477},
	url = {http://genesdev.cshlp.org/content/15/12/1577},
	doi = {10/b2rhkq},
	abstract = {The aerial architecture of flowering plants is determined to a large extent by shoot growth and shoot branching arising from the initiation and growth of axillary meristems. We have identified anArabidopsis mutant, supershoot (sps), which is characterized by a massive overproliferation of shoots, such that a single plant can generate 500 or more inflorescences. Analysis of the mutant plants shows that the primary defect is because of an increase in the number of meristems formed in leaf axils, together with release of bud arrest, resulting in reiterative branch formation from rosette and cauline leaves. The SPS gene is shown here to encode a cytochrome P450, and together with a 3- to 9-fold increase in levels of Z-type cytokinins in sps mutant plants, indicate a role forSPS in modulating hormone levels. The expression pattern ofSPS, with strong expression at the leaf axils, correlates well with the phenotypic defects. Our results indicate that control of shoot branching in Arabidopsis may be accomplished in part by suppression of axillary meristem initiation and growth through the localized attenuation of cytokinin levels at sites of bud initiation.},
	language = {en},
	number = {12},
	urldate = {2021-11-02},
	journal = {Genes \& Development},
	author = {Tantikanjana, Titima and Yong, Jean W. H. and Letham, D. Stuart and Griffith, Megan and Hussain, Mumtaz and Ljung, Karin and Sandberg, Göran and Sundaresan, Venkatesan},
	month = jun,
	year = {2001},
	pmid = {11410537},
	note = {Company: Cold Spring Harbor Laboratory Press
Distributor: Cold Spring Harbor Laboratory Press
Institution: Cold Spring Harbor Laboratory Press
Label: Cold Spring Harbor Laboratory Press
Publisher: Cold Spring Harbor Lab},
	keywords = {Arabidopsis, Axillary meristem, apical dominance, branching, bud initiation, cytochrome P450, cytokinins},
	pages = {1577--1588},
}

The aerial architecture of flowering plants is determined to a large extent by shoot growth and shoot branching arising from the initiation and growth of axillary meristems. We have identified anArabidopsis mutant, supershoot (sps), which is characterized by a massive overproliferation of shoots, such that a single plant can generate 500 or more inflorescences. Analysis of the mutant plants shows that the primary defect is because of an increase in the number of meristems formed in leaf axils, together with release of bud arrest, resulting in reiterative branch formation from rosette and cauline leaves. The SPS gene is shown here to encode a cytochrome P450, and together with a 3- to 9-fold increase in levels of Z-type cytokinins in sps mutant plants, indicate a role forSPS in modulating hormone levels. The expression pattern ofSPS, with strong expression at the leaf axils, correlates well with the phenotypic defects. Our results indicate that control of shoot branching in Arabidopsis may be accomplished in part by suppression of axillary meristem initiation and growth through the localized attenuation of cytokinin levels at sites of bud initiation.

@article{ljung_developmental_2001,
	title = {Developmental {Regulation} of {Indole}-3-{Acetic} {Acid} {Turnover} in {Scots} {Pine} {Seedlings1}},
	volume = {125},
	issn = {0032-0889},
	url = {https://doi.org/10.1104/pp.125.1.464},
	doi = {10.1104/pp.125.1.464},
	abstract = {Indole-3-acetic acid (IAA) homeostasis was investigated during seed germination and early seedling growth in Scots pine (Pinus sylvestris). IAA-ester conjugates were initially hydrolyzed in the seed to yield a peak of free IAA prior to initiation of root elongation. Developmental regulation of IAA synthesis was observed, with tryptophan-dependent synthesis being initiated around 4 d and tryptophan-independent synthesis occurring around 7 d after imbibition. Induction of catabolism to yield 2-oxindole-3-acetic acid and irreversible conjugation to indole-3-acetyl-N-aspartic acid was noticed at the same time as de novo synthesis was first detected. As a part of the homeostatic regulation IAA was further metabolized to two new conjugates: glucopyranosyl-1-N-indole-3-acetyl-N-aspartic acid and glucopyranosyl-1-N-indole-3-acetic acid. The initial supply of IAA thus originates from stored pools of IAA-ester conjugates, mainly localized in the embryo itself rather than in the general nutrient storage tissue, the megagametophyte. We have found that de novo synthesis is first induced when the stored pool of conjugated IAA is used up and additional hormone is needed for elongation growth. It is interesting that when de novo synthesis is induced, a distinct induction of catabolic events occurs, indicating that the seedling needs mechanisms to balance synthesis rates for the homeostatic regulation of the IAA pool.},
	number = {1},
	urldate = {2021-11-02},
	journal = {Plant Physiology},
	author = {Ljung, Karin and Östin, Anders and Lioussanne, Laetitia and Sandberg, Göran},
	month = jan,
	year = {2001},
	pages = {464--475},
}

Indole-3-acetic acid (IAA) homeostasis was investigated during seed germination and early seedling growth in Scots pine (Pinus sylvestris). IAA-ester conjugates were initially hydrolyzed in the seed to yield a peak of free IAA prior to initiation of root elongation. Developmental regulation of IAA synthesis was observed, with tryptophan-dependent synthesis being initiated around 4 d and tryptophan-independent synthesis occurring around 7 d after imbibition. Induction of catabolism to yield 2-oxindole-3-acetic acid and irreversible conjugation to indole-3-acetyl-N-aspartic acid was noticed at the same time as de novo synthesis was first detected. As a part of the homeostatic regulation IAA was further metabolized to two new conjugates: glucopyranosyl-1-N-indole-3-acetyl-N-aspartic acid and glucopyranosyl-1-N-indole-3-acetic acid. The initial supply of IAA thus originates from stored pools of IAA-ester conjugates, mainly localized in the embryo itself rather than in the general nutrient storage tissue, the megagametophyte. We have found that de novo synthesis is first induced when the stored pool of conjugated IAA is used up and additional hormone is needed for elongation growth. It is interesting that when de novo synthesis is induced, a distinct induction of catabolic events occurs, indicating that the seedling needs mechanisms to balance synthesis rates for the homeostatic regulation of the IAA pool.

@article{swarup_localization_2001,
	title = {Localization of the auxin permease {AUX1} suggests two functionally distinct hormone transport pathways operate in the {Arabidopsis} root apex},
	volume = {15},
	url = {https://www.ncbi.nlm.nih.gov/sites/ppmc/articles/PMC312818/},
	doi = {10.1101/gad.210501},
	abstract = {Auxins represent an important class of plant hormone that regulate plant development. Plants use specialized carrier proteins to transport the auxin indole-3-acetic acid (IAA) to target tissues. To date, efflux carrier-mediated polar auxin transport has ...},
	language = {en},
	number = {20},
	urldate = {2021-11-02},
	journal = {Genes \& Development},
	author = {Swarup, Ranjan and Friml, Jirí and Marchant, Alan and Ljung, Karin and Sandberg, Goran and Palme, Klaus and Bennett, Malcolm},
	month = oct,
	year = {2001},
	pmid = {11641271},
	note = {Publisher: Cold Spring Harbor Laboratory Press},
	keywords = {AUX1, Auxin transport, auxin influx carrier, membrane localization, phloem unloading, root gravitropism},
	pages = {2648},
}

Auxins represent an important class of plant hormone that regulate plant development. Plants use specialized carrier proteins to transport the auxin indole-3-acetic acid (IAA) to target tissues. To date, efflux carrier-mediated polar auxin transport has ...

@article{ljung_sites_2001,
	title = {Sites and homeostatic control of auxin biosynthesis in {Arabidopsis} during vegetative growth},
	volume = {28},
	issn = {1365-313X},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1046/j.1365-313X.2001.01173.x},
	doi = {10.1046/j.1365-313X.2001.01173.x},
	abstract = {The distribution and biosynthesis of indole-3-acetic acid (IAA) was investigated during early plant development in Arabidopsis. The youngest leaves analysed, less than 0.5 mm in length, contained 250 pg mg−1 of IAA and also exhibited the highest relative capacity to synthesize this hormone. A decrease of nearly one hundred-fold in IAA content occurred as the young leaves expanded to their full size, and this was accompanied by a clear shift in both pool size and IAA synthesis capacity. The correlation between high IAA content and intense cell division was further verified in tobacco leaves, where a detailed analysis revealed that dividing mesophyll tissue contained ten-fold higher IAA levels than tissue growing solely by elongation. We demonstrated that all parts of the young Arabidopsis plant can potentially contribute to the auxin needed for growth and development, as not only young leaves, but also all other parts of the plant such as cotyledons, expanding leaves and root tissues have the capacity to synthesize IAA de novo. We also observed that naphthylphthalamic acid (NPA) treatment induced tissue-dependent feedback inhibition of IAA biosynthesis in expanding leaves and cotyledons, but intriguingly not in young leaves or in the root system. This observation supports the hypothesis that there is a sophisticated tissue-specific regulatory mechanism for auxin biosynthesis. Finally, a strict requirement for maintaining the pool sizes of IAA was revealed as reductions in leaf expansion followed both decreases and increases in the IAA levels in developing leaves. This indicates that leaves are not only important sources for IAA synthesis, but that normal leaf expansion depends on rigorous control of IAA homeostasis.},
	language = {en},
	number = {4},
	urldate = {2021-11-02},
	journal = {The Plant Journal},
	author = {Ljung, Karin and Bhalerao, Rishikesh P. and Sandberg, Göran},
	year = {2001},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1046/j.1365-313X.2001.01173.x},
	keywords = {auxin, distribution and biosynthesis, feedback inhibition, indole-3-acetic acid, leaf expansion, naphthylphthalamic acid},
	pages = {465--474},
}

The distribution and biosynthesis of indole-3-acetic acid (IAA) was investigated during early plant development in Arabidopsis. The youngest leaves analysed, less than 0.5 mm in length, contained 250 pg mg−1 of IAA and also exhibited the highest relative capacity to synthesize this hormone. A decrease of nearly one hundred-fold in IAA content occurred as the young leaves expanded to their full size, and this was accompanied by a clear shift in both pool size and IAA synthesis capacity. The correlation between high IAA content and intense cell division was further verified in tobacco leaves, where a detailed analysis revealed that dividing mesophyll tissue contained ten-fold higher IAA levels than tissue growing solely by elongation. We demonstrated that all parts of the young Arabidopsis plant can potentially contribute to the auxin needed for growth and development, as not only young leaves, but also all other parts of the plant such as cotyledons, expanding leaves and root tissues have the capacity to synthesize IAA de novo. We also observed that naphthylphthalamic acid (NPA) treatment induced tissue-dependent feedback inhibition of IAA biosynthesis in expanding leaves and cotyledons, but intriguingly not in young leaves or in the root system. This observation supports the hypothesis that there is a sophisticated tissue-specific regulatory mechanism for auxin biosynthesis. Finally, a strict requirement for maintaining the pool sizes of IAA was revealed as reductions in leaf expansion followed both decreases and increases in the IAA levels in developing leaves. This indicates that leaves are not only important sources for IAA synthesis, but that normal leaf expansion depends on rigorous control of IAA homeostasis.

@article{barlier_sur2_2000,
	title = {The {SUR2} gene of {Arabidopsis} thaliana encodes the cytochrome {P450} {CYP83B1}, a modulator of auxin homeostasis},
	volume = {97},
	copyright = {Copyright © 2000, The National Academy of Sciences},
	issn = {0027-8424, 1091-6490},
	url = {https://www.pnas.org/content/97/26/14819},
	doi = {10/c36wb6},
	abstract = {Genetic screens have been performed to identify mutants with altered auxin homeostasis in Arabidopsis. A tagged allele of the auxin-overproducing mutant sur2 was identified within a transposon mutagenized population. The SUR2 gene was cloned and shown to encode the CYP83B1 protein, which belongs to the large family of the P450-dependent monooxygenases. SUR2 expression is up-regulated in sur1 mutants and induced by exogenous auxin in the wild type. Analysis of indole-3-acetic acid (IAA) synthesis and metabolism in sur2 plants indicates that the mutation causes a conditional increase in the pool size of IAA through up-regulation of IAA synthesis.},
	language = {en},
	number = {26},
	urldate = {2021-11-08},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Barlier, Isabelle and Kowalczyk, Mariusz and Marchant, Alan and Ljung, Karin and Bhalerao, Rishikesh and Bennett, Malcolm and Sandberg, Goeran and Bellini, Catherine},
	month = dec,
	year = {2000},
	pmid = {11114200},
	note = {Publisher: National Academy of Sciences
Section: Biological Sciences},
	keywords = {metabolism},
	pages = {14819--14824},
}

Genetic screens have been performed to identify mutants with altered auxin homeostasis in Arabidopsis. A tagged allele of the auxin-overproducing mutant sur2 was identified within a transposon mutagenized population. The SUR2 gene was cloned and shown to encode the CYP83B1 protein, which belongs to the large family of the P450-dependent monooxygenases. SUR2 expression is up-regulated in sur1 mutants and induced by exogenous auxin in the wild type. Analysis of indole-3-acetic acid (IAA) synthesis and metabolism in sur2 plants indicates that the mutation causes a conditional increase in the pool size of IAA through up-regulation of IAA synthesis.

@article{philippar_auxin-induced_1999,
	title = {Auxin-induced {K}+ channel expression represents an essential step in coleoptile growth and gravitropism},
	volume = {96},
	copyright = {Copyright © 1999, The National Academy of Sciences},
	issn = {0027-8424, 1091-6490},
	url = {https://www.pnas.org/content/96/21/12186},
	doi = {10/c6st7j},
	abstract = {Auxin-induced growth of coleoptiles depends on the presence of potassium and is suppressed by K+ channel blockers. To evaluate the role of K+ channels in auxin-mediated growth, we isolated and functionally expressed ZMK1 and ZMK2 (Zea mays K+ channel 1 and 2), two potassium channels from maize coleoptiles. In growth experiments, the time course of auxin-induced expression of ZMK1 coincided with the kinetics of coleoptile elongation. Upon gravistimulation of maize seedlings, ZMK1 expression followed the gravitropic-induced auxin redistribution. K+ channel expression increased even before a bending of the coleoptile was observed. The transcript level of ZMK2, expressed in vascular tissue, was not affected by auxin. In patch-clamp studies on coleoptile protoplasts, auxin increased K+ channel density while leaving channel properties unaffected. Thus, we conclude that coleoptile growth depends on the transcriptional up-regulation of ZMK1, an inwardly rectifying K+ channel expressed in the nonvascular tissue of this organ.},
	language = {en},
	number = {21},
	urldate = {2021-11-08},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Philippar, Katrin and Fuchs, Ines and Lüthen, Hartwig and Hoth, Stefan and Bauer, Claudia S. and Haga, Ken and Thiel, Gerhard and Ljung, Karin and Sandberg, Göran and Böttger, Michael and Becker, Dirk and Hedrich, Rainer},
	month = oct,
	year = {1999},
	pmid = {10518597},
	note = {Publisher: National Academy of Sciences
Section: Biological Sciences},
	pages = {12186--12191},
}

Auxin-induced growth of coleoptiles depends on the presence of potassium and is suppressed by K+ channel blockers. To evaluate the role of K+ channels in auxin-mediated growth, we isolated and functionally expressed ZMK1 and ZMK2 (Zea mays K+ channel 1 and 2), two potassium channels from maize coleoptiles. In growth experiments, the time course of auxin-induced expression of ZMK1 coincided with the kinetics of coleoptile elongation. Upon gravistimulation of maize seedlings, ZMK1 expression followed the gravitropic-induced auxin redistribution. K+ channel expression increased even before a bending of the coleoptile was observed. The transcript level of ZMK2, expressed in vascular tissue, was not affected by auxin. In patch-clamp studies on coleoptile protoplasts, auxin increased K+ channel density while leaving channel properties unaffected. Thus, we conclude that coleoptile growth depends on the transcriptional up-regulation of ZMK1, an inwardly rectifying K+ channel expressed in the nonvascular tissue of this organ.