@article{wahl_plant_2026,
	title = {The plant energy management machinery: an essential hub for stress resilience and developmental dynamics with great potential for crop improvement},
	volume = {77},
	issn = {0022-0957},
	shorttitle = {The plant energy management machinery},
	url = {https://doi.org/10.1093/jxb/erag032},
	doi = {10.1093/jxb/erag032},
	abstract = {Plants coordinate resource uptake, developmental pace, and morphological efficiency. This ensures that energy use is balanced across time and tissues, enabling resilience and stable growth under fluctuating environmental conditions. The plant energy management machinery encompasses the interconnected signalling and metabolic networks that coordinate energy acquisition, storage, mobilization, and utilization to support growth, development, and environmental adaptation. In contrast to animals, where dedicated organs such as fat bodies in Drosophila and the liver in mammals, play crucial roles in energy metabolism and sensing (Chatterjee and Perrimon, 2021), plants exhibit a more integrative concept of nutrient and energy regulation. Here, the term ‘nutrients’ extends beyond simple energy carriers to include a broad spectrum of organic and inorganic compounds, such as sugars, amino acids, nitrate, phosphate, and lipids, that function both as metabolic substrates and as signalling molecules, influencing gene expression, enzyme activity, developmental transitions, and growth.},
	number = {5},
	urldate = {2026-03-10},
	journal = {Journal of Experimental Botany},
	author = {Wahl, Vanessa and Hanson, Johannes and Menand, Benoît},
	month = mar,
	year = {2026},
	pages = {1357--1361},
}

Plants coordinate resource uptake, developmental pace, and morphological efficiency. This ensures that energy use is balanced across time and tissues, enabling resilience and stable growth under fluctuating environmental conditions. The plant energy management machinery encompasses the interconnected signalling and metabolic networks that coordinate energy acquisition, storage, mobilization, and utilization to support growth, development, and environmental adaptation. In contrast to animals, where dedicated organs such as fat bodies in Drosophila and the liver in mammals, play crucial roles in energy metabolism and sensing (Chatterjee and Perrimon, 2021), plants exhibit a more integrative concept of nutrient and energy regulation. Here, the term ‘nutrients’ extends beyond simple energy carriers to include a broad spectrum of organic and inorganic compounds, such as sugars, amino acids, nitrate, phosphate, and lipids, that function both as metabolic substrates and as signalling molecules, influencing gene expression, enzyme activity, developmental transitions, and growth.

@article{wang_ribosome_2025,
	title = {Ribosome biogenesis in plants requires the nuclear envelope and mitochondria localized {OPENER} complex},
	volume = {16},
	copyright = {2025 The Author(s)},
	issn = {2041-1723},
	url = {https://www.nature.com/articles/s41467-025-62652-7},
	doi = {10.1038/s41467-025-62652-7},
	abstract = {Eukaryotic ribosome biogenesis proceeds from nucleolus to cytosol assisted by various assembly factors. The process is evolutionarily conserved across eukaryotes but differences between the kingdoms are emerging. Here, we describe how the OPENER (OPNR) protein complex is required for 60S ribosome assembly in the model plant Arabidopsis thaliana. The complex is observed on both nuclear envelope and mitochondria, and contains OPNR, OPENER ASSOCIATED PROTEIN 1 (OAP1), OAP2, Cell Division Cycle 48 D (CDC48D) and Calmodulin-interacting protein 111 (CIP111). Depletion of the OPNR complex components results in reproductive lethality and cytoplasmic retention of assembly factors on 60S ribosomes. Subsequent biochemical analyses and structural modelling suggest that OPNR, OAP1 and OAP2 form a claw-like trimer which grabs the ribosome assembly factor RIBOSOMAL PROTEIN L24C (RPL24C) on the pre-60S ribosome. Our results reveal previously unrecognised subcellular complexity of ribosome biogenesis in plants, and point to mitochondria association as a feature to ensure sufficient translational capacity.},
	language = {en},
	number = {1},
	urldate = {2025-08-12},
	journal = {Nature Communications},
	publisher = {Nature Publishing Group},
	author = {Wang, Wei and Mahboubi, Amir and Zhu, Shaochun and Hanson, Johannes and Mateus, André and Niittylä, Totte},
	month = aug,
	year = {2025},
	keywords = {Plant cell biology, Plant molecular biology, Ribosome},
	pages = {7301},
}

Eukaryotic ribosome biogenesis proceeds from nucleolus to cytosol assisted by various assembly factors. The process is evolutionarily conserved across eukaryotes but differences between the kingdoms are emerging. Here, we describe how the OPENER (OPNR) protein complex is required for 60S ribosome assembly in the model plant Arabidopsis thaliana. The complex is observed on both nuclear envelope and mitochondria, and contains OPNR, OPENER ASSOCIATED PROTEIN 1 (OAP1), OAP2, Cell Division Cycle 48 D (CDC48D) and Calmodulin-interacting protein 111 (CIP111). Depletion of the OPNR complex components results in reproductive lethality and cytoplasmic retention of assembly factors on 60S ribosomes. Subsequent biochemical analyses and structural modelling suggest that OPNR, OAP1 and OAP2 form a claw-like trimer which grabs the ribosome assembly factor RIBOSOMAL PROTEIN L24C (RPL24C) on the pre-60S ribosome. Our results reveal previously unrecognised subcellular complexity of ribosome biogenesis in plants, and point to mitochondria association as a feature to ensure sufficient translational capacity.

@article{kreisz_s1_2024,
	title = {S1 basic leucine zipper transcription factors shape plant architecture by controlling {C}/{N} partitioning to apical and lateral organs},
	volume = {121},
	url = {https://www.pnas.org/doi/10.1073/pnas.2313343121},
	doi = {10.1073/pnas.2313343121},
	abstract = {Plants tightly control growth of their lateral organs, which led to the concept of apical dominance. However, outgrowth of the dormant lateral primordia is sensitive to the plant’s nutritional status, resulting in an immense plasticity in plant architecture. While the impact of hormonal regulation on apical dominance is well characterized, the prime importance of sugar signaling to unleash lateral organ formation has just recently emerged. Here, we aimed to identify transcriptional regulators, which control the trade-off between growth of apical versus lateral organs. Making use of locally inducible gain-of-function as well as single and higher-order loss-of-function approaches of the sugar-responsive S1-basic-leucine-zipper (S1-bZIP) transcription factors, we disclosed their largely redundant function in establishing apical growth dominance. Consistently, comprehensive phenotypical and analytical studies of S1-bZIP mutants show a clear shift of sugar and organic nitrogen (N) allocation from apical to lateral organs, coinciding with strong lateral organ outgrowth. Tissue-specific transcriptomics reveal specific clade III SWEET sugar transporters, crucial for long-distance sugar transport to apical sinks and the glutaminase GLUTAMINE AMIDO-TRANSFERASE 1\_2.1, involved in N homeostasis, as direct S1-bZIP targets, linking the architectural and metabolic mutant phenotypes to downstream gene regulation. Based on these results, we propose that S1-bZIPs control carbohydrate (C) partitioning from source leaves to apical organs and tune systemic N supply to restrict lateral organ formation by C/N depletion. Knowledge of the underlying mechanisms controlling plant C/N partitioning is of pivotal importance for breeding strategies to generate plants with desired architectural and nutritional characteristics.},
	number = {7},
	urldate = {2024-02-09},
	journal = {Proceedings of the National Academy of Sciences},
	publisher = {Proceedings of the National Academy of Sciences},
	author = {Kreisz, Philipp and Hellens, Alicia M. and Fröschel, Christian and Krischke, Markus and Maag, Daniel and Feil, Regina and Wildenhain, Theresa and Draken, Jan and Braune, Gabriel and Erdelitsch, Leon and Cecchino, Laura and Wagner, Tobias C. and Ache, Peter and Mueller, Martin J. and Becker, Dirk and Lunn, John E. and Hanson, Johannes and Beveridge, Christine A. and Fichtner, Franziska and Barbier, Francois F. and Weiste, Christoph},
	month = feb,
	year = {2024},
	pages = {e2313343121},
}

Plants tightly control growth of their lateral organs, which led to the concept of apical dominance. However, outgrowth of the dormant lateral primordia is sensitive to the plant’s nutritional status, resulting in an immense plasticity in plant architecture. While the impact of hormonal regulation on apical dominance is well characterized, the prime importance of sugar signaling to unleash lateral organ formation has just recently emerged. Here, we aimed to identify transcriptional regulators, which control the trade-off between growth of apical versus lateral organs. Making use of locally inducible gain-of-function as well as single and higher-order loss-of-function approaches of the sugar-responsive S1-basic-leucine-zipper (S1-bZIP) transcription factors, we disclosed their largely redundant function in establishing apical growth dominance. Consistently, comprehensive phenotypical and analytical studies of S1-bZIP mutants show a clear shift of sugar and organic nitrogen (N) allocation from apical to lateral organs, coinciding with strong lateral organ outgrowth. Tissue-specific transcriptomics reveal specific clade III SWEET sugar transporters, crucial for long-distance sugar transport to apical sinks and the glutaminase GLUTAMINE AMIDO-TRANSFERASE 1_2.1, involved in N homeostasis, as direct S1-bZIP targets, linking the architectural and metabolic mutant phenotypes to downstream gene regulation. Based on these results, we propose that S1-bZIPs control carbohydrate (C) partitioning from source leaves to apical organs and tune systemic N supply to restrict lateral organ formation by C/N depletion. Knowledge of the underlying mechanisms controlling plant C/N partitioning is of pivotal importance for breeding strategies to generate plants with desired architectural and nutritional characteristics.

@article{hoffmann_cauliflower_2023,
	title = {Cauliflower mosaic virus protein {P6} is a multivalent node for {RNA} granule proteins and interferes with stress granule responses during plant infection},
	volume = {35},
	issn = {1040-4651},
	url = {https://doi.org/10.1093/plcell/koad101},
	doi = {10.1093/plcell/koad101},
	abstract = {Biomolecular condensation is a multipurpose cellular process that viruses use ubiquitously during their multiplication. Cauliflower mosaic virus replication complexes are condensates that differ from those of most viruses, as they are nonmembranous assemblies that consist of RNA and protein, mainly the viral protein P6. Although these viral factories (VFs) were described half a century ago, with many observations that followed since, functional details of the condensation process and the properties and relevance of VFs have remained enigmatic. Here, we studied these issues in Arabidopsis thaliana and Nicotiana benthamiana. We observed a large dynamic mobility range of host proteins within VFs, while the viral matrix protein P6 is immobile, as it represents the central node of these condensates. We identified the stress granule (SG) nucleating factors G3BP7 and UBP1 family members as components of VFs. Similarly, as SG components localize to VFs during infection, ectopic P6 localizes to SGs and reduces their assembly after stress. Intriguingly, it appears that soluble rather than condensed P6 suppresses SG formation and mediates other essential P6 functions, suggesting that the increased condensation over the infection time-course may accompany a progressive shift in selected P6 functions. Together, this study highlights VFs as dynamic condensates and P6 as a complex modulator of SG responses.},
	number = {9},
	urldate = {2023-09-07},
	journal = {The Plant Cell},
	author = {Hoffmann, Gesa and López-González, Silvia and Mahboubi, Amir and Hanson, Johannes and Hafrén, Anders},
	month = sep,
	year = {2023},
	pages = {3363--3382},
}

Biomolecular condensation is a multipurpose cellular process that viruses use ubiquitously during their multiplication. Cauliflower mosaic virus replication complexes are condensates that differ from those of most viruses, as they are nonmembranous assemblies that consist of RNA and protein, mainly the viral protein P6. Although these viral factories (VFs) were described half a century ago, with many observations that followed since, functional details of the condensation process and the properties and relevance of VFs have remained enigmatic. Here, we studied these issues in Arabidopsis thaliana and Nicotiana benthamiana. We observed a large dynamic mobility range of host proteins within VFs, while the viral matrix protein P6 is immobile, as it represents the central node of these condensates. We identified the stress granule (SG) nucleating factors G3BP7 and UBP1 family members as components of VFs. Similarly, as SG components localize to VFs during infection, ectopic P6 localizes to SGs and reduces their assembly after stress. Intriguingly, it appears that soluble rather than condensed P6 suppresses SG formation and mediates other essential P6 functions, suggesting that the increased condensation over the infection time-course may accompany a progressive shift in selected P6 functions. Together, this study highlights VFs as dynamic condensates and P6 as a complex modulator of SG responses.

@article{bai_seedtransnet_2023,
	title = {{SeedTransNet}: a directional translational network revealing regulatory patterns during seed maturation and germination},
	volume = {74},
	issn = {0022-0957},
	shorttitle = {{SeedTransNet}},
	url = {https://doi.org/10.1093/jxb/erac394},
	doi = {10.1093/jxb/erac394},
	abstract = {Seed maturation is the developmental process that prepares the embryo for the desiccated waiting period before germination. It is associated with a series of physiological changes leading to the establishment of seed dormancy, seed longevity, and desiccation tolerance. We studied translational changes during seed maturation and observed a gradual reduction in global translation during seed maturation. Transcriptome and translatome profiling revealed specific reduction in the translation of thousands of genes. By including previously published data on germination and seedling establishment, a regulatory network based on polysome occupancy data was constructed: SeedTransNet. Network analysis predicted translational regulatory pathways involving hundreds of genes with distinct functions. The network identified specific transcript sequence features suggesting separate translational regulatory circuits. The network revealed several seed maturation-associated genes as central nodes, and this was confirmed by specific seed phenotypes of the respective mutants. One of the regulators identified, an AWPM19 family protein, PM19-Like1 (PM19L1), was shown to regulate seed dormancy and longevity. This putative RNA-binding protein also affects the translational regulation of its target mRNA, as identified by SeedTransNet. Our data show the usefulness of SeedTransNet in identifying regulatory pathways during seed phase transitions.},
	number = {7},
	urldate = {2023-04-14},
	journal = {Journal of Experimental Botany},
	author = {Bai, Bing and Schiffthaler, Bastian and van der Horst, Sjors and Willems, Leo and Vergara, Alexander and Karlström, Jacob and Mähler, Niklas and Delhomme, Nicolas and Bentsink, Leónie and Hanson, Johannes},
	month = apr,
	year = {2023},
	pages = {2416--2432},
}

Seed maturation is the developmental process that prepares the embryo for the desiccated waiting period before germination. It is associated with a series of physiological changes leading to the establishment of seed dormancy, seed longevity, and desiccation tolerance. We studied translational changes during seed maturation and observed a gradual reduction in global translation during seed maturation. Transcriptome and translatome profiling revealed specific reduction in the translation of thousands of genes. By including previously published data on germination and seedling establishment, a regulatory network based on polysome occupancy data was constructed: SeedTransNet. Network analysis predicted translational regulatory pathways involving hundreds of genes with distinct functions. The network identified specific transcript sequence features suggesting separate translational regulatory circuits. The network revealed several seed maturation-associated genes as central nodes, and this was confirmed by specific seed phenotypes of the respective mutants. One of the regulators identified, an AWPM19 family protein, PM19-Like1 (PM19L1), was shown to regulate seed dormancy and longevity. This putative RNA-binding protein also affects the translational regulation of its target mRNA, as identified by SeedTransNet. Our data show the usefulness of SeedTransNet in identifying regulatory pathways during seed phase transitions.

@article{hoffmann_arabidopsis_2022,
	title = {Arabidopsis {RNA} processing body components {LSM1} and {DCP5} aid in the evasion of translational repression during {Cauliflower} mosaic virus infection},
	issn = {1532-298X},
	doi = {10.1093/plcell/koac132},
	abstract = {Viral infections impose extraordinary RNA stress, triggering cellular RNA surveillance pathways such as RNA decapping, nonsense-mediated decay, and RNA silencing. Viruses need to maneuver among these pathways to establish infection and succeed in producing high amounts of viral proteins. Processing bodies (PBs) are integral to RNA triage in eukaryotic cells, with several distinct RNA quality control pathways converging for selective RNA regulation. In this study, we investigated the role of Arabidopsis thaliana PBs during Cauliflower mosaic virus (CaMV) infection. We found that several PB components are co-opted into viral factories that support virus multiplication. This pro-viral role was not associated with RNA decay pathways but instead, we established that PB components are helpers in viral RNA translation. While CaMV is normally resilient to RNA silencing, dysfunctions in PB components expose the virus to this pathway, which is similar to previous observations for transgenes. Transgenes, however, undergo RNA quality control-dependent RNA degradation and transcriptional silencing, whereas CaMV RNA remains stable but becomes translationally repressed through decreased ribosome association, revealing a unique dependence among PBs, RNA silencing, and translational repression. Together, our study shows that PB components are co-opted by the virus to maintain efficient translation, a mechanism not associated with canonical PB functions.},
	language = {eng},
	journal = {The Plant Cell},
	author = {Hoffmann, Gesa and Mahboubi, Amir and Bente, Heinrich and Garcia, Damien and Hanson, Johannes and Hafrén, Anders},
	month = may,
	year = {2022},
	pages = {koac132},
}

Viral infections impose extraordinary RNA stress, triggering cellular RNA surveillance pathways such as RNA decapping, nonsense-mediated decay, and RNA silencing. Viruses need to maneuver among these pathways to establish infection and succeed in producing high amounts of viral proteins. Processing bodies (PBs) are integral to RNA triage in eukaryotic cells, with several distinct RNA quality control pathways converging for selective RNA regulation. In this study, we investigated the role of Arabidopsis thaliana PBs during Cauliflower mosaic virus (CaMV) infection. We found that several PB components are co-opted into viral factories that support virus multiplication. This pro-viral role was not associated with RNA decay pathways but instead, we established that PB components are helpers in viral RNA translation. While CaMV is normally resilient to RNA silencing, dysfunctions in PB components expose the virus to this pathway, which is similar to previous observations for transgenes. Transgenes, however, undergo RNA quality control-dependent RNA degradation and transcriptional silencing, whereas CaMV RNA remains stable but becomes translationally repressed through decreased ribosome association, revealing a unique dependence among PBs, RNA silencing, and translational repression. Together, our study shows that PB components are co-opted by the virus to maintain efficient translation, a mechanism not associated with canonical PB functions.

@article{prior_arabidopsis_2021,
	title = {Arabidopsis {bZIP11} {Is} a {Susceptibility} {Factor} {During} {Pseudomonas} syringae {Infection}},
	volume = {34},
	issn = {0894-0282},
	url = {https://apsjournals.apsnet.org/doi/10.1094/MPMI-11-20-0310-R},
	doi = {10/gj6p4s},
	abstract = {The induction of plant nutrient secretion systems is critical for successful pathogen infection. Some bacterial pathogens (e.g., Xanthomonas spp.) use transcription activator-like (TAL) effectors to induce transcription of SWEET sucrose efflux transporters. Pseudomonas syringae pv. tomato strain DC3000 lacks TAL effectors yet is able to induce multiple SWEETs in Arabidopsis thaliana by unknown mechanisms. Because bacteria require other nutrients in addition to sugars for efficient reproduction, we hypothesized that Pseudomonas spp. may depend on host transcription factors involved in secretory programs to increase access to essential nutrients. Bioinformatic analyses identified the Arabidopsis basic-leucine zipper transcription factor bZIP11 as a potential regulator of nutrient transporters, including SWEETs and UmamiT amino acid transporters. Inducible downregulation of bZIP11 expression in Arabidopsis resulted in reduced growth of P. syringae pv. tomato strain DC3000, whereas inducible overexpression of bZIP11 resulted in increased bacterial growth, supporting the hypothesis that bZIP11-regulated transcription programs are essential for maximal pathogen titer in leaves. Our data are consistent with a model in which a pathogen alters host transcription factor expression upstream of secretory transcription networks to promote nutrient efflux from host cells. Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.},
	number = {4},
	urldate = {2021-06-21},
	journal = {Molecular Plant-Microbe Interactions®},
	author = {Prior, Matthew J. and Selvanayagam, Jebasingh and Kim, Jung-Gun and Tomar, Monika and Jonikas, Martin and Mudgett, Mary Beth and Smeekens, Sjef and Hanson, Johannes and Frommer, Wolf B.},
	month = apr,
	year = {2021},
	pages = {439--447},
}

The induction of plant nutrient secretion systems is critical for successful pathogen infection. Some bacterial pathogens (e.g., Xanthomonas spp.) use transcription activator-like (TAL) effectors to induce transcription of SWEET sucrose efflux transporters. Pseudomonas syringae pv. tomato strain DC3000 lacks TAL effectors yet is able to induce multiple SWEETs in Arabidopsis thaliana by unknown mechanisms. Because bacteria require other nutrients in addition to sugars for efficient reproduction, we hypothesized that Pseudomonas spp. may depend on host transcription factors involved in secretory programs to increase access to essential nutrients. Bioinformatic analyses identified the Arabidopsis basic-leucine zipper transcription factor bZIP11 as a potential regulator of nutrient transporters, including SWEETs and UmamiT amino acid transporters. Inducible downregulation of bZIP11 expression in Arabidopsis resulted in reduced growth of P. syringae pv. tomato strain DC3000, whereas inducible overexpression of bZIP11 resulted in increased bacterial growth, supporting the hypothesis that bZIP11-regulated transcription programs are essential for maximal pathogen titer in leaves. Our data are consistent with a model in which a pathogen alters host transcription factor expression upstream of secretory transcription networks to promote nutrient efflux from host cells. Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

@article{muralidhara_perturbations_2021,
	title = {Perturbations in plant energy homeostasis prime lateral root initiation via {SnRK1}-{bZIP63}-{ARF19} signaling},
	volume = {118},
	copyright = {© 2021 . https://www.pnas.org/site/aboutpnas/licenses.xhtmlPublished under the PNAS license.},
	issn = {0027-8424, 1091-6490},
	url = {https://www.pnas.org/content/118/37/e2106961118},
	doi = {10/gmvnsg},
	abstract = {Plants adjust their energy metabolism to continuous environmental fluctuations, resulting in a tremendous plasticity in their architecture. The regulatory circuits involved, however, remain largely unresolved. In Arabidopsis, moderate perturbations in photosynthetic activity, administered by short-term low light exposure or unexpected darkness, lead to increased lateral root (LR) initiation. Consistent with expression of low-energy markers, these treatments alter energy homeostasis and reduce sugar availability in roots. Here, we demonstrate that the LR response requires the metabolic stress sensor kinase Snf1-RELATED-KINASE1 (SnRK1), which phosphorylates the transcription factor BASIC LEUCINE ZIPPER63 (bZIP63) that directly binds and activates the promoter of AUXIN RESPONSE FACTOR19 (ARF19), a key regulator of LR initiation. Consistently, starvation-induced ARF19 transcription is impaired in bzip63 mutants. This study highlights a positive developmental function of SnRK1. During energy limitation, LRs are initiated and primed for outgrowth upon recovery. Hence, this study provides mechanistic insights into how energy shapes the agronomically important root system.},
	language = {en},
	number = {37},
	urldate = {2021-11-12},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Muralidhara, Prathibha and Weiste, Christoph and Collani, Silvio and Krischke, Markus and Kreisz, Philipp and Draken, Jan and Feil, Regina and Mair, Andrea and Teige, Markus and Müller, Martin J. and Schmid, Markus and Becker, Dirk and Lunn, John E. and Rolland, Filip and Hanson, Johannes and Dröge-Laser, Wolfgang},
	month = sep,
	year = {2021},
	keywords = {ARF19, SnRK1, bZIP63, lateral root, metabolic homeostasis},
}

Plants adjust their energy metabolism to continuous environmental fluctuations, resulting in a tremendous plasticity in their architecture. The regulatory circuits involved, however, remain largely unresolved. In Arabidopsis, moderate perturbations in photosynthetic activity, administered by short-term low light exposure or unexpected darkness, lead to increased lateral root (LR) initiation. Consistent with expression of low-energy markers, these treatments alter energy homeostasis and reduce sugar availability in roots. Here, we demonstrate that the LR response requires the metabolic stress sensor kinase Snf1-RELATED-KINASE1 (SnRK1), which phosphorylates the transcription factor BASIC LEUCINE ZIPPER63 (bZIP63) that directly binds and activates the promoter of AUXIN RESPONSE FACTOR19 (ARF19), a key regulator of LR initiation. Consistently, starvation-induced ARF19 transcription is impaired in bzip63 mutants. This study highlights a positive developmental function of SnRK1. During energy limitation, LRs are initiated and primed for outgrowth upon recovery. Hence, this study provides mechanistic insights into how energy shapes the agronomically important root system.

@article{mahboubi_small-scale_2021,
	title = {Small-scale sequencing enables quality assessment of {Ribo}-{Seq} data: an example from {Arabidopsis} cell culture},
	volume = {17},
	issn = {1746-4811},
	shorttitle = {Small-scale sequencing enables quality assessment of {Ribo}-{Seq} data},
	url = {https://doi.org/10.1186/s13007-021-00791-w},
	doi = {10.1186/s13007-021-00791-w},
	abstract = {Translation is a tightly regulated process, controlling the rate of protein synthesis in cells. Ribosome sequencing (Ribo-Seq) is a recently developed tool for studying actively translated mRNA and can thus directly address translational regulation. Ribo-Seq libraries need to be sequenced to a great depth due to high contamination by rRNA and other contaminating nucleic acid fragments. Deep sequencing is expensive, and it generates large volumes of data, making data analysis complicated and time consuming.},
	number = {1},
	urldate = {2021-10-14},
	journal = {Plant Methods},
	author = {Mahboubi, Amir and Delhomme, Nicolas and Häggström, Sara and Hanson, Johannes},
	month = aug,
	year = {2021},
	keywords = {Evaluation of sequencing library quality, Ribo-Seq, Ribosomal profiling, Translation, Translational profiling},
	pages = {92},
}

Translation is a tightly regulated process, controlling the rate of protein synthesis in cells. Ribosome sequencing (Ribo-Seq) is a recently developed tool for studying actively translated mRNA and can thus directly address translational regulation. Ribo-Seq libraries need to be sequenced to a great depth due to high contamination by rRNA and other contaminating nucleic acid fragments. Deep sequencing is expensive, and it generates large volumes of data, making data analysis complicated and time consuming.

@article{van_der_horst_metabolite_2020,
	title = {Metabolite {Control} of {Translation} by {Conserved} {Peptide} {uORFs}: {The} {Ribosome} as a {Metabolite} {Multisensor}},
	volume = {182},
	issn = {0032-0889, 1532-2548},
	shorttitle = {Metabolite {Control} of {Translation} by {Conserved} {Peptide} {uORFs}},
	url = {https://academic.oup.com/plphys/article/182/1/110-122/6116065},
	doi = {10.1104/pp.19.00940},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Plant Physiology},
	author = {van der Horst, Sjors and Filipovska, Teodora and Hanson, Johannes and Smeekens, Sjef},
	month = jan,
	year = {2020},
	pages = {110--122},
}

@article{bai_seed-stored_2020,
	title = {Seed-{Stored} {mRNAs} that {Are} {Specifically} {Associated} to {Monosomes} {Are} {Translationally} {Regulated} during {Germination1}  [{OPEN}]},
	volume = {182},
	issn = {0032-0889},
	url = {https://doi.org/10.1104/pp.19.00644},
	doi = {10.1104/pp.19.00644},
	abstract = {The life cycle of many organisms includes a quiescent stage, such as bacterial or fungal spores, insect larvae, or plant seeds. Common to these stages is their low water content and high survivability during harsh conditions. Upon rehydration, organisms need to reactivate metabolism and protein synthesis. Plant seeds contain many mRNAs that are transcribed during seed development. Translation of these mRNAs occurs during early seed germination, even before the requirement of transcription. Therefore, stored mRNAs are postulated to be important for germination. How these mRNAs are stored and protected during long-term storage is unknown. The aim of this study was to investigate how mRNAs are stored in dry seeds and whether they are indeed translated during seed germination. We investigated seed polysome profiles and the mRNAs and protein complexes that are associated with these ribosomes in seeds of the model organism Arabidopsis (Arabidopsis thaliana). We showed that most stored mRNAs are associated with monosomes in dry seeds; therefore, we focus on monosomes in this study. Seed ribosome complexes are associated with mRNA-binding proteins, stress granule, and P-body proteins, which suggests regulated packing of seed mRNAs. Interestingly, ∼17\% of the mRNAs that are specifically associated with monosomes are translationally up-regulated during seed germination. These mRNAs are transcribed during seed maturation, suggesting a role for this developmental stage in determining the translational fate of mRNAs during early germination.},
	number = {1},
	urldate = {2021-06-07},
	journal = {Plant Physiology},
	author = {Bai, Bing and van der Horst, Sjors and Cordewener, Jan H.G. and America, Twan A.H.P. and Hanson, Johannes and Bentsink, Leónie},
	month = jan,
	year = {2020},
	pages = {378--392},
}

The life cycle of many organisms includes a quiescent stage, such as bacterial or fungal spores, insect larvae, or plant seeds. Common to these stages is their low water content and high survivability during harsh conditions. Upon rehydration, organisms need to reactivate metabolism and protein synthesis. Plant seeds contain many mRNAs that are transcribed during seed development. Translation of these mRNAs occurs during early seed germination, even before the requirement of transcription. Therefore, stored mRNAs are postulated to be important for germination. How these mRNAs are stored and protected during long-term storage is unknown. The aim of this study was to investigate how mRNAs are stored in dry seeds and whether they are indeed translated during seed germination. We investigated seed polysome profiles and the mRNAs and protein complexes that are associated with these ribosomes in seeds of the model organism Arabidopsis (Arabidopsis thaliana). We showed that most stored mRNAs are associated with monosomes in dry seeds; therefore, we focus on monosomes in this study. Seed ribosome complexes are associated with mRNA-binding proteins, stress granule, and P-body proteins, which suggests regulated packing of seed mRNAs. Interestingly, ∼17% of the mRNAs that are specifically associated with monosomes are translationally up-regulated during seed germination. These mRNAs are transcribed during seed maturation, suggesting a role for this developmental stage in determining the translational fate of mRNAs during early germination.

@article{westman_defence_2019,
	title = {Defence priming in {Arabidopsis} – a {Meta}-{Analysis}},
	volume = {9},
	copyright = {2019 The Author(s)},
	issn = {2045-2322},
	url = {https://www.nature.com/articles/s41598-019-49811-9},
	doi = {10/gh92kh},
	abstract = {Defence priming by organismal and non-organismal stimulants can reduce effects of biotic stress in plants. Thus, it could help efforts to enhance the sustainability of agricultural production by reducing use of agrochemicals in protection of crops from pests and diseases. We have explored effects of applying this approach to both Arabidopsis plants and seeds of various crops in meta-analyses. The results show that its effects on Arabidopsis plants depend on both the priming agent and antagonist. Fungi and vitamins can have strong priming effects, and priming is usually more effective against bacterial pathogens than against herbivores. Moreover, application of bio-stimulants (particularly vitamins and plant defence elicitors) to seeds can have promising defence priming effects. However, the published evidence is scattered, does not include Arabidopsis, and additional studies are required before we can draw general conclusions and understand the molecular mechanisms involved in priming of seeds’ defences. In conclusion, defence priming of plants has clear potential and application of bio-stimulants to seeds may protect plants from an early age, promises to be both labour- and resource-efficient, poses very little environmental risk, and is thus both economically and ecologically promising.},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Scientific Reports},
	publisher = {Nature Publishing Group},
	author = {Westman, Sara M. and Kloth, Karen J. and Hanson, Johannes and Ohlsson, Anna B. and Albrectsen, Benedicte R.},
	month = sep,
	year = {2019},
	note = {Number: 1},
	pages = {13309},
}

Defence priming by organismal and non-organismal stimulants can reduce effects of biotic stress in plants. Thus, it could help efforts to enhance the sustainability of agricultural production by reducing use of agrochemicals in protection of crops from pests and diseases. We have explored effects of applying this approach to both Arabidopsis plants and seeds of various crops in meta-analyses. The results show that its effects on Arabidopsis plants depend on both the priming agent and antagonist. Fungi and vitamins can have strong priming effects, and priming is usually more effective against bacterial pathogens than against herbivores. Moreover, application of bio-stimulants (particularly vitamins and plant defence elicitors) to seeds can have promising defence priming effects. However, the published evidence is scattered, does not include Arabidopsis, and additional studies are required before we can draw general conclusions and understand the molecular mechanisms involved in priming of seeds’ defences. In conclusion, defence priming of plants has clear potential and application of bio-stimulants to seeds may protect plants from an early age, promises to be both labour- and resource-efficient, poses very little environmental risk, and is thus both economically and ecologically promising.

@article{van_der_horst_novel_2019,
	title = {Novel pipeline identifies new upstream {ORFs} and non-{AUG} initiating main {ORFs} with conserved amino acid sequences in the 5′ leader of {mRNAs} in \textit{{Arabidopsis} thaliana}},
	volume = {25},
	issn = {1355-8382, 1469-9001},
	url = {http://rnajournal.cshlp.org/lookup/doi/10.1261/rna.067983.118},
	doi = {10.1261/rna.067983.118},
	language = {en},
	number = {3},
	urldate = {2021-06-07},
	journal = {RNA},
	author = {van der Horst, Sjors and Snel, Berend and Hanson, Johannes and Smeekens, Sjef},
	month = mar,
	year = {2019},
	pages = {292--304},
}

@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{dubreuil_establishment_2018,
	title = {Establishment of {Photosynthesis} through {Chloroplast} {Development} {Is} {Controlled} by {Two} {Distinct} {Regulatory} {Phases}},
	volume = {176},
	issn = {0032-0889, 1532-2548},
	url = {https://academic.oup.com/plphys/article/176/2/1199-1214/6117139},
	doi = {10/gb2hj6},
	language = {en},
	number = {2},
	urldate = {2021-06-07},
	journal = {Plant Physiology},
	author = {Dubreuil, Carole and Jin, Xu and Barajas-López, Juan de Dios and Hewitt, Timothy C. and Tanz, Sandra K. and Dobrenel, Thomas and Schröder, Wolfgang P. and Hanson, Johannes and Pesquet, Edouard and Grönlund, Andreas and Small, Ian and Strand, Åsa},
	month = feb,
	year = {2018},
	pages = {1199--1214},
}

@article{yazdanpanah_differentially_2017,
	title = {Differentially expressed genes during the imbibition of dormant and after-ripened seeds – a reverse genetics approach},
	volume = {17},
	issn = {1471-2229},
	url = {http://bmcplantbiol.biomedcentral.com/articles/10.1186/s12870-017-1098-z},
	doi = {10/gbx65c},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {BMC Plant Biology},
	author = {Yazdanpanah, Farzaneh and Hanson, Johannes and Hilhorst, Henk W.M. and Bentsink, Leónie},
	month = dec,
	year = {2017},
	pages = {151},
}

@article{bai_extensive_2017,
	title = {Extensive translational regulation during seed germination revealed by polysomal profiling},
	volume = {214},
	issn = {0028-646X, 1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/nph.14355},
	doi = {10.1111/nph.14355},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {New Phytologist},
	author = {Bai, Bing and Peviani, Alessia and Horst, Sjors and Gamm, Magdalena and Snel, Berend and Bentsink, Leónie and Hanson, Johannes},
	month = apr,
	year = {2017},
	pages = {233--244},
}

@article{baena-gonzalez_shaping_2017,
	title = {Shaping plant development through the {SnRK1}–{TOR} metabolic regulators},
	volume = {35},
	issn = {13695266},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S1369526616302242},
	doi = {10.1016/j.pbi.2016.12.004},
	language = {en},
	urldate = {2021-06-07},
	journal = {Current Opinion in Plant Biology},
	author = {Baena-González, Elena and Hanson, Johannes},
	month = feb,
	year = {2017},
	pages = {152--157},
}

@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{he_effects_2016,
	title = {Effects of {Parental} {Temperature} and {Nitrate} on {Seed} {Performance} are {Reflected} by {Partly} {Overlapping} {Genetic} and {Metabolic} {Pathways}},
	volume = {57},
	issn = {0032-0781, 1471-9053},
	url = {https://academic.oup.com/pcp/article-lookup/doi/10.1093/pcp/pcv207},
	doi = {10.1093/pcp/pcv207},
	language = {en},
	number = {3},
	urldate = {2021-06-07},
	journal = {Plant and Cell Physiology},
	author = {He, Hanzi and Willems, Leo A. J. and Batushansky, Albert and Fait, Aaron and Hanson, Johannes and Nijveen, Harm and Hilhorst, Henk W.M. and Bentsink, Leónie},
	month = mar,
	year = {2016},
	pages = {473--487},
}

@article{nukarinen_quantitative_2016,
	title = {Quantitative phosphoproteomics reveals the role of the {AMPK} plant ortholog {SnRK1} as a metabolic master regulator under energy deprivation},
	volume = {6},
	issn = {2045-2322},
	url = {http://www.nature.com/articles/srep31697},
	doi = {10/f3rwtq},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Scientific Reports},
	author = {Nukarinen, Ella and Nägele, Thomas and Pedrotti, Lorenzo and Wurzinger, Bernhard and Mair, Andrea and Landgraf, Ramona and Börnke, Frederik and Hanson, Johannes and Teige, Markus and Baena-Gonzalez, Elena and Dröge-Laser, Wolfgang and Weckwerth, Wolfram},
	month = aug,
	year = {2016},
	pages = {31697},
}

@article{dobrenel_tor_2016,
	title = {{TOR} {Signaling} and {Nutrient} {Sensing}},
	volume = {67},
	issn = {1543-5008, 1545-2123},
	url = {http://www.annualreviews.org/doi/10.1146/annurev-arplant-043014-114648},
	doi = {10.1146/annurev-arplant-043014-114648},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Annual Review of Plant Biology},
	author = {Dobrenel, Thomas and Caldana, Camila and Hanson, Johannes and Robaglia, Christophe and Vincentz, Michel and Veit, Bruce and Meyer, Christian},
	month = apr,
	year = {2016},
	pages = {261--285},
}

@article{dekkers_arabidopsis_2016,
	title = {The {Arabidopsis} \textit{{DELAY} {OF} {GERMINATION} 1} gene affects \textit{{ABSCISIC} {ACID} {INSENSITIVE} 5 ({ABI5})} expression and genetically interacts with \textit{{ABI3}} during {Arabidopsis} seed development},
	volume = {85},
	issn = {09607412},
	url = {http://doi.wiley.com/10.1111/tpj.13118},
	doi = {10.1111/tpj.13118},
	language = {en},
	number = {4},
	urldate = {2021-06-07},
	journal = {The Plant Journal},
	author = {Dekkers, Bas J.W. and He, Hanzi and Hanson, Johannes and Willems, Leo A.J. and Jamar, Diaan C.L. and Cueff, Gwendal and Rajjou, Loïc and Hilhorst, Henk W.M. and Bentsink, Leónie},
	month = feb,
	year = {2016},
	pages = {451--465},
}

@article{dobrenel_arabidopsis_2016,
	title = {The {Arabidopsis} {TOR} {Kinase} {Specifically} {Regulates} the {Expression} of {Nuclear} {Genes} {Coding} for {Plastidic} {Ribosomal} {Proteins} and the {Phosphorylation} of the {Cytosolic} {Ribosomal} {Protein} {S6}},
	volume = {7},
	issn = {1664-462X},
	url = {http://journal.frontiersin.org/article/10.3389/fpls.2016.01611/full},
	doi = {10.3389/fpls.2016.01611},
	urldate = {2021-06-07},
	journal = {Frontiers in Plant Science},
	author = {Dobrenel, Thomas and Mancera-Martínez, Eder and Forzani, Céline and Azzopardi, Marianne and Davanture, Marlène and Moreau, Manon and Schepetilnikov, Mikhail and Chicher, Johana and Langella, Olivier and Zivy, Michel and Robaglia, Christophe and Ryabova, Lyubov A. and Hanson, Johannes and Meyer, Christian},
	month = nov,
	year = {2016},
}

@article{peviani_phylogeny_2016,
	title = {The phylogeny of {C}/{S1} {bZIP} transcription factors reveals a shared algal ancestry and the pre-angiosperm translational regulation of {S1} transcripts},
	volume = {6},
	issn = {2045-2322},
	url = {http://www.nature.com/articles/srep30444},
	doi = {10/f3sc79},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Scientific Reports},
	author = {Peviani, Alessia and Lastdrager, Jeroen and Hanson, Johannes and Snel, Berend},
	month = jul,
	year = {2016},
	pages = {30444},
}

@article{hartmann_crosstalk_2015,
	title = {Crosstalk between {Two} {bZIP} {Signaling} {Pathways} {Orchestrates} {Salt}-{Induced} {Metabolic} {Reprogramming} in {Arabidopsis} {Roots}},
	volume = {27},
	issn = {1532-298X (Electronic) 1040-4651 (Linking)},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/26276836},
	doi = {10.1105/tpc.15.00163},
	abstract = {Soil salinity increasingly causes crop losses worldwide. Although roots are the primary targets of salt stress, the signaling networks that facilitate metabolic reprogramming to induce stress tolerance are less understood than those in leaves. Here, a combination of transcriptomic and metabolic approaches was performed in salt-treated Arabidopsis thaliana roots, which revealed that the group S1 basic leucine zipper transcription factors bZIP1 and bZIP53 reprogram primary C- and N-metabolism. In particular, gluconeogenesis and amino acid catabolism are affected by these transcription factors. Importantly, bZIP1 expression reflects cellular stress and energy status in roots. In addition to the well-described abiotic stress response pathway initiated by the hormone abscisic acid (ABA) and executed by SnRK2 (Snf1-RELATED-PROTEIN-KINASE2) and AREB-like bZIP factors, we identify a structurally related ABA-independent signaling module consisting of SnRK1s and S1 bZIPs. Crosstalk between these signaling pathways recruits particular bZIP factor combinations to establish at least four distinct gene expression patterns. Understanding this signaling network provides a framework for securing future crop productivity.},
	language = {en},
	number = {8},
	urldate = {2021-06-07},
	journal = {Plant Cell},
	author = {Hartmann, L. and Pedrotti, L. and Weiste, C. and Fekete, A. and Schierstaedt, J. and Gottler, J. and Kempa, S. and Krischke, M. and Dietrich, K. and Mueller, M. J. and Vicente-Carbajosa, J. and Hanson, J. and Droge-Laser, W.},
	month = aug,
	year = {2015},
	note = {Edition: 2015/08/16},
	keywords = {Abscisic Acid/pharmacology, Amino Acids/metabolism, Arabidopsis Proteins/*genetics/metabolism, Arabidopsis/drug effects/*genetics/metabolism, Basic-Leucine Zipper Transcription Factors/*genetics/metabolism, Calcium/metabolism, Carbohydrate Metabolism/drug effects/genetics, Gene Expression Regulation, Plant/drug effects, Gluconeogenesis/drug effects/genetics, Immunoblotting, Mutation, Plant Growth Regulators/pharmacology, Plant Roots/drug effects/genetics/metabolism, Promoter Regions, Genetic/genetics, Protein Binding/drug effects, Protein-Serine-Threonine Kinases, Reverse Transcriptase Polymerase Chain Reaction, Salt-Tolerant Plants/drug effects/genetics/metabolism, Signal Transduction/drug effects/*genetics, Sodium Chloride/pharmacology, Transcriptome/drug effects/genetics},
	pages = {2244--60},
}

Soil salinity increasingly causes crop losses worldwide. Although roots are the primary targets of salt stress, the signaling networks that facilitate metabolic reprogramming to induce stress tolerance are less understood than those in leaves. Here, a combination of transcriptomic and metabolic approaches was performed in salt-treated Arabidopsis thaliana roots, which revealed that the group S1 basic leucine zipper transcription factors bZIP1 and bZIP53 reprogram primary C- and N-metabolism. In particular, gluconeogenesis and amino acid catabolism are affected by these transcription factors. Importantly, bZIP1 expression reflects cellular stress and energy status in roots. In addition to the well-described abiotic stress response pathway initiated by the hormone abscisic acid (ABA) and executed by SnRK2 (Snf1-RELATED-PROTEIN-KINASE2) and AREB-like bZIP factors, we identify a structurally related ABA-independent signaling module consisting of SnRK1s and S1 bZIPs. Crosstalk between these signaling pathways recruits particular bZIP factor combinations to establish at least four distinct gene expression patterns. Understanding this signaling network provides a framework for securing future crop productivity.

@article{hummel_proteomic_2015,
	title = {Proteomic {LC}-{MS} analysis of {Arabidopsis} cytosolic ribosomes: {Identification} of ribosomal protein paralogs and re-annotation of the ribosomal protein genes},
	volume = {128},
	issn = {1876-7737 (Electronic) 1874-3919 (Linking)},
	shorttitle = {Proteomic {LC}–{MS} analysis of {Arabidopsis} cytosolic ribosomes},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/26232565},
	doi = {10.1016/j.jprot.2015.07.004},
	abstract = {UNLABELLED: Arabidopsis thaliana cytosolic ribosomes are large complexes containing eighty-one distinct ribosomal proteins (r-proteins), four ribosomal RNAs (rRNA) and a plethora of associated (non-ribosomal) proteins. In plants, r-proteins of cytosolic ribosomes are each encoded by two to seven different expressed and similar genes, forming an r-protein family. Distinctions in the r-protein coding sequences of gene family members are a source of variation between ribosomes. We performed proteomic investigation of actively translating cytosolic ribosomes purified using both immunopurification and a classic sucrose cushion centrifugation-based protocol from plants of different developmental stages. Both 1D and 2D LC-MS(E) with data-independent acquisition as well as conventional data-dependent MS/MS procedures were applied. This approach provided detailed identification of 165 r-protein paralogs with high coverage based on proteotypic peptides. The detected r-proteins were the products of the majority (68\%) of the 242 cytosolic r-protein genes encoded by the genome. A total of 70 distinct r-proteins were identified. Based on these results and information from DNA microarray and ribosome footprint profiling studies a re-annotation of Arabidopsis r-proteins and genes is proposed. This compendium of the cytosolic r-protein proteome will serve as a template for future investigations on the dynamic structure and function of plant ribosomes. BIOLOGICAL SIGNIFICANCE: Translation is one of the most energy demanding processes in a living cell and is therefore carefully regulated. Translational activity is tightly linked to growth control and growth regulating mechanism. Recently established translational profiling technologies, including the profiling of mRNAs associated with polysomes and the mapping of ribosome footprints on mRNAs, have revealed that the expression of gene expression is often fine-tuned by differential translation of gene transcripts. The eukaryotic ribosome, the hub of these important processes, consists of close to eighty different proteins (depending on species) and four large RNAs assembled into two highly conserved subunits. In plants and to lesser extent in yeast, the r-proteins are encoded by more than one actively transcribed gene. As r-protein gene paralogs frequently do not encode identical proteins and are regulated by growth conditions and development, in vivo ribosomes are heterogeneous in their protein content. The regulatory and physiological importance of this heterogeneity is unknown. Here, an improved annotation of the more than two hundred r-protein genes of Arabidopsis is presented that combines proteomic and advanced mRNA expression data. This proteomic investigation and re-annotation of Arabidopsis ribosomes establish a base for future investigations of translational control in plants.},
	language = {en},
	urldate = {2021-06-07},
	journal = {J Proteomics},
	author = {Hummel, M. and Dobrenel, T. and Cordewener, J. J. and Davanture, M. and Meyer, C. and Smeekens, S. J. and Bailey-Serres, J. and America, T. A. and Hanson, J.},
	month = oct,
	year = {2015},
	note = {Edition: 2015/08/02},
	keywords = {A. thaliana, Amino Acid Sequence, Arabidopsis Proteins/*metabolism, Arabidopsis/*metabolism, Chromatography, Liquid/*methods, Data-independent acquisition, Dia, Gene Expression Profiling/methods, Lc-ms, Mass Spectrometry/*methods, Molecular Sequence Data, Paralogs, Proteome/chemistry/metabolism, Ribosomal Proteins/*chemistry/*metabolism, Ribosomal protein, Ribosomes},
	pages = {436--49},
}

UNLABELLED: Arabidopsis thaliana cytosolic ribosomes are large complexes containing eighty-one distinct ribosomal proteins (r-proteins), four ribosomal RNAs (rRNA) and a plethora of associated (non-ribosomal) proteins. In plants, r-proteins of cytosolic ribosomes are each encoded by two to seven different expressed and similar genes, forming an r-protein family. Distinctions in the r-protein coding sequences of gene family members are a source of variation between ribosomes. We performed proteomic investigation of actively translating cytosolic ribosomes purified using both immunopurification and a classic sucrose cushion centrifugation-based protocol from plants of different developmental stages. Both 1D and 2D LC-MS(E) with data-independent acquisition as well as conventional data-dependent MS/MS procedures were applied. This approach provided detailed identification of 165 r-protein paralogs with high coverage based on proteotypic peptides. The detected r-proteins were the products of the majority (68%) of the 242 cytosolic r-protein genes encoded by the genome. A total of 70 distinct r-proteins were identified. Based on these results and information from DNA microarray and ribosome footprint profiling studies a re-annotation of Arabidopsis r-proteins and genes is proposed. This compendium of the cytosolic r-protein proteome will serve as a template for future investigations on the dynamic structure and function of plant ribosomes. BIOLOGICAL SIGNIFICANCE: Translation is one of the most energy demanding processes in a living cell and is therefore carefully regulated. Translational activity is tightly linked to growth control and growth regulating mechanism. Recently established translational profiling technologies, including the profiling of mRNAs associated with polysomes and the mapping of ribosome footprints on mRNAs, have revealed that the expression of gene expression is often fine-tuned by differential translation of gene transcripts. The eukaryotic ribosome, the hub of these important processes, consists of close to eighty different proteins (depending on species) and four large RNAs assembled into two highly conserved subunits. In plants and to lesser extent in yeast, the r-proteins are encoded by more than one actively transcribed gene. As r-protein gene paralogs frequently do not encode identical proteins and are regulated by growth conditions and development, in vivo ribosomes are heterogeneous in their protein content. The regulatory and physiological importance of this heterogeneity is unknown. Here, an improved annotation of the more than two hundred r-protein genes of Arabidopsis is presented that combines proteomic and advanced mRNA expression data. This proteomic investigation and re-annotation of Arabidopsis ribosomes establish a base for future investigations of translational control in plants.

@article{zamioudis_rhizobacterial_2015,
	title = {Rhizobacterial volatiles and photosynthesis-related signals coordinate {MYB72} expression in {Arabidopsis} roots during onset of induced systemic resistance and iron-deficiency responses},
	volume = {84},
	issn = {1365-313X (Electronic) 0960-7412 (Linking)},
	shorttitle = {Rhizobacterial volatiles and photosynthesis‐related signals coordinate},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/26307542},
	doi = {10/f3m6j7},
	abstract = {In Arabidopsis roots, the transcription factor MYB72 plays a dual role in the onset of rhizobacteria-induced systemic resistance (ISR) and plant survival under conditions of limited iron availability. Previously, it was shown that MYB72 coordinates the expression of a gene module that promotes synthesis and excretion of iron-mobilizing phenolic compounds in the rhizosphere, a process that is involved in both iron acquisition and ISR signaling. Here, we show that volatile organic compounds (VOCs) from ISR-inducing Pseudomonas bacteria are important elicitors of MYB72. In response to VOC treatment, MYB72 is co-expressed with the iron uptake-related genes FERRIC REDUCTION OXIDASE 2 (FRO2) and IRON-REGULATED TRANSPORTER 1 (IRT1) in a manner that is dependent on FER-LIKE IRON DEFICIENCY TRANSCRIPTION FACTOR (FIT), indicating that MYB72 is an intrinsic part of the plant's iron-acquisition response that is typically activated upon iron starvation. However, VOC-induced MYB72 expression is activated independently of iron availability in the root vicinity. Moreover, rhizobacterial VOC-mediated induction of MYB72 requires photosynthesis-related signals, while iron deficiency in the rhizosphere activates MYB72 in the absence of shoot-derived signals. Together, these results show that the ISR- and iron acquisition-related transcription factor MYB72 in Arabidopsis roots is activated by rhizobacterial volatiles and photosynthesis-related signals, and enhances the iron-acquisition capacity of roots independently of the iron availability in the rhizosphere. This work highlights the role of MYB72 in plant processes by which root microbiota simultaneously stimulate systemic immunity and activate the iron-uptake machinery in their host plants.},
	language = {en},
	number = {2},
	urldate = {2021-06-07},
	journal = {Plant J},
	author = {Zamioudis, C. and Korteland, J. and Van Pelt, J. A. and van Hamersveld, M. and Dombrowski, N. and Bai, Y. and Hanson, J. and Van Verk, M. C. and Ling, H. Q. and Schulze-Lefert, P. and Pieterse, C. M.},
	month = oct,
	year = {2015},
	note = {Edition: 2015/08/27},
	keywords = {Arabidopsis Proteins/genetics/*metabolism, Arabidopsis thaliana, Arabidopsis/drug effects/*metabolism, Gene Expression Regulation, Plant/drug effects/genetics, Iron/*deficiency, MYB transcription factor, Photosynthesis/drug effects, Plant Roots/drug effects/*metabolism, Rhizobium/*chemistry, Volatile Organic Compounds/*pharmacology, induced resistance, iron homeostasis, plant growth-promoting rhizobacteria, volatile organic compounds},
	pages = {309--22},
}

In Arabidopsis roots, the transcription factor MYB72 plays a dual role in the onset of rhizobacteria-induced systemic resistance (ISR) and plant survival under conditions of limited iron availability. Previously, it was shown that MYB72 coordinates the expression of a gene module that promotes synthesis and excretion of iron-mobilizing phenolic compounds in the rhizosphere, a process that is involved in both iron acquisition and ISR signaling. Here, we show that volatile organic compounds (VOCs) from ISR-inducing Pseudomonas bacteria are important elicitors of MYB72. In response to VOC treatment, MYB72 is co-expressed with the iron uptake-related genes FERRIC REDUCTION OXIDASE 2 (FRO2) and IRON-REGULATED TRANSPORTER 1 (IRT1) in a manner that is dependent on FER-LIKE IRON DEFICIENCY TRANSCRIPTION FACTOR (FIT), indicating that MYB72 is an intrinsic part of the plant's iron-acquisition response that is typically activated upon iron starvation. However, VOC-induced MYB72 expression is activated independently of iron availability in the root vicinity. Moreover, rhizobacterial VOC-mediated induction of MYB72 requires photosynthesis-related signals, while iron deficiency in the rhizosphere activates MYB72 in the absence of shoot-derived signals. Together, these results show that the ISR- and iron acquisition-related transcription factor MYB72 in Arabidopsis roots is activated by rhizobacterial volatiles and photosynthesis-related signals, and enhances the iron-acquisition capacity of roots independently of the iron availability in the rhizosphere. This work highlights the role of MYB72 in plant processes by which root microbiota simultaneously stimulate systemic immunity and activate the iron-uptake machinery in their host plants.

@article{mair_snrk1-triggered_2015,
	title = {{SnRK1}-triggered switch of {bZIP63} dimerization mediates the low-energy response in plants},
	volume = {4},
	issn = {2050-084X (Electronic) 2050-084X (Linking)},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/26263501},
	doi = {10.7554/eLife.05828},
	abstract = {Metabolic adjustment to changing environmental conditions, particularly balancing of growth and defense responses, is crucial for all organisms to survive. The evolutionary conserved AMPK/Snf1/SnRK1 kinases are well-known metabolic master regulators in the low-energy response in animals, yeast and plants. They act at two different levels: by modulating the activity of key metabolic enzymes, and by massive transcriptional reprogramming. While the first part is well established, the latter function is only partially understood in animals and not at all in plants. Here we identified the Arabidopsis transcription factor bZIP63 as key regulator of the starvation response and direct target of the SnRK1 kinase. Phosphorylation of bZIP63 by SnRK1 changed its dimerization preference, thereby affecting target gene expression and ultimately primary metabolism. A bzip63 knock-out mutant exhibited starvation-related phenotypes, which could be functionally complemented by wild type bZIP63, but not by a version harboring point mutations in the identified SnRK1 target sites.},
	language = {en},
	urldate = {2021-06-07},
	journal = {Elife},
	author = {Mair, A. and Pedrotti, L. and Wurzinger, B. and Anrather, D. and Simeunovic, A. and Weiste, C. and Valerio, C. and Dietrich, K. and Kirchler, T. and Nagele, T. and Vicente Carbajosa, J. and Hanson, J. and Baena-Gonzalez, E. and Chaban, C. and Weckwerth, W. and Droge-Laser, W. and Teige, M.},
	month = aug,
	year = {2015},
	note = {Edition: 2015/08/12},
	keywords = {*Gene Expression Regulation, Plant, *Protein Multimerization, Adaptation, Physiological, Arabidopsis Proteins/*metabolism, Arabidopsis/*genetics/metabolism, Basic-Leucine Zipper Transcription Factors/deficiency/*metabolism, Gene Knockout Techniques, Genetic Complementation Test, Phosphorylation, Protein Processing, Post-Translational, Protein-Serine-Threonine Kinases/*metabolism, SnRK1 kinase, arabidopsis, bZIP transcription factor, cell biology, metabolic reprogramming, plant biology},
	pages = {e05828},
}

Metabolic adjustment to changing environmental conditions, particularly balancing of growth and defense responses, is crucial for all organisms to survive. The evolutionary conserved AMPK/Snf1/SnRK1 kinases are well-known metabolic master regulators in the low-energy response in animals, yeast and plants. They act at two different levels: by modulating the activity of key metabolic enzymes, and by massive transcriptional reprogramming. While the first part is well established, the latter function is only partially understood in animals and not at all in plants. Here we identified the Arabidopsis transcription factor bZIP63 as key regulator of the starvation response and direct target of the SnRK1 kinase. Phosphorylation of bZIP63 by SnRK1 changed its dimerization preference, thereby affecting target gene expression and ultimately primary metabolism. A bzip63 knock-out mutant exhibited starvation-related phenotypes, which could be functionally complemented by wild type bZIP63, but not by a version harboring point mutations in the identified SnRK1 target sites.

@article{gamm_increased_2014,
	title = {Increased sucrose levels mediate selective {mRNA} translation in {Arabidopsis}},
	volume = {14},
	issn = {1471-2229},
	url = {http://bmcplantbiol.biomedcentral.com/articles/10.1186/s12870-014-0306-3},
	doi = {10/f3nrb4},
	language = {en},
	number = {1},
	urldate = {2021-06-08},
	journal = {BMC Plant Biology},
	author = {Gamm, Magdalena and Peviani, Alessia and Honsel, Anne and Snel, Berend and Smeekens, Sjef and Hanson, Johannes},
	month = dec,
	year = {2014},
	pages = {306},
}

@article{lastdrager_sugar_2014,
	title = {Sugar signals and the control of plant growth and development},
	volume = {65},
	issn = {1460-2431, 0022-0957},
	url = {https://academic.oup.com/jxb/article-lookup/doi/10.1093/jxb/ert474},
	doi = {10/f239qn},
	language = {en},
	number = {3},
	urldate = {2021-06-08},
	journal = {Journal of Experimental Botany},
	author = {Lastdrager, Jeroen and Hanson, Johannes and Smeekens, Sjef},
	month = mar,
	year = {2014},
	pages = {799--807},
}

@article{zamioudis_-glucosidase_2014,
	title = {β-{Glucosidase} {BGLU42} is a {MYB72}-dependent key regulator of rhizobacteria-induced systemic resistance and modulates iron deficiency responses in \textit{{Arabidopsis}} roots},
	volume = {204},
	issn = {0028646X},
	url = {http://doi.wiley.com/10.1111/nph.12980},
	doi = {10/f3nsht},
	language = {en},
	number = {2},
	urldate = {2021-06-08},
	journal = {New Phytologist},
	author = {Zamioudis, Christos and Hanson, Johannes and Pieterse, Corné M. J.},
	month = oct,
	year = {2014},
	pages = {368--379},
}

@article{wind_abi4_2013,
	title = {{ABI4}: versatile activator and repressor},
	volume = {18},
	issn = {13601385},
	shorttitle = {{ABI4}},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S1360138512002312},
	doi = {10/f22p4f},
	language = {en},
	number = {3},
	urldate = {2021-06-08},
	journal = {Trends in Plant Science},
	author = {Wind, Julia J. and Peviani, Alessia and Snel, Berend and Hanson, Johannes and Smeekens, Sjef C.},
	month = mar,
	year = {2013},
	pages = {125--132},
}

@article{hummel_dynamic_2012,
	title = {Dynamic protein composition of {Arabidopsis} thaliana cytosolic ribosomes in response to sucrose feeding as revealed by label free {MSE} proteomics},
	volume = {12},
	issn = {16159853},
	url = {http://doi.wiley.com/10.1002/pmic.201100413},
	doi = {10/f23s9x},
	language = {en},
	number = {7},
	urldate = {2021-06-08},
	journal = {PROTEOMICS},
	author = {Hummel, Maureen and Cordewener, Jan H. G. and de Groot, Joost C. M. and Smeekens, Sjef and America, Antoine H. P. and Hanson, Johannes},
	month = apr,
	year = {2012},
	pages = {1024--1038},
}

@article{li_fructose_2011,
	chapter = {Biological Sciences},
	title = {Fructose sensitivity is suppressed in {Arabidopsis} by the transcription factor {ANAC089} lacking the membrane-bound domain},
	volume = {108},
	issn = {0027-8424, 1091-6490},
	url = {https://www.pnas.org/content/108/8/3436},
	doi = {10/bpszjb},
	abstract = {In living organisms sugars not only provide energy and carbon skeletons but also act as evolutionarily conserved signaling molecules. The three major soluble sugars in plants are sucrose, glucose, and fructose. Information on plant glucose and sucrose signaling is available, but to date no fructose-specific signaling pathway has been reported. In this study, sugar repression of seedling development was used to study fructose sensitivity in the Landsberg erecta (Ler)/Cape Verde Islands (Cvi) recombinant inbred line population, and eight fructose-sensing quantitative trait loci (QTLs) (FSQ1–8) were mapped. Among them, FSQ6 was confirmed to be a fructose-specific QTL by analyzing near-isogenic lines in which Cvi genomic fragments were introgressed in the Ler background. These results indicate the existence of a fructose-specific signaling pathway in Arabidopsis. Further analysis demonstrated that the FSQ6-associated fructose-signaling pathway functions independently of the hexokinase1 (HXK1) glucose sensor. Remarkably, fructose-specific FSQ6 downstream signaling interacts with abscisic acid (ABA)- and ethylene-signaling pathways, similar to HXK1-dependent glucose signaling. The Cvi allele of FSQ6 acts as a suppressor of fructose signaling. The FSQ6 gene was identified using map-based cloning approach, and FSQ6 was shown to encode the transcription factor gene Arabidopsis NAC (petunia No apical meristem and Arabidopsis transcription activation factor 1, 2 and Cup-shaped cotyledon 2) domain containing protein 89 (ANAC089). The Cvi allele of FSQ6/ANAC089 is a gain-of-function allele caused by a premature stop in the third exon of the gene. The truncated Cvi FSQ6/ANAC089 protein lacks a membrane association domain that is present in ANAC089 proteins from other Arabidopsis accessions. As a result, Cvi FSQ6/ANAC089 is constitutively active as a transcription factor in the nucleus.},
	language = {en},
	number = {8},
	urldate = {2021-06-08},
	journal = {Proceedings of the National Academy of Sciences},
	publisher = {National Academy of Sciences},
	author = {Li, Ping and Wind, Julia J. and Shi, Xiaoliang and Zhang, Honglei and Hanson, Johannes and Smeekens, Sjef C. and Teng, Sheng},
	month = feb,
	year = {2011},
	keywords = {fructose quantitative trait locus, map based cloning, natural variation, sugar signaling},
	pages = {3436--3441},
}

In living organisms sugars not only provide energy and carbon skeletons but also act as evolutionarily conserved signaling molecules. The three major soluble sugars in plants are sucrose, glucose, and fructose. Information on plant glucose and sucrose signaling is available, but to date no fructose-specific signaling pathway has been reported. In this study, sugar repression of seedling development was used to study fructose sensitivity in the Landsberg erecta (Ler)/Cape Verde Islands (Cvi) recombinant inbred line population, and eight fructose-sensing quantitative trait loci (QTLs) (FSQ1–8) were mapped. Among them, FSQ6 was confirmed to be a fructose-specific QTL by analyzing near-isogenic lines in which Cvi genomic fragments were introgressed in the Ler background. These results indicate the existence of a fructose-specific signaling pathway in Arabidopsis. Further analysis demonstrated that the FSQ6-associated fructose-signaling pathway functions independently of the hexokinase1 (HXK1) glucose sensor. Remarkably, fructose-specific FSQ6 downstream signaling interacts with abscisic acid (ABA)- and ethylene-signaling pathways, similar to HXK1-dependent glucose signaling. The Cvi allele of FSQ6 acts as a suppressor of fructose signaling. The FSQ6 gene was identified using map-based cloning approach, and FSQ6 was shown to encode the transcription factor gene Arabidopsis NAC (petunia No apical meristem and Arabidopsis transcription activation factor 1, 2 and Cup-shaped cotyledon 2) domain containing protein 89 (ANAC089). The Cvi allele of FSQ6/ANAC089 is a gain-of-function allele caused by a premature stop in the third exon of the gene. The truncated Cvi FSQ6/ANAC089 protein lacks a membrane association domain that is present in ANAC089 proteins from other Arabidopsis accessions. As a result, Cvi FSQ6/ANAC089 is constitutively active as a transcription factor in the nucleus.

@article{ma_sucroseregulated_2011,
	title = {The sucrose‐regulated {Arabidopsis} transcription factor {bZIP11} reprograms metabolism and regulates trehalose metabolism},
	volume = {191},
	issn = {0028-646X, 1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/j.1469-8137.2011.03735.x},
	doi = {10/b9vhbj},
	language = {en},
	number = {3},
	urldate = {2021-06-08},
	journal = {New Phytologist},
	author = {Ma, Jingkun and Hanssen, Micha and Lundgren, Krister and Hernández, Lázaro and Delatte, Thierry and Ehlert, Andrea and Liu, Chun‐Ming and Schluepmann, Henriette and Dröge‐Laser, Wolfgang and Moritz, Thomas and Smeekens, Sjef and Hanson, Johannes},
	month = aug,
	year = {2011},
	pages = {733--745},
}

@article{bentsink_natural_2010,
	title = {Natural variation for seed dormancy in {Arabidopsis} is regulated by additive genetic and molecular pathways},
	volume = {107},
	issn = {1091-6490},
	doi = {10/c2gjzz},
	abstract = {Timing of germination is presumably under strong natural selection as it determines the environmental conditions in which a plant germinates and initiates its postembryonic life cycle. To investigate how seed dormancy is controlled, quantitative trait loci (QTL) analyses has been performed in six Arabidopsis thaliana recombinant inbred line populations by analyzing them simultaneously using a mixed model QTL approach. The recombinant inbred line populations were derived from crosses between the reference accession Landsberg erecta (Ler) and accessions from different world regions. In total, 11 delay of germination (DOG) QTL have been identified, and nine of them have been confirmed by near isogenic lines (NILs). The absence of strong epistatic interactions between the different DOG loci suggests that they affect dormancy mainly by distinct genetic pathways. This was confirmed by analyzing the transcriptome of freshly harvested dry seeds of five different DOG NILs. All five DOG NILs showed discernible and different expression patterns compared with the expression of their genetic background Ler. The genes identified in the different DOG NILs represent largely different gene ontology profiles. It is proposed that natural variation for seed dormancy in Arabidopsis is mainly controlled by different additive genetic and molecular pathways rather than epistatic interactions, indicating the involvement of several independent pathways.},
	language = {eng},
	number = {9},
	journal = {Proceedings of the National Academy of Sciences of the United States of America},
	author = {Bentsink, Leónie and Hanson, Johannes and Hanhart, Corrie J. and Blankestijn-de Vries, Hetty and Coltrane, Colin and Keizer, Paul and El-Lithy, Mohamed and Alonso-Blanco, Carlos and de Andrés, M. Teresa and Reymond, Matthieu and van Eeuwijk, Fred and Smeekens, Sjef and Koornneef, Maarten},
	month = mar,
	year = {2010},
	keywords = {Arabidopsis, Arabidopsis Proteins, Gene Expression Profiling, Genetic Variation, Quantitative Trait Loci, Seeds},
	pages = {4264--4269},
}

Timing of germination is presumably under strong natural selection as it determines the environmental conditions in which a plant germinates and initiates its postembryonic life cycle. To investigate how seed dormancy is controlled, quantitative trait loci (QTL) analyses has been performed in six Arabidopsis thaliana recombinant inbred line populations by analyzing them simultaneously using a mixed model QTL approach. The recombinant inbred line populations were derived from crosses between the reference accession Landsberg erecta (Ler) and accessions from different world regions. In total, 11 delay of germination (DOG) QTL have been identified, and nine of them have been confirmed by near isogenic lines (NILs). The absence of strong epistatic interactions between the different DOG loci suggests that they affect dormancy mainly by distinct genetic pathways. This was confirmed by analyzing the transcriptome of freshly harvested dry seeds of five different DOG NILs. All five DOG NILs showed discernible and different expression patterns compared with the expression of their genetic background Ler. The genes identified in the different DOG NILs represent largely different gene ontology profiles. It is proposed that natural variation for seed dormancy in Arabidopsis is mainly controlled by different additive genetic and molecular pathways rather than epistatic interactions, indicating the involvement of several independent pathways.

@article{wind_sucrose_2010,
	title = {Sucrose: metabolite and signaling molecule},
	volume = {71},
	issn = {1873-3700},
	shorttitle = {Sucrose},
	doi = {10/bcnsm2},
	abstract = {Sucrose is a molecule that is synthesized only by oxygenic photosynthetic organisms. In plants, sucrose is synthesized in source tissues and then can be transported to sink tissues, where it is utilized or stored. Interestingly, sucrose is both a metabolite and a signaling molecule. Manipulating the rate of the synthesis, transport or degradation of sucrose affects plant growth, development and physiology. Altered sucrose levels changes the quantity of sucrose derived metabolites and sucrose-specific signaling. In this paper, these changes are summarized. Better understanding of sucrose metabolism and sucrose sensing systems in plants will lead to opportunities to adapt plant metabolism and growth.},
	language = {eng},
	number = {14-15},
	journal = {Phytochemistry},
	author = {Wind, Julia and Smeekens, Sjef and Hanson, Johannes},
	month = oct,
	year = {2010},
	keywords = {Arabidopsis, Molecular Structure, Photosynthesis, Plant Development, Plants, Signal Transduction, Sucrose},
	pages = {1610--1614},
}

Sucrose is a molecule that is synthesized only by oxygenic photosynthetic organisms. In plants, sucrose is synthesized in source tissues and then can be transported to sink tissues, where it is utilized or stored. Interestingly, sucrose is both a metabolite and a signaling molecule. Manipulating the rate of the synthesis, transport or degradation of sucrose affects plant growth, development and physiology. Altered sucrose levels changes the quantity of sucrose derived metabolites and sucrose-specific signaling. In this paper, these changes are summarized. Better understanding of sucrose metabolism and sucrose sensing systems in plants will lead to opportunities to adapt plant metabolism and growth.

@article{smeekens_sugar_2010,
	title = {Sugar signals and molecular networks controlling plant growth},
	volume = {13},
	issn = {1369-5266},
	url = {https://www.sciencedirect.com/science/article/pii/S1369526609001782},
	doi = {10/d9t45g},
	abstract = {In recent years, several regulatory systems that link carbon nutrient status to plant growth and development have emerged. In this paper, we discuss the growth promoting functions of the hexokinase (HXK) glucose sensor, the trehalose 6-phosphate (T6P) signal and the Target of Rapamycin (TOR) kinase pathway, and the growth inhibitory function of the SNF1-related Protein Kinase1 (SnRK1) and the C/S1 bZIP transcription factor network. It is crucial that these systems interact closely in regulating growth and in several cases crosstalk has been demonstrated. Importantly, these nutrient controlled systems must interact with other growth regulatory pathways.},
	language = {en},
	number = {3},
	urldate = {2021-06-08},
	journal = {Current Opinion in Plant Biology},
	author = {Smeekens, Sjef and Ma, Jingkun and Hanson, Johannes and Rolland, Filip},
	month = jun,
	year = {2010},
	pages = {273--278},
}

In recent years, several regulatory systems that link carbon nutrient status to plant growth and development have emerged. In this paper, we discuss the growth promoting functions of the hexokinase (HXK) glucose sensor, the trehalose 6-phosphate (T6P) signal and the Target of Rapamycin (TOR) kinase pathway, and the growth inhibitory function of the SNF1-related Protein Kinase1 (SnRK1) and the C/S1 bZIP transcription factor network. It is crucial that these systems interact closely in regulating growth and in several cases crosstalk has been demonstrated. Importantly, these nutrient controlled systems must interact with other growth regulatory pathways.

@article{weltmeier_expression_2009,
	title = {Expression patterns within the {Arabidopsis} {C}/{S1} {bZIP} transcription factor network: availability of heterodimerization partners controls gene expression during stress response and development},
	volume = {69},
	issn = {0167-4412},
	shorttitle = {Expression patterns within the {Arabidopsis} {C}/{S1} {bZIP} transcription factor network},
	doi = {10/dqff6q},
	abstract = {Members of the Arabidopsis group C/S1 basic leucine zipper (bZIP) transcription factor (TF) network are proposed to implement transcriptional reprogramming of plant growth in response to energy deprivation and environmental stresses. The four group C and five group S1 members form specific heterodimers and are, therefore, considered to cooperate functionally. For example, the interplay of C/S1 bZIP TFs in regulating seed maturation genes was analyzed by expression studies and target gene regulation in both protoplasts and transgenic plants. The abundance of the heterodimerization partners significantly affects target gene transcription. Therefore, a detailed analysis of the developmental and stress related expression patterns was performed by comparing promoter: GUS and transcription data. The idea that the C/S1 network plays a role in the allocation of nutrients is supported by the defined and partially overlapping expression patterns in sink leaves, seeds and anthers. Accordingly, metabolic signals strongly affect bZIP expression on the transcriptional and/or post-transcriptional level. Sucrose induced repression of translation (SIRT) was demonstrated for all group S1 bZIPs. In particular, transcription of group S1 genes strongly responds to various abiotic stresses, such as salt (AtbZIP1) or cold (AtbZIP44). In summary, heterodimerization and expression data provide a basic framework to further determine the functional impact of the C/S1 network in regulating the plant energy balance and nutrient allocation.},
	language = {eng},
	number = {1-2},
	journal = {Plant Molecular Biology},
	author = {Weltmeier, Fridtjof and Rahmani, Fatima and Ehlert, Andrea and Dietrich, Katrin and Schütze, Katia and Wang, Xuan and Chaban, Christina and Hanson, Johannes and Teige, Markus and Harter, Klaus and Vicente-Carbajosa, Jesus and Smeekens, Sjef and Dröge-Laser, Wolfgang},
	month = jan,
	year = {2009},
	keywords = {Arabidopsis, Basic-Leucine Zipper Transcription Factors, Dimerization, Gene Expression Regulation, Plant, Stress, Physiological},
	pages = {107--119},
}

Members of the Arabidopsis group C/S1 basic leucine zipper (bZIP) transcription factor (TF) network are proposed to implement transcriptional reprogramming of plant growth in response to energy deprivation and environmental stresses. The four group C and five group S1 members form specific heterodimers and are, therefore, considered to cooperate functionally. For example, the interplay of C/S1 bZIP TFs in regulating seed maturation genes was analyzed by expression studies and target gene regulation in both protoplasts and transgenic plants. The abundance of the heterodimerization partners significantly affects target gene transcription. Therefore, a detailed analysis of the developmental and stress related expression patterns was performed by comparing promoter: GUS and transcription data. The idea that the C/S1 network plays a role in the allocation of nutrients is supported by the defined and partially overlapping expression patterns in sink leaves, seeds and anthers. Accordingly, metabolic signals strongly affect bZIP expression on the transcriptional and/or post-transcriptional level. Sucrose induced repression of translation (SIRT) was demonstrated for all group S1 bZIPs. In particular, transcription of group S1 genes strongly responds to various abiotic stresses, such as salt (AtbZIP1) or cold (AtbZIP44). In summary, heterodimerization and expression data provide a basic framework to further determine the functional impact of the C/S1 network in regulating the plant energy balance and nutrient allocation.

@article{rahmani_sucrose_2009,
	title = {Sucrose control of translation mediated by an upstream open reading frame-encoded peptide},
	volume = {150},
	issn = {0032-0889},
	doi = {10/dzt95k},
	abstract = {Regulation of gene expression through translational control is common in many organisms. The Arabidopsis (Arabidopsis thaliana) transcription factor bZIP11 is translational repressed in response to sucrose (Suc), resulting in Suc-regulated changes in amino acid metabolism. The 5' leader of the bZIP11 mRNA harbors several upstream open reading frames (uORFs), of which the second uORF is well conserved among bZIP11 homologous genes. The uORF2 element encodes a Suc control peptide (SC-peptide) of 28 residues that is sufficient for imposing Suc-induced repression of translation (SIRT) on a heterologous mRNA. Detailed analysis of the SC-peptide suggests that it functions as an attenuator peptide. Results suggest that the SC-peptide inhibits bZIP11 translation in response to high Suc levels by stalling the ribosome on the mRNA. The conserved noncanonical AUG contexts of bZIP11 uORFs allow inefficient translational initiation of the uORF, resulting in translation initiation of the scanning ribosome at the AUG codon of the bZIP11 main ORF. The results presented show that Suc-dependent signaling mediates differential translation of mRNAs containing SC-peptides encoding uORFs.},
	language = {eng},
	number = {3},
	journal = {Plant Physiology},
	author = {Rahmani, Fatemeh and Hummel, Maureen and Schuurmans, Jolanda and Wiese-Klinkenberg, Anika and Smeekens, Sjef and Hanson, Johannes},
	month = jul,
	year = {2009},
	keywords = {Amino Acid Sequence, Arabidopsis, Arabidopsis Proteins, Base Sequence, Basic-Leucine Zipper Transcription Factors, Conserved Sequence, Gene Expression Regulation, Plant, Molecular Sequence Data, Open Reading Frames, Protein Biosynthesis, RNA, Messenger, Sequence Analysis, RNA, Sucrose},
	pages = {1356--1367},
}

Regulation of gene expression through translational control is common in many organisms. The Arabidopsis (Arabidopsis thaliana) transcription factor bZIP11 is translational repressed in response to sucrose (Suc), resulting in Suc-regulated changes in amino acid metabolism. The 5' leader of the bZIP11 mRNA harbors several upstream open reading frames (uORFs), of which the second uORF is well conserved among bZIP11 homologous genes. The uORF2 element encodes a Suc control peptide (SC-peptide) of 28 residues that is sufficient for imposing Suc-induced repression of translation (SIRT) on a heterologous mRNA. Detailed analysis of the SC-peptide suggests that it functions as an attenuator peptide. Results suggest that the SC-peptide inhibits bZIP11 translation in response to high Suc levels by stalling the ribosome on the mRNA. The conserved noncanonical AUG contexts of bZIP11 uORFs allow inefficient translational initiation of the uORF, resulting in translation initiation of the scanning ribosome at the AUG codon of the bZIP11 main ORF. The results presented show that Suc-dependent signaling mediates differential translation of mRNAs containing SC-peptides encoding uORFs.

@article{hummel_sucrose-mediated_2009,
	title = {Sucrose-mediated translational control},
	volume = {104},
	issn = {1095-8290},
	doi = {10/bwnw47},
	abstract = {BACKGROUND: Environmental factors greatly impact plant gene expression and concentrations of cellular metabolites such as sugars and amino acids. The changed metabolite concentrations affect the expression of many genes both transcriptionally and post-transcriptionally.
RECENT PROGRESS: Sucrose acts as a signalling molecule in the control of translation of the S1 class basic leucine zipper transcription factor (bZIP) genes. In these genes the main bZIP open reading frames (ORFs) are preceded by upstream open reading frames (uORFs). The presence of uORFs generally inhibits translation of the following ORF but can also be instrumental in specific translational control. bZIP11, a member of the S1 class bZIP genes, harbours four uORFs of which uORF2 is required for translational control in response to sucrose concentrations. This uORF encodes the Sucrose Control peptide (SC-peptide), which is evolutionarily conserved among all S1 class bZIP genes in different plant species. Arabidopsis thaliana bZIP11 and related bZIP genes seem to be important regulators of metabolism. These proteins are targets of the Snf1-related protein kinase 1 (SnRK1) KIN10 and KIN11, which are responsive to energy deprivation as well as to various stresses. In response to energy deprivation, ribosomal biogenesis is repressed to preserve cellular function and maintenance. Other key regulators of ribosomal biogenesis such as the protein kinase Target of Rapamycin (TOR) are tightly regulated in response to stress.
CONCLUSIONS: Plants use translational control of gene expression to optimize growth and development in response to stress as well as to energy deprivation. This Botanical Briefing discusses the role of sucrose signalling in the translational control of bZIP11 and the regulation of ribosomal biogenesis in response to metabolic changes and stress conditions.},
	language = {eng},
	number = {1},
	journal = {Annals of Botany},
	author = {Hummel, Maureen and Rahmani, Fatima and Smeekens, Sjef and Hanson, Johannes},
	month = jul,
	year = {2009},
	keywords = {Arabidopsis, Basic-Leucine Zipper Transcription Factors, Gene Expression Regulation, Plant, Open Reading Frames, Plant Proteins, Sucrose},
	pages = {1--7},
}

BACKGROUND: Environmental factors greatly impact plant gene expression and concentrations of cellular metabolites such as sugars and amino acids. The changed metabolite concentrations affect the expression of many genes both transcriptionally and post-transcriptionally. RECENT PROGRESS: Sucrose acts as a signalling molecule in the control of translation of the S1 class basic leucine zipper transcription factor (bZIP) genes. In these genes the main bZIP open reading frames (ORFs) are preceded by upstream open reading frames (uORFs). The presence of uORFs generally inhibits translation of the following ORF but can also be instrumental in specific translational control. bZIP11, a member of the S1 class bZIP genes, harbours four uORFs of which uORF2 is required for translational control in response to sucrose concentrations. This uORF encodes the Sucrose Control peptide (SC-peptide), which is evolutionarily conserved among all S1 class bZIP genes in different plant species. Arabidopsis thaliana bZIP11 and related bZIP genes seem to be important regulators of metabolism. These proteins are targets of the Snf1-related protein kinase 1 (SnRK1) KIN10 and KIN11, which are responsive to energy deprivation as well as to various stresses. In response to energy deprivation, ribosomal biogenesis is repressed to preserve cellular function and maintenance. Other key regulators of ribosomal biogenesis such as the protein kinase Target of Rapamycin (TOR) are tightly regulated in response to stress. CONCLUSIONS: Plants use translational control of gene expression to optimize growth and development in response to stress as well as to energy deprivation. This Botanical Briefing discusses the role of sucrose signalling in the translational control of bZIP11 and the regulation of ribosomal biogenesis in response to metabolic changes and stress conditions.

@article{hanson_sugar_2009,
	title = {Sugar perception and signaling--an update},
	volume = {12},
	issn = {1879-0356},
	doi = {10/b87fkq},
	abstract = {Sugars act as potent signaling molecules in plants. Several sugar sensors, including the highly studied glucose sensor HEXOKINASE1 (HXK1), have been identified or proposed. Many additional sensors likely exist, as plants respond to other sugars and sugar metabolites, such as sucrose and trehalose 6-phosphate. Sugar sensing and signaling is a highly complex process resulting in many changes in physiology and development and is integrated with other signaling pathways in plants such as those for inorganic nutrients, hormones, and different stress factors. Importantly, KIN10 and KIN11 protein kinases are central in coordinating several of the responses to sugars and stress. bZIP transcription factors were found to mediate effects of sugar signaling on gene expression and metabolite content.},
	language = {eng},
	number = {5},
	journal = {Current Opinion in Plant Biology},
	author = {Hanson, Johannes and Smeekens, Sjef},
	month = oct,
	year = {2009},
	keywords = {Basic-Leucine Zipper Transcription Factors, Carbohydrate Metabolism, Gene Expression Regulation, Plant, Hexokinase, Plant Development, Plant Proteins, Plants, Signal Transduction, Sucrose, Sugar Phosphates, Trehalose},
	pages = {562--567},
}

Sugars act as potent signaling molecules in plants. Several sugar sensors, including the highly studied glucose sensor HEXOKINASE1 (HXK1), have been identified or proposed. Many additional sensors likely exist, as plants respond to other sugars and sugar metabolites, such as sucrose and trehalose 6-phosphate. Sugar sensing and signaling is a highly complex process resulting in many changes in physiology and development and is integrated with other signaling pathways in plants such as those for inorganic nutrients, hormones, and different stress factors. Importantly, KIN10 and KIN11 protein kinases are central in coordinating several of the responses to sugars and stress. bZIP transcription factors were found to mediate effects of sugar signaling on gene expression and metabolite content.

@article{hanson_sucrose_2008,
	title = {The sucrose regulated transcription factor {bZIP11} affects amino acid metabolism by regulating the expression of {ASPARAGINE} {SYNTHETASE1} and {PROLINE} {DEHYDROGENASE2}},
	volume = {53},
	copyright = {© 2008 The Authors},
	issn = {1365-313X},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1365-313X.2007.03385.x},
	doi = {10/cqhtc6},
	abstract = {Translation of the transcription factor bZIP11 is repressed by sucrose in a process that involves a highly conserved peptide encoded by the 5′ leaders of bZIP11 and other plant basic region leucine zipper (bZip) genes. It is likely that a specific signaling pathway operating at physiological sucrose concentrations controls metabolism via a feedback mechanism. In this paper bZIP11 target processes are identified using transiently increased nuclear bZIP11 levels and genome-wide expression analysis. bZIP11 affects the expression of hundreds of genes with proposed functions in biochemical pathways and signal transduction. The expression levels of approximately 80\% of the genes tested are not affected by bZIP11 promoter-mediated overexpression of bZIP11. This suggests that {\textless}20\% of the identified genes appear to be physiologically relevant targets of bZIP11. ASPARAGINE SYNTHETASE1 and PROLINE DEHYDROGENASE2 are among the rapidly activated bZIP11 targets, whose induction is independent of protein translation. Transient expression experiments in Arabidopsis protoplasts show that the bZIP11-dependent activation of the ASPARAGINE SYNTHETASE1 gene is dependent on a G-box element present in the promoter. Increased bZIP11 expression leads to decreased proline and increased phenylalanine levels. A model is proposed in which sugar signals control amino acid levels via the bZIP11 transcription factor.},
	language = {en},
	number = {6},
	urldate = {2021-06-10},
	journal = {The Plant Journal},
	author = {Hanson, Johannes and Hanssen, Micha and Wiese, Anika and Hendriks, Margriet M. W. B. and Smeekens, Sjef},
	year = {2008},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1365-313X.2007.03385.x},
	keywords = {ATB2, nitrogen metabolism, sucrose, sugar signaling, target gene},
	pages = {935--949},
}

Translation of the transcription factor bZIP11 is repressed by sucrose in a process that involves a highly conserved peptide encoded by the 5′ leaders of bZIP11 and other plant basic region leucine zipper (bZip) genes. It is likely that a specific signaling pathway operating at physiological sucrose concentrations controls metabolism via a feedback mechanism. In this paper bZIP11 target processes are identified using transiently increased nuclear bZIP11 levels and genome-wide expression analysis. bZIP11 affects the expression of hundreds of genes with proposed functions in biochemical pathways and signal transduction. The expression levels of approximately 80% of the genes tested are not affected by bZIP11 promoter-mediated overexpression of bZIP11. This suggests that \textless20% of the identified genes appear to be physiologically relevant targets of bZIP11. ASPARAGINE SYNTHETASE1 and PROLINE DEHYDROGENASE2 are among the rapidly activated bZIP11 targets, whose induction is independent of protein translation. Transient expression experiments in Arabidopsis protoplasts show that the bZIP11-dependent activation of the ASPARAGINE SYNTHETASE1 gene is dependent on a G-box element present in the promoter. Increased bZIP11 expression leads to decreased proline and increased phenylalanine levels. A model is proposed in which sugar signals control amino acid levels via the bZIP11 transcription factor.

@article{johannesson_arabidopsis_2003,
	title = {The {Arabidopsis} thaliana homeobox gene {ATHB5} is a potential regulator of abscisic acid responsiveness in developing seedlings},
	volume = {51},
	issn = {0167-4412},
	doi = {10.1023/a:1022567625228},
	abstract = {ATHB5 is a member of the homeodomain-leucine zipper (HDZip) transcription factor gene family of Arabidopsis thaliana. In this report we show that increased expression levels of ATHB5 in transgenic Arabidopsis plants cause an enhanced sensitivity to the inhibitory effect of abscisic acid (ABA) on seed germination and seedling growth. Consistent with this finding we demonstrate in northern blot experiments that the ABA-responsive gene RAB18 is hyperinduced by ABA in transgenic overexpressor lines as compared to the wild type. Northern blot and promoter-GUS fusion analyses show that ATHB5 gene transcription is initiated rapidly after the onset of germination and localized primarily to the hypocotyl of germinating seedlings. Moreover, analysis of ATHB5 gene expression during post-germinative growth in different ABA response mutants shows that ATHB5 gene activity is down-regulated in the abil-1, abi3-1 and abi5-1 mutant lines, but not in abi2-1 or abi4-1. The identification of a T-DNA insertion mutant line of ATHB5 is described and no phenotypic alterations could be discerned, suggesting that ATHB5 may act redundantly with other HDZip genes. Taken together, these data suggest that ATHB5 is a positive regulator of ABA-responsiveness, mediating the inhibitory effect of ABA on growth during seedling establishment.},
	language = {eng},
	number = {5},
	journal = {Plant Molecular Biology},
	author = {Johannesson, Henrik and Wang, Yan and Hanson, Johannes and Engström, Peter},
	month = mar,
	year = {2003},
	keywords = {Abscisic Acid, Arabidopsis, Arabidopsis Proteins, Blotting, Northern, Gene Expression Regulation, Developmental, Gene Expression Regulation, Plant, Germination, Glucuronidase, Homeodomain Proteins, Plants, Genetically Modified, Recombinant Fusion Proteins, Seeds, Signal Transduction, Transcription Factors},
	pages = {719--729},
}

ATHB5 is a member of the homeodomain-leucine zipper (HDZip) transcription factor gene family of Arabidopsis thaliana. In this report we show that increased expression levels of ATHB5 in transgenic Arabidopsis plants cause an enhanced sensitivity to the inhibitory effect of abscisic acid (ABA) on seed germination and seedling growth. Consistent with this finding we demonstrate in northern blot experiments that the ABA-responsive gene RAB18 is hyperinduced by ABA in transgenic overexpressor lines as compared to the wild type. Northern blot and promoter-GUS fusion analyses show that ATHB5 gene transcription is initiated rapidly after the onset of germination and localized primarily to the hypocotyl of germinating seedlings. Moreover, analysis of ATHB5 gene expression during post-germinative growth in different ABA response mutants shows that ATHB5 gene activity is down-regulated in the abil-1, abi3-1 and abi5-1 mutant lines, but not in abi2-1 or abi4-1. The identification of a T-DNA insertion mutant line of ATHB5 is described and no phenotypic alterations could be discerned, suggesting that ATHB5 may act redundantly with other HDZip genes. Taken together, these data suggest that ATHB5 is a positive regulator of ABA-responsiveness, mediating the inhibitory effect of ABA on growth during seedling establishment.

@article{hanson_expression_2002,
	title = {The expression pattern of the homeobox gene {ATHB13} reveals a conservation of transcriptional regulatory mechanisms between {Arabidopsis} and hybrid aspen},
	volume = {21},
	issn = {1432-203X},
	url = {https://doi.org/10.1007/s00299-002-0476-6},
	doi = {10/cvzt76},
	abstract = {ATHB13 belongs to a family of homeodomain leucine zipper (HDZip) transcription factors in Arabidopsis thaliana. To understand the temporal and spatial distribution of ATHB13 gene expression, we examined the ATHB13 promoter activity by means of fusions to the uidA (GUS, β-glucuronidase) reporter gene in transgenic plants. The strongest promoter activity was detected in the vasculature of the basal portion of petioles for both rosette leaves and cotyledons and at the base of cauline leaves. Activity was also detected in the stem at the base of the cauline leaf in an area corresponding to the leaf gap in the vasculature. In flowers, promoter activity was also present in the receptacle and in the stigma. Transformation of the same promoter-GUS construct into hybrid aspen (Populus tremula × P. tremuloides) resulted in an analogous expression pattern in the petioles of leaves. The similarity of these expression patterns indicates that the trans-acting factors responsible for ATHB13 expression are conserved between aspen and Arabidopsis. The conserved expression pattern of the highly specific Arabidopsis ATHB13 promoter in hybrid aspen demonstrates the potential utility of Arabidopsis promoters for tissue-specific expression in angiosperm trees.},
	language = {en},
	number = {1},
	urldate = {2021-08-26},
	journal = {Plant Cell Reports},
	author = {Hanson, J. and Regan, S. and Engström, P.},
	month = jul,
	year = {2002},
	pages = {81--89},
}

ATHB13 belongs to a family of homeodomain leucine zipper (HDZip) transcription factors in Arabidopsis thaliana. To understand the temporal and spatial distribution of ATHB13 gene expression, we examined the ATHB13 promoter activity by means of fusions to the uidA (GUS, β-glucuronidase) reporter gene in transgenic plants. The strongest promoter activity was detected in the vasculature of the basal portion of petioles for both rosette leaves and cotyledons and at the base of cauline leaves. Activity was also detected in the stem at the base of the cauline leaf in an area corresponding to the leaf gap in the vasculature. In flowers, promoter activity was also present in the receptacle and in the stigma. Transformation of the same promoter-GUS construct into hybrid aspen (Populus tremula × P. tremuloides) resulted in an analogous expression pattern in the petioles of leaves. The similarity of these expression patterns indicates that the trans-acting factors responsible for ATHB13 expression are conserved between aspen and Arabidopsis. The conserved expression pattern of the highly specific Arabidopsis ATHB13 promoter in hybrid aspen demonstrates the potential utility of Arabidopsis promoters for tissue-specific expression in angiosperm trees.

@article{hanson_sugar-dependent_2001,
	title = {Sugar-dependent alterations in cotyledon and leaf development in transgenic plants expressing the {HDZhdip} gene {ATHB13}},
	volume = {45},
	issn = {1573-5028},
	url = {https://doi.org/10.1023/A:1006464907710},
	doi = {10.1023/A:1006464907710},
	abstract = {ATHB13 is a new member of the homeodomain leucine zipper (HDZip) transcription factor family of Arabidopsis thaliana. Constitutive high-level expression of the ATHB13 cDNA in transgenic plants results in altered development of cotyledons and leaves, specifically in plants grown on media containing metabolizable sugars. Cotyledons and leaves of sugar-grown transgenic plants are more narrow and the junction between the petiole and the leaf blade less distinct, as compared to the wild type. High-level expression of ATHB13 affects cotyledon shape by inhibiting lateral expansion of epidermal cells in sugar-treated seedlings. Experiments with non-metabolizable sugars indicate that the alteration in leaf shape in the ATHB13 transgenics is mediated by sucrose sensing. ATHB13 further affects a subset of the gene expression responses of the wild-type plant to sugars. The expression of genes encoding β-amylase and vegetative storage protein is induced to higher levels in response to sucrose in the transgenic plants as compared to the wild type. The expression of other sugar-regulated genes examined is unaffected by ATHB13. These data suggest that ATHB13 may be a component of the sucrose-signalling pathway, active close to the targets of the signal transduction.},
	language = {en},
	number = {3},
	urldate = {2021-11-02},
	journal = {Plant Molecular Biology},
	author = {Hanson, Johannes and Johannesson, Henrik and Engström, Peter},
	month = feb,
	year = {2001},
	pages = {247--262},
}

ATHB13 is a new member of the homeodomain leucine zipper (HDZip) transcription factor family of Arabidopsis thaliana. Constitutive high-level expression of the ATHB13 cDNA in transgenic plants results in altered development of cotyledons and leaves, specifically in plants grown on media containing metabolizable sugars. Cotyledons and leaves of sugar-grown transgenic plants are more narrow and the junction between the petiole and the leaf blade less distinct, as compared to the wild type. High-level expression of ATHB13 affects cotyledon shape by inhibiting lateral expansion of epidermal cells in sugar-treated seedlings. Experiments with non-metabolizable sugars indicate that the alteration in leaf shape in the ATHB13 transgenics is mediated by sucrose sensing. ATHB13 further affects a subset of the gene expression responses of the wild-type plant to sugars. The expression of genes encoding β-amylase and vegetative storage protein is induced to higher levels in response to sucrose in the transgenic plants as compared to the wild type. The expression of other sugar-regulated genes examined is unaffected by ATHB13. These data suggest that ATHB13 may be a component of the sucrose-signalling pathway, active close to the targets of the signal transduction.

@article{bellini_synthetic_2024,
	title = {A synthetic auxin for cloning mature trees},
	copyright = {2024 Springer Nature America, Inc.},
	issn = {1546-1696},
	url = {https://www.nature.com/articles/s41587-024-02132-3},
	doi = {10.1038/s41587-024-02132-3},
	abstract = {A synthetic auxin improves the growth of adventitious roots in various plant species.},
	language = {en},
	urldate = {2024-10-07},
	journal = {Nature Biotechnology},
	publisher = {Nature Publishing Group},
	author = {Bellini, Catherine},
	month = jan,
	year = {2024},
	keywords = {Auxin, Plant regeneration},
	pages = {1--2},
}

A synthetic auxin improves the growth of adventitious roots in various plant species.

@incollection{mishra_adventitious_2024,
	edition = {5},
	title = {Adventitious {Root} {Development} in {Dicotyledons}},
	isbn = {978-1-00-332494-2},
	abstract = {The plant's root system is comprised of primary, lateral, and adventitious roots (ARs). Lateral roots emerge exclusively from existing roots, whereas ARs originate from stem- or leaf-derived cells. The progression of adventitious root development is a natural part of a plant's growth, commonly observed in most monocotyledonous species where they establish the primary root system or in various dicotyledonous plants that reproduce vegetatively. Adventitious rooting holds particular significance in the propagation of economically valuable horticultural and woody species, enabling the cloning of plants and swift establishment of superior genotypes before integrating them into production or breeding schemes. The process of AR development is intricate and influenced by numerous intrinsic and environmental factors, encompassing phytohormones, light exposure, nutritional state, stress responses like injury, and genetic traits. This chapter provides an overview of the latest advancements in research concerning adventitious root formation, with a specific focus on the interplay of key hormones and their interactions, as well as the influence of light, a significant environmental factor.},
	booktitle = {Plant {Roots}},
	publisher = {CRC Press},
	author = {Mishra, Priyanka and Kidwai, Maria and Lakehal, Abdellah and Bellini, Catherine},
	year = {2024},
	note = {Num Pages: 13},
}

The plant's root system is comprised of primary, lateral, and adventitious roots (ARs). Lateral roots emerge exclusively from existing roots, whereas ARs originate from stem- or leaf-derived cells. The progression of adventitious root development is a natural part of a plant's growth, commonly observed in most monocotyledonous species where they establish the primary root system or in various dicotyledonous plants that reproduce vegetatively. Adventitious rooting holds particular significance in the propagation of economically valuable horticultural and woody species, enabling the cloning of plants and swift establishment of superior genotypes before integrating them into production or breeding schemes. The process of AR development is intricate and influenced by numerous intrinsic and environmental factors, encompassing phytohormones, light exposure, nutritional state, stress responses like injury, and genetic traits. This chapter provides an overview of the latest advancements in research concerning adventitious root formation, with a specific focus on the interplay of key hormones and their interactions, as well as the influence of light, a significant environmental factor.

@article{zeng_chemical_2023,
	title = {Chemical induction of hypocotyl rooting reveals extensive conservation of auxin signalling controlling lateral and adventitious root formation},
	volume = {240},
	copyright = {© 2023 The Authors. New Phytologist © 2023 New Phytologist Foundation},
	issn = {1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/nph.19292},
	doi = {10.1111/nph.19292},
	abstract = {Upon exposure to light, etiolated Arabidopsis seedlings form adventitious roots (AR) along the hypocotyl. While processes underlying lateral root formation are studied intensively, comparatively little is known about the molecular processes involved in the initiation of hypocotyl AR. AR and LR formation were studied using a small molecule named Hypocotyl Specific Adventitious Root INducer (HYSPARIN) that strongly induces AR but not LR formation. HYSPARIN does not trigger rapid DR5-reporter activation, DII-Venus degradation or Ca2+ signalling. Transcriptome analysis, auxin signalling reporter lines and mutants show that HYSPARIN AR induction involves nuclear TIR1/AFB and plasma membrane TMK auxin signalling, as well as multiple downstream LR development genes (SHY2/IAA3, PUCHI, MAKR4 and GATA23). Comparison of the AR and LR induction transcriptome identified SAURs, AGC kinases and OFP transcription factors as specifically upregulated by HYSPARIN. Members of the SAUR19 subfamily, OFP4 and AGC2 suppress HYS-induced AR formation. While SAUR19 and OFP subfamily members also mildly modulate LR formation, AGC2 regulates only AR induction. Analysis of HYSPARIN-induced AR formation uncovers an evolutionary conservation of auxin signalling controlling LR and AR induction in Arabidopsis seedlings and identifies SAUR19, OFP4 and AGC2 kinase as novel regulators of AR formation.},
	language = {en},
	number = {5},
	urldate = {2023-11-10},
	journal = {New Phytologist},
	author = {Zeng, Yinwei and Verstraeten, Inge and Trinh, Hoang Khai and Lardon, Robin and Schotte, Sebastien and Olatunji, Damilola and Heugebaert, Thomas and Stevens, Christian and Quareshy, Mussa and Napier, Richard and Nastasi, Sara Paola and Costa, Alex and De Rybel, Bert and Bellini, Catherine and Beeckman, Tom and Vanneste, Steffen and Geelen, Danny},
	month = oct,
	year = {2023},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/nph.19292},
	keywords = {adventitious root, auxin signalling, root branching, root development, synthetic auxin},
	pages = {1883--1899},
}

Upon exposure to light, etiolated Arabidopsis seedlings form adventitious roots (AR) along the hypocotyl. While processes underlying lateral root formation are studied intensively, comparatively little is known about the molecular processes involved in the initiation of hypocotyl AR. AR and LR formation were studied using a small molecule named Hypocotyl Specific Adventitious Root INducer (HYSPARIN) that strongly induces AR but not LR formation. HYSPARIN does not trigger rapid DR5-reporter activation, DII-Venus degradation or Ca2+ signalling. Transcriptome analysis, auxin signalling reporter lines and mutants show that HYSPARIN AR induction involves nuclear TIR1/AFB and plasma membrane TMK auxin signalling, as well as multiple downstream LR development genes (SHY2/IAA3, PUCHI, MAKR4 and GATA23). Comparison of the AR and LR induction transcriptome identified SAURs, AGC kinases and OFP transcription factors as specifically upregulated by HYSPARIN. Members of the SAUR19 subfamily, OFP4 and AGC2 suppress HYS-induced AR formation. While SAUR19 and OFP subfamily members also mildly modulate LR formation, AGC2 regulates only AR induction. Analysis of HYSPARIN-induced AR formation uncovers an evolutionary conservation of auxin signalling controlling LR and AR induction in Arabidopsis seedlings and identifies SAUR19, OFP4 and AGC2 kinase as novel regulators of AR formation.

@article{kidwai_species-specific_2023,
	title = {Species-specific transcriptional reprogramming during adventitious root initiation},
	volume = {28},
	issn = {1360-1385},
	url = {https://www.sciencedirect.com/science/article/pii/S1360138522003028},
	doi = {10.1016/j.tplants.2022.11.003},
	abstract = {Adventitious roots or shoot-borne roots transdifferentiate from cells close to vascular tissues after cell reprogramming, which is associated with increased transcriptional activity. Recently, Garg et al. provided a genome-wide landscape of transcriptional signatures during the early stages of adventitious root initiation in rice and showed that conserved transcription factors acquire species-specific function.},
	language = {en},
	number = {2},
	urldate = {2023-01-26},
	journal = {Trends in Plant Science},
	author = {Kidwai, Maria and Mishra, Priyanka and Bellini, Catherine},
	month = feb,
	year = {2023},
	keywords = {adventitious root, dicotyledons, epigenetic regulation, monocotyledons, transcription factors},
	pages = {128--130},
}

Adventitious roots or shoot-borne roots transdifferentiate from cells close to vascular tissues after cell reprogramming, which is associated with increased transcriptional activity. Recently, Garg et al. provided a genome-wide landscape of transcriptional signatures during the early stages of adventitious root initiation in rice and showed that conserved transcription factors acquire species-specific function.

@article{aubry_vacuolar_2022,
	title = {A vacuolar hexose transport is required for xylem development in the inflorescence stem},
	volume = {188},
	issn = {0032-0889},
	url = {https://doi.org/10.1093/plphys/kiab551},
	doi = {10.1093/plphys/kiab551},
	abstract = {In Angiosperms, the development of the vascular system is controlled by a complex network of transcription factors. However, how nutrient availability in the vascular cells affects their development remains to be addressed. At the cellular level, cytosolic sugar availability is regulated mainly by sugar exchanges at the tonoplast through active and/or facilitated transport. In Arabidopsis (Arabidopsis thaliana), among the genes encoding tonoplastic transporters, SUGAR WILL EVENTUALLY BE EXPORTED TRANSPORTER 16 (SWEET16) and SWEET17 expression has been previously detected in the vascular system. Here, using a reverse genetics approach, we propose that sugar exchanges at the tonoplast, regulated by SWEET16, are important for xylem cell division as revealed in particular by the decreased number of xylem cells in the swt16 mutant and the accumulation of SWEET16 at the procambium–xylem boundary. In addition, we demonstrate that transport of hexoses mediated by SWEET16 and/or SWEET17 is required to sustain the formation of the xylem secondary cell wall. This result is in line with a defect in the xylem cell wall composition as measured by Fourier-transformed infrared spectroscopy in the swt16swt17 double mutant and by upregulation of several genes involved in secondary cell wall synthesis. Our work therefore supports a model in which xylem development partially depends on the exchange of hexoses at the tonoplast of xylem-forming cells.},
	number = {2},
	urldate = {2022-03-31},
	journal = {Plant Physiology},
	author = {Aubry, Emilie and Hoffmann, Beate and Vilaine, Françoise and Gilard, Françoise and Klemens, Patrick A W and Guérard, Florence and Gakière, Bertrand and Neuhaus, H Ekkehard and Bellini, Catherine and Dinant, Sylvie and Le Hir, Rozenn},
	month = feb,
	year = {2022},
	pages = {1229--1247},
}

In Angiosperms, the development of the vascular system is controlled by a complex network of transcription factors. However, how nutrient availability in the vascular cells affects their development remains to be addressed. At the cellular level, cytosolic sugar availability is regulated mainly by sugar exchanges at the tonoplast through active and/or facilitated transport. In Arabidopsis (Arabidopsis thaliana), among the genes encoding tonoplastic transporters, SUGAR WILL EVENTUALLY BE EXPORTED TRANSPORTER 16 (SWEET16) and SWEET17 expression has been previously detected in the vascular system. Here, using a reverse genetics approach, we propose that sugar exchanges at the tonoplast, regulated by SWEET16, are important for xylem cell division as revealed in particular by the decreased number of xylem cells in the swt16 mutant and the accumulation of SWEET16 at the procambium–xylem boundary. In addition, we demonstrate that transport of hexoses mediated by SWEET16 and/or SWEET17 is required to sustain the formation of the xylem secondary cell wall. This result is in line with a defect in the xylem cell wall composition as measured by Fourier-transformed infrared spectroscopy in the swt16swt17 double mutant and by upregulation of several genes involved in secondary cell wall synthesis. Our work therefore supports a model in which xylem development partially depends on the exchange of hexoses at the tonoplast of xylem-forming cells.

@incollection{bellini_adventitious_2022,
	title = {Adventitious {Roots}},
	copyright = {Copyright © 2022 John Wiley \& Sons, Ltd.},
	isbn = {978-0-470-01590-2},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/9780470015902.a0029521},
	doi = {10.1002/9780470015902.a0029521},
	abstract = {The root system of a plant is composed of the primary, lateral and adventitious roots (ARs). Lateral roots always develop from roots, whereas ARs form from stem or leaf-derived cells. AR development (ARD) is part of the normal development of the plant and occurs naturally, like in most monocotyledonous for which they constitute the main root system or in many dicotyledonous species that propagate vegetatively. Adventitious rooting is an essential step for vegetative propagation of economically important horticultural and woody species as it allows clonal propagation and rapid fixation of superior genotypes prior to their introduction into production or breeding programmes. Development of ARs is a complex process that is affected by multiple endogenous and environmental factors, including phytohormones, light, nutritional status, associated stress responses, such as wounding, and genetic characteristics. Key Concepts ARs are a prerequisite for vegetative propagation of plants. ARs arise from any organ of the plant but the root. ARs originate from different cell types depending on the organ or the species. Adventitious rooting is a complex quantitative genetic trait. ARs are the main root system for monocots. ARs can be adaptative response to environmental changes. ARs can be induced by interaction with micro-organisms such as mycorrhizae or bacteria Auxin cross-talks with other hormones to control adventitious rooting.},
	language = {en},
	urldate = {2024-10-07},
	booktitle = {{eLS}},
	publisher = {John Wiley \& Sons, Ltd},
	author = {Bellini, Catherine},
	year = {2022},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/9780470015902.a0029521},
	keywords = {abiotic stress, adventitious root, biotic stress, in vitro culture, plant hormones, root development, vegetative propagation},
	pages = {1--9},
}

The root system of a plant is composed of the primary, lateral and adventitious roots (ARs). Lateral roots always develop from roots, whereas ARs form from stem or leaf-derived cells. AR development (ARD) is part of the normal development of the plant and occurs naturally, like in most monocotyledonous for which they constitute the main root system or in many dicotyledonous species that propagate vegetatively. Adventitious rooting is an essential step for vegetative propagation of economically important horticultural and woody species as it allows clonal propagation and rapid fixation of superior genotypes prior to their introduction into production or breeding programmes. Development of ARs is a complex process that is affected by multiple endogenous and environmental factors, including phytohormones, light, nutritional status, associated stress responses, such as wounding, and genetic characteristics. Key Concepts ARs are a prerequisite for vegetative propagation of plants. ARs arise from any organ of the plant but the root. ARs originate from different cell types depending on the organ or the species. Adventitious rooting is a complex quantitative genetic trait. ARs are the main root system for monocots. ARs can be adaptative response to environmental changes. ARs can be induced by interaction with micro-organisms such as mycorrhizae or bacteria Auxin cross-talks with other hormones to control adventitious rooting.

@article{cardoso_editorial_2022,
	title = {Editorial: {Advances} on the {Biological} {Mechanisms} {Involved} in {Adventitious} {Root} {Formation}: {From} {Signaling} to {Morphogenesis}},
	volume = {13},
	issn = {1664-462X},
	shorttitle = {Editorial},
	url = {https://www.frontiersin.org/article/10.3389/fpls.2022.867651},
	doi = {10.3389/fpls.2022.867651},
	urldate = {2022-03-25},
	journal = {Frontiers in Plant Science},
	author = {Cardoso, Hélia and Peixe, Augusto and Bellini, Catherine and Porfírio, Sara and Druege, Uwe},
	year = {2022},
}

@article{ranjan_molecular_2022,
	title = {Molecular basis of differential adventitious rooting competence in poplar genotypes},
	volume = {73},
	issn = {0022-0957},
	url = {https://doi.org/10.1093/jxb/erac126},
	doi = {10.1093/jxb/erac126},
	abstract = {Recalcitrant adventitious root (AR) development is a major hurdle in propagating commercially important woody plants. Although significant progress has been made to identify genes involved in subsequent steps of AR development, the molecular basis of differences in apparent recalcitrance to form AR between easy-to-root and difficult-to-root genotypes remains unknown. To address this, we generated cambium tissue-specific transcriptomic data from stem cuttings of hybrid aspen, T89 (difficult-to-root) and hybrid poplar OP42 (easy-to-root), and used transgenic approaches to verify the role of several transcription factors in the control of adventitious rooting. Increased peroxidase activity was positively correlated with better rooting. We found differentially expressed genes encoding reactive oxygen species scavenging proteins to be enriched in OP42 compared with T89. A greater number of differentially expressed transcription factors in cambium cells of OP42 compared with T89 was revealed by a more intense transcriptional reprograming in the former. PtMYC2, a potential negative regulator, was less expressed in OP42 compared with T89. Using transgenic approaches, we demonstrated that PttARF17.1 and PttMYC2.1 negatively regulate adventitious rooting. Our results provide insights into the molecular basis of genotypic differences in AR and implicate differential expression of the master regulator MYC2 as a critical player in this process.},
	number = {12},
	urldate = {2022-06-30},
	journal = {Journal of Experimental Botany},
	author = {Ranjan, Alok and Perrone, Irene and Alallaq, Sanaria and Singh, Rajesh and Rigal, Adeline and Brunoni, Federica and Chitarra, Walter and Guinet, Frederic and Kohler, Annegret and Martin, Francis and Street, Nathaniel R and Bhalerao, Rishikesh and Legué, Valérie and Bellini, Catherine},
	month = jun,
	year = {2022},
	pages = {4046--4064},
}

Recalcitrant adventitious root (AR) development is a major hurdle in propagating commercially important woody plants. Although significant progress has been made to identify genes involved in subsequent steps of AR development, the molecular basis of differences in apparent recalcitrance to form AR between easy-to-root and difficult-to-root genotypes remains unknown. To address this, we generated cambium tissue-specific transcriptomic data from stem cuttings of hybrid aspen, T89 (difficult-to-root) and hybrid poplar OP42 (easy-to-root), and used transgenic approaches to verify the role of several transcription factors in the control of adventitious rooting. Increased peroxidase activity was positively correlated with better rooting. We found differentially expressed genes encoding reactive oxygen species scavenging proteins to be enriched in OP42 compared with T89. A greater number of differentially expressed transcription factors in cambium cells of OP42 compared with T89 was revealed by a more intense transcriptional reprograming in the former. PtMYC2, a potential negative regulator, was less expressed in OP42 compared with T89. Using transgenic approaches, we demonstrated that PttARF17.1 and PttMYC2.1 negatively regulate adventitious rooting. Our results provide insights into the molecular basis of genotypic differences in AR and implicate differential expression of the master regulator MYC2 as a critical player in this process.

@article{chardon_natural_2022,
	title = {Natural variation in the long-distance transport of nutrients and photoassimilates in response to {N} availability},
	volume = {273},
	issn = {0176-1617},
	url = {https://www.sciencedirect.com/science/article/pii/S0176161722000931},
	doi = {10.1016/j.jplph.2022.153707},
	abstract = {Phloem and xylem tissues are necessary for the allocation of nutrients and photoassimilates. However, how the long-distance transport of carbon (C) and nitrogen (N) is coordinated with the central metabolism is largely unknown. To better understand how the genetic and environmental factors influence C and N transport, we analysed the metabolite profiles of phloem exudates and xylem saps of five Arabidopsis thaliana accessions grown in low or non-limiting N supply. We observed that xylem saps were composed of 46 or 56\% carbohydrates, 27 or 45\% amino acids, and 5 or 13\% organic acids in low or non-limiting N supply, respectively. In contrast, phloem exudates were composed of 76 or 86\% carbohydrates, 7 or 18\% amino acids, and 5 or 6\% organic acids. Variation in N supply impacted amino acid, organic acid and sugar contents. When comparing low N and non-limiting N, the most striking differences were variations of glutamine, aspartate, and succinate abundance in the xylem saps and citrate and fumarate abundance in phloem exudates. In addition, we observed a substantial variation of metabolite content between genotypes, particularly under high N. The content of several organic acids, such as malate, citrate, fumarate, and succinate was affected by the genotype alone or by the interaction between genotype and N supply. This study confirmed that the response of the transport of nutrients in the phloem and the xylem to N availability is associated with the regulation of the central metabolism and could be an adaptive trait.},
	language = {en},
	urldate = {2022-05-30},
	journal = {Journal of Plant Physiology},
	author = {Chardon, Fabien and De Marco, Federica and Marmagne, Anne and Le Hir, Rozenn and Vilaine, Françoise and Bellini, Catherine and Dinant, Sylvie},
	month = jun,
	year = {2022},
	keywords = {Allocation, Pipecolate, Raffinose, Succinate, Sucrose, Transport},
	pages = {153707},
}

Phloem and xylem tissues are necessary for the allocation of nutrients and photoassimilates. However, how the long-distance transport of carbon (C) and nitrogen (N) is coordinated with the central metabolism is largely unknown. To better understand how the genetic and environmental factors influence C and N transport, we analysed the metabolite profiles of phloem exudates and xylem saps of five Arabidopsis thaliana accessions grown in low or non-limiting N supply. We observed that xylem saps were composed of 46 or 56% carbohydrates, 27 or 45% amino acids, and 5 or 13% organic acids in low or non-limiting N supply, respectively. In contrast, phloem exudates were composed of 76 or 86% carbohydrates, 7 or 18% amino acids, and 5 or 6% organic acids. Variation in N supply impacted amino acid, organic acid and sugar contents. When comparing low N and non-limiting N, the most striking differences were variations of glutamine, aspartate, and succinate abundance in the xylem saps and citrate and fumarate abundance in phloem exudates. In addition, we observed a substantial variation of metabolite content between genotypes, particularly under high N. The content of several organic acids, such as malate, citrate, fumarate, and succinate was affected by the genotype alone or by the interaction between genotype and N supply. This study confirmed that the response of the transport of nutrients in the phloem and the xylem to N availability is associated with the regulation of the central metabolism and could be an adaptive trait.

@article{bannoud_adventitious_2021,
	title = {Adventitious {Rooting} in {Populus} {Species}: {Update} and {Perspectives}},
	volume = {12},
	issn = {1664-462X},
	shorttitle = {Adventitious {Rooting} in {Populus} {Species}},
	url = {https://www.frontiersin.org/articles/10.3389/fpls.2021.668837/full},
	doi = {10/gkhp7k},
	abstract = {Populus spp. are among the most economically important species worldwide. These trees are used not only for wood and fiber production, but also in the rehabilitation of degraded lands. Since they are clonally propagated, the ability of stem cuttings to form adventitious roots is a critical point for plant establishment and survival in the field, and consequently for the forest industry. Adventitious rooting in different Populus clones has been an agronomic trait targeted in breeding programs for many years, and many factors have been identified that affect this quantitative trait. A huge variation in the rooting capacity has been observed among the species in the Populus genus, and the responses to some of the factors affecting this trait have been shown to be genotype-dependent. This review analyses similarities and differences between results obtained from studies examining the role of internal and external factors affecting rooting of Populus species cuttings. Since rooting is the most important requirement for stand establishment in clonally propagated species, understanding the physiological and genetic mechanisms that promote this trait is essential for successful commercial deployment.},
	language = {English},
	urldate = {2021-06-17},
	journal = {Frontiers in Plant Science},
	author = {Bannoud, Florencia and Bellini, Catherine},
	year = {2021},
	keywords = {Adventitious rooting, Populus, Vegetative propagation, adventitious rooting, endogenous factors, environmental factors, vegetative propagation},
}

Populus spp. are among the most economically important species worldwide. These trees are used not only for wood and fiber production, but also in the rehabilitation of degraded lands. Since they are clonally propagated, the ability of stem cuttings to form adventitious roots is a critical point for plant establishment and survival in the field, and consequently for the forest industry. Adventitious rooting in different Populus clones has been an agronomic trait targeted in breeding programs for many years, and many factors have been identified that affect this quantitative trait. A huge variation in the rooting capacity has been observed among the species in the Populus genus, and the responses to some of the factors affecting this trait have been shown to be genotype-dependent. This review analyses similarities and differences between results obtained from studies examining the role of internal and external factors affecting rooting of Populus species cuttings. Since rooting is the most important requirement for stand establishment in clonally propagated species, understanding the physiological and genetic mechanisms that promote this trait is essential for successful commercial deployment.

@article{dob_jasmonate_2021,
	title = {Jasmonate inhibits adventitious root initiation through repression of {CKX1} and activation of {RAP2}.{6L} transcription factor in {Arabidopsis}},
	volume = {72},
	issn = {0022-0957},
	url = {https://doi.org/10.1093/jxb/erab358},
	doi = {10.1093/jxb/erab358},
	abstract = {Adventitious rooting is a de novo organogenesis process that enables plants to propagate clonally and cope with environmental stresses. Adventitious root initiation (ARI) is controlled by interconnected transcriptional and hormonal networks, but there is little knowledge of the genetic and molecular programs orchestrating these networks. Thus, we have applied genome-wide transcriptome profiling to elucidate the profound transcriptional reprogramming events preceding ARI. These reprogramming events are associated with the downregulation of cytokinin (CK) signaling and response genes, which could be triggers for ARI. Interestingly, we found that CK free-base (iP, tZ, cZ and DHZ) content declined during ARI, due to downregulation of de novo CK biosynthesis and upregulation of CK inactivation pathways. We also found that MYC2-dependent jasmonate (JA) signaling inhibits ARI by downregulating the expression of the CYTOKININ OXIDASE/DEHYDROGENASE1 (CKX1) gene. We also demonstrated that JA and CK synergistically activate expression of RELATED to APETALA2.6 LIKE (RAP2.6L) transcription factor, and constitutive expression of this transcription factor strongly inhibits ARI. Collectively, our findings reveal that previously unknown genetic interactions between JA and CK play key roles in ARI},
	number = {20},
	urldate = {2021-08-18},
	journal = {Journal of Experimental Botany},
	author = {Dob, Asma and Lakehal, Abdellah and Novak, Ondrej and Bellini, Catherine},
	month = jul,
	year = {2021},
	keywords = {Adventitious roots, Arabidopsis, Arabidopsis Proteins, CKX1, Cyclopentanes, Gene Expression Regulation, Plant, MYC2, Oxylipins, Plant Roots, RAP2.6L, Transcription Factors, cytokinins, jasmonate, light, vegetative propagation},
	pages = {7107--7118},
}

Adventitious rooting is a de novo organogenesis process that enables plants to propagate clonally and cope with environmental stresses. Adventitious root initiation (ARI) is controlled by interconnected transcriptional and hormonal networks, but there is little knowledge of the genetic and molecular programs orchestrating these networks. Thus, we have applied genome-wide transcriptome profiling to elucidate the profound transcriptional reprogramming events preceding ARI. These reprogramming events are associated with the downregulation of cytokinin (CK) signaling and response genes, which could be triggers for ARI. Interestingly, we found that CK free-base (iP, tZ, cZ and DHZ) content declined during ARI, due to downregulation of de novo CK biosynthesis and upregulation of CK inactivation pathways. We also found that MYC2-dependent jasmonate (JA) signaling inhibits ARI by downregulating the expression of the CYTOKININ OXIDASE/DEHYDROGENASE1 (CKX1) gene. We also demonstrated that JA and CK synergistically activate expression of RELATED to APETALA2.6 LIKE (RAP2.6L) transcription factor, and constitutive expression of this transcription factor strongly inhibits ARI. Collectively, our findings reveal that previously unknown genetic interactions between JA and CK play key roles in ARI

@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{lakehal_ethylene_2020,
	title = {{ETHYLENE} {RESPONSE} {FACTOR} 115 integrates jasmonate and cytokinin signaling machineries to repress adventitious rooting in {Arabidopsis}},
	volume = {228},
	copyright = {©2020 The Authors. New Phytologist ©2020 New Phytologist Trust},
	issn = {1469-8137},
	url = {https://nph.onlinelibrary.wiley.com/doi/abs/10.1111/nph.16794},
	doi = {10/ghhwk4},
	abstract = {Adventitious root initiation (ARI) is a de novo organogenesis program and a key adaptive trait in plants. Several hormones regulate ARI but the underlying genetic architecture that integrates the hormonal crosstalk governing this process remains largely elusive. In this study, we use genetics, genome editing, transcriptomics, hormone profiling and cell biological approaches to demonstrate a crucial role played by the APETALA2/ETHYLENE RESPONSE FACTOR 115 transcription factor. We demonstrate that ERF115 functions as a repressor of ARI by activating the cytokinin (CK) signaling machinery. We also demonstrate that ERF115 is transcriptionally activated by jasmonate (JA), an oxylipin-derived phytohormone, which represses ARI in NINJA-dependent and independent manners. Our data indicate that NINJA-dependent JA signaling in pericycle cells blocks early events of ARI. Altogether, our results reveal a previously unreported molecular network involving cooperative crosstalk between JA and CK machineries that represses ARI.},
	language = {en},
	number = {5},
	urldate = {2021-06-21},
	journal = {New Phytologist},
	author = {Lakehal, Abdellah and Dob, Asma and Rahneshan, Zahra and Novák, Ondřej and Escamez, Sacha and Alallaq, Sanaria and Strnad, Miroslav and Tuominen, Hannele and Bellini, Catherine},
	year = {2020},
	keywords = {AP2/ERF transcription factors, adventitious rooting, cytokinins, de novo organogenesis, jasmonate},
	pages = {1611--1626},
}

Adventitious root initiation (ARI) is a de novo organogenesis program and a key adaptive trait in plants. Several hormones regulate ARI but the underlying genetic architecture that integrates the hormonal crosstalk governing this process remains largely elusive. In this study, we use genetics, genome editing, transcriptomics, hormone profiling and cell biological approaches to demonstrate a crucial role played by the APETALA2/ETHYLENE RESPONSE FACTOR 115 transcription factor. We demonstrate that ERF115 functions as a repressor of ARI by activating the cytokinin (CK) signaling machinery. We also demonstrate that ERF115 is transcriptionally activated by jasmonate (JA), an oxylipin-derived phytohormone, which represses ARI in NINJA-dependent and independent manners. Our data indicate that NINJA-dependent JA signaling in pericycle cells blocks early events of ARI. Altogether, our results reveal a previously unreported molecular network involving cooperative crosstalk between JA and CK machineries that represses ARI.

@incollection{champion_multiple_2020,
	address = {New York, NY},
	title = {Multiple {Roles} of {Jasmonates} in {Shaping} {Rhizotaxis}: {Emerging} {Integrators}},
	volume = {2085},
	isbn = {978-1-07-160141-9 978-1-07-160142-6},
	shorttitle = {Multiple {Roles} of {Jasmonates} in {Shaping} {Rhizotaxis}},
	url = {http://link.springer.com/10.1007/978-1-0716-0142-6_1},
	language = {en},
	urldate = {2021-06-07},
	booktitle = {Jasmonate in {Plant} {Biology}},
	publisher = {Springer US},
	author = {Lakehal, Abdellah and Ranjan, Alok and Bellini, Catherine},
	editor = {Champion, Antony and Laplaze, Laurent},
	year = {2020},
	pages = {3--22},
}

@article{alallaq_red_2020,
	title = {Red {Light} {Controls} {Adventitious} {Root} {Regeneration} by {Modulating} {Hormone} {Homeostasis} in {Picea} abies {Seedlings}},
	volume = {11},
	issn = {1664-462X},
	url = {https://www.frontiersin.org/article/10.3389/fpls.2020.586140/full},
	doi = {10.3389/fpls.2020.586140},
	urldate = {2021-06-07},
	journal = {Frontiers in Plant Science},
	author = {Alallaq, Sanaria and Ranjan, Alok and Brunoni, Federica and Novák, Ondřej and Lakehal, Abdellah and Bellini, Catherine},
	month = sep,
	year = {2020},
	pages = {586140},
}

@article{lakehal_dao1-mediated_2019,
	title = {A {DAO1}-{Mediated} {Circuit} {Controls} {Auxin} and {Jasmonate} {Crosstalk} {Robustness} during {Adventitious} {Root} {Initiation} in {Arabidopsis}},
	volume = {20},
	issn = {1422-0067},
	url = {https://www.mdpi.com/1422-0067/20/18/4428},
	doi = {10/gjcs2h},
	abstract = {Adventitious rooting is a post-embryonic developmental program governed by a multitude of endogenous and environmental cues. Auxin, along with other phytohormones, integrates and translates these cues into precise molecular signatures to provide a coherent developmental output. Auxin signaling guides every step of adventitious root (AR) development from the early event of cell reprogramming and identity transitions until emergence. We have previously shown that auxin signaling controls the early events of AR initiation (ARI) by modulating the homeostasis of the negative regulator jasmonate (JA). Although considerable knowledge has been acquired about the role of auxin and JA in ARI, the genetic components acting downstream of JA signaling and the mechanistic basis controlling the interaction between these two hormones are not well understood. Here we provide evidence that COI1-dependent JA signaling controls the expression of DAO1 and its closely related paralog DAO2. In addition, we show that the dao1-1 loss of function mutant produces more ARs than the wild type, probably due to its deficiency in accumulating JA and its bioactive metabolite JA-Ile. Together, our data indicate that DAO1 controls a sensitive feedback circuit that stabilizes the auxin and JA crosstalk during ARI.},
	language = {en},
	number = {18},
	urldate = {2021-06-07},
	journal = {International Journal of Molecular Sciences},
	author = {Lakehal, Abdellah and Dob, Asma and Novák, Ondřej and Bellini, Catherine},
	month = sep,
	year = {2019},
	pages = {4428},
}

Adventitious rooting is a post-embryonic developmental program governed by a multitude of endogenous and environmental cues. Auxin, along with other phytohormones, integrates and translates these cues into precise molecular signatures to provide a coherent developmental output. Auxin signaling guides every step of adventitious root (AR) development from the early event of cell reprogramming and identity transitions until emergence. We have previously shown that auxin signaling controls the early events of AR initiation (ARI) by modulating the homeostasis of the negative regulator jasmonate (JA). Although considerable knowledge has been acquired about the role of auxin and JA in ARI, the genetic components acting downstream of JA signaling and the mechanistic basis controlling the interaction between these two hormones are not well understood. Here we provide evidence that COI1-dependent JA signaling controls the expression of DAO1 and its closely related paralog DAO2. In addition, we show that the dao1-1 loss of function mutant produces more ARs than the wild type, probably due to its deficiency in accumulating JA and its bioactive metabolite JA-Ile. Together, our data indicate that DAO1 controls a sensitive feedback circuit that stabilizes the auxin and JA crosstalk during ARI.

@article{lakehal_molecular_2019,
	title = {A {Molecular} {Framework} for the {Control} of {Adventitious} {Rooting} by {TIR1}/{AFB2}-{Aux}/{IAA}-{Dependent} {Auxin} {Signaling} in {Arabidopsis}},
	volume = {12},
	issn = {16742052},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S1674205219302904},
	doi = {10.1016/j.molp.2019.09.001},
	language = {en},
	number = {11},
	urldate = {2021-06-07},
	journal = {Molecular Plant},
	author = {Lakehal, Abdellah and Chaabouni, Salma and Cavel, Emilie and Le Hir, Rozenn and Ranjan, Alok and Raneshan, Zahra and Novák, Ondřej and Păcurar, Daniel I. and Perrone, Irene and Jobert, François and Gutierrez, Laurent and Bakó, Laszlo and Bellini, Catherine},
	month = nov,
	year = {2019},
	pages = {1499--1514},
}

@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{lakehal_control_2019,
	title = {Control of adventitious root formation: insights into synergistic and antagonistic hormonal interactions},
	volume = {165},
	issn = {00319317},
	shorttitle = {Control of adventitious root formation},
	url = {http://doi.wiley.com/10.1111/ppl.12823},
	doi = {10.1111/ppl.12823},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Physiologia Plantarum},
	author = {Lakehal, Abdellah and Bellini, Catherine},
	month = jan,
	year = {2019},
	pages = {90--100},
}

@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{aubry_lateral_2019,
	title = {Lateral {Transport} of {Organic} and {Inorganic} {Solutes}},
	volume = {8},
	issn = {2223-7747},
	url = {http://www.mdpi.com/2223-7747/8/1/20},
	doi = {10/gjdwmf},
	abstract = {Organic (e.g., sugars and amino acids) and inorganic (e.g., K+, Na+, PO42−, and SO42−) solutes are transported long-distance throughout plants. Lateral movement of these compounds between the xylem and the phloem, and vice versa, has also been reported in several plant species since the 1930s, and is believed to be important in the overall resource allocation. Studies of Arabidopsis thaliana have provided us with a better knowledge of the anatomical framework in which the lateral transport takes place, and have highlighted the role of specialized vascular and perivascular cells as an interface for solute exchanges. Important breakthroughs have also been made, mainly in Arabidopsis, in identifying some of the proteins involved in the cell-to-cell translocation of solutes, most notably a range of plasma membrane transporters that act in different cell types. Finally, in the future, state-of-art imaging techniques should help to better characterize the lateral transport of these compounds on a cellular level. This review brings the lateral transport of sugars and inorganic solutes back into focus and highlights its importance in terms of our overall understanding of plant resource allocation.},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Plants},
	author = {Aubry, Emilie and Dinant, Sylvie and Vilaine, Françoise and Bellini, Catherine and Le Hir, Rozenn},
	month = jan,
	year = {2019},
	pages = {20},
}

Organic (e.g., sugars and amino acids) and inorganic (e.g., K+, Na+, PO42−, and SO42−) solutes are transported long-distance throughout plants. Lateral movement of these compounds between the xylem and the phloem, and vice versa, has also been reported in several plant species since the 1930s, and is believed to be important in the overall resource allocation. Studies of Arabidopsis thaliana have provided us with a better knowledge of the anatomical framework in which the lateral transport takes place, and have highlighted the role of specialized vascular and perivascular cells as an interface for solute exchanges. Important breakthroughs have also been made, mainly in Arabidopsis, in identifying some of the proteins involved in the cell-to-cell translocation of solutes, most notably a range of plasma membrane transporters that act in different cell types. Finally, in the future, state-of-art imaging techniques should help to better characterize the lateral transport of these compounds on a cellular level. This review brings the lateral transport of sugars and inorganic solutes back into focus and highlights its importance in terms of our overall understanding of plant resource allocation.

@article{dinant_synchrotron_2019,
	title = {Synchrotron {FTIR} and {Raman} spectroscopy provide unique spectral fingerprints for {Arabidopsis} floral stem vascular tissues},
	volume = {70},
	issn = {0022-0957, 1460-2431},
	url = {https://academic.oup.com/jxb/article/70/3/871/5165365},
	doi = {10.1093/jxb/ery396},
	language = {en},
	number = {3},
	urldate = {2021-06-07},
	journal = {Journal of Experimental Botany},
	author = {Dinant, S and Wolff, N and De Marco, F and Vilaine, F and Gissot, L and Aubry, E and Sandt, C and Bellini, C. and Le Hir, R},
	month = feb,
	year = {2019},
	pages = {871--884},
}

@incollection{geiss_adventitious_2018,
	title = {Adventitious {Root} {Formation}: {New} {Insights} and {Perspectives}},
	copyright = {Copyright © 2010 by Blackwell Publishing Ltd},
	isbn = {978-1-119-31299-4},
	shorttitle = {Adventitious {Root} {Formation}},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/9781119312994.apr0400},
	doi = {10.1002/9781119312994.apr0400},
	abstract = {The root system of a plant consists of the primary, lateral and adventitious roots. Lateral roots always develop from roots whereas adventitious roots form from stem or leaf-derived cells. Adventitious rooting is an essential step in the vegetative propagation of economically important horticultural and woody species. It allows clonal propagation and rapid fixation of superior genotypes prior to their introduction into production or breeding programs. Problems associated with rooting of cuttings frequently result in significant economic losses. Development of adventitious roots is a complex process that is affected by multiple factors including phytohormones, light, nutritional status, associated stress responses such as wounding, and genetic characteristics. How endogenous and environmental factors interact to control adventitious root formation is still poorly understood, although significant progress has been made in the understanding of the molecular control of root and lateral root development. In this review, we will summarize the current knowledge on the physiological aspects of AR formation and highlight the recent progress made in the identification of putative molecular players involved in the control of adventitious rooting.},
	language = {en},
	urldate = {2024-10-07},
	booktitle = {Annual {Plant} {Reviews} online},
	publisher = {John Wiley \& Sons, Ltd},
	author = {Geiss, Gaia and Gutierrez, Laurent and Bellini, Catherine},
	year = {2018},
	note = {Section: 5
\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/9781119312994.apr0400},
	keywords = {adventitious roots, clonal propagation, light, molecular markers, phyto-hormones, quantitative trait},
	pages = {127--156},
}

The root system of a plant consists of the primary, lateral and adventitious roots. Lateral roots always develop from roots whereas adventitious roots form from stem or leaf-derived cells. Adventitious rooting is an essential step in the vegetative propagation of economically important horticultural and woody species. It allows clonal propagation and rapid fixation of superior genotypes prior to their introduction into production or breeding programs. Problems associated with rooting of cuttings frequently result in significant economic losses. Development of adventitious roots is a complex process that is affected by multiple factors including phytohormones, light, nutritional status, associated stress responses such as wounding, and genetic characteristics. How endogenous and environmental factors interact to control adventitious root formation is still poorly understood, although significant progress has been made in the understanding of the molecular control of root and lateral root development. In this review, we will summarize the current knowledge on the physiological aspects of AR formation and highlight the recent progress made in the identification of putative molecular players involved in the control of adventitious rooting.

@article{rahneshan_unravelling_2018,
	title = {Unravelling salt stress responses in two pistachio ({Pistacia} vera {L}.) genotypes},
	volume = {40},
	issn = {0137-5881, 1861-1664},
	url = {http://link.springer.com/10.1007/s11738-018-2745-1},
	doi = {10.1007/s11738-018-2745-1},
	language = {en},
	number = {9},
	urldate = {2021-06-07},
	journal = {Acta Physiologiae Plantarum},
	author = {Rahneshan, Zahra and Nasibi, Fatemeh and Lakehal, Abdellah and Bellini, Catherine},
	month = sep,
	year = {2018},
	pages = {172},
}

@article{le_hir_at_2017,
	title = {At \textit{{bHLH68}} transcription factor contributes to the regulation of {ABA} homeostasis and drought stress tolerance in \textit{{Arabidopsis} thaliana}},
	volume = {160},
	issn = {00319317},
	url = {http://doi.wiley.com/10.1111/ppl.12549},
	doi = {10.1111/ppl.12549},
	language = {en},
	number = {3},
	urldate = {2021-06-07},
	journal = {Physiologia Plantarum},
	author = {Le Hir, Rozenn and Castelain, Mathieu and Chakraborti, Dipankar and Moritz, Thomas and Dinant, Sylvie and Bellini, Catherine},
	month = jul,
	year = {2017},
	pages = {312--327},
}

@article{pacurar_arabidopsis_2017,
	title = {The {Arabidopsis} {Cop9} signalosome subunit 4 ({CSN4}) is involved in adventitious root formation},
	volume = {7},
	issn = {2045-2322},
	url = {http://www.nature.com/articles/s41598-017-00744-1},
	doi = {10.1038/s41598-017-00744-1},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Scientific Reports},
	author = {Pacurar, Daniel Ioan and Pacurar, Monica Lacramioara and Lakehal, Abdellah and Pacurar, Andrea Mariana and Ranjan, Alok and Bellini, Catherine},
	month = dec,
	year = {2017},
	pages = {628},
}

@article{le_hir_disruption_2015,
	title = {Disruption of the {Sugar} {Transporters} {AtSWEET11} and {AtSWEET12} {Affects} {Vascular} {Development} and {Freezing} {Tolerance} in {Arabidopsis}},
	volume = {8},
	issn = {1752-9867 (Electronic) 1674-2052 (Linking)},
	url = {https://www.ncbi.nlm.nih.gov/pubmed/26358680},
	doi = {10.1016/j.molp.2015.08.007},
	language = {en},
	number = {11},
	urldate = {2021-06-07},
	journal = {Mol Plant},
	author = {Le Hir, R. and Spinner, L. and Klemens, P. A. and Chakraborti, D. and de Marco, F. and Vilaine, F. and Wolff, N. and Lemoine, R. and Porcheron, B. and Gery, C. and Teoule, E. and Chabout, S. and Mouille, G. and Neuhaus, H. E. and Dinant, S. and Bellini, C.},
	month = nov,
	year = {2015},
	note = {Edition: 2015/09/12},
	keywords = {Adaptation, Physiological, Arabidopsis Proteins/genetics/*physiology, Arabidopsis/growth \& development/metabolism/*physiology, Carbohydrates, Cell Wall/metabolism, Freezing, Membrane Transport Proteins/genetics/*physiology, Phloem/metabolism, Xylem/metabolism},
	pages = {1687--90},
}

@article{pacurar_novel_2014,
	title = {A {Novel} {Viable} {Allele} of {Arabidopsis} {CULLIN1} {Identified} in a {Screen} for {Superroot2} {Suppressors} by {Next} {Generation} {Sequencing}-{Assisted} {Mapping}},
	volume = {9},
	issn = {1932-6203},
	url = {https://dx.plos.org/10.1371/journal.pone.0100846},
	doi = {10/f22p63},
	language = {en},
	number = {6},
	urldate = {2021-06-08},
	journal = {PLoS ONE},
	author = {Pacurar, Daniel I. and Pacurar, Monica L. and Pacurar, Andrea M. and Gutierrez, Laurent and Bellini, Catherine},
	editor = {Zwick, Michael Edward.},
	month = jun,
	year = {2014},
	pages = {e100846},
}

@incollection{bellini_adventitious_2014,
	title = {Adventitious {Roots}},
	copyright = {Copyright © 2014 John Wiley \& Sons, Ltd. All rights reserved.},
	isbn = {978-0-470-01590-2},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/9780470015902.a0002061.pub2},
	doi = {10.1002/9780470015902.a0002061.pub2},
	abstract = {The root system of a plant is composed of the primary, lateral and adventitious roots (ARs). Lateral roots always develop from roots, whereas ARs form from stem or leaf-derived cells. AR formation is part of the normal development of the plant and occurs naturally, like in most monocotyledonous for which they constitute the main root system or in many dicotyledonous species that propagate vegetatively. Adventitious rooting is an essential step for vegetative propagation of economically important horticultural and woody species as it allows clonal propagation and rapid fixation of superior genotypes prior to their introduction into production or breeding programmes. Development of ARs is a complex process that is affected by multiple endogenous and environmental factors, including phytohormones; light; nutritional status; associated stress responses, such as wounding; and genetic characteristics. Key Concepts: ARs are the main root system for monocots. ARs are an adaptative response to environmental changes. ARs are required for vegetative propagation of plants. ARs arise from any organ of the plant but the root. ARs originate from different cell types depending on the organ or the species. ARs can be induced by ECMs or Agrobacterium rhizogenes. ARdevelopment is controlled by environmental factors. Adventitious rooting is an age-dependant process. Auxin cross talks with other hormones to control adventitious rooting. Adventitious rooting is a complex quantitative genetic trait.},
	language = {en},
	urldate = {2024-10-07},
	booktitle = {{eLS}},
	publisher = {John Wiley \& Sons, Ltd},
	author = {Bellini, Catherine},
	year = {2014},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/9780470015902.a0002061.pub2},
	keywords = {abiotic factors, adventitious roots, biotic factors, plant hormones, vegetative propagation},
}

The root system of a plant is composed of the primary, lateral and adventitious roots (ARs). Lateral roots always develop from roots, whereas ARs form from stem or leaf-derived cells. AR formation is part of the normal development of the plant and occurs naturally, like in most monocotyledonous for which they constitute the main root system or in many dicotyledonous species that propagate vegetatively. Adventitious rooting is an essential step for vegetative propagation of economically important horticultural and woody species as it allows clonal propagation and rapid fixation of superior genotypes prior to their introduction into production or breeding programmes. Development of ARs is a complex process that is affected by multiple endogenous and environmental factors, including phytohormones; light; nutritional status; associated stress responses, such as wounding; and genetic characteristics. Key Concepts: ARs are the main root system for monocots. ARs are an adaptative response to environmental changes. ARs are required for vegetative propagation of plants. ARs arise from any organ of the plant but the root. ARs originate from different cell types depending on the organ or the species. ARs can be induced by ECMs or Agrobacterium rhizogenes. ARdevelopment is controlled by environmental factors. Adventitious rooting is an age-dependant process. Auxin cross talks with other hormones to control adventitious rooting. Adventitious rooting is a complex quantitative genetic trait.

@article{bellini_adventitious_2014,
	title = {Adventitious {Roots} and {Lateral} {Roots}: {Similarities} and {Differences}},
	volume = {65},
	issn = {1543-5008, 1545-2123},
	shorttitle = {Adventitious {Roots} and {Lateral} {Roots}},
	url = {http://www.annualreviews.org/doi/10.1146/annurev-arplant-050213-035645},
	doi = {10/f2z6rb},
	language = {en},
	number = {1},
	urldate = {2021-06-08},
	journal = {Annual Review of Plant Biology},
	author = {Bellini, Catherine and Pacurar, Daniel I. and Perrone, Irene},
	month = apr,
	year = {2014},
	pages = {639--666},
}

@article{pacurar_auxin_2014,
	title = {Auxin is a central player in the hormone cross-talks that control adventitious rooting},
	volume = {151},
	issn = {00319317},
	url = {http://doi.wiley.com/10.1111/ppl.12171},
	doi = {10/f2264z},
	language = {en},
	number = {1},
	urldate = {2021-06-08},
	journal = {Physiologia Plantarum},
	author = {Pacurar, Daniel Ioan and Perrone, Irene and Bellini, Catherine},
	month = may,
	year = {2014},
	pages = {83--96},
}

@article{mauriat_gibberellins_2014,
	title = {Gibberellins inhibit adventitious rooting in hybrid aspen and {Arabidopsis} by affecting auxin transport},
	volume = {78},
	issn = {09607412},
	url = {http://doi.wiley.com/10.1111/tpj.12478},
	doi = {10/f22tk3},
	language = {en},
	number = {3},
	urldate = {2021-06-08},
	journal = {The Plant Journal},
	author = {Mauriat, Mélanie and Petterle, Anna and Bellini, Catherine and Moritz, Thomas},
	month = may,
	year = {2014},
	pages = {372--384},
}

@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{le_hir_abcg9_2013,
	title = {{ABCG9}, {ABCG11} and {ABCG14} {ABC} transporters are required for vascular development in {Arabidopsis}},
	volume = {76},
	issn = {09607412},
	url = {http://doi.wiley.com/10.1111/tpj.12334},
	doi = {10/f22xd4},
	language = {en},
	number = {5},
	urldate = {2021-06-08},
	journal = {The Plant Journal},
	author = {Le Hir, Rozenn and Sorin, Clément and Chakraborti, Dipankar and Moritz, Thomas and Schaller, Hubert and Tellier, Frédérique and Robert, Stéphanie and Morin, Halima and Bakó, Laszlo and Bellini, Catherine},
	month = dec,
	year = {2013},
	pages = {811--824},
}

@article{chardon_leaf_2013,
	title = {Leaf {Fructose} {Content} {Is} {Controlled} by the {Vacuolar} {Transporter} {SWEET17} in {Arabidopsis}},
	volume = {23},
	issn = {09609822},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S096098221300287X},
	doi = {10/f24bg2},
	language = {en},
	number = {8},
	urldate = {2021-06-08},
	journal = {Current Biology},
	author = {Chardon, Fabien and Bedu, Magali and Calenge, Fanny and Klemens, Patrick A.W. and Spinner, Lara and Clement, Gilles and Chietera, Giorgiana and Léran, Sophie and Ferrand, Marina and Lacombe, Benoit and Loudet, Olivier and Dinant, Sylvie and Bellini, Catherine and Neuhaus, H. Ekkehard and Daniel-Vedele, Françoise and Krapp, Anne},
	month = apr,
	year = {2013},
	pages = {697--702},
}

@article{klemens_overexpression_2013,
	title = {Overexpression of the {Vacuolar} {Sugar} {Carrier} \textit{{AtSWEET16}} {Modifies} {Germination}, {Growth}, and {Stress} {Tolerance} in {Arabidopsis}},
	volume = {163},
	issn = {1532-2548},
	url = {https://academic.oup.com/plphys/article/163/3/1338/6112737},
	doi = {10/f23t2h},
	abstract = {Abstract
            Here, we report that SUGARS WILL EVENTUALLY BE EXPORTED TRANSPORTER (SWEET16) from Arabidopsis (Arabidopsis thaliana) is a vacuole-located carrier, transporting glucose (Glc), fructose (Fru), and sucrose (Suc) after heterologous expression in Xenopus laevis oocytes. The SWEET16 gene, similar to the homologs gene SWEET17, is mainly expressed in vascular parenchyma cells. Application of Glc, Fru, or Suc, as well as cold, osmotic stress, or low nitrogen, provoke the down-regulation of SWEET16 messenger RNA accumulation. SWEET16 overexpressors (35SPro:SWEET16) showed a number of peculiarities related to differences in sugar accumulation, such as less Glc, Fru, and Suc at the end of the night. Under cold stress, 35SPro:SWEET16 plants are unable to accumulate Fru, while under nitrogen starvation, both Glc and Fru, but not Suc, were less abundant. These changes of individual sugars indicate that the consequences of an increased SWEET16 activity are dependent upon the type of external stimulus. Remarkably, 35SPro:SWEET16 lines showed improved germination and increased freezing tolerance. The latter observation, in combination with the modified sugar levels, points to a superior function of Glc and Suc for frost tolerance. 35SPro:SWEET16 plants exhibited increased growth efficiency when cultivated on soil and showed improved nitrogen use efficiency when nitrate was sufficiently available, while under conditions of limiting nitrogen, wild-type biomasses were higher than those of 35SPro:SWEET16 plants. Our results identify SWEET16 as a vacuolar sugar facilitator, demonstrate the substantial impact of SWEET16 overexpression on various critical plant traits, and imply that SWEET16 activity must be tightly regulated to allow optimal Arabidopsis development under nonfavorable conditions.},
	language = {en},
	number = {3},
	urldate = {2021-06-08},
	journal = {Plant Physiology},
	author = {Klemens, Patrick A.W. and Patzke, Kathrin and Deitmer, Joachim and Spinner, Lara and Le Hir, Rozenn and Bellini, Catherine and Bedu, Magali and Chardon, Fabien and Krapp, Anne and Neuhaus, H. Ekkehard},
	month = oct,
	year = {2013},
	pages = {1338--1352},
}

Abstract Here, we report that SUGARS WILL EVENTUALLY BE EXPORTED TRANSPORTER (SWEET16) from Arabidopsis (Arabidopsis thaliana) is a vacuole-located carrier, transporting glucose (Glc), fructose (Fru), and sucrose (Suc) after heterologous expression in Xenopus laevis oocytes. The SWEET16 gene, similar to the homologs gene SWEET17, is mainly expressed in vascular parenchyma cells. Application of Glc, Fru, or Suc, as well as cold, osmotic stress, or low nitrogen, provoke the down-regulation of SWEET16 messenger RNA accumulation. SWEET16 overexpressors (35SPro:SWEET16) showed a number of peculiarities related to differences in sugar accumulation, such as less Glc, Fru, and Suc at the end of the night. Under cold stress, 35SPro:SWEET16 plants are unable to accumulate Fru, while under nitrogen starvation, both Glc and Fru, but not Suc, were less abundant. These changes of individual sugars indicate that the consequences of an increased SWEET16 activity are dependent upon the type of external stimulus. Remarkably, 35SPro:SWEET16 lines showed improved germination and increased freezing tolerance. The latter observation, in combination with the modified sugar levels, points to a superior function of Glc and Suc for frost tolerance. 35SPro:SWEET16 plants exhibited increased growth efficiency when cultivated on soil and showed improved nitrogen use efficiency when nitrate was sufficiently available, while under conditions of limiting nitrogen, wild-type biomasses were higher than those of 35SPro:SWEET16 plants. Our results identify SWEET16 as a vacuolar sugar facilitator, demonstrate the substantial impact of SWEET16 overexpression on various critical plant traits, and imply that SWEET16 activity must be tightly regulated to allow optimal Arabidopsis development under nonfavorable conditions.

@article{le_hir_plant-specific_2013,
	title = {The {Plant}-{Specific} {Dof} {Transcription} {Factors} {Family}: {New} {Players} {Involved} in {Vascular} {System} {Development} and {Functioning} in {Arabidopsis}},
	volume = {4},
	issn = {1664-462X},
	shorttitle = {The {Plant}-{Specific} {Dof} {Transcription} {Factors} {Family}},
	url = {http://journal.frontiersin.org/article/10.3389/fpls.2013.00164/abstract},
	doi = {10/f2ztrr},
	urldate = {2021-06-08},
	journal = {Frontiers in Plant Science},
	author = {Le Hir, Rozenn and Bellini, Catherine},
	year = {2013},
}

@article{pacurar_collection_2012,
	title = {A collection of {INDEL} markers for map-based cloning in seven {Arabidopsis} accessions},
	volume = {63},
	issn = {1460-2431, 0022-0957},
	url = {https://academic.oup.com/jxb/article-lookup/doi/10.1093/jxb/err422},
	doi = {10/fxrh28},
	language = {en},
	number = {7},
	urldate = {2021-06-08},
	journal = {Journal of Experimental Botany},
	author = {Păcurar, Daniel Ioan and Păcurar, Monica Lăcrămioara and Street, Nathaniel and Bussell, John Desmond and Pop, Tiberia Ioana and Gutierrez, Laurent and Bellini, Catherine},
	month = apr,
	year = {2012},
	pages = {2491--2501},
}

@article{gutierrez_auxin_2012,
	title = {Auxin {Controls} {Arabidopsis} {Adventitious} {Root} {Initiation} by {Regulating} {Jasmonic} {Acid} {Homeostasis}},
	volume = {24},
	issn = {1040-4651},
	url = {https://doi.org/10.1105/tpc.112.099119},
	doi = {10/f22j9d},
	abstract = {Vegetative shoot-based propagation of plants, including mass propagation of elite genotypes, is dependent on the development of shoot-borne roots, which are also called adventitious roots. Multiple endogenous and environmental factors control the complex process of adventitious rooting. In the past few years, we have shown that the auxin response factors ARF6 and ARF8, targets of the microRNA miR167, are positive regulators of adventitious rooting, whereas ARF17, a target of miR160, is a negative regulator. We showed that these genes have overlapping expression profiles during adventitious rooting and that they regulate each other's expression at the transcriptional and posttranscriptional levels by modulating the homeostasis of miR160 and miR167. We demonstrate here that this complex network of transcription factors regulates the expression of three auxin-inducible Gretchen Hagen3 (GH3) genes, GH3.3, GH3.5, and GH3.6, encoding acyl-acid-amido synthetases. We show that these three GH3 genes are required for fine-tuning adventitious root initiation in the Arabidopsis thaliana hypocotyl, and we demonstrate that they act by modulating jasmonic acid homeostasis. We propose a model in which adventitious rooting is an adaptive developmental response involving crosstalk between the auxin and jasmonate regulatory pathways.},
	number = {6},
	urldate = {2021-06-08},
	journal = {The Plant Cell},
	author = {Gutierrez, Laurent and Mongelard, Gaëlle and Floková, Kristýna and Păcurar, Daniel I. and Novák, Ondřej and Staswick, Paul and Kowalczyk, Mariusz and Păcurar, Monica and Demailly, Hervé and Geiss, Gaia and Bellini, Catherine},
	month = jun,
	year = {2012},
	pages = {2515--2527},
}

Vegetative shoot-based propagation of plants, including mass propagation of elite genotypes, is dependent on the development of shoot-borne roots, which are also called adventitious roots. Multiple endogenous and environmental factors control the complex process of adventitious rooting. In the past few years, we have shown that the auxin response factors ARF6 and ARF8, targets of the microRNA miR167, are positive regulators of adventitious rooting, whereas ARF17, a target of miR160, is a negative regulator. We showed that these genes have overlapping expression profiles during adventitious rooting and that they regulate each other's expression at the transcriptional and posttranscriptional levels by modulating the homeostasis of miR160 and miR167. We demonstrate here that this complex network of transcription factors regulates the expression of three auxin-inducible Gretchen Hagen3 (GH3) genes, GH3.3, GH3.5, and GH3.6, encoding acyl-acid-amido synthetases. We show that these three GH3 genes are required for fine-tuning adventitious root initiation in the Arabidopsis thaliana hypocotyl, and we demonstrate that they act by modulating jasmonic acid homeostasis. We propose a model in which adventitious rooting is an adaptive developmental response involving crosstalk between the auxin and jasmonate regulatory pathways.

@article{rigal_aintegumenta_2012,
	title = {The {AINTEGUMENTA} {LIKE1} homeotic transcription factor {PtAIL1} controls the formation of adventitious root primordia in poplar},
	volume = {160},
	issn = {1532-2548},
	doi = {10/f2ztb6},
	abstract = {Adventitious rooting is an essential but sometimes rate-limiting step in the clonal multiplication of elite tree germplasm, because the ability to form roots declines rapidly with age in mature adult plant tissues. In spite of the importance of adventitious rooting, the mechanism behind this developmental process remains poorly understood. We have described the transcriptional profiles that are associated with the developmental stages of adventitious root formation in the model tree poplar (Populus trichocarpa). Transcriptome analyses indicate a highly specific temporal induction of the AINTEGUMENTA LIKE1 (PtAIL1) transcription factor of the AP2 family during adventitious root formation. Transgenic poplar samples that overexpressed PtAIL1 were able to grow an increased number of adventitious roots, whereas RNA interference mediated the down-expression of PtAIL1 expression, which led to a delay in adventitious root formation. Microarray analysis showed that the expression of 15 genes, including the transcription factors AGAMOUS-Like6 and MYB36, was overexpressed in the stem tissues that generated root primordia in PtAIL1-overexpressing plants, whereas their expression was reduced in the RNA interference lines. These results demonstrate that PtAIL1 is a positive regulator of poplar rooting that acts early in the development of adventitious roots.},
	language = {eng},
	number = {4},
	journal = {Plant Physiology},
	author = {Rigal, Adeline and Yordanov, Yordan S. and Perrone, Irene and Karlberg, Anna and Tisserant, Emilie and Bellini, Catherine and Busov, Victor B. and Martin, Francis and Kohler, Annegret and Bhalerao, Rishikesh P. and Legué, Valérie},
	month = dec,
	year = {2012},
	keywords = {Gene Expression Regulation, Developmental, Gene Expression Regulation, Plant, Genes, Homeobox, Plant Proteins, Plant Roots, Plants, Genetically Modified, Populus, RNA Interference, RNA, Messenger, Transcription Factors, Transcriptome},
	pages = {1996--2006},
}

Adventitious rooting is an essential but sometimes rate-limiting step in the clonal multiplication of elite tree germplasm, because the ability to form roots declines rapidly with age in mature adult plant tissues. In spite of the importance of adventitious rooting, the mechanism behind this developmental process remains poorly understood. We have described the transcriptional profiles that are associated with the developmental stages of adventitious root formation in the model tree poplar (Populus trichocarpa). Transcriptome analyses indicate a highly specific temporal induction of the AINTEGUMENTA LIKE1 (PtAIL1) transcription factor of the AP2 family during adventitious root formation. Transgenic poplar samples that overexpressed PtAIL1 were able to grow an increased number of adventitious roots, whereas RNA interference mediated the down-expression of PtAIL1 expression, which led to a delay in adventitious root formation. Microarray analysis showed that the expression of 15 genes, including the transcription factors AGAMOUS-Like6 and MYB36, was overexpressed in the stem tissues that generated root primordia in PtAIL1-overexpressing plants, whereas their expression was reduced in the RNA interference lines. These results demonstrate that PtAIL1 is a positive regulator of poplar rooting that acts early in the development of adventitious roots.

@article{castelain_non-dna-binding_2012,
	title = {The non-{DNA}-binding {bHLH} transcription factor {PRE3}/{bHLH135}/{ATBS1}/{TMO7} is involved in the regulation of light signaling pathway in {Arabidopsis}},
	volume = {145},
	issn = {00319317},
	url = {http://doi.wiley.com/10.1111/j.1399-3054.2012.01600.x},
	doi = {10/f2z8jx},
	language = {en},
	number = {3},
	urldate = {2021-06-08},
	journal = {Physiologia Plantarum},
	author = {Castelain, Mathieu and Le Hir, Rozenn and Bellini, Catherine},
	month = jul,
	year = {2012},
	pages = {450--460},
}

@article{pacurar_agrobacterium_2011,
	title = {Agrobacterium tumefaciens: {From} crown gall tumors to genetic transformation},
	volume = {76},
	issn = {08855765},
	shorttitle = {Agrobacterium tumefaciens},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0885576511000580},
	doi = {10/drwscf},
	language = {en},
	number = {2},
	urldate = {2021-06-08},
	journal = {Physiological and Molecular Plant Pathology},
	author = {Păcurar, Daniel I. and Thordal-Christensen, Hans and Păcurar, Monica L. and Pamfil, Doru and Botez, Constantin and Bellini, Catherine},
	month = aug,
	year = {2011},
	pages = {76--81},
}

@article{pop_auxin_2011,
	title = {Auxin {Control} in the {Formation} of {Adventitious} {Roots}},
	volume = {39},
	doi = {10/gc8s37},
	abstract = {Adventitious rooting is a complex process and a key step in the vegetative propagation of economically important woody, horticultural and agricultural species, playing an important role in the successful production of elite clones. The formation of adventitious roots is a quantitative genetic trait regulated by both environmental and endogenous factors. Among phytohormones, auxin plays an essential role in regulating roots development and it has been shown to be intimately involved in the process of adventitious rooting. Great progress has been made in elucidating the auxin-induced genes and auxin signaling pathway, especially in auxin response Aux/IAA and Auxin Response Factor gene families. Although some important aspects of adventitious and lateral rooting signaling have been revealed, the intricate signaling network remains poorly understood. This review summarizes some of the current knowledge on the physiological aspects of adventitious root formation and highlights the recent progress made in the identification of putative molecular players involved in the control of adventitious rooting. Despite much has been discovered regarding the effects and regulation of auxins on plant growth since the Darwin experiments, there is much that remains unknown.},
	journal = {Notulae Botanicae Horti Agrobotanici Cluj-Napoca},
	author = {Pop, Tiberia and Pamfil, Doru and Bellini, Catherine},
	month = jun,
	year = {2011},
	pages = {307--316},
}

Adventitious rooting is a complex process and a key step in the vegetative propagation of economically important woody, horticultural and agricultural species, playing an important role in the successful production of elite clones. The formation of adventitious roots is a quantitative genetic trait regulated by both environmental and endogenous factors. Among phytohormones, auxin plays an essential role in regulating roots development and it has been shown to be intimately involved in the process of adventitious rooting. Great progress has been made in elucidating the auxin-induced genes and auxin signaling pathway, especially in auxin response Aux/IAA and Auxin Response Factor gene families. Although some important aspects of adventitious and lateral rooting signaling have been revealed, the intricate signaling network remains poorly understood. This review summarizes some of the current knowledge on the physiological aspects of adventitious root formation and highlights the recent progress made in the identification of putative molecular players involved in the control of adventitious rooting. Despite much has been discovered regarding the effects and regulation of auxins on plant growth since the Darwin experiments, there is much that remains unknown.

@article{keech_leaf_2010,
	title = {Leaf {Senescence} {Is} {Accompanied} by an {Early} {Disruption} of the {Microtubule} {Network} in {Arabidopsis}},
	volume = {154},
	issn = {1532-2548},
	url = {https://academic.oup.com/plphys/article/154/4/1710/6108651},
	doi = {10/cp2qs5},
	abstract = {Abstract
            The dynamic assembly and disassembly of microtubules (MTs) is essential for cell function. Although leaf senescence is a well-documented process, the role of the MT cytoskeleton during senescence in plants remains unknown. Here, we show that both natural leaf senescence and senescence of individually darkened Arabidopsis (Arabidopsis thaliana) leaves are accompanied by early degradation of the MT network in epidermis and mesophyll cells, whereas guard cells, which do not senesce, retain their MT network. Similarly, entirely darkened plants, which do not senesce, retain their MT network. While genes encoding the tubulin subunits and the bundling/stabilizing MT-associated proteins (MAPs) MAP65 and MAP70-1 were repressed in both natural senescence and dark-induced senescence, we found strong induction of the gene encoding the MT-destabilizing protein MAP18. However, induction of MAP18 gene expression was also observed in leaves from entirely darkened plants, showing that its expression is not sufficient to induce MT disassembly and is more likely to be part of a Ca2+-dependent signaling mechanism. Similarly, genes encoding the MT-severing protein katanin p60 and two of the four putative regulatory katanin p80s were repressed in the dark, but their expression did not correlate with degradation of the MT network during leaf senescence. Taken together, these results highlight the earliness of the degradation of the cortical MT array during leaf senescence and lead us to propose a model in which suppression of tubulin and MAP genes together with induction of MAP18 play key roles in MT disassembly during senescence.},
	language = {en},
	number = {4},
	urldate = {2021-06-08},
	journal = {Plant Physiology},
	author = {Keech, Olivier and Pesquet, Edouard and Gutierrez, Laurent and Ahad, Abdul and Bellini, Catherine and Smith, Steven M. and Gardeström, Per},
	month = dec,
	year = {2010},
	pages = {1710--1720},
}

Abstract The dynamic assembly and disassembly of microtubules (MTs) is essential for cell function. Although leaf senescence is a well-documented process, the role of the MT cytoskeleton during senescence in plants remains unknown. Here, we show that both natural leaf senescence and senescence of individually darkened Arabidopsis (Arabidopsis thaliana) leaves are accompanied by early degradation of the MT network in epidermis and mesophyll cells, whereas guard cells, which do not senesce, retain their MT network. Similarly, entirely darkened plants, which do not senesce, retain their MT network. While genes encoding the tubulin subunits and the bundling/stabilizing MT-associated proteins (MAPs) MAP65 and MAP70-1 were repressed in both natural senescence and dark-induced senescence, we found strong induction of the gene encoding the MT-destabilizing protein MAP18. However, induction of MAP18 gene expression was also observed in leaves from entirely darkened plants, showing that its expression is not sufficient to induce MT disassembly and is more likely to be part of a Ca2+-dependent signaling mechanism. Similarly, genes encoding the MT-severing protein katanin p60 and two of the four putative regulatory katanin p80s were repressed in the dark, but their expression did not correlate with degradation of the MT network during leaf senescence. Taken together, these results highlight the earliness of the degradation of the cortical MT array during leaf senescence and lead us to propose a model in which suppression of tubulin and MAP genes together with induction of MAP18 play key roles in MT disassembly during senescence.

@article{contesto_auxin-signaling_2010,
	title = {The auxin-signaling pathway is required for the lateral root response of {Arabidopsis} to the rhizobacterium {Phyllobacterium} brassicacearum},
	volume = {232},
	issn = {0032-0935, 1432-2048},
	url = {http://link.springer.com/10.1007/s00425-010-1264-0},
	doi = {10/c99m2s},
	language = {en},
	number = {6},
	urldate = {2021-06-08},
	journal = {Planta},
	author = {Contesto, Céline and Milesi, Sandrine and Mantelin, Sophie and Zancarini, Anouk and Desbrosses, Guilhem and Varoquaux, Fabrice and Bellini, Catherine and Kowalczyk, Mariusz and Touraine, Bruno},
	month = nov,
	year = {2010},
	pages = {1455--1470},
}

@article{guenin_normalization_2009,
	title = {Normalization of {qRT}-{PCR} data: the necessity of adopting a systematic, experimental conditions-specific, validation of references},
	volume = {60},
	issn = {0022-0957, 1460-2431},
	shorttitle = {Normalization of {qRT}-{PCR} data},
	url = {https://academic.oup.com/jxb/article-lookup/doi/10.1093/jxb/ern305},
	doi = {10/bf946c},
	language = {en},
	number = {2},
	urldate = {2021-06-08},
	journal = {Journal of Experimental Botany},
	author = {Guenin, S. and Mauriat, M. and Pelloux, J. and Van Wuytswinkel, O. and Bellini, C. and Gutierrez, L.},
	month = jan,
	year = {2009},
	pages = {487--493},
}

@article{gutierrez_phenotypic_2009,
	title = {Phenotypic {Plasticity} of {Adventitious} {Rooting} in \textit{{Arabidopsis}} {Is} {Controlled} by {Complex} {Regulation} of {AUXIN} {RESPONSE} {FACTOR} {Transcripts} and {MicroRNA} {Abundance}},
	volume = {21},
	issn = {1532-298X, 1040-4651},
	url = {https://academic.oup.com/plcell/article/21/10/3119/6096289},
	doi = {10/c7kpnr},
	abstract = {Abstract
            The development of shoot-borne roots, or adventitious roots, is indispensable for mass propagation of elite genotypes. It is a complex genetic trait with a high phenotypic plasticity due to multiple endogenous and environmental regulatory factors. We demonstrate here that a subtle balance of activator and repressor AUXIN RESPONSE FACTOR (ARF) transcripts controls adventitious root initiation. Moreover, microRNA activity appears to be required for fine-tuning of this process. Thus, ARF17, a target of miR160, is a negative regulator, and ARF6 and ARF8, targets of miR167, are positive regulators of adventitious rooting. The three ARFs display overlapping expression domains, interact genetically, and regulate each other's expression at both transcriptional and posttranscriptional levels by modulating miR160 and miR167 availability. This complex regulatory network includes an unexpected feedback regulation of microRNA homeostasis by direct and nondirect target transcription factors. These results provide evidence of microRNA control of phenotypic variability and are a significant step forward in understanding the molecular mechanisms regulating adventitious rooting.},
	language = {en},
	number = {10},
	urldate = {2021-06-08},
	journal = {The Plant Cell},
	author = {Gutierrez, Laurent and Bussell, John D. and Păcurar, Daniel I. and Schwambach, Josèli and Păcurar, Monica and Bellini, Catherine},
	month = dec,
	year = {2009},
	pages = {3119--3132},
}

Abstract The development of shoot-borne roots, or adventitious roots, is indispensable for mass propagation of elite genotypes. It is a complex genetic trait with a high phenotypic plasticity due to multiple endogenous and environmental regulatory factors. We demonstrate here that a subtle balance of activator and repressor AUXIN RESPONSE FACTOR (ARF) transcripts controls adventitious root initiation. Moreover, microRNA activity appears to be required for fine-tuning of this process. Thus, ARF17, a target of miR160, is a negative regulator, and ARF6 and ARF8, targets of miR167, are positive regulators of adventitious rooting. The three ARFs display overlapping expression domains, interact genetically, and regulate each other's expression at both transcriptional and posttranscriptional levels by modulating miR160 and miR167 availability. This complex regulatory network includes an unexpected feedback regulation of microRNA homeostasis by direct and nondirect target transcription factors. These results provide evidence of microRNA control of phenotypic variability and are a significant step forward in understanding the molecular mechanisms regulating adventitious rooting.

@article{le_hir_gene_2008,
	title = {Gene expression profiling: keys for investigating phloem functions},
	volume = {13},
	issn = {13601385},
	shorttitle = {Gene expression profiling},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S1360138508001301},
	doi = {10/b4c2q3},
	language = {en},
	number = {6},
	urldate = {2021-06-10},
	journal = {Trends in Plant Science},
	author = {Le Hir, Rozenn and Beneteau, Julie and Bellini, Catherine and Vilaine, Françoise and Dinant, Sylvie},
	month = jun,
	year = {2008},
	pages = {273--280},
}

@article{gutierrez_lack_2008,
	title = {The lack of a systematic validation of reference genes: a serious pitfall undervalued in reverse transcription-polymerase chain reaction ({RT}-{PCR}) analysis in plants},
	volume = {6},
	issn = {14677644, 14677652},
	shorttitle = {The lack of a systematic validation of reference genes},
	url = {http://doi.wiley.com/10.1111/j.1467-7652.2008.00346.x},
	doi = {10/d6bcb9},
	language = {en},
	number = {6},
	urldate = {2021-06-10},
	journal = {Plant Biotechnology Journal},
	author = {Gutierrez, Laurent and Mauriat, Mlanie and Gunin, Stphanie and Pelloux, Jrme and Lefebvre, Jean-Franois and Louvet, Romain and Rusterucci, Christine and Moritz, Thomas and Guerineau, Franois and Bellini, Catherine and Van Wuytswinkel, Olivier},
	month = aug,
	year = {2008},
	pages = {609--618},
}

@article{gutierrez_towards_2008,
	title = {Towards a {Systematic} {Validation} of {References} in {Real}-{Time} {RT}-{PCR}},
	volume = {20},
	issn = {1040-4651, 1532-298X},
	url = {https://academic.oup.com/plcell/article/20/7/1734-1735/6092386},
	doi = {10/drh6vn},
	language = {en},
	number = {7},
	urldate = {2021-06-10},
	journal = {The Plant Cell},
	author = {Gutierrez, Laurent and Mauriat, Mélanie and Pelloux, Jérôme and Bellini, Catherine and Van Wuytswinkel, Olivier},
	month = jul,
	year = {2008},
	pages = {1734--1735},
}

@article{gutierrez_combined_2007,
	title = {Combined networks regulating seed maturation},
	volume = {12},
	issn = {13601385},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S1360138507001343},
	doi = {10/d2p7pf},
	language = {en},
	number = {7},
	urldate = {2021-06-10},
	journal = {Trends in Plant Science},
	author = {Gutierrez, Laurent and Van Wuytswinkel, Olivier and Castelain, Mathieu and Bellini, Catherine},
	month = jul,
	year = {2007},
	pages = {294--300},
}

@article{svennerstam_comprehensive_2007,
	title = {Comprehensive {Screening} of {Arabidopsis} {Mutants} {Suggests} the {Lysine} {Histidine} {Transporter} 1 to {Be} {Involved} in {Plant} {Uptake} of {Amino} {Acids}},
	volume = {143},
	issn = {1532-2548},
	url = {https://academic.oup.com/plphys/article/143/4/1853/6106923},
	doi = {10/cgtd2h},
	abstract = {Abstract
            Plant nitrogen (N) uptake is a key process in the global N cycle and is usually considered a “bottleneck” for biomass production in land ecosystems. Earlier, mineral N was considered the only form available to plants. Recent studies have questioned this dogma and shown that plants may access organic N sources such as amino acids. The actual mechanism enabling plants to access amino acid N is still unknown. However, a recent study suggested the Lysine Histidine Transporter 1 (LHT1) to be involved in root amino acid uptake. In this study, we isolated mutants defective in root amino acid uptake by screening Arabidopsis (Arabidopsis thaliana) seeds from ethyl methanesulfonate-treated plants and seeds from amino acid transporter T-DNA knockout mutants for resistance against the toxic d-enantiomer of alanine (Ala). Both ethyl methanesulfonate and T-DNA knockout plants identified as d-Ala resistant were found to be mutated in the LHT1 gene. LHT1 mutants displayed impaired capacity for uptake of a range of amino acids from solutions, displayed impaired growth when N was supplied in organic forms, and acquired substantially lower amounts of amino acids than wild-type plants from solid growth media. LHT1 mutants grown on mineral N did not display a phenotype until at the stage of flowering, when premature senescence of old leaf pairs occurred, suggesting that LHT1 may fulfill an important function at this developmental stage. Based on the broad and unbiased screening of mutants resistant to d-Ala, we suggest that LHT1 is an important mediator of root uptake of amino acids. This provides a molecular background for plant acquisition of organic N from the soil.},
	language = {en},
	number = {4},
	urldate = {2021-06-10},
	journal = {Plant Physiology},
	author = {Svennerstam, Henrik and Ganeteg, Ulrika and Bellini, Catherine and Näsholm, Torgny},
	month = apr,
	year = {2007},
	pages = {1853--1860},
}

Abstract Plant nitrogen (N) uptake is a key process in the global N cycle and is usually considered a “bottleneck” for biomass production in land ecosystems. Earlier, mineral N was considered the only form available to plants. Recent studies have questioned this dogma and shown that plants may access organic N sources such as amino acids. The actual mechanism enabling plants to access amino acid N is still unknown. However, a recent study suggested the Lysine Histidine Transporter 1 (LHT1) to be involved in root amino acid uptake. In this study, we isolated mutants defective in root amino acid uptake by screening Arabidopsis (Arabidopsis thaliana) seeds from ethyl methanesulfonate-treated plants and seeds from amino acid transporter T-DNA knockout mutants for resistance against the toxic d-enantiomer of alanine (Ala). Both ethyl methanesulfonate and T-DNA knockout plants identified as d-Ala resistant were found to be mutated in the LHT1 gene. LHT1 mutants displayed impaired capacity for uptake of a range of amino acids from solutions, displayed impaired growth when N was supplied in organic forms, and acquired substantially lower amounts of amino acids than wild-type plants from solid growth media. LHT1 mutants grown on mineral N did not display a phenotype until at the stage of flowering, when premature senescence of old leaf pairs occurred, suggesting that LHT1 may fulfill an important function at this developmental stage. Based on the broad and unbiased screening of mutants resistant to d-Ala, we suggest that LHT1 is an important mediator of root uptake of amino acids. This provides a molecular background for plant acquisition of organic N from the soil.

@article{sorin_proteomic_2006,
	title = {Proteomic analysis of different mutant genotypes of {Arabidopsis} led to the identification of 11 proteins correlating with adventitious root development},
	volume = {140},
	issn = {0032-0889},
	doi = {10/bqsw6z},
	abstract = {A lack of competence to form adventitious roots by cuttings or explants in vitro occurs routinely and is an obstacle for the clonal propagation and rapid fixation of elite genotypes. Adventitious rooting is known to be a quantitative genetic trait. We performed a proteomic analysis of Arabidopsis ( Arabidopsis thaliana) mutants affected in their ability to develop adventitious roots in order to identify associated molecular markers that could be used to select genotypes for their rooting ability and/or to get further insight into the molecular mechanisms controlling adventitious rooting. Comparison of two-dimensional gel electrophoresis protein profiles resulted in the identification of 11 proteins whose abundance could be either positively or negatively correlated with endogenous auxin content, the number of adventitious root primordia, and/or the number of mature adventitious roots. One protein was negatively correlated only to the number of root primordia and two were negatively correlated to the number of mature adventitious roots. Two putative chaperone proteins were positively correlated only to the number of primordia, and, interestingly, three auxin-inducible GH3-like proteins were positively correlated with the number of mature adventitious roots. The others were correlated with more than one parameter. The 11 proteins are predicted to be involved in different biological processes, including the regulation of auxin homeostasis and light-associated metabolic pathways. The results identify regulatory pathways associated with adventitious root formation and represent valuable markers that might be used for the future identification of genotypes with better rooting abilities.},
	language = {English},
	number = {1},
	journal = {Plant Physiology},
	publisher = {Amer Soc Plant Biologists},
	author = {Sorin, C. and Negroni, L. and Balliau, T. and Corti, H. and Jacquemot, M. P. and Davanture, M. and Sandberg, G. and Zivy, M. and Bellini, C.},
	month = jan,
	year = {2006},
	note = {Place: Rockville
WOS:000234492100031},
	keywords = {ago1, auxin, cuttings, cyp83b1, cytochrome-p450, expression, genetic-analysis, glucosinolate biosynthesis, light, locus},
	pages = {349--364},
}

A lack of competence to form adventitious roots by cuttings or explants in vitro occurs routinely and is an obstacle for the clonal propagation and rapid fixation of elite genotypes. Adventitious rooting is known to be a quantitative genetic trait. We performed a proteomic analysis of Arabidopsis ( Arabidopsis thaliana) mutants affected in their ability to develop adventitious roots in order to identify associated molecular markers that could be used to select genotypes for their rooting ability and/or to get further insight into the molecular mechanisms controlling adventitious rooting. Comparison of two-dimensional gel electrophoresis protein profiles resulted in the identification of 11 proteins whose abundance could be either positively or negatively correlated with endogenous auxin content, the number of adventitious root primordia, and/or the number of mature adventitious roots. One protein was negatively correlated only to the number of root primordia and two were negatively correlated to the number of mature adventitious roots. Two putative chaperone proteins were positively correlated only to the number of primordia, and, interestingly, three auxin-inducible GH3-like proteins were positively correlated with the number of mature adventitious roots. The others were correlated with more than one parameter. The 11 proteins are predicted to be involved in different biological processes, including the regulation of auxin homeostasis and light-associated metabolic pathways. The results identify regulatory pathways associated with adventitious root formation and represent valuable markers that might be used for the future identification of genotypes with better rooting abilities.

@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{bennett_integrative_2005,
	title = {Integrative biology: dissecting cross-talk between plant signalling pathways},
	volume = {123},
	issn = {0031-9317},
	shorttitle = {Integrative biology},
	doi = {10/bwb463},
	language = {English},
	number = {2},
	journal = {Physiologia Plantarum},
	publisher = {Wiley},
	author = {Bennett, M. and Bellini, C. and Van Der Straeten, D.},
	month = feb,
	year = {2005},
	note = {Place: Hoboken
WOS:000226966400001},
	keywords = {ethylene, gene, growth},
	pages = {109--110},
}

@article{baud_gurke_2004,
	title = {gurke and pasticcino3 mutants affected in embryo development are impaired in acetyl-{CoA} carboxylase},
	volume = {5},
	issn = {1469-221X},
	url = {https://www.embopress.org/doi/full/10.1038/sj.embor.7400124},
	doi = {10.1038/sj.embor.7400124},
	abstract = {Normal embryo development is required for correct seedling formation. The Arabidopsis gurke and pasticcino3 mutants were isolated from different developmental screens and the corresponding embryos exhibit severe defects in their apical region, affecting bilateral symmetry. We have recently identified lethal acc1 mutants affected in acetyl-CoA carboxylase 1 (ACCase 1) that display a similar embryo phenotype. A series of crosses showed that gk and pas3 are allelic to acc1 mutants, and direct sequencing of the ACC1 gene revealed point mutations in these new alleles. The isolation of leaky acc1 alleles demonstrated that ACCase 1 is essential for correct plant development and that mutations in ACCase affect cellular division in plants, as is the case in yeast. Interestingly, significant metabolic complementation of the mutant phenotype was obtained by exogenous supply of malonate, suggesting that the lack of cytosolic malonyl-CoA is likely to be the initial factor leading to abnormal development in the acc1 mutants.},
	number = {5},
	urldate = {2021-06-30},
	journal = {EMBO reports},
	publisher = {John Wiley \& Sons, Ltd},
	author = {Baud, Sébastien and Bellec, Yannick and Miquel, Martine and Bellini, Catherine and Caboche, Michel and Lepiniec, Loïc and Faure, Jean-Denis and Rochat, Christine},
	month = may,
	year = {2004},
	keywords = {cell division, embryo development, plant development, very-long-chain fatty acids},
	pages = {515--520},
}

Normal embryo development is required for correct seedling formation. The Arabidopsis gurke and pasticcino3 mutants were isolated from different developmental screens and the corresponding embryos exhibit severe defects in their apical region, affecting bilateral symmetry. We have recently identified lethal acc1 mutants affected in acetyl-CoA carboxylase 1 (ACCase 1) that display a similar embryo phenotype. A series of crosses showed that gk and pas3 are allelic to acc1 mutants, and direct sequencing of the ACC1 gene revealed point mutations in these new alleles. The isolation of leaky acc1 alleles demonstrated that ACCase 1 is essential for correct plant development and that mutations in ACCase affect cellular division in plants, as is the case in yeast. Interestingly, significant metabolic complementation of the mutant phenotype was obtained by exogenous supply of malonate, suggesting that the lack of cytosolic malonyl-CoA is likely to be the initial factor leading to abnormal development in the acc1 mutants.

@article{schrick_interactions_2002,
	title = {Interactions between sterol biosynthesis genes in embryonic development of {Arabidopsis}},
	volume = {31},
	issn = {1365-313X},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1046/j.1365-313X.2002.01333.x},
	doi = {10/fv724z},
	abstract = {The sterol biosynthesis pathway of Arabidopsis produces a large set of structurally related phytosterols including sitosterol and campesterol, the latter being the precursor of the brassinosteroids (BRs). While BRs are implicated as phytohormones in post-embryonic growth, the functions of other types of steroid molecules are not clear. Characterization of the fackel (fk) mutants provided the first hint that sterols play a role in plant embryogenesis. FK encodes a sterol C-14 reductase that acts upstream of all known enzymatic steps corresponding to BR biosynthesis mutants. Here we report that genetic screens for fk-like seedling and embryonic phenotypes have identified two additional genes coding for sterol biosynthesis enzymes: CEPHALOPOD (CPH), a C-24 sterol methyl transferase, and HYDRA1 (HYD1), a sterol C-8,7 isomerase. We describe genetic interactions between cph, hyd1 and fk, and studies with 15-azasterol, an inhibitor of sterol C-14 reductase. Our experiments reveal that FK and HYD1 act sequentially, whereas CPH acts independently of these genes to produce essential sterols. Similar experiments indicate that the BR biosynthesis gene DWF1 acts independently of FK, whereas BR receptor gene BRI1 acts downstream of FK to promote post-embryonic growth. We found embryonic patterning defects in cph mutants and describe a GC–MS analysis of cph tissues which suggests that steroid molecules in addition to BRs play critical roles during plant embryogenesis. Taken together, our results imply that the sterol biosynthesis pathway is not a simple linear pathway but a complex network of enzymes that produce essential steroid molecules for plant growth and development.},
	language = {en},
	number = {1},
	urldate = {2021-10-19},
	journal = {The Plant Journal},
	author = {Schrick, Kathrin and Mayer, Ulrike and Martin, Gottfried and Bellini, Catherine and Kuhnt, Christine and Schmidt, Jürgen and Jürgens, Gerd},
	year = {2002},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1046/j.1365-313X.2002.01333.x},
	keywords = {15-azasterol, Arabidopsis, GC–MS, brassinosteroids., embryogenesis, sterols},
	pages = {61--73},
}

The sterol biosynthesis pathway of Arabidopsis produces a large set of structurally related phytosterols including sitosterol and campesterol, the latter being the precursor of the brassinosteroids (BRs). While BRs are implicated as phytohormones in post-embryonic growth, the functions of other types of steroid molecules are not clear. Characterization of the fackel (fk) mutants provided the first hint that sterols play a role in plant embryogenesis. FK encodes a sterol C-14 reductase that acts upstream of all known enzymatic steps corresponding to BR biosynthesis mutants. Here we report that genetic screens for fk-like seedling and embryonic phenotypes have identified two additional genes coding for sterol biosynthesis enzymes: CEPHALOPOD (CPH), a C-24 sterol methyl transferase, and HYDRA1 (HYD1), a sterol C-8,7 isomerase. We describe genetic interactions between cph, hyd1 and fk, and studies with 15-azasterol, an inhibitor of sterol C-14 reductase. Our experiments reveal that FK and HYD1 act sequentially, whereas CPH acts independently of these genes to produce essential sterols. Similar experiments indicate that the BR biosynthesis gene DWF1 acts independently of FK, whereas BR receptor gene BRI1 acts downstream of FK to promote post-embryonic growth. We found embryonic patterning defects in cph mutants and describe a GC–MS analysis of cph tissues which suggests that steroid molecules in addition to BRs play critical roles during plant embryogenesis. Taken together, our results imply that the sterol biosynthesis pathway is not a simple linear pathway but a complex network of enzymes that produce essential steroid molecules for plant growth and development.

@article{bellec_pasticcino2_2002,
	title = {Pasticcino2 is a protein tyrosine phosphatase-like involved in cell proliferation and differentiation in {Arabidopsis}},
	volume = {32},
	issn = {1365-313X},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1046/j.1365-313X.2002.01456.x},
	doi = {10/cgckd9},
	abstract = {The pasticcino2 (pas2) mutant shows impaired embryo and seedling development associated with cell de-differentiation and proliferation. This process is specifically enhanced in presence of cytokinins leading to callus-like structure of the apical part of the seedling. Cell proliferation concerns localized and stochastic nodules of dividing cells. In absence of cytokinins, cell proliferation leads to small calli on stems but, most often, cell proliferation is associated with post-genital organ fusion. The PAS2 gene was identified by positional cloning. PAS2 expression was found in every plant organ and was not regulated by PAS1 and PAS3 genes. PAS2 encodes the Arabidopsis member of the protein tyrosine phosphatase-like (Ptpl) family, a new PTP family originally described in mice and humans and characterized by a mutated PTP active site. This family of proteins has a yeast homolog that is essential for cell viability. The absence of yeast PAS2 homolog can be functionally replaced by the Arabidopsis PAS2 protein, demonstrating that PAS2 function is conserved between higher and lower eukaryotes.},
	language = {en},
	number = {5},
	urldate = {2021-10-19},
	journal = {The Plant Journal},
	author = {Bellec, Yannick and Harrar, Yaël and Butaeye, Christelle and Darnet, Sylvain and Bellini, Catherine and Faure, Jean-Denis},
	year = {2002},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1046/j.1365-313X.2002.01456.x},
	keywords = {Ptpl, YJL097w, cytokinins, protein tyrosine phosphatase, tumor},
	pages = {713--722},
}

The pasticcino2 (pas2) mutant shows impaired embryo and seedling development associated with cell de-differentiation and proliferation. This process is specifically enhanced in presence of cytokinins leading to callus-like structure of the apical part of the seedling. Cell proliferation concerns localized and stochastic nodules of dividing cells. In absence of cytokinins, cell proliferation leads to small calli on stems but, most often, cell proliferation is associated with post-genital organ fusion. The PAS2 gene was identified by positional cloning. PAS2 expression was found in every plant organ and was not regulated by PAS1 and PAS3 genes. PAS2 encodes the Arabidopsis member of the protein tyrosine phosphatase-like (Ptpl) family, a new PTP family originally described in mice and humans and characterized by a mutated PTP active site. This family of proteins has a yeast homolog that is essential for cell viability. The absence of yeast PAS2 homolog can be functionally replaced by the Arabidopsis PAS2 protein, demonstrating that PAS2 function is conserved between higher and lower eukaryotes.

@article{camilleri_arabidopsis_2002,
	title = {The {Arabidopsis} {TONNEAU2} {Gene} {Encodes} a {Putative} {Novel} {Protein} {Phosphatase} {2A} {Regulatory} {Subunit} {Essential} for the {Control} of the {Cortical} {Cytoskeleton}},
	volume = {14},
	issn = {1040-4651},
	url = {https://doi.org/10.1105/tpc.010402},
	doi = {10/d79s3z},
	abstract = {In Arabidopsis ton2 mutants, abnormalities of the cortical microtubular cytoskeleton, such as disorganization of the interphase microtubule array and lack of the preprophase band before mitosis, markedly affect cell shape and arrangement as well as overall plant morphology. We present the molecular isolation of the TON2 gene, which is highly conserved in higher plants and has a vertebrate homolog of unknown function. It encodes a protein similar in its C-terminal part to B″ regulatory subunits of type 2A protein phosphatases (PP2As). We show that the TON2 protein interacts with an Arabidopsis type A subunit of PP2A in the yeast two-hybrid system and thus likely defines a novel subclass of PP2A subunits that are possibly involved in the control of cytoskeletal structures in plants.},
	number = {4},
	urldate = {2021-10-19},
	journal = {The Plant Cell},
	author = {Camilleri, Christine and Azimzadeh, Juliette and Pastuglia, Martine and Bellini, Catherine and Grandjean, Olivier and Bouchez, David},
	month = apr,
	year = {2002},
	pages = {833--845},
}

In Arabidopsis ton2 mutants, abnormalities of the cortical microtubular cytoskeleton, such as disorganization of the interphase microtubule array and lack of the preprophase band before mitosis, markedly affect cell shape and arrangement as well as overall plant morphology. We present the molecular isolation of the TON2 gene, which is highly conserved in higher plants and has a vertebrate homolog of unknown function. It encodes a protein similar in its C-terminal part to B″ regulatory subunits of type 2A protein phosphatases (PP2As). We show that the TON2 protein interacts with an Arabidopsis type A subunit of PP2A in the yeast two-hybrid system and thus likely defines a novel subclass of PP2A subunits that are possibly involved in the control of cytoskeletal structures in plants.

@article{harrar_fkbps_2001,
	title = {{FKBPs}: at the crossroads of folding and transduction},
	volume = {6},
	issn = {1360-1385},
	shorttitle = {{FKBPs}},
	url = {https://www.sciencedirect.com/science/article/pii/S1360138501020441},
	doi = {10/c79bct},
	abstract = {FK506-binding proteins (FKBPs) belong to the large family of peptidyl–prolyl cis–trans isomerases, which are known to be involved in many cellular processes, such as cell signalling, protein trafficking and transcription. FKBPs associate into protein complexes, although the involvement and precise role of their foldase activity remain to be elucidated. FKBPs represent a large gene family in plants that is involved in growth and development. Disruption of genes encoding FKBPs in plants and animals has underlined the importance of this family of proteins in the regulation of cell division and differentiation.},
	language = {en},
	number = {9},
	urldate = {2021-11-02},
	journal = {Trends in Plant Science},
	author = {Harrar, Yaël and Bellini, Catherine and Faure, Jean-Denis},
	month = sep,
	year = {2001},
	keywords = {Heat shock protein, Ppiase, calcineurin, calcium channel, cell division and differentiation, immunophilin, pasticcino1, receptors, rotamase, salt stress, steroid and TGFβ},
	pages = {426--431},
}

FK506-binding proteins (FKBPs) belong to the large family of peptidyl–prolyl cis–trans isomerases, which are known to be involved in many cellular processes, such as cell signalling, protein trafficking and transcription. FKBPs associate into protein complexes, although the involvement and precise role of their foldase activity remain to be elucidated. FKBPs represent a large gene family in plants that is involved in growth and development. Disruption of genes encoding FKBPs in plants and animals has underlined the importance of this family of proteins in the regulation of cell division and differentiation.

@article{carol_pasticcino1_2001,
	title = {{PASTICCINO1} ({AtFKBP70}) is a nuclear-localised immunophilin required during {Arabidopsis} thaliana embryogenesis},
	volume = {161},
	issn = {0168-9452},
	url = {https://www.sciencedirect.com/science/article/pii/S016894520100437X},
	doi = {10/bwth5k},
	abstract = {The PASTICCINO1 (PAS1) gene of Arabidopsis thaliana encodes a protein with homology to the FK506-binding protein (FKBP) class of immunophilins. To begin to understand more about the possible function of PAS1, we tested some properties of recombinant PAS1 protein and analysed the expression of the gene in Arabidopsis embryos and cell cultures and in tobacco cells. In pas1-1/+ heterozygote embryos the pas1-1 allele is expressed at very low levels in all cells, but it is misexpressed in the pas1-1 homozygote mutant at the same stage. Anti-PAS1 affinity-purified antibodies recognise a 70 kDa protein from dividing cell cultures of Arabidopsis. In indirect immunofluorescence, the same antibodies label the nuclei of dividing tobacco BY-2 cells. In a protease-coupled assay, recombinant PAS1 protein has low peptidylprolyl cis–trans isomerase (PPIase) activity, which is inhibited by the immunosuppressive drugs FK506 and rapamycin, but not by cyclosporin. PAS1 also binds calmodulin in vitro. This data suggests the importance of the correctly regulated production of functional PAS1 protein, a likely nuclear-localised FKBP, for the correct development of the plant embryo.},
	language = {en},
	number = {3},
	urldate = {2021-11-02},
	journal = {Plant Science},
	author = {Carol, Rachel J. and Breiman, Adina and Erel, Noa and Vittorioso, Paola and Bellini, Catherine},
	month = aug,
	year = {2001},
	keywords = {Calmodulin, Embryogenesis, FKBP, Nucleus, PPIase},
	pages = {527--535},
}

The PASTICCINO1 (PAS1) gene of Arabidopsis thaliana encodes a protein with homology to the FK506-binding protein (FKBP) class of immunophilins. To begin to understand more about the possible function of PAS1, we tested some properties of recombinant PAS1 protein and analysed the expression of the gene in Arabidopsis embryos and cell cultures and in tobacco cells. In pas1-1/+ heterozygote embryos the pas1-1 allele is expressed at very low levels in all cells, but it is misexpressed in the pas1-1 homozygote mutant at the same stage. Anti-PAS1 affinity-purified antibodies recognise a 70 kDa protein from dividing cell cultures of Arabidopsis. In indirect immunofluorescence, the same antibodies label the nuclei of dividing tobacco BY-2 cells. In a protease-coupled assay, recombinant PAS1 protein has low peptidylprolyl cis–trans isomerase (PPIase) activity, which is inhibited by the immunosuppressive drugs FK506 and rapamycin, but not by cyclosporin. PAS1 also binds calmodulin in vitro. This data suggests the importance of the correctly regulated production of functional PAS1 protein, a likely nuclear-localised FKBP, for the correct development of the plant embryo.

@article{fagard_ago1_2000,
	chapter = {Biological Sciences},
	title = {{AGO1}, {QDE}-2, and {RDE}-1 are related proteins required for post-transcriptional gene silencing in plants, quelling in fungi, and {RNA} interference in animals},
	volume = {97},
	copyright = {Copyright © 2000, The National Academy of Sciences},
	issn = {0027-8424, 1091-6490},
	url = {https://www.pnas.org/content/97/21/11650},
	doi = {10/dbx439},
	abstract = {Introduction of transgene DNA may lead to specific degradation of RNAs that are homologous to the transgene transcribed sequence through phenomena named post-transcriptional gene silencing (PTGS) in plants, quelling in fungi, and RNA interference (RNAi) in animals. It was shown previously that PTGS, quelling, and RNAi require a set of related proteins (SGS2, QDE-1, and EGO-1, respectively). Here we report the isolation of Arabidopsis mutants impaired in PTGS which are affected at the Argonaute1 (AGO1) locus. AGO1 is similar to QDE-2 required for quelling and RDE-1 required for RNAi. Sequencing of ago1 mutants revealed one amino acid essential for PTGS that is also present in QDE-2 and RDE-1 in a highly conserved motif. Taken together, these results confirm the hypothesis that these processes derive from a common ancestral mechanism that controls expression of invading nucleic acid molecules at the post-transcriptional level. As opposed to rde-1 and qde-2 mutants, which are viable, ago1 mutants display several developmental abnormalities, including sterility. These results raise the possibility that PTGS, or at least some of its elements, could participate in the regulation of gene expression during development in plants.},
	language = {en},
	number = {21},
	urldate = {2021-11-08},
	journal = {Proceedings of the National Academy of Sciences},
	publisher = {National Academy of Sciences},
	author = {Fagard, Mathilde and Boutet, Stéphanie and Morel, Jean-Benoit and Bellini, Catherine and Vaucheret, Hervé},
	month = oct,
	year = {2000},
	pages = {11650--11654},
}

Introduction of transgene DNA may lead to specific degradation of RNAs that are homologous to the transgene transcribed sequence through phenomena named post-transcriptional gene silencing (PTGS) in plants, quelling in fungi, and RNA interference (RNAi) in animals. It was shown previously that PTGS, quelling, and RNAi require a set of related proteins (SGS2, QDE-1, and EGO-1, respectively). Here we report the isolation of Arabidopsis mutants impaired in PTGS which are affected at the Argonaute1 (AGO1) locus. AGO1 is similar to QDE-2 required for quelling and RDE-1 required for RNAi. Sequencing of ago1 mutants revealed one amino acid essential for PTGS that is also present in QDE-2 and RDE-1 in a highly conserved motif. Taken together, these results confirm the hypothesis that these processes derive from a common ancestral mechanism that controls expression of invading nucleic acid molecules at the post-transcriptional level. As opposed to rde-1 and qde-2 mutants, which are viable, ago1 mutants display several developmental abnormalities, including sterility. These results raise the possibility that PTGS, or at least some of its elements, could participate in the regulation of gene expression during development in plants.

@article{schrick_fackel_2000,
	title = {{FACKEL} is a sterol {C}-14 reductase required for organized cell division and expansion in {Arabidopsis} embryogenesis},
	volume = {14},
	url = {https://www.ncbi.nlm.nih.gov/sites/ppmc/articles/PMC316688/},
	abstract = {In flowering plants, the developing embryo consists of growing populations of cells whose fates are determined in a position-dependent manner to form the adult organism. Mutations in the FACKEL (FK) gene affect body organization of the Arabidopsis seedling. ...},
	language = {en},
	number = {12},
	urldate = {2021-11-08},
	journal = {Genes \& Development},
	publisher = {Cold Spring Harbor Laboratory Press},
	author = {Schrick, Kathrin and Mayer, Ulrike and Horrichs, Andrea and Kuhnt, Christine and Bellini, Catherine and Dangl, Jeff and Schmidt, Jürgen and Jürgens, Gerd},
	month = jun,
	year = {2000},
	pages = {1471},
}

In flowering plants, the developing embryo consists of growing populations of cells whose fates are determined in a position-dependent manner to form the adult organism. Mutations in the FACKEL (FK) gene affect body organization of the Arabidopsis seedling. ...

@article{barlier_sur2_2000,
	chapter = {Biological Sciences},
	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},
	publisher = {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},
	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{delarue_increased_1999,
	title = {Increased auxin efflux in the {IAA}-overproducing sur1 mutant of {Arabidopsis} thaliana: {A} mechanism of reducing auxin levels?},
	volume = {107},
	issn = {1399-3054},
	shorttitle = {Increased auxin efflux in the {IAA}-overproducing sur1 mutant of {Arabidopsis} thaliana},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1034/j.1399-3054.1999.100116.x},
	doi = {10.1034/j.1399-3054.1999.100116.x},
	abstract = {With the aim of investigating the mechanisms that maintain auxin homeostasis in plants, we have monitored the net uptake and metabolism of exogenously supplied indole-3-acetic acid (IAA) and naphthalene-1-acetic acid (NAA) in seedlings of wild type and the IAA-overproducing mutant sur1 of Arabidopsis thaliana. Tritiated IAA and NAA entered the seedling tissues within minutes and were mostly accumulated as metabolites, probably amino acid and sugar conjugates. The mutant seedlings were marked by a strong increase of [3H]IAA metabolism and a reduction of the accumulation levels of both free [3H]IAA and [3H]NAA. The same characteristics were observed in wild-type seedlings grown on 5 μM picloram. We measured [3H]NAA uptake in the presence of high concentrations of unlabeled NAA or the auxin efflux carrier inhibitor naphthylphthalamic acid (NPA). This abolished the difference in free [3H]NAA accumulation between the mutant or picloram-treated seedlings and wild-type seedlings. These data indicated that active auxin efflux carriers were present in Arabidopsis seedling tissues. Picloram-treated seedlings and seedlings of the IAA-overproducing mutant sur1 displayed increased auxin efflux carrier activity as well as elevated conjugation of IAA. There is previous evidence to suggest that conjugation is a means to remove excess IAA in plant cells. Here, we discuss the possibility of efflux constituting an additional mechanism for regulating free IAA levels in the face of an excess auxin supply.},
	language = {en},
	number = {1},
	urldate = {2021-11-08},
	journal = {Physiologia Plantarum},
	author = {Delarue, Marianne and Muller, Philimppe and Bellini, Catherine and Delbarre, Alain},
	year = {1999},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1034/j.1399-3054.1999.100116.x},
	pages = {120--127},
}

With the aim of investigating the mechanisms that maintain auxin homeostasis in plants, we have monitored the net uptake and metabolism of exogenously supplied indole-3-acetic acid (IAA) and naphthalene-1-acetic acid (NAA) in seedlings of wild type and the IAA-overproducing mutant sur1 of Arabidopsis thaliana. Tritiated IAA and NAA entered the seedling tissues within minutes and were mostly accumulated as metabolites, probably amino acid and sugar conjugates. The mutant seedlings were marked by a strong increase of [3H]IAA metabolism and a reduction of the accumulation levels of both free [3H]IAA and [3H]NAA. The same characteristics were observed in wild-type seedlings grown on 5 μM picloram. We measured [3H]NAA uptake in the presence of high concentrations of unlabeled NAA or the auxin efflux carrier inhibitor naphthylphthalamic acid (NPA). This abolished the difference in free [3H]NAA accumulation between the mutant or picloram-treated seedlings and wild-type seedlings. These data indicated that active auxin efflux carriers were present in Arabidopsis seedling tissues. Picloram-treated seedlings and seedlings of the IAA-overproducing mutant sur1 displayed increased auxin efflux carrier activity as well as elevated conjugation of IAA. There is previous evidence to suggest that conjugation is a means to remove excess IAA in plant cells. Here, we discuss the possibility of efflux constituting an additional mechanism for regulating free IAA levels in the face of an excess auxin supply.