@article{van_dijk_single_2022,
	title = {Single, but not dual, attack by a biotrophic pathogen and a sap-sucking insect affects the oak leaf metabolome},
	volume = {13},
	issn = {1664-462X},
	url = {https://www.frontiersin.org/articles/10.3389/fpls.2022.897186},
	abstract = {Plants interact with a multitude of microorganisms and insects, both below- and above ground, which might influence plant metabolism. Despite this, we lack knowledge of the impact of natural soil communities and multiple aboveground attackers on the metabolic responses of plants, and whether plant metabolic responses to single attack can predict responses to dual attack. We used untargeted metabolic fingerprinting (gas chromatography-mass spectrometry, GC-MS) on leaves of the pedunculate oak, Quercus robur, to assess the metabolic response to different soil microbiomes and aboveground single and dual attack by oak powdery mildew (Erysiphe alphitoides) and the common oak aphid (Tuberculatus annulatus). Distinct soil microbiomes were not associated with differences in the metabolic profile of oak seedling leaves. Single attacks by aphids or mildew had pronounced but different effects on the oak leaf metabolome, but we detected no difference between the metabolomes of healthy seedlings and seedlings attacked by both aphids and powdery mildew. Our findings show that aboveground attackers can have species-specific and non-additive effects on the leaf metabolome of oak. The lack of a metabolic signature detected by GC-MS upon dual attack might suggest the existence of a potential negative feedback, and highlights the importance of considering the impacts of multiple attackers to gain mechanistic insights into the ecology and evolution of species interactions and the structure of plant-associated communities, as well as for the development of sustainable strategies to control agricultural pests and diseases and plant breeding.},
	urldate = {2022-08-12},
	journal = {Frontiers in Plant Science},
	author = {van Dijk, Laura J. A. and Regazzoni, Emilia D. E. and Albrectsen, Benedicte R. and Ehrlén, Johan and Abdelfattah, Ahmed and Stenlund, Hans and Pawlowski, Katharina and Tack, Ayco J. M.},
	month = aug,
	year = {2022},
}

Plants interact with a multitude of microorganisms and insects, both below- and above ground, which might influence plant metabolism. Despite this, we lack knowledge of the impact of natural soil communities and multiple aboveground attackers on the metabolic responses of plants, and whether plant metabolic responses to single attack can predict responses to dual attack. We used untargeted metabolic fingerprinting (gas chromatography-mass spectrometry, GC-MS) on leaves of the pedunculate oak, Quercus robur, to assess the metabolic response to different soil microbiomes and aboveground single and dual attack by oak powdery mildew (Erysiphe alphitoides) and the common oak aphid (Tuberculatus annulatus). Distinct soil microbiomes were not associated with differences in the metabolic profile of oak seedling leaves. Single attacks by aphids or mildew had pronounced but different effects on the oak leaf metabolome, but we detected no difference between the metabolomes of healthy seedlings and seedlings attacked by both aphids and powdery mildew. Our findings show that aboveground attackers can have species-specific and non-additive effects on the leaf metabolome of oak. The lack of a metabolic signature detected by GC-MS upon dual attack might suggest the existence of a potential negative feedback, and highlights the importance of considering the impacts of multiple attackers to gain mechanistic insights into the ecology and evolution of species interactions and the structure of plant-associated communities, as well as for the development of sustainable strategies to control agricultural pests and diseases and plant breeding.

@article{andre_flowering_2022,
	title = {{FLOWERING} {LOCUS} {T} paralogs control the annual growth cycle in {Populus} trees},
	volume = {32},
	issn = {0960-9822},
	url = {https://www.cell.com/current-biology/abstract/S0960-9822(22)00782-5},
	doi = {10.1016/j.cub.2022.05.023},
	language = {English},
	number = {13},
	urldate = {2022-08-12},
	journal = {Current Biology},
	author = {André, Domenique and Marcon, Alice and Lee, Keh Chien and Goretti, Daniela and Zhang, Bo and Delhomme, Nicolas and Schmid, Markus and Nilsson, Ove},
	month = jul,
	year = {2022},
	pmid = {35660141},
	note = {Publisher: Elsevier},
	keywords = {FLOWERING LOCUS T, Populus, annual growth cycle, bud flush, dormancy, paralogs},
	pages = {2988--2996.e4},
}

@article{liebsch_metabolic_2022,
	title = {Metabolic control of arginine and ornithine levels paces the progression of leaf senescence},
	volume = {189},
	issn = {0032-0889},
	url = {https://doi.org/10.1093/plphys/kiac244},
	doi = {10.1093/plphys/kiac244},
	abstract = {Leaf senescence can be induced by stress or aging, sometimes in a synergistic manner. It is generally acknowledged that the ability to withstand senescence-inducing conditions can provide plants with stress resilience. Although the signaling and transcriptional networks responsible for a delayed senescence phenotype, often referred to as a functional stay-green trait, have been actively investigated, very little is known about the subsequent metabolic adjustments conferring this aptitude to survival. First, using the individually darkened leaf (IDL) experimental setup, we compared IDLs of wild-type (WT) Arabidopsis (Arabidopsis thaliana) to several stay-green contexts, that is IDLs of two functional stay-green mutant lines, oresara1-2 (ore1-2) and an allele of phytochrome-interacting factor 5 (pif5), as well as to leaves from a WT plant entirely darkened (DP). We provide compelling evidence that arginine and ornithine, which accumulate in all stay-green contexts—likely due to the lack of induction of amino acids (AAs) transport—can delay the progression of senescence by fueling the Krebs cycle or the production of polyamines (PAs). Secondly, we show that the conversion of putrescine to spermidine (SPD) is controlled in an age-dependent manner. Thirdly, we demonstrate that SPD represses senescence via interference with ethylene signaling by stabilizing the ETHYLENE BINDING FACTOR1 and 2 (EBF1/2) complex. Taken together, our results identify arginine and ornithine as central metabolites influencing the stress- and age-dependent progression of leaf senescence. We propose that the regulatory loop between the pace of the AA export and the progression of leaf senescence provides the plant with a mechanism to fine-tune the induction of cell death in leaves, which, if triggered unnecessarily, can impede nutrient remobilization and thus plant growth and survival.},
	number = {4},
	urldate = {2022-08-08},
	journal = {Plant Physiology},
	author = {Liebsch, Daniela and Juvany, Marta and Li, Zhonghai and Wang, Hou-Ling and Ziolkowska, Agnieszka and Chrobok, Daria and Boussardon, Clément and Wen, Xing and Law, Simon R and Janečková, Helena and Brouwer, Bastiaan and Lindén, Pernilla and Delhomme, Nicolas and Stenlund, Hans and Moritz, Thomas and Gardeström, Per and Guo, Hongwei and Keech, Olivier},
	month = aug,
	year = {2022},
	pages = {1943--1960},
}

Leaf senescence can be induced by stress or aging, sometimes in a synergistic manner. It is generally acknowledged that the ability to withstand senescence-inducing conditions can provide plants with stress resilience. Although the signaling and transcriptional networks responsible for a delayed senescence phenotype, often referred to as a functional stay-green trait, have been actively investigated, very little is known about the subsequent metabolic adjustments conferring this aptitude to survival. First, using the individually darkened leaf (IDL) experimental setup, we compared IDLs of wild-type (WT) Arabidopsis (Arabidopsis thaliana) to several stay-green contexts, that is IDLs of two functional stay-green mutant lines, oresara1-2 (ore1-2) and an allele of phytochrome-interacting factor 5 (pif5), as well as to leaves from a WT plant entirely darkened (DP). We provide compelling evidence that arginine and ornithine, which accumulate in all stay-green contexts—likely due to the lack of induction of amino acids (AAs) transport—can delay the progression of senescence by fueling the Krebs cycle or the production of polyamines (PAs). Secondly, we show that the conversion of putrescine to spermidine (SPD) is controlled in an age-dependent manner. Thirdly, we demonstrate that SPD represses senescence via interference with ethylene signaling by stabilizing the ETHYLENE BINDING FACTOR1 and 2 (EBF1/2) complex. Taken together, our results identify arginine and ornithine as central metabolites influencing the stress- and age-dependent progression of leaf senescence. We propose that the regulatory loop between the pace of the AA export and the progression of leaf senescence provides the plant with a mechanism to fine-tune the induction of cell death in leaves, which, if triggered unnecessarily, can impede nutrient remobilization and thus plant growth and survival.

@article{biniaz_transcriptome_2022,
	title = {Transcriptome {Meta}-{Analysis} {Identifies} {Candidate} {Hub} {Genes} and {Pathways} of {Pathogen} {Stress} {Responses} in {Arabidopsis} thaliana},
	volume = {11},
	copyright = {http://creativecommons.org/licenses/by/3.0/},
	issn = {2079-7737},
	url = {https://www.mdpi.com/2079-7737/11/8/1155},
	doi = {10.3390/biology11081155},
	abstract = {Following a pathogen attack, plants defend themselves using multiple defense mechanisms to prevent infections. We used a meta-analysis and systems-biology analysis to search for general molecular plant defense responses from transcriptomic data reported from different pathogen attacks in Arabidopsis thaliana. Data from seven studies were subjected to meta-analysis, which revealed a total of 3694 differentially expressed genes (DEGs), where both healthy and infected plants were considered. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis further suggested that the DEGs were involved in several biosynthetic metabolic pathways, including those responsible for the biosynthesis of secondary metabolites and pathways central to photosynthesis and plant–pathogen interactions. Using network analysis, we highlight the importance of WRKY40, WRKY46 and STZ, and suggest that they serve as major points in protein–protein interactions. This is especially true regarding networks of composite-metabolic responses by pathogens. In summary, this research provides a new approach that illuminates how different mechanisms of transcriptome responses can be activated in plants under pathogen infection and indicates that common genes vary in their ability to regulate plant responses to the pathogens studied herein.},
	language = {en},
	number = {8},
	urldate = {2022-08-02},
	journal = {Biology},
	author = {Biniaz, Yaser and Tahmasebi, Ahmad and Tahmasebi, Aminallah and Albrectsen, Benedicte Riber and Poczai, Péter and Afsharifar, Alireza},
	month = aug,
	year = {2022},
	note = {Number: 8
Publisher: Multidisciplinary Digital Publishing Institute},
	keywords = {\textit{Arabidopsis thaliana}, biotic stress, plant–pathogen interaction, transcriptome data},
	pages = {1155},
}

Following a pathogen attack, plants defend themselves using multiple defense mechanisms to prevent infections. We used a meta-analysis and systems-biology analysis to search for general molecular plant defense responses from transcriptomic data reported from different pathogen attacks in Arabidopsis thaliana. Data from seven studies were subjected to meta-analysis, which revealed a total of 3694 differentially expressed genes (DEGs), where both healthy and infected plants were considered. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis further suggested that the DEGs were involved in several biosynthetic metabolic pathways, including those responsible for the biosynthesis of secondary metabolites and pathways central to photosynthesis and plant–pathogen interactions. Using network analysis, we highlight the importance of WRKY40, WRKY46 and STZ, and suggest that they serve as major points in protein–protein interactions. This is especially true regarding networks of composite-metabolic responses by pathogens. In summary, this research provides a new approach that illuminates how different mechanisms of transcriptome responses can be activated in plants under pathogen infection and indicates that common genes vary in their ability to regulate plant responses to the pathogens studied herein.

@article{yu_structure_2022,
	title = {Structure of {Arabidopsis} {SOQ1} lumenal region unveils {C}-terminal domain essential for negative regulation of photoprotective {qH}},
	volume = {8},
	copyright = {2022 The Author(s), under exclusive licence to Springer Nature Limited},
	issn = {2055-0278},
	url = {https://www.nature.com/articles/s41477-022-01177-z},
	doi = {10.1038/s41477-022-01177-z},
	abstract = {Non-photochemical quenching (NPQ) plays an important role for phototrophs in decreasing photo-oxidative damage. qH is a sustained form of NPQ and depends on the plastid lipocalin (LCNP). A thylakoid membrane-anchored protein SUPPRESSOR OF QUENCHING1 (SOQ1) prevents qH formation by inhibiting LCNP. SOQ1 suppresses qH with its lumen-located thioredoxin (Trx)-like and NHL domains. Here we report structural data, genetic modification and biochemical characterization of Arabidopsis SOQ1 lumenal domains. Our results show that the Trx-like and NHL domains are associated together, with the cysteine motif located at their interface. Residue E859, required for SOQ1 function, is pivotal for maintaining the Trx–NHL association. Importantly, the C-terminal region of SOQ1 forms an independent β-stranded domain that has structural homology to the N-terminal domain of bacterial disulfide bond protein D and is essential for negative regulation of qH. Furthermore, SOQ1 is susceptible to cleavage at the loops connecting the neighbouring lumenal domains both in vitro and in vivo, which could be a regulatory process for its suppression function of qH.},
	language = {en},
	number = {7},
	urldate = {2022-07-22},
	journal = {Nature Plants},
	author = {Yu, Guimei and Hao, Jingfang and Pan, Xiaowei and Shi, Lifang and Zhang, Yong and Wang, Jifeng and Fan, Hongcheng and Xiao, Yang and Yang, Fuquan and Lou, Jizhong and Chang, Wenrui and Malnoë, Alizée and Li, Mei},
	month = jul,
	year = {2022},
	note = {Number: 7
Publisher: Nature Publishing Group},
	keywords = {Photosynthesis, Plant sciences},
	pages = {840--855},
}

Non-photochemical quenching (NPQ) plays an important role for phototrophs in decreasing photo-oxidative damage. qH is a sustained form of NPQ and depends on the plastid lipocalin (LCNP). A thylakoid membrane-anchored protein SUPPRESSOR OF QUENCHING1 (SOQ1) prevents qH formation by inhibiting LCNP. SOQ1 suppresses qH with its lumen-located thioredoxin (Trx)-like and NHL domains. Here we report structural data, genetic modification and biochemical characterization of Arabidopsis SOQ1 lumenal domains. Our results show that the Trx-like and NHL domains are associated together, with the cysteine motif located at their interface. Residue E859, required for SOQ1 function, is pivotal for maintaining the Trx–NHL association. Importantly, the C-terminal region of SOQ1 forms an independent β-stranded domain that has structural homology to the N-terminal domain of bacterial disulfide bond protein D and is essential for negative regulation of qH. Furthermore, SOQ1 is susceptible to cleavage at the loops connecting the neighbouring lumenal domains both in vitro and in vivo, which could be a regulatory process for its suppression function of qH.

@article{wang_aspen_2022,
	title = {Aspen growth is not limited by starch reserves},
	issn = {0960-9822},
	url = {https://www.sciencedirect.com/science/article/pii/S0960982222010181},
	doi = {10.1016/j.cub.2022.06.056},
	abstract = {All photosynthetic organisms balance CO2 assimilation with growth and carbon storage. Stored carbon is used for growth at night and when demand exceeds assimilation. Gaining a mechanistic understanding of carbon partitioning between storage and growth in trees is important for biological studies and for estimating the potential of terrestrial photosynthesis to sequester anthropogenic CO2 emissions.1,2 Starch represents the main carbon storage in plants.3,4 To examine the carbon storage mechanism and role of starch during tree growth, we generated and characterized low-starch hybrid aspen (Populus tremula × tremuloides) trees using CRISPR-Cas9-mediated gene editing of two PHOSPHOGLUCOMUTASE (PGM) genes coding for plastidial PGM isoforms essential for starch biosynthesis. We demonstrate that starch deficiency does not reduce tree growth even in short days, showing that starch is not a critical carbon reserve during diel growth of aspen. The low-starch trees assimilated up to ∼30\% less CO2 compared to the wild type under a range of irradiance levels, but this did not reduce growth or wood density. This implies that aspen growth is not limited by carbon assimilation under benign growth conditions. Moreover, the timing of bud set and bud flush in the low-starch trees was not altered, implying that starch reserves are not critical for the seasonal growth-dormancy cycle. The findings are consistent with a passive starch storage mechanism that contrasts with the annual Arabidopsis and indicate that the capacity of the aspen to absorb CO2 is limited by the rate of sink tissue growth.},
	language = {en},
	urldate = {2022-07-11},
	journal = {Current Biology},
	author = {Wang, Wei and Talide, Loic and Viljamaa, Sonja and Niittylä, Totte},
	month = jul,
	year = {2022},
	keywords = {carbon partitioning, phosphoglucomutase, starch},
}

All photosynthetic organisms balance CO2 assimilation with growth and carbon storage. Stored carbon is used for growth at night and when demand exceeds assimilation. Gaining a mechanistic understanding of carbon partitioning between storage and growth in trees is important for biological studies and for estimating the potential of terrestrial photosynthesis to sequester anthropogenic CO2 emissions.1,2 Starch represents the main carbon storage in plants.3,4 To examine the carbon storage mechanism and role of starch during tree growth, we generated and characterized low-starch hybrid aspen (Populus tremula × tremuloides) trees using CRISPR-Cas9-mediated gene editing of two PHOSPHOGLUCOMUTASE (PGM) genes coding for plastidial PGM isoforms essential for starch biosynthesis. We demonstrate that starch deficiency does not reduce tree growth even in short days, showing that starch is not a critical carbon reserve during diel growth of aspen. The low-starch trees assimilated up to ∼30% less CO2 compared to the wild type under a range of irradiance levels, but this did not reduce growth or wood density. This implies that aspen growth is not limited by carbon assimilation under benign growth conditions. Moreover, the timing of bud set and bud flush in the low-starch trees was not altered, implying that starch reserves are not critical for the seasonal growth-dormancy cycle. The findings are consistent with a passive starch storage mechanism that contrasts with the annual Arabidopsis and indicate that the capacity of the aspen to absorb CO2 is limited by the rate of sink tissue growth.

@article{ranade_enhanced_2022,
	title = {Enhanced lignin synthesis and ecotypic variation in defense-related gene expression in response to shade in {Norway} spruce.},
	volume = {n/a},
	issn = {1365-3040},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/pce.14387},
	doi = {10.1111/pce.14387},
	abstract = {ABSTRACTDuring the growth season, northern forests in Sweden daily receive more hours of far-red (FR)-enriched light or twilight (shade) as compared to southern forests. Norway spruce (shade-tolerant) are adapted to latitudinal variation in twilight characterized by a northward increase in FR requirement to maintain growth. Shade is a stressful condition that affects plant growth and increases plant's susceptibility to pathogen attack. Lignin plays a central role in plant defense and its metabolism is regulated by light wavelength composition (light quality). In the current work, we studied regulation of lignin synthesis and defense-related genes (growth-defense trade-offs) in response to shade in Norway spruce. In most angiosperms, light promotes lignin synthesis, whereas shade decreases lignin production leading to weaker stem, which may make plants more disease susceptible. In contrast, enhanced lignin synthesis was detected in response to shade in Norway spruce. We detected a higher number of immunity/defense-related genes up-regulated in northern populations as compared to south ones in response to shade. Enhanced lignin synthesis coupled with higher defense-related gene expression can be interpreted as an adaptive strategy for better survival in northern populations. Findings will contribute to ensuring deployment of well-adapted genetic material and identifying tree families with enhanced disease resistance.This article is protected by copyright. All rights reserved.},
	language = {en},
	number = {n/a},
	urldate = {2022-07-08},
	journal = {Plant, Cell \& Environment},
	author = {Ranade, Sonali Sachin and Seipel, George and Gorzsás, András and García-Gil, María Rosario},
	month = jul,
	year = {2022},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/pce.14387},
	keywords = {Conifer, Defense, Ecotypic variation, Immunity, Light quality, Lignin, Local adaptation, Norway spruce, R:FR ratio, RNA sequencing, Response to shade},
}

ABSTRACTDuring the growth season, northern forests in Sweden daily receive more hours of far-red (FR)-enriched light or twilight (shade) as compared to southern forests. Norway spruce (shade-tolerant) are adapted to latitudinal variation in twilight characterized by a northward increase in FR requirement to maintain growth. Shade is a stressful condition that affects plant growth and increases plant's susceptibility to pathogen attack. Lignin plays a central role in plant defense and its metabolism is regulated by light wavelength composition (light quality). In the current work, we studied regulation of lignin synthesis and defense-related genes (growth-defense trade-offs) in response to shade in Norway spruce. In most angiosperms, light promotes lignin synthesis, whereas shade decreases lignin production leading to weaker stem, which may make plants more disease susceptible. In contrast, enhanced lignin synthesis was detected in response to shade in Norway spruce. We detected a higher number of immunity/defense-related genes up-regulated in northern populations as compared to south ones in response to shade. Enhanced lignin synthesis coupled with higher defense-related gene expression can be interpreted as an adaptive strategy for better survival in northern populations. Findings will contribute to ensuring deployment of well-adapted genetic material and identifying tree families with enhanced disease resistance.This article is protected by copyright. All rights reserved.

@article{diamanti_comparative_2022,
	title = {Comparative structural analysis provides new insights into the function of {R2}-like ligand-binding oxidase},
	volume = {596},
	copyright = {© 2022 The Authors. FEBS Letters published by John Wiley \& Sons Ltd on behalf of Federation of European Biochemical Societies},
	issn = {1873-3468},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/1873-3468.14319},
	doi = {10.1002/1873-3468.14319},
	abstract = {R2-like ligand-binding oxidase (R2lox) is a ferritin-like protein that harbours a heterodinuclear manganese–iron active site. Although R2lox function is yet to be established, the enzyme binds a fatty acid ligand coordinating the metal centre and catalyses the formation of a tyrosine–valine ether cross-link in the protein scaffold upon O2 activation. Here, we characterized the ligands copurified with R2lox by mass spectrometry-based metabolomics. Moreover, we present the crystal structures of two new homologs of R2lox, from Saccharopolyspora erythraea and Sulfolobus acidocaldarius, at 1.38 Å and 2.26 Å resolution, respectively, providing the highest resolution structure for R2lox, as well as new insights into putative mechanisms regulating the function of the enzyme.},
	language = {en},
	number = {12},
	urldate = {2022-06-30},
	journal = {FEBS Letters},
	author = {Diamanti, Riccardo and Srinivas, Vivek and Johansson, Annika I. and Nordström, Anders and Griese, Julia J. and Lebrette, Hugo and Högbom, Martin},
	year = {2022},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/1873-3468.14319},
	keywords = {R2-like ligand-binding oxidase, R2lox, aldehyde deformylating oxygenase, ferritin-like protein, hydroxy fatty acids, long-chain fatty acids},
	pages = {1600--1610},
}

R2-like ligand-binding oxidase (R2lox) is a ferritin-like protein that harbours a heterodinuclear manganese–iron active site. Although R2lox function is yet to be established, the enzyme binds a fatty acid ligand coordinating the metal centre and catalyses the formation of a tyrosine–valine ether cross-link in the protein scaffold upon O2 activation. Here, we characterized the ligands copurified with R2lox by mass spectrometry-based metabolomics. Moreover, we present the crystal structures of two new homologs of R2lox, from Saccharopolyspora erythraea and Sulfolobus acidocaldarius, at 1.38 Å and 2.26 Å resolution, respectively, providing the highest resolution structure for R2lox, as well as new insights into putative mechanisms regulating the function of the enzyme.

@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{fataftah_nitrate_2022,
	title = {Nitrate fertilization may delay autumn leaf senescence, while amino acid treatments do not},
	volume = {174},
	issn = {1399-3054},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/ppl.13690},
	doi = {10.1111/ppl.13690},
	abstract = {Fertilization with nitrogen (N)-rich compounds leads to increased growth but may compromise phenology and winter survival of trees in boreal regions. During autumn, N is remobilized from senescing leaves and stored in other parts of the tree to be used in the next growing season. However, the mechanism behind the N fertilization effect on winter survival is not well understood, and it is unclear how N levels or forms modulate autumn senescence. We performed fertilization experiments and showed that treating Populus saplings with inorganic nitrogen resulted in a delay in senescence. In addition, by using precise delivery of solutes into the xylem stream of Populus trees in their natural environment, we found that delay of autumn senescence was dependent on the form of N administered: inorganic N (NO3−) delayed senescence, but amino acids (Arg, Glu, Gln, and Leu) did not. Metabolite profiling of leaves showed that the levels of tricarboxylic acids, arginine catabolites (ammonium, ornithine), glycine, glycine-serine ratio and overall carbon-to-nitrogen (C/N) ratio were affected differently by the way of applying NO3− and Arg treatments. In addition, the onset of senescence did not coincide with soluble sugar accumulation in control trees or in any of the treatments. We propose that different regulation of C and N status through direct molecular signaling of NO3− and/or different allocation of N between tree parts depending on N forms could account for the contrasting effects of NO3− and tested here amino acids (Arg, Glu, Gln, and Leu) on autumn senescence.},
	language = {en},
	number = {3},
	urldate = {2022-06-30},
	journal = {Physiologia Plantarum},
	author = {Fataftah, Nazeer and Edlund, Erik and Lihavainen, Jenna and Bag, Pushan and Björkén, Lars and Näsholm, Torgny and Jansson, Stefan},
	year = {2022},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/ppl.13690},
	pages = {e13690},
}

Fertilization with nitrogen (N)-rich compounds leads to increased growth but may compromise phenology and winter survival of trees in boreal regions. During autumn, N is remobilized from senescing leaves and stored in other parts of the tree to be used in the next growing season. However, the mechanism behind the N fertilization effect on winter survival is not well understood, and it is unclear how N levels or forms modulate autumn senescence. We performed fertilization experiments and showed that treating Populus saplings with inorganic nitrogen resulted in a delay in senescence. In addition, by using precise delivery of solutes into the xylem stream of Populus trees in their natural environment, we found that delay of autumn senescence was dependent on the form of N administered: inorganic N (NO3−) delayed senescence, but amino acids (Arg, Glu, Gln, and Leu) did not. Metabolite profiling of leaves showed that the levels of tricarboxylic acids, arginine catabolites (ammonium, ornithine), glycine, glycine-serine ratio and overall carbon-to-nitrogen (C/N) ratio were affected differently by the way of applying NO3− and Arg treatments. In addition, the onset of senescence did not coincide with soluble sugar accumulation in control trees or in any of the treatments. We propose that different regulation of C and N status through direct molecular signaling of NO3− and/or different allocation of N between tree parts depending on N forms could account for the contrasting effects of NO3− and tested here amino acids (Arg, Glu, Gln, and Leu) on autumn senescence.

@article{arshad_kaleidoscope_2022,
	title = {A kaleidoscope of photosynthetic antenna proteins and their emerging roles},
	volume = {189},
	issn = {1532-2548},
	doi = {10.1093/plphys/kiac175},
	abstract = {Photosynthetic light-harvesting antennae are pigment-binding proteins that perform one of the most fundamental tasks on Earth, capturing light and transferring energy that enables life in our biosphere. Adaptation to different light environments led to the evolution of an astonishing diversity of light-harvesting systems. At the same time, several strategies have been developed to optimize the light energy input into photosynthetic membranes in response to fluctuating conditions. The basic feature of these prompt responses is the dynamic nature of antenna complexes, whose function readily adapts to the light available. High-resolution microscopy and spectroscopic studies on membrane dynamics demonstrate the crosstalk between antennae and other thylakoid membrane components. With the increased understanding of light-harvesting mechanisms and their regulation, efforts are focusing on the development of sustainable processes for effective conversion of sunlight into functional bio-products. The major challenge in this approach lies in the application of fundamental discoveries in light-harvesting systems for the improvement of plant or algal photosynthesis. Here, we underline some of the latest fundamental discoveries on the molecular mechanisms and regulation of light harvesting that can potentially be exploited for the optimization of photosynthesis.},
	language = {eng},
	number = {3},
	journal = {Plant Physiology},
	author = {Arshad, Rameez and Saccon, Francesco and Bag, Pushan and Biswas, Avratanu and Calvaruso, Claudio and Bhatti, Ahmad Farhan and Grebe, Steffen and Mascoli, Vincenzo and Mahbub, Moontaha and Muzzopappa, Fernando and Polyzois, Alexandros and Schiphorst, Christo and Sorrentino, Mirella and Streckaité, Simona and van Amerongen, Herbert and Aro, Eva-Mari and Bassi, Roberto and Boekema, Egbert J. and Croce, Roberta and Dekker, Jan and van Grondelle, Rienk and Jansson, Stefan and Kirilovsky, Diana and Kouřil, Roman and Michel, Sylvie and Mullineaux, Conrad W. and Panzarová, Klára and Robert, Bruno and Ruban, Alexander V. and van Stokkum, Ivo and Wientjes, Emilie and Büchel, Claudia},
	month = jun,
	year = {2022},
	pmid = {35512089},
	keywords = {Adaptation, Physiological, Light-Harvesting Protein Complexes, Photosynthesis, Plants, Thylakoids},
	pages = {1204--1219},
}

Photosynthetic light-harvesting antennae are pigment-binding proteins that perform one of the most fundamental tasks on Earth, capturing light and transferring energy that enables life in our biosphere. Adaptation to different light environments led to the evolution of an astonishing diversity of light-harvesting systems. At the same time, several strategies have been developed to optimize the light energy input into photosynthetic membranes in response to fluctuating conditions. The basic feature of these prompt responses is the dynamic nature of antenna complexes, whose function readily adapts to the light available. High-resolution microscopy and spectroscopic studies on membrane dynamics demonstrate the crosstalk between antennae and other thylakoid membrane components. With the increased understanding of light-harvesting mechanisms and their regulation, efforts are focusing on the development of sustainable processes for effective conversion of sunlight into functional bio-products. The major challenge in this approach lies in the application of fundamental discoveries in light-harvesting systems for the improvement of plant or algal photosynthesis. Here, we underline some of the latest fundamental discoveries on the molecular mechanisms and regulation of light harvesting that can potentially be exploited for the optimization of photosynthesis.

@article{blasko_carbon_2022,
	title = {The carbon sequestration response of aboveground biomass and soils to nutrient enrichment in boreal forests depends on baseline site productivity},
	volume = {838},
	issn = {0048-9697},
	url = {https://www.sciencedirect.com/science/article/pii/S0048969722034246},
	doi = {10.1016/j.scitotenv.2022.156327},
	abstract = {Nutrient enrichment can alleviate productivity limitations and thus substantially increase carbon (C) uptake in northern coniferous forests. Yet, factors controlling stand-to-stand variation of forest ecosystem responses to nutrient enrichment remain unclear. We used five long-term (13 years) nutrient-enrichment experiments across Sweden, where nitrogen (N), phosphorus, and potassium were applied annually to young Norway spruce forests that varied in their baseline ecosystem properties. We measured tree biomass and soil C and N stocks, litterfall C inputs, soil CO2 efflux, and shifts in composition and biomass of soil microbial communities to understand the links between above and belowground responses to nutrient enrichment. We found that the strongest responses in tree biomass occurred when baseline site productivity was lowest. High increases in tree biomass C stocks were generally balanced by weaker responses in organic soil C stocks. The average ecosystem C–N response rate was 35 kg C kg−1 N added, with a nearly five-fold greater response rate in tree biomass than in soil. The positive nutrient enrichment effects on ecosystem C sinks were driven by a 95\% increase in tree biomass C stocks, 150\% increase in litter production, 67\% increase in organic layer C stocks, and a 46\% reduction in soil CO2 efflux accompanied by compositional changes in soil microbial communities. Our results show that ecosystem C uptake in spruce forests in northern Europe can be substantially enhanced by nutrient enrichment; however, the strength of the responses and whether the enhancement occurs mainly in tree biomass or soils are dependent on baseline forest productivity.},
	language = {en},
	urldate = {2022-06-30},
	journal = {Science of The Total Environment},
	author = {Blaško, Róbert and Forsmark, Benjamin and Gundale, Michael J. and Lim, Hyungwoo and Lundmark, Tomas and Nordin, Annika},
	month = sep,
	year = {2022},
	keywords = {Ecosystem carbon stocks, Litterfall, Soil carbon, Soil microbial community, Soil nitrogen, Soil respiration},
	pages = {156327},
}

Nutrient enrichment can alleviate productivity limitations and thus substantially increase carbon (C) uptake in northern coniferous forests. Yet, factors controlling stand-to-stand variation of forest ecosystem responses to nutrient enrichment remain unclear. We used five long-term (13 years) nutrient-enrichment experiments across Sweden, where nitrogen (N), phosphorus, and potassium were applied annually to young Norway spruce forests that varied in their baseline ecosystem properties. We measured tree biomass and soil C and N stocks, litterfall C inputs, soil CO2 efflux, and shifts in composition and biomass of soil microbial communities to understand the links between above and belowground responses to nutrient enrichment. We found that the strongest responses in tree biomass occurred when baseline site productivity was lowest. High increases in tree biomass C stocks were generally balanced by weaker responses in organic soil C stocks. The average ecosystem C–N response rate was 35 kg C kg−1 N added, with a nearly five-fold greater response rate in tree biomass than in soil. The positive nutrient enrichment effects on ecosystem C sinks were driven by a 95% increase in tree biomass C stocks, 150% increase in litter production, 67% increase in organic layer C stocks, and a 46% reduction in soil CO2 efflux accompanied by compositional changes in soil microbial communities. Our results show that ecosystem C uptake in spruce forests in northern Europe can be substantially enhanced by nutrient enrichment; however, the strength of the responses and whether the enhancement occurs mainly in tree biomass or soils are dependent on baseline forest productivity.

@article{kleczkowski_effects_2022,
	title = {Effects of {Magnesium}, {Pyrophosphate} and {Phosphonates} on {Pyrophosphorolytic} {Reaction} of {UDP}-{Glucose} {Pyrophosphorylase}},
	volume = {11},
	copyright = {http://creativecommons.org/licenses/by/3.0/},
	issn = {2223-7747},
	url = {https://www.mdpi.com/2223-7747/11/12/1611},
	doi = {10.3390/plants11121611},
	abstract = {UDP-glucose pyrophosphorylase (UGPase) carries a freely reversible reaction, using glucose-1-P and UTP to produce UDP-glucose (UDPG) and pyrophosphate (PPi), with UDPG being essential for glycosylation reactions in all organisms including, e.g., synthesis of sucrose, cellulose and glycoproteins. In the present study, we found that free magnesium (Mg2+) had profound effects on the reverse reaction of purified barley UGPase, and was absolutely required for its activity, with an apparent Km of 0.13 mM. More detailed analyses with varied concentrations of MgPPi allowed us to conclude that it is the MgPPi complex which serves as true substrate for UGPase in its reverse reaction, with an apparent Km of 0.06 mM. Free PPi was an inhibitor in this reaction. Given the key role of PPi in the UGPase reaction, we have also tested possible effects of phosphonates, which are analogs of PPi and phosphate (Pi). Clodronate and etidronate (PPi analogs) had little or no effect on UGPase activity, whereas fosetyl-Al (Pi analog), a known fungicide, acted as effective near-competitive inhibitor versus PPi, with Ki of 0.15 mM. The data are discussed with respect to the role of magnesium in the UGPase reaction and elucidating the use of inhibitors in studies on cellular function of UGPase and related enzymes.},
	language = {en},
	number = {12},
	urldate = {2022-06-30},
	journal = {Plants},
	author = {Kleczkowski, Leszek A. and Decker, Daniel},
	month = jun,
	year = {2022},
	note = {Number: 12
Publisher: Multidisciplinary Digital Publishing Institute},
	keywords = {\textit{Phytophthora}, Dixon plot, chemical genetics, fosetyl-Al, inhibitor kinetics, magnesium activation},
	pages = {1611},
}

UDP-glucose pyrophosphorylase (UGPase) carries a freely reversible reaction, using glucose-1-P and UTP to produce UDP-glucose (UDPG) and pyrophosphate (PPi), with UDPG being essential for glycosylation reactions in all organisms including, e.g., synthesis of sucrose, cellulose and glycoproteins. In the present study, we found that free magnesium (Mg2+) had profound effects on the reverse reaction of purified barley UGPase, and was absolutely required for its activity, with an apparent Km of 0.13 mM. More detailed analyses with varied concentrations of MgPPi allowed us to conclude that it is the MgPPi complex which serves as true substrate for UGPase in its reverse reaction, with an apparent Km of 0.06 mM. Free PPi was an inhibitor in this reaction. Given the key role of PPi in the UGPase reaction, we have also tested possible effects of phosphonates, which are analogs of PPi and phosphate (Pi). Clodronate and etidronate (PPi analogs) had little or no effect on UGPase activity, whereas fosetyl-Al (Pi analog), a known fungicide, acted as effective near-competitive inhibitor versus PPi, with Ki of 0.15 mM. The data are discussed with respect to the role of magnesium in the UGPase reaction and elucidating the use of inhibitors in studies on cellular function of UGPase and related enzymes.

@article{kauppi_managing_2022,
	title = {Managing existing forests can mitigate climate change},
	volume = {513},
	issn = {0378-1127},
	url = {https://www.sciencedirect.com/science/article/pii/S0378112722001803},
	doi = {10.1016/j.foreco.2022.120186},
	abstract = {Planting new forests has received scientific and political attention as a measure to mitigate climate change. Large, new forests have been planted in places like China and Ethiopia and, over time, a billion hectares could become available globally for planting new forests. Sustainable management of forests, which are available to wood production, has received less attention despite these forests covering at least two billion hectares globally. Better management of existing forests would improve forest growth and help mitigate climate change by increasing the forest carbon (C) stock, by storing C in forest products, and by generating wood-based materials substituting fossil C based materials or other CO2-emission-intensive materials. Some published research assumes a trade-off between the timber harvested from existing forests and the stock of C in those forest ecosystems, asserting that both cannot increase simultaneously. We tested this assumption using the uniquely detailed forest inventory data available from Finland, Norway and Sweden, hereafter denoted northern Europe. We focused on the period 1960 – 2017, that saw little change in the total area covered by forests in northern Europe. At the start of the period, rotational forestry practices began to diffuse, eventually replacing selective felling management systems as the most common management practice. Looking at data over the period we find that despite significant increases in timber and pulp wood harvests, the growth of the forest C stock accelerated. Over the study period, the C stock of the forest ecosystems in northern Europe increased by nearly 70\%, while annual timber harvests increased at the about 40\% over the same period. This increase in the forest C stock was close to on par with the CO2-emissions from the region (other greenhouse gases not included). Our results suggest that the important effects of management on forest growth allows the forest C stock and timber harvests to increase simultaneously. The development in northern Europe raises the question of how better forest management can improve forest growth elsewhere around the globe while at the same time protecting biodiversity and preserving landscapes.},
	language = {en},
	urldate = {2022-06-27},
	journal = {Forest Ecology and Management},
	author = {Kauppi, Pekka E. and Stål, Gustav and Arnesson-Ceder, Lina and Hallberg Sramek, Isabella and Hoen, Hans Fredrik and Svensson, Arvid and Wernick, Iddo K. and Högberg, Peter and Lundmark, Tomas and Nordin, Annika},
	month = jun,
	year = {2022},
	keywords = {Boreal forests, Carbon cycle, Carbon mitigation, Forest ecosystems, Forest management, Global forests},
	pages = {120186},
}

Planting new forests has received scientific and political attention as a measure to mitigate climate change. Large, new forests have been planted in places like China and Ethiopia and, over time, a billion hectares could become available globally for planting new forests. Sustainable management of forests, which are available to wood production, has received less attention despite these forests covering at least two billion hectares globally. Better management of existing forests would improve forest growth and help mitigate climate change by increasing the forest carbon (C) stock, by storing C in forest products, and by generating wood-based materials substituting fossil C based materials or other CO2-emission-intensive materials. Some published research assumes a trade-off between the timber harvested from existing forests and the stock of C in those forest ecosystems, asserting that both cannot increase simultaneously. We tested this assumption using the uniquely detailed forest inventory data available from Finland, Norway and Sweden, hereafter denoted northern Europe. We focused on the period 1960 – 2017, that saw little change in the total area covered by forests in northern Europe. At the start of the period, rotational forestry practices began to diffuse, eventually replacing selective felling management systems as the most common management practice. Looking at data over the period we find that despite significant increases in timber and pulp wood harvests, the growth of the forest C stock accelerated. Over the study period, the C stock of the forest ecosystems in northern Europe increased by nearly 70%, while annual timber harvests increased at the about 40% over the same period. This increase in the forest C stock was close to on par with the CO2-emissions from the region (other greenhouse gases not included). Our results suggest that the important effects of management on forest growth allows the forest C stock and timber harvests to increase simultaneously. The development in northern Europe raises the question of how better forest management can improve forest growth elsewhere around the globe while at the same time protecting biodiversity and preserving landscapes.

@article{law_metatranscriptomics_2022,
	title = {Metatranscriptomics captures dynamic shifts in mycorrhizal coordination in boreal forests},
	volume = {119},
	url = {https://www.pnas.org/doi/full/10.1073/pnas.2118852119},
	doi = {10.1073/pnas.2118852119},
	abstract = {Carbon storage and cycling in boreal forests—the largest terrestrial carbon store—is moderated by complex interactions between trees and soil microorganisms. However, existing methods limit our ability to predict how changes in environmental conditions will alter these associations and the essential ecosystem services they provide. To address this, we developed a metatranscriptomic approach to analyze the impact of nutrient enrichment on Norway spruce fine roots and the community structure, function, and tree–microbe coordination of over 350 root-associated fungal species. In response to altered nutrient status, host trees redefined their relationship with the fungal community by reducing sugar efflux carriers and enhancing defense processes. This resulted in a profound restructuring of the fungal community and a collapse in functional coordination between the tree and the dominant Basidiomycete species, and an increase in functional coordination with versatile Ascomycete species. As such, there was a functional shift in community dominance from Basidiomycetes species, with important roles in enzymatically cycling recalcitrant carbon, to Ascomycete species that have melanized cell walls that are highly resistant to degradation. These changes were accompanied by prominent shifts in transcriptional coordination between over 60 predicted fungal effectors, with more than 5,000 Norway spruce transcripts, providing mechanistic insight into the complex molecular dialogue coordinating host trees and their fungal partners. The host–microbe dynamics captured by this study functionally inform how these complex and sensitive biological relationships may mediate the carbon storage potential of boreal soils under changing nutrient conditions.},
	number = {26},
	urldate = {2022-06-22},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Law, Simon R. and Serrano, Alonso R. and Daguerre, Yohann and Sundh, John and Schneider, Andreas N. and Stangl, Zsofia R. and Castro, David and Grabherr, Manfred and Näsholm, Torgny and Street, Nathaniel R. and Hurry, Vaughan},
	month = jun,
	year = {2022},
	pages = {e2118852119},
}

Carbon storage and cycling in boreal forests—the largest terrestrial carbon store—is moderated by complex interactions between trees and soil microorganisms. However, existing methods limit our ability to predict how changes in environmental conditions will alter these associations and the essential ecosystem services they provide. To address this, we developed a metatranscriptomic approach to analyze the impact of nutrient enrichment on Norway spruce fine roots and the community structure, function, and tree–microbe coordination of over 350 root-associated fungal species. In response to altered nutrient status, host trees redefined their relationship with the fungal community by reducing sugar efflux carriers and enhancing defense processes. This resulted in a profound restructuring of the fungal community and a collapse in functional coordination between the tree and the dominant Basidiomycete species, and an increase in functional coordination with versatile Ascomycete species. As such, there was a functional shift in community dominance from Basidiomycetes species, with important roles in enzymatically cycling recalcitrant carbon, to Ascomycete species that have melanized cell walls that are highly resistant to degradation. These changes were accompanied by prominent shifts in transcriptional coordination between over 60 predicted fungal effectors, with more than 5,000 Norway spruce transcripts, providing mechanistic insight into the complex molecular dialogue coordinating host trees and their fungal partners. The host–microbe dynamics captured by this study functionally inform how these complex and sensitive biological relationships may mediate the carbon storage potential of boreal soils under changing nutrient conditions.

@article{lopez-lopez_maturation_2022,
	title = {Maturation and {Assembly} of {Iron}-{Sulfur} {Cluster}-{Containing} {Subunits} in the {Mitochondrial} {Complex} {I} {From} {Plants}},
	volume = {13},
	issn = {1664-462X},
	url = {https://www.frontiersin.org/article/10.3389/fpls.2022.916948},
	abstract = {In plants, the mitochondrial complex I is the protein complex encompassing the largest number of iron-sulfur (Fe-S) clusters. The whole, membrane-embedded, holo-complex is assembled stepwise from assembly intermediates. The Q and N modules are combined to form a peripheral arm in the matrix, whereas the so-called membrane arm is formed after merging a carbonic anhydrase (CA) module with so-called Pp (proximal) and the Pd (distal) domains. A ferredoxin bridge connects both arms. The eight Fe-S clusters present in the peripheral arm for electron transfer reactions are synthesized via a dedicated protein machinery referred to as the iron-sulfur cluster (ISC) machinery. The de novo assembly occurs on ISCU scaffold proteins from iron, sulfur and electron delivery proteins. In a second step, the preformed Fe-S clusters are transferred, eventually converted and inserted in recipient apo-proteins. Diverse molecular actors, including a chaperone-cochaperone system, assembly factors among which proteins with LYR motifs, and Fe-S cluster carrier/transfer proteins, have been identified as contributors to the second step. This mini-review highlights the recent progresses in our understanding of how specificity is achieved during the delivery of preformed Fe-S clusters to complex I subunits.},
	urldate = {2022-06-07},
	journal = {Frontiers in Plant Science},
	author = {López-López, Alicia and Keech, Olivier and Rouhier, Nicolas},
	month = may,
	year = {2022},
	keywords = {⛔ No DOI found},
}

In plants, the mitochondrial complex I is the protein complex encompassing the largest number of iron-sulfur (Fe-S) clusters. The whole, membrane-embedded, holo-complex is assembled stepwise from assembly intermediates. The Q and N modules are combined to form a peripheral arm in the matrix, whereas the so-called membrane arm is formed after merging a carbonic anhydrase (CA) module with so-called Pp (proximal) and the Pd (distal) domains. A ferredoxin bridge connects both arms. The eight Fe-S clusters present in the peripheral arm for electron transfer reactions are synthesized via a dedicated protein machinery referred to as the iron-sulfur cluster (ISC) machinery. The de novo assembly occurs on ISCU scaffold proteins from iron, sulfur and electron delivery proteins. In a second step, the preformed Fe-S clusters are transferred, eventually converted and inserted in recipient apo-proteins. Diverse molecular actors, including a chaperone-cochaperone system, assembly factors among which proteins with LYR motifs, and Fe-S cluster carrier/transfer proteins, have been identified as contributors to the second step. This mini-review highlights the recent progresses in our understanding of how specificity is achieved during the delivery of preformed Fe-S clusters to complex I subunits.

@article{nilsson_winter_2022,
	title = {Winter dormancy in trees},
	volume = {32},
	issn = {0960-9822},
	url = {https://www.sciencedirect.com/science/article/pii/S0960982222005802},
	doi = {10.1016/j.cub.2022.04.011},
	abstract = {Plants growing in temperate and boreal regions of the world have to face strikingly different environmental conditions during summer and winter. Being sessile organisms, plants have had to develop various strategies to adapt to these changes in light, temperature, and water availability, thereby optimizing their ‘economy of growth’. While annual plants can endure unfavorable winter conditions in the form of a seed, or under a protective cover of thick snow, perennial plants such as trees adapt by going into a stage of deep sleep called winter dormancy. To enter dormancy, vegetative growth is stopped in the late summer or early autumn and the shoots are converted into buds, where the shoot apical meristems are protected by tightly closed and hardened bud scales (Figures 1 and 2). At the same time, cold hardiness develops and the need for water and nutrient uptake is drastically reduced. Deciduous trees also go through leaf senescence whereby the leaves develop their autumn colors and are shed (Figure 1A). The trees then spend the beginning of the winter in a state of deep sleep in which they are completely unreceptive to any environmental signals telling them to wake up. However, as winter progresses, the trees are gradually released from this slumber and will eventually flush their buds in the spring. Vegetative growth then resumes with the formation of new leaves and shoots during summer until the trees again go into growth cessation and the cycle is closed (Figures 1 and 2). This cycle of growth and dormancy is central for the ability of trees to adapt to growth at different latitudes and elevations. The further north, or the higher the elevation at which the trees grow, the earlier in the season the trees enter growth cessation and the later they flush their buds in the spring. This is because meteorological winter arrives earlier in the season and lasts longer into the spring. The trees therefore have to stop growth earlier in the season to ensure that they have enough time to complete bud formation and to develop cold hardiness and dormancy. They also have to be sure that winter is really over before flushing their buds. Winter dormancy is therefore a clear case of a trade-off between the length of the growing season and the protection against winter damage — a nice example of ‘economy in biology’, the theme of this special issue. This primer will briefly summarize what we know about the environmental signals that influence the annual growth cycle in trees, as well as our current understanding of the genetic pathways and molecular mechanisms regulated by these signals.},
	language = {en},
	number = {12},
	urldate = {2022-06-21},
	journal = {Current Biology},
	author = {Nilsson, Ove},
	month = jun,
	year = {2022},
	pages = {R630--R634},
}

Plants growing in temperate and boreal regions of the world have to face strikingly different environmental conditions during summer and winter. Being sessile organisms, plants have had to develop various strategies to adapt to these changes in light, temperature, and water availability, thereby optimizing their ‘economy of growth’. While annual plants can endure unfavorable winter conditions in the form of a seed, or under a protective cover of thick snow, perennial plants such as trees adapt by going into a stage of deep sleep called winter dormancy. To enter dormancy, vegetative growth is stopped in the late summer or early autumn and the shoots are converted into buds, where the shoot apical meristems are protected by tightly closed and hardened bud scales (Figures 1 and 2). At the same time, cold hardiness develops and the need for water and nutrient uptake is drastically reduced. Deciduous trees also go through leaf senescence whereby the leaves develop their autumn colors and are shed (Figure 1A). The trees then spend the beginning of the winter in a state of deep sleep in which they are completely unreceptive to any environmental signals telling them to wake up. However, as winter progresses, the trees are gradually released from this slumber and will eventually flush their buds in the spring. Vegetative growth then resumes with the formation of new leaves and shoots during summer until the trees again go into growth cessation and the cycle is closed (Figures 1 and 2). This cycle of growth and dormancy is central for the ability of trees to adapt to growth at different latitudes and elevations. The further north, or the higher the elevation at which the trees grow, the earlier in the season the trees enter growth cessation and the later they flush their buds in the spring. This is because meteorological winter arrives earlier in the season and lasts longer into the spring. The trees therefore have to stop growth earlier in the season to ensure that they have enough time to complete bud formation and to develop cold hardiness and dormancy. They also have to be sure that winter is really over before flushing their buds. Winter dormancy is therefore a clear case of a trade-off between the length of the growing season and the protection against winter damage — a nice example of ‘economy in biology’, the theme of this special issue. This primer will briefly summarize what we know about the environmental signals that influence the annual growth cycle in trees, as well as our current understanding of the genetic pathways and molecular mechanisms regulated by these signals.

@article{zacharaki_impaired_2022,
	title = {Impaired {KIN10} function restores developmental defects in the {Arabidopsis} trehalose 6-phosphate synthase1 (tps1) mutant},
	volume = {235},
	issn = {1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/nph.18104},
	doi = {10.1111/nph.18104},
	abstract = {Sensing carbohydrate availability is essential for plants to coordinate their growth and development. In Arabidopsis thaliana, TREHALOSE 6-PHOSPHATE SYNTHASE 1 (TPS1) and its product, trehalose 6-phosphate (T6P), are important for the metabolic control of development. tps1 mutants are embryo-lethal and unable to flower when embryogenesis is rescued. T6P regulates development in part through inhibition of SUCROSE NON-FERMENTING1 RELATED KINASE1 (SnRK1). Here, we explored the role of SnRK1 in T6P-mediated plant growth and development using a combination of a mutant suppressor screen and genetic, cellular and transcriptomic approaches. We report nonsynonymous amino acid substitutions in the catalytic KIN10 and regulatory SNF4 subunits of SnRK1 that can restore both embryogenesis and flowering of tps1 mutant plants. The identified SNF4 point mutations disrupt the interaction with the catalytic subunit KIN10. Contrary to the common view that the two A. thaliana SnRK1 catalytic subunits act redundantly, we found that loss-of-function mutations in KIN11 are unable to restore embryogenesis and flowering, highlighting the important role of KIN10 in T6P signalling.},
	language = {en},
	number = {1},
	urldate = {2022-06-09},
	journal = {New Phytologist},
	author = {Zacharaki, Vasiliki and Ponnu, Jathish and Crepin, Nathalie and Langenecker, Tobias and Hagmann, Jörg and Skorzinski, Noemi and Musialak-Lange, Magdalena and Wahl, Vanessa and Rolland, Filip and Schmid, Markus},
	year = {2022},
	keywords = {Arabidopsis thaliana, SnRK1 complex, T6P pathway, TPS1, embryogenesis, flowering time},
	pages = {220--233},
}

Sensing carbohydrate availability is essential for plants to coordinate their growth and development. In Arabidopsis thaliana, TREHALOSE 6-PHOSPHATE SYNTHASE 1 (TPS1) and its product, trehalose 6-phosphate (T6P), are important for the metabolic control of development. tps1 mutants are embryo-lethal and unable to flower when embryogenesis is rescued. T6P regulates development in part through inhibition of SUCROSE NON-FERMENTING1 RELATED KINASE1 (SnRK1). Here, we explored the role of SnRK1 in T6P-mediated plant growth and development using a combination of a mutant suppressor screen and genetic, cellular and transcriptomic approaches. We report nonsynonymous amino acid substitutions in the catalytic KIN10 and regulatory SNF4 subunits of SnRK1 that can restore both embryogenesis and flowering of tps1 mutant plants. The identified SNF4 point mutations disrupt the interaction with the catalytic subunit KIN10. Contrary to the common view that the two A. thaliana SnRK1 catalytic subunits act redundantly, we found that loss-of-function mutations in KIN11 are unable to restore embryogenesis and flowering, highlighting the important role of KIN10 in T6P signalling.

@article{wang_sucrose_2022,
	title = {Sucrose synthase activity is not required for cellulose biosynthesis in {Arabidopsis}},
	volume = {110},
	issn = {1365-313X},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/tpj.15752},
	doi = {10.1111/tpj.15752},
	abstract = {Biosynthesis of plant cell walls requires UDP-glucose as the substrate for cellulose biosynthesis, and as an intermediate for the synthesis of other matrix polysaccharides. The sucrose cleaving enzyme sucrose synthase (SUS) is thought to have a central role in UDP-glucose biosynthesis, and a long-held and much debated hypothesis postulates that SUS is required to supply UDP-glucose to cellulose biosynthesis. To investigate the role of SUS in cellulose biosynthesis of Arabidopsis thaliana we characterized mutants in which four or all six Arabidopsis SUS genes were disrupted. These sus mutants showed no growth phenotypes, vascular tissue cell wall defects, or changes in cellulose content. Moreover, the UDP-glucose content of rosette leaves of the sextuple sus mutants was increased by approximately 20\% compared with wild type. It can thus be concluded that cellulose biosynthesis is able to employ alternative UDP-glucose biosynthesis pathway(s), and thereby the model of SUS requirements for cellulose biosynthesis in Arabidopsis can be refuted.},
	language = {en},
	number = {5},
	urldate = {2022-06-09},
	journal = {The Plant Journal},
	author = {Wang, Wei and Viljamaa, Sonja and Hodek, Ondrej and Moritz, Thomas and Niittylä, Totte},
	year = {2022},
	keywords = {Arabidopsis thaliana, UDP-glucose, cellulose, sucrose synthase},
	pages = {1493--1497},
}

Biosynthesis of plant cell walls requires UDP-glucose as the substrate for cellulose biosynthesis, and as an intermediate for the synthesis of other matrix polysaccharides. The sucrose cleaving enzyme sucrose synthase (SUS) is thought to have a central role in UDP-glucose biosynthesis, and a long-held and much debated hypothesis postulates that SUS is required to supply UDP-glucose to cellulose biosynthesis. To investigate the role of SUS in cellulose biosynthesis of Arabidopsis thaliana we characterized mutants in which four or all six Arabidopsis SUS genes were disrupted. These sus mutants showed no growth phenotypes, vascular tissue cell wall defects, or changes in cellulose content. Moreover, the UDP-glucose content of rosette leaves of the sextuple sus mutants was increased by approximately 20% compared with wild type. It can thus be concluded that cellulose biosynthesis is able to employ alternative UDP-glucose biosynthesis pathway(s), and thereby the model of SUS requirements for cellulose biosynthesis in Arabidopsis can be refuted.

@article{nibbering_cages_2022,
	title = {{CAGEs} are {Golgi}-localized {GT31} enzymes involved in cellulose biosynthesis in {Arabidopsis}},
	volume = {110},
	issn = {1365-313X},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/tpj.15734},
	doi = {10.1111/tpj.15734},
	abstract = {Cellulose is the main structural component in the plant cell walls. We show that two glycosyltransferase family 31 (GT31) enzymes of Arabidopsis thaliana, here named cellulose synthesis associated glycosyltransferases 1 and 2 (CAGE1 and 2), influence both primary and secondary cell wall cellulose biosynthesis. cage1cage2 mutants show primary cell wall defects manifesting as impaired growth and cell expansion in seedlings and etiolated hypocotyls, along with secondary cell wall defects, apparent as collapsed xylem vessels and reduced xylem wall thickness in the inflorescence stem. Single and double cage mutants also show increased sensitivity to the cellulose biosynthesis inhibitor isoxaben. The cage1cage2 phenotypes were associated with an approximately 30\% reduction in cellulose content, an approximately 50\% reduction in secondary cell wall CELLULOSE SYNTHASE (CESA) protein levels in stems and reduced cellulose biosynthesis rate in seedlings. CESA transcript levels were not significantly altered in cage1cage2 mutants, suggesting that the reduction in CESA levels was caused by a post-transcriptional mechanism. Both CAGE1 and 2 localize to the Golgi apparatus and are predicted to synthesize β-1,3-galactans on arabinogalactan proteins. In line with this, the cage1cage2 mutants exhibit reduced levels of β-Yariv binding to arabinogalactan protein linked β-1,3-galactan. This leads us to hypothesize that defects in arabinogalactan biosynthesis underlie the cellulose deficiency of the mutants.},
	language = {en},
	number = {5},
	urldate = {2022-06-09},
	journal = {The Plant Journal},
	author = {Nibbering, Pieter and Castilleux, Romain and Wingsle, Gunnar and Niittylä, Totte},
	year = {2022},
	keywords = {Arabidopsis, Golgi, arabinogalactan protein, cell wall, cellulose, glycosyltransferase family 31},
	pages = {1271--1285},
}

Cellulose is the main structural component in the plant cell walls. We show that two glycosyltransferase family 31 (GT31) enzymes of Arabidopsis thaliana, here named cellulose synthesis associated glycosyltransferases 1 and 2 (CAGE1 and 2), influence both primary and secondary cell wall cellulose biosynthesis. cage1cage2 mutants show primary cell wall defects manifesting as impaired growth and cell expansion in seedlings and etiolated hypocotyls, along with secondary cell wall defects, apparent as collapsed xylem vessels and reduced xylem wall thickness in the inflorescence stem. Single and double cage mutants also show increased sensitivity to the cellulose biosynthesis inhibitor isoxaben. The cage1cage2 phenotypes were associated with an approximately 30% reduction in cellulose content, an approximately 50% reduction in secondary cell wall CELLULOSE SYNTHASE (CESA) protein levels in stems and reduced cellulose biosynthesis rate in seedlings. CESA transcript levels were not significantly altered in cage1cage2 mutants, suggesting that the reduction in CESA levels was caused by a post-transcriptional mechanism. Both CAGE1 and 2 localize to the Golgi apparatus and are predicted to synthesize β-1,3-galactans on arabinogalactan proteins. In line with this, the cage1cage2 mutants exhibit reduced levels of β-Yariv binding to arabinogalactan protein linked β-1,3-galactan. This leads us to hypothesize that defects in arabinogalactan biosynthesis underlie the cellulose deficiency of the mutants.

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

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

@article{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{hernandez-verdeja_genomes_2022,
	title = {{GENOMES} {UNCOUPLED1} plays a key role during the de-etiolation process in {Arabidopsis}},
	volume = {235},
	issn = {1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/nph.18115},
	doi = {10.1111/nph.18115},
	abstract = {One of the most dramatic challenges in the life of a plant occurs when the seedling emerges from the soil and exposure to light triggers expression of genes required for establishment of photosynthesis. This process needs to be tightly regulated, as premature accumulation of light-harvesting proteins and photoreactive Chl precursors causes oxidative damage when the seedling is first exposed to light. Photosynthesis genes are encoded by both nuclear and plastid genomes, and to establish the required level of control, plastid-to-nucleus (retrograde) signalling is necessary to ensure correct gene expression. We herein show that a negative GENOMES UNCOUPLED1 (GUN1)-mediated retrograde signal restricts chloroplast development in darkness and during early light response by regulating the transcription of several critical transcription factors linked to light response, photomorphogenesis, and chloroplast development, and consequently their downstream target genes in Arabidopsis. Thus, the plastids play an essential role during skotomorphogenesis and the early light response, and GUN1 acts as a safeguard during the critical step of seedling emergence from darkness.},
	language = {en},
	number = {1},
	urldate = {2022-06-09},
	journal = {New Phytologist},
	author = {Hernández-Verdeja, Tamara and Vuorijoki, Linda and Jin, Xu and Vergara, Alexander and Dubreuil, Carole and Strand, Åsa},
	year = {2022},
	keywords = {GUN1, chloroplast, greening, light signalling, plastid retrograde signalling, transcriptional regulation},
	pages = {188--203},
}

One of the most dramatic challenges in the life of a plant occurs when the seedling emerges from the soil and exposure to light triggers expression of genes required for establishment of photosynthesis. This process needs to be tightly regulated, as premature accumulation of light-harvesting proteins and photoreactive Chl precursors causes oxidative damage when the seedling is first exposed to light. Photosynthesis genes are encoded by both nuclear and plastid genomes, and to establish the required level of control, plastid-to-nucleus (retrograde) signalling is necessary to ensure correct gene expression. We herein show that a negative GENOMES UNCOUPLED1 (GUN1)-mediated retrograde signal restricts chloroplast development in darkness and during early light response by regulating the transcription of several critical transcription factors linked to light response, photomorphogenesis, and chloroplast development, and consequently their downstream target genes in Arabidopsis. Thus, the plastids play an essential role during skotomorphogenesis and the early light response, and GUN1 acts as a safeguard during the critical step of seedling emergence from darkness.

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

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

@article{gaur_compensatory_2022,
	title = {Compensatory phenolic induction dynamics in aspen after aphid infestation},
	volume = {12},
	copyright = {2022 The Author(s)},
	issn = {2045-2322},
	url = {https://www.nature.com/articles/s41598-022-13225-x},
	doi = {10.1038/s41598-022-13225-x},
	abstract = {Condensed tannins (CTs) are polyphenolics and part of the total phenolic (TP) pool that shape resistance in aspen (Populus tremula). CTs are negatively associated with pathogens, but their resistance properties against herbivores are less understood. CTs shape resistance to pathogens and chewing herbivores and could also shape resistance to aphids. Being chemical pools that are highly variable it can further be questioned whether CT-shaped resistance is better described by constitutive levels, by the induced response potential, or by both. Here, aspen genotypes were propagated and selected to represent a range of inherent abilities to produce and store foliar CTs; the plantlets were then exposed to Chaitophorus aphid infestation and to mechanical (leaf rupture) damage, and the relative abundance of constitutive and induced CTs was related to aphid fitness parameters. As expected, aphid fecundity was negatively related to CT-concentrations of the aphid infested plants although more consistently related to TPs. While TPs increased in response to damage, CT induction was generally low and it even dropped below constitutive levels in more CT-rich genotypes, suggesting that constitutive CTs are more relevant measurements of resistance compared to induced CT-levels. Relating CT and TP dynamics with phenolic low molecular compounds further suggested that catechin (the building block of CTs) increased in response to aphid damage in amounts that correlated negatively with CT-induction and positively with constitutive CT-levels and aphid fecundity. Our study portrays dynamic phenolic responses to two kinds of damage detailed for major phenylpropanoid classes and suggests that the ability of a genotype to produce and store CTs may be a measurement of resistance, caused by other, more reactive, phenolic compounds such as catechin. Rupture damage however appeared to induce catechin levels oppositely supporting that CTs may respond differently to different kinds of damage.},
	language = {en},
	number = {1},
	urldate = {2022-06-13},
	journal = {Scientific Reports},
	author = {Gaur, Rajarshi Kumar and de Abreu, Ilka Nacif and Albrectsen, Benedicte Riber},
	month = jun,
	year = {2022},
	keywords = {Biochemistry, Plant sciences},
	pages = {9582},
}

Condensed tannins (CTs) are polyphenolics and part of the total phenolic (TP) pool that shape resistance in aspen (Populus tremula). CTs are negatively associated with pathogens, but their resistance properties against herbivores are less understood. CTs shape resistance to pathogens and chewing herbivores and could also shape resistance to aphids. Being chemical pools that are highly variable it can further be questioned whether CT-shaped resistance is better described by constitutive levels, by the induced response potential, or by both. Here, aspen genotypes were propagated and selected to represent a range of inherent abilities to produce and store foliar CTs; the plantlets were then exposed to Chaitophorus aphid infestation and to mechanical (leaf rupture) damage, and the relative abundance of constitutive and induced CTs was related to aphid fitness parameters. As expected, aphid fecundity was negatively related to CT-concentrations of the aphid infested plants although more consistently related to TPs. While TPs increased in response to damage, CT induction was generally low and it even dropped below constitutive levels in more CT-rich genotypes, suggesting that constitutive CTs are more relevant measurements of resistance compared to induced CT-levels. Relating CT and TP dynamics with phenolic low molecular compounds further suggested that catechin (the building block of CTs) increased in response to aphid damage in amounts that correlated negatively with CT-induction and positively with constitutive CT-levels and aphid fecundity. Our study portrays dynamic phenolic responses to two kinds of damage detailed for major phenylpropanoid classes and suggests that the ability of a genotype to produce and store CTs may be a measurement of resistance, caused by other, more reactive, phenolic compounds such as catechin. Rupture damage however appeared to induce catechin levels oppositely supporting that CTs may respond differently to different kinds of damage.

@article{funfgeld_sucrose_2022,
	title = {Sucrose synthases are not involved in starch synthesis in {Arabidopsis} leaves},
	volume = {8},
	copyright = {2022 The Author(s)},
	issn = {2055-0278},
	url = {https://www.nature.com/articles/s41477-022-01140-y},
	doi = {10.1038/s41477-022-01140-y},
	abstract = {Many plants accumulate transitory starch reserves in their leaves during the day to buffer their carbohydrate supply against fluctuating light conditions, and to provide carbon and energy for survival at night. It is universally accepted that transitory starch is synthesized from ADP-glucose (ADPG) in the chloroplasts. However, the consensus that ADPG is made in the chloroplasts by ADPG pyrophosphorylase has been challenged by a controversial proposal that ADPG is made primarily in the cytosol, probably by sucrose synthase (SUS), and then imported into the chloroplasts. To resolve this long-standing controversy, we critically re-examined the experimental evidence that appears to conflict with the consensus pathway. We show that when precautions are taken to avoid artefactual changes during leaf sampling, Arabidopsis thaliana mutants that lack SUS activity in mesophyll cells (quadruple sus1234) or have no SUS activity (sextuple sus123456) have wild-type levels of ADPG and starch, while ADPG is 20 times lower in the pgm and adg1 mutants that are blocked in the consensus chloroplastic pathway of starch synthesis. We conclude that the ADPG needed for starch synthesis in leaves is synthesized primarily by ADPG pyrophosphorylase in the chloroplasts.},
	language = {en},
	number = {5},
	urldate = {2022-05-30},
	journal = {Nature Plants},
	author = {Fünfgeld, Maximilian M. F. F. and Wang, Wei and Ishihara, Hirofumi and Arrivault, Stéphanie and Feil, Regina and Smith, Alison M. and Stitt, Mark and Lunn, John E. and Niittylä, Totte},
	month = may,
	year = {2022},
	keywords = {Plant molecular biology, Plant physiology},
	pages = {574--582},
}

Many plants accumulate transitory starch reserves in their leaves during the day to buffer their carbohydrate supply against fluctuating light conditions, and to provide carbon and energy for survival at night. It is universally accepted that transitory starch is synthesized from ADP-glucose (ADPG) in the chloroplasts. However, the consensus that ADPG is made in the chloroplasts by ADPG pyrophosphorylase has been challenged by a controversial proposal that ADPG is made primarily in the cytosol, probably by sucrose synthase (SUS), and then imported into the chloroplasts. To resolve this long-standing controversy, we critically re-examined the experimental evidence that appears to conflict with the consensus pathway. We show that when precautions are taken to avoid artefactual changes during leaf sampling, Arabidopsis thaliana mutants that lack SUS activity in mesophyll cells (quadruple sus1234) or have no SUS activity (sextuple sus123456) have wild-type levels of ADPG and starch, while ADPG is 20 times lower in the pgm and adg1 mutants that are blocked in the consensus chloroplastic pathway of starch synthesis. We conclude that the ADPG needed for starch synthesis in leaves is synthesized primarily by ADPG pyrophosphorylase in the chloroplasts.

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

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

@article{rabe_combining_2022,
	title = {Combining metabolic phenotype determination with metabolomics and transcriptional analyses to reveal pathways regulated by hydroxycarboxylic acid receptor 2},
	volume = {13},
	issn = {2730-6011},
	url = {https://doi.org/10.1007/s12672-022-00503-3},
	doi = {10.1007/s12672-022-00503-3},
	abstract = {The adaptation of cellular metabolism is considered a hallmark of cancer. Oncogenic signaling pathways support tumorigenesis and cancer progression through the induction of certain metabolic phenotypes associated with altered regulation of key metabolic enzymes. Hydroxycarboxylic acid receptor 2 (HCA2) is a G protein-coupled receptor previously shown to act as a tumor suppressor. Here, we aimed to unveil the connection between cellular metabolism and HCA2 in BT-474 cells. Moreover, we intend to clarify how well this metabolic phenotype is reflected in transcriptional changes and metabolite levels as determined by global metabolomics analyses.},
	language = {en},
	number = {1},
	urldate = {2022-06-17},
	journal = {Discover Oncology},
	author = {Rabe, Philipp and Gehmlich, Mareike and Peters, Anna and Krumbholz, Petra and Nordström, Anders and Stäubert, Claudia},
	month = jun,
	year = {2022},
	keywords = {Cancer metabolism, GPR109A, HCA2, LC-MS, Metabolite profile, Metabolite-sensing GPCR},
	pages = {47},
}

The adaptation of cellular metabolism is considered a hallmark of cancer. Oncogenic signaling pathways support tumorigenesis and cancer progression through the induction of certain metabolic phenotypes associated with altered regulation of key metabolic enzymes. Hydroxycarboxylic acid receptor 2 (HCA2) is a G protein-coupled receptor previously shown to act as a tumor suppressor. Here, we aimed to unveil the connection between cellular metabolism and HCA2 in BT-474 cells. Moreover, we intend to clarify how well this metabolic phenotype is reflected in transcriptional changes and metabolite levels as determined by global metabolomics analyses.

@article{heuchel_genetic_2022,
	title = {Genetic diversity and background pollen contamination in {Norway} spruce and {Scots} pine seed orchard crops},
	volume = {2},
	copyright = {2022 The Author(s)},
	issn = {2767-3812},
	url = {https://www.maxapress.com/rticle/doi/10.48130/FR-2022-0008},
	doi = {10.48130/FR-2022-0008},
	abstract = {Seed orchards are the key link between tree breeding and production forest for conifer trees. In Sweden, Scots pine and Norway spruce seed orchards currently supply ca. 85\% of seedlings used in annual reforestation. The functionality of these seed orchards is thus crucial for supporting long-term production gain and sustainable diversity. We conducted a large-scale genetic investigation of pine and spruce orchards across Sweden using genotyping-by-sequencing. We genotyped 3,300 seedlings/trees from six orchards and 10 natural stands to gain an overview of mating structure and genetic diversity in orchard crops. We found clear differences in observed heterozygosity (\textit{H}$_{\textrm{O}}$) and background pollen contamination (BPC) rates between species, with pine orchard crops showing higher \textit{H}$_{\textrm{O}}$ and BPC than spruce. BPC in pine crops varied from 87\% at young orchard age to 12\% at mature age, wherease this rate ranged between 27\%−4\% in spruce crops. Substantial variance in parental contribution was observed in all orchards with 30\%−50\% parents contibuting to 80\% of the progeny. Selfing was low (2\%−6\%) in all seed crops. Compared to natural stands, orchard crops had slightly lower \textit{H}$_{\textrm{O}}$ but no strong signal of inbreeding. Our results provide valuable references for orchard management.},
	language = {en},
	number = {1},
	urldate = {2022-06-03},
	journal = {Forestry Research},
	author = {Heuchel, Alisa and Hall, David and Zhao, Wei and Gao, Jie and Wennström, Ulfstand and Wang, Xiao-Ru and Heuchel, Alisa and Hall, David and Zhao, Wei and Gao, Jie and Wennström, Ulfstand and Wang, Xiao-Ru},
	month = jun,
	year = {2022},
	pages = {1--12},
}

Seed orchards are the key link between tree breeding and production forest for conifer trees. In Sweden, Scots pine and Norway spruce seed orchards currently supply ca. 85% of seedlings used in annual reforestation. The functionality of these seed orchards is thus crucial for supporting long-term production gain and sustainable diversity. We conducted a large-scale genetic investigation of pine and spruce orchards across Sweden using genotyping-by-sequencing. We genotyped 3,300 seedlings/trees from six orchards and 10 natural stands to gain an overview of mating structure and genetic diversity in orchard crops. We found clear differences in observed heterozygosity (H$_{\textrm{O}}$) and background pollen contamination (BPC) rates between species, with pine orchard crops showing higher H$_{\textrm{O}}$ and BPC than spruce. BPC in pine crops varied from 87% at young orchard age to 12% at mature age, wherease this rate ranged between 27%−4% in spruce crops. Substantial variance in parental contribution was observed in all orchards with 30%−50% parents contibuting to 80% of the progeny. Selfing was low (2%−6%) in all seed crops. Compared to natural stands, orchard crops had slightly lower H$_{\textrm{O}}$ but no strong signal of inbreeding. Our results provide valuable references for orchard management.

@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{long_dgat1_2022,
	title = {{DGAT1} activity synchronises with mitophagy to protect cells from metabolic rewiring by iron  depletion},
	issn = {0261-4189},
	url = {https://www.embopress.org/doi/full/10.15252/embj.2021109390},
	doi = {10.15252/embj.2021109390},
	abstract = {Mitophagy removes defective mitochondria via lysosomal elimination. Increased mitophagy coincides with metabolic reprogramming, yet it remains unknown whether mitophagy is a cause or consequence of such state changes. The signalling pathways that integrate with mitophagy to sustain cell and tissue integrity also remain poorly defined. We performed temporal metabolomics on mammalian cells treated with deferiprone, a therapeutic iron chelator that stimulates PINK1/PARKIN-independent mitophagy. Iron depletion profoundly rewired the metabolome, hallmarked by remodelling of lipid metabolism within minutes of treatment. DGAT1-dependent lipid droplet biosynthesis occurred several hours before mitochondrial clearance, with lipid droplets bordering mitochondria upon iron chelation. We demonstrate that DGAT1 inhibition restricts mitophagy in vitro, with impaired lysosomal homeostasis and cell viability. Importantly, genetic depletion of DGAT1 in vivo significantly impaired neuronal mitophagy and locomotor function in Drosophila. Our data define iron depletion as a potent signal that rapidly reshapes metabolism and establishes an unexpected synergy between lipid homeostasis and mitophagy that safeguards cell and tissue integrity.},
	urldate = {2022-04-19},
	journal = {The EMBO Journal},
	author = {Long, Maeve and Sanchez-Martinez, Alvaro and Longo, Marianna and Suomi, Fumi and Stenlund, Hans and Johansson, Annika I. and Ehsan, Homa and Salo, Veijo T. and Montava-Garriga, Lambert and Naddafi, Seyedehshima and Ikonen, Elina and Ganley, Ian G. and Whitworth, Alexander J. and McWilliams, Thomas G.},
	month = apr,
	year = {2022},
	keywords = {DGAT1, iron, lipid droplet, metabolism, mitophagy},
	pages = {e109390},
}

Mitophagy removes defective mitochondria via lysosomal elimination. Increased mitophagy coincides with metabolic reprogramming, yet it remains unknown whether mitophagy is a cause or consequence of such state changes. The signalling pathways that integrate with mitophagy to sustain cell and tissue integrity also remain poorly defined. We performed temporal metabolomics on mammalian cells treated with deferiprone, a therapeutic iron chelator that stimulates PINK1/PARKIN-independent mitophagy. Iron depletion profoundly rewired the metabolome, hallmarked by remodelling of lipid metabolism within minutes of treatment. DGAT1-dependent lipid droplet biosynthesis occurred several hours before mitochondrial clearance, with lipid droplets bordering mitochondria upon iron chelation. We demonstrate that DGAT1 inhibition restricts mitophagy in vitro, with impaired lysosomal homeostasis and cell viability. Importantly, genetic depletion of DGAT1 in vivo significantly impaired neuronal mitophagy and locomotor function in Drosophila. Our data define iron depletion as a potent signal that rapidly reshapes metabolism and establishes an unexpected synergy between lipid homeostasis and mitophagy that safeguards cell and tissue integrity.

@article{jonsson_plant_2022,
	title = {Plant cell walls as mechanical signaling hubs for morphogenesis},
	volume = {32},
	issn = {0960-9822},
	url = {https://www.sciencedirect.com/science/article/pii/S0960982222002585},
	doi = {10.1016/j.cub.2022.02.036},
	abstract = {The instructive role of mechanical cues during morphogenesis is increasingly being recognized in all kingdoms. Patterns of mechanical stress depend on shape, growth and external factors. In plants, the cell wall integrates these three parameters to function as a hub for mechanical feedback. Plant cells are interconnected by cell walls that provide structural integrity and yet are flexible enough to act as both targets and transducers of mechanical cues. Such cues may act locally at the subcellular level or across entire tissues, requiring tight control of both cell-wall composition and cell–cell adhesion. Here we focus on how changes in cell-wall chemistry and mechanics act in communicating diverse cues to direct growth asymmetries required for plant morphogenesis. We explore the role of cellulose microfibrils, microtubule arrays and pectin methylesterification in the transduction of mechanical cues during morphogenesis. Plant hormones can affect the mechanochemical composition of the cell wall and, in turn, the cell wall can modulate hormone signaling pathways, as well as the tissue-level distribution of these hormones. This also leads us to revisit the position of biochemical growth factors, such as plant hormones, acting both upstream and downstream of mechanical signaling. Finally, while the structure of the cell wall is being elucidated with increasing precision, existing data clearly show that the integration of genetic, biochemical and theoretical studies will be essential for a better understanding of the role of the cell wall as a hub for the mechanical control of plant morphogenesis.},
	language = {en},
	number = {7},
	urldate = {2022-05-20},
	journal = {Current Biology},
	author = {Jonsson, Kristoffer and Hamant, Olivier and Bhalerao, Rishikesh P.},
	month = apr,
	year = {2022},
	pages = {R334--R340},
}

The instructive role of mechanical cues during morphogenesis is increasingly being recognized in all kingdoms. Patterns of mechanical stress depend on shape, growth and external factors. In plants, the cell wall integrates these three parameters to function as a hub for mechanical feedback. Plant cells are interconnected by cell walls that provide structural integrity and yet are flexible enough to act as both targets and transducers of mechanical cues. Such cues may act locally at the subcellular level or across entire tissues, requiring tight control of both cell-wall composition and cell–cell adhesion. Here we focus on how changes in cell-wall chemistry and mechanics act in communicating diverse cues to direct growth asymmetries required for plant morphogenesis. We explore the role of cellulose microfibrils, microtubule arrays and pectin methylesterification in the transduction of mechanical cues during morphogenesis. Plant hormones can affect the mechanochemical composition of the cell wall and, in turn, the cell wall can modulate hormone signaling pathways, as well as the tissue-level distribution of these hormones. This also leads us to revisit the position of biochemical growth factors, such as plant hormones, acting both upstream and downstream of mechanical signaling. Finally, while the structure of the cell wall is being elucidated with increasing precision, existing data clearly show that the integration of genetic, biochemical and theoretical studies will be essential for a better understanding of the role of the cell wall as a hub for the mechanical control of plant morphogenesis.

@article{domevscik_large-scale_2022,
	title = {Large-scale assessment of artificially coated seeds for forest regeneration across {Sweden}},
	issn = {1573-5095},
	url = {https://doi.org/10.1007/s11056-022-09920-2},
	doi = {10.1007/s11056-022-09920-2},
	abstract = {We report the results of two years’ field performance of Scots pine (Pinus sylvestris) seedlings regenerated using artificially coated seeds. The coated seeds were used for regeneration on 12 clearcut sites, covering a 1000 km latitudinal gradient across Sweden. The coating was either combined with arginine-phosphate fertilizer (10 mg N per seed) or had no additions. Interactions with environmental variables associated with sites were also assessed. Coated seeds were deployed in May–June 2017 and surveyed in August–September of 2018 and 2019. After two years, the mean establishment rate of seedlings from coated seeds was 56 ± 4\% across the 12 sites. The fertilizer addition did not affect survival, and the biomass response to fertilizer varied significantly between sites. Maximum precipitation and wind speed during the first six weeks after deployment were correlated with seedling survival, regardless of fertilization treatment. Establishment increased with increasing precipitation and decreased with increasing wind speed. This highlights the importance of initial weather conditions for the seeds’ establishment. Our data suggest that Scots pine regeneration using coated seeds can be practiced in boreal forests, but also that the method is sensitive to the weather conditions at the time of deployment of the seeds.},
	language = {en},
	urldate = {2022-05-20},
	journal = {New Forests},
	author = {Domevscik, Matej and Häggström, Bodil and Lim, Hyungwoo and Öhlund, Jonas and Nordin, Annika},
	month = may,
	year = {2022},
	keywords = {Boreal forest, Coated seeds, Forest regeneration, Scots pine, SeedPAD, Seeding},
}

We report the results of two years’ field performance of Scots pine (Pinus sylvestris) seedlings regenerated using artificially coated seeds. The coated seeds were used for regeneration on 12 clearcut sites, covering a 1000 km latitudinal gradient across Sweden. The coating was either combined with arginine-phosphate fertilizer (10 mg N per seed) or had no additions. Interactions with environmental variables associated with sites were also assessed. Coated seeds were deployed in May–June 2017 and surveyed in August–September of 2018 and 2019. After two years, the mean establishment rate of seedlings from coated seeds was 56 ± 4% across the 12 sites. The fertilizer addition did not affect survival, and the biomass response to fertilizer varied significantly between sites. Maximum precipitation and wind speed during the first six weeks after deployment were correlated with seedling survival, regardless of fertilization treatment. Establishment increased with increasing precipitation and decreased with increasing wind speed. This highlights the importance of initial weather conditions for the seeds’ establishment. Our data suggest that Scots pine regeneration using coated seeds can be practiced in boreal forests, but also that the method is sensitive to the weather conditions at the time of deployment of the seeds.

@incollection{anjam_rna_2022,
	address = {New York, NY},
	series = {Methods in {Molecular} {Biology}},
	title = {{RNA} {Isolation} from {Nematode}-{Induced} {Feeding} {Sites} in {Arabidopsis} {RootsRoots} {Using} {Laser} {Capture} {Microdissection}},
	isbn = {978-1-07-162297-1},
	url = {https://doi.org/10.1007/978-1-0716-2297-1_22},
	abstract = {Nematodes are diverse multicellular organisms that are most abundantly found in the soil. Most nematodes are free-living and feed on a range of organisms. Based on their feeding habits, soil nematodes can be classified into four groups: bacterial, omnivorous, fungal, and plant-feeding. Plant-parasitic nematodes (PPNs) are a serious threat to global food security, causing substantial losses to the agricultural sector. Root-knot and cyst nematodes are the most important of PPNs, significantly limiting the yield of commercial crops such as sugar beet, mustard, and cauliflower. The life cycle of these nematodes consists of four molting stages (J1–J4) that precede adulthood. Nonetheless, only second-stage juveniles (J2), which hatch from eggs, are infective worms that can parasitize the host’s roots. The freshly hatched juveniles (J2) of beet cyst nematode, Heterodera schachtii, establish a permanent feeding site inside the roots of the host plant. A cocktail of proteinaceous secretions is injected into a selected cell which later develops into a syncytium via local cell wall dissolution of several hundred neighboring cells. The formation of syncytium is accompanied by massive transcriptional, metabolic, and proteomic changes inside the host tissues. It creates a metabolic sink in which solutes are translocated to feed the nematodes throughout their life cycle. Deciphering the molecular signaling cascades during syncytium establishment is thus essential in studying the plant-nematode interactions and ensuring sustainability in agricultural practices. However, isolating RNA, protein, and metabolites from syncytial cells remains challenging. Extensive use of laser capture microdissection (LCM) in animal and human tissues has shown this approach to be a powerful technique for isolating a single cell from complex tissues. Here, we describe a simplified protocol for Arabidopsis-Heterodera schachtii infection assays, which is routinely applied in several plant-nematode laboratories. Next, we provide a detailed protocol for isolating high-quality RNA from syncytial cells induced by Heterodera schachtii in the roots of Arabidopsis thaliana plants.},
	language = {en},
	urldate = {2022-04-29},
	booktitle = {Environmental {Responses} in {Plants}: {Methods} and {Protocols}},
	publisher = {Springer US},
	author = {Anjam, Muhammad Shahzad and Siddique, Shahid and Marhavy, Peter},
	editor = {Duque, Paula and Szakonyi, Dóra},
	year = {2022},
	keywords = {Arabidopsis root dissection, Laser capture dissection, Plant-nematode infection, RNA extraction, Syncytial cell isolation},
	pages = {313--324},
}

Nematodes are diverse multicellular organisms that are most abundantly found in the soil. Most nematodes are free-living and feed on a range of organisms. Based on their feeding habits, soil nematodes can be classified into four groups: bacterial, omnivorous, fungal, and plant-feeding. Plant-parasitic nematodes (PPNs) are a serious threat to global food security, causing substantial losses to the agricultural sector. Root-knot and cyst nematodes are the most important of PPNs, significantly limiting the yield of commercial crops such as sugar beet, mustard, and cauliflower. The life cycle of these nematodes consists of four molting stages (J1–J4) that precede adulthood. Nonetheless, only second-stage juveniles (J2), which hatch from eggs, are infective worms that can parasitize the host’s roots. The freshly hatched juveniles (J2) of beet cyst nematode, Heterodera schachtii, establish a permanent feeding site inside the roots of the host plant. A cocktail of proteinaceous secretions is injected into a selected cell which later develops into a syncytium via local cell wall dissolution of several hundred neighboring cells. The formation of syncytium is accompanied by massive transcriptional, metabolic, and proteomic changes inside the host tissues. It creates a metabolic sink in which solutes are translocated to feed the nematodes throughout their life cycle. Deciphering the molecular signaling cascades during syncytium establishment is thus essential in studying the plant-nematode interactions and ensuring sustainability in agricultural practices. However, isolating RNA, protein, and metabolites from syncytial cells remains challenging. Extensive use of laser capture microdissection (LCM) in animal and human tissues has shown this approach to be a powerful technique for isolating a single cell from complex tissues. Here, we describe a simplified protocol for Arabidopsis-Heterodera schachtii infection assays, which is routinely applied in several plant-nematode laboratories. Next, we provide a detailed protocol for isolating high-quality RNA from syncytial cells induced by Heterodera schachtii in the roots of Arabidopsis thaliana plants.

@article{hallberg-sramek_bringing_2022,
	title = {Bringing “{Climate}-{Smart} {Forestry}” {Down} to the {Local} {Level}—{Identifying} {Barriers}, {Pathways} and {Indicators} for {Its} {Implementation} in {Practice}},
	volume = {13},
	copyright = {http://creativecommons.org/licenses/by/3.0/},
	issn = {1999-4907},
	url = {https://www.mdpi.com/1999-4907/13/1/98},
	doi = {10/gn3n2b},
	abstract = {The theoretical concept of “climate-smart forestry” aims to integrate climate change mitigation and adaptation to maintain and enhance forests’ contributions to people and global agendas. We carried out two local transdisciplinary collaboration processes with the aim of developing local articulations of climate-smart forestry and to identify barriers, pathways and indicators to applying it in practice. During workshops in northern and southern Sweden, local stakeholders described how they would like forests to be managed, considering their past experiences, future visions and climate change. As a result, the stakeholders framed climate-smart forestry as active and diverse management towards multiple goals. They identified several conditions that could act both as barriers and pathways for its implementation in practice, such as value chains for forest products and services, local knowledge and experiences of different management alternatives, and the management of ungulates. Based on the workshop material, a total of 39 indicators for climate-smart forestry were identified, of which six were novel indicators adding to the existing literature. Our results emphasize the importance of understanding the local perspectives to promote climate-smart forestry practices across Europe. We also suggest how the concept of climate-smart forestry can be further developed, through the interplay between theory and practice.},
	language = {en},
	number = {1},
	urldate = {2022-03-16},
	journal = {Forests},
	author = {Hallberg-Sramek, Isabella and Reimerson, Elsa and Priebe, Janina and Nordström, Eva-Maria and Mårald, Erland and Sandström, Camilla and Nordin, Annika},
	month = jan,
	year = {2022},
	keywords = {adaptation, climate change, forest policy, interdisciplinary research, mitigation, nature’s contributions to people, stakeholder participation, sustainable forest management, transdisciplinary collaboration},
	pages = {98},
}

The theoretical concept of “climate-smart forestry” aims to integrate climate change mitigation and adaptation to maintain and enhance forests’ contributions to people and global agendas. We carried out two local transdisciplinary collaboration processes with the aim of developing local articulations of climate-smart forestry and to identify barriers, pathways and indicators to applying it in practice. During workshops in northern and southern Sweden, local stakeholders described how they would like forests to be managed, considering their past experiences, future visions and climate change. As a result, the stakeholders framed climate-smart forestry as active and diverse management towards multiple goals. They identified several conditions that could act both as barriers and pathways for its implementation in practice, such as value chains for forest products and services, local knowledge and experiences of different management alternatives, and the management of ungulates. Based on the workshop material, a total of 39 indicators for climate-smart forestry were identified, of which six were novel indicators adding to the existing literature. Our results emphasize the importance of understanding the local perspectives to promote climate-smart forestry practices across Europe. We also suggest how the concept of climate-smart forestry can be further developed, through the interplay between theory and practice.

@article{miao_katanin-dependent_2022,
	title = {Katanin-{Dependent} {Microtubule} {Ordering} in {Association} with {ABA} {Is} {Important} for {Root} {Hydrotropism}},
	volume = {23},
	copyright = {http://creativecommons.org/licenses/by/3.0/},
	issn = {1422-0067},
	url = {https://www.mdpi.com/1422-0067/23/7/3846},
	doi = {10.3390/ijms23073846},
	abstract = {Root hydrotropism refers to root directional growth toward soil moisture. Cortical microtubule arrays are essential for determining the growth axis of the elongating cells in plants. However, the role of microtubule reorganization in root hydrotropism remains elusive. Here, we demonstrate that the well-ordered microtubule arrays and the microtubule-severing protein KATANIN (KTN) play important roles in regulating root hydrotropism in Arabidopsis. We found that the root hydrotropic bending of the ktn1 mutant was severely attenuated but not root gravitropism. After hydrostimulation, cortical microtubule arrays in cells of the elongation zone of wild-type (WT) Col-0 roots were reoriented from transverse into an oblique array along the axis of cell elongation, whereas the microtubule arrays in the ktn1 mutant remained in disorder. Moreover, we revealed that abscisic acid (ABA) signaling enhanced the root hydrotropism of WT and partially rescued the oryzalin (a microtubule destabilizer) alterative root hydrotropism of WT but not ktn1 mutants. These results suggest that katanin-dependent microtubule ordering is required for root hydrotropism, which might work downstream of ABA signaling pathways for plant roots to search for water.},
	language = {en},
	number = {7},
	urldate = {2022-04-19},
	journal = {International Journal of Molecular Sciences},
	author = {Miao, Rui and Siao, Wei and Zhang, Na and Lei, Zuliang and Lin, Deshu and Bhalerao, Rishikesh P. and Lu, Congming and Xu, Weifeng},
	month = jan,
	year = {2022},
	keywords = {KATANIN, abscisic acid, cortical microtubule arrays, oryzalin, root hydrotropism},
	pages = {3846},
}

Root hydrotropism refers to root directional growth toward soil moisture. Cortical microtubule arrays are essential for determining the growth axis of the elongating cells in plants. However, the role of microtubule reorganization in root hydrotropism remains elusive. Here, we demonstrate that the well-ordered microtubule arrays and the microtubule-severing protein KATANIN (KTN) play important roles in regulating root hydrotropism in Arabidopsis. We found that the root hydrotropic bending of the ktn1 mutant was severely attenuated but not root gravitropism. After hydrostimulation, cortical microtubule arrays in cells of the elongation zone of wild-type (WT) Col-0 roots were reoriented from transverse into an oblique array along the axis of cell elongation, whereas the microtubule arrays in the ktn1 mutant remained in disorder. Moreover, we revealed that abscisic acid (ABA) signaling enhanced the root hydrotropism of WT and partially rescued the oryzalin (a microtubule destabilizer) alterative root hydrotropism of WT but not ktn1 mutants. These results suggest that katanin-dependent microtubule ordering is required for root hydrotropism, which might work downstream of ABA signaling pathways for plant roots to search for water.

@article{niu_chinese_2022,
	title = {The {Chinese} pine genome and methylome unveil key features of conifer evolution},
	volume = {185},
	issn = {0092-8674, 1097-4172},
	url = {https://www.cell.com/cell/abstract/S0092-8674(21)01428-8},
	doi = {10/gnw8q5},
	abstract = {Conifers dominate the world’s forest ecosystems and are the most widely planted tree species. Their giant and complex genomes present great challenges for assembling a complete reference genome for evolutionary and genomic studies. We present a 25.4-Gb chromosome-level assembly of Chinese pine (Pinus tabuliformis) and revealed that its genome size is mostly attributable to huge intergenic regions and long introns with high transposable element (TE) content. Large genes with long introns exhibited higher expressions levels. Despite a lack of recent whole-genome duplication, 91.2\% of genes were duplicated through dispersed duplication, and expanded gene families are mainly related to stress responses, which may underpin conifers’ adaptation, particularly in cold and/or arid conditions. The reproductive regulation network is distinct compared with angiosperms. Slow removal of TEs with high-level methylation may have contributed to genomic expansion. This study provides insights into conifer evolution and resources for advancing research on conifer adaptation and development.},
	language = {English},
	number = {1},
	urldate = {2022-02-04},
	journal = {Cell},
	author = {Niu, Shihui and Li, Jiang and Bo, Wenhao and Yang, Weifei and Zuccolo, Andrea and Giacomello, Stefania and Chen, Xi and Han, Fangxu and Yang, Junhe and Song, Yitong and Nie, Yumeng and Zhou, Biao and Wang, Peiyi and Zuo, Quan and Zhang, Hui and Ma, Jingjing and Wang, Jun and Wang, Lvji and Zhu, Qianya and Zhao, Huanhuan and Liu, Zhanmin and Zhang, Xuemei and Liu, Tao and Pei, Surui and Li, Zhimin and Hu, Yao and Yang, Yehui and Li, Wenzhao and Zan, Yanjun and Zhou, Linghua and Lin, Jinxing and Yuan, Tongqi and Li, Wei and Li, Yue and Wei, Hairong and Wu, Harry X.},
	month = jan,
	year = {2022},
	keywords = {Chinese pine, chromosome-level genome, climate adaptation, conifer evolution, conifer reproduction, gene expression, genome expansion, long intron, methylome},
	pages = {204--217.e14},
}

Conifers dominate the world’s forest ecosystems and are the most widely planted tree species. Their giant and complex genomes present great challenges for assembling a complete reference genome for evolutionary and genomic studies. We present a 25.4-Gb chromosome-level assembly of Chinese pine (Pinus tabuliformis) and revealed that its genome size is mostly attributable to huge intergenic regions and long introns with high transposable element (TE) content. Large genes with long introns exhibited higher expressions levels. Despite a lack of recent whole-genome duplication, 91.2% of genes were duplicated through dispersed duplication, and expanded gene families are mainly related to stress responses, which may underpin conifers’ adaptation, particularly in cold and/or arid conditions. The reproductive regulation network is distinct compared with angiosperms. Slow removal of TEs with high-level methylation may have contributed to genomic expansion. This study provides insights into conifer evolution and resources for advancing research on conifer adaptation and development.

@article{kolbeck_casp_2022,
	title = {{CASP} microdomain formation requires cross cell wall stabilization of domains and non-cell autonomous action of {LOTR1}},
	volume = {11},
	issn = {2050-084X},
	url = {https://doi.org/10.7554/eLife.69602},
	doi = {10/gpjfdm},
	abstract = {Efficient uptake of nutrients in both animal and plant cells requires tissue-spanning diffusion barriers separating inner tissues from the outer lumen/soil. However, we poorly understand how such contiguous three-dimensional superstructures are formed in plants. Here, we show that correct establishment of the plant Casparian Strip (CS) network relies on local neighbor communication. We show that positioning of Casparian Strip membrane domains (CSDs) is tightly coordinated between neighbors in wild-type and that restriction of domain formation involves the putative extracellular protease LOTR1. Impaired domain restriction in lotr1 leads to fully functional CSDs at ectopic positions, forming ‘half strips’. LOTR1 action in the endodermis requires its expression in the stele. LOTR1 endodermal expression cannot complement, while cortex expression causes a dominant-negative phenotype. Our findings establish LOTR1 as a crucial player in CSD positioning acting in a directional, non-cell-autonomous manner to restrict and coordinate CS positioning.},
	urldate = {2022-02-17},
	journal = {eLife},
	author = {Kolbeck, Andreas and Marhavý, Peter and De Bellis, Damien and Li, Baohai and Kamiya, Takehiro and Fujiwara, Toru and Kalmbach, Lothar and Geldner, Niko},
	editor = {Benitez-Alfonso, Yoselin and Kleine-Vehn, Jürgen and Jallais, Yvon and Somssich, Marc},
	month = jan,
	year = {2022},
	keywords = {arabidopsis, casparian strip, endodermis, microdomains, neprosin, network},
	pages = {e69602},
}

Efficient uptake of nutrients in both animal and plant cells requires tissue-spanning diffusion barriers separating inner tissues from the outer lumen/soil. However, we poorly understand how such contiguous three-dimensional superstructures are formed in plants. Here, we show that correct establishment of the plant Casparian Strip (CS) network relies on local neighbor communication. We show that positioning of Casparian Strip membrane domains (CSDs) is tightly coordinated between neighbors in wild-type and that restriction of domain formation involves the putative extracellular protease LOTR1. Impaired domain restriction in lotr1 leads to fully functional CSDs at ectopic positions, forming ‘half strips’. LOTR1 action in the endodermis requires its expression in the stele. LOTR1 endodermal expression cannot complement, while cortex expression causes a dominant-negative phenotype. Our findings establish LOTR1 as a crucial player in CSD positioning acting in a directional, non-cell-autonomous manner to restrict and coordinate CS positioning.

@article{hodek_mixed-mode_2022,
	title = {Mixed-mode chromatography-mass spectrometry enables targeted and untargeted screening of carboxylic acids in biological samples},
	volume = {14},
	issn = {1759-9679},
	url = {https://pubs.rsc.org/en/content/articlelanding/2022/ay/d1ay02143e},
	doi = {10/gpkx25},
	abstract = {Carboxylic acids are crucial metabolites in the tricarboxylic acid (TCA) cycle and thus participate in central carbon metabolism (CCM). Research dependent on the analysis of metabolites involved in central carbon metabolism requires fast separation and sensitive detection of carboxylic acids using liquid chromatography-mass spectrometry (LC-MS). However, successful separation of all carboxylic acids from the TCA cycle by liquid chromatography remains a challenging task because of their high polarity and thus low retention on the conventional reversed-phase columns. In this study, we tested a reversed-phase/anion exchange mixed-mode stationary phase (Waters BEH C18 AX) using liquid chromatography-tandem mass spectrometry (LC-MS/MS). We developed and optimized a method that enables a 10 minute separation of all carboxylic acids from the TCA cycle and lactic acid without prior derivatization or addition of ion-pair reagents in the mobile phase. The developed method was validated for quantification of 8 acids in murine brown preadipocytes, 5 acids in human plasma and 6 acids in Arabidopsis thaliana leaves with limits of quantification ranging from 0.1 μM for malic acid to 10 μM for isocitric acid. Moreover, the mixed-mode chromatography enabled untargeted screening of medium- to long-chain fatty acids in murine brown preadipocytes, Arabidopsis thaliana, and human plasma, where 23 fatty acids were identified by using liquid chromatography with high-resolution mass spectrometry (HRMS).},
	language = {en},
	number = {10},
	urldate = {2022-02-25},
	journal = {Analytical Methods},
	author = {Hodek, Ondřej and Argemi-Muntadas, Lidia and Khan, Adnan and Moritz, Thomas},
	month = jan,
	year = {2022},
	pages = {1015--1022},
}

Carboxylic acids are crucial metabolites in the tricarboxylic acid (TCA) cycle and thus participate in central carbon metabolism (CCM). Research dependent on the analysis of metabolites involved in central carbon metabolism requires fast separation and sensitive detection of carboxylic acids using liquid chromatography-mass spectrometry (LC-MS). However, successful separation of all carboxylic acids from the TCA cycle by liquid chromatography remains a challenging task because of their high polarity and thus low retention on the conventional reversed-phase columns. In this study, we tested a reversed-phase/anion exchange mixed-mode stationary phase (Waters BEH C18 AX) using liquid chromatography-tandem mass spectrometry (LC-MS/MS). We developed and optimized a method that enables a 10 minute separation of all carboxylic acids from the TCA cycle and lactic acid without prior derivatization or addition of ion-pair reagents in the mobile phase. The developed method was validated for quantification of 8 acids in murine brown preadipocytes, 5 acids in human plasma and 6 acids in Arabidopsis thaliana leaves with limits of quantification ranging from 0.1 μM for malic acid to 10 μM for isocitric acid. Moreover, the mixed-mode chromatography enabled untargeted screening of medium- to long-chain fatty acids in murine brown preadipocytes, Arabidopsis thaliana, and human plasma, where 23 fatty acids were identified by using liquid chromatography with high-resolution mass spectrometry (HRMS).

@article{marabita_multiomics_2022,
	title = {Multiomics and digital monitoring during lifestyle changes reveal independent dimensions of human biology and health},
	volume = {13},
	issn = {2405-4712},
	url = {https://www.cell.com/cell-systems/abstract/S2405-4712(21)00451-8},
	doi = {10.1016/j.cels.2021.11.001},
	language = {English},
	number = {3},
	urldate = {2022-04-08},
	journal = {Cell Systems},
	author = {Marabita, Francesco and James, Tojo and Karhu, Anu and Virtanen, Heidi and Kettunen, Kaisa and Stenlund, Hans and Boulund, Fredrik and Hellström, Cecilia and Neiman, Maja and Mills, Robert and Perheentupa, Teemu and Laivuori, Hannele and Helkkula, Pyry and Byrne, Myles and Jokinen, Ilkka and Honko, Harri and Kallonen, Antti and Ermes, Miikka and Similä, Heidi and Lindholm, Mikko and Widén, Elisabeth and Ripatti, Samuli and Perälä-Heape, Maritta and Engstrand, Lars and Nilsson, Peter and Moritz, Thomas and Miettinen, Timo and Sallinen, Riitta and Kallioniemi, Olli},
	month = mar,
	year = {2022},
	keywords = {P4 medicine, lifestyle changes, multiomics data integration, personalized medicine, precision health, precision medicine, systems medicine},
	pages = {241--255.e7},
}

@incollection{chantreau_spatio-temporal_2022,
	title = {Spatio-temporal regulation of lignification},
	url = {https://www.sciencedirect.com/science/article/pii/S0065229622000398},
	abstract = {Lignin is a poly-aromatic polymer found in plant cell walls. This polymer, mainly composed of three phenylpropanoid units, confers exceptional properties to the cell wall such as hydrophobicity, mechanical strength, or resistance against stresses. Thereby the cell wall deposition of lignin represents often the main molecular event that defines the biological function(s) of the lignified cell or tissue. The time and localization of lignin deposition as well as the composition of the polymer can be considered as the three essential components of the polymer that will define the biological function of the lignified tissue. In this review, we will cover the localizations, types and functions of lignin found in various part of land plants. Then, for the various lignified tissues, the mechanisms controlling the developmental deposition of lignin such as transcriptional regulation, intercellular coordinated control of lignification or posttranslational modification of proteins will be discussed. Finally, a focus will be made on the environmental cues that influence the lignification during radial tree growth, as well as the plant responses that these signals trigger in the regulation of lignification.},
	language = {en},
	urldate = {2022-04-26},
	booktitle = {Advances in {Botanical} {Research}},
	publisher = {Academic Press},
	author = {Chantreau, Maxime and Tuominen, Hannele},
	month = apr,
	year = {2022},
	keywords = {Lignification, Lignin, Non-cell autonomous lignification, Regulation},
}

Lignin is a poly-aromatic polymer found in plant cell walls. This polymer, mainly composed of three phenylpropanoid units, confers exceptional properties to the cell wall such as hydrophobicity, mechanical strength, or resistance against stresses. Thereby the cell wall deposition of lignin represents often the main molecular event that defines the biological function(s) of the lignified cell or tissue. The time and localization of lignin deposition as well as the composition of the polymer can be considered as the three essential components of the polymer that will define the biological function of the lignified tissue. In this review, we will cover the localizations, types and functions of lignin found in various part of land plants. Then, for the various lignified tissues, the mechanisms controlling the developmental deposition of lignin such as transcriptional regulation, intercellular coordinated control of lignification or posttranslational modification of proteins will be discussed. Finally, a focus will be made on the environmental cues that influence the lignification during radial tree growth, as well as the plant responses that these signals trigger in the regulation of lignification.

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

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

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

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

@article{chen_lncrna_2022,
	title = {{LncRNA} {PMAT}–{PtoMYB46} module represses {PtoMATE} and {PtoARF2} promoting {Pb2}+ uptake and plant growth in poplar},
	volume = {433},
	issn = {0304-3894},
	url = {https://www.sciencedirect.com/science/article/pii/S0304389422005581},
	doi = {10.1016/j.jhazmat.2022.128769},
	abstract = {Lead (Pb2+) is one of the most toxic heavy-metal contaminants. Fast-growing woody plants with substantial biomass are ideal for bioremediation. However, the transcriptional regulation of Pb2+ uptake in woody plants remains unclear. Here, we identified 226 Pb2+-induced, differentially expressed long non-coding RNAs (DELs) in Populus tomentosa. Functional annotation revealed that these DELs mainly regulate carbon metabolism, biosynthesis of secondary metabolites, energy metabolism, and signal transduction through their potential target genes. Association and epistasis analysis showed that the lncRNA PMAT (Pb2+-induced multidrug and toxic compound extrusion (MATE) antisense lncRNA) interacts epistatically with PtoMYB46 to regulate leaf dry weight, photosynthesis rate, and transketolase activity. Genetic transformation and molecular assays showed that PtoMYB46 reduces the expression of PtoMATE directly or indirectly through PMAT, thereby reducing the secretion of citric acid (CA) and ultimately promoting Pb2+ uptake. Meanwhile, PtoMYB46 targets auxin response factor 2 (ARF2) and reduces its expression, thus positively regulating plant growth. We concluded that the PMAT–PtoMYB46–PtoMATE–PtoARF2 regulatory module control Pb2+ tolerance, uptake, and plant growth. This study demonstrates the involvement of lncRNAs in response to Pb2+ in poplar, yielding new insight into the potential for developing genetically improved woody plant varieties for phytoremediating lead-contaminated soils.},
	language = {en},
	urldate = {2022-04-22},
	journal = {Journal of Hazardous Materials},
	author = {Chen, Panfei and Song, Yuepeng and Liu, Xin and Xiao, Liang and Bu, Chenhao and Liu, Peng and Zhao, Lei and Ingvarsson, Pär K. and Wu, Harry X. and El-Kassaby, Yousry A. and Zhang, Deqiang},
	month = jul,
	year = {2022},
	keywords = {Association genetics, Lead, Long non-coding RNAs, Phytoremediation},
	pages = {128769},
}

Lead (Pb2+) is one of the most toxic heavy-metal contaminants. Fast-growing woody plants with substantial biomass are ideal for bioremediation. However, the transcriptional regulation of Pb2+ uptake in woody plants remains unclear. Here, we identified 226 Pb2+-induced, differentially expressed long non-coding RNAs (DELs) in Populus tomentosa. Functional annotation revealed that these DELs mainly regulate carbon metabolism, biosynthesis of secondary metabolites, energy metabolism, and signal transduction through their potential target genes. Association and epistasis analysis showed that the lncRNA PMAT (Pb2+-induced multidrug and toxic compound extrusion (MATE) antisense lncRNA) interacts epistatically with PtoMYB46 to regulate leaf dry weight, photosynthesis rate, and transketolase activity. Genetic transformation and molecular assays showed that PtoMYB46 reduces the expression of PtoMATE directly or indirectly through PMAT, thereby reducing the secretion of citric acid (CA) and ultimately promoting Pb2+ uptake. Meanwhile, PtoMYB46 targets auxin response factor 2 (ARF2) and reduces its expression, thus positively regulating plant growth. We concluded that the PMAT–PtoMYB46–PtoMATE–PtoARF2 regulatory module control Pb2+ tolerance, uptake, and plant growth. This study demonstrates the involvement of lncRNAs in response to Pb2+ in poplar, yielding new insight into the potential for developing genetically improved woody plant varieties for phytoremediating lead-contaminated soils.

@article{dominguez_mobile_2022,
	title = {Mobile forms of carbon in trees: metabolism and transport},
	volume = {42},
	issn = {1758-4469},
	shorttitle = {Mobile forms of carbon in trees},
	url = {https://doi.org/10.1093/treephys/tpab123},
	doi = {10.1093/treephys/tpab123},
	abstract = {Plants constitute 80\% of the biomass on earth, and almost two thirds of this biomass is found in wood. Wood formation is a carbon demanding process and relies on carbon transport from photosynthetic tissues. Thus, understanding the transport process is of major interest for understanding terrestrial biomass formation. Here we review the molecules and mechanisms used to transport and allocate carbon in trees. Sucrose is the major form in which carbon is transported, found in the phloem sap of all so far investigated tree species. However, in several tree species sucrose is accompanied by other molecules, notably polyols and the raffinose family of oligosaccharides. We describe the molecules that constitute each of these transport groups, and their distribution across different tree species. Further, we detail the metabolic reactions for their synthesis, the mechanisms by which trees load and unload these compounds in and out of the vascular system, and how they are radially transported in the trunk and finally catabolized during wood formation. We also address a particular carbon recirculation process between phloem and xylem that occurs in trees during the annual cycle of growth and dormancy. A search of possible evolutionary drivers behind the diversity of C carrying molecules in trees reveals no consistent differences in carbon transport mechanisms between angiosperm and gymnosperm trees. Furthermore, the distribution of C forms across species suggests that climate related environmental factors will not either explain the diversity of carbon transport forms. However, the consideration of C transport mechanisms in relation to tree—rhizosphere coevolution deserves further attention. To conclude the review, we identify possible future lines of research in this field.},
	number = {3},
	urldate = {2021-09-21},
	journal = {Tree Physiology},
	author = {Dominguez, Pia Guadalupe and Niittylä, Totte},
	month = mar,
	year = {2022},
	pages = {458--487},
}

Plants constitute 80% of the biomass on earth, and almost two thirds of this biomass is found in wood. Wood formation is a carbon demanding process and relies on carbon transport from photosynthetic tissues. Thus, understanding the transport process is of major interest for understanding terrestrial biomass formation. Here we review the molecules and mechanisms used to transport and allocate carbon in trees. Sucrose is the major form in which carbon is transported, found in the phloem sap of all so far investigated tree species. However, in several tree species sucrose is accompanied by other molecules, notably polyols and the raffinose family of oligosaccharides. We describe the molecules that constitute each of these transport groups, and their distribution across different tree species. Further, we detail the metabolic reactions for their synthesis, the mechanisms by which trees load and unload these compounds in and out of the vascular system, and how they are radially transported in the trunk and finally catabolized during wood formation. We also address a particular carbon recirculation process between phloem and xylem that occurs in trees during the annual cycle of growth and dormancy. A search of possible evolutionary drivers behind the diversity of C carrying molecules in trees reveals no consistent differences in carbon transport mechanisms between angiosperm and gymnosperm trees. Furthermore, the distribution of C forms across species suggests that climate related environmental factors will not either explain the diversity of carbon transport forms. However, the consideration of C transport mechanisms in relation to tree—rhizosphere coevolution deserves further attention. To conclude the review, we identify possible future lines of research in this field.

@article{hasegawa_tgnee_2022,
	title = {The {TGN}/{EE} {SNARE} protein {SYP61} and the ubiquitin ligase {ATL31} cooperatively regulate plant responses to carbon/nitrogen conditions in {Arabidopsis}},
	volume = {34},
	issn = {1040-4651},
	url = {https://doi.org/10.1093/plcell/koac014},
	doi = {10.1093/plcell/koac014},
	abstract = {Ubiquitination is a post-translational modification involving the reversible attachment of the small protein ubiquitin to a target protein. Ubiquitination is involved in numerous cellular processes, including the membrane trafficking of cargo proteins. However, the ubiquitination of the trafficking machinery components and their involvement in environmental responses are not well understood. Here, we report that the Arabidopsis thaliana trans-Golgi network/early endosome localized SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptor) protein SYP61 interacts with the transmembrane ubiquitin ligase ATL31, a key regulator of resistance to disrupted carbon (C)/nitrogen/(N)-nutrient conditions. SYP61 is a key component of membrane trafficking in Arabidopsis. The subcellular localization of ATL31 was disrupted in knockdown mutants of SYP61, and the insensitivity of ATL31-overexpressing plants to high C/low N-stress was repressed in these mutants, suggesting that SYP61 and ATL31 cooperatively function in plant responses to nutrient stress. SYP61 is ubiquitinated in plants, and its ubiquitination level is upregulated under low C/high N-nutrient conditions. These findings provide important insights into the ubiquitin signaling and membrane trafficking machinery in plants.},
	number = {4},
	urldate = {2022-04-08},
	journal = {The Plant Cell},
	author = {Hasegawa, Yoko and Huarancca Reyes, Thais and Uemura, Tomohiro and Baral, Anirban and Fujimaki, Akari and Luo, Yongming and Morita, Yoshie and Saeki, Yasushi and Maekawa, Shugo and Yasuda, Shigetaka and Mukuta, Koki and Fukao, Yoichiro and Tanaka, Keiji and Nakano, Akihiko and Takagi, Junpei and Bhalerao, Rishikesh P and Yamaguchi, Junji and Sato, Takeo},
	month = apr,
	year = {2022},
	pages = {1354--1374},
}

Ubiquitination is a post-translational modification involving the reversible attachment of the small protein ubiquitin to a target protein. Ubiquitination is involved in numerous cellular processes, including the membrane trafficking of cargo proteins. However, the ubiquitination of the trafficking machinery components and their involvement in environmental responses are not well understood. Here, we report that the Arabidopsis thaliana trans-Golgi network/early endosome localized SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptor) protein SYP61 interacts with the transmembrane ubiquitin ligase ATL31, a key regulator of resistance to disrupted carbon (C)/nitrogen/(N)-nutrient conditions. SYP61 is a key component of membrane trafficking in Arabidopsis. The subcellular localization of ATL31 was disrupted in knockdown mutants of SYP61, and the insensitivity of ATL31-overexpressing plants to high C/low N-stress was repressed in these mutants, suggesting that SYP61 and ATL31 cooperatively function in plant responses to nutrient stress. SYP61 is ubiquitinated in plants, and its ubiquitination level is upregulated under low C/high N-nutrient conditions. These findings provide important insights into the ubiquitin signaling and membrane trafficking machinery in plants.

@article{nie_genome-wide_2022,
	title = {Genome-wide {TCP} transcription factors analysis provides insight into their new functions in seasonal and diurnal growth rhythm in {Pinus} tabuliformis},
	volume = {22},
	issn = {1471-2229},
	url = {https://doi.org/10.1186/s12870-022-03554-4},
	doi = {10.1186/s12870-022-03554-4},
	abstract = {Pinus tabuliformis adapts to cold climate with dry winter in northern China, serving as important commercial tree species. The TEOSINTE BRANCHED 1, CYCLOIDEA, and PROLIFERATING CELL FACTOR family(TCP)transcription factors were found to play a role in the circadian clock system in Arabidopsis. However, the role of TCP transcription factors in P. tabuliformis remains little understood.},
	number = {1},
	urldate = {2022-04-08},
	journal = {BMC Plant Biology},
	author = {Nie, Yu-meng and Han, Fang-xu and Ma, Jing-jing and Chen, Xi and Song, Yi-tong and Niu, Shi-Hui and Wu, Harry X.},
	month = apr,
	year = {2022},
	keywords = {Diurnal, Gene family, Oscillation, Pinus tabuliformis, Seasonal, TCP},
	pages = {167},
}

Pinus tabuliformis adapts to cold climate with dry winter in northern China, serving as important commercial tree species. The TEOSINTE BRANCHED 1, CYCLOIDEA, and PROLIFERATING CELL FACTOR family(TCP)transcription factors were found to play a role in the circadian clock system in Arabidopsis. However, the role of TCP transcription factors in P. tabuliformis remains little understood.

@article{liu_demographic_2022,
	title = {Demographic history and natural selection shape patterns of deleterious mutation load and barriers to introgression across {Populus} genome},
	volume = {39},
	issn = {1537-1719},
	url = {https://doi.org/10.1093/molbev/msac008},
	doi = {10/gn9jc6},
	abstract = {Hybridization and resulting introgression are important processes shaping the tree of life and appear to be far more common than previously thought. However, how the genome evolution was shaped by various genetic and evolutionary forces after hybridization remains unresolved. Here we used whole genome resequencing data of 227 individuals from multiple widespread Populus species to characterize their contemporary patterns of hybridization and to quantify genomic signatures of past introgression. We observe a high frequency of contemporary hybridization and confirm that multiple previously ambiguous species are in fact F1 hybrids. Seven species were identified, which experienced different demographic histories that resulted in strikingly varied efficacy of selection and burdens of deleterious mutations. Frequent past introgression has been found to be a pervasive feature throughout the speciation of these Populus species. The retained introgressed regions, more generally, tend to contain reduced genetic load and to be located in regions of high recombination. We also find that in pairs of species with substantial differences in effective population size, introgressed regions are inferred to have undergone selective sweeps at greater than expected frequencies in the species with lower effective population size, suggesting that introgression likely have higher potential to provide beneficial variation for species with small populations. Our results, therefore, illustrate that demography and recombination have interplayed with both positive and negative selection in determining the genomic evolution after hybridization.},
	number = {2},
	urldate = {2022-01-24},
	journal = {Molecular Biology and Evolution},
	author = {Liu, Shuyu and Zhang, Lei and Sang, Yupeng and Lai, Qiang and Zhang, Xinxin and Jia, Changfu and Long, Zhiqin and Wu, Jiali and Ma, Tao and Mao, Kangshan and Street, Nathaniel R and Ingvarsson, Pär K and Liu, Jianquan and Wang, Jing},
	month = jan,
	year = {2022},
	pages = {msac008},
}

Hybridization and resulting introgression are important processes shaping the tree of life and appear to be far more common than previously thought. However, how the genome evolution was shaped by various genetic and evolutionary forces after hybridization remains unresolved. Here we used whole genome resequencing data of 227 individuals from multiple widespread Populus species to characterize their contemporary patterns of hybridization and to quantify genomic signatures of past introgression. We observe a high frequency of contemporary hybridization and confirm that multiple previously ambiguous species are in fact F1 hybrids. Seven species were identified, which experienced different demographic histories that resulted in strikingly varied efficacy of selection and burdens of deleterious mutations. Frequent past introgression has been found to be a pervasive feature throughout the speciation of these Populus species. The retained introgressed regions, more generally, tend to contain reduced genetic load and to be located in regions of high recombination. We also find that in pairs of species with substantial differences in effective population size, introgressed regions are inferred to have undergone selective sweeps at greater than expected frequencies in the species with lower effective population size, suggesting that introgression likely have higher potential to provide beneficial variation for species with small populations. Our results, therefore, illustrate that demography and recombination have interplayed with both positive and negative selection in determining the genomic evolution after hybridization.

@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.

@article{przybyla-toscano_protein_2022,
	title = {Protein lipoylation in mitochondria requires {Fe}–{S} cluster assembly factors {NFU4} and {NFU5}},
	volume = {188},
	issn = {0032-0889},
	url = {https://doi.org/10.1093/plphys/kiab501},
	doi = {10.1093/plphys/kiab501},
	abstract = {Plants have evolutionarily conserved NifU-like (NFU)-domain proteins that are targeted to plastids or mitochondria. ‘Plastid-type’ NFU1, NFU2 and NFU3 in Arabidopsis (Arabidopsis thaliana) play a role in iron-sulfur (Fe-S) cluster assembly in this organelle, whereas the type-II NFU4 and NFU5 proteins have not been subjected to mutant studies in any plant species to determine their biological role. Here, we confirmed that NFU4 and NFU5 are targeted to the mitochondria. The proteins were constitutively produced in all parts of the plant, suggesting a housekeeping function. Double nfu4 nfu5 knockout mutants were embryonic lethal, and depletion of NFU4 and NFU5 proteins led to growth arrest of young seedlings. Biochemical analyses revealed that NFU4 and NFU5 are required for lipoylation of the H proteins of the glycine decarboxylase complex and the E2 subunits of other mitochondrial dehydrogenases, with little impact on Fe-S cluster-containing respiratory complexes or aconitase. Consequently, the Gly-to-Ser ratio was increased in mutant seedlings and early growth improved with elevated CO2 treatment. In addition, pyruvate, 2-oxoglutarate and branched-chain amino acids accumulated in nfu4 nfu5 mutants, further supporting defects in the other three mitochondrial lipoate-dependent enzyme complexes. NFU4 and NFU5 interacted with mitochondrial lipoyl synthase (LIP1) in yeast 2-hybrid and bimolecular fluorescence complementation assays. These data indicate that NFU4 and NFU5 have a more specific function than previously thought, most likely providing Fe-S clusters to lipoyl synthase.},
	number = {2},
	urldate = {2021-11-04},
	journal = {Plant Physiology},
	author = {Przybyla-Toscano, Jonathan and Maclean, Andrew E and Franceschetti, Marina and Liebsch, Daniela and Vignols, Florence and Keech, Olivier and Rouhier, Nicolas and Balk, Janneke},
	month = feb,
	year = {2022},
	pages = {997--1013},
}

Plants have evolutionarily conserved NifU-like (NFU)-domain proteins that are targeted to plastids or mitochondria. ‘Plastid-type’ NFU1, NFU2 and NFU3 in Arabidopsis (Arabidopsis thaliana) play a role in iron-sulfur (Fe-S) cluster assembly in this organelle, whereas the type-II NFU4 and NFU5 proteins have not been subjected to mutant studies in any plant species to determine their biological role. Here, we confirmed that NFU4 and NFU5 are targeted to the mitochondria. The proteins were constitutively produced in all parts of the plant, suggesting a housekeeping function. Double nfu4 nfu5 knockout mutants were embryonic lethal, and depletion of NFU4 and NFU5 proteins led to growth arrest of young seedlings. Biochemical analyses revealed that NFU4 and NFU5 are required for lipoylation of the H proteins of the glycine decarboxylase complex and the E2 subunits of other mitochondrial dehydrogenases, with little impact on Fe-S cluster-containing respiratory complexes or aconitase. Consequently, the Gly-to-Ser ratio was increased in mutant seedlings and early growth improved with elevated CO2 treatment. In addition, pyruvate, 2-oxoglutarate and branched-chain amino acids accumulated in nfu4 nfu5 mutants, further supporting defects in the other three mitochondrial lipoate-dependent enzyme complexes. NFU4 and NFU5 interacted with mitochondrial lipoyl synthase (LIP1) in yeast 2-hybrid and bimolecular fluorescence complementation assays. These data indicate that NFU4 and NFU5 have a more specific function than previously thought, most likely providing Fe-S clusters to lipoyl synthase.

@article{atakhani_characterising_2022,
	title = {Characterising the mechanics of cell–cell adhesion in plants},
	volume = {3},
	issn = {2632-8828},
	url = {https://www.cambridge.org/core/journals/quantitative-plant-biology/article/characterising-the-mechanics-of-cellcell-adhesion-in-plants/9D165A5D6EA6F2B1927B9F0F38F88AAC},
	doi = {10/gpjfdn},
	abstract = {, 

Cell–cell adhesion is a fundamental feature of multicellular organisms. To ensure multicellular integrity, adhesion needs to be tightly controlled and maintained. In plants, cell–cell adhesion remains poorly understood. Here, we argue that to be able to understand how cell–cell adhesion works in plants, we need to understand and quantitatively measure the mechanics behind it. We first introduce cell–cell adhesion in the context of multicellularity, briefly explain the notions of adhesion strength, work and energy and present the current knowledge concerning the mechanisms of cell–cell adhesion in plants. Because still relatively little is known in plants, we then turn to animals, but also algae, bacteria, yeast and fungi, and examine how adhesion works and how it can be quantitatively measured in these systems. From this, we explore how the mechanics of cell adhesion could be quantitatively characterised in plants, opening future perspectives for understanding plant multicellularity.},
	language = {en},
	urldate = {2022-02-16},
	journal = {Quantitative Plant Biology},
	author = {Atakhani, Asal and Bogdziewiez, Léa and Verger, Stéphane},
	month = feb,
	year = {2022},
	keywords = {adhesion strength, cell–cell adhesion, multicellularity, plant, single cell, tissue},
}

, Cell–cell adhesion is a fundamental feature of multicellular organisms. To ensure multicellular integrity, adhesion needs to be tightly controlled and maintained. In plants, cell–cell adhesion remains poorly understood. Here, we argue that to be able to understand how cell–cell adhesion works in plants, we need to understand and quantitatively measure the mechanics behind it. We first introduce cell–cell adhesion in the context of multicellularity, briefly explain the notions of adhesion strength, work and energy and present the current knowledge concerning the mechanisms of cell–cell adhesion in plants. Because still relatively little is known in plants, we then turn to animals, but also algae, bacteria, yeast and fungi, and examine how adhesion works and how it can be quantitatively measured in these systems. From this, we explore how the mechanics of cell adhesion could be quantitatively characterised in plants, opening future perspectives for understanding plant multicellularity.

@article{maqdasy_impaired_2022,
	title = {Impaired phosphocreatine metabolism in white adipocytes promotes inflammation},
	volume = {4},
	copyright = {2022 The Author(s)},
	issn = {2522-5812},
	url = {https://www.nature.com/articles/s42255-022-00525-9},
	doi = {10.1038/s42255-022-00525-9},
	abstract = {The mechanisms promoting disturbed white adipocyte function in obesity remain largely unclear. Herein, we integrate white adipose tissue (WAT) metabolomic and transcriptomic data from clinical cohorts and find that the WAT phosphocreatine/creatine ratio is increased and creatine kinase-B expression and activity is decreased in the obese state. In human in vitro and murine in vivo models, we demonstrate that decreased phosphocreatine metabolism in white adipocytes alters adenosine monophosphate-activated protein kinase activity via effects on adenosine triphosphate/adenosine diphosphate levels, independently of WAT beigeing. This disturbance promotes a pro-inflammatory profile characterized, in part, by increased chemokine (C-C motif) ligand 2 (CCL2) production. These data suggest that the phosphocreatine/creatine system links cellular energy shuttling with pro-inflammatory responses in human and murine white adipocytes. Our findings provide unexpected perspectives on the mechanisms driving WAT inflammation in obesity and may present avenues to target adipocyte dysfunction.},
	language = {en},
	number = {2},
	urldate = {2022-02-17},
	journal = {Nature Metabolism},
	author = {Maqdasy, Salwan and Lecoutre, Simon and Renzi, Gianluca and Frendo-Cumbo, Scott and Rizo-Roca, David and Moritz, Thomas and Juvany, Marta and Hodek, Ondrej and Gao, Hui and Couchet, Morgane and Witting, Michael and Kerr, Alastair and Bergo, Martin O. and Choudhury, Robin P. and Aouadi, Myriam and Zierath, Juleen R. and Krook, Anna and Mejhert, Niklas and Rydén, Mikael},
	month = feb,
	year = {2022},
	keywords = {Fat metabolism, Mechanisms of disease, Obesity},
	pages = {1--13},
}

The mechanisms promoting disturbed white adipocyte function in obesity remain largely unclear. Herein, we integrate white adipose tissue (WAT) metabolomic and transcriptomic data from clinical cohorts and find that the WAT phosphocreatine/creatine ratio is increased and creatine kinase-B expression and activity is decreased in the obese state. In human in vitro and murine in vivo models, we demonstrate that decreased phosphocreatine metabolism in white adipocytes alters adenosine monophosphate-activated protein kinase activity via effects on adenosine triphosphate/adenosine diphosphate levels, independently of WAT beigeing. This disturbance promotes a pro-inflammatory profile characterized, in part, by increased chemokine (C-C motif) ligand 2 (CCL2) production. These data suggest that the phosphocreatine/creatine system links cellular energy shuttling with pro-inflammatory responses in human and murine white adipocytes. Our findings provide unexpected perspectives on the mechanisms driving WAT inflammation in obesity and may present avenues to target adipocyte dysfunction.

@article{ding_transcriptome-based_2022,
	title = {A transcriptome-based association study of growth, wood quality, and oleoresin traits in a slash pine breeding population},
	volume = {18},
	issn = {1553-7404},
	url = {https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1010017},
	doi = {10/gpn67c},
	abstract = {Slash pine (Pinus elliottii Engelm.) is an important timber and resin species in the United States, China, Brazil and other countries. Understanding the genetic basis of these traits will accelerate its breeding progress. We carried out a genome-wide association study (GWAS), transcriptome-wide association study (TWAS) and weighted gene co-expression network analysis (WGCNA) for growth, wood quality, and oleoresin traits using 240 unrelated individuals from a Chinese slash pine breeding population. We developed high quality 53,229 single nucleotide polymorphisms (SNPs). Our analysis reveals three main results: (1) the Chinese breeding population can be divided into three genetic groups with a mean inbreeding coefficient of 0.137; (2) 32 SNPs significantly were associated with growth and oleoresin traits, accounting for the phenotypic variance ranging from 12.3\% to 21.8\% and from 10.6\% to 16.7\%, respectively; and (3) six genes encoding PeTLP, PeAP2/ERF, PePUP9, PeSLP, PeHSP, and PeOCT1 proteins were identified and validated by quantitative real time polymerase chain reaction for their association with growth and oleoresin traits. These results could be useful for tree breeding and functional studies in advanced slash pine breeding program.},
	language = {en},
	number = {2},
	urldate = {2022-03-03},
	journal = {PLOS Genetics},
	author = {Ding, Xianyin and Diao, Shu and Luan, Qifu and Wu, Harry X. and Zhang, Yini and Jiang, Jingmin},
	month = feb,
	year = {2022},
	keywords = {Gene expression, Genetics, Genome-wide association studies, Phenotypes, Phylogenetic analysis, Pines, Single nucleotide polymorphisms, Transcriptome analysis},
	pages = {e1010017},
}

Slash pine (Pinus elliottii Engelm.) is an important timber and resin species in the United States, China, Brazil and other countries. Understanding the genetic basis of these traits will accelerate its breeding progress. We carried out a genome-wide association study (GWAS), transcriptome-wide association study (TWAS) and weighted gene co-expression network analysis (WGCNA) for growth, wood quality, and oleoresin traits using 240 unrelated individuals from a Chinese slash pine breeding population. We developed high quality 53,229 single nucleotide polymorphisms (SNPs). Our analysis reveals three main results: (1) the Chinese breeding population can be divided into three genetic groups with a mean inbreeding coefficient of 0.137; (2) 32 SNPs significantly were associated with growth and oleoresin traits, accounting for the phenotypic variance ranging from 12.3% to 21.8% and from 10.6% to 16.7%, respectively; and (3) six genes encoding PeTLP, PeAP2/ERF, PePUP9, PeSLP, PeHSP, and PeOCT1 proteins were identified and validated by quantitative real time polymerase chain reaction for their association with growth and oleoresin traits. These results could be useful for tree breeding and functional studies in advanced slash pine breeding program.

@article{pervaiz_microrna_2022,
	title = {{MicroRNA} and {cDNA}-{Microarray} as {Potential} {Targets} against {Abiotic} {Stress} {Response} in {Plants}: {Advances} and {Prospects}},
	volume = {12},
	copyright = {http://creativecommons.org/licenses/by/3.0/},
	issn = {2073-4395},
	shorttitle = {{MicroRNA} and {cDNA}-{Microarray} as {Potential} {Targets} against {Abiotic} {Stress} {Response} in {Plants}},
	url = {https://www.mdpi.com/2073-4395/12/1/11},
	doi = {10/gpjfdp},
	abstract = {Abiotic stresses, such as temperature (heat and cold), salinity, and drought negatively affect plant productivity; hence, the molecular responses of abiotic stresses need to be investigated. Numerous molecular and genetic engineering studies have made substantial contributions and revealed that abiotic stresses are the key factors associated with production losses in plants. In response to abiotic stresses, altered expression patterns of miRNAs have been reported, and, as a result, cDNA-microarray and microRNA (miRNA) have been used to identify genes and their expression patterns against environmental adversities in plants. MicroRNA plays a significant role in environmental stresses, plant growth and development, and regulation of various biological and metabolic activities. MicroRNAs have been studied for over a decade to identify those susceptible to environmental stimuli, characterize expression patterns, and recognize their involvement in stress responses and tolerance. Recent findings have been reported that plants assign miRNAs as critical post-transcriptional regulators of gene expression in a sequence-specific manner to adapt to multiple abiotic stresses during their growth and developmental cycle. In this study, we reviewed the current status and described the application of cDNA-microarray and miRNA to understand the abiotic stress responses and different approaches used in plants to survive against different stresses. Despite the accessibility to suitable miRNAs, there is a lack of simple ways to identify miRNA and the application of cDNA-microarray. The elucidation of miRNA responses to abiotic stresses may lead to developing technologies for the early detection of plant environmental stressors. The miRNAs and cDNA-microarrays are powerful tools to enhance abiotic stress tolerance in plants through multiple advanced sequencing and bioinformatics techniques, including miRNA-regulated network, miRNA target prediction, miRNA identification, expression profile, features (disease or stress, biomarkers) association, tools based on machine learning algorithms, NGS, and tools specific for plants. Such technologies were established to identify miRNA and their target gene network prediction, emphasizing current achievements, impediments, and future perspectives. Furthermore, there is also a need to identify and classify new functional genes that may play a role in stress resistance, since many plant genes constitute an unexplained fraction.},
	language = {en},
	number = {1},
	urldate = {2022-02-14},
	journal = {Agronomy},
	author = {Pervaiz, Tariq and Amjid, Muhammad Waqas and El-kereamy, Ashraf and Niu, Shi-Hui and Wu, Harry X.},
	month = jan,
	year = {2022},
	keywords = {abiotic stress tolerance, adaptation, cold stress, drought stress, miRNA target gene expression, salinity stress},
	pages = {11},
}

Abiotic stresses, such as temperature (heat and cold), salinity, and drought negatively affect plant productivity; hence, the molecular responses of abiotic stresses need to be investigated. Numerous molecular and genetic engineering studies have made substantial contributions and revealed that abiotic stresses are the key factors associated with production losses in plants. In response to abiotic stresses, altered expression patterns of miRNAs have been reported, and, as a result, cDNA-microarray and microRNA (miRNA) have been used to identify genes and their expression patterns against environmental adversities in plants. MicroRNA plays a significant role in environmental stresses, plant growth and development, and regulation of various biological and metabolic activities. MicroRNAs have been studied for over a decade to identify those susceptible to environmental stimuli, characterize expression patterns, and recognize their involvement in stress responses and tolerance. Recent findings have been reported that plants assign miRNAs as critical post-transcriptional regulators of gene expression in a sequence-specific manner to adapt to multiple abiotic stresses during their growth and developmental cycle. In this study, we reviewed the current status and described the application of cDNA-microarray and miRNA to understand the abiotic stress responses and different approaches used in plants to survive against different stresses. Despite the accessibility to suitable miRNAs, there is a lack of simple ways to identify miRNA and the application of cDNA-microarray. The elucidation of miRNA responses to abiotic stresses may lead to developing technologies for the early detection of plant environmental stressors. The miRNAs and cDNA-microarrays are powerful tools to enhance abiotic stress tolerance in plants through multiple advanced sequencing and bioinformatics techniques, including miRNA-regulated network, miRNA target prediction, miRNA identification, expression profile, features (disease or stress, biomarkers) association, tools based on machine learning algorithms, NGS, and tools specific for plants. Such technologies were established to identify miRNA and their target gene network prediction, emphasizing current achievements, impediments, and future perspectives. Furthermore, there is also a need to identify and classify new functional genes that may play a role in stress resistance, since many plant genes constitute an unexplained fraction.

@article{svennerstam_timing_2022,
	title = {Timing is everything – obtaining accurate measures of plant uptake of amino acids},
	volume = {234},
	issn = {1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/nph.17964},
	doi = {10/gn9jc5},
	abstract = {Plants are known to have the capacity to take up and utilise amino acids for growth. The significance of this uptake, however, remains elusive, partly due to methodological challenges and biological implications associated with acquiring and interpreting data. This study compared bulk stable isotope analysis and compound-specific liquid chromatography-mass spectrometry, two established methods for determining amino acid uptake. Root amino acid uptake was assayed using U-13C5-15N2-l-glutamine and axenically grown Arabidopsis thaliana. After 15–120 min of exposure, the content of intact glutamine measured in the roots was constant, whilst the 15N and 13C content increased over time, resulting in very different estimated uptake rates. The 13C : 15N ratio in roots declined with time, suggesting a loss of glutamine carbon of up to 15\% within 120 min. The results presented indicate that, regardless of method used, time is a crucial factor when determining plant amino acid uptake. Due to post-uptake metabolism, compound-specific methods should primarily be used in experiments with a time frame of minutes rather than hours or days. Post-uptake metabolism in plants may account for significant loss of carbon, suggesting that it is not just pre-uptake metabolism by microbes that accounts for the 15N–13C mismatch reported in ecological studies, but also post-uptake metabolism in the plant.},
	language = {en},
	number = {1},
	urldate = {2022-02-14},
	journal = {New Phytologist},
	author = {Svennerstam, Henrik and Jämtgård, Sandra},
	month = jan,
	year = {2022},
	keywords = {Arabidopsis thaliana, EA-IRMS, LC-MS, amino acids, glutamine, isotopes, organic nitrogen, plant uptake},
	pages = {311--318},
}

Plants are known to have the capacity to take up and utilise amino acids for growth. The significance of this uptake, however, remains elusive, partly due to methodological challenges and biological implications associated with acquiring and interpreting data. This study compared bulk stable isotope analysis and compound-specific liquid chromatography-mass spectrometry, two established methods for determining amino acid uptake. Root amino acid uptake was assayed using U-13C5-15N2-l-glutamine and axenically grown Arabidopsis thaliana. After 15–120 min of exposure, the content of intact glutamine measured in the roots was constant, whilst the 15N and 13C content increased over time, resulting in very different estimated uptake rates. The 13C : 15N ratio in roots declined with time, suggesting a loss of glutamine carbon of up to 15% within 120 min. The results presented indicate that, regardless of method used, time is a crucial factor when determining plant amino acid uptake. Due to post-uptake metabolism, compound-specific methods should primarily be used in experiments with a time frame of minutes rather than hours or days. Post-uptake metabolism in plants may account for significant loss of carbon, suggesting that it is not just pre-uptake metabolism by microbes that accounts for the 15N–13C mismatch reported in ecological studies, but also post-uptake metabolism in the plant.

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

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

@article{andre_populus_2022,
	title = {Populus {SVL} {Acts} in {Leaves} to {Modulate} the {Timing} of {Growth} {Cessation} and {Bud} {Set}},
	volume = {13},
	issn = {1664-462X},
	url = {https://www.frontiersin.org/article/10.3389/fpls.2022.823019},
	doi = {10.3389/fpls.2022.823019},
	abstract = {SHORT VEGETATIVE PHASE (SVP) is an important regulator of FLOWERING LOCUS T (FT) in the thermosensory pathway of Arabidopsis. It is a negative regulator of flowering and represses FT transcription. In poplar trees, FT2 is central for the photoperiodic control of growth cessation, which also requires the decrease of bioactive gibberellins (GAs). In angiosperm trees, genes similar to SVP, sometimes named DORMANCY-ASSOCIATED MADS-BOX genes, control temperature-mediated bud dormancy. Here we show that SVL, an SVP ortholog in aspen trees, besides its role in controlling dormancy through its expression in buds, is also contributing to the regulation of short day induced growth cessation and bud set through its expression in leaves. SVL is upregulated during short days in leaves and binds to the FT2 promoter to repress its transcription. It furthermore decreases the amount of active GAs, whose downregulation is essential for growth cessation, by repressing the transcription of GA20 oxidase. Finally, the SVL protein is more stable in colder temperatures, thus integrating the temperature signal into the response. We conclude that the molecular function of SVL in the photoperiodic pathway has been conserved between Arabidopsis and poplar trees, albeit the physiological process it controls has changed. SVL is thus both involved in regulating the photoperiod response in leaves, modulating the timing of growth cessation and bud set, and in the subsequent temperature regulation of dormancy in the buds.},
	urldate = {2022-02-17},
	journal = {Frontiers in Plant Science},
	author = {André, Domenique and Zambrano, José Alfredo and Zhang, Bo and Lee, Keh Chien and Rühl, Mark and Marcon, Alice and Nilsson, Ove},
	month = feb,
	year = {2022},
}

SHORT VEGETATIVE PHASE (SVP) is an important regulator of FLOWERING LOCUS T (FT) in the thermosensory pathway of Arabidopsis. It is a negative regulator of flowering and represses FT transcription. In poplar trees, FT2 is central for the photoperiodic control of growth cessation, which also requires the decrease of bioactive gibberellins (GAs). In angiosperm trees, genes similar to SVP, sometimes named DORMANCY-ASSOCIATED MADS-BOX genes, control temperature-mediated bud dormancy. Here we show that SVL, an SVP ortholog in aspen trees, besides its role in controlling dormancy through its expression in buds, is also contributing to the regulation of short day induced growth cessation and bud set through its expression in leaves. SVL is upregulated during short days in leaves and binds to the FT2 promoter to repress its transcription. It furthermore decreases the amount of active GAs, whose downregulation is essential for growth cessation, by repressing the transcription of GA20 oxidase. Finally, the SVL protein is more stable in colder temperatures, thus integrating the temperature signal into the response. We conclude that the molecular function of SVL in the photoperiodic pathway has been conserved between Arabidopsis and poplar trees, albeit the physiological process it controls has changed. SVL is thus both involved in regulating the photoperiod response in leaves, modulating the timing of growth cessation and bud set, and in the subsequent temperature regulation of dormancy in the buds.

@article{zuch_cell_2022,
	title = {Cell biology of the leaf epidermis: {Fate} specification, morphogenesis, and coordination},
	volume = {34},
	issn = {1040-4651},
	shorttitle = {Cell biology of the leaf epidermis},
	url = {https://doi.org/10.1093/plcell/koab250},
	doi = {10/gpjfdq},
	abstract = {As the outermost layer of plants, the epidermis serves as a critical interface between plants and the environment. During leaf development, the differentiation of specialized epidermal cell types, including stomatal guard cells, pavement cells, and trichomes, occurs simultaneously, each providing unique and pivotal functions for plant growth and survival. Decades of molecular-genetic and physiological studies have unraveled key players and hormone signaling specifying epidermal differentiation. However, most studies focus on only one cell type at a time, and how these distinct cell types coordinate as a unit is far from well-comprehended. Here we provide a review on the current knowledge of regulatory mechanisms underpinning the fate specification, differentiation, morphogenesis, and positioning of these specialized cell types. Emphasis is given to their shared developmental origins, fate flexibility, as well as cell cycle and hormonal controls. Furthermore, we discuss computational modeling approaches to integrate how mechanical properties of individual epidermal cell types and entire tissue/organ properties mutually influence each other. We hope to illuminate the underlying mechanisms coordinating the cell differentiation that ultimately generate a functional leaf epidermis.},
	number = {1},
	urldate = {2022-02-14},
	journal = {The Plant Cell},
	author = {Zuch, Daniel T and Doyle, Siamsa M and Majda, Mateusz and Smith, Richard S and Robert, Stéphanie and Torii, Keiko U},
	month = jan,
	year = {2022},
	pages = {209--227},
}

As the outermost layer of plants, the epidermis serves as a critical interface between plants and the environment. During leaf development, the differentiation of specialized epidermal cell types, including stomatal guard cells, pavement cells, and trichomes, occurs simultaneously, each providing unique and pivotal functions for plant growth and survival. Decades of molecular-genetic and physiological studies have unraveled key players and hormone signaling specifying epidermal differentiation. However, most studies focus on only one cell type at a time, and how these distinct cell types coordinate as a unit is far from well-comprehended. Here we provide a review on the current knowledge of regulatory mechanisms underpinning the fate specification, differentiation, morphogenesis, and positioning of these specialized cell types. Emphasis is given to their shared developmental origins, fate flexibility, as well as cell cycle and hormonal controls. Furthermore, we discuss computational modeling approaches to integrate how mechanical properties of individual epidermal cell types and entire tissue/organ properties mutually influence each other. We hope to illuminate the underlying mechanisms coordinating the cell differentiation that ultimately generate a functional leaf epidermis.

@article{witzell_aspen_2022,
	title = {Aspen {Leaves} as a “{Chemical} {Landscape}” for {Fungal} {Endophyte} {Diversity}—{Effects} of {Nitrogen} {Addition}},
	volume = {13},
	issn = {1664-302X},
	url = {https://www.frontiersin.org/article/10.3389/fmicb.2022.846208},
	doi = {10/gpq8cc},
	abstract = {Abiotic and biotic factors may shape the mycobiome communities in plants directly but also indirectly by modifying the quality of host plants as a substrate. We hypothesized that nitrogen fertilization (N) would determine the quality of aspen (Populus tremula) leaves as a substrate for the endophytic fungi, and that by subjecting the plants to N, we could manipulate the concentrations of positive (nutritious) and negative (antifungal) chemicals in leaves, thus changing the internal “chemical landscape” for the fungi. We expected that this would lead to changes in the fungal community composition, in line with the predictions of heterogeneity–diversity relationship and resource availability hypotheses. To test this, we conducted a greenhouse study where aspen plants were subjected to N treatment. The chemical status of the leaves was confirmed using GC/MS (114 metabolites, including amino acids and sugars), LC/MS (11 phenolics), and UV-spectrometry (antifungal condensed tannins, CTs), and the endophytic communities were characterized using culture-dependent sequencing. We found that N treatment reduced foliar concentrations of CT precursor catechin but not that of CTs. Nitrogen treatment also increased the concentrations of the amino acids and reduced the concentration of some sugars. We introduced beetle herbivores (H) as a second treatment but found no rapid changes in chemical traits nor strong effect on the diversity of endophytes induced by herbivores. A few rare fungi were associated with and potentially vectored by the beetle herbivores. Our findings indicate that in a controlled environment, the externally induced changes did not strongly alter endophyte diversity in aspen leaves.},
	urldate = {2022-03-22},
	journal = {Frontiers in Microbiology},
	author = {Witzell, Johanna and Decker, Vicki Huizu Guo and Agostinelli, Marta and Romeralo, Carmen and Cleary, Michelle and Albrectsen, Benedicte Riber},
	month = mar,
	year = {2022},
}

Abiotic and biotic factors may shape the mycobiome communities in plants directly but also indirectly by modifying the quality of host plants as a substrate. We hypothesized that nitrogen fertilization (N) would determine the quality of aspen (Populus tremula) leaves as a substrate for the endophytic fungi, and that by subjecting the plants to N, we could manipulate the concentrations of positive (nutritious) and negative (antifungal) chemicals in leaves, thus changing the internal “chemical landscape” for the fungi. We expected that this would lead to changes in the fungal community composition, in line with the predictions of heterogeneity–diversity relationship and resource availability hypotheses. To test this, we conducted a greenhouse study where aspen plants were subjected to N treatment. The chemical status of the leaves was confirmed using GC/MS (114 metabolites, including amino acids and sugars), LC/MS (11 phenolics), and UV-spectrometry (antifungal condensed tannins, CTs), and the endophytic communities were characterized using culture-dependent sequencing. We found that N treatment reduced foliar concentrations of CT precursor catechin but not that of CTs. Nitrogen treatment also increased the concentrations of the amino acids and reduced the concentration of some sugars. We introduced beetle herbivores (H) as a second treatment but found no rapid changes in chemical traits nor strong effect on the diversity of endophytes induced by herbivores. A few rare fungi were associated with and potentially vectored by the beetle herbivores. Our findings indicate that in a controlled environment, the externally induced changes did not strongly alter endophyte diversity in aspen leaves.

@article{siddique_optimization_2022,
	title = {Optimization of {Protocol} for {Construction} of {Fungal} {ITS} {Amplicon} {Library} for {High}-{Throughput} {Illumina} {Sequencing} to {Study} the {Mycobiome} of {Aspen} {Leaves}},
	volume = {12},
	copyright = {http://creativecommons.org/licenses/by/3.0/},
	issn = {2076-3417},
	url = {https://www.mdpi.com/2076-3417/12/3/1136},
	doi = {10.3390/app12031136},
	abstract = {High-Throughput Illumina Sequencing (HTS) can be used to study metagenomes, for example, those of importance for plant health. However, protocols must be optimized according to the plant system in question, the focal microorganisms in the samples, the marker genes selected, and the number of environmental samples. We optimized the protocol for metagenomic studies of aspen leaves, originating from varied genotypes sampled across the growing season, and consequently varying in phenolic composition and in the abundance of endo- and epiphytic fungal species. We optimized the DNA extraction protocol by comparing commercial kits and evaluating five fungal ribosomal specific primers (Ps) alone, and with extended primers that allow binding to sample-specific index primers, and we then optimized the amplification with these composite Ps for 380 samples. The fungal DNA concentration in the samples varied from 561 ng/\µL to 1526 ng/\µL depending on the DNA extraction kit used. However, binding to phenolic compounds affected DNA quality as assessed by Nanodrop measurements (0.63\–2.04 and 0.26\–2.00 absorbance ratios for 260/280 and 260/230, respectively), and this was judged to be more important in making our choice of DNA extraction kit. We initially modified the PCR conditions after determining the concentration of DNA extract in a few subsamples and then evaluated and optimized the annealing temperature, duration, and number of cycles to obtain the required amplification and PCR product bands. For three specific Ps, the extended Ps produced dimers and unexpected amplicon fragments due to nonspecific binding. However, we found that the specific Ps that targeted the ITS2 region of fungal rDNA successfully amplified this region for every sample (with and without the extension PP) resulting in the desired PCR bands, and also allowing the addition of sample-specific index primers, findings which were successfully verified in a second PCR. The optimized protocol allowed us to successfully prepare an amplicon library in order to subject the intended 380 environmental samples to HTS.},
	language = {en},
	number = {3},
	urldate = {2022-01-24},
	journal = {Applied Sciences},
	author = {Siddique, Abu Bakar and Albrectsen, Benedicte Riber and Ilbi, Hulya and Siddique, Abu Bakar},
	month = jan,
	year = {2022},
	keywords = {ITS, NGS, amplicon, aspen, eDNA, endophytes, metabarcoding, metagenomics, rDNA},
	pages = {1136},
}

High-Throughput Illumina Sequencing (HTS) can be used to study metagenomes, for example, those of importance for plant health. However, protocols must be optimized according to the plant system in question, the focal microorganisms in the samples, the marker genes selected, and the number of environmental samples. We optimized the protocol for metagenomic studies of aspen leaves, originating from varied genotypes sampled across the growing season, and consequently varying in phenolic composition and in the abundance of endo- and epiphytic fungal species. We optimized the DNA extraction protocol by comparing commercial kits and evaluating five fungal ribosomal specific primers (Ps) alone, and with extended primers that allow binding to sample-specific index primers, and we then optimized the amplification with these composite Ps for 380 samples. The fungal DNA concentration in the samples varied from 561 ng/µL to 1526 ng/µL depending on the DNA extraction kit used. However, binding to phenolic compounds affected DNA quality as assessed by Nanodrop measurements (0.63–2.04 and 0.26–2.00 absorbance ratios for 260/280 and 260/230, respectively), and this was judged to be more important in making our choice of DNA extraction kit. We initially modified the PCR conditions after determining the concentration of DNA extract in a few subsamples and then evaluated and optimized the annealing temperature, duration, and number of cycles to obtain the required amplification and PCR product bands. For three specific Ps, the extended Ps produced dimers and unexpected amplicon fragments due to nonspecific binding. However, we found that the specific Ps that targeted the ITS2 region of fungal rDNA successfully amplified this region for every sample (with and without the extension PP) resulting in the desired PCR bands, and also allowing the addition of sample-specific index primers, findings which were successfully verified in a second PCR. The optimized protocol allowed us to successfully prepare an amplicon library in order to subject the intended 380 environmental samples to HTS.

@article{jurca_zeitlupe_2022,
	title = {{ZEITLUPE} {Promotes} {ABA}-{Induced} {Stomatal} {Closure} in {Arabidopsis} and {Populus}},
	volume = {13},
	issn = {1664-462X},
	url = {https://www.frontiersin.org/article/10.3389/fpls.2022.829121},
	abstract = {Plants balance water availability with gas exchange and photosynthesis by controlling stomatal aperture. This control is regulated in part by the circadian clock, but it remains unclear how signalling pathways of daily rhythms are integrated into stress responses. The serine/threonine protein kinase OPEN STOMATA 1 (OST1) contributes to the regulation of stomatal closure via activation of S-type anion channels. OST1 also mediates gene regulation in response to ABA/drought stress. We show that ZEITLUPE (ZTL), a blue light photoreceptor and clock component, also regulates ABA-induced stomatal closure in Arabidopsis thaliana, establishing a link between clock and ABA-signalling pathways. ZTL sustains expression of OST1 and ABA-signalling genes. Stomatal closure in response to ABA is reduced in ztl mutants, which maintain wider stomatal apertures and show higher rates of gas exchange and water loss than wild-type plants. Detached rosette leaf assays revealed a stronger water loss phenotype in ztl-3, ost1-3 double mutants, indicating that ZTL and OST1 contributed synergistically to the control of stomatal aperture. Experimental studies of Populus sp., revealed that ZTL regulated the circadian clock and stomata, indicating ZTL function was similar in these trees and Arabidopsis. PSEUDO-RESPONSE REGULATOR 5 (PRR5), a known target of ZTL, affects ABA-induced responses, including stomatal regulation. Like ZTL, PRR5 interacted physically with OST1 and contributed to the integration of ABA responses with circadian clock signalling. This suggests a novel mechanism whereby the PRR proteins—which are expressed from dawn to dusk—interact with OST1 to mediate ABA-dependent plant responses to reduce water loss in time of stress.},
	urldate = {2022-03-02},
	journal = {Frontiers in Plant Science},
	author = {Jurca, Manuela and Sjölander, Johan and Ibáñez, Cristian and Matrosova, Anastasia and Johansson, Mikael and Kozarewa, Iwanka and Takata, Naoki and Bakó, Laszlo and Webb, Alex A. R. and Israelsson-Nordström, Maria and Eriksson, Maria E.},
	month = mar,
	year = {2022},
	keywords = {⛔ No DOI found},
}

Plants balance water availability with gas exchange and photosynthesis by controlling stomatal aperture. This control is regulated in part by the circadian clock, but it remains unclear how signalling pathways of daily rhythms are integrated into stress responses. The serine/threonine protein kinase OPEN STOMATA 1 (OST1) contributes to the regulation of stomatal closure via activation of S-type anion channels. OST1 also mediates gene regulation in response to ABA/drought stress. We show that ZEITLUPE (ZTL), a blue light photoreceptor and clock component, also regulates ABA-induced stomatal closure in Arabidopsis thaliana, establishing a link between clock and ABA-signalling pathways. ZTL sustains expression of OST1 and ABA-signalling genes. Stomatal closure in response to ABA is reduced in ztl mutants, which maintain wider stomatal apertures and show higher rates of gas exchange and water loss than wild-type plants. Detached rosette leaf assays revealed a stronger water loss phenotype in ztl-3, ost1-3 double mutants, indicating that ZTL and OST1 contributed synergistically to the control of stomatal aperture. Experimental studies of Populus sp., revealed that ZTL regulated the circadian clock and stomata, indicating ZTL function was similar in these trees and Arabidopsis. PSEUDO-RESPONSE REGULATOR 5 (PRR5), a known target of ZTL, affects ABA-induced responses, including stomatal regulation. Like ZTL, PRR5 interacted physically with OST1 and contributed to the integration of ABA responses with circadian clock signalling. This suggests a novel mechanism whereby the PRR proteins—which are expressed from dawn to dusk—interact with OST1 to mediate ABA-dependent plant responses to reduce water loss in time of stress.

@article{vergara_norway_2022,
	title = {Norway spruce deploys tissue-specific responses during acclimation to cold},
	volume = {45},
	issn = {1365-3040},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/pce.14241},
	doi = {10.1111/pce.14241},
	abstract = {Climate change in the conifer-dominated boreal forest is expected to lead to warmer but more dynamic winter air temperatures, reducing the depth and duration of snow cover, which in turn results in colder winter soils. To gain insight into the mechanisms that have enabled conifers to dominate when exposed to extremes of long exposure to freezing temperatures, we performed genome-wide RNA-Seq analysis from needles and roots of non-dormant two-year Norway spruce (Picea abies (L.) H. Karst), and contrasted these response to herbaceous model Arabidopsis We show that, relative to Arabidopsis leaves, the main transcriptional response of Norway spruce (Picea abies (L.) H. Karst) needles exposed to cold was delayed, and this delay was associated with slower development of freezing tolerance. However, despite this difference in timing, our results indicate that Norway spruce principally utilizes early response transcription factors (TFs) belonging to the same gene families as used by Arabidopsis, indicating broad evolutionary conservation of cold response networks. However, needles and root of Norway spruce showed contrasting results, in keeping with their different metabolic and developmental states. Regulatory network analysis identified conserved TFs, including a root-specific bHLH101 homolog, and other members of the same TF family with a pervasive role in cold regulation, such as homologs of ICE1 and AKS3, and also homologs of the NAC (anac47 and anac28) and AP2/ERF superfamilies (DREB2 and ERF3), providing new functional insights into cold stress response strategies in Norway spruce. This article is protected by copyright. All rights reserved.},
	language = {en},
	number = {2},
	urldate = {2021-12-09},
	journal = {Plant, Cell \& Environment},
	author = {Vergara, Alexander and Haas, Julia Christa and Aro, Tuuli and Stachula, Paulina and Street, Nathaniel Robert and Hurry, Vaughan},
	month = feb,
	year = {2022},
	keywords = {Norway spruce, cold, transcriptome},
}

Climate change in the conifer-dominated boreal forest is expected to lead to warmer but more dynamic winter air temperatures, reducing the depth and duration of snow cover, which in turn results in colder winter soils. To gain insight into the mechanisms that have enabled conifers to dominate when exposed to extremes of long exposure to freezing temperatures, we performed genome-wide RNA-Seq analysis from needles and roots of non-dormant two-year Norway spruce (Picea abies (L.) H. Karst), and contrasted these response to herbaceous model Arabidopsis We show that, relative to Arabidopsis leaves, the main transcriptional response of Norway spruce (Picea abies (L.) H. Karst) needles exposed to cold was delayed, and this delay was associated with slower development of freezing tolerance. However, despite this difference in timing, our results indicate that Norway spruce principally utilizes early response transcription factors (TFs) belonging to the same gene families as used by Arabidopsis, indicating broad evolutionary conservation of cold response networks. However, needles and root of Norway spruce showed contrasting results, in keeping with their different metabolic and developmental states. Regulatory network analysis identified conserved TFs, including a root-specific bHLH101 homolog, and other members of the same TF family with a pervasive role in cold regulation, such as homologs of ICE1 and AKS3, and also homologs of the NAC (anac47 and anac28) and AP2/ERF superfamilies (DREB2 and ERF3), providing new functional insights into cold stress response strategies in Norway spruce. This article is protected by copyright. All rights reserved.

@article{tunnermann_have_2022,
	title = {To have or not to have: expression of amino acid transporters during pathogen infection},
	issn = {1573-5028},
	shorttitle = {To have or not to have},
	url = {https://doi.org/10.1007/s11103-022-01244-1},
	doi = {10/gpjfdr},
	abstract = {The interaction between plants and plant pathogens can have significant effects on ecosystem performance. For their growth and development, both bionts rely on amino acids. While amino acids are key transport forms of nitrogen and can be directly absorbed from the soil through specific root amino acid transporters, various pathogenic microbes can invade plant tissues to feed on different plant amino acid pools. In parallel, plants may initiate an immune response program to restrict this invasion, employing various amino acid transporters to modify the amino acid pool at the site of pathogen attack. The interaction between pathogens and plants is sophisticated and responses are dynamic. Both avail themselves of multiple tools to increase their chance of survival. In this review, we highlight the role of amino acid transporters during pathogen infection. Having control over the expression of those transporters can be decisive for the fate of both bionts but the underlying mechanism that regulates the expression of amino acid transporters is not understood to date. We provide an overview of the regulation of a variety of amino acid transporters, depending on interaction with biotrophic, hemibiotrophic or necrotrophic pathogens. In addition, we aim to highlight the interplay of different physiological processes on amino acid transporter regulation during pathogen attack and chose the LYSINE HISTIDINE TRANSPORTER1 (LHT1) as an example.},
	language = {en},
	urldate = {2022-02-14},
	journal = {Plant Molecular Biology},
	author = {Tünnermann, Laura and Colou, Justine and Näsholm, Torgny and Gratz, Regina},
	month = feb,
	year = {2022},
}

The interaction between plants and plant pathogens can have significant effects on ecosystem performance. For their growth and development, both bionts rely on amino acids. While amino acids are key transport forms of nitrogen and can be directly absorbed from the soil through specific root amino acid transporters, various pathogenic microbes can invade plant tissues to feed on different plant amino acid pools. In parallel, plants may initiate an immune response program to restrict this invasion, employing various amino acid transporters to modify the amino acid pool at the site of pathogen attack. The interaction between pathogens and plants is sophisticated and responses are dynamic. Both avail themselves of multiple tools to increase their chance of survival. In this review, we highlight the role of amino acid transporters during pathogen infection. Having control over the expression of those transporters can be decisive for the fate of both bionts but the underlying mechanism that regulates the expression of amino acid transporters is not understood to date. We provide an overview of the regulation of a variety of amino acid transporters, depending on interaction with biotrophic, hemibiotrophic or necrotrophic pathogens. In addition, we aim to highlight the interplay of different physiological processes on amino acid transporter regulation during pathogen attack and chose the LYSINE HISTIDINE TRANSPORTER1 (LHT1) as an example.

@article{ohlund_transcriptome_2022,
	title = {Transcriptome {Analysis} of an {Aedes} albopictus {Cell} {Line} {Single}- and {Dual}-{Infected} with {Lammi} {Virus} and {WNV}},
	volume = {23},
	issn = {1422-0067},
	url = {https://www.mdpi.com/1422-0067/23/2/875},
	doi = {10.3390/ijms23020875},
	abstract = {Understanding the flavivirus infection process in mosquito hosts is important and fundamental in the search for novel control strategies that target the mosquitoes' ability to carry and transmit pathogenic arboviruses. A group of viruses known as insect-specific viruses (ISVs) has been shown to interfere with the infection and replication of a secondary arbovirus infection in mosquitoes and mosquito-derived cell lines. However, the molecular mechanisms behind this interference are unknown. Therefore, in the present study, we infected the Aedes albopictus cell line U4.4 with either the West Nile virus (WNV), the insect-specific Lammi virus (LamV) or an infection scheme whereby cells were pre-infected with LamV 24 h prior to WNV challenge. The qPCR analysis showed that the dual-infected U4.4 cells had a reduced number of WNV RNA copies compared to WNV-only infected cells. The transcriptome profiles of the different infection groups showed a variety of genes with altered expression. WNV-infected cells had an up-regulation of a broad range of immune-related genes, while in LamV-infected cells, many genes related to stress, such as different heat-shock proteins, were up-regulated. The transcriptome profile of the dual-infected cells was a mix of up- and down-regulated genes triggered by both viruses. Furthermore, we observed an up-regulation of signal peptidase complex (SPC) proteins in all infection groups. These SPC proteins have shown importance for flavivirus assembly and secretion and could be potential targets for gene modification in strategies for the interruption of flavivirus transmission by mosquitoes.},
	language = {eng},
	number = {2},
	journal = {International Journal of Molecular Sciences},
	author = {Öhlund, Pontus and Delhomme, Nicolas and Hayer, Juliette and Hesson, Jenny C. and Blomström, Anne-Lie},
	month = jan,
	year = {2022},
	keywords = {\textit{Aedes albopictus}, Aedes albopictus, West Nile virus, insect-specific flaviviruses, transcriptome, viral interference},
	pages = {875},
}

Understanding the flavivirus infection process in mosquito hosts is important and fundamental in the search for novel control strategies that target the mosquitoes' ability to carry and transmit pathogenic arboviruses. A group of viruses known as insect-specific viruses (ISVs) has been shown to interfere with the infection and replication of a secondary arbovirus infection in mosquitoes and mosquito-derived cell lines. However, the molecular mechanisms behind this interference are unknown. Therefore, in the present study, we infected the Aedes albopictus cell line U4.4 with either the West Nile virus (WNV), the insect-specific Lammi virus (LamV) or an infection scheme whereby cells were pre-infected with LamV 24 h prior to WNV challenge. The qPCR analysis showed that the dual-infected U4.4 cells had a reduced number of WNV RNA copies compared to WNV-only infected cells. The transcriptome profiles of the different infection groups showed a variety of genes with altered expression. WNV-infected cells had an up-regulation of a broad range of immune-related genes, while in LamV-infected cells, many genes related to stress, such as different heat-shock proteins, were up-regulated. The transcriptome profile of the dual-infected cells was a mix of up- and down-regulated genes triggered by both viruses. Furthermore, we observed an up-regulation of signal peptidase complex (SPC) proteins in all infection groups. These SPC proteins have shown importance for flavivirus assembly and secretion and could be potential targets for gene modification in strategies for the interruption of flavivirus transmission by mosquitoes.

@incollection{johansson_perennial_2022,
	address = {New York, NY},
	series = {Methods in {Molecular} {Biology}},
	title = {The {Perennial} {Clock} {Is} an {Essential} {Timer} for {Seasonal} {Growth} {Events} and {Cold} {Hardiness}},
	isbn = {978-1-07-161912-4},
	url = {https://doi.org/10.1007/978-1-0716-1912-4_18},
	abstract = {Over the last several decades, changes in global temperatures have led to changes in local environments affecting the growth conditions for many species. This is a trend that makes it even more important to understand how plants respond to local variations and seasonal changes in climate.To detect daily and seasonal changes as well as acute stress factors such as cold and drought, plants rely on a circadian clock. This chapter introduces the current knowledge and literature about the setup and function of the circadian clock in various tree and perennial species, with a focus on the Populus genus.},
	language = {en},
	urldate = {2021-12-01},
	booktitle = {Plant {Circadian} {Networks}: {Methods} and {Protocols}},
	publisher = {Springer US},
	author = {Johansson, Mikael and Ibáñez, Cristian and Takata, Naoki and Eriksson, Maria E.},
	editor = {Staiger, Dorothee and Davis, Seth and Davis, Amanda Melaragno},
	month = jan,
	year = {2022},
	keywords = {Bud burst, Bud set, Circadian clock, Cold tolerance, Growth, Perennial plants, Populus, Seasonal regulation},
	pages = {227--242},
}

Over the last several decades, changes in global temperatures have led to changes in local environments affecting the growth conditions for many species. This is a trend that makes it even more important to understand how plants respond to local variations and seasonal changes in climate.To detect daily and seasonal changes as well as acute stress factors such as cold and drought, plants rely on a circadian clock. This chapter introduces the current knowledge and literature about the setup and function of the circadian clock in various tree and perennial species, with a focus on the Populus genus.

@incollection{johansson_monitoring_2022,
	address = {New York, NY},
	series = {Methods in {Molecular} {Biology}},
	title = {Monitoring {Seasonal} {Bud} {Set}, {Bud} {Burst}, and {Cold} {Hardiness} in {Populus}},
	isbn = {978-1-07-161912-4},
	url = {https://doi.org/10.1007/978-1-0716-1912-4_17},
	abstract = {Using a perennial model plant allows the study of reoccurring seasonal events in a way that is not possible using a fast-growing annual such as A. thaliana (Arabidopsis). In this study, we present a hybrid aspen (Populus tremula × P. tremuloides) as our perennial model plant. These plants can be grown in growth chambers to shorten growth periods and manipulate day length and temperature in ways that would be impossible under natural conditions. In addition, the use of growth chambers allows easy monitoring of height and diameter expansion, accelerating the collection of data from new strategies that allow evaluation of promoters or inhibitors of growth. Here, we describe how to study and quantify responses to seasonal changes (mainly using P. tremula × P. tremuloides) by measuring growth rate and key events under different photoperiodic cycles.},
	language = {en},
	urldate = {2021-12-01},
	booktitle = {Plant {Circadian} {Networks}: {Methods} and {Protocols}},
	publisher = {Springer US},
	author = {Johansson, Mikael and Takata, Naoki and Ibáñez, Cristian and Eriksson, Maria E.},
	editor = {Staiger, Dorothee and Davis, Seth and Davis, Amanda Melaragno},
	month = jan,
	year = {2022},
	keywords = {Bud burst, Bud set, Cold acclimation, Critical day length, Freezing tolerance, Perennial, Photoperiod, Populus},
	pages = {215--226},
}

Using a perennial model plant allows the study of reoccurring seasonal events in a way that is not possible using a fast-growing annual such as A. thaliana (Arabidopsis). In this study, we present a hybrid aspen (Populus tremula × P. tremuloides) as our perennial model plant. These plants can be grown in growth chambers to shorten growth periods and manipulate day length and temperature in ways that would be impossible under natural conditions. In addition, the use of growth chambers allows easy monitoring of height and diameter expansion, accelerating the collection of data from new strategies that allow evaluation of promoters or inhibitors of growth. Here, we describe how to study and quantify responses to seasonal changes (mainly using P. tremula × P. tremuloides) by measuring growth rate and key events under different photoperiodic cycles.

@article{ivanov_decreased_2022,
	title = {The decreased {PG} content of pgp1 inhibits {PSI} photochemistry and limits reaction center and light-harvesting polypeptide accumulation in response to cold acclimation},
	volume = {255},
	issn = {1432-2048},
	url = {https://doi.org/10.1007/s00425-022-03819-0},
	doi = {10/gn64qq},
	abstract = {Decreased PG constrains PSI activity due to inhibition of transcript and polypeptide abundance of light-harvesting and reaction center polypeptides generating a reversible, yellow phenotype during cold acclimation of pgp1.},
	language = {en},
	number = {2},
	urldate = {2022-01-17},
	journal = {Planta},
	author = {Ivanov, Alexander G. and Krol, Marianna and Savitch, Leonid V. and Szyszka-Mroz, Beth and Roche, Jessica and Sprott, D. P. and Selstam, Eva and Wilson, Kenneth W. and Gardiner, Richard and Öquist, Gunnar and Hurry, Vaughan M. and Hüner, Norman P. A.},
	month = jan,
	year = {2022},
	pages = {36},
}

Decreased PG constrains PSI activity due to inhibition of transcript and polypeptide abundance of light-harvesting and reaction center polypeptides generating a reversible, yellow phenotype during cold acclimation of pgp1.

@incollection{boussardon_cell_2022,
	address = {New York, NY},
	series = {Methods in {Molecular} {Biology}},
	title = {Cell {Type}–{Specific} {Isolation} of {Mitochondria} in {Arabidopsis}},
	isbn = {978-1-07-161653-6},
	url = {https://doi.org/10.1007/978-1-0716-1653-6_2},
	abstract = {Membrane-bound organelles are unique features of eukaryotic cell structures. Among them, mitochondria host key metabolic functions and pathways, including the aerobic respiration. In plants, several procedures are available to isolate mitochondria from the other cell compartments, as high-quality purified extracts are often necessary for accurate molecular biology or biochemistry investigations. Protocols based on differential centrifugations and subsequent density gradients are an effective way to extract rather pure and intact mitochondria within a few hours. However, while mitochondria from seedlings, large leaves or tubers are relatively easy to extract, tissue-specific isolation of organelles had remained a challenge. This has recently been circumvented, only in transformable plants though, by the use of affinity-tagged mitochondria and their isolation with magnetic beads.We hereby describe a step-by-step protocol for the rapid and tissue-specific isolation of Arabidopsis thaliana mitochondria, a method named IMTACT (Isolation of Mitochondria TAgged in specific Cell Types). Cell-specific biotinylated mitochondria are isolated with streptavidin magnetic beads in less than 30 min from sampling to final extract. Key steps, enrichment, bead size comparison, and mitochondrial depletion in the sample are also reported in order to facilitate the experimental setup of the user.},
	language = {en},
	urldate = {2021-09-23},
	booktitle = {Plant {Mitochondria}: {Methods} and {Protocols}},
	publisher = {Springer US},
	author = {Boussardon, Clément and Keech, Olivier},
	editor = {Van Aken, Olivier and Rasmusson, Allan G.},
	month = jan,
	year = {2022},
	keywords = {Biotin–streptavidin interaction, Editable Golden Gate plasmids, Mitochondria, Tagged outer membrane, Tissue-specific isolation},
	pages = {13--23},
}

Membrane-bound organelles are unique features of eukaryotic cell structures. Among them, mitochondria host key metabolic functions and pathways, including the aerobic respiration. In plants, several procedures are available to isolate mitochondria from the other cell compartments, as high-quality purified extracts are often necessary for accurate molecular biology or biochemistry investigations. Protocols based on differential centrifugations and subsequent density gradients are an effective way to extract rather pure and intact mitochondria within a few hours. However, while mitochondria from seedlings, large leaves or tubers are relatively easy to extract, tissue-specific isolation of organelles had remained a challenge. This has recently been circumvented, only in transformable plants though, by the use of affinity-tagged mitochondria and their isolation with magnetic beads.We hereby describe a step-by-step protocol for the rapid and tissue-specific isolation of Arabidopsis thaliana mitochondria, a method named IMTACT (Isolation of Mitochondria TAgged in specific Cell Types). Cell-specific biotinylated mitochondria are isolated with streptavidin magnetic beads in less than 30 min from sampling to final extract. Key steps, enrichment, bead size comparison, and mitochondrial depletion in the sample are also reported in order to facilitate the experimental setup of the user.

@article{li_towards_2022,
	title = {Towards understanding the biological foundations of perenniality},
	volume = {27},
	issn = {1360-1385},
	url = {https://www.sciencedirect.com/science/article/pii/S1360138521002181},
	doi = {10.1016/j.tplants.2021.08.007},
	abstract = {Perennial life cycles enable plants to have remarkably long lifespans, as exemplified by trees that can live for thousands of years. For this, they require sophisticated regulatory networks that sense environmental changes and initiate adaptive responses in their growth patterns. Recent research has gradually elucidated fundamental mechanisms underlying the perennial life cycle. Intriguingly, several conserved components of the floral transition pathway in annuals such as Arabidopsis thaliana also participate in these regulatory mechanisms underpinning perenniality. Here, we provide an overview of perennials’ physiological features and summarise their recently discovered molecular foundations. We also highlight the importance of deepening our understanding of perenniality in the development of perennial grain crops, which are promising elements of future sustainable agriculture.},
	language = {en},
	number = {1},
	urldate = {2021-09-30},
	journal = {Trends in Plant Science},
	author = {Li, Zheng and Lathe, Rahul S. and Li, Jinping and He, Hong and Bhalerao, Rishikesh P.},
	month = jan,
	year = {2022},
	keywords = {perenniality, polycarpy, seasonal adaptation, sustainable agriculture},
	pages = {56--68},
}

Perennial life cycles enable plants to have remarkably long lifespans, as exemplified by trees that can live for thousands of years. For this, they require sophisticated regulatory networks that sense environmental changes and initiate adaptive responses in their growth patterns. Recent research has gradually elucidated fundamental mechanisms underlying the perennial life cycle. Intriguingly, several conserved components of the floral transition pathway in annuals such as Arabidopsis thaliana also participate in these regulatory mechanisms underpinning perenniality. Here, we provide an overview of perennials’ physiological features and summarise their recently discovered molecular foundations. We also highlight the importance of deepening our understanding of perenniality in the development of perennial grain crops, which are promising elements of future sustainable agriculture.

@article{marhava_recent_2022,
	title = {Recent developments in the understanding of {PIN} polarity},
	volume = {233},
	issn = {1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/nph.17867},
	doi = {10/gnr3sd},
	abstract = {Polar localization of PIN-FORMED proteins (PINs) at the plasma membrane is essential for plant development as they direct the transport of phytohormone auxin between cells. PIN polar localization to certain sides of a given cell is dynamic, strictly regulated and provides directionality to auxin flow. Signals that act upstream to control subcellular PIN localization modulate auxin distribution, thereby regulating diverse aspects of plant development. Here I summarize the current understanding of mechanisms by which PIN polarity is established, maintained and rearranged to provide a glimpse into the complexity of PIN polarity.},
	language = {en},
	number = {2},
	urldate = {2021-12-14},
	journal = {New Phytologist},
	author = {Marhava, Petra},
	month = jan,
	year = {2022},
	keywords = {PIN clustering, PIN polarity establishment, PIN polarity maintenance, auxin transport, self-reinforcing polarity},
	pages = {624--630},
}

Polar localization of PIN-FORMED proteins (PINs) at the plasma membrane is essential for plant development as they direct the transport of phytohormone auxin between cells. PIN polar localization to certain sides of a given cell is dynamic, strictly regulated and provides directionality to auxin flow. Signals that act upstream to control subcellular PIN localization modulate auxin distribution, thereby regulating diverse aspects of plant development. Here I summarize the current understanding of mechanisms by which PIN polarity is established, maintained and rearranged to provide a glimpse into the complexity of PIN polarity.

@article{peters_hydroxycarboxylic_2022,
	title = {Hydroxycarboxylic acid receptor 3 and {GPR84} – {Two} metabolite-sensing {G} protein-coupled receptors with opposing functions in innate immune cells},
	volume = {176},
	issn = {1043-6618},
	url = {https://www.sciencedirect.com/science/article/pii/S1043661821006319},
	doi = {10/gn29gj},
	abstract = {G protein-coupled receptors (GPCRs) are key regulatory proteins of immune cell function inducing signaling in response to extracellular (pathogenic) stimuli. Although unrelated, hydroxycarboxylic acid receptor 3 (HCA3) and GPR84 share signaling via Gαi/o proteins and the agonist 3-hydroxydecanoic acid (3HDec). Both receptors are abundantly expressed in monocytes, macrophages and neutrophils but have opposing functions in these innate immune cells. Detailed insights into the molecular mechanisms and signaling components involved in immune cell regulation by GPR84 and HCA3 are still lacking. Here, we report that GPR84-mediated pro-inflammatory signaling depends on coupling to the hematopoietic cell-specific Gα15 protein in human macrophages, while HCA3 exclusively couples to Gαi protein. We show that activated GPR84 induces Gα15-dependent ERK activation, increases intracellular Ca2+ and IP3 levels as well as ROS production. In contrast, HCA3 activation shifts macrophage metabolism to a less glycolytic phenotype, which is associated with anti-inflammatory responses. This is supported by an increased release of anti-inflammatory IL-10 and a decreased secretion of pro-inflammatory IL-1β. In primary human neutrophils, stimulation with HCA3 agonists counteracts the GPR84-induced neutrophil activation. Our analyses reveal that 3HDec acts solely through GPR84 but not HCA3 activation in macrophages. In summary, this study shows that HCA3 mediates hyporesponsiveness in response to metabolites derived from dietary lactic acid bacteria and uncovers that GPR84, which is already targeted in clinical trials, promotes pro-inflammatory signaling via Gα15 protein in macrophages.},
	language = {en},
	urldate = {2022-01-10},
	journal = {Pharmacological Research},
	author = {Peters, Anna and Rabe, Philipp and Liebing, Aenne-Dorothea and Krumbholz, Petra and Nordström, Anders and Jäger, Elisabeth and Kraft, Robert and Stäubert, Claudia},
	month = feb,
	year = {2022},
	keywords = {D-phenyllactic acid, GPR84, Hydroxycarboxylic acid receptor 3, Lactic acid bacteria, Macrophages, Neutrophils},
	pages = {106047},
}

G protein-coupled receptors (GPCRs) are key regulatory proteins of immune cell function inducing signaling in response to extracellular (pathogenic) stimuli. Although unrelated, hydroxycarboxylic acid receptor 3 (HCA3) and GPR84 share signaling via Gαi/o proteins and the agonist 3-hydroxydecanoic acid (3HDec). Both receptors are abundantly expressed in monocytes, macrophages and neutrophils but have opposing functions in these innate immune cells. Detailed insights into the molecular mechanisms and signaling components involved in immune cell regulation by GPR84 and HCA3 are still lacking. Here, we report that GPR84-mediated pro-inflammatory signaling depends on coupling to the hematopoietic cell-specific Gα15 protein in human macrophages, while HCA3 exclusively couples to Gαi protein. We show that activated GPR84 induces Gα15-dependent ERK activation, increases intracellular Ca2+ and IP3 levels as well as ROS production. In contrast, HCA3 activation shifts macrophage metabolism to a less glycolytic phenotype, which is associated with anti-inflammatory responses. This is supported by an increased release of anti-inflammatory IL-10 and a decreased secretion of pro-inflammatory IL-1β. In primary human neutrophils, stimulation with HCA3 agonists counteracts the GPR84-induced neutrophil activation. Our analyses reveal that 3HDec acts solely through GPR84 but not HCA3 activation in macrophages. In summary, this study shows that HCA3 mediates hyporesponsiveness in response to metabolites derived from dietary lactic acid bacteria and uncovers that GPR84, which is already targeted in clinical trials, promotes pro-inflammatory signaling via Gα15 protein in macrophages.