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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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