@article{tronnet_extracellular_2025,
	title = {Extracellular {ATP} is an environmental cue in bacteria},
	volume = {44},
	issn = {2211-1247},
	url = {https://www.sciencedirect.com/science/article/pii/S2211124725011271},
	doi = {10.1016/j.celrep.2025.116356},
	abstract = {In animals and plants, extracellular ATP (eATP) functions as a signal and regulates the immune response. During inflammation, intestinal bacteria are exposed to elevated eATP originating from the mucosa. However, whether bacteria respond to eATP is unclear. Here, we show that non-pathogenic Escherichia coli responds to eATP by modifying its transcriptional and metabolic landscapes. A genome-scale promoter library showed that the response is dependent on time, concentration, and medium and ATP specific. Second messengers and genes related to metabolism, biofilm formation, and envelope stress were regulated downstream of eATP. Metabolomics confirmed that eATP triggers enrichment of compounds with bioactive properties in the host or bacteria. Combined genome-scale modeling revealed modifications to global metabolic and biomass building blocks. Consequently, eATP altered the sensitivity to antibiotics and antimicrobial peptides. Finally, in pathogens, eATP controlled virulence factor expression. Our results indicate that eATP is an environmental cue in prokaryotes, which broadly regulates physiology, antimicrobial resistance, and virulence.},
	number = {10},
	urldate = {2025-10-17},
	journal = {Cell Reports},
	author = {Tronnet, Sophie and Pandey, Vikash and Lloret-Berrocal, Miriam and Pérez-del-Pozo, Mario and Hernández-Ortego, Carlos and Söderholm, Niklas and Billker, Oliver and Nordström, Anders and Puhar, Andrea},
	month = oct,
	year = {2025},
	keywords = {Enterobacteriaceae, antimicrobial resistance, extracellular ATP, gene expression, inflammation, intestinal bacteria, metabolites, physiology, purinergic signaling, virulence},
	pages = {116356},
}

In animals and plants, extracellular ATP (eATP) functions as a signal and regulates the immune response. During inflammation, intestinal bacteria are exposed to elevated eATP originating from the mucosa. However, whether bacteria respond to eATP is unclear. Here, we show that non-pathogenic Escherichia coli responds to eATP by modifying its transcriptional and metabolic landscapes. A genome-scale promoter library showed that the response is dependent on time, concentration, and medium and ATP specific. Second messengers and genes related to metabolism, biofilm formation, and envelope stress were regulated downstream of eATP. Metabolomics confirmed that eATP triggers enrichment of compounds with bioactive properties in the host or bacteria. Combined genome-scale modeling revealed modifications to global metabolic and biomass building blocks. Consequently, eATP altered the sensitivity to antibiotics and antimicrobial peptides. Finally, in pathogens, eATP controlled virulence factor expression. Our results indicate that eATP is an environmental cue in prokaryotes, which broadly regulates physiology, antimicrobial resistance, and virulence.

@article{fenech_cyp71a_2025,
	title = {The {CYP71A}, {NIT}, {AMI}, and {IAMH} gene families are dispensable for indole-3-acetaldoxime-mediated auxin biosynthesis in {Arabidopsis}},
	issn = {1040-4651},
	url = {https://doi.org/10.1093/plcell/koaf242},
	doi = {10.1093/plcell/koaf242},
	abstract = {The auxin indole-3-acetic acid (IAA) governs plant development and environmental responses. Although the indole-3-pyruvic acid (IPyA) pathway is the predominant route for IAA biosynthesis, other pathways have been proposed, such as the indole-3-acetaldoxime (IAOx) pathway. The IAOx pathway has garnered attention due to its supposed activation in auxin-overproducing mutants (e.g., sur1, sur2, ugt74b1) and the auxin-like responses triggered by exogenous application of its proposed intermediates IAOx, indole-3-acetonitrile (IAN), and indole-3-acetamide (IAM). However, despite the supporting evidence for individual steps of the IAOx pathway, its overall physiological relevance remains inconclusive. Here, using a comprehensive genetic approach combined with metabolic and phenotypic profiling, we demonstrate that mutating gene families proposed to function in the IAOx pathway in Arabidopsis (Arabidopsis thaliana) does not result in prominent auxin-deficient phenotypes, nor are these genes required for the high auxin production in the sur2 mutant. Our findings also challenge the previously postulated linear IAOx pathway. Exogenously provided IAOx, IAN, and IAM can be converted to IAA in vivo, but they do not act as precursors for each other. Finally, our findings question the physiological relevance of IAM and IAN as IAA precursors in plants and suggest the existence of a yet-uncharacterized route for IAA production in the sur2 mutant, likely involving IAOx as an intermediate. The identification of the metabolic steps and the corresponding genes in this pathway may uncover another IAA biosynthesis route in plants.},
	urldate = {2025-10-17},
	journal = {The Plant Cell},
	author = {Fenech, M and Brumos, J and Pěnčík, A and Edwards, B and Belcapo, S and DeLacey, J and Patel, A and Kater, M M and Li, X and Ljung, K and Novak, O and Alonso, J M and Stepanova, A N},
	month = oct,
	year = {2025},
	pages = {koaf242},
}

The auxin indole-3-acetic acid (IAA) governs plant development and environmental responses. Although the indole-3-pyruvic acid (IPyA) pathway is the predominant route for IAA biosynthesis, other pathways have been proposed, such as the indole-3-acetaldoxime (IAOx) pathway. The IAOx pathway has garnered attention due to its supposed activation in auxin-overproducing mutants (e.g., sur1, sur2, ugt74b1) and the auxin-like responses triggered by exogenous application of its proposed intermediates IAOx, indole-3-acetonitrile (IAN), and indole-3-acetamide (IAM). However, despite the supporting evidence for individual steps of the IAOx pathway, its overall physiological relevance remains inconclusive. Here, using a comprehensive genetic approach combined with metabolic and phenotypic profiling, we demonstrate that mutating gene families proposed to function in the IAOx pathway in Arabidopsis (Arabidopsis thaliana) does not result in prominent auxin-deficient phenotypes, nor are these genes required for the high auxin production in the sur2 mutant. Our findings also challenge the previously postulated linear IAOx pathway. Exogenously provided IAOx, IAN, and IAM can be converted to IAA in vivo, but they do not act as precursors for each other. Finally, our findings question the physiological relevance of IAM and IAN as IAA precursors in plants and suggest the existence of a yet-uncharacterized route for IAA production in the sur2 mutant, likely involving IAOx as an intermediate. The identification of the metabolic steps and the corresponding genes in this pathway may uncover another IAA biosynthesis route in plants.

@article{rydman_metabolomics_2025,
	title = {A {Metabolomics} and {Transcriptomics} {Resource} for {Identifying} {Candidate} {Genes} in the {Biosynthesis} of {Specialised} {Metabolites} in {Populus} tremula},
	volume = {177},
	copyright = {© 2025 The Author(s). Physiologia Plantarum published by John Wiley \& Sons Ltd on behalf of Scandinavian Plant Physiology Society.},
	issn = {1399-3054},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/ppl.70567},
	doi = {10.1111/ppl.70567},
	abstract = {This study aims to identify candidate genes involved in the biosynthesis of salicinoid phenolic glycosides (SPGs), a group of specialised metabolites characteristic of the Salicaceae family. While the integration of multi-omics data represents a powerful approach to link genes encoding enzymes and their regulatory factors to metabolite biosynthesis, suitable multi-omics data resources are scarce. We present a comprehensive dataset comprising untargeted liquid chromatography–mass spectrometry (LC–MS) and mRNA-sequencing data from various organs of European aspen (Populus tremula L.) and from genotypes that produce contrasting sets of SPGs. We present a reproducible pipeline for the analysis of the LC–MS data, including predicted annotation of potential novel SPGs. We demonstrate the utility of the resource by identifying candidate genes involved in the biosynthesis of SPGs with a cinnamoyl moiety. By integrating gene and metabolite differential analyses with a gene co-expression network, we identified two HXXXD-type acyltransferase genes and one UDP-glucosyltransferase gene as candidates for future downstream characterisation. The combined gene expression and metabolomics resource is integrated into PlantGenIE.org to facilitate easy access and data mining. All raw data are available in public databases, and all data and results files are available at an associated Figshare repository.},
	language = {en},
	number = {5},
	urldate = {2025-10-13},
	journal = {Physiologia Plantarum},
	author = {Rydman, Sara M. and Lihavainen, Jenna and Robinson, Kathryn M. and Jansson, Stefan and Albrectsen, Benedicte R. and Street, Nathaniel R.},
	year = {2025},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/ppl.70567},
	keywords = {Populus tremula, RNA-Seq, aspen, biosynthesis, chemotype, liquid chromatography–mass spectrometry (LC–MS), metabolomics, phenolic glycosides, salicinoid, specialised metabolite},
	pages = {e70567},
}

This study aims to identify candidate genes involved in the biosynthesis of salicinoid phenolic glycosides (SPGs), a group of specialised metabolites characteristic of the Salicaceae family. While the integration of multi-omics data represents a powerful approach to link genes encoding enzymes and their regulatory factors to metabolite biosynthesis, suitable multi-omics data resources are scarce. We present a comprehensive dataset comprising untargeted liquid chromatography–mass spectrometry (LC–MS) and mRNA-sequencing data from various organs of European aspen (Populus tremula L.) and from genotypes that produce contrasting sets of SPGs. We present a reproducible pipeline for the analysis of the LC–MS data, including predicted annotation of potential novel SPGs. We demonstrate the utility of the resource by identifying candidate genes involved in the biosynthesis of SPGs with a cinnamoyl moiety. By integrating gene and metabolite differential analyses with a gene co-expression network, we identified two HXXXD-type acyltransferase genes and one UDP-glucosyltransferase gene as candidates for future downstream characterisation. The combined gene expression and metabolomics resource is integrated into PlantGenIE.org to facilitate easy access and data mining. All raw data are available in public databases, and all data and results files are available at an associated Figshare repository.

@article{zacharaki_convergent_2025,
	title = {Convergent antisense transcription primes hosting genes for stress responsiveness in plants.},
	issn = {1674-2052},
	url = {https://www.sciencedirect.com/science/article/pii/S167420522500351X},
	doi = {10.1016/j.molp.2025.10.001},
	abstract = {Plants need to constantly surveil their surroundings to adapt to environmental fluctuations, which they achieve primarily through transcriptional reprogramming. Thus, plants are excellent models for identifying novel transcriptional regulatory mechanisms. Here, we characterize regulation conveyed by long non-coding transcription that initiates on the complementary strand in the 5ʹ-end of coding genes (Convergent Antisense transcription (CASt)). In Arabidopsis, CASt is associated with stress-responsive genes that are highly expressed. Our analysis shows that CASt depends on a specific gene architecture that is evolutionarily conserved in higher plants. CASt is present in genes with an extended first intron and over-represented in genes with a transporter function in Arabidopsis, such as the AAP transporter family. Experimental evidence points to a role for CASt in priming their host genes for stress-responsiveness in evolutionary divergent plant species. Furthermore, we were able to predict stress responsiveness in AAP rice genes based on the presence of a long first intron and CASt. Overall, we show an evolutionary strategy and regulatory mechanism specific to plants for enhancing stress responsiveness through modification of gene architecture and antisense transcription.},
	urldate = {2025-10-13},
	journal = {Molecular Plant},
	author = {Zacharaki, Vasiliki and Quevedo, Marti and Nardeli, Sarah Muniz and Meena, Shiv Kumar and Monte, Elena and Kindgren, Peter},
	month = oct,
	year = {2025},
	keywords = {Antisense transcription, Arabidopsis, Cold acclimation, Transporters},
}

Plants need to constantly surveil their surroundings to adapt to environmental fluctuations, which they achieve primarily through transcriptional reprogramming. Thus, plants are excellent models for identifying novel transcriptional regulatory mechanisms. Here, we characterize regulation conveyed by long non-coding transcription that initiates on the complementary strand in the 5ʹ-end of coding genes (Convergent Antisense transcription (CASt)). In Arabidopsis, CASt is associated with stress-responsive genes that are highly expressed. Our analysis shows that CASt depends on a specific gene architecture that is evolutionarily conserved in higher plants. CASt is present in genes with an extended first intron and over-represented in genes with a transporter function in Arabidopsis, such as the AAP transporter family. Experimental evidence points to a role for CASt in priming their host genes for stress-responsiveness in evolutionary divergent plant species. Furthermore, we were able to predict stress responsiveness in AAP rice genes based on the presence of a long first intron and CASt. Overall, we show an evolutionary strategy and regulatory mechanism specific to plants for enhancing stress responsiveness through modification of gene architecture and antisense transcription.

@article{alonso-serra_water_2024,
	title = {Water fluxes pattern growth and identity in shoot meristems},
	volume = {15},
	copyright = {2024 The Author(s)},
	issn = {2041-1723},
	url = {https://www.nature.com/articles/s41467-024-51099-x},
	doi = {10.1038/s41467-024-51099-x},
	abstract = {In multicellular organisms, tissue outgrowth creates a new water sink, modifying local hydraulic patterns. Although water fluxes are often considered passive by-products of development, their contribution to morphogenesis remains largely unexplored. Here, we mapped cell volumetric growth across the shoot apex in Arabidopsis thaliana. We found that, as organs grow, a subpopulation of cells at the organ-meristem boundary shrinks. Growth simulations using a model that integrates hydraulics and mechanics revealed water fluxes and predicted a water deficit for boundary cells. In planta, a water-soluble dye preferentially allocated to fast-growing tissues and failed to enter the boundary domain. Cell shrinkage next to fast-growing domains was also robust to different growth conditions and different topographies. Finally, a molecular signature of water deficit at the boundary confirmed our conclusion. Taken together, we propose that the differential sink strength of emerging organs prescribes the hydraulic patterns that define boundary domains at the shoot apex.},
	language = {en},
	number = {1},
	urldate = {2025-10-08},
	journal = {Nature Communications},
	author = {Alonso-Serra, Juan and Cheddadi, Ibrahim and Kiss, Annamaria and Cerutti, Guillaume and Lang, Marianne and Dieudonné, Sana and Lionnet, Claire and Godin, Christophe and Hamant, Olivier},
	month = aug,
	year = {2024},
	note = {Publisher: Nature Publishing Group},
	keywords = {Computational biophysics, Patterning, Plant morphogenesis},
	pages = {6944},
}

In multicellular organisms, tissue outgrowth creates a new water sink, modifying local hydraulic patterns. Although water fluxes are often considered passive by-products of development, their contribution to morphogenesis remains largely unexplored. Here, we mapped cell volumetric growth across the shoot apex in Arabidopsis thaliana. We found that, as organs grow, a subpopulation of cells at the organ-meristem boundary shrinks. Growth simulations using a model that integrates hydraulics and mechanics revealed water fluxes and predicted a water deficit for boundary cells. In planta, a water-soluble dye preferentially allocated to fast-growing tissues and failed to enter the boundary domain. Cell shrinkage next to fast-growing domains was also robust to different growth conditions and different topographies. Finally, a molecular signature of water deficit at the boundary confirmed our conclusion. Taken together, we propose that the differential sink strength of emerging organs prescribes the hydraulic patterns that define boundary domains at the shoot apex.