Biology subjects

Pateyron, S.

Publications and source records attributed to Pateyron, S..

7 recordsLinked to original sources

bioRxiv2026

Genetic coupling of hydathode formation with leaf morphogenesis maintains water homeostasis

Hydathodes are specialized leaf structures present across vascular plants that allow guttation by connecting the xylem to the external environment through epithem tissue and permanently open water pores. However, the genetic mechanisms controlling their formation and physiological roles remain poorly understood. Here, we identify a genetic regulatory network that controls hydathode formation and links this process to leaf morphogenesis. This network converges on auxin signaling to coordinate the formation of the three hydathode cell types. We further show that epithem development requires sustained cell proliferation with limited endoreduplication. Analysis of hydathode mutants demonstrates that hydathode size and number are required to prevent reversible leaf flooding. Together, these findings establish a genetic framework for hydathode morphogenesis and uncover a central role for hydathodes in maintaining leaf water homeostasis under fluctuating environmental conditions.

plant biology↗

bioRxiv2026

How to be dispensable: genomic and transcriptomic determinants in maize genes

BackgroundPlant genomes harbour a substantial proportion of dispensable genes - present only in a subset of individuals - that differ from ubiquitously shared core genes in multiple genomic and expression features. While these differences have been repeatedly documented, the factors shaping gene dispensability remain poorly understood. ResultsWe assembled a pan-gene set from eight maize inbred lines from American and European germplasms, together with their transcriptomic profile across 22 tissues/conditions, revealing the genomic and transcriptomic determinants of maize gene dispensability. Multivariate analysis demonstrates that gene expression level and purifying selection - rather than gene size - are the primary factors distinguishing core from dispensable genes. Dispensable genes overlap Helitrons at 4.6 times the rate of core genes, implicating Helitron-mediated gene capture as a major mechanism of dispensable gene formation. Classifying genes into stably expressed, variably expressed, and on-off categories shows that all three classes contain dispensable genes, though in different proportions than for core genes. Contrary to previous assumptions, we show that dispensable genes can participate in basal biological functions just as core genes, and that gene duplication likely provides only a partial mechanism for functional complementation of accessory genes absence. ConclusionsOur results provide novel insights into the molecular and evolutionary factors distinguishing core from dispensable genes and into the biological mechanisms shaping gene dispensability in maize, and demonstrate that classifying genes by transcriptional patterns provides a powerful framework for understanding the biological functions and evolutionary dynamics of both core and dispensable genes.

plant biology↗

bioRxiv2026

Comparative cross-species transcriptomic analysis identifies new candidates of Pooideae nitrate response

Nitrogen fertilizers are essential for crop productivity but cause environmental harm, necessitating the development of cultivars that thrive under limited nitrogen. This study investigates the transcriptomic response to nitrate in Arabidopsis thaliana (a model dicot), Brachypodium distachyon (a model Pooideae), and Hordeum vulgare (barley, a domesticated Pooideae) to identify conserved and species-specific molecular mechanisms. Using RNA-seq after 1.5 and 3 hours of nitrate treatment, we found that core nitrate-responsive biological processes - such as nitrate transport, assimilation, carbon metabolism, and hormone signaling - are largely conserved across species. However, comparative analysis at gene level based on orthology revealed specificities between the species. For instance, rRNA processing was uniquely stimulated in Arabidopsis, while cysteine biosynthesis from serine and gibberellin biosynthesis were specifically regulated in Brachypodium and barley. Orthologs of key nitrate-responsive genes (e.g., NRT, NLP, TCP20) exhibited variable regulation, reflecting potential adaptations linked to domestication or nutrient acquisition strategies. These findings highlight the importance of integrating model and crop species to uncover targets for improving nitrogen use efficiency in cereals. This study provides a general pipeline combining Gene Ontology enrichment and orthology analysis to compare transcriptomic responses across species. This workflow is highly useful for any comparative transcriptomic study in which differences in annotation quality and gene divergence between genomes may bias interpretation.

plant biology↗

bioRxiv2026

The role of reactive oxygen species and calcium signaling in antiviral defense in Arabidopsis

Plant viruses interfere with host signaling pathways, but it remains unclear how calcium (Ca2+) signaling, reactive oxygen species (ROS), and changes in the plasma membrane interact during viral infection. Here, we investigated how plantago asiatica mosaic virus (PlAMV) modulates host Ca2+ and ROS-associated signaling in Arabidopsis thaliana. Using live-cell imaging and the R-GECO1.2 Ca2+ sensor, we observed a rapid increase in cytoplasmic Ca2+ before the virus was detected, indicating that Ca2+ release occurs early in infection. Genetic analysis showed that GLR, CPK3, and CNGC, core components of Ca2+ signaling, limit PlAMV spread between cells, while the usual pattern-triggered immunity (PTI) co-receptors were not needed. This means that Ca2+-based antiviral restriction operates independently of PTI. With the plasma membrane-tethered and cytosolic HyPer7 biosensor, we found that ROS levels were lower inside infection foci in the inoculated leaves, but higher in nearby cells, respectively. The NADPH oxidases RBOHD and RBOHF, which produce ROS, slowed down the local viral propagation. The PM sphingolipid biosynthetic enzyme MOCA1 altered ROS patterns and reduced the viruss spread. Epistasis analysis revealed a functional interaction between RBOHD and MOCA1, suggesting that ROS signaling and plasma membrane sphingolipid homeostasis are interconnected in antiviral defense. Overall, our findings suggest that PlAMV triggers Ca2+ influx and ROS signaling at the plasma membrane, which induces sphingolipid reorganization and helps restrict the propagation of the virus. This study shows how Ca2+, ROS, and membrane sphingolipid signaling work together in plant antiviral immunity and points to possible ways to improve resistance to viruses.

plant biology↗

bioRxiv2025

Enhancement of Arabidopsis growth by Enterobacter sp. SA187 under elevated CO2 is dependent on ethylene signalling activation and primary metabolism reprogramming

As atmospheric CO2 levels continue to increase, optimizing the CO2 fertilization effect which often falls short of its potential due to the physiological and metabolic limitations of plants becomes crucial. This study investigates the role of Enterobacter sp. SA187 (SA187), a plant growth-promoting bacterium, in enhancing growth and development of Arabidopsis thaliana under elevated atmospheric CO2 (eCO2) conditions. While SA187 inoculation did not have major effects under ambient CO2, it was found to significantly enhance root and shoot biomass, and to increase N- and reduce C-contents under eCO2. Moreover, transcriptomics and metabolomics suggested that SA187 modulated phytohormonal homeostasis, with activation of the salicylic acid, jasmonic acid and ethylene signalling pathways, and increased primary metabolism including the TCA cycle, N and carbohydrate metabolisms. Finally, the growth-promoting effects of SA187 were shown to be mediated through ethylene-dependent pathways, as evidenced with the ethylene-insensitive mutant ein2-1 which did not show similar benefits in plant fresh weight and altered gene expression. This beneficial plant-microbe interaction under eCO2 in a non-leguminous plant highlights a novel aspect of microbial influence on plant physiology in the context of climate change. These insights underscore the potential of utilizing SA187 to enhance plant performance and adaptability in future high CO2 environments, providing a sustainable approach to agricultural productivity as global CO2 levels increase.

plant biology↗

bioRxiv2023

Cell specialization and coordination in Arabidopsis leaves upon pathogenic attack revealed by scRNA-seq.

Plant defense responses involve several biological processes that allow plants to fight against pathogenic attacks. How these different processes are orchestrated within organs and depend on specific cell types is poorly known. Here, using scRNA-seq technology on three independent biological replicates, we identified 10 distinct cell populations in wild-type Arabidopsis leaves inoculated with the bacterial pathogen Pseudomonas syringae DC3000. Among those, we retrieved major cell types of the leaves (mesophyll, guard, epidermal, companion and vascular S cells) to which we could associate characteristic transcriptional reprogramming and regulators, thereby specifying different cell-type responses to the pathogen. Further analyses of transcriptional dynamics, based on inference of cell trajectories, indicated that the different cell types, in addition to their characteristic defense responses, can also share similar modules of gene reprogramming, allowing for instance vascular S cells, epidermal cells and mesophyll cells to converge towards an identical cell fate, mostly characterized by lignification and detoxification functions. Moreover, it appeared that the defense responses of these three cell types can evolve along a second separate path. As this divergence does not correspond to the differentiation between immune and susceptible cells, we speculate that this might reflect the discrimination between cell-autonomous and non-cell-autonomous responses. Altogether our data provide an upgraded framework to describe, explore and explain the specialization and the coordination of plant cell responses upon pathogenic challenge.

plant biology↗

bioRxiv2020

Identification of key tissue-specific, biological processes by integrating enhancer information in maize gene regulatory networks

Enhancers are important regulators of gene expression during numerous crucial processes including tissue differentiation across development. In plants, their recent molecular characterization revealed their capacity to activate the expression of several target genes through the binding of transcription factors. Nevertheless, identifying these target genes at a genome-wide level remains a challenge, in particular in species with large genomes, where enhancers and target genes can be hundreds of kilobases away. Therefore, the contribution of enhancers to regulatory network is still poorly understood in plants. In this study, we investigate the enhancer-driven regulatory network of two maize tissues at different stages: leaves at seedling stage and husks (bracts) at flowering. Using a systems biology approach, we integrate genomic, epigenomic and transcriptomic data to model the regulatory relationship between transcription factors and their potential target genes. We identify regulatory modules specific to husk and V2-IST, and show that they are involved in distinct functions related to the biology of each tissue. We evidence enhancers exhibiting binding sites for two distinct transcription factor families (DOF and AP2/ERF) that drive the tissue-specificity of gene expression in seedling immature leaf and husk. Analysis of the corresponding enhancer sequences reveals that two different transposable element families (TIR transposon Mutator and MITE Pif/Harbinger) have shaped the regulatory network in each tissue, and that MITEs have provided new transcription factor binding sites that are involved in husk tissue-specificity.Significance Enhancers play a major role in regulating tissue-specific gene expression in higher eukaryotes, including angiosperms. While molecular characterization of enhancers has improved over the past years, identifying their target genes at the genome-wide scale remains challenging. Here, we integrate genomic, epigenomic and transcriptomic data to decipher the tissue-specific gene regulatory network controlled by enhancers at two different stages of maize leaf development. Using a systems biology approach, we identify transcription factor families regulating gene tissue-specific expression in husk and seedling leaves, and characterize the enhancers likely to be involved. We show that a large part of maize enhancers is derived from transposable elements, which can provide novel transcription factor binding sites crucial to the regulation of tissue-specific biological functions.Competing Interest StatementThe authors have declared no competing interest.View Full Text

systems biology↗