Biology subjects

Canessa, P.

Publications and source records attributed to Canessa, P..

3 recordsLinked to original sources

bioRxiv2026

Salicylic acid contributes to plant defense against a necrotroph: evidence from a transgenic NahG-expressing strain in Botrytis cinerea.

Botrytis cinerea is a plant pathogen that causes significant agricultural losses worldwide. Although this necrotroph disrupts extensive plant hormonal networks, the role of salicylic acid (SA) in plant defense against B. cinerea remains controversial across plant species. To investigate its role from a pathogen perspective, B. cinerea mutants constitutively expressing the Pseudomonas putida salicylate hydroxylase NahG, an enzyme that catalyzes salicylic acid degradation, were generated. The NahG-expressing B. cinerea mutants exhibited enhanced in vitro growth on SA-supplemented media, indicating that SA catabolism confers an advantage. In planta, these mutants displayed increased virulence in Arabidopsis thaliana and Phaseolus vulgaris. Notably, the increase in lesion formation was strictly dependent on host SA biosynthesis, as no differences were observed when infecting the SA-deficient Arabidopsis sid2-2 mutant. This result provides evidence that SA degradation increases the virulence of B. cinerea in the interaction with A. thaliana. Genome inspection revealed that the fungus encodes four salicylate hydroxylase-like genes. Analysis of publicly available transcriptomic data from virulence assays across multiple plant hosts revealed that all these genes are expressed during the plant-pathogen interaction, with distinct expression patterns across infection stages and hosts. Together, these observations suggest that B. cinerea may have endogenous mechanisms for SA degradation during host colonization, thereby conferring the capacity to control its accumulation during the infection process. HIGHLIGHTSO_LIBotrytis cinerea expressing the salicylate hydroxylase (SH) ppNahG shows enhanced virulence in Arabidopsis and bean plants. C_LIO_LIEnhanced virulence of NahG-expressing strains depends on host salicylic acid biosynthesis. C_LIO_LIThe Botrytis cinerea genome encodes four SH-like genes. C_LIO_LISH-like genes display distinct expression patterns during infection across different plant hosts. C_LI VISUAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=128 SRC="FIGDIR/small/698134v1_ufig1.gif" ALT="Figure 1"> View larger version (24K): org.highwire.dtl.DTLVardef@135adorg.highwire.dtl.DTLVardef@16b2947org.highwire.dtl.DTLVardef@62fd40org.highwire.dtl.DTLVardef@e07e2e_HPS_FORMAT_FIGEXP M_FIG C_FIG

plant biology↗

bioRxiv2022

The Botrytis cinerea Gene Expression Browser.

To analyze and visualize comprehensive gene expression patterns in the phytopathogenic fungus Botrytis cinerea, we developed BEB -- a web-based B. cinerea gene expression browser. This tool and associated databases (DB) contain manually-curated RNA-Seq experiments conducted in B. cinerea. BEB allows easy gene expression analyses of genes of interest under different culture conditions by providing publication-ready heatmaps depicting transcripts levels. BEB is a computationally-inexpensive web-based application and gene expression DB that allows effortless visualization of the transcript levels of genes of interest without needing advanced computational skills. BEB also provides details of each experiment under analysis and user-defined gene expression clustering and visualization options. If needed, tables of gene expression values can be downloaded for further exploration, employing more sophisticated bioinformatics tools. The BEB implementation is based on open-source computational technologies that can be easily deployed for other organisms of interest with little additional effort. To demonstrate BEBs usability and potential, we selected genes of interest in B. cinerea to determine their expression patterns across different conditions. We thus focused our analysis on secondary metabolite gene clusters, chromosome-wide gene expression, previously described virulence factors, and reference genes, leading to a comprehensive expression overview of these groups of genes in this relevant fungal phytopathogen.

bioinformatics↗

bioRxiv2021

Uncovering divergence in gene expression regulation in the adaptation of yeast to nitrogen scarcity

Saccharomyces cerevisiae rewires its transcriptional output to survive stressful environments, such as nitrogen scarcity under fermentative conditions. Although divergence in nitrogen metabolism has been described among natural yeast populations, the impact of regulatory genetic variants modulating gene expression and nitrogen consumption remains to be investigated. Here, we employed an F1 hybrid from two contrasting S. cerevisiae strains, providing a controlled genetic environment to map cis factors involved in the divergence of gene expression regulation in response to nitrogen scarcity. We used a dual approach to obtain genome-wide allele-specific profiles of chromatin accessibility, transcription factor binding, and gene expression through ATAC-seq and RNA-seq. We observed large variability in allele-specific expression and accessibility between the two genetic backgrounds, with a third of these differences specific to a deficient nitrogen environment. Furthermore, we discovered events of allelic bias in gene expression correlating with allelic bias in transcription factor binding solely under nitrogen scarcity, where the majority of these transcription factors orchestrates the Nitrogen Catabolite Repression regulatory pathway and demonstrates a cis x environment-specific response. Our approach allowed us to find cis variants modulating gene expression, chromatin accessibility and allelic differences in transcription factor binding in response to low nitrogen culture conditions. ImportanceHistorically, coding variants were prioritized when searching for causal mechanisms driving adaptation of natural populations to stressful environments. However, the recent focus on non-coding variants demonstrated their ubiquitous role in adaptation. Here we performed genome-wide regulatory variation profiles between two divergent yeast strains when facing nitrogen nutritional stress. The open chromatin availability of several regulatory regions changes in response to nitrogen scarcity. Importantly we describe regulatory events that deviate between strains. Our results demonstrate a widespread variation in gene expression regulation between naturally occurring populations in response to stressful environments.

genomics↗