Biology subjects

Clairet, C.

Publications and source records attributed to Clairet, C..

3 recordsLinked to original sources

bioRxiv2021

Regulation of effector gene expression as concerted waves in Leptosphaeria maculans: a two-players game

During infection, plant pathogenic fungi secrete a set of molecules collectively known as effectors, involved in overcoming the host immune system and in disease establishment. Effector genes are concertedly expressed as waves all along plant pathogenic fungi lifecycle. However, little is known about how coordinated expression of effector genes is regulated. Since many effector genes are located in repeat-rich regions, the role of chromatin remodeling in the regulation of effector expression was recently investigated. In Leptosphaeria maculans, causing stem canker of oilseed rape, we established that the repressive histone modification H3K9me3 (trimethylation of Lysine 9 of Histone H3), deposited by the histone methyltransferase KMT1, was involved in the regulation of expression of genes highly expressed during infection, including effectors. Nevertheless, inactivation of KMT1 did not induce expression of these genes at the same level as observed during infection of oilseed rape, suggesting that a second regulator, such as a transcription factor (TF), might be involved. Pf2, a TF belonging to the Zn2Cys6 fungal specific TF family, was described in several Dothideomycete species as essential for pathogenicity and effector gene expression. We identified the orthologue of Pf2 in L. maculans, LmPf2, and investigated the role of LmPf2 together with KMT1, by inactivating and over-expressing LmPf2 in a wild type (WT) strain and a{Delta} kmt1 mutant. Functional analyses of the corresponding transformants highlighted an essential role of LmPf2 in the establishment of pathogenesis. Transcriptomic analyses during axenic growth showed that LmPf2 is involved in the control of effector gene expression. We observed an enhanced effect of the over-expression of LmPf2 on effector gene expression in a{Delta} kmt1 background, suggesting an antagonist role between KMT1 and LmPf2.

plant biology↗

bioRxiv2021

Nucleosome patterns in four plant pathogenic fungi with contrasted genome structures

AO_SCPLOWBSTRACTC_SCPLOWFungal pathogens represent a serious threat towards agriculture, health, and environment. Control of fungal diseases on crops necessitates a global understanding of fungal pathogenicity determinants and their expression during infection. Genomes of phytopathogenic fungi are often compartmentalized: the core genome contains housekeeping genes whereas the fast-evolving genome mainly contains transposable elements and species-specific genes. In this study, we analysed nucleosome landscapes of four phytopathogenic fungi with contrasted genome organizations to describe and compare nucleosome repartition patterns in relation with genome structure and gene expression level. We combined MNase-seq and RNA-seq analyses to concomitantly map nucleosome-rich and transcriptionally active regions during fungal growth in axenic culture; we developed the MNase-seq Tool Suite (MSTS) to analyse and visualise data obtained from MNase-seq experiments in combination with other genomic data and notably RNA-seq expression data. We observed different characteristics of nucleosome profiles between species, as well as between genomic regions within the same species. We further linked nucleosome repartition and gene expression. Our findings support that nucleosome positioning and occupancies are subjected to evolution, in relation with underlying genome sequence modifications. Understanding genomic organization and its role in expression regulation is the next gear to understand complex cellular mechanisms and their evolution.

genomics↗

bioRxiv2020

Genome-wide mapping of histone modifications in two species of Leptosphaeria maculans showing contrasting genomic organization and host specialization

In plant-associated fungi, the role of the epigenome is increasingly recognized as an important regulator of genome structure and of the expression of genes involved in interaction(s) with the host plant. Two closely-related phytopathogenic species, Leptosphaeria maculans brassicae (Lmb) and L. maculans lepidii (Lml) exhibit a large conservation of genome synteny but contrasting genome structure. Lmb has undergone massive invasion of its genome by transposable elements amounting to one third of its genome and clustered in large TE-rich regions on chromosomal arms, while Lml genome has only a small amount of repeats (3% of the genome). Previous studies showed that the TE-rich regions of Lmb harbour a few species-specific effector genes, expressed during plant infection. The distinct genome structures shown by Lmb and Lml thus provides an excellent model for comparing the organization of pathogenicity/effector genes in relation to the chromatin landscape in two closely related phytopathogenic fungi. Here, we performed chromatin immunoprecipitation during axenic culture, targeting either histone modifications typical for heterochromatin or euchromatin, combined with transcriptomic analysis to analyse the influence of chromatin organisation on gene expression. In both species, we found that facultative heterochromatin landscapes associated with H3K27me3-domains are enriched with genes lacking functional annotation, including numerous candidate effector and species-specific genes. Notably, orthologous genes located in H3K27me3-domains in both species are enriched with genes encoding putative proteinaceous and metabolic effectors. These genes are mostly silenced in axenic growth conditions and are likely to be involved in interaction with the host. Compared to other fungal species, including Lml, Lmb is distinct in having large H3K9me3-domains associated with TE-rich regions that contain numerous species-specific effector-encoding genes. Discovery of these two distinctive heterochromatin landscapes now raises questions about their involvement in the regulation of pathogenicity, the dynamics of these domains during plant infection, and the selective advantage to the fungus to host effector genes in H3K9me3- or H3K27me3-domains.

genomics↗