Institut de Biologie de l'École Normale Supérieure ENS . CNRS UMR8197 . Inserm U1024 Directeur : Pierre Paoletti

Small RNA-directed Control of the Host Immune Response and its Targeting by Bacterial Effectors

Our current research interests are to understand the role and regulation of small RNAs in plant innate immunity and to unravel the mechanisms by which bacterial effectors interfere with RNA silencing in plants and humans. We are mostly using the phytopathogenic bacterium Pseudomonas syringae pv. tomato strain DC3000 and the human pathogenic bacterium Shigella flexneri as model systems.

Current projects

Mechanisms of bacterial-mediated suppression of the microRNA pathway. The innate immune response is the first line of defence against pathogens, which plays a critical role in antimicrobial defence. This response is initiated by the perception of pathogen-derived signatures referred to as Pathogen or Microbe associated molecular patterns (PAMPs or MAMPs). Both plants and animals sense PAMPs and in turn differentially regulate a large set of immune responsive genes, among which microRNA (miRNAs) were recently identified. These small regulatory RNAs control gene expression mostly at the post-transcriptional level by inducing degradation and/or translational silencing of target mRNAs.We recently showed that growth of a type III secretion-defective mutant of Pseudomonas syringae as well as non-pathogenic bacteria was significantly enhanced in Arabidopsis miRNA-deficient mutants, implicating the miRNA pathway as major component of antibacterial defense. Accordingly, we have identified P. syringae type III secreted proteins that suppress multiple steps of the miRNA pathway. Our goal is now to identify the modes of action of these bacterial silencing suppressors and to determine whether analogous mechanisms of RNA silencing suppression are used by human pathogenic bacteria.

Role of the RNA-directed DNA methylation pathway in the regulation of the Arabidopsis immune response and the evolution of immune-response genes. In higher eukaryotes, the vast majority of the genome appears to be transcribed, leading to an extraordinary diversity of non- coding RNAs (ncRNAs). Whereas the functional significance of these ncRNAs is mostly unknown, increasing evidence suggests a role for these molecules in guiding chromatin modifications. In plants, a large proportion of ncRNAs is processed by the RNA silencing machinery to produce short interfering (si)RNAs. Some of them guide sequence specific DNA methylation through a phenomenon referred to as RNA-directed DNA methylation (RdDM). The RdDM pathway contributes to the transcriptional silencing (TGS) of transposons, repeats as well as some genes that carry repeats in their vicinity. We have recently shown that DNA demethylation is part of a plant immune response and, accordingly, have identified functionally relevant defense genes that are directly controlled by this epigenetic regulatory mechanism. Our goal is now to determine whether bacterial effectors could have evolved strategies to interfere directly with the Arabidopsis TGS machinery to enable disease. We are also investigating the contribution of the RdDM pathway in transgenerational immune priming and its eventual implication in the evolution of immune-response genes.