Transcriptome analysis of Xylella fastidiosa strains isolated from distinct hosts and search for regulatory RNAs

Abstract

Pathogenic bacteria use gene regulation specific mechanisms to rapidly respond to changes in the hostile environment of their hosts. Traditionally, these regulations have been credited to the activities of protein transcription factors that activate and deactivate sets of genes relevant to survival in the host. However, some recent studies suggest that non-coding RNAs (ncRNAs) also play a role in regulating mechanisms of bacterial pathogenesis. Our group recently sequenced the genome of six South American strains of the phytopathogen Xylella fastidiosa, three isolated from citrus (J1a12, U24D and Fb7) and three strains isolated from plum (Pr8x), coffee (3124) and hibiscus (Hib4). The comparative analysis of these X. fastidiosa genomes allowed us to associate genotypic differences to the phenotypes of the distinct isolates. In this project, we propose an extension of these studies by analyzing the complete transcriptome of these strains through RNAseq. The full analysis of the transcriptome will enable the discovery of new genes, particularly ncRNAs, a more precise definition of the structure of genes and operons as well as the detection of non-translated regions, including riboswitches and binding sites of small regulatory RNAs (sRNAs). The expression of some sRNAs candidates identified will be confirmed. We also intend to identify targets of regulation by such ncRNAs. The phenotypic analysis of strains of X. fastidiosa will be further analysed by electron microscopy and adhesion and motility assays in microfluidic chambers. (AU)