Extracellular Vesicles From Xylella fastidiosa Carry sRNAs and Genomic Islands, Suggesting Roles in Recipient Cells

Abstract

Xylella fastidiosa (Xf) is a Gram-negative bacterial plant pathogen responsible for severe diseases in a variety of economically important crops. A critical aspect of its virulence is the production of extracellular vesicles (EVs). In this study, we discovered that DNA-binding proteins and nonribosomal RNA-binding proteins are abundant in the corona of Xf-EVs. DNA-seq revealed enrichment of three genomic islands (GIs) in EVs, which carry molecular signatures indicative of horizontal gene transfer (HGT). The most abundant GI encodes five homologous small RNAs designated sXFs. RNA sequencing revealed a distinct pattern of noncoding RNAs enriched in EVs, including four island-encoded sXFs. One of the sXF’s stem-loops contains motifs for binding the RNA chaperone Hfq, which is also abundant in EVs. Predicted target analysis suggests that sXFs play a role in regulation of natural competence in bacteria. Additionally, sXF plant target prediction identifies a coiled-coil nucleotide-binding domain leucine-rich repeat receptor (CNL) immune gene that is downregulated following Xf infection and Xf-EV treatment. We propose a model where Xf releases nucleic acid carrying EVs with two functions: one to deliver RNA-related cargo that regulates gene expression in both bacterial and plant cells, and another to deliver DNA-related cargo for the genetic transfer of genomic islands. We highlight island-encoded sXFs as potential virulence factors and vesiduction as a mechanism of HGT of sXFs in Xf. Taken together, our data on Xf-EV cargoes provide a molecular framework for understanding the virulence of Xf.