Global discovery of small RNAs in Yersinia pseudotuberculosis identifies Yersinia -specific small, noncoding RNAs required for virulence

Abstract

A major class of bacterial small, noncoding RNAs (sRNAs) acts by base-pairing with mRNAs to alter the translation from and/or stability of the transcript. Our laboratory has shown that Hfq, the chaperone that mediates the interaction of many sRNAs with their targets, is required for the virulence of the enteropathogen Yersinia pseudotuberculosis. This finding suggests that sRNAs play a critical role in the regulation of virulence in this pathogen, but these sRNAs are not known. Using a deep sequencing approach, we identified the global set of sRNAs expressed in vitro by Y. pseudotuberculosis. Sequencing of RNA libraries from bacteria grown at 26°C and 37°C resulted in the identification of 150 unannotated sRNAs. The majority of these sRNAs are Yersinia specific, without orthologs in either Escherichia coli or Salmonella typhimurium. Six sRNAs are Y. pseudotuberculosis specific and are absent from the genome of the closely related species Yersinia pestis. We found that the expression of many sRNAs conserved between Y. pseudotuberculosis and Y. pestis differs in both timing and dependence on Hfq, suggesting evolutionary changes in posttranscriptional regulation between these species. Deletion of multiple sRNAs in Y. pseudotuberculosis leads to attenuation of the pathogen in a mouse model of yersiniosis, as does the inactivation in Y. pestis of a conserved, Yersinia-specific sRNA in a mouse model of pneumonic plague. Finally, we determined the regulon controlled by one of these sRNAs, revealing potential virulence determinants in Y. pseudotuberculosis that are regulated in a posttranscriptional manner.Ysr29 | RybB | stress | Illumina-Solexa | 2D-DIGE

Absence of YbeY RNase compromises the growth and enhances the virulence plasmid gene expression of Yersinia enterocolitica O:3

“…Two of them, csrB and csrC, are Hfqindependent and were previously implicated in the global carbon storage regulatory system (Liu & Romeo, 1997;Schiano & Lathem, 2012). The gcvB sRNA has been shown to repress dppA, a gene encoding the periplasmic-binding protein component of the dipeptide transport system in Y. pestis and is known to bind Hfq (Koo et al, 2011). Our results show that both the Hfq-dependent and Hfqindependent regulation pathways were affected.…”

“…Two of them (csrB and csrC) that have been implicated in the global carbon storage regulatory system (Liu & Romeo, 1997), were downregulated. The expression of csrB was significantly decreased at both 22 and 37 uC while that of csrC was decreased only at 22 u C. The expression of gcvB, encoding a sRNA shown to repress the dppA gene that encodes the periplasmic-binding protein component of the dipeptide transport system in Yersinia pestis (Koo et al, 2011) was upregulated at 37 u C. In addition, 4.5S RNA was strongly upregulated at 37 u C and rtT at both analysed temperatures.…”

Genome‐wide identification of novel small RNAs in Pseudomonas aeruginosa

“…The latter approach, in particular, has revolutionized sRNA discovery by enabling interrogation of the transcriptome at unprecedented depths. Deep sequencing has revealed hundreds of previously undetected transcripts in diverse bacteria including Bacillus subtilis (Irnov et al, 2010 (Koo et al, 2011). The detected transcripts derive from reads that map to both intergenic and coding regions, and in the sense and antisense directions relative to annotated genes.…”

Genome-Wide Analysis of Small RNAs Expressed by Yersinia pestis Identifies a Regulator of the Yop-Ysc Type III Secretion System

“…For instance, Hfq and sRNAs participate in the regulation of biofilms produced by uropathogenic E. coli, V. cholerae, and Y. pestis, as well as in the regulation of alpha-toxin synthesis in Staphylococcus aureus (23,(25)(26)(27)(28)(29). Indeed, Hfq and sRNAs have been shown to contribute to the virulence of a number of pathogens, including both Y. pestis and Y. pseudotuberculosis (20,(30)(31)(32).…”