Comparative profiling of Pseudomonas aeruginosa strains reveals differential expression of novel unique and conserved small RNAs

In recent years, it has become increasingly clear that regulation of gene expression at both transcriptional and post-transcriptional levels by small RNAs (sRNAs) is widespread in bacteria. Furthermore, several studies suggest that sRNAs can play key roles in regulating cellular processes linked to pathogenesis. Pseudomonas aeruginosa is a widely distributed opportunistic pathogen for which complete genomic sequences of several strains - with varying pathogenic characteristics – are available. We have performed a comparative sRNA profiling via deep-sequencing of P. aeruginosa PAO1 and PA14 strains which share the same host range but differ in pathogenicity, PA14 being considerably more virulent in several model organisms. Altogether, we have identified more than 150 novel candidate sRNAs and validated a third of them by Northern blotting. Interestingly, a number of these novel sRNAs are strain-specific or showed strain-specific expression, strongly suggesting that they could be involved in determining specific phenotypic traits. About 20 validated sRNAs showed potential virulence hallmarks such as: specific expression in PA14 or PAO1; responsiveness to infection-relevant host stimuli (e.g. oxygen availability, temperature shift) or invasion signals (e.g. quorum sensing). Our future studies will focus on the impact of this panel of sRNAs on P. aeruginosa virulence and infection, and on the dissection of the regulatory role via identification of target mRNAs and characterization of sRNA/target mRNA interactions.