Comparative small RNA profiling in the PAO1 and PA14 strains of the opportunistic pathogen Pseudomonas aeruginosa

Small RNAs (sRNAs) play fundamental roles in the control of gene expression, both in eukaryotes and prokaryotes, by modulating transcription, translation, mRNA stability, and DNA maintenance or silencing. In bacteria, sRNAs participate in regulatory circuits of cell viability, stress adaptation, metabolism, virulence and pathogenicity. Unlike the most studied bacterial pathogens where hundreds of sRNAs have been identified, only 30 sRNAs have been annotated in the opportunistic pathogen Pseudomonas aeruginosa, in particular in the attenuated strain PAO1. In this work, we aimed at the comparative sRNA profiling of the P. aeruginosa PAO1 and virulent PA14 strains by systematic identification via a massive sequencing approach tailored for low molecular weight RNA. Overall, by this approach we identified about 300 genomic regions significantly expressing short sRNA-like transcripts. Some of these regions are unique to either PAO1 or PA14, whereas the majority is conserved in both strains. In the latter case, we could detect either similar or differential expression levels between the two strains. We also validated by Northern blotting the actual sRNA expression from a selected panel of both unique and orthologous genomic regions. We are currently analyzing their expression in response to pathogenesis-relevant signals such as temperature, O2 availability and quorum sensing. In addition, we aim to build up a genetic system for the identification of target genes in order to dissect sRNA-based regulatory mechanisms involved in cell viability and pathogenesis.