Abstract
Pseudomonas aeruginosa is a highly adaptable bacterium that thrives in a broad range of ecological niches and can infect multiple hosts as diverse as plants, nematodes and mammals. In humans, it is an important opportunistic pathogen. This wide adaptability correlates with its broad genetic diversity. In this study, we used a deep-sequencing approach to explore the complement of small RNAs (sRNAs) in P. aeruginosa as the number of such regulatory molecules previously identified in this organism is relatively low, considering its genome size, phenotypic diversity and adaptability. We have performed a comparative analysis of PAO1 and PA14 strains which share the same host range but differ in virulence, 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.
Highlights
Small RNAs are widespread in bacteria and play critical regulatory roles in several cellular processes [1,2,3,4]
We aimed at small RNAs (sRNAs) profiling in the P. aeruginosa PAO1 and PA14 strains by sRNA-Seq [26], a massive sequencing approach tailored for unbiased identification of low molecular weight RNA
The 39 ends of PAO1 and PA14 sRNA20–500 were tagged by ligation with linker L1, a mixed ribo-deoxyribo-oligonucleotide with its 39-end protected by an inverted dT (Table S1), obtaining L1-sRNA20–500. sRNA preparations are expected to contain a high proportion of the stable
Summary
Small RNAs (sRNAs) are widespread in bacteria and play critical regulatory roles in several cellular processes [1,2,3,4]. SRNA-target interaction may lead to modulation of mRNA translation and/or stability [2,4]. Some sRNAs modulate the activity of target proteins or act as mRNAs coding for short proteins. The prevalent view is that sRNAs might target almost all bacterial cell processes [6]. Genome-scale searches have led to a remarkable increase in the number of identified sRNAs in bacteria [2]. In this context, our knowledge of the sRNA complement of Pseudomonas aeruginosa seemed limited
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