Experimental identification of small non-coding regulatory RNAs in the opportunistic human pathogen Burkholderia cenocepacia J2315

Small non-coding regulatory RNAs (sRNAs) play important roles in regulating gene expression at the post-transcriptional level and often require the RNA chaperone Hfq. The human opportunistic pathogen Burkholderia cenocepacia J2315 encodes two distinct RNA chaperones, Hfq and Hfq2. The present work describes the experimental identification and validation of 24 sRNAs from B. cenocepacia J2315, based on the co-purification of sRNAs with the bacterium Hfq protein, followed by conversion into cDNA, cloning, computational analysis of sequences and validation by Northern blot analysis. The sRNAs here reported escaped identification by previous studies based on transcriptomics or bioinformatic analyses. Results presented indicate that 3 sRNAs are exclusive to bacteria of the Burkholderia cepacia complex and have no homologues in other bacteria, while the other 21 share homology, at different extents, to sRNAs of other bacterial species.

► 24 B. cenocepacia J2315 sRNAs were identified by co-purification with Hfq.
► Transcripts corresponding to all 24 sRNAs were confirmed by Northern blot.
► 3 sRNAs were unique to the Burholderia cepacia complex.
► The 24 sRNAs were not identified by bioinformatics predictions.