Assessing the conservation and targets of putative sRNAs in Streptococcus pneumoniae

RNA regulators are often found in regulatory networks and mediate growth and virulence in bacteria. Small RNAs (sRNAs) are non-coding RNAs that modulate translation initiation and mRNA degradation by base-pairing. To better understand the role of sRNAs in pathogenicity several studies identified sRNAs in Streptococcus pneumoniae; however, little functional characterization has followed. This study's goals are: 1) survey putative sRNAs in S. pneumoniae; 2) assess the conservation of these sRNAs; and 3) examine their predicted targets. Three previous studies in S. pneumoniae identified 287 putative sRNAs by high-throughput sequencing. This study narrows the candidates to a list of 58 putative sRNAs. BLAST analysis indicates that the 58 sequences are highly conserved across the S. pneumoniae pangenome, and 25 of them are identified sporadically in other Streptococcus species. However, only 2 have corresponding sequences identified across several Streptococcus species. We used four RNA-target prediction programs to predict targets for each of the 58 putative sRNAs. Across all probable predictions, six sRNAs have overlapping targets predicted by multiple programs, four of which target numerous transposase encoding transcripts. sRNAs targeting transposase genes display nearly identical and perfect base-pairing. One sRNA, M63 (Spd_sr37), has several probable targets in the CcpA regulon, a network responsible for global catabolite repression, suggesting a possible biological function in carbon metabolism control. Each M63-target interaction exhibits unique base-pairing increasing confidence in the biological relevance of the result. This study produces a list of S. pneumoniae putative sRNAs whose predicted targets suggest functional significance in transposon and carbon metabolism regulation.