Assessing the conservation and targets of putative sRNAs in .

RNA regulators are often found in complex regulatory networks and may mediate metabolism and virulence in bacteria. Small RNAs (sRNA's), a class of non-coding RNAs that interact with an mRNA transcript via base pairing, modulate translation initiation and mRNA degradation. To better understand the role of sRNAs in pathogenicity several studies identified sRNAs in , however little functional characterization has followed. The goal of this study is threefold: 1) take an inventory of putative sRNAs in ; 2) assess the conservation of these sRNAs; and 3) examine their predicted targets. Three previous studies in identified 287 putative sRNAs by high-throughput sequencing using a variety of distinct inclusion criteria. This study narrows the candidates to a list of 59 putative sRNAs. BLAST analysis shows that each of the 59 sequences are highly conserved across the pangenome while only 5 sRNAs have corresponding sequences with substantial similarity in other members of the Streptococcus genus. We used four RNA-RNA interaction prediction programs (IntaRNA, CopraRNA, sRNARFTarget, and TargetRNA3) to predict targets for each of the 59 putative sRNAs. Across all probable predictions, only seven sRNAs have overlap in the targets predicted by multiple programs, four of which target numerous transposases. Moreover, sRNAs targeting transposases do so with nearly identical and perfect base pairing. One sRNA, named M63 (Spd_sr37), has several probable targets in the CcpA regulon, a network responsible for global catabolite repression, suggesting a possible biological function in control of carbon metabolism. Further, each M63-target interaction exhibits unique base pairing increasing confidence in the biological relevance of the result. This study produces a curated list of S putative sRNAs whose predicted targets suggest functional significance in transposon and carbon metabolism regulation.