Computational prediction of small non-coding RNA within distal 3´region of 16SrRNA gene of Bacillus sp. strain SJ-101

Computational ribonucleomics of heavy metal stress tolerant Bacillus sp. strain SJ-101 16SrRNA gene has led to the identification of a novel small non-coding RNA (sRNA) and promoter-like sequences within 3´ region of the gene. Using RNAz web server, a 123 bp long functional sRNA with significant thermodynamic stability (Energy contribution: -25.2) and evolutionary conservation (structure conservation index: 0.63) with a SVM RNA class probability (p) of 0.98 was predicted. The clustal W alignment revealed ~79% sequence homology with OxySRNA of Salmonella spp. in sRNAMap database. The Hfq binding site mapped within sRNA showed high sequence similarity with the Hfq elements in OxySRNA family. The target sites for SJ-101 sRNA were identified as ywqE, glpD, yomN and ywjE genes of Bacillus subtilis employing TargetRNA tool. Furthermore, using BPROM software, the regulatory motifs like -35 and -10 boxes were mapped at 1166 and 1187 positions, respectively. The cis-acting elements as the binding sites for transcription factors (TF) were identified at positions 1184 and 1188 within the same region. Thus, it is concluded that sRNAs are widely distributed and that these functional elements are implicated in fine tuning of gene regulatory processes under stress conditions.