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

Content Provider	IEEE Xplore Digital Library
Author	Singh, B.R. Al-Khedhairy, A.A. Alarifi, S.A. Musarrat, J.
Copyright Year	2010
Description	Author affiliation: DNA Research Chair, College of Science, King Saud University, P.O. Box 2455, Riyadh-11451, Saudi Arabia (Singh, B.R.; Al-Khedhairy, A.A.; Alarifi, S.A.; Musarrat, J.)
Abstract	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.
Starting Page	257
Ending Page	261
File Size	524065
Page Count	5
File Format	PDF
ISBN	9781424467754
e-ISBN	9781424467754
DOI	10.1109/ICBBT.2010.5478967
Language	English
Publisher	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Publisher Date	2010-04-16
Publisher Place	China
Access Restriction	Subscribed
Rights Holder	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Subject Keyword	Sequences OxySRNA RNA Genomics In silico analysis Capacitive sensors Computational ribonucleomics Proteins Microorganisms Hfq SRNA DNA Bacillus 16SrRNA gene Genetics Performance analysis Bioinformatics
Content Type	Text
Resource Type	Article

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