Identification of regulatory RNAs in Bacillus subtilis.
Post-transcriptional regulatory mechanisms are widespread in bacteria. Interestingly, current published data hint that some of these mechanisms may be non-random with respect to their phylogenetic distribution. Although small, trans-acting regulatory RNAs commonly occur in bacterial genomes, they have been better characterized in Gram-negative bacteria, leaving the impression that they may be less important for Firmicutes. It has been presumed that Gram-positive bacteria, in particular the Firmicutes, are likely to utilize cis-acting regulatory RNAs located within the 5' mRNA leader region more often than trans-acting regulatory RNAs. In this analysis we catalog, by a deep sequencing-based approach, both classes of regulatory RNA candidates for Bacillus subtilis, the model microorganism for Firmicutes. We successfully recover most of the known small RNA regulators while also identifying a greater number of new candidate RNAs. We anticipate these data to be a broadly useful resource for analysis of post-transcriptional regulatory strategies in B. subtilis and other Firmicutes.
Irnov
Irnov
I
Department of Biochemistry, The University of Texas Southwestern Medical Center, Dallas, TX 75390-9038, USA.
Sharma
Cynthia M
CM
Vogel
Jörg
J
Winkler
Wade C
WC
D020121:5' Untranslated Regions; D001412:Bacillus subtilis / Q000235:genetics*; D001427:Bacterial Toxins / Q000235:genetics; D001483:Base Sequence; D008969:Molecular Sequence Data; D039002:Prophages / Q000235:genetics; D016372:RNA, Antisense / Q000032:analysis; D012329:RNA, Bacterial / Q000032:analysis / Q000737:chemistry / Q000235:genetics; D058727:RNA, Small Untranslated / Q000032:analysis* / Q000737:chemistry / Q000235:genetics; D017423:Sequence Analysis, RNA
D020121:5' Untranslated Regions; D001427:Bacterial Toxins; D016372:RNA, Antisense; D012329:RNA, Bacterial; D058727:RNA, Small Untranslated