title: 6S RNA is a widespread regulator of eubacterial RNA polymerase that resembles an open promoter.
abstract: 6S RNA is an abundant noncoding RNA in Escherichia coli that binds to sigma70 RNA polymerase holoenzyme to globally regulate gene expression in response to the shift from exponential growth to stationary phase. We have computationally identified >100 new 6S RNA homologs in diverse eubacterial lineages. Two abundant Bacillus subtilis RNAs of unknown function (BsrA and BsrB) and cyanobacterial 6Sa RNAs are now recognized as 6S homologs. Structural probing of E. coli 6S RNA and a B. subtilis homolog supports a common secondary structure derived from comparative sequence analysis. The conserved features of 6S RNA suggest that it binds RNA polymerase by mimicking the structure of DNA template in an open promoter complex. Interestingly, the two B. subtilis 6S RNAs are discoordinately expressed during growth, and many proteobacterial 6S RNAs could be cotranscribed with downstream homologs of the E. coli ygfA gene encoding a putative methenyltetrahydrofolate synthetase. The prevalence and robust expression of 6S RNAs emphasize their critical role in bacterial adaptation.
authors.affiliation: Department of Molecular, Cellular, and Developmental Biology, Yale University, P.O. Box 208103, New Haven, CT 06520, USA.
authors.forename: Jeffrey E
authors.initials: JE
authors.lastname: Barrick
authors.forename: Narasimhan
authors.initials: N
authors.lastname: Sudarsan
authors.forename: Zasha
authors.initials: Z
authors.lastname: Weinberg
authors.forename: Walter L
authors.initials: WL
authors.lastname: Ruzzo
authors.forename: Ronald R
authors.initials: RR
authors.lastname: Breaker
mesh_terms: D001412:Bacillus subtilis / Q000235:genetics / Q000254:growth & development; D001419:Bacteria / Q000201:enzymology* / Q000235:genetics*; D001483:Base Sequence; D017124:Conserved Sequence / Q000235:genetics; D012321:DNA-Directed RNA Polymerases / Q000378:metabolism*; D015964:Gene Expression Regulation, Bacterial; D005798:Genes, Bacterial / Q000235:genetics; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D009876:Operon / Q000235:genetics; D010802:Phylogeny; D011401:Promoter Regions, Genetic / Q000235:genetics*; D012329:RNA, Bacterial / Q000737:chemistry / Q000235:genetics*; D022661:RNA, Untranslated; D012689:Sequence Homology, Nucleic Acid; D009626:Terminology as Topic
chemical_list: C411065:6S RNA; D012329:RNA, Bacterial; D022661:RNA, Untranslated; D012321:DNA-Directed RNA Polymerases