Non-coding RNAs (ncRNAs) are regulatory molecules encoded in the intergenic or intragenic regions of the genome. In prokaryotes, biocomputational identification of homologs of known ncRNAs in other species often fails due to weakly evolutionarily conserved sequences, structures, synteny and genome localization, except in the case of evolutionarily closely related species. To eliminate results from weak conservation, we focused on RNA structure, which is the most conserved ncRNA property. Analysis of the structure of one of the few well-studied bacterial ncRNAs, 6S RNA, demonstrated that unlike optimal and consensus structures, suboptimal structures are capable of capturing RNA homology even in divergent bacterial species. A computational procedure for the identification of homologous ncRNAs using suboptimal structures was created. The suggested procedure was applied to strongly divergent bacterial species and was capable of identifying homologous ncRNAs.

Laboratory of Bioinformatics Institute of Microbiology Academy of Sciences of the Czech Republic Vídeňská 1073 14220 Prague Czech Republic

Zobrazit více v PubMed

Wassarman KM, Storz G. 6S RNA regulates E. coli RNA polymerase activity. Cell. 2000;101:613–623. PubMed

Tucker BJ, Breaker RR. Riboswitches as versatile gene control elements. Curr. Opin. Struct. Biol. 2005;15:342–348. PubMed

Vogel J, Sharma CM. How to find small non-coding RNAs in bacteria. Biol. Chem. 2005;386:1219–1238. PubMed

Wolfsberg TG, McEntyre J, Schuler GD. Guide to the draft human genome. Nature. 2001;409:824–826. PubMed

Gardner PP, Giegerich R. A comprehensive comparison of comparative RNA structure prediction approaches. BMC Bioinformatics. 2004;5:140. PubMed PMC

Gardner PP, Daub J, Tate JG, Nawrocki EP, Kolbe DL, Lindgreen S, Wilkinson AC, Finn RD, Griffiths-Jones S, Eddy SR, et al. Rfam: updates to the RNA families database. Nucleic Acids Res. 2009;37:D136–D140. PubMed PMC

Ando Y, Asari S, Suzuma S, Yamane K, Nakamura K. Expression of a small RNA, BS203 RNA, from the yocI-yocJ intergenic region of Bacillus subtilis genome. FEMS Microbiol. Lett. 2002;207:29–33. PubMed

Suzuma S, Asari S, Bunai K, Yoshino K, Ando Y, Kakeshita H, Fujita M, Nakamura K, Yamane K. Identification and characterization of novel small RNAs in the aspS-yrvM intergenic region of the Bacillus subtilis genome. Microbiology. 2002;148:2591–2598. PubMed

Trotochaud AE, Wassarman KM. A highly conserved 6S RNA structure is required for regulation of transcription. Nat. Struct. Mol. Biol. 2005;12:313–319. PubMed

Barrick JE, Sudarsan N, Weinberg Z, Ruzzo WL, Breaker RR. 6S RNA is a widespread regulator of eubacterial RNA polymerase that resembles an open promoter. RNA. 2005;11:774–784. PubMed PMC

Kingsford CL, Ayanbule K, Salzberg SL. Rapid, accurate, computational discovery of Rho-independent transcription terminators illuminates their relationship to DNA uptake. Genome Biol. 2007;8:R22. PubMed PMC

Korf I, Yandell M, Bedell J. BLAST. Sebastopol: O’Reilly & Associates; 2003.

Hopwood DA, Bibb MJ, Chater KF, Kieser T, Bruton CJ, Kieser HM, Lydiate DJ, Smith CP, Ward JM, Schrempf H. Genetic Manipulation of Streptomyces – A Laboratory Manual. Norwich: The John Innes Foundation; 1985.

Krasny L, Tiserova H, Jonak J, Rejman D, Sanderova H. The identity of the transcription +1 position is crucial for changes in gene expression in response to amino acid starvation in Bacillus subtilis. Mol. Microbiol. 2008;69:42–54. PubMed

Griffiths-Jones S, Bateman A, Marshall M, Khanna A, Eddy SR. Rfam: an RNA family database. Nucleic Acids Res. 2003;31:439–441. PubMed PMC

Markham NR, Zuker M. DINAMelt web server for nucleic acid melting prediction. Nucleic Acids Res. 2005;33:W577–W581. PubMed PMC

Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J. Mol. Biol. 1990;215:403–410. PubMed

Hofacker IL. RNA secondary structure analysis using the Vienna RNA package. Curr. Protoc. Bioinformatics. 2004 Chapter 12, Unit 12 12. PubMed

Panek J, Bobek J, Mikulik K, Basler M, Vohradsky J. Biocomputational prediction of small non-coding RNAs in Streptomyces. BMC Genomics. 2008;9:217. PubMed PMC

Jaeger JA, Turner DH, Zuker M. Improved predictions of secondary structures for RNA. Proc. Natl Acad. Sci. USA. 1989;86:7706–7710. PubMed PMC

Tran TT, Zhou F, Marshburn S, Stead M, Kushner SR, Xu Y. De novo computational prediction of non-coding RNA genes in prokaryotic genomes. Bioinformatics. 2009;25:2897–2905. PubMed PMC

MoaB2, a newly identified transcription factor, binds to σA in Mycobacterium smegmatis

RIP-seq reveals RNAs that interact with RNA polymerase and primary sigma factors in bacteria

Ms1 RNA Interacts With the RNA Polymerase Core in Streptomyces coelicolor and Was Identified in Majority of Actinobacteria Using a Linguistic Gene Synteny Search

6S-Like scr3559 RNA Affects Development and Antibiotic Production in Streptomyces coelicolor

rboAnalyzer: A Software to Improve Characterization of Non-coding RNAs From Sequence Database Search Output

rPredictorDB: a predictive database of individual secondary structures of RNAs and their formatted plots

Ms1, a novel sRNA interacting with the RNA polymerase core in mycobacteria