Molecular Biology

, Volume 37, Issue 5, pp 707–715 | Cite as

Search for Alternative RNA Secondary Structures Regulating Expression of Bacterial Genes

  • E. V. Lyubetskaya
  • L. A. Leont'ev
  • M. S. Gelfand
  • V. A. Lyubetsky
Article

Abstract

Expression of many bacterial genes is regulated by formation of alternative secondary RNA structure within the leader mRNA sequence. Our algorithm designed to search for these structures (basing on analysis of one nucleotide sequence) was applied to analyze operons of amino acid biosynthesis in alpha- and gamma-proteobacteria. The attenuators of these operons are predicted for genomes of some poorly known gamma-proteobacteria including Shewanella putrefaciens, attenuators of the tryptophan operon in some alpha-proteobacteria are also predicted.

attenuator structure proteobacteria expression regulation search algorithm 

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

REFERENCES

  1. 1.
    Vitreschak A.G., Gelfand M.S. 2000. Computer-assisted analysis of regulatory signals in bacterial genomes. Attenuators of the operons involved metabolism of aromatic amino acids. Mol. Biol., 34, 545–552.Google Scholar
  2. 2.
    Landick R., Yanofsky C. 1996. Transcription Attenuation. In Escherichia coli and Salmonella. Cellular and Molecular Biology. Ed. Neidhardt F.C. Washington DC: ASM Press, 1, Ch. 81, 1263–1286.Google Scholar
  3. 3.
    Gorbunov K.Yu, Lyubetskaya E.V., Lyubetsky V.A. 2001. On two algorithms to search for alternative secondary RNA structure. Informatsionnye Protsessy. 1, 178–187. (http://www.jip.ru/).Google Scholar
  4. 4.
    Gorodkin J., Stricklin S.L., Stormo G.D. 2001. Discovering common stem-loop motifs in unaligned RNA sequence. Nucleic Acids Res. 29, 2035–2044.Google Scholar
  5. 5.
    Eddy S.R. 2002. A memory-efficient dynamic programming algorithm for optimal alignment of a sequence to an RNA secondary structure. BMC Bioinformatics. 3, 1–16.Google Scholar
  6. 6.
    Waterman M.S. 1989. In Mathematical Methods for DNA Sequences. Ed. Waterman M.S. Boca Raton, FL: CRC Press, 185–224.Google Scholar
  7. 7.
    Mironov A.A., Vinokurova N.P., Gelfand M.S. 2000. Software for analysis of bacterial genomes. Mol. Biol. 34, 253–262.Google Scholar
  8. 8.
    Vereshchagin N.K., Lyubetsky V.A. 2000. An algorithm to analyze secondary structure of RNA. Trudy Nauch.-Issled. Semin. Logich. Tsentra IF RAN. Moscow: Izd. RAN, 14, 99–109.Google Scholar
  9. 9.
    Leont'ev L.A., Lyubetskaya E.V., Lyubetsky V.A. 2002. A modified algorithm to search for alternative RNA secondary structures and results of calculations. Informatsionnye Protsessy. 2, 100–105 (http://www.jip.ru/).Google Scholar
  10. 10.
    Jeanmougin F., Thompson J.D., Gouy M., Higgins D.G., Gibson T.J. 1998. Multiple sequence alignment with Clustal X. Trends Biochem. Sci. 23, 403–405.Google Scholar
  11. 11.
    Lathe W., Suyama M., Bork P. 2002. Identification of attenuation and antitermination regulation in prokaryotes. Genome Biology. 3, preprint 0003. (http://genome-biology. com/2002/3/6/preprint/0003).Google Scholar
  12. 12.
    Vereshchagin N.K., Lyubetsky V.A. 2000. An algorithm to analyze secondary structure of RNA. Trudy Nauch.-Issled. Semin. Logich. Tsentra IF RAN. Moscow: Izd. RAN, 14, 99–109.Google Scholar
  13. 13.
    Pesole G., Liuni S., D'souza M. 2000. PatSearch: a pattern matcher software that finds functional elements in nucleotide and protein sequences and assesses their statistical significance. Bioinformatics. 16, 439–450.Google Scholar
  14. 14.
    Vitreschak A.G., Rodionov D.A., Mironov A.A, Gelfand M.S. 2002. Regulation of riboflavin biosynthesis and transport genes in bacteria by transcriptional and translational attenuation. Nucleic Acids Res. 30, 3141–3151.Google Scholar
  15. 15.
    Rodionov D.A., Vitreschak A.G., Mironov A.A., Gelfand M.S. 2002. Comparative genomics of thiamin biosynthesis in procaryotes: new genes and regulatory mechanisms. J. Biol. Chem. 277, 48949–48959.Google Scholar
  16. 16.
    Vitreschak A.G., Bansal A.K., Titov I.I., Gelfand M.S. 1999. Computer-assisted analysis of regulatory signals in complete bacterial genomes. Initiation of translation in operons of the ribosomal proteins. Biofizika.44, 601–610.Google Scholar
  17. 17.
    Switzer R.L., Turner R.J., Lu Y. 1999. Regulation of the Bacillus subtilis pyrimidine biosynthetic operon by transcriptional attenuation: control of gene expression by an mRNA-binding protein. Progress Nucleic Acid Res. Mol. Biol. 62, 329–367.Google Scholar
  18. 18.
    Liu J., Turnbough C.L. Jr. 1994. Effects of transcriptional start site sequence and position on nucleotide-sensitive selection of alternative start sites at the pyrC promoter in Escherichia coli. J. Bacteriol. 176, 2938–2945.Google Scholar
  19. 19.
    Rutberg B. 1997. Antitermination of transcription of catabolic operons. Mol. Microbiol. 23, 413–421.Google Scholar
  20. 20.
    Perkins J.B., Pero J.G. 2001. In Bacillus subtilis and its relatives: from genes to cells. Eds. Sonenshein A.L., Hoch J.A., Losick R. Washington, DC: American Soc. Microbiol., 279–293.Google Scholar
  21. 21.
    Miranda-Rios J., Navarro M., Soberon M. 2001. A conserved RNA structure (thi box) is involved in regulation of thiamin biosynthetic gene expression in bacteria. Proc. Natl. Acad. Sci. USA. 98, 9736–9741.Google Scholar
  22. 22.
    Stasinopoulos S.J., Farr G.A., Bechhofer D.H. 1998. Bacillus subtilis tetA(L) gene expression: evidence for regulation by translational reinitiation. Mol. Microbiol. 30, 923–932.Google Scholar
  23. 23.
    Keener J., Nomura M. 1996. Regulation of ribosome synthesis. In Escherichia coli and Salmonella. Cellular and Molecular Biology. Ed. Neidhardt F.C. Washington DC: ASM Press, 1, Ch. 90, 1417–1431.Google Scholar
  24. 24.
    Decatur A., McMurry M.T., Kunkel B.N., Losick R. 1997. Translation of the mRNA for the sporulation gene spoIIID of Bacillus subtilis is dependent upon translation of a small upstream open reading frame. J. Bacteriol. 179, 1324–1328.Google Scholar

Copyright information

© MAIK “Nauka/Interperiodica” 2003

Authors and Affiliations

  • E. V. Lyubetskaya
    • 1
  • L. A. Leont'ev
    • 1
  • M. S. Gelfand
    • 2
  • V. A. Lyubetsky
    • 1
  1. 1.Institute for Information Transmission ProblemsRussian Academy of SciencesMoscowRussia
  2. 2.State Research Center GosNIIGenetikaMoscowRussia

Personalised recommendations