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Molecular Biology

, Volume 37, Issue 5, pp 716–722 | Cite as

Computer-Assisted Analysis of Regulation of the Glycerol-3-Phosphate Metabolism in Genomes of Proteobacteria

  • L. V. Danilova
  • M. S. Gelfand
  • V. A. Lyubetsky
  • O. N. Laikova
Article

Abstract

Comparative computer-assisted analysis was used to study putative GlpR regulons responsible for metabolism of glycerol and glycerol-3-phosphate in genomes of α-, β-, and γ-proteobacteria. New palindromic GlpR-binding signals were identified in γ-proteobacteria, consensus sequences being TGTTCGATAACGAACA for Enterobacteriaceae, wTTTTCGTATACGAAAAw for Pseudomonadaceae, and AATGCTCGATCGAGCATT for Vibrionaceae. The signals in α- and β-proteobacteria were also identified: they contained 3–4 direct TTTCGTT repeats separated by 3–4 nucleotide pairs.

GlpR tandem repeats computer-assisted analysis operon structure α-proteobacteria β-proteobacteria γ-proteobacteria 

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REFERENCES

  1. 1.
    Weissenborn D.L., Wittekindt N., Larson T.J. 1992. Structure and regulation of the glpFK operon encoding glycerol diffusion facilitator and glycerol kinase of Escherichia coli K-12. J. Biol. Chem. 267, 6122–6131.Google Scholar
  2. 2.
    Larson T.J., Cantwell J.S., van Loo-Bhattacharya A.T. 1992. Interaction at a distance between multiple operators controls the adjacent, divergently transcribed glpTQ-glpABC operons of Escherichia coli K-12. J. Biol. Chem. 267, 6114–6121.Google Scholar
  3. 3.
    Yang B., Larson T.J. 1996. Action at a distance for negative control of transcription of the glpD gene encoding sn-glycerol 3-Phosphate dehydrogenase of Escherichia coli K-12. J. Bacteriol. 178, 7090–7098.Google Scholar
  4. 4.
    Schweizer H.P., Po C. 1996. Regulation of glycerol metabolism in Pseudomonas aeruginosa: characterization of glpR repressor gene. J. Bacteriol. 178, 5215–5221.Google Scholar
  5. 5.
    Blattner F.R., Plunkett G. 3rd, Bloch C.A. et al. 1997. The complete genome sequence of Escherichia coli K-12. Science. 277, 1453–1474.Google Scholar
  6. 6.
    Parkhill J., Dougan G., James K.D. et al. 2000. Complete genome sequence of a multiple drug resistant Salmonella enterica serovar typhi CT18. Nature. 413, 848–852.Google Scholar
  7. 7.
    McClelland M., Sanderson K.E., Spieth J. et al. 2001. Complete genome sequence of Salmonella enterica serovar typhimurium LT2. Nature. 413, 852–856.Google Scholar
  8. 8.
    http://genome.wustl.eduGoogle Scholar
  9. 9.
    http://www.ncbi.nlm.nih.gov/Genbank/index.htmlGoogle Scholar
  10. 10.
    Parkhill J., Wren B.W., Thomson N.R. et al. 2001. Genome sequence of Yersinia pestis, the causative agent of plague. Nature. 413, 523–527.Google Scholar
  11. 11.
    Heidelberg J.F., Eisen J.A., Nelson W.C. et al. 2000. DNA sequence of both chromosomes of the cholera pathogen Vibrio cholerae. Nature. 406, 477–483.Google Scholar
  12. 12.
    May B.J., Zhang Q., Li L.L., Paustian M.L., Whittam T.S., Kapur V. 2001. Complete genomic sequence of Pasteurella multocida Pm70. Proc. Natl. Acad. Sci. USA. 98, 3460–3465.Google Scholar
  13. 13.
    Fleischmann R.D., Adams M.D., White O. et al. 1995. Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science. 269, 496–512.Google Scholar
  14. 14.
    http://spider.jgi-psf.org/JGI_microbial/html/Google Scholar
  15. 15.
    http://www.tigr.orgGoogle Scholar
  16. 16.
    http://www.genome.ou.edu/act.htmlGoogle Scholar
  17. 17.
    Thompson J.D., Higgins D.G., Gibson T.J. 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positionspecific gap penalties and weight matrix choice. Nucleic Acids Res. 22, 4673–4680.Google Scholar
  18. 18.
    Lim A., Zhang L. 1999. WebPHYLIP: a web interface to PHYLIP. Bioinformatics. 15, 1068–1069.Google Scholar
  19. 19.
    Mironov A.A., Vinokurova N.P., Gelfand M.S. 2000. Software for analysis of bacterial genomes. Mol. Biol.34, 253–262.Google Scholar
  20. 20.
    Danilova L.V., Gorbunov K.Yu., Gelfand M.S., Lyubetsky V.A. 2001. An algorithm to detect regulatory signals in DNA sequences. Mol Biol.35, 987–995.Google Scholar
  21. 21.
    Gennis R.B., Stewart V. 1996. Escherichia coli and Salmonella. Cellular and Molecular biology. Washington DC: ASM Press. 2822 p.Google Scholar
  22. 22.
    Panina E.M., Mironov A.A., Gelfand M.S. 2001. Comparative analysis of FUR regulons in gamma-proteobacteria. Nucleic Acids Res. 29, 5195–5206.Google Scholar
  23. 23.
    http://www.bio.cam.ac.uk/seqlogo/logo.cgiGoogle Scholar

Copyright information

© MAIK “Nauka/Interperiodica” 2003

Authors and Affiliations

  • L. V. Danilova
    • 1
  • M. S. Gelfand
    • 2
  • V. A. Lyubetsky
    • 1
  • O. N. Laikova
    • 2
  1. 1.Institute for Information Transmission ProblemsRussian Academy of SciencesMoscowRussia
  2. 2.State Research Center GosNIIGenetikaMoscowRussia

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