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Evolution of Regulatory Systems in Bacteria (Invited Keynote Talk)

  • Mikhail S. Gelfand
  • Alexei E. Kazakov
  • Yuri D. Korostelev
  • Olga N. Laikova
  • Andrei A. Mironov
  • Alexandra B. Rakhmaninova
  • Dmitry A. Ravcheev
  • Dmitry A. Rodionov
  • Alexei G. Vitreschak
Part of the Lecture Notes in Computer Science book series (LNCS, volume 5542)

Abstract

Recent comparative studies indicate surprising flexibility of regulatory systems in bacteria. These systems can be analyzed on several levels, and I plan to consider two of them. At the level of regulon evolution, one can attempt to characterize the evolution of regulon content formed by loss, gain and duplications of regulators and regulated genes, as well as gain and loss of individual regulatory sites and horizontal gene transfer. At the level of transcription factor families, one can study co-evolution of DNA-binding proteins and the motifs they recognize. While this area is not yet ripe for fully automated analysis, the results of systematic comparative studies gradually start to coalesce into an understanding of how bacteria regulatory systems evolve.

Keywords

Comparative genomics bacteria regulation of transcription regulation of translation transcription factor binding site T-box 

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References

  1. 1.
    Rodionov, D.A., Gelfand, M.S., Todd, J.D., Curson, A.R.J., Johnston, A.W.B.: Comparative Reconstruction of Transcriptional Network Controlling Iron and Manganese Homeostasis in Alpha-Proteobacteria. PLoS Comp. Biol. 2, e163 (2006)CrossRefGoogle Scholar
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    Kazakov, A.E., Rodionov, D.A., Alm, E., Arkin, A., Dubchak, I., Gelfand, M.S.: Comparative Genomics of Regulation of Fatty Acid and Branched-Chain Amino Acid Utilization in Proteobacteria. J. Bacteriol. 191, 52–64 (2009)CrossRefPubMedGoogle Scholar
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    Vitreschak, A.G., Mironov, A.A., Lyubetsky, V.A., Gelfand, M.S.: Functional and Evolutionary Analysis of the T-box Regulon in Bacteria. RNA 14, 717–735 (2008)CrossRefPubMedPubMedCentralGoogle Scholar
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    Desai, T., Rodionov, D., Gelfand, M., Alm, E., Rao, C.: Engineering Transcription Factors with Novel DNA-binding Specificity Using Comparative Genomics. Nucleic Acids Res. (in press)Google Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2009

Authors and Affiliations

  • Mikhail S. Gelfand
    • 1
    • 2
  • Alexei E. Kazakov
    • 1
  • Yuri D. Korostelev
    • 2
  • Olga N. Laikova
    • 3
  • Andrei A. Mironov
    • 1
    • 2
  • Alexandra B. Rakhmaninova
    • 1
    • 2
  • Dmitry A. Ravcheev
    • 1
  • Dmitry A. Rodionov
    • 1
    • 4
  • Alexei G. Vitreschak
    • 1
  1. 1.A.A.Kharkevich Institute for Information Transmission Problems, RASMoscowRussia
  2. 2.Faculty of Bioengineering and BioinformaticsM.V.Lomonosov Moscow State UniversityMoscowRussia
  3. 3.Research Institute for Genetics and Selection of Industrial MicroorganismsMoscowRussia
  4. 4.A.A. Burnham Institute for Medical ResearchLa JollaUSA

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