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Molecular Biology

, Volume 41, Issue 5, pp 836–842 | Cite as

Reconstruction of ancestral regulatory signals along a transcription factor tree

  • K. Yu. Gorbunov
  • V. A. Lyubetsky
Mathematical and System Biology

Abstract

A model and an algorithm were developed to reconstruct the ancestral regulatory signals, first and foremost, for DNA-protein interactions, at inner nodes of a transcription factor phylogenetic tree on the basis of the modern signal distribution. The algorithm simultaneously infers the evolutionary scenario as a set of tree edges along which the signal diverged to the greatest extent. The model and algorithm were tested with simulation data and biological findings on the NrdR, MntR, and LacI signals.

Key words

evolutionary scenario regulatory signal frequency matrix evolution along a tree transcription factor tree 

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References

  1. 1.
    Lyubetsky V., Gorbunov K., Rusin L., V’yugin V. 2005. Algorithms to reconstruct evolutionary events at molecular level and infer species phylogeny. In: Bioinformatics of Genome Regulation and Structure II. Springer, 189–204.Google Scholar
  2. 2.
    Gorbunov K.Yu., Lyubetsky V.A. 2005. Identification of ancestral genes that introduce incongruence between protein and species trees. Mol. Biol. 39,5, 847–858.CrossRefGoogle Scholar
  3. 3.
    Rodionov D.A., Gelfand M.S. 2005. A universal regulatory system of ribonucleotide reductase genes in bacterial genomes. Trends Genet. 21, 385–398PubMedCrossRefGoogle Scholar
  4. 4.
    Kotelnikova E.A., Makeev V.J., Gelfand M.S. 2005. Evolution of transcription factor DNA binding sites. Gene. 347, 255–263.PubMedCrossRefGoogle Scholar
  5. 5.
    Fitch W.M. 1971. Towards defining the course of evolution: Minimum change for a specific tree topology. Syst. Zool. 20, 406–416.CrossRefGoogle Scholar
  6. 6.
    Schneider T.D. 1986. Information content of binding sites on nucleotide sequences. J. Mol. Biol. 188, 415–431.PubMedCrossRefGoogle Scholar
  7. 7.
    Stormo G.D., Fields D.S. 1998. Specificity, energy and information in DNA-protein interactions. Trends Biochem. Sci. 23, 109–113.PubMedCrossRefGoogle Scholar
  8. 8.
    Berg O.G., von Hippel P.H. 1987. Selection of DNA binding sites by regulatory proteins. J. Mol. Biol. 193, 723–750.PubMedCrossRefGoogle Scholar
  9. 9.
  10. 10.
    Gorbunov K.Yu., Lyubetsky V.A. 2006. Inferring regulatory signal profiles and evolutionary events. Proc. 5th Int. Conf. Bioinformatics Genome Regul. Struct. (BGRS’2006). Novosibirsk: IC&G, vol. 3, pp. 151–154.Google Scholar
  11. 11.
    Laikova O.N. 2002. Systematic prediction of regulatory interactions in the LacI family of transcriptional regulators. Proc. 5th Int. Conf. Bioinformatics Genome Regul. Struct. (BGRS’2002). Novosibirsk: IC&G, vol. 2, pp. 26–28.Google Scholar
  12. 12.
    Gelfand M.S., Laikova O.N. 2003. Prolegomena to the evolution of transcriptional regulation in bacterial genomes. In: Frontiers in Computitional Genomics. Eds. Galperin M.Y., Koonin E.V. Wymondham, U.K.: Caiser Acad. Press, pp. 195–216.Google Scholar

Copyright information

© Pleiades Publishing, Inc. 2007

Authors and Affiliations

  1. 1.Kharkevich Institute for Information Transmission ProblemsRussian Academy of SciencesMoscowRussia

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