Advertisement

Evolutionary and Temporal Dynamics of Transcriptional Regulatory Networks

  • M. Madan Babu
Part of the Lecture Notes in Computer Science book series (LNCS, volume 5151)

Abstract

Transcriptional regulation is a key mechanism that allows cells to make the appropriate amount of proteins at the right time. This is mediated by transcription factors that respond to specific signals and regulate expression of the relevant genes. The set of all regulatory interactions in a cell can now be investigated and this is best represented as the transcriptional network where nodes represent transcription factors or target genes and edges represent regulatory interactions. In this manuscript, I will first discuss the current understanding of the organization of such networks from the model organisms E. coli and yeast. I will then demonstrate that such networks are extremely dynamic and adapt rapidly to changing environments. This will be illustrated by discussing the changes in the network structure in two different time scales: (i) those that occur during different cellular conditions and (ii) those that occur across different organisms living in diverse environments.

Keywords

network evolution dynamics transcription and gene regulation 

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. 1.
    Barabasi, A.L., Oltvai, Z.N.: Network biology: understanding the cell’s functional organization. Nat. Rev. Genet. 5(2), 101–113 (2004)CrossRefGoogle Scholar
  2. 2.
    Babu, M.M., Luscombe, N.M., Aravind, L., Gerstein, M., Teichmann, S.A.: Structure and evolution of transcriptional regulatory networks. Curr. Opin. Struct. Biol. 14(3), 283–291 (2004)CrossRefGoogle Scholar
  3. 3.
    Lee, T.I., Rinaldi, N.J., Robert, F., Odom, D.T., Bar-Joseph, Z., Gerber, G.K., Hannett, N.M., Harbison, C.T., Thompson, C.M., Simon, I., Zeitlinger, J., Jennings, E.G., Murray, H.L., Gordon, D.B., Ren, B., Wyrick, J.J., Tagne, J.B., Volkert, T.L., Fraenkel, E., Gifford, D.K., Young, R.A.: Transcriptional regulatory networks in Saccharomyces cerevisiae. Science 298(5594), 799–804 (2002)CrossRefGoogle Scholar
  4. 4.
    Shen-Orr, S.S., Milo, R., Mangan, S., Alon, U.: Network motifs in the transcriptional regulation network of Escherichia coli. Nat. Genet. 31(1), 64–68 (2002)CrossRefGoogle Scholar
  5. 5.
    Alon, U.: Network motifs: theory and experimental approaches. Nat. Rev. Genet. 8(6), 450–461 (2007)CrossRefGoogle Scholar
  6. 6.
    Barabasi, A.L., Albert, R.: Emergence of scaling in random networks. Science 286(5439), 509–512 (1999)MathSciNetCrossRefzbMATHGoogle Scholar
  7. 7.
    Albert, R., Jeong, H., Barabasi, A.L.: Error and attack tolerance of complex networks. Nature 406(6794), 378–382 (2000)CrossRefGoogle Scholar
  8. 8.
    Albert, R.: Scale-free networks in cell biology. J. Cell Sci. 118(pt 21), 4947–4957 (2005)CrossRefGoogle Scholar
  9. 9.
    Kitano, H.: Biological robustness. Nat. Rev. Genet. 5(11), 826–837 (2004)CrossRefGoogle Scholar
  10. 10.
    Thieffry, D., Huerta, A.M., Perez-Rueda, E., Collado-Vides, J.: From specific gene regulation to genomic networks: a global analysis of transcriptional regulation in Escherichia coli. Bioessays 20(5), 433–440 (1998)CrossRefGoogle Scholar
  11. 11.
    Guelzim, N., Bottani, S., Bourgine, P., Kepes, F.: Topological and causal structure of the yeast transcriptional regulatory network. Nat. Genet. 31(1), 60–63 (2002)CrossRefGoogle Scholar
  12. 12.
    Teichmann, S.A., Babu, M.M.: Gene regulatory network growth by duplication. Nat. Genet. 36(5), 492–496 (2004)CrossRefGoogle Scholar
  13. 13.
    Luscombe, N.M., Babu, M.M., Yu, H., Snyder, M., Teichmann, S.A., Gerstein, M.: Genomic analysis of regulatory network dynamics reveals large topological changes. Nature 431(7006), 308–312 (2004)CrossRefGoogle Scholar
  14. 14.
    Madan Babu, M., Teichmann, S.A., Aravind, L.: Evolutionary dynamics of prokaryotic transcriptional regulatory networks. J. Mol. Biol. 358(2), 614–633 (2006)CrossRefGoogle Scholar
  15. 15.
    Wuchty, S., Oltvai, Z.N., Barabasi, A.L.: Evolutionary conservation of motif constituents in the yeast protein interaction network. Nat. Genet. 35(2), 176–179 (2003)CrossRefGoogle Scholar
  16. 16.
    Jeong, H., Mason, S.P., Barabasi, A.L., Oltvai, Z.N.: Lethality and centrality in protein networks. Nature 411(6833), 41–42 (2001)CrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2008

Authors and Affiliations

  • M. Madan Babu
    • 1
  1. 1.MRC Laboratory of Molecular BiologyCambridgeUK

Personalised recommendations