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Bioinformatics pp 417-430 | Cite as

Inferring Ancestral Protein Interaction Networks

  • José M. Peregrín-Alvarez
Part of the Methods in Molecular Biology™ book series (MIMB, volume 452)

Abstract

With the recent sequencing of numerous complete genomes and the advent of high throughput technologies (e.g., yeast two-hybrid assays or tandem-affinity purification experiments), it is now possible to estimate the ancestral form of protein interaction networks. This chapter combines protein interaction data and comparative genomics techniques in an attempt to reconstruct a network of core proteins and interactions in yeast that potentially represents an ancestral state of the budding yeast protein interaction network.

Key words

Ancestral state protein interaction networks phylogenetic profiles comparative genomics bioinformatics 

Notes

Acknowledgments

The author thanks John Parkinson for reading the manuscript and making useful comments. This work was supported by the Hospital for Sick Children (Toronto, Ontario, Canada) Research Training Center.

References

  1. 1.
    Uetz, P., Giot, L., Cagney, G., et al. (2000) A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature 403, 623–627.PubMedCrossRefGoogle Scholar
  2. 2.
    Gavin, A. C., Bosche, M., Krause, R., et al. (2002) Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 415, 141–147.PubMedCrossRefGoogle Scholar
  3. 3.
    Giot, L., Bader, J. S., Brouwer, C., et al. (2003) A protein interaction map of Drosophila melanogaster. Science 302, 1727–1736.PubMedCrossRefGoogle Scholar
  4. 4.
    Li, S., Armstrong, C. M., Bertin, N., et al. (2004) A map of the interactome network of the metazoan C. elegans. Science 303, 540–543.PubMedCrossRefGoogle Scholar
  5. 5.
    Butland, G., Peregrin-Alvarez, J. M., Li, J., et al. (2005) Interaction network containing conserved and essential protein complexes in Escherichia coli. Nature 433, 531–537.CrossRefGoogle Scholar
  6. 6.
    Pereira-Leal, J. B., Audit, B., Peregrin-Alvarez, J. M., et al. (2005) An exponential core in the heart of the yeast protein interaction network. Mol Biol Evol 22, 421–425.PubMedCrossRefGoogle Scholar
  7. 7.
    Peregrin-Alvarez, J. M., Tsoka, S., Ouzounis, C. A. (2003) The phylogenetic extent of metabolic enzymes and pathways. Genome Res 13, 422–427.PubMedCrossRefGoogle Scholar
  8. 8.
    Makarova, K. S., Aravind, L., Galperin, M. Y., et al. (1999) Comparative genomics of the Archaea (Euryarchaeota): evolution of conserved protein families, the stable core, and the variable shell. Genome Res 9, 608–628.PubMedGoogle Scholar
  9. 9.
    Harris, J. K., Kelley, S. T., Spiegelman, G. B., et al. (2003) The genetic core of the universal ancestor. Genome Res 13, 407– 412.PubMedCrossRefGoogle Scholar
  10. 10.
    Kyrpides, N., Overbeek, R., Ouzounis, C. (1999) Universal protein families and the functional content of the last universal common ancestor. J Mol Evol 49, 413–423.PubMedCrossRefGoogle Scholar
  11. 11.
    Deane, C. M., Salwinski, L., Xenarios, I., et al. (2002) Protein interactions: two methods for assessment of the reliability of high-throughput observations. Mol Cell Prot 1, 349–356.CrossRefGoogle Scholar
  12. 12.
    Altschul, S. F., Gish, W., Miller, W., et al. (1990) Basic local alignment search tool. J Mol Biol 215, 403–410.PubMedGoogle Scholar
  13. 13.
    Goldovsky, L., Cases, I., Enright, A. J., et al. (2005) BioLayout (Java): versatile network visualisation of structural and functional relationships. Appl Bioinformatics 4, 71–74.PubMedCrossRefGoogle Scholar
  14. 14.
    Pellegrini, M., Marcotte, E. M., Thompson, M. J., et al. (1999) Assigning protein functions by comparative genome analysis: protein phylogenetic profiles. Proc Natl Acad Sci U S A 96, 4285–4288.PubMedCrossRefGoogle Scholar
  15. 15.
    Woese, C. (1998) The universal ancestor. Proc Natl Acad Sci U S A 9, 6854–6859.CrossRefGoogle Scholar
  16. 16.
    Ouzounis, C. A., Kunin, V., Darzentas, N., et al. (2005) A minimal estimate for the gene content of the last common ancestor: exobiology from a terrestrial perspective. Res Microbiol 2005; Epub ahead of print.Google Scholar
  17. 17.
    Ouzounis, C. A. (2005) Ancestral state reconstructions for genomes. Curr Opin Genet Dev 15, 595–600.PubMedCrossRefGoogle Scholar

Copyright information

© Humana Press, a part of Springer Science+Business Media, LLC 2008

Authors and Affiliations

  • José M. Peregrín-Alvarez
    • 1
  1. 1.SickKids Research InstituteTorontoCanada

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