Protein interaction maps for complete genomes based on gene fusion events (original) (raw)

References

  1. Mendelsohn,A. R. & Brent,R. Protein interaction methods—toward an endgame. Science 284, 1948–1950 (1999).
    Article CAS Google Scholar
  2. Blackstock,W. P. & Weir,M. P. Proteomics: quantitative and physical mapping of cellular proteins. Trends Biotechnol. 17, 121–127 (1999).
    Article CAS Google Scholar
  3. Phizicky,E. M. & Fields,S. Protein–protein interactions: methods for detection and analysis. Microbiol. Rev. 59, 94–123 (1995).
    CAS PubMed PubMed Central Google Scholar
  4. Luban,J. & Goff,S. P. The yeast two-hybrid system for studying protein–protein interactions. Curr. Opin. Biotechnol. 6, 59–64 (1995).
    Article CAS Google Scholar
  5. Lecrenier,N., Foury,F. & Goffeau,A. Two-hybrid systematic screening of the yeast proteome. BioEssays 20, 1–5 (1998).
    Article CAS Google Scholar
  6. Lakey,J. H. & Raggett,E. M. Measuring protein–protein interactions. Curr. Opin. Struct. Biol. 8, 119–123 (1998).
    Article CAS Google Scholar
  7. Janin,J. & Rodier,F. Protein–protein interaction at crystal contacts. Proteins 23, 580–587 (1995).
    Article CAS Google Scholar
  8. Jones,S. & Thornton,J. M. Principles of protein–protein interactions. Proc. Natl Acad. Sci. USA 93, 13–20 (1996).
    Article ADS CAS Google Scholar
  9. Larsen,T. A., Olson,A. J. & Goodsell,D. S. Morphology of protein–protein interfaces. Structure 6, 421–427 (1998).
    Article CAS Google Scholar
  10. Dandekar,T., Snel,B., Huynen,M. & Bork,P. Conservation of gene order: a finger-print of proteins that physically interact. Trends Biochem. Sci. 23, 324–328 (1998).
    Article CAS Google Scholar
  11. Overbeek,R., Fonstein,M., D'Souza,M., Pusch,G. D. & Maltsev,N. The use of gene clusters to infer functional coupling. Proc. Natl Acad. Sci. USA 96, 2896–2901 (1999).
    Article ADS CAS Google Scholar
  12. Tamames,J., Casari,G., Ouzounis,C. & Valencia,A. Conserved clusters of functionally related genes in two bacterial genomes. J. Mol. Evol. 44, 66–73 (1997).
    Article ADS CAS Google Scholar
  13. Pellegrini,M., Marcotte,E. M., Thompson,M. J., Eisenberg,D. & Yeates,T. O. Assigning protein functions by comparative genome analysis: protein phylogenetic profiles. Proc. Natl Acad. Sci. USA 96, 4285–4288 (1999).
    Article ADS CAS Google Scholar
  14. Bülow,I. Preparation of artificial bifunctional enzymes by gene fusion. Biochem. Soc. Symp. 57, 123–133 (1990).
    PubMed Google Scholar
  15. Wales,M. E. & Wild,J. R. Analysis of structure–function relationships by formation of chimeric enzymes produced by gene fusion. Methods Enzymol. 202, 687–706 (1991).
    Article CAS Google Scholar
  16. Burns,D. M., Horn,V., Paluh,J. & Yanofsky,C. Evolution of the tryptophan synthetase of fungi. Analysis of experimentally fused Escherichia coli tryptophan synthetase alpha and beta chains. J. Biol. Chem. 265, 2060–2069 (1990).
    CAS PubMed Google Scholar
  17. Duncan,K., Edwards,R. M. & Coggins,J. R. The Saccharomyces cerevisiae ARO1 gene. An example of the co-ordinate regulation of five enzymes on a single biosynthetic pathway. FEBS Lett. 241, 83–88 (1988).
    Article CAS Google Scholar
  18. Denis-Duphil,M. Pyrimidine biosynthesis in Saccharomyces cerevisiae: the ura2 cluster gene, its multifunctional enzyme product, and other structural or regulatory genes involved in de novo UMP synthesis. Biochem. Cell Biol. 67, 612–631 (1989).
    Article CAS Google Scholar
  19. Ouzounis,C. A. & Kyrpides,N. C. ThiD-TenA: a gene pair fusion in eukaryotes. J. Mol. Evol. 45, 708–711 (1997).
    Article ADS CAS Google Scholar
  20. Smith,S. The animal fatty acid synthase: one gene, one polypeptide, seven enzymes. FASEB J. 8, 1248–1259 (1994).
    Article CAS Google Scholar
  21. Welch,G. R. & Easterby,J. S. Metabolic channeling versus free diffusion: transition-time analysis. Trends Biochem. Sci. 19, 193–197 (1994).
    Article CAS Google Scholar
  22. Marcotte,E. M. et al. Detecting protein function and protein–protein interactions from genome sequences. Science 285, 751–753 (1999).
    Article CAS Google Scholar
  23. Altschul,S. F., Gish,W., Miller,W., Myers,E. W. & Lipman,D. J. Basic local alignment search tool. J. Mol. Biol. 215, 403–410 (1990).
    Article CAS Google Scholar
  24. Andrade,M. A. et al. Automated genome sequence analysis and annotation. Bioinformatics 15, 391–412 (1999).
    Article CAS Google Scholar
  25. Rivera,M. C., Jain,R., Moore,J. E. & Lake,J. A. Genomic evidence for two functionally distinct gene classes. Proc. Natl Acad. Sci. USA 95, 6239–6244 (1998).
    Article ADS CAS Google Scholar
  26. Smith,T. F. & Waterman,M. Identification of common molecular subsequences. J. Mol. Biol. 147, 195–197 (1981).
    Article CAS Google Scholar
  27. Pearson,W. R. Effective protein sequence comparison. Methods Enzymol. 266, 227–258 (1996).
    Article CAS Google Scholar

Download references