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Graph Theoretical Insights into Evolution of Multidomain Proteins

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Research in Computational Molecular Biology (RECOMB 2005)

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 3500))

Abstract

We study properties of multidomain proteins from a graph theoretical perspective. In particular, we demonstrate connections between properties of the domain overlap graph and certain variants of Dollo parsimony models. We apply our graph theoretical results to address several interrelated questions: do proteins acquire new domains infrequently, or often enough that the same combinations of domains will be created repeatedly through independent events? Once domain architectures are created, do they persist? In other words, is the existence of ancestral proteins with domain compositions not observed in contemporary proteins unlikely? Our experimental results indicate that independent merges of domain pairs are not uncommon in large superfamilies.

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References

  1. Apic, G., Gough, J., Teichmann, S.A.: Domain combinations in archaeal, eubacterial and eukaryotic proteomes. J. Mol. Biol. 310, 311–325 (2001)

    Article  Google Scholar 

  2. Apic, G., Huber, W., Teichmann, S.A.: Multi-domain protein families and domain pairs: Comparison with known structures and a random model of domain recombination. J. Struc. Func. Genomics 4, 67–78 (2003)

    Article  Google Scholar 

  3. Barabasi, A.-L., Albert, R.: Emergence of scaling in random networks. Science 286, 509–512 (1999)

    Article  MathSciNet  Google Scholar 

  4. Bashton, M., Chothia, C.: The geometry of domain combination in proteins. J. Mol. Biol. 315, 927–939 (2002)

    Article  Google Scholar 

  5. Bateman, A., Birney, E., Durbin, R., Eddy, S.R., Howe, K.L., Sonnhammer, E.L.: The Pfam protein families database. Nucleic Acids Res. 28(1), 263–266 (2000)

    Article  Google Scholar 

  6. Boeckmann, B., Bairoch, A., Apweiler, R., Blatter, M.-C., Estreicher, A., Gasteiger, E., Martin, M.J., Michoud, K., O’Donovan, C., Phan, I., Pilbout, S., Schneider, M.: The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. Nucleic Acids Res. 31, 365–370 (2003)

    Article  Google Scholar 

  7. Bollobas, B.: Random Graph Theory. Cambridge University Press, Cambridge (2001)

    Google Scholar 

  8. Cheek, S., Zhang, H., Grishin, N.V.: Sequence and structure classification of kinases. J. Mol. Biol. 320(4), 855–881 (2002)

    Article  Google Scholar 

  9. Danzer, L., Grunbaum, B., Klee, V.: Helly’s theorem and its relatives. Convexity, AMS 7, 101–180 (1963)

    MathSciNet  Google Scholar 

  10. Day, W.H.E., Johnson, D., Sankoff, D.: The computational complexity of inferring rooted phylogenies by parsimony. Mathematical Biosciences 81, 33–42 (1986)

    Article  MATH  MathSciNet  Google Scholar 

  11. Gusfield, D.: Efficient methods for inferring evolutionary history. Networks 21, 19–28 (1991)

    Article  MATH  MathSciNet  Google Scholar 

  12. Felsenstein, J.: Inferring Phylogenies. Sinauer Associates (2004)

    Google Scholar 

  13. Gavril, F.: The intersection graphs of subtrees in trees are exactly the chordal graphs. J. Comb. Theory (B) 16, 47–56 (1974)

    Article  MATH  MathSciNet  Google Scholar 

  14. Geer, L.Y., Domrachev, M., Lipman, D.J., Bryant, S.H.: CDART: protein homology by domain architecture. Genome Res. 12(10), 1619–1623 (2002)

    Article  Google Scholar 

  15. Gerstein, M.: How representative are the known structures of the proteins in a complete genome? A comprehensive structural census. Fold des. 3, 497–512 (1998)

    Article  Google Scholar 

  16. Golumbic, M.: Algorithmic Graph Theory and Perfect Graphs. Academic Press, New York (1980)

    MATH  Google Scholar 

  17. Gu, J., Gu, X.: Natural history and functional divergence of protein tyrosine kinases. Gene. 317, 49–57 (2003)

    Article  Google Scholar 

  18. Hanks, S.K.: Genomic analysis of the eukaryotic protein kinase superfamily: a perspective. Genome Biol. 4(5), 111 (2003)

    Article  Google Scholar 

  19. Heger, A., Holm, L.: Exhaustive enumeration of protein domain families. J. Mol. Biol. 328, 749–767 (2003)

    Article  Google Scholar 

  20. Yanai, I., Wolf, Y.I., Koonin, E.V.: Evolution of gene fusions: horizontal transfer versus independent events. Genome Biol. 3 (2002), research:0024

    Google Scholar 

  21. Farris, J.S.: Phylogenetic analysis under Dollo’s law. Systematic Zoology 26(1), 77–88 (1977)

    Article  MathSciNet  Google Scholar 

  22. Krause, A., Stoye, J., Vingron, M.: The SYSTERS protein sequence cluster set. Nucleic Acids Res. 28(1), 270–272 (2000)

    Article  Google Scholar 

  23. Kummerfeld, S., Vogel, C., Madera, M., Teichmann, S.: Evolution of multi-domain proteins by gene fusion and fission. In: ISMB 2004 (2004)

    Google Scholar 

  24. Letunic, I., Goodstadt, L., Dickens, N.J., Doerks, T., Schultz, J., Mott, R., Ciccarelli, F., Copley, R.R., Ponting, C.P., Bork, P.: Recent improvements to the SMART domain-based sequence annotation resource. Nucleic Acids Res. 31(1), 242–244 (2002)

    Article  Google Scholar 

  25. Liu, Y., Gerstein, M., Engelman, D.M.: Evolutionary use of domain recombination: a distinction between membrane and soluble proteins. Proc. Natl. Acad. Sci. USA, 3495–3497 (2004)

    Google Scholar 

  26. Long, M.: Evolution of novel genes. Curr. Opin. Genet. Dev. 11(6), 673–680 (2001)

    Article  Google Scholar 

  27. Patthy, L.: Genome evolution and the evolution of exon-shuffling–a review. Gene 238, 103–114 (1999)

    Article  Google Scholar 

  28. Marcotte, E.M., Pellegrini, M., Ng, H.L., Rice, D.W., Yeates, T.O., Eisenberg, D.: Detecting protein function and protein-protein interactions from genome sequences. Science 285, 751–753 (1999)

    Article  Google Scholar 

  29. Mehlhorn, K., Naher, S.: The LEDA Platform of Combinatorial and Geometric Computing. Cambridge University Press, Cambridge (1999)

    Google Scholar 

  30. Robinson, D.R., Wu, Y.M., Lin, S.F.: The protein tyrosine kinase family of the human genome. Oncogene 19(49), 5548–5558 (2000)

    Article  Google Scholar 

  31. Teichmann, S.A., Park, J., Chothia, C.: Structural assignments to the mycoplasma genitalium proteins show extensive gene duplications and domain rearrangements (1998)

    Google Scholar 

  32. Snel, B., Bork, P., Huynen, M.: Genome evolution gene fusion versus gene fission. Trends Genet. 16, 9–11 (2002)

    Article  Google Scholar 

  33. Wuchty, S.: Scale-free behavior in protein domain networks. Mol. Biol. Evol. 18, 1694–1702 (2001)

    Google Scholar 

  34. Yona, G., Linial, N., Linial, M.: Protomap: Automatic classification of protein sequences, a hierarchy of protein families, and local maps of the protein space. Proteins: Structure, Function and Genetics 37, 360–378 (1999)

    Article  Google Scholar 

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Author information

Authors and Affiliations

  1. National Center for Biotechnology Information, US National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA

    Teresa Przytycka

  2. Program in Computation, Organizations and Society, Carnegie Mellon University,  

    George Davis

  3. Department of Biological Sciences, Carnegie Mellon University,  

    Nan Song & Dannie Durand

  4. Computer Science Department, Carnegie Mellon University,  

    Dannie Durand

Authors
  1. Teresa Przytycka
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  2. George Davis
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  3. Nan Song
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  4. Dannie Durand
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Editor information

Editors and Affiliations

  1. Human Genome Center, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, 108-8639, Minato-ku, Tokyo, Japan

    Satoru Miyano

  2. Broad Institute of MIT and Harvard, 320 Charles Street, 02141-2023, Cambridge, MA, USA

    Jill Mesirov

  3. Computational Genomics Laboratory, Department of Bioengineering, Boston University, 44 Cummington St., 02215, Boston, MA, USA

    Simon Kasif

  4. Center for Molecular Biology and Computer Sciecne Department, Brown University, 115 Waterman St., 02912, Providence, RI, USA

    Sorin Istrail

  5. University of California, San Diego, USA

    Pavel A. Pevzner

  6. Department of Molecular and Computational Biology, University of Southern California, 1050 Childs Way, 90089-2910, Los Angeles, CA, USA

    Michael Waterman

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© 2005 Springer-Verlag Berlin Heidelberg

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Przytycka, T., Davis, G., Song, N., Durand, D. (2005). Graph Theoretical Insights into Evolution of Multidomain Proteins. In: Miyano, S., Mesirov, J., Kasif, S., Istrail, S., Pevzner, P.A., Waterman, M. (eds) Research in Computational Molecular Biology. RECOMB 2005. Lecture Notes in Computer Science(), vol 3500. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11415770_24

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  • DOI: https://doi.org/10.1007/11415770_24

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-25866-7

  • Online ISBN: 978-3-540-31950-4

  • eBook Packages: Computer ScienceComputer Science (R0)

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