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Global Versus Local Centrality in Evolution of Yeast Protein Network

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Abstract

It is shown here that in the yeast protein interaction network the global centrality measure (betweenness) depends on the protein evolutionary age (i.e., on historic contingency) more weakly than the local centrality measure (degree). This phenomenon is not observed in mutational duplication-and-divergence models. The network domains responsible for this difference deal with DNA/RNA information processing, regulation, and cell cycle. A selection vector can operate in these domains, which integrates the network activity and thus compensates for the process of mutational divergence.

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References

  • Aravind L, Iyer LM, Koonin EV (2006) Comparative genomics and structural biology of the molecular innovations of eukaryotes. Curr Opin Struct Biol 16:409–419

    Article  PubMed  CAS  Google Scholar 

  • Batada NN, Reguly T, Breitkreutz A, Boucher L, Breitkreutz BJ, Hurst LD, Tyers M (2007) Still stratus not altocumulus: further evidence against the date/party hub distinction. PLoS Biol 5:e154

    Article  PubMed  Google Scholar 

  • Beltrao P, Serrano L (2007) Specificity and evolvability in eukaryotic protein interaction networks. PLoS Comput Biol 3:e25

    Article  Google Scholar 

  • Davids W, Zhang Z (2008) The impact of horizontal gene transfer in shaping operons and protein interaction networks—direct evidence of preferential attachment. BMC Evol Biol 8:23

    Article  PubMed  Google Scholar 

  • Dosztányi Z, Chen J, Dunker AK, Simon I, Tompa P (2006) Disorder and sequence repeats in hub proteins and their implications for network evolution. J Proteome Res 5:2985–2995

    Article  PubMed  Google Scholar 

  • D’Souza RM, Borgs C, Chayes JT, Berger N, Kleinberg RD (2007) Emergence of tempered preferential attachment from optimization. Proc Natl Acad Sci USA 104:6112–6117

    Article  PubMed  CAS  Google Scholar 

  • Gene Ontology Consortium (2008) The Gene Ontology project in 2008. Nucleic Acids Res 36:D440–D444

    Article  Google Scholar 

  • Hahn MW, Conant GC, Wagner A (2004) Molecular evolution in large genetic networks: does connectivity equal constraint? J Mol Evol 58:203–211

    Article  PubMed  CAS  Google Scholar 

  • Kim PM, Korbel JO, Gerstein MB (2007) Positive selection at the protein network periphery: evaluation in terms of structural constraints and cellular context. Proc Natl Acad Sci USA 104:20274–20279

    Article  PubMed  CAS  Google Scholar 

  • Koonin EV, Fedorova ND, Jackson JD, Jacobs AR, Krylov DM, Makarova KS, Mazumder R, Mekhedov SL, Nikolskaya AN, Rao BS, Rogozin IB, Smirnov S, Sorokin AV, Sverdlov AV, Vasudevan S, Wolf YI, Yin JJ, Natale DA (2004) A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes. Genome Biol 5:R7

    Article  PubMed  Google Scholar 

  • Maglott D, Ostell J, Pruitt KD, Tatusova T (2007) Entrez Gene: gene-centered information at NCBI. Nucleic Acids Res 35:D26–D31

    Article  PubMed  CAS  Google Scholar 

  • Pastor-Satorras R, Smith B, Sole RV (2003) Evolving protein interaction networks through gene duplication. J Theor Biol 222:199–210

    Article  PubMed  CAS  Google Scholar 

  • Rivera MC, Lake JA (2004) The ring of life provides evidence for a genome fusion origin of eukaryotes. Nature 431:152–155

    Article  PubMed  CAS  Google Scholar 

  • Storey JD, Tibshirani R (2003) Statistical significance for genomewide studies. Proc Natl Acad Sci USA 100:9440–9445

    Article  PubMed  CAS  Google Scholar 

  • Stumpf MP, Kelly WP, Thorne T, Wiuf C (2007) Evolution at the system level: the natural history of protein interaction networks. Trends Ecol Evol 22:366–373

    Article  PubMed  Google Scholar 

  • Tatusov RL, Fedorova ND, Jackson JD, Jacobs AR, Kiryutin B, Koonin EV, Krylov DM, Mazumder R, Mekhedov SL, Nikolskaya AN, Rao BS, Smirnov S, Sverdlov AV, Vasudevan S, Wolf YI, Yin JJ, Natale DA (2003) The COG database: an updated version includes eukaryotes. BMC Bioinformatics 4:41

    Article  PubMed  Google Scholar 

  • Vazquez A, Flammini A, Maritan A, Vespignani A (2003) Modeling of protein interaction networks. ComPlexUs 1:38–44

    Article  Google Scholar 

  • Vinogradov AE, Anatskaya OV (2007) Organismal complexity, cell differentiation and gene expression: human over mouse. Nucleic Acids Res 35:6350–6356

    Article  PubMed  CAS  Google Scholar 

  • von Mering C, Jensen LJ, Kuhn M, Chaffron S, Doerks T, Krüger B, Snel B, Bork P (2007) STRING 7—recent developments in the integration and prediction of protein interactions. Nucleic Acids Res 35:D358–D362

    Article  Google Scholar 

  • Wagner A (2003) How the global structure of protein interaction networks evolves. Proc Biol Sci 270:457–466

    Article  PubMed  CAS  Google Scholar 

  • Wang Z, Zhang J (2007) In search of the biological significance of modular structures in protein networks. PLoS Comput Biol 3:e107

    Article  PubMed  Google Scholar 

  • Wheeler DL, Barrett T, Benson DA, Bryant SH, Canese K, Chetvernin V, Church DM, DiCuccio M, Edgar R, Federhen S, Geer LY, Helmberg W, Kapustin Y, Kenton DL, Khovayko O, Lipman DJ, Madden TL, Maglott DR, Ostell J, Pruitt KD, Schuler GD, Schriml LM, Sequeira E, Sherry ST, Sirotkin K, Souvorov A, Starchenko G, Suzek TO, Tatusov R, Tatusova TA, Wagner L, Yaschenko E (2006) Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 34:D173–D180

    Article  PubMed  CAS  Google Scholar 

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Acknowledgments

I thank two anonymous reviewers for helpful comments. This work was supported by the Russian Foundation for Basic Research (RFBR) and by the Programme of the Russian Academy of Sciences ‘Molecular and Cellular Biology’ (MCB RAS).

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Correspondence to Alexander E. Vinogradov.

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Vinogradov, A.E. Global Versus Local Centrality in Evolution of Yeast Protein Network. J Mol Evol 68, 192–196 (2009). https://doi.org/10.1007/s00239-008-9185-2

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  • DOI: https://doi.org/10.1007/s00239-008-9185-2

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