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Volumn 439, Issue 1-2, 2009, Pages 11-16

Multifunctionality dominantly determines the rate of human housekeeping and tissue specific interacting protein evolution

Author keywords

Connectivity; Evolutionary rate; Multi interface protein; Multifunctionality; Protein protein interaction network; Single interface proteins

Indexed keywords

AMINO ACID SEQUENCE; ARTICLE; CONTROLLED STUDY; GENE EXPRESSION; HOUSEKEEPING GENE; HUMAN; MOLECULAR EVOLUTION; MOUSE; NONHUMAN; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN EXPRESSION; PROTEIN FUNCTION; PROTEIN PROTEIN INTERACTION; TISSUE SPECIFICITY;

EID: 67349114852     PISSN: 03781119     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.gene.2009.03.005     Document Type: Article
Times cited : (25)

References (53)
  • 1
    • 0041817645 scopus 로고    scopus 로고
    • Translational selection and yeast proteome evolution
    • Akashi H. Translational selection and yeast proteome evolution. Genetics 164 (2003) 1291-1303
    • (2003) Genetics , vol.164 , pp. 1291-1303
    • Akashi, H.1
  • 3
    • 9144252016 scopus 로고    scopus 로고
    • The Gene Ontology Annotation (GOA) Database: sharing knowledge in Uniprot with Gene Ontology
    • Camon E., Magrane M., Barrell D., et al. The Gene Ontology Annotation (GOA) Database: sharing knowledge in Uniprot with Gene Ontology. Nucleic Acids Res. 1 32 (2004) D262-D266
    • (2004) Nucleic Acids Res. , vol.1 , Issue.32
    • Camon, E.1    Magrane, M.2    Barrell, D.3
  • 4
    • 0242380296 scopus 로고    scopus 로고
    • Conservation, relocation and duplication in genome evolution
    • Castillo-Davis C.I., and Hartl D.L. Conservation, relocation and duplication in genome evolution. Trends Genet. 19 (2003) 593-597
    • (2003) Trends Genet. , vol.19 , pp. 593-597
    • Castillo-Davis, C.I.1    Hartl, D.L.2
  • 5
    • 30744441602 scopus 로고    scopus 로고
    • A single determinant dominates the rate of Yeast protein evolution
    • Drummond D.A., Raval A., and Wilke C.O. A single determinant dominates the rate of Yeast protein evolution. Mol. Biol. Evol. 23 (2006) 327-337
    • (2006) Mol. Biol. Evol. , vol.23 , pp. 327-337
    • Drummond, D.A.1    Raval, A.2    Wilke, C.O.3
  • 6
    • 0033977618 scopus 로고    scopus 로고
    • Determinants of substitution rates in mammalian genes: expression pattern affects selection intensity but not mutation rate
    • Duret L., and Mouchiroud D. Determinants of substitution rates in mammalian genes: expression pattern affects selection intensity but not mutation rate. Mol. Biol. Evol. 17 (2000) 68-74
    • (2000) Mol. Biol. Evol. , vol.17 , pp. 68-74
    • Duret, L.1    Mouchiroud, D.2
  • 7
    • 0033551151 scopus 로고    scopus 로고
    • Expression pattern and, surprisingly, gene length shape codon usage in Caenorhabditis, Drosophila, and Arabidopsis
    • Duret L., and Mouchiroud D. Expression pattern and, surprisingly, gene length shape codon usage in Caenorhabditis, Drosophila, and Arabidopsis. Proc. Natl. Acad. 96 8 (1999) 4482-4487
    • (1999) Proc. Natl. Acad. , vol.96 , Issue.8 , pp. 4482-4487
    • Duret, L.1    Mouchiroud, D.2
  • 8
    • 16844363315 scopus 로고    scopus 로고
    • Modularity and evolutionary constraint on proteins
    • Fraser H.B. Modularity and evolutionary constraint on proteins. Nat. Genet. 37 (2005) 351-352
    • (2005) Nat. Genet. , vol.37 , pp. 351-352
    • Fraser, H.B.1
  • 9
    • 2942678187 scopus 로고    scopus 로고
    • Evolutionary rate depends on number of protein-protein interactions independently of gene expression level
    • Fraser H.B., and Hirsh A.E. Evolutionary rate depends on number of protein-protein interactions independently of gene expression level. BMC Evol. Biol. 4 (2004) 13
    • (2004) BMC Evol. Biol. , vol.4 , pp. 13
    • Fraser, H.B.1    Hirsh, A.E.2
  • 11
    • 0242284421 scopus 로고    scopus 로고
    • A simple dependence between protein evolution rate and the number of protein-protein interactions
    • Fraser H.B., Wall D.P., and Hirsh A.E. A simple dependence between protein evolution rate and the number of protein-protein interactions. BMC Evol. Biol. 3 (2003) 11
    • (2003) BMC Evol. Biol. , vol.3 , pp. 11
    • Fraser, H.B.1    Wall, D.P.2    Hirsh, A.E.3
  • 12
    • 16344381521 scopus 로고    scopus 로고
    • Comparative genomics of centrality and essentiality in three eukaryotic protein interaction networks
    • Hahn M.W., and Kern A.D. Comparative genomics of centrality and essentiality in three eukaryotic protein interaction networks. Mol. Biol. Evol. 22 (2005) 803-806
    • (2005) Mol. Biol. Evol. , vol.22 , pp. 803-806
    • Hahn, M.W.1    Kern, A.D.2
  • 13
    • 0029888297 scopus 로고    scopus 로고
    • Strong evolutionary conservation of broadly expressed protein isoforms in the troponin I gene family and other vertebrate gene families
    • Hastings K.E. Strong evolutionary conservation of broadly expressed protein isoforms in the troponin I gene family and other vertebrate gene families. J. Mol. Evol. 42 (1996) 631-640
    • (1996) J. Mol. Evol. , vol.42 , pp. 631-640
    • Hastings, K.E.1
  • 14
    • 33747817940 scopus 로고    scopus 로고
    • Toward a molecular understanding of pleiotropy
    • He X., and Zhang J. Toward a molecular understanding of pleiotropy. Genetics 173 (2006) 1885-1891
    • (2006) Genetics , vol.173 , pp. 1885-1891
    • He, X.1    Zhang, J.2
  • 15
    • 33745712594 scopus 로고    scopus 로고
    • Why do hubs tend to be essential in protein networks?
    • He X., and Zhang J. Why do hubs tend to be essential in protein networks?. PloS Genet. 2 (2006) e88
    • (2006) PloS Genet. , vol.2
    • He, X.1    Zhang, J.2
  • 16
    • 0035963414 scopus 로고    scopus 로고
    • Protein dispensability and rate of evolution
    • Hirsh A.E., and Fraser H.B. Protein dispensability and rate of evolution. Nature 411 (2001) 1046-1049
    • (2001) Nature , vol.411 , pp. 1046-1049
    • Hirsh, A.E.1    Fraser, H.B.2
  • 17
    • 37549002450 scopus 로고    scopus 로고
    • Identification of transient hub proteins and the possible structural basis for their multiple interactions
    • Higurashi M., Ishida T., and Kinoshita K. Identification of transient hub proteins and the possible structural basis for their multiple interactions. Protein Sci. 17 1 (2007) 72-78
    • (2007) Protein Sci. , vol.17 , Issue.1 , pp. 72-78
    • Higurashi, M.1    Ishida, T.2    Kinoshita, K.3
  • 18
    • 0033565762 scopus 로고    scopus 로고
    • Do essential genes evolve slowly?
    • Hurst L.D., and Smith N.G. Do essential genes evolve slowly?. Curr. Biol. 9 (1999) 747-750
    • (1999) Curr. Biol. , vol.9 , pp. 747-750
    • Hurst, L.D.1    Smith, N.G.2
  • 19
    • 0035799707 scopus 로고    scopus 로고
    • Lethality and centrality in protein networks
    • Jeong H., Mason S.P., Barabasi A.L., and Oltvai Z.N. Lethality and centrality in protein networks. Nature 411 (2001) 41-42
    • (2001) Nature , vol.411 , pp. 41-42
    • Jeong, H.1    Mason, S.P.2    Barabasi, A.L.3    Oltvai, Z.N.4
  • 20
    • 0036078078 scopus 로고    scopus 로고
    • Essential genes are more evolutionarily conserved than are nonessential genes in bacteria
    • Jordan I.K., Rogozin I.B., Wolf Y.I., and Koonin E.V. Essential genes are more evolutionarily conserved than are nonessential genes in bacteria. Genome Res. 12 (2002) 962-968
    • (2002) Genome Res. , vol.12 , pp. 962-968
    • Jordan, I.K.1    Rogozin, I.B.2    Wolf, Y.I.3    Koonin, E.V.4
  • 21
    • 0842291785 scopus 로고    scopus 로고
    • No simple dependence between protein evolution rate and the number of protein-protein interactions: only the most prolific interactors tend to evolve slowly
    • Jordan I.K., Wolf Y.I., and Koonin E.V. No simple dependence between protein evolution rate and the number of protein-protein interactions: only the most prolific interactors tend to evolve slowly. BMC Evol. Biol. 3 (2003) 1
    • (2003) BMC Evol. Biol. , vol.3 , pp. 1
    • Jordan, I.K.1    Wolf, Y.I.2    Koonin, E.V.3
  • 22
    • 57049156519 scopus 로고    scopus 로고
    • Exploring the evolutionary rate differences of party hub and date hub proteins in Saccharomyces cerevisiae protein-protein interaction network
    • Kahali B., Ahmad S., and Ghosh T.C. Exploring the evolutionary rate differences of party hub and date hub proteins in Saccharomyces cerevisiae protein-protein interaction network. Gene 429 1-2 (2009) 18-22
    • (2009) Gene , vol.429 , Issue.1-2 , pp. 18-22
    • Kahali, B.1    Ahmad, S.2    Ghosh, T.C.3
  • 23
    • 33845875196 scopus 로고    scopus 로고
    • Relating three-dimensional structures to protein networks provides evolutionary insights
    • Kim P.M., Lu L.J., Xia Y., and Gerstein M.B. Relating three-dimensional structures to protein networks provides evolutionary insights. Science 314 (2006) 1938-1941
    • (2006) Science , vol.314 , pp. 1938-1941
    • Kim, P.M.1    Lu, L.J.2    Xia, Y.3    Gerstein, M.B.4
  • 24
    • 41149119083 scopus 로고    scopus 로고
    • The role of disorder in interaction networks: a structural analysis
    • Kim P.M., Sboner A., Xia Y., and Gerstein M. The role of disorder in interaction networks: a structural analysis. Mol. Syst. Biol. 4 (2008) 179
    • (2008) Mol. Syst. Biol. , vol.4 , pp. 179
    • Kim, P.M.1    Sboner, A.2    Xia, Y.3    Gerstein, M.4
  • 25
    • 13444291526 scopus 로고    scopus 로고
    • Codon bias as a factor in regulating expression via translation rate in the human genome
    • Lavner Y., and Kotlar D. Codon bias as a factor in regulating expression via translation rate in the human genome. Gene 345 1 (2005) 127-138
    • (2005) Gene , vol.345 , Issue.1 , pp. 127-138
    • Lavner, Y.1    Kotlar, D.2
  • 26
    • 33646882591 scopus 로고    scopus 로고
    • Low rates of expression profile divergence in highly expressed genes and tissue-specific genes during mammalian evolution
    • Liao B.Y., and Zhang J. Low rates of expression profile divergence in highly expressed genes and tissue-specific genes during mammalian evolution. Mol. Biol. Evol. 23 (2006) 1119-1128
    • (2006) Mol. Biol. Evol. , vol.23 , pp. 1119-1128
    • Liao, B.Y.1    Zhang, J.2
  • 27
    • 33749579409 scopus 로고    scopus 로고
    • Impacts of gene essentiality, expression pattern, and gene compactness on the evolutionary rate of mammalian proteins
    • Liao B.Y., Scott N.M., and Zhang J. Impacts of gene essentiality, expression pattern, and gene compactness on the evolutionary rate of mammalian proteins. Mol. Biol. Evol. 11 (2006) 2072-2080
    • (2006) Mol. Biol. Evol. , vol.11 , pp. 2072-2080
    • Liao, B.Y.1    Scott, N.M.2    Zhang, J.3
  • 28
    • 33644909094 scopus 로고    scopus 로고
    • The evolutionary rate of a protein is influenced by features of the interacting partners
    • Makino T., and Gojobori T. The evolutionary rate of a protein is influenced by features of the interacting partners. Mol. Biol. Evol. 23 (2006) 784-789
    • (2006) Mol. Biol. Evol. , vol.23 , pp. 784-789
    • Makino, T.1    Gojobori, T.2
  • 29
    • 33947419351 scopus 로고    scopus 로고
    • An evaluation of human protein-protein interaction data in the public domain
    • Mathivanan S., et al. An evaluation of human protein-protein interaction data in the public domain. BMC Bioinform. 18 7 Suppl 5 (2006) S19
    • (2006) BMC Bioinform. , vol.18 , Issue.7 SUPPL. 5
    • Mathivanan, S.1
  • 30
    • 33644877439 scopus 로고    scopus 로고
    • Human protein reference database-2006 update
    • Mishra G.R., et al. Human protein reference database-2006 update. Nucleic Acids Res. 1 34 (2006) D411-D414
    • (2006) Nucleic Acids Res. , vol.1 , Issue.34
    • Mishra, G.R.1
  • 31
    • 33845790070 scopus 로고    scopus 로고
    • Correlation of mRNA expression and protein abundance affected by multiple sequence features related to translational efficiency in Desulfovibrio vulgaris: a quantitative analysis
    • Nie L., Wu G., and Zhang W. Correlation of mRNA expression and protein abundance affected by multiple sequence features related to translational efficiency in Desulfovibrio vulgaris: a quantitative analysis. Genetics 174 (2006) 2229-2243
    • (2006) Genetics , vol.174 , pp. 2229-2243
    • Nie, L.1    Wu, G.2    Zhang, W.3
  • 32
    • 0036737630 scopus 로고    scopus 로고
    • Impact of the presence of paralogs on sequence divergence in a set of mouse-human orthologs
    • Nembaware V., Crum K., Kelso J., and Seoighe C. Impact of the presence of paralogs on sequence divergence in a set of mouse-human orthologs. Genome Res. 12 (2002) 1370-1376
    • (2002) Genome Res. , vol.12 , pp. 1370-1376
    • Nembaware, V.1    Crum, K.2    Kelso, J.3    Seoighe, C.4
  • 33
    • 0036667702 scopus 로고    scopus 로고
    • Accounting for Background Nucleotide Composition When Measuring Codon Usage Bias
    • Novembre J.A. Accounting for Background Nucleotide Composition When Measuring Codon Usage Bias. Mol. Biol. Evol. 19 8 (2002) 1390-1394
    • (2002) Mol. Biol. Evol. , vol.19 , Issue.8 , pp. 1390-1394
    • Novembre, J.A.1
  • 34
    • 13144257707 scopus 로고    scopus 로고
    • The genetic theory of adaptation: a brief history
    • Orr H.A. The genetic theory of adaptation: a brief history. Nat. Rev., Genet. 6 (2005) 119-127
    • (2005) Nat. Rev., Genet. , vol.6 , pp. 119-127
    • Orr, H.A.1
  • 35
    • 0035207792 scopus 로고    scopus 로고
    • Does the recombination rate affect the efficiency of purifying selection? The yeast genome provides a partial answer
    • Pal C., Papp B., and Hurst L.D. Does the recombination rate affect the efficiency of purifying selection? The yeast genome provides a partial answer. Mol. Biol. Evol. 18 (2001) 2323-2326
    • (2001) Mol. Biol. Evol. , vol.18 , pp. 2323-2326
    • Pal, C.1    Papp, B.2    Hurst, L.D.3
  • 36
    • 33646182934 scopus 로고    scopus 로고
    • An integrated view of protein evolution
    • Pal C., Papp B., and Lercher M.J. An integrated view of protein evolution. Nat. Rev., Genet. 7 (2006) 337-348
    • (2006) Nat. Rev., Genet. , vol.7 , pp. 337-348
    • Pal, C.1    Papp, B.2    Lercher, M.J.3
  • 37
    • 4344647504 scopus 로고    scopus 로고
    • Tissue-specific codon usage and the expression of human genes
    • Plotkin J.B., Robins H., and Levine A.J. Tissue-specific codon usage and the expression of human genes. Proc. Natl. Acad. 101 (2004) 12588-12591
    • (2004) Proc. Natl. Acad. , vol.101 , pp. 12588-12591
    • Plotkin, J.B.1    Robins, H.2    Levine, A.J.3
  • 38
    • 28944434076 scopus 로고    scopus 로고
    • Protein function, connectivity and duplicability in yeast
    • Prachumwat A., and Li W.H. Protein function, connectivity and duplicability in yeast. Mol. Biol. Evol. 23 1 (2006) 30-39
    • (2006) Mol. Biol. Evol. , vol.23 , Issue.1 , pp. 30-39
    • Prachumwat, A.1    Li, W.H.2
  • 40
    • 1242284655 scopus 로고    scopus 로고
    • An analysis of determinants of amino acids substitution rates in bacterial proteins
    • Rocha E.P., and Danchin A. An analysis of determinants of amino acids substitution rates in bacterial proteins. Mol. Biol. Evol. 21 (2004) 108-116
    • (2004) Mol. Biol. Evol. , vol.21 , pp. 108-116
    • Rocha, E.P.1    Danchin, A.2
  • 41
    • 33644907774 scopus 로고    scopus 로고
    • The effect of multifunctionality on the rate of evolution in yeast
    • Salathe M., Ackermann M., and Bonhoeffer S. The effect of multifunctionality on the rate of evolution in yeast. Mol. Biol. Evol. 23 (2006) 721-722
    • (2006) Mol. Biol. Evol. , vol.23 , pp. 721-722
    • Salathe, M.1    Ackermann, M.2    Bonhoeffer, S.3
  • 42
    • 33244484877 scopus 로고    scopus 로고
    • No Evidence for Tissue-Specific Adaptation of Synonymous Codon Usage in Humans
    • Semon M., Lobry J.R., and Duret L. No Evidence for Tissue-Specific Adaptation of Synonymous Codon Usage in Humans. Mol. Biol. Evol. 23 (2006) 523-529
    • (2006) Mol. Biol. Evol. , vol.23 , pp. 523-529
    • Semon, M.1    Lobry, J.R.2    Duret, L.3
  • 43
    • 11144358198 scopus 로고    scopus 로고
    • A gene atlas of the mouse and human protein-encoding transcriptomes
    • Su A.I., et al. A gene atlas of the mouse and human protein-encoding transcriptomes. Proc. Natl. Acad. Sci. U. S. A. 101 (2004) 6062-6067
    • (2004) Proc. Natl. Acad. Sci. U. S. A. , vol.101 , pp. 6062-6067
    • Su, A.I.1
  • 44
    • 5044252972 scopus 로고    scopus 로고
    • Gene expression intensity shapes evolutionary rates of the proteins encoded by the vertebrate genome
    • Subramanian S., and Kumar S. Gene expression intensity shapes evolutionary rates of the proteins encoded by the vertebrate genome. Genetics 168 (2004) 373-381
    • (2004) Genetics , vol.168 , pp. 373-381
    • Subramanian, S.1    Kumar, S.2
  • 45
    • 17244367886 scopus 로고    scopus 로고
    • Functional genomic analysis of the rates of protein evolution
    • Wall D.P., et al. Functional genomic analysis of the rates of protein evolution. Proc. Natl. Acad. Sci. U. S. A. 102 (2005) 5483-5488
    • (2005) Proc. Natl. Acad. Sci. U. S. A. , vol.102 , pp. 5483-5488
    • Wall, D.P.1
  • 46
    • 0347766006 scopus 로고    scopus 로고
    • Elevated rates of protein secretion, evolution, and disease among tissue-specific genes
    • Winter E.E., Goodstadt L., and Ponting C.P. Elevated rates of protein secretion, evolution, and disease among tissue-specific genes. Genome Res. 14 (2004) 54-61
    • (2004) Genome Res. , vol.14 , pp. 54-61
    • Winter, E.E.1    Goodstadt, L.2    Ponting, C.P.3
  • 47
    • 77149167227 scopus 로고    scopus 로고
    • Alternative isoforms regulation in human tissue transcriptomes
    • 10.1038
    • Wang E.T., et al. Alternative isoforms regulation in human tissue transcriptomes. Nature (2008) 456 10.1038
    • (2008) Nature , pp. 456
    • Wang, E.T.1
  • 48
    • 0025318864 scopus 로고
    • The 'effective number of codons' used in a gene
    • Wright F. The 'effective number of codons' used in a gene. Gene 87 (1990) 23-29
    • (1990) Gene , vol.87 , pp. 23-29
    • Wright, F.1
  • 49
    • 20144376345 scopus 로고    scopus 로고
    • Genome-wide midrange transcription profiles reveal expression level relationships in human tissue specification
    • Yanai I.H., et al. Genome-wide midrange transcription profiles reveal expression level relationships in human tissue specification. Bioinformatics 21 (2005) 650-659
    • (2005) Bioinformatics , vol.21 , pp. 650-659
    • Yanai, I.H.1
  • 50
    • 0038708556 scopus 로고    scopus 로고
    • Rate of protein evolution versus fitness effect of gene deletion
    • Yang J., Gu Z., and Li W.H. Rate of protein evolution versus fitness effect of gene deletion. Mol. Biol. Evol. 20 (2003) 772-774
    • (2003) Mol. Biol. Evol. , vol.20 , pp. 772-774
    • Yang, J.1    Gu, Z.2    Li, W.H.3
  • 51
    • 0033979433 scopus 로고    scopus 로고
    • Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models
    • Yang Z., and Nielsen R. Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models. Mol. Biol. Evol. 17 (2000) 32-39
    • (2000) Mol. Biol. Evol. , vol.17 , pp. 32-39
    • Yang, Z.1    Nielsen, R.2
  • 52
    • 16344369543 scopus 로고    scopus 로고
    • Significant impact of protein dispensability on the instantaneous rate of protein evolution
    • Zhang J., and He X. Significant impact of protein dispensability on the instantaneous rate of protein evolution. Mol. Biol. Evol. 22 (2005) 1147-1155
    • (2005) Mol. Biol. Evol. , vol.22 , pp. 1147-1155
    • Zhang, J.1    He, X.2
  • 53
    • 1542286776 scopus 로고    scopus 로고
    • Mammalian housekeeping genes evolve more slowly than tissue-specific genes
    • Zhang L., and Li W.H. Mammalian housekeeping genes evolve more slowly than tissue-specific genes. Mol. Biol. Evol. 21 (2004) 236-239
    • (2004) Mol. Biol. Evol. , vol.21 , pp. 236-239
    • Zhang, L.1    Li, W.H.2


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