메뉴 건너뛰기




Volumn 277, Issue 1686, 2010, Pages 1403-1408

Systemic factors dominate mammal protein evolution

Author keywords

Cell integrity; Coevolution; Gene expression; Protein evolution

Indexed keywords

COEVOLUTION; CORRELATION; EVOLUTIONARY BIOLOGY; GENE EXPRESSION; MAMMAL; PROTEIN; TOXICITY;

EID: 77952261765     PISSN: 09628452     EISSN: 14712970     Source Type: Journal    
DOI: 10.1098/rspb.2009.1865     Document Type: Article
Times cited : (20)

References (31)
  • 1
    • 33750238153 scopus 로고    scopus 로고
    • Stratus not altocumulus: A new view of the yeast protein interaction network
    • doi:10.1371/ journal.pbio.0040317
    • Batada, N. N., Reguly, T., Breitkreutz, A., Boucher, L., Breitkreutz, B. J., Hurst, L. D. & Tyers, M. 2006 Stratus not altocumulus: a new view of the yeast protein interaction network. PLoS Biol. 4, e317. (doi:10.1371/ journal.pbio.0040317)
    • (2006) PLoS Biol. , vol.4
    • Batada, N.N.1    Reguly, T.2    Breitkreutz, A.3    Boucher, L.4    Breitkreutz, B.J.5    Hurst, L.D.6    Tyers, M.7
  • 3
    • 47549097539 scopus 로고    scopus 로고
    • Mistranslationinduced protein misfolding as a dominant constraint on coding-sequence evolution
    • doi:10. 1016/j.cell.2008.05.042
    • Drummond, D. A. & Wilke, C. O. 2008 Mistranslationinduced protein misfolding as a dominant constraint on coding-sequence evolution. Cell 134, 341-352. (doi:10. 1016/j.cell.2008.05.042)
    • (2008) Cell , vol.134 , pp. 341-352
    • Drummond, D.A.1    Wilke, C.O.2
  • 4
    • 30744441602 scopus 로고    scopus 로고
    • A single determinant dominates the rate of yeast protein evolution
    • DOI 10.1093/molbev/msj038
    • Drummond, D. A., Raval, A. & Wilke, C. O. 2006 A single determinant dominates the rate of yeast protein evolution. Mol Biol. Evol. 23, 327-337. (doi:10.1093/molbev/ msj038) (Pubitemid 43100047)
    • (2006) Molecular Biology and Evolution , vol.23 , Issue.2 , pp. 327-337
    • Drummond, D.A.1    Raval, A.2    Wilke, C.O.3
  • 5
    • 0038692119 scopus 로고    scopus 로고
    • Human housekeeping genes are compact
    • DOI 10.1016/S0168-9525(03)00140-9
    • Eisenberg, E. & Levanon, E. Y. 2003 Human housekeeping genes are compact. Trends Genet. 19, 362-365. (doi:10. 1016/S0168-9525(03)00140-9) (Pubitemid 36794535)
    • (2003) Trends in Genetics , vol.19 , Issue.7 , pp. 362-365
    • Eisenberg, E.1    Levanon, E.Y.2
  • 6
    • 0037177560 scopus 로고    scopus 로고
    • Evolutionary rate in the protein interaction network
    • DOI 10.1126/science.1068696
    • Fraser, H. B., Hirsh, A. E., Steinmetz, L. M., Scharfe, C. & Feldman, M. W. 2002 Evolutionary rate in the protein interaction network. Science 296, 750-752. (doi:10.1126/science.1068696) (Pubitemid 34442006)
    • (2002) Science , vol.296 , Issue.5568 , pp. 750-752
    • Fraser, H.B.1    Hirsh, A.E.2    Steinmetz, L.M.3    Scharfe, C.4    Feldman, M.W.5
  • 7
    • 2942695714 scopus 로고    scopus 로고
    • Coevolution of gene expression among interacting proteins
    • doi:10.1073/pnas.0402591101
    • Fraser, H. B., Hirsh, A. E., Wall, D. P. & Eisen, M. B. 2004 Coevolution of gene expression among interacting proteins. Proc. Natl Acad. Sci USA 101, 9033-9038. (doi:10.1073/pnas.0402591101)
    • (2004) Proc. Natl Acad. Sci USA , vol.101 , pp. 9033-9038
    • Fraser, H.B.1    Hirsh, A.E.2    Wall, D.P.3    Eisen, M.B.4
  • 8
    • 34249945479 scopus 로고    scopus 로고
    • Specificity in protein interactions and its relationship with sequence diversity and coevolution
    • doi:10.1073/pnas. 0609962104
    • Hakes, L., Lovell, S. C., Oliver, S. G. & Robertson, D. L. 2007 Specificity in protein interactions and its relationship with sequence diversity and coevolution. Proc. Natl Acad. Sci USA 104, 7999-8004. (doi:10.1073/pnas. 0609962104)
    • (2007) Proc. Natl Acad. Sci USA , vol.104 , pp. 7999-8004
    • Hakes, L.1    Lovell, S.C.2    Oliver, S.G.3    Robertson, D.L.4
  • 9
    • 58149193234 scopus 로고    scopus 로고
    • STRING 8-a global view on proteins and their functional interactions in 630 organisms
    • doi:10.1093/nar/ gkn760
    • Jensen, L. J. et al. 2009 STRING 8-a global view on proteins and their functional interactions in 630 organisms. Nucleic Acids Res. 37, D412-D416. (doi:10.1093/nar/ gkn760)
    • (2009) Nucleic Acids Res. , vol.37
    • Jensen, L.J.1
  • 10
    • 6344241652 scopus 로고    scopus 로고
    • Conservation and coevolution in the scale-free human gene coexpression network
    • DOI 10.1093/molbev/msh222
    • Jordan, I. K., Marino-Ramirez, L., Wolf, Y. I. & Koonin, E. V. 2004 Conservation and coevolution in the scalefree human gene coexpression network. Mol. Biol. Evol. 21, 2058-2070. (doi:10.1093/molbev/msh222) (Pubitemid 39391982)
    • (2004) Molecular Biology and Evolution , vol.21 , Issue.11 , pp. 2058-2070
    • Jordan, I.K.1    Marino-Ramirez, L.2    Wolf, Y.I.3    Koonin, E.V.4
  • 11
    • 33749563056 scopus 로고    scopus 로고
    • Protein evolution is faster outside the cell
    • DOI 10.1093/molbev/msl081
    • Julenius, K. & Pedersen, A. G. 2006 Protein evolution is faster outside the cell. Mol Biol. Evol. 23, 2039-2048. (doi: 10.109 3/molbev/ms1081 ) (Pubitemid 44536813)
    • (2006) Molecular Biology and Evolution , vol.23 , Issue.11 , pp. 2039-2048
    • Julenius, K.1    Pedersen, A.G.2
  • 12
    • 33846675265 scopus 로고    scopus 로고
    • A genome-wide survey of changes in protein evolutionary rates across four closely related species of Saccharomyces sensu stricto group. BMC
    • Kawahara, Y. & Imanishi, T. 2007 A genome-wide survey of changes in protein evolutionary rates across four closely related species of Saccharomyces sensu stricto group. BMC Evol. Biol. 7, 9.
    • (2007) Evol. Biol. , vol.7 , pp. 9
    • Kawahara, Y.1    Imanishi, T.2
  • 13
    • 33748980210 scopus 로고    scopus 로고
    • Evolutionary systems biology: Links between gene evolution and function
    • doi:10.1016/j.copbio.2006.08.003
    • Koonin, E. V. & Wolf, Y. I. 2006 Evolutionary systems biology: links between gene evolution and function. Curr. Opin. Biotechnol. 17, 481-487. (doi:10.1016/j.copbio.2006.08.003)
    • (2006) Curr. Opin. Biotechnol. , vol.17 , pp. 481-487
    • Koonin, E.V.1    Wolf, Y.I.2
  • 14
    • 16444381885 scopus 로고    scopus 로고
    • A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes
    • doi:10.1186/gb-2004-52-r7
    • Koonin, E. V. et al. 2004 A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes. Genome Biol. 5, R7. (doi:10.1186/gb-2004-52-r7)
    • (2004) Genome Biol. , vol.5
    • Koonin, E.V.1
  • 15
    • 36448991500 scopus 로고    scopus 로고
    • doi: 10.1093/ bioinformatics/btm404 version 2.0. Bioinformatics
    • Larkin, M. A. et al. 2007 CLUSTAL Wand CLUSTAL X version 2.0. Bioinformatics 23, 2947-2948. (doi: 10.1093/ bioinformatics/btm404)
    • (2007) CLUSTAL Wand CLUSTAL X , vol.23 , pp. 2947-2948
    • Larkin, M.A.1
  • 16
    • 33644909094 scopus 로고    scopus 로고
    • The evolutionary rate of a protein is influenced by features of the interacting partners
    • doi: 10.1093/ molbev/msj090
    • Makino, T. & Gojobori, T 2006 The evolutionary rate of a protein is influenced by features of the interacting partners. Mol. Biol. Evol. 23, 784-789. (doi: 10.1093/ molbev/msj090)
    • (2006) Mol. Biol. Evol. , vol.23 , pp. 784-789
    • Makino, T.1    Gojobori, T.2
  • 17
    • 0033990061 scopus 로고    scopus 로고
    • Flexible similarity searching with the FASTA3 program package
    • (eds S. Misener & S. A. Krawetz), Totowa, NJ: Humana Press
    • Pearson, W. R. 1999 Flexible similarity searching with the FASTA3 program package. In Bioinformatics methods and protocols (eds S. Misener & S. A. Krawetz), pp. 185-219. Totowa, NJ: Humana Press.
    • (1999) Bioinformatics Methods and Protocols , pp. 185-219
    • Pearson, W.R.1
  • 18
    • 47549108636 scopus 로고    scopus 로고
    • Costly mistakes: Translational infidelity and protein homeostasis
    • doi:10.1016/j.cell.2008.07.005
    • Powers, E. T. & Balch, W. E. 2008 Costly mistakes: translational infidelity and protein homeostasis. Cell 134, 204-206. (doi:10.1016/j.cell.2008. 07.005)
    • (2008) Cell , vol.134 , pp. 204-206
    • Powers, E.T.1    Balch, W.E.2
  • 19
    • 58149200954 scopus 로고    scopus 로고
    • Database resources of the National Center for Biotechnology Information
    • doi:10.1093/nar/gkn741
    • Sayers, E. W. et al. 2009 Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 37, D5-D15. (doi:10.1093/nar/ gkn741)
    • (2009) Nucleic Acids Res. , vol.37
    • Sayers, E.W.1
  • 20
    • 23644445492 scopus 로고    scopus 로고
    • Fixation of conserved sequences shapes human intron size and influences transposon-insertion dynamics
    • DOI 10.1016/j.tig.2005.06.009, PII S0168952505001721
    • Sironi, M., Menozzi, G., Comi, G. P., Bresolin, N., Cagliani, R. & Pozzoli, U. 2005a Fixation of conserved sequences shapes human intron size and influences transposon-insertion dynamics. Trends Genet. 21, 484-488. (doi:10.1016/j.tig.2005.06.009) (Pubitemid 41132580)
    • (2005) Trends in Genetics , vol.21 , Issue.9 , pp. 484-488
    • Sironi, M.1    Menozzi, G.2    Comi, G.P.3    Bresolin, N.4    Cagliani, R.5    Pozzoli, U.6
  • 21
    • 24144466902 scopus 로고    scopus 로고
    • Analysis of intronic conserved elements indicates that functional complexity might represent a major source of negative selection on non-coding sequences
    • DOI 10.1093/hmg/ddi257
    • Sironi, M., Menozzi, G., Comi, G. P., Cagliani, R., Bresolin, N. & Pozzoli, U. 2005 b Analysis of intronic conserved elements indicates that functional complexity might represent a major source of negative selection on non-coding sequences. Hum. Mol. Genet. 14, 2533-2546. (doi:10.1093/hmg/ddi257) (Pubitemid 41236066)
    • (2005) Human Molecular Genetics , vol.14 , Issue.17 , pp. 2533-2546
    • Sironi, M.1    Menozzi, G.2    Comi, G.P.3    Cagliani, R.4    Bresolin, N.5    Pozzoli, U.6
  • 22
    • 11144358198 scopus 로고    scopus 로고
    • A gene atlas of the mouse and human protein-encoding transcriptomes
    • doi:10.1073/pnas. 0400782101
    • Su, A. I. et al. 2004 A gene atlas of the mouse and human protein-encoding transcriptomes. Proc. Natl Acad. Sci. USA 101, 6062-6067. (doi:10.1073/pnas. 0400782101)
    • (2004) Proc. Natl Acad. Sci. USA , vol.101 , pp. 6062-6067
    • Su, A.I.1
  • 23
    • 36549027355 scopus 로고    scopus 로고
    • GSEA-P: A desktop application for gene set enrichment analysis
    • DOI 10.1093/bioinformatics/btm369
    • Subramanian, A., Kuehn, H., Gould, J., Tamayo, P. & Mesirov, J. P. 2007 GSEA-P: a desktop application for gene set enrichment analysis. Bioinformatics 23, 3251-3253. (doi: 10.1093/bioinformatics/btm369) (Pubitemid 350187532)
    • (2007) Bioinformatics , vol.23 , Issue.23 , pp. 3251-3253
    • Subramanian, A.1    Kuehn, H.2    Gould, J.3    Tamayo, P.4    Mesirov, J.P.5
  • 24
    • 0142092546 scopus 로고    scopus 로고
    • The signature of selection mediated by expression on human genes
    • doi:10.1101/gr. 641103
    • Urrutia, A. O. & Hurst, L. D. 2003 The signature of selection mediated by expression on human genes. Genome Res. 13, 2260-2264. (doi:10.1101/gr. 641103)
    • (2003) Genome Res. , vol.13 , pp. 2260-2264
    • Urrutia, A.O.1    Hurst, L.D.2
  • 25
    • 4744355710 scopus 로고    scopus 로고
    • Compactness of human housekeeping genes: Selection for economy or genomic design?
    • doi:10.1016/j.tig.2004. 03.006
    • Vinogradov, A. E. 2004 Compactness of human housekeeping genes: selection for economy or genomic design? Trends Genet. 20, 248-253. (doi:10.1016/j.tig. 2004. 03.006)
    • (2004) Trends Genet. , vol.20 , pp. 248-253
    • Vinogradov, A.E.1
  • 26
    • 33644652318 scopus 로고    scopus 로고
    • 'Genome design' model: Evidence from conserved intronic sequence in human-mouse comparison
    • doi:10.1101/gr. 4318206
    • Vinogradov, A. E. 2006 'Genome design' model: evidence from conserved intronic sequence in human-mouse comparison. Genome Res. 16, 347-354. (doi:10.1101/gr. 4318206)
    • (2006) Genome Res. , vol.16 , pp. 347-354
    • Vinogradov, A.E.1
  • 27
    • 61349126118 scopus 로고    scopus 로고
    • Global versus local centrality in evolution of yeast protein network
    • doi: 10.1007/S00239-008-9185-2
    • Vinogradov, A. E. 2009 Global versus local centrality in evolution of yeast protein network. J. Mol. Evol. 68, 192-196. (doi: 10.1007/S00239-008-9185- 2)
    • (2009) J. Mol. Evol. , vol.68 , pp. 192-196
    • Vinogradov, A.E.1
  • 28
    • 0043123111 scopus 로고    scopus 로고
    • RevTrans: Multiple alignment of coding DNA from aligned amino acid sequences
    • DOI 10.1093/nar/gkg609
    • Wernersson, R. & Pedersen, A. G. 2003 RevTrans: multiple alignment of coding DNA from aligned amino acid sequences. Nucleic Acids Res. 31, 3537-3539. (doi: 10. 1093/nar/gkg609) (Pubitemid 37442193)
    • (2003) Nucleic Acids Research , vol.31 , Issue.13 , pp. 3537-3539
    • Wernersson, R.1    Pedersen, A.G.2
  • 29
    • 33745744354 scopus 로고    scopus 로고
    • Coping with the quantitative genomics 'elephant': The correlation between the gene dispensability and evolution rate
    • doi: 10. 1016/j.tig.2006.04.009
    • Wolf, Y. I. 2006 Coping with the quantitative genomics 'elephant': The correlation between the gene dispensability and evolution rate. Trends Genet. 22, 354-357. (doi: 10. 1016/j.tig.2006.04.009)
    • (2006) Trends Genet. , vol.22 , pp. 354-357
    • Wolf, Y.I.1
  • 30
    • 54949151498 scopus 로고    scopus 로고
    • Comparable contributions of structural-functional constraints and expression level to the rate of protein sequence evolution
    • doi:10.1186/1745-6150-3-40
    • Wolf, M. Y., Wolf, Y. I. & Koonin, E. V. 2008 Comparable contributions of structural-functional constraints and expression level to the rate of protein sequence evolution. Biol. Direct. 3, 40. (doi:10.1186/1745-6150- 3-40)
    • (2008) Biol. Direct. , vol.3 , pp. 40
    • Wolf, M.Y.1    Wolf, Y.I.2    Koonin, E.V.3
  • 31
    • 34547803197 scopus 로고    scopus 로고
    • PAML 4: Phylogenetic analysis by maximum likelihood
    • DOI 10.1093/molbev/msm088
    • Yang, Z. 2007 PAML 4: a program package for phylogenetic analysis likelihood. Mol. Biol. Evol. 24, 1586-1591. (doi:10.1093/molbev/msm088) (Pubitemid 47236688)
    • (2007) Molecular Biology and Evolution , vol.24 , Issue.8 , pp. 1586-1591
    • Yang, Z.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.