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Volumn 336, Issue 4, 2004, Pages 871-887

Evolution of Protein Superfamilies and Bacterial Genome Size

Author keywords

Bacteria; Domain distribution; Genome size; Protein family; Three dimensional structure

Indexed keywords

PROTEOME;

EID: 1042298811     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2003.12.044     Document Type: Article
Times cited : (86)

References (54)
  • 1
    • 0037079014 scopus 로고    scopus 로고
    • The structure of the protein universe and genome evolution
    • Koonin E.V., Wolf Y.I., Karev G.P. The structure of the protein universe and genome evolution. Nature. 420:2002;218-223.
    • (2002) Nature , vol.420 , pp. 218-223
    • Koonin, E.V.1    Wolf, Y.I.2    Karev, G.P.3
  • 2
    • 0034799370 scopus 로고    scopus 로고
    • Whole genome plasticity in pathogenic bacteria
    • Dobrindt U., Hacker J. Whole genome plasticity in pathogenic bacteria. Curr. Opin. Microbiol. 4:2001;550-557.
    • (2001) Curr. Opin. Microbiol. , vol.4 , pp. 550-557
    • Dobrindt, U.1    Hacker, J.2
  • 3
    • 0035479142 scopus 로고    scopus 로고
    • Deletional bias and the evolution of bacterial genomes
    • Mira. A., Ochman, H., Moran, N.A. (2001). Deletional bias and the evolution of bacterial genomes. Trends Genet. 17, 589-596.
    • (2001) Trends Genet , vol.17 , pp. 589-596
    • Mira, A.1    Ochman, H.2    Moran, N.A.3
  • 4
    • 0037040394 scopus 로고    scopus 로고
    • Microbial minimalism: Genome reduction in bacterial pathogens
    • Moran N.A. Microbial minimalism: genome reduction in bacterial pathogens. Cell. 108:2002;583-586.
    • (2002) Cell , vol.108 , pp. 583-586
    • Moran, N.A.1
  • 5
    • 0034682335 scopus 로고    scopus 로고
    • Lateral gene transfer and the nature of bacterial innovation
    • Ochman H., Lawrence J.G., Groisman E.A. Lateral gene transfer and the nature of bacterial innovation. Nature. 405:2000;299-304.
    • (2000) Nature , vol.405 , pp. 299-304
    • Ochman, H.1    Lawrence, J.G.2    Groisman, E.A.3
  • 9
    • 0037414465 scopus 로고    scopus 로고
    • Exhaustive enumeration of protein domain families
    • Heger A., Holm L. Exhaustive enumeration of protein domain families. J. Mol. Biol. 328:2003;749-767.
    • (2003) J. Mol. Biol. , vol.328 , pp. 749-767
    • Heger, A.1    Holm, L.2
  • 11
    • 0036322695 scopus 로고    scopus 로고
    • Target space for structural genomics revisited
    • Liu J., Rost B. Target space for structural genomics revisited. Bioinformatics. 18:2002;922-933.
    • (2002) Bioinformatics , vol.18 , pp. 922-933
    • Liu, J.1    Rost, B.2
  • 16
    • 0033537993 scopus 로고    scopus 로고
    • GenTHREADER: An efficient and reliable protein fold recognition method for genomic sequences
    • Jones D. GenTHREADER: an efficient and reliable protein fold recognition method for genomic sequences. J. Mol. Biol. 287:1999;797-815.
    • (1999) J. Mol. Biol. , vol.287 , pp. 797-815
    • Jones, D.1
  • 17
    • 0036087169 scopus 로고    scopus 로고
    • SUPERFAMILY: HMMs representing all proteins of known structure. SCOP sequence searches, alignments and genome assignments
    • Gough J., Chothia C. SUPERFAMILY: HMMs representing all proteins of known structure. SCOP sequence searches, alignments and genome assignments. Nucl. Acids Res. 30:2002;268-272.
    • (2002) Nucl. Acids Res. , vol.30 , pp. 268-272
    • Gough, J.1    Chothia, C.2
  • 25
    • 0028961335 scopus 로고
    • SCOP: A structural classification of proteins database for the investigation of sequences and structures
    • Murzin A.G., Brenner S.E., Hubbard T., Chothia C. SCOP: a structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol. 247:1995;536-540.
    • (1995) J. Mol. Biol. , vol.247 , pp. 536-540
    • Murzin, A.G.1    Brenner, S.E.2    Hubbard, T.3    Chothia, C.4
  • 27
    • 0035816218 scopus 로고    scopus 로고
    • Domain combinations in archaeal, eubacterial and eukaryotic proteomes
    • Apic G., Gough J., Teichmann S.A. Domain combinations in archaeal, eubacterial and eukaryotic proteomes. J. Mol. Biol. 310:2001;311-325.
    • (2001) J. Mol. Biol. , vol.310 , pp. 311-325
    • Apic, G.1    Gough, J.2    Teichmann, S.A.3
  • 28
    • 0036568328 scopus 로고    scopus 로고
    • Structural genomics analysis: Characteristics of atypical, common, and horizontally transferred folds
    • Hegyi H., Lin J., Greenbaum D., Gerstein M. Structural genomics analysis: characteristics of atypical, common, and horizontally transferred folds. Proteins: Struct. Funct. Genet. 47:2002;126-141.
    • (2002) Proteins: Struct. Funct. Genet. , vol.47 , pp. 126-141
    • Hegyi, H.1    Lin, J.2    Greenbaum, D.3    Gerstein, M.4
  • 29
    • 0036295212 scopus 로고    scopus 로고
    • Classification and evolution of P-loop GTPases and related ATPases
    • Leipe D.D., Wolf Y.I., Koonin E.V., Aravind L. Classification and evolution of P-loop GTPases and related ATPases. J. Mol. Biol. 317:2002;41-72.
    • (2002) J. Mol. Biol. , vol.317 , pp. 41-72
    • Leipe, D.D.1    Wolf, Y.I.2    Koonin, E.V.3    Aravind, L.4
  • 30
    • 0035815113 scopus 로고    scopus 로고
    • Evolution of function in protein superfamilies, from a structural perspective
    • Todd A.E., Orengo C.A., Thornton J.M. Evolution of function in protein superfamilies, from a structural perspective. J. Mol. Biol. 307:2001;1113-1143.
    • (2001) J. Mol. Biol. , vol.307 , pp. 1113-1143
    • Todd, A.E.1    Orengo, C.A.2    Thornton, J.M.3
  • 31
    • 0037440734 scopus 로고    scopus 로고
    • Evolution of transcription factors and the gene regulatory network in Escherichia coli
    • Babu M.M., Teichmann S.A. Evolution of transcription factors and the gene regulatory network in Escherichia coli. Nucl. Acids Res. 31:2003;1234-1244.
    • (2003) Nucl. Acids Res. , vol.31 , pp. 1234-1244
    • Babu, M.M.1    Teichmann, S.A.2
  • 32
    • 0032034821 scopus 로고    scopus 로고
    • Signal transduction in bacteria: Molecular mechanisms of stimulus-response coupling
    • Goudreau P.N., Stock A.M. Signal transduction in bacteria: molecular mechanisms of stimulus-response coupling. Curr. Opin. Microbiol. 1:1998;160-169.
    • (1998) Curr. Opin. Microbiol. , vol.1 , pp. 160-169
    • Goudreau, P.N.1    Stock, A.M.2
  • 33
    • 0027256676 scopus 로고
    • Structural, functional, and evolutionary relationships among extracellular solute-binding receptors of bacteria
    • Tam R., Saier M.H. Jr. Structural, functional, and evolutionary relationships among extracellular solute-binding receptors of bacteria. Microbiol. Rev. 57:1993;320-346.
    • (1993) Microbiol. Rev. , vol.57 , pp. 320-346
    • Tam, R.1    Saier Jr., M.H.2
  • 34
    • 0028955458 scopus 로고
    • Response regulators of bacterial signal transduction systems: Selective domain shuffling during evolution
    • Pao G.M., Saier M.H. Jr. Response regulators of bacterial signal transduction systems: selective domain shuffling during evolution. J. Mol. Evol. 40:1995;136-154.
    • (1995) J. Mol. Evol. , vol.40 , pp. 136-154
    • Pao, G.M.1    Saier Jr., M.H.2
  • 35
    • 0344780875 scopus 로고    scopus 로고
    • A role for a highly conserved protein of unknown function in regulation of Bacillus subtilis purA by the purine repressor
    • Rappu P., Shin B.S., Zalkin H., Mantsala P. A role for a highly conserved protein of unknown function in regulation of Bacillus subtilis purA by the purine repressor. J. Bacteriol. 181:1999;3810-3815.
    • (1999) J. Bacteriol. , vol.181 , pp. 3810-3815
    • Rappu, P.1    Shin, B.S.2    Zalkin, H.3    Mantsala, P.4
  • 36
    • 0033575262 scopus 로고    scopus 로고
    • Ribonuclease activity of rat liver perchloric acid-soluble protein, a potent inhibitor of protein synthesis
    • Morishita R., Kawagoshi A., Sawasaki T., Madin K., Ogasawara T., Oka T., Endo Y. Ribonuclease activity of rat liver perchloric acid-soluble protein, a potent inhibitor of protein synthesis. J. Biol. Chem. 274:1999;20688-20692.
    • (1999) J. Biol. Chem. , vol.274 , pp. 20688-20692
    • Morishita, R.1    Kawagoshi, A.2    Sawasaki, T.3    Madin, K.4    Ogasawara, T.5    Oka, T.6    Endo, Y.7
  • 38
    • 0030954208 scopus 로고    scopus 로고
    • GCN5-related histone N-acetyltransferases belong to a diverse superfamily that includes the yeast SPT10 protein
    • Neuwald A.F., Landsman D. GCN5-related histone N-acetyltransferases belong to a diverse superfamily that includes the yeast SPT10 protein. Trends Biochem. Sci. 22:1997;154-155.
    • (1997) Trends Biochem. Sci. , vol.22 , pp. 154-155
    • Neuwald, A.F.1    Landsman, D.2
  • 39
    • 0038728733 scopus 로고    scopus 로고
    • Kinetic mechanism of the GCN5-related chromosomal aminoglycoside acetyltransferase AAC(6')-Ii from Enterococcus faecium: Evidence of dimer subunit cooperativity
    • Draker K.A., Northrop D.B., Wright G.D. Kinetic mechanism of the GCN5-related chromosomal aminoglycoside acetyltransferase AAC(6')-Ii from Enterococcus faecium: evidence of dimer subunit cooperativity. Biochemistry. 42:2003;6565-6574.
    • (2003) Biochemistry , vol.42 , pp. 6565-6574
    • Draker, K.A.1    Northrop, D.B.2    Wright, G.D.3
  • 40
    • 0036145551 scopus 로고    scopus 로고
    • The CATH extended protein-family database: Providing structural annotations for genome sequences
    • Pearl F., Lee D., Bray J., Buchan D., Shepherd A., Orengo C. The CATH extended protein-family database: providing structural annotations for genome sequences. Protein Sci. 11:2002;233-244.
    • (2002) Protein Sci. , vol.11 , pp. 233-244
    • Pearl, F.1    Lee, D.2    Bray, J.3    Buchan, D.4    Shepherd, A.5    Orengo, C.6
  • 41
    • 0032411225 scopus 로고    scopus 로고
    • How representative are the known structures of the proteins in a complete genome? a comprehensive structural census
    • Gerstein M. How representative are the known structures of the proteins in a complete genome? A comprehensive structural census. Fold. Des. 3:1998;497-512.
    • (1998) Fold. Des. , vol.3 , pp. 497-512
    • Gerstein, M.1
  • 42
    • 0032499698 scopus 로고    scopus 로고
    • The universal ancestor
    • Woese C. The universal ancestor. Proc. Natl Acad. Sci. USA. 95:1998;6854-6859.
    • (1998) Proc. Natl Acad. Sci. USA , vol.95 , pp. 6854-6859
    • Woese, C.1
  • 43
    • 0037154986 scopus 로고    scopus 로고
    • Ribosome structure and the mechanism of translation
    • Ramakrishnan V. Ribosome structure and the mechanism of translation. Cell. 108:2002;557-572.
    • (2002) Cell , vol.108 , pp. 557-572
    • Ramakrishnan, V.1
  • 44
    • 0032127258 scopus 로고    scopus 로고
    • Reductive evolution of resident genomes
    • Andersson S.G., Kurland C.G. Reductive evolution of resident genomes. Trends Microbiol. 6:1998;263-268.
    • (1998) Trends Microbiol. , vol.6 , pp. 263-268
    • Andersson, S.G.1    Kurland, C.G.2
  • 46
    • 0028940587 scopus 로고
    • Gene number, noise reduction and biological complexity
    • Bird A.P. Gene number, noise reduction and biological complexity. Trends Genet. 11:1995;94-100.
    • (1995) Trends Genet. , vol.11 , pp. 94-100
    • Bird, A.P.1
  • 47
    • 0037665941 scopus 로고    scopus 로고
    • Transcription regulation and environmental adaptation in bacteria
    • Cases I., de Lorenzo V., Ouzounis C.A. Transcription regulation and environmental adaptation in bacteria. Trends Microbiol. 11:2003;248-253.
    • (2003) Trends Microbiol. , vol.11 , pp. 248-253
    • Cases, I.1    De Lorenzo, V.2    Ouzounis, C.A.3
  • 48
    • 0041828241 scopus 로고    scopus 로고
    • Scaling laws in the functional content of genomes
    • Nimwegen E. Scaling laws in the functional content of genomes. Trends Genet. 19:2003;479-484.
    • (2003) Trends Genet. , vol.19 , pp. 479-484
    • Nimwegen, E.1
  • 49
    • 0038438514 scopus 로고    scopus 로고
    • IMPALA: Matching a protein sequence against a collection of PSI-BLAST-constructed position-specific score matrices
    • Schaffer A.A., Wolf Y.I., Ponting C.P., Koonin E.V., Aravind L., Altschul S.F. IMPALA: matching a protein sequence against a collection of PSI-BLAST-constructed position-specific score matrices. Bioinformatics. 15:1999;1000-1011.
    • (1999) Bioinformatics , vol.15 , pp. 1000-1011
    • Schaffer, A.A.1    Wolf, Y.I.2    Ponting, C.P.3    Koonin, E.V.4    Aravind, L.5    Altschul, S.F.6
  • 50
    • 0033618555 scopus 로고    scopus 로고
    • Detecting protein function and protein-protein interactions from genome sequences
    • Marcotte E., Pellegrini M., Ng H., Rice D., Yeates T., Eisenberg D. Detecting protein function and protein-protein interactions from genome sequences. Science. 285:1999;751-753.
    • (1999) Science , vol.285 , pp. 751-753
    • Marcotte, E.1    Pellegrini, M.2    Ng, H.3    Rice, D.4    Yeates, T.5    Eisenberg, D.6
  • 54
    • 0035162592 scopus 로고    scopus 로고
    • The COG database: New developments in phylogenetic classification of proteins from complete genomes
    • Tatusov R., Natale D., Garkavtsev I., Tatusova T., Shankavaram U., Rao B., et al. The COG database: new developments in phylogenetic classification of proteins from complete genomes. Nucl. Acids Res. 29:2001;22-28.
    • (2001) Nucl. Acids Res. , vol.29 , pp. 22-28
    • Tatusov, R.1    Natale, D.2    Garkavtsev, I.3    Tatusova, T.4    Shankavaram, U.5    Rao, B.6


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.