메뉴 건너뛰기




Volumn 58, Issue 5, 2004, Pages 615-631

Detection of lateral gene transfer events in the prokaryotic tRNA synthetases by the ratios of evolutionary distances method

Author keywords

Aminoacyl tRNA synthetases; Lateral gene transfers; Ratios of evolutionary distances; RED T; Ribosomal proteins

Indexed keywords

PROTEIN DERIVATIVE; RIBOSOME PROTEIN; RNA; SYNTHETASE;

EID: 2342661195     PISSN: 00222844     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00239-004-2582-2     Document Type: Article
Times cited : (19)

References (54)
  • 2
    • 0028092214 scopus 로고
    • Amino acid substitution during functionally constrained divergent evolution of protein sequences
    • Benner SA, Cohen MA, Gonnet GH (1994) Amino acid substitution during functionally constrained divergent evolution of protein sequences. Protein Eng 7:1323-1332
    • (1994) Protein Eng , vol.7 , pp. 1323-1332
    • Benner, S.A.1    Cohen, M.A.2    Gonnet, G.H.3
  • 3
    • 0034939491 scopus 로고    scopus 로고
    • Bacterial origin foi the isoprenoid biosynthesis enzyme HMG-CoA reductase of the archaeal orders Thermoplasmatales and Archaeoglobales
    • Boucher Y, Huber H, L'Haridon S, Stetter KO, Doolittle WF (2001) Bacterial origin foi the isoprenoid biosynthesis enzyme HMG-CoA reductase of the archaeal orders Thermoplasmatales and Archaeoglobales. Mol Biol Evol 18:1378-1388
    • (2001) Mol Biol Evol , vol.18 , pp. 1378-1388
    • Boucher, Y.1    Huber, H.2    L'Haridon, S.3    Stetter, K.O.4    Doolittle, W.F.5
  • 4
    • 0034565944 scopus 로고    scopus 로고
    • The evolutionary history of ribosomal protein RpS14: Horizontal gene transfer at the heart of the ribosome
    • Brochier C, Philippe H, Moreira D (2000) The evolutionary history of ribosomal protein RpS14: Horizontal gene transfer at the heart of the ribosome. Trends Genet 16:529-533
    • (2000) Trends Genet , vol.16 , pp. 529-533
    • Brochier, C.1    Philippe, H.2    Moreira, D.3
  • 5
    • 0035527409 scopus 로고    scopus 로고
    • Genomic and phylogenetic perspectives on the evolution of prokaryotes
    • Brown JR (2001) Genomic and phylogenetic perspectives on the evolution of prokaryotes. Syst Biol 50:497-512
    • (2001) Syst Biol , vol.50 , pp. 497-512
    • Brown, J.R.1
  • 6
    • 0032554795 scopus 로고    scopus 로고
    • A bacterial antibiotic resistance gene with eukaryotic origins
    • Brown JR, Zhang J, Hodgson JE (1998) A bacterial antibiotic resistance gene with eukaryotic origins. Curr Biol 8:R365-R367
    • (1998) Curr Biol , vol.8
    • Brown, J.R.1    Zhang, J.2    Hodgson, J.E.3
  • 7
    • 0002929101 scopus 로고
    • A model of evolutionary change in proteins
    • Dayhoff MO (ed) National Biomedical Research Foundation, Washington, DC
    • Dayhoff MO, Eck FV, Park CM (1972) A model of evolutionary change in proteins. In: Dayhoff MO (ed) Atlas of protein sequence and structure, vol. 5. National Biomedical Research Foundation, Washington, DC, pp 89-99
    • (1972) Atlas of Protein Sequence and Structure , vol.5 , pp. 89-99
    • Dayhoff, M.O.1    Eck, F.V.2    Park, C.M.3
  • 8
    • 0000228203 scopus 로고
    • A model of evolutionary change in proteins
    • Dayhoff MO (ed) National Biomedical Research Foundation, Washington, DC
    • Dayhoff MO, Schwartz RM, Orcutt BC (1978) A model of evolutionary change in proteins. In: Dayhoff MO (ed) Atlas of protein sequence, vol. 5, Supplement 3. National Biomedical Research Foundation, Washington, DC, pp 345-352
    • (1978) Atlas of Protein Sequence , vol.5 , Issue.3 SUPPL. , pp. 345-352
    • Dayhoff, M.O.1    Schwartz, R.M.2    Orcutt, B.C.3
  • 10
    • 0033603539 scopus 로고    scopus 로고
    • Phylogenetic classification and the universal tree
    • Doolittle WF (1999b) Phylogenetic classification and the universal tree. Science 284:2124-2129
    • (1999) Science , vol.284 , pp. 2124-2129
    • Doolittle, W.F.1
  • 11
    • 0033783996 scopus 로고    scopus 로고
    • Assessing evolutionary relationships among microbes from whole-genome analysis
    • Eisen JA (2000) Assessing evolutionary relationships among microbes from whole-genome analysis. Curr Opin Microbiol 3:475-480
    • (2000) Curr Opin Microbiol , vol.3 , pp. 475-480
    • Eisen, J.A.1
  • 13
    • 0242391988 scopus 로고    scopus 로고
    • RED-T: Utilizing the Ratios of Evolutionary Distances for determination of alternative phylogenetic events
    • Farahi K, Whitman WB, Kraemer ET (2003) RED-T: Utilizing the Ratios of Evolutionary Distances for determination of alternative phylogenetic events. Bioinformatics 19:2152-2154
    • (2003) Bioinformatics , vol.19 , pp. 2152-2154
    • Farahi, K.1    Whitman, W.B.2    Kraemer, E.T.3
  • 14
  • 16
    • 0014211361 scopus 로고
    • Construction of phylogenetic trees
    • Fitch WM, Margoliash E (1967) Construction of phylogenetic trees. Science 155:279-284
    • (1967) Science , vol.155 , pp. 279-284
    • Fitch, W.M.1    Margoliash, E.2
  • 17
    • 0026712536 scopus 로고
    • Mitochondrial Eve: Wounded, but not dead yet
    • Gibbons A (1992) Mitochondrial Eve: Wounded, but not dead yet. Science 257:873-875
    • (1992) Science , vol.257 , pp. 873-875
    • Gibbons, A.1
  • 18
    • 0033752775 scopus 로고    scopus 로고
    • About the last common ancestor, the universal life-tree and lateral gene transfer: A reappraisal
    • Glansdorff N (2000) About the last common ancestor, the universal life-tree and lateral gene transfer: A reappraisal. Mol Microbiol 38:177-185
    • (2000) Mol Microbiol , vol.38 , pp. 177-185
    • Glansdorff, N.1
  • 20
    • 0027073347 scopus 로고
    • The endosymbiont hypothesis revisited
    • Gray MW (1992) The endosymbiont hypothesis revisited. Int Rev Cytol 141:233-357
    • (1992) Int Rev Cytol , vol.141 , pp. 233-357
    • Gray, M.W.1
  • 21
    • 0033859839 scopus 로고    scopus 로고
    • Phylogeny of 33 ribosomal and six other proteins encoded in an ancient gene cluster that is conserved across prokaryotic genomes: Influence of excluding poorly alignable sites from analysis
    • Hansmann S, Martin W (2000) Phylogeny of 33 ribosomal and six other proteins encoded in an ancient gene cluster that is conserved across prokaryotic genomes: Influence of excluding poorly alignable sites from analysis. Int J Syst Evol Microbiol 50:1655-1663
    • (2000) Int J Syst Evol Microbiol , vol.50 , pp. 1655-1663
    • Hansmann, S.1    Martin, W.2
  • 22
    • 0026458378 scopus 로고
    • Amino acid substitution matrices from protein blocks
    • Henikoff S, Henikoff JG (1992) Amino acid substitution matrices from protein blocks. Proc Natl Acad Sci USA 89:10915-10919
    • (1992) Proc Natl Acad Sci USA , vol.89 , pp. 10915-10919
    • Henikoff, S.1    Henikoff, J.G.2
  • 23
    • 0027738868 scopus 로고
    • Horizontal transfer of ATPase genes - The tree of life becomes a net of life
    • Hilario E, Gogarten JP (1993) Horizontal transfer of ATPase genes - The tree of life becomes a net of life. Biosystems 31:111-119
    • (1993) Biosystems , vol.31 , pp. 111-119
    • Hilario, E.1    Gogarten, J.P.2
  • 24
    • 0034991910 scopus 로고    scopus 로고
    • The renaissance of aminoacyl-tRNA synthesis
    • Ibba M, Soll D (2001) The renaissance of aminoacyl-tRNA synthesis. EMBO Rep 2:382-387
    • (2001) EMBO Rep , vol.2 , pp. 382-387
    • Ibba, M.1    Soll, D.2
  • 25
    • 0033616714 scopus 로고    scopus 로고
    • Horizontal gene transfer among genomes: The complexity hypothesis
    • Jain R, Rivera MC, Lake JA (1999) Horizontal gene transfer among genomes: the complexity hypothesis. Proc Natl Acad Sci USA 96:3801-3806
    • (1999) Proc Natl Acad Sci USA , vol.96 , pp. 3801-3806
    • Jain, R.1    Rivera, M.C.2    Lake, J.A.3
  • 27
    • 0027992228 scopus 로고
    • Evolution of the Glx-tRNA synthetase family: The glutaminyl enzyme as a case of horizontal gene transfer
    • Lamour V, Quevillon S, Diriong S, N'Guyen VC, Lipinski M, Mirande M (1994) Evolution of the Glx-tRNA synthetase family: The glutaminyl enzyme as a case of horizontal gene transfer. Proc Natl Acad Sci USA 91:8670-8674
    • (1994) Proc Natl Acad Sci USA , vol.91 , pp. 8670-8674
    • Lamour, V.1    Quevillon, S.2    Diriong, S.3    N'Guyen, V.C.4    Lipinski, M.5    Mirande, M.6
  • 28
    • 0032482924 scopus 로고    scopus 로고
    • Molecular archaeology of the Escherichia coli genome
    • Lawrence JG, Ochman H (1998) Molecular archaeology of the Escherichia coli genome. Proc Natl Acad Sci USA 95:9413-9417
    • (1998) Proc Natl Acad Sci USA , vol.95 , pp. 9413-9417
    • Lawrence, J.G.1    Ochman, H.2
  • 29
    • 0036145420 scopus 로고    scopus 로고
    • Reconciling the many faces of lateral gene transfer
    • Lawrence JG, Ochman H (2002) Reconciling the many faces of lateral gene transfer. Trends Microbiol 10:1-4
    • (2002) Trends Microbiol , vol.10 , pp. 1-4
    • Lawrence, J.G.1    Ochman, H.2
  • 31
    • 0035225012 scopus 로고    scopus 로고
    • Two C or not two C: Recurrent disruption of Zn-ribbons, gene duplication, lineage-specific gene loss, and horizontal gene transfer in evolution of bacterial ribosomal proteins
    • RESEARCH 0033
    • Makarova KS, Ponomarev VA, Koonin EV (2001) Two C or not two C: recurrent disruption of Zn-ribbons, gene duplication, lineage-specific gene loss, and horizontal gene transfer in evolution of bacterial ribosomal proteins. Genome Biol 2:RESEARCH 0033
    • (2001) Genome Biol , vol.2
    • Makarova, K.S.1    Ponomarev, V.A.2    Koonin, E.V.3
  • 34
    • 0033082247 scopus 로고    scopus 로고
    • Mosaic bacterial chromosomes: A challenge en route to a tree of genomes
    • Martin W (1999) Mosaic bacterial chromosomes: a challenge en route to a tree of genomes. Bioessays 21:99-104
    • (1999) Bioessays , vol.21 , pp. 99-104
    • Martin, W.1
  • 36
    • 0033609333 scopus 로고    scopus 로고
    • Evidence for lateral gene transfer between Archaea and bacteria from genome sequence of Thermotoga maritima
    • Nelson KE, Clayton RA, Gill SR et al. (1999) Evidence for lateral gene transfer between Archaea and bacteria from genome sequence of Thermotoga maritima. Nature 399:323-329
    • (1999) Nature , vol.399 , pp. 323-329
    • Nelson, K.E.1    Clayton, R.A.2    Gill, S.R.3
  • 37
    • 0034831587 scopus 로고    scopus 로고
    • Defining the core of nontransferable prokaryotic genes: The euryarchaeal core
    • Nesbo CL, Boucher Y, Doolittle WF (2001) Defining the core of nontransferable prokaryotic genes: The euryarchaeal core. J Mol Evol 53:340-350
    • (2001) J Mol Evol , vol.53 , pp. 340-350
    • Nesbo, C.L.1    Boucher, Y.2    Doolittle, W.F.3
  • 40
    • 0029853148 scopus 로고    scopus 로고
    • WWW-query: An on-line retrieval system for biological sequence banks
    • Perriere G, Gouy M (1996) WWW-query: An on-line retrieval system for biological sequence banks. Biochimie 78:364-369
    • (1996) Biochimie , vol.78 , pp. 364-369
    • Perriere, G.1    Gouy, M.2
  • 41
    • 0018213316 scopus 로고
    • Coupled evolution: Adaptive interactions among the genomes of plasmids, viruses, and cells
    • Reanney DC (1978) Coupled evolution: Adaptive interactions among the genomes of plasmids, viruses, and cells. Int Rev Cytol Suppl (Suppl):1-68
    • (1978) Int Rev Cytol Suppl , Issue.SUPPL. , pp. 1-68
    • Reanney, D.C.1
  • 42
    • 0023375195 scopus 로고
    • The neighbor-joining method: A new method for reconstructing phylogenetic trees
    • Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406-425
    • (1987) Mol Biol Evol , vol.4 , pp. 406-425
    • Saitou, N.1    Nei, M.2
  • 43
    • 0026490002 scopus 로고
    • Evolution by acquisition: The case for horizontal gene transfers
    • Smith MW, Feng DF, Doolittle RF (1992) Evolution by acquisition: the case for horizontal gene transfers. Trends Biochem Sci 17:489-493
    • (1992) Trends Biochem Sci , vol.17 , pp. 489-493
    • Smith, M.W.1    Feng, D.F.2    Doolittle, R.F.3
  • 45
    • 0036143446 scopus 로고    scopus 로고
    • Genomes in flux: The evolution of archaeal and proteobacterial gene content
    • Snel B, Bork P, Huynen MA (2002) Genomes in flux: The evolution of archaeal and proteobacterial gene content. Genome Res 12:17-25
    • (2002) Genome Res , vol.12 , pp. 17-25
    • Snel, B.1    Bork, P.2    Huynen, M.A.3
  • 46
    • 0017002184 scopus 로고
    • Towards a new bacteriology
    • Sonea S, Paniset M (1976) Towards a new bacteriology. Rev Can Biol 35:103-167
    • (1976) Rev Can Biol , vol.35 , pp. 103-167
    • Sonea, S.1    Paniset, M.2
  • 49
    • 0027968068 scopus 로고
    • CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
    • Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673-4680
    • (1994) Nucleic Acids Res , vol.22 , pp. 4673-4680
    • Thompson, J.D.1    Higgins, D.G.2    Gibson, T.J.3
  • 50
    • 0031574072 scopus 로고    scopus 로고
    • The CLUSTAL_X windows interface: Flexible strategies for multiple sequence alignment aided by quality analysis tools
    • Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The CLUSTAL_X windows interface: Flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25:4876-4882
    • (1997) Nucleic Acids Res , vol.25 , pp. 4876-4882
    • Thompson, J.D.1    Gibson, T.J.2    Plewniak, F.3    Jeanmougin, F.4    Higgins, D.G.5
  • 51
    • 0032499698 scopus 로고    scopus 로고
    • The universal ancestor
    • Woese CR (1998) The universal ancestor. Proc Natl Acad Sci USA 95:6854-6859
    • (1998) Proc Natl Acad Sci USA , vol.95 , pp. 6854-6859
    • Woese, C.R.1
  • 52
    • 0037173066 scopus 로고    scopus 로고
    • On the evolution of cells
    • Woese CR (2002) On the evolution of cells. Proc Natl Acad Sci USA 99:8742-8747
    • (2002) Proc Natl Acad Sci USA , vol.99 , pp. 8742-8747
    • Woese, C.R.1
  • 54
    • 0034053846 scopus 로고    scopus 로고
    • Aminoacyl-tRNA synthetases, the genetic code, and the evolutionary process
    • Woese CR, Olsen GJ, Ibba M, Soll D (2000) Aminoacyl-tRNA synthetases, the genetic code, and the evolutionary process. Microbiol Mol Biol Rev 64:202-236
    • (2000) Microbiol Mol Biol Rev , vol.64 , pp. 202-236
    • Woese, C.R.1    Olsen, G.J.2    Ibba, M.3    Soll, D.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.