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Volumn 21, Issue 10, 2004, Pages 1884-1894

Successful lateral transfer requires codon usage compatibility between foreign genes and recipient genomes

Author keywords

Bayesian model; Codon usage compatibility; Comparative genomics; Evolution; Horizontal gene transfer

Indexed keywords

ARTICLE; CODON USAGE; EVOLUTION; GENE FUNCTION; GENE STRUCTURE; GENOME; HORIZONTAL GENE TRANSFER; HUMAN; INTROGRESSION; NONHUMAN; PHYLOGENY; PROKARYOTE;

EID: 4944262629     PISSN: 07374038     EISSN: None     Source Type: Journal    
DOI: 10.1093/molbev/msh202     Document Type: Article
Times cited : (63)

References (53)
  • 1
    • 0345827436 scopus 로고    scopus 로고
    • SOS response promotes horizontal dissemination of antibiotic resistance genes
    • Beaber, J. W., B. Hochhut, and M. K. Waldor. 2004. SOS response promotes horizontal dissemination of antibiotic resistance genes. Nature 427:72-74.
    • (2004) Nature , vol.427 , pp. 72-74
    • Beaber, J.W.1    Hochhut, B.2    Waldor, M.K.3
  • 2
    • 0036899896 scopus 로고    scopus 로고
    • Evolution of microbial genomes: Sequence acquisition and loss
    • Berg, O. G., and C. G. Kurland. 2002. Evolution of microbial genomes: sequence acquisition and loss. Mol. Biol. Evol. 19:2265-2276.
    • (2002) Mol. Biol. Evol. , vol.19 , pp. 2265-2276
    • Berg, O.G.1    Kurland, C.G.2
  • 4
    • 0037306453 scopus 로고    scopus 로고
    • Ancient horizontal gene transfer
    • Brown, J. R. 2003. Ancient horizontal gene transfer. Nat. Rev. Genet. 4:121-132.
    • (2003) Nat. Rev. Genet. , vol.4 , pp. 121-132
    • Brown, J.R.1
  • 5
    • 0033529862 scopus 로고    scopus 로고
    • Genome signature comparisons among prokaryote, plasmid, and mitochondrial DNA
    • Campbell, A., J. Mrazek, and S. Karlin. 1999. Genome signature comparisons among prokaryote, plasmid, and mitochondrial DNA. Proc. Natl. Acad. Sci. USA 96:9184-9189.
    • (1999) Proc. Natl. Acad. Sci. USA , vol.96 , pp. 9184-9189
    • Campbell, A.1    Mrazek, J.2    Karlin, S.3
  • 6
    • 0034043778 scopus 로고    scopus 로고
    • Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis
    • Castresana, J. 2000. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol. Biol. Evol. 17:540-552.
    • (2000) Mol. Biol. Evol. , vol.17 , pp. 540-552
    • Castresana, J.1
  • 7
    • 0034703744 scopus 로고    scopus 로고
    • Evolutionary implications of the frequent horizontal transfer of mismatch repair genes
    • Denamur, E., G. Lecointre, P. Darlu et al. (12 co-authors). 2000. Evolutionary implications of the frequent horizontal transfer of mismatch repair genes. Cell 103:711-721.
    • (2000) Cell , vol.103 , pp. 711-721
    • Denamur, E.1    Lecointre, G.2    Darlu, P.3
  • 9
    • 0000122573 scopus 로고
    • PHYLIP: Phylogeny inference package. Version 3.2
    • Felsenstein, J. 1989. PHYLIP: phylogeny inference package. Version 3.2. Cladistics 5:164-166.
    • (1989) Cladistics , vol.5 , pp. 164-166
    • Felsenstein, J.1
  • 10
    • 0037250391 scopus 로고    scopus 로고
    • HGT-DB: A database of putative horizontally transferred genes in prokaryotic complete genomes
    • Garcia-Vallvé, S., E. Guzman, M. A. Montera, and A. Romeu. 2003. HGT-DB: a database of putative horizontally transferred genes in prokaryotic complete genomes. Nucleic Acids Res. 31:187-189.
    • (2003) Nucleic Acids Res. , vol.31 , pp. 187-189
    • Garcia-Vallvé, S.1    Guzman, E.2    Montera, M.A.3    Romeu, A.4
  • 11
    • 0033670249 scopus 로고    scopus 로고
    • Horizontal gene transfer in bacterial and archaeal complete genomes
    • Garcia-Vallvé, S., A. Romeu, and J. Palau. 2000. Horizontal gene transfer in bacterial and archaeal complete genomes. Genome Res. 10:1719-1725.
    • (2000) Genome Res. , vol.10 , pp. 1719-1725
    • Garcia-Vallvé, S.1    Romeu, A.2    Palau, J.3
  • 13
    • 0034864223 scopus 로고    scopus 로고
    • The evolution of bacterial LuxI and LuxR quorum sensing regulators
    • Gray, K. M., and J. R. Garey. 2001. The evolution of bacterial LuxI and LuxR quorum sensing regulators. Microbiology 147:2379-2387.
    • (2001) Microbiology , vol.147 , pp. 2379-2387
    • Gray, K.M.1    Garey, J.R.2
  • 14
    • 0242578620 scopus 로고    scopus 로고
    • A simple, fast, and accurate algorithm to estimate large phytogenies by maximum likelihood
    • Guindon, S., and O. Gascuel. 2003. A simple, fast, and accurate algorithm to estimate large phytogenies by maximum likelihood. Syst. Biol. 52:696-704.
    • (2003) Syst. Biol. , vol.52 , pp. 696-704
    • Guindon, S.1    Gascuel, O.2
  • 15
    • 0030888233 scopus 로고    scopus 로고
    • RecQ DNA helicase is a suppressor of illegitimate recombination in Escherichia coli
    • Hanada, K., T. Ukita, Y. Kohno, K. Saito, J. Kato, and H. Ikeda. 1997. RecQ DNA helicase is a suppressor of illegitimate recombination in Escherichia coli. Proc. Natl. Acad. Sci. USA 94:3860-3865.
    • (1997) Proc. Natl. Acad. Sci. USA , vol.94 , pp. 3860-3865
    • Hanada, K.1    Ukita, T.2    Kohno, Y.3    Saito, K.4    Kato, J.5    Ikeda, H.6
  • 16
    • 0642344263 scopus 로고    scopus 로고
    • Duplication is more common among laterally transferred genes than among indigenous genes
    • Hooper, S. D., and O. G. Berg. 2003. Duplication is more common among laterally transferred genes than among indigenous genes. Genome Biol. 4:R48.
    • (2003) Genome Biol. , vol.4
    • Hooper, S.D.1    Berg, O.G.2
  • 17
    • 0019824131 scopus 로고
    • Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes: A proposal for a synonymous codon choice that is optimal for the E. coli translational system
    • Ikemura, T. 1981. Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes: a proposal for a synonymous codon choice that is optimal for the E. coli translational system. J. Mol. Biol. 151:389-409.
    • (1981) J. Mol. Biol. , vol.151 , pp. 389-409
    • Ikemura, T.1
  • 18
    • 0019949369 scopus 로고
    • Correlation between the abundance of yeast transfer RNAs and the occurrence of the respective codons in protein genes. Differences in synonymous codon choice patterns of yeast and Escherichia coli with reference to the abundance of isoaccepting transfer RNAs
    • -. 1982. Correlation between the abundance of yeast transfer RNAs and the occurrence of the respective codons in protein genes. Differences in synonymous codon choice patterns of yeast and Escherichia coli with reference to the abundance of isoaccepting transfer RNAs. J. Mol. Biol. 158:573-597.
    • (1982) J. Mol. Biol. , vol.158 , pp. 573-597
  • 19
    • 0034739881 scopus 로고    scopus 로고
    • Complete genome structure of the nitrogen-fixing symbiotic bacterium Mesorhizobium loti
    • Kaneko, T., Y. Nakamura, S. Sato et al. (24 co-authors). 2000. Complete genome structure of the nitrogen-fixing symbiotic bacterium Mesorhizobium loti. DNA Res. 7:331-338.
    • (2000) DNA Res. , vol.7 , pp. 331-338
    • Kaneko, T.1    Nakamura, Y.2    Sato, S.3
  • 20
    • 0035399931 scopus 로고    scopus 로고
    • Detecting anomalous gene clusters and pathogenicity islands in diverse bacterial genomes
    • Karlin, S. 2001. Detecting anomalous gene clusters and pathogenicity islands in diverse bacterial genomes. Trends Microbiol. 9:335-343.
    • (2001) Trends Microbiol. , vol.9 , pp. 335-343
    • Karlin, S.1
  • 21
    • 0031720281 scopus 로고    scopus 로고
    • Codon usages in different gene classes of the Escherichia coli genome
    • Karlin, S., J. Mrázek, and A. M. Campbell. 1998. Codon usages in different gene classes of the Escherichia coli genome. Mol. Microbiol. 29:1341-1355.
    • (1998) Mol. Microbiol. , vol.29 , pp. 1341-1355
    • Karlin, S.1    Mrázek, J.2    Campbell, A.M.3
  • 22
    • 0034992826 scopus 로고    scopus 로고
    • The closest Blast hit is often not the nearest neighbor
    • Koski, L. B., and G. B. Golding. 2001. The closest Blast hit is often not the nearest neighbor. J. Mol. Evol. 52:540-542.
    • (2001) J. Mol. Evol. , vol.52 , pp. 540-542
    • Koski, L.B.1    Golding, G.B.2
  • 23
    • 0035099964 scopus 로고    scopus 로고
    • Codon bias and base composition are poor indicators of horizontally transferred genes
    • Koski, L. B., R. A. Morton, and G. B. Golding. 2001. Codon bias and base composition are poor indicators of horizontally transferred genes. Mol. Biol. Evol. 18:404-412.
    • (2001) Mol. Biol. Evol. , vol.18 , pp. 404-412
    • Koski, L.B.1    Morton, R.A.2    Golding, G.B.3
  • 24
    • 0032514693 scopus 로고    scopus 로고
    • Natural genetic exchange between Haemophilus and Neisseria: Intergeneric transfer of chromosomal genes between major human pathogens
    • Krall, J. S., K. E. Wilks, J. L. Farrant, and P. R. Langford. 1998. Natural genetic exchange between Haemophilus and Neisseria: intergeneric transfer of chromosomal genes between major human pathogens. Proc. Natl. Acad. Sci. USA 95:12381-12385.
    • (1998) Proc. Natl. Acad. Sci. USA , vol.95 , pp. 12381-12385
    • Krall, J.S.1    Wilks, K.E.2    Farrant, J.L.3    Langford, P.R.4
  • 25
    • 0342768762 scopus 로고    scopus 로고
    • Archaeal and bacterial hyperthermophiles: Horizontal gene exchange or common ancestry?
    • Kyrpides, N. C., and G. J. Olsen. 1999. Archaeal and bacterial hyperthermophiles: horizontal gene exchange or common ancestry? Trends Genet. 15:298-299.
    • (1999) Trends Genet. , vol.15 , pp. 298-299
    • Kyrpides, N.C.1    Olsen, G.J.2
  • 26
    • 0030994798 scopus 로고    scopus 로고
    • Amelioration of bacterial genomes: Rates of change and exchange
    • Lawrence, J. G., and H. Ochman. 1997. Amelioration of bacterial genomes: rates of change and exchange. J. Mol. Evol. 44:383-397.
    • (1997) J. Mol. Evol. , vol.44 , pp. 383-397
    • Lawrence, J.G.1    Ochman, H.2
  • 27
    • 0032482924 scopus 로고    scopus 로고
    • Molecular archaeology of the Escherichia coli genome
    • -. 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
  • 28
    • 0036145420 scopus 로고    scopus 로고
    • Reconciling the many faces of lateral gene transfer
    • -. 2002. Reconciling the many faces of lateral gene transfer. Trends Microbiol. 10:1-4.
    • (2002) Trends Microbiol. , vol.10 , pp. 1-4
  • 29
    • 0035972889 scopus 로고    scopus 로고
    • Sexual isolation in bacteria
    • Majewski, J. 2001. Sexual isolation in bacteria. FEMS Microbiol. Lett. 199:161-169.
    • (2001) FEMS Microbiol. Lett. , vol.199 , pp. 161-169
    • Majewski, J.1
  • 30
    • 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
  • 31
    • 0026332291 scopus 로고
    • Evidence for horizontal gene transfer in Escherichia coli speciation
    • Médigue, C., T. Rouxel, P. Vigier, A. Henaut, and A. Danchin. 1991. Evidence for horizontal gene transfer in Escherichia coli speciation. J. Mol. Biol. 222:851-856.
    • (1991) J. Mol. Biol. , vol.222 , pp. 851-856
    • Médigue, C.1    Rouxel, T.2    Vigier, P.3    Henaut, A.4    Danchin, A.5
  • 32
    • 0001291140 scopus 로고    scopus 로고
    • A powerful non-homology method for the prediction of operons in prokaryotes
    • Moreno-Hagelsieb, G., and J. Collado-Vides. 2002a. A powerful non-homology method for the prediction of operons in prokaryotes. Bioinformatics 18(Suppl 1):S329-S336.
    • (2002) Bioinformatics. , vol.18 , Issue.SUPPL. 1
    • Moreno-Hagelsieb, G.1    Collado-Vides, J.2
  • 33
    • 0036014557 scopus 로고    scopus 로고
    • Operon conservation from the point of view of Escherichia coli, and inference of functional interdependence of gene products from genome context
    • -. 2002b. Operon conservation from the point of view of Escherichia coli, and inference of functional interdependence of gene products from genome context. In Silico Biol. 2:87-95.
    • (2002) In Silico Biol. , vol.2 , pp. 87-95
  • 34
    • 0032870941 scopus 로고    scopus 로고
    • Codon usage and lateral gene transfer in Bacillus subtilis
    • Moszer, I., E. P. Rocha, and A. Danchin. 1999. Codon usage and lateral gene transfer in Bacillus subtilis. Curr. Opin. Microbiol. 2:524-528.
    • (1999) Curr. Opin. Microbiol. , vol.2 , pp. 524-528
    • Moszer, I.1    Rocha, E.P.2    Danchin, A.3
  • 35
    • 0014757386 scopus 로고
    • A general method applicable to the search for similarities in the amino acid sequence of two proteins
    • Needleman, S. B., and C. D. Wunsch. 1970. A general method applicable to the search for similarities in the amino acid sequence of two proteins. J. Mol. Biol. 48:443-453.
    • (1970) J. Mol. Biol. , vol.48 , pp. 443-453
    • Needleman, S.B.1    Wunsch, C.D.2
  • 36
    • 0033609333 scopus 로고    scopus 로고
    • Evidence for lateral gene transfer between Archaea and bacteria from genome sequence of Thermotoga maritima
    • Nelson, K. E., R. A. Clayton, S. R. Gill et al. (25 co-authors). 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
    • 0035106010 scopus 로고    scopus 로고
    • Phylogenetic analyses of two "archaeal" genes in Thermotoga maritima reveal multiple transfers between archaea and bacteria
    • Nesbo, C. L., S. L'Haridon, K. O. Stetter, and W. F. Doolittle. 2001. Phylogenetic analyses of two "archaeal" genes in Thermotoga maritima reveal multiple transfers between archaea and bacteria. Mol. Biol. Evol. 18:362-375.
    • (2001) Mol. Biol. Evol. , vol.18 , pp. 362-375
    • Nesbo, C.L.1    L'Haridon, S.2    Stetter, K.O.3    Doolittle, W.F.4
  • 38
    • 0032173633 scopus 로고    scopus 로고
    • Rates and patterns of chromosome evolution in enteric bacteria
    • Ochman, H., and U. Bergthorsson. 1998. Rates and patterns of chromosome evolution in enteric bacteria. Curr. Opin. Microbiol. 1:580-583.
    • (1998) Curr. Opin. Microbiol. , vol.1 , pp. 580-583
    • Ochman, H.1    Bergthorsson, U.2
  • 39
    • 0036513591 scopus 로고    scopus 로고
    • EMBOSS opens up sequence analysis. European molecular biology open software suite
    • Olson, S. A. 2002. EMBOSS opens up sequence analysis. European molecular biology open software suite. Brief Bioinform. 3:87-91.
    • (2002) Brief Bioinform. , vol.3 , pp. 87-91
    • Olson, S.A.1
  • 40
    • 0035546223 scopus 로고    scopus 로고
    • Detection of lateral gene transfer among microbial genomes
    • Ragan, M. A. 2001a. Detection of lateral gene transfer among microbial genomes. Curr. Opin. Genet. Dev. 11:620-626.
    • (2001) Curr. Opin. Genet. Dev. , vol.11 , pp. 620-626
    • Ragan, M.A.1
  • 41
    • 0035943134 scopus 로고    scopus 로고
    • On surrogate methods for detecting lateral gene transfer
    • -. 2001b. On surrogate methods for detecting lateral gene transfer. FEMS Microbiol. Lett. 201:187-191.
    • (2001) FEMS Microbiol. Lett , vol.201 , pp. 187-191
  • 42
    • 0036145420 scopus 로고    scopus 로고
    • Reconciling the many faces of lateral gene transfer
    • -. 2002. Reconciling the many faces of lateral gene transfer. Trends Microbiol. 10:4.
    • (2002) Trends Microbiol. , vol.10 , pp. 4
  • 43
    • 0032102374 scopus 로고    scopus 로고
    • Ribosomal protein structures: Insights into the architecture, machinery and evolution of the ribosome
    • Ramakrishnan, V., and S. W. White. 1998. Ribosomal protein structures: insights into the architecture, machinery and evolution of the ribosome. Trends Biochem. Sci. 23:208-212.
    • (1998) Trends Biochem. Sci. , vol.23 , pp. 208-212
    • Ramakrishnan, V.1    White, S.W.2
  • 45
    • 0036966861 scopus 로고    scopus 로고
    • The role of conjugative transposons in spreading antibiotic resistance between bacteria that inhabit the gastrointestinal tract
    • Scott, K. P. 2002. The role of conjugative transposons in spreading antibiotic resistance between bacteria that inhabit the gastrointestinal tract. Cell Mol. Life Sci. 59:2071-2082.
    • (2002) Cell Mol. Life Sci. , vol.59 , pp. 2071-2082
    • Scott, K.P.1
  • 46
    • 0023650543 scopus 로고
    • The codon adaptation index - A measure of directional synonymous codon usage bias, and its potential applications
    • Sharp, P. M., and W. H. Li. 1987. The codon Adaptation Index-a measure of directional synonymous codon usage bias, and its potential applications. Nucleic Acids Res. 15:1281-1295.
    • (1987) Nucleic Acids Res. , vol.15 , pp. 1281-1295
    • Sharp, P.M.1    Li, W.H.2
  • 47
    • 0034871459 scopus 로고    scopus 로고
    • Why are translationally sub-optimal synonymous codons used in Escherichia coli?
    • Smith, N. G., and A. Eyre-Walker. 2001. Why are translationally sub-optimal synonymous codons used in Escherichia coli? J. Mol. Evol. 53:225-236.
    • (2001) J. Mol. Evol. , vol.53 , pp. 225-236
    • Smith, N.G.1    Eyre-Walker, A.2
  • 48
    • 0028606283 scopus 로고
    • Horizontal gene transfer: Evidence and possible consequences
    • Syvanen, M. 1994. Horizontal gene transfer: evidence and possible consequences. Annu. Rev. Genet. 28:237-261.
    • (1994) Annu. Rev. Genet. , vol.28 , pp. 237-261
    • Syvanen, M.1
  • 49
    • 0031574072 scopus 로고    scopus 로고
    • The ClustalX windows interface: Flexible strategies for multiple sequence alignment aided by quality analysis tools
    • Thompson, J. D., T. J. Gibson, F. Plewniak, F. Jeanmougin, and D. G. Higgins. 1997. The ClustalX 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
  • 50
    • 0034872741 scopus 로고    scopus 로고
    • Limitations of compositional approach to identifying horizontally transferred genes
    • Wang, B. 2001. Limitations of compositional approach to identifying horizontally transferred genes. J. Mol. Evol. 53:244-250.
    • (2001) J. Mol. Evol. , vol.53 , pp. 244-250
    • Wang, B.1
  • 52
    • 0033565598 scopus 로고    scopus 로고
    • Genetic recombination: Helicases and topoisomerases link up
    • Wu, L., J. K. Karow, and I. D. Hickson. 1999. Genetic recombination: helicases and topoisomerases link up. Curr. Biol. 9:R518-R520.
    • (1999) Curr. Biol. , vol.9
    • Wu, L.1    Karow, J.K.2    Hickson, I.D.3
  • 53
    • 0345328128 scopus 로고    scopus 로고
    • Gene sequences useful for predicting relatedness of whole genomes in bacteria
    • Zeigler, D. R. 2003. Gene sequences useful for predicting relatedness of whole genomes in bacteria. Int. J. Syst. Evol. Microbiol. 53:1893-1900.
    • (2003) Int. J. Syst. Evol. Microbiol. , vol.53 , pp. 1893-1900
    • Zeigler, D.R.1


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