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Volumn 5, Issue , 2005, Pages

Evolution of a microbial nitrilase gene family: A comparative and environmental genomics study

Author keywords

[No Author keywords available]

Indexed keywords

HYDROLASE; NITRILASE;

EID: 24344443169     PISSN: 14712148     EISSN: None     Source Type: Journal    
DOI: 10.1186/1471-2148-5-42     Document Type: Article
Times cited : (70)

References (68)
  • 1
    • 0030982247 scopus 로고    scopus 로고
    • A molecular view of microbial diversity and the biosphere
    • Pace NR: A molecular view of microbial diversity and the biosphere. Science 1997, 276:734-740.
    • (1997) Science , vol.276 , pp. 734-740
    • Pace, N.R.1
  • 3
    • 1842560595 scopus 로고    scopus 로고
    • Tapping into microbial diversity
    • Keller M, Zengler K: Tapping into microbial diversity. Nat Rev Microbiol 2004, 2:141-150.
    • (2004) Nat Rev Microbiol , vol.2 , pp. 141-150
    • Keller, M.1    Zengler, K.2
  • 4
    • 10344227692 scopus 로고    scopus 로고
    • Metagenomics: Application of genomics to uncultured microorganisms
    • Handelsman J: Metagenomics: application of genomics to uncultured microorganisms. Microbiol Mol Biol Rev 2004, 68:669-685.
    • (2004) Microbiol Mol Biol Rev , vol.68 , pp. 669-685
    • Handelsman, J.1
  • 12
    • 6944240079 scopus 로고    scopus 로고
    • Darwinian adaptation of proteorhodopsin to different light intensities in the marine environment
    • Bielawski JP, Dunn KA, Sabehi G, Beja O: Darwinian adaptation of proteorhodopsin to different light intensities in the marine environment. Proc Natl Acad Sci U S A 2004, 101:14824-14829.
    • (2004) Proc Natl Acad Sci U S A , vol.101 , pp. 14824-14829
    • Bielawski, J.P.1    Dunn, K.A.2    Sabehi, G.3    Beja, O.4
  • 14
    • 19144366814 scopus 로고    scopus 로고
    • Metagenomics and industrial applications 1
    • Lorenz P, Eck J: Metagenomics and industrial applications 1. Nat Rev Microbiol 2005, 3:510-516.
    • (2005) Nat Rev Microbiol , vol.3 , pp. 510-516
    • Lorenz, P.1    Eck, J.2
  • 16
    • 0037805644 scopus 로고    scopus 로고
    • Biotechnological prospects from metagenomics
    • Schloss PD, Handelsman J: Biotechnological prospects from metagenomics. Curr Opin Biotechnol 2003, 14:303-310.
    • (2003) Curr Opin Biotechnol , vol.14 , pp. 303-310
    • Schloss, P.D.1    Handelsman, J.2
  • 17
    • 0031300142 scopus 로고    scopus 로고
    • Recombinant approaches for accessing biodiversity
    • Short JM: Recombinant approaches for accessing biodiversity. Nat Biotechnol 1997, 15:1322-1323.
    • (1997) Nat Biotechnol , vol.15 , pp. 1322-1323
    • Short, J.M.1
  • 18
    • 0036909261 scopus 로고    scopus 로고
    • Catalysis in the nitrilase superfamily
    • Brenner C: Catalysis in the nitrilase superfamily. Curr Opin Struct Biol 2002, 12:775-782.
    • (2002) Curr Opin Struct Biol , vol.12 , pp. 775-782
    • Brenner, C.1
  • 19
    • 0345167149 scopus 로고    scopus 로고
    • The nitrilase family of CN hydrolysing enzymes - A comparative study
    • O'Reilly C, Turner PD: The nitrilase family of CN hydrolysing enzymes - a comparative study. J Appl Microbiol 2003, 95:1161-1174.
    • (2003) J Appl Microbiol , vol.95 , pp. 1161-1174
    • O'Reilly, C.1    Turner, P.D.2
  • 20
    • 0035114118 scopus 로고    scopus 로고
    • The nitrilase superfamily: Classification, structure and function
    • reviews0001.1-0001.9
    • Pace HC, Brenner C: The nitrilase superfamily: classification, structure and function. Genome Biol 2001, 2:reviews0001.1-0001.9.
    • (2001) Genome Biol , vol.2
    • Pace, H.C.1    Brenner, C.2
  • 21
    • 0034306448 scopus 로고    scopus 로고
    • Gene context conservation of a higher order than operons
    • Lathe WCIII, Snel B, Bork P: Gene context conservation of a higher order than operons. Trends Biochem Sci 2000, 25:474-479.
    • (2000) Trends Biochem Sci , vol.25 , pp. 474-479
    • Lathe III, W.C.1    Snel, B.2    Bork, P.3
  • 23
    • 0242440314 scopus 로고    scopus 로고
    • Gene organization: Selection, selfishness, and serendipity
    • Lawrence JG: Gene organization: selection, selfishness, and serendipity. Annu Rev Microbiol 2003, 57:419-440.
    • (2003) Annu Rev Microbiol , vol.57 , pp. 419-440
    • Lawrence, J.G.1
  • 24
    • 13944268797 scopus 로고    scopus 로고
    • A novel method for accurate operon predictions in all sequenced prokaryotes 3
    • Price MN, Huang KH, Alm EJ, Arkin AP: A novel method for accurate operon predictions in all sequenced prokaryotes 3. Nucleic Acids Res 2005, 33:880-892.
    • (2005) Nucleic Acids Res , vol.33 , pp. 880-892
    • Price, M.N.1    Huang, K.H.2    Alm, E.J.3    Arkin, A.P.4
  • 25
    • 0035798406 scopus 로고    scopus 로고
    • Assignment of homology to genome sequences using a library of hidden Markov models that represent all proteins of known structure
    • Gough J, Karplus K, Hughey R, Chothia C: Assignment of homology to genome sequences using a library of hidden Markov models that represent all proteins of known structure. J Mol Biol 2001, 313:903-919.
    • (2001) J Mol Biol , vol.313 , pp. 903-919
    • Gough, J.1    Karplus, K.2    Hughey, R.3    Chothia, C.4
  • 26
    • 0035282866 scopus 로고    scopus 로고
    • Radical SAM, a novel protein superfamily linking unresolved steps in familiar biosynthetic pathways with radical mechanisms: Functional characterization using new analysis and information visualization methods
    • Sofia HJ, Chen G, Hetzler BG, Reyes-Spindola JF, Miller NE: Radical SAM, a novel protein superfamily linking unresolved steps in familiar biosynthetic pathways with radical mechanisms: functional characterization using new analysis and information visualization methods. Nucleic Acids Res 2001, 29:1097-1106.
    • (2001) Nucleic Acids Res , vol.29 , pp. 1097-1106
    • Sofia, H.J.1    Chen, G.2    Hetzler, B.G.3    Reyes-Spindola, J.F.4    Miller, N.E.5
  • 27
    • 0033135707 scopus 로고    scopus 로고
    • Crystal structure of an aminoglycoside 6′-N-acetyltransferase: Defining the GCN5-related N-acetyltransferase superfamily fold
    • Wybenga-Groot LE, Draker K, Wright GD, Berghuis AM: Crystal structure of an aminoglycoside 6′-N-acetyltransferase: defining the GCN5-related N-acetyltransferase superfamily fold. Structure Fold Des 1999, 7:497-507.
    • (1999) Structure Fold Des , vol.7 , pp. 497-507
    • Wybenga-Groot, L.E.1    Draker, K.2    Wright, G.D.3    Berghuis, A.M.4
  • 28
    • 0029295437 scopus 로고
    • The MarR repressor of the multiple antibiotic resistance (mar) operon in Escherichia coli: Prototypic member of a family of bacterial regulatory proteins involved in sensing phenolic compounds
    • Sulavik MC, Gambino LF, Miller PF: The MarR repressor of the multiple antibiotic resistance (mar) operon in Escherichia coli: prototypic member of a family of bacterial regulatory proteins involved in sensing phenolic compounds. Mol Med 1995, 1:436-446.
    • (1995) Mol Med , vol.1 , pp. 436-446
    • Sulavik, M.C.1    Gambino, L.F.2    Miller, P.F.3
  • 30
    • 0036005636 scopus 로고    scopus 로고
    • Understanding nature's strategies for enzymecatalyzed racemization and epimerization
    • Tanner ME: Understanding nature's strategies for enzymecatalyzed racemization and epimerization. Acc Chem Res 2002, 35:237-246.
    • (2002) Acc Chem Res , vol.35 , pp. 237-246
    • Tanner, M.E.1
  • 31
    • 0034534035 scopus 로고    scopus 로고
    • Epoxide hydrolases: Biochemistry and molecular biology
    • Fretland AJ, Omiecinski CJ: Epoxide hydrolases: biochemistry and molecular biology. Chem Biol Interact 2000, 129:41-59.
    • (2000) Chem Biol Interact , vol.129 , pp. 41-59
    • Fretland, A.J.1    Omiecinski, C.J.2
  • 32
    • 0033639150 scopus 로고    scopus 로고
    • Statistical methods for detecting molecular adaptation
    • Yang Z, Bielawski JP: Statistical methods for detecting molecular adaptation. Trends Ecol Evol 2000, 15:496-503.
    • (2000) Trends Ecol Evol , vol.15 , pp. 496-503
    • Yang, Z.1    Bielawski, J.P.2
  • 33
    • 0036889183 scopus 로고    scopus 로고
    • Inference of selection from multiple species alignments
    • Yang Z: Inference of selection from multiple species alignments. Curr Opin Genet Dev 2002, 12:688-694.
    • (2002) Curr Opin Genet Dev , vol.12 , pp. 688-694
    • Yang, Z.1
  • 34
    • 0037270595 scopus 로고    scopus 로고
    • Maximum likelihood methods for detecting adaptive evolution after gene duplication
    • Bielawski JP, Yang Z: Maximum likelihood methods for detecting adaptive evolution after gene duplication. J Struct Funct Genomics 2003, 3:201-212.
    • (2003) J Struct Funct Genomics , vol.3 , pp. 201-212
    • Bielawski, J.P.1    Yang, Z.2
  • 35
    • 0032584099 scopus 로고    scopus 로고
    • Positive Darwinian selection after gene duplication in primate ribonuclease genes
    • Zhang J, Rosenberg HF, Nei M: Positive Darwinian selection after gene duplication in primate ribonuclease genes. Proc Natl Acad Sci U S A 1998, 95:3708-3713.
    • (1998) Proc Natl Acad Sci U S A , vol.95 , pp. 3708-3713
    • Zhang, J.1    Rosenberg, H.F.2    Nei, M.3
  • 36
    • 0028024626 scopus 로고
    • A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution rates, with application to the chloroplast genome
    • Muse SV, Gaut BS: A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution rates, with application to the chloroplast genome. Mol Biol Evol 1994, 11:715-724.
    • (1994) Mol Biol Evol , vol.11 , pp. 715-724
    • Muse, S.V.1    Gaut, B.S.2
  • 38
    • 0019255001 scopus 로고
    • Selective neutrality of 6PGD allozymes in E. coli and the effects of genetic background
    • Dykhuizen D, Hartl DL: Selective neutrality of 6PGD allozymes in E. coli and the effects of genetic background. Genetics 1980, 96:801-817.
    • (1980) Genetics , vol.96 , pp. 801-817
    • Dykhuizen, D.1    Hartl, D.L.2
  • 39
    • 0344824014 scopus 로고    scopus 로고
    • Convergent neofunctionalization by positive Darwinian selection after ancient recurrent duplications of the xanthine dehydrogenase gene
    • Rodriguez-Trelles F, Tarrio R, Ayala FJ: Convergent neofunctionalization by positive Darwinian selection after ancient recurrent duplications of the xanthine dehydrogenase gene. Proc Natl Acad Sci U S A 2003, 100:13413-13417.
    • (2003) Proc Natl Acad Sci U S A , vol.100 , pp. 13413-13417
    • Rodriguez-Trelles, F.1    Tarrio, R.2    Ayala, F.J.3
  • 40
    • 0037500141 scopus 로고    scopus 로고
    • Evolution by gene duplication: An update
    • Zhang J: Evolution by gene duplication: an update. Trends Ecol Evol 2003, 18:292-298.
    • (2003) Trends Ecol Evol , vol.18 , pp. 292-298
    • Zhang, J.1
  • 41
    • 0036855372 scopus 로고    scopus 로고
    • Simulation study of the reliability and robustness of the statistical methods for detecting positive selection at single amino acid sites
    • Suzuki Y, Nei M: Simulation study of the reliability and robustness of the statistical methods for detecting positive selection at single amino acid sites. Mol Biol Evol 2002, 19:1865-1869.
    • (2002) Mol Biol Evol , vol.19 , pp. 1865-1869
    • Suzuki, Y.1    Nei, M.2
  • 42
    • 1942533483 scopus 로고    scopus 로고
    • False positive selection identified by ML-based methods: Examples from the Sig1 gene of the diatom Thalassiosira weissflogii and the tax gene of a human T-cell lymphotropic virus
    • Suzuki Y, Nei M: False positive selection identified by ML-based methods: examples from the Sig1 gene of the diatom Thalassiosira weissflogii and the tax gene of a human T-cell lymphotropic virus. Mol Biol Evol 2004, 21:914-921.
    • (2004) Mol Biol Evol , vol.21 , pp. 914-921
    • Suzuki, Y.1    Nei, M.2
  • 43
    • 8544225780 scopus 로고    scopus 로고
    • Accuracy and power of statistical methods for detecting adaptive evolution in protein coding sequences and for identifying positively selected sites
    • Wong WS, Yang Z, Goldman N, Nielsen R: Accuracy and power of statistical methods for detecting adaptive evolution in protein coding sequences and for identifying positively selected sites. Genetics 2004, 168:1041-1051.
    • (2004) Genetics , vol.168 , pp. 1041-1051
    • Wong, W.S.1    Yang, Z.2    Goldman, N.3    Nielsen, R.4
  • 44
    • 0034097381 scopus 로고    scopus 로고
    • Codon-substitution models for heterogeneous selection pressure at amino acid sites
    • Yang Z, Nielsen R, Goldman N, Pedersen AM: Codon-substitution models for heterogeneous selection pressure at amino acid sites. Genetics 2000, 155:431-449.
    • (2000) Genetics , vol.155 , pp. 431-449
    • Yang, Z.1    Nielsen, R.2    Goldman, N.3    Pedersen, A.M.4
  • 45
    • 0030007094 scopus 로고    scopus 로고
    • Large-scale search for genes on which positive selection may operate 5
    • Endo T, Ikeo K, Gojobori T: Large-scale search for genes on which positive selection may operate 5. Mol Biol Evol 1996, 13:685-690.
    • (1996) Mol Biol Evol , vol.13 , pp. 685-690
    • Endo, T.1    Ikeo, K.2    Gojobori, T.3
  • 46
    • 0036270185 scopus 로고    scopus 로고
    • Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages
    • Yang Z, Nielsen R: Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages. Mol Biol Evol 2002, 19:908-917.
    • (2002) Mol Biol Evol , vol.19 , pp. 908-917
    • Yang, Z.1    Nielsen, R.2
  • 48
    • 0035895433 scopus 로고    scopus 로고
    • Crystal structure and site-directed mutagenesis studies of N-carbamoyl-D-aminoacid amidohydrolase from Agrobacterium radiobacter reveals a homotetramer and insight into a catalytic cleft
    • Wang WC, Hsu WH, Chien FT, Chen CY: Crystal structure and site-directed mutagenesis studies of N-carbamoyl-D-aminoacid amidohydrolase from Agrobacterium radiobacter reveals a homotetramer and insight into a catalytic cleft. J Mol Biol 2001, 306:251-261.
    • (2001) J Mol Biol , vol.306 , pp. 251-261
    • Wang, W.C.1    Hsu, W.H.2    Chien, F.T.3    Chen, C.Y.4
  • 50
    • 0033058895 scopus 로고    scopus 로고
    • Evolutionary instability of operon structures disclosed by sequence comparisons of complete microbial genomes
    • Itoh T, Takemoto K, Mori H, Gojobori T: Evolutionary instability of operon structures disclosed by sequence comparisons of complete microbial genomes. Mol Biol Evol 1999, 16:332-346.
    • (1999) Mol Biol Evol , vol.16 , pp. 332-346
    • Itoh, T.1    Takemoto, K.2    Mori, H.3    Gojobori, T.4
  • 51
    • 0035051602 scopus 로고    scopus 로고
    • A comparative genomics approach to prediction of new members of regulons
    • Tan K, Moreno-Hagelsieb G, Collado-Vides J, Stormo GD: A comparative genomics approach to prediction of new members of regulons. Genome Res 2001, 11:566-584.
    • (2001) Genome Res , vol.11 , pp. 566-584
    • Tan, K.1    Moreno-Hagelsieb, G.2    Collado-Vides, J.3    Stormo, G.D.4
  • 52
    • 0037398732 scopus 로고    scopus 로고
    • Missing genes in metabolic pathways: A comparative genomics approach
    • Osterman A, Overbeek R: Missing genes in metabolic pathways: a comparative genomics approach. Curr Opin Chem Biol 2003, 7:238-251.
    • (2003) Curr Opin Chem Biol , vol.7 , pp. 238-251
    • Osterman, A.1    Overbeek, R.2
  • 53
    • 0010414313 scopus 로고    scopus 로고
    • Evolution of gene order conservation in prokaryotes
    • Research0020
    • Tamames J: Evolution of gene order conservation in prokaryotes. Genome Biol 2001, 2(6):Research0020.
    • (2001) Genome Biol , vol.2 , Issue.6
    • Tamames, J.1
  • 54
    • 0043011009 scopus 로고    scopus 로고
    • Comparative genomics of Archaea: How much have we learned in six years, and what's next?
    • Makarova KS, Koonin EV: Comparative genomics of Archaea: how much have we learned in six years, and what's next? Genome Biol 2003, 4:115.
    • (2003) Genome Biol , vol.4 , pp. 115
    • Makarova, K.S.1    Koonin, E.V.2
  • 55
    • 0037397439 scopus 로고    scopus 로고
    • Definitions of enzyme function for the structural genomics era
    • Babbitt PC: Definitions of enzyme function for the structural genomics era. Curr Opin Chem Biol 2003, 7:230-237.
    • (2003) Curr Opin Chem Biol , vol.7 , pp. 230-237
    • Babbitt, P.C.1
  • 56
    • 4344685409 scopus 로고    scopus 로고
    • Microbial population genomics and ecology: The road ahead
    • DeLong EF: Microbial population genomics and ecology: the road ahead. Environ Microbiol 2004, 6:875-878.
    • (2004) Environ Microbiol , vol.6 , pp. 875-878
    • DeLong, E.F.1
  • 57
    • 1342300599 scopus 로고    scopus 로고
    • Environmental genomics, the big picture
    • Rodriguez-Valera F: Environmental genomics, the big picture. FEMS Microbiol Lett 2004, 231:153-158.
    • (2004) FEMS Microbiol Lett , vol.231 , pp. 153-158
    • Rodriguez-Valera, F.1
  • 58
    • 24344473498 scopus 로고    scopus 로고
    • The Institute for Genome Research 2005 [http://www.tigr.org].
    • (2005)
  • 59
    • 24344478308 scopus 로고    scopus 로고
    • DOE Joint Genome Institute 2005 [http://www.jgi.doe.gov/].
    • (2005)
  • 60
    • 24344497598 scopus 로고    scopus 로고
    • Hall T: BioEdit. 2005 [http://www.mbio.ncsu.edu/BioEdit/bioedit.html].
    • (2005) BioEdit
    • Hall, T.1
  • 61
    • 0000122573 scopus 로고
    • PHYLIP - Phylogeny Inference Package (Version3.2)
    • Felsenstein J: PHYLIP - Phylogeny Inference Package (Version3.2). Cladistics 1989, 5:164-166.
    • (1989) Cladistics , vol.5 , pp. 164-166
    • Felsenstein, J.1
  • 62
    • 0036205377 scopus 로고    scopus 로고
    • TREE-PUZZLE: Maximum likelihood phylogenetic analysis using quartets and parallel computing
    • Schmidt HA, Strimmer K, Vingron M, von Haeseler A: TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing. Bioinformatics 2002, 18:502-504.
    • (2002) Bioinformatics , vol.18 , pp. 502-504
    • Schmidt, H.A.1    Strimmer, K.2    Vingron, M.3    Von Haeseler, A.4
  • 64
    • 0031773680 scopus 로고    scopus 로고
    • MODELTEST: Testing the model of DNA substitution
    • Posada D, Crandall KA: MODELTEST: testing the model of DNA substitution. Bioinformatics 1998, 14:817-818.
    • (1998) Bioinformatics , vol.14 , pp. 817-818
    • Posada, D.1    Crandall, K.A.2
  • 65
    • 0030683599 scopus 로고    scopus 로고
    • PAML: A program package for phylogenetic analysis by maximum likelihood
    • Yang Z: PAML: a program package for phylogenetic analysis by maximum likelihood. Comput Appl Biosci 1997, 13:555-556.
    • (1997) Comput Appl Biosci , vol.13 , pp. 555-556
    • Yang, Z.1
  • 66
    • 0031897964 scopus 로고    scopus 로고
    • Likelihood ratio tests for detecting positive selection and application to primate lysozyme evolution
    • Yang Z: Likelihood ratio tests for detecting positive selection and application to primate lysozyme evolution. Mol Biol Evol 1998, 15:568-573.
    • (1998) Mol Biol Evol , vol.15 , pp. 568-573
    • Yang, Z.1


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