메뉴 건너뛰기




Volumn 56, Issue 12, 2011, Pages 1246-1255

Prediction of sites under adaptive evolution in flavin-containing monooxygenases: Selection pattern revisited

Author keywords

adaptive evolution; evolutionary fingerprint; flavin containing monooxygenase; insertion domain; maximum likelihood; positive selection

Indexed keywords

ANURA; INVERTEBRATA; MAMMALIA; TAKIFUGU; TETRAODONTIDAE; VERTEBRATA;

EID: 79955156938     PISSN: 10016538     EISSN: 18619541     Source Type: Journal    
DOI: 10.1007/s11434-011-4380-8     Document Type: Article
Times cited : (8)

References (44)
  • 1
    • 19444375492 scopus 로고    scopus 로고
    • Mammalian flavin-containing monooxygenases: Structure/function, genetic polymorphisms and role in drug metabolism
    • Krueger S K, Williams D E. Mammalian flavin-containing monooxygenases: Structure/function, genetic polymorphisms and role in drug metabolism. Pharmacol Ther, 2005, 106: 357-387.
    • (2005) Pharmacol Ther , vol.106 , pp. 357-387
    • Krueger, S.K.1    Williams, D.E.2
  • 2
    • 44549087470 scopus 로고    scopus 로고
    • Flavin-containing monooxygenases: Mutations, disease and drug response
    • Phillips I R, Shephard E A. Flavin-containing monooxygenases: Mutations, disease and drug response. Trends Pharmacol Sci, 2008, 29: 294-301.
    • (2008) Trends Pharmacol Sci , vol.29 , pp. 294-301
    • Phillips, I.R.1    Shephard, E.A.2
  • 3
    • 38549120238 scopus 로고    scopus 로고
    • CYP3 phylogenomics: Evidence for positive selection of CYP3A4 and CYP3A7
    • Qiu H, Taudien S, Herlyn H, et al. CYP3 phylogenomics: Evidence for positive selection of CYP3A4 and CYP3A7. Pharmacogenet Genomics, 2008, 18: 53-66.
    • (2008) Pharmacogenet Genomics , vol.18 , pp. 53-66
    • Qiu, H.1    Taudien, S.2    Herlyn, H.3
  • 4
    • 44649143137 scopus 로고    scopus 로고
    • Prediction of sites under adaptive evolution in cytochrome P450 sequences and their relationship to substrate recognition sites
    • Zawaira A, Matimba A, Masimirembwa C. Prediction of sites under adaptive evolution in cytochrome P450 sequences and their relationship to substrate recognition sites. Pharmacogenet Genomics, 2008, 18: 467-476.
    • (2008) Pharmacogenet Genomics , vol.18 , pp. 467-476
    • Zawaira, A.1    Matimba, A.2    Masimirembwa, C.3
  • 5
    • 70449569063 scopus 로고    scopus 로고
    • Molecular population genetics of human CYP3A locus: Signatures of positive selection and implications for evolutionary environmental medicine
    • Chen X, Wang H, Zhou G, et al. Molecular population genetics of human CYP3A locus: Signatures of positive selection and implications for evolutionary environmental medicine. Environ Health Perspect, 2009, 117: 1541-1548.
    • (2009) Environ Health Perspect , vol.117 , pp. 1541-1548
    • Chen, X.1    Wang, H.2    Zhou, G.3
  • 6
    • 34648847287 scopus 로고    scopus 로고
    • Molecular evolution and balancing selection in the flavin-containing monooxygenase 3 gene (FMO 3)
    • Allerston C K, Shimizu M, Fujieda M, et al. Molecular evolution and balancing selection in the flavin-containing monooxygenase 3 gene (FMO 3). Pharmacogenet Genomics, 2007, 17: 827-839.
    • (2007) Pharmacogenet Genomics , vol.17 , pp. 827-839
    • Allerston, C.K.1    Shimizu, M.2    Fujieda, M.3
  • 7
    • 70350102615 scopus 로고    scopus 로고
    • Molecular phylogeny, long-term evolution, and functional divergence of flavin-containing monooxygenases
    • Hao D C, Chen S L, Xiao P G, et al. Molecular phylogeny, long-term evolution, and functional divergence of flavin-containing monooxygenases. Genetica, 2009, 137: 173-187.
    • (2009) Genetica , vol.137 , pp. 173-187
    • Hao, D.C.1    Chen, S.L.2    Xiao, P.G.3
  • 8
    • 33750995860 scopus 로고    scopus 로고
    • The genome of the sea urchin Strongylocentrotus purpuratus
    • Sea Urchin Genome Sequencing Consortium
    • Sea Urchin Genome Sequencing Consortium. The genome of the sea urchin Strongylocentrotus purpuratus. Science, 2006, 314: 941-952.
    • (2006) Science , vol.314 , pp. 941-952
  • 9
    • 0031743421 scopus 로고    scopus 로고
    • Profile hidden Markov models
    • Eddy S R. Profile hidden Markov models. Bioinformatics, 1998, 14: 755-763.
    • (1998) Bioinformatics , vol.14 , pp. 755-763
    • Eddy, S.R.1
  • 12
  • 13
    • 0043123111 scopus 로고    scopus 로고
    • RevTrans: Multiple alignment of coding DNA from aligned amino acid sequences
    • Wernersson R, Pedersen A G. RevTrans: Multiple alignment of coding DNA from aligned amino acid sequences. Nucleic Acids Res, 2003, 31: 3537-3539.
    • (2003) Nucleic Acids Res , vol.31 , pp. 3537-3539
    • Wernersson, R.1    Pedersen, A.G.2
  • 14
    • 0023375195 scopus 로고
    • The neighbor-joining method: A new method for reconstructing phylogenetic trees
    • Saitou N, Nei M. The neighbor-joining method: A new method for reconstructing phylogenetic trees. Mol Biol Evol, 1987, 4: 406-425.
    • (1987) Mol Biol Evol , vol.4 , pp. 406-425
    • Saitou, N.1    Nei, M.2
  • 15
    • 34547781750 scopus 로고    scopus 로고
    • MEGA4: Molecular evolutionary genetics analysis (MEGA) software version 4.0
    • Tamura K, Dudley J, Nei M. MEGA4: Molecular evolutionary genetics analysis (MEGA) software version 4. 0. Mol Biol Evol, 2007, 24: 1596-1599.
    • (2007) Mol Biol Evol , vol.24 , pp. 1596-1599
    • Tamura, K.1    Dudley, J.2    Nei, M.3
  • 16
    • 18744382506 scopus 로고    scopus 로고
    • ProtTest: Selection of best-fit models of protein evolution
    • Abascal F, Zardoya R, Posada D. ProtTest: Selection of best-fit models of protein evolution. Bioinformatics, 2005, 21: 2104-2105.
    • (2005) Bioinformatics , vol.21 , pp. 2104-2105
    • Abascal, F.1    Zardoya, R.2    Posada, D.3
  • 17
    • 0041386108 scopus 로고    scopus 로고
    • MrBayes 3: Bayesian phylogenetic inference under mixed models
    • Ronquist F, Huelsenbeck J P. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics, 2003, 19: 1572-1574.
    • (2003) Bioinformatics , vol.19 , pp. 1572-1574
    • Ronquist, F.1    Huelsenbeck, J.P.2
  • 19
  • 20
    • 0037099627 scopus 로고    scopus 로고
    • Molecular cloning and characterization of a full-length flavin-dependent monooxygenase from yeast
    • Zhang M, Robertus J D. Molecular cloning and characterization of a full-length flavin-dependent monooxygenase from yeast. Arch Biochem Biophys, 2002, 403: 277-283.
    • (2002) Arch Biochem Biophys , vol.403 , pp. 277-283
    • Zhang, M.1    Robertus, J.D.2
  • 21
    • 0034097381 scopus 로고    scopus 로고
    • Codon-substitution models for heterogeneous selection pressure at amino acid sites
    • Yang Z, Nielsen R, Goldman N. 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
  • 22
    • 34547803197 scopus 로고    scopus 로고
    • PAML 4: A program package for phylogenetic analysis by maximum likelihood
    • Yang Z. PAML 4: A program package for phylogenetic analysis by maximum likelihood. Mol Biol Evol, 2007, 24: 1586-1591.
    • (2007) Mol Biol Evol , vol.24 , pp. 1586-1591
    • Yang, Z.1
  • 23
    • 33846818777 scopus 로고    scopus 로고
    • Combined empirical and mechanistic codon model
    • Doron-Faigenboim A, Pupko T A. Combined empirical and mechanistic codon model. Mol Biol Evol, 2007, 24: 388-397.
    • (2007) Mol Biol Evol , vol.24 , pp. 388-397
    • Doron-Faigenboim, A.1    Pupko, T.A.2
  • 24
    • 17744396121 scopus 로고    scopus 로고
    • Not so different after all: A comparison of methods for detecting amino acid sites under selection
    • Kosakovsky P S L, Frost S D. Not so different after all: A comparison of methods for detecting amino acid sites under selection. Mol Biol Evol, 2005, 22: 1208-1222.
    • (2005) Mol Biol Evol , vol.22 , pp. 1208-1222
    • Kosakovsky, P.S.L.1    Frost, S.D.2
  • 25
    • 17744395033 scopus 로고    scopus 로고
    • Datamonkey: Rapid detection of selective pressure on individual sites of codon alignments
    • Kosakovsky P S L, Frost S D. Datamonkey: Rapid detection of selective pressure on individual sites of codon alignments. Bioinformatics, 2005, 21: 2531-2533.
    • (2005) Bioinformatics , vol.21 , pp. 2531-2533
    • Kosakovsky, P.S.L.1    Frost, S.D.2
  • 27
    • 0041571683 scopus 로고    scopus 로고
    • Parallel functional changes in the digestive RNases of ruminants and colobines by divergent amino acid substitutions
    • Zhang J. Parallel functional changes in the digestive RNases of ruminants and colobines by divergent amino acid substitutions. Mol Biol Evol, 2003, 20: 1310-1317.
    • (2003) Mol Biol Evol , vol.20 , pp. 1310-1317
    • Zhang, J.1
  • 28
    • 0028820333 scopus 로고
    • A new method of inference of ancestral nucleotide and amino acid sequences
    • Yang Z, Kumar S, Nei M. A new method of inference of ancestral nucleotide and amino acid sequences. Genetics, 1995, 141: 1641-1650.
    • (1995) Genetics , vol.141 , pp. 1641-1650
    • Yang, Z.1    Kumar, S.2    Nei, M.3
  • 29
    • 0016197604 scopus 로고
    • Amino-acid difference formula to help explain protein evolution
    • Grantham R. Amino-acid difference formula to help explain protein evolution. Science, 1974, 185: 862-864.
    • (1974) Science , vol.185 , pp. 862-864
    • Grantham, R.1
  • 30
    • 3242768556 scopus 로고    scopus 로고
    • A universal evolutionary index for amino acid changes
    • Tang H, Wyckoff G J, Lu J, et al. A universal evolutionary index for amino acid changes. Mol Biol Evol, 2004, 21: 1548-1556.
    • (2004) Mol Biol Evol , vol.21 , pp. 1548-1556
    • Tang, H.1    Wyckoff, G.J.2    Lu, J.3
  • 31
    • 44349089600 scopus 로고    scopus 로고
    • Revealing the moonlighting role of NADP in the structure of a flavin-containing monooxygenase
    • Alfieri A, Malito E, Orru R, et al. Revealing the moonlighting role of NADP in the structure of a flavin-containing monooxygenase. Proc Natl Acad Sci USA, 2008, 105: 6572-6577.
    • (2008) Proc Natl Acad Sci USA , vol.105 , pp. 6572-6577
    • Alfieri, A.1    Malito, E.2    Orru, R.3
  • 32
    • 53549126881 scopus 로고    scopus 로고
    • The potentially deleterious functional variant flavin-containing monooxygenase 2*1 is at high frequency throughout sub-Saharan Africa
    • Veeramah K R, Thomas M G, Weale M E. The potentially deleterious functional variant flavin-containing monooxygenase 2*1 is at high frequency throughout sub-Saharan Africa. Pharmacogenet Genomics, 2008, 18: 877-886.
    • (2008) Pharmacogenet Genomics , vol.18 , pp. 877-886
    • Veeramah, K.R.1    Thomas, M.G.2    Weale, M.E.3
  • 33
    • 27944477670 scopus 로고    scopus 로고
    • Concerted and birth-and-death evolution of multigene families
    • Nei M, Rooney A P. Concerted and birth-and-death evolution of multigene families. Annu Rev Genet, 2005, 39: 121-152.
    • (2005) Annu Rev Genet , vol.39 , pp. 121-152
    • Nei, M.1    Rooney, A.P.2
  • 34
    • 1342309263 scopus 로고    scopus 로고
    • Organization and evolution of the flavin-containing monooxygenase genes of human and mouse: Identification of novel gene and pseudogene clusters
    • Hernandez D, Janmohamed A, Chandan P. Organization and evolution of the flavin-containing monooxygenase genes of human and mouse: Identification of novel gene and pseudogene clusters. Pharmacogenetics, 2004, 14: 117-130.
    • (2004) Pharmacogenetics , vol.14 , pp. 117-130
    • Hernandez, D.1    Janmohamed, A.2    Chandan, P.3
  • 35
    • 0021710490 scopus 로고
    • Nonrandomness of point mutation as reflected in nucleotide substitutions in pseudogenes and its evolutionary implications
    • Li W H, Wu C I, Luo C C. Nonrandomness of point mutation as reflected in nucleotide substitutions in pseudogenes and its evolutionary implications. J Mol Evol, 1984, 21: 58-71.
    • (1984) J Mol Evol , vol.21 , pp. 58-71
    • Li, W.H.1    Wu, C.I.2    Luo, C.C.3
  • 36
    • 29944437885 scopus 로고    scopus 로고
    • Quantitative analysis of FMO gene mRNA levels in human tissues
    • Zhang J, Cashman J R. Quantitative analysis of FMO gene mRNA levels in human tissues. Drug Metab Dispos, 2006, 34: 19-26.
    • (2006) Drug Metab Dispos , vol.34 , pp. 19-26
    • Zhang, J.1    Cashman, J.R.2
  • 37
    • 0028930879 scopus 로고
    • Characterization of flavin-containing monooxygenase 5 (FMO 5) cloned from human and guinea pig: Evidence that the unique catalytic properties of FMO 5 are not confined to the rabbit ortholog
    • Overby L H, Buckpitt A R, Lawton M P. Characterization of flavin-containing monooxygenase 5 (FMO 5) cloned from human and guinea pig: Evidence that the unique catalytic properties of FMO 5 are not confined to the rabbit ortholog. Arch Biochem Biophys, 1995, 317: 275-284.
    • (1995) Arch Biochem Biophys , vol.317 , pp. 275-284
    • Overby, L.H.1    Buckpitt, A.R.2    Lawton, M.P.3
  • 38
    • 0031878122 scopus 로고    scopus 로고
    • Physiological factors affecting protein expression of flavin-containing monooxygenases 1, 3 and 5
    • Cherrington N J, Cao Y, Cherrington J W. Physiological factors affecting protein expression of flavin-containing monooxygenases 1, 3 and 5. Xenobiotica, 1998, 28: 673-682.
    • (1998) Xenobiotica , vol.28 , pp. 673-682
    • Cherrington, N.J.1    Cao, Y.2    Cherrington, J.W.3
  • 39
    • 1642498339 scopus 로고    scopus 로고
    • S-oxidation of S-methylesonarimod by flavin-containing monooxygenases in human liver microsomes
    • Ohmi N, Yoshida H, Endo H. S-oxidation of S-methylesonarimod by flavin-containing monooxygenases in human liver microsomes. Xenobiotica, 2003, 33: 1221-1231.
    • (2003) Xenobiotica , vol.33 , pp. 1221-1231
    • Ohmi, N.1    Yoshida, H.2    Endo, H.3
  • 40
    • 38149024191 scopus 로고    scopus 로고
    • Transcriptome and proteome profiling of colon mucosa from quercetin fed F344 rats point to tumor preventive mechanisms, increased mitochondrial fatty acid degradation and decreased glycolysis
    • Dihal A A, van der Woude H, Hendriksen P J, et al. Transcriptome and proteome profiling of colon mucosa from quercetin fed F344 rats point to tumor preventive mechanisms, increased mitochondrial fatty acid degradation and decreased glycolysis. Proteomics, 2008, 8: 45-61.
    • (2008) Proteomics , vol.8 , pp. 45-61
    • Dihal, A.A.1    van der Woude, H.2    Hendriksen, P.J.3
  • 41
    • 78650726697 scopus 로고    scopus 로고
    • A Baeyer-Villiger oxidation specifically catalyzed by human flavin-containing monooxygenase 5 (FMO 5)
    • Lai W G, Farah N, Moniz G A, et al. A Baeyer-Villiger oxidation specifically catalyzed by human flavin-containing monooxygenase 5 (FMO 5). Drug Metab Dispos, 2011, 39: 61-70.
    • (2011) Drug Metab Dispos , vol.39 , pp. 61-70
    • Lai, W.G.1    Farah, N.2    Moniz, G.A.3
  • 42
    • 77951294696 scopus 로고    scopus 로고
    • Modulation of stress genes expression profile by nitric oxide-releasing aspirin in Jurkat T leukemia cells
    • Nath N, Chattopadhyay M, Kodela R, et al. Modulation of stress genes expression profile by nitric oxide-releasing aspirin in Jurkat T leukemia cells. Biochem Pharmacol, 2010, 79: 1759-1771.
    • (2010) Biochem Pharmacol , vol.79 , pp. 1759-1771
    • Nath, N.1    Chattopadhyay, M.2    Kodela, R.3
  • 43
    • 0037974644 scopus 로고    scopus 로고
    • Two new polymorphisms of the FMO 3 gene in Caucasian and African-American populations: Comparative genetic and functional studies
    • Lattard V, Zhang J, Tran Q, et al. Two new polymorphisms of the FMO 3 gene in Caucasian and African-American populations: Comparative genetic and functional studies. Drug Metab Dispos, 2003, 31: 854-860.
    • (2003) Drug Metab Dispos , vol.31 , pp. 854-860
    • Lattard, V.1    Zhang, J.2    Tran, Q.3
  • 44
    • 33751535481 scopus 로고    scopus 로고
    • Investigation of structure and function of a catalytically efficient variant of the human flavin-containing monooxygenase form 3
    • Orbás T, Zhang J, Cerny M A, et al. Investigation of structure and function of a catalytically efficient variant of the human flavin-containing monooxygenase form 3. Drug Metab Dispos, 2006, 34: 1995-2002.
    • (2006) Drug Metab Dispos , vol.34 , pp. 1995-2002
    • Orbás, T.1    Zhang, J.2    Cerny, M.A.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.