Structural divergence and adaptive evolution in mammalian cytochromes P450 2C

Gene

Volumn 387, Issue 1-2, 2007, Pages 58-66

  da Fonseca, Rute R ^a   Antunes, Agostinho ^a   Melo, André ^a   Ramos, Maria João ^a  

^a UNIVERSITY OF PORTO   (Portugal)

Author keywords

3D structure; Enzyme; Functional divergence; Positive selection

Indexed keywords

CARCINOGEN; CYTOCHROME P450 2C; XENOBIOTIC AGENT;

ARTICLE; ENZYME ACTIVE SITE; ENZYME SPECIFICITY; ENZYME STRUCTURE; GENETIC SELECTION; GENETIC VARIABILITY; MAMMALIAN GENETICS; MOLECULAR EVOLUTION; NONHUMAN; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN FUNCTION; THREE DIMENSIONAL IMAGING;

ANIMALS; COMPUTATIONAL BIOLOGY; CYTOCHROME P-450 ENZYME SYSTEM; EVOLUTION, MOLECULAR; GENOMICS; MAMMALS; PROTEIN FOLDING; PROTEIN STRUCTURE, SECONDARY; PROTEIN STRUCTURE, TERTIARY; STRUCTURE-ACTIVITY RELATIONSHIP; SUBSTRATE SPECIFICITY;

MAMMALIA;

EID: 33845624599     PISSN: 03781119     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.gene.2006.08.017     Document Type: Article

References (46)

1. Anzenbacher P., and Anzenbacherova E. Cytochromes P450 and metabolism of xenobiotics. Cell. Mol. Life Sci. 58 (2001) 737-747
2. Delaforge M., Pruvost A., Perrin L., and Andre F. Cytochrome P450-mediated oxidation of glucuronide derivatives: example of estradiol-17 beta-glucuronide oxidation to 2-hydroxyestradiol-17 beta-glucuronide by CYP2C8. Drug Metab. Dispos. 33 (2005) 466-473
3. Fares M.A. SWAPSC: sliding window analysis procedure to detect selective constraints. Bioinformatics 20 (2004) 2867-2868
4. Fares M.A., Barrio E., Sabater-Munoz B., and Moya A. The evolution of the heat-shock protein GroEL from Buchnera, the primary endosymbiont of aphids, is governed by positive selection. Mol. Biol. Evol. 19 (2002) 1162-1170
5. Fares M.A., Elena S.F., Ortiz J., Moya A., and Barrio E. A sliding window-based method to detect selective constraints in protein-coding genes and its application to RNA viruses. J. Mol. Evol. 55 (2002) 509-521
6. Galtier N., Gouy M., and Gautier C. SEAVIEW and PHYLO_WIN: two graphic tools for sequence alignment and molecular phylogeny. Comput. Appl. Biosci. 12 (1996) 543-548
7. Gaucher E.A., Miyamoto M.M., and Benner S.A. Function-structure analysis of proteins using covarion-based evolutionary approaches: elongation factors. PNAS 98 (2001) 548-552
8. Gotoh O. Substrate recognition sites in cytochrome P450 family 2 (CYP2) proteins inferred from comparative analyses of amino acid and coding nucleotide sequences. J. Biol. Chem. 267 (1992) 83-90
9. Gu X. Functional divergence in protein (family) sequence evolution. Genetica 118 (2003) 133-141
10. Guengerich F.P. Common and uncommon cytochrome P450 reactions related to metabolism and chemical toxicity. Chem. Res. Toxicol. 14 (2001) 611-650
11. Johnson E.F., Barnes H.J., Griffin K.J., Okino S., and Tukey R.H. Characterization of A 2Nd gene-product related to rabbit cytochrome-P-450-1. J. Biol. Chem. 262 (1987) 5918-5923
12. Jones D.T., Taylor W.R., and Thornton J.M. The rapid generation of mutation data matrices from protein sequences. Comput. Appl. Biosci. 8 (1992) 275-282
13. Knudsen B., and Farid N.R. Evolutionary divergence of thyrotropin receptor structure. Mol. Genet. Metab. 81 (2004) 322-334
14. Knudsen B., and Miyamoto M.M. A likelihood ratio test for evolutionary rate shifts and functional divergence among proteins. Proc. Natl. Acad. Sci. U. S. A. 98 (2001) 14512-14517
15. Knudsen B., Miyamoto M.M., Laipis P.J., and Silverman D.N. Using evolutionary rates to investigate protein functional divergence and conservation: a case study of the carbonic anhydrases (vol 164, pg 1261, 2002). Genetics 165 (2003) 453
16. Laethem R.M., and Koop D.R. Identification of rabbit cytochromes P450 2C1 and 2C2 as arachidonic acid epoxygenases. Molecular (1992) 958-963
17. Li W.H. Unbiased estimation of the rates of synonymous and nonsynonymous substitution. J. Mol. Evol. 36 (1993) 96-99
18. Luo G., Zeldin D.C., Blaisdell J.A., Hodgson E., and Goldstein J.A. Cloning and expression of murine CYP2Cs and their ability to metabolize arachidonic acid. Arch. Biochem. Biophys. 357 (1998) 45-57
19. McClellan D.A., Palfreyman E.J., Smith M.J., Moss J.L., Christensen R.G., and Sailsbery A.K. Physicochemical evolution and molecular adaptation of the cetacean and artiodactyl cytochrome b proteins. Mol. Biol. Evol. 22 (2005) 437-455
20. Miners J.O., and Birkett D.J. Cytochrome P4502C9: an enzyme of major importance in human drug metabolism. Br. J. Clin. Pharmacol. 45 (1998) 525-538
21. Nei M., and Gojobori T. Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol. Biol. Evol. 3 (1986) 418-426
22. Nelson D.R., Zeldin D.C., Hoffman S.M., Maltais L.J., Wain H.M., and Nebert D.W. Comparison of cytochrome P450 (CYP) genes from the mouse and human genomes, including nomenclature recommendations for genes, pseudogenes and alternative-splice variants. Pharmacogenetics 14 (2004) 1-18
23. Omiecinski C.J., Remmel R.P., and Hosagrahara V.P. Concise review of the cytochrome P450s and their roles in toxicology. Toxicol. Sci. 48 (1999) 151-156
24. Posada D., and Crandall K.A. MODELTEST: testing the model of DNA substitution. Bioinformatics 14 (1998) 817-818
25. Poulos T.L. Cytochrome P450. Curr. Opin. Struct. Biol. 5 (1995) 767-774
26. Pride D.T. SWAAP - a Tool for Analysing Substitutions and Similarity in Multiple Alignments (2000)
27. Ranson H., et al. Evolution of supergene families associated with insecticide resistance. Science 298 (2002) 179-181
28. Rifkind A.B., Lee C., Chang T.K.H., and Waxman D.J. Arachidonic-acid metabolism by human cytochrome P450S-2C8, cytochrome P450S-2C9, cytochrome P450S-2E1, and cytochrome P450S-1A2 - regioselective oxygenation and evidence for a role for Cyp2C enzymes in arachidonic-acid epoxygenation in human liver-microsomes. Arch. Biochem. Biophys. 320 (1995) 380-389
29. Sandberg M., Johansson I., Christensen M., Rane A., and Eliasson E. The impact of CYP2C9 genetics and oral contraceptives on cytochrome P4502C9 phenotype. Drug Metab. Dispos. 32 (2004) 484-489
30. Sawyer S.A. GENECONV: a computer package for the statistical detection of gene conversion. Distributed by the author, Department of Mathematics, Washington University in St. Louis. available at (1999). http://www.math.wustl.edu/~sawyer
31. Schleinkofer K., Winn P.J., Lüdemann S.K., and Wade R.C. Do mammalian cytochrome P450s show multiple ligand access pathways and ligand channelling?. EMBO Rep. 6 (2005) 584-589
32. * and Other Methods) (1998), Sinauer Associates, Sunderland, Massachusetts Version 4
33. Thompson J.D., Higgins D.G., and Gibson T.J. 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 (1994) 4673-4680
34. Totah R.A., and Rettie A.E. Cytochrome P4502C8: substrates, inhibitors, pharmacogenetics, and clinical relevance. Clin. Pharmacol. Ther. 77 (2005) 341-352
35. Uno T., Imai Y., Nakamura M., Okamoto N., and Fukuda T. Importance of successive prolines in the carboxy-terminal region of P450-2C2 and P450-2C14 for the hydroxylase-activities. J. Biochem. 114 (1993) 363-369
36. Wang B., Sanchez R.I., Franklin R.B., Evans D.C., and Huskey S.E.W. The involvement of CYP3A4 and CYP2C9 in the metabolism of 17 alpha-ethinylestradiol. Drug Metab. Dispos. 32 (2004) 1209-1212
37. Werck-Reichhart D., and Feyereisen R. Cytochromes P450: a success story. Genome Biol. 1 (2000) reviews 3003.1-3003.9
38. Williams P.A., Cosme J., Sridhar V., Johnson E.F., and McRee D.E. Microsomal cytochrome P450 2C5: comparison to microbial P450s and unique features. J. Inorg. Biochem. 81 (2000) 183-190
39. Wong W.S.W., Yang Z., Goldman N., and Nielsen R. Accuracy and power of statistical methods for detecting adaptive evolution in protein coding sequences and for identifying positively selected sites. Genetics 168 (2004) 1041-1051
40. Woolley S., Johnson J., Smith M.J., Crandall K.A., and McClellan D.A. TreeSAAP: selection on amino acid properties using phylogenetic trees. Bioinformatics 19 (2003) 671-672
41. Yang Z.H. PAML: a program package for phylogenetic analysis by maximum likelihood. Comput. Appl. Biosci. 13 (1997) 555-556
42. Yang Z.H. Likelihood ratio tests for detecting positive selection and application to primate lysozyme evolution. Mol. Biol. Evol. 15 (1998) 568-573
43. Yang Z.H. Maximum likelihood estimation on large phylogenies and analysis of adaptive evolution in human influenza virus A. J. Mol. Evol. 51 (2000) 423-432
44. Yang Z., Nielsen R., Goldman N., and Pedersen A.M.K. Codon-substitution models for heterogeneous selection pressure at amino acid sites. Genetics 155 (2000) 431-449
45. Yang Z.H., Wong W.S.W., and Nielsen R. Bayes empirical Bayes inference of amino acid sites under positive selection. Mol. Biol. Evol. 22 (2005) 1107-1118
46. Zhou S., et al. Therapeutic drugs that behave as mechanism-based inhibitors of cytochrome P450 3A4. Curr. Drug Metab. 5 (2004) 415-442