A revised evolutionary history of the CYP1A subfamily: Gene duplication, gene conversion, and positive selection

Journal of Molecular Evolution

Volumn 62, Issue 6, 2006, Pages 708-717

  Goldstone, Heather M H ^a,b   Stegeman, John J ^a  

^a WOODS HOLE OCEANOGRAPHIC INSTITUTION   (United States)

^b MARINE BIOLOGICAL LABORATORY   (United States)

Author keywords

Chicken; Cytochrome P450; Gene conversion; Gene duplication; Mammalian

Indexed keywords

CYTOCHROME P450 1A; CYTOCHROME P450 1A1; CYTOCHROME P450 1A2; CYTOCHROME P450 1A4; CYTOCHROME P450 1A5; PROTEIN; UNCLASSIFIED DRUG;

ANIMAL CELL; ARTICLE; BIRD; CHICKEN; CHROMOSOME PAIRING; COMPARATIVE STUDY; CONTROLLED STUDY; FOWL; GENE; GENE CONVERSION; GENE DUPLICATION; GENE SEQUENCE; GENOMICS; MAMMAL; MOLECULAR EVOLUTION; MULTIGENE FAMILY; NONHUMAN; NUCLEOTIDE SEQUENCE; PARALOGY; SYNTENY;

ANIMALS; CHICKENS; CYTOCHROME P-450 CYP1A1; EVOLUTION, MOLECULAR; GENE CONVERSION; GENE DUPLICATION; HUMANS; MICE; MULTIGENE FAMILY; PHYLOGENY; RECOMBINATION, GENETIC; SELECTION (GENETICS); SEQUENCE ALIGNMENT; SYNTENY;

AVES; MAMMALIA; VERTEBRATA;

EID: 33744911365     PISSN: 00222844     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00239-005-0134-z     Document Type: Article

References (42)

1. Aguileta G, Bielawski JP, Yang Z (2004) Gene conversion and functional divergence in the beta-globin gene family. J Mol Evol 59:177-189
2. Atchison M, Adesnik M (1986) Gene conversion in a cytochrome P-450 gene family. Proc Natl Acad Sci U S A 83:2300-2304
3. Balding DJ, Nichols RA, Hunt DM (1992) Detecting gene conversion: primate visual pigment genes. Proc Biol Sci 249:275-280
4. Crooijmans RP, Dijkhof RJ, Veenendaal T, van der Poel JJ, Nicholls RD, Bovenhuis H, Groenen MA (2001) The gene orders on human chromosome 15 and chicken chromosome 10 reveal multiple inter- and intrachromosomal rearrangements. Mol Biol Evol 18:2102-2109
5. Drouin G, Prat F, Ell M, Clarke GD (1999) Detecting and characterizing gene conversions between multigene family members. Mol Biol Evol 16:1369-1390
6. Elskus AA, Monosson E, McElroy AE, Stegeman JJ, Woltering DS (1999) Altered CYP1A expression in Fundulus heteroclitus adults and larvae: a sign of pollutant resistance? Aquatic Toxicol 45:99-113
7. Fujita Y, Ohi H, Murayama N, Saguchi K, Higuchi S (1999) Molecular cloning and sequence analysis of cDNAs coding for 3-methylcholanthrene-inducible cytochromes P450 in Xenopus laevis liver. Arch Biochem Biophys 371:24-28
8. Gilday D, Gannon M, Yutzey K, Bader D, Rifkind AB (1996a) Molecular cloning and expression of two novel avian cytochrome P450 1A enzymes induced by 2,3,7,8-tetrachlorodibenzo-p-dioxin. J Biol Chem 271:33054-33059
9. Gilday D, Yutzey K, Bader D, Rifkind AB (1996b) Molecular cloning of two TCDD-induced chicken CYP1A related enzymes distinct from mammalian CYP1A1 and 1A2. FASEB J 10:A283
10. Godard CAJ, Goldstone JV, Said MR, Dickerson RL, Woodin BR, Stegeman JJ (2005) The new vertebrate CYP1C family: cloning of new subfamily members and phylogenetic analysis. Biochem Biophys Res Commun 331:1016-1024
11. Gonzalez FJ, Kimura S (2003) Study of P450 function using gene knockout and transgenic mice. Arch Biochem Biophys 409:153-158
12. Gorman N, Walton HS, Sinclair JF, Sinclair PR (1998) CYP1A-catalyzed uroporphyrinogen oxidation in hepatic microsomes from non-mammalian vertebrates (chicken and duck embryos, scup and alligator). Comp Biochem Physiol 121C:405-412
13. Innan H (2003) A two-locus gene conversion model with selection and its application to the human RHCE and RHD genes. Proc Natl Acad Sci USA 100:8793-8798
14. Jeffreys AJ, May CA (2004) Intense and highly localized gene conversion activity in human meiotic crossover hot spots. Nat Genet 36:151-156
15. Jouvin-Marche E, Heller M, Rudikoff S (1986) Gene correction in the evolution of the T cell receptor beta chain. J Exp Med 164:2083-2088
16. 3-450 cDNA nucleotide and amino acid sequences. J Biol Chem 259:10705-10713
17. Mahajan SS, Rifkind AB (1999) Transcriptional activation of avian CYP1A4 and CYP1A5 by 2,3,7, 8-tetrachlorodibenzo-p-dioxin: differences in gene expression and regulation compared to mammalian CYP1A1 and CYP1A2. Toxicol Appl Pharmacol 155:96-106
18. Mahata SC, Mitsuo R, Aoki J-y, Kato H, Itakura T (2003) Two forms of cytochrome P450 cDNA from 3-methylcholanthrene-treated European eel Anguilla anguilla. Fish Sci 69:615-624
19. Martin DP, Williamson C, Posada D (2005) RDP2: recombination detection and analysis from sequence alignments. Bioinformatics 21:260-262
20. Michelson AM, Orkin SH (1983) Boundaries of gene conversion within the duplicated human alpha-globin genes. Concerted evolution by segmental recombination. J Biol Chem 258:15245-15254
21. Morrison HG, Oleksiak MF, Cornell NW, Sogin ML, Stegeman JJ (1995) Identification of cytochrome P-450 1A (CYP1A) genes from two teleost fish, toadfish (Opsanus tau) and scup (Stenotomus chrysops), and phylogenetic analysis of CYP1A genes. Biochem J 308(Pt 1):97-104
22. Morrison HG, Weil EJ, Karchner SI, Sogin ML, Stegeman JJ (1998) Molecular cloning of CYP1A from the estuarine fish Fundulus heteroclitus and phylogenetic analysis of CYP1A genes: Update with new sequences. Comp Biochem Physiol 121C:231-240
23. Nasar F, Jankowski C, Nag DK (2000) Long palindromic sequences induce double-strand breaks during meiosis in yeast. Mol Cell Biol 20:3449-3458
24. Okino ST, Quattrochi LC, Barnes HJ, Osanto S, Griffin KJ, Johnson EF, Tukey RH (1985) Cloning and characterization of cDNAs encoding 2,3,7,8-tetrachlorodibenzo-p-dioxin-inducible rabbit mRNAs for cytochrome P-450 isozymes 4 and 6. Proc Natl Acad Sci USA 82:5310-5314
25. Paraskevis D, Deforche K, Lemey P, Magiorkinis G, Hatzakis A, Vandamme AM (2005) SlidingBayes: exploring recombination using a sliding window approach based on Bayesian phylogenetic inference. Bioinformatics 21:1274-1275
26. Pascoe L, Curnow KM, Slutsker L, Connell JM, Speiser PW, New MI, White PC (1992) Glucocorticoid-suppressible hyperaldosteronism results from hybrid genes created by unequal crossovers between CYP11B1 and CYP11B2. Proc Natl Acad Sci USA 89:8327-8331
27. Posada D (2002) Evaluation of methods for detecting recombination from DNA sequences: empirical data. Mol Biol Evol 19:708-717
28. Posada D, Crandall KA (2001) Evaluation of methods for detecting recombination from DNA sequences: computer simulations. Proc Natl Acad Sci U S A 98:13757-13762
29. Quattrochi LC, Okino ST, Pendurthi UR, Tukey RH (1985) Cloning and isolation of human cytochrome P-450 cDNAs homologous to dioxin-inducible rabbit mRNAs encoding P-450 4 and P-450 6. DNA 4:395-400
30. Rabergh CM, Vrolijk NH, Lipsky MM, Chen TT (2000) Differential expression of two CYP1A genes in rainbow trout (Oncorhynchus mykiss). Toxicol Appl Pharmacol 165:195-205
31. Rifkind AB, Kanetoshi A, Orlinick J, Capdevila JH, Lee C (1994) Purification and biochemical characterization of two major cytochrome P-450 isoforms induced by 2,3,7,8-tetrachlorodibenzo-p-dioxin in chick embryo liver. J Biol Chem 269:3387-3396
32. Rozen S, Skaletsky H, Marszalek JD, Minx PJ, Cordum HS, Waterston RH, Wilson RK, Page DC (2003) Abundant gene conversion between arms of palindromes in human and ape Y chromosomes. Nature 423:873-876
33. Rudikoff S, Fitch WM, Heller M (1992) Exon-specific gene correction (conversion) during short evolutionary periods: homogenization in a two-gene family encoding the beta-chain constant region of the T-lymphocyte antigen receptor. Mol Biol Evol 9:14-26
34. Sinclair PR, Gorman N, Tsyrlov IB, Fuhr U, Walton HS, Sinclair JF (1998) Uroporphyrinogen oxidation catalyzed by human cytochromes P450. Drug Metab Dispos 26:1019-1025
35. Sinnott P, Collier S, Costigan C, Dyer PA, Harris R, Strachan T (1990) Genesis by meiotic unequal crossover of a de novo deletion that contributes to steroid 21-hydroxylase deficiency. Proc Natl Acad Sci U S A 87:2107-2111
36. Teraoka H, Dong W, Tsujimoto Y, Iwasa H, Endoh D, Ueno N, Stegeman JJ, Peterson RE, Hiraga T (2003) Induction of cytochrome P450 1A is required for circulation failure and edema by 2,3,7,8-tetrachlorodibenzo-p-dioxin in zebrafish. Biochem Biophys Res Commun 304:223-228
37. Teshima KM, Innan H (2004) The effect of gene conversion on the divergence between duplicated genes. Genetics 166:1553-1560
38. 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
39. Werck-Reichhart D, Feyereisen R (2000) Cytochromes P450: A success story. Genome Biol (6): reviews 3003.1-9
40. Wiuf C, Christensen T, Hein J (2001) A simulation study of the reliability of recombination detection methods. Mol Biol Evol 18:1929-1239
41. Yang Z (1997) PAML: a program package for phylogenetic analysis by maximum likelihood. Comput Appl Biosci 13:555-556
42. Yawetz A, Woodin BR, Stegeman JJ (1998) Cytochromes P450 (CYP) in liver of the turtle Chysemys picta picta and the induction and partial purification of CYP1A-like proteins. Biochim Biophys Acta 1381:12-26