The CYP1D Subfamily of Genes in Mammals and Other Vertebrates

Overview

Journal Mamm Genome

Specialty Genetics

Date 2010 May 25

PMID 20495808

Citations 9

Authors

Yusuke K Kawai

Yoshinori Ikenaka

Shoichi Fujita

Mayumi Ishizuka

Affiliations

Soon will be listed here.

Abstract

Members of the cytochrome P450 family 1 (CYP1s) are involved in the detoxification and bioactivation of numerous environmental pollutants and phytochemicals such as polycyclic aromatic hydrocarbons (PAHs), aromatic amines, and flavonoids. The vertebrate CYP1 gene comprises four subfamilies: CYP1A, CYP1B, CYP1C, and CYP1D. Recently, the CYP1D gene was identified in fish, and subsequently in the platypus. These findings indicate the possibility that all vertebrates have a functional CYP1D subfamily. However, there is no information on the mammalian CYP1D gene. In this study we investigated the genomic location of CYP1D genes in mammals and other vertebrates in silico. We also performed phylogenetic analysis and calculated the identities and similarities of CYP1D sequences. The data from synteny and phylogenetic analyses of CYP1D genes demonstrated the evolutionary history of the CYP1 gene family. The results suggested that CYP1D became a nonfunctional pseudogene in human and bovine species; however, several other mammals possess functional CYP1D genes. The promoter regions of CYP1D genes were also examined. Unlike other CYP1 isoforms, few xenobiotic responsive element (XRE)-like sequences were found upstream of the CYP1D genes. Analysis of mammalian CYP1Ds also provided new insight into the relationship between CYP1 genes and the aryl hydrocarbon receptor.

Citing Articles

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References

Canestro C, Catchen J, Rodriguez-Mari A, Yokoi H, Postlethwait J . Consequences of lineage-specific gene loss on functional evolution of surviving paralogs: ALDH1A and retinoic acid signaling in vertebrate genomes. PLoS Genet. 2009; 5(5):e1000496. PMC: 2682703. DOI: 10.1371/journal.pgen.1000496. View

Goldstone J, Jonsson M, Behrendt L, Woodin B, Jenny M, Nelson D . Cytochrome P450 1D1: a novel CYP1A-related gene that is not transcriptionally activated by PCB126 or TCDD. Arch Biochem Biophys. 2008; 482(1-2):7-16. PMC: 2661202. DOI: 10.1016/j.abb.2008.12.002. View

Godard C, Goldstone J, Said M, Dickerson R, Woodin B, Stegeman J . The new vertebrate CYP1C family: cloning of new subfamily members and phylogenetic analysis. Biochem Biophys Res Commun. 2005; 331(4):1016-24. DOI: 10.1016/j.bbrc.2005.03.231. View

Jonsson M, Franks D, Woodin B, Jenny M, Garrick R, Behrendt L . The tryptophan photoproduct 6-formylindolo[3,2-b]carbazole (FICZ) binds multiple AHRs and induces multiple CYP1 genes via AHR2 in zebrafish. Chem Biol Interact. 2009; 181(3):447-54. PMC: 2838191. DOI: 10.1016/j.cbi.2009.07.003. View

Yang Z . PAML 4: phylogenetic analysis by maximum likelihood. Mol Biol Evol. 2007; 24(8):1586-91. DOI: 10.1093/molbev/msm088. View

Fujita Y, Ohi H, Murayama N, Saguchi K, Higuchi S . Molecular cloning and sequence analysis of cDNAs coding for 3-methylcholanthrene-inducible cytochromes P450 in Xenopus laevis liver. Arch Biochem Biophys. 1999; 371(1):24-8. DOI: 10.1006/abbi.1999.1425. View

Goldstone J, Goldstone H, Morrison A, Tarrant A, Kern S, Woodin B . Cytochrome P450 1 genes in early deuterostomes (tunicates and sea urchins) and vertebrates (chicken and frog): origin and diversification of the CYP1 gene family. Mol Biol Evol. 2007; 24(12):2619-31. DOI: 10.1093/molbev/msm200. View

Ronquist F, Huelsenbeck J . MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics. 2003; 19(12):1572-4. DOI: 10.1093/bioinformatics/btg180. View

Tamura K, Dudley J, Nei M, Kumar S . MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol Biol Evol. 2007; 24(8):1596-9. DOI: 10.1093/molbev/msm092. View

10.

Heinemeyer T, Wingender E, Reuter I, Hermjakob H, Kel A, Kel O . Databases on transcriptional regulation: TRANSFAC, TRRD and COMPEL. Nucleic Acids Res. 1998; 26(1):362-7. PMC: 147251. DOI: 10.1093/nar/26.1.362. View

11.

Zanette J, Jenny M, Goldstone J, Woodin B, Watka L, Bainy A . New cytochrome P450 1B1, 1C2 and 1D1 genes in the killifish Fundulus heteroclitus: Basal expression and response of five killifish CYP1s to the AHR agonist PCB126. Aquat Toxicol. 2009; 93(4):234-43. PMC: 2761021. DOI: 10.1016/j.aquatox.2009.05.008. View

12.

Keane T, Creevey C, Pentony M, Naughton T, Mclnerney J . Assessment of methods for amino acid matrix selection and their use on empirical data shows that ad hoc assumptions for choice of matrix are not justified. BMC Evol Biol. 2006; 6:29. PMC: 1435933. DOI: 10.1186/1471-2148-6-29. View

13.

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. 1992; 267(1):83-90. View

14.

Nebert D, Dalton T, Okey A, Gonzalez F . Role of aryl hydrocarbon receptor-mediated induction of the CYP1 enzymes in environmental toxicity and cancer. J Biol Chem. 2004; 279(23):23847-50. DOI: 10.1074/jbc.R400004200. View

15.

Rice P, Longden I, Bleasby A . EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000; 16(6):276-7. DOI: 10.1016/s0168-9525(00)02024-2. View

16.

Drummond A, Rambaut A . BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol Biol. 2007; 7:214. PMC: 2247476. DOI: 10.1186/1471-2148-7-214. View

17.

Jonsson M, Orrego R, Woodin B, Goldstone J, Stegeman J . Basal and 3,3',4,4',5-pentachlorobiphenyl-induced expression of cytochrome P450 1A, 1B and 1C genes in zebrafish. Toxicol Appl Pharmacol. 2007; 221(1):29-41. PMC: 4428972. DOI: 10.1016/j.taap.2007.02.017. View

18.

Sogawa K, Numayama-Tsuruta K, Takahashi T, Matsushita N, Miura C, Nikawa J . A novel induction mechanism of the rat CYP1A2 gene mediated by Ah receptor-Arnt heterodimer. Biochem Biophys Res Commun. 2004; 318(3):746-55. DOI: 10.1016/j.bbrc.2004.04.090. View

19.

Goldstone J, Stegeman J . Gene structure of the novel cytochrome P4501D1 genes in stickleback (Gasterosteus aculeatus) and medaka (Oryzias latipes). Mar Environ Res. 2008; 66(1):19-20. PMC: 3529149. DOI: 10.1016/j.marenvres.2008.02.011. View

20.

Goldstone H, Stegeman J . A revised evolutionary history of the CYP1A subfamily: gene duplication, gene conversion, and positive selection. J Mol Evol. 2006; 62(6):708-17. DOI: 10.1007/s00239-005-0134-z. View