Mammalian Genome

, Volume 21, Issue 5–6, pp 320–329 | Cite as

The CYP1D subfamily of genes in mammals and other vertebrates

  • Yusuke K. Kawai
  • Yoshinori Ikenaka
  • Shoichi Fujita
  • Mayumi Ishizuka
Article

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.

References

  1. Cañestro C, Catchen JM, Rodríguez-Marí A, Yokoi H, Postlethwait JH (2009) Consequences of lineage-specific gene loss on functional evolution of surviving paralogs: ALDH1A and retinoic acid signaling in vertebrate genomes. PLoS Genet 5:e1000496CrossRefPubMedGoogle Scholar
  2. Drummond AJ, Rambaut A (2007) BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol Biol 7:214CrossRefPubMedGoogle Scholar
  3. Fujita Y, Ohi H, Murayama N, Saguchi KI, 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(1):24–28CrossRefPubMedGoogle Scholar
  4. Godard CA, Goldstone JV, Said MR, Dickerson RL, Woodin BR et al (2005) The new vertebrate CYP1C family: Cloning of new subfamily members and phylogenetic analysis. Biochem Biophys Res Commun 331(4):1016–1024CrossRefPubMedGoogle Scholar
  5. Goldstone HM, Stegeman JJ (2006) A revised evolutionary history of the CYP1A subfamily: gene duplication, gene conversion, and positive selection. J Mol Evol 62:708–717CrossRefPubMedGoogle Scholar
  6. Goldstone JV, Stegeman JJ (2008) Gene structure of the novel cytochrome P4501D1 genes in stickleback (Gasterosteus aculeatus) and medaka (Oryzias latipes). Mar Environ Res 66(1):19–20CrossRefPubMedGoogle Scholar
  7. Goldstone JV, Goldstone HMH, Morrison AM, Tarrant A, Kern SE et al (2007) 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 Evol 24(12):2619–2631CrossRefGoogle Scholar
  8. Goldstone JV, Jönsson ME, Behrendt L, Woodin BR, Jenny MJ et al (2009) Cytochrome P450 1D1: a novel CYP1A-related gene that is not transcriptionally activated by PCB126 or TCDD. Arch Biochem Biophys 482(1–2):7–16CrossRefPubMedGoogle Scholar
  9. Gotoh O (1992) Substrate recognition sites in cytochrome P450 family 2 (CYP2) proteins inferred from comparative analyses of amino acid and coding nucleotide sequences. J Biol Chem 267:83–90PubMedGoogle Scholar
  10. Heinemeyer T, Wingender E, Reuter I, Hermjakob H, Kel AE et al (1998) Databases on transcriptional regulation: TRANSFAC, TRRD, and COMPEL. Nucleic Acids Res 26:364–370CrossRefGoogle Scholar
  11. Jönsson ME, Orrego R, Woodin BR, Goldstone JV, Stegeman JJ (2007) Basal and 3,3′,4,4′,5-pentachlorobiphenyl-induced expression of cytochrome P450 1A, 1B and 1C genes in zebrafish. Toxicol Appl Pharmacol 221(1):29–41CrossRefPubMedGoogle Scholar
  12. Jönsson ME, Franks DG, Woodin BR, Jenny MJ, Garrick RA et al (2009) 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 181(3):447–454CrossRefPubMedGoogle Scholar
  13. Keane TM, Creevey CJ, Pentony MM, Naughton TJ, Mclnerney JO (2006) 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 6:29CrossRefPubMedGoogle Scholar
  14. Nebert DW, Dalton TP, Okey AB, Gonzalez FJ (2004) Role of aryl hydrocarbon receptor-mediated induction of the CYP1 enzymes in environmental toxicity and cancer. J Biol Chem 279(23):23847–23850CrossRefPubMedGoogle Scholar
  15. Rice P, Longden I, Bleasby A (2000) EMBOSS: The European Molecular Biology Open Software Suite. Trends Genet 16(6):276–277CrossRefPubMedGoogle Scholar
  16. Ronquist F, Huelsenbeck JP (2003) MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19(12):1572–1574CrossRefPubMedGoogle Scholar
  17. Sogawa K, Numayama-Tsuruta K, Takahashi T, Matsushita N, Miura C et al (2004) A novel induction mechanism of the rat CYP1A2 gene mediated by Ah receptor-Arnt heterodimer. Biochem Biophys Res Commun 318:746–755CrossRefPubMedGoogle Scholar
  18. Sutter TR, Tang YM, Hayes CL, Wo YY, Jabs EW et al (1994) Complete cDNA sequence of a human dioxin-inducible mRNA identifies a new gene subfamily of cytochrome P450 that maps to chromosome 2. J Biol Chem 269(18):13092–13099PubMedGoogle Scholar
  19. Tamura K, Dudley J, Nei M, Kumar S (2007) MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol Biol Evol 24(8):1596–1599CrossRefPubMedGoogle Scholar
  20. Yang Z (2007) PAML 4: phylogenetic analysis by maximum likelihood. Mol Biol Evol 24(8):1586–1591CrossRefPubMedGoogle Scholar
  21. Zanette J, Jenny MJ, Goldstone JV, Woodin BR, Watka LA et al (2009) New cytochrome P450 1B1, 1C2, and 1D1 genes in killifish Fundulus heteroclitus: basal expression and response of five killifish CYP1s to the AHR agonist PCB126. Aquat Toxicol 93(4):234–243CrossRefPubMedGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC 2010

Authors and Affiliations

  • Yusuke K. Kawai
    • 1
  • Yoshinori Ikenaka
    • 1
  • Shoichi Fujita
    • 1
  • Mayumi Ishizuka
    • 1
  1. 1.Laboratory of Toxicology, Department of Environmental Veterinary ScienceGraduate School of Veterinary Medicine, Hokkaido UniversitySapporoJapan

Personalised recommendations