Abstract
Cytochrome P450 (CYP) proteins compose a highly diverse superfamily found in all domains of life. These proteins are enzymes involved in metabolism of endogenous and exogenous compounds. In vertebrates, the CYP2 family is one of the largest, most diverse and plays an important role in mammalian drug metabolism. However, there are more than 20 vertebrate CYP2 subfamilies with uncertain evolution and fairly discrete subfamily composition within vertebrate classes, hindering extrapolation of knowledge across subfamilies. To better understand CYP2 diversity, a phylogenetic analysis of 196 CYP2 protein sequences from 16 species was performed using a maximum likelihood approach and Bayesian inference. The analyses included the CYP2 compliment from human, fugu, zebrafish, stickleback, medaka, cow, and dog genomes. Additional sequences were included from rabbit, marsupial, platypus, chicken, frog, and salmonid species. Three CYP2 sequences from the tunicate Ciona intestinalis were utilized as the outgroup. Results indicate a single ancestral vertebrate CYP2 gene and monophyly of all CYP2 subfamilies. Two subfamilies (CYP2R and CYP2U) pre-date vertebrate diversification, allowing direct comparison across vertebrate classes, while all other subfamilies originated during vertebrate diversification, often within specific vertebrate lineages. Analysis of site-specific evolution indicates that some substrate recognition sites (SRS) previously proposed for CYP genes do not have elevated rates of evolution, suggesting that these regions of the protein are not necessarily important in recognition of CYP2 substrates. Type II functional divergence analysis identified multiple residues in the active site of CYP2F, CYP2A, and CYP2B proteins that have undergone radical biochemical changes and may be functionally important.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
References
Abascal F, Zardoya R, Posada D (2005) ProtTest: selection of best-fit models of protein evolution. Bioinformatics 21:2104–2105
Boissinot S, Chevret P, Furano AV (2000) L1 (LINE-1) retrotransposon evolution and amplification in recent human history. Mol Biol Evol 17:915–928
de Graaf C, Vermeulen NP, Feenstra KA (2005) Cytochrome p450 in silico: an integrative modeling approach. J Med Chem 48:2725–2755
DeVore NM, Smith BD, Urban MJ, Scott EE (2008) Key residues controlling phenacetin metabolism by human cytochrome P450 2A enzymes. Drug Metab Dispos 36:2582–2590
Goldstone JV, Hamdoun A, Cole BJ, Howard-Ashby M, Nebert DW, Scally M, Dean M, Epel D, Hahn ME, Stegeman JJ (2006) The chemical defensome: environmental sensing and response genes in the Strongylocentrotus purpuratus genome. Dev Biol 300:366–384
Goldstone JV, Goldstone HM, Morrison AM, Tarrant A, Kern SE, Woodin BR, Stegeman JJ (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 Biol Evol 24:2619–2631
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 267:83–90
Gu X (1999) Statistical methods for testing functional divergence after gene duplication. Mol Biol Evol 16:1664–1674
Gu X (2006) A simple statistical method for estimating type-II (cluster-specific) functional divergence of protein sequences. Mol Biol Evol 23:1937–1945
Hall TA (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl Acids Symp Ser 95–98
Hasemann CA, Kurumbail RG, Boddupalli SS, Peterson JA, Deisenhofer J (1995) Structure and function of cytochromes P450: a comparative analysis of three crystal structures. Structure 3:41–62
Huelsenbeck JP, Ronquist F, Nielsen R, Bollback JP (2001) Bayesian inference of phylogeny and its impact on evolutionary biology. Science 294:2310–2314
Jones DT, Taylor WR, Thornton JM (1992) The rapid generation of mutation data matrices from protein sequences. Comput Appl Biosci 8:275–282
Lee TS (2008) Reverse conservation analysis reveals the specificity determining residues of cytochrome P450 family 2 (CYP 2). Evol Bioinform Online 4:7–16
Lee HS, Park EJ, Ji HY, Kim SY, Im GJ, Lee SM, Jang IJ (2008) Identification of cytochrome P450 enzymes responsible for N-dealkylation of a new oral erectogenic, mirodenafil. Xenobiotica 38:21–33
Lewis DF (2002) Homology modelling of human CYP2 family enzymes based on the CYP2C5 crystal structure. Xenobiotica 32:305–323
Lewis DF (2003) Human cytochromes P450 associated with the phase 1 metabolism of drugs and other xenobiotics: a compilation of substrates and inhibitors of the CYP1, CYP2 and CYP3 families. Curr Med Chem 10:1955–1972
Li C, Orti G, Zhang G, Lu G (2007) A practical approach to phylogenomics: the phylogeny of ray-finned fish (Actinopterygii) as a case study. BMC Evol Biol 7:44
Maddison DR, Maddison WP (2000) MacClade version 4: analysis of phylogeny and character evolution. Sinauer Associates, Sunderland
Maddison WP, Maddison DR (2009) Mesquite: a modular system for evolutionary analysis, 2.72 version
McArthur AG, Hegelund T, Cox RL, Stegeman JJ, Liljenberg M, Olsson U, Sundberg P, Celander MC (2003) Phylogenetic analysis of the cytochrome P450 3 (CYP3) gene family. J Mol Evol 57:200–211
Mestres J (2005) Structure conservation in cytochromes P450. Proteins 58:596–609
Nelson DR (1998) Metazoan cytochrome P450 evolution. Comp Biochem Physiol C Pharmacol Toxicol Endocrinol 121:15–22
Nelson DR (2003) Comparison of P450s from human and fugu: 420 million years of vertebrate P450 evolution. Arch Biochem Biophys 409:18–24
Nelson DR (2009) The cytochrome P450 homepage. Human Genomics 4:59–65
Nelson DR, Kamataki T, Waxman DJ, Guengerich FP, Estabrook RW, Feyereisen R, Gonzalez FJ, Coon MJ, Gunsalus IC, Gotoh O et al (1993) The P450 superfamily: update on new sequences, gene mapping, accession numbers, early trivial names of enzymes, and nomenclature. DNA Cell Biol 12:1–51
Nelson DR, Zeldin DC, Hoffman SM, Maltais LJ, Wain HM, Nebert DW (2004) Comparison of cytochrome P450 (CYP) genes from the mouse and human genomes, including nomenclature recommendations for genes, pseudogenes and alternative-splice variants. Pharmacogenetics 14:1–18
Nylander JA, Wilgenbusch JC, Warren DL, Swofford DL (2008) AWTY (are we there yet?): a system for graphical exploration of MCMC convergence in Bayesian phylogenetics. Bioinformatics 24:581–583
Oleksiak MF, Wu S, Parker C, Karchner SI, Stegeman JJ, Zeldin DC (2000) Identification, functional characterization, and regulation of a new cytochrome P450 subfamily, the CYP2Ns. J Biol Chem 275:2312–2321
Oleksiak MF, Wu S, Parker C, Qu W, Cox R, Zeldin DC, Stegeman JJ (2003) Identification and regulation of a new vertebrate cytochrome P450 subfamily, the CYP2Ps, and functional characterization of CYP2P3, a conserved arachidonic acid epoxygenase/19-hydroxylase. Arch Biochem Biophys 411:223–234
Poulos TL, Finzel BC, Howard AJ (1987) High-resolution crystal structure of cytochrome P450cam. J Mol Biol 195:687–700
Prasad JC, Goldstone JV, Camacho CJ, Vajda S, Stegeman JJ (2007) Ensemble modeling of substrate binding to cytochromes P450: analysis of catalytic differences between CYP1A orthologs. Biochemistry 46:2640–2654
Prasad AB, Allard MW, Green ED (2008) Confirming the phylogeny of mammals by use of large comparative sequence data sets. Mol Biol Evol 25:1795–1808
Rewitz KF, Styrishave B, Lobner-Olsen A, Andersen O (2006) Marine invertebrate cytochrome P450: emerging insights from vertebrate and insects analogies. Comp Biochem Physiol C Toxicol Pharmacol 143:363–381
Rogers J, Wall R (1980) A mechanism for RNA splicing. Proc Natl Acad Sci USA 77:1877–1879
Rowland P, Blaney FE, Smyth MG, Jones JJ, Leydon VR, Oxbrow AK, Lewis CJ, Tennant MG, Modi S, Eggleston DS, Chenery RJ, Bridges AM (2006) Crystal structure of human cytochrome P450 2D6. J Biol Chem 281:7614–7622
Scarborough PE, Ma J, Qu W, Zeldin DC (1999) P450 subfamily CYP2J and their role in the bioactivation of arachidonic acid in extrahepatic tissues. Drug Metab Rev 31:205–234
Stamatakis A, Hoover P, Rougemont J (2008) A rapid bootstrap algorithm for the RAxML Web servers. Syst Biol 57:758–771
Thomas JH (2007) Rapid birth-death evolution specific to xenobiotic cytochrome P450 genes in vertebrates. PLoS Genet 3:e67
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
Tournel G, Cauffiez C, Billaut-Laden I, Allorge D, Chevalier D, Bonnifet F, Mensier E, Lafitte JJ, Lhermitte M, Broly F, Lo-Guidice JM (2007) Molecular analysis of the CYP2F1 gene: identification of a frequent non-functional allelic variant. Mutat Res 617:79–89
Wang H, Tompkins LM (2008) CYP2B6: new insights into a historically overlooked cytochrome P450 isozyme. Curr Drug Metab 9:598–610
Yano JK, Denton TT, Cerny MA, Zhang X, Johnson EF, Cashman JR (2006) Synthetic inhibitors of cytochrome P-450 2A6: inhibitory activity, difference spectra, mechanism of inhibition, and protein cocrystallization. J Med Chem 49:6987–7001
Acknowledgments
We would like to thank Dr. David Nelson (University of Tennessee) for assigning nomenclature to our de novo gene annotations and Drs. Brian Golding and Jonathan Stone (McMaster University) for computer cluster access to run our Bayesian analyses and access to PAUP* software for posterior probability node analysis, respectively. We are thankful to Emily Smith and Dr. Golding for helpful comments and suggestions during manuscript revision. This work was supported by the Natural Sciences and Engineering Research Council of Canada (NSERC Discovery Grant #328204 to JYW). The Department of Biology, McMaster University provided partial support for N.K.
Author information
Authors and Affiliations
Corresponding author
Electronic supplementary material
Below is the link to the electronic supplementary material.
Rights and permissions
About this article
Cite this article
Kirischian, N., McArthur, A.G., Jesuthasan, C. et al. Phylogenetic and Functional Analysis of the Vertebrate Cytochrome P450 2 Family. J Mol Evol 72, 56–71 (2011). https://doi.org/10.1007/s00239-010-9402-7
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s00239-010-9402-7