Comparison of cytochrome P450 (CYP) genes from the mouse and human genomes, including nomenclature recommendations for genes, pseudogenes and alternative-splice variants

Pharmacogenetics

Volumn 14, Issue 1, 2004, Pages 1-18

  Nelson, David R ^a,b   Zeldin, Darryl C ^c   Hoffman, Susan M G ^d   Maltais, Lois J ^e   Wain, Hester M ^f   Nebert, Daniel W ^g  

^a UNIVERSITY OF TENNESSEE HEALTH SCIENCE CENTER   (United States)

^b UT Ctr Excellence Genom Bioinfo   (United States)

^c NATIONAL INSTITUTE OF ENVIRONMENTAL HEALTH SCIENCES   (United States)

^d MIAMI UNIVERSITY   (United States)

^e JACKSON LABORATORY   (United States)

^f UNIVERSITY COLLEGE LONDON   (United Kingdom)

^g UNIVERSITY OF CINCINNATI MEDICAL CENTER   (United States)

Author keywords

Cytochrome P450; Human; Mouse; Nomenclature; Pseudogenes

Indexed keywords

CYTOCHROME P450; ISOENZYME;

ALTERNATIVE RNA SPLICING; DETRITUS; EUKARYOTE; EXON; GENE; GENE CLUSTER; GENE CONVERSION; GENE SEQUENCE; GENETIC TRANSCRIPTION; GENETIC VARIABILITY; GENOME; GENOTYPE; HUMAN; HUMAN GENOME; MULTIGENE FAMILY; NOMENCLATURE; NONHUMAN; NUCLEOTIDE SEQUENCE; PHARMACOGENETICS; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; PSEUDOGENE; REVIEW; SPECIES DIFFERENCE;

ALTERNATIVE SPLICING; ANIMALS; CYTOCHROME P-450 ENZYME SYSTEM; HUMANS; MICE; MULTIGENE FAMILY; PSEUDOGENES; TERMINOLOGY;

MAMMALIA;

EID: 0842312531     PISSN: 0960314X     EISSN: None     Source Type: Journal    
DOI: 10.1097/00008571-200401000-00001     Document Type: Review

References (53)

1. Nebert DW, Russell DW. Clinical importance of the cytochromes P450. Lancet 2002; 360:1155-1162.
2. Waterston RH, Lindblad-Toh K, Birney E, Rogers J, Abril JF, Agarwal P, et al. Initial sequencing and comparative analysis of the mouse genome. Nature 2002; 420:520-562.
3. Nelson DR. Cytochrome P450 gene superfamily. 2003. (web site) http:// drnelson.utmem.edu/cytochromeP450.html/
4. Nebert DW, Adesnik M, Coon MJ, Estabrook RW, Gonzalez FJ, Guengerich FP, et al. The P450 gene superfamily. Recommended nomenclature. DNA 1987; 6:1-11.
5. Nelson DR, Koymans L, Kamataki T, Stegeman JJ, Feyereisen R, Waxman DJ, et al. P450 superfamily: update on new sequences, gene mapping, accession numbers and nomenclature. Pharmacogenetics 1996; 6:1-41.
6. Ranson R, Claudianos C, Ortelli F, Abgrall, C, Hemingway J, Sharakhova MV, et al. Evolution of supergene families associated with insecticide resistance. Science 2002; 298: 179-181.
7. Nelson DR. Mining databases for cytochrome P450 genes. Methods Enzymol 2002; 357:3-15.
8. Hoffman SMG, Nelson DR, Keeney DS. Organization, structure and evolution of the CYP2 gene cluster on human chromosome 19. Pharmacogenetics 2001; 11:687-698.
9. Nelson DR. Metazoan cytochrome P450 evolution. Comp Biochem Physiol Part C 1998; 121:15-22.
10. Nelson DR. Cytochrome P450 and the individuality of species. Arch Biochem Biophys 1999; 369:1-10.
11. Nelson DR. Comparison of P450s from Human and Fugu. 420 million years of vertebrate P450 evolution. Arch Biochem Biophys 2003; 409:18-24.
12. Xuan Z, Wang J, Zhang MQ. Computational comparison of two mouse draft genomes and the human golden path. Genome Biol 2003; 4:R1.
13. Flicek P, Keibler E, Hu P, Korf I, Brent MR. Leveraging the mouse genome for gene prediction in human: from whole-genome shotgun reads to a global synteny map. Genome Res 2003; 13:46-54.
14. Venter JC, Adams MD, Myers EW, Li PW, Mural RJ, Sutton GG, et al. The sequence of the human genome. Science 2001; 291:1304-1351.
15. Harrison PM, Hegyi H, Balasubramanian S, Luscombe NM, Bertone P, Echols N, et al. Molecular fossils in the human genome: identification and analysis of the pseudogenes in chromosomes 21 and 22. Genome Res 2002; 12:272-280.
16. Zhang Z, Harrison P, Gerstein M. Identification and analysis of over 2000 ribosomal protein pseudogenes in the human genome. Genome Res 2002; 12:1466-1482.
17. 7 Glazko GV, Nei M. Estimation of divergence times for major lineages of primate species. Mol Biol Evol 2003; 20:424-434.
18. Springer MS, Murphy WJ, Eizirik E, O'Brien SJ. Placental mammal diversification and the Cretaceous-Tertiary boundary. Proc Natl Acad Sci U S A 2003; 100:1056-1061.
19. Oscarson M, Ingelman-Sundberg M, Daly AK, Nebert DW. Human cytochrome P450 (CYP) alleles. 2003. (web site) http://www.imm.ki.se/ CYPalleles/
20. Nevilie M, Selzer R, Aizenstein B, Maguire M, Hogan K, Walton R, et al. Characterization of cytochrome P450 2D6 alleles using the Invader system. Biotechniques 2002; (suppl 34-8):40-43.
21. Hirotsune S, Yoshida N, Chen A, Garrett L, Sugiyama F, Takahashi S, et al. An expressed pseudogene regulates the messenger-RNA stability of its homologous coding gene. Nature 2003; 423:91-96.
22. Piechaczyk M, Blanchard JM, Riaad-el Sabouty S, Dani C, Marty L, Jeanteur P. Unusual abundance of vertebrate 3-phosphate dehydrogenase pseudogenes. Nature 1984; 312:469-471.
23. Riad-el Sabouty S, Blanchard JM, Marty L, Jeanteur P, Piechaczyk M. The muridae glyceraldehyde-3-phosphate dehydrogenase family. J Mol Evol 1989; 29:212-222.
24. Garcia-Meunier P, Etienne-Julan M, Fort P, Piechaczyk M, Bonhomme F. Concerted evolution in the GAPDH family of retro-transposed pseudogenes. Mamm Genome 1993; 4:695-703.
25. Burge C, Karlin S. Prediction of complete gene structures in human genomic DNA. J Mol Biol 1997; 268:78-94.
26. Hua Z, Zhang QY, Su T, Lipinskas TW, Ding X. cDNA cloning, heterologous expression, and characterization of mouse CYP2G1, an olfactory-specific steroid hydroxylase. Arch Biochem Biophys 1997; 340:208-214.
27. Ding XX, Porter TD, Peng HM, Coon MJ. cDNA and derived amino acid sequence of rabbit nasal cytochrome P450NMb (P450IIG1), a unique isozyme possibly involved in olfaction. Arch Biochem Biophys 1991; 285:120-125.
28. Zhang Z. 2003. http://bioinfo.mbb.yale.edu/genome/pseudogene/human-all/ index.html
29. Maltais LJ, Blake JA, Chu T, Lutz CM, Eppig JT, Jackson I. Rules and guidelines for mouse gene, allele, and mutation nomenclature: a condensed version. Genomics 2002; 79:471-474.
30. Finta C, Zaphiropoulos PG. The human cytochrome P450 3A locus. Gene evolution by capture of downstream exons. Gene 2000; 260: 13-23.
31. Wain HM, Bruford EA, Lovering RC, Lush MJ, Wright MW, Povey S. Guidelines for Human Gene Nomenclature (2002). Genomics 2002; 79:464-470.
32. Schuetz JD, Guzelian PS. Isolation of CYP3A5P cDNA from human liver: a reflection of a novel cytochrome P-450 pseudogene. Biochim Biophys Acta 1995; 1261:161-165.
33. Meinhardt U, Mullis PE. The essential role of the aromatase/p450arom. Semin Reprod Med 2002; 20:277-284.
34. Hoffman S, Fernandez-Salguero P, Gonzalez F, Mohrenweiser H. Organization and evolution of the cytochrome P450 CYP2A-2B-2F subfamily gene cluster on human chromosome 19. J Molec Evol 1995; 41: 894-900.
35. Wang H, Donley KM, Keeney DS, Hoffman SM. Organization and evolution of the Cyp2 gene cluster on mouse chromosome 7, and comparison with the syntenic human cluster. 2003; Environ Health Perspect 2003; 111:1835-1842.
36. Oscarson M, McLellan RA, Asp V, Ledesma M, Ruiz ML, Sinues B, et al. Characterization of a novel CYP2A7/CYP2A6 hybrid allele (CYP2A6*12) that causes reduced CYP2A6 activity. Hum Mutat 2002; 20:275-283.
37. Fernandez-Salguero P, Hoffman SM, Cholerton S, Mohrenweiser H, Raunio H, Rautio A, et al. A genetic polymorphism in coumarin 7-hydroxylation: Sequence of the human CYP2A genes and identification of variant CYP2A6 alleles. Amer Jour Human Genet 1995; 57:651-660.
38. Nebert DW, Jorge-Nebert LF. Pharmacogenetics and pharmacogenomics. In: Rimoin DL, Connor JM, Pyeritz RE, Korf BR, eds. Emery & Rimoin's Principles and Practice of Medical Genetics, 4th ed. London: Churchill Livingstone; 2002. pp. 590-631.
39. Ingelman-Sundberg M. Duplication, multi-duplication, and amplification of genes encoding drug-metabolizing enzymes: evolutionary, toxicological, and clinical pharmacological aspects. Drug Metab Rev 1999; 31: 449-459.
40. Yu AM, Idle JR, Herraiz T, Kupfer A, Gonzalez FJ. Screening for endogenous substrates reveals that CYP2D6 is a 5-methoxyindolethylamine O-demethylase. Pharmacogenetics 2003; 13:307-319.
41. Yu AM, Idle JR, Byrd LG, Krausz KW, Kupfer A, Gonzalez FJ. Regeneration of serotonin from 5-methoxytryptamine by polymorphic human CYP2D6. Pharmacogenetics 2003; 13:173-181.
42. Heim MH, Meyer UA. Evolution of a highly polymorphic human cytochrome P450 gene cluster: CYP2D6. Genomics 1992; 14:49-58.
43. Ma J, Bradbury JA, King L, Maronpot R, Davis LS, Breyer MD, et al. Molecular cloning and characterization of mouse CYP2J6, an unstable cytochrome P450 isoform. Biochem Pharmacol 2002; 64:1447-1460.
44. King LM, Ma J, Srettabunjong S, Graves J, Bradbury JA, Li L, et al. Cloning of CYP2J2 gene and identification of functional polymorphisms. Mol Pharmacol 2002: 61:840-852.
45. Qu W, Bradbury JA, Tsao CC, Maronpot R, Harry GJ, Parker CE, et al. Cytochrome P450 CYP2J9, a new mouse arachidonic acid omega-1 hydroxylase predominantly expressed in brain. J Biol Chem 2001; 276:25467-25479.
46. Scarborough PE, Ma J, Qu W, Zeldin DC. P450 subfamily CYP2J and their role in the bioactivation of arachidonic acid in extrahepatic tissues. Drug Metab Rev 1999: 31:205-234.
47. Oleksiak MF, Wu S, Parker C, Karchner SI, Stegeman JJ, Zeldin DC. Identification, functional characterization, and regulation of a new cytochrome P450 subfamily, the CYP2Ns. J Biol Chem 2000; 275: 2312-2321.
48. Oleksiak MF, Wu S, Parker C, Qu W, Cox R, Zeldin DC, et al. 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 2003; 411:223-234.
49. Smith SF, Snell P, Gruetzner F, Bench AJ, Haaf T, Metcalfe JA, et al. Analyses of the extent of shared synteny and conserved gene orders between the genome of Fugu rubripes and human 20q. Genome Res 2002; 12:776-784.
50. Taylor JS, Braasch I, Frickey T, Meyer A, Van de Peer Y. Genome duplication, a trait shared by 22,000 species of ray-finned fish. Genome Res 2003; 13:382-390.
51. Lifton RP, Dluhy RG, Powers M, Rich GM, Cook S, Ulick S, et al. A chimaeric 11 β-hydroxylase/aldosterone synthase gene causes glucocorticoid-remediable aldosteronism and human hypertension. Nature 1992; 355:262-265.
52. Oscarson M, McLellan RA, Gullsten H, Agundez JA, Benitez J, Rautio A, et al. Identification and characterisation of novel polymorphisms in the CYP2A locus: implications for nicotine metabolism. FEBS Lett 1999; 460:321-327.
53. Cok I, Aygun Kocabas N, Cholerton S, Karakaya AE, Sardas S. Determination of coumarin metabolism in a Turkish population. Hum Exp Toxicol 2001; 20:179-184.