Evolutionary toxicogenomics: Diversification of the Cyp12d1 and Cyp12d3 genes in Drosophila species

Journal of Molecular Evolution

Volumn 74, Issue 5-6, 2012, Pages 281-296

  McDonnell, Cynthia M ^a,b   King, Darrin ^a   Comeron, Josep M ^c   Li, Hongmei ^a   Sun, Weilin ^a   Berenbaum, May R ^a   Schuler, Mary A ^d   Pittendrigh, Barry R ^a  

^a UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

^b Laboratoire de Toxicologie Environnementale   (France)

^c UNIVERSITY OF IOWA   (United States)

^d UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

Author keywords

12 Drosophila genomes; 30 UTR; Comparative genomics; Cyp12d1; Cytochrome P450 monooxygenase genes; Drosophila melanogaster; Evolutionary toxicology; Gene duplication; Polyadenylation signal; Xenobiotics

Indexed keywords

AMINO ACID; CYTOCHROME P 450 12D1, DROSOPHILA; CYTOCHROME P-450 12D1, DROSOPHILA; CYTOCHROME P450; DROSOPHILA PROTEIN;

ANIMAL; ARTICLE; DNA SEQUENCE; DROSOPHILA; DROSOPHILA MELANOGASTER; ENVIRONMENT; ENZYMOLOGY; GENE; GENE DOSAGE; GENE EXPRESSION REGULATION; GENE LOCUS; GENETIC POLYMORPHISM; GENETIC VARIABILITY; GENETICS; MOLECULAR EVOLUTION; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PHYLOGENY; PHYSIOLOGICAL STRESS; POLYMERASE CHAIN REACTION; SEQUENCE HOMOLOGY; SPECIES DIFFERENCE; TIME; TOXICOGENETICS;

AMINO ACIDS; ANIMALS; BASE SEQUENCE; CYTOCHROME P-450 ENZYME SYSTEM; DROSOPHILA; DROSOPHILA MELANOGASTER; DROSOPHILA PROTEINS; ENVIRONMENT; EVOLUTION, MOLECULAR; GENE DOSAGE; GENE EXPRESSION REGULATION, ENZYMOLOGIC; GENES, INSECT; GENETIC LOCI; GENETIC VARIATION; MOLECULAR SEQUENCE DATA; PHYLOGENY; POLYMERASE CHAIN REACTION; POLYMORPHISM, GENETIC; SEQUENCE ANALYSIS, DNA; SEQUENCE HOMOLOGY, AMINO ACID; SPECIES SPECIFICITY; STRESS, PHYSIOLOGICAL; TIME FACTORS; TOXICOGENETICS;

DROSOPHILA ANANASSAE; DROSOPHILA MELANOGASTER; DROSOPHILA SECHELLIA; MELANOGASTER; MYA; OBSCURA GROUP;

EID: 84865791720     PISSN: 00222844     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00239-012-9506-3     Document Type: Article

References (57)

1. Amlou M, Moreteau B, David JR (1998) Larval tolerance in the Drosophila melanogaster species complex toward the two toxic acids of the D. sechellia host plant. Hereditas 129:7-14
2. Bak S, Beisson F, Bishop G, Hamberger B, Hofer R, Paquette S, Werck-Reichhart D (2011) Cytochrome P450s. In: Somerville CR, Meyerowitz EM (eds) The arabidopsis book. American Society of Plant Biologists, Rockville. URL:http://www.aspb. org/publications/arabidopsis
3. Bass C, Field LM (2011) Gene amplification and insecticide resistance. Pest Manag Sci 67:886-890
4. Betran E, Ashburner M (2000) Duplication, dicistronic transcription, and subsequent evolution of the Alcohol dehydrogenase and Alcohol dehydrogenase-related genes in Drosophila. Mol Biol Evol 17:1344-1352
5. Brandt A, Scharf M, Pedra JHF, Holmes G, Dean A, Kreitman M, Pittendrigh BR (2002) Differential expression and induction of two Drosophila cytochrome P450 genes near the Rst(2)DDT locus. Insect Mol Biol 11:337-341
6. Drosophila 12 Genomes Consortium, Clark AG, Eisen MB et al (2007) Evolution of genes and genomes on the Drosophila phylogeny. Nature 450:203-218
7. Daborn P, Boundy S, Yen J, Pittendrigh B, ffrench-Constant R (2001) DDT resistance in Drosophila correlates with Cyp6g1 overexpression and confers cross-resistance to the neonicotinoid imidacloprid. Mol Genet Genomics 266:556-563
8. Dapkus D, Merrell DJ (1977) Chromosomal analysis of DDTresistance in long-term selected population of Drosophila melanogaster. Genetics 87:685-697
9. Emerson JJ, Cardoso-Moreira M, Borevitz JO, Long M (2008) Natural selection shapes genome-wide patterns of copy-number polymorphism in Drosophila melanogaster. Science 320:1629-1631
10. Farine J, Legal L, Moreteau B, Le Quere JL (1996) Volatile components of ripe fruits of Morinda citrifolia and their effects on Drosophila. Phytochemistry 41:433-438
11. Festucci-Buselli RA, Carvalho-Dias AS, de Oliveira-Andrade M, Caixeta-Nunes C, Li HM, Stuart JJ, Muir W, Scharf ME, Pittendrigh BR (2005) Expression of Cyp6g1 and Cyp12d1 in DDT resistant and susceptible strains of Drosophila melanogaster. Insect Mol Biol 14:69-77
12. Feyereisen R (2011) Arthropod CYPomes illustrate the tempo and mode in P450 evolution. Biochim Biophys Acta 1814:19-28
13. Feyereisen R (2012) Insect CYP genes and P450 enzymes. In: Gilbert LI (ed) Insect molecular biology and biochemistry. Elsevier Press, Oxford, pp 236-316
14. Guengerich FP (2005) Human cytochrome P450 enzymes. In: Ortiz de Montellano PR (ed) Cytochrome P450: structure, mechanism, and biochemistry, 3rd edn. Kluwer Academic, New York, pp 377-530
15. Innan H, Kondrashov F (2010) The evolution of gene duplications: classifying and distinguishing between models. Nature Rev Genet 11:97-108
16. Jensen HR, Scott IM, Sims S, Trudeau VL, Arnason JT (2006) Gene expression profiles of Drosophila melanogaster exposed to an insecticidal extract of Piper nigrum. J Agric Food Chem 54:1289-1295
17. Jones DT, Taylor WR, Thornton JM (1992) The rapid generation of mutation data matrices from protein sequences. Comput Appl Biosci 8:275-282
18. Kelly SL, Kelly DE, Jackson CJ, Warrilow AGS, Lamb DC (2005) The diversity and importance of microbial cytochromes P450. In: Ortiz de Montellano PR (ed) Cytochrome P450: structure, mechanism, and biochemistry, 3rd edn. Kluwer Academic, New York, pp 585-618
19. Kondrashov FA, Rogozin IB, Wolf YI, Koonin EV (2002) Selection in the evolution of gene duplications. Genome Biol 3:research0008- research0008.9
20. Le Goff G, Hilliou F, Siegfried BD, Boundy S, Wajnberg E, Sofer L, Audant P, ffrench-Constant RH, Feyereisen R (2006) Xenobiotic response in Drosophila melanogaster: sex dependence of P450 and GST gene induction. Insect Biochem Mol Biol 36:674-682
21. Legal L, Chappe B, Jallon J (1994)Molecular basis of Morinda citrifolia (L.): toxicity on Drosophila. J Chem Ecol 20:1931-1943
22. Li WH (1999) Molecular evolution. Sinauer Associates, Sunderland
23. Li H, Durbin R (2010) Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics 26:589-595
24. Li X, Schuler MA, Berenbaum MR (2007) Molecular mechanisms of metabolic resistance to synthetic and natural xenobiotics. Annu Rev Entomol 52:231-253
25. Li HM, Buczkowski G, Mittapalli O, Xie J, Wu J, Westerman R, Schemerhorn BJ, Murdock LL, Pittendrigh BR (2008) Transcriptomic profiles of Drosophila melanogaster third instar larval midgut and responses to oxidative stress. Insect Mol Biol 17:325-339
26. Li H, Handsaker B, Wysoker A, Fennell T, Ruan R et al (2009) The sequence alignment/map format and SAMtools. Bioinformatics 25:2078-2079
27. Lupski JR (2007) Genomic rearrangements and sporadic disease. Nat Genet 39:S43-S47
28. Matzkin LM, Eanes WF (2003) Sequence variation of alcohol dehydrogenase (Adh) paralogs in cactophilic Drosophila. Genetics 163:181-194
29. Mizutani M, Ohta D (2010) Diversification of P450 genes during land plant evolution. Annu Rev Plant Biol 61:291-315
30. Nelson DR (1998) Metazoan cytochrome P450 evolution. Comp Biochem Phyiol C Pharmacol Toxicol Endocrinol 121:15-22
31. Nelson DR (2009) The cytochrome P450 homepage. Hum Genomics 4:59-65
32. Nelson DR, Koymans L, Kamataki T, Stegeman JJ, Feyereisen R, Waxman DJ, Waterman MR, Gotoh O, Coon MJ, Estabrook RW, Gunsalus IC, Nebert DW (1996) P450 superfamily: update on new sequences, gene mapping, accession numbers and nomenclature. Pharmacogenetics 6:1-42
33. Nielsen R, Yang Z (1998) Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene. Genetics 148:929-936
34. Ohno S (1970) Evolution by gene duplication. Springer, New York
35. Oppentocht JE, van Delden W, van de Zande L (2002) Isolation and characterization of the genomic region from Drosophila kuntzei containing the Adh and Adhr genes. Mol Biol Evol 19:1026-1040
36. Pearson WR (1990) Rapid and sensitive sequence comparison with FASTP and FASTA. Method Enzymol 183:63-98
37. Pedra JH, McIntyre LM, Scharf ME, Pittendrigh BR (2004) Genomewide transcription profile of field- and laboratory-selected dichlorodiphenyltrichloroethane (DDT)-resistant Drosophila. Proc Natl Acad Sci USA 101:7034-7039
38. R'Kha S, Capy P, David JR (1991) Host-plant specialization in the Drosophila melanogaster species complex: a physiological, behavioral, and genetical analysis. Proc Natl Acad Sci USA 88:1835-1839
39. Schmidt JM, Good RT, Appleton B, Sherrard J, Raymant GC, Bogwitz MR, Martin J, Daborn PJ, Goddard ME, Batterham P, Robin C (2010) Copy number variation and transposable elements feature in recent, ongoing adaptation at the Cyp6g1 locus. PLoS Genet 6:e1000998
40. Schuler MA (2011) P450s in plant-insect interactions. Biochim Biophys Acta 1814:36-45
41. Schuler MA, Duan H, Bilgin M, Ali S (2006) Arabidopsis P450s through the looking glass: a window on plant biochemistry. Phytochem Reviews 5:205-237
42. Sebat J, Lakshmi B, Troge J, Alexander J, Young J, Lundin P, Maner S, Massa H, Walker M, Chi M et al (2004) Large-scale copy number polymorphism in the human genome. Science 305: 525-528
43. Singh ND, Larracuente AM, Sackton TB, Clark AG (2009) Comparative genomics on the Drosophila phylogenetic tree. Annu Rev Ecol Evol Syst 40:459-480
44. Sun L (2009) The response of Drosophila melanogaster to methamphetamine and oxidative stress. Ph.D. dissertation, Purdue University
45. Sun W, Margam VM, Sun L, Buczkowski G, Bennett GW, Schemerhorn B, Muir WM, Pittendrigh BR (2006) Genomewide analysis of phenobarbital-inducible genes in Drosophila melanogaster. Insect Mol Biol 15:455-464
46. Swofford DL (2002) PAUP*. Phylogenetic analysis using parsimony (*and other methods). Version 4. Sinauer Associates, Sunderland, M.A.
47. Tamura K, Subramanian S, Kumar S (2004) Temporal patterns of fruit fly (Drosophila) evolution revealed by mutation clocks. Mol Biol Evol 21:36-44
48. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28:2731-2739
49. Thomas JH (2007) Rapid birth-death evolution specific to xenobiotic cytochrome P450 genes in vertebrates. PLoS Genet 3:e67
50. Willoughby L, Chung H, Lumb C, Robin C, Batterham P, Daborn PJ (2006) A comparison of Drosophila melanogaster detoxification gene induction responses for six insecticides, caffeine and phenobarbital. Insect Biochem Mol Biol 36:934-942
51. Willoughby L, Batterham P, Daborn PJ (2007) Piperonyl butoxide induces the expression of cytochrome P450 and glutathione S-transferase genes in Drosophila melanogaster. Pest Manag Sci 63:803-808
52. Wong WS, Yang Z, Goldman N, Nielsen R (2004) Accuracy and power of statistical methods for detecting adaptive evolution in protein coding sequences and for identifying positively selected sites. Genetics 168:1041-1051
53. Yang Z (1997) PAML: a program package for phylogenetic analysis by maximum likelihood. Comput Appl Biosci 13:555-556
54. Yang Z, Nielsen R, Goldman N, Pedersen AM (2000) Codonsubstitution models for heterogeneous selection pressure at amino acid sites. Genetics 155:431-449
55. Yang Z, Wong WS, Nielsen R (2005) Bayes empirical Bayes inference of amino acid sites under positive selection. Mol Biol Evol 22:1107-1118
56. Zhang F, GuW, Hurles ME, Lupski JR (2009) Copy number variation in human health, disease, and evolution. Ann Rev Genom Hum G. 10:451-481
57. Zhou Q, Zhang G, Zhang Y, Xu S, Zhao R, Zhan Z, Li X, Ding Y, Yang S, Wang W (2008) On the origin of new genes in Drosophila. Genome Res 18:1446-1455