Publication Cover
Xenobiotica
the fate of foreign compounds in biological systems
Volume 50, 2020 - Issue 12
115
Views
0
CrossRef citations to date
0
Altmetric
General Xenobiochemistry

Diversifying selection detected in only a minority of xenobiotic-metabolizing CYP1-3 genes among primate species

ORCID Icon, ORCID Icon, ORCID Icon & ORCID Icon
Pages 1406-1412 | Received 30 Apr 2020, Accepted 17 Jun 2020, Published online: 29 Jun 2020

References

  • Baer BR, Rettie AE. (2006). CYP4B1: An enigmatic P450 at the interface between xenobiotic and endobiotic metabolism. Drug Metab Rev 38:451–76.
  • Bak S, Paquette SM, Morant M, et al. (2006). Cyanogenic glycosides: a case study for evolution and application of cytochromes P450. Phytochem. Rev 5:309–29.
  • Bass C, Puinean AM, Zimmer CT, et al. (2014). The evolution of insecticide resistance in the peach potato aphid, Myzus persicae. Insect Biochem Mol Biol 51:41–51.
  • Bielawski JP, Yang Z. 2005. Maximum likelihood methods for detecting adaptive protein evolution. In: Nielsen R, ed. Statistical methods in molecular evolution. New York: Springer New York, 103–124.
  • Cabana F, Dierenfeld E, Wirdateti W, et al. (2017). The seasonal feeding ecology of the javan slow loris (Nycticebus javanicus). Am J Phys Anthropol 162:768–81.
  • Chaney ME, Piontkivska H, Tosi AJ. (2018). Retained duplications and deletions of CYP2C genes among primates. Mol Phylogenet Evol 125:204–12.
  • Darriba D, Taboada GL, Doallo R, Posada D. (2012). jModelTest 2: more models, new heuristics and parallel computing. Nat Methods 9:772.
  • Edgar RC. (2004). MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32:1792–7.
  • Eronen JT, Zohdy S, Evans AR, et al. (2017). Feeding ecology and morphology make a bamboo specialist vulnerable to climate change. Curr Biol 27:3384–9.
  • Eschler BM, Pass DM, Willis R, Foley WJ. (2000). Distribution of foliar formylated phloroglucinol derivatives amongst Eucalyptus species. Biochem Syst Ecol 28:813–24.
  • Felton AM, Felton A, Lindenmayer DB, Foley WJ. (2009). Nutritional goals of wild primates. Funct Ecol 23:70–8.
  • Feyereisen R. (2011). Arthropod CYPomes illustrate the tempo and mode in P450 evolution. Biochim Biophys Acta 1814:19–28.
  • Ghenu A-H, Bolker BM, Melnick DJ, Evans BJ. (2016). Multicopy gene family evolution on primate Y chromosomes. BMC Genomics 17:17.
  • 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.
  • Gotoh O. (2012). Evolution of cytochrome P450 genes from the viewpoint of genome informatics. Biol Pharm Bull 35:812–17.
  • Guengerich FP. 2015. Human cytochrome P450 enzymes. In: Ortiz de Montellano PR, editor. Cytochrome P450: structure, mechanism, and biochemistry. 4th ed. New York: Springer International Publishing, 523–785.
  • Guindon S, Dufayard J-F, Lefort V, et al. (2010). New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol 59:307–21.
  • Gursky S. 2011. Tarsiiformes. In: Campbell CJ, Fuentes A, MacKinnon KC, Bearder SK, Stumpf RM, ed. Primates in perspective. 2nd ed. New York: Oxford University Press, 79–90.
  • Hanya G, Noma N, Agetsuma N. (2003). Altitudinal and seasonal variations in the diet of Japanese macaques in Yakushima. Primates 44:51–9.
  • Hasi S, Yao J, Yu S, Tian Y. (2018). Diversity and distribution of CYP gene family in Bactrian camel. Funct Integr Genomics 18:23–9.
  • Hulo N, Bairoch A, Bulliard V, et al. (2006). The PROSITE database. Nucleic Acids Res 34:D227–30.
  • Ingelman-Sundberg M. (2005). Genetic polymorphisms of cytochrome P450 2D6 (CYP2D6): clinical consequences, evolutionary aspects and functional diversity. Pharmacogenomics J 5:6–13.
  • Jablonski NG, Crompton RH. (1994). Feeding behavior, mastication, and tooth wear in the western tarsier (Tarsius bancanus). Int J Primatol 15:29–59.
  • Janha RE, Worwui A, Linton KJ, et al. (2014). Inactive alleles of cytochrome P450 2C19 may be positively selected in human evolution. BMC Evol. Biol 14:71.
  • Janiak MC, Chaney ME, Tosi AJ. (2018). Evolution of acidic mammalian chitinase genes (CHIA) is related to body mass and insectivory in primates. Mol. Biol. Evol 35:607–22.
  • Jarvey JC, Low BS, Pappano DJ, et al. (2018). Graminivory and fallback foods: annual diet profile of geladas (Theropithecus gelada) living in the Simien Mountains National Park. Ethiopia Int J Primatol 39:105–26.
  • Johnson RN, O'Meally D, Chen Z, et al. (2018). Adaptation and conservation insights from the koala genome. Nat Genet 50:1102–11.
  • Katoh K, Standley DM. (2013). MAFFT multiple sequence alignment software version 7: Improvements in performance and usability. Mol Biol Evol 30:772–80.
  • Kay RF, Covert HH. 1984. Anatomy and behavior of extinct primates. In: Chivers DJ, Wood BA, Bilsborough A, ed. Food acquisition and processing in primates. New York: Springer Science + Business Media, LLC, 467–508.
  • Kay RF. 1984. On the use of anatomical features to infer foraging behavior in extinct primates. In: Cant J, Rodman P, ed. Adaptations for foraging in nonhuman primates. New York: Columbia University Press, 21–53.
  • Kearse M, Moir R, Wilson A, et al. (2012). Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics 28:1647–9.
  • Kitanovic S, Orr TJ, Spalink D, et al. (2018). Role of cytochrome P450 2B sequence variation and gene copy number in facilitating dietary specialization in mammalian herbivores. Mol Ecol 12:3218–21.
  • Kosakovsky Pond SL, Murrell B, Fourment M, et al. (2011). A random effects branch-site model for detecting episodic diversifying selection. Mol Biol Evol 28:3033–43.
  • Kumar S, Stecher G, Li M, et al. (2018). MEGA X: Molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol 35:1547–9.
  • Lambert JE. (1998). Primate digestion: interactions among anatomy, physiology, and feeding ecology. Evol Anthropol 7:8–20.
  • Lewis DV, Watson E, Lake BG. (1998). Evolution of the cytochrome P450 superfamily: sequence alignments and pharmacogenetics. Mutat Res 410:245–70.
  • Li YM. (2006). Seasonal variation of diet and food availability in a group of Sichuan snub-nosed monkeys in Shennongjia Nature Reserve, China. Am J Primatol 68:217–33.
  • Liu N, Li T, Reid WR, et al. (2011). Multiple cytochrome P450 genes: Their constitutive overexpression and permethrin induction in insecticide resistant mosquitoes, Culex quinquefasciatus. PLoS One 6:e23403.
  • Marotta M, Piontkivska H, Tanaka H. (2012). Molecular trajectories leading to the alternative fates of duplicate genes. PLoS One 7:e38958.
  • Milton K. 1980. The foraging strategy of howler monkeys: a study in primate economics. New York: Columbia University Press.
  • Murrell B, Wertheim JO, Moola S, et al. (2012). Detecting individual sites subject to episodic diversifying selection. PLoS Genet 8:e1002764.
  • Nelson DR. 2006. Cytochrome P450 Nomenclature, 2004. In: Phillips IR, Shephard EA, ed. Cytochrome P450 Protocols. 2nd ed. Totowa (NJ): Humana Press, 1–10.
  • Nelson DR. (2009). The cytochrome p450 homepage. Hum Genomics 4:59–65.
  • Nelson DR. (2013). A world of cytochrome P450s. Philos Trans R Soc Lond B Biol Sci 368:20120430.
  • Nelson DR. (2018). Cytochrome P450 diversity in the tree of life. Biochim Biophys Acta Proteins Proteom 1866:141–54.
  • Nelson DR, Goldstone JV, Stegeman JJ. (2013). The cytochrome P450 genesis locus: the origin and evolution of animal cytochrome P450s. Philos Trans R Soc B 368:1–22.
  • Norconk MA, Conklin-Brittain NL. (2016). Bearded saki feeding strategies on an island in Lago Guri, Venezuela. Am J Primatol 78:507–22.
  • Norlin M, Wikvall K. (2007). Enzymes in the conversion of cholesterol into bile acids. Curr Mol Med 7:199–218.
  • Osada N, Uno Y, Mineta K, et al. (2010). Ancient genome-wide admixture extends beyond the current hybrid zone between Macaca fascicularis and M. mulatta. Mol Ecol 19:2884–95.
  • Pass GJ, McLean S, Stupans I, Davies N. (2001). Microsomal metabolism of the terpene 1,8-cineole in the common brushtail possum (Trichosurus vulpecula), koala (Phascolarctos cinereus), rat and human. Xenobiotica 31:205–21.
  • Porter LM. (2001). Dietary differences among sympatric callitrichinae in northern Bolivia: Callimico goeldii, Saguinus fuscicollis and S. labiatus. Int J Primatol 22:961–92.
  • Qiu H, Taudien S, Herlyn H, et al. (2008). CYP3 phylogenomics: evidence for positive selection of CYP3A4 and CYP3A7. Pharmacogenet Genomics 18:53–66.
  • Sayers KA, Norconk MA. (2008). Himalayan Semnopithecus entellus at Langtang National Park, Nepal: Diet, activity patterns, and resources. Int J Primatol 29:509–30.
  • Sharma V, Hecker N, Roscito JG, et al. (2018). A genomics approach reveals insights into the importance of gene losses for mammalian adaptations. Nat Commun 9:1–9.
  • Smith RJ. (2018). The continuing misuse of null hypothesis significance testing in biological anthropology. Am J Phys Anthropol 166:236–45.
  • Tan CL. (1999). Group composition, home range size, and diet of three sympatric bamboo lemur species (genus Hapalemur) in Ranomafana National Park, Madagascar. Int J Primatol 20:547–66.
  • Thibaud-Nissen F, Sourorov A, Murphy T, DiCuccio M, Kitts P. 2013. Eukaryotic genome annotation pipeline. In: Beck J, Benson D, Coleman J, Hoeppner M, Johnson M, Maglott D, Mizrachi I, Morris R, Ostell J, Pruitt K, et al. ed. The NCBI handbook. 2nd ed. Bethesda, MD: National Center for Biotechnology Information, 1–34.
  • Thomas JH. (2007). Rapid birth-death evolution specific to xenobiotic cytochrome P450 genes in vertebrates. PLoS Genet 3:e67.
  • Thompson CL, Gapp LM, Melo LCO, et al. In press. Nocturnal foragers exploit tree exudates from holes gouged by diurnal common marmoset monkeys (Callithrix jacchus). Integr Zool.doi:10.1111/1749-4877.12448
  • Tomasco IH, Boullosa N, Hoffmann FG, Lessa EP. (2017). Molecular adaptive convergence in the α-globin gene in subterranean octodontid rodents. Gene 628:275–80.
  • Uehara S, Uno Y, Hagihira Y, et al. (2015). Marmoset cytochrome P450 2D8 in livers and small intestines metabolizes typical human P450 2D6 substrates, metoprolol, bufuralol and dextromethorphan. Xenobiotica 45:766–72.
  • Vogel ER, Alavi SE, Utami‐Atmoko SS, et al. (2017). Nutritional ecology of wild Bornean orangutans (Pongo pygmaeus wurmbii) in a peat swamp habitat: Effects of age, sex, and season. Am J Primatol 79:e22618.
  • Yang Z, Wong WSW, Nielsen R. (2005). Bayes empirical Bayes inference of amino acid sites under positive selection. Mol. Biol. Evol 22:1107–18.
  • Yasukochi Y, Satta Y. (2015). Molecular evolution of the CYP2D subfamily in primates: purifying selection on substrate recognition sites without the frequent or long-tract gene conversion. Genome Biol Evol 7:1053–67.
  • Zanger UM, Schwab M. (2013). Cytochrome P450 enzymes in drug metabolism: regulation of gene expression, enzyme activities, and impact of genetic variation. Pharmacol Ther 138:103–41.
  • Zawaira A, Ching LY, Coulson L, Blackburn J, et al. (2011). An expanded, unified substrate recognition site map for mammalian cytochrome P450s: analysis of molecular interactions between 15 mammalian CYP450 isoforms and 868 substrates. Curr Drug Metab 12:684–700.
  • Zhang J, Nielsen R, Yang Z. (2005). Evaluation of an improved branch-site likelihood method for detecting positive selection at the molecular level. Mol Biol Evol 22:2472–9.

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.