Probabilistic orthology analysis of the ATP-binding cassette transporters: Implications for the development of multiple drug resistance phenotype

Drug Metabolism and Disposition

Volumn 40, Issue 7, 2012, Pages 1397-1402

  Fisher, Ciaran ^a   Coleman, Tanya ^b   Plant, Nick ^a  

^a UNIVERSITY OF SURREY   (United Kingdom)

^b ASTRAZENECA   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ABC TRANSPORTER; DNA;

AMINO ACID SEQUENCE; ARTICLE; CONTROLLED STUDY; DOG; DRUG EFFICACY; DRUG SAFETY; GENE CLUSTER; GENE SEQUENCE; GENETIC CODE; HUMAN; MACACA; MOUSE; MULTIDRUG RESISTANCE; NONHUMAN; ORTHOLOGY; PHENOTYPE; PHYLOGENETIC TREE; PRIORITY JOURNAL; PROBABILITY; PROTEIN FAMILY; RAT; SPECIES DIFFERENCE;

ANIMALS; ATP-BINDING CASSETTE TRANSPORTERS; BIOLOGICAL TRANSPORT; DOGS; DRUG RESISTANCE, MULTIPLE; DRUG TOXICITY; HUMANS; MACACA; MICE; PHYLOGENY; RATS;

EID: 84862669767     PISSN: 00909556     EISSN: 1521009X     Source Type: Journal    
DOI: 10.1124/dmd.112.045062     Document Type: Article

References (47)

1. Abascal F, Zardoya R, and Posada D (2005) ProtTest: selection of best fit models of protein evolution. Bioinformatics 21:2104-2105.
2. Altschul SF, Gish W, Miller W, Myers EW, and Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403-410.
3. Ambudkar SV, Dey S, Hrycyna CA, Ramachandra M, Pastan I, and Gottesman MM (1999) Biochemical, cellular, and pharmacological aspects of the multidrug transporter. Annu Rev Pharmacol Toxicol 39:361-398.
4. Arvestad L, Berglund AC, Lagergren J, and Sennblad B (2003) Bayesian gene/species tree reconciliation and orthology analysis using MCMC. Bioinformatics 19:i7-i15.
5. Barille FA (2008) Principles of Toxicology Testing. CRC Press, Boca Raton.
6. Bisbal C, Martinand C, Silhol M, Lebleu B, and Salehzada T (1995) Cloning and characterization of a RNAse L inhibitor. A new component of the interferon-regulated 2-5A pathway. J Biol Chem 270:13308-13317.
7. Cedernaes J, Olszewski PK, Almén MS, Stephansson O, Levine AS, Fredriksson R, Nylander O, and Schiöth HB (2011) Comprehensive analysis of localization of 78 solute carrier genes throughout the subsections of the rat gastrointestinal tract. Biochem Biophys Res Commun 411:702-707.
8. Cervenak J, Andrikovics H, Ozvegy-Laczka C, Tordai A, Német K, Váradi A, and Sarkadi B (2006) The role of the human ABCG2 multidrug transporter and its variants in cancer therapy and toxicology. Cancer Lett 234:62-72.
9. Childs S, Yeh RL, Hui D, and Ling V (1998) Taxol resistance mediated by transfection of the liver-specific sister gene of P-glycoprotein. Cancer Res 58:4160-4167.
10. Choi CH (2005) ABC transporters as multidrug resistance mechanisms and the development of chemosensitizers for their reversal. Cancer Cell Int 5:30.
11. Coley HM (2008) Mechanisms and strategies to overcome chemotherapy resistance in metastatic breast cancer. Cancer Treat Rev 34:378-390.
12. Cotton JA and Page RD (2005) Rates and patterns of gene duplication and loss in the human genome. Proc Biol Sci 272:277-283.
13. Davidson AL and Chen J (2004) ATP-binding cassette transporters in bacteria. Annu Rev Biochem 73:241-268.
14. Dean M and Allikmets R (1995) Evolution of ATP-binding cassette transporter genes. Curr Opin Genet Dev 5:779-785.
15. Dean M and Annilo T (2005) Evolution of the ATP-binding cassette (ABC) transporter superfamily in vertebrates. Annu Rev Genomics Hum Genet 6:123-142.
16. Deeley RG, Westlake C, and Cole SP (2006) Transmembrane transport of endo- and xenobiotics by mammalian ATP-binding cassette multidrug resistance proteins. Physiol Rev 86:849-899.
17. Dressman JB, Thelen K, and Willmann S (2011) An update on computational oral absorption simulation. Expert Opin Drug Metab Toxicol 7:1345-1364.
18. Fan J, Chen S, Chow EC, and Pang KS (2010) PBPK modeling of intestinal and liver enzymes and transporters in drug absorption and sequential metabolism. Curr Drug Metab 11:743-761.
19. Fath MJ and Kolter R (1993) ABC transporters: bacterial exporters. Microbiol Rev 57:995-1017.
20. Felenstein J (1989) Phylip-Phlylogeny Interface Package (Version 3.2). Cladistics 164-166.
21. Felsenstein J (1997) An alternating least squares approach to inferring phylogenies from pairwise distances. Syst Biol 46:101-111.
22. Gillet JP, Efferth T, and Remacle J (2007) Chemotherapy-induced resistance by ATP-binding cassette transporter genes. Biochim Biophys Acta 1775:237-262.
23. Glavinas H, Krajcsi P, Cserepes J, and Sarkadi B (2004) The role of ABC transporters in drug resistance, metabolism and toxicity. Curr Drug Deliv 1:27-42.
24. Guindon S and Gascuel O (2003) A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 52:696-704.
25. Hembruff SL, Laberge ML, Villeneuve DJ, Guo BQ, Veitch Z, Cecchetto M, and Parissenti AM (2008) Role of drug transporters and drug accumulation in the temporal acquisition of drug resistance. BMC Cancer 8:318.
26. Higgins DG and Sharp PM (1988) CLUSTAL: a package for performing multiple sequence aligment on a microcomputes. Gene 73:237-244.
27. Huang Y, Anderle P, Bussey KJ, Barbacioru C, Shankavaram U, Dai Z, Reinhold WC, Papp A, Weinstein JN, and Sadée W (2004) Membrane transporters and channels: role of the transportome in cancer chemosensitivity and chemoresistance. Cancer Res 64:4294-4301.
28. Jacobs LL and Downs WR (1994) The evolution of murine rodents, in Rodents and Lagomorph Families of Asian Origin and Diversification (Tomida Y, Li C, and Setoguchi T eds), pp 149-156, National Science Museum Monograph, Tokyo.
29. Kalliokoski A and Niemi M (2009) Impact of OATP transporters on pharmacokinetics. Br J Pharmacol 158:693-705.
30. Koski LB and Golding GB (2001) The closest BLAST hit is often not the nearest neighbor. J Mol Evol 52:540-542.
31. Kumar S and Hedges SB (1998) A molecular timescale for vertebrate evolution. Nature 392:917-920.
32. Le SQ and Gascuel O (2008) An improved general amino acid replacement matrix. Mol Biol Evol 25:1307-1320.
33. Lynch M and Conery JS (2003) The evolutionary demography of duplicate genes. J Struct Funct Genomics 3:35-44.
34. Lynch M and Conery JS (2000) The evolutionary fate and consequences of duplicate genes. Science 290:1151-1155.
35. Pang KS, Maeng HJ, and Fan J (2009) Interplay of transporters and enzymes in drug and metabolite processing. Mol Pharm 6:1734-1755.
36. Rannala B and Yang Z (2007) Inferring speciation times under an episodic molecular clock. Syst Biol 56:453-466.
37. Rees DC, Johnson E, and Lewinson O (2009) ABC transporters: the power to change. Nat Rev Mol Cell Biol 10:218-227.
38. Richard M, Drouin R, and Beaulieu AD (1998) ABC50, a novel human ATP-Binding cassette protein found in tumor necrosis factor-alpha-stimulated synoviocytes. Genomics 53:137-145.
39. Saier MH and Paulsen IT (2001) Phylogeny of multidrug transporters. Semin Cell Dev Biol 12:205-213.
40. Sennblad B and Lagergren J (2009) Probabilistic orthology analysis. Syst Biol 58:411-424.
41. Sheps JA, Ralph S, Zhao ZY, Baillie DL, and Ling V (2004) The ABC transporter gene family of Caenorhabditis elegans has implications for the evolutionary dynamics of multidrug resistance in eukaryotes. Genome Biol 5: R15.
42. Smith AJ, van Helvoort A, van Meer G, Szabo K, Welker E, Szakacs G, Varadi A, Sarkadi B, and Borst P (2000) MDR3 P-glycoprotein, a phosphatidylcholine translocase, transports several cytotoxic drugs and directly interacts with drugs as judged by interference with nucleotide trapping. J Biol Chem 275:23530-23539.
43. Takahashi M, Washio T, Suzuki N, Igeta K, Fujii Y, Hayashi M, Shirasaka Y, and Yamashita S (2008) Characterization of gastrointestinal drug absorption in cynomolgus monkeys. Mol Pharm 5:340-348.
44. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, and 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.
45. Tiwari AK, Sodani K, Dai CL, Ashby CR Jr, and Chen ZS (2011) Revisiting the ABCs of multidrug resistance in cancer chemotherapy. Curr Pharm Biotechnol 12:570-594.
46. Zhang Z, Schwartz S, Wagner L, and Miller W (2000) A greedy algorithm for aligning DNA sequences. J Comput Biol 7:203-214.
47. Zhou SF, Wang LL, Di YM, Xue CC, Duan W, Li CG, and Li Y (2008) Substrates and inhibitors of human multidrug resistance associated proteins and the implications in drug development. Curr Med Chem 15:1981-2039.