Genome-wide analysis of the ATP-binding cassette (ABC) transporter gene family in the silkworm, Bombyx mori

Molecular Biology Reports

Volumn 39, Issue 7, 2012, Pages 7281-7291

  Xie, Xiaodong ^a   Cheng, Tingcai ^a   Wang, Genhong ^a   Duan, Jun ^a   Niu, Weihuan ^a   Xia, Qingyou ^b  

^a CHONGQING UNIVERSITY   (China)

^b SOUTHWEST UNIVERSITY   (China)

Author keywords

ABC transporter; Biochemical defense; Bombyx mori; Phylogenetic analysis

Indexed keywords

ABC TRANSPORTER; ABC TRANSPORTER B; ABC TRANSPORTER C; ABC TRANSPORTER C4; ABC TRANSPORTER D; ABC TRANSPORTER E; ABC TRANSPORTER F; ABC TRANSPORTER G; ABC TRANSPORTER H; UNCLASSIFIED DRUG;

ARTICLE; CONTROLLED STUDY; DOMESTICATION; GENE EXPRESSION; GENETIC CONSERVATION; GENETIC SELECTION; GENETIC VARIABILITY; GENOME ANALYSIS; INSECT GENOME; MICROARRAY ANALYSIS; MULTIDRUG RESISTANCE; MULTIGENE FAMILY; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PROTEIN ANALYSIS; PROTEIN FAMILY; PROTEIN FUNCTION; SILKWORM;

ANIMALS; ATP-BINDING CASSETTE TRANSPORTERS; BOMBYX; DRUG RESISTANCE, MULTIPLE; GENE EXPRESSION PROFILING; GENETIC VARIATION; GENOME, INSECT; MULTIGENE FAMILY; PHYLOGENY; PROTEIN STRUCTURE, SECONDARY;

BOMBYX MORI; CAENORHABDITIS ELEGANS; HOMO SAPIENS; PHYLO;

EID: 84864288759     PISSN: 03014851     EISSN: 15734978     Source Type: Journal    
DOI: 10.1007/s11033-012-1558-3     Document Type: Article

References (56)

1. Schneider E, Hunke S (1998) ATP-binding-cassette (ABC) transport systems: functional and structural aspects of the ATP-hydrolyzing subunits/domains. FEMS Microbiol Rev 22(1):1-20 (Pubitemid 28270522)
2. Berntsson RP, Smits SH, Schmitt L, Slotboom DJ, Poolman B (2010) A structural classification of substrate-binding proteins. FEBS Lett 584(12):2606-2617
3. Hyde SC, Emsley P, Hartshorn MJ, Mimmack MM, Gileadi U, Pearce SR, Gallagher MP, Gill DR, Hubbard RE, Higgins CF (1990) Structural model of ATP-binding proteins associated with cystic fibrosis, multidrug resistance and bacterial transport. Nature 346(6282):362-365
4. Walker JE, Saraste M, Runswick MJ, Gay NJ (1982) Distantly related sequences in the alpha-and beta-subunits of ATP syn-thase, myosin, kinases and other ATP-requiring enzymes and a common nucleotide binding fold. EMBO J 1(8):945-951
5. Dean M (2009) ABC transporters, drug resistance, and cancer stem cells. J Mammary Gland Biol Neoplasia 14(1):3-9
6. Dean M, Rzhetsky A, Allikmets R (2001) The human ATP-binding cassette (ABC) transporter superfamily. Genome Res 11(7):1156-1166 (Pubitemid 32677289)
7. Higgins CF (1992) ABC transporters: from microorganisms to man. Annu Rev Cell Biol 8:67-113 (Pubitemid 23000992)
8. Klein I, Sarkadi B, Varadi A (1999) An inventory of the human ABC proteins. Biochim Biophys Acta 1461(2):237-262
9. Gottesman MM, Fojo T, Bates SE (2002) Multidrug resistance in cancer: role of ATP-dependent transporters. Nat Rev Cancer 2(1):48-58 (Pubitemid 37328807)
10. Grailles M, Brey PT, Roth CW (2003) The Drosophila melano-gaster multidrug-resistance protein 1 (MRP1) homolog has a novel gene structure containing two variable internal exons. Gene 307:41-50 (Pubitemid 36428861)
11. Broeks A, Gerrard B, Allikmets R, Dean M, Plasterk RH (1996) Homologues of the human multidrug resistance genes MRP and MDR contribute to heavy metal resistance in the soil nematode Caenorhabditis elegans. EMBO J 15(22):6132-6143 (Pubitemid 26397885)
12. de Waard MA, Andrade AC, Hayashi K, Schoonbeek HJ, Ster-giopoulos I, Zwiers LH (2006) Impact of fungal drug transporters on fungicide sensitivity, multidrug resistance and virulence. Pest Manag Sci 62(3):195-207
13. Webber MA, Piddock LJ (2003) The importance of efflux pumps in bacterial antibiotic resistance. J Antimicrob Chemother 51(1):9-11 (Pubitemid 36163821)
14. Mackenzie SM, Brooker MR, Gill TR, Cox GB, Howells AJ, Ewart GD (1999) Mutations in the white gene of Drosophila melanogaster affecting ABC transporters that determine eye colouration. Biochim Biophys Acta 1419(2):173-185 (Pubitemid 29322708)
15. Ricardo S, Lehmann R (2009) An ABC transporter controls export of a Drosophila germ cell attractant. Science 323(5916): 943-946
16. Tarnay JN, Szeri F, Ilias A, Annilo T, Sung C, Le Saux O, Varadi A, Dean M, Boyd CD, Robinow S (2004) The dMRP/CG6214 gene of Drosophila is evolutionarily and functionally related to the human multidrug resistance-associated protein family. Insect Mol Biol 13(5):539-548 (Pubitemid 39333195)
17. Komoto N, Quan GX, Sezutsu H, Tamura T (2009) A single-base deletion in an ABC transporter gene causes white eyes, white eggs, and translucent larval skin in the silkworm w-3(oe) mutant. Insect Biochem Mol Biol 39(2):152-156
18. Murray CL, Quaglia M, Arnason JT, Morris CE (1994) A putative nicotine pump at the metabolic blood-brain barrier of the tobacco hornworm. J Neurobiol 25(1):23-34 (Pubitemid 23358281)
19. Gaertner LS, Murray CL, Morris CE (1998) Transepithelial transport of nicotine and vinblastine in isolated malpighian tubules of the tobacco hornworm (Manduca sexta) suggests a P-glycoprotein-like mechanism. J Exp Biol 201(18):2637-2645 (Pubitemid 28514562)
20. Zhou Z, Yang H, Zhong B (2008) From genome to proteome: great progress in the domesticated silkworm (Bombyx mori L.). Acta Biochim Biophys Sin (Shanghai) 40(7):601-611 (Pubitemid 352009076)
21. Xia Q, Zhou Z, Lu C, Cheng D, Dai F, Li B, Zhao P, Zha X, Cheng T, Chai C, Pan G, Xu J, Liu C, Lin Y, Qian J, Hou Y, Wu Z, Li G, Pan M, Li C, Shen Y, Lan X, Yuan L, Li T, Xu H, Yang G, Wan Y, Zhu Y, Yu M, Shen W, Wu D, Xiang Z, Yu J, Wang J, Li R, Shi J, Li H, Su J, Wang X, Zhang Z, Wu Q, Li J, Zhang Q, Wei N, Sun H, Dong L, Liu D, Zhao S, Zhao X, Meng Q, Lan F, Huang X, Li Y, Fang L, Li D, Sun Y, Yang Z, Huang Y, Xi Y, Qi Q, He D, Huang H, Zhang X, Wang Z, Li W, Cao Y, Yu Y, Yu H, Ye J, Chen H, Zhou Y, Liu B, Ji H, Li S, Ni P, Zhang J, Zhang Y, Zheng H, Mao B, Wang W, Ye C, Wong GK, Yang H (2004) A draft sequence for the genome of the domesticated silkworm (Bombyx mori). Science 306(5703):1937-1940 (Pubitemid 39627858)
22. Bateman A, Birney E, Durbin R, Eddy SR, Finn RD, Sonnhammer EL (1999) Pfam 3.1: 1313 multiple alignments and profile HMMs match the majority of proteins. Nucleic Acids Res 27(1):260-262 (Pubitemid 29209455)
23. Eddy SR (1995) Multiple alignment using hidden Markov models. Proc Int Conf Intell Syst Mol Biol 3:114-120
24. Dean M, Annilo T (2005) Evolution of the ATP-binding cassette (ABC) transporter superfamily in vertebrates. Annu Rev Genomics Hum Genet 6:123-142 (Pubitemid 41397078)
25. Verrier PJ, Bird D, Burla B, Dassa E, Forestier C, Geisler M, Klein M, Kolukisaoglu U, Lee Y, Martinoia E, Murphy A, Rea PA, Samuels L, Schulz B, Spalding EJ, Yazaki K, Theodoulou FL (2008) Plant ABC proteins-a unified nomenclature and updated inventory. Trends Plant Sci 13(4):151-159
26. 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(24):4876-4882
27. Tamura K, Dudley J, Nei M, Kumar S (2007) MEGA4: molecular evolutionary genetics analysis (mega) software version 4.0. Mol Biol Evol 24(8):1596-1599 (Pubitemid 47236692)
28. Xia Q, Guo Y, Zhang Z, Li D, Xuan Z, Li Z, Dai F, Li Y, Cheng D, Li R, Cheng T, Jiang T, Becquet C, Xu X, Liu C, Zha X, Fan W, Lin Y, Shen Y, Jiang L, Jensen J, Hellmann I, Tang S, Zhao P, Xu H, Yu C, Zhang G, Li J, Cao J, Liu S, He N, Zhou Y, Liu H, Zhao J, Ye C, Du Z, Pan G, Zhao A, Shao H, Zeng W, Wu P, Li C, Pan M, Yin X, Wang J, Zheng H, Wang W, Zhang X, Li S, Yang H, Lu C, Nielsen R, Zhou Z, Xiang Z (2009) Complete re-sequencing of 40 genomes reveals domestication events and genes in silkworm (Bombyx). Science 326(5951):433-436
29. Yang Z (1997) PAML: a program package for phylogenetic analysis by maximum likelihood. Comput Appl Biosci 13(5):555-556 (Pubitemid 27480216)
30. Xia Q, Cheng D, Duan J, Wang G, Cheng T, Zha X, Liu C, Zhao P, Dai F, Zhang Z, He N, Zhang L, Xiang Z (2007) Microarray-based gene expression profiles in multiple tissues of the domesticated silkworm Bombyx mori. Genome Biol 8(8):R162
31. Vasiliou V, Vasiliou K, Nebert DW (2009) Human ATP-binding cassette (ABC) transporter family. Hum Genomics 3(3):281-290
32. Hogue DL, Liu L, Ling V (1999) Identification and characterization of a mammalian mitochondrial ATP-binding cassette membrane protein. J Mol Biol 285(1):379-389 (Pubitemid 29034051)
33. Abele R, Tampe R (2004) The ABCs of immunology: structure and function of TAP, the transporter associated with antigen processing. Physiology (Bethesda) 19:216-224 (Pubitemid 39481937)
34. Rommens JM, Iannuzzi MC, Kerem B, Drumm ML, Melmer G, Dean M, Rozmahel R, Cole JL, Kennedy D, Hidaka N et al (1989) Identification of the cystic fibrosis gene: chromosome walking and jumping. Science 245(4922):1059-1065 (Pubitemid 19231813)
35. Shani N, Valle D (1998) Peroxisomal ABC transporters. Methods Enzymol 292:753-776 (Pubitemid 29343930)
36. Mosser J, Lutz Y, Stoeckel ME, Sarde CO, Kretz C, Douar AM, Lopez J, Aubourg P, Mandel JL (1994) The gene responsible for adrenoleukodystrophy encodes a peroxisomal membrane protein. Hum Mol Genet 3(2):265-271 (Pubitemid 24060941)
37. Kuwana H, Shimizu-Nishikawa K, Iwahana H, Yamamoto D (1996) Molecular cloning and characterization of the ABC transporter expressed in Trachea (ATET) gene from Drosophila melanogaster. Biochim Biophys Acta 1309(1-2):47-52 (Pubitemid 26382348)
38. Abraham EG, Sezutsu H, Kanda T, Sugasaki T, Shimada T, Tamura T (2000) Identification and characterisation of a silkworm ABC transporter gene homologous to Drosophila white. Mol Gen Genet 264(1-2):11-19
39. Labbe R, Caveney S, Donly C (2011) Genetic analysis of the xenobiotic resistance-associated ABC gene subfamilies of the Lepidoptera. Insect Mol Biol 20(2):243-256
40. Anjard C, Loomis WF (2002) Evolutionary analyses of ABC transporters of Dictyostelium discoideum. Eukaryot Cell 1(4):643-652 (Pubitemid 36562390)
41. Berger J, Gartner J (2006) X-linked adrenoleukodystrophy: clinical, biochemical and pathogenetic aspects. Biochim Biophys Acta 1763(12):1721-1732 (Pubitemid 44880457)
42. Zhou A, Hassel BA, Silverman RH (1993) Expression cloning of 2-5A-dependent RNAase: a uniquely regulated mediator of interferon action. Cell 72(5):753-765 (Pubitemid 23093883)
43. Gerrard B, Stewart C, Dean M (1993) Analysis of Mdr50: a Drosophila P-glycoprotein/multidrug resistance gene homolog. Genomics 17(1):83-88 (Pubitemid 23205061)
44. Wu CT, Budding M, Griffin MS, Croop JM (1991) Isolation and characterization of Drosophila multidrug resistance gene homologs. Mol Cell Biol 11(8):3940-3948 (Pubitemid 21895783)
45. Begun DJ, Whitley P (2000) Genetics of alpha-amanitin resistance in a natural population of Drosophila melanogaster. Heredity 85(2):184-190
46. Borst P, Evers R, Kool M, Wijnholds J (2000) A family of drug transporters: the multidrug resistance-associated proteins. J Natl Cancer Inst 92(16):1295-1302 (Pubitemid 30662093)
47. Reid G, Wielinga P, Zelcer N, van der Heijden I, Kuil A, de Haas M, Wijnholds J, Borst P (2003) The human multidrug resistance protein MRP4 functions as a prostaglandin efflux transporter and is inhibited by nonsteroidal antiinflammatory drugs. Proc Natl Acad Sci U S A 100(16):9244-9249 (Pubitemid 37033914)
48. van de Ven R, Oerlemans R, van der Heijden JW, Scheffer GL, de Gruijl TD, Jansen G, Scheper RJ (2009) ABC drug transporters and immunity: novel therapeutic targets in autoimmunity and cancer. J Leukoc Biol 86(5):1075-1087
49. Leier I, Jedlitschky G, Buchholz U, Cole SP, Deeley RG, Keppler D (1994) The MRP gene encodes an ATP-dependent export pump for leukotriene C4 and structurally related conjugates. J Biol Chem 269(45):27807-27810 (Pubitemid 24354499)
50. Cui Y, Konig J, Buchholz JK, Spring H, Leier I, Keppler D (1999) Drug resistance and ATP-dependent conjugate transport mediated by the apical multidrug resistance protein, MRP2, permanently expressed in human and canine cells. Mol Pharmacol 55(5):929-937 (Pubitemid 29214613)
51. Zeng H, Liu G, Rea PA, Kruh GD (2000) Transport of amphi-pathic anions by human multidrug resistance protein 3. Cancer Res 60(17):4779-4784
52. Rius M, Hummel-Eisenbeiss J, Keppler D (2008) ATP-dependent transport of leukotrienes B4 and C4 by the multidrug resistance protein ABCC4 (MRP4). J Pharmacol Exp Ther 324(1):86-94 (Pubitemid 350294174)
53. Laberge RM, Karwatsky J, Lincoln MC, Leimanis ML, Georges E (2007) Modulation of GSH levels in ABCC1 expressing tumor cells triggers apoptosis through oxidative stress. Biochem Pharmacol 73(11):1727-1737 (Pubitemid 46601409)
54. Kusuhara H, Sugiyama Y (2007) ATP-binding cassette, subfamily G (ABCG family). Pflugers Arch 453(5):735-744 (Pubitemid 46192543)
55. Chen H, Rossier C, Lalioti MD, Lynn A, Chakravarti A, Perrin G, Antonarakis SE (1996) Cloning of the cDNA for a human homologue of the Drosophila white gene and mapping to chromosome 21q22.3. Am J Hum Genet 59(1):66-75 (Pubitemid 26189730)
56. Quan GX, Kanda T, Tamura T (2002) Induction of the white egg 3 mutant phenotype by injection of the double-stranded RNA of the silkworm white gene. Insect Mol Biol 11(3):217-222 (Pubitemid 34536273)