The evolutionary repertoires of the eukaryotic-type ABC transporters in terms of the phylogeny of ATP-binding domains in eukaryotes and prokaryotes

Molecular Biology and Evolution

Volumn 21, Issue 11, 2004, Pages 2149-2160

  Igarashi, Yoshinobu ^a   Aoki, Kiyoko F ^a   Mamitsuka, Hiroshi ^a   Kuma, Kei Ichi ^a   Kanehisa, Minoru ^a  

^a KYOTO UNIVERSITY   (Japan)

Author keywords

ABC transporter; Comparative genomics; Multidrug

Indexed keywords

ABC TRANSPORTER; ADENOSINE TRIPHOSPHATE;

ARTICLE; CELL MEMBRANE; EUKARYOTE EVOLUTION; GENE CLUSTER; GENE LOCATION; GENETIC VARIABILITY; NONHUMAN; PHYLOGENY; PROKARYOTE;

ADENOSINE TRIPHOSPHATE; ANIMALS; ATP-BINDING CASSETTE TRANSPORTERS; BACTERIAL PROTEINS; BIOLOGICAL TRANSPORT; CLUSTER ANALYSIS; COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; DRUG RESISTANCE, MULTIPLE; EUKARYOTIC CELLS; EVOLUTION, MOLECULAR; HUMANS; MEMBRANE TRANSPORT PROTEINS; MOLECULAR SEQUENCE DATA; PHYLOGENY; PROKARYOTIC CELLS; PROTEIN STRUCTURE, TERTIARY;

BACTERIA (MICROORGANISMS); EUKARYOTA; PROKARYOTA;

EID: 6344225693     PISSN: 07374038     EISSN: None     Source Type: Journal    
DOI: 10.1093/molbev/msh226     Document Type: Article

References (58)

1. Ahn, J. H., J. G. Pan, and J. S. Rhee. 1999. Identification of the tliDEF ABC transporter specific for lipase in Pseudomonas fluorescens S1K W1. J Bacteriol. 181:1847-1852.
2. Bateman, A., E. Birney, L. Cerruti, R. Durbin, L. Etwiller, S. R. Eddy, S. Griffiths-Jones, K. L. Howe, M. Marshall, and E. L. Sonnhammer. 2002. The Pfam protein families database. Nucleic Acids Res. 30:276-280.
3. Becker, A., H. Kuster, K. Niehaus, and A. Puhler. 1995. Extension of the Rhizobium meliloti succinoglycan biosynthesis gene cluster: identification of the exsA gene encoding an ABC transporter protein, and the exsB gene which probably codes for a regulator of succinoglycan biosynthesis. Mol. Gen. Genet. 249:487-497.
4. Benabdelhak, H., S. Kiontke, C. Horn, R. Ernst, M. A. Blight, I. B. Holland, and L. Schmitt. 2003. A specific interaction between the NBD of the ABC-transporter HlyB and a C-terminal fragment of its transport substrate haemolysin A. J. Mol. Biol. 327:1169-1179.
5. Chang, G., and C. B. Roth. 2001. Structure of MsbA from E. coli: a homolog of the multidrug resistance ATP binding cassette (ABC) transporters. Science 293:1793-1800.
6. Chenna, R., H. Sugawara, T. Koike, R. Lopez, T. J. Gibson, D. G. Higgins, and J. D. Thompson. 2003. Multiple sequence alignment with the Clustal series of programs. Nucleic Acids Res. 31:3497-3500.
7. Christensen, P. U., J. Davey, and O. Nielsen. 1997. The Schizosaccharomyces pombe mam1 gene encodes an ABC transporter mediating secretion of M-factor. Mol. Gen. Genet. 255:226-236.
8. Cole, S. P., G. Bhardwaj, J. H. Gerlach, J. E. Mackie, C. E. Grant, K. C. Almquist, A. J. Stewart, E. U. Kurz, A. M. Duncan, and R. G. Deeley. 1992. Overexpression of a transporter gene in a multidrug-resistant human lung cancer cell line. Science 258:1650-1654.
9. Cole, S. P., and R. G. Deeley. 1996. Multidrug resistance associated with overexpression of MRP. Cancer Treat Res. 87:39-62.
10. de Leeuw, E., B. Graham, G. J. Phillips, C. M. ten Hagen-Jongman, B. Oudega, and J. Luirink. 1999. Molecular characterization of Excherichia coli FtsE and FtsX. Mol. Microbiol. 31:983-993.
11. Dean, M., A. Rzhetsky, and R. Allikmets. 2001. The human ATP-binding cassette (ABC) transporter superfamily. Genome Res. 11:1156-1166.
12. Decoltignies, A., and A. Goffeau. 1997. Complete inventory of the yeast ABC proteins. Nat. Genet. 15:137-145.
13. Eddy, S. R. 1998. Profile hidden Markov models. Bioinformatics 14:755-763.
14. Ewart, G. D., and A. J. Howells. 1998. ABC transporters involved in transport of eye pigment precursors in Drosophila melanogaster. Methods Enzymol. 292:213-224.
15. Fetherston, J. D., V. J. Bertolino, and R. D. Perry. 1999. YbtP and YbtQ: two ABC transporters required for iron uptake in Yersinia pestis. Mol. Microbiol. 32:289-299.
16. Gorodkin, J., L. J. Heyer, S. Brunak, and G. D. Stormo. 1997. Displaying the information contents of structural RNA alignments: the structure logos. Comput. Appl. Biosci. 13:583-586.
17. Havarstein, L. S., D. B. Diep, and I. F. Nes. 1995. A family of bacteriocin ABC transporters carry out proteolytic processing of their substrates concomitant with export. Mol. Microbiol. 16:229-240.
18. Higgins, D. G., A. J. Bleasby, and R. Fuchs. 1992. CLUSTAL V: improved software for multiple sequence alignment. Comput. Appl. Biosci. 8:189-191.
19. Hwang, J., M. Manuvakhova, and P. C. Tai. 1997. Characterization of in-frame proteins encoded by cvaA, an essential gene in the colicin V secretion system: CvaA* stabilizes CvaA to enhance secretion. J. Bacteriol. 179:689-696.
20. Idei, A., E. Kawai, H. Akatsuka, and K. Omori. 1999. Cloning and characterization of the Pseudomonas fluorescens ATP-binding cassette exporter, HasDEF, for the heme acquisition protein HasA. J. Bacteriol. 181:7545-7551.
21. Jedlitschky, G., I. Leier, U. Buchholz, K. Barnouin, G. Kurz, and D. Keppler. 1996. Transport of glutathione, glucuronate, and sulfate conjugates by the MRP gene-encoded conjugate export pump. Cancer Res. 56:988-994.
22. Kanehisa, M., S. Goto, S. Kawashima, and A. Nakaya. 2002. The KEGG databases at GenomeNet. Nucleic Acids Res. 30:42-46.
23. Ketchum, C. J., W. K. Schmidt, G. V. Rajendrakumar, S. Michaelis, and P. C. Maloney. 2001. The yeast a-factor transporter Ste6p, a member of the ABC superfamily, couples ATP hydrolysis to pheromone export. J. Biol. Chem. 276:29007-29011.
24. Khudyakov, I., and C. P. Wolk. 1997. hetC, a gene coding for a protein similar to bacterial ABC protein exporters, is involved in early regulation of heterocyst differentiation in Anabaena sp. strain PCC 7120. J. Bacteriol. 179:6971-6978.
25. Kispal, G., P. Csere, C. Prohl, and R. Lill. 1999. The mitochondrial proteins Atm1p and Nfs1p are essential for biogenesis of cytosolic Fe/S proteins. EMBO J. 18: 3981-3989.
26. Kobayashi, N., K. Nishino, and A. Yamaguchi. 2001. Novel macrolide-specific ABC-type efflux transporter in Escherichia coli. J. Bacteriol. 183:5639-5644.
27. Kolaczkowski, M., A. Kolaczowska, J. Luczynski, S. Witek, and A. Goffeau. 1998. In vivo characterization of the drug resistance profile of the major ABC transporters and other components of the yeast pleiotropic drug resistance network. Microbiol. Drug Resist. 4:143-158.
28. Krogh, A., B. Larsson, G. von Heijne, and E. L. Sonnhammer. 2001. Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J. Mol. Biol. 305:567-580.
29. Kullback, S., and R. A. Leibler. 1951. On information and sufficiency. Ann. Math. Stat. 22:76-86.
30. Lin, W., K. J. Fullner, R. Clayton, J. A. Sexton, M. B. Rogers, K. E. Calia, S. B. Calderwood, C. Fraser, and J. J. Mekalanos. 1999. Identification of a vibrio cholerae RTX toxin gene cluster that is tightly linked to the cholera toxin prophage. Proc. Natl. Acad. Sci. USA 96:1071-1076.
31. Locher, K. P., A. T. Lee, and D. C. Rees. 2002. The E. coli BtuCD structure: a framework for ABC transporter architecture and mechanism. Science 296:1091-1098.
32. Marcotte, E. M., M. Pellegrini, H. L. Ng, D. W. Rice, T. O. Yeates, and D. Eisenberg. 1999. Detecting protein function and protein-protein interactions from genome sequences. Science 285:751-753.
33. Mauel, C., M. Young, P. Margot, and D. Karamata. 1989. The essential nature of teichoic acids in Bacillus subtilis as revealed by insertional mutagenesis. Mol. Gen. Genet. 215:388-394.
34. McMorran, B. J., M. E. Merriman, I. T. Rombel, and I. L. Lamont. 1996. Characterisation of the pvdE gene which is required for pyoverdine synthesis in Pseudomonas aeruginosa. Gene 176:55-59.
35. Ortiz, D. F., T. Ruscitti, K. F. McCue, and D. W. Ow. 1995. Transport of metal-binding peptides by HMTI, a fission yeast ABC-type vacuolar membrane protein. J. Biol. Chem. 270:4721-4728.
36. Pearson, W. R. 1996. Effective protein sequence comparison. Methods Enzymol. 266:227-258.
37. Pestova, E. V., L. S. Havarstein, and D. A. Morrison. 1996. Regulation of competence for genetic transformation in Streptococcus pneumoniae by an auto-induced peptide pheromone and a two-component regulatory system. Mol. Microbiol. 21:853-862.
38. Pittman, M. S., H. Corker, G. Wu, M. B. Binet, A. J. Moir, and R. K. Poole. 2002. Cysteine is exported from the Escherichia coli cytoplasm by CydDC, an ATP-binding cassette-type transporter required for cytochrome assembly. J. Biol. Chem. 277:49841-49849.
39. Quigley, N. B., Y. Y. Mo, and D. C. Gross. 1993. SyrD is required for syringomycin production by Pseudomonas syringae pathovar syringae and is related to a family of ATP-binding secretion proteins. Mol. Microbiol. 9:787-801.
40. Reizer, J., A. Reizer, and M. H. Saier Jr. 1992. A new subfamily of bacterial ABC-type transport systems catalyzing export of drugs and carbohydrates. Protein Sci. 1:1326-1332.
41. Reuter, G., T. Janvilisri, H. Venter, S. Shahi, L. Balakrishnan, and H. W. van Veen. 2003. The ATP binding cassette multidrug transporter LmrA and lipid transporter MsbA have overlapping substrate specificities. J. Biol. Chem. 278:35193-35198.
42. Saitou, N., and M. Nei. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4:406-425.
43. Sanchez-Fernandez, R., T. G. Davies, J. O. Coleman, and P. A. Rea. 2001. The Arabidopsis thaliana ABC protein superfamily, a complete inventory. J Biol Chem 276:30231-30244.
44. Saraste, M., P. R. Sibbald, and A. Wittinghofer. 1990. The P-loop - a common motif in ATP- and GTP-binding proteins. Trends Biochem. Sci. 15:430-434.
45. Saurin, W., and E. Dassa. 1994. Sequence relationships between integral inner membrane proteins of binding protein-dependent transport systems: evolution by recurrent gene duplications. Protein Sci. 3:325-344.
46. Saurin, W., M. Hofnung, and E. Dassa. 1999. Getting in or out: early segregation between importers and exporters in the evolution of ATP-binding cassette (ABC) transporters. J. Mol. Evol. 48:22-41.
47. Schmitt, L., H. Benabdelhak, M. A. Blight, I. B. Holland, and M. T. Stubbs. 2003. Crystal structure of the nucleotide-binding domain of the ABC-transporter haemolysin B: identification of a variable region within ABC helical domains. J. Mol. Biol. 330:333-342.
48. Sharom, F. J. 1997. The P-glycoprotein efflux pump: how does it transport drugs? J. Membr. Biol. 160:161-175.
49. Smith, T. F., and M. S. Waterman. 1981. Identification of common molecular subsequences. J. Mol. Biol. 147:195-197.
50. Sokal, R. R., and C. D. Michener. 1958. A statistical method for evaluating systematic relationships. University of Kansas Science Bulletin, 38:1409-1438.
51. Stanfield, S. W., L. Ielpi, D. O'Brochta, D. R. Helinski, and G. S. Ditta. 1988. The ndvA gene product of Rhizobium meliloti is required for beta-(1-2)glucan production and has homology to the ATP-binding export protein HlyB. J. Bacteriol. 170: 3523-3530.
52. Tam, R., and M. H. Saier Jr. 1993. Structural, functional, and evolutionary relationships among extracellular solute-binding receptors of bacteria. Microbiol. Rev. 57:320-346.
53. Tauch, A., S. Krieft, A. Puhler, and J. Kalinowski. 1999. The tetAB genes of the Corynebacterium striatum R-plasmid pTP10 encode an ABC transporter and confer tetracycline, oxytetracycline and oxacillin resistance in Corynebacterium glutamicum. FEMS Microbiol. Lett. 173:203-209.
54. Tomii, K., and M. Kanehisa. 1998. A comparative analysis of ABC transporters in complete microbial genomes. Genome Res. 8:1048-1059.
55. Verleur, N., E. H. Hettema, C. W. van Roermund, H. F. Tabak, and R. J. Wanders. 1997. Transport of activated fatty acids by the peroxisomal ATP-binding-cassette transporter Pxa2 in a semi-intact yeast cell system. Eur. J. Biochem. 249:657-661.
56. Wooff, E., S. L. Michell, S. V. Gordon, M. A. Chambers, S. Bardarov, W. R. Jacobs Jr., R. G. Hewinson, and P. R. Wheeler. 2002. Functional genomics reveals the sole sulphate transporter of the Mycobacterium tuberculosis complex and its relevance to the acquisition of sulphur in vivo. Mol. Microbiol. 43:653-663.
57. Wu, Y. C., and H. R. Horvitz. 1998. The C. elegans cell corpse engulfment gene ced-7 encodes a protein similar to ABC transporters. Cell 93:951-960.
58. York, G. M., and G. C. Walker. 1998. The Rhizobium meliloti ExoK and ExsH glycanases specifically depolymerize nascent succinoglycan chains. Proc. Natl. Acad. Sci. USA 95:4912-4917.