TRAP transporters: An ancient family of extracytoplasmic solute-receptor-dependent secondary active transporters

Microbiology

Volumn 145, Issue 12, 1999, Pages 3431-3445

  Rabus, Ralf ^a,c   Jack, Donald L ^a   Kelly, David J ^b   Saier Jr , Milton H ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF SHEFFIELD   (United Kingdom)

^c MAX PLANCK INSTITUTE FOR MARINE MICROBIOLOGY   (Germany)

Author keywords

Dicarboxylates; Ion transport; Molecular evolution; Phylogeny; TRAP T family

Indexed keywords

ADENOSINE TRIPHOSPHATE; CARRIER PROTEIN; CELL RECEPTOR; DICARBOXYLIC ACID; MEMBRANE PROTEIN;

AMINO ACID SEQUENCE; ARCHAEBACTERIUM; ARTICLE; BACILLUS SUBTILIS; BACTERIAL MEMBRANE; EVOLUTION; NONHUMAN; PHYLOGENY; PRIORITY JOURNAL; PROTON MOTIVE FORCE; RHODOBACTER CAPSULATUS; SEQUENCE HOMOLOGY; TRANSCRIPTION REGULATION;

ARCHAEA; BACILLUS SUBTILIS; BACTERIA (MICROORGANISMS); POSIBACTERIA; RHODOBACTER CAPSULATUS; RHODOPSEUDOMONAS;

EID: 0033374883     PISSN: 13500872     EISSN: None     Source Type: Journal    
DOI: 10.1099/00221287-145-12-3431     Document Type: Article

References (49)

1. Altschul, S. F., Gish, W., Miller, W., Myers, E. W. & Lipman, D. J. (1990). Basic local alignment search tool. J Mol Biol 215, 403-410.
2. Altschul, S. F., Madden, T. L., Schäffer, A. A., Zhang, J., Zhang, Z., Miller, W. & Lipman, D. J. (1997). Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25, 3389-3402.
3. Ames, G. F.-L. (1986). Bacterial periplasmic transport systems: structure, mechanism, and evolution. Annu Rev Biochem 55, 397-425.
4. Bailey, T. L. & Gribskov, M. (1998). Combining evidence using p-values: application to sequence homology searches. Bioinformatics 14, 48-54.
5. Bairoch, A., Bucher, P. & Hofmann, K. (1997). The PROSITE database, its status in 1997. Nucleic Acids Res 25, 217-221.
6. Berks, B. C., Richardson, D. J., Reilly, A., Willis, A. C. & Ferguson, S. J. (1995). The napEDABC gene cluster encoding the periplasmic nitrate reductase system of Thiosphaera pantotropha. Biochem J 309, 983-992.
7. 1-ATPases of bacteria, chloroplasts and mitochondria. Microbiology 142, 17-32.
8. Boos, W. & Lucht, J. M. (1996). Periplasmic binding protein-dependent ABC transporters. In Escherichia coli and Salmonella: Cellular and Molecular Biology, 2nd edn, pp. 1175-1209. Edited by F. C. Neidhardt and others. Washington, DC: American Society for Microbiology.
9. Cangelosi, G. A., Ankenbauer, R. G. & Nester, E. W. (1990). Sugars induce the Agrobacterium virulence genes through a periplasmic binding protein and a transmembrane signal protein. Proc Natl Acad Sci USA 87, 6708-6712.
10. Dayhoff, M. O., Barker, W. C. & Hunt, L. T. (1983). Establishing homologies in protein sequences. Methods Enzymol 91, 524-545.
11. Devereux, J., Haeberli, P. & Smithies, O. (1984). A comprehensive set of sequence analysis programs for the VAX. Nucleic Acids Res 12, 387-395.
12. Felsenstein, J. (1985). Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39, 783-791.
13. Feng, D.-F. & Doolittle, R. F. (1990). Progressive alignment and phylogenetic tree construction of protein sequences. Methods Enzymol 183, 375-387.
14. Forward, J. A., Behrendt, M. C., Wyborn, N. R., Cross, R. & Kelly, D. J. (1997). TRAP transporters: a new family of periplasmic solute transport systems encoded by the dctPQM genes of Rhodobacter capsulatus and by homologs in diverse Gramnegative bacteria. J Bacteriol 179, 5482-5493.
15. Grundy, W. N., Bailey, T. L., Elkan, C. P. & Baker, M. E. (1997). Mera-MEME: motif-based hidden Markov models of protein families. Comput Appl Biosci 13, 397-406.
16. 4-dicarboxylate transport genes from Rhodobacter capsulatus. Mol Microbiol 4, 1567-1574.
17. Higgins, C. F. (1992). ABC transporters: from microorganisms to man. Annu Rev Cell Biol 8, 67-113.
18. Higgins, C. F., Hyde, S. C., Mimmack, M. M., Gileadi, U., Gill, D. R. & Gallagher, M. P. (1990). Binding protein-dependent transport systems. J Bioenerg Biomembr 22, 571-592.
19. Huala, E., Stigter, J. & Ausubel, F. M. (1992). The central domain of Rhizobium leguminosarum DctD functions independently to activate transcription. J Bacteriol 174, 1428-1431.
20. Hyde, S. C., Emsley, P., Hartshorn, M. J. & 7 other authors (1990). Structural model of ATP-binding proteins associated with cystic fibrosis, multidrug resistance and bacterial transport. Nature 346, 362-365.
21. Jacobs, M. H. J., van der Heide, T., Driessen, A. J. M. & Konings, W. N. (1996). Glutamate transport in Rhodobacter sphaeroides is mediated by a novel binding protein-dependent secondary transport system. Proc Natl Acad Sci USA 93, 12786-12790.
22. Kemner, J. M., Liang, X. & Nester, E. W. (1997). The Agrobacterium tumefaciens virulence gene chvE is part of a putative ABC-type sugar transport operon. J Bacteriol 179, 2452-2458.
23. Klenk, H.-P., Clayton, R. A., Tomb, J.-F. & 48 other authors (1997). The complete genome sequence of the hyperthermophilic, sulphate-reducing archaeon Archaeoglobus fulgidus. Nature 390, 364-370.
24. Kuan, G., Dassa, E., Saurin, W., Hofnung, M. & Saier, M. H., Jr (1995). Phylogenetic analyses of the ATP-binding constituents of bacterial extracytoplasmic receptor-dependent ABC-type nutrient uptake permeases. Res Microbiol 146, 271-278.
25. Kuroda, M., Dey, S., Sanders, O. I. & Rosen, B. P. (1997). Alternate energy coupling of ArsB, the membrane subunit of the Ars aniontranslocating ATPase. J Biol Chem 272, 326-331.
26. Kyte, J. & Doolittle, R. F. (1982). A simple method for displaying the hydropathic character of a protein. J Mol Biol 157, 105-132.
27. Le, T., Tseng, T.-T. & Saier, M. H., Jr (1999). Flexible programs for the prediction of average amphipathicity of multiply aligned homologous proteins: application to integral membrane transport proteins. Mol Membr Biol 16, 173-179.
28. Maloney, P. C. (1994). Bacterial transporters. Curr Opin Cell Biol 6, 571-582.
29. Maloney, P. C. & Wilson, T. H. (1996). Ion-coupled transport and transporters. In Escherichia coli and Salmonella: Cellular and Molecular Biology, 2nd edn, pp. 1130-1148. Edited by F. C. Neidhardt and others. Washington, DC: American Society for Microbiology.
30. Nakatsu, C. H., Korona, R., Lenski, R. E., DeBruijn, F. J., Marsh, T. L. & Forney, L. J. (1998). Parallel and divergent genotypic evolution in experimental populations of Ralstonia sp. J Bacteriol 180, 4325-4331.
31. Nikaido, H. & Saier, M. H., Jr (1992). Transport proteins in bacteria: common themes in their design. Science 258, 936-942.
32. Obis, D., Guillot, A., Gripon, J.-C., Renault, P., Bolotine, A. & Mistou, M. Y. (1999). Genetic and biochemical characterization of a high-affinity betaine uptake system (BusA) in Lactococcus lactis reveals a new functional organization within bacterial ABC transporters. J Bacteriol (in press).
33. Pearson, W. R. & Lipman, D. J. (1988). Improved tools for biological sequence comparison. Proc Natl Acad Sci USA 85, 2444-2448.
34. Postma, P. W., Lengeler, J. W. & Jacobson, G. R. (1993). Phosphoenolpyruvate : carbohydrate phosphotransferase systems of bacteria. Microbiol Rev 57, 543-594.
35. Quiocho, F. A. & Ledvina, P. S. (1996). Atomic structure and specificity of bacterial periplasmic receptors for active transport and chemotaxis : variation of common themes. Mol Microbiol 20, 17-25.
36. Saier, M. H., Jr (1994). Computer-aided analyses of transport protein sequences: gleaning evidence concerning function, structure, biogenesis, and evolution. Microbiol Rev 58, 71-93.
37. Saier, M. H., Jr (1998). Molecular phylogeny as a basis for the classification of transport proteins from Bacteria, Archaea and Eukarya. Adv Microb Physiol 40, 81-136.
38. Saier, M. H., Jr (1999). Eukaryotic transmembrane solute transport systems. In International Review of Cytology: a Survey of Cell Biology, pp. 61-136. Edited by K. W. Jeon. San Diego: Academic Press.
39. Saier, M. H., Jr & Tseng, T.-T. (1999). Evolutionary origins of transmembrane transport systems. In Transport of Molecules Across Microbial Membranes, Society for General Microbiology Symposium 58, pp. 252-274. Cambridge: Cambridge University Press.
40. Saurin, W., Hofnung, M. & Dassa, E. (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.
41. 4-dicarboxylates in Rhodobacter capsulatus. Arch Microbiol 155, 466-472.
42. 4-dicarboxylate-binding protein (DctP) from Rhodobacter capsulatus. Mol Microbiol 5, 3055-3062.
43. Silver, S., Ji, G., Bröer, S., Dey, S., Du, D. & Rosen, B. P. (1993). Orphan enzyme or patriarch of a new tribe: the arsenic resistance ATPase of bacterial plasmids. Mol Microbiol 8, 637-642.
44. Tam, R. & Saier, M. H., Jr (1993). Structural, functional, and evolutionary relationships among extracellular solute-binding receptors of bacteria. Microbiol Rev 57, 320-346.
45. Thompson, J. D., Gibson, T. J., Plewniak, F., Jeanmougin, F. & Higgins, D. G. (1997). The CLUSTAL x windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25, 4876-4882.
46. Tseng, T.-T., Gratwick, K. S., Kollman, J., Park, D., Nies, D. H., Goffeau, A. & Saier, M. H., Jr (1999). The RND permease superfamily: an ancient, ubiquitous and diverse family that includes human disease and development proteins. J Mol Microbiol Biotechnol 1, 107-125.
47. 4-dicarboxylate binding protein (DctP) from Rhodobacter capsulatus. J Biol Chem 267, 8064-8072.
48. Winans, S. C. (1991). An Agrobacterium two-component regulatory system for the detection of chemicals released from plant wounds. Mol Microbiol 5, 2345-2350.
49. Young, G. B., Jack, D. L., Smith, D. W. & Saier, M. H., Jr (1999). The amino acid/auxin:proton symport permease family. Biochim Biophys Acta 1415, 306-322.