Membrane topology of the Mep/Amt family of ammonium transporters

Molecular Microbiology

Volumn 37, Issue 2, 2000, Pages 331-344

  Thomas, Gavin H ^a   Mullins, Jonathan G L ^b   Merrick, Mike ^a  

^a JOHN INNES CENTRE   (United Kingdom)

^b UNIVERSITY OF BEDFORDSHIRE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL PROTEIN; CARRIER PROTEIN; HYBRID PROTEIN;

AMINO TERMINAL SEQUENCE; ARTICLE; CARBOXY TERMINAL SEQUENCE; ESCHERICHIA COLI; MEMBRANE STRUCTURE; NONHUMAN; PRIORITY JOURNAL; PROTEIN FAMILY;

ALKALINE PHOSPHATASE; AMINO ACID SEQUENCE; BACTERIAL PROTEINS; BETA-GALACTOSIDASE; BIOLOGICAL TRANSPORT; BLOTTING, WESTERN; CARRIER PROTEINS; CATION TRANSPORT PROTEINS; CELL MEMBRANE; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; EVOLUTION, MOLECULAR; GENES, REPORTER; HUMANS; MEMBRANE PROTEINS; METHYLAMINES; MODELS, BIOLOGICAL; MOLECULAR SEQUENCE DATA; POLYMERASE CHAIN REACTION; RECOMBINANT FUSION PROTEINS; SEQUENCE HOMOLOGY, AMINO ACID;

EID: 0033913267     PISSN: 0950382X     EISSN: None     Source Type: Journal    
DOI: 10.1046/j.1365-2958.2000.01994.x     Document Type: Article

References (62)

1. Alibhai, M., and Villafranca, J.J. (1994) Kinetic and mutagenic studies of the role of the active site residues Asp-50 and Glu-327 of Escherichia coli glutamine synthetase. Biochemistry 33: 682-686.
2. Anstee, D.J., and Tanner, M.J. (1988) Blood group antigen deficiencies associated with abnormal red cell shape. Blood Rev 2: 115-120.
3. Arcondéguy, T., van Heeswijk, W.C., and Merrick, M. (1999) Studies on the roles of GlnK and GlnB in regulating Klebsiella pneumoniae NifL-dependent nitrogen control. FEMS Microbiol Lett 180: 263-270.
4. Atkinson, M.R., and Ninfa, A.J. (1998) Role of the GlnK signal transduction protein in the regulation of nitrogen assimilation in Escherichia coli. Mol Microbiol 29: 431-447.
5. Atkinson, M.R., and Ninfa, A.J. (1999) Characterization of the GlnK protein of Escherichia coli. Mol Microbiol 32: 301-313.
6. Avent, N.D., and Reid, M.E. (2000) The Rh blood group system: a review. Blood 95: 375-387.
7. Avent, N.D., Liu, W., Warner, K.M., Mawby, W.J., Jones, J.W., Ridgwell, K., et al. (1996) Immunochemical analysis of the human erythrocyte Rh polypeptides. J Biol Chem 271: 14233-14239.
8. Ballas, S.K., Clark, M.R., Mohandas, N., Golfer, H.F., Caswell, M.S., Bergren, M.O., et al. (1984) Red cell membrane and cation deficiency in Rh null syndrome. Blood 63: 1046-1055.
9. Boyd, D., Traxler, B., and Beckwith, J. (1993) Analysis of the topology of a membrane protein by using a minimum number of alkaline phosphatase fusions. J Bacteriol 175: 553-536.
10. Chothia, C., Levitt, M., and Richardson, D. (1981) Helix to helix packing in proteins. J Mol Biol 145: 215-250.
11. Chou, P.Y., and Fasman, G.D. (1979) Prediction of beta-turns. Biophys J 26: 367-373.
12. Dandekar, T., Snel, B., Huynen, M., and Bork, P. (1998) Conservation of gene order: a fingerprint of proteins that physically interact. Trends Biochem Sci 23: 324-328.
13. Deleage, G., and Roux, B. (1987) An algorithm for protein secondary structure prediction based on class prediction. Protein Eng 1: 289-294.
14. van Dommelen, A., Keijers, V., Vanderleyden, J., and de Zamaroczy, M. (1998) (Methyl)ammonium transport in the nitrogen-fixing bacterium Azospirillum brasilense. J Bacteriol 180: 2652-2659.
15. Donnelly, D., Overington, J.P., Ruffle, S.V., Nugent, J.H., and Blundell, T.L. (1993) Modeling alpha-helical transmembrane domains: the calculation and use of substitution tables for lipid-facing residues. Protein Sci 2: 55-70.
16. Eyers, S.A., Ridgwell, K., Mawby, W.J., and Tanner, M.J. (1994) Topology and organization of human Rh (rhesus) blood group-related polypeptides. J Biol Chem 269: 6417-6423.
17. Geest, M., and Lolkema, J.S. (2000) Membrane topology and insertion of membrane proteins: search for topogenic signals. Microbiol Mol Biol Rev 64: 13-33.
18. II protein in the regulation of glutamine synthetase in Escherichia coli. Mol Microbiol 21: 133-146.
19. von Heijne. G. (1992) Membrane protein structure prediction, hydrophobicity analysis and the positive-inside rule. J Mol Biol 225: 487-494.
20. Hennessey, E.S., and Broome-Smith, J.K. (1993) Gene-fusion techniques for determining membrane-protein topology. Curr Opin Struct Biol 3: 524-531.
21. Hofmann, J., and Stoffel, W. (1993) TMBASE - a database of membrane spanning proteins segments. Biol Chem Hoppe-Seyler 347: 166-168.
22. Jack, R., de Zamaroczy, M., and Merrick, M. (1999) The signal transduction protein GlnK is required for NifL-dependent nitrogen control of nif gene expression in Klebsiella pneumoniae. J Bacteriol 181: 1156-1162.
23. Jayakumar, A., Schulman, D., MacNeil, D., and Barnes, E.M., Jr (1986) Role of the Escherichia coli glnALG operon in regulation of ammonium transport. J Bacteriol 166: 281-284.
24. Jones, D.T. (1998) Do transmembrane protein superfolds exist? FEBS Lett 423: 281-285.
25. Jones, D.T., Taylor, W.R., and Thornton, J.M. (1994) A model recognition approach to the prediction of all-helical membrane protein structure and topology. Biochemistry 33: 3038-3049.
26. Kleiner, D. (1993) Ammonium transport systems - an overview. In Alkali Cation Transport Systems in Prokaryotes. Bakker, E.P. (ed.). Florida: CRC Press, pp. 379-396.
27. Kyte, J., and Doolittle, R.F. (1982) A simple method for displaying the hydropathic character of a protein. J Mol Biol 157: 105-132.
28. Knepper, M.A., Packer, R., and Good, D.W. (1989) Ammonium transport in the kidney. Physiol Rev 69: 179-249.
29. Liaw, S.H., Kuo, I., and Eisenberg, D. (1995) Discovery of the ammonium substrate site on glutamine synthetase, a third cation binding site. Protein Sci 4: 2358-2365.
30. Link, A.J., Phillips, D.R., and Church, G.M. (1997) Methods for generating precise deletions and insertions in the genome of wild-type Escherichia coli: application to open reading frame characterization. J Bacteriol 179: 6228-6237.
31. Lolkema, J.S., and Slotboom, D.-J. (1998) Estimation of structural similarity of membrane proteins by hydropathy profile alignment. Mol Membr Biol 15: 33-42.
32. McEwan, A.J., Jackson, J.B., and Ferguson, S.J. (1984) Rationalisation of properties of nitrate reductases in Rhodopseudomonas capsulata. Arch Microbiol 137: 344-349.
33. Manoil, C. (1991) Analysis of membrane protein topology using alkaline phosphatase and β-galactosidase gene fusions. Methods Cell Biol 34: 61-75.
34. Manoil, C., and Bailey, J. (1997) A simple screen for permissive sites in proteins: analysis of Escherichia coli lac permease. J Mol Biol 267: 250-263.
35. Manoil, C., and Beckwith, J. (1985) TnphoA: a transposon probe for protein export signals. Proc Natl Acad Sci USA 82: 8129-8133.
36. Marini, A.M., Vissers, S., Urrestarazu, A., and Andre, B. (1994) Cloning and expression of the MEP1 gene encoding an ammonium transporter in Saccharomyces cerevisiae. EMBO J 13: 3456-3463.
37. + transporters. Trends Biochem Sci 22: 460-461.
38. Meletzus, D., Rudnick, P., Doetsch, N., Green, A., and Kennedy, C. (1998) Characterization of the glnK-amtB operon of Azotobacter vinelandii. J Bacteriol 180: 3260-3264.
39. Michel-Reydellet, N., Desnoues, N., de Zamaroczy, M., Elmerich, C., and Kaminski, P.A. (1998) Characterisation of the glnK-amtB operon and the involvement of AmtB in methylammonium uptake in Azorhizobium caulinodans. Mol Gen Genet 258: 671-677.
40. Miller, J.H. (1972) Experiments in Molecular Genetics. Cold Spring Harbour, NY: Cold Spring Harbour Laboratory Press.
41. Minton, N.P. (1984) Improved vectors for the isolation of translational lac gene fusions. Gene 31: 269-273.
42. Montesinos, M.L., Muro-Pastor, A.M., Herrero, A., and Flores, E. (1998) Ammonium/methylammonium permeases of a cyanobacterium. Identification and analysis of three nitrogen-regulated amt genes in Synechocystis sp. PCC 6803. J Biol Chem 273: 31463-31470.
43. + transporter from plants. EMBO J 13: 3464-3471.
44. Paulsen, I.T., Brown, M.H., Dunstan, S.J., and Skurray, R.A. (1995) Molecular characterization of the Staphylococcal multidrug resistance export protein QacC. J Bacteriol 177: 2827-2833.
45. Persson, B., and Argos, P. (1997) Prediction of membrane protein topology utilizing multiple sequence alignments. J Protein Chem 16: 453-457.
46. Sääf, A., Johansson, M., Wallin, E., and von Heijne, G. (1999) Divergent evolution of membrane protein topology: the Escherichia coli RnfA and RnfE homologues. Proc Natl Acad Sci USA 96: 8540-8544.
47. Saier, M.H., Jr, Eng, B.H., Fard, S., Garg, J., Haggerty, D.A., Hutchinson, W.J., et al. (1999) Phylogenetic characterization of novel transport protein families revealed by genome analyses. Biochim Biophys Acta 1422: 1-56.
48. Sambrook, J., Fritsch, E.F., and Maniatis, T. (1989) Molecular Cloning. A Laboratory Manual, 2nd edn. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press.
49. Sarsero, J.P., and Pittard, A.J. (1995) Membrane topology analysis of Escherichia coli K-12 Mtr permease by alkaline phosphatase and β-galactosidase fusions. J Bacteriol 177: 297-306.
50. Servín-González, L., and Bastarrachea, F. (1984) Nitrogen regulation of synthesis of the high affinity methylammonium transport system of Escherichia coli. J Gen Microbiol 130: 3071-3077.
51. Siewe, R.M., Weil, B., Burkovski, A., Eikmanns, B.J., Eikmanns, M., and Krämer, R. (1996) Functional and genetic characterization of the (methyl)ammonium uptake carrier of Corynebacterium glutamicum. J Biol Chem 271: 5398-5403.
52. Sonnhammer, E.L.L., von Heijne, G., Krogh, A. (1998) A hidden Markov model for predicting transmembrane helices in protein sequences. In Proceedings of the Sixth International Conference on Intelligent Systems for Molecular Biology. Glasgow, J., Littlejohn, T., Major, F., Lathrop, R., Sankoff, D., and Sensen, C. (eds). Menlo Park, CA: AAAI Press, pp. 177-183.
53. + antiporter of Escherichia coli. J Biol Chem 275: 210-214.
54. Soupene, E., He, L., Yan, D., and Kustu, S. (1998) Ammonia acquisition in enteric bacteria: physiological role of the ammonium/methylammonium transport B (AmtB) protein. Proc Natl Acad Sci USA 95: 7030-7034.
55. + transporter is down-regulated early during bacteroid differentiation. Mol Plant-Microbe Interact 11: 188-198.
56. Thomas, G., Coutts, G., and Merrick, M. (2000) The glnKamtB operon: a conserved gene pair in prokaryotes. Trends Genet 16: 11-14.
57. Thompson, J.D., Gibson, T.J., Plewniak, F., Jeanmougin, F., and Higgins, D.G. (1997) The CLUSTALX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25: 4876-4882.
58. Traxler, B., Boyd, D., and Beckwith, J. (1993) The trpological analysis of integral cytoplasmic membrane proteins. J Membr Biol 132: 1-11.
59. Tusnády, G.E., and Simon, I. (1998) Principles governing amino acid composition of integral membrane proteins: application to topology prediction. J Mol Biol 283: 489-506.
60. Vieira, J., and Messing, J. (1987) Production of single-stranded plasmid DNA. Methods Enzymol 153: 3-11.
61. Wallin, E., and von Heijne, G. (1998) Genome-wide analysis of integral membrane proteins from eubacterial, archaean, and eukaryotic organisms. Protein Sci 7: 1029-1038.
62. Wang, R.F., and Kushner, S.R. (1991) Construction of versatile low-copy-number vectors for cloning, sequencing and gene expression in Escherichia coli. Gene 100: 195-199.