Tandem clusters of membrane proteins in complete genome sequences

Genome Research

Volumn 10, Issue 6, 2000, Pages 731-743

  Kihara, Daisuke ^a,b   Kanehisa, Minoru ^a  

^a KYOTO UNIVERSITY   (Japan)

^b DONALD DANFORTH PLANT SCIENCE CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ADENOSINE TRIPHOSPHATE; BINDING PROTEIN; MEMBRANE PROTEIN;

AMINO TERMINAL SEQUENCE; ARTICLE; CELL MEMBRANE; CELL MOTILITY; COMPLEX FORMATION; ELECTRON TRANSPORT; GENE CLUSTER; GENE LOCATION; GENE SEQUENCE; GENOME; NONHUMAN; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN TRANSPORT;

ALGORITHMS; ATP-BINDING CASSETTE TRANSPORTERS; COMPUTATIONAL BIOLOGY; CONSERVED SEQUENCE; DATABASES, FACTUAL; GENE DUPLICATION; GENOME, BACTERIAL; MEMBRANE PROTEINS; MULTIGENE FAMILY; SEQUENCE ANALYSIS, DNA; TANDEM REPEAT SEQUENCES;

ARCHAEA; EUKARYOTA;

EID: 0033945491     PISSN: 10889051     EISSN: None     Source Type: Journal    
DOI: 10.1101/gr.10.6.731     Document Type: Article

References (62)

1. Arkin, I.T., A.T. Brünger, and D.M. Engelman. 1997. Are there dominant membrane protein families with a given number of helices? Proteins: Struct. Funct. Genet. 28: 465-466.
2. Aurora, R. and G.D. Rose. 1998. Seeking an ancient enzyme in Methanococcus jannaschii using ORF, a program based on predicted secondary structure comparisons. Proc. Natl. Acad. Sci. 95: 2818-2823.
3. Bairoch, A. and R. Apweiler. 1998. The SWISS-PROT protein sequence data bank and its supplement TrEMBL in 1998. Nucleic Acids Res. 26: 38-42.
4. Blattner, F.R., G. Plunkett, III, C.A. Bloch, N.T. Perna, V. Burland, M. Riley, J. Collado-Vides, J.D. Glasner, C.K. Rode, G.F. Mayhew et al. 1997. The complete genome sequence of Escherichia coli K-12. Science 277: 1453-1462.
5. Bork, P. and E.V. Koonin. 1998. Predicting functions from protein sequences-where are the bottlenecks? Nature Genet. 18: 313-318.
6. Boyd, D., C. Schierle, and J. Beckwith. 1998. How many membrane proteins are there? Protein Sci. 7: 201-205.
7. Brenner, S.E., T. Hubbard, A. Murzin, and C. Chothia. 1995. Gene duplications in H. influenzae. Nature 378: 140.
8. Brown, P.O. and D. Botstein. 1999. Exploring the new world of the genome with DNA microarrays. Nat. Genet. 21: 33-37.
9. Bult, C.J., O. White, G.J. Olsen, L. Zhou, R.D. Fleischmann, G.G. Sutton, J.A. Blake, L.M. Fitzgerald, R.A. Clayton, J.D. Gocayne et al. 1996. Complete genome sequence of the Methanogenic archaeon, Methanococcus jannaschii. Science 273: 1058-1073.
10. Cole, S.T., R. Brosch, J. Parkhill, T. Garnier, C. Churcher, D. Harris, S.V. Gordon, K. Eiglmeier, S. Gas, C.E. Barry, III et al. 1998. Deciphering the biology of Mycrobacterium tuberculosis from the complete genome sequence. Nature 393: 537-544.
11. Dandekar, T., B. Snel, M. Huynen M, and P. Bork. 1998. Conservation of gene order: A fingerprint of proteins that physically interact. Trends Biochem. Sci. 23: 324-328.
12. Dean, M. and R. Allikmets. 1995. Evolution of ATP-binding cassette transporter genes. Curr. Opin. Genet. & Development. 5: 779-785.
13. Deckert, G., P.V. Warren, T. Gaasterland, W.G. Young, A.L. Lenox, D.E. Graham, R. Overbeek, M.A. Snead, M. Keller, M. Aujay et al. 1998. The complete genome of the hyperthermophilic bacterium Aquifex aeolicus. Nature 392: 353-358.
14. Fath, M,J. and R. Kolter. 1993. ABC transporters: Bacterial exporters. Micobiol. Rev. 57: 995-1017.
15. 1 ribonucleases. J. Mol. Biol. 281: 949-968.
16. Fleischmann, R.D., M.D. Adams, O. White, R.A. Clayton, E.F. Kirkness, A.R. Kerlavage, C.J. Bult, J.-F. Tomb, B.A. Dougherty, J.M. Merrick et al. 1995. Whole-genome random sequencing and assembly of Haemophilus influenzae. Science 269: 496-512.
17. Fraser, C.M., J.D. Gocayne, O. White, M.D. Adams, R.A. Clayton, R.D. Fleischmann, C.J. Bult, A.R. Kerlavage, G. Sutton, J.M. Kelley et al. 1995. The minimal gene complement of Mycoplasma genitalium. Science 270: 397-403.
18. Fraser, C.M., S. Casjens, W.M. Huang, G.G. Sutton, R. Clayton, R. Lathigra, O. White, K.A. Ketchum, R. Dodson, E.K. Hickey et al. 1997. Genomic sequence of a lyme disease spirochete, Borrelia burgdorferi. Nature 390: 580-586.
19. Fraser. C,M, S.J. Norris, G.M. Weinstock, O. White, G.G. Sutton, R. Dodson, M. Gwinn, E.K. Hickey, R. Clayton, K.A. Ketchum et al. 1998. Complete genome sequence of Treponema pallidum, the syphilis spirochete. Science 281: 375-388.
20. Frishman, D. and H.W. Mewes. 1997. Protein structural classes in five complete genomes. Nature Struct. Biol. 4: 626-628.
21. Froshauer, S., G.N. Green, D. Boyd, K. McGovern, and J. Beckwidth. 1988. Genetic analysis of the membrane insertion and topology of MalF, a cytoplasmic membrane protein of Escherichia coli. Mol. Biol. 200: 501-511.
22. Goffeau A., R. Aert, M.L. Agostini-Carbone, A. Ahmed, M. Aigle, L. Alberghina, K. Albermann, M. Albers, M. Aldea, D. Alexandraki et al. 1997. The yeast genome directory. Nature 387(6632 Suppl.).
23. Higgins, C.F. 1992. ABC transporters. From microorganisms to man. Annu. Rev. Cell. Biol. 8: 67-113.
24. Himmelreich, R., H. Hilbert, H. Plagens, E. Pirkl, B.-C. Li, and R. Herrmann. 1996. Complete sequence analysis of the genome of the bacterium Mycoplasma pneumoniae. Nucleic Acid Res. 24: 4420-4449.
25. Hobohm, U., M. Scharf, R. Schneider, and C. Sander. 1992. Selection of a representative set of structures from the Brookhaven Protein Data Bank. Prot. Sci. 1: 409-417.
26. Hofmann, K., P. Bucher, L. Falquet, and A. Bairoch. 1999. The PROSITE database, its status in 1999. Nucleic Acid Res. 1: 215-219.
27. Jones D.T. 1998. Do transmembrane protein superfold exist? FEBS Lett. 423: 281-285.
28. Jungnickel, B., T.A. Rapoport, E. Hartmann. 1994. Protein translocation: common themes from bacteria to man. FEBS Lett. 346: 73-77.
29. Kanehisa, M. 2000. Pathway databases and higher order function. Adv. Protein Chem. 54: in press.
30. Kaneko, T., S. Sato, H. Kotani, A. Tanaka, E. Asamizu, Y. Nakamura, N. Miyajima, M. Hirosawa, M. Sugiura, S. Sasamoto et al. 1996. Sequence analysis of the genome of the unicellular Cyanobacterium Synechocystis sp. Strain PCC6803. II. Sequence determination of the entire genome and assignment of potential protein-coding regions. DNA Res. 3: 109-136.
31. Kawarabayasi, Y., M. Sawada, H. Horikawa, Y. Haikawa, Y. Hino, S Yamamoto, M. Sekine, S. Baba, H. Kosugi, A. Hosoyama et al. 1998. Complete sequence and gene organization of the genome of a hyper-thermophilic archaebacterium, Pyrococcus horikoshii OT3. DNA Res. 5: 55-76.
32. Kihara, D. and M. Kanehisa. 1997. Detection of membrane proteins in the whole genome sequences. Genome Informatics 1997. pp.300-301. Universal Academy Press, Tokyo, Japan.
33. Kihara, D., T. Shimizu, and M. Kanehisa. 1998. Prediction of membrane proteins based on classification of transmembrane segments. Protein Eng. 11: 961-970.
34. Klenk, H.P., R.A. Clayton, J.-F. Tomb, O. White, K.E. Nelson, K.A. Ketchum, R.J. Dodson, M. Gwinn, E.K. Hickey, J.D. Peterson et al. 1997. The complete genome sequence of the hyperthermophilic, sulphate-reducing archaeon Archaeoglobus fulgidus. Nature 390: 364-370.
35. Kunst, F., N. Ogasawara, I. Moszer, A.M. Albertini, G. Alloni, V. Azevedo, M.G. Bertero, P. Bessieres, A. Bologin, S. Borchert et al. 1997. The complete genome sequence of the gram-positive bacterium Bacillus subtilis. Nature 390: 249-256.
36. Kyte, J. and R.F. Doolittle. 1982. A simple method for displaying the hydropathic character of a protein. J. Mol. Biol. 157: 105-132.
37. Lyman, S.K. and R. Schekman. 1996. Polypeptide translocation machinery of the yeast endoplasmic reticulum. Experientia 52: 1042-1049.
38. McGeoch, D.J. 1985. On the predictive recognition of signal peptide sequences. Virus Res. 3: 271-286.
39. Nakai, K. and M. Kanehisa. 1991. Expert system for predicting protein localization sites in gram-negative bacteria. Proteins: Struct. Funct. Genet. 11: 95-110.
40. Nakai, K. and P. Horton. 1999. PSORT: A program for detecting sorting signals in proteins and predicting their subcellular localization. Trends Biochem. Sci. 24: 34-6.
41. Overbeek, R., M. Fonstein, M. D'Souza, G.D. Pusch, and N. Maltsev. 1999. The use of gene clusters to infer functional coupling. Proc. Natl. Acad. Sci. USA 96: 2896-2901.
42. Ogata, H., S. Goto, K. Sato, W. Fujibuchi, H. Bono, and M. Kanehisa. 1999. KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acid Res. 27: 29-34.
43. Paulsen, I.T., M.K. Sliwinski, and H. Saier, Jr. 1998. Microbial genome analyses: Global comparisons of transport capabilities based on phylogenies, bioenergetics and substrate specificities. J. Mol. Biol. 277: 573-592.
44. Pearson, W.R. 1991. Searching protein sequence libraries: Comparison of the sensitivity and selectivity of the Smith-Waterman and FASTA algorithms. Genomics 11: 635-650.
45. _1996. Effective protein sequence comparison. Methods Enzymol. 266: 227-258.
46. _1998. Empirical statistical estimates for sequence similarity searches. J. Mol. Biol. 276: 71-84.
47. Randall, L.L., S.J.S. Hardy, T.B. Topping, V.F. Smith, J.E. Bruce, and R.D. Smith. 1998. The interaction between the chaperone SecB and its ligands: Evidence for multiple subsites for binding. Protein Sci. 7: 2384-2390.
48. 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.
49. Smith, D.R, L.A. Doucette-Stamm, C. Deloughery, H. Lee, J. Dubois, T. Aldredge, R. Bashirzadeh, D. Blakely, R. Cook, K. Gilbert et al. 1997. Complete genome sequence of Methanobacterium thermoautotrophicum deltaH: Functional analysis and comparative genomics. J. Bacteriol. 179: 7135-7155.
50. 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.
51. Tamames, J., G. Casari, C. Ouzounis, and A. Valencia. 1997. Conserved clusters of functionally related genes in two bacterial genomes. J. Mol. Evol. 44: 66-73.
52. Tatusov, R.L., E.V. Koonin, and D.J. Lipman. 1997. A genomic perspective on protein families. Science 278: 631-637.
53. Tokuda, H. 1994. Biochemical characterization of the presecretory protein translocation machinery of Escherichia coli. FEBS Lett. 346: 65-68.
54. Tomb, J.-F., O. White, A.R. Kerlavage, R.A. Clayton, G.G. Sutton, R.D. Fleischmann, K.A. Ketchum, H.P. Klenk, S. Gill, B.A. Dougherty et al. 1997. The complete genome sequence of the gastric pathogen Helicobacter pylori. Nature 388: 539-547.
55. Tomii, K. and M. Kanehisa. 1998. A comparative analysis of ABC transporters in complete microbial genomes. Genome Res. 8: 1048-1059.
56. Ulbrandt, N.D., J.A. Newitt, and H.D. Bernstein. 1997. The E. coli signal recognition particle is required for the insertion of a subset of inner membrane proteins. Cell 88: 187-196.
57. Valent, Q.A., P.A. Scotti, S. High, J.W. de Gier, G. von Heijne, G. Lentzen, W. Wintermeyer, B. Oudega, and J. Luirink. 1998. The Escherichia coli SRP and SecB targeting pathways converge at the translocon. EMBO J. 17: 2504-2512.
58. von Heijne, G. 1986. A new method for predicting signal sequence cleavage sites. Nucleic Acid Res. 14: 4683-4690.
59. Wallin, E. and G. von Heijne. 1998. Genome-wide analysis of integral membrane proteins from eubacterial, archaean, and eukaryotic organisms. Protein Sci. 7: 1029-1038.
60. Wooton, J.C. and S. Federhen. 1993. Statistics of local complexity in amino acid sequences and sequence databases. Computers and Chem. 17: 149-163.
61. Xu, Y., B.E. Murray, and G.M. Weinstock. 1998. A cluster of genes involved in polysaccharide biosynthesis from Enterococcus faecalis OG1RF. Infect. Immun. 66: 4313-4323.
62. Zhang, X. and T.F. Smith. 1998. Yeast "Operons". Microbial Comp. Gen. 3: 133-140.