Gene and context: Integrative approaches to genome analysis

Advances in Protein Chemistry

Volumn 54, Issue , 2000, Pages 345-379

  Huynen, Martijn A ^a,b,c   Snel, Berend ^a  

^a EUROPEAN MOLECULAR BIOLOGY LABORATORY   (Germany)

^b MAX DELBRÜCK CENTER FOR MOLECULAR MEDICINE   (Germany)

^c Bioinformatics Group   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIUM; CITRIC ACID CYCLE; EXON; GENE CLUSTER; GENE DUPLICATION; GENE FUNCTION; GENE FUSION; GENE ORDER; GENOME; MOLECULAR EVOLUTION; NONHUMAN; OPERON; PHYLOGENY; PRIORITY JOURNAL; PROMOTER REGION; REVIEW;

EID: 0033940941     PISSN: 00653233     EISSN: None     Source Type: Book Series    
DOI: 10.1016/s0065-3233(00)54010-8     Document Type: Review

References (81)

1. Adams, M. W., and Kletzin, A. (1996). Adv. Protein Chem. 48, 101-80.
2. Akhmanova, A., Voncken, F., van Alen, T., van Hoek, A., Boxma, B., Volgels, G., Veenhuis, M., and Hackstein, J. H. (1998). Nature 396, 527-528.
3. Beach, R., Aogaichi, T., and Plaut, G. W. (1977). J. Biol. Chem. 252, 2702-2709.
4. Beck, C. F., and Warren, R. A. (1988). Microbiol. Rev. 52, 318-326.
5. Bellgard, M. I., and Gojobori, T. (1999). FEBS Lett. 19, 6-8.
6. Bharathan, G., Janssen, B. J., Kellog, E. A., and Sinha, N. (1999). Mol. Biol. Evol. 16, 553-563.
7. Blumenthal, T. (1998). Bioessays 20, 480-487.
8. Bork, P., Dandekar, T., Diaz-Lazcoz, Y., Eisenhaber, F., Huynen, M., and Yuan, Y. (1998). J. Mol. Biol. 283, 707-725.
9. Borodovsky, M., Rudd, K. E., and Koonin, E. V. (1994). Nucleic Acids Res. 22, 4756-4767.
10. Bult, C. J., White, O., Olsen, G. J., Zhou, L., Fleischmann, R. D., Sutton, G. G., Blake, J. A., Fitzgerald, L. M., Clayton, R. A., Gocayne, J. D., Kervalage, A. R., Dougherty, B. A., Tomb, J. F., Adams, M. D., Reich, C. I., Overbeek, R., Kirkness, E. F., Weinstock, K. G., Merrick, J. M., Glodeck, A., Scott, J. L., Geoghagen, N., Weidman, J. F., Fuhrmann, J. L., Nguyen, D., utterback, T. R., Kelley, J. M., Peterson, J. D., Sadow, P. W., Hanna, M. C., Cotton, M. D., Roberts, K. M., Hurst, M. A., Kaine, B. P., Borodovsky, M., Klenk, H.-P., Fraser, C. M., Smith, H. O., Woese, C. R., and Venter, J. C. (1996). Science 273, 1058-1072.
11. elegans Sequencing Consortium (1998). Science 282, 2012-2018.
12. Clarke, A. R., Atkinson, T., and Holbrook, J. H. (1989). Trends Biochem. Sci. 14, 145-148.
13. Cordwell, S. J., Basseal, D. J., Pollack, J. D., and Humphery-Smith, I. (1997). Gene 195, 113-120.
14. Corthesy-Theulaz, I. E., Bergonzelli, G. E., Henry, H., Bachmann, D., Schorderet, D. F., Blum, A. L., and Ornston, L. N. (1997). J. Biol. Chem. 41, 25659-25667.
15. Dandekar, T., Snel, B., Huynen, M., and Bork, P. (1998). Trends Biochem. Sci. 23, 324-328.
16. Deckert, G., Warren, P. V., Gaasterland, T., Young, W. G., Lenox, A. L., Graham, D. E., Overbeek, R., Snead, M. A., Keller, M., Aujay, M., Huber, R., Feldman, R. A., Short, J. M., Olsen, G. J., and Swanson, R. V. (1998). Nature 392, 353-358.
17. Falke, J., Bass, R. B., Butler, S. L., Chervitz, S. A., and Danielson, M. A. (1997). Annu. Rev. Cell. Dev. Biol. 13, 457-512.
18. Fani, R., Mori, E., Tamburini, E., and Lazcano, A. (1998). Orig. Life Evol. Biosph. 28, 555-570.
19. Felsenstein, J. (1993). Distributed by the author. Department of Genetics, University of Washington, Seattle.
20. Fitch, W. M. (1970). Syst. Zool. 19, 99-110.
21. Fitch, W. M., and Margoliash, E. (1967). Science 155, 279-284.
22. Florea, L., Hartzell, G., Zhang, Z., Rubin, G. M., and Miller, W. (1998). Genome Res. 8, 967-974.
23. Fuchs, G., and Stupperich, E. (1978). Arch. Microbiol. 118, 121-125.
24. Gaasterland, T., and Ragan, M. A. (1998). Microb. Comp. Genomics 3, 199-217.
25. Galperin, M., and Koonin, E. V. (1997). Mol. Microbiol. 24, 443-445.
26. Galperin, M. Y., Walker, D. R., and Koonin, E. V. (1998). Genome Res. 8, 779-790.
27. Gelfand, M., Mironov, A. A., and Pezmei, P. A. (1996). Proc. Natl. Acad. Sci. U.S.A. 93, 9061-9066.
28. Gerike, U., Hough, D. W., Russell, N. J., Dyall-Smith, M. L., and Danson, M. J. (1998). Microbiology 144, 929-935.
29. Hacker, J., Blum-Oehler, G., Muhldorfer, I., and Tschape, H. (1997). Mol. Microbiol. 23, 1089-1097.
30. Heim, S., Kunkel, A., Thauer, R. K., and Hedderich, R. (1998). Eur. J. Biochem. 253, 292-299.
31. Honka, E., Fabry, S., Niermann, T., Palm, P., and Hensel, R. (1990). Eur. J. Biochem. 188, 623-632.
32. Horswill, A. R., and Escalante-Semerena, J. C. (1997). J. Bacteriol. 179, 928-940.
33. Hughes, N., Clayton, C. L., Chalk, P. A., and Kelly, D. J. (1998). J. Bacteriol. 180, 1119-1128.
34. Huynen, M., Diaz-Lazcoz, Y., and Bork, P. (1997). Trends Genet. 13, 389-390.
35. Huynen, M. A., and Bork, P. (1998). Proc. Natl. Acad. Sci. U.S.A. 95, 5849-5856.
36. Huynen, M. A., Dandekar, T., and Bork, P. (1999). Trends Microbiol. 7, 281-291.
37. Huynen, M. A., and Konings, D. A. M. (1998). In "Viral Regulatory Structures and Their Degeneracy" (G. Myers, ed.), pp. 143-160. Addison Wesley Longman, Reading, Massachusetts.
38. Itoh, T., Takemoto, K., Mori, H., and Gojobori, T. (1999). Mol. Biol. Evol. 16, 332-346.
39. Janssen, S., Schafer, G., Anemuller, S., and Moll, R. (1997). J. Bacteriol. 179, 5560-5569.
40. Jeanmougin, F., Thompson, J. D., Gouy, M., Higgins, D. G., and Gibson, T. J. (1998). Trends Biochem. Sci. 23, 403-405.
41. Kimura, M. (1980). J. Mol. Evol. 16, 111-120.
42. Kolsto, A. B. (1997). Mol. Microbiol. 24, 241-248.
43. Koonin, E. V., Mushegian, A. R., and Bork, P. (1996). Trends Genet. 12, 334-336.
44. Lawrence, J. G., and Ochman, H. (1997). J. Mol. Evol. 44, 383-397.
45. Lawrence, J. G., and Roth, J. R. (1996). Genetics 143, 1843-1860.
46. Le, S.-Y., Chen, J.-H., Currey, K., and Maizel, J. (1988). CABIOS 4, 153-159.
47. Lindbladh, C., Brodeur, R. D., Small, W. C., Lilius, G., Bulow, L., and Srere, K. M. P. A. (1994). Biochemistry 33, 11684-11691.
48. Maidak, B. L., Cole, J. R., Parker, C. T., Jr, Garrity, G. M., Larsen, N., Li, B., Lilburn, T. G., McCaughey, M. J., Olsen, G. J., Overbeek, R., Pramanik, S., Schmidt, T. M., Tiedje, J. M., and Woese, C. R. (1999). Nucleic Acids Res. 27, 171-173.
49. Marcotte, E. M., Pellegrini, M., Ng, H., Rice, W. D., Yeates, T. O., and Eisenberg, D. (1999). Science 285, 751-753.
50. Medigue, C., Rouxel, Y., Vigier, P., Henaut, A., and Danchin, A. (1991). J. Mol. Biol. 222, 851-856.
51. Mewes, H. W., Albermann, K., Bahr, M., Frishman, D., Gleissner, A., Hani, J., Heumann, K., Kleine, K., Maierl, A., Oliver, S., Pfeiffer, F., and Zollner, A. (1997). Nature 387, 7-65.
52. Mushegian, A. R., and Koonin, E. V. (1996). Trends Genet. 12, 289-290.
53. Olsen, G. J., Woese, C. R., and Overbeek, R. (1994). J. Bacteriol. 176, 1-6.
54. Overbeek, R., Fonstein, M., D'Souza, M., Pusch, G. D., and Maltsev, N. (1999). Proc. Natl. Acad. Sci. U.S.A. 96, 2896-2901.
55. Paulsen, I. T., Sliwinski, M. K., and Saier, M. H. (1998). J. Mol. Biol. 277, 573-592.
56. Pellegrini, M., Marcotte, E. M., Thompson, M. J., Eisenberg, D., and Yeats, T. O. (1999). Proc. Natl. Acad. Sci. U.S.A. 96, 4285-4288.
57. Piatigorsky, J., and Wistow, G. J. (1989). Cell 57, 197-199.
58. Pitson, S. M., Mendz, G. L., Srinivasan, S., and Hazell, S. L. (1999). Eur. J. Biochem. 260, 258-267.
59. Riley, M. (1998). Curr. Opin. Struct. Biol. 8, 388-392.
60. Rosario, M. M., and Ordal, G. W. (1996). Mol. Microbiol. 21, 511-518.
61. Salmond, G. P. C., Bycroft, B. W., Stewart, G. S. A. B., and Williams, P. (1995). Mol. Microbiol. 16, 615-624.
62. Schloss, J. V., Emptage, M. H., and Cleland, W. W. (1984). Biochemistry 23, 4572-4580.
63. Selkov, E., Grechkin, Y., Mikhailova, N., and Selkov, E. (1998). Nucleic Acids Res. 26, 43-45.
64. Selkov, E., Maltsev, N., Olsen, G. J., Overbeek, R., and Whitman, W. B. (1997). Gene 197, GC11-26.
65. Shieh, J., and Whitman, W. B. (1987). J. Bacteriol. 169, 5327-5329.
66. Snel, B., Bork, P., and Huynen, M. (1999). Nat. Genet. 21, 108-110.
67. Steen, I. H., Lein, T., and Birkeland, N.-K. (1997). Arch. Microbiol. 168, 412-420.
68. StJohn, T. P., and Davis, R. W. (1981). J. Mol. Biol. 152, 285-315.
69. Sunnarborg, A., Klumpp, D., Chung, T., and LaPorte, D. C. (1990). J. Bacteriol. 172, 2642-2649.
70. Tamames, J., Casari, G., Ouzounis, C., and Valencia, A. (1997). J. Mol. Evol. 44, 66-73.
71. Tatusov, R. L., Koonin, E. V., and Lipman, D. J. (1997). Science 278, 631-637.
72. Tatusov, R. L., Mushegian, A. R., Bork, P., Brown, N. P., Hayes, W. S., Borodovsky, M., Rudd, K., and Koonin, E. V. (1996). Curr. Biol. 6, 279-291.
73. Taylor, K., Hradecna, Z., and Szybalski, W. (1967). Proc. Natl. Acad. Sci. U.S.A. 57, 1618-1625.
74. Tekaia, F., Lazcano, A., and Dujon, B. (1999). Genome Res. 9, 550-557.
75. Tersteegen, A., Linder, D., Thauer, R. K., and Hedderich, R. (1997). Eur. J. Biochem. 244, 862-868.
76. Textor, S., Wendisch, V. F., Graaf, A. A. D., Muller, U., Linder, M. I., Linder, D., and Buckel, W. (1997). Arch. Microbiol. 168, 428-436.
77. Tsang, A. W., Horswill, A. R., and Escalante-Semerena, J. C. (1998). J. Bacteriol. 180, 6511-6518.
78. Watanabe, H., Mori, H., Itoh, T., and Gojobori, T. (1997). J. Mol. Evol. 44, 57-64.
79. Wilcox, G., Meuris, P., Bass, P., and Engelsberg, E. (1974). J. Biol. Chem. 249, 2946-2952.
80. Wu, G., Fiser, A., ter Kuile, B., Sali, A., and Muller, M. (1999). Proc. Natl. Acad. Sci. U.S.A. 96, 6285-6290.
81. Zhang, X., and Smith, T. F. (1998). Microb. Comp. Genomics 3, 133-140.