The repertoire of DNA-binding transcriptional regulators in Escherichia coli K-12

Nucleic Acids Research

Volumn 28, Issue 8, 2000, Pages 1838-1847

  Pérez Rueda, Ernesto ^a   Collado Vides, Julio ^a  

^a INSTITUTO DE CIENCIAS FÍSICAS   (Mexico)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL PROTEIN; DNA BINDING PROTEIN; REGULATOR PROTEIN; TRANSCRIPTION FACTOR;

AMINO ACID SYNTHESIS; ANTIBIOTIC RESISTANCE; ARTICLE; BACTERIAL GENETICS; CARBOHYDRATE METABOLISM; CARBON DIOXIDE FIXATION; CONTROLLED STUDY; ESCHERICHIA COLI K 12; EUKARYOTIC CELL; GENE ACTIVATION; GENE CONTROL; GENE REPRESSION; MOLECULAR EVOLUTION; NITROGEN FIXATION; NONHUMAN; PRIORITY JOURNAL; PROKARYOSIS; PROTEIN FAMILY; TRANSCRIPTION REGULATION;

DNA-BINDING PROTEINS; ESCHERICHIA COLI; GENE EXPRESSION REGULATION, BACTERIAL; GENES, BACTERIAL; HELIX-TURN-HELIX MOTIFS; TRANSCRIPTION FACTORS;

BACTERIA (MICROORGANISMS); ESCHERICHIA; ESCHERICHIA COLI K12; EUKARYOTA; NEGIBACTERIA; PROKARYOTA;

EID: 0343963178     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/28.8.1838     Document Type: Article

References (71)

1. Neidhardt, F.C., Ingraham, J.L., Low, K.B., Magasanik, B., Schaechter, M. and Umbarger, H.E. (eds) (1987) Escherichia coli and Salmonella typhimurium, Cellular and Molecular Biology. American Society for Microbiology, Washington, DC.
2. Neidhardt, F.C., Curtiss, R., Ingraham, J.L., Lin, E.C.C., Low, K.B., Magasanik, B., Reznikoff, W.S., Riley, M., Schaerchter, M. and Umbarger, H.E. (eds) (1996) Escherichia coli and Salmonella typhimurium. Cellular and Molecular Biology. American Society for Microbiology, Washington, DC.
3. Huerta, A.M., Salgado, H., Thieffry, D. and Collado-Vides, J. (1998) Nucleic Acids Res., 26, 55-59.
4. Salgado, H., Santos-Zavaleta, A., Gama-Castro, S., Millán-Zárate, D., Blattner, F.R. and Collado-Vides, J. (2000) Nucleic Acids Res., 28, 65-67
5. Blattner, F.R., Plunkett, G., Bloch, C.A., Pema, N.T., Burland, V., Riley, M., Collado-Vides, J., Glasner, J.D., Rode, C.K., Mayhew, G.F. et al. (1997) Science, 277, 1453-1462.
6. Thieffry, D., Huerta, A., Pérez-Rueda, E. and Collado-Vides, J. (1998) Bioessays, 20, 433-440.
7. Collado-Vides, J., Magasanik, B. and Gralla, J.D. (1991) Microbiol. Rev., 55, 371-394.
8. Gralla, J.D. and Collado-Vides, J. (1996) In Neidhart, F.C., Curtiss, R., Ingraham, J.L., Lin, E.C.C., Low, K.B., Magasanik, B., Reznikoff, W., Riley, M., Schaechter, M. and Umbarger, H.E. (eds), Escherichia coli and Salmonella typhimurium. Cellular and Molecular Biology. American Society for Microbiology, Washington, DC, pp. 1232-1246.
9. Pérez-Rueda, E., Gralla, J. and Collado-Vides, J. (1998) J. Mol. Biol., 275, 165-170.
10. Bork, P. and Koonin, E.V. (1998) Nature Genet., 18, 313-318.
11. Bairoch, A. and Apweiler, R. (1996) Nucleic Acids Res., 24, 21-25.
12. Bairoch, A. and Boeckmann, B. (1992) Nucleic Acids Res., 20, 2019-2022.
13. Bairoch, A., Bucher, P. and Hoffman, K. (1997) Nucleic Acids Res., 25, 217-221.
14. Brazma, A., Jonassen, I., Eidhammer, I. and Gilbert, D. (1998) J. Comput. Biol., 5, 279-305.
15. Harrison, S.C. (1991) Nature, 353, 715-719.
16. Dodd, I.B. and Egan, J.B. (1987) J. Mol. Biol., 194, 557-564.
17. Yudkin, M.D. (1987) Protein Eng., 1, 371-372.
18. Lawrence, C.E., Altschul, S.F., Boguski, M.S., Liu, J.S., Neuwald, A.F. and Wooton, J.C. (1993) Science, 262, 208-214.
19. Kabsch, W. and Sander, C. (1983) Biopolymers, 22, 2577-2637.
20. Weickert, M.J. and Adhya, S. (1992) J. Biol. Chem., 267, 15869-15874.
21. Altschul, S.F., Madden, T.L., Schäffer, A.A., Zhang, J., Zhang, Z., Miller, W. and Lipman, D. (1997) Nucleic Acids Res., 25, 3389-3402.
22. Holm, L. (1998) Curr. Opin. Struct. Biol., 8, 372-379.
23. Jones, D.T. (1999) J. Mol. Biol., 287, 797-815.
24. Thompson, J.D., Higgins, D.G. and Gibson, T.J. (1994) Nucleic Acids Res., 22, 4673-4680.
25. Henikoff, S., Wallace, J.C. and Brown, J.P. (1990) Methods Enzymol., 183, 111-132.
26. Pao, G.M. and Saier, M.H., Jr (1995) J. Mol. Evol., 40, 136-154.
27. Henikoff, S., Haughn, G.W., Calvo, J.M. and Wallace, J.C. (1988) Proc. Natl Acad. Sci. USA, 85, 6602-6606.
28. Schell, M.A. (1993) Annu. Rev. Microbiol., 47, 597-626.
29. Gallegos, M.-T., Schelif, R., Bairoch, A., Hoffman, K. and Ramos, J.L. (1997) Microbiol. Mol. Biol. Rev., 61, 393-410.
30. Bairoch, A. (1993) Nucleic Acids Res., 21, 2515.
31. Spiro, S. (1994) Antonie van Leewenhoek, 66, 23-36.
32. Salgado, H., Santos, A., Garza-Ramos, U., Van Helden, J., Diaz, E. and Collado-Vides, J. (1999) Nucleic Acids Res., 27, 59-60.
33. Rey, L., Murillo, J., Hernando, Y., Hidalgo, E., Cabrera, E., Imperial, J. and Ruiz-Argueso, T. (1993) Mol. Microbiol., 8, 471-481.
34. Somers, W.S. and Phillips, S.E. (1992) Nature, 359, 387-393.
35. Graumman, P. and Marahiel, M.A. (1996) Bioessays, 18, 309-315.
36. Roth, A. and Messer, W. (1995) EMBOJ., 14, 2106-2111.
37. Kolb, A., Busby, S., Buc, H., Garges, S. and Adhya, S. (1993) Annu. Rev. Biochem., 62, 749-795.
38. Newman, E.B., Lin, R.T. and D'Ari, R. (1996) In Neidhardt, F.C., Curtiss, R., Ingraham, J.L., Lin, E.C.C., Low, K.B., Magasanik, B., Reznikoff, W.S., Riley, M., Schaerchter, M. and Umbarger, H.E. (eds). Escherichia coli and Salmonella typhimurium, Cellular and Molecular Biology. American Society for Microbiology, Washington, DC, pp. 1513-1526.
39. Magasanik, B. and Neidhardt, F.C. (1987) In Neidhart, F.C., Ingraham, J.L., Low, K.B., Magasanik, B., Schaechter, M. and Umbarger, H.E. (eds), Escherichia coli and Salmonella typhimurium. Cellular and Molecular Biology. American Society for Microbiology, Washington, DC, pp. 1318-1325.
40. Death, A. and Ferenci, T. (1994) J. Bacteriol., 176, 5101-5107.
41. Tomb, J.F., White, O., Kerlavage, A.R., Clayton, R.A., Sutton, G.G., Fleischmann, R.D., Ketchum, K.A., Klenk, H.P., Gill, S., Dougherty, B.A. et al. (1997) Nature, 388, 539-547.
42. Fleischmann, R.D., Adam, M.D., White, O., Clayton, R.A., Kirkness, E.F., Kerlavage, A.R., Bult, C.J., Tomb, J.F., Dougherty, B.A., Merrick, J.M. et al. (1995) Science, 269, 496-512.
43. Kunst, F., Ogasawara, N., Moszer, I., Albertini, A.M., Alloni, G., Azevedo, V., Bertero, M.G., Bessieres, P., Bolotin, A., Borchert, S. et al. (1997) Nature, 390, 249-256.
44. Van Rooijen, R.T.J., Dechering, K.J., Niek, C., Wilmink, J. and de Vos, W.M. (1993) Protein Eng., 6, 201-206.
45. Rosey, E.L. and Stewart, G.C. (1992) J. Bacteriol., 174, 6159-6170.
46. Kim, H. and Farrand, S.K. (1997) J. Bacteriol., 179, 7559-7572.
47. Schweizer, H.P. and Po, C. (1996) J. Bacteriol., 178, 5215-5221.
48. Olsen, G.J., Woese, C.R. and Overbeek, R. (1994) J. Bacteriol., 176, 1-6.
49. Haydon, D. and Guest, J. (1991) FEMS Microbiol. Lett., 79, 291-296.
50. Kyrpides, N.C. and Ouzounis, C.A. (1995) Trends Biochem. Sci., 20, 140-141.
51. Haldenwang, W.G. (1995) Microbiol. Rev., 59, 1-30.
52. Ninfa, A.J. (1996) In Neidhardt, F.C., Curtiss, R., Ingraham, J.L., Lin, E.C.C., Low, K.B., Magasanik, B., Reznikoff, W.S., Riley, M., Schaerchter, M. and Umbarger, H.E. (eds), Escherichia coli and Salmonella typhimurium. Cellular and Molecular Biology. American Society for Microbiology, Washington, DC, pp. 1246-1262.
53. Nguyen, C.C. and Saier, M.H., Jr (1995) FEBS Lett., 377, 98-102.
54. Savageau, M. (1986) Proc. Natl Acad. Sci. USA, 83, 1198-1202.
55. Yamanaka, K., Fang, L. and Inouye, M. (1998) Mol. Microbiol, 27, 247-255.
56. Huynen, M.A. and van Nimwegen, E. (1998) Mol. Biol. Evol., 15, 583-589.
57. Brewer, B.J. (1988) Cell, 53, 679-686.
58. Sunnerhagen, M., Nilges, M., Otting, G. and Carey, J. (1997) Nature Struct. Biol., 4, 819-825.
59. Streaker, E.D. and Beckett, D. (1998) J. Mol. Biol., 278, 787-800.
60. Wilson, K.P., Shewchuk, L.M., Brennan, R.G., Otsuka, A.J. and Matthews, B.W. (1992) Proc. Natl Acad. Sci. USA, 89, 9257-9261.
61. Weber, I.T. and Steitz, T.A. (1987) J. Mol. Biol., 198, 311-326.
62. Kostrewa, D., Granzin, J., Stock, D., Choe, H.-W., Labahn, J. and Saenger. W. (1992) J. Mol. Biol., 226, 209-226.
63. Penin, F., Georjon, C., Montserret, R., Bockmann, A., Lesage, A., Yang, Y., Bonod-Bidaud, C., Cortay, J.C., Negre, D., Cozzone, A.J. and Deleage, G. (1997) J. Mol. Biol., 270, 496-510.
64. Lewis, M., Chang, G., Horton, N.C., Kercher, M.A., Pace, H.C., Schumacher, M.A., Brennan, R.R. and Lu, P. (1996) Science. 271, 1247-1254.
65. Fogh, R.H., Ottleben, G., Rueterjans, H., Schnarr, M., Boelens, R. and Kaptein, R. (1994) EMBO J., 13, 3936-3944.
66. Baikalov, I., Schroeder, I., Kaczor-Grzeskowiak, M., Cascio,D., Gunsalus, R.P. and Dickerson, R.E. (1998) Biochemistry, 37, 3665-3676.
67. Martinez-Hackert, E. and Stock, M. (1997) J. Mol. Biol., 269, 301-312.
68. Schumacher, M.A., Glasfeld, A., Zalkin, H. and Brennan, R.G. (1997) J. Biol. Chem., 272, 22648-22653.
69. Hinrichs, W., Kisker, C., Duevel, C., Mueller, A., Tovar, K., Hillen, W. and Saenger, W. (1994) Science, 264, 418-420.
70. Kisker, C., Hinrichs, W., Tovar, K., Hillen, W. and Saenger, W. (1995) J. Mol. Biol., 247, 260-280.
71. Zhang, R.-G., Joachimiak, A., Lawson, C.L., Schevitz, R.W., Otwinowski, Z. and Sigler, P.B. (1987) Nature, 327, 591-597.