Protein-nucleic acid interactions during open complex formation investigated by systematic alteration of the protein and DNA binding partners

Biochemistry

Volumn 38, Issue 19, 1999, Pages 5959-5967

  Helmann, John D ^a   DeHaseth, Pieter L ^b  

^a Cornell University ^*  (United States)

^b CASE WESTERN RESERVE UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

RNA POLYMERASE;

BINDING SITE; COMPLEX FORMATION; CONFORMATIONAL TRANSITION; DNA FOOTPRINTING; DNA TEMPLATE; MOLECULAR INTERACTION; NUCLEIC ACID STRUCTURE; PRIORITY JOURNAL; PROTEIN DNA BINDING; PROTEIN PROTEIN INTERACTION; REVIEW; STRUCTURE ANALYSIS;

BACTERIA; DNA; DNA-BINDING PROTEINS; DNA-DIRECTED RNA POLYMERASES; NUCLEIC ACID CONFORMATION; PROTEIN CONFORMATION;

EID: 18344418394     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi990206g     Document Type: Review

References (105)

1. Gross, C. A., Lonetto, M., and Losick, R. (1992) in Transcriptional Regulation (McKnight, S. L., and Yamamoto, K. R., Eds.) pp 129-176, Cold Spring Harbor Press, Cold Spring Harbor, NY.
2. Helmann, J. D., and Chamberlin, M. J. (1988) Annu. Rev. Biochem. 57, 839-872.
3. Helmann, J. D. (1994) in Transcription: Mechanisms and Regulation (Conaway, R. C., and Conaway, J. W., Eds.) pp 1-17, Raven Press, New York.
4. Lonetto, M., Gribskov, M., and Gross, C. A. (1992) J. Bacteriol. 174, 3843-3849.
5. Blatter, E. E., Ross, W., Tang, H., Gourse, R. L., and Ebright, R. H. (1994) Cell 78, 889-896.
6. Gaal, T., Ross, W., Blatter, E. E., Tang, H., Jia, X., Krishnan, V. V., Assa-Munt, N., Ebright, R. H., and Gourse, R. L. (1996) Genes Dev. 10, 16-26.
7. Jeon, Y. H., Negishi, T., Shirakawa, M., Yamazaki, T., Fujita, N., Ishihama, A., and Kyogoku, Y. (1995) Science 270, 1495-1497.
8. Jeon, Y. H., Yamazaki, T., Otomo, T., Ishihama, A., and Kyogoku, Y. (1997) J. Mol. Biol. 267, 953-962.
9. Kimura, M., and Ishihama, A. (1995) J. Mol. Biol. 248, 756-767.
10. Malhotra, A., Severinova, E., and Darst, S. A. (1996) Cell 87, 127-136.
11. Murakami, K., Owens, J. T., Belyaeva, T. A., Meares, C. F., Busby, S. J., and Ishihama, A. (1997) Proc. Natl. Acad. Sci. U.S.A. 94, 11274-11278.
12. Polyakov, A., Severinova, E., and Darst, S. A. (1995) Cell 83, 365-373.
13. Severinova, E., Severinov, K., Fenyo, D., Marr, M., Brody, E., Roberts, J. W., Chait, B. T., and Darst, S. A. (1996) J. Mol. Biol. 263, 637-647.
14. Kim, T. K., Lagrange, T., Wang, Y. H., Griffith, J. D., Reinberg, D., and Ebright, R. H. (1997) Proc. Natl. Acad. Sci. U.S.A. 94, 12268-73.
15. deHaseth, P. L., and Helmann, J. D. (1995) Mol. Microbiol. 16, 817-824.
16. Ross, W., Gosink, K. K., Salomon, J., Igarashi, K., Zou, C., Ishihama, A., Severinov, K., and Gourse, R. L. (1993) Science 262, 1407-1413.
17. Ross, W., Aiyar, S. E., Salomon, J., and Gourse, R. L. (1998) J. Bacteriol. 180, 5375-5383.
18. Estrem, S. T., Gaal, T., Ross, W., and Gourse, R. L. (1998) Proc. Natl. Acad. Sci. U.S.A. 95, 9761-9766.
19. Helmann, J. D. (1995) Nucleic Acids Res. 23, 2351-2360.
20. Leirmo, S., and Gourse, R. L. (1991) J. Mol. Biol. 220, 555-568.
21. Landini, P., and Volkert, M. R. (1995) EMBO J. 14, 4329-4335.
22. Strainic, M. G., Jr., Sullivan, J. J., Velevis, A., and deHaseth, P. L. (1998) Biochemistry 37, 18074-18080.
23. Bown, J., Barne, K., Minchin, S., and Busby, S. (1997) Nucleic Acids Mol. Biol. 11, 41-52.
24. Kirkegaard, K., Buc, H., Spassky, A., and Wang, J. (1983) Proc. Natl. Acad. Sci. U.S.A. 80, 2544-2548.
25. Sasse-Dwight, S., and Gralla, J. D. (1989) J. Biol. Chem. 264, 8074-8081.
26. Siebenlist, U., Simpson, R. B., and Gilbert, W. (1980) Cell 20, 269-281.
27. Suh, W.-C., Ross, W., and Record, M. T., Jr. (1993) Science 259, 358-361.
28. Zaychikov, E., Denissova, L., Meier, T., Gotte, M., and Heumann, H. (1997) J. Biol. Chem. 272, 2259-2267.
29. Heumann, H., Ricchetti, M., and Werel, W. (1988) EMBO J. 7, 4379-4381.
30. Rees, W. A., Keller, W. R., Vesenka, J. P., Yang, G., and Bustamante, C. (1993) Science 260, 1646-1649.
31. Record, M. T., Jr., Reznikoff, W. S., Craig, M. L., McQuade, K. L., and Schlax, P. J. (1996) in Escherichia coli and Salmonella, cellular and molecular biology (Neidhardt, F. C., Ed.) pp 792-820, ASM Press, Washington, DC.
32. Craig, M. L., Suh, W.-C., and Record, M. T., Jr. (1995) Biochemistry 34, 15624-15632.
33. Gaal, T., Bartlett, M. S., Ross, W., Turnbough, C. L., Jr., and Gourse, R. L. (1997) Science 278, 2092-2097.
34. Gourse, R. L. (1988) Nucleic Acids Res. 16, 9789-9809.
35. deHaseth, P. L., Zupancic, M., and Record, M. T., Jr. (1998) J. Bacteriol. 180, 3019-3025.
36. Craig, M. L., Tsodikov, O. V., McQuade, K. L., Schlax, P. E., Jr., Capp, M. W., Saecker, R. M., and Record, M. T., Jr. (1998) J. Mol. Biol. 283, 741-756.
37. Buckle, M., Pemberton, I. K., Jacquet, M. A., and Buc, H. (1999) J. Mol. Biol. 285, 955-964.
38. Roy, S., Garges, S., and Adhya, S. (1998) J. Biol. Chem. 273, 14059-14062.
39. Chen, Y.-F., and Helmann, J. D. (1997) J. Mol. Biol. 267, 47-59.
40. Juang, Y.-L., and Helmann, J. D. (1995) Biochemistry 34, 8465-8473.
41. Rowe-Magnus, D. A., and Spiegelman, G. B. (1998) Proc. Natl. Acad. Sci. U.S.A. 95, 5305-5310.
42. Meier, T., Schickor, P., Wedel, A., Cellai, L., and Heumann, H. (1995) Nucleic Acids Res 23, 988-994.
43. Burns, H., and Minchin, S. (1994) Nucleic Acids Res. 22, 3840-3845.
44. Mooney, R. A., Artsimovitch, I., and Landick, R. (1998) J. Bacteriol. 180, 3265-3275.
45. Simpson, R. B. (1979) Cell 18, 277-285.
46. Dombroski, A. J., Walter, W. A., Record, M. T., Jr., Siegele, D. A., and Gross, C. A. (1992) Cell 70, 501-512.
47. Huang, X., Lopez de Saro, F. J., and Helmann, J. D. (1997) Nucleic Acids Res. 25, 2603-2609.
48. Callaci, S., and Heyduk, T. (1998) Biochemistry 37, 3312-3320.
49. Severinov, K., and Darst, S. A. (1997) Proc. Natl. Acad. Sci. U.S.A. 94, 13481-13486.
50. Owens, J. T., Miyake, R., Murakami, K., Chmura, A. J., Fujita, N., Ishihama, A., and Meares, C. F. (1998) Proc. Natl. Acad. Sci. U.S.A. 95, 6021-6026.
51. Dombroski, A. J., Walter, W. A., and Gross, C. A. (1993) Genes Dev. 7, 2446-2455.
52. Chen, Y.-F., and Helmann, J. D. (1995) J. Mol. Biol. 249, 743-753.
53. Callaci, S., Heyduk, E., and Heyduk, T. (1998) J. Biol. Chem. 273, 32995-33001.
54. Callaci, S., Heyduk, E., and Heyduk, T. (1999) Mol. Cell 3, 229-238.
55. Bowers, C. W., and Dombroski, A. J. (1999) EMBO J. 18, 709-716.
56. Gopal, V., Ma, H.-W., Kumaran, M. K., and Chatterji, D. (1994) J. Mol. Biol. 242, 9-22.
57. Juang, Y.-L., and Helmann, J. D. (1994) J. Mol. Biol. 235, 1470-1488.
58. Rong, J. C., and Helmann, J. D. (1994) J. Bacteriol. 176, 5218-24.
59. Aiyar, S. E., Juang, Y.-L., Helmann, J. D., and deHaseth, P. L. (1994) Biochemistry 33, 11501-11507.
60. Marr, M. T., and Roberts, J. W. (1997) Science 276, 1258-1260.
61. Daniels, D., Zuber, P., and Losick, R. (1990) Proc. Natl. Acad. Sci. U.S.A. 87, 8075-8079.
62. Waldburger, C., Gardella, T., Wong, R., and Susskind, M. M. (1990) J. Mol. Biol. 215, 1-10.
63. Barne, K. A., Bown, J. A., Busby, S. J. W., and Minchin, S. D. (1997) EMBO J. 16, 4034-4040.
64. Bown, J. A., Owens, J. T., Meares, C. F., Fujita, N., Ishihama, A., Busby, S. J., and Minchin, S. D. (1999) J. Biol. Chem. 274, 2263-2270.
65. Owens, J. T., Chmura, A. J., Murakami, K., Fujita, N., Ishihama, A., and Meares, C. (1998) Biochemistry 37, 7670-7675.
66. Heyduk, E., and Heyduk, T. (1999) J. Biol. Chem. 274, 3315-3322.
67. Siegele, D. A., Hu, J. C., Walter, W. A., and Gross, C. A. (1989) J. Mol. Biol. 206, 591-603.
68. Roberts, R. J., and Cheng, X. (1998) Annu. Rev. Biochem. 67, 181-198.
69. deHaseth, P. L., Lohman, T. M., Burgess, R. R., and Record, M. T., Jr. (1978) Biochemistry 17, 1612-1622.
70. Dedrick, R. L., and Chamberlin, M. J. (1985) Biochemistry 24, 2245-2253.
71. Kadesch, T. R., and Chamberlin, M. J. (1982) J. Biol. Chem. 257, 5286-5295.
72. Kane, C., and Chamberlin, M. J. (1985) Biochemistry 24, 2254-2262.
73. Sluder, A. E., Price, D. H., and Greenleaf, A. L. (1988) J. Biol. Chem. 263, 9917-9925.
74. Campbell, F. E., and Setzer, D. R. (1992) Mol. Cell. Biol. 12, 2260-2272.
75. Kane, C. M. (1988) Biochemistry 27, 3187-3196.
76. Aiyar, S. E., Helmann, J. D., and deHaseth, P. L. (1994) J. Biol. Chem. 269, 13179-13184.
77. Tripatara, A., and deHaseth, P. (1993) J. Mol. Biol. 233, 349-358.
78. Ring, B. Z., Yamell, W. S., and Roberts, J. W. (1996) Cell 86, 485-493.
79. Dombroski, A. J. (1997) J. Biol Chem. 272, 3487-3494.
80. Fredrick, K., and Helmann, J. D. (1997) Proc. Natl. Acad. Sci. U.S.A. 94, 4982-4987.
81. Tantin, D., and Carey, M. (1994) J. Biol. Chem. 269, 17397-17400.
82. Pan, G., and Greenblatt, J. (1994) J. Biol. Chem. 269, 30101-30104.
83. Usheva, A., and Shenk, T. (1996) Proc. Natl. Acad. Sci. U.S.A. 93, 13571-13576.
84. Mollegaard, N. E., Buchardt, O., Egholm, M., and Nielsen, P. E. (1994) Proc. Natl. Acad. Sci. U.S.A. 91, 3892-3895.
85. Daube, S., and von Hippel, P. H. (1992) Science 258, 1320-1324.
86. Daube, S. S., Hart, C. R., and von Hippel, P. H. (1994) Proc. Natl. Acad. Sci. U.S.A. 91, 9539-9543.
87. Daube, S. S., and von Hippel, P. H. (1994) Biochemistry 33, 340-347.
88. Sidorenkov, I., Komissarova, N., and Kashlev, M. (1998) Mol. Cell 2, 55-64.
89. Jeon, C. J., and Agarwal, K. (1996) Proc. Natl. Acad. Sci. U.S.A. 93, 13677-13682.
90. Roberts, C. W., and Roberts, J. W. (1996) Cell 86, 495-501.
91. Li, X.-Y., and McClure, W. R. (1998) J. Biol Chem. 273, 23558-23566.
92. Breslauer, K. J., Frank, R., Blocker, H., and Marky, L. A. (1986) Proc. Natl. Acad. Sci. U.S.A. 83, 3746-3750.
93. Spassky, A., Rimsky, S., Buc, H., and Busby, S. (1988) EMBO J. 7, 1871-1879.
94. Schaeffer, F., Kolb, A., and Buc, H. (1982) EMBO J. 1, 99-105.
95. Drew, H. R., Weeks, J. R., and Travers, A. A. (1985) EMBO J. 4, 1025-1032.
96. Fedoriw, A. M., Liu, H., Anderson, V. E., and deHaseth, P. L. (1998) Biochemistry 37, 11971-11979.
97. Guo, Y., and Gralla, J. D. (1998) Proc. Natl. Acad. Sci. U.S.A. 95, 11655-11660.
98. Roe, J. H., Burgess, R. R., and Record, M. T., Jr. (1985) J. Mol. Biol. 184, 441-453.
99. Kaguni, J. M., and Kornberg, A. (1982) J. Biol. Chem. 257, 5437-5443.
100. Higashitani, A., Higashitani, N., and Horiuchi, K. (1997) Proc. Natl. Acad. Sci. U.S.A. 94, 2909-2914.
101. Masai, H., and Arai, K. (1997) Cell 89, 897-907.
102. McClure, W. R. (1985) Annu. Rev. Biochem. 54, 171-204.
103. von Hippel, P. H., Bear, D. G., Morgan, W. D., and McSwiggen, J. A. (1984) Annu. Rev. Biochem. 53, 389-446.
104. Fredrick, K., Caramori, T., Chen, Y. F., Galizzi, A., and Helmann, J. D. (1995) Proc. Natl. Acad. Sci. U.S.A. 92, 2582-2586.
105. Nudler, E., Gusarov, I., Avetissova, E., Kozlov, M., and Goldfarb, A. (1998) Science 281, 424-428.