Mechanisms by which T7 lysozyme specifically regulates T7 RNA polymerase during different phases of transcription

Journal of Molecular Biology

Volumn 293, Issue 3, 1999, Pages 457-475

  Huang, Jianbin ^a   Villemain, Jana ^a   Padilla, Robert ^a   Sousa, Rui ^a  

^a UNIVERSITY OF TEXAS HEALTH SCIENCE CENTER AT SAN ANTONIO   (United States)

Author keywords

Kinetics; Phage RNA polymerase; T7 lysozyme; T7 RNA polymerase; Transcription regulation

Indexed keywords

LYSOZYME; RNA POLYMERASE;

ARTICLE; BACTERIOPHAGE T7; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN DEGRADATION; PROTEIN PROTEIN INTERACTION; TRANSCRIPTION INITIATION; TRANSCRIPTION REGULATION;

EID: 0032732424     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1999.3135     Document Type: Article

References (44)

1. Axelrod V. D., Kramer F. R. Transcription from bacteriophage T7 and SP6 RNA polymerase promoters in the presence of 3′-deoxyribonucleoside chain terminators. Biochemistry. 24:1985;5716-5723.
2. Bonner G., Patra D., Lafer E. M., Sousa R. Mutations in T7 RNA polymerase that support the proposal for a common polymerase active site structure. EMBO J. 11:1992;3676-3775.
3. Beynon R. J., Bond J. S. Proteolytic Enzymes, A Practical Approach. 1993;IRL Press, Oxford.
4. Cheetham G. M. T., Jeruzalmi D., Steitz T. A. Structural basis of transcription initiation by T7 RNA polymerase. Nature. 399:1999;80-83.
5. Diaz G. A., Rong M., McAllister W. T. The stability of abortively cycling T7 RNA polymerase complexes depends upon template conformation. Biochemistry. 35:1996;10837-10843.
6. Gardner L. P., Mookhtiar K. A., Coleman J. E. Initiation, elongation, and processivity of carboxyl-terminal mutants of T7 RNA polymerase. Biochemistry. 36:1997;2908-2918.
7. Gopal V., Briebas L. D., Guajardo R., McAllister W. T., Sousa R. Characterization of structural features of T7 RNA polymerase important for elongation complex stability reveals alternate elongation complex conformations and a role for the non-template strand in RNA displacement. J. Mol. Biol. 290:1999;410-431.
8. Gross L., Chen W. J., McAlester W. T. Characterization of bacteriophage T7 RNA polymerase by linker insertion mutagenesis. J. Mol. Biol. 228:1992;488-505.
9. Guajardo R., Sousa R. A model for the mechanism of polymerase translocation. J. Mol. Biol. 265:1997;8-19.
10. Guajardo R., Lopez P., Dreyfus M., Sousa R. NTP concentration effects during initial transcription by T7RNAP indicates that translocation occurs by passive sliding and reveal that divergent promoters have increased NTP concentration requirements for initiation. J. Mol. Biol. 281:1998;783-792.
11. He B., Rong M., Durbin R. K., McAllister W. T. A mutant T7 RNA polymerase that is defective in RNA binding and blocked in the early stages of transcription. J. Mol. Biol. 265:1997;275-288.
12. Huang Y., Padilla R., Eckstein F., Sousa R. The mechanism of ribose 2′-group discrimination by an RNA polymerase. Biochemistry. 36:1997;8231-8242.
13. ++ and dNMP incorporation into transcripts. Biochemistry. 36:1997b;13718-13728.
14. Ikeda R. A., Bailey P. A. Inhibition of T7 RNA polymerase by T7 lysozyme in vitro. J. Biol. Chem. 267:1992;20153-20158.
15. Ikeda R. A., Richardson C. C. Interactions of a proteolytically nicked RNA polymerase of bacteriophage T7 with its promoter. J. Biol. Chem. 262:1987a;3800-3808.
16. Ikeda R. A., Richardson C. C. Enzymatic properties of a proteolytically nicked RNA polymerase of bacteriophage T7. J. Biol. Chem. 262:1987b;3790-3799.
17. Jeruzalmi D., Steitz T. A. Structure of T7 RNA polymerase complexed to the transcriptional inhibitor T7 lysozyme. EMBO J. 17:1998;4101-4113.
18. Jia Y., Patel S. S. Kinetic mechanism of transcription initiation by bacteriophage T7 RNA polymerase. Biochemistry. 36:1997a;4223-4232.
19. Jia Y., Patel S. S. Kinetic mechanism of GTP binding and RNA synthesis during transcription initiation by T7 RNA polymerase. J. Biol. Chem. 272:1997b;30147-30153.
20. Jia Y., Kumar A., Patel S. S. Equilibrium and stopped-flow kinetic studies of interaction between T7 RNA polymerase and its promoters measured by protein and 2-aminopurine fluorescence Changes. J. Biol. Chem. 271:1996;30451-30458.
21. Klement J. F., Ling M. L., McAllister W. T. Sequencing of DNA using T3 RNA polymerase and chain terminating ribonucleotide analogs. Gene Anal. Techn. 3:1986;59-66.
22. Kumar A., Patel S. S. Inhibition of T7 RNA polymerase transcription initiation and transition from initiation to elongation are inhibited by T7 lysozyme via a ternary complex with RNA polymerase and promoter DNA. Biochemistry. 36:1997;13954-13962.
23. Lyakhov D. L., He B., Zhang X., Studier F. W., McAllister W. T. Pausing and termination by bacteriophage T7 RNA polymerase. J. Mol. Biol. 280:1998;201-213.
24. Matthews B. W. Structural and genetic analysis of protein stability. Annu. Rev. Biochem. 62:1993;139-160.
25. McAllister W. T. Structure and function of the bacteriophage T7 RNA polymerase (or, the virtues of simplicity). Cell Mol. Biol. Res. 39:1993a;385-391.
26. McAllister W. T. The phage RNA polymerases are related to DNA polymerases and reverse transcriptases. Mol. Microbiol. 10:1993b;1-6.
27. McAllister W. T., Wu H. L. Regulation of transcription of the late genes of bacteriophage T7. Proc. Natl Acad. Sci. USA. 75:1978;804-808.
28. McAllister W. T., Morris C., Rosenberg A. H., Studier F. W. Utilization of bacteriophage T7 late promoters in recombinant plasmids during infection. J. Mol. Biol. 153:1981;527-544.
29. Moffat B. A., Studier F. W. T7 lysozyme inhibits transcription by T7 RNA polymerase. Cell. 49:1987;221-227.
30. Mookhtiar K. A., Peluso P. S., Muller D. K., Dunn J. J., Coleman J. E. Processivity of T7 RNA polymerase requires the C-terminal Phe882-Ala883-COO- or 'foot'. Biochemistry. 30:1991;6305-6313.
31. Muller D., Martin C. T., Coleman J. E. Processivity of proteolytically modified forms of T7 RNA polymerase. Biochemistry. 27:1988;5763-5771.
32. Nudler E. Transcription elongation: structural basis and mechanisms. J. Mol. Biol. 288:1999;1-12.
33. Patra D., Lafer E. M., Sousa R. Isolation and characterization of mutant bacteriophage T7 RNA polymerases. J. Mol. Biol. 243:1992;368-387.
34. Sastry S., Ross B. M. RNA-binding site in T7 RNA polymerase. Proc. Natl Acad. Sci. USA. 95:1998;9111-9116.
35. Sousa R. Structural and mechanistic relationships between nucleic acid polymerases. Trends Biochem. Sci. 21:1996;186-190.
36. Sousa R., Padilla R. A mutant T7 RNA polymerase as a DNA polymerase. EMBO J. 14:1995;4609-4621.
37. Sousa R., Patra D., Lafer E. M. Model for the mechanism of bacteriophage T7RNAP transcription initiation and termination. J. Mol. Biol. 224:1992;319-334.
38. Sousa R., Chung Y. J., Rose J. R., Wang B. C. Crystal structure of bacteriophage T7 RNA polymerase at 3.3 Å resolution. Nature. 364:1993;593-599.
39. Tabor S., Richardson C. C. A bacteriophage T7 RNA polymerase/promoter system for controlled exclusive expression of specific genes. Proc. Natl Acad. Sci. USA. 82:1985;1074-1078.
40. Ujvari A., Martin C. T. Thermodynamic and kinetic measurements of promoter binding by T7 RNA polymerase. Biochemistry. 35:1996;14574-14582.
41. Villemain J., Sousa R. Specificity in transcriptional regulation in the absence of specific DNA binding sites: the case of T7 lysozyme. J. Mol. Biol. 281:1998;793-802.
42. Villemain J., Guajardo R., Sousa R. The role of open complex instability in kinetic promoter selection by T7 RNA polymerize. J. Mol. Biol. 273:1997;958-977.
43. Woody A. Y. M., Osumi-Davis P. A., Hiremath M. M., Woody R. W. Pre-steady-state and steady-state kinetic studies on transcription initiation catalyzed by T7 RNA polymerase and its active-site mutants K631R and Y639F. Biochemistry. 37:1998;15958-15964.
44. Zhang X., Studier F. W. Mechanism of inhibition of bacteriophage T7 RNA polymerase by T7 lysozyme. J. Mol. Biol. 269:1997;10-27.