Reversible stalling of transcription elongation complexes by high pressure

Biophysical Journal

Volumn 75, Issue 1, 1998, Pages 453-462

  Erijman, Leonardo ^a   Clegg, Robert M ^a,b  

^a MAX PLANCK INSTITUTE FOR BIOPHYSICAL CHEMISTRY   (Germany)

^b University of Illinois at Urbana Champaign   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ELONGATION FACTOR; RNA POLYMERASE;

ARTICLE; ENZYME STABILITY; ESCHERICHIA COLI; HYDROSTATIC PRESSURE; NONHUMAN; PROTEIN QUATERNARY STRUCTURE; PROTEIN STABILITY; REACTION ANALYSIS; TEMPERATURE DEPENDENCE; TRANSCRIPTION REGULATION;

EID: 0031863612     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0006-3495(98)77533-2     Document Type: Article

References (45)

1. Arndt, K. M., and M. J. Chamberlin. 1990. RNA chain elongation by Escherichia coli RNA polymerase. Factors affecting the stability of elongating ternary complexes. J. Mol. Biol. 213:79-108.
2. Asano, T., and W. J. Le Noble. 1978. Activation and reaction volumes in solution. Chem. Rev. 78:407-489.
3. Beabealashvilly, R. S., and L. P. Savotchkina. 1973. RNA polymerase-DNA complexes. IV. Influences of the ionic strength on the integrity of the complexes. Biochim. Biophys. Acta. 294:434-441.
4. Buchanan, J., and S. D. Hammann. 1953. The chemical effects of pressure. Trans. Faraday Soc. 49:1425-1433.
5. Burgess, R. R. 1976. Purification and physical properties of E. coli RNA polymerase. In RNA Polymerase. R. Losick and M. J. Chamberlin, editors. Cold Spring Harbor Laboratory, Cold Spring Harbor, NY. 69-100.
6. Chamberlin, M. J. 1994. New models for the mechanism of transcription elongation and its regulation. Harvey Lect. 88:1-21.
7. Cioni, P., and G. B. Strambini. 1994. Pressure effects on protein flexibility monomeric proteins. J. Mol. Biol. 242:291-301.
8. Cooper, A. 1976. Thermodynamic fluctuations in protein molecules. Proc. Natl. Acad. Sci. USA. 73:2740-2741.
9. Erie, D. A., T. D. Yager, and P. H. von Hippel. 1992. The single-nucleotide addition cycle in transcription: a biophysical and biochemical perspective. Annu. Rev. Biophys. Biomol. Struct. 21:379-415.
10. Erijman, L., and R. M. Clegg. 1995. Heterogeneity of E. coli RNA polymerase revealed by high pressure. J. Mol. Biol. 253:259-265.
11. Erijman, L., and R. M. Clegg. 1997. Transcriptional inhibition by high pressure in vitro. In High Pressure Research in the Biosciences and Biotechnology. K. Heremans, editor. University of Leuven Press, Leuven, Belgium. 103-106.
12. Fukuda, R., and A. Ishihama. 1974. Subunits of RNA polymerase in function and structure. Maturation in vitro of core enzyme from Escherichia coli. J. Mol. Biol. 87:523-540.
13. Gross, M., G. Auerbach, and R. Jaenicke. 1993. The catalytic activities of monomeric enzymes show complex pressure dependence. FEBS Lett. 321:256-260.
14. Hawley, S. A., and R. M. MacLeod. 1974. Pressure-temperature stability of DNA in neutral salt solutions. Biopolymers. 13:1417-1426.
15. Krummel, B., and M. J. Chamberlin. 1992. Structural analysis of ternary complexes of Escherichia coli RNA polymerase. Deoxyribonuclease I footprinting of defined complexes. J. Mol. Biol. 225:239-250.
16. Liu, B., and B. M. Alberts. 1995. Head-on collision between a DNA replication apparatus and RNA polymerase transcription complex. Science. 267:1131-1137.
17. Liu, B., M. L. Wong, and B. Alberts. 1994. A transcribing RNA polymerase molecule survives DNA replication without aborting its growing RNA chain. Proc. Natl. Acad. Sci. USA. 91:10660-10664.
18. Low, P. S., and G. N. Somero. 1975. Activation volumes in enzymic catalysis: their sources and modification by low-molecular-weight solutes. Proc. Natl. Acad. Sci. USA. 72:3014-3018.
19. Markovtsov, V., A. Mustaev, and A. Goldfarb. 1996. Protein-RNA interactions in the active center of transcription elongation complex. Proc. Natl. Acad. Sci. USA. 93:3221-3226.
20. Metzger, W., P. Schickor, and H. Heumann. 1989. A cinematographic view of Escherichia coli RNA polymerase translocation. EMBO J. 8:2745-2754.
21. Miner, C. S., and N. N. Dalton. 1953. Glycerol. ACS Monograph Series, no. 117. Reinhold Publishers, New York. 282-283.
22. Naito, S., and A. Ishihama. 1975. Isolation and properties of the transcription complex of Escherichia coli RNA polymerase. Biochim. Biophys. Acta. 402:88-104.
23. Neff, N. F., and M. J. Chamberlin. 1980. Termination of transcription by Escherichia coli ribonucleic acid polymerase in vitro. Effect of altered reaction conditions and mutations in the enzyme protein on termination with T7 and T3 deoxyribonucleic acids. Biochemistry. 19:3005-3015.
24. Nudler, E., A. Goldfarb, and M. Kashlev. 1994. Discontinuous mechanism of transcription elongation. Science. 265:793-796.
25. Nudler, E., M. Kashlev, V. Nikiforov, and A. Goldfarb. 1995. Coupling between transcription termination and RNA polymerase inchworming. Cell. 81:351-357.
26. Reynolds, R., R. M. Bermudez-Cruz, and M. J. Chamberlin. 1992. Parameters affecting transcription termination by Escherichia coli RNA polymerase. I. Analysis of 13 rho-independent terminators. J. Mol. Biol. 224:31-51.
27. Rhodes, G., and M. J. Chamberlin. 1974. Ribonucleic acid chain elongation by Escherichia coli ribonucleic acid polymerase. I. Isolation of ternary complexes and the kinetics of elongation. J. Biol. Chem. 249: 6675-6683.
28. Richardson, J. P. 1966. The binding of RNA polymerase to DNA. J. Mol. Biol. 21:83-114.
29. Robinson, C. R., and S. G. Sligar. 1994. Hydrostatic pressure reverses osmotic pressure effects on the specificity of EcoRI-DNA interactions. Biochemistry. 33:3787-3793.
30. Roe, J. H., R. R. Burgess, and M. Record, Jr. 1985. Temperature dependence of the rate constants of the Escherichia coli RNA polymerase-lambda PR promoter interaction. Assignment of the kinetic steps corresponding to protein conformational change and DNA opening. J. Mol. Biol. 184:441-453.
31. Royer, C. A., A. E. Chakerian, and K. S. Matthews. 1990. Macromolecular binding equilibria in the lac repressor system: studies using high-pressure fluorescence spectroscopy. Biochemistry. 29:4959-4966.
32. Schäfer, R., W. Zillig, and K. Zechel. 1973. A model for the initiation of transcription by DNA-dependent RNA polymerase from Escherichia coli. Eur. J. Biochem. 33:207-214.
33. Schlageck, J. G., M. Baughman, and L. R. Yarbrough. 1979. Spectroscopic techniques for study of phosphodiester bond formation by Escherichia coli RNA polymerase. J. Biol. Chem. 254:12074-12077.
34. Thomas, C. A. J., and J. Abelson. 1966. The isolation and characterization of DNA from bacteriophage. In Procedures in Nucleic Acid Research. G. L. Cantoni and D. R. Davies, editors. Harper and Row, New York. 553-561.
35. Villas-Boas, M., A. Sepulveda de Rezende, J. L. Silva, A. Zechel, and R. M. Clegg. 1996. Exploring structural, functional and kinetic aspects of nucleic acid-protein complexes with pressure: nucleosomes and RNA polymerase. In P. H. von Hippel and T. D. Yager. 1991. Transcript elongation and termination are competitive kinetic processes. Proc. Natl. Acad. Sci. USA. 88:2307-2311.
36. Wang, D., T. I. Meier, C. L. Chan, G. Feng, D. N. Lee, and R. Landick. 1995. Discontinuous movements of DNA and RNA in RNA polymerase accompany formation of a paused transcription complex. Cell. 81: 341-50.
37. Weast, R. C., and M. J. Astle. 1980. CRC Handbook of Chemistry and Physics. CRC Press, Boca Raton, FL.
38. Wilson, K. S., and P. H. von Hippel. 1994. Stability of Escherichia coli transcription complexes near an intrinsic terminator. J. Mol. Biol. 244: 36-51.
39. Wilson, K. S., and P. H. von Hippel. 1995. Transcription termination at intrinsic terminators: the role of the RNA hairpin. Proc. Natl. Acad. Sci. USA. 92:8793-8797.
40. Wu, J. Q., and R. Macgregor, Jr. 1993. Pressure dependence of the melting temperature of dA · dT polymers. Biochemistry. 32:12531-12537.
41. Yager, T. D., and P. H. von Hippel. 1987. Transcript elongation and termination in Escherichia coli. In Escherichia coli and Salmonella typhimurium. F. C. Neidhardt, editor. American Society for Microbiology, Washington, DC. 1241-1275.
42. Yager, T. D., and P. H. von Hippel. 1991. A thermodynamic analysis of RNA transcript elongation and termination in Escherichia coli. Biochemistry. 30:1097-1118.
43. Yarbrough, L. R., J. G. Schlageck, and M. Baughman. 1979. Synthesis and properties of fluorescent nucleotide substrates for DNA-dependent RNA polymerases. J. Biol. Chem. 254:12069-12073.
44. Yin, H., M. D. Wang, K. Svoboda, R. Landick, S. M. Block, and J. Gelles. 1995. Transcription against an applied force. Science. 270:1653-1657.
45. Zaychikov, E., L. Denissova, and H. Heumann. 1995. Translocation of the Escherichia coli transcription complex observed in the registers 11 to 20: "jumping" of RNA polymerase and asymmetric expansion and contraction of the "transcription bubble." Proc. Natl. Acad. Sci. USA. 92:1739-1743.