Effects of reaction conditions on RNA secondary structure and on the helicase activity of Escherichia coli transcription termination factor rho

Journal of Molecular Biology

Volumn 279, Issue 4, 1998, Pages 713-726

  Walstrom, Katherine M ^a,b   Dozono, Jody M ^a   Von Hippel, Peter H ^a  

^a UNIVERSITY OF OREGON   (United States)

^b NEW COLLEGE OF FLORIDA   (United States)

Author keywords

ATPase activity; Presteady state kinetics; Processivity; RNA secondary structure; RNA DNA helicase activity

Indexed keywords

ADENOSINE TRIPHOSPHATASE; HELICASE; POTASSIUM CHLORIDE; RHO FACTOR; RNA;

ARTICLE; CHEMICAL REACTION; ENZYME ACTIVITY; ESCHERICHIA COLI; PRIORITY JOURNAL; PROTEIN SECONDARY STRUCTURE; RNA STRUCTURE; TRANSCRIPTION TERMINATION;

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI;

EID: 0032546731     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1998.1814     Document Type: Article

References (46)

1. Alifano, P., Rivellini, F., Limauro, D., Bruni, C. B. & Carlomagno, S. M. (1991). A consensus motif common to all rho-dependent prokaryotic transcription terminators. Cell, 64, 553-563.
2. Allison, T. J., Wood, T. C., Briercheck, D. M., Rastinejad, F., Richardson, J. P. & Rule, G. S. (1998). Crystal structure of the RNA-binding domain from transcription termination factor rho. Nature Struct. Biol. In the press.
3. Bear, D. G. & Peabody, D. S. (1988). The E. coli rho protein: an ATPase that terminates transcription. Trends Biochem. Sci. 13, 343-347.
4. Brennan, C. A. & Platt, T. (1991). Mutations in an RNP1 consensus sequence of rho protein reduce RNA binding affinity but facilitate helicase turnover. J. Biol. Chem. 266, 17296-17305.
5. Brennan, C. A., Dombroski, A. J. & Platt, T. (1987). Transcription termination factor rho is an RNA-DNA helicase. Cell, 48, 945-952.
6. Brennan, C. A., Steinmetz, E. J., Spear, P. & Platt, T. (1990). Specificity and efficiency of rho-factor helicase activity depends on magnesium concentration and energy coupling to NTP hydrolysis. J. Biol. Chem. 265, 5440-5447.
7. 13C resonance assignments and secondary structure determination of the RNA-binding domain of E. coli rho protein. J. Biomol. NMR, 8, 429-444.
8. Briercheck, D. M., Wood, T. C., Allison, T. J., Richardson, J. P. & Rule, G. S. (1998). The NMR structure of the RNA binding domain of E. coli rho factor suggests possible RNA-protein interactions. Nature Struct. Biol. In the press.
9. Ceruzzi, M. A. F., Bektesh, S. L. & Richardson, J. P. (1985). Interaction of rho factor with bacteriophage lambda cro gene transcripts. J. Biol. Chem. 260, 9412-9418.
10. Chamberlin, M. J. & Patterson, D. L. (1965). Physical and chemical characterization of the ordered complexes formed between polyinosinic acid, polycytidylic acid, and their deoxyribo-analogues. J. Mol. Biol. 12, 410-428.
11. R1. J. Biol. Chem. 262, 11292-11299.
12. Faus, I. & Richardson, J. P. (1989). Thermodynamic and enzymological characterization of the interaction between transcription termination factor rho and lambda cro mRNA. Biochemistry, 28, 3510-3517.
13. Finger, L. R. & Richardson, J. P. (1982). Stabilization of the hexameric form of Escherichia coli protein rho under ATP hydrolysis conditions. J. Mol. Biol. 156, 203-219.
14. Galluppi, G. R. & Richardson, J. P. (1980). ATP-induced changes in the binding of RNA synthesis termination protein rho to RNA. J. Mol. Biol. 138, 513-539.
15. Geiselmann, J. & von Hippel, P. H. (1992). Functional interactions of ligand cofactors with E. coli transcription termination factor rho. I Binding of ATP. Protein Sci. 1, 850-860.
16. Geiselmann, J., Yager, T. D., Gill, S. C., Calmettes, P. & von Hippel, P. H. (1992a). Physical properties of the E. coli transcription termination factor rho. Association states and geometry of the rho hexamer. Biochemistry, 31, 111-121.
17. Geiselmann, J., Yager, T. D. & von Hippel, P. H. (1992b). Functional interactions of ligand cofactors with E. coli transcription termination factor rho: binding of RNA. Protein Sci. 1, 861-873.
18. Greenblatt, J., McLimont, M. & Hanly, S. (1981). Termination of transcription by NusA gene protein of Escherichia coli. Nature, 292, 215-220.
19. Jin, D. J., Burgess, R. R., Richardson, J. P. & Gross, C. A. (1992). Termination and efficiency at rho-dependent terminators depends on kinetic coupling between RNA polymerase and rho. Proc. Natl Acad. Sci. USA, 89, 1453-1457.
20. Leirmo, S., Harrison, C., Cayley, D. S., Burgess, R. R. & Record, M. T., Jr (1987). Replacement of potassium chloride by potassium glutamate dramatically enhances protein-DNA interactions in vitro. Biochemistry, 26, 2095-2101.
21. Lowery-Goldhammer, C. & Richardson, J. P. (1974). An RNA-dependent nucleoside triphosphate phosphohydrolase (ATPase) associated with rho termination factor. Proc. Natl Acad. Sci. USA, 71, 2003-2007.
22. 1 nuclease. J. Biol. Chem. 261, 5396-5403.
23. Martinez, A., Opperman, T. & Richardson, J. P. (1995). Mutational analysis and secondary structure model of the RNP1-like sequence motif of transcription termination factor rho. J. Mol. Biol. 257, 895-908.
24. Mascotti, D. P. & Lohman, T. M. (1997). Thermodynamics of oligoarginines binding to RNA and DNA. Biochemistry, 36, 7272-7279.
25. McSwiggen, J. A., Bear, D. G. & von Hippel, P. H. (1988). Interactions of Escherichia coli transcription termination factor rho with RNA I. Binding stoichiometries and free energies. J. Mol. Biol. 199, 609-622.
26. Morgan, W. D., Bear, D. G., Litchman, B. L. & von Hippel, P. H. (1985). RNA sequence and secondary structure requirements for rho-dependent transcription termination. Nucl. Acids Res, 13, 3739-3754.
27. Murzin, A. G. (1993). OB(oligonucleotide/oligosaccharide binding)-fold: common structural and functional solution for non-homologous sequences. EMBO J. 12, 861-867.
28. Nehrke, K. W., Seifried, S. E. & Platt, T. (1992). Overproduced rho factor from p39AS has lysine replacing glutamic acid at residue 155 in the linker region between its RNA and ATP binding domains. Nucl. Acids Res. 20, 6107.
29. O'Sullivan, W. J. & Smithers, G. W. (1979). Stability constants for biologically important metal-ligand complexes. Methods Enzymol. 63, 294-336.
30. Oubridge, C., Ito, N., Evans, P. R., Teo, C.-H. & Nagai, K. (1994). Crystal structure at 1. 92 Å resolution of the RNA-binding domain of the U1A spliceosomal protein complexed with an RNA hairpin. Nature, 372, 432-438.
31. Platt, T. (1986). Transcription termination and the regulation of gene expression. Annu. Rev. Biochem. 55, 339-372.
32. Platt, T. (1994). Rho and RNA: models for recognition and response. Mol. Microbiol. 11, 983-990.
33. Platt, T. & Richardson, J. P. (1992). Escherichia coli rho factor: protein and enzyme of transcription termination. In Transcriptional Regulation (McKnight, S. L. & Yamamoto, K. R., eds), pp. 365-388, Cold Spring Harbor Laboratory Press, Plainview, NY.
34. Record, J., M, T., deHaseth, P. L. & Lohman, T. M. (1977). Interpretation of monovalent and divalent cation effects on the lac repressor-operator interaction. Biochemistry, 16, 4791-4796.
35. Richardson, J. P. (1982). Activation of rho protein ATPase requires simultaneous interaction at two kinds of nucleic acid-binding sites. J. Biol. Chem. 257, 5760-5766.
36. Richardson, J. P. (1996). Structural organization of transcription termination factor rho. J. Biol. Chem. 271, 1251-1254.
37. Richardson, J. P. & Macy, M. R. (1981). Ribonucleic acid synthesis termination protein p function: effects of conditions that destabilize ribonucleic acid secondary structure. Biochemistry, 20, 1133-1139.
38. Richey, B., Cayley, D. S., Mossing, M. C., Kolka, C., Anderson, C. F., Farrar, T. C. & Record, M. T., Jr (1987). Variability of the intracellular ionic environment of Escherichia coli. Differences between in vitro and in vivo effects of ion concentrations on protein-DNA interactions and gene expression. J. Biol. Chem. 262, 7157-7164.
39. Ruteshouser, E. C. & Richardson, J. P. (1989). Identification and characterization of transcription termination sites in the Escherichia coli lacZ gene. J. Mol. Biol. 208, 23-43.
40. Steinmetz, E. J., Brennan, C. A. & Platt, T. (1990). A short intervening structure can block rho factor helicase action at a distance. J. Biol. Chem. 265, 18408-18413.
41. Ts'o, P. O. P., Rapaport, S. A. & Bollum, F. J. (1966). A comparative study of polydeoxyribonucleotides and polyribonucleotides by optical rotary dispersion. Biochemistry, 5, 4153-4170.
42. Walstrom, K. M., Dozono, J. M., Robic, S. & von Hippel, P. H. (1997a). Kinetics of the RNA-DNA helicase activity of the Escherichia coli transcription termination factor rho. I. Characterization and analysis of the reaction. Biochemistry, 36, 7980-7992.
43. Walstrom, K. M., Dozono, J. M. & von Hippel, P. H. (1997b). Kinetics of the RNA-DNA helicase activity of the Escherichia coli transcription termination factor rho. II. Processivity, ATP consumption, and RNA binding. Biochemistry, 36, 7993-8004.
44. Yager, T. D. & von Hippel, P. H. (1987). Transcript elongation and termination in Escherichia coli. In E. coli and S. typhimurium: Cellular and Molecular Biology (Neidhardt, F. C., ed.), pp. 1241-1275, American Society of Microbiology, Washington, DC.
45. Yang, X. J. & Roberts, J. W. (1989). Gene Q antiterminator proteins of Escherichia coli phages 82 and lambda suppress pausing by RNA polymerase at a rho-dependent terminator and at other sites. Proc. Natl Acad. Sci. USA, 86, 5301-5305.
46. Zou, L. & Richardson, J. P. (1991). Enhancement of transcription termination factor rho activity with potassium glutamate. J. Biol. Chem. 266, 10201-10209.