Mechanochemistry of Transcription Termination Factor Rho

Molecular Cell

Volumn 22, Issue 5, 2006, Pages 611-621

  Adelman, Joshua L ^a   Jeong, Yong Joo ^c   Liao, Jung Chi ^a,b   Patel, Gayatri ^c   Kim, Dong Eun ^c   Oster, George ^a,b   Patel, Smita S ^c  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c RUTGERS ROBERT WOOD JOHNSON MEDICAL SCHOOL   (United States)

Author keywords

DNA

Indexed keywords

ADENOSINE TRIPHOSPHATASE; ARGININE; MUTANT PROTEIN; PHOSPHATE; PROTEIN SUBUNIT; TRANSCRIPTION TERMINATION FACTOR RHO;

ALGORITHM; ARTICLE; CATALYSIS; DATA ANALYSIS; ENZYME INHIBITION; HYDROLYSIS; RNA TRANSPORT; STEADY STATE; STRESS;

ADENOSINE TRIPHOSPHATE; ALGORITHMS; BINDING SITES; HYDROLYSIS; KINETICS; MODELS, MOLECULAR; MUTATION; NUCLEOTIDES; PHOSPHATES; PROTEIN CONFORMATION; PROTEIN SUBUNITS; RHO FACTOR; RNA; TERMINATOR REGIONS (GENETICS); TRANSCRIPTION, GENETIC; TRANSLOCATION, GENETIC;

EID: 33744529571     PISSN: 10972765     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.molcel.2006.04.022     Document Type: Article

References (42)

1. Browne R.J., and Stitt B.L. Active site occupancy required for catalytic cooperativity by Escherichia coli transcription termination factor Rho. J. Biol. Chem. 280 (2005) 13300-13303
2. Browne R.J., Barr E.W., and Stitt B.L. Catalytic cooperativity among subunits of Escherichia coli transcription termination factor Rho. Kinetics and substrate structural requirements. J. Biol. Chem. 280 (2005) 13292-13299
3. Brune M., Hunter J.L., Corrie J.E., and Webb M.R. Direct, real-time measurement of rapid inorganic phosphate release using a novel fluorescent probe and its application to actomyosin subfragment 1 ATPase. Biochemistry 33 (1994) 8262-8271
4. Bujalowski W., and Jezewska M.J. Kinetic mechanism of nucleotide cofactor binding to Escherichia coli replicative helicase DnaB protein. stopped-flow kinetic studies using fluorescent, ribose-, and base-modified nucleotide analogues. Biochemistry 39 (2000) 2106-2122
5. Burgess B.R., and Richardson J.P. RNA passes through the hole of the protein hexamer in the complex with the Escherichia coli Rho factor. J. Biol. Chem. 276 (2001) 4182-4189
6. Chen X., and Stitt B.L. The binding of C10 oligomers to Escherichia coli transcription termination factor Rho. J. Biol. Chem. 279 (2004) 16301-16310
7. DeLaBarre B., and Brunger A.T. Nucleotide dependent motion and mechanism of action of p97/VCP. J. Mol. Biol. 347 (2005) 437-452
8. Faus I., and Richardson J.P. Thermodynamic and enzymological characterization of the interaction between transcription termination factor rho and lambda cro mRNA. Biochemistry 28 (1989) 3510-3517
9. Finger L.R., and Richardson J.P. Procedure for purification of Escherichia coli ribonucleic acid synthesis termination protein rho. Biochemistry 20 (1981) 1640-1645
10. Fisher A.J., Smith C.A., Thoden J.B., Smith R., Sutoh K., Holden H.M., and Rayment I. X-ray structures of the myosin motor domain of Dictyostelium discoideum complexed with MgADP.BeFx and MgADP.AlF4. Biochemistry 34 (1995) 8960-8972
11. Gai D., Zhao R., Li D., Finkielstein C.V., and Chen X.S. Mechanisms of conformational change for a replicative hexameric helicase of SV40 large tumor antigen. Cell 119 (2004) 47-60
12. Geiselmann J., and von Hippel P.H. Functional interactions of ligand cofactors with Escherichia coli transcription termination factor rho. I. Binding of ATP. Protein Sci. 1 (1992) 850-860
13. Geiselmann J., Seifried S.E., Yager T.D., Liang C., and von Hippel P.H. Physical properties of the Escherichia coli transcription termination factor rho. 2. Quaternary structure of the rho hexamer. Biochemistry 31 (1992) 121-132
14. Geiselmann J., Yager T.D., Gill S.C., Calmettes P., and von Hippel P.H. Physical properties of the Escherichia coli transcription termination factor rho. 1. Association states and geometry of the rho hexamer. Biochemistry 31 (1992) 111-121
15. Geiselmann J., Wang Y., Seifried S.E., and von Hippel P.H. A physical model for the translocation and helicase activities of Escherichia coli transcription termination protein Rho. Proc. Natl. Acad. Sci. USA 90 (1993) 7754-7758
16. Hingorani M.M., and Patel S.S. Cooperative interactions of nucleotide ligands are linked to oligomerization and DNA binding in bacteriophage T7 gene 4 helicases. Biochemistry 35 (1996) 2218-2228
17. Hinnerwisch J., Fenton W.A., Furtak K.J., Farr G.W., and Horwich A.L. Loops in the central channel of ClpA chaperone mediate protein binding, unfolding, and translocation. Cell 121 (2005) 1029-1041
18. Jeong Y.J., Kim D.E., and Patel S.S. Kinetic pathway of dTTP hydrolysis by hexameric T7 helicase-primase in the absence of DNA. J. Biol. Chem. 277 (2002) 43778-43784
19. Jeong Y.J., Kim D.E., and Patel S.S. Nucleotide binding induces conformational changes in Escherichia coli transcription termination factor Rho. J. Biol. Chem. 279 (2004) 18370-18376
20. Jezewska M.J., Lucius A.L., and Bujalowski W. Binding of six nucleotide cofactors to the hexameric helicase RepA protein of plasmid RSF1010. 1. Direct evidence of cooperative interactions between the nucleotide-binding sites of a hexameric helicase. Biochemistry 44 (2005) 3865-3876
21. Jezewska M.J., Lucius A.L., and Bujalowski W. Binding of six nucleotide cofactors to the hexameric helicase RepA protein of plasmid RSF1010. 2. Base specificity, nucleotide structure, magnesium, and salt effect on the cooperative binding of the cofactors. Biochemistry 44 (2005) 3877-3890
22. Kim D.E., and Patel S.S. The mechanism of ATP hydrolysis at the noncatalytic sites of the transcription termination factor Rho. J. Biol. Chem. 274 (1999) 32667-32671
23. Kim D.E., and Patel S.S. The kinetic pathway of RNA binding to the Escherichia coli transcription termination factor Rho. J. Biol. Chem. 276 (2001) 13902-13910
24. Kim D.E., Shigesada K., and Patel S.S. Transcription termination factor Rho contains three noncatalytic nucleotide binding sites. J. Biol. Chem. 274 (1999) 11623-11628
25. Liao J.C., Jeong Y.J., Kim D.E., Patel S.S., and Oster G. Mechanochemistry of t7 DNA helicase. J. Mol. Biol. 350 (2005) 452-475
26. Mancini E.J., Kainov D.E., Grimes J.M., Tuma R., Bamford D.H., and Stuart D.I. Atomic snapshots of an RNA packaging motor reveal conformational changes linking ATP hydrolysis to RNA translocation. Cell 118 (2004) 743-755
27. Miwa Y., Horiguchi T., and Shigesada K. Structural and functional dissections of transcription termination factor rho by random mutagenesis. J. Mol. Biol. 254 (1995) 815-837
28. Oster G., and Wang H. Reverse engineering a protein: the mechanochemistry of ATP synthase. Biochim. Biophys. Acta 1458 (2000) 482-510
29. Ponomarev M.A., Timofeev V.P., and Levitsky D.I. The difference between ADP-beryllium fluoride and ADP-aluminium fluoride complexes of the spin-labeled myosin subfragment 1. FEBS Lett. 371 (1995) 261-263
30. Rajendran S., Jezewska M.J., and Bujalowski W. Multiple-step kinetic mechanism of DNA-independent ATP binding and hydrolysis by Escherichia coli replicative helicase DnaB protein: quantitative analysis using the rapid quench-flow method. J. Mol. Biol. 303 (2000) 773-795
31. Richardson J.P. Activation of rho protein ATPase requires simultaneous interaction at two kinds of nucleic acid-binding sites. J. Biol. Chem. 257 (1982) 5760-5766
32. Richardson J.P., and Ruteshouser E.C. rho factor-dependent transcription termination. Interference by a mutant rho. J. Mol. Biol. 189 (1986) 413-419
33. Skordalakes E., and Berger J.M. Structure of the Rho transcription terminator: mechanism of mRNA recognition and helicase loading. Cell 114 (2003) 135-146
34. Stitt B.L. Escherichia coli transcription termination protein rho has three hydrolytic sites for ATP. J. Biol. Chem. 263 (1988) 11130-11137
35. Stitt B.L. Escherichia coli transcription termination factor Rho binds and hydrolyzes ATP using a single class of three sites. Biochemistry 40 (2001) 2276-2281
36. Stitt B.L., and Xu Y. Sequential hydrolysis of ATP molecules bound in interacting catalytic sites of Escherichia coli transcription termination protein Rho. J. Biol. Chem. 273 (1998) 26477-26486
37. Wei R.R., and Richardson J.P. Identification of an RNA-binding Site in the ATP binding domain of Escherichia coli Rho by H2O2/Fe-EDTA cleavage protection studies. J. Biol. Chem. 276 (2001) 28380-28387
38. Wei R.R., and Richardson J.P. Mutational changes of conserved residues in the Q-loop region of transcription factor Rho greatly reduce secondary site RNA-binding. J. Mol. Biol. 314 (2001) 1007-1015
39. Xu Y., Kohn H., and Widger W.R. Mutations in the rho transcription termination factor that affect RNA tracking. J. Biol. Chem. 277 (2002) 30023-30030
40. Xu Y., Johnson J., Kohn H., and Widger W.R. ATP binding to Rho transcription termination factor. Mutant F355W ATP-induced fluorescence quenching reveals dynamic ATP binding. J. Biol. Chem. 278 (2003) 13719-13727
41. Ye J., Osborne A.R., Groll M., and Rapoport T.A. RecA-like motor ATPases-lessons from structures. Biochim. Biophys. Acta 1659 (2004) 1-18
42. Yu X., Hingorani M.M., Patel S.S., and Egelman E.H. DNA is bound within the central hole to one or two of the six subunits of the T7 DNA helicase. Nat. Struct. Biol. 3 (1996) 740-743