Controlling the motor activity of a transcription-repair coupling factor: Autoinhibition and the role of RNA polymerase

Nucleic Acids Research

Volumn 35, Issue 6, 2007, Pages 1802-1811

  Smith, Abigail J ^a   Szczelkun, Mark D ^a   Savery, Nigel J ^a  

^a UNIVERSITY OF BRISTOL   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ADENOSINE TRIPHOSPHATASE; ADENOSINE TRIPHOSPHATE; DNA; DOUBLE STRANDED DNA; HELICASE; MFD HELICASE; MOLECULAR MOTOR; NUCLEIC ACID; OLIGONUCLEOTIDE; RNA POLYMERASE; UNCLASSIFIED DRUG; BACTERIAL PROTEIN; DNA DIRECTED RNA POLYMERASE; TRANSCRIPTION ELONGATION FACTOR; TRANSCRIPTION FACTOR; TRANSCRIPTION REPAIR COUPLING FACTOR PROTEIN, BACTERA; TRIPLEX DNA;

ANIMAL CELL; ARTICLE; CARBOXY TERMINAL SEQUENCE; CONTROLLED STUDY; COUPLING FACTOR; DNA METABOLISM; ENZYME ACTIVITY; ESCHERICHIA COLI; GENE DELETION; GENE TRANSLOCATION; GENETIC TRANSCRIPTION; HYDROLYSIS; INHIBITION KINETICS; MACROMOLECULE; NONHUMAN; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN DOMAIN; PROTEIN FAMILY; PROTEIN TRANSPORT; CHEMICAL STRUCTURE; CHEMISTRY; GENETICS; HOMEOSTASIS; METABOLISM; PHYSIOLOGY; PROTEIN TERTIARY STRUCTURE; TRANSPORT AT THE CELLULAR LEVEL;

BACTERIA (MICROORGANISMS);

ADENOSINE TRIPHOSPHATASES; BACTERIAL PROTEINS; BIOLOGICAL TRANSPORT; DNA; DNA-DIRECTED RNA POLYMERASES; HOMEOSTASIS; MODELS, MOLECULAR; PROTEIN STRUCTURE, TERTIARY; SEQUENCE DELETION; TRANSCRIPTION FACTORS; TRANSCRIPTIONAL ELONGATION FACTORS;

EID: 34247859353     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkm019     Document Type: Article

References (33)

1. Gorbalenya,A.E. and Koonin,E.V. (1993) Helicases - amino-acid-sequence comparisons and structure-function-relationships. Curr. Opin. Struct. Biol., 3, 419-429.
2. Caruthers,J.M. and McKay,D.B. (2002) Helicase structure and mechanism. Curr. Opin. Struct. Biol., 12, 123-133.
3. Selby,C.P. and Sancar,A. (1993) Molecular mechanism of transcription-repair coupling. Science, 260, 53-58.
4. Tornaletti,S. and Hanawalt,P.C. (1999) Effect of DNA lesions on transcription elongation. Biochimie, 81, 139-146.
5. Scicchitano,D.A., Olesnicky,E.C. and Dimitri,A. (2004) Transcription and DNA adducts: What happens when the message gets cut off? DNA Repair 3, 1537-1548.
6. Saxowsky,T.T. and Doetsch,P.W. (2006) RNA polymerase encounters with DNA damage: Transcription-coupled repair or transcriptional mutagenesis? Chem. Rev., 106, 474-488.
7. Selby,C.P. and Sancar,A. (1990) Transcription preferentially inhibits nucleotide excision repair of the template DNA strand in vitro. J. Biol. Chem., 265, 21330-21336.
8. Mellon,I. and Hanawalt,P.C. (1989) Induction of the Escherichia coli lactose operon selectively increases repair of its transcribed DNA strand. Nature, 342, 95-98.
9. Mellon,I., Spivak,G. and Hanawalt,P.C. (1987) Selective removal of transcription-blocking DNA damage from the transcribed strand of the mammalian DHFR gene. Cell, 51, 241-249.
10. Zalieckas,J.M., Wray,L.V.,Jr, Ferson,A.E. and Fisher,S.H. (1998) Transcription-repair coupling factor is involved in carbon catabolite repression of the Bacillus subtilis hut and gnt operons. Mol. Microbiol., 27, 1031-1038.
11. Washburn,R.S., Wang,Y. and Gottesman,M.E. (2003) Role of E. coli transcription-repair coupling factor Mfd in Nun-mediated transcription termination. J. Mol. Biol., 329, 655-662.
12. Deaconescu,A.M., Chambers,A.L., Smith,A.J., Nickels,B.E., Hochschild,A., Savery,N.J. and Darst,S.A. (2006) Structural basis for bacterial transcription-coupled DNA repair. Cell, 124, 507-520.
13. Assenmacher,N., Wenig,K., Lammens,A. and Hopfner,K.P. (2006) Structural basis for transcription-coupled repair: The N terminus of Mfd resembles UvrB with degenerate ATPase motifs. J. Mol. Biol., 355, 675-683.
14. Selby,C.P. and Sancar,A. (1995) Structure and function of transcription-repair coupling factor. I. Structural domains and binding properties. J. Biol. Chem., 270, 4882-4889.
15. Park,J.S., Marr,M.T. and Roberts,J.W. (2002) E. coli transcription repair coupling factor (Mfd Protein) rescues arrested complexes by promoting forward translocation. Cell, 109, 757-767.
16. Mahdi,A.A., Briggs,G.S., Sharples,G.J., Wen,Q. and Lloyd,R.G. (2003) A model for dsDNA translocation revealed by a structural motif common to RecG and Mfd proteins. EMBO J., 22, 724-734.
17. Chambers,A.L., Smith,A.J. and Savery,N.J. (2003) A DNA translocation motif in the bacterial transcription-repair coupling factor, Mfd. Nucleic Acids Res., 31, 6409-6418.
18. Park,J.S. and Roberts,J.W. (2006) Role of DNA bubble rewinding in enzymatic transcription termination. Proc. Natl. Acad. Sci. U.S.A. 103, 4870-4875.
19. Briggs,G.S., Mahdi,A.A., Wen,Q. and Lloyd,R.G. (2005) DNA binding by the substrate specificity (wedge) domain of RecG helicase suggests a role in processivity. J. Biol. Chem., 280, 13921-13927.
20. Singleton,M.R., Scaife,S. and Wigley,D.B. (2001) Structural analysis of DNA replication fork reversal by RecG. Cell, 107, 79-89.
21. Smith,A.J. and Savery,N.J. (2005) RNA polymerase mutants defective in the initiation of transcription-coupled DNA repair. Nucleic Acids Res., 33, 755-764.
22. Kolb,A., Kotlarz,D., Kusano,S. and Ishihama,A. (1995) Selectivity of the Escherichia coli RNA polymerase E sigma 38 for overlapping promoters and ability to support CRP activation. Nucleic Acids Res. 23, 819-826.
23. Levin,J.R., Krummel,B. and Chamberlin,M.J. (1987) Isolation and properties of transcribing ternary complexes of Escherichia coli RNA polymerase positioned at a single template base. J. Mol. Biol. 196, 85-100.
24. Kiianitsa,K., Solinger,J.A. and Heyer,W.D. (2003) NADH-coupled microplate photometric assay for kinetic studies of ATP-hydrolyzing enzymes with low and high specific activities. Anal. Biochem., 321, 266-271.
25. Firman,K. and Szczelkun,M.D. (2000) Measuring motion on DNA by the type I restriction endonuclease EcoR124I using triplex displacement. EMBO J., 19, 2094-2102.
26. Krummel,B. and Chamberlin,M.J. (1992) Structural analysis of ternary complexes of Escherichia coli RNA polymerase. Individual complexes halted along different transcription units have distinct and unexpected biochemical properties. J. Mol. Biol., 225, 221-237.
27. Mahdi,A.A., McGlynn,P., Levett,S.D. and Lloyd,R.G. (1997) DNA binding and helicase domains of the Escherichia coli recombination protein RecG. Nucleic Acids Res., 25, 3875-3880.
28. Darst,S.A. (2001) Bacterial RNA polymerase. Curr. Opin. Struct. Biol. 11, 155-162.
29. Murakami,K.S. and Darst,S.A. (2003) Bacterial RNA polymerases: The whole story. Curr. Opin. Struct. Biol., 13, 31-39.
30. Komissarova,N. and Kashlev,M. (1997) RNA polymerase switches between inactivated and activated states by translocating back and forth along the DNA and the RNA. J. Biol. Chem., 272, 15329-15338.
31. Nudler,E., Mustaev,A., Lukhtanov,E. and Goldfarb,A. (1997) The RNA-DNA hybrid maintains the register of transcription by preventing backtracking of RNA polymerase. Cell, 89, 33-41.
32. Brendza,K.M., Cheng,W., Fischer,C.J., Chesnik,M.A., Niedziela-Majka,A. and Lohman,T.M. (2005) Autoinhibition of Escherichia coli Rep monomer helicase activity by its 2B subdomain. Proc. Natl. Acad. Sci. U.S.A., 102, 10076-10081.
33. Wang,H., DellaVecchia,M.J., Skorvaga,M., Croteau,D.L., Erie,D.A. and Van Houten,B. (2006) UvrB Domain 4, an autoinhibitory gate for regulation of DNA binding and ATPase activity. J. Biol. Chem., 281, 15227-15237.