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Volumn 38, Issue 22, 2010, Pages 8357-8369

Structural basis for the bacterial transcription-repair coupling factor/RNA polymerase interaction

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL PROTEIN; PROTEIN CARD; REGULATOR PROTEIN; RNA POLYMERASE; TRANSCRIPTION REPAIR COUPLING FACTOR; UNCLASSIFIED DRUG;

EID: 78650415624     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkq692     Document Type: Article
Times cited : (57)

References (46)
  • 1
    • 0021905437 scopus 로고
    • DNA repair in an active gene: Removal of pyrimidine dimers from the DHFR gene of CHO cells is much more efficient than in the genome overall
    • Bohr, V.A., Smith, C.A., Okumoto, D.S. and Hanawalt, P.C. (1985) DNA repair in an active gene: removal of pyrimidine dimers from the DHFR gene of CHO cells is much more efficient than in the genome overall. Cell, 40, 359-369.
    • (1985) Cell , vol.40 , pp. 359-369
    • Bohr, V.A.1    Smith, C.A.2    Okumoto, D.S.3    Hanawalt, P.C.4
  • 2
    • 0024426244 scopus 로고
    • Induction of the Escherichia coli lactose operon selectively increases repair of its transcribed DNA strand
    • 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.
    • (1989) Nature , vol.342 , pp. 95-98
    • Mellon, I.1    Hanawalt, P.C.2
  • 3
    • 0025610725 scopus 로고
    • Transcription preferentially inhibits nucleotide excision repair of the template DNA strand in vitro
    • 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.
    • (1990) J. Biol. Chem. , vol.265 , pp. 21330-21336
    • Selby, C.P.1    Sancar, A.2
  • 4
    • 84961002510 scopus 로고
    • Time, temperature, and protein synthesis: A study of ultraviolet-induced mutation in bacteria
    • Witkin, E.M. (1956) Time, temperature, and protein synthesis: a study of ultraviolet-induced mutation in bacteria. Cold Spring Harbor Symp. Quant. Biol., 21, 123-140.
    • (1956) Cold Spring Harbor Symp. Quant. Biol. , vol.21 , pp. 123-140
    • Witkin, E.M.1
  • 5
    • 0014004977 scopus 로고
    • Radiation-induced mutations and their repair
    • Witkin, E.M. (1966) Radiation-induced mutations and their repair. Science, 152, 1345-1353.
    • (1966) Science , vol.152 , pp. 1345-1353
    • Witkin, E.M.1
  • 6
    • 0027905034 scopus 로고
    • Molecular mechanism of transcription-repair coupling
    • Selby, C.P. and Sancar, A. (1993) Molecular mechanism of transcription-repair coupling. Science, 260, 53-58.
    • (1993) Science , vol.260 , pp. 53-58
    • Selby, C.P.1    Sancar, A.2
  • 7
    • 0026354699 scopus 로고
    • Escherichia coli mfd mutant deficient in "mutation frequency decline" lacks strand-specific repair: In vitro complementation with purified coupling factor
    • Selby, C.P., Witkin, E.M. and Sancar, A. (1991) Escherichia coli mfd mutant deficient in "mutation frequency decline" lacks strand-specific repair: in vitro complementation with purified coupling factor. Proc. Natl Acad. Sci. USA, 88, 11574-11578.
    • (1991) Proc. Natl Acad. Sci. USA , vol.88 , pp. 11574-11578
    • Selby, C.P.1    Witkin, E.M.2    Sancar, A.3
  • 9
    • 67649730094 scopus 로고    scopus 로고
    • A structural model for the damage-sensing complex in bacterial nucleotide excision repair
    • Pakotiprapha, D., Liu, Y., Verdine, G.L. and Jeruzalmi, D. (2009) A structural model for the damage-sensing complex in bacterial nucleotide excision repair. J. Biol. Chem., 284, 12837-12844.
    • (2009) J. Biol. Chem. , vol.284 , pp. 12837-12844
    • Pakotiprapha, D.1    Liu, Y.2    Verdine, G.L.3    Jeruzalmi, D.4
  • 10
    • 0028969976 scopus 로고
    • Structure and function of transcription-repair coupling factor. I. Structural domains and binding properties
    • 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.
    • (1995) J. Biol. Chem. , vol.270 , pp. 4882-4889
    • Selby, C.P.1    Sancar, A.2
  • 11
    • 0024344173 scopus 로고
    • Two related superfamilies of putative helicases involved in replication, recombination, repair and expression of DNA and RNA genomes
    • Gorbalenya, A.E., Koonin, E.V., Domchenko, A.P. and Blinov, V.M. (1989) Two related superfamilies of putative helicases involved in replication, recombination, repair and expression of DNA and RNA genomes. Nucleic Acids Res., 17, 4713-4729.
    • (1989) Nucleic Acids Res. , vol.17 , pp. 4713-4729
    • Gorbalenya, A.E.1    Koonin, E.V.2    Domchenko, A.P.3    Blinov, V.M.4
  • 12
    • 70350643700 scopus 로고    scopus 로고
    • An N-terminal clamp restrains the motor domains of the bacterial transcription-repair coupling factor Mfd
    • Murphy, M.N., Gong, P., Ralto, K., Manelyte, L., Savery, N.J. and Theis, K. (2009) An N-terminal clamp restrains the motor domains of the bacterial transcription-repair coupling factor Mfd. Nucleic Acids Res., 37, 6042-6053.
    • (2009) Nucleic Acids Res. , vol.37 , pp. 6042-6053
    • Murphy, M.N.1    Gong, P.2    Ralto, K.3    Manelyte, L.4    Savery, N.J.5    Theis, K.6
  • 13
    • 34247859353 scopus 로고    scopus 로고
    • Controlling the motor activity of a transcription-repair coupling factor: Autoinhibition and the role of RNA polymerase
    • Smith, A.G., Szczelkun, M.D. and Savery, N.J. (2007) Controlling the motor activity of a transcription-repair coupling factor: autoinhibition and the role of RNA polymerase. Nucleic Acids Res., 35, 1802-1811.
    • (2007) Nucleic Acids Res. , vol.35 , pp. 1802-1811
    • Smith, A.G.1    Szczelkun, M.D.2    Savery, N.J.3
  • 14
    • 13844317928 scopus 로고    scopus 로고
    • RNA polymerase mutants defective in the initiation of transcription-coupled DNA repair
    • 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.
    • (2005) Nucleic Acids Res. , vol.33 , pp. 755-764
    • Smith, A.J.1    Savery, N.J.2
  • 15
    • 33645514260 scopus 로고    scopus 로고
    • Role of DNA bubble rewinding in enzymatic transcription termination
    • Park, J.S. and Roberts, J.W. (2006) Role of DNA bubble rewinding in enzymatic transcription termination. Proc. Natl. Acad. Sci. USA, 103, 4870-4875.
    • (2006) Proc. Natl. Acad. Sci. USA , vol.103 , pp. 4870-4875
    • Park, J.S.1    Roberts, J.W.2
  • 16
    • 0037077154 scopus 로고    scopus 로고
    • E. coli transcription repair coupling factor (Mfd protein) rescues arrested complexes by promoting forward translocation
    • 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.
    • (2002) Cell , vol.109 , pp. 757-767
    • Park, J.-S.1    Marr, M.T.2    Roberts, J.W.3
  • 17
    • 0037610124 scopus 로고    scopus 로고
    • The Stigmatella aurantiaca homolog of Myxococcus xanthus high-mobility-group A-type transcription factor CarD: Insights into the functional modules of CarD and their distribution in bacteria
    • Cayuela, M.L., Elias-Arnanz, M., Penalver-Mellado, M., Padmanabhan, S. and Murillo, F.J. (2003) The Stigmatella aurantiaca homolog of Myxococcus xanthus high-mobility-group A-type transcription factor CarD: insights into the functional modules of CarD and their distribution in bacteria. J. Bacteriol., 185, 3527-3537.
    • (2003) J. Bacteriol. , vol.185 , pp. 3527-3537
    • Cayuela, M.L.1    Elias-Arnanz, M.2    Penalver-Mellado, M.3    Padmanabhan, S.4    Murillo, F.J.5
  • 18
    • 77955144096 scopus 로고    scopus 로고
    • CdnL, a member of the large CarD-like family of bacterial proteins, is vital for Myxococcus xanthus and differs functionally from the global transcriptional regulator CarD
    • Garcia-Moreno, D., Abellon-Ruiz, J., Garcia-Heras, F., Murillo, F.J., Padmanabhan, S. and Elias-Arnanz, M. (2010) CdnL, a member of the large CarD-like family of bacterial proteins, is vital for Myxococcus xanthus and differs functionally from the global transcriptional regulator CarD. Nucleic Acids Res., 38, 4586-4598.
    • (2010) Nucleic Acids Res. , vol.38 , pp. 4586-4598
    • Garcia-Moreno, D.1    Abellon-Ruiz, J.2    Garcia-Heras, F.3    Murillo, F.J.4    Padmanabhan, S.5    Elias-Arnanz, M.6
  • 19
    • 67649660560 scopus 로고    scopus 로고
    • CarD is an essential regulator of rRNA transcription required for Mycobacterium tuberculosis persistence
    • Stallings, C.L., Stphanou, N.C., Chu, L., Hochschild, A., Nickels, B.E. and Glickman, M.S. (2009) CarD is an essential regulator of rRNA transcription required for Mycobacterium tuberculosis persistence. Cell, 138, 149-159.
    • (2009) Cell , vol.138 , pp. 149-159
    • Stallings, C.L.1    Stphanou, N.C.2    Chu, L.3    Hochschild, A.4    Nickels, B.E.5    Glickman, M.S.6
  • 20
    • 0030986177 scopus 로고    scopus 로고
    • Cross-validated maximum likelihood enhances crystallographic simulated annealing refinement
    • Adams, P.D., Pannu, N.S., Read, R.J. and Brunger, A.T. (1997) Cross-validated maximum likelihood enhances crystallographic simulated annealing refinement. Proc. Natl Acad. Sci. USA, 94, 5018-5023.
    • (1997) Proc. Natl Acad. Sci. USA , vol.94 , pp. 5018-5023
    • Adams, P.D.1    Pannu, N.S.2    Read, R.J.3    Brunger, A.T.4
  • 21
    • 24044475924 scopus 로고    scopus 로고
    • Phase translation function revisited: Structure solution of the cofilin-homology domain from yeast actin-binding protein 1 using six-dimensional searches
    • Strokopytov, B.V., Fedorov, A., Mahoney, N.M., Kessels, M., Drubin, D.G. and Almo, S.C. (2005) Phase translation function revisited: structure solution of the cofilin-homology domain from yeast actin-binding protein 1 using six-dimensional searches. Acta Crystallogr. D Biol. Crystallogr., 61, 285-293.
    • (2005) Acta Crystallogr. D Biol. Crystallogr. , vol.61 , pp. 285-293
    • Strokopytov, B.V.1    Fedorov, A.2    Mahoney, N.M.3    Kessels, M.4    Drubin, D.G.5    Almo, S.C.6
  • 23
    • 0030907304 scopus 로고    scopus 로고
    • Activation of prokaryotic transcription through arbitrary protein-protein contacts
    • Dove, S.L., Joung, K. and Hochschild, A. (1997) Activation of prokaryotic transcription through arbitrary protein-protein contacts. Nature, 386, 627-630.
    • (1997) Nature , vol.386 , pp. 627-630
    • Dove, S.L.1    Joung, K.2    Hochschild, A.3
  • 24
    • 1542346163 scopus 로고    scopus 로고
    • High-throughput beta-galactosidase assay for bacterial cell-based reporter systems
    • Thibodeau, S.A., Fang, R. and Joung, J.K. (2004) High-throughput beta-galactosidase assay for bacterial cell-based reporter systems. Biotechniques, 36, 410-415.
    • (2004) Biotechniques , vol.36 , pp. 410-415
    • Thibodeau, S.A.1    Fang, R.2    Joung, J.K.3
  • 25
    • 73649093377 scopus 로고    scopus 로고
    • Molecular evolution of multi-subunit RNA polymerases: Structural analysis
    • Lane, W.J. and Darst, S.A. (2009) Molecular evolution of multi-subunit RNA polymerases: structural analysis. J. Mol. Biol., 395, 686-704.
    • (2009) J. Mol. Biol. , vol.395 , pp. 686-704
    • Lane, W.J.1    Darst, S.A.2
  • 26
    • 0033578701 scopus 로고    scopus 로고
    • Crystal structure of Thermus aquaticus core RNA polymerase at 3.3 A resolution
    • Zhang, G., Campbell, E.A., Minakhin, L., Richter, C., Severinov, K. and Darst, S.A. (1999) Crystal structure of Thermus aquaticus core RNA polymerase at 3.3 A resolution. Cell, 98, 811-824.
    • (1999) Cell , vol.98 , pp. 811-824
    • Zhang, G.1    Campbell, E.A.2    Minakhin, L.3    Richter, C.4    Severinov, K.5    Darst, S.A.6
  • 27
    • 0034733377 scopus 로고    scopus 로고
    • F, contacting multiple conserved regions of the s factor
    • F, contacting multiple conserved regions of the s factor. J. Mol. Biol., 300, 17-28.
    • (2000) J. Mol. Biol. , vol.300 , pp. 17-28
    • Campbell, E.A.1    Darst, S.A.2
  • 28
  • 29
    • 0346325753 scopus 로고    scopus 로고
    • Kinetics of multisubunit RNA polymerases: Experimental methods and data analysis
    • Holmes, S.F., Foster, J.E. and Erie, D.A. (2003) Kinetics of multisubunit RNA polymerases: experimental methods and data analysis. Methods Enzymol., 371, 71-81.
    • (2003) Methods Enzymol. , vol.371 , pp. 71-81
    • Holmes, S.F.1    Foster, J.E.2    Erie, D.A.3
  • 30
    • 34447499995 scopus 로고    scopus 로고
    • Structural basis for transcription elongation by bacterial RNA polymerase
    • DOI 10.1038/nature05932, PII NATURE05932
    • Vassylyev, D.G., Vassylyeva, M.N., Perederina, A., Tahirov, T.H. and Artsimovitch, I. (2007) Structural basis for transcription elongation by bacterial RNA polymerase. Nature, 448, 157-162. (Pubitemid 47067370)
    • (2007) Nature , vol.448 , Issue.7150 , pp. 157-162
    • Vassylyev, D.G.1    Vassylyeva, M.N.2    Perederina, A.3    Tahirov, T.H.4    Artsimovitch, I.5
  • 31
    • 0034691146 scopus 로고    scopus 로고
    • Pausing by bacterial RNA polymerase is mediated by mechanistically distinct classes of signals
    • Artsimovitch, I. and Landick, R. (2000) Pausing by bacterial RNA polymerase is mediated by mechanistically distinct classes of signals. Proc. Natl Acad. Sci. USA, 97, 7090-7095.
    • (2000) Proc. Natl Acad. Sci. USA , vol.97 , pp. 7090-7095
    • Artsimovitch, I.1    Landick, R.2
  • 32
    • 0035957687 scopus 로고    scopus 로고
    • Allosteric control of RNA polymerase by a site that contacts nascent RNA hairpins
    • Toulokhonov, I., Artsimovitch, I. and Landick, R. (2001) Allosteric control of RNA polymerase by a site that contacts nascent RNA hairpins. Science, 292, 730-733.
    • (2001) Science , vol.292 , pp. 730-733
    • Toulokhonov, I.1    Artsimovitch, I.2    Landick, R.3
  • 34
    • 0037123659 scopus 로고    scopus 로고
    • Structural basis of transcription initiation: RNA polymerase holoenzyme at 4 A resolution
    • DOI 10.1126/science.1069594
    • Murakami, K., Masuda, S. and Darst, S.A. (2002) Structural basis of transcription initiation: RNA polymerase holoenzyme at 4 A resolution. Science, 296, 1280-1284. (Pubitemid 34522777)
    • (2002) Science , vol.296 , Issue.5571 , pp. 1280-1284
    • Murakami, K.S.1    Masuda, S.2    Darst, S.A.3
  • 35
    • 0037071844 scopus 로고    scopus 로고
    • Crystal structure of a bacterial RNA polymerase holoenzyme at 2.6. A resolution
    • DOI 10.1038/nature752
    • Vassylyev, D.G., Sekine, S., Laptenko, O., Lee, J., Vassylyeva, M.N., Borukhov, S. and Yokoyama, S. (2002) Crystal structure of a bacterial RNA polymerase holoenzyme at 2.6 A resolution. Nature, 417, 712-719. (Pubitemid 34640620)
    • (2002) Nature , vol.417 , Issue.6890 , pp. 712-719
    • Vassylyev, D.G.1    Sekine, S.-I.2    Laptenko, O.3    Lee, J.4    Vassylyeva, M.N.5    Borukhov, S.6    Yokoyama, S.7
  • 37
    • 10644220255 scopus 로고    scopus 로고
    • The bacteriophage T4 late-transcription coactivator gp33 binds the flap domain of Escherichia coli RNA polymerase
    • Nechaev, S., Kamali-Moghaddam, M., Andre, E., Leonetti, J.-P. and Geiduschek, E.P. (2004) The bacteriophage T4 late-transcription coactivator gp33 binds the flap domain of Escherichia coli RNA polymerase. Proc. Natl Acad. Sci. USA, 101, 17365-17370.
    • (2004) Proc. Natl Acad. Sci. USA , vol.101 , pp. 17365-17370
    • Nechaev, S.1    Kamali-Moghaddam, M.2    Andre, E.3    Leonetti, J.-P.4    Geiduschek, E.P.5
  • 38
    • 55749096593 scopus 로고    scopus 로고
    • The bacteriophage lambda Q antiterminator protein contacts the eta-flap domain of RNA polymerase
    • Deighan, P., Diez, C.M., Leibman, M., Hochschild, A. and Nickels, B.E. (2008) The bacteriophage lambda Q antiterminator protein contacts the eta-flap domain of RNA polymerase. Proc. Natl Acad. Sci. USA, 105, 15305-15310.
    • (2008) Proc. Natl Acad. Sci. USA , vol.105 , pp. 15305-15310
    • Deighan, P.1    Diez, C.M.2    Leibman, M.3    Hochschild, A.4    Nickels, B.E.5
  • 39
    • 0346243938 scopus 로고    scopus 로고
    • Transcript cleavage factors GreA and GreB act as transient catalytic components of RNA polymerase
    • Laptenko, O., Lee, J., Lomakin, I. and Borukhov, S. (2003) Transcript cleavage factors GreA and GreB act as transient catalytic components of RNA polymerase. EMBO J., 23, 6322-6334.
    • (2003) EMBO J. , vol.23 , pp. 6322-6334
    • Laptenko, O.1    Lee, J.2    Lomakin, I.3    Borukhov, S.4
  • 40
    • 0043244877 scopus 로고    scopus 로고
    • Structure and function of the transcription elongation factor GreB bound to bacterial RNA polymerase
    • Opalka, N., Chlenov, M., Chacon, P., Rice, W.J., Wriggers, W. and Darst, S.A. (2003) Structure and function of the transcription elongation factor GreB bound to bacterial RNA polymerase. Cell, 114, 335-345.
    • (2003) Cell , vol.114 , pp. 335-345
    • Opalka, N.1    Chlenov, M.2    Chacon, P.3    Rice, W.J.4    Wriggers, W.5    Darst, S.A.6
  • 42
    • 4043135220 scopus 로고    scopus 로고
    • Regulation of RNA polymerase through the secondary channel
    • Nickels, B.E. and Hochschild, A. (2004) Regulation of RNA polymerase through the secondary channel. Cell, 118, 281-284.
    • (2004) Cell , vol.118 , pp. 281-284
    • Nickels, B.E.1    Hochschild, A.2
  • 43
    • 4043108470 scopus 로고    scopus 로고
    • Regulation through the secondary channel - Structural framework for ppGpp-DksA synergism during transcription
    • Perederina, A., Svetlov, V., Vassylyeva, M., Tahirov, T., Yokoyama, S., Artsimovitch, I. and Vassylyev, D. (2004) Regulation through the secondary channel - structural framework for ppGpp-DksA synergism during transcription. Cell, 118, 297-309.
    • (2004) Cell , vol.118 , pp. 297-309
    • Perederina, A.1    Svetlov, V.2    Vassylyeva, M.3    Tahirov, T.4    Yokoyama, S.5    Artsimovitch, I.6    Vassylyev, D.7
  • 44
    • 38949110771 scopus 로고    scopus 로고
    • The elongation factor RfaH and the initiation factor s bind to the same site on the transcription elongation complex
    • Sevostyanova, A., Svetlov, V., Vassylyev, D.G. and Artsimovitch, I. (2008) The elongation factor RfaH and the initiation factor s bind to the same site on the transcription elongation complex. Proc. Natl Acad. Sci. USA, 105, 865-870.
    • (2008) Proc. Natl Acad. Sci. USA , vol.105 , pp. 865-870
    • Sevostyanova, A.1    Svetlov, V.2    Vassylyev, D.G.3    Artsimovitch, I.4
  • 45
    • 57349097787 scopus 로고    scopus 로고
    • Genetic assays to define and characterize protein-protein interactions involved in gene regulation
    • Nickels, B.E. (2009) Genetic assays to define and characterize protein-protein interactions involved in gene regulation. Methods, 47, 53-62.
    • (2009) Methods , vol.47 , pp. 53-62
    • Nickels, B.E.1
  • 46
    • 0000243829 scopus 로고
    • PROCHECK - A program to check the stereochemical quality of protein structures
    • Laskowski, R.A., MacArthur, M.W., Moss, D.S. and Thornton, J.M. (1993) PROCHECK - a program to check the stereochemical quality of protein structures. J. appl. Crystallogr., 26, 283-291.
    • (1993) J. Appl. Crystallogr. , vol.26 , pp. 283-291
    • Laskowski, R.A.1    MacArthur, M.W.2    Moss, D.S.3    Thornton, J.M.4


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