Adebali O, Chiou YY, Hu J, et al. 2017 Genome-wide transcription-coupled repair in Escherichia coli is mediated by the Mfd translocase. Proc. Natl. Acad. Sci. USA 114 E2116–E2125

Article  CAS  PubMed  PubMed Central  Google Scholar 

Bharati BK, Gowder M, Zheng F, et al. 2022 Crucial role and mechanism of transcription-coupled DNA repair in bacteria. Nature 604 152–159

Article  CAS  PubMed  PubMed Central  Google Scholar 

Caron PR, Kushner SR and Grossman L 1985 Involvement of helicase II (uvrD gene product) and DNA polymerase I in excision mediated by the uvrABC protein complex. Proc. Natl. Acad. Sci. USA 82 4925–4929

Article  CAS  PubMed  PubMed Central  Google Scholar 

Case BC, Hartley S, Osuga M, et al. 2019 The ATPase mechanism of UvrA2 reveals the distinct roles of proximal and distal ATPase sites in nucleotide excision repair. Nucleic Acids Res. 47 4136–4152

Article  CAS  PubMed  PubMed Central  Google Scholar 

Chatterjee N and Walker GC 2017 Mechanisms of DNA damage, repair, and mutagenesis. Environ. Mol. Mutagen. 58 235–263

Article  CAS  PubMed  PubMed Central  Google Scholar 

Epshtein V, Kamarthapu V, McGary K, et al. 2014 UvrD facilitates DNA repair by pulling RNA polymerase backwards. Nature 505 372–377

Article  CAS  PubMed  PubMed Central  Google Scholar 

Friedberg E 2003 DNA damage and repair. Nature 421 436–440

Article  PubMed  Google Scholar 

Ghodke H, Ho HN and van Oijen AM 2020 Single-molecule live-cell imaging visualizes parallel pathways of prokaryotic nucleotide excision repair. Nat. Commun. 11 1477

Article  CAS  PubMed  PubMed Central  Google Scholar 

Hoeijmakers JH 2001 Genome maintenance mechanisms for preventing cancer. Nature 411 366–374

Article  CAS  PubMed  Google Scholar 

Hu J, Selby CP, Adar S, Adebali O and Sancar A 2017 Molecular mechanisms and genomic maps of DNA excision repair in Escherichia coli and humans. J. Biol. Chem. 292 15588–15597

Article  CAS  PubMed  PubMed Central  Google Scholar 

Husain I, van Houten B, Thomas DC, et al. 1985 Effect of DNA polymerase I and DNA helicase II on the turnover rate of UvrABC excision nuclease. Proc. Natl. Acad. Sci. USA 82 6774–6778

Article  CAS  PubMed  PubMed Central  Google Scholar 

Jaciuk M, Swuec P, Gaur V, et al. 2020 A combined structural and biochemical approach reveals translocation and stalling of UvrB on the DNA lesion as a mechanism of damage verification in bacterial nucleotide excision repair. DNA Repair 85 102746

Article  CAS  PubMed  Google Scholar 

Jain S, Gupta R and Sen R 2019 Rho-dependent transcription termination in bacteria recycles RNA polymerases stalled at DNA lesions. Nat. Commun. 10 1207

Article  PubMed  PubMed Central  Google Scholar 

Kad NM, Wang H, Kennedy GG, et al. 2010 Collaborative dynamic DNA scanning by nucleotide excision repair proteins investigated by single-molecule imaging of quantum-dot-labeled proteins. Mol. Cell 37 702–713

Article  CAS  PubMed  PubMed Central  Google Scholar 

Kamarthapu V, Epshtein V, Benjamin B, et al. 2016 ppGpp couples transcription to DNA repair in E. coli. Science 352 993–996

Article  CAS  PubMed  PubMed Central  Google Scholar 

Kang JY, Llewellyn E, Chen J, et al. 2021 Structural basis for transcription complex disruption by the Mfd translocase. eLife 10 e62117

Article  CAS  PubMed  PubMed Central  Google Scholar 

Kisker C, Kuper J and Van Houten B 2013 Prokaryotic nucleotide excision repair. Cold Spring Harb. Perspect. Biol. 5 a012591

Article  PubMed  PubMed Central  Google Scholar 

Kraithong T, Hartley S, Jeruzalmi D, et al. 2021 A peek inside the machines of bacterial nucleotide excision repair. Int. J. Mol. Sci. 22 952

Article  CAS  PubMed  PubMed Central  Google Scholar 

Kreuzer KN 2013 DNA damage responses in prokaryotes: regulating gene expression, modulating growth patterns, and manipulating replication forks. Cold Spring Harb. Perspect. Biol. 5 a012674

Article  PubMed  PubMed Central  Google Scholar 

Lee SJ, Sung RJ and Verdine GL 2019 Mechanism of DNA lesion homing and recognition by the Uvr nucleotide excision repair system. Research 2019 5641746

Article  PubMed  PubMed Central  Google Scholar 

Lindsey-Boltz LA and Sancar A 2021 The transcription-repair coupling factor Mfd prevents and promotes mutagenesis in a context-dependent manner. Front. Mol. Biosci. 8 668290

Article  CAS  PubMed  PubMed Central  Google Scholar 

Machius M, Henry L, Palnitkar M, et al. 1999 Crystal structure of the DNA nucleotide excision repair enzyme UvrB from Thermus thermophilus Proc. Natl. Acad. Sci. USA 96 11717–11722

Article  CAS  Google Scholar 

Martinez B, Bharati BK, Epshtein V, et al. 2022 Pervasive Transcription-coupled DNA repair in E. coli. Nat Commun. 13 1702

Article  CAS  PubMed  PubMed Central  Google Scholar 

Moolenaar GF, Franken KL, Dijkstra DM, et al. 1995 The C-terminal region of the UvrB protein of Escherichia coli contains an important determinant for UvrC binding to the preincision complex but not the catalytic site for 3’-incision. J. Biol. Chem. 270 30508–30515

Article  CAS  PubMed  Google Scholar 

Moolenaar GF, Moorman C and Goosen N 2000 Role of the Escherichia coli nucleotide excision repair proteins in DNA replication. J Bacteriol. 182 5706–5714

Article  CAS  PubMed  PubMed Central  Google Scholar 

Morita R, Nakane S, Shimada A, et al. 2010 Molecular mechanisms of the whole DNA repair system: a comparison of bacterial and eukaryotic systems. J. Nucleic Acids 14 179594

Google Scholar 

Myles GM, Hearst JE and Sancar A 1991 Site-specific mutagenesis of conserved residues within Walker A and B sequences of Escherichia coli UvrA protein. Biochemistry 30 3824–3834

Article  CAS  PubMed  Google Scholar 

Nakagawa N, Sugahara M, Masui R, et al. 1999 Crystal structure of Thermus thermophilus HB8 UvrB protein, a key enzyme of nucleotide excision repair. J. Biochem. 126 986–990

Article  CAS  PubMed  Google Scholar 

Pakotiprapha D, Liu Y, Verdine GL, et al. 2009 A structural model for the damage-sensing complex in bacterial nucleotide excision repair. J. Biol. Chem. 284 12837–12844

Article  CAS  PubMed  PubMed Central  Google Scholar 

Pakotiprapha D, Samuels M, Shen K, et al. 2012 Structure and mechanism of the UvrA-UvrB DNA damage sensor. Nat. Struct. Mol. Biol. 19 291–298

Article  CAS  PubMed  Google Scholar 

Paudel BP, Xu ZQ, Jergic S, et al. 2022 Mechanism of transcription modulation by the transcription-repair coupling factor. Nucleic Acids Res. 50 5688–5712

Article  CAS  PubMed  PubMed Central  Google Scholar 

Rossi F, Khanduja JS, Bortoluzzi A, et al. 2011 The biological and structural characterization of Mycobacterium tuberculosis UvrA provides novel insights into its mechanism of action. Nucleic Acids Res. 39 7316–7328

Article  CAS  PubMed  PubMed Central  Google Scholar 

Sale JE, Lehmann AR and Woodgate R 2012 Y-family DNA polymerases and their role in tolerance of cellular DNA damage. Nat. Rev. Mol. Cell Biol. 13 141–152

Article  CAS  PubMed  PubMed Central  Google Scholar 

Seck A, De Bonis S, Stelter M, et al. 2023 Structural and functional insights into the activation of the dual incision activity of UvrC, a key player in bacterial NER. Nucleic Acids Res. 51 2931–2949

Article  CAS  PubMed  PubMed Central  Google Scholar 

Selby CP 2017 Mfd protein and transcription-repair coupling in Escherichia coli. Photochem. Photobiol. 93 280–295

Article  CAS  PubMed  PubMed Central  Google Scholar 

Selby CP and Sancar A 1993 Molecular mechanism of transcription-repair coupling. Science