Prokaryotic Nucleotide Excision Repair

Kisker, C.; Kuper, J.; Van Houten, B.

doi:10.1101/cshperspect.a012591

Cited by 192DNA Repair MechanismsBacterial Genetics and BiotechnologyDNA and Nucleic Acid Chemistry

Prokaryotic Nucleotide Excision Repair

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Kisker, C., Kuper, J., Van Houten, B.·2013·Cold Spring Harbor Perspectives in Biology

DOI 10.1101/cshperspect.a012591PMC PMC3578354

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Abstract

Nucleotide excision repair (NER) has allowed bacteria to flourish in many different niches around the globe that inflict harsh environmental damage to their genetic material. NER is remarkable because of its diverse substrate repertoire, which differs greatly in chemical composition and structure. Recent advances in structural biology and single-molecule studies have given great insight into the structure and function of NER components. This ensemble of proteins orchestrates faithful removal of toxic DNA lesions through a multistep process. The damaged nucleotide is recognized by dynamic probing of the DNA structure that is then verified and marked for dual incisions followed by excision of the damage and surrounding nucleotides. The opposite DNA strand serves as a template for repair, which is completed after resynthesis and ligation.

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A 12-13 nt long damage-containing fragment is released (16 nt in the case of Cho protein).
“Finally, 12–13 nt. long damage containing fragment is released (16 nt in the case of Cho protein).”
From Focus on UV-Induced DNA Damage and Repair—Disease Relevance and Protective Strategies (2020) · cites this paper as [90]
TRCF allows removal of RNA polymerase from the damaged site and subsequent UvrABC-mediated repair.
“TRCF allows for the removal of RNA polymerase from the damaged site and subsequent UvrABC-mediated repair.”
From Focus on UV-Induced DNA Damage and Repair—Disease Relevance and Protective Strategies (2020) · cites this paper as [90]
Transcription-coupled repair is induced mainly by stalling of RNA polymerase at sites of damage.
“The transcription-coupled repair is induced mainly by the stalling of RNA polymerase at the sites of damage.”
From Focus on UV-Induced DNA Damage and Repair—Disease Relevance and Protective Strategies (2020) · cites this paper as [90]
In prokaryotes, DNA damage is detected by a dimer of UvrA working together with UvrB.
“In prokaryotes, DNA damage is detected by dimer of UvrABC system protein (UvrA) working together with UvrB.”
From Focus on UV-Induced DNA Damage and Repair—Disease Relevance and Protective Strategies (2020) · cites this paper as [90]
UvrC acts as an endonuclease that nicks DNA 7-8 nucleotides from the 5′-end and 4-5 nucleotides from the 3′-end of the damaged site.
“UvrC acts as an endonuclease that nicks the DNA 7-8 nucleotides from 5′-end and 4–5 nucleotides from the 3′-end of the damaged site.”
From Focus on UV-Induced DNA Damage and Repair—Disease Relevance and Protective Strategies (2020) · cites this paper as [90]

UvrA dimer dissociates from the complex, leaving UvrB bound to DNA waiting for UvrC engagement.
“In the next step, the UvrA dimer dissociates form the complex, leaving UvrB bound to the DNA waiting for UvrC engagement in the repair process.”
From Focus on UV-Induced DNA Damage and Repair—Disease Relevance and Protective Strategies (2020) · cites this paper as [90]
DNA polymerase I and DNA ligase restore the proper DNA sequence.
“The DNA polymerase I (Pol 1) and DNA ligase restores the proper DNA sequence [90,91,92].”
From Focus on UV-Induced DNA Damage and Repair—Disease Relevance and Protective Strategies (2020) · cites this paper as [90]
The 3′-incision precedes the 5′-incision for both Cho and UvrC-mediated repair.
“The 3′-incision precedes the 5′-incision for both Cho and UvrC-mediated repair.”
From Focus on UV-Induced DNA Damage and Repair—Disease Relevance and Protective Strategies (2020) · cites this paper as [90]
Detection can also be carried out by transcriptional-repair coupling factor (TRCF, also known as Mfd).
“The detection step can also be carried out by transcriptional-repair coupling factor (TRCF, also known as Mfd).”
From Focus on UV-Induced DNA Damage and Repair—Disease Relevance and Protective Strategies (2020) · cites this paper as [90]
UvrA dimer is the key complex for damage recognition that scans DNA; UvrB catalyzes local dissociation of the DNA helix and provides a scaffold for UvrC.
“The UvrA dimer is the key complex for the damage recognition that scans DNA in the search of damage, while UvrB catalyzes the local dissociation of the DNA helix and provides a scaffold for UvrC protein.”
From Focus on UV-Induced DNA Damage and Repair—Disease Relevance and Protective Strategies (2020) · cites this paper as [90]
UvrC homolog Cho may be incorporated; Cho cleaves DNA 4 nucleotides farther away than the normal cleavage site on the 3′ side of the lesion.
“Alternatively, UvrC homolog excinuclease (Cho) may be incorporated in the DNA process; however, this nuclease cleaves DNA molecule 4 nucleotides farther away than the normal cleavage site on the 3′ side of the lesion.”
From Focus on UV-Induced DNA Damage and Repair—Disease Relevance and Protective Strategies (2020) · cites this paper as [90]
UvrD protein acts as a helicase that removes hydrogen bonds between complementary nucleotides.
“In this process, the UvrD protein acts as a helicase that removes hydrogen bonds between the complementary nucleotides.”
From Focus on UV-Induced DNA Damage and Repair—Disease Relevance and Protective Strategies (2020) · cites this paper as [90]

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Solution structure and DNA‐binding properties of the C‐terminal domain of UvrC from E.coli
Singh, S., Folkers, G. E., Bonvin, A. M. J. J., Boelens, R., Wechselberger, R. W., Niztayev, A., & Kaptein, R. (2002) · The EMBO Journal · doi:10.1093/emboj/cdf627 · Cited by 51 · see citing works
Characterization of the Escherichia coliDamage-independent UvrBC Endonuclease Activity
Moolenaar, G. F., Bazuine, M., van Knippenberg, I. C., Visse, R., & Goosen, N. (1998) · Journal of Biological Chemistry · doi:10.1074/jbc.273.52.34896 · Cited by 50 · see citing works
DNA wrapping is required for DNA damage recognition in the Escherichia coli DNA nucleotide excision repair pathway
Wang, H., Lü, M., Tang, M., Houten, B. V., Ross, J. B. A., Weinfeld, M., & Le, X. C. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0902281106 · Cited by 50 · see citing works
Differential Nucleotide Excision Repair Susceptibility of Bulky DNA Adducts in Different Sequence Contexts: Hierarchies of Recognition Signals
Cai, Y., Patel, D. J., Geacintov, N. E., & Broyde, S. B. (2008) · Journal of Molecular Biology · doi:10.1016/j.jmb.2008.09.087 · Cited by 48 · see citing works
Crystal structure of Escherichia coli UvrB C‐terminal domain, and a model for UvrB‐UvrC interaction
Sohi, M. K., Alexandrovich, A., Moolenaar, G. F., Visse, R., Goosen, N., Vernède, X., Fontecilla-Camps, J. C., Champness, J. N., & Sanderson, M. R. (2000) · FEBS Letters · doi:10.1016/s0014-5793(99)01690-7 · Cited by 48 · see citing works
Probing for DNA damage with β-hairpins: Similarities in incision efficiencies of bulky DNA adducts by prokaryotic and human nucleotide excision repair systems in vitro
Liu, Y., Reeves, D. A., Kropachev, K. Y., Cai, Y., Ding, S., Kolbanovskiy, M., Kolbanovskiy, A., Bolton, J. L., Broyde, S. B., Houten, B. V., et al. (2011) · DNA repair · doi:10.1016/j.dnarep.2011.04.020 · Cited by 47 · see citing works
Dynamics of the UvrABC Nucleotide Excision Repair Proteins Analyzed by Fluorescence Resonance Energy Transfer
Malta, E., Moolenaar, G. F., & Goosen, N. (2007) · Biochemistry · doi:10.1021/bi7002235 · Cited by 47 · see citing works
Base Flipping in Nucleotide Excision Repair
Malta, E., Moolenaar, G. F., & Goosen, N. (2005) · Journal of Biological Chemistry · doi:10.1074/jbc.m508901200 · Cited by 47 · see citing works
Structural and Mutational Analyses of Deinococcus radiodurans UvrA2 Provide Insight into DNA Binding and Damage Recognition by UvrAs
Timmins, J., Gordon, E. J., Caria, S., Leonard, G. A., Acajjaoui, S., Kuo, M.-S., Monchois, V., & McSweeney, S. M. (2009) · Structure · doi:10.1016/j.str.2009.02.008 · Cited by 46 · see citing works
UvrB Domain 4, an Autoinhibitory Gate for Regulation of DNA Binding and ATPase Activity
Wang, H., DellaVecchia, M. J., Škorvaga, M., Croteau, D. L., Erie, D. A., & Houten, B. V. (2006) · Journal of Biological Chemistry · doi:10.1074/jbc.m601476200 · Cited by 46 · see citing works
DNA Tandem Lesion Repair by Strand Displacement Synthesis and Nucleotide Excision Repair
Imoto, S., Bransfield, L. A., Croteau, D. L., Houten, B. V., & Greenberg, M. M. (2008) · Biochemistry · doi:10.1021/bi7021427 · Cited by 45 · see citing works
The Role of ATP Binding and Hydrolysis by UvrB during Nucleotide Excision Repair
Moolenaar, G. F., Herron, M. F. P., Monaco, V., van der MAREL, G. A., van Boom, J. H., Visse, R., & Goosen, N. (2000) · Journal of Biological Chemistry · doi:10.1074/jbc.275.11.8044 · Cited by 44 · see citing works
A cut above: Discovery of an alternative excision repair pathway in bacteria
Van Houten, B., Eisen, J. A., & Hanawalt, P. C. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.062062599 · Cited by 44 · see citing works
Identification of Residues within UvrB That Are Important for Efficient DNA Binding and Damage Processing
Škorvaga, M., DellaVecchia, M. J., Croteau, D. L., Theis, K. W., Truglio, J. J., Mandavilli, B. S., Kisker, C., & Houten, B. V. (2004) · Journal of Biological Chemistry · doi:10.1074/jbc.m409266200 · Cited by 43 · see citing works
Self-citation
Nucleotide excision repair (NER) machinery recruitment by the transcription-repair coupling factor involves unmasking of a conserved intramolecular interface
Deaconescu, A. M., Sevostyanova, A., Artsimovitch, I., & Grigorieff, N. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1115105109 · Cited by 43 · see citing works
The C-terminal region of Escherichia coli UvrC contributes to the flexibility of the UvrABC nucleotide excision repair system
Verhoeven, E. E. A. (2002) · Nucleic Acids Research · doi:10.1093/nar/30.11.2492 · Cited by 39 · see citing works
Damage detection by the UvrABC pathway: Crystal structure of UvrB bound to fluorescein‐adducted DNA
Waters, T. R., Eryilmaz, J., Geddes, S., & Barrett, T. E. (2006) · FEBS Letters · doi:10.1016/j.febslet.2006.10.051 · Cited by 38 · see citing works
Sequence Context- and Temperature-Dependent Nucleotide Excision Repair of a Benzo[a]pyrene Diol Epoxide-Guanine DNA Adduct Catalyzed by Thermophilic UvrABC Proteins
Ruan, Q., Liu, T., Kolbanovskiy, A., Liu, Y., Ren, J., Škorvaga, M., Zou, Y., Lader, J. M., Malkani, B., Amin, S., et al. (2007) · Biochemistry · doi:10.1021/bi700294k · Cited by 38 · see citing works
Cooperative damage recognition by UvrA and UvrB: Identification of UvrA residues that mediate DNA binding
Croteau, D. L., DellaVecchia, M. J., Perera, L., & Houten, B. V. (2008) · DNA repair · doi:10.1016/j.dnarep.2007.11.013 · Cited by 38 · see citing works
A Point Mutation in Escherichia coli DNA Helicase II Renders the Enzyme Nonfunctional in Two DNA Repair Pathways
Brosh, R. M., & Matson, S. W. (1997) · Journal of Biological Chemistry · doi:10.1074/jbc.272.1.572 · Cited by 38 · see citing works
Stimulation of UvrD Helicase by UvrAB
Atkinson, J., Guy, C. P., Cadman, C. J., Moolenaar, G. F., Goosen, N., & McGlynn, P. (2009) · Journal of Biological Chemistry · doi:10.1074/jbc.m808030200 · Cited by 37 · see citing works
Genetic Analysis of Repair and Damage Tolerance Mechanisms for DNA-Protein Cross-Links in Escherichia coli
Salem, A. M. H., Nakano, T., Takuwa, M., Matoba, N., Tsuboi, T., Terato, H., Yamamoto, K., Yamada, M., Nohmi, T., & Ide, H. (2009) · Journal of Bacteriology · doi:10.1128/jb.00417-09 · Cited by 36 · see citing works
An N-terminal clamp restrains the motor domains of the bacterial transcription-repair coupling factor Mfd
Murphy, M. N., Gong, P., Ralto, K. M., Manelytė, L., Savery, N. J., & Theis, K. W. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkp680 · Cited by 34 · see citing works
Structural Basis for Transcription-coupled Repair: the N Terminus of Mfd Resembles UvrB with Degenerate ATPase Motifs
Aßenmacher, N., Wenig, K., Lammens, A., & Hopfner, K. (2005) · Journal of Molecular Biology · doi:10.1016/j.jmb.2005.10.033 · Cited by 33 · see citing works
Structural Insights into the Cryptic DNA-dependent ATPase Activity of UvrB
Eryilmaz, J., Ceschini, S., Ryan, J., Geddes, S., Waters, T. R., & Barrett, T. E. (2006) · Journal of Molecular Biology · doi:10.1016/j.jmb.2005.12.059 · Cited by 32 · see citing works
A mutational study of the C-terminal zinc-finger motif of the Escherichia coli UvrA protein.
Wang, J., Mueller, K. L., & Grossman, L. I. (1994) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(17)34126-1 · Cited by 29 · see citing works
Binding of the UvrB dimer to non-damaged and damaged DNA: Residues Y92 and Y93 influence the stability of both subunits
Moolenaar, G. F., Schut, M. H., & Goosen, N. (2005) · DNA repair · doi:10.1016/j.dnarep.2005.03.001 · Cited by 28 · see citing works
Effects of the bacterial transcription-repair coupling factor during transcription of DNA containing non-bulky lesions
SMITH, A., & Savery, N. J. (2008) · DNA repair · doi:10.1016/j.dnarep.2008.06.020 · Cited by 27 · see citing works
A Physical Interaction of UvrD with Nucleotide Excision Repair Protein UvrB
Ahn, B. (2000) · Molecules and Cells · doi:10.1007/s10059-000-0592-5 · Cited by 27 · see citing works
The first zinc-binding domain of UvrA is not essential for UvrABC-mediated DNA excision repair
Visse, R., de Ruijter, M., Ubbink, M., Brandsma, J. A., & van de Putte, P. (1993) · Mutation Research/DNA Repair · doi:10.1016/0921-8777(93)90009-6 · Cited by 25 · see citing works
DNA Damage Recognition of Mutated Forms of UvrB Proteins in Nucleotide Excision Repair
Zou, Y., Ma, H., Minko, I. G., Shell, S. M., Yang, Z., Qu, Y., Xu, Y., Geacintov, N. E., & Lloyd, R. S. (2004) · Biochemistry · doi:10.1021/bi035992a · Cited by 25 · see citing works
NMR analysis of [methyl-13C]methionine UvrB from Bacillus caldotenax reveals UvrB–domain 4 heterodimer formation in solution
DellaVecchia, M. J., Merritt, W. K., Ye, P., Kirby, T. W., DeRose, E. F., Mueller, G. A., Houten, B. V., & London, R. E. (2007) · Journal of Molecular Biology · doi:10.1016/j.jmb.2007.07.045 · Cited by 24 · see citing works
Exploring Damage Recognition Models in Prokaryotic Nucleotide Excision Repair with a Benzo[a]pyrene-Derived Lesion in UvrB
Jia, L., Kropachev, K. Y., Ding, S., Houten, B. V., Geacintov, N. E., & Broyde, S. B. (2009) · Biochemistry · doi:10.1021/bi9010072 · Cited by 23 · see citing works
Prokaryotic Nucleotide Excision Repair: The UvrABC System
Truglio, J. J., Croteau, D. L., Houten, B. V., & Kisker, C. (2006) · ChemInform · doi:10.1002/chin.200620265 · Cited by 23 · see citing works
Self-citation
Functions of base flipping in E. coli nucleotide excision repair
Malta, E., VERHAGEN, C., Moolenaar, G. F., Filippov, D. V., VANDERMAREL, G., & Goosen, N. (2008) · DNA repair · doi:10.1016/j.dnarep.2008.06.011 · Cited by 22 · see citing works
New discoveries linking transcription to DNA repair and damage tolerance pathways
Cohen, S., & Walker, G. C. (2011) · Transcription · doi:10.4161/trns.2.1.14228 · Cited by 22 · see citing works
Crystal structure of the UvrB dimer: insights into the nature and functioning of the UvrAB damage engagement and UvrB–DNA complexes
Webster, M. P. J., Jukes, R., Zamfir, V. S., Kay, C. W. M., Bagnéris, C., & Barrett, T. E. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks633 · Cited by 22 · see citing works
Oligomerization of the UvrB Nucleotide Excision Repair Protein of Escherichia coli
Hildebrand, E. L., & Grossman, L. I. (1999) · Journal of Biological Chemistry · doi:10.1074/jbc.274.39.27885 · Cited by 21 · see citing works
Solution Structure, Hydrodynamics and Thermodynamics of the UvrB C-terminal Domain
Alexandrovich, A., Czisch, M., Frenkiel, T. A., Kelly, G. P., Goosen, N., Moolenaar, G. F., Chowdhry, B. Z., Sanderson, M. R., & Lane, A. N. (2001) · Journal of Biomolecular Structure and Dynamics · doi:10.1080/07391102.2001.10506734 · Cited by 21 · see citing works
Scanning the DNA for damage by the nucleotide excision repair machinery
Goosen, N. (2010) · DNA repair · doi:10.1016/j.dnarep.2010.02.015 · Cited by 20 · see citing works
Direct Restart of a Replication Fork Stalled by a Head-On RNA Polymerase
Pomerantz, R. T., & O’Donnell, M. E. (2010) · Journal of Visualized Experiments · doi:10.3791/1919 · Cited by 11 · see citing works
Direct Restart of a Replication Fork Stalled by a Head-On RNA Polymerase
Pomerantz, R. T., & O’Donnell, M. E. (2010) · Journal of Visualized Experiments · doi:10.3791/1919-v · Cited by 11 · see citing works
The Origin And Early Evolution Of Life On Earth
Oró, J. (1990) · Annual Review of Earth and Planetary Sciences · doi:10.1146/annurev.earth.18.1.317 · Cited by 10 · see citing works
Activity of nucleotide excision repair enzymes for oxanine cross-link lesions
Nakano, T., Katafuchi, A., Terato, H., Suzuki, T., Houten, B. V., & Ide, H. (2005) · Nucleic Acids Symposium Series · doi:10.1093/nass/49.1.293 · Cited by 8 · see citing works
Prioritizing the repair of DNA damage that is encountered by RNA polymerase
Savery, N. J. (2011) · Transcription · doi:10.4161/trns.2.4.16146 · Cited by 8 · see citing works
Flow Linear Dichroism and Electron Microscopic Analysis of Protein-DNA Complexes of a Mutant UvrB Protein that Binds to but cannot Kink DNA
Hsu, D. S., Takahashi, M., Delagoutte, E., Bertrand-Burggraf, E., Wang, Y.-H., Nordén, B., Fuchs, R. P., Griffith, J. D., & Sancar, A. (1994) · Journal of Molecular Biology · doi:10.1006/jmbi.1994.1541 · Cited by 8 · see citing works
Variations on the ABC
Lebbink, J. H. G., & Sixma, T. K. (2005) · Structure · doi:10.1016/j.str.2005.03.003 · Cited by 7 · see citing works
Escherichia coli DNA photolyase stimulates uvrABC excision nuclease in vitro.
Franklin, K. A., Sancar, A., & Sancar, G. B. (2020) · Carolina Digital Repository (University of North Carolina at Chapel Hill) · doi:10.17615/fnzt-9z98 · Cited by 7 · see citing works
DNA Damage and Transcription Elongation: Consequences and RNA Integrity
Dreij, K., Burns, J. A., Dimitri, A., Nirenstein, L., Noujnykh, T., & Scicchitano, D. A. (2010) · Wiley eBooks · doi:10.1002/9783527630110.ch17 · Cited by 5 · see citing works
The (A)BC excinuclease of Escherichia coli has only the UvrB and UvrC subunits in the incision complex.
Orren, D. K., & Sancar, A. (2020) · Carolina Digital Repository (University of North Carolina at Chapel Hill) · doi:10.17615/2gq0-n988 · Cited by 5 · see citing works
Structure and Function of the UvrB Protein
Kim, S. T., Hsu, D. S., Sancar, A., et al. (2021) · Carolina Digital Repository (University of North Carolina at Chapel Hill) · doi:10.17615/5xew-n212 · Cited by 3 · see citing works
Active site of (A) BC excinuclease. I. Evidence for 5'incision by UvrC through a catalytic site involving Asp399, Asp438, Asp466, and His538 residues.
Lin, J.-J., & Sancar, A. (2021) · Carolina Digital Repository (University of North Carolina at Chapel Hill) · doi:10.17615/xst9-sh33 · Cited by 3 · see citing works
A Physical Interaction of UvrD with Nucleotide Excision Repair Protein UvrB
Ahn, B. (2000) · Molecules and Cells · doi:10.1007/s100590000017 · Cited by 2 · see citing works
CRYSTAL STRUCTURE OF THE DNA NUCLEOTIDE EXCISION REPAIR ENZYME UVRB FROM THERMUS THERMOPHILUS
Machius, M., Henry, L., Palnitkar, M., & Deisenhofer, J. (1999) · Worldwide Protein Data Bank · doi:10.2210/pdb1c4o/pdb · Cited by 1 · see citing works

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Nucleotide Excision Repair in EukaryotesPreprint
Schärer, O. D. (2013) · Cold Spring Harbor Perspectives in Biology · doi:10.1101/cshperspect.a012609 · Cited by 801 · see citing works
Microbial response to acid stress: mechanisms and applications
Guan, N., & Liu, L. (2019) · Applied Microbiology and Biotechnology · doi:10.1007/s00253-019-10226-1 · Cited by 667 · see citing works
Bacterial defences: mechanisms, evolution and antimicrobial resistance
Smith, W. P. J., Wucher, B. R., Nadell, C. D., & Foster, K. R. (2023) · Nature Reviews Microbiology · doi:10.1038/s41579-023-00877-3 · Cited by 404 · see citing works
Uracil‐DNA glycosylases—Structural and functional perspectives on an essential family of DNA repair enzymes
Schormann, N., Ricciardi, R. P., & Chattopadhyay, D. (2014) · Protein Science · doi:10.1002/pro.2554 · Cited by 203 · see citing works
Direct observation of structure-function relationship in a nucleic acid–processing enzyme
Comstock, M., Whitley, K. D., Jia, H., Sokoloski, J. E., Lohman, T. M., Ha, T., & Chemla, Y. R. (2015) · Science · doi:10.1126/science.aaa0130 · Cited by 177 · see citing works
Focus on UV-Induced DNA Damage and Repair—Disease Relevance and Protective Strategies
Kciuk, M., Marciniak, B., Mojzych, M., & Kontek, R. (2020) · International Journal of Molecular Sciences · doi:10.3390/ijms21197264 · Cited by 168 · see citing works
Distinctive Genome Reduction Rates Revealed by Genomic Analyses of TwoCoxiella-Like Endosymbionts in Ticks
Gottlieb, Y., Lalzar, I., & Klasson, L. (2015) · Genome Biology and Evolution · doi:10.1093/gbe/evv108 · Cited by 161 · see citing works
Vibrio natriegens : an ultrafast‐growing marine bacterium as emerging synthetic biology chassis
Hoff, J., Daniel, B. B. J., Stukenberg, D., Thuronyi, B. W., Waldminghaus, T., & Fritz, G. (2020) · Environmental Microbiology · doi:10.1111/1462-2920.15128 · Cited by 132 · see citing works
ADP-ribosylation of DNA and RNA
Groslambert, J., Prokhorova, E. A., & Ahel, I. (2021) · DNA repair · doi:10.1016/j.dnarep.2021.103144 · Cited by 112 · see citing works
Single-molecule imaging of UvrA and UvrB recruitment to DNA lesions in living Escherichia coli
Stracy, M., Jaciuk, M., Uphoff, S., Kapanidis, A. N., Nowotny, M., Sherratt, D. J., & Zawadzki, P. (2016) · Nature Communications · doi:10.1038/ncomms12568 · Cited by 95 · see citing works
Xer Site Specific Recombination: Double and Single Recombinase Systems
Martinez, F. A. C., Benmohamed, A., & Szatmari, G. B. (2017) · Frontiers in Microbiology · doi:10.3389/fmicb.2017.00453 · Cited by 87 · see citing works
An underlying mechanism for the increased mutagenesis of lagging-strand genes in Bacillus subtilis
Million‐Weaver, S., Samadpour, A. N., Moreno-Habel, D. A., Nugent, P., Brittnacher, M., Weiss, E. J., Hayden, H. S., Miller, S. I., Liachko, I., & Merrikh, H. (2015) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1416651112 · Cited by 82 · see citing works
Degradation and deactivation of a plasmid-encoded extracellular antibiotic resistance gene during separate and combined exposures to UV254 and radicals
Nihemaiti, M., Yoon, Y., He, H., Dodd, M. C., Croué, J., & Lee, Y. (2020) · Water Research · doi:10.1016/j.watres.2020.115921 · Cited by 83 · see citing works
Redox Chemistry in the Genome: Emergence of the [4Fe4S] Cofactor in Repair and Replication
Barton, J. K., Silva, R. M. B., & O’Brien, E. (2019) · Annual Review of Biochemistry · doi:10.1146/annurev-biochem-013118-110644 · Cited by 81 · see citing works
The BER necessities: the repair of DNA damage in human-adapted bacterial pathogens
van der Veen, S., & Tang, C. M. (2015) · Nature Reviews Microbiology · doi:10.1038/nrmicro3391 · Cited by 80 · see citing works
Structural basis for the recognition of diastereomeric 5′,8-cyclo-2′-deoxypurine lesions by the human nucleotide excision repair system
Kropachev, K. Y., Ding, S., Terzidis, M. A., Masi, A., Liu, Z., Cai, Y., Kolbanovskiy, M., Chatgilialoglu, C., Broyde, S. B., Geacintov, N. E., et al. (2014) · Nucleic Acids Research · doi:10.1093/nar/gku162 · Cited by 76 · see citing works
Crucial role and mechanism of transcription-coupled DNA repair in bacteria
Bharati, B. K., Gowder, M., Zheng, F., Alzoubi, K., Svetlov, V. V., Kamarthapu, V., Weaver, J. W., Epshtein, V., Vasilyev, N., Shen, L., et al. (2022) · Nature · doi:10.1038/s41586-022-04530-6 · Cited by 69 · see citing works
Dr. NO and Mr. Toxic – the versatile role of nitric oxide
Porrini, C., Ramarao, N., & Tran, S. (2019) · Biological Chemistry · doi:10.1515/hsz-2019-0368 · Cited by 70 · see citing works
Transcription-coupled repair: An update
Spivak, G. (2016) · Archives of Toxicology · doi:10.1007/s00204-016-1820-x · Cited by 65 · see citing works
Structural basis of DNA lesion recognition for eukaryotic transcription-coupled nucleotide excision repair
Wang, W., Xu, J., Chong, J. P. C., & Wang, D. (2018) · DNA repair · doi:10.1016/j.dnarep.2018.08.006 · Cited by 64 · see citing works
Oxidative stress drives mutagenesis through transcription-coupled repair in bacteria
Carvajal-Garcia, J., Samadpour, A. N., Viera, A. J. H., & Merrikh, H. (2023) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2300761120 · Cited by 63 · see citing works
Repair-Resistant DNA Lesions
Geacintov, N. E., & Broyde, S. B. (2017) · Chemical Research in Toxicology · doi:10.1021/acs.chemrestox.7b00128 · Cited by 63 · see citing works
Elimination of transforming activity and gene degradation during UV and UV/H 2 O 2 treatment of plasmid-encoded antibiotic resistance genes
Yoon, Y., Dodd, M. C., & Lee, Y. (2018) · Environmental Science Water Research & Technology · doi:10.1039/c8ew00200b · Cited by 62 · see citing works
Mfd Protein and Transcription–Repair Coupling in Escherichia coli
Selby, C. P. (2016) · Photochemistry and Photobiology · doi:10.1111/php.12675 · Cited by 62 · see citing works
Photochemistry and Photobiology of the Spore Photoproduct: A 50‐Year Journey
Setlow, P., & Li, L. (2015) · Photochemistry and Photobiology · doi:10.1111/php.12506 · Cited by 59 · see citing works
The transcription-repair coupling factor Mfd associates with RNA polymerase in the absence of exogenous damage
Ho, H. N., van Oijen, A. M., & Ghodke, H. B. (2018) · Nature Communications · doi:10.1038/s41467-018-03790-z · Cited by 59 · see citing works
Bacterial IAA-Delivery into Medicago Root Nodules Triggers a Balanced Stimulation of C and N Metabolism Leading to a Biomass Increase
Defez, R., Andreozzi, A., Romano, S., Pòcsfalvi, G., Fiume, I., Esposito, R., Angelini, C., & Bianco, C. (2019) · Microorganisms · doi:10.3390/microorganisms7100403 · Cited by 58 · see citing works
A Decade of Biochemical and Structural Studies of the DNA Repair Machinery of Deinococcus radiodurans : Major Findings, Functional and Mechanistic Insight and Challenges
Timmins, J., & Moe, E. (2016) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2016.04.001 · Cited by 57 · see citing works
The complex choreography of transcription-coupled repair
Spivak, G., & Ganesan, A. K. (2014) · DNA Repair · doi:10.1016/j.dnarep.2014.03.025 · Cited by 51 · see citing works
Reprograming the Replisome of a Semisynthetic Organism for the Expansion of the Genetic Alphabet
Ledbetter, M. P., Karadeema, R. J., & Romesberg, F. E. (2018) · Journal of the American Chemical Society · doi:10.1021/jacs.7b11488 · Cited by 53 · see citing works
DNA ADP-Ribosylation Stalls Replication and Is Reversed by RecF-Mediated Homologous Recombination and Nucleotide Excision Repair
Lawarée, E., Jankevicius, G., Cooper, C., Ahel, I., Uphoff, S., & Tang, C. M. (2020) · Cell Reports · doi:10.1016/j.celrep.2020.01.014 · Cited by 50 · see citing works
Application of UVC and UVC based advanced disinfection technologies for the inactivation of antibiotic resistance genes and elimination of horizontal gene transfer activities: Opportunities and challenges
Ghosh, S., Chen, Y., & Hu, J. (2022) · Chemical Engineering Journal · doi:10.1016/j.cej.2022.138234 · Cited by 52 · see citing works
Mechanisms of stationary-phase mutagenesis in bacteria: mutational processes in pseudomonads
Kivisaar, M. (2010) · FEMS Microbiology Letters · doi:10.1111/j.1574-6968.2010.02027.x · Cited by 52 · see citing works
An RNA Repair Operon Regulated by Damaged tRNAs
Hughes, K. J., Chen, X., Burroughs, A. M., Aravind, L., & Wolin, S. L. (2020) · Cell Reports · doi:10.1016/j.celrep.2020.108527 · Cited by 51 · see citing works
Degradation and deactivation of plasmid-encoded antibiotic resistance genes during exposure to ozone and chlorine
Yoon, Y., He, H., Dodd, M. C., & Lee, Y. (2021) · Water Research · doi:10.1016/j.watres.2021.117408 · Cited by 51 · see citing works
TFIIH: A multi-subunit complex at the cross-roads of transcription and DNA repair
Kolesnikova, O., Radu, L., & Poterszman, A. (2019) · Advances in protein chemistry and structural biology · doi:10.1016/bs.apcsb.2019.01.003 · Cited by 50 · see citing works
Stalled transcription complexes promote DNA repair at a distance
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Authors: Kisker, C., Kuper, J., & Van Houten, B.
Affiliations: University of Würzburg (DE)
ORCID: Kisker, C.
Kuper, J.
Venue: Cold Spring Harbor Perspectives in Biology
Publisher: Cold Spring Harbor Laboratory
Published: 2013-03-01
Volume: 5
Issue: 3
Pages: a012591-a012591
ISSN: 1943-0264 (ISSN-L)
DOI: 10.1101/cshperspect.a012591
PMC: PMC3578354
OpenAlex: W2078446890
Cited by: 192
References: 122
Citations by year: 2026: 14 · 2025: 8 · 2024: 4 · 2023: 14 · 2022: 18 · 2021: 20 · 2020: 19 · 2019: 18 · 2018: 14 · 2017: 16 · 2016: 20 · 2015: 11 · 2014: 11 · 2013: 4
Type: posted content
Language: en
Open access: bronze
doi.org
Locations: Cold Spring Harbor Perspectives in Biology (publishedVersion)
Europe PMC (PubMed Central) (publishedVersion)
PubMed Central (publishedVersion)
PubMed (publishedVersion)
Funders: National Institutes of Health
National Institute of Environmental Health Sciences (R01ES019566)
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA Repair Mechanisms
Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Bacterial Genetics and Biotechnology
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA and Nucleic Acid Chemistry
Keywords: nucleotide excision repair, prokaryotes, DNA damage, DNA damage recognition, DNA repair proteins, DNA damage tolerance, single-molecule analysis, structural biology
MeSH terms: DNA Damage, DNA Repair, Endodeoxyribonucleases, Models, Molecular, Nucleotides, Prokaryotic Cells, Protein Conformation, Transcription, Genetic, Escherichia coli Proteins, Multiprotein Complexes

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Prokaryotic Nucleotide Excision Repair

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