Zeman, M. K. & Cimprich, K. A. Causes and consequences of replication stress. Nat. Cell Biol. 16, 2–9 (2014).
Gaillard, H., García-Muse, T. & Aguilera, A. Replication stress and cancer. Nat. Rev. Cancer 15, 276–289 (2015).
Tubbs, A. & Nussenzweig, A. Endogenous DNA damage as a source of genomic instability in cancer. Cell 168, 644–656 (2017).
Srivatsan, A., Tehranchi, A., MacAlpine, D. M. & Wang, J. D. Co-orientation of replication and transcription preserves genome integrity. PLoS Genet. 6, e1000810 (2010).
Tehranchi, A. K. et al. The transcription factor DksA prevents conflicts between DNA replication and transcription machinery. Cell 141, 595–605 (2010).
Dutta, D., Shatalin, K., Epshtein, V., Gottesman, M. E. & Nudler, E. Linking RNA polymerase backtracking to genome instability in E. coli. Cell 146, 533–543 (2011).
Wahba, L., Amon, J. D., Koshland, D. & Vuica-Ross, M. RNase H and multiple RNA biogenesis factors cooperate to prevent RNA: DNA hybrids from generating genome instability. Mol. Cell 44, 978–988 (2011).
Wimberly, H. et al. R-loops and nicks initiate DNA breakage and genome instability in non-growing Escherichia coli. Nat. Commun. 4, 2115 (2013).
Hamperl, S., Bocek, M. J., Saldivar, J. C., Swigut, T. & Cimprich, K. A. Transcription–replication conflict orientation modulates R-loop levels and activates distinct DNA damage responses. Cell 170, 774–786.e719 (2017).
Lang, K. S. et al. Replication–transcription conflicts generate R-loops that orchestrate bacterial stress survival and pathogenesis. Cell 170, 787–799.e718 (2017).
Konforti, B. & Davis, R. DNA substrate requirements for stable joint molecule formation by the RecA and single-stranded DNA-binding proteins of Escherichia coli. J. Biol. Chem. 266, 10112–10121 (1991).
Razavy, H., Szigety, S. K. & Rosenberg, S. M. Evidence for both 3′ and 5′ single-strand DNA ends in intermediates in Chi-stimulated recombination in vivo. Genetics 142, 333–339 (1996).
Adams, P. P. et al. Regulatory roles of Escherichia coli 5′ UTR and ORF-internal RNAs detected by 3′ end mapping. eLife 10, e62438 (2021).
Ju, X., Li, D. & Liu, S. Full-length RNA profiling reveals pervasive bidirectional transcription terminators in bacteria. Nat. Microbiol. 4, 1907–1918 (2019).
Hou, Y., Song, H., Croteau, D. L., Akbari, M. & Bohr, V. A. Genome instability in Alzheimer disease. Mech. Ageing Dev. 161, 83–94 (2017).
Vermeij, W. et al. Restricted diet delays accelerated ageing and genomic stress in DNA-repair-deficient mice. Nature 537, 427–431 (2016).
Xia, J. et al. Bacteria-to-human protein networks reveal origins of endogenous DNA damage. Cell 176, 127–143.e124 (2019).
Seigneur, M., Bidnenko, V., Ehrlich, S. D. & Michel, B. RuvAB acts at arrested replication forks. Cell 95, 419–430 (1998).
Neelsen, K. J. & Lopes, M. Replication fork reversal in eukaryotes: from dead end to dynamic response. Nat. Rev. Mol. Cell Biol. 16, 207–220 (2015).
Rupp, W. D. & Howard-Flanders, P. Discontinuities in the DNA synthesized in an excision-defective strain of Escherichia coli following ultraviolet irradiation. J. Mol. Biol. 31, 291–304 (1968).
Sogo, J. M., Lopes, M. & Foiani, M. Fork reversal and ssDNA accumulation at stalled replication forks owing to checkpoint defects. Science 297, 599–602 (2002).
Yeeles, J. T. & Marians, K. J. The Escherichia coli replisome is inherently DNA damage tolerant. Science 334, 235–238 (2011).
Xia, J. et al. Holliday junction trap shows how cells use recombination and a junction-guardian role of RecQ helicase. Sci. Adv. 2, e1601605 (2016).
Pennington, J. M. & Rosenberg, S. M. Spontaneous DNA breakage in single living Escherichia coli cells. Nat. Genet. 39, 797–802 (2007).
Paull, T. T. et al. A critical role for histone H2AX in recruitment of repair factors to nuclear foci after DNA damage. Curr. Biol. 10, 886–895 (2000).
Britton, S., Coates, J. & Jackson, S. P. A new method for high-resolution imaging of Ku foci to decipher mechanisms of DNA double-strand break repair. J. Cell Biol. 202, 579–595 (2013).
Shee, C. et al. Engineered proteins detect spontaneous DNA breakage in human and bacterial cells. eLife 2, e01222 (2013).
Canela, A. et al. DNA breaks and end resection measured genome-wide by end sequencing. Mol. Cell 63, 898–911 (2016).
Lensing, S. V. et al. DSBCapture: in situ capture and sequencing of DNA breaks. Nat. Methods 13, 855–857 (2016).
Mei, Q. et al. Two mechanisms of chromosome fragility at replication-termination sites in bacteria. Sci. Adv. 7, eabe2846 (2021).
Caldecott, K. W. Single-strand break repair and genetic disease. Nat. Rev. Genet. 9, 619–631 (2008).
Sassanfar, M. & Roberts, J. W. Nature of the SOS-inducing signal in Escherichia coli: the involvement of DNA replication. J. Mol. Biol. 212, 79–96 (1990).
Blackford, A. N. & Jackson, S. P. ATM, ATR, and DNA-PK: the trinity at the heart of the DNA damage response. Mol. Cell 66, 801–817 (2017).
Sivaramakrishnan, P. et al. The transcription fidelity factor GreA impedes DNA break repair. Nature 550, 214–218 (2017).
Sollier, J. et al. Transcription-coupled nucleotide excision repair factors promote R-loop-induced genome instability. Mol. Cell 56, 777–785 (2014).
Kuzminov, A. & Stahl, F. W. Double-strand end repair via the RecBC pathway in Escherichia coli primes DNA replication. Genes Dev. 13, 345–356 (1999).
Pomerantz, R. T. & O’donnell, M. The replisome uses mRNA as a primer after colliding with RNA polymerase. Nature 456, 762 (2008).
Kushner, S. R., Nagaishi, H., Templin, A. & Clark, A. J. Genetic recombination in Escherichia coli: the role of exonuclease I. Proc. Natl Acad. Sci. USA 68, 824–827 (1971).
Thoms, B., Borchers, I. & Wackernagel, W. Effects of single-strand DNases ExoI, RecJ, ExoVII, and SbcCD on homologous recombination of recBCD+ strains of Escherichia coli and roles of SbcB15 and XonA2 ExoI mutant enzymes. J. Bacteriol. 190, 179–192 (2008).
Lloyd, R. G. & Buckman, C. Identification and genetic analysis of sbcC mutations in commonly used recBC sbcB strains of Escherichia coli K-12. J. Bacteriol. 164, 836–844 (1985).
Dillingham, M. S. & Kowalczykowski, S. C. RecBCD enzyme and the repair of double-stranded DNA breaks. Microbiol. Mol. Biol. Rev. 72, 642–671 (2008).
Gumbiner-Russo, L. M., Lombardo, M.-J., Ponder, R. G. & Rosenberg, S. M. The TGV transgenic vectors for single-copy gene expression from the Escherichia coli chromosome. Gene 273, 97–104 (2001).
Kim, J. J., Kumbhar, R., Gong, F. & Miller, K. M. In time and space: laser microirradiation and the DNA damage response. Methods Mol. Biol. 1999, 61–74 (2019).
Joshi, M. C. et al. Regulation of sister chromosome cohesion by the replication fork tracking protein SeqA. PLoS Genet. 9, e1003673 (2013).
Fehér, T., Cseh, B., Umenhoffer, K., Karcagi, I. & Pósfai, G. Characterization of cycA mutants of Escherichia coli: an assay for measuring in vivo mutation rates. Mutat. Res. 595, 184–190 (2006).
Hastings, P. et al. Competition of Escherichia coli DNA polymerases I, II and III with DNA Pol IV in stressed cells. PLoS ONE 5, e10862 (2010).
Kath, J. E. et al. Exchange between Escherichia coli polymerases II and III on a processivity clamp. Nucleic Acids Res. 44, 1681–1690 (2016).
Maki, H., Horiuchi, T. & Kornberg, A. The polymerase subunit of DNA polymerase III of Escherichia coli. I. Amplification of the dnaE gene product and polymerase activity of the alpha subunit. J. Biol. Chem. 260, 12982–12986 (1985).
Miko, I. Epistasis: gene interaction and phenotype effects. Nat. Educ. 1, 197 (2008).
Yanofsky, C. & Horn, V. Rifampin resistance mutations that alter the efficiency of transcription termination at the tryptophan operon attenuator. J. Bacteriol. 145, 1334–1341 (1981).
McDowell, J. C., Roberts, J. W., Jin, D. J. & Gross, C. Determination of intrinsic transcription termination efficiency by RNA polymerase elongation rate. Science 266, 822–825 (1994).
Kogoma, T. Escherichia coli RNA polymerase mutants that enhance or diminish the SOS response constitutively expressed in the absence of RNase HI activity. J. Bacteriol. 176, 1521–1523 (1994).
Gusarov, I. & Nudler, E. The mechanism of intrinsic transcription termination. Mol. Cell 3, 495–504 (1999).
Kotlajich, M. V. et al. Bridged filaments of histone-like nucleoid structuring protein pause RNA polymerase and aid termination in bacteria. eLife 4, e04970 (2015).
Zenkin, N., Yuzenkova, Y. & Severinov, K. Transcript-assisted transcriptional proofreading. Science 313, 518–520 (2006).
Dey, S. et al. Structural insights into RNA-mediated transcription regulation in bacteria. Mol. Cell 82, 3885–3900.e10 (2022).
Mirkin, E. V., Castro Roa, D., Nudler, E. & Mirkin, S. M. Transcription regulatory elements are punctuation marks for DNA replication. Proc. Natl Acad. Sci. USA 103, 7276–7281 (2006).
Borukhov, S., Sagitov, V. & Goldfarb, A. Transcript cleavage factors from E. coli. Cell 72, 459–466 (1993).
Phillips, G. J., Prasher, D. & Kushner, S. R. Physical and biochemical characterization of cloned sbcB and xonA mutations from Escherichia coli K-12. J. Bacteriol. 170, 2089–2094 (1988).
Liu, J., Mei, Q., Nimer, S., Fitzgerald, D. M. & Rosenberg, S. M. in Methods in Enzymology, Vol. 661 (ed. Eichman, B. F.) 155–181 (Elsevier, 2021).
Cohen, A. & Clark, A. J. Synthesis of linear plasmid multimers in Escherichia coli K-12. J. Bacteriol. 167, 327–335 (1986).
Datsenko, K. A. & Wanner, B. L. One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. Proc. Natl Acad. Sci. USA 97, 6640–6645 (2000).
Bonura, T. & Smith, K. C. Sensitization of Escherichia coli C to gamma-radiation by 5-bromouracil incorporation. Int. J. Radiat. Biol. Relat. Stud. Phys. Chem. Med. 32, 457–464 (1977).
Gong, F., Clouaire, T., Aguirrebengoa, M., Legube, G. & Miller, K. M. Histone demethylase KDM5A regulates the ZMYND8–NuRD chromatin remodeler to promote DNA repair. J. Cell Biol. 216, 1959–1974 (2017).
Henricksen, L. A., Umbricht, C. B. & Wold, M. S. Recombinant replication protein A: expression, complex formation, and functional characterization. J. Biol. Chem. 269, 11121–11132 (1994).
Ducret, A., Quardokus, E. M. & Brun, Y. V. MicrobeJ, a tool for high throughput bacterial cell detection and quantitative analysis. Nat. Microbiol. 1, 16077 (2016).
Bolte, S. & Cordelieres, F. A guided tour into subcellular colocalization analysis in light microscopy. J. Microsc. 224, 213–232 (2006).
Kim, D. R., Pritchard, A. E. & McHenry, C. S. Localization of the active site of the alpha subunit of the Escherichia coli DNA polymerase III holoenzyme. J. Bacteriol. 179, 6721–6728 (1997).
Zheng, Q. rSalvador: an R package for the fluctuation experiment. G3: Genes Genomes Genet. 7, 3849–3856 (2017).
Bonocora, R. P. & Wade, J. T. in Bacterial Transcriptional Control (eds Artsimovitch, I. & Santangelo, T. J.) 327–340 (Springer, 2015).
Thomason, L. C., Sawitzke, J. A., Li, X., Costantino, N. & Court, D. L. Recombineering: genetic engineering in bacteria using homologous recombination. Curr. Protoc. Mol. Biol. 106, 1.16.11–11.16. 39 (2014).
Reisch, C. R. & Prather, K. L. The no-SCAR (Scarless Cas9 Assisted Recombineering) system for genome editing in Escherichia coli. Sci. Rep. 5, 15096 (2015).
Ramirez, F. et al. deepTools2: a next generation web server for deep-sequencing data analysis. Nucleic Acids Res. 44, W160–W165 (2016).
Lawrence, M. et al. Software for computing and annotating genomic ranges. PLoS Comput. Biol. 9, e1003118 (2013).
Wold, M. S., Weinberg, D. H., Virshup, D. M., Li, J. J. & Kelly, T. J. Identification of cellular proteins required for simian virus 40 DNA replication. J. Biol. Chem. 264, 2801–2809 (1989).
Razavy, H. Single-Strand DNA Ends in Recombination In Vivo. MSc thesis, Univ. of Alberta (1997).
Rinken, R., Thomas, B. & Wackernagel, W. Evidence that recBC-dependent degradation of duplex DNA in Escherichia coli recD mutants involves DNA unwinding. J. Bacteriol. 174, 5424–5429 (1992).
Connelly, J. C., de Leau, E. S. & Leach, D. R. DNA cleavage and degradation by the SbcCD protein complex from Escherichia coli. Nucleic Acids Res. 27, 1039–1046 (1999).
Chase, J. W. & Richardson, C. C. Exonuclease VII of Escherichia coli: mechanism of action. J. Biol. Chem. 249, 4553–4561 (1974).
Schaaper, R. M. Base selection, proofreading, and mismatch repair during DNA replication in Escherichia coli. J. Biol. Chem. 268, 23762–23765 (1993).
Robinson, J. T. et al. Integrative genomics viewer. Nat. Biotechnol. 29, 24–26 (2011).
Skordalakes, E., Brogan, A. P., Park, B. S., Kohn, H. & Berger, J. M. Structural mechanism of inhibition of the Rho transcription termination factor by the antibiotic bicyclomycin. Structure 13, 99–109 (2005).
Zhou, Y. & Martin, C. T. Observed instability of T7 RNA polymerase elongation complexes can be dominated by collision-induced “bumping”. J. Biol. Chem. 281, 24441–24448 (2006).
Source link
