1. McHenry,C.S. (2003) Chromosomal replicases as asymmetric dimers: studies of subunit arrangement and functional consequences. Mol. Microbiol., 49, 1157-1165. 

2. Yao,N. and O'Donnell,M. (2016) Bacterial and eukaryotic replisome machines. JSM Biochem. Mol. Biol., 3, 1013. 

3. Zechner,E.L., Wu,C.A. and Marians,K.J. (1992) Coordinated leadingand lagging-strand synthesis at the Escherichia coli DNA replication fork. III. A polymerase-primase interaction governs primer size. J. Biol. Chem., 267, 4054-4063. 

4. Ogawa,T. and Okazaki,T. (1984) Function of RNase H in DNA replication revealed by RNase H defective mutants of Escherichia coli. Mol. Gen. Genet., 193, 231-237. 

Downloaded from https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkad038/7033787 by ABE Marketing user on 14 February 2023 leading strand and lagging strand DNA replication on the Escherichia coli chromosome. Proc. Natl. Acad. Sci. U.S.A., 95, 10020-10025.

8. Maslowska,K.H., Makiela-Dzbenska,K., Mo,J.-Y., Fijalkowska,I.J. and Schaaper,R.M. (2018) High-accuracy lagging-strand DNA

replication mediated by DNA polymerase dissociation. Proc. Natl. Acad. Sci. U.S.A., 115, 4212-4217.

9. Makiela-Dzbenska,K., Maslowska,K.H., Kuban,W., Gawel,D., Jonczyk,P., Schaaper,R.M. and Fijalkowska,I.J. (2019) Replication fidelity in E. coli: differential leading and lagging strand effects for dnaE antimutator alleles. DNA Repair (Amst.), 83, 4-10.

10. Maliszewska-Tkaczyk,M., Jonczyk,P., Bialoskorska,M., Schaaper,R.M. and Fijalkowska,I.J. (2000) SOS mutator activity: unequal mutagenesis on leading and lagging strands. Proc. Natl. Acad. Sci. U.S.A., 97, 12678-12683.

11. Vandewiele,D., Fernández de Henestrosa,A.R., Timms,A.R., Bridges,B.A. and Woodgate,R. (2002) Sequence analysis and phenotypes of five temperature sensitive mutator alleles of dnaE, encoding modified ␣-catalytic subunits of Escherichia coli DNA polymerase III holoenzyme. Mutat. Res., 499, 85-95.

12. Banach-Orlowska,M., Fijalkowska,I.J., Schaaper,R.M. and Jonczyk,P. (2005) DNA polymerase II as a fidelity factor in chromosomal DNA synthesis in Escherichia coli. Mol. Microbiol., 58, 61-70.

13. Kuban,W., Banach-Orlowska,M., Schaaper,R.M., Jonczyk,P. and Fijalkowska,I.J. (2006) Role of DNA polymerase IV in Escherichia coli SOS mutator activity. J. Bacteriol., 188, 7977-7980.

14. Makiela-Dzbenska,K., Jaszczur,M.M., Banach-Orlowska,M., Jonczyk,P., Schaaper,R.M. and Fijalkowska,I.J. (2009) Role of Escherichia coli DNA polymerase I in chromosomal DNA replication fidelity. Mol. Microbiol., 74, 1114-1127.

15. Joyce,C.M. (1997) Choosing the right sugar: how polymerases select a nucleotide substrate. Proc. Natl. Acad. Sci. U.S.A., 94, 1619-1622.

16. Williams,J.S. and Kunkel,T.A. (2014) Ribonucleotides in DNA: origins, repair and consequences. DNA Repair (Amst.), 19, 27-37.

17. Vaisman,A. and Woodgate,R. (2015) Redundancy in ribonucleotide excision repair: competition, compensation, and cooperation. DNA Repair (Amst.), 29, 74-82.

18. Clausen,A.R., Lujan,S.A., Burkholder,A.B., Orebaugh,C.D., Williams,J.S., Clausen,M.F., Malc,E.P., Mieczkowski,P.A., Fargo,D.C., Smith,D.J. et al. (2015) Tracking replication enzymology in vivo by genome-wide mapping of ribonucleotide incorporation. Nat. Struct. Mol. Biol., 22, 185-191.

19. Brown,J.A. and Suo,Z. (2011) Unlocking the sugar “steric gate” of DNA polymerases. Biochemistry, 50, 1135-1142.

20. Parasuram,R., Coulther,T.A., Hollander,J.M., Keston-Smith,E., Ondrechen,M.J. and Beuning,P.J. (2018) Prediction of active site and distal residues in E.coli DNA polymerase III alpha polymerase activity. Biochemistry, 57, 1063-1072.

21. Vaisman,A., Łazowski,K., Reijns,M.A.M., Walsh,E., McDonald,J.P., Moreno,K.C., Quiros,D.R., Schmidt,M., Kranz,H., Yang,W. et al. (2021) Novel Escherichia coli active site dnaE alleles with altered base and sugar selectivity. Mol. Microbiol., 116, 909-925.

22. Vaisman,A., Kuban,W., McDonald,J.P., Karata,K., Yang,W., Goodman,M.F. and Woodgate,R. (2012) Critical amino acids in Escherichia coli UmuC responsible for sugar discrimination and base-substitution fidelity. Nucleic Acids Res., 40, 6144-6157.

23. Vaisman,A., McDonald,J.P., Noll,S., Huston,D., Loeb,G., Goodman,M.F. and Woodgate,R. (2014) Investigating the

mechanisms of ribonucleotide excision repair in Escherichia coli. Mutat. Res., 761, 21-33.

24. Cerritelli,S.M. and Crouch,R.J. (2016) The balancing act of ribonucleotides in DNA. Trends Biochem. Sci, 41, 434-445.

25. Itaya,M. (1990) Isolation and characterization of a second RNase H (RNase HII) of Escherichia coli K-12 encoded by the rnhB gene. Proc. Natl. Acad. Sci. U.S.A., 87, 8587-8591.

26. Tadokoro,T. and Kanaya,S. (2009) Ribonuclease H: molecular diversities, substrate binding domains, and catalytic mechanism of the (1990) RecA protein of Escherichia coli has a third essential role in prokaryotic enzymes. FEBS J., 276, 1482-1493. 

27. Hyjek,M., Figiel,M. and Nowotny,M. (2019) RNases H: structure and mechanism. DNA Repair (Amst.), 84, 102672. 

28. Reijns,M.A.M., Rabe,B., Rigby,R.E., Mill,P., Astell,K.R., Lettice,L.A., Boyle,S., Leitch,A., Keighren,M., Kilanowski,F. et al. Escherichia coli that allow rapid detection of each of the six base (2012) Enzymatic removal of ribonucleotides from DNA is essential 48. Sweasy,J.B., Witkin,E.M., Sinha,N. and Roegner-Maniscalco,V.

SOS mutator activity. J. Bacteriol., 172, 3030-3036.

49. Wanner,B.L. (1986) Novel regulatory mutants of the phosphate

regulon in Escherichia coli K-12. J. Mol. Biol., 191, 39-58. 50. Cupples,C.G. and Miller,J.H. (1989) A set of lacZ mutations in

substitutions. Proc. Natl. Acad. Sci. U.S.A., 86, 5345-5349. for mammalian genome integrity and development. Cell, 149, 1008-1022. 

29. Tannous,E., Kanaya,E. and Kanaya,S. (2015) Role of RNase H1 in DNA repair: removal of single ribonucleotide misincorporated into DNA in collaboration with RNase H2. Sci. Rep., 5, 9969.

30. Lee,H., Cho,H., Kim,J., Lee,S., Yoo,J., Park,D. and Lee,G. (2022) RNase H is an exoand endoribonuclease with asymmetric directionality, depending on the binding mode to the structural variants of RNA:DNA hybrids. Nucleic Acids Res., 50, 1801-1814.

31. Gowrishankar,J., Krishna Leela,J. and Anupama,K. (2013) R-loops in bacterial transcription: their causes and consequences. Transcription, 4, 153-157. 

32. Drolet,M. and Brochu,J. (2019) R-loop-dependent replication and genomic instability in bacteria. DNA Repair (Amst.)., 84, 102693.

33. Naito,S. and Uchida,H. (1986) RNase H and replication of ColE1 DNA in Escherichia coli. J. Bacteriol., 166, 143-147.

34. Wendel,B.M., Hernandez,A.J., Courcelle,C.T. and Courcelle,J. (2021) human genome. Genome Biol., 10, R25. Ligase A and RNase HI participate in completing replication on the chromosome in Escherichia coli. DNA, 1, 13-25. 

35. Cerritelli,S.M., Frolova,E.G., Feng,C., Grinberg,A., Love,P.E. and Crouch,R.J. (2003) Failure to produce mitochondrial DNA results in embryonic lethality in Rnaseh1 null mice. Mol. Cell, 11, 807-815.

36. Arora,R., Lee,Y., Wischnewski,H., Brun,C.M., Schwarz,T. and Azzalin,C.M. (2014) RNaseH1 regulates TERRA-telomeric DNA hybrids and telomere maintenance in ALT tumour cells. Nat. Commun., 5, 5220. 

37. Maduike,N.Z., Tehranchi,A.K., Wang,J.D. and Kreuzer,K.N. (2014) Replication of the Escherichia coli chromosome in RNase HI-deficient cells: multiple initiation regions and fork dynamics. Mol. Orozco,M. (2015) The structural impact of DNA mismatches. Microbiol., 91, 39-56. 

38. Kouzminova,E.A., Kadyrov,F.F. and Kuzminov,A. (2017) RNase HII saves rnhA mutant Escherichia coli from R-loop-associated chromosomal fragmentation. J. Mol. Biol., 429, 2873-2894.

39. Kouzminova,E.A. and Kuzminov,A. (2021) Ultraviolet-induced RNA:DNA hybrids interfere with chromosomal DNA synthesis. Nucleic Acids Res., 49, 3888-3906. 

40. Walsh,E., Henrikus,S.S., Vaisman,A., Makiela-Dzbenska,K., Armstrong,T.J., Łazowski,K., McDonald,J.P., Goodman,M.F., van Oijen,A.M., Jonczyk,P. et al. (2019) Role of RNase H enzymes in maintaining genome stability in Escherichia coli expressing a steric-gate mutant of pol VICE391 . DNA Repair (Amst.), 84, 102685. 65. Lujan,S.A., Williams,J.S. and Kunkel,T.A. (2016) DNA polymerases

41. Vaisman,A., McDonald,J.P., Huston,D., Kuban,W., Liu,L., Van Houten,B. and Woodgate,R. (2013) Removal of misincorporated ribonucleotides from prokaryotic genomes: an unexpected role for nucleotide excision repair. PLoS Genet., 9, e1003878.

42. Faraz,M., Woodgate,R. and Clausen,A.R. (2021) Tracking Escherichia coli DNA polymerase V to the entire genome during the SOS response. DNA Repair (Amst.)., 101, 103075. 

43. Fijalkowska,I.J., Dunn,R.L. and Schaaper,R.M. (1997) Genetic requirements and mutational specificity of the Escherichia coli SOS 68. Kornberg,A. and Baker,T.A. (1992) In: DNA Replication. 2nd edn. mutator activity. J. Bacteriol., 179, 7435-7445. 

44. Curti,E., McDonald,J.P., Mead,S. and Woodgate,R. (2009) DNA polymerase switching: effects on spontaneous mutagenesis in Escherichia coli. Mol. Microbiol., 71, 315-331. 

45. Niccum,B.A., Coplen,C.P., Lee,H., Mohammed Ismail,W., Tang,H. and Foster,P.L. (2020) New complexities of SOS-induced “untargeted” mutagenesis in Escherichia coli as revealed by mutation 71. Yao,N.Y. and O'Donnell,M. (2008) Replisome dynamics and use of accumulation and whole-genome sequencing. DNA Repair (Amst.), 90, 102852. 

46. Watanabe-Akanuma,M., Woodgate,R. and Ohta,T. (1997) Enhanced generation of A:T → T:A transversions in a recA730 lexA51(Def) mutant of Escherichia coli. Mutat. Res. - Fundam. Mol. Mech. Mutagen., 373, 61-66. 

47. Gawel,D., Maliszewska-Tkaczyk,M., Jonczyk,P., Schaaper,R.M. and Fijalkowska,I.J. (2002) Lack of strand bias in UV-induced mutagenesis in Escherichia coli. J. Bacteriol., 184, 4449-4454.

Downloaded from https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkad038/7033787 by ABE Marketing user on 14 February 2023

51. Fijalkowska,I.J. and Schaaper,R.M. (1995) Effects of Escherichia coli

dnaE antimutator alleles in a proofreadingdeficient mutD5 strain. J.

Bacteriol., 177, 5979-5986. 52. Swerdlow,S.J. and Schaaper,R.M. (2014) Mutagenesis in the lacI gene

target of E. Coli: improved analysis for lacId and lacO mutants.

Mutat. Res. - Fundam. Mol. Mech. Mutagen., 770, 79-84. 53. Zheng,Q. (2005) New algorithms for Luria-Delbruck ¨ fluctuation

analysis. Math. Biosci., 196, 198-214.

54. Zheng,Q. (2017) rSalvador: an R package for the fluctuation

experiment. G3: Genes Genomes Genet., 7, 3849-3856.

55. Zheng,Q. (2021) New approaches to mutation rate fold change in

Luria-Delbruck¨ fluctuation experiments. Math. Biosci., 335, 108572.

56. Martin,M. (2011) Cutadapt removes adapter sequences from

high-throughput sequencing reads. EMBnet. J., 17, 10.

57. Langmead,B., Trapnell,C., Pop,M. and Salzberg,S.L. (2009) Ultrafast

and memory-efficient alignment of short DNA sequences to the 58. Goodman,M.F., McDonald,J.P., Jaszczur,M.M. and Woodgate,R.

(2016) Insights into the complex levels of regulation imposed on

Escherichia coli DNA polymerase V. DNA Repair (Amst.), 44, 42-50. 59. Henrikus,S.S., van Oijen,A.M. and Robinson,A. (2018) Specialised

DNA polymerases in Escherichia coli: roles within multiple pathways. Curr. Genet., 64, 1189-1196. 60. Creighton,S., Huang,M.M., Cai,H., Arnheim,N. and Goodman,M.F. (1992) Base mispair extension kinetics. Binding of avian

myeloblastosis reverse transcriptase to matched and mismatched base

pair termini. J. Biol. Chem., 267, 2633-2639. 61. Rossetti,G., Dans,P.D., Gomez-Pinto,I., Ivani,I., Gonzalez,C. and

Nucleic Acids Res., 43, 4309-4321.

62. Schaaper,R.M. (1993) Base selection, proofreading, and mismatch repair during DNA replication in Escherichia coli. J. Biol. Chem., 268, 23762-23765.

63. Niccum,B.A., Lee,H., MohammedIsmail,W., Tang,H. and Foster,P.L. (2018) The spectrum of replication errors in the absence of

error correction assayed across the whole genome of Escherichia coli. Genetics, 209, 1043-1054.

64. Reijns,M.A.M., Kemp,H., Ding,J., De Procé,S.M., Jackson,A.P. and

Taylor,M.S. (2015) Lagging-strand replication shapes the mutational landscape of the genome. Nature, 518, 502-506. divide the labor of genome replication. Trends Cell Biol., 26, 640-654.

66. Oka,A., Sugimoto,K., Takanami,M. and Hirota,Y. (1980)

Replication origin of the Escherichia coli K-12 chromosome: the size

and structure of the minimum DNA segment carrying the

information for autonomous replication. Mol. Gen. Genet., 178, 9-20. 67. Duggin,I.G. and Bell,S.D. (2009) Termination structures in the

Escherichia coli chromosome replication fork trap. J. Mol. Biol., 387, 532-539.

W.H. Freeman & Co, California, NY.

69. O'Donnell,M. (2006) Replisome architecture and dynamics in Escherichia coli. J. Biol. Chem., 281, 10653-10656.

70. Pomerantz,R.T. and O'Donnell,M. (2007) Replisome mechanics: insights into a twin DNA polymerase machine. Trends Microbiol., 15,

156-164. DNA trombone loops to bypass replication blocks. Mol. Biosyst., 4,

1075.

72. Langston,L.D., Indiani,C. and O'Donnell,M. (2009) Whither the

replisome: emerging perspectives on the dynamic nature of the DNA replication machinery. Cell Cycle, 8, 2686-2691.

73. McHenry,C.S. (2011) Bacterial replicases and related polymerases.

Curr. Opin. Chem. Biol., 15, 587-594. 74. Williams,J.S., Clausen,A.R., Nick McElhinny,S.A., Watts,B.E.,

Johansson,E. and Kunkel,T.A. (2012) Proofreading of ribonucleotides inserted into DNA by yeast DNA polymerase ε. DNA Repair (Amst.), 11, 649-656. 

75. Clausen,A.R., Zhang,S., Burgers,P.M., Lee,M.Y. and Kunkel,T.A. (2013) Ribonucleotide incorporation, proofreading and bypass by human DNA polymerase ␦. DNA Repair (Amst.), 12, 121-127.

76. Cronan,G.E., Kouzminova,E.A. and Kuzminov,A. (2019) Near-continuously synthesized leading strands in Escherichia coli are bacterial chromosome duplication without an active replication broken by ribonucleotide excision. Proc. Natl. Acad. Sci. U.S.A., 116, origin. mBio, 6, 1-13.

81. Pomerantz,R.T. and O'Donnell,M. (2008) The replisome uses mRNA

as a primer after colliding with RNA polymerase. Nature, 456,

762-767.

82. Dimude,J.U., Stockum,A., Midgley-Smith,S.L., Upton,A.L.,

Foster,H.A., Khan,A., Saunders,N.J., Retkute,R. and Rudolph,C.J.

(2015) The consequences of replicating in the wrong orientation: 1251-1260. 

77. Petzold,C., Marceau,A.H., Miller,K.H., Marqusee,S. and Keck,J.L. (2015) Interaction with single-stranded DNA-binding protein stimulates Escherichia coli ribonuclease HI enzymatic activity. J. Biol. Syst., 8, 212-225. Chem., 290, 14626-14636. 

78. Wolak,C., Ma,H.J., Soubry,N., Sandler,S.J., Reyes-Lamothe,R. and Keck,J.L. (2020) Interaction with single-stranded DNA-binding protein localizes ribonuclease HI to DNA replication forks and facilitates R-loop removal. Mol. Microbiol., 114, 495-509.

79. Kuban,W., Banach-Orlowska,M., Bialoskorska,M., Lipowska,A., Schaaper,R.M., Jonczyk,P. and Fijalkowska,I.J. (2005) Mutator phenotype resulting from DNA polymerase IV overproduction in Escherichia coli: preferential mutagenesis on the lagging strand. J. transcription. Nucleic Acids Res., 43, 2232-2241. Bacteriol., 187, 6862-6866.

80. Kogoma,T. (1997) Stable DNA replication: interplay between DNA replication, homologous recombination, and transcription. Microbiol. Mol. Biol. Rev., 61, 212-238.

Downloaded from https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkad038/7033787 by ABE Marketing user on 14 February 2023

83. Scholz,S.A., Diao,R., Wolfe,M.B., Fivenson,E.M., Lin,X.N. and

Freddolino,P.L. (2019) High-resolution mapping of the Escherichia coli chromosome reveals positions of high and low transcription. Cell

84. Rocha,E.P.C. (2004) Order and disorder in bacterial genomes. Curr.

Opin. Microbiol., 7, 519-527.

85. Mehta,A.P., Wang,Y., Reed,S.A., Supekova,L., Javahishvili,T., Chaput,J.C. and Schultz,P.G. (2018) Bacterial genome containing chimeric DNA-RNA sequences. J. Am. Chem. Soc., 140, 11464-11473.

86. Xu,L., Wang,W., Zhang,L., Chong,J., Huang,X. and Wang,D. (2015) Impact of template backbone heterogeneity on RNA polymerase II