Vulnerabilities on the Lagging-Strand Template: Opportunities for Mobile Elements

Literature Cited

1. Bidnenko V, Ehrlich SD, Michel B. 1.  2002. Replication fork collapse at replication terminator sequences. EMBO J 21:143898–907 [Google Scholar]
2. Bobay LM, Touchon M, Rocha EPC. 2.  2013. Manipulating or superseding host recombination functions: a dilemma that shapes phage evolvability. PLOS Genet 9:9e1003825 [Google Scholar]
3. Chandler M, de la Cruz F, Dyda F, Hickman AB, Moncalian G, Ton-Hoang B. 3.  2013. Breaking and joining single-stranded DNA: the HUH endonuclease superfamily. Nat. Rev. Microbiol. 11:8525–38 [Google Scholar]
4. Claverys JP, Prudhomme M, Martin B. 4.  2006. Induction of competence regulons as a general response to stress in Gram-positive bacteria. Annu. Rev. Microbiol. 60:1451–75 [Google Scholar]
5. Coros AM, Twiss E, Tavakoli NP, Derbyshire KM. 5.  2005. Genetic evidence that GTP is required for transposition of IS903 and Tn552 in Escherichia coli. J. Bacteriol 187:134598–606 [Google Scholar]
6. Coros CJ, Piazza CL, Chalamcharla VR, Smith D, Belfort M. 6.  2009. Global regulators orchestrate group II intron retromobility. Mol. Cell 34:2250–56 [Google Scholar]
7. Costantino N, Court DL. 7.  2003. Enhanced levels of λ Red-mediated recombinants in mismatch repair mutants. Proc. Natl. Acad. Sci. USA 100:2615748–53 [Google Scholar]
8. Cousineau B, Lawrence S, Smith D, Belfort M. 8.  2000. Retrotransposition of a bacterial group II intron. Nature 404:67811018–21 [Google Scholar]
9. Cousineau B, Smith D, Lawrence-Cavanagh S, Mueller JE, Yang J. 9.  et al. 1998. Retrohoming of a bacterial group II intron: mobility via complete reverse splicing, independent of homologous DNA recombination. Cell 94:4451–62 [Google Scholar]
10. Craig NL, Roberts JW. 10.  1980. E. coli RecA protein-directed cleavage of phage λ repressor requires polynucleotide. Nature 283:574226–30 [Google Scholar]
11. Dalrymple BP, Kongsuwan K, Wijffels G, Dixon NE, Jennings PA. 11.  2001. A universal protein-protein interaction motif in the eubacterial DNA replication and repair systems. Proc. Natl. Acad. Sci. USA 98:2011627–32 [Google Scholar]
12. DeBoy RT, Craig NL. 12.  2000. Target site selection by Tn7:attTn7 transcription and target activity. J Bacteriol 182:113310–13 [Google Scholar]
13. DeNapoli J, Tehranchi AK, Wang JD. 13.  2013. Dose-dependent reduction of replication elongation rate by (p)ppGpp in Escherichia coli and Bacillus subtilis. Mol. Microbiol 88:193–104 [Google Scholar]
14. De Septenville AL, Duigou S, Boubakri H, Michel B. 14.  2012. Replication fork reversal after replication-transcription collision. PLOS Genet 8:4e1002622 [Google Scholar]
15. Duderstadt KE, Reyes-Lamothe R, van Oijen AM, Sherratt DJ. 15.  2014. Replication-fork dynamics. Cold Spring Harb. Perspect. Biol. 6:1a010157 [Google Scholar]
16. Duggin IG, Wake RG, Bell SD, Hill TM. 16.  2008. The replication fork trap and termination of chromosome replication. Mol. Microbiol. 70:61323–33 [Google Scholar]
17. Ellis HM, Yu D, DiTizio T, Court DL. 17.  2001. High efficiency mutagenesis, repair, and engineering of chromosomal DNA using single-stranded oligonucleotides. Proc. Natl. Acad. Sci. USA 98:126742–46 [Google Scholar]
18. Eykelenboom JK, Blackwood JK, Okely E, Leach DRF. 18.  2008. SbcCD causes a double-strand break at a DNA palindrome in the Escherichia coli chromosome. Mol. Cell 29:5644–51 [Google Scholar]
19. Feschotte C, Mouchès C. 19.  2000. Evidence that a family of miniature inverted-repeat transposable elements (MITES) from the Arabidopsis thaliana genome has arisen from a pogo-like DNA transposon. Mol. Biol. Evol 17:5730–37 [Google Scholar]
20. Fijalkowska IJ, Jonczyk P, Tkaczyk MM, Bialoskorska M, Schaaper RM. 20.  1998. Unequal fidelity of leading strand and lagging strand DNA replication on the Escherichia coli chromosome. Proc. Natl. Acad. Sci USA 95:1710020–25 [Google Scholar]
21. Finn JA, Parks AR, Peters JE. 21.  2007. Transposon Tn7 directs transposition into the genome of filamentous bacteriophage M13 using the element-encoded TnsE protein. J. Bacteriol. 189:249122–25 [Google Scholar]
22. Frank AC, Lobry JR. 22.  1999. Asymmetric substitution patterns: a review of possible underlying mutational or selective mechanisms. Gene 238:165–77 [Google Scholar]
23. Freudenreich CH, Stavenhagen JB, Zakian VA. 23.  1997. Stability of a CTG/CAG trinucleotide repeat in yeast is dependent on its orientation in the genome. Mol. Cell. Biol. 17:42090–98 [Google Scholar]
24. Fukui K. 24.  2010. DNA mismatch repair in eukaryotes and bacteria. J. Nucleic Acids 27:260512 [Google Scholar]
25. Galkin VE, Yu X, Bielnicki J, Ndjonka D, Bell CE, Egelman EH. 25.  2009. Cleavage of bacteriophage λ cI repressor involves the RecA C-terminal domain. J. Mol. Biol. 385:3779–87 [Google Scholar]
26. Garsin DA, Urbach J, Huguet-Tapia JC, Peters JE, Ausubel FM. 26.  2004. Construction of an Enterococcus faecalis Tn917-mediated-gene-disruption library offers insight into Tn917 insertion patterns. J. Bacteriol 186:217280–89 [Google Scholar]
27. Georgescu RE, Kim SS, Yurieva O, Kuriyan J, Kong XP, O'Donnell M. 27.  2008. Structure of a sliding clamp on DNA. Cell 132:143–54 [Google Scholar]
28. Georgescu RE, Kurth I, O'Donnell ME. 28.  2012. Single-molecule studies reveal the function of a third polymerase in the replisome. Nat. Struct. Mol. Biol. 19:1113–16 [Google Scholar]
29. Guo H, Zimmerly S, Perlman PS, Lambowitz AM. 29.  1997. Group II intron endonucleases use both RNA and protein subunits for recognition of specific sequences in double-stranded DNA. EMBO J 16:226835–48 [Google Scholar]
30. Guynet C, Hickman AB, Barabas O, Dyda F, Chandler M, Ton-Hoang B. 30.  2008. In vitro reconstitution of a single-stranded transposition mechanism of IS608. Mol. Cell 29:3302–12 [Google Scholar]
31. Heller RC, Marians KJ. 31.  2006. Replication fork reactivation downstream of a blocked nascent leading strand. Nature 439:7076557–62 [Google Scholar]
32. Hillyar CRT. 32.  2012. Genetic recombination in bacteriophage lambda. Biosci. Horiz. 5:hzs001 [Google Scholar]
33. Hu WY, Derbyshire KM. 33.  1998. Target choice and orientation preference of the insertion sequence IS903. J. Bacteriol. 180:123039–48 [Google Scholar]
34. Huen MSY, Li X, Lu LY, Watt RM, Liu DP, Huang JD. 34.  2006. The involvement of replication in single stranded oligonucleotide-mediated gene repair. Nucleic Acids Res 34:216183–94 [Google Scholar]
35. Ichiyanagi K, Beauregard A, Belfort M. 35.  2003. A bacterial group II intron favors retrotransposition into plasmid targets. Proc. Natl. Acad. Sci. USA 100:2615742–47 [Google Scholar]
36. Ichiyanagi K, Beauregard A, Lawrence S, Smith D, Cousineau B, Belfort M. 36.  2002. Retrotransposition of the Ll.LtrB group II intron proceeds predominantly via reverse splicing into DNA targets. Mol. Microbiol 46:51259–72 [Google Scholar]
37. Indiani C, Patel M, Goodman MF, O'Donnell ME. 37.  2013. RecA acts as a switch to regulate polymerase occupancy in a moving replication fork. Proc. Natl. Acad. Sci. USA 110:145410–15 [Google Scholar]
38. Iyer RR, Pluciennik A, Burdett V, Modrich PL. 38.  2006. DNA mismatch repair: functions and mechanisms. Chem. Rev. 106:2302–23 [Google Scholar]
39. Joshi MC, Magnan D, Montminy TP, Lies M, Stepankiw N, Bates D. 39.  2013. Regulation of sister chromosome cohesion by the replication fork tracking protein SeqA. PLOS Genet 9:8e1003673 [Google Scholar]
40. Kantartzis A, Williams GM, Balakrishnan L, Roberts RL, Surtees JA, Bambara RA. 40.  2012. Msh2-Msh3 interferes with Okazaki fragment processing to promote trinucleotide repeat expansions. Cell Rep 2:2216–22 [Google Scholar]
41. Kersulyte D, Velapatiño B, Dailide G, Mukhopadhyay AK, Ito Y. 41.  et al. 2002. Transposable element ISHp608 of Helicobacter pylori: nonrandom geographic distribution, functional organization, and insertion specificity. J. Bacteriol 184:4992–1002 [Google Scholar]
42. Kim S, Dallmann HG, McHenry CS, Marians KJ. 42.  1996. Coupling of a replicative polymerase and helicase: a τ-DnaB interaction mediates rapid replication fork movement. Cell 84:4643–50 [Google Scholar]
43. Kolter R, Siegele DA, Tormo A. 43.  1993. The stationary phase of the bacterial life cycle. Annu. Rev. Microbiol 47:855–74 [Google Scholar]
44. Kowalczykowski SC. 44.  2000. Initiation of genetic recombination and recombination-dependent replication. Trends Biochem. Sci. 25:4156–65 [Google Scholar]
45. Lajoie MJ, Gregg CJ, Mosberg JA, Washington GC, Church GM. 45.  2012. Manipulating replisome dynamics to enhance lambda Red-mediated multiplex genome engineering. Nucleic Acids Res. 40:22e170 [Google Scholar]
46. Lambowitz AM, Zimmerly S. 46.  2010. Group II introns: mobile ribozymes that invade DNA. Cold Spring Harb. Perspect. Biol. 3:8a003616 [Google Scholar]
47. Leu FP, Georgescu R, O'Donnell M. 47.  2003. Mechanism of the E. coli tau processivity switch during lagging-strand synthesis. Mol. Cell 11:2315–27 [Google Scholar]
48. Li X, Costantino N, Lu L, Liu D, Watt RM. 48.  et al. 2003. Identification of factors influencing strand bias in oligonucleotide-mediated recombination in Escherichia coli. Nucleic Acids Res 31:226674–87 [Google Scholar]
49. Li X, Thomason LC, Sawitzke JA, Costantino N, Court DL. 49.  2013. Bacterial DNA polymerases participate in oligonucleotide recombination. Mol. Microbiol. 88:5906–20 [Google Scholar]
50. Li Z, Craig NL, Peters JE. 50.  2013. Transposon Tn7. Bacterial Integrative Mobile Genetic Elements AP Roberts, P Mullany 1–32 Austin, TX: Landes Biosci. [Google Scholar]
51. Lia G, Michel B, Allemand JF. 51.  2012. Polymerase exchange during Okazaki fragment synthesis observed in living cells. Science 335:6066328–31 [Google Scholar]
52. Lia G, Rigato A, Long E, Chagneau C, Le Masson M. 52.  et al. 2013. RecA-promoted, RecFOR-independent progressive disassembly of replisomes stalled by helicase inactivation. Mol. Cell 49:3547–57 [Google Scholar]
53. Lopez de Saro FJ, O'Donnell M. 53.  2001. Interaction of the β sliding clamp with MutS, ligase, and DNA polymerase I. Proc. Natl. Acad. Sci. USA 98:158376–80 [Google Scholar]
54. Lorenz MG, Wackernagel W. 54.  1994. Bacterial gene transfer by natural genetic transformation in the environment. Microbiol. Rev. 58:3563–602 [Google Scholar]
55. Lundquist RC, Olivera BM. 55.  1982. Transient generation of displaced single-stranded DNA during nick translation. Cell 31:153–60 [Google Scholar]
56. Lusetti SL, Cox MM. 56.  2002. The bacterial RecA protein and the recombinational DNA repair of stalled replication forks. Annu. Rev. Biochem. 71:71–100 [Google Scholar]
57. Lyamichev V, Brow MA, Dahlberg JE. 57.  1993. Structure-specific endonucleolytic cleavage of nucleic acids by eubacterial DNA polymerases. Science 260:5109778–83 [Google Scholar]
58. Maciąg M, Kochanowska M, Łyżeń R, Węgrzyn G, Szalewska-Pałasz A. 58.  2010. ppGpp inhibits the activity of Escherichia coli DnaG primase. Plasmid 63:161–67 [Google Scholar]
59. Maliszewska-Tkaczyk M, Jonczyk P, Bialoskorska M, Schaaper RM, Fijalkowska IJ. 59.  2000. SOS mutator activity: unequal mutagenesis on leading and lagging strands. Proc. Natl. Acad. Sci. USA 97:2312678–83 [Google Scholar]
60. Martínez-Abarca F, Barrientos-Durán A, Fernández-López M, Toro N. 60.  2004. The RmInt1 group II intron has two different retrohoming pathways for mobility using predominantly the nascent lagging strand at DNA replication forks for priming. Nucleic Acids Res 32:92880–88 [Google Scholar]
61. Martinsohn JT, Radman M, Petit MA. 61.  2008. The λ Red proteins promote efficient recombination between diverged sequences: implications for bacteriophage genome mosaicism. PLOS Genet 4:5e1000065 [Google Scholar]
62. Matsuura M, Saldanha R, Ma H, Wank H, Yang J. 62.  et al. 1997. A bacterial group II intron encoding reverse transcriptase, maturase, and DNA endonuclease activities: biochemical demonstration of maturase activity and insertion of new genetic information within the intron. Genes Dev 11:212910–24 [Google Scholar]
63. Mills DA, McKay LL, Dunny GM. 63.  1996. Splicing of a group II intron involved in the conjugative transfer of pRS01 in lactococci. J. Bacteriol. 178:123531–38 [Google Scholar]
64. Mirkin EV, Mirkin SM. 64.  2007. Replication fork stalling at natural impediments. Microbiol. Mol. Biol. Rev. 71:113–35 [Google Scholar]
65. Mohr G, Smith D, Belfort M, Lambowitz AM. 65.  2000. Rules for DNA target-site recognition by a lactococcal group II intron enable retargeting of the intron to specific DNA sequences. Genes Dev 14:5559–73 [Google Scholar]
66. Mosberg JA, Lajoie MJ, Church GM. 66.  2010. Lambda Red recombineering in Escherichia coli occurs through a fully single-stranded intermediate. Genetics 186:3791–99 [Google Scholar]
67. Muñoz-Adelantado E, San Filippo J, Martínez-Abarca F, García-Rodríguez FM, Lambowitz AM, Toro N. 67.  2003. Mobility of the Sinorhizobium meliloti group II intron RmInt1 occurs by reverse splicing into DNA, but requires an unknown reverse transcriptase priming mechanism. J. Mol. Biol 327:5931–43 [Google Scholar]
68. Murphy KC. 68.  1991. Lambda Gam protein inhibits the helicase and chi-stimulated recombination activities of Escherichia coli RecBCD enzyme. J. Bacteriol 173:185808–21 [Google Scholar]
69. Murphy KC. 69.  2012. Phage recombinases and their applications. Advances in Virus Research M Łobocka, W Szybalski 367–414 Waltham, MA: Acad. Press [Google Scholar]
70. Myers RS, Stahl FW. 70.  1994. Chi and the RecBCD enzyme of Escherichia coli. Annu. Rev. Genet 28:49–70 [Google Scholar]
71. Neylon C, Kralicek AV, Hill TM, Dixon NE. 71.  2005. Replication termination in Escherichia coli: structure and antihelicase activity of the Tus-ter complex. Microbiol. Mol. Biol. Rev 69:3501–26 [Google Scholar]
72. Nicolas E, Upton AL, Uphoff S, Henry O, Badrinarayanan A, Sherratt D. 72.  2014. The SMC complex MukBEF recruits topoisomerase IV to the origin of replication region in live Escherichia coli. mBio 5:1e01001–13 [Google Scholar]
73. Parks AR, Li Z, Shi Q, Owens RM, Jin MM, Peters JE. 73.  2009. Transposition into replicating DNA occurs through interaction with the processivity factor. Cell 138:4685–95 [Google Scholar]
74. Parks AR, Peters JE. 74.  2009. Tn7 elements: engendering diversity from chromosomes to episomes. Plasmid 6111–14
75. Pasternak C, Ton-Hoang B, Coste G, Bailone A, Chandler M, Sommer S. 75.  2010. Irradiation-induced Deinococcus radiodurans genome fragmentation triggers transposition of a single resident insertion sequence. PLOS Genet 6:1e1000799 [Google Scholar]
76. Persky NS, Ferullo DJ, Cooper DL, Moore HR, Lovett ST. 76.  2009. The ObgE/CgtA GTPase influences the stringent response to amino acid starvation in Escherichia coli. Mol. Microbiol 73:2253–66 [Google Scholar]
77. Peters JE, Craig NL. 77.  2000. Tn7 transposes proximal to DNA double-strand breaks and into regions where chromosomal DNA replication terminates. Mol. Cell 6:3573–82 [Google Scholar]
78. Peters JE, Craig NL. 78.  2001. Tn7 recognizes transposition target structures associated with DNA replication using the DNA-binding protein TnsE. Genes Dev. 15:6737–47 [Google Scholar]
79. Peters JE, Craig NL. 79.  2001. Tn7: smarter than we thought. Nat. Rev. Mol. Cell Biol. 2:11806–14 [Google Scholar]
80. Pluciennik A, Burdett V, Lukianova O, O'Donnell M, Modrich P. 80.  2009. Involvement of the β clamp in methyl-directed mismatch repair in vitro. J. Biol. Chem. 284:4732782–91 [Google Scholar]
81. Pomerantz RT, O'Donnell M. 81.  2008. The replisome uses mRNA as a primer after colliding with RNA polymerase. Nature 456:7223762–66 [Google Scholar]
82. Possoz C, Filipe SR, Grainge I, Sherratt DJ. 82.  2006. Tracking of controlled Escherichia coli replication fork stalling and restart at repressor-bound DNA in vivo. EMBO J 25:112596–604 [Google Scholar]
83. Postow L, Ullsperger C, Keller RW, Bustamante C, Vologodskii AV, Cozzarelli NR. 83.  2001. Positive torsional strain causes the formation of a four-way junction at replication forks. J. Biol. Chem. 276:42790–96 [Google Scholar]
84. Poteete AR, Fenton AC. 84.  1993. Efficient double-strand break-stimulated recombination promoted by the general recombination systems of phages λ and p22. Genetics 134:41013–21 [Google Scholar]
85. Reyes-Lamothe R, Sherratt DJ, Leake MC. 85.  2010. Stoichiometry and architecture of active DNA replication machinery in Escherichia coli. Science 328:5977498–501 [Google Scholar]
86. Roberts D, Hoopes BC, McClure WR, Kleckner N. 86.  1985. IS10 transposition is regulated by DNA adenine methylation. Cell 43:1117–30 [Google Scholar]
87. Roitzsch M, Pyle AM. 87.  2009. The linear form of a group II intron catalyzes efficient autocatalytic reverse splicing, establishing a potential for mobility. RNA 15:3473–82 [Google Scholar]
88. Ros F, Kunze R. 88.  2001. Regulation of activator/dissociation transposition by replication and DNA methylation. Genetics 157:41723–33 [Google Scholar]
89. Roszak DB, Colwell RR. 89.  1987. Survival strategies of bacteria in the natural environment. Microbiol. Rev 51:3365–79 [Google Scholar]
90. Rymer RU, Solorio FA, Tehranchi AK, Chu C, Corn JE. 90.  et al. 2012. Binding mechanism of metal·NTP substrates and stringent-response alarmones to bacterial DnaG-type primases. Structure 20:91478–89 [Google Scholar]
91. Sandler SJ. 91.  2000. Multiple genetic pathways for restarting DNA replication forks in Escherichia coli K-12. Genetics 155:2487–97 [Google Scholar]
92. San Filippo J, Lambowitz AM. 92.  2002. Characterization of the C-terminal DNA-binding/DNA endonuclease region of a group II intron-encoded protein. J. Mol. Biol. 324:5933–51 [Google Scholar]
93. Sawitzke JA, Costantino N, Li X, Thomason LC, Bubunenko M. 93.  et al. 2011. Probing cellular processes with oligo-mediated recombination and using the knowledge gained to optimize recombineering. J. Mol. Biol. 407:145–59 [Google Scholar]
94. Segawa T, Tomizawa J. 94.  1971. Formation of concatemers of lambda phage DNA in a recombination-deficient system. Mol. Gen. Genet. 111:3197–201 [Google Scholar]
95. Sharpe PL, Craig NL. 95.  1998. Host proteins can stimulate Tn7 transposition: a novel role for the ribosomal protein L29 and the acyl carrier protein. EMBO J. 17:195822–31 [Google Scholar]
96. Shi Q, Huguet-Tapia JC, Peters JE. 96.  2009. Tn917 targets the region where DNA replication terminates in Bacillus subtilis, highlighting a difference in chromosome processing in the Firmicutes. J. Bacteriol 191:247623–27 [Google Scholar]
97. Shi Q, Parks AR, Potter BD, Safir IJ, Luo Y. 97.  et al. 2008. DNA damage differentially activates regional chromosomal loci for Tn7 transposition in Escherichia coli. Genetics 179:31237–50 [Google Scholar]
98. Singh NN, Lambowitz AM. 98.  2001. Interaction of a group II intron ribonucleoprotein endonuclease with its DNA target site investigated by DNA footprinting and modification interference. J. Mol. Biol. 309:2361–86 [Google Scholar]
99. Spradling AC, Bellen HJ, Hoskins RA. 99.  2011. Drosophila P elements preferentially transpose to replication origins. Proc. Natl. Acad. Sci. USA 108:3815948–53 [Google Scholar]
100. Swingle B, Bao Z, Markel E, Chambers A, Cartinhour S. 100.  2010. Recombineering using RecTE from Pseudomonas syringae. Appl. Environ. Microbiol. 76:154960–68 [Google Scholar]
101. Swingle B, Markel E, Costantino N, Bubunenko MG, Cartinhour S, Court DL. 101.  2010. Oligonucleotide recombination in Gram-negative bacteria. Mol. Microbiol. 75:1138–48 [Google Scholar]
102. Swingle B, O'Carroll M, Haniford D, Derbyshire KM. 102.  2004. The effect of host-encoded nucleoid proteins on transposition: H-NS influences targeting of both IS903 and Tn10. Mol. Microbiol. 52:41055–67 [Google Scholar]
103. Taylor MS, LaCava J, Mita P, Molloy KR, Huang CRL. 103.  et al. 2013. Affinity proteomics reveals human host factors implicated in discrete stages of LINE-1 retrotransposition. Cell 155:51034–48 [Google Scholar]
104. Ton-Hoang B, Pasternak C, Siguier P, Guynet C, Hickman AB. 104.  et al. 2010. Single-stranded DNA transposition is coupled to host replication. Cell 142:3398–408 [Google Scholar]
105. Twiss E, Coros AM, Tavakoli NP, Derbyshire KM. 105.  2005. Transposition is modulated by a diverse set of host factors in Escherichia coli and is stimulated by nutritional stress: host factors and transposition. Mol. Microbiol. 57:61593–607 [Google Scholar]
106. Van Kessel JC, Hatfull GF. 106.  2007. Recombineering in Mycobacterium tuberculosis. Nat. Methods 4:2147–52 [Google Scholar]
107. Wang HH, Isaacs FJ, Carr PA, Sun ZZ, Xu G. 107.  et al. 2009. Programming cells by multiplex genome engineering and accelerated evolution. Nature 460:7257894–98 [Google Scholar]
108. Wang HH, Xu G, Vonner AJ, Church G. 108.  2011. Modified bases enable high-efficiency oligonucleotide-mediated allelic replacement via mismatch repair evasion. Nucleic Acids Res. 39:167336–47 [Google Scholar]
109. Wang JD, Sanders GM, Grossman AD. 109.  2007. Nutritional control of elongation of DNA replication by (p)ppGpp. Cell 128:5865–75 [Google Scholar]
110. Wang X, Liu X, Possoz C, Sherratt DJ. 110.  2006. The two Escherichia coli chromosome arms locate to separate cell halves. Genes Dev. 20:131727–31 [Google Scholar]
111. Wang X, Reyes-Lamothe R, Sherratt DJ. 111.  2008. Modulation of Escherichia coli sister chromosome cohesion by topoisomerase IV. Genes Dev 22:172426–33 [Google Scholar]
112. Warbrick E. 112.  2000. The puzzle of PCNA's many partners. BioEssays 22:11997–1006 [Google Scholar]
113. Warbrick E, Lane DP, Glover DM, Heatherington W. 113.  1998. PCNA binding proteins in Drosophila melanogaster: the analysis of a conserved PCNA binding domain. Nucleic Acids Res. 26:173925–32 [Google Scholar]
114. Wardle SJ, O'Carroll M, Derbyshire KM, Haniford DB. 114.  2005. The global regulator H-NS acts directly on the transpososome to promote Tn10 transposition. Genes Dev. 19:182224–35 [Google Scholar]
115. Waters VL, Guiney DG. 115.  1993. Processes at the nick region link conjugation, t-DNA transfer and rolling circle replication. Mol. Microbiol. 9:61123–30 [Google Scholar]
116. White MA, Eykelenboom JK, Lopez-Vernaza MA, Wilson E, Leach DRF. 116.  2008. Non-random segregation of sister chromosomes in Escherichia coli. Nature 455:72171248–50 [Google Scholar]
117. Wolkow CA, DeBoy RT, Craig NL. 117.  1996. Conjugating plasmids are preferred targets for Tn7. Genes Dev 10:172145–57 [Google Scholar]
118. Yang Y, Sharan SK. 118.  2003. A simple two-step, “hit and fix” method to generate subtle mutations in BACs using short denatured PCR fragments. Nucleic Acids Res 31:15e80 [Google Scholar]
119. Yeeles JTP, Marians KJ. 119.  2013. Dynamics of leading-strand lesion skipping by the replisome. Mol. Cell 52:6855–65 [Google Scholar]
120. Yin JCP, Krebs MP, Reznikoff WS. 120.  1988. Effect of DAM methylation on Tn5 transposition. J. Mol. Biol. 199:135–45 [Google Scholar]
121. Yuan Q, McHenry CS. 121.  2013. Cycling of the E. coli lagging strand polymerase is triggered exclusively by the availability of a new primer at the replication fork. Nucleic Acids Res. 42:31747–56 [Google Scholar]
122. Zhong J, Lambowitz AM. 122.  2003. Group II intron mobility using nascent strands at DNA replication forks to prime reverse transcription. EMBO J. 22:174555–65 [Google Scholar]
123. Zimmerly S, Guo H, Perlman PS, Lambowitz AM. 123.  1995. Group II intron mobility occurs by target DNA-primed reverse transcription. Cell 82:4545–54 [Google Scholar]