Recombinational DNA repair of damaged repliction forks in Eschericha coli: Questions

Annual Review of Genetics

Volumn 35, Issue , 2001, Pages 53-82

  Cox, M M ^a  

^a UNIVERSITY OF WISCONSIN MADISON   (United States)

Author keywords

PriA protein; RecA protein; Recombination; Repair; Replication

Indexed keywords

DOUBLE STRANDED DNA; RECA PROTEIN;

BACTERIAL GENETICS; DNA RECOMBINATION; DNA REPAIR; DNA REPLICATION; DNA STRUCTURE; ESCHERICHIA COLI; GENETIC RECOMBINATION; HOLLIDAY JUNCTION; NONHUMAN; PRIORITY JOURNAL; RECA GENE; REVIEW;

BACTERIAL PROTEINS; CHROMOSOMES, BACTERIAL; DNA DAMAGE; DNA REPAIR; DNA REPLICATION; DNA, BACTERIAL; ESCHERICHIA COLI; RECOMBINATION, GENETIC; REPLICATION ORIGIN; SOS RESPONSE (GENETICS);

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI; NEGIBACTERIA;

EID: 0035679232     PISSN: 00664197     EISSN: None     Source Type: Book Series    
DOI: 10.1146/annurev.genet.35.102401.090016     Document Type: Review

References (182)

1. Modulation of recombination and DNA repair by the RecG and PriA helicases of Escherichia coli K-12
2. The recombination hot spot chi is a regulatory element that switches the polarity of DNA degradation by the RecBCD enzyme
3. The translocating RecBCD enzyme stimulates recombination by directing RecA protein onto ssDNA in a chiregulated manner
4. Survey and summary: Holliday junction resolvases and related nucleases: Identification of new families, phyletic distribution and evolutionary trajectories
5. Quantitative analysis of the kinetics of end-dependent disassembly of RecA filaments from ssDNA
6. DNA replication triggered by double-stranded breaks in E. coli: Dependence on homologous recombination functions
7. Frequency and spectrum of mutations produced by a single cis-syn thymine-thymine cyclobutane dimer in a single-stranded vector
8. Circles: The replication-recombination-chromosome segregation connection
9. Effect of single DNA lesions on in vitro replication with DNA polymerase III holoenzyme. Comparison with other polymerases
10. RuvC protein resolves Holliday junctions via cleavage of the continuous (noncrossover) strands
11. Genetic damage, mutation, and the evolution of sex
12. Is meiotic recombination an adaptation for repairing DNA, producing genetic variation, or both?
13. Molecular analysis of the recF gene of Escherichia coli
14. The complete genome sequence of Escherichia coli K- 12
15. Chromosome break-induced DNA replication leads to nonreciprocal translocations and telomere capture
16. DNA chain elongation and joining in normal human and xeroderma pigmentosum cells after ultraviolet irradiation
17. Defending genome integrity during DNA replication: A proposed role for RecQ family helicases
18. Recognition and manipulation of branched DNA by the RusA Holliday junction resolvase of Escherichia coli
19. Resolution of an early RecA-recombination intermediate by a junction-specific endonuclease
20. The RecBC enzyme loads RecA protein onto ssDNA asymmetrically and independently of chi, resulting in constitutive recombination activation
21. Progress toward a metabolic interpretation of genetic recombination of Escherichia coli and bacteriophage lambda
22. Homologous genetic recombination: The pieces begin to fall into place
23. Review: SMCs in the world of chromosome biology - From prokaryotes to higher eukaryotes
24. Methyl-directed mismatch repair is bidirectional
25. Analysis of DNA replication forks encountering a pyrimidine dimer in the template to the leading strand
26. Relating biochemistry to biology: How the recombinational repair function of the RecA system is manifested in its molecular properties
27. Recombinational cross-roads - Eukaryotic enzymes and the limits of bacterial precedents
28. A broadening view of recombinational DNA repair in bacteria
29. Recombinational DNA repair in bacteria and the RecA protein
30. Historical overview: Searching for replication help in all the rec places
31. The importance of repairing stalled replication forks
32. Control of crossing over
33. A mutation (radA100) in Escherichia coli that selectively sensitizes cells grown in rich medium to x- or u.v.-radiation, or methyl methanesulphonate
34. Comparative evolution and the origin of sexuality
35. The effects on strand exchange of 5′ versus 3′ ends of single-stranded DNA in RecA nucleoprotein filaments
36. The Bloom's syndrome gene product is homologous to RecQ helicases
37. Identification of the Escherichia coli recN gene product as a major SOS protein
38. Impairment of lagging strand synthesis triggers the formation of a RuvABC substrate at replication forks
39. Transcriptional organization of the Escherichia coli dnaX gene
40. RecQ-like helicases: The DNA replication checkpoint connection
41. Pathways for homologous recombination between chromosomal direct repeats in Salmonella typhimurium
42. Architecture of the replication fork stalled at the 3′ end of yeast ribosomal genes
43. DNA recombination: The replication connection
44. RecQ helicase and topoisomerase III comprise a novel DNA strand passage function: A conserved mechanism for control of DNA recombination
45. A model for replication repair in mammalian cells
46. Escherichia coli Tus protein acts to arrest the progression of DNA replication forks in vitro
47. Genetic analysis of the RecF pathway to genetic recombination in Escherichia coli K12: Isolation and characterization of mutants
48. Mechanisms and consequences of replication fork arrest
49. Bimodal pattern of killing of DNA-repair-defective or anoxicallygrown Escherichia coli by hydrogen peroxide
50. Methodology for the study of the effect of drugs on development and DNA replication in Drosophila melanogaster embryonic tissue
51. Blocked RecA protein-mediated DNA strand exchange reactions are reversed by the RuvA and RuvB proteins
52. On the role of ATP hydrolysis in RecA protein-mediated DNA strand exchange III. Unidirectional branch migration and extensive hybrid DNA formation
53. Mechanisms of inhibition of DNA replication by ultraviolet light in normal human and xeroderma pigmentosum fibroblasts
54. Superoxide and the production of oxidative DNA damage
55. Mechanism of transient inhibition of DNA synthesis in ultraviolet-irradiated E. coli: Inhibition is independent of recA whilst recovery requires RecA protein itself and an additional, inducible SOS function
56. Stable DNA replication: Interplay between DNA replication, homologous recombination, and transcription
57. DNA replication in Escherichia coli: Replication in absence of protein synthesis after replication inhibition
58. Characterization of the replication of Escherichia coli DNA in the absence of protein synthesis: Stable DNA replication
59. Genetic recombination of bacterial plasmid DNA: Effect of RecF pathway mutations on plasmid recombination in Escherichia coli
60. The preference for a 3′ homologous end is intrinsic to RecA-promoted strand exchange
61. Initiation of genetic recombination and recombination-dependent replication
62. Biochemistry of homologous recombination in Escherichia coli
63. Recombination-dependent DNA replication in phage T4
64. Recombinational repair of DNA damage in Escherichia coli and bacteriophage lambda
65. DNA replication meets genetic exchange: Generation of chromosomal damage and its repair by homologous recombination
66. Single-strand interruptions in replicating chromosomes cause double-strand breaks
67. Mutation frequency and spectrum resulting from a single abasic site in a single-stranded vector
68. RAD50 and RAD51 define two pathways that collaborate to maintain telomeres in the absence of telomerase
69. Postreplication repair of DNA in ultraviolet-irradiated mammalian cells
70. Genetic exchanges caused by ultraviolet photoproducts in phage lambda DNA molecules: The role of DNA replication
71. Instability and decay of the primary structure of DNA
72. Toxicity, mutagenesis and stress responses induced in Escherichia coli by hydrogen peroxide
73. PriA-directed assembly of a primosome on D loop DNA
74. Replication of UV-irradiated single-stranded DNA by DNA polymerase III holoenzyme of Escherichia coli: Evidence for bypass of pyrimidine photodimers
75. Inducible expression of a gene specific to the RecF pathway for recombination in Escherichia coli K12
76. Dissociation of synthetic Holliday junctions by E. coli RecG protein
77. Genetic analysis of the recJ gene of Escherichia coli K-12
78. Identification and purification of a single-stranded-DNA-specific exonuclease encoded by the recJ gene of Escherichia coli
79. Two alternative mechanisms for initiation of DNA replication forks in bacteriophage T4: Priming by RNA polymerase and by recombination
80. Identification of the recR locus of Escherichia coli K-12 and analysis of its role in recombination and DNA repair
81. The recR locus of Escherichia coli K-12: Molecular cloning, DNA sequencing and identification of the gene product
82. Double-strand break repair in the absence of RAD51 in yeast: A possible role for break-induced DNA replication
83. PriA: At the cross-roads of DNA replication and recombination
84. PriA-directed replication fork restart in Escherichia coli
85. RecA protein-catalyzed strand assimilation: Stimulation by Escherichia coli single-stranded DNA-binding protein
86. The DNA replication protein PriA and the recombination protein RecG bind D-loops
87. RecG helicase activity at three- and four-strand DNA structures
88. Modulation of RNA polymerase by (p)ppGpp reveals a RecG-dependent mechanism for replication fork progression
89. Formation of Holliday junctions by regression of nascent DNA in intermediates containing stalled replication forks: RecG stimulates regression even when the DNA is negatively supercoiled
90. Gaps in DNA synthesized by ultraviolet light-irradiated WI38 human cells
91. T4-endonuclease V-sensitive sites in DNA from ultraviolet-irradiated human cells
92. Chromosome breakage accompanying genetic recombination in bacteriophage
93. Replication fork arrest and DNA recombination
94. Rescue of arrested replication forks by homologous recombination
95. Resolution of Holliday junctions by Ruv ABC prevents dimer formation in rep mutants and UV-irradiated cells
96. Repair of near-ultraviolet (365 nm)-induced strand breaks in Escherichia coli DNA. The role of the polA and recA gene products
97. Methyl-directed DNA mismatch correction
98. Sites of termination of in vitro DNA synthesis on ultraviolet- and N-acetylaminofluorene-treated phi X174 templates by prokaryotic and eukaryotic DNA polymerases
99. Anaerobic incubation enhances the colony formation of a polA recB strain of Escherichia coli K-12
100. Mechanisms of assembly of the enzyme-ssDNA complexes required for recombination-dependent DNA synthesis and repair in bacteriophage T4
101. "Break copy" duplication: A model for chromosome fragment formation in Saccharomyces cerevisiae
102. Induction of error-prone repair as a consequence of DNA ligase deficiency in Escherichia coli
103. The essential role of recombination in phage T4 growth
104. Recombination and recombination-dependent DNA replication in bacteriophage T4
105. Isolation and genetic characterization of a thymineless death-resistant mutant of Escherichia coli K12: Identification of a new mutation (recQ1) that blocks the RecF recombination pathway
106. Unusual base-pairing of newly synthesized DNA in HeLa cells
107. Formation of a single base mismatch impedes spontaneous DNA branch migration
108. The kinetics of spontaneous DNA branch migration
109. Construction and complementation of a recA deletion mutant of Mycobacterium smegmatis reveals that the intein in Mycobacterium tuberculosis recA does not affect RecA function
110. Mycobacterial recA is cotranscribed with a potential regulatory gene called recX
111. Assay of excised oxidative DNA lesions: Isolation of 8-oxoguanine and its nucleoside derivatives from biological fluids with a monoclonal antibody column
112. Structure of a multisubunit complex that promotes DNA branch migration
113. Repair of DNA containing O6-alkylguanine
114. Positive and negative regulatory elements in the dnaA-dnaN-recF operon of Escherichia coli
115. Repair of DNA double-strand breaks in Escherichia coli K12 requires a functional recN product
116. Positive torsional strain causes the formation of a four-way junction at replication forks
117. Genetic recombination: Molecular biology, biochemistry, and evolution
118. Activity of the purified mutagenesis proteins UmuC, UmuD', and RecA in replicative bypass of an abasic DNA lesion by DNA polymerase III
119. A phenotype for enigmatic DNA polymerase II: A pivotal role for pol H in replication restart in UV-irradiated Escherichia coli
120. The direction of RecA protein assembly onto single strand DNA is the same as the direction of strand assimilation during strand exchange
121. Normal oxidative damage to mitochondrial and nuclear DNA is extensive
122. RecA protein promotes the regression of stalled replication forks in vitro
123. RecA protein: Structure, function, and role in recombinational DNA repair
124. Nucleotide sequence and LexA regulation of the Escherichia coli recN gene
125. Replication fork pausing and recombination or "gimme a break"
126. Discontinuities in the DNA synthesized in an excision-defective strain of Escherichia coli following ultraviolet irradiation
127. Exchanges between DNA strands in ultraviolet-irradiated Escherichia coli
128. Insertion of nucleotides opposite apurinic/apyrimidinic sites in deoxyribonucleic acid during in vitro synthesis: Uniqueness of adenine nucleotides
129. ScII: An abundant chromosome scaffold protein is a member of a family of putative ATPases with an unusual predicted tertiary structure
130. DNA repair enzymes
131. Multiple genetic pathways for restarting DNA replication forks in Escherichia coli K-12
132. Role of PriA in replication fork reactivation in Escherichia coli
133. Differential suppression of priA2::kan phenotypes in Escherichia coli K-12 by mutations in priA, lexA, and dnaC
134. Tandem repeat recombination induced by replication fork defects in Escherichia coli requires a novel factor, RadC
135. RuvAB acts at arrested replication forks
136. RuvABC-dependent double-strand breaks in dnaBts mutants require RecA
137. RecA protein filaments: End-dependent dissociation from ssDNA and stabilization by RecO and RecR proteins
138. The Werner syndrome gene: The molecular basis of RecQ helicase-deficiency diseases
139. Site-specific recombination and circular chromosome segregation
140. Homologous pairing in genetic recombination: Formation of D loops by combined action of RecA protein and a helix-destabilizing protein
141. SOS response as an adaptive response to DNA damage in prokaryotes
142. Replic. I. Conversion of viral DNA to a supercoiled, biologically active duplexation of phi X174 dna with purified enzymes
143. Mutagenesis and more: UmuDC and the Escherichia coli SOS response
144. Conjugational recombination in E. coli: Myths and mechanisms
145. DNA double-strand break repair and recombination in E. coli
146. Escherichia coli DNA repair genes radA and sms are the same gene
147. Sister chromatid exchange frequencies in Escherichia coli analyzed by recombination at the dif resolvase site
148. Oxidative stress
149. Differential replication of a single. UV-induced lesion in the leading or lagging strand by a human cell extract - Fork uncoupling or gap formation
150. Biochemical basis of SOS-induced mutagenesis in Escherichia coli: Reconstitution of in vitro lesion bypass dependent on the UmuD'2C mutagenic complex and RecA protein
151. Production of DNA bifilarly substituted with bromodeoxyuridine in the first round of synthesis: Branch migration during isolation of cellular DNA
152. Frequency and fidelity of translesion synthesis of site-specific N-2acetylaminofluorene adducts during DNA replication in a human cell extract
153. Mutagenic replication in human cell extracts of DNA containing site-specific N-2-acetylaminofluorene adducts
154. Kinetics of branch migration in double-stranded DNA
155. Protein interactions in genetic recombination in Escherichia coli. Interactions involving RecO and RecR overcome the inhibition of RecA by single-stranded DNA-binding protein
156. RecQ DNA helicase of Escherichia coli. Characterization of the helix-unwinding activity with emphasis on the effect of single-stranded DNA-binding protein
157. Escherichia coli RecQ protein is a DNA helicase
158. Assembly of the Escherichia coli RuvABC resolvasome directs the orientation of Holliday junction resolution
159. Transcriptional and mutational analyses of the Streptomyces lividans recX gene and its interference with RecA activity
160. Single-strand DNA-specific exonucleases in Escherichia coli. Roles in repair and mutation avoidance
161. Gene conversion tracts stimulated by HOT1-promoted transcription are long and continuous
162. The SOS response to DNA damage
163. Cosuppression of recF, recR and recO mutations by mutant recA alleles in Escherichia coli cells
164. Inviability of dam recA and dam recB cells of Escherichia coli is correlated with their inability to repair DNA double-strand breaks produced by mismatch repair
165. The origin of nascent single-stranded DNA extracted from mammalian cells
166. An interaction between the Escherichia coli RecF and RecR proteins dependent on ATP and double-stranded DNA
167. Recombinational DNA repair - The RecF and RecR proteins limit the extension of RecA filaments beyond single-strand DNA gaps
168. Processing of recombination intermediates by the Ruv ABC proteins
169. Heteroduplex formation by RecA protein: Polarity of strand exchanges
170. Reverse branch migration of Holliday junctions by RecG protein: A new mechanism for resolution of intermediates in recombination and DNA repair
171. Branch migration of Holliday junctions: Identification of RecG protein as a junction specific DNA helicase
172. Association of phiX174 DNA-dependent ATPase activity with an Escherichia coli protein, replication factor Y, required for in vitro synthesis of phiX174 DNA
173. Over-production of DnaE protein (alpha subunit of DNA polymerase III) restores viability in a conditionally inviable Escherichia coli strain deficient in DNA polymerase I
174. + strains of Escherichia coli
175. Positional cloning of the Werner's syndrome gene
176. The remarkable instability of replication loops provides a general method for the isolation of origins of DNA replication