Action of RuvAB at Replication Fork Structures

McGlynn, Peter; Lloyd, Robert G.

doi:10.1074/jbc.m107945200

Cited by 58 publications

(78 citation statements)

References 41 publications

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“…RecG binds and unwinds DNA forks with completely double-stranded (ds) DNA arms (Fig. 1B, structure d) (11,28) in a reaction that mimics replication fork regression. RecG protein also promotes branch migration in Holliday junctions, the first activity reported for RecG (Fig.…”

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confidence: 99%

“…All in vitro experiments demonstrating fork regression-like reactions in model structures with ssDNA arms used small forks assembled from synthetic oligonucleotides, creating arms that are 25-26 nt long and are heterologous to each other (13,27,30). In the case of RecG-mediated unwinding/branch migration of forks with no ssDNA gaps, the DNA substrates have been designed to permit a reaction encompassing from a few dozen (13) to a few hundred (11,28) base pairs.…”

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confidence: 99%

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Situational Repair of Replication Forks

Robu

Inman

Cox

2004

Journal of Biological Chemistry

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Replication forks often stall or collapse when they encounter a DNA lesion. Fork regression is part of several major paths to the repair of stalled forks, allowing nonmutagenic bypass of the lesion. We have shown previously that Escherichia coli RecA protein can promote extensive regression of a forked DNA substrate that mimics a possible structure of a replication fork stalled at a leading strand lesion. Using electron microscopy and gel electrophoresis, we demonstrate that another protein, E. coli RecG helicase, promotes extensive fork regression in the same system. The RecG-catalyzed fork regression is very efficient and faster than the

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confidence: 99%

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confidence: 99%

Situational Repair of Replication Forks

Robu

Inman

Cox

2004

Journal of Biological Chemistry

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“…Origin forks accumulate at early times of infection and disappear as the infection progresses. Origin replication is repressed at late times by UvsW, an RNA-DNA helicase that displaces the ori (34) transcript from the R loops (24). The disappearance of the origin fork as new initiation is repressed implies processing and resolution of the origin fork.…”

Section: T4 Origins Provide a Model For Stalled Fork Processingmentioning

confidence: 99%

“…Replication of ori (34) involves the formation of a transient fork-shaped intermediate, which we call the origin fork ( Fig. 1) (2).…”

Section: T4 Origins Provide a Model For Stalled Fork Processingmentioning

confidence: 99%

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Regression supports two mechanisms of fork processing in phage T4

Long

Kreuzer

2008

Proc. Natl. Acad. Sci. U.S.A.

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Replication forks routinely encounter damaged DNA and tightly bound proteins, leading to fork stalling and inactivation. To complete DNA synthesis, it is necessary to remove fork-blocking lesions and reactivate stalled fork structures, which can occur by multiple mechanisms. To study the mechanisms of stalled fork reactivation, we used a model fork intermediate, the origin fork, which is formed during replication from the bacteriophage T4 origin, ori(34). The origin fork accumulates within the T4 chromosome in a site-specific manner without the need for replication inhibitors or DNA damage. We report here that the origin fork is processed in vivo to generate a regressed fork structure. Furthermore, origin fork regression supports two mechanisms of fork resolution that can potentially lead to fork reactivation. Fork regression generates both a site-specific double-stranded end (DSE) and a Holliday junction. Each of these DNA elements serves as a target for processing by the T4 ATPase/exonuclease complex [gene product (gp) 46/47] and Holliday junction-cleaving enzyme (EndoVII), respectively. In the absence of both gp46 and EndoVII, regressed origin forks are stabilized and persist throughout infection. In the presence of EndoVII, but not gp46, there is significantly less regressed origin fork accumulation apparently due to cleavage of the regressed fork Holliday junction. In the presence of gp46, but not EndoVII, regressed origin fork DSEs are processed by degradation of the DSE and a pathway that includes recombination proteins. Although both mechanisms can occur independently, they may normally function together as a single fork reactivation pathway.2D gel electrophoresis ͉ DNA replication ͉ recombination ͉ restart R eplication forks routinely encounter various lesions, ranging from damaged nucleotide residues to covalent protein-DNA complexes. The consequences of these encounters depend on the type and position of the lesion (1). Although some lesions result in fork breakage, many result in fork stalling and replisome inactivation. Presumably, replisome disassembly is important for the repair of the original DNA lesion. However, it is then necessary to reactivate stalled forks to complete replication and maintain genome stability. Therefore, it is critical to understand the mechanisms of stalled fork resolution and reactivation.To identify the pathways of stalled fork reactivation, we have used a model fork intermediate that is formed during replication from bacteriophage T4 origin, ori(34). Replication from ori(34) occurs bidirectionally through a two-step process (Fig. 1) (2). A middle-mode promoter and DNA unwinding element promote the formation of an R loop that initiates the first replication fork (3). The mechanism of T4 replication from an R loop has been analyzed in vitro (4). Initially, the branch structure of the R loop supports the binding of the replicative helicase loader [gene product (gp) 59], which promotes removal of the ssDNA-binding protein (gp32) in favor of the replicative helicase (gp41). ...

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SSB and the RecG DNA helicase: an intimate association to rescue a stalled replication fork

Bianco

Lyubchenko

2017

Protein Science

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In E. coli, the regression of stalled DNA replication forks is catalyzed by the DNA helicase RecG. One means of gaining access to the fork is by binding to the single strand binding protein or SSB. This interaction occurs via the wedge domain of RecG and the intrinsically disordered linker (IDL) of SSB, in a manner similar to that of SH3 domains binding to PXXP motif-containing ligands in eukaryotic cells. During loading, SSB remodels the wedge domain so that the helicase domains bind to the parental, duplex DNA, permitting the helicase to translocate using thermal energy. This translocation may be used to clear the fork of obstacles, prior to the initiation of fork regression.

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Action of RuvAB at Replication Fork Structures

Cited by 58 publications

References 41 publications

Situational Repair of Replication Forks

Situational Repair of Replication Forks

Regression supports two mechanisms of fork processing in phage T4

SSB and the RecG DNA helicase: an intimate association to rescue a stalled replication fork

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