Gaps and forks in DNA replication: Rediscovering old models

Lehmann, Alan R.; Fuchs, Robert P. P.

doi:10.1016/j.dnarep.2006.07.002

Cited by 154 publications

(128 citation statements)

References 17 publications

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“…The ratio of kan R /cm R E. coli colonies is a measure of the efficiency of TLS in the mammalian cells, and sequence analysis of plasmids extracted from individual colonies provides data on DNA sequence changes during TLS. The assay was found to be very useful to study TLS in mammalian cells (8,16,17), perhaps because it is a good model system of postreplication gaps (18). Using this system we have shown that TLS across a TT CPD is an order of magnitude more mutagenic in XPV cells compared with normal cells (19), consistent with the hypermutability of XPV cells (12), and the relatively accurate TLS across CPD by purified pol (10,20).…”

Section: Resultssupporting

confidence: 50%

DNA polymerase ζ cooperates with polymerases κ and ι in translesion DNA synthesis across pyrimidine photodimers in cells from XPV patients

Ziv

Geacintov

Nakajima

et al. 2009

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

117

125

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Human cells tolerate UV-induced cyclobutane pyrimidine dimers (CPD) by translesion DNA synthesis (TLS), carried out by DNA polymerase , the POLH gene product. A deficiency in DNA polymerase due to germ-line mutations in POLH causes the hereditary disease xeroderma pigmentosum variant (XPV), which is characterized by sunlight sensitivity and extreme predisposition to sunlight-induced skin cancer. XPV cells are UV hypermutable due to the activity of mutagenic TLS across CPD, which explains the cancer predisposition of the patients. However, the identity of the backup polymerase that carries out this mutagenic TLS was unclear. Here, we show that DNA polymerase cooperates with DNA polymerases and to carry out error-prone TLS across a TT CPD. Moreover, DNA polymerases and , but not , protect XPV cells against UV cytotoxicity, independently of nucleotide excision repair. This presents an extreme example of benefit-risk balance in the activity of TLS polymerases, which provide protection against UV cytotoxicity at the cost of increased mutagenic load.carcinogenesis ͉ DNA repair ͉ lesion bypass ͉ replication ͉ ultraviolet T LS is a fundamental mechanism for tolerating DNA damage that has escaped repair, carried out by specialized lowfidelity DNA polymerases, which synthesize across a wide variety of DNA lesions (1). At least 5 TLS DNA polymerases are present in mammals, four of which, DNA polymerases , , , and REV1, belong to the Y superfamily. The fifth TLS polymerase is pol, which belongs to the B family, and is the only TLS polymerase known to be essential in mammals (2-5). TLS polymerases exhibit a certain degree of specificity for their substrate DNA lesions, and their activity is tightly regulated (6-9). The most well characterized TLS polymerase is pol, which is specialized to bypass cyclobutane pyrimidine dimers (CPD) in a relatively error-free manner. The biological significance of pol is illustrated by the hereditary disease xeroderma pigmentosum variant (XPV), in which germ-line mutations in the POLH gene, encoding pol, cause an extreme 1000-fold increased predisposition to sunlight-induced skin cancer (10, 11). Cells from XPV patients exhibit a slightly increased UV sensitivity, and a dramatic UV hypermutability (12), which is responsible for their extreme cancer predisposition. The UV hypermutability is explained by the activity of a back-up DNA polymerase that performs TLS across CPD with lower efficiency and higher error-frequency. Although there is evidence that pol is involved in TLS across CPD in XPV cells (13-15), additional polymerases may be involved, and the picture is far from being complete. This is an important issue because these polymerases are likely to be driving sunlight-induced skin carcinogenesis in XPV patients.Here, we show that 3 TLS polymerases, pol, pol, and pol, are involved in TLS across CPD in XPV cells. Moreover, pol and pol, but not pol, also provide protection against UV cytotoxicity, independently of nucleotide excision repair (NER). Results Pol, pol, and pol Are Involved in T...

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Section: Resultssupporting

confidence: 50%

DNA polymerase ζ cooperates with polymerases κ and ι in translesion DNA synthesis across pyrimidine photodimers in cells from XPV patients

Ziv

Geacintov

Nakajima

et al. 2009

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

117

125

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“…The ssDNA gap would then be filled by pol IV, by other polymerases such as pol V or pol II, or even by pol III*. Consistent with this speculation, it has been shown that a replication fork keeps moving even when a lesion exists on both strands in vivo, leaving an ssDNA gap behind it (30,31). Heller and Marians showed (32) that the primase bound to DnaB helicase on the lagging strand can prime on the leading strand in vitro, implying that the replication fork restarts on the leading strand.…”

Section: Discussionmentioning

confidence: 58%

A Dynamic Polymerase Exchange with Escherichia coli DNA Polymerase IV Replacing DNA Polymerase III on the Sliding Clamp*

Furukohri

Goodman

Maki

2008

Journal of Biological Chemistry

133

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An assay that measures synchronized, processive DNA replication by Escherichia coli DNA polymerase III holoenzyme was used to reveal replacement of pol III by the specialized lesion bypass DNA polymerase IV when the replicative polymerase is stalled. When idled replication is restarted, a rapid burst of pol III-catalyzed synthesis accompanied by ϳ7-kb full-length products is strongly inhibited by the presence of pol IV. The production of slower-forming, shorter length DNA reflects a rapid takeover of DNA synthesis by pol IV. Here we demonstrate that pol IV rapidly (<15 s) obstructs the stable interaction between pol III* and the ␤ clamp (the lifetime of the complex is >5 min), causing the removal of pol III* from template DNA. We propose that the rapid replacement of pol III* on the ␤ clamp with pol IV is mediated by two processes, an interaction between pol IV and the ␤ clamp and a separate interaction between pol IV and pol III*. This newly discovered property of pol IV facilitates a dynamic exchange between the two free polymerases at the primer terminus. Our study suggests a model in which the interaction between pol III* and the ␤ clamp is mediated by pol IV to ensure that DNA replication proceeds with minimal interruption.Successful DNA replication requires a high fidelity DNA polymerase to replicate the entire genome accurately. In Escherichia coli, DNA polymerase III holoenzyme (pol III HE) 2 is a replicative polymerase that catalyzes elongation of DNA chains at a rate of about 1 kb/s with high fidelity. pol III HE is a multisubunit complex that contains two pol III core catalytic subassemblies, each linked to a subunit of the DnaX complex. Polymerase activity resides in the ␣ subunit, the largest subunit of pol III HE. pol III*, a subassembly composed of two pol III cores and one DnaX complex, binds to a dimer of the ␤ subunit (the ␤ clamp) loaded onto the primer/template by the DnaX complex to form a stable structure, pol III HE, which can synthesize DNA processively (over 50 kb per binding event) (1, 2).When a replisome encounters a lesion, pol III is generally believed to stall on DNA at a lesion site on the leading strand, resulting in uncoupling of leading and lagging strand DNA synthesis and arrest of the replication fork (3-5). Two major pathways are thought to play a role in overcoming DNA damage at the replication fork; one is recombinational repair, and the other is the translesion synthesis (TLS). In the TLS pathway, a switch is likely to occur from the stalled replicative polymerase to a specialized polymerase, which replaces the former to bypass the lesion. It is not yet clear, however, how a specialized polymerase gains access to the primer terminus when a stalled replicative polymerase exists at the site or how it acts in coordination with the replicative polymerase (6).In E. coli, three polymerases, pol II, pol IV, and pol V, have been identified as specialized polymerases. pol IV, encoded by the dinB gene, belongs to the Y family and is up-regulated by the SOS response (7). pol IV can r...

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“…In some instances, replication may be restarted downstream of the unrepaired parental strand lesion, leaving a "daughter strand gap" (DSG)-a ssDNA lesion that cannot be filled by a conventional DNA polymerase, due to the presence of the DNA polymerase blocking lesion. The DSG has received less attention than its illustrious cousin, the DSB, but recent work in model organisms has reawakened interest in the DSG as a potential intermediate in genomic instability and cancer [7]. DSBs and DSGs can be repaired in an error-free manner by sister chromatid recombination (SCR), a mechanism whereby the damaged chromatid uses the intact sister as a template for repair by homologous recombination (HR) [5,8,9].…”

Section: Introductionmentioning

confidence: 99%

Minding the gap: The underground functions of BRCA1 and BRCA2 at stalled replication forks

Nagaraju

Scully

2007

DNA Repair

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The hereditary breast and ovarian cancer predisposition genes, BRCA1 and BRCA2, participate in the repair of DNA double strand breaks by homologous recombination. Circumstantial evidence implicates these genes in recombinational responses to DNA polymerase stalling during the S phase of the cell cycle. These responses play a key role in preventing genomic instability and cancer. Here, we review the current literature implicating the BRCA pathway in HR at stalled replication forks and explore the hypothesis that BRCA1 and BRCA2 participate in the recombinational resolution of single stranded DNA lesions termed "daughter strand gaps", generated during replication across a damaged DNA template.

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Gaps and forks in DNA replication: Rediscovering old models

Abstract: (2006) Gaps and forks in DNA replication: Rediscovering old models.

Cited by 154 publications

References 17 publications

DNA polymerase ζ cooperates with polymerases κ and ι in translesion DNA synthesis across pyrimidine photodimers in cells from XPV patients

DNA polymerase ζ cooperates with polymerases κ and ι in translesion DNA synthesis across pyrimidine photodimers in cells from XPV patients

A Dynamic Polymerase Exchange with Escherichia coli DNA Polymerase IV Replacing DNA Polymerase III on the Sliding Clamp*

Minding the gap: The underground functions of BRCA1 and BRCA2 at stalled replication forks

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