Increased contribution of DNA polymerase delta to the leading strand replication in yeast with an impaired CMG helicase complex

Dmowski, Michal; Jedrychowska, Malgorzata; Makiela‐Dzbenska, Karolina; Denkiewicz-Kruk, Milena; Sharma, Sushma; Chabes, Andrei; Araki, Hideki; Fijałkowska, Iwona J.

doi:10.1016/j.dnarep.2022.103272

Cited by 6 publications

(5 citation statements)

References 82 publications

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“…Our DNA sequencing data enable the observation of changes in the mutational spectra in the URA3 reporter gene cloned in two orientations regarding the nearest ARS. The data presented in this article support the study "Increased contribution of DNA polymerase delta to the leading strand replication in yeast with an impaired CMG helicase complex” [1] .…”

supporting

confidence: 83%

“…PSF1 encodes the psf1 essential subunit of the GINS complex, a component of the CMG helicase [3] . The psf1-1 subunit demonstrates impaired interaction with another GINS subunit - Psf3 [ 1 , 4 ], resulting in impaired functioning of the complex, what can affect the contribution of Pol ε to DNA replication. Deletion of REV3 inactivates DNA polymerase zeta (Pol ζ) activity partially responsible for the increased mutation rates in the psf1-1 mutant [4] .…”

Section: Data Descriptionmentioning

confidence: 99%

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Mutation spectrum data for Saccharomyces cerevisiae psf1-1 pol2-M644G mutants

et al. 2022

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supporting

confidence: 83%

Section: Data Descriptionmentioning

confidence: 99%

Mutation spectrum data for Saccharomyces cerevisiae psf1-1 pol2-M644G mutants

et al. 2022

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“…Another possibility is that the contribution of TLS polymerases to DNA replication is affected by the excess of PCNA in ATAD5-/- . A defective interaction between polymerase epsilon and CMG was reported to result in an increased leading strand synthesis by polymerase delta (45) and in enhanced activity of the error-prone polymerase zeta (46).…”

Section: Resultsmentioning

confidence: 99%

Comprehensive Whole Genome Sequencing Reveals Origins of Mutational Signatures Associated with Aging and Temozolomide Chemotherapy

Hwang,

Sitko,

Khoirunnisa

et al. 2024

Preprint

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In a comprehensive study to decipher the multi-layered response to the chemotherapeutic agent temozolomide (TMZ), we analyzed 427 genomes and determined mutational patterns in a collection of ~40 isogenic DNA repair-deficient human TK6 lymphoblast cell lines. We demonstrate that the spontaneous mutational background is very similar to the aging-associated mutational signature SBS40 and mainly caused by polymerase zeta-mediated translesion synthesis (TLS). MSH2-/- mismatch repair knockout in conjunction with additional repair deficiencies uncovers cryptic mutational patterns. We report how distinct mutational signatures are induced by TMZ upon sequential inactivation of DNA repair pathways, mirroring the acquisition of chemotherapy resistance by glioblastomas. The most toxic adduct induced by TMZ, O6-meG, is directly repaired by the O6-methylguanine-DNA methyltransferase (MGMT). In MGMT-/- cells, mismatch repair (MMR) leads to cell death and limits mutagenesis. MMR deficiency results in TMZ resistance, allowing the accumulation of ~10^5 C>T substitutions corresponding to signature SBS11. Under these conditions, N-alkylated bases, processed by base excision repair (BER), limit cell survival. Without BER, 3-meA is read through via error-prone TLS, causing T>A substitutions but not affecting survival. Blocking BER after abasic site formation results in large deletions and TMZ hypersensitization. Our findings reveal potential vulnerabilities of TMZ-resistant tumors.

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“…Interestingly, it has been shown that besides lagging strand synthesis, in some circumstances of helicase/polymerase uncoupling, Pol δ can also take over leading-strand synthesis ( 58 ). For example, in conditions where DNA mismatches cannot be properly repaired ( 59 ) and when in vitro replication of the leading strand was impeded by a dimer, Pol δ binds and synthesizes the nascent leading strand ( 60 ).…”

Section: Discussionmentioning

confidence: 99%

“…For example, in conditions where DNA mismatches cannot be properly repaired ( 59 ) and when in vitro replication of the leading strand was impeded by a dimer, Pol δ binds and synthesizes the nascent leading strand ( 60 ). Pol δ can perform proofreading on the leading strand ( 61 ) and, in mutants of replisome components such as the CMG helicase, Pol δ could also be involved in leading strand replication ( 58 ). Also, it has been reported that during break-induced replication (BIR) ( 32 ), and during replication forks restart mediated by homologous recombination both strands are replicated by Pol δ ( 33 ).…”

Section: Discussionmentioning

confidence: 99%

S-phase checkpoint prevents leading strand degradation from strand-associated nicks at stalled replication forks

Bugallo,

Sánchez,

Fernández-García

et al. 2024

Nucleic Acids Research

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The S-phase checkpoint is involved in coupling DNA unwinding with nascent strand synthesis and is critical to maintain replication fork stability in conditions of replicative stress. However, its role in the specific regulation of leading and lagging strands at stalled forks is unclear. By conditionally depleting RNaseH2 and analyzing polymerase usage genome-wide, we examine the enzymology of DNA replication during a single S-phase in the presence of replicative stress and show that there is a differential regulation of lagging and leading strands. In checkpoint proficient cells, lagging strand replication is down-regulated through an Elg1-dependent mechanism. Nevertheless, when checkpoint function is impaired we observe a defect specifically at the leading strand, which was partially dependent on Exo1 activity. Further, our genome-wide mapping of DNA single-strand breaks reveals that strand discontinuities highly accumulate at the leading strand in HU-treated cells, whose dynamics are affected by checkpoint function and Exo1 activity. Our data reveal an unexpected role of Exo1 at the leading strand and support a model of fork stabilization through prevention of unrestrained Exo1-dependent resection of leading strand-associated nicks after fork stalling.

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Increased contribution of DNA polymerase delta to the leading strand replication in yeast with an impaired CMG helicase complex

Cited by 6 publications

References 82 publications

Mutation spectrum data for Saccharomyces cerevisiae psf1-1 pol2-M644G mutants

Mutation spectrum data for Saccharomyces cerevisiae psf1-1 pol2-M644G mutants

Comprehensive Whole Genome Sequencing Reveals Origins of Mutational Signatures Associated with Aging and Temozolomide Chemotherapy

S-phase checkpoint prevents leading strand degradation from strand-associated nicks at stalled replication forks

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