DNA Polymerases Divide the Labor of Genome Replication

Lujan, Scott A.; Williams, Jessica S.; Kunkel, Thomas A.

doi:10.1016/j.tcb.2016.04.012

Cited by 124 publications

(117 citation statements)

References 88 publications

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“…Alterations in replicative DNA polymerases that increase the rate of base pairing errors were regarded as the most obvious source of such infidelity. In the 40+ years that followed, it has been established that DNA replication in eukaryotic cells is accomplished by a concerted action of three DNA polymerases, Polα, Polδ and Polε [2,3], and the high fidelity of synthesis relies on accurate nucleotide selection by these enzymes, exonucleolytic proofreading by Polδ and Polε, and post-replicative DNA mismatch repair (MMR) [4–6]. MMR defects had been recognized as the cause of hereditary colorectal cancer (CRC) predisposition in Lynch syndrome almost 25 years ago [7] and were soon shown to be widespread in sporadic cancers.…”

Section: Prehistorymentioning

confidence: 99%

Replicative DNA polymerase defects in human cancers: Consequences, mechanisms, and implications for therapy

Barbari

Shcherbakova

2017

DNA Repair

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The fidelity of DNA replication relies on three error avoidance mechanisms acting in series: nucleotide selectivity of replicative DNA polymerases, exonucleolytic proofreading, and post-replicative DNA mismatch repair (MMR). MMR defects are well known to be associated with increased cancer incidence. Due to advances in DNA sequencing technologies, the past several years have witnessed a long-predicted discovery of replicative DNA polymerase defects in sporadic and hereditary human cancers. The polymerase mutations preferentially affect conserved amino acid residues in the exonuclease domain and occur in tumors with an extremely high mutation load. Thus, a concept has formed that defective proofreading of replication errors triggers the development of these tumors. Recent studies of the most common DNA polymerase variants, however, suggested that their pathogenicity may be determined by functional alterations other than loss of proofreading. In this review, we summarize our current understanding of the consequences of DNA polymerase mutations in cancers and the mechanisms of their mutator effects. We also discuss likely explanations for a high recurrence of some but not other polymerase variants and new ideas for therapeutic interventions emerging from the mechanistic studies.

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Section: Prehistorymentioning

confidence: 99%

Replicative DNA polymerase defects in human cancers: Consequences, mechanisms, and implications for therapy

Barbari

Shcherbakova

2017

DNA Repair

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“…Each time a cell divides, the genome must be faithfully copied and transferred to a daughter cell for genetic inheritance. The former relies on replicative DNA polymerases (pols) that read a template strand in the 3′ to 5′ direction and synthesize complementary DNA in the 5′ to 3′ direction 4 . In eukaryotes, DNA replication emanates from many replication origins ( Ori ) that are activated at different times over the course of an extended S-phase 5 .…”

Section: Introductionmentioning

confidence: 99%

“…The leading strand template is replicated continuously in the direction of replication fork progression while the nascent DNA on the lagging strand template is synthesized in short fragments (i.e., discontinuously) in the opposite direction. These short fragments, referred to as Okazaki fragments, are subsequently processed and ligated together to form a continuous, mature DNA strand 4 .…”

Section: Introductionmentioning

confidence: 99%

Eukaryotic Translesion DNA Synthesis on the Leading and Lagging Strands: Unique Detours around the Same Obstacle

Hedglin

Benkovic

2017

Chem. Rev.

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During S-phase, minor DNA damage may be overcome by DNA damage tolerance (DDT) pathways that bypass such obstacles, postponing repair of the offending damage to complete the cell cycle and maintain cell survival. In translesion DNA synthesis (TLS), specialized DNA polymerases replicate the damaged DNA, allowing stringent DNA synthesis by a replicative polymerase to resume beyond the offending damage. Dysregulation of this DDT pathway in human cells leads to increased mutations rates that may contribute to the onset of cancer. Furthermore, TLS affords human cancer cells the ability to counteract chemotherapeutic agents that elicit cell death by damaging DNA in actively replicating cells. Currently, it is unclear how this critical pathway unfolds, in particular where and when TLS occurs on each template strand. Given the semi-discontinuous nature of DNA replication, it is likely that TLS on the leading and lagging strand templates is unique for each strand. Since the discovery of DDT in the late 1960’s, most studies on TLS in eukaryotes have focused on DNA lesions resulting from ultraviolet (UV) radiation exposure. In this review, we re-visit these and other related studies to dissect the step-by-step intricacies of this complex process, provide our current understanding of TLS on leading and lagging strand templates, and propose testable hypotheses to gain further insights.

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“…Pole replicates the leading strand, whereas Polδ synthesizes the lagging strand. This "division of labor during eukaryotic DNA replication" model (20) was initially proposed based on the characterization of S. cerevisiae strains carrying activesite mutations in DNA polymerases (e.g., pol2-M644G and pol3-L612M), which confer a weak mutator phenotype with a characteristic mutator signature, without compromising DNA polymerase proofreading activity (21,22).…”

mentioning

confidence: 99%

Alterations in cellular metabolism triggered by URA7 or GLN3 inactivation cause imbalanced dNTP pools and increased mutagenesis

Schmidt

Reyes

Gries

et al. 2017

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

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Eukaryotic DNA replication fidelity relies on the concerted action of DNA polymerase nucleotide selectivity, proofreading activity, and DNA mismatch repair (MMR). Nucleotide selectivity and proofreading are affected by the balance and concentration of deoxyribonucleotide (dNTP) pools, which are strictly regulated by ribonucleotide reductase (RNR). Mutations preventing DNA polymerase proofreading activity or MMR function cause mutator phenotypes and consequently increased cancer susceptibility. To identify genes not previously linked to high-fidelity DNA replication, we conducted a genome-wide screen in Saccharomyces cerevisiae using DNA polymerase active-site mutants as a "sensitized mutator background." Among the genes identified in our screen, three metabolism-related genes (GLN3, URA7, and SHM2) have not been previously associated to the suppression of mutations. Loss of either the transcription factor Gln3 or inactivation of the CTP synthetase Ura7 both resulted in the activation of the DNA damage response and imbalanced dNTP pools. Importantly, these dNTP imbalances are strongly mutagenic in genetic backgrounds where DNA polymerase function or MMR activity is partially compromised. Previous reports have shown that dNTP pool imbalances can be caused by mutations altering the allosteric regulation of enzymes involved in dNTP biosynthesis (e.g., RNR or dCMP deaminase). Here, we provide evidence that mutations affecting genes involved in RNR substrate production can cause dNTP imbalances, which cannot be compensated by RNR or other enzymatic activities. Moreover, Gln3 inactivation links nutrient deprivation to increased mutagenesis. Our results suggest that similar genetic interactions could drive mutator phenotypes in cancer cells.DNA replication fidelity | mismatch repair | CTP biosynthesis | DNA polymerases | dNTP pool imbalance T he fidelity of DNA replication is strongly influenced by three processes (1-3): (i) nucleotide selectivity, wherein replicative DNA polymerases select the correct dNTP to be incorporated; (ii) DNA polymerase proofreading activity, which excises wrongly incorporated nucleotides by using the DNA polymerase 3′-to-5′ exonuclease activity; and (iii) mismatch repair (MMR) (4, 5), a DNA replication-coupled repair mechanism (6, 7), which corrects errors that escaped proofreading. Furthermore, the balance and overall concentration of dNTPs not only affect nucleotide selection but also influence DNA polymerase proofreading activity (8). A central player in the biosynthesis of dNTPs is the ribonucleotide reductase (RNR) holoenzyme, which catalyzes the reduction of NDPs to dNDPs (9, 10). In Saccharomyces cerevisiae, RNR is composed of two identical Rnr1 large subunits that associate with two smaller subunits represented by Rnr2 and Rnr4 (11,12). In addition, a second large subunit has been identified (Rnr3), which is induced upon DNA damage and when overexpressed can rescue the rnr1 lethal phenotype (13).The interplay between nucleotide selectivity, DNA polymerase proofreading activity, and MM...

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DNA Polymerases Divide the Labor of Genome Replication

Cited by 124 publications

References 88 publications

Replicative DNA polymerase defects in human cancers: Consequences, mechanisms, and implications for therapy

Replicative DNA polymerase defects in human cancers: Consequences, mechanisms, and implications for therapy

Eukaryotic Translesion DNA Synthesis on the Leading and Lagging Strands: Unique Detours around the Same Obstacle

Alterations in cellular metabolism triggered by URA7 or GLN3 inactivation cause imbalanced dNTP pools and increased mutagenesis

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