The Polymerase Activity of Mammalian DNA Pol ζ Is Specifically Required for Cell and Embryonic Viability

DNA polymerase ζ (pol ζ) is exceptionally important for maintaining genome stability. Inactivation of the Rev3l gene encoding the polymerase catalytic subunit causes a high frequency of chromosomal breaks, followed by lethality in mouse embryos and in primary cells. Yet it is not known whether the DNA polymerase activity of pol ζ is specifically essential, as the large REV3L protein also serves as a multiprotein scaffold for translesion DNA synthesis via multiple conserved structural domains. We report that Rev3l cDNA rescues the genomic instability and DNA damage sensitivity of Rev3l-null immortalized mouse fibroblast cell lines. A cDNA harboring mutations of conserved catalytic aspartate residues in the polymerase domain of REV3L could not rescue these phenotypes. To investigate the role of REV3L DNA polymerase activity in vivo, a Rev3l knock-in mouse was constructed with this polymerase-inactivating alteration. No homozygous mutant mice were produced, with lethality occurring during embryogenesis. Primary fibroblasts from mutant embryos showed growth defects, elevated DNA double-strand breaks and cisplatin sensitivity similar to Rev3l-null fibroblasts. We tested whether the severe Rev3l^-/- phenotypes could be rescued by deletion of DNA polymerase η, as has been reported with chicken DT40 cells. However, Rev3l^-/- Polh^-/- mice were inviable, and derived primary fibroblasts were as sensitive to DNA damage as Rev3l^-/- Polh^+/+ fibroblasts. Therefore, the functions of REV3L in maintaining cell viability, embryonic viability and genomic stability are directly dependent on its polymerase activity, and cannot be ameliorated by an additional deletion of pol η. These results validate and encourage the approach of targeting the DNA polymerase activity of pol ζ to sensitize tumors to DNA damaging agents.     

Human DNA Polymerase η Is Required for Common Fragile Site Stability during Unperturbed DNA Replication

Human DNA polymerase η (Pol η) modulates susceptibility to skin cancer by promoting translesion DNA synthesis (TLS) past sunlight-induced cyclobutane pyrimidine dimers. Despite its well-established role in TLS synthesis, the role of Pol η in maintaining genome stability in the absence of external DNA damage has not been well explored. We show here that short hairpin RNA-mediated depletion of Pol η from undamaged human cells affects cell cycle progression and the rate of cell proliferation and results in increased spontaneous chromosome breaks and common fragile site expression with the activation of ATM-mediated DNA damage checkpoint signaling. These phenotypes were also observed in association with modified replication factory dynamics during S phase. In contrast to that seen in Pol η-depleted cells, none of these cellular or karyotypic defects were observed in cells depleted for Pol ι, the closest relative of Pol η. Our results identify a new role for Pol η in maintaining genomic stability during unperturbed S phase and challenge the idea that the sole functional role of Pol η in human cells is in TLS DNA damage tolerance and/or repair pathways following exogenous DNA damage.Mutations in the POLH gene that encodes DNA polymerase η (Pol η) are responsible for the variant form of xeroderma pigmentosum (XP-V). XP-V is a rare autosomal recessive disorder characterized by extreme sensitivity to sunlight and a very high incidence of sunlight-induced skin cancer, as are the other forms of “classical” XP (17, 27). However, in contrast to the other nucleotide excision repair (NER)-defective XP complementation groups (XP-A to XP-G), XP-V cells have normal NER but cannot support translesion synthesis (TLS) past DNA-containing cyclobutane pyrimidine dimers (CPDs) (27). Purified Pol η, the TLS polymerase that is mutated in XP-V, is able to synthesize past this lesion with a high level of efficiency (28), and in a majority of cases it inserts the correct nucleotide, adenine, opposite the two thymines contained in the cyclobutane pyrimidine dimer ring (26).The ability to replicate efficiently past UV pyrimidine dimers has been the principal—or sole—function assigned thus far to Pol η. In the absence of Pol η, cells display an increased rate of UV-induced mutagenesis and carcinogenesis (23) that may reflect inefficient or error-prone synthesis by another polymerase. In mouse cells, this back-up polymerase may be Pol ι (12). Despite its ability to replicate past cyclobutane pyrimidine dimers, Pol η does not appear to be able to carry out TLS past the other major UV photoproduct, the pyrimidine (6-4) pyrimidone photoproduct [(6-4)PP] in vitro or in vivo. It can, however, replicate past a limited number of other types of DNA damage in vitro, albeit with a lower level of efficiency than past CPDs (21). Whether the bypass of these lesions is performed in vivo by Pol η is less clear. For example, XP-V cells are sensitive to cisplatin, suggesting that bypass of cisplatin lesions may depend on Pol η (1). Combined NER- and Pol η-mediated lesion bypass has also been suggested as the likely mechanism for repairing DNA interstrand cross-links formed by mitomycin C (46) and psoralen (32). In contrast, Pol η does not appear to play a role in replication past endogenous lesions such as 8-oxoguanine (3) or abasic sites (2).It has been difficult to visualize or identify sites of action of Pol η or any of the other TLS polymerases by immunofluorescence due to their low levels of expression. However, in cells that mildly overexpress Pol η, it has been possible to localize the polymerase to nuclear replication factories during S phase. This localization depends on several motifs located close to the C terminus of Pol η, including an NLS and a ubiquitin-binding zinc finger domain (7, 18). Localization of Pol η in replication factories may concentrate the polymerase near sites of replication to facilitate recruitment to carry out TLS. If cells cannot remove or synthesize through a lesion blocking the replication fork, then homology-dependent recombinational repair (HRR) may be used to restart the replication fork (11, 34). RAD51-mediated HRR has been shown to be important for the repair of DNA damage during replication in all organisms (20, 31, 42). Recent evidence has suggested that Pol η, in addition to its role in TLS, may participate in HRR. This has been suggested by analyses of gene conversion in chicken DT40 cells during immunoglobulin gene diversification (19), as well as by in vitro experiments showing that Pol η is capable of promoting extension of the invading strand in D-loop structures to facilitate RAD52-mediated second-end capture during recombination-mediated repair (29, 30). The functional importance of this observation is less clear. Recent evidence from yeast argues that the bulk of heteroduplex DNA strand extension during HRR is mediated by the preferential recruitment of a replicative DNA polymerase, Pol δ (25). Moreover, there is no obvious recombination deficit in XP-V patients or in XP-V cells beyond a modest elevation in the frequency of UV-induced sister chromatid exchanges (10).In order to better understand the functional roles and importance of Pol η in human cells, we used short hairpin RNAs (shRNAs) to selectively deplete Pol η from cells and then determined how the loss of Pol η affected cell cycle progression, DNA replication dynamics, and cell proliferation in otherwise unperturbed cells. These experiments revealed an unexpected role for Pol η in maintaining chromosomal stability and preventing common fragile site (CFS) breakage during unperturbed S phase. Our results thus broaden the functional role of Pol η in human cells to include the maintenance of genomic stability during unperturbed DNA replication in S phase.     

The Human Lagging Strand DNA Polymerase δ Holoenzyme Is Distributive

Polymerase δ is widely accepted as the lagging strand replicative DNA polymerase in eukaryotic cells. It forms a replication complex in the presence of replication factor C and proliferating cell nuclear antigen to perform efficient DNA synthesis in vivo. In this study, the human lagging strand holoenzyme was reconstituted in vitro. The rate of DNA synthesis of this holoenzyme, measured with a singly primed ssM13 DNA substrate, is 4.0 ± 0.4 nucleotides. Results from adenosine 5′-(3-thiotriphosphate) tetralithium salt (ATPγS) inhibition experiments revealed the nonprocessive characteristic of the human DNA polymerase (Pol δ) holoenzyme (150 bp for one binding event), consistent with data from chase experiments with catalytically inactive mutant Pol δ^AA. The ATPase activity of replication factor C was characterized and found to be stimulated ∼10-fold in the presence of both proliferating cell nuclear antigen and DNA, but the activity was not shut down by Pol δ in accord with rapid association/dissociation of the holoenzyme to/from DNA. It is noted that high concentrations of ATP inhibit the holoenzyme DNA synthesis activity, most likely due to its inhibition of the clamp loading process.     

Active Site Mutations in Mammalian DNA Polymerase δ Alter Accuracy and Replication Fork Progression

DNA polymerase δ (pol δ) is one of the two main replicative polymerases in eukaryotes; it synthesizes the lagging DNA strand and also functions in DNA repair. In previous work, we demonstrated that heterozygous expression of the pol δ L604G variant in mice results in normal life span and no apparent phenotype, whereas a different substitution at the same position, L604K, is associated with shortened life span and accelerated carcinogenesis. Here, we report in vitro analysis of the homologous mutations at position Leu-606 in human pol δ. Four-subunit human pol δ variants that harbor or lack 3′ → 5′-exonucleolytic proofreading activity were purified from Escherichia coli. The pol δ L606G and L606K holoenzymes retain catalytic activity and processivity similar to that of wild type pol δ. pol δ L606G is highly error prone, incorporating single noncomplementary nucleotides at a high frequency during DNA synthesis, whereas pol δ L606K is extremely accurate, with a higher fidelity of single nucleotide incorporation by the active site than that of wild type pol δ. However, pol δ L606K is impaired in the bypass of DNA adducts, and the homologous variant in mouse embryonic fibroblasts results in a decreased rate of replication fork progression in vivo. These results indicate that different substitutions at a single active site residue in a eukaryotic polymerase can either increase or decrease the accuracy of synthesis relative to wild type and suggest that enhanced fidelity of base selection by a polymerase active site can result in impaired lesion bypass and delayed replication fork progression.     

Bacillus subtilis DNA Polymerase III Is Required for the Replication of the Virulent Bacteriophage φe

The virulent phage phie of Bacillus subtilis which contains hydroxymethyluracil in its DNA requires host DNA polymerase III for its DNA replication. DNA polymerase III(ts) mutant cells infected with phie at restrictive temperatures do not support phage DNA synthesis. However, phie grows normally both at low and high temperatures in the mutant's parent strain and in spontaneous DNA polymerase III(+) revertants isolated from the mutant strain. Temperature-shift-down experiments with phie-infected cells having thermosensitive DNA polymerase III (pol III(ts)) indicate that at 48 C the thermolabile DNA polymerase III is irreversibly inactivated and has to be synthesized de novo after the shift to 37 C, before phage DNA synthesis can begin. Temperature-shift-up experiments with phie-infected mutant cells show that phage replication is arrested immediately after the temperature shift and indicate that phie requires DNA polymerase III throughout its replication stage.     

Involvement of the Yeast DNA Polymerase δ in DNA Repair in Vivo

The POL3 encoded catalytic subunit of DNA polymerase δ possesses a highly conserved C-terminal cysteine-rich domain in Saccharomyces cerevisiae. Mutations in some of its cysteine codons display a lethal phenotype, which demonstrates an essential function of this domain. The thermosensitive mutant pol3-13, in which a serine replaces a cysteine of this domain, exhibits a range of defects in DNA repair, such as hypersensitivity to different DNA-damaging agents and deficiency for induced mutagenesis and for recombination. These phenotypes are observed at 24°, a temperature at which DNA replication is almost normal; this differentiates the functions of POL3 in DNA repair and DNA replication. Since spontaneous mutagenesis and spontaneous recombination are efficient in pol3-13, we propose that POL3 plays an important role in DNA repair after irradiation, particularly in the error-prone and recombinational pathways. Extragenic suppressors of pol3-13 are allelic to sdp5-1, previously identified as an extragenic suppressor of pol3-11. SDP5, which is identical to HYS2, encodes a protein homologous to the p50 subunit of bovine and human DNA polymerase δ. SDP5 is most probably the p55 subunit of Polδ of S. cerevisiae and seems to be associated with the catalytic subunit for both DNA replication and DNA repair.     

Interaction of Loach DNA Polymerase δ with DNA Duplexes with Single-Strand Gaps

The interaction of DNA polymerase purified from eggs of the teleost fish Misgurnus fossilis (loach) with DNA duplexes with single-strand gaps of 1-13 nucleotides was studied. In the absence of template-restricting DNA, the enzyme elongated primers on single-stranded DNA templates in a distributive manner. However, in the presence of the proximal 5"-terminus restricting the template, the enzyme activity significantly increased. In this case, the enzyme was capable of processive synthesis by filling gaps of 5-9 nucleotides in DNA duplexes. These data indicate that DNA polymerase can interact with both the 3"- and 5"-termini located upstream and downstream from the gap. Analysis of the complexes formed by DNA polymerase and different DNA substrates by electrophoretic mobility shift assay confirmed the assumption that this enzyme can interact with the proximal 5"-terminus restricting the gap. DNA polymerase displayed much higher affinity in duplexes with gaps of approximately 10 nucleotides compared to the standard template–primer complexes. Maximal affinity was observed in experiments with DNA substrates containing unpaired 3"-tails in primers. The results of this study suggest that DNA polymerase exerts high activity in the cell nuclei during repair of DNA intermediates with single strand gaps and unpaired 3"-termini.     

A Specific Docking Site for DNA Polymerase α-Primase on the SV40 Helicase Is Required for Viral Primosome Activity,but Helicase Activity Is Dispensable

Replication of simian virus 40 (SV40) DNA, a model for eukaryotic chromosomal replication, can be reconstituted in vitro using the viral helicase (large tumor antigen, or Tag) and purified human proteins. Tag interacts physically with two cellular proteins, replication protein A and DNA polymerase α-primase (pol-prim), constituting the viral primosome. Like the well characterized primosomes of phages T7 and T4, this trio of proteins coordinates parental DNA unwinding with primer synthesis to initiate the leading strand at the viral origin and each Okazaki fragment on the lagging strand template. We recently determined the structure of a previously unrecognized pol-prim domain (p68N) that docks on Tag, identified the p68N surface that contacts Tag, and demonstrated its vital role in primosome function. Here, we identify the p68N-docking site on Tag by using structure-guided mutagenesis of the Tag helicase surface. A charge reverse substitution in Tag disrupted both p68N-binding and primosome activity but did not affect docking with other pol-prim subunits. Unexpectedly, the substitution also disrupted Tag ATPase and helicase activity, suggesting a potential link between p68N docking and ATPase activity. To assess this possibility, we examined the primosome activity of Tag with a single residue substitution in the Walker B motif. Although this substitution abolished ATPase and helicase activity as expected, it did not reduce pol-prim docking on Tag or primosome activity on single-stranded DNA, indicating that Tag ATPase is dispensable for primosome activity in vitro.     

A DNA Polymerase α Accessory Protein,Mcl1, Is Required for Propagation of Centromere Structures in Fission Yeast

Specialized chromatin exists at centromeres and must be precisely transmitted during DNA replication. The mechanisms involved in the propagation of these structures remain elusive. Fission yeast centromeres are composed of two chromatin domains: the central CENP-A^Cnp1 kinetochore domain and flanking heterochromatin domains. Here we show that fission yeast Mcl1, a DNA polymerase α (Polα) accessory protein, is critical for maintenance of centromeric chromatin. In a screen for mutants that alleviate both central domain and outer repeat silencing, we isolated several cos mutants, of which cos1 is allelic to mcl1. The mcl1-101 mutation causes reduced CENP-A^Cnp1 in the central domain and an aberrant increase in histone acetylation in both domains. These phenotypes are also observed in a mutant of swi7⁺, which encodes a catalytic subunit of Polα. Mcl1 forms S-phase-specific nuclear foci, which colocalize with those of PCNA and Polα. These results suggest that Mcl1 and Polα are required for propagation of centromere chromatin structures during DNA replication.     

Neurospora Importin α Is Required for Normal Heterochromatic Formation and DNA Methylation

Heterochromatin and associated gene silencing processes play roles in development, genome defense, and chromosome function. In many species, constitutive heterochromatin is decorated with histone H3 tri-methylated at lysine 9 (H3K9me3) and cytosine methylation. In Neurospora crassa, a five-protein complex, DCDC, catalyzes H3K9 methylation, which then directs DNA methylation. Here, we identify and characterize a gene important for DCDC function, dim-3 (defective in methylation-3), which encodes the nuclear import chaperone NUP-6 (Importin α). The critical mutation in dim-3 results in a substitution in an ARM repeat of NUP-6 and causes a substantial loss of H3K9me3 and DNA methylation. Surprisingly, nuclear transport of all known proteins involved in histone and DNA methylation, as well as a canonical transport substrate, appear normal in dim-3 strains. Interactions between DCDC members also appear normal, but the nup-6dim-3 allele causes the DCDC members DIM-5 and DIM-7 to mislocalize from heterochromatin and NUP-6^dim-3 itself is mislocalized from the nuclear envelope, at least in conidia. GCN-5, a member of the SAGA histone acetyltransferase complex, also shows altered localization in dim-3, raising the possibility that NUP-6 is necessary to localize multiple chromatin complexes following nucleocytoplasmic transport.     

Replication Stress Leads to Genome Instabilities in Arabidopsis DNA Polymerase δ Mutants

Impeded DNA replication or a deficiency of its control may critically threaten the genetic information of cells, possibly resulting in genome alterations, such as gross chromosomal translocations, microsatellite instabilities, or increased rates of homologous recombination (HR). We examined an Arabidopsis thaliana line derived from a forward genetic screen, which exhibits an elevated frequency of somatic HR. These HR events originate from replication stress in endoreduplicating cells caused by reduced expression of the gene coding for the catalytic subunit of the DNA polymerase δ (POLδ1). The analysis of recombination types induced by diverse alleles of polδ1 and by replication inhibitors allows the conclusion that two not mutually exclusive mechanisms lead to the generation of recombinogenic breaks at replication forks. In plants with weak polδ1 alleles, we observe genome instabilities predominantly at sites with inverted repeats, suggesting the formation and processing of aberrant secondary DNA structures as a result of the accumulation of unreplicated DNA. Stalled and collapsed replication forks account for the more drastic enhancement of HR in plants with strong polδ1 mutant alleles. Our data suggest that efficient progression of DNA replication, foremost on the lagging strand, relies on the physiological level of the polymerase δ complex and that even a minor disturbance of the replication process critically threatens genomic integrity of Arabidopsis cells.     

DNA Polymerase α Subunit Residues and Interactions Required for Efficient Initiation Complex Formation Identified by a Genetic Selection

Biophysical and structural studies have defined many of the interactions that occur between individual components or subassemblies of the bacterial replicase, DNA polymerase III holoenzyme (Pol III HE). Here, we extended our knowledge of residues and interactions that are important for the first step of the replicase reaction: the ATP-dependent formation of an initiation complex between the Pol III HE and primed DNA. We exploited a genetic selection using a dominant negative variant of the polymerase catalytic subunit that can effectively compete with wild-type Pol III α and form initiation complexes, but cannot elongate. Suppression of the dominant negative phenotype was achieved by secondary mutations that were ineffective in initiation complex formation. The corresponding proteins were purified and characterized. One class of mutant mapped to the PHP domain of Pol III α, ablating interaction with the ϵ proofreading subunit and distorting the polymerase active site in the adjacent polymerase domain. Another class of mutation, found near the C terminus, interfered with τ binding. A third class mapped within the known β-binding domain, decreasing interaction with the β₂ processivity factor. Surprisingly, mutations within the β binding domain also ablated interaction with τ, suggesting a larger τ binding site than previously recognized.