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1.
DNA Repair (Amst) ; 141: 103715, 2024 Sep.
Article in English | MEDLINE | ID: mdl-39029375

ABSTRACT

Glioblastoma (GBM) is a highly aggressive brain tumor associated with poor patient survival. The current standard treatment involves invasive surgery, radiotherapy, and chemotherapy employing temozolomide (TMZ). Resistance to TMZ is, however, a major challenge. Previous work from our group has identified candidate genes linked to TMZ resistance, including genes encoding translesion synthesis (TLS) DNA polymerases iota (PolÉ©) and kappa (Polκ). These specialized enzymes are known for bypassing lesions and tolerating DNA damage. Here, we investigated the roles of PolÉ© and Polκ in TMZ resistance, employing MGMT-deficient U251-MG glioblastoma cells, with knockout of either POLI or POLK genes encoding PolÉ© and Polκ, respectively, and assess their viability and genotoxic stress responses upon subsequent TMZ treatment. Cells lacking either of these polymerases exhibited a significant decrease in viability following TMZ treatment compared to parental counterparts. The restoration of the missing polymerase led to a recovery of cell viability. Furthermore, knockout cells displayed increased cell cycle arrest, mainly in late S-phase, and lower levels of genotoxic stress after TMZ treatment, as assessed by a reduction of γH2AX foci and flow cytometry data. This implies that TMZ treatment does not trigger a significant H2AX phosphorylation response in the absence of these proteins. Interestingly, combining TMZ with Mirin (double-strand break repair pathway inhibitor) further reduced the cell viability and increased DNA damage and γH2AX positive cells in TLS KO cells, but not in parental cells. These findings underscore the crucial roles of PolÉ© and Polκ in conferring TMZ resistance and the potential backup role of homologous recombination in the absence of these TLS polymerases. Targeting these TLS enzymes, along with double-strand break DNA repair inhibition, could, therefore, provide a promising strategy to enhance TMZ's effectiveness in treating GBM.


Subject(s)
DNA Modification Methylases , DNA Polymerase iota , DNA Repair Enzymes , DNA-Directed DNA Polymerase , Drug Resistance, Neoplasm , Glioblastoma , Temozolomide , Temozolomide/pharmacology , Humans , Glioblastoma/genetics , Glioblastoma/drug therapy , Glioblastoma/metabolism , Glioblastoma/pathology , DNA-Directed DNA Polymerase/metabolism , DNA-Directed DNA Polymerase/genetics , Cell Line, Tumor , DNA Modification Methylases/metabolism , DNA Modification Methylases/genetics , DNA Repair Enzymes/metabolism , DNA Repair Enzymes/genetics , Tumor Suppressor Proteins/metabolism , Tumor Suppressor Proteins/genetics , Tumor Suppressor Proteins/deficiency , Antineoplastic Agents, Alkylating/pharmacology , Antineoplastic Agents, Alkylating/therapeutic use , DNA Damage , Cell Survival/drug effects , Brain Neoplasms/drug therapy , Brain Neoplasms/genetics , Brain Neoplasms/metabolism , Brain Neoplasms/pathology , DNA Repair , Gene Knockout Techniques
2.
DNA Repair (Amst) ; 141: 103712, 2024 Sep.
Article in English | MEDLINE | ID: mdl-38959714

ABSTRACT

Epigenetic cytosine methylation covers most of genomic CpG dinucleotides in human cells. In addition to common deamination-mediated mutagenesis at CpG sites, an alternative deamination-independent pathway associated with DNA polymerase activity was previously described. This mutagenesis is characterized by the TCG→TTG mutational signature and is believed to arise from dAMP misincorporation opposite 5-methylcytosine (mC) or its oxidized derivative 5-hydroxymethylcytosine (hmC) by B-family replicative DNA polymerases with disrupted proofreading 3→5'-exonuclease activity. In addition to being less stable and pro-mutagenic themselves, cytosine modifications also increase the risk of adjacent nucleotides damage, including the formation of 8-oxo-2'-deoxyguanosine (8-oxoG), a well-known mutagenic lesion. The effect of cytosine methylation on error-prone DNA polymerases lacking proofreading activity and involved in repair and DNA translesion synthesis remains unexplored. Here we analyze the efficiency and fidelity of translesion Y-family polymerases (Pol κ, Pol η, Pol ι and REV1) and primase-polymerase PrimPol opposite mC and hmC as well as opposite 8-oxoG adjacent to mC in the TCG context. We demonstrate that epigenetic cytosine modifications suppress Pol ι and REV1 activities and lead to increasing dAMP misincorporation by PrimPol, Pol κ and Pol ι in vitro. Cytosine methylation also increases misincorporation of dAMP opposite the adjacent 8-oxoG by PrimPol, decreases the TLS activity of Pol η opposite the lesion but increases dCMP incorporation opposite 8-oxoG by REV1. Altogether, these data suggest that methylation and hydroxymethylation of cytosine alter activity and fidelity of translesion DNA polymerases.


Subject(s)
5-Methylcytosine , Cytosine , DNA Methylation , DNA-Directed DNA Polymerase , Humans , DNA-Directed DNA Polymerase/metabolism , Cytosine/metabolism , Cytosine/analogs & derivatives , 5-Methylcytosine/metabolism , 5-Methylcytosine/analogs & derivatives , DNA Repair , DNA Damage , Nucleotidyltransferases/metabolism , Nucleotidyltransferases/genetics , DNA Polymerase iota , DNA/metabolism , Multifunctional Enzymes/metabolism , DNA Replication , 8-Hydroxy-2'-Deoxyguanosine/metabolism
3.
Biochim Biophys Acta Mol Cell Res ; 1871(5): 119743, 2024 Jun.
Article in English | MEDLINE | ID: mdl-38705361

ABSTRACT

Human DNA polymerase ι (Polι) belongs to the Y-family of specialized DNA polymerases engaged in the DNA damage tolerance pathway of translesion DNA synthesis that is crucial to the maintenance of genome integrity. The extreme infidelity of Polι and the fact that both its up- and down-regulation correlate with various cancers indicate that Polι expression and access to the replication fork should be strictly controlled. Here, we identify RNF2, an E3 ubiquitin ligase, as a new interacting partner of Polι that is responsible for Polι stabilization in vivo. Interestingly, while we report that RNF2 does not directly ubiquitinate Polι, inhibition of the E3 ubiquitin ligase activity of RNF2 affects the cellular level of Polι thereby protecting it from destabilization. Additionally, we indicate that this mechanism is more general, as DNA polymerase η, another Y-family polymerase and the closest paralogue of Polι, share similar features.


Subject(s)
DNA Polymerase iota , DNA-Directed DNA Polymerase , Ubiquitin-Protein Ligases , Ubiquitination , Humans , Ubiquitin-Protein Ligases/metabolism , Ubiquitin-Protein Ligases/genetics , DNA-Directed DNA Polymerase/metabolism , DNA-Directed DNA Polymerase/genetics , DNA Replication , DNA Damage , HEK293 Cells , Enzyme Stability , Polycomb Repressive Complex 1
4.
Nucleic Acids Res ; 52(7): 3740-3760, 2024 Apr 24.
Article in English | MEDLINE | ID: mdl-38321962

ABSTRACT

It is well-established that, through canonical functions in transcription and DNA repair, the tumor suppressor p53 plays a central role in safeguarding cells from the consequences of DNA damage. Recent data retrieved in tumor and stem cells demonstrated that p53 also carries out non-canonical functions when interacting with the translesion synthesis (TLS) polymerase iota (POLι) at DNA replication forks. This protein complex triggers a DNA damage tolerance (DDT) mechanism controlling the DNA replication rate. Given that the levels of p53 trigger non-binary rheostat-like functions in response to stress or during differentiation, we explore the relevance of the p53 levels for its DDT functions at the fork. We show that subtle changes in p53 levels modulate the contribution of some DDT factors including POLι, POLη, POLζ, REV1, PCNA, PRIMPOL, HLTF and ZRANB3 to the DNA replication rate. Our results suggest that the levels of p53 are central to coordinate the balance between DDT pathways including (i) fork-deceleration by the ZRANB3-mediated fork reversal factor, (ii) POLι-p53-mediated fork-slowing, (iii) POLι- and POLη-mediated TLS and (iv) PRIMPOL-mediated fork-acceleration. Collectively, our study reveals the relevance of p53 protein levels for the DDT pathway choice in replicating cells.


Subject(s)
DNA Damage , DNA Polymerase iota , DNA Replication , DNA-Directed DNA Polymerase , Tumor Suppressor Protein p53 , Tumor Suppressor Protein p53/metabolism , Tumor Suppressor Protein p53/genetics , DNA-Directed DNA Polymerase/metabolism , Humans , Proliferating Cell Nuclear Antigen/metabolism , Proliferating Cell Nuclear Antigen/genetics , DNA Repair , Nucleotidyltransferases/metabolism , Nucleotidyltransferases/genetics , DNA-Binding Proteins/metabolism , DNA-Binding Proteins/genetics , Multifunctional Enzymes/metabolism , Multifunctional Enzymes/genetics , DNA Primase/metabolism , DNA Primase/genetics , DNA Damage Tolerance
5.
Cell Death Dis ; 15(2): 171, 2024 Feb 24.
Article in English | MEDLINE | ID: mdl-38402183

ABSTRACT

Esophageal squamous cell carcinoma (ESCC) is one of the most lethal cancer types, with a low 5-year survival rate of ~20%. Our prior research has suggested that DNA Polymerase iota (Pol ι), a member of Y-family DNA polymerase, plays a crucial role in the invasion and metastasis of ESCC. However, the underlying mechanism is not well understood. In this study, we utilized ChIP-PCR and luciferase reporter assays to investigate the binding of HIF-1α to the promoter of the Pol ι gene. Transwell, wound healing, and mouse models were employed to assess the impact of Pol ι and HIF-1α on the motility of ESCC cells. Co-immunoprecipitation and Western blot were carried out to explore the interaction between Pol ι and HIF-1α, while qRT-PCR and Western blot were conducted to confirm the regulation of Pol ι and HIF-1α on their downstream targets. Our results demonstrate that HIF-1α activates the transcription of the Pol ι gene in ESCC cells under hypoxic conditions. Furthermore, the knockdown of Pol ι impeded HIF-1α-induced invasion and metastasis. Additionally, we found that Pol ι regulates the expression of genes involved in epithelial-mesenchymal transition (EMT) and initiates EMT through the stabilization of HIF-1α. Mechanistically, Pol ι maintains the protein stability of HIF-1α by recruiting USP7 to mediate the deubiquitination of HIF-1α, with the residues 446-578 of Pol being crucial for the interaction between Pol ι and USP7. Collectively, our findings unveil a novel feedforward molecular axis of HIF-1α- Pol ι -USP7 in ESCC that contributes to ESCC metastasis. Hence, our results present an attractive target for intervention in ESCC.


Subject(s)
Esophageal Neoplasms , Esophageal Squamous Cell Carcinoma , Animals , Mice , Cell Line, Tumor , Cell Movement , DNA Polymerase iota , Epithelial-Mesenchymal Transition/genetics , Esophageal Neoplasms/pathology , Esophageal Squamous Cell Carcinoma/genetics , Gene Expression Regulation, Neoplastic , Ubiquitin-Specific Peptidase 7/metabolism
6.
Photochem Photobiol ; 100(1): 4-18, 2024.
Article in English | MEDLINE | ID: mdl-37926965

ABSTRACT

Xeroderma pigmentosum (XP) variant cells are deficient in the translesion synthesis (TLS) DNA polymerase Polη (eta). This protein contributes to DNA damage tolerance, bypassing unrepaired UV photoproducts and allowing S-phase progression with minimal delay. In the absence of Polη, backup polymerases perform TLS of UV lesions. However, which polymerase plays this role in human cells remains an open question. Here, we investigated the potential role of Polι (iota) in bypassing ultraviolet (UV) induced photoproducts in the absence of Polη, using NER-deficient (XP-C) cells knocked down for Polι and/or Polη genes. Our results indicate that cells lacking either Polι or Polη have increased sensitivity to UVC radiation. The lack of both TLS polymerases led to increased cell death and defects in proliferation and migration. Loss of both polymerases induces a significant replication fork arrest and G1/S-phase blockage, compared to the lack of Polη alone. In conclusion, we propose that Polι acts as a bona fide backup for Polη in the TLS of UV-photoproducts.


Subject(s)
DNA Polymerase iota , Xeroderma Pigmentosum , Humans , DNA Damage , Translesion DNA Synthesis , DNA Replication , Xeroderma Pigmentosum/genetics , Ultraviolet Rays , DNA Repair
7.
Hist Sci ; 62(1): 23-53, 2024 Mar.
Article in English | MEDLINE | ID: mdl-37421137

ABSTRACT

This paper presents a case study of the "electric hypothesis" of the causes of earthquakes, which emerged in the second half of the eighteenth century as part of the first studies of seismology. This hypothesis was related to Franklin's views on atmospheric electricity and developed in a period when electric phenomena were widely studied, and was essentially based on solid empirical evidence and confirmed by model experiments. Even though it resulted from scientific reasoning, the theory remained strongly empirical, and was supported by Italian scholars who were familiar with seismic events. Among these, Giuseppe Saverio Poli, a follower of Franklin, was able to provide a careful and comprehensive explanation of the disastrous earthquake of 1783, which occurred in Calabria, a region of southern Italy, and the St. Anne earthquake of 1805, by drawing not just upon the electric evidence, but all the relevant phenomenology available. We outline here the emergence, the development, and the later evolution (up to the beginning of the nineteenth century) of the "electric earthquake" paradigm by focusing on different works by Poli, including a previously unknown manuscript containing a thorough account of the Calabria earthquake prepared by the Neapolitan scholar for the Royal Society. The present case study therefore offers the opportunity to illustrate how electrical science shaped earthquake science to a degree not usually appreciated in the literature, and is also supported to some extent by the transition from Enlightenment scientific ideals to the Romantic conception of unity in the natural world, in search of common causes among phenomena belonging to different fields.


Subject(s)
Disasters , Earthquakes , Italy , Electricity , DNA Polymerase iota
8.
J Mol Biol ; 435(24): 168353, 2023 12 15.
Article in English | MEDLINE | ID: mdl-37935254

ABSTRACT

The Y-family DNA polymerases - Pol ι, Pol η, Pol κ and Rev1 - are most well-known for their roles in the DNA damage tolerance pathway of translesion synthesis (TLS). They function to overcome replication barriers by bypassing DNA damage lesions that cannot be normally replicated, allowing replication forks to continue without stalling. In this work, we demonstrate a novel interaction between each Y-family polymerase and the nucleotide excision repair (NER) proteins, RAD23A and RAD23B. We initially focus on the interaction between RAD23A and Pol ι, and through a series of biochemical, cell-based, and structural assays, find that the RAD23A ubiquitin-binding domains (UBA1 and UBA2) interact with separate sites within the Pol ι catalytic domain. While this interaction involves the ubiquitin-binding cleft of UBA2, Pol ι interacts with a distinct surface on UBA1. We further find that mutating or deleting either UBA domain disrupts the RAD23A-Pol ι interaction, demonstrating that both interactions are necessary for stable binding. We also provide evidence that both RAD23 proteins interact with Pol ι in a similar manner, as well as with each of the Y-family polymerases. These results shed light on the interplay between the different functions of the RAD23 proteins and reveal novel binding partners for the Y-family TLS polymerases.


Subject(s)
DNA Repair Enzymes , DNA-Binding Proteins , DNA-Directed DNA Polymerase , DNA Damage , DNA Polymerase iota/chemistry , DNA Repair , DNA Replication , DNA-Directed DNA Polymerase/metabolism , Ubiquitins/chemistry , DNA-Binding Proteins/chemistry , DNA Repair Enzymes/chemistry
9.
Chem Res Toxicol ; 34(12): 2567-2578, 2021 12 20.
Article in English | MEDLINE | ID: mdl-34860508

ABSTRACT

The lipid peroxidation product malondialdehyde and the DNA peroxidation product base-propenal react with dG to generate the exocyclic adduct, M1dG. This mutagenic lesion has been found in human genomic and mitochondrial DNA. M1dG in genomic DNA is enzymatically oxidized to 6-oxo-M1dG, a lesion of currently unknown mutagenic potential. Here, we report the synthesis of an oligonucleotide containing 6-oxo-M1dG and the results of extension experiments aimed at determining the effect of the 6-oxo-M1dG lesion on the activity of human polymerase iota (hPol ι). For this purpose, a liquid chromatography-tandem mass spectrometry (LC-MS/MS) assay was developed to obtain reliable quantitative data on the utilization of poorly incorporated nucleotides. Results demonstrate that hPol ι primarily incorporates deoxycytidine triphosphate (dCTP) and thymidine triphosphate (dTTP) across from 6-oxo-M1dG with approximately equal efficiency, whereas deoxyadenosine triphosphate (dATP) and deoxyguanosine triphosphate (dGTP) are poor substrates. Following the incorporation of a single nucleotide opposite the lesion, 6-oxo-M1dG blocks further replication by the enzyme.


Subject(s)
DNA-Directed DNA Polymerase/metabolism , Deoxyguanosine/metabolism , Oligonucleotides/metabolism , Chromatography, Liquid , Deoxyguanosine/analogs & derivatives , Deoxyguanosine/chemistry , Humans , Molecular Structure , Oligonucleotides/chemical synthesis , Oligonucleotides/chemistry , Tandem Mass Spectrometry , DNA Polymerase iota
10.
Cell Death Dis ; 12(10): 941, 2021 10 13.
Article in English | MEDLINE | ID: mdl-34645785

ABSTRACT

The recently discovered p53-dependent DNA damage tolerance (DDT) pathway relies on its biochemical activities in DNA-binding, oligomerization, as well as complex formation with the translesion synthesis (TLS) polymerase iota (POLι). These p53-POLι complexes slow down nascent DNA synthesis for safe, homology-directed bypass of DNA replication barriers. In this study, we demonstrate that the alternative p53-isoforms p53ß, p53γ, Δ40p53α, Δ133p53α, and Δ160p53α differentially affect this p53-POLι-dependent DDT pathway originally described for canonical p53α. We show that the C-terminal isoforms p53ß and p53γ, comprising a truncated oligomerization domain (OD), bind PCNA. Conversely, N-terminally truncated isoforms have a reduced capacity to engage in this interaction. Regardless of the specific loss of biochemical activities required for this DDT pathway, all alternative isoforms were impaired in promoting POLι recruitment to PCNA in the chromatin and in decelerating DNA replication under conditions of enforced replication stress after Mitomycin C (MMC) treatment. Consistent with this, all alternative p53-isoforms no longer stimulated recombination, i.e., bypass of endogenous replication barriers. Different from the other isoforms, Δ133p53α and Δ160p53α caused a severe DNA replication problem, namely fork stalling even in untreated cells. Co-expression of each alternative p53-isoform together with p53α exacerbated the DDT pathway defects, unveiling impaired POLι recruitment and replication deceleration already under unperturbed conditions. Such an inhibitory effect on p53α was particularly pronounced in cells co-expressing Δ133p53α or Δ160p53α. Notably, this effect became evident after the expression of the isoforms in tumor cells, as well as after the knockdown of endogenous isoforms in human hematopoietic stem and progenitor cells. In summary, mimicking the situation found to be associated with many cancer types and stem cells, i.e., co-expression of alternative p53-isoforms with p53α, carved out interference with p53α functions in the p53-POLι-dependent DDT pathway.


Subject(s)
DNA Damage , DNA-Directed DNA Polymerase/metabolism , Tumor Suppressor Protein p53/metabolism , DNA Replication , Humans , K562 Cells , Mitomycin/pharmacology , Models, Biological , Proliferating Cell Nuclear Antigen/metabolism , Protein Binding/drug effects , Protein Isoforms/chemistry , Protein Isoforms/metabolism , Protein Multimerization , Recombination, Genetic/genetics , Subcellular Fractions/metabolism , Tumor Suppressor Protein p53/chemistry , Ubiquitination , DNA Polymerase iota
11.
Nucleic Acids Res ; 49(13): 7457-7475, 2021 07 21.
Article in English | MEDLINE | ID: mdl-34165573

ABSTRACT

Using human embryonic, adult and cancer stem cells/stem cell-like cells (SCs), we demonstrate that DNA replication speed differs in SCs and their differentiated counterparts. While SCs decelerate DNA replication, differentiated cells synthesize DNA faster and accumulate DNA damage. Notably, both replication phenotypes depend on p53 and polymerase iota (POLι). By exploring protein interactions and newly synthesized DNA, we show that SCs promote complex formation of p53 and POLι at replication sites. Intriguingly, in SCs the translocase ZRANB3 is recruited to POLι and required for slow-down of DNA replication. The known role of ZRANB3 in fork reversal suggests that the p53-POLι complex mediates slow but safe bypass of replication barriers in SCs. In differentiated cells, POLι localizes more transiently to sites of DNA synthesis and no longer interacts with p53 facilitating fast POLι-dependent DNA replication. In this alternative scenario, POLι associates with the p53 target p21, which antagonizes PCNA poly-ubiquitination and, thereby potentially disfavors the recruitment of translocases. Altogether, we provide evidence for diametrically opposed DNA replication phenotypes in SCs and their differentiated counterparts putting DNA replication-based strategies in the spotlight for the creation of therapeutic opportunities targeting SCs.


Subject(s)
DNA Replication , DNA-Directed DNA Polymerase/metabolism , Stem Cells/metabolism , Tumor Suppressor Protein p53/metabolism , Cell Differentiation/genetics , Cells, Cultured , DNA Helicases/metabolism , Embryonic Stem Cells/metabolism , Humans , Neoplastic Stem Cells/metabolism , Stress, Physiological/genetics , DNA Polymerase iota
12.
PLoS One ; 16(6): e0252587, 2021.
Article in English | MEDLINE | ID: mdl-34061890

ABSTRACT

Living organisms are continuously under threat from a vast array of DNA-damaging agents, which impact genome DNA. DNA replication machinery stalls at damaged template DNA. The stalled replication fork is restarted via bypass replication by translesion DNA-synthesis polymerases, including the Y-family polymerases Polη, Polι, and Polκ, which possess the ability to incorporate nucleotides opposite the damaged template. To investigate the division of labor among these polymerases in vivo, we generated POLη-/-, POLι-/-, POLκ-/-, double knockout (KO), and triple knockout (TKO) mutants in all combinations from human TK6 cells. TKO cells exhibited a hypersensitivity to ultraviolet (UV), cisplatin (CDDP), and methyl methanesulfonate (MMS), confirming the pivotal role played by these polymerases in bypass replication of damaged template DNA. POLη-/- cells, but not POLι-/- or POLκ-/- cells, showed a strong sensitivity to UV and CDDP, while TKO cells showed a slightly higher sensitivity to UV and CDDP than did POLη-/- cells. On the other hand, TKO cells, but not all single KO cells, exhibited a significantly higher sensitivity to MMS than did wild-type cells. Consistently, DNA-fiber assay revealed that Polη plays a crucial role in bypassing lesions caused by UV-mimetic agent 4-nitroquinoline-1-oxide and CDDP, while all three polymerases play complementary roles in bypassing MMS-induced damage. Our findings indicate that the three Y-family polymerases play distinctly different roles in bypass replication, according to the type of DNA damage generated on the template strand.


Subject(s)
DNA Damage , DNA-Directed DNA Polymerase/metabolism , DNA/metabolism , Cell Line , Cisplatin/pharmacology , DNA/genetics , DNA Damage/drug effects , DNA Damage/radiation effects , DNA Repair , DNA Replication , DNA-Directed DNA Polymerase/deficiency , DNA-Directed DNA Polymerase/genetics , Gene Knockout Techniques , Humans , Methyl Methanesulfonate/pharmacology , Ultraviolet Rays , DNA Polymerase iota
13.
Biochem J ; 478(7): 1399-1412, 2021 04 16.
Article in English | MEDLINE | ID: mdl-33600564

ABSTRACT

Y-family DNA polymerase iota (Pol ι) is involved in DNA damage response and tolerance. Mutations and altered expression level of POLI gene are linked to a higher incidence of cancer. We biochemically characterized five active site polymorphic variants of human Pol ι: R71G (rs3218778), P118L (rs554252419), I236M (rs3218784), E251K (rs3218783) and P365R (rs200852409). We analyzed fidelity of nucleotide incorporation on undamaged DNA, efficiency and accuracy of DNA damage bypass, as well as 5'-deoxyribophosphate lyase (dRP-lyase) activity. The I236M and P118L variants were indistinguishable from the wild-type Pol ι in activity. The E251K and P365R substitutions altered the spectrum of nucleotide incorporation opposite several undamaged DNA bases. The P365R variant also reduced the dRP-lyase activity and possessed the decreased TLS activity opposite 8-oxo-G. The R71G mutation dramatically affected the catalytic activities of Pol ι. The reduced DNA polymerase activity of the R71G variant correlated with an enhanced fidelity of nucleotide incorporation on undamaged DNA, altered lesion-bypass activity and reduced dRP-lyase activity. Therefore, this amino acid substitution likely alters Pol ι functions in vivo.


Subject(s)
DNA Replication , DNA-Directed DNA Polymerase/metabolism , DNA/metabolism , Phosphorus-Oxygen Lyases/metabolism , Polymorphism, Single Nucleotide , Catalytic Domain , DNA/genetics , DNA-Directed DNA Polymerase/chemistry , DNA-Directed DNA Polymerase/genetics , Humans , Phosphorus-Oxygen Lyases/genetics , DNA Polymerase iota
14.
J Mol Biol ; 433(2): 166733, 2021 01 22.
Article in English | MEDLINE | ID: mdl-33279577

ABSTRACT

Reversible protein ubiquitination is an essential signaling mechanism within eukaryotes. Deubiquitinating enzymes are critical to this process, as they mediate removal of ubiquitin from substrate proteins. Ubiquitin-specific protease 7 (USP7) is a prominent deubiquitinating enzyme, with an extensive network of interacting partners and established roles in cell cycle activation, immune responses and DNA replication. Characterized USP7 substrates primarily interact with one of two major binding sites outside the catalytic domain. These are located on the USP7 N-terminal TRAF-like (TRAF) domain and the first and second UBL domains (UBL1-2) within the C-terminal tail. Here, we report that DNA polymerase iota (Pol ι) is a novel USP7 substrate that interacts with both TRAF and UBL1-2. Through the use of biophysical approaches and mutational analysis, we characterize both interfaces and demonstrate that bipartite binding to both USP7 domains is required for efficient Pol ι deubiquitination. Together, these data establish a new bipartite mode of USP7 substrate binding.


Subject(s)
DNA-Directed DNA Polymerase/chemistry , DNA-Directed DNA Polymerase/metabolism , Protein Interaction Domains and Motifs , Ubiquitin-Specific Peptidase 7/chemistry , Ubiquitin-Specific Peptidase 7/metabolism , Binding Sites , Catalytic Domain , Cell Line , DNA-Directed DNA Polymerase/genetics , Humans , Kinetics , Models, Molecular , Protein Binding , Protein Conformation , Recombinant Proteins , Structure-Activity Relationship , Substrate Specificity , Ubiquitin-Specific Peptidase 7/genetics , Ubiquitination , DNA Polymerase iota
15.
Proc Natl Acad Sci U S A ; 117(52): 33436-33445, 2020 12 29.
Article in English | MEDLINE | ID: mdl-33376220

ABSTRACT

Fanconi anemia (FA) is caused by defects in cellular responses to DNA crosslinking damage and replication stress. Given the constant occurrence of endogenous DNA damage and replication fork stress, it is unclear why complete deletion of FA genes does not have a major impact on cell proliferation and germ-line FA patients are able to progress through development well into their adulthood. To identify potential cellular mechanisms that compensate for the FA deficiency, we performed dropout screens in FA mutant cells with a whole genome guide RNA library. This uncovered a comprehensive genome-wide profile of FA pathway synthetic lethality, including POLI and CDK4 As little is known of the cellular function of DNA polymerase iota (Pol ι), we focused on its role in the loss-of-function FA knockout mutants. Loss of both FA pathway function and Pol ι leads to synthetic defects in cell proliferation and cell survival, and an increase in DNA damage accumulation. Furthermore, FA-deficient cells depend on the function of Pol ι to resume replication upon replication fork stalling. Our results reveal a critical role for Pol ι in DNA repair and replication fork restart and suggest Pol ι as a target for therapeutic intervention in malignancies carrying an FA gene mutation.


Subject(s)
DNA Replication , DNA-Directed DNA Polymerase/metabolism , Fanconi Anemia/enzymology , Stress, Physiological , CRISPR-Cas Systems/genetics , Cyclin-Dependent Kinase 4 , DNA Damage , Genome, Human , HCT116 Cells , Humans , Mutation/genetics , Synthetic Lethal Mutations/genetics , DNA Polymerase iota
16.
Biochem Soc Trans ; 48(6): 2811-2822, 2020 12 18.
Article in English | MEDLINE | ID: mdl-33196097

ABSTRACT

Interaction of PCNA with DNA polymerase is vital to efficient and processive DNA synthesis. PCNA being a homotrimeric ring possesses three hydrophobic pockets mostly involved in an interaction with its binding partners. PCNA interacting proteins contain a short sequence of eight amino acids, popularly coined as PIP motif, which snuggly fits into the hydrophobic pocket of PCNA to stabilize the interaction. In the last two decades, several PIP motifs have been mapped or predicted in eukaryotic DNA polymerases. In this review, we summarize our understandings of DNA polymerase-PCNA interaction, the function of such interaction during DNA synthesis, and emphasize the lacunae that persist. Because of the presence of multiple ligands in the replisome complex and due to many interaction sites in DNA polymerases, we also propose two modes of DNA polymerase positioning on PCNA required for DNA synthesis to rationalize the tool-belt model of DNA replication.


Subject(s)
DNA Damage , DNA Replication , DNA-Directed DNA Polymerase/metabolism , Models, Genetic , Proliferating Cell Nuclear Antigen/chemistry , Proliferating Cell Nuclear Antigen/genetics , Amino Acid Motifs , Animals , Binding Sites , DNA/biosynthesis , DNA Polymerase I/metabolism , DNA Polymerase II/metabolism , DNA Polymerase III/metabolism , Humans , Ligands , Mutation , Protein Binding , Protein Interaction Mapping , Recombination, Genetic , DNA Polymerase iota
17.
Nucleic Acids Res ; 48(21): 12188-12203, 2020 12 02.
Article in English | MEDLINE | ID: mdl-33166398

ABSTRACT

We have previously reported that p53 decelerates nascent DNA elongation in complex with the translesion synthesis (TLS) polymerase ι (POLι) which triggers a homology-directed DNA damage tolerance (DDT) pathway to bypass obstacles during DNA replication. Here, we demonstrate that this DDT pathway relies on multiple p53 activities, which can be disrupted by TP53 mutations including those frequently found in cancer tissues. We show that the p53-mediated DDT pathway depends on its oligomerization domain (OD), while its regulatory C-terminus is not involved. Mutation of residues S315 and D48/D49, which abrogate p53 interactions with the DNA repair and replication proteins topoisomerase I and RPA, respectively, and residues L22/W23, which disrupt formation of p53-POLι complexes, all prevent this DDT pathway. Our results demonstrate that the p53-mediated DDT requires the formation of a DNA binding-proficient p53 tetramer, recruitment of such tetramer to RPA-coated forks and p53 complex formation with POLι. Importantly, our mutational analysis demonstrates that transcriptional transactivation is dispensable for the POLι-mediated DDT pathway, which we show protects against DNA replication damage from endogenous and exogenous sources.


Subject(s)
DNA Repair , DNA Topoisomerases, Type I/genetics , DNA-Directed DNA Polymerase/genetics , DNA/genetics , Gene Expression Regulation, Neoplastic , Tumor Suppressor Protein p53/genetics , Cell Line, Tumor , DNA/metabolism , DNA Damage , DNA Replication/drug effects , DNA Topoisomerases, Type I/metabolism , DNA-Directed DNA Polymerase/metabolism , Humans , Hydrogen Peroxide/pharmacology , K562 Cells , Mutation , Osteoblasts/drug effects , Osteoblasts/metabolism , Osteoblasts/pathology , Oxidants/pharmacology , Protein Binding/drug effects , Protein Multimerization , Signal Transduction , Tumor Suppressor Protein p53/metabolism , DNA Polymerase iota
18.
DNA Repair (Amst) ; 93: 102914, 2020 09.
Article in English | MEDLINE | ID: mdl-33087280

ABSTRACT

With the publication of the first paper describing the biochemical properties of DNA polymerase iota (polɩ), the question immediately arose as to why cells harbor such a low-fidelity enzyme which often violates the Watson-Crick base pairing rules? Yet 20 years after its discovery, the cellular function of polɩ remains unknown. Here, we provide a graphical review of the unique biochemical properties of polɩ and speculate about the cellular pathways in which enigmatic polɩ may participate.


Subject(s)
DNA Replication , DNA-Directed DNA Polymerase/metabolism , Models, Molecular , DNA/metabolism , DNA Repair , Humans , DNA Polymerase iota
19.
Chem Res Toxicol ; 33(8): 2120-2129, 2020 08 17.
Article in English | MEDLINE | ID: mdl-32635723

ABSTRACT

Human Y-family DNA polymerase (pol) ι is involved in translesion DNA synthesis (TLS) and base excision repair (BER) of oxidative DNA damage. Genetic variations may alter the function of pol ι and affect cellular susceptibility to oxidative genotoxic agents, but their effects remain unclear. We investigated the impacts of 10 human missense germline variations on pol ι function by biochemical and cell-based assays. Both polymerase and deoxyribose phosphate (dRP) lyase activities were determined utilizing recombinant pol ι (residues 1-445) proteins. The K209Q, K228I, and Q386R variants showed 4- to 53-fold decreases in specificity constants (kcat/Km) for dCTP insertion opposite G and 8-oxo-7,8-dihydroguanine compared to the wild-type. The R126C and K345E variants showed wild-type-like polymerase activity, although these two variants (as well as the R209Q, K228I, and Q386R variants) showed greater than 6-fold decreases in dRP lyase activity compared to the wild-type. A CRISPR/Cas9-mediated POLI knockout conferred higher sensitivity to H2O2 in human embryonic kidney (HEK293) cells. Exogenous expression of the full-length wild-type, R126C, and K345E variants fully rescued the H2O2 sensitivity in POLI-deficient cells, while full-length R209Q, K228I, and Q386R variants did not rescue the sensitivity. Our results indicate that the R126C and K345E variants (having wild-type-like polymerase activity, albeit impaired in dRP lyase activity) could fully rescue the H2O2 sensitivity in POLI-deficient cells, while the R209Q, K228I, and Q386R variants, all impaired in polymerase and dRP lyase activity, failed to rescue the sensitivity, indicating the relative importance of TLS-related polymerase function of pol ι rather than its BER-related dRP lyase function in protection from oxidative stress. The possibility exists that the hypoactive pol ι variants increase the individual susceptibility to oxidative genotoxic agents.


Subject(s)
DNA-Directed DNA Polymerase/metabolism , Hydrogen Peroxide/metabolism , DNA-Directed DNA Polymerase/deficiency , DNA-Directed DNA Polymerase/genetics , HEK293 Cells , Humans , Hydrogen Peroxide/analysis , Models, Molecular , DNA Polymerase iota
20.
Biochemistry (Mosc) ; 85(4): 425-435, 2020 Apr.
Article in English | MEDLINE | ID: mdl-32569550

ABSTRACT

Tens of thousands of DNA lesions are formed in mammalian cells each day. DNA translesion synthesis is the main mechanism of cell defense against unrepaired DNA lesions. DNA polymerases iota (Pol ι), eta (Pol η), kappa (Pol κ), and zeta (Pol ζ) have active sites that are less stringent toward the DNA template structure and efficiently incorporate nucleotides opposite DNA lesions. However, these polymerases display low accuracy of DNA synthesis and can introduce mutations in genomic DNA. Impaired functioning of these enzymes can lead to an increased risk of cancer.


Subject(s)
DNA Damage , DNA Repair , DNA Replication , DNA-Directed DNA Polymerase/metabolism , Neoplasms/pathology , Animals , Humans , Neoplasms/genetics , Neoplasms/metabolism , DNA Polymerase iota
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