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Tdp1 processes chromate-induced single-strand DNA breaks that collapse replication forks. PLoS Genet 2018; 14:e1007595. [PMID: 30148840 PMCID: PMC6128646 DOI: 10.1371/journal.pgen.1007595] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Revised: 09/07/2018] [Accepted: 07/26/2018] [Indexed: 01/20/2023] Open
Abstract
Hexavalent chromium [Cr(VI)] damages DNA and causes cancer, but it is unclear which DNA damage responses (DDRs) most critically protect cells from chromate toxicity. Here, genome-wide quantitative functional profiling, DDR measurements and genetic interaction assays in Schizosaccharomyces pombe reveal a chromate toxicogenomic profile that closely resembles the cancer chemotherapeutic drug camptothecin (CPT), which traps Topoisomerase 1 (Top1)-DNA covalent complex (Top1cc) at the 3’ end of single-stand breaks (SSBs), resulting in replication fork collapse. ATR/Rad3-dependent checkpoints that detect stalled and collapsed replication forks are crucial in Cr(VI)-treated cells, as is Mus81-dependent sister chromatid recombination (SCR) that repairs single-ended double-strand breaks (seDSBs) at broken replication forks. Surprisingly, chromate resistance does not require base excision repair (BER) or interstrand crosslink (ICL) repair, nor does co-elimination of XPA-dependent nucleotide excision repair (NER) and Rad18-mediated post-replication repair (PRR) confer chromate sensitivity in fission yeast. However, co-elimination of Tdp1 tyrosyl-DNA phosphodiesterase and Rad16-Swi10 (XPF-ERCC1) NER endonuclease synergistically enhances chromate toxicity in top1Δ cells. Pnk1 polynucleotide kinase phosphatase (PNKP), which restores 3’-hydroxyl ends to SSBs processed by Tdp1, is also critical for chromate resistance. Loss of Tdp1 ameliorates pnk1Δ chromate sensitivity while enhancing the requirement for Mus81. Thus, Tdp1 and PNKP, which prevent neurodegeneration in humans, repair an important class of Cr-induced SSBs that collapse replication forks. Hexavalent chromium is a carcinogen that is found at toxic waste sites and in some groundwater supplies. Cellular metabolism converts chromium into DNA-damaging chromate, but it is unclear which types of chromate-DNA lesions are most dangerous, and which cellular mechanisms most critically prevent chromium toxicity. This study uses whole-genome profiling to identify DNA repair pathways that are crucial for chromate resistance in fission yeast. The resulting ‘toxicogenomic’ profile of chromate closely matches camptothecin, a natural product representing a class of chemotherapeutic drugs that cause replication fork collapse by poisoning Topoisomerase 1 (Top1), which relaxes supercoiled DNA by creating and resealing single-strand breaks (SSBs). Genetic interaction analyses uncover important roles for Tdp1 tyrosyl-DNA phosphodiesterase and Pnk1 polynucleotide 5’-kinase 3’-phosphatase (PNKP), which repair camptothecin-induced SSBs and prevent neurological disease in humans. However, chromium toxicity does not involve Top1. As Tdp1 and Pnk1 repair SSBs with 3’-blocked termini, these data suggest that Top1-independent 3’-blocked SSBs contribute to the carcinogenic and mutagenic properties of chromium.
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Chalasani SL, Kawale AS, Akopiants K, Yu Y, Fanta M, Weinfeld M, Povirk LF. Persistent 3'-phosphate termini and increased cytotoxicity of radiomimetic DNA double-strand breaks in cells lacking polynucleotide kinase/phosphatase despite presence of an alternative 3'-phosphatase. DNA Repair (Amst) 2018; 68:12-24. [PMID: 29807321 DOI: 10.1016/j.dnarep.2018.05.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 05/07/2018] [Indexed: 02/08/2023]
Abstract
Polynucleotide kinase/phosphatase (PNKP) has been implicated in non-homologous end joining (NHEJ) of DNA double-strand breaks (DSBs). To assess the consequences of PNKP deficiency for NHEJ of 3'-phosphate-ended DSBs, PNKP-deficient derivatives of HCT116 and of HeLa cells were generated using CRISPR/CAS9. For both cell lines, PNKP deficiency conferred sensitivity to ionizing radiation as well as to neocarzinostatin (NCS), which specifically induces DSBs bearing protruding 3'-phosphate termini. Moreover, NCS-induced DSBs, detected as 53BP1 foci, were more persistent in PNKP -/- HCT116 cells compared to their wild-type (WT) counterparts. Surprisingly, PNKP-deficient whole-cell and nuclear extracts were biochemically competent in removing both protruding and recessed 3'-phosphates from synthetic DSB substrates, albeit much less efficiently than WT extracts, suggesting an alternative 3'-phosphatase. Measurements by ligation-mediated PCR showed that PNKP-deficient HeLa cells contained significantly more 3'-phosphate-terminated and fewer 3'-hydroxyl-terminated DSBs than parental cells 5-15 min after NCS treatment, but this difference disappeared by 1 h. These results suggest that, despite presence of an alternative 3'-phosphatase, loss of PNKP significantly sensitizes cells to 3'-phosphate-terminated DSBs, due to a 3'-dephosphorylation defect.
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Affiliation(s)
- Sri Lakshmi Chalasani
- Department of Pharmacology and Toxicology and Massey Cancer Center, Virginia Commonwealth University, Richmond, VA 23298, United States
| | - Ajinkya S Kawale
- Department of Pharmacology and Toxicology and Massey Cancer Center, Virginia Commonwealth University, Richmond, VA 23298, United States
| | - Konstantin Akopiants
- Department of Pharmacology and Toxicology and Massey Cancer Center, Virginia Commonwealth University, Richmond, VA 23298, United States
| | - Yaping Yu
- Centre for Genome Engineering, University of Calgary, Calgary, AB, Canada
| | - Mesfin Fanta
- Department of Oncology, Cross Cancer Institute and University of Alberta, Edmonton, AB, Canada
| | - Michael Weinfeld
- Department of Oncology, Cross Cancer Institute and University of Alberta, Edmonton, AB, Canada
| | - Lawrence F Povirk
- Department of Pharmacology and Toxicology and Massey Cancer Center, Virginia Commonwealth University, Richmond, VA 23298, United States.
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53
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Shire Z, Vakili MR, Morgan TDR, Hall DG, Lavasanifar A, Weinfeld M. Nanoencapsulation of Novel Inhibitors of PNKP for Selective Sensitization to Ionizing Radiation and Irinotecan and Induction of Synthetic Lethality. Mol Pharm 2018; 15:2316-2326. [PMID: 29688721 DOI: 10.1021/acs.molpharmaceut.8b00169] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
There is increasing interest in developing and applying DNA repair inhibitors in cancer treatment to augment the efficacy of radiation and conventional genotoxic chemotherapy. However, targeting the inhibitor is required to avoid reducing the repair capacity of normal tissue. The aim of this study was to develop nanodelivery systems for the encapsulation of novel imidopiperidine-based inhibitors of the DNA 3'-phosphatase activity of polynucleotide kinase/phosphatase (PNKP), a DNA repair enzyme that plays a critical role in rejoining DNA single- and double-strand breaks. For this purpose, newly identified hit compounds with potent PNKP inhibitory activity, imidopiperidines A12B4C50 and A83B4C63 were encapsulated in polymeric micelles of different poly(ethylene oxide)- b-poly(ε-caprolactone) (PEO- b-PCL)-based structures. Our results showed efficient loading of A12B4C50 and A83B4C63 in PEO- b-PCLs with pendent carboxyl and benzyl carboxylate groups, respectively, and relatively slow release over 24 h. Both free and encapsulated inhibitors were able to sensitize HCT116 cells to radiation and the topoisomerase I poison, irinotecan. In addition, the encapsulated inhibitors were capable of inducing synthetic lethalilty in phosphatase and tensin homologue (PTEN)-deficient cells. We also established the validity of the peptide GE11 as a suitable ligand for active targeted delivery of nanoencapsulated drugs to colorectal cancer cells overexpressing epidermal growth factor receptor (EGFR). Our results show the potential of nanoencapsulated inhibitors of PNKP as either mono or combined therapeutic agents for colorectal cancer.
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Affiliation(s)
- Zahra Shire
- Department of Oncology, Faculty of Medicine and Dentistry , University of Alberta , Edmonton , AB , Canada T6G 1Z2.,Faculty of Pharmacy and Pharmaceutical Sciences , University of Alberta , Edmonton , AB , Canada T6G 2E1
| | - Mohammad Reza Vakili
- Faculty of Pharmacy and Pharmaceutical Sciences , University of Alberta , Edmonton , AB , Canada T6G 2E1
| | - Timothy D R Morgan
- Department of Chemistry, Faculty of Science , University of Alberta , Edmonton , AB , Canada T6G 2G2
| | - Dennis G Hall
- Department of Chemistry, Faculty of Science , University of Alberta , Edmonton , AB , Canada T6G 2G2
| | - Afsaneh Lavasanifar
- Faculty of Pharmacy and Pharmaceutical Sciences , University of Alberta , Edmonton , AB , Canada T6G 2E1
| | - Michael Weinfeld
- Department of Oncology, Faculty of Medicine and Dentistry , University of Alberta , Edmonton , AB , Canada T6G 1Z2
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54
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Pillon MC, Sobhany M, Stanley RE. Characterization of the molecular crosstalk within the essential Grc3/Las1 pre-rRNA processing complex. RNA (NEW YORK, N.Y.) 2018; 24:721-738. [PMID: 29440475 PMCID: PMC5900568 DOI: 10.1261/rna.065037.117] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Accepted: 02/06/2018] [Indexed: 06/08/2023]
Abstract
Grc3 is an essential well-conserved eukaryotic polynucleotide kinase (PNK) that cooperates with the endoribonuclease Las1 to process the preribosomal RNA (rRNA). Aside from being dependent upon Las1 for coordinated kinase and nuclease function, little is known about Grc3 substrate specificity and the molecular mechanisms governing kinase activity. Here we characterize the kinase activity of Grc3 and identify key similarities and differences between Grc3 and other polynucleotide kinase family members. In contrast to other PNK family members, Grc3 has distinct substrate preference for RNA substrates in vitro. By disrupting conserved residues found at the Grc3 kinase active site, we identified specific residues required to support Grc3-directed Las1-mediated pre-rRNA cleavage in vitro and in vivo. The crosstalk between Grc3 and Las1 ensures the direct coupling of cleavage and phosphorylation during pre-rRNA processing. Taken together, our studies provide key insight into the polynucleotide kinase activity of the essential enzyme Grc3 and its molecular crosstalk with the endoribonuclease Las1.
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Affiliation(s)
- Monica C Pillon
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina 27709, USA
| | - Mack Sobhany
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina 27709, USA
| | - Robin E Stanley
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina 27709, USA
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55
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Horton JK, Stefanick DF, Çağlayan M, Zhao ML, Janoshazi AK, Prasad R, Gassman NR, Wilson SH. XRCC1 phosphorylation affects aprataxin recruitment and DNA deadenylation activity. DNA Repair (Amst) 2018; 64:26-33. [DOI: 10.1016/j.dnarep.2018.02.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Revised: 02/05/2018] [Accepted: 02/08/2018] [Indexed: 11/26/2022]
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56
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Abstract
Topoisomerase I (Top1) resolves torsional stress that accumulates during transcription, replication and chromatin remodeling by introducing a transient single-strand break in DNA. The cleavage activity of Top1 has opposing roles, either promoting or destabilizing genome integrity depending on the context. Resolution of transcription-associated negative supercoils, for example, prevents pairing of the nascent RNA with the DNA template (R-loops) as well as DNA secondary structure formation. Reduced Top1 levels thus enhance CAG repeat contraction, somatic hypermutation, and class switch recombination. Actively transcribed ribosomal DNA is also destabilized in the absence of Top1, reflecting the importance of Top1 in ensuring efficient transcription. In terms of promoting genome instability, an aborted Top1 catalytic cycle stimulates deletions at short tandem repeats and the enzyme's transesterification activity supports illegitimate recombination. Finally, Top1 incision at ribonucleotides embedded in DNA generates deletions in tandem repeats, and induces gross chromosomal rearrangements and mitotic recombination.
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Affiliation(s)
- Jang-Eun Cho
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, 213 Research Drive, CARL 384, Durham, NC, 27710, USA
| | - Sue Jinks-Robertson
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, 213 Research Drive, CARL 384, Durham, NC, 27710, USA.
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57
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Processing-Challenges Generated by Clusters of DNA Double-Strand Breaks Underpin Increased Effectiveness of High-LET Radiation and Chromothripsis. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1044:149-168. [DOI: 10.1007/978-981-13-0593-1_10] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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58
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Horton JK, Stefanick DF, Zhao ML, Janoshazi AK, Gassman NR, Seddon HJ, Wilson SH. XRCC1-mediated repair of strand breaks independent of PNKP binding. DNA Repair (Amst) 2017; 60:52-63. [PMID: 29100039 PMCID: PMC5696015 DOI: 10.1016/j.dnarep.2017.10.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Revised: 10/03/2017] [Accepted: 10/12/2017] [Indexed: 10/18/2022]
Abstract
Repair of DNA-protein crosslinks and oxidatively damaged DNA base lesions generates intermediates with nicks or gaps with abnormal and blocked 3'-phosphate and 5'-OH ends that prevent the activity of DNA polymerases and ligases. End cleaning in mammalian cells by Tdp1 and PNKP produces the conventional 3'-OH and 5'-phosphate DNA ends suitable for completion of repair. This repair function of PNKP is facilitated by its binding to the scaffold protein XRCC1, and phosphorylation of XRCC1 by CK2 at several consensus sites enables PNKP binding and recruitment to DNA damage. To evaluate this documented repair process, a phosphorylation mutant of XRCC1, designed to eliminate PNKP binding, was stably expressed in Xrcc1-/- mouse fibroblast cells. Analysis of PNKP-GFP accumulation at micro-irradiation induced damage confirmed that the XRCC1 phosphorylation mutant failed to support efficient PNKP recruitment, whereas there was rapid recruitment in cells expressing wild-type XRCC1. Recruitment of additional fluorescently-tagged repair factors PARP-1-YFP, GFF-XRCC1, PNKP-GFP and Tdp1-GFP to micro-irradiation induced damage was assessed in wild-type XRCC1-expressing cells. PARP-1-YFP recruitment was best fit to two exponentials, whereas kinetics for the other proteins were fit to a single exponential. The similar half-times of recruitment suggest that XRCC1 may be recruited with other proteins possibly as a pre-formed complex. Xrcc1-/- cells are hypersensitive to the DNA-protein cross-link inducing agent camptothecin (CPT) and the DNA oxidative agent H2O2 due in part to compromised PNKP-mediated repair. However, cells expressing the PNKP interaction mutant of XRCC1 demonstrated marked reversal of CPT hypersensitivity. This reversal represents XRCC1-dependent repair in the absence of the phosphorylation-dependent PNKP recruitment and suggests either an XRCC1-independent mechanism of PNKP recruitment or a functional back-up pathway for cleaning of blocked DNA ends.
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Affiliation(s)
- Julie K Horton
- Genomic Integrity and Structural Biology Laboratory, NIEHS, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Donna F Stefanick
- Genomic Integrity and Structural Biology Laboratory, NIEHS, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Ming-Lang Zhao
- Genomic Integrity and Structural Biology Laboratory, NIEHS, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Agnes K Janoshazi
- Signal Transduction Laboratory, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina 27709, USA
| | - Natalie R Gassman
- Genomic Integrity and Structural Biology Laboratory, NIEHS, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Hannah J Seddon
- Genomic Integrity and Structural Biology Laboratory, NIEHS, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Samuel H Wilson
- Genomic Integrity and Structural Biology Laboratory, NIEHS, National Institutes of Health, Research Triangle Park, NC 27709, USA.
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59
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Prasad R, Çağlayan M, Dai DP, Nadalutti CA, Zhao ML, Gassman NR, Janoshazi AK, Stefanick DF, Horton JK, Krasich R, Longley MJ, Copeland WC, Griffith JD, Wilson SH. DNA polymerase β: A missing link of the base excision repair machinery in mammalian mitochondria. DNA Repair (Amst) 2017; 60:77-88. [PMID: 29100041 PMCID: PMC5919216 DOI: 10.1016/j.dnarep.2017.10.011] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Mitochondrial genome integrity is fundamental to mammalian cell viability. Since mitochondrial DNA is constantly under attack from oxygen radicals released during ATP production, DNA repair is vital in removing oxidatively generated lesions in mitochondrial DNA, but the presence of a strong base excision repair system has not been demonstrated. Here, we addressed the presence of such a system in mammalian mitochondria involving the primary base lesion repair enzyme DNA polymerase (pol) β. Pol β was localized to mammalian mitochondria by electron microscopic-immunogold staining, immunofluorescence co-localization and biochemical experiments. Extracts from purified mitochondria exhibited base excision repair activity that was dependent on pol β. Mitochondria from pol β-deficient mouse fibroblasts had compromised DNA repair and showed elevated levels of superoxide radicals after hydrogen peroxide treatment. Mitochondria in pol β-deficient fibroblasts displayed altered morphology by electron microscopy. These results indicate that mammalian mitochondria contain an efficient base lesion repair system mediated in part by pol β and thus pol β plays a role in preserving mitochondrial genome stability.
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Affiliation(s)
- Rajendra Prasad
- Genome Integrity and Structural Biology Laboratory, National Institutes of Health, NIEHS, 111 T.W. Alexander Drive, P.O. Box 12233, Research Triangle Park, NC 27709, USA
| | - Melike Çağlayan
- Genome Integrity and Structural Biology Laboratory, National Institutes of Health, NIEHS, 111 T.W. Alexander Drive, P.O. Box 12233, Research Triangle Park, NC 27709, USA
| | - Da-Peng Dai
- Genome Integrity and Structural Biology Laboratory, National Institutes of Health, NIEHS, 111 T.W. Alexander Drive, P.O. Box 12233, Research Triangle Park, NC 27709, USA
| | - Cristina A Nadalutti
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Ming-Lang Zhao
- Genome Integrity and Structural Biology Laboratory, National Institutes of Health, NIEHS, 111 T.W. Alexander Drive, P.O. Box 12233, Research Triangle Park, NC 27709, USA
| | - Natalie R Gassman
- Genome Integrity and Structural Biology Laboratory, National Institutes of Health, NIEHS, 111 T.W. Alexander Drive, P.O. Box 12233, Research Triangle Park, NC 27709, USA; University of South Alabama Mitchell Cancer Institute, 1660 Springhill Ave, Mobile, AL 36604, USA
| | - Agnes K Janoshazi
- Signal Transduction Laboratory, National Institutes of Health, NIEHS, 111 T.W. Alexander Drive, P.O. Box 12233, Research Triangle Park, NC 27709, USA
| | - Donna F Stefanick
- Genome Integrity and Structural Biology Laboratory, National Institutes of Health, NIEHS, 111 T.W. Alexander Drive, P.O. Box 12233, Research Triangle Park, NC 27709, USA
| | - Julie K Horton
- Genome Integrity and Structural Biology Laboratory, National Institutes of Health, NIEHS, 111 T.W. Alexander Drive, P.O. Box 12233, Research Triangle Park, NC 27709, USA
| | - Rachel Krasich
- Genome Integrity and Structural Biology Laboratory, National Institutes of Health, NIEHS, 111 T.W. Alexander Drive, P.O. Box 12233, Research Triangle Park, NC 27709, USA
| | - Matthew J Longley
- Genome Integrity and Structural Biology Laboratory, National Institutes of Health, NIEHS, 111 T.W. Alexander Drive, P.O. Box 12233, Research Triangle Park, NC 27709, USA
| | - William C Copeland
- Genome Integrity and Structural Biology Laboratory, National Institutes of Health, NIEHS, 111 T.W. Alexander Drive, P.O. Box 12233, Research Triangle Park, NC 27709, USA
| | - Jack D Griffith
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Samuel H Wilson
- Genome Integrity and Structural Biology Laboratory, National Institutes of Health, NIEHS, 111 T.W. Alexander Drive, P.O. Box 12233, Research Triangle Park, NC 27709, USA.
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60
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Aceytuno RD, Piett CG, Havali-Shahriari Z, Edwards RA, Rey M, Ye R, Javed F, Fang S, Mani R, Weinfeld M, Hammel M, Tainer JA, Schriemer DC, Lees-Miller SP, Glover JNM. Structural and functional characterization of the PNKP-XRCC4-LigIV DNA repair complex. Nucleic Acids Res 2017; 45:6238-6251. [PMID: 28453785 PMCID: PMC5449630 DOI: 10.1093/nar/gkx275] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Accepted: 04/25/2017] [Indexed: 01/14/2023] Open
Abstract
Non-homologous end joining (NHEJ) repairs DNA double strand breaks in non-cycling eukaryotic cells. NHEJ relies on polynucleotide kinase/phosphatase (PNKP), which generates 5΄-phosphate/3΄-hydroxyl DNA termini that are critical for ligation by the NHEJ DNA ligase, LigIV. PNKP and LigIV require the NHEJ scaffolding protein, XRCC4. The PNKP FHA domain binds to the CK2-phosphorylated XRCC4 C-terminal tail, while LigIV uses its tandem BRCT repeats to bind the XRCC4 coiled-coil. Yet, the assembled PNKP-XRCC4–LigIV complex remains uncharacterized. Here, we report purification and characterization of a recombinant PNKP–XRCC4–LigIV complex. We show that the stable binding of PNKP in this complex requires XRCC4 phosphorylation and that only one PNKP protomer binds per XRCC4 dimer. Small angle X-ray scattering (SAXS) reveals a flexible multi-state complex that suggests that both the PNKP FHA and catalytic domains contact the XRCC4 coiled-coil and LigIV BRCT repeats. Hydrogen-deuterium exchange indicates protection of a surface on the PNKP phosphatase domain that may contact XRCC4–LigIV. A mutation on this surface (E326K) causes the hereditary neuro-developmental disorder, MCSZ. This mutation impairs PNKP recruitment to damaged DNA in human cells and provides a possible disease mechanism. Together, this work unveils multipoint contacts between PNKP and XRCC4–LigIV that regulate PNKP recruitment and activity within NHEJ.
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Affiliation(s)
- R Daniel Aceytuno
- Department of Biochemistry, University of Alberta, Edmonton, AB T6G-2H7, Canada
| | - Cortt G Piett
- Department of Biochemistry & Molecular Biology, Robson DNA Science Centre, Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, AB T2N 1N4, Canada
| | | | - Ross A Edwards
- Department of Biochemistry, University of Alberta, Edmonton, AB T6G-2H7, Canada
| | - Martial Rey
- Department of Biochemistry & Molecular Biology, Robson DNA Science Centre, Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Ruiqiong Ye
- Department of Biochemistry & Molecular Biology, Robson DNA Science Centre, Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Fatima Javed
- Department of Biochemistry, University of Alberta, Edmonton, AB T6G-2H7, Canada
| | - Shujuan Fang
- Department of Biochemistry & Molecular Biology, Robson DNA Science Centre, Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Rajam Mani
- Department of Oncology, University of Alberta, Cross Cancer Institute, 11560 University Avenue, Edmonton, Alberta T6G 1Z2, Canada
| | - Michael Weinfeld
- Department of Oncology, University of Alberta, Cross Cancer Institute, 11560 University Avenue, Edmonton, Alberta T6G 1Z2, Canada
| | - Michal Hammel
- Molecular Biophysics & Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - John A Tainer
- Molecular Biophysics & Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.,Department of Molecular and Cellular Oncology, The University of Texas M. D. Anderson Cancer Center, Houston, TX 77030, USA
| | - David C Schriemer
- Department of Biochemistry & Molecular Biology, Robson DNA Science Centre, Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Susan P Lees-Miller
- Department of Biochemistry & Molecular Biology, Robson DNA Science Centre, Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - J N Mark Glover
- Department of Biochemistry, University of Alberta, Edmonton, AB T6G-2H7, Canada
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61
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Zheng F, Yu X, Huang J, Dai Y. Circular RNA expression profiles of peripheral blood mononuclear cells in rheumatoid arthritis patients, based on microarray chip technology. Mol Med Rep 2017; 16:8029-8036. [PMID: 28983619 PMCID: PMC5779885 DOI: 10.3892/mmr.2017.7638] [Citation(s) in RCA: 92] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Accepted: 09/07/2017] [Indexed: 12/15/2022] Open
Abstract
Rheumatoid arthritis (RA) is a systemic autoimmune disease characterized by chronic synovial inflammation and finally leads to variable degrees of bone and cartilage erosion. The diagnosis of RA is not an accurate indicator, but a series of scores and the mechanisms underlying it remain only partially understood. The present study explored whether circular RNAs (circRNAs) contribute to the RA pathophysiological mechanism. Total RNA from peripheral blood mononuclear cells of 10 RA patients and 10 healthy controls were extracted and circRNA expression profiling was followed by microarray analysis. In addition, circRNA interactions with microRNAs were performed and microRNA response elements were listed to identify differentially expressed binding site targets in RA. Reverse transcription-quantitative polymerase chain reaction amplification (RT-qPCR) was used to verify the differential expression of circRNAs. A total of 584 circRNAs were differentially expressed in RA patients vs. healthy controls, by circRNA microarray, including 255 circRNAs which were significantly upregulated and 329 downregulated among the RA samples. RT-qPCR validation demonstrated that the expression levels of hsa_circRNA_104194, hsa_circRNA_104593, hsa_circRNA_103334, hsa_circRNA_101407 and hsa_circRNA_102594 were consistent with the results from the microarray analysis. The current study presented differentially expressed circRNAs and their corresponding microRNA binding sites in RA. circRNAs may exhibit a role in the regulation of expression of symbol genes that influence the occurrence and development of RA.
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Affiliation(s)
- Fengping Zheng
- Clinical Medical Research Center, The Second Clinical Medical College of Jinan University, Shenzhen People's Hospital, Shenzhen, Guangdong 518020, P.R. China
| | - Xiangqi Yu
- Clinical Medical Research Center, The Second Clinical Medical College of Jinan University, Shenzhen People's Hospital, Shenzhen, Guangdong 518020, P.R. China
| | - Jiahuang Huang
- Clinical Medical Research Center, The Second Clinical Medical College of Jinan University, Shenzhen People's Hospital, Shenzhen, Guangdong 518020, P.R. China
| | - Yong Dai
- Clinical Medical Research Center, The Second Clinical Medical College of Jinan University, Shenzhen People's Hospital, Shenzhen, Guangdong 518020, P.R. China
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Ramdzan ZM, Ginjala V, Pinder JB, Chung D, Donovan CM, Kaur S, Leduy L, Dellaire G, Ganesan S, Nepveu A. The DNA repair function of CUX1 contributes to radioresistance. Oncotarget 2017; 8:19021-19038. [PMID: 28147323 PMCID: PMC5386666 DOI: 10.18632/oncotarget.14875] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 01/19/2017] [Indexed: 01/19/2023] Open
Abstract
Ionizing radiation generates a broad spectrum of oxidative DNA lesions, including oxidized base products, abasic sites, single-strand breaks and double-strand breaks. The CUX1 protein was recently shown to function as an auxiliary factor that stimulates enzymatic activities of OGG1 through its CUT domains. In the present study, we investigated the requirement for CUX1 and OGG1 in the resistance to radiation. Cancer cell survival following ionizing radiation is reduced by CUX1 knockdown and increased by higher CUX1 expression. However, CUX1 knockdown is sufficient by itself to reduce viability in many cancer cell lines that exhibit high levels of reactive oxygen species (ROS). Consequently, clonogenic results expressed relative to that of non-irradiated cells indicate that CUX1 knockdown confers no or modest radiosensitivity to cancer cells with high ROS. A recombinant protein containing only two CUT domains is sufficient for rapid recruitment to DNA damage, acceleration of DNA repair and increased survival following radiation. In agreement with these findings, OGG1 knockdown and treatment of cells with OGG1 inhibitors sensitize cancer cells to radiation. Together, these results validate CUX1 and more specifically the CUT domains as therapeutic targets.
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Affiliation(s)
- Zubaidah M Ramdzan
- Goodman Cancer Research Centre, McGill University, Montreal, Quebec, H3A 1A3, Canada
| | - Vasudeva Ginjala
- Department of Medicine, Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, New Jersey 08903, USA
| | - Jordan B Pinder
- Department of Pathology, Dalhousie University, Halifax, Nova Scotia, B3H 4R2, Canada
| | - Dudley Chung
- Department of Pathology, Dalhousie University, Halifax, Nova Scotia, B3H 4R2, Canada
| | - Caroline M Donovan
- Goodman Cancer Research Centre, McGill University, Montreal, Quebec, H3A 1A3, Canada.,Department of Biochemistry, McGill University, Montreal, Quebec, H3A 1A3, Canada
| | - Simran Kaur
- Goodman Cancer Research Centre, McGill University, Montreal, Quebec, H3A 1A3, Canada.,Department of Biochemistry, McGill University, Montreal, Quebec, H3A 1A3, Canada
| | - Lam Leduy
- Goodman Cancer Research Centre, McGill University, Montreal, Quebec, H3A 1A3, Canada
| | - Graham Dellaire
- Department of Pathology, Dalhousie University, Halifax, Nova Scotia, B3H 4R2, Canada
| | - Shridar Ganesan
- Department of Medicine, Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, New Jersey 08903, USA
| | - Alain Nepveu
- Goodman Cancer Research Centre, McGill University, Montreal, Quebec, H3A 1A3, Canada.,Department of Biochemistry, McGill University, Montreal, Quebec, H3A 1A3, Canada.,Department of Medicine, McGill University, Montreal, Quebec, H3A 1A3, Canada.,Department of Oncology, McGill University, Montreal, Quebec, H3A 1A3, Canada
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63
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Sanchez A, Gadaleta MC, Limbo O, Russell P. Lingering single-strand breaks trigger Rad51-independent homology-directed repair of collapsed replication forks in the polynucleotide kinase/phosphatase mutant of fission yeast. PLoS Genet 2017; 13:e1007013. [PMID: 28922417 PMCID: PMC5626526 DOI: 10.1371/journal.pgen.1007013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Revised: 10/03/2017] [Accepted: 09/08/2017] [Indexed: 11/19/2022] Open
Abstract
The DNA repair enzyme polynucleotide kinase/phosphatase (PNKP) protects genome integrity by restoring ligatable 5'-phosphate and 3'-hydroxyl termini at single-strand breaks (SSBs). In humans, PNKP mutations underlie the neurological disease known as MCSZ, but these individuals are not predisposed for cancer, implying effective alternative repair pathways in dividing cells. Homology-directed repair (HDR) of collapsed replication forks was proposed to repair SSBs in PNKP-deficient cells, but the critical HDR protein Rad51 is not required in PNKP-null (pnk1Δ) cells of Schizosaccharomyces pombe. Here, we report that pnk1Δ cells have enhanced requirements for Rad3 (ATR/Mec1) and Chk1 checkpoint kinases, and the multi-BRCT domain protein Brc1 that binds phospho-histone H2A (γH2A) at damaged replication forks. The viability of pnk1Δ cells depends on Mre11 and Ctp1 (CtIP/Sae2) double-strand break (DSB) resection proteins, Rad52 DNA strand annealing protein, Mus81-Eme1 Holliday junction resolvase, and Rqh1 (BLM/WRN/Sgs1) DNA helicase. Coupled with increased sister chromatid recombination and Rad52 repair foci in pnk1Δ cells, these findings indicate that lingering SSBs in pnk1Δ cells trigger Rad51-independent homology-directed repair of collapsed replication forks. From these data, we propose models for HDR-mediated tolerance of persistent SSBs with 3' phosphate in pnk1Δ cells.
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Affiliation(s)
- Arancha Sanchez
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, United States of America
| | - Mariana C. Gadaleta
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, United States of America
| | - Oliver Limbo
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, United States of America
| | - Paul Russell
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, United States of America
- * E-mail:
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64
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Breslin C, Mani RS, Fanta M, Hoch N, Weinfeld M, Caldecott KW. The Rev1 interacting region (RIR) motif in the scaffold protein XRCC1 mediates a low-affinity interaction with polynucleotide kinase/phosphatase (PNKP) during DNA single-strand break repair. J Biol Chem 2017; 292:16024-16031. [PMID: 28821613 PMCID: PMC5625035 DOI: 10.1074/jbc.m117.806638] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Revised: 08/15/2017] [Indexed: 11/22/2022] Open
Abstract
The scaffold protein X-ray repair cross-complementing 1 (XRCC1) interacts with multiple enzymes involved in DNA base excision repair and single-strand break repair (SSBR) and is important for genetic integrity and normal neurological function. One of the most important interactions of XRCC1 is that with polynucleotide kinase/phosphatase (PNKP), a dual-function DNA kinase/phosphatase that processes damaged DNA termini and that, if mutated, results in ataxia with oculomotor apraxia 4 (AOA4) and microcephaly with early-onset seizures and developmental delay (MCSZ). XRCC1 and PNKP interact via a high-affinity phosphorylation-dependent interaction site in XRCC1 and a forkhead-associated domain in PNKP. Here, we identified using biochemical and biophysical approaches a second PNKP interaction site in XRCC1 that binds PNKP with lower affinity and independently of XRCC1 phosphorylation. However, this interaction nevertheless stimulated PNKP activity and promoted SSBR and cell survival. The low-affinity interaction site required the highly conserved Rev1-interacting region (RIR) motif in XRCC1 and included three critical and evolutionarily invariant phenylalanine residues. We propose a bipartite interaction model in which the previously identified high-affinity interaction acts as a molecular tether, holding XRCC1 and PNKP together and thereby promoting the low-affinity interaction identified here, which then stimulates PNKP directly.
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Affiliation(s)
- Claire Breslin
- From the Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Science Park Road, Falmer, Brighton BN19RQ, United Kingdom
| | - Rajam S Mani
- the Department of Experimental Oncology, Cross Cancer Institute, Edmonton, Alberta T6G 1Z2, Canada, and
| | - Mesfin Fanta
- the Department of Experimental Oncology, Cross Cancer Institute, Edmonton, Alberta T6G 1Z2, Canada, and
| | - Nicolas Hoch
- From the Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Science Park Road, Falmer, Brighton BN19RQ, United Kingdom.,the CAPES Foundation, Ministry of Education of Brazil, Brasilia/DF 70040-020, Brazil
| | - Michael Weinfeld
- the Department of Experimental Oncology, Cross Cancer Institute, Edmonton, Alberta T6G 1Z2, Canada, and
| | - Keith W Caldecott
- From the Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Science Park Road, Falmer, Brighton BN19RQ, United Kingdom,
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65
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Dutta A, Eckelmann B, Adhikari S, Ahmed KM, Sengupta S, Pandey A, Hegde PM, Tsai MS, Tainer JA, Weinfeld M, Hegde ML, Mitra S. Microhomology-mediated end joining is activated in irradiated human cells due to phosphorylation-dependent formation of the XRCC1 repair complex. Nucleic Acids Res 2017; 45:2585-2599. [PMID: 27994036 PMCID: PMC5389627 DOI: 10.1093/nar/gkw1262] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 12/15/2016] [Indexed: 02/06/2023] Open
Abstract
Microhomology-mediated end joining (MMEJ), an error-prone pathway for DNA double-strand break (DSB) repair, is implicated in genomic rearrangement and oncogenic transformation; however, its contribution to repair of radiation-induced DSBs has not been characterized. We used recircularization of a linearized plasmid with 3΄-P-blocked termini, mimicking those at X-ray-induced strand breaks, to recapitulate DSB repair via MMEJ or nonhomologous end-joining (NHEJ). Sequence analysis of the circularized plasmids allowed measurement of relative activity of MMEJ versus NHEJ. While we predictably observed NHEJ to be the predominant pathway for DSB repair in our assay, MMEJ was significantly enhanced in preirradiated cells, independent of their radiation-induced arrest in the G2/M phase. MMEJ activation was dependent on XRCC1 phosphorylation by casein kinase 2 (CK2), enhancing XRCC1's interaction with the end resection enzymes MRE11 and CtIP. Both endonuclease and exonuclease activities of MRE11 were required for MMEJ, as has been observed for homology-directed DSB repair (HDR). Furthermore, the XRCC1 co-immunoprecipitate complex (IP) displayed MMEJ activity in vitro, which was significantly elevated after irradiation. Our studies thus suggest that radiation-mediated enhancement of MMEJ in cells surviving radiation therapy may contribute to their radioresistance and could be therapeutically targeted.
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Affiliation(s)
- Arijit Dutta
- Department of Radiation Oncology, Houston Methodist Research Institute, Houston, TX 77030, USA.,Department of Biochemistry and Molecular Biology, University of Texas Medical Branch (UTMB), Galveston, TX 77555, USA
| | - Bradley Eckelmann
- Department of Radiation Oncology, Houston Methodist Research Institute, Houston, TX 77030, USA.,Texas A&M Health Science Center, College of Medicine, Bryan, TX 77807, USA
| | | | - Kazi Mokim Ahmed
- Department of Radiation Oncology, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Shiladitya Sengupta
- Department of Radiation Oncology, Houston Methodist Research Institute, Houston, TX 77030, USA.,Weill Cornell Medical College, New York, NY 10065, USA
| | - Arvind Pandey
- Department of Radiation Oncology, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Pavana M Hegde
- Department of Radiation Oncology, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Miaw-Sheue Tsai
- Department of Cell and Molecular Biology, Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA 94720, USA
| | - John A Tainer
- Department of Cell and Molecular Biology, Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA 94720, USA.,Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Michael Weinfeld
- Department of Oncology, University of Alberta, Cross Cancer Institute, Edmonton, Alberta T6G 1Z2, Canada
| | - Muralidhar L Hegde
- Department of Radiation Oncology, Houston Methodist Research Institute, Houston, TX 77030, USA.,Weill Cornell Medical College, New York, NY 10065, USA.,Houston Methodist Neurological Institute, Houston, TX 77030, USA
| | - Sankar Mitra
- Department of Radiation Oncology, Houston Methodist Research Institute, Houston, TX 77030, USA.,Department of Biochemistry and Molecular Biology, University of Texas Medical Branch (UTMB), Galveston, TX 77555, USA.,Texas A&M Health Science Center, College of Medicine, Bryan, TX 77807, USA.,Weill Cornell Medical College, New York, NY 10065, USA
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66
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Seol JH, Shim EY, Lee SE. Microhomology-mediated end joining: Good, bad and ugly. Mutat Res 2017; 809:81-87. [PMID: 28754468 DOI: 10.1016/j.mrfmmm.2017.07.002] [Citation(s) in RCA: 149] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 06/21/2017] [Accepted: 07/03/2017] [Indexed: 01/06/2023]
Abstract
DNA double-strand breaks (DSBs) are induced by a variety of genotoxic agents, including ionizing radiation and chemotherapy drugs for treating cancers. The elimination of DSBs proceeds via distinctive error-free and error-prone pathways. Repair by homologous recombination (HR) is largely error-free and mediated by RAD51/BRCA2 gene products. Classical non-homologous end joining (C-NHEJ) requires the Ku heterodimer and can efficiently rejoin breaks, with occasional loss or gain of DNA information. Recently, evidence has unveiled another DNA end-joining mechanism that is independent of recombination factors and Ku proteins, termed alternative non-homologous end joining (A-NHEJ). While A-NHEJ-mediated repair does not require homology, in a subtype of A-NHEJ, DSB breaks are sealed by microhomology (MH)-mediated base-pairing of DNA single strands, followed by nucleolytic trimming of DNA flaps, DNA gap filling, and DNA ligation, yielding products that are always associated with DNA deletion. This highly error-prone DSB repair pathway is termed microhomology-mediated end joining (MMEJ). Dissecting the mechanisms of MMEJ is of great interest because of its potential to destabilize the genome through gene deletions and chromosomal rearrangements in cells deficient in canonical repair pathways, including HR and C-NHEJ. In addition, evidence now suggests that MMEJ plays a physiological role in normal cells.
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Affiliation(s)
- Ja-Hwan Seol
- Department of Molecular Medicine, Institute of Biotechnology, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX 78229-3900, United States
| | - Eun Yong Shim
- Department of Radiation Oncology, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX 78229-3900, United States
| | - Sang Eun Lee
- Department of Molecular Medicine, Institute of Biotechnology, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX 78229-3900, United States; Department of Radiation Oncology, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX 78229-3900, United States.
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67
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Abstract
Multiple DNA repair pathways maintain genome stability and ensure that DNA remains essentially unchanged over the life of a cell. Various human diseases occur if DNA repair is compromised, and most of these impact the nervous system, in some cases exclusively. However, it is often unclear what specific endogenous damage underpins disease pathology. Generally, the types of causative DNA damage are associated with replication, transcription, or oxidative metabolism; other direct sources of endogenous lesions may arise from aberrant topoisomerase activity or ribonucleotide incorporation into DNA. This review focuses on the etiology of DNA damage in the nervous system and the genome stability pathways that prevent human neurologic disease.
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Affiliation(s)
- Peter J McKinnon
- Department of Genetics, St Jude Children's Research Hospital, Memphis, Tennessee 38105, USA
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68
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Abbotts R, Wilson DM. Coordination of DNA single strand break repair. Free Radic Biol Med 2017; 107:228-244. [PMID: 27890643 PMCID: PMC5443707 DOI: 10.1016/j.freeradbiomed.2016.11.039] [Citation(s) in RCA: 144] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Revised: 11/21/2016] [Accepted: 11/23/2016] [Indexed: 12/28/2022]
Abstract
The genetic material of all organisms is susceptible to modification. In some instances, these changes are programmed, such as the formation of DNA double strand breaks during meiotic recombination to generate gamete variety or class switch recombination to create antibody diversity. However, in most cases, genomic damage is potentially harmful to the health of the organism, contributing to disease and aging by promoting deleterious cellular outcomes. A proportion of DNA modifications are caused by exogenous agents, both physical (namely ultraviolet sunlight and ionizing radiation) and chemical (such as benzopyrene, alkylating agents, platinum compounds and psoralens), which can produce numerous forms of DNA damage, including a range of "simple" and helix-distorting base lesions, abasic sites, crosslinks and various types of phosphodiester strand breaks. More significant in terms of frequency are endogenous mechanisms of modification, which include hydrolytic disintegration of DNA chemical bonds, attack by reactive oxygen species and other byproducts of normal cellular metabolism, or incomplete or necessary enzymatic reactions (such as topoisomerases or repair nucleases). Both exogenous and endogenous mechanisms are associated with a high risk of single strand breakage, either produced directly or generated as intermediates of DNA repair. This review will focus upon the creation, consequences and resolution of single strand breaks, with a particular focus on two major coordinating repair proteins: poly(ADP-ribose) polymerase 1 (PARP1) and X-ray repair cross-complementing protein 1 (XRCC1).
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Affiliation(s)
- Rachel Abbotts
- Laboratory of Molecular Gerontology, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - David M Wilson
- Laboratory of Molecular Gerontology, National Institute on Aging, Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA.
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69
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Havali-Shahriari Z, Weinfeld M, Glover JNM. Characterization of DNA Substrate Binding to the Phosphatase Domain of the DNA Repair Enzyme Polynucleotide Kinase/Phosphatase. Biochemistry 2017; 56:1737-1745. [PMID: 28276686 DOI: 10.1021/acs.biochem.6b01236] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Polynucleotide kinase/phosphatase (PNKP) is a DNA strand break repair enzyme that uses separate 5' kinase and 3' phosphatase active sites to convert damaged 5'-hydroxyl/3'-phosphate strand termini to ligatable 5'-phosphate/3'-hydroxyl ends. The phosphatase active site has received particular attention as a target of inhibition in cancer therapy development. The phosphatase domain dephosphorylates a range of single- and double-stranded substrates; however, structural studies have shown that the phosphatase catalytic cleft can bind only single-stranded substrates. Here we use a catalytically inactive but structurally intact phosphatase mutant to probe interactions between PNKP and a variety of single- and double-stranded DNA substrates using an electrophoretic mobility shift assay. This work indicates that the phosphatase domain binds 3'-phosphorylated single-stranded DNAs in a manner that is highly dependent on the presence of the 3'-phosphate. Double-stranded substrate binding, in contrast, is not as dependent on the 3'-phosphate. Experiments comparing blunt-end, 3'-overhanging, and frayed-end substrates indicate that the predicted loss of energy due to base pair disruption upon binding of the phosphatase active site is likely balanced by favorable interactions between the liberated complementary strand and PNKP. Comparison of the effects on substrate binding of mutations within the phosphatase active site cleft with mutations in surrounding positively charged surfaces suggests that the surrounding surfaces are important for binding to double-stranded substrates. We further show that while fluorescence polarization methods can detect specific binding of single-stranded DNAs with the phosphatase domain, this method does not detect specific interactions between the PNKP phosphatase and double-stranded substrates.
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Affiliation(s)
| | - Michael Weinfeld
- Department of Oncology, University of Alberta, Cross Cancer Institute , 11560 University Avenue, Edmonton, Alberta T6G 1Z2, Canada
| | - J N Mark Glover
- Department of Biochemistry, University of Alberta , Edmonton, Alberta T6G 2H7, Canada
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70
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Whitaker AM, Schaich MA, Smith MR, Flynn TS, Freudenthal BD. Base excision repair of oxidative DNA damage: from mechanism to disease. Front Biosci (Landmark Ed) 2017; 22:1493-1522. [PMID: 28199214 DOI: 10.2741/4555] [Citation(s) in RCA: 139] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Reactive oxygen species continuously assault the structure of DNA resulting in oxidation and fragmentation of the nucleobases. Both oxidative DNA damage itself and its repair mediate the progression of many prevalent human maladies. The major pathway tasked with removal of oxidative DNA damage, and hence maintaining genomic integrity, is base excision repair (BER). The aphorism that structure often dictates function has proven true, as numerous recent structural biology studies have aided in clarifying the molecular mechanisms used by key BER enzymes during the repair of damaged DNA. This review focuses on the mechanistic details of the individual BER enzymes and the association of these enzymes during the development and progression of human diseases, including cancer and neurological diseases. Expanding on these structural and biochemical studies to further clarify still elusive BER mechanisms, and focusing our efforts toward gaining an improved appreciation of how these enzymes form co-complexes to facilitate DNA repair is a crucial next step toward understanding how BER contributes to human maladies and how it can be manipulated to alter patient outcomes.
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Affiliation(s)
- Amy M Whitaker
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, Kansas, 66160
| | - Matthew A Schaich
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, Kansas, 66160
| | - Mallory R Smith
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, Kansas, 66160
| | - Tony S Flynn
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, Kansas, 66160
| | - Bret D Freudenthal
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, Kansas, 66160,
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71
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Jones L, Houlden H, Tabrizi SJ. DNA repair in the trinucleotide repeat disorders. Lancet Neurol 2017; 16:88-96. [PMID: 27979358 DOI: 10.1016/s1474-4422(16)30350-7] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Revised: 09/22/2016] [Accepted: 10/27/2016] [Indexed: 02/07/2023]
Abstract
BACKGROUND Inherited diseases caused by unstable repeated DNA sequences are rare, but together represent a substantial cause of morbidity. Trinucleotide repeat disorders are severe, usually life-shortening, neurological disorders caused by nucleotide expansions, and most have no disease-modifying treatments. Longer repeat expansions are associated with genetic anticipation (ie, earlier disease onset in successive generations), although the differences in age at onset are not entirely accounted for by repeat length. Such phenotypic variation within disorders implies the existence of additional modifying factors in pathways that can potentially be modulated to treat disease. RECENT DEVELOPMENTS A genome-wide association study detected genetic modifiers of age at onset in Huntington's disease. Similar findings were seen in the spinocerebellar ataxias, indicating an association between DNA damage-response and repair pathways and the age at onset of disease. These studies also suggest that a common genetic mechanism modulates age at onset across polyglutamine diseases and could extend to other repeat expansion disorders. Genetic defects in DNA repair underlie other neurodegenerative disorders (eg, ataxia-telangiectasia), and DNA double-strand breaks are crucial to the modulation of early gene expression, which provides a mechanistic link between DNA repair and neurodegeneration. Mismatch and base-excision repair are important in the somatic expansion of repeated sequences in mouse models of trinucleotide repeat disorders, and somatic expansion of the expanded CAG tract in HTT correlates with age at onset of Huntington's disease and other trinucleotide repeat disorders. WHERE NEXT?: To understand the common genetic architecture of trinucleotide repeat disorders and any further genetic susceptibilities in individual disorders, genetic analysis with increased numbers of variants and sample sizes is needed, followed by sequencing approaches to define the phenotype-modifying variants. The findings must then be translated into cell biology analyses to elucidate the mechanisms through which the genetic variants operate. Genes that have roles in the DNA damage response could underpin a common DNA repeat-based mechanism and provide new therapeutic targets (and hence therapeutics) in multiple trinucleotide repeat disorders.
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Affiliation(s)
- Lesley Jones
- MRC Centre for Neuropsychiatric Genetics and Genomics, Institute of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, UK.
| | - Henry Houlden
- Department of Molecular Neuroscience and MRC Centre for Neuromuscular Diseases, Institute of Neurology, Queen Square, London, UK
| | - Sarah J Tabrizi
- UCL Huntington's Disease Centre, Department of Neurodegenerative Disease, Institute of Neurology, University College London, London, UK
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72
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Barzilai A, Schumacher B, Shiloh Y. Genome instability: Linking ageing and brain degeneration. Mech Ageing Dev 2017; 161:4-18. [DOI: 10.1016/j.mad.2016.03.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Revised: 03/23/2016] [Accepted: 03/26/2016] [Indexed: 02/06/2023]
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73
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Hall DG, Rybak T, Verdelet T. Multicomponent Hetero-[4 + 2] Cycloaddition/Allylboration Reaction: From Natural Product Synthesis to Drug Discovery. Acc Chem Res 2016; 49:2489-2500. [PMID: 27753496 DOI: 10.1021/acs.accounts.6b00403] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Multicomponent reactions (MCR), transformations employing three or more simple substrates in a single and highly atom-economical operation, are very attractive in both natural product synthesis and diversity-oriented synthesis of druglike molecules. Several popular multicomponent reactions were designed by combining two well-established individual reactions that utilize mutually compatible substrates. In this regard, it is not surprising that the merging of two reactions deemed as workhorses of stereoselective synthesis, the Diels-Alder cycloaddition and carbonyl allylboration, would produce a powerful and highly versatile tandem MCR process. The idea of using 1,3-dienylboronates in [4 + 2] cycloadditions as a means to produce cyclic allylic boronates was first reported by Vaultier and Hoffmann in 1987. In their seminal study, a 1-boronodiene was reacted with electron-poor alkenes, and the intermediate cycloadducts were isolated and added to aldehydes in a separate step leading to α-hydroxyalkylated carbocycles via a highly diastereoselective allylboration reaction. The one-pot three-component variant was realized in 1999 by Lallemand and co-workers, and soon after groups led by Hall and Carboni reported heterocyclic variants of the tandem [4 + 2] cycloaddition/allylboration to prepare α-hydroxyalkylated piperidine and pyran containing compounds, respectively. These classes of heterocycles are ubiquitous in Nature and are important components of pharmaceuticals. This Account summarizes the development and evolution of this powerful multicomponent reaction for accessing nonaromatic heterocycles and its many applications in natural products synthesis and drug discovery. The aza[4 + 2]cycloaddition/allylboration MCR was first optimized in our laboratory using 4-boronylhydrazonobutadienes and N-substituted maleimides, and it was exploited in the preparation of combinatorial libraries of polysubstituted imidopiperidines that feature as many as four elements of chemical diversity. Biological screening of these druglike imidopiperidine libraries unveiled promising bioactive agents such as A12B4C3, the first reported inhibitor of the human DNA repair enzyme, polynucleotide kinase-phosphatase (hPNKP). Related applications of this MCR in target-oriented synthesis also led to total syntheses of palustrine alkaloids. The inverse electron-demand oxa[4 + 2] cycloaddition/allyboration variant can take advantage of Jacobsen's chiral Cr(III)salen catalyst, affording a rare example of catalytic enantioselective MCR, one that provides a rapid access to α-hydroxyalkyl dihydropyrans in high enantio- and diastereoselectivity. This process exploits 3-boronoacrolein pinacolate as the heterodiene with ethyl vinyl ether or various 2-substituted enol ethers, along with a wide variety of aldehydes in the allylation stage. This versatile methodology was deployed in total syntheses of thiomarinol antibiotics, goniodiol and its derivatives, and the complex anticancer macrolide palmerolide A. More recent work from our laboratory centered on the regio- and stereoselective Suzuki-Miyaura cross-coupling of the dihydropyranyl boronates, thus providing a glimpse of the potential for new multicomponent variants that merge hetero[4 + 2] cycloadditions of 1-borylated heterodienes with transition metal-catalyzed transformations. This stereoselective MCR strategy holds great promise for provoking continuing applications in complex molecule synthesis and drug discovery, and is likely to inspire new and innovative MCR-based approaches to nonaromatic heterocycles.
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Affiliation(s)
- Dennis G. Hall
- Department of Chemistry, University of Alberta, 4-010 Centennial Centre for Interdisciplinary Science, Edmonton, Alberta, Canada, T6G 2G2
| | - Taras Rybak
- Department of Chemistry, University of Alberta, 4-010 Centennial Centre for Interdisciplinary Science, Edmonton, Alberta, Canada, T6G 2G2
| | - Tristan Verdelet
- Department of Chemistry, University of Alberta, 4-010 Centennial Centre for Interdisciplinary Science, Edmonton, Alberta, Canada, T6G 2G2
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74
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Antisense oligonucleotide-mediated exon skipping as a strategy to reduce proteolytic cleavage of ataxin-3. Sci Rep 2016; 6:35200. [PMID: 27731380 PMCID: PMC5059676 DOI: 10.1038/srep35200] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Accepted: 09/27/2016] [Indexed: 12/04/2022] Open
Abstract
Spinocerebellar ataxia type-3 (SCA3) is a neurodegenerative disorder caused by a polyglutamine repeat expansion in the ataxin-3 protein. Cleavage of mutant ataxin-3 by proteolytic enzymes yields ataxin-3 fragments containing the polyglutamine stretch. These shorter ataxin-3 fragments are thought to be involved in SCA3 pathogenesis due to their increased cellular toxicity and their involvement in formation of the characteristic neuronal aggregates. As a strategy to prevent formation of toxic cleavage fragments, we investigated an antisense oligonucleotide-mediated modification of the ataxin-3 pre-mRNA through exon skipping of exon 8 and 9, resulting in the removal of a central 88 amino acid region of the ataxin-3 protein. This removed protein region contains several predicted cleavage sites and two ubiquitin-interacting motifs. In contrast to unmodified mutant ataxin-3, the internally truncated ataxin-3 protein did not give rise to potentially toxic cleavage fragments when incubated with caspases. In vitro experiments did not show cellular toxicity of the modified ataxin-3 protein. However, the modified protein was incapable of binding poly-ubiquitin chains, which may interfere with its normal deubiquitinating function. Low exon skipping efficiencies combined with reduction in important ataxin-3 protein functions suggest that skipping of exon 8 and 9 is not a viable therapeutic option for SCA3.
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75
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Chakraborty A, Tapryal N, Venkova T, Horikoshi N, Pandita RK, Sarker AH, Sarkar PS, Pandita TK, Hazra TK. Classical non-homologous end-joining pathway utilizes nascent RNA for error-free double-strand break repair of transcribed genes. Nat Commun 2016; 7:13049. [PMID: 27703167 PMCID: PMC5059474 DOI: 10.1038/ncomms13049] [Citation(s) in RCA: 121] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Accepted: 08/30/2016] [Indexed: 12/30/2022] Open
Abstract
DNA double-strand breaks (DSBs) leading to loss of nucleotides in the transcribed region can be lethal. Classical non-homologous end-joining (C-NHEJ) is the dominant pathway for DSB repair (DSBR) in adult mammalian cells. Here we report that during such DSBR, mammalian C-NHEJ proteins form a multiprotein complex with RNA polymerase II and preferentially associate with the transcribed genes after DSB induction. Depletion of C-NHEJ factors significantly abrogates DSBR in transcribed but not in non-transcribed genes. We hypothesized that nascent RNA can serve as a template for restoring the missing sequences, thus allowing error-free DSBR. We indeed found pre-mRNA in the C-NHEJ complex. Finally, when a DSB-containing plasmid with several nucleotides deleted within the E. coli lacZ gene was allowed time to repair in lacZ-expressing mammalian cells, a functional lacZ plasmid could be recovered from control but not C-NHEJ factor-depleted cells, providing important mechanistic insights into C-NHEJ-mediated error-free DSBR of the transcribed genome. Most adult mammalian cells prefer to repair double-strand DNA breaks though the classical nonhomologous end-joining pathway. Here the authors present evidence that a nascent RNA transcript can serve as a template to facilitate error-free repair.
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Affiliation(s)
- Anirban Chakraborty
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Sealy Center for Molecular Medicine, University of Texas Medical Branch, Galveston, Texas 77555, USA
| | - Nisha Tapryal
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Sealy Center for Molecular Medicine, University of Texas Medical Branch, Galveston, Texas 77555, USA
| | - Tatiana Venkova
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Sealy Center for Molecular Medicine, University of Texas Medical Branch, Galveston, Texas 77555, USA
| | - Nobuo Horikoshi
- Department of Radiation Oncology, The Houston Methodist Research Institute, Houston, Texas 77030, USA
| | - Raj K Pandita
- Department of Radiation Oncology, The Houston Methodist Research Institute, Houston, Texas 77030, USA
| | - Altaf H Sarker
- Division of Life Sciences, Department of Cancer and DNA Damage Responses, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Partha S Sarkar
- Department of Neurology and Neuroscience and Cell Biology, University of Texas Medical Branch, Galveston, Texas 77555, USA
| | - Tej K Pandita
- Department of Radiation Oncology, The Houston Methodist Research Institute, Houston, Texas 77030, USA
| | - Tapas K Hazra
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Sealy Center for Molecular Medicine, University of Texas Medical Branch, Galveston, Texas 77555, USA
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76
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Nagel R, Semenova EA, Berns A. Drugging the addict: non-oncogene addiction as a target for cancer therapy. EMBO Rep 2016; 17:1516-1531. [PMID: 27702988 PMCID: PMC5090709 DOI: 10.15252/embr.201643030] [Citation(s) in RCA: 96] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2016] [Accepted: 08/24/2016] [Indexed: 12/13/2022] Open
Abstract
Historically, cancers have been treated with chemotherapeutics aimed to have profound effects on tumor cells with only limited effects on normal tissue. This approach was followed by the development of small‐molecule inhibitors that can target oncogenic pathways critical for the survival of tumor cells. The clinical targeting of these so‐called oncogene addictions, however, is in many instances hampered by the outgrowth of resistant clones. More recently, the proper functioning of non‐mutated genes has been shown to enhance the survival of many cancers, a phenomenon called non‐oncogene addiction. In the current review, we will focus on the distinct non‐oncogenic addictions found in cancer cells, including synthetic lethal interactions, the underlying stress phenotypes, and arising therapeutic opportunities.
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Affiliation(s)
- Remco Nagel
- Division of Molecular Genetics, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Ekaterina A Semenova
- Division of Molecular Genetics, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Anton Berns
- Division of Molecular Genetics, The Netherlands Cancer Institute, Amsterdam, The Netherlands
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77
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Kaur S, Coulombe Y, Ramdzan ZM, Leduy L, Masson JY, Nepveu A. Special AT-rich Sequence-binding Protein 1 (SATB1) Functions as an Accessory Factor in Base Excision Repair. J Biol Chem 2016; 291:22769-22780. [PMID: 27590341 DOI: 10.1074/jbc.m116.735696] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Revised: 09/01/2016] [Indexed: 01/19/2023] Open
Abstract
Base excision repair is initiated by DNA glycosylases that recognize specific altered bases. DNA glycosylases for oxidized bases carry both a glycosylase activity that removes the faulty base and an apyrimidinic/apurinic lyase activity that introduces a single-strand DNA incision. In particular, the CUT domains within the CUX1 and CUX2 proteins were recently shown to interact with the 8-oxoguanine (8-oxoG) DNA glycosylase and stimulate its enzymatic activities. SATB1, which contains two CUT domains, was originally characterized as a T cell-specific genome organizer whose aberrant overexpression in breast cancer can promote tumor progression. Here we investigated the involvement of SATB1 in DNA repair. SATB1 knockdown caused a delay in DNA repair following exposure to H2O2, an increase in OGG1-sensitive oxidized bases within genomic DNA, and a decrease in 8-oxoG cleavage activity in cell extracts. In parallel, we observed an increase in phospho-CHK1 and γ-H2AX levels and a decrease in DNA synthesis. Conversely, ectopic expression of SATB1 accelerated DNA repair and reduced the levels of oxidized bases in genomic DNA. Moreover, an enhanced GFP-SATB1 fusion protein was rapidly recruited to laser microirradiation-induced DNA damage. Using purified proteins, we showed that SATB1 interacts directly with OGG1, increases its binding to 8-oxoG-containing DNA, promotes Schiff base formation, and stimulates its glycosylase and apyrimidinic/apurinic lyase enzymatic activities. Structure/function analysis demonstrated that CUT domains, but not the homeodomain, are responsible for the stimulation of OGG1. Together, these results identify another CUT domain protein that functions both as a transcription factor and an accessory factor in base excision repair.
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Affiliation(s)
- Simran Kaur
- From the Goodman Cancer Research Centre and.,Departments of Biochemistry
| | - Yan Coulombe
- the Genome Stability Laboratory, CHU de Québec Research Center, Québec City, Québec G1R 2J6, Canada, and.,the Department of Molecular Biology, Medical Biochemistry, and Pathology, Laval University Cancer Research Center, Québec City, Québec G1V 0A6, Canada
| | | | - Lam Leduy
- From the Goodman Cancer Research Centre and
| | - Jean-Yves Masson
- the Genome Stability Laboratory, CHU de Québec Research Center, Québec City, Québec G1R 2J6, Canada, and.,the Department of Molecular Biology, Medical Biochemistry, and Pathology, Laval University Cancer Research Center, Québec City, Québec G1V 0A6, Canada
| | - Alain Nepveu
- From the Goodman Cancer Research Centre and .,Departments of Biochemistry.,Oncology, and.,Medicine, McGill University, Montreal, Quebec H3A 1A3, Canada
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78
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Jiang B, Glover JNM, Weinfeld M. Neurological disorders associated with DNA strand-break processing enzymes. Mech Ageing Dev 2016; 161:130-140. [PMID: 27470939 DOI: 10.1016/j.mad.2016.07.009] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Revised: 07/21/2016] [Accepted: 07/23/2016] [Indexed: 12/24/2022]
Abstract
The termini of DNA strand breaks induced by reactive oxygen species or by abortive DNA metabolic intermediates require processing to enable subsequent gap filling and ligation to proceed. The three proteins, tyrosyl DNA-phosphodiesterase 1 (TDP1), aprataxin (APTX) and polynucleotide kinase/phosphatase (PNKP) each act on a discrete set of modified strand-break termini. Recently, a series of neurodegenerative and neurodevelopmental disorders have been associated with mutations in the genes coding for these proteins. Mutations in TDP1 and APTX have been linked to Spinocerebellar ataxia with axonal neuropathy (SCAN1) and Ataxia-ocular motor apraxia 1 (AOA1), respectively, while mutations in PNKP are considered to be responsible for Microcephaly with seizures (MCSZ) and Ataxia-ocular motor apraxia 4 (AOA4). Here we present an overview of the mechanisms of these proteins and how their impairment may give rise to their respective disorders.
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Affiliation(s)
- Bingcheng Jiang
- Department of Oncology, University of Alberta, Cross Cancer Institute, 11560 University Avenue, Edmonton, Alberta, T6G 1Z2, Canada.
| | - J N Mark Glover
- Department of Biochemistry, Medical Sciences Building, University of Alberta, Edmonton, Alberta, T6G 2H7, Canada.
| | - Michael Weinfeld
- Department of Oncology, University of Alberta, Cross Cancer Institute, 11560 University Avenue, Edmonton, Alberta, T6G 1Z2, Canada.
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79
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Mladenova V, Mladenov E, Iliakis G. Novel Biological Approaches for Testing the Contributions of Single DSBs and DSB Clusters to the Biological Effects of High LET Radiation. Front Oncol 2016; 6:163. [PMID: 27446809 PMCID: PMC4923065 DOI: 10.3389/fonc.2016.00163] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Accepted: 06/15/2016] [Indexed: 01/28/2023] Open
Abstract
The adverse biological effects of ionizing radiation (IR) are commonly attributed to the generation of DNA double-strand breaks (DSBs). IR-induced DSBs are generated by clusters of ionizations, bear damaged terminal nucleotides, and frequently comprise base damages and single-strand breaks in the vicinity generating a unique DNA damage-clustering effect that increases DSB "complexity." The number of ionizations in clusters of different radiation modalities increases with increasing linear energy transfer (LET), and is thought to determine the long-known LET-dependence of the relative biological effectiveness (RBE). Multiple ionizations may also lead to the formation of DSB clusters, comprising two or more DSBs that destabilize chromatin further and compromise overall processing. DSB complexity and DSB-cluster formation are increasingly considered in the development of mathematical models of radiation action, which are then "tested" by fitting available experimental data. Despite a plethora of such mathematical models the ultimate goal, i.e., the "a priori" prediction of the radiation effect, has not yet been achieved. The difficulty partly arises from unsurmountable difficulties in testing the fundamental assumptions of such mathematical models in defined biological model systems capable of providing conclusive answers. Recently, revolutionary advances in methods allowing the generation of enzymatic DSBs at random or in well-defined locations in the genome, generate unique testing opportunities for several key assumptions frequently fed into mathematical modeling - including the role of DSB clusters in the overall effect. Here, we review the problematic of DSB-cluster formation in radiation action and present novel biological technologies that promise to revolutionize the way we address the biological consequences of such lesions. We describe new ways of exploiting the I-SceI endonuclease to generate DSB-clusters at random locations in the genome and describe the possible utility of Zn-finger nucleases and of TALENs in generating DSBs at defined genomic locations. Finally, we describe ways to harness the revolution of CRISPR/Cas9 technology to advance our understanding of the biological effects of DSBs. Collectively, these approaches promise to improve the focus of mathematical modeling of radiation action by providing testing opportunities for key assumptions on the underlying biology. They are also likely to further strengthen interactions between experimental radiation biologists and mathematical modelers.
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Affiliation(s)
- Veronika Mladenova
- Institute of Medical Radiation Biology, University of Duisburg-Essen Medical School , Essen , Germany
| | - Emil Mladenov
- Institute of Medical Radiation Biology, University of Duisburg-Essen Medical School , Essen , Germany
| | - George Iliakis
- Institute of Medical Radiation Biology, University of Duisburg-Essen Medical School , Essen , Germany
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80
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Dumitrache LC, McKinnon PJ. Polynucleotide kinase-phosphatase (PNKP) mutations and neurologic disease. Mech Ageing Dev 2016; 161:121-129. [PMID: 27125728 DOI: 10.1016/j.mad.2016.04.009] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Revised: 04/12/2016] [Accepted: 04/24/2016] [Indexed: 12/30/2022]
Abstract
A variety of human neurologic diseases are caused by inherited defects in DNA repair. In many cases, these syndromes almost exclusively impact the nervous system, underscoring the critical requirement for genome stability in this tissue. A striking example of this is defective enzymatic activity of polynucleotide kinase-phosphatase (PNKP), leading to microcephaly or neurodegeneration. Notably, the broad neural impact of mutations in PNKP can result in markedly different disease entities, even when the inherited mutation is the same. For example microcephaly with seizures (MCSZ) results from various hypomorphic PNKP mutations, as does ataxia with oculomotor apraxia 4 (AOA4). Thus, other contributing factors influence the neural phenotype when PNKP is disabled. Here we consider the role for PNKP in maintaining brain function and how perturbation in its activity can account for the varied pathology of neurodegeneration or microcephaly present in MCSZ and AOA4 respectively.
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Affiliation(s)
- Lavinia C Dumitrache
- Dept. of Genetics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Peter J McKinnon
- Dept. of Genetics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.
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81
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Overcash JM, Aryan A, Myles KM, Adelman ZN. Understanding the DNA damage response in order to achieve desired gene editing outcomes in mosquitoes. Chromosome Res 2015; 23:31-42. [PMID: 25596822 DOI: 10.1007/s10577-014-9450-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Mosquitoes are high-impact disease vectors with the capacity to transmit pathogenic agents that cause diseases such as malaria, yellow fever, chikungunya, and dengue. Continued growth in knowledge of genetic, molecular, and physiological pathways in mosquitoes allows for the development of novel control methods and for the continued optimization of existing ones. The emergence of site-specific nucleases as genomic engineering tools promises to expedite research of crucial biological pathways in these disease vectors. The utilization of these nucleases in a more precise and efficient manner is dependent upon knowledge and manipulation of the DNA repair pathways utilized by the mosquito. While progress has been made in deciphering DNA repair pathways in some model systems, research into the nature of the hierarchy of mosquito DNA repair pathways, as well as in mechanistic differences that may exist, is needed. In this review, we will describe progress in the use of site-specific nucleases in mosquitoes, along with the hierarchy of DNA repair in the context of mosquito chromosomal organization and structure, and how this knowledge may be manipulated to achieve precise chromosomal engineering in mosquitoes.
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Affiliation(s)
- Justin M Overcash
- Fralin Life Science Institute and Department of Entomology, Virginia Tech, 305 Fralin Life Science Institute, 360 West Campus Dr., Blacksburg, VA, 24061, USA
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82
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Reprint of "Oxidant and environmental toxicant-induced effects compromise DNA ligation during base excision DNA repair". DNA Repair (Amst) 2015; 36:86-90. [PMID: 26596511 DOI: 10.1016/j.dnarep.2015.11.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
DNA lesions arise from many endogenous and environmental agents, and such lesions can promote deleterious events leading to genomic instability and cell death. Base excision repair (BER) is the main DNA repair pathway responsible for repairing single strand breaks, base lesions and abasic sites in mammalian cells. During BER, DNA substrates and repair intermediates are channeled from one step to the next in a sequential fashion so that release of toxic repair intermediates is minimized. This includes handoff of the product of gap-filling DNA synthesis to the DNA ligation step. The conformational differences in DNA polymerase β (pol β) associated with incorrect or oxidized nucleotide (8-oxodGMP) insertion could impact channeling of the repair intermediate to the final step of BER, i.e., DNA ligation by DNA ligase I or the DNA Ligase III/XRCC1 complex. Thus, modified DNA ligase substrates produced by faulty pol β gap-filling could impair coordination between pol β and DNA ligase. Ligation failure is associated with 5'-AMP addition to the repair intermediate and accumulation of strand breaks that could be more toxic than the initial DNA lesions. Here, we provide an overview of the consequences of ligation failure in the last step of BER. We also discuss DNA-end processing mechanisms that could play roles in reversal of impaired BER.
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83
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Label-free and sensitive detection of T4 polynucleotide kinase activity via coupling DNA strand displacement reaction with enzymatic-aided amplification. Biosens Bioelectron 2015; 73:138-145. [DOI: 10.1016/j.bios.2015.05.059] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Revised: 05/05/2015] [Accepted: 05/26/2015] [Indexed: 01/04/2023]
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84
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Bartlett EJ, Brissett NC, Plocinski P, Carlberg T, Doherty AJ. Molecular basis for DNA strand displacement by NHEJ repair polymerases. Nucleic Acids Res 2015; 44:2173-86. [PMID: 26405198 PMCID: PMC4797286 DOI: 10.1093/nar/gkv965] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Accepted: 09/14/2015] [Indexed: 11/22/2022] Open
Abstract
The non-homologous end-joining (NHEJ) pathway repairs DNA double-strand breaks (DSBs) in all domains of life. Archaea and bacteria utilize a conserved set of multifunctional proteins in a pathway termed Archaeo-Prokaryotic (AP) NHEJ that facilitates DSB repair. Archaeal NHEJ polymerases (Pol) are capable of strand displacement synthesis, whilst filling DNA gaps or partially annealed DNA ends, which can give rise to unligatable intermediates. However, an associated NHEJ phosphoesterase (PE) resects these products to ensure that efficient ligation occurs. Here, we describe the crystal structures of these archaeal (Methanocella paludicola) NHEJ nuclease and polymerase enzymes, demonstrating their strict structural conservation with their bacterial NHEJ counterparts. Structural analysis, in conjunction with biochemical studies, has uncovered the molecular basis for DNA strand displacement synthesis in AP-NHEJ, revealing the mechanisms that enable Pol and PE to displace annealed bases to facilitate their respective roles in DSB repair.
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Affiliation(s)
- Edward J Bartlett
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, BN1 9RQ, UK
| | - Nigel C Brissett
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, BN1 9RQ, UK
| | - Przemyslaw Plocinski
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, BN1 9RQ, UK
| | - Tom Carlberg
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, BN1 9RQ, UK
| | - Aidan J Doherty
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, BN1 9RQ, UK
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85
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Çağlayan M, Wilson SH. Oxidant and environmental toxicant-induced effects compromise DNA ligation during base excision DNA repair. DNA Repair (Amst) 2015; 35:85-9. [PMID: 26466358 DOI: 10.1016/j.dnarep.2015.09.010] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
DNA lesions arise from many endogenous and environmental agents, and such lesions can promote deleterious events leading to genomic instability and cell death. Base excision repair (BER) is the main DNA repair pathway responsible for repairing single strand breaks, base lesions and abasic sites in mammalian cells. During BER, DNA substrates and repair intermediates are channeled from one step to the next in a sequential fashion so that release of toxic repair intermediates is minimized. This includes handoff of the product of gap-filling DNA synthesis to the DNA ligation step. The conformational differences in DNA polymerase β (pol β) associated with incorrect or oxidized nucleotide (8-oxodGMP) insertion could impact channeling of the repair intermediate to the final step of BER, i.e., DNA ligation by DNA ligase I or the DNA Ligase III/XRCC1 complex. Thus, modified DNA ligase substrates produced by faulty pol β gap-filling could impair coordination between pol β and DNA ligase. Ligation failure is associated with 5'-AMP addition to the repair intermediate and accumulation of strand breaks that could be more toxic than the initial DNA lesions. Here, we provide an overview of the consequences of ligation failure in the last step of BER. We also discuss DNA-end processing mechanisms that could play roles in reversal of impaired BER.
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Affiliation(s)
- Melike Çağlayan
- Genome Integrity and Structural Biology Laboratory, NIEHS, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Samuel H Wilson
- Genome Integrity and Structural Biology Laboratory, NIEHS, National Institutes of Health, Research Triangle Park, NC 27709, USA.
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86
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Enns L, Rasouli-Nia A, Hendzel M, Marples B, Weinfeld M. Association of ATM activation and DNA repair with induced radioresistance after low-dose irradiation. RADIATION PROTECTION DOSIMETRY 2015; 166:131-6. [PMID: 25904696 PMCID: PMC4572139 DOI: 10.1093/rpd/ncv203] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Mammalian cells often exhibit a hyper-radiosensitivity (HRS) to radiation doses <20 cGy, followed by increased radioresistance (IRR) at slightly higher doses (∼20-30 cGy). Here, the influence of DNA double-strand break repair (DSBR) on IRR was examined. The failure of Ataxia telangiectasia (AT) cells to undergo IRR reported by others was confirmed. Flow cytometric analysis indicated that normal cells fail to show a measurable increase in serine 1981 phosphorylated AT-mutated (ATM) protein after 10 cGy up to 4 h post irradiation, but a two- to fourfold increase after 25 cGy. Similarly, more proficient reduction of phosphorylated histone H2AX was observed 24 h after 25 cGy than after 10 cGy, suggesting that DSBR is more efficient during IRR than HRS. A direct examination of the consequences of inefficient DNA repair per se (as opposed to ATM-mediated signal transduction/cell cycle responses), by determining the clonogenic survival of cells lacking the DNA repair enzyme polynucleotide kinase/phosphatase, indicated that these cells have a response similar to AT cells, i.e. HRS but no IRR, strongly linking IRR to DSBR.
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Affiliation(s)
- L Enns
- Department of Oncology, University of Alberta, Cross Cancer Institute, 11560 University Ave., Edmonton, Alberta T6G 1Z2, Canada
| | - A Rasouli-Nia
- Department of Oncology, University of Alberta, Cross Cancer Institute, 11560 University Ave., Edmonton, Alberta T6G 1Z2, Canada
| | - M Hendzel
- Department of Oncology, University of Alberta, Cross Cancer Institute, 11560 University Ave., Edmonton, Alberta T6G 1Z2, Canada
| | - B Marples
- Department of Radiation Oncology, William Beaumont Hospital, 3811 W. Thirteen Mile Rd., 105-RI, Royal Oak, MI 48073, USA
| | - M Weinfeld
- Department of Oncology, University of Alberta, Cross Cancer Institute, 11560 University Ave., Edmonton, Alberta T6G 1Z2, Canada
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87
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Shimada M, Dumitrache LC, Russell HR, McKinnon PJ. Polynucleotide kinase-phosphatase enables neurogenesis via multiple DNA repair pathways to maintain genome stability. EMBO J 2015; 34:2465-80. [PMID: 26290337 DOI: 10.15252/embj.201591363] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Accepted: 07/09/2015] [Indexed: 11/09/2022] Open
Abstract
Polynucleotide kinase-phosphatase (PNKP) is a DNA repair factor possessing both 5'-kinase and 3'-phosphatase activities to modify ends of a DNA break prior to ligation. Recently, decreased PNKP levels were identified as the cause of severe neuropathology present in the human microcephaly with seizures (MCSZ) syndrome. Utilizing novel murine Pnkp alleles that attenuate expression and a T424GfsX48 frame-shift allele identified in MCSZ individuals, we determined how PNKP inactivation impacts neurogenesis. Mice with PNKP inactivation in neural progenitors manifest neurodevelopmental abnormalities and postnatal death. This severe phenotype involved defective base excision repair and non-homologous end-joining, pathways required for repair of both DNA single- and double-strand breaks. Although mice homozygous for the T424GfsX48 allele were lethal embryonically, attenuated PNKP levels (akin to MCSZ) showed general neurodevelopmental defects, including microcephaly, indicating a critical developmental PNKP threshold. Directed postnatal neural inactivation of PNKP affected specific subpopulations including oligodendrocytes, indicating a broad requirement for genome maintenance, both during and after neurogenesis. These data illuminate the basis for selective neural vulnerability in DNA repair deficiency disease.
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Affiliation(s)
- Mikio Shimada
- Department of Genetics, St Jude Children's Research Hospital, Memphis, TN, USA
| | | | - Helen R Russell
- Department of Genetics, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Peter J McKinnon
- Department of Genetics, St Jude Children's Research Hospital, Memphis, TN, USA
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88
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Abstract
Scaffold proteins play a central role in DNA repair by recruiting and organizing sets of enzymes required to perform multi-step repair processes. X-ray cross complementing group 1 protein (XRCC1) forms enzyme complexes optimized for single-strand break repair, but participates in other repair pathways as well. Available structural data for XRCC1 interactions is summarized and evaluated in terms of its proposed roles in DNA repair. Mutational approaches related to the abrogation of specific XRCC1 interactions are also discussed. Although substantial progress has been made in elucidating the structural basis for XRCC1 function, the molecular mechanisms of XRCC1 recruitment related to several proposed roles of the XRCC1 DNA repair complex remain undetermined.
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Affiliation(s)
- Robert E London
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC 27709, United States.
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89
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Knobloch G, Jabari N, Stadlbauer S, Schindelin H, Köhn M, Gohla A. Synthesis of hydrolysis-resistant pyridoxal 5′-phosphate analogs and their biochemical and X-ray crystallographic characterization with the pyridoxal phosphatase chronophin. Bioorg Med Chem 2015; 23:2819-27. [DOI: 10.1016/j.bmc.2015.02.049] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Revised: 02/24/2015] [Accepted: 02/25/2015] [Indexed: 12/12/2022]
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90
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Heo J, Li J, Summerlin M, Hays A, Katyal S, McKinnon PJ, Nitiss KC, Nitiss JL, Hanakahi LA. TDP1 promotes assembly of non-homologous end joining protein complexes on DNA. DNA Repair (Amst) 2015; 30:28-37. [PMID: 25841101 DOI: 10.1016/j.dnarep.2015.03.003] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Revised: 02/25/2015] [Accepted: 03/09/2015] [Indexed: 11/16/2022]
Abstract
The repair of DNA double-strand breaks (DSB) is central to the maintenance of genomic integrity. In tumor cells, the ability to repair DSBs predicts response to radiation and many cytotoxic anti-cancer drugs. DSB repair pathways include homologous recombination and non-homologous end joining (NHEJ). NHEJ is a template-independent mechanism, yet many NHEJ repair products carry limited genetic changes, which suggests that NHEJ includes mechanisms to minimize error. Proteins required for mammalian NHEJ include Ku70/80, the DNA-dependent protein kinase (DNA-PKcs), XLF/Cernunnos and the XRCC4:DNA ligase IV complex. NHEJ also utilizes accessory proteins that include DNA polymerases, nucleases, and other end-processing factors. In yeast, mutations of tyrosyl-DNA phosphodiesterase (TDP1) reduced NHEJ fidelity. TDP1 plays an important role in repair of topoisomerase-mediated DNA damage and 3'-blocking DNA lesions, and mutation of the human TDP1 gene results in an inherited human neuropathy termed SCAN1. We found that human TDP1 stimulated DNA binding by XLF and physically interacted with XLF to form TDP1:XLF:DNA complexes. TDP1:XLF interactions preferentially stimulated TDP1 activity on dsDNA as compared to ssDNA. TDP1 also promoted DNA binding by Ku70/80 and stimulated DNA-PK activity. Because Ku70/80 and XLF are the first factors recruited to the DSB at the onset of NHEJ, our data suggest a role for TDP1 during the early stages of mammalian NHEJ.
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Affiliation(s)
- Jinho Heo
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois, Chicago, Rockford Health Sciences Campus, 1601 Parkview Avenue, Rockford, IL 61107, USA
| | - Jing Li
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois, Chicago, Rockford Health Sciences Campus, 1601 Parkview Avenue, Rockford, IL 61107, USA
| | - Matthew Summerlin
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois, Chicago, Rockford Health Sciences Campus, 1601 Parkview Avenue, Rockford, IL 61107, USA
| | - Annette Hays
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois, Chicago, Rockford Health Sciences Campus, 1601 Parkview Avenue, Rockford, IL 61107, USA
| | - Sachin Katyal
- University of Manitoba, Department of Pharmacology and Therapeutics, Manitoba Institute of Cell Biology, 675 McDermot Avenue, Winnipeg, Manitoba, Canada R3E 0V9
| | - Peter J McKinnon
- Department of Genetics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Karin C Nitiss
- Department of Biopharmaceutical Sciences, College of Pharmacy, University of Illinois, Chicago, Rockford Health Sciences Campus, 1601 Parkview Avenue, Rockford, IL 61107, USA
| | - John L Nitiss
- Department of Biopharmaceutical Sciences, College of Pharmacy, University of Illinois, Chicago, Rockford Health Sciences Campus, 1601 Parkview Avenue, Rockford, IL 61107, USA
| | - Leslyn A Hanakahi
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois, Chicago, Rockford Health Sciences Campus, 1601 Parkview Avenue, Rockford, IL 61107, USA; Department of Biopharmaceutical Sciences, College of Pharmacy, University of Illinois, Chicago, Rockford Health Sciences Campus, 1601 Parkview Avenue, Rockford, IL 61107, USA.
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91
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Bras J, Alonso I, Barbot C, Costa M, Darwent L, Orme T, Sequeiros J, Hardy J, Coutinho P, Guerreiro R. Mutations in PNKP cause recessive ataxia with oculomotor apraxia type 4. Am J Hum Genet 2015; 96:474-9. [PMID: 25728773 PMCID: PMC4375449 DOI: 10.1016/j.ajhg.2015.01.005] [Citation(s) in RCA: 99] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Accepted: 01/09/2015] [Indexed: 11/13/2022] Open
Abstract
Hereditary autosomal-recessive cerebellar ataxias are a genetically and clinically heterogeneous group of disorders. We used homozygosity mapping and exome sequencing to study a cohort of nine Portuguese families who were identified during a nationwide, population-based, systematic survey as displaying a consistent phenotype of recessive ataxia with oculomotor apraxia (AOA). The integration of data from these analyses led to the identification of the same homozygous PNKP (polynucleotide kinase 3′-phosphatase) mutation, c.1123G>T (p.Gly375Trp), in three of the studied families. When analyzing this particular gene in the exome sequencing data from the remaining cohort, we identified homozygous or compound-heterozygous mutations in five other families. PNKP is a dual-function enzyme with a key role in different pathways of DNA-damage repair. Mutations in this gene have previously been associated with an autosomal-recessive syndrome characterized by microcephaly; early-onset, intractable seizures; and developmental delay (MCSZ). The finding of PNKP mutations associated with recessive AOA extends the phenotype associated with this gene and identifies a fourth locus that causes AOA. These data confirm that MCSZ and some forms of ataxia share etiological features, most likely reflecting the role of PNKP in DNA-repair mechanisms.
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92
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Andres SN, Schellenberg MJ, Wallace BD, Tumbale P, Williams RS. Recognition and repair of chemically heterogeneous structures at DNA ends. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2015; 56:1-21. [PMID: 25111769 PMCID: PMC4303525 DOI: 10.1002/em.21892] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2014] [Accepted: 07/28/2014] [Indexed: 05/13/2023]
Abstract
Exposure to environmental toxicants and stressors, radiation, pharmaceutical drugs, inflammation, cellular respiration, and routine DNA metabolism all lead to the production of cytotoxic DNA strand breaks. Akin to splintered wood, DNA breaks are not "clean." Rather, DNA breaks typically lack DNA 5'-phosphate and 3'-hydroxyl moieties required for DNA synthesis and DNA ligation. Failure to resolve damage at DNA ends can lead to abnormal DNA replication and repair, and is associated with genomic instability, mutagenesis, neurological disease, ageing and carcinogenesis. An array of chemically heterogeneous DNA termini arises from spontaneously generated DNA single-strand and double-strand breaks (SSBs and DSBs), and also from normal and/or inappropriate DNA metabolism by DNA polymerases, DNA ligases and topoisomerases. As a front line of defense to these genotoxic insults, eukaryotic cells have accrued an arsenal of enzymatic first responders that bind and protect damaged DNA termini, and enzymatically tailor DNA ends for DNA repair synthesis and ligation. These nucleic acid transactions employ direct damage reversal enzymes including Aprataxin (APTX), Polynucleotide kinase phosphatase (PNK), the tyrosyl DNA phosphodiesterases (TDP1 and TDP2), the Ku70/80 complex and DNA polymerase β (POLβ). Nucleolytic processing enzymes such as the MRE11/RAD50/NBS1/CtIP complex, Flap endonuclease (FEN1) and the apurinic endonucleases (APE1 and APE2) also act in the chemical "cleansing" of DNA breaks to prevent genomic instability and disease, and promote progression of DNA- and RNA-DNA damage response (DDR and RDDR) pathways. Here, we provide an overview of cellular first responders dedicated to the detection and repair of abnormal DNA termini.
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Affiliation(s)
- Sara N Andres
- Laboratory of Structural Biology, National Institute of Environmental Health Sciences, NIH, DHHS, North Carolina
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93
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Gao R, Liu Y, Silva-Fernandes A, Fang X, Paulucci-Holthauzen A, Chatterjee A, Zhang HL, Matsuura T, Choudhary S, Ashizawa T, Koeppen AH, Maciel P, Hazra TK, Sarkar PS. Inactivation of PNKP by mutant ATXN3 triggers apoptosis by activating the DNA damage-response pathway in SCA3. PLoS Genet 2015; 11:e1004834. [PMID: 25590633 PMCID: PMC4295939 DOI: 10.1371/journal.pgen.1004834] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2014] [Accepted: 10/16/2014] [Indexed: 12/30/2022] Open
Abstract
Spinocerebellar ataxia type 3 (SCA3), also known as Machado-Joseph disease (MJD), is an untreatable autosomal dominant neurodegenerative disease, and the most common such inherited ataxia worldwide. The mutation in SCA3 is the expansion of a polymorphic CAG tri-nucleotide repeat sequence in the C-terminal coding region of the ATXN3 gene at chromosomal locus 14q32.1. The mutant ATXN3 protein encoding expanded glutamine (polyQ) sequences interacts with multiple proteins in vivo, and is deposited as aggregates in the SCA3 brain. A large body of literature suggests that the loss of function of the native ATNX3-interacting proteins that are deposited in the polyQ aggregates contributes to cellular toxicity, systemic neurodegeneration and the pathogenic mechanism in SCA3. Nonetheless, a significant understanding of the disease etiology of SCA3, the molecular mechanism by which the polyQ expansions in the mutant ATXN3 induce neurodegeneration in SCA3 has remained elusive. In the present study, we show that the essential DNA strand break repair enzyme PNKP (polynucleotide kinase 3'-phosphatase) interacts with, and is inactivated by, the mutant ATXN3, resulting in inefficient DNA repair, persistent accumulation of DNA damage/strand breaks, and subsequent chronic activation of the DNA damage-response ataxia telangiectasia-mutated (ATM) signaling pathway in SCA3. We report that persistent accumulation of DNA damage/strand breaks and chronic activation of the serine/threonine kinase ATM and the downstream p53 and protein kinase C-δ pro-apoptotic pathways trigger neuronal dysfunction and eventually neuronal death in SCA3. Either PNKP overexpression or pharmacological inhibition of ATM dramatically blocked mutant ATXN3-mediated cell death. Discovery of the mechanism by which mutant ATXN3 induces DNA damage and amplifies the pro-death signaling pathways provides a molecular basis for neurodegeneration due to PNKP inactivation in SCA3, and for the first time offers a possible approach to treatment.
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Affiliation(s)
- Rui Gao
- Department of Neurology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Yongping Liu
- Department of Neurology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Anabela Silva-Fernandes
- Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, Braga, Portugal
- ICVS/3B’s PT Government Associate Laboratory, Braga/Guimarặes, Portugal
| | - Xiang Fang
- Department of Neurology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Adriana Paulucci-Holthauzen
- Department of Biomedical Engineering, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Arpita Chatterjee
- Department of Internal Medicine, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Hang L. Zhang
- Department of Neurology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Tohru Matsuura
- Department of Neurology, Jichi Medical School, Shimotsuke, Japan
| | - Sanjeev Choudhary
- Department of Internal Medicine, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Tetsuo Ashizawa
- Department of Neurology and McNight Brain Research Institute, University of Florida, Gainesville, Florida, United States of America
| | - Arnulf H. Koeppen
- Department of Neurology, Albany Stratton VA Medical Center, Albany, New York, United States of America
| | - Patricia Maciel
- Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, Braga, Portugal
- ICVS/3B’s PT Government Associate Laboratory, Braga/Guimarặes, Portugal
| | - Tapas K. Hazra
- Department of Internal Medicine, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Partha S. Sarkar
- Department of Neurology, University of Texas Medical Branch, Galveston, Texas, United States of America
- Neuroscience and Cell Biology, University of Texas Medical Branch, Galveston, Texas, United States of America
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94
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Abdou I, Poirier GG, Hendzel MJ, Weinfeld M. DNA ligase III acts as a DNA strand break sensor in the cellular orchestration of DNA strand break repair. Nucleic Acids Res 2014; 43:875-92. [PMID: 25539916 PMCID: PMC4333375 DOI: 10.1093/nar/gku1307] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
In the current model of DNA SSBR, PARP1 is regarded as the sensor of single-strand breaks (SSBs). However, biochemical studies have implicated LIG3 as another possible SSB sensor. Using a laser micro-irradiation protocol that predominantly generates SSBs, we were able to demonstrate that PARP1 is dispensable for the accumulation of different single-strand break repair (SSBR) proteins at sites of DNA damage in live cells. Furthermore, we show in live cells for the first time that LIG3 plays a role in mediating the accumulation of the SSBR proteins XRCC1 and PNKP at sites of DNA damage. Importantly, the accumulation of LIG3 at sites of DNA damage did not require the BRCT domain-mediated interaction with XRCC1. We were able to show that the N-terminal ZnF domain of LIG3 plays a key role in the enzyme's SSB sensing function. Finally, we provide cellular evidence that LIG3 and not PARP1 acts as the sensor for DNA damage caused by the topoisomerase I inhibitor, irinotecan. Our results support the existence of a second damage-sensing mechanism in SSBR involving the detection of nicks in the genome by LIG3.
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Affiliation(s)
- Ismail Abdou
- Department of Oncology, University of Alberta, and Cross Cancer Institute, Edmonton, Alberta, Canada
| | - Guy G Poirier
- Cancer Axis, CHUQ Research Center and Faculty of Medicine, Laval University, Quebec City, Quebec, Canada
| | - Michael J Hendzel
- Department of Oncology, University of Alberta, and Cross Cancer Institute, Edmonton, Alberta, Canada
| | - Michael Weinfeld
- Department of Oncology, University of Alberta, and Cross Cancer Institute, Edmonton, Alberta, Canada
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95
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Shiloh Y. ATM: expanding roles as a chief guardian of genome stability. Exp Cell Res 2014; 329:154-61. [PMID: 25218947 DOI: 10.1016/j.yexcr.2014.09.002] [Citation(s) in RCA: 85] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2014] [Revised: 08/19/2014] [Accepted: 09/01/2014] [Indexed: 01/10/2023]
Affiliation(s)
- Yosef Shiloh
- The David and Inez Myers Laboratory for Cancer Research, Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel.
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96
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Rahmanian S, Taleei R, Nikjoo H. Radiation induced base excision repair (BER): a mechanistic mathematical approach. DNA Repair (Amst) 2014; 22:89-103. [PMID: 25117268 DOI: 10.1016/j.dnarep.2014.07.011] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Revised: 07/17/2014] [Accepted: 07/18/2014] [Indexed: 01/24/2023]
Abstract
This paper presents a mechanistic model of base excision repair (BER) pathway for the repair of single-stand breaks (SSBs) and oxidized base lesions produced by ionizing radiation (IR). The model is based on law of mass action kinetics to translate the biochemical processes involved, step-by-step, in the BER pathway to translate into mathematical equations. The BER is divided into two subpathways, short-patch repair (SPR) and long-patch repair (LPR). SPR involves in replacement of single nucleotide via Pol β and ligation of the ends via XRCC1 and Ligase III, while LPR involves in replacement of multiple nucleotides via PCNA, Pol δ/ɛ and FEN 1, and ligation via Ligase I. A hallmark of IR is the production of closely spaced lesions within a turn of DNA helix (named complex lesions), which have been attributed to a slower repair process. The model presented considers fast and slow component of BER kinetics by assigning SPR for simple lesions and LPR for complex lesions. In the absence of in vivo reaction rate constants for the BER proteins, we have deduced a set of rate constants based on different published experimental measurements including accumulation kinetics obtained from UVA irradiation, overall SSB repair kinetic experiments, and overall BER kinetics from live-cell imaging experiments. The model was further used to calculate the repair kinetics of complex base lesions via the LPR subpathway and compared to foci kinetic experiments for cells irradiated with γ rays, Si, and Fe ions. The model calculation show good agreement with experimental measurements for both overall repair and repair of complex lesions. Furthermore, using the model we explored different mechanisms responsible for inhibition of repair when higher LET and HZE particles are used and concluded that increasing the damage complexity can inhibit initiation of LPR after the AP site removal step in BER.
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Affiliation(s)
- Shirin Rahmanian
- Radiation Biophysics Group, Department of Oncology-Pathology, Karolinska Institutet, Box 260 P9-02, Stockholm 17176, Sweden
| | - Reza Taleei
- Radiation Physics, MD Anderson Cancer Center, 1515 Holcombe Blvd., Unit 94, Houston, TX 77030-4409, USA
| | - Hooshang Nikjoo
- Radiation Biophysics Group, Department of Oncology-Pathology, Karolinska Institutet, Box 260 P9-02, Stockholm 17176, Sweden.
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97
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Du J, Xu Q, Lu X, Zhang CY. A label-free bioluminescent sensor for real-time monitoring polynucleotide kinase activity. Anal Chem 2014; 86:8481-8. [PMID: 25048013 DOI: 10.1021/ac502240c] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Polynucleotide kinase (PNK) plays a crucial role in maintaining the genomic stability of cells and is becoming a potential target in the radio-therapeutic treatment of cancers. The fluorescent method is usually used to measure the PNK activity, but it is impossible to obtain the real-time monitoring without the employment of the labeled DNA probes. Here, we report a label-free bioluminescent sensor for PNK activity assay through real-time monitoring of the phosphorylation-dependent DNA ligation reaction. In this bioluminescent sensor, two hairpin DNA probes with 5'-protruding terminal are designed as the phosphate acceptor, and the widely used phosphate donor of ATP is substituted by dCTP. In the absence of PNK, the ligation reaction cannot be triggered due to the lack of 5'-phosphoryl groups in the probes, and the background signal is negligible. With the addition of PNK, the phosphorylation-ligation reaction of the probes is initiated with the release of AMP, and the subsequent conversion of AMP to ATP leads to the generation of distinct bioluminescence signal. The PNK activity assay can be performed in real time by continuously monitoring the bioluminescence signal. This bioluminescent sensor is much simpler, label-free, cost-effective, and free from the autofluorescence interference of biological matrix, and can be further used for quantitative, kinetic, and inhibition assay.
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Affiliation(s)
- Jiao Du
- Key Laboratory of Bioelectrochemistry & Environmental analysis of Gansu Province, College of Chemistry & Chemical Engineering, Northwest Normal University , Lanzhou 730070, China
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98
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Causative novel PNKP mutations and concomitant PCDH15 mutations in a patient with microcephaly with early-onset seizures and developmental delay syndrome and hearing loss. J Hum Genet 2014; 59:471-4. [PMID: 24965255 DOI: 10.1038/jhg.2014.51] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2014] [Revised: 05/03/2014] [Accepted: 06/05/2014] [Indexed: 12/25/2022]
Abstract
We report on a 1-year-old boy with microcephaly with a simplified gyral pattern, early-onset seizures, congenital hearing loss and a severe developmental delay. Trio-based whole-exome sequencing identified candidate compound heterozygous mutations in two genes: c.163G>T (p.Ala55Ser) and c.874G>A (p.Gly292Arg) in polynucleotide kinase 3'-phosphatase gene (PNKP), and c.195G>A (p.Met65Ile) and c.1210A>C (p.Ser404Arg) in PCDH15. PNKP and PCDH15 mutations have been reported in autosomal recessive microcephaly with early-onset seizures and developmental delay syndrome, and Usher syndrome type 1F, respectively. Our patient showed neurological features similar to reported cases of both syndromes that could be explained by the observed mutations in both PNKP and PCDH15, which therefore appear to be pathogenic in this case.
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99
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Alcantara D, O'Driscoll M. Congenital microcephaly. AMERICAN JOURNAL OF MEDICAL GENETICS. PART C, SEMINARS IN MEDICAL GENETICS 2014; 166C:124-39. [PMID: 24816482 DOI: 10.1002/ajmg.c.31397] [Citation(s) in RCA: 94] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The underlying etiologies of genetic congenital microcephaly are complex and multifactorial. Recently, with the exponential growth in the identification and characterization of novel genetic causes of congenital microcephaly, there has been a consolidation and emergence of certain themes concerning underlying pathomechanisms. These include abnormal mitotic microtubule spindle structure, numerical and structural abnormalities of the centrosome, altered cilia function, impaired DNA repair, DNA Damage Response signaling and DNA replication, along with attenuated cell cycle checkpoint proficiency. Many of these processes are highly interconnected. Interestingly, a defect in a gene whose encoded protein has a canonical function in one of these processes can often have multiple impacts at the cellular level involving several of these pathways. Here, we overview the key pathomechanistic themes underlying profound congenital microcephaly, and emphasize their interconnected nature.
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100
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Radhakrishnan SK, Jette N, Lees-Miller SP. Non-homologous end joining: emerging themes and unanswered questions. DNA Repair (Amst) 2014; 17:2-8. [PMID: 24582502 PMCID: PMC4084493 DOI: 10.1016/j.dnarep.2014.01.009] [Citation(s) in RCA: 108] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2013] [Revised: 01/03/2014] [Accepted: 01/24/2014] [Indexed: 11/25/2022]
Abstract
Non-homologous end joining (NHEJ) is the major pathway for the repair of ionizing radiation induced DNA double strand breaks in human cells. Here, we discuss current insights into the mechanism of NHEJ and the interplay between NHEJ and other pathways for repair of IR-induced DNA damage.
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Affiliation(s)
- Sarvan Kumar Radhakrishnan
- Department of Biochemistry & Molecular Biology and Southern Alberta Cancer Research Institute, University of Calgary, 3330 Hospital Drive, NW, Calgary, Alberta, Canada T2N 4N1
| | - Nicholas Jette
- Department of Biochemistry & Molecular Biology and Southern Alberta Cancer Research Institute, University of Calgary, 3330 Hospital Drive, NW, Calgary, Alberta, Canada T2N 4N1
| | - Susan P Lees-Miller
- Department of Biochemistry & Molecular Biology and Southern Alberta Cancer Research Institute, University of Calgary, 3330 Hospital Drive, NW, Calgary, Alberta, Canada T2N 4N1.
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