1
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Alajlan H, Raducanu VS, Lopez de Los Santos Y, Tehseen M, Alruwaili H, Al-Mazrou A, Mohammad R, Al-Alwan M, De Biasio A, Merzaban JS, Al-Mousa H, Hamdan SM, Alazami AM. Severe Combined Immunodeficiency from a Homozygous DNA Ligase 1 Mutant with Reduced Catalytic Activity but Increased Ligation Fidelity. J Clin Immunol 2024; 44:151. [PMID: 38896336 PMCID: PMC11186889 DOI: 10.1007/s10875-024-01754-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Accepted: 06/10/2024] [Indexed: 06/21/2024]
Abstract
A cell's ability to survive and to evade cancer is contingent on its ability to retain genomic integrity, which can be seriously compromised when nucleic acid phosphodiester bonds are disrupted. DNA Ligase 1 (LIG1) plays a key role in genome maintenance by sealing single-stranded nicks that are produced during DNA replication and repair. Autosomal recessive mutations in a limited number of individuals have been previously described for this gene. Here we report a homozygous LIG1 mutation (p.A624T), affecting a universally conserved residue, in a patient presenting with leukopenia, neutropenia, lymphopenia, pan-hypogammaglobulinemia, and diminished in vitro response to mitogen stimulation. Patient fibroblasts expressed normal levels of LIG1 protein but exhibited impaired growth, poor viability, high baseline levels of gamma-H2AX foci, and an enhanced susceptibility to DNA-damaging agents. The mutation reduced LIG1 activity by lowering its affinity for magnesium 2.5-fold. Remarkably, it also increased LIG1 fidelity > 50-fold against 3' end 8-Oxoguanine mismatches, exhibiting a marked reduction in its ability to process such nicks. This is expected to yield increased ss- and dsDNA breaks. Molecular dynamic simulations, and Residue Interaction Network studies, predicted an allosteric effect for this mutation on the protein loops associated with the LIG1 high-fidelity magnesium, as well as on DNA binding within the adenylation domain. These dual alterations of suppressed activity and enhanced fidelity, arising from a single mutation, underscore the mechanistic picture of how a LIG1 defect can lead to severe immunological disease.
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Affiliation(s)
- Huda Alajlan
- Translational Genomics, Centre for Genomic Medicine, King Faisal Specialist Hospital & Research Centre, MBC 3, P.O. Box 3354, 11211, Riyadh, Saudi Arabia
| | - Vlad-Stefan Raducanu
- Bioscience Program, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, 23955, Thuwal, Saudi Arabia
| | - Yossef Lopez de Los Santos
- Cell Migration and Signaling Laboratory, Bioscience Program, Division of Biological & Environmental Science & Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Muhammad Tehseen
- Bioscience Program, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, 23955, Thuwal, Saudi Arabia
| | - Hibah Alruwaili
- Translational Genomics, Centre for Genomic Medicine, King Faisal Specialist Hospital & Research Centre, MBC 3, P.O. Box 3354, 11211, Riyadh, Saudi Arabia
| | - Amer Al-Mazrou
- Cell Therapy and Immunobiology Department, King Faisal Specialist Hospital & Research Centre, Riyadh, Saudi Arabia
| | - Reem Mohammad
- Pediatric Allergy & Immunology, Department of Pediatrics, King Faisal Specialist Hospital & Research Centre, MBC 3, P.O. Box 3354, 11211, Riyadh, Saudi Arabia
| | - Monther Al-Alwan
- Cell Therapy and Immunobiology Department, King Faisal Specialist Hospital & Research Centre, Riyadh, Saudi Arabia
- College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | - Alfredo De Biasio
- Bioscience Program, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, 23955, Thuwal, Saudi Arabia
| | - Jasmeen S Merzaban
- Cell Migration and Signaling Laboratory, Bioscience Program, Division of Biological & Environmental Science & Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Hamoud Al-Mousa
- Pediatric Allergy & Immunology, Department of Pediatrics, King Faisal Specialist Hospital & Research Centre, MBC 3, P.O. Box 3354, 11211, Riyadh, Saudi Arabia.
- College of Medicine, Alfaisal University, Riyadh, Saudi Arabia.
| | - Samir M Hamdan
- Bioscience Program, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, 23955, Thuwal, Saudi Arabia.
| | - Anas M Alazami
- Translational Genomics, Centre for Genomic Medicine, King Faisal Specialist Hospital & Research Centre, MBC 3, P.O. Box 3354, 11211, Riyadh, Saudi Arabia.
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2
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Chatterjee S, Chaubet L, van den Berg A, Mukhortava A, Gulkis M, Çağlayan M. Uncovering nick DNA binding by LIG1 at the single-molecule level. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.28.587287. [PMID: 38586032 PMCID: PMC10996606 DOI: 10.1101/2024.03.28.587287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
DNA ligases repair the strand breaks are made continually and naturally throughout the genome, if left unrepaired and allowed to persist, they can lead to genome instability in the forms of lethal double-strand (ds) breaks, deletions, and duplications. DNA ligase 1 (LIG1) joins Okazaki fragments during the replication machinery and seals nicks at the end of most DNA repair pathways. Yet, how LIG1 recognizes its target substrate is entirely missing. Here, we uncover the dynamics of nick DNA binding by LIG1 at the single-molecule level. Our findings reveal that LIG1 binds to dsDNA both specifically and non-specifically and exhibits diffusive behavior to form a stable complex at the nick. Furthermore, by comparing with the LIG1 C-terminal protein, we demonstrate that the N-terminal non-catalytic region promotes binding enriched at nick sites and facilitates an efficient nick search process by promoting 1D diffusion along the DNA. Our findings provide a novel single-molecule insight into the nick binding by LIG1, which is critical to repair broken phosphodiester bonds in the DNA backbone to maintain genome integrity.
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3
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Sallmyr A, Bhandari SK, Naila T, Tomkinson AE. Mammalian DNA ligases; roles in maintaining genome integrity. J Mol Biol 2024; 436:168276. [PMID: 37714297 PMCID: PMC10843057 DOI: 10.1016/j.jmb.2023.168276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Revised: 09/07/2023] [Accepted: 09/08/2023] [Indexed: 09/17/2023]
Abstract
The joining of breaks in the DNA phosphodiester backbone is essential for genome integrity. Breaks are generated during normal processes such as DNA replication, cytosine demethylation during differentiation, gene rearrangement in the immune system and germ cell development. In addition, they are generated either directly by a DNA damaging agent or indirectly due to damage excision during repair. Breaks are joined by a DNA ligase that catalyzes phosphodiester bond formation at DNA nicks with 3' hydroxyl and 5' phosphate termini. Three human genes encode ATP-dependent DNA ligases. These enzymes have a conserved catalytic core consisting of three subdomains that encircle nicked duplex DNA during ligation. The DNA ligases are targeted to different nuclear DNA transactions by specific protein-protein interactions. Both DNA ligase IIIα and DNA ligase IV form stable complexes with DNA repair proteins, XRCC1 and XRCC4, respectively. There is functional redundancy between DNA ligase I and DNA ligase IIIα in DNA replication, excision repair and single-strand break repair. Although DNA ligase IV is a core component of the major double-strand break repair pathway, non-homologous end joining, the other enzymes participate in minor, alternative double-strand break repair pathways. In contrast to the nucleus, only DNA ligase IIIα is present in mitochondria and is essential for maintaining the mitochondrial genome. Human immunodeficiency syndromes caused by mutations in either LIG1 or LIG4 have been described. Preclinical studies with DNA ligase inhibitors have identified potentially targetable abnormalities in cancer cells and evidence that DNA ligases are potential targets for cancer therapy.
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Affiliation(s)
- Annahita Sallmyr
- University of New Mexico Comprehensive Cancer Center and the Departments of Internal Medicine, and Molecular Genetics & Microbiology, University of New Mexico Health Sciences Center, United States
| | - Seema Khattri Bhandari
- University of New Mexico Comprehensive Cancer Center and the Departments of Internal Medicine, and Molecular Genetics & Microbiology, University of New Mexico Health Sciences Center, United States
| | - Tasmin Naila
- University of New Mexico Comprehensive Cancer Center and the Departments of Internal Medicine, and Molecular Genetics & Microbiology, University of New Mexico Health Sciences Center, United States
| | - Alan E Tomkinson
- University of New Mexico Comprehensive Cancer Center and the Departments of Internal Medicine, and Molecular Genetics & Microbiology, University of New Mexico Health Sciences Center, United States.
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4
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Magrino J, Munford V, Martins DJ, Homma TK, Page B, Gaubitz C, Freire BL, Lerario AM, Vilar JB, Amorin A, Leão EKE, Kok F, Menck CF, Jorge AA, Kelch BA. A thermosensitive PCNA allele underlies an ataxia-telangiectasia-like disorder. J Biol Chem 2023; 299:104656. [PMID: 36990216 PMCID: PMC10165274 DOI: 10.1016/j.jbc.2023.104656] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 02/25/2023] [Accepted: 03/10/2023] [Indexed: 03/29/2023] Open
Abstract
Proliferating cell nuclear antigen (PCNA) is a sliding clamp protein that coordinates DNA replication with various DNA maintenance events that are critical for human health. Recently, a hypomorphic homozygous serine to isoleucine (S228I) substitution in PCNA was described to underlie a rare DNA repair disorder known as PCNA-associated DNA repair disorder (PARD). PARD symptoms range from UV sensitivity, neurodegeneration, telangiectasia, and premature aging. We, and others, previously showed that the S228I variant changes the protein-binding pocket of PCNA to a conformation that impairs interactions with specific partners. Here, we report a second PCNA substitution (C148S) that also causes PARD. Unlike PCNA-S228I, PCNA-C148S has WT-like structure and affinity toward partners. In contrast, both disease-associated variants possess a thermostability defect. Furthermore, patient-derived cells homozygous for the C148S allele exhibit low levels of chromatin-bound PCNA and display temperature-dependent phenotypes. The stability defect of both PARD variants indicates that PCNA levels are likely an important driver of PARD disease. These results significantly advance our understanding of PARD and will likely stimulate additional work focused on clinical, diagnostic, and therapeutic aspects of this severe disease.
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Affiliation(s)
- Joseph Magrino
- Department of Biochemistry and Biotechnology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Veridiana Munford
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Davi Jardim Martins
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Thais K Homma
- Genetic Endocrinology Unit, Cellular and Molecular Endocrinology Laboratory LIM25, Endocrinology Discipline of the Faculty of Medicine of the University of São Paulo, São Paulo, Brazil; Developmental Endocrinology Unit, Laboratory of Hormones and Molecular Genetics LIM42, Faculty of Medicine of the University of São Paulo, São Paulo, Brazil
| | - Brendan Page
- Department of Biochemistry and Biotechnology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Christl Gaubitz
- Department of Biochemistry and Biotechnology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Bruna L Freire
- Genetic Endocrinology Unit, Cellular and Molecular Endocrinology Laboratory LIM25, Endocrinology Discipline of the Faculty of Medicine of the University of São Paulo, São Paulo, Brazil; Developmental Endocrinology Unit, Laboratory of Hormones and Molecular Genetics LIM42, Faculty of Medicine of the University of São Paulo, São Paulo, Brazil
| | - Antonio M Lerario
- Developmental Endocrinology Unit, Laboratory of Hormones and Molecular Genetics LIM42, Faculty of Medicine of the University of São Paulo, São Paulo, Brazil; Department of Internal Medicine, Division of Metabolism, Endocrinology and Diabetes, University of Michigan, Ann Arbor, Michigan, USA
| | - Juliana Brandstetter Vilar
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Antonio Amorin
- Neurogenetics, Neurology Department, Faculty of Medicine of the University of São Paulo, São Paulo, Brazil
| | - Emília K E Leão
- Medical Genetics Service of the Professor Edgard Santos University Hospital - Federal University of Bahia, Salvador, Brazil
| | - Fernando Kok
- Neurogenetics, Neurology Department, Faculty of Medicine of the University of São Paulo, São Paulo, Brazil; Mendelics Genomic Analysis, São Paulo, São Paulo, Brazil
| | - Carlos Fm Menck
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Alexander Al Jorge
- Genetic Endocrinology Unit, Cellular and Molecular Endocrinology Laboratory LIM25, Endocrinology Discipline of the Faculty of Medicine of the University of São Paulo, São Paulo, Brazil
| | - Brian A Kelch
- Department of Biochemistry and Biotechnology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA.
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5
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Gulkis M, Tang Q, Petrides M, Çağlayan M. Structures of LIG1 active site mutants reveal the importance of DNA end rigidity for mismatch discrimination. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.21.533718. [PMID: 36993234 PMCID: PMC10055324 DOI: 10.1101/2023.03.21.533718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
ATP-dependent DNA ligases catalyze phosphodiester bond formation in the conserved three-step chemical reaction of nick sealing. Human DNA ligase I (LIG1) finalizes almost all DNA repair pathways following DNA polymerase-mediated nucleotide insertion. We previously reported that LIG1 discriminates mismatches depending on the architecture of the 3'-terminus at a nick, however the contribution of conserved active site residues to faithful ligation remains unknown. Here, we comprehensively dissect the nick DNA substrate specificity of LIG1 active site mutants carrying Ala(A) and Leu(L) substitutions at Phe(F)635 and Phe(F)F872 residues and show completely abolished ligation of nick DNA substrates with all 12 non-canonical mismatches. LIG1 EE/AA structures of F635A and F872A mutants in complex with nick DNA containing A:C and G:T mismatches demonstrate the importance of DNA end rigidity, as well as uncover a shift in a flexible loop near 5'-end of the nick, which causes an increased barrier to adenylate transfer from LIG1 to the 5'-end of the nick. Furthermore, LIG1 EE/AA /8oxoG:A structures of both mutants demonstrated that F635 and F872 play critical roles during steps 1 or 2 of the ligation reaction depending on the position of the active site residue near the DNA ends. Overall, our study contributes towards a better understanding of the substrate discrimination mechanism of LIG1 against mutagenic repair intermediates with mismatched or damaged ends and reveals the importance of conserved ligase active site residues to maintain ligation fidelity.
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6
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Bhandari SK, Wiest N, Sallmyr A, Du R, Ferry L, Defossez PA, Tomkinson AE. Unchanged PCNA and DNMT1 dynamics during replication in DNA ligase I-deficient cells but abnormal chromatin levels of non-replicative histone H1. Sci Rep 2023; 13:4363. [PMID: 36928068 PMCID: PMC10020546 DOI: 10.1038/s41598-023-31367-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 03/10/2023] [Indexed: 03/18/2023] Open
Abstract
DNA ligase I (LigI), the predominant enzyme that joins Okazaki fragments, interacts with PCNA and Pol δ. LigI also interacts with UHRF1, linking Okazaki fragment joining with DNA maintenance methylation. Okazaki fragments can also be joined by a relatively poorly characterized DNA ligase IIIα (LigIIIα)-dependent backup pathway. Here we examined the effect of LigI-deficiency on proteins at the replication fork. Notably, LigI-deficiency did not alter the kinetics of association of the PCNA clamp, the leading strand polymerase Pol ε, DNA maintenance methylation proteins and core histones with newly synthesized DNA. While the absence of major changes in replication and methylation proteins is consistent with the similar proliferation rate and DNA methylation levels of the LIG1 null cells compared with the parental cells, the increased levels of LigIIIα/XRCC1 and Pol δ at the replication fork and in bulk chromatin indicate that there are subtle replication defects in the absence of LigI. Interestingly, the non-replicative histone H1 variant, H1.0, is enriched in the chromatin of LigI-deficient mouse CH12F3 and human 46BR.1G1 cells. This alteration was not corrected by expression of wild type LigI, suggesting that it is a relatively stable epigenetic change that may contribute to the immunodeficiencies linked with inherited LigI-deficiency syndrome.
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Affiliation(s)
- Seema Khattri Bhandari
- Cancer Research Facility, Departments of Internal Medicine and Molecular Genetics & Microbiology, University of New Mexico Comprehensive Cancer Center, University of New Mexico Health Sciences Center, 915 Camino de Salud, 1 University of New Mexico, Albuquerque, NM, 87131, USA
| | - Nathaniel Wiest
- Cancer Research Facility, Departments of Internal Medicine and Molecular Genetics & Microbiology, University of New Mexico Comprehensive Cancer Center, University of New Mexico Health Sciences Center, 915 Camino de Salud, 1 University of New Mexico, Albuquerque, NM, 87131, USA
- Division of Hematology and Medical Oncology, Department of Internal Medicine, Mayo Clinic, Jacksonville, FL, 32224, USA
| | - Annahita Sallmyr
- Cancer Research Facility, Departments of Internal Medicine and Molecular Genetics & Microbiology, University of New Mexico Comprehensive Cancer Center, University of New Mexico Health Sciences Center, 915 Camino de Salud, 1 University of New Mexico, Albuquerque, NM, 87131, USA
| | - Ruofei Du
- Cancer Research Facility, Departments of Internal Medicine and Molecular Genetics & Microbiology, University of New Mexico Comprehensive Cancer Center, University of New Mexico Health Sciences Center, 915 Camino de Salud, 1 University of New Mexico, Albuquerque, NM, 87131, USA
- Department of Biostatistics, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA
| | - Laure Ferry
- Epigenetics and Cell Fate, CNRS, Université Paris Cité, 750013, Paris, France
| | | | - Alan E Tomkinson
- Cancer Research Facility, Departments of Internal Medicine and Molecular Genetics & Microbiology, University of New Mexico Comprehensive Cancer Center, University of New Mexico Health Sciences Center, 915 Camino de Salud, 1 University of New Mexico, Albuquerque, NM, 87131, USA.
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7
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Yilmaz Demirdag Y, Gupta S. Infections in DNA Repair Defects. Pathogens 2023; 12:pathogens12030440. [PMID: 36986362 PMCID: PMC10054915 DOI: 10.3390/pathogens12030440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 03/03/2023] [Accepted: 03/09/2023] [Indexed: 03/14/2023] Open
Abstract
DNA repair defects are heterogenous conditions characterized by a wide spectrum of clinical phenotypes. The common presentations of DNA repair defects include increased risk of cancer, accelerated aging, and defects in the development of various organs and systems. The immune system can be affected in a subset of these disorders leading to susceptibility to infections and autoimmunity. Infections in DNA repair defects may occur due to primary defects in T, B, or NK cells and other factors such as anatomic defects, neurologic disorders, or during chemotherapy. Consequently, the characteristics of the infections may vary from mild upper respiratory tract infections to severe, opportunistic, and even fatal infections with bacteria, viruses, or fungi. Here, infections in 15 rare and sporadic DNA repair defects that are associated with immunodeficiencies are discussed. Because of the rarity of some of these conditions, limited information is available regarding infectious complications.
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8
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Sun H, Ma L, Tsai YF, Abeywardana T, Shen B, Zheng L. Okazaki fragment maturation: DNA flap dynamics for cell proliferation and survival. Trends Cell Biol 2023; 33:221-234. [PMID: 35879148 PMCID: PMC9867784 DOI: 10.1016/j.tcb.2022.06.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 06/28/2022] [Accepted: 06/30/2022] [Indexed: 01/24/2023]
Abstract
Unsuccessful processing of Okazaki fragments leads to the accumulation of DNA breaks which are associated with many human diseases including cancer and neurodegenerative disorders. Recently, Okazaki fragment maturation (OFM) has received renewed attention regarding how unprocessed Okazaki fragments are sensed and repaired, and how inappropriate OFM impacts on genome stability and cell viability, especially in cancer cells. We provide an overview of the highly efficient and faithful canonical OFM pathways and their regulation of genomic integrity and cell survival. We also discuss how cells induce alternative error-prone OFM processes to promote cell survival in response to environmental stresses. Such stress-induced OFM processes may be important mechanisms driving mutagenesis, cellular evolution, and resistance to radio/chemotherapy and targeted therapeutics in human cancers.
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Affiliation(s)
- Haitao Sun
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute of City of Hope, 1500 East Duarte Road, Duarte, CA 91010, USA
| | - Lingzi Ma
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute of City of Hope, 1500 East Duarte Road, Duarte, CA 91010, USA
| | - Ya-Fang Tsai
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute of City of Hope, 1500 East Duarte Road, Duarte, CA 91010, USA
| | - Tharindu Abeywardana
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute of City of Hope, 1500 East Duarte Road, Duarte, CA 91010, USA
| | - Binghui Shen
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute of City of Hope, 1500 East Duarte Road, Duarte, CA 91010, USA.
| | - Li Zheng
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute of City of Hope, 1500 East Duarte Road, Duarte, CA 91010, USA.
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9
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McNally JR, Ames AM, Admiraal SJ, O’Brien PJ. Human DNA ligases I and III have stand-alone end-joining capability, but differ in ligation efficiency and specificity. Nucleic Acids Res 2023; 51:796-805. [PMID: 36625284 PMCID: PMC9881130 DOI: 10.1093/nar/gkac1263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Revised: 12/13/2022] [Accepted: 12/16/2022] [Indexed: 01/11/2023] Open
Abstract
Double-strand DNA breaks (DSBs) are toxic to cells, and improper repair can cause chromosomal abnormalities that initiate and drive cancer progression. DNA ligases III and IV (LIG3, LIG4) have long been credited for repair of DSBs in mammals, but recent evidence suggests that DNA ligase I (LIG1) has intrinsic end-joining (EJ) activity that can compensate for their loss. To test this model, we employed in vitro biochemical assays to compare EJ by LIG1 and LIG3. The ligases join blunt-end and 3'-overhang-containing DNA substrates with similar catalytic efficiency, but LIG1 joins 5'-overhang-containing DNA substrates ∼20-fold less efficiently than LIG3 under optimal conditions. LIG1-catalyzed EJ is compromised at a physiological concentration of Mg2+, but its activity is restored by increased molecular crowding. In contrast to LIG1, LIG3 efficiently catalyzes EJ reactions at a physiological concentration of Mg2+ with or without molecular crowding. Under all tested conditions, LIG3 has greater affinity than LIG1 for DNA ends. Remarkably, LIG3 can ligate both strands of a DSB during a single binding encounter. The weaker DNA binding affinity of LIG1 causes significant abortive ligation that is sensitive to molecular crowding and DNA terminal structure. These results provide new insights into mechanisms of alternative nonhomologous EJ.
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Affiliation(s)
- Justin R McNally
- Department of Biological Chemistry, Michigan Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Amanda M Ames
- Department of Biological Chemistry, Michigan Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Suzanne J Admiraal
- Department of Biological Chemistry, Michigan Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Patrick J O’Brien
- Department of Biological Chemistry, Michigan Medicine, University of Michigan, Ann Arbor, MI 48109, USA
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10
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Dabrowska-Leonik N, Pastorczak AK, Bąbol-Pokora K, Bernat-Sitarz K, Piątosa B, Heropolitańska-Pliszka E, Kacprzak MM, Kalwak K, Gul K, van der Burg M, Ussowicz M, Pac M. Case report: Severe combined immunodeficiency with ligase 1 deficiency and Omenn-like manifestation. Front Immunol 2022; 13:1033338. [PMID: 36341401 PMCID: PMC9626757 DOI: 10.3389/fimmu.2022.1033338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 10/03/2022] [Indexed: 11/24/2022] Open
Abstract
DNA ligase I deficiency is an extremely rare primary immunodeficiency with only 6 patients reported in the literature. Most common manifestations include radiosensitivity, macrocytic anemia, lymphopenia with an increased percentage of gamma-delta T cells, and hypogammaglobulinemia requiring replacement therapy. Two-month-old girl with delayed development, T-B-NK+ SCID, and macrocytic anemia presented features of Omenn syndrome. Whole exome sequencing revealed two novel, heterozygous variants (c.2312 G>A, p.Arg771Gly and c.776+5G>T, p.Pro260*) in the LIG1 gene (NM_000234.1). Hematopoietic stem cell transplantation from a fully matched unrelated donor was performed at the age of 4 months using GEFA03 protocol. Mixed donor-recipient chimerism was observed, with 60-70% chimerism in the mononucleated cell compartment and over 90% in T-lymphocyte compartment, but autologous myeloid recovery. Stable CD4+ and CD8+ T-cell counts above 200/µL were achieved after 2 months, but the patient remained transfusion-dependent. Despite satisfactory immunological reconstitution, the second transplantation due to constitutional hemolytic defect has been considered. In light of possible re-transplantation, an issue of optimal conditioning protocol with sufficient myeloid engraftment is important. For the first time Omenn syndrome is described in a compound heterozygote carrying two the novel variants p.Arg771Gly and p.Pro260* in the LIG1 gene. Patients diagnosed with SCID and Omenn syndrome showing macrocytic anemia, should be screened for DNA ligase I deficiency.
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Affiliation(s)
- Nel Dabrowska-Leonik
- Department of Immunology, Children’s Memorial Health Institute, Warsaw, Poland
- *Correspondence: Nel Dabrowska-Leonik,
| | | | - Katarzyna Bąbol-Pokora
- Department of Pediatrics, Oncology and Hematology, Medical University of Lodz, Lodz, Poland
| | | | - Barbara Piątosa
- Histocompatibility Laboratory, Children’s Memorial Health Institute (IPCZD), Warsaw, Poland
| | | | | | - Krzysztof Kalwak
- Department of Paediatric Bone Marrow Transplantation, Oncology and Hematology, Wroclaw Medical University, Wroclaw, Poland
| | - Katarzyna Gul
- Department of Paediatric Bone Marrow Transplantation, Oncology and Hematology, Wroclaw Medical University, Wroclaw, Poland
| | - Mirjam van der Burg
- Department of Pediatrics, Leiden University Medical Center (LUMC), Leiden, Netherlands
| | - Marek Ussowicz
- Department of Paediatric Bone Marrow Transplantation, Oncology and Hematology, Wroclaw Medical University, Wroclaw, Poland
| | - Malgorzata Pac
- Department of Immunology, Children’s Memorial Health Institute, Warsaw, Poland
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11
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Boulund U, Bastos DM, Ferwerda B, van den Born BJ, Pinto-Sietsma SJ, Galenkamp H, Levin E, Groen AK, Zwinderman AH, Nieuwdorp M. Gut microbiome associations with host genotype vary across ethnicities and potentially influence cardiometabolic traits. Cell Host Microbe 2022; 30:1464-1480.e6. [PMID: 36099924 DOI: 10.1016/j.chom.2022.08.013] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 06/16/2022] [Accepted: 08/17/2022] [Indexed: 12/13/2022]
Abstract
Previous studies in mainly European populations have reported that the gut microbiome composition is associated with the human genome. However, the genotype-microbiome interaction in different ethnicities is largely unknown. We performed a large fecal microbiome genome-wide association study of a single multiethnic cohort, the Healthy Life in an Urban Setting (HELIUS) cohort (N = 4,117). Mendelian randomization was performed using the multiethnic Pan-UK Biobank (N = 460,000) to dissect potential causality. We identified ethnicity-specific associations between host genomes and gut microbiota. Certain microbes were associated with genotype in multiple ethnicities. Several of the microbe-associated loci were found to be related to immune functions, interact with glutamate and the mucus layer, or be expressed in the gut or brain. Additionally, we found that gut microbes potentially influence cardiometabolic health factors such as BMI, cholesterol, and blood pressure. This provides insight into the relationship of ethnicity and gut microbiota and into the possible causal effects of gut microbes on cardiometabolic traits.
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Affiliation(s)
- Ulrika Boulund
- Department of Internal and Vascular Medicine, Amsterdam University Medical Centers, location AMC, 1105 AZ Amsterdam, the Netherlands
| | - Diogo M Bastos
- Department of Internal and Vascular Medicine, Amsterdam University Medical Centers, location AMC, 1105 AZ Amsterdam, the Netherlands
| | - Bart Ferwerda
- Department of Clinical Epidemiology and Biostatistics, Amsterdam University Medical Centers, location AMC, 1105 AZ Amsterdam, the Netherlands
| | - Bert-Jan van den Born
- Department of Internal and Vascular Medicine, Amsterdam University Medical Centers, location AMC, 1105 AZ Amsterdam, the Netherlands; Department of Public and Occupational Health, Amsterdam University Medical Centers, location AMC, 1105 AZ Amsterdam, the Netherlands
| | - Sara-Joan Pinto-Sietsma
- Department of Internal and Vascular Medicine, Amsterdam University Medical Centers, location AMC, 1105 AZ Amsterdam, the Netherlands; Department of Clinical Epidemiology and Biostatistics, Amsterdam University Medical Centers, location AMC, 1105 AZ Amsterdam, the Netherlands
| | - Henrike Galenkamp
- Department of Public and Occupational Health, Amsterdam University Medical Centers, location AMC, 1105 AZ Amsterdam, the Netherlands
| | - Evgeni Levin
- Department of Internal and Vascular Medicine, Amsterdam University Medical Centers, location AMC, 1105 AZ Amsterdam, the Netherlands; HorAIzon BV, 2645 LT Delfgauw, the Netherlands
| | - Albert K Groen
- Department of Internal and Vascular Medicine, Amsterdam University Medical Centers, location AMC, 1105 AZ Amsterdam, the Netherlands
| | - Aeilko H Zwinderman
- Department of Clinical Epidemiology and Biostatistics, Amsterdam University Medical Centers, location AMC, 1105 AZ Amsterdam, the Netherlands
| | - Max Nieuwdorp
- Department of Internal and Vascular Medicine, Amsterdam University Medical Centers, location AMC, 1105 AZ Amsterdam, the Netherlands.
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12
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Wang Y, Abolhassani H, Hammarström L, Pan-Hammarström Q. SARS-CoV-2 infection in patients with inborn errors of immunity due to DNA repair defects. Acta Biochim Biophys Sin (Shanghai) 2022; 54:836-846. [PMID: 35713311 PMCID: PMC9827799 DOI: 10.3724/abbs.2022071] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Clinical information on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in patients with inborn errors of immunity (IEI) during the current Coronavirus disease 2019 (COVID-19) pandemic is still limited. Proper DNA repair machinery is required for the development of the adaptive immune system, which provides specific and long-term protection against SARS-CoV-2. This review highlights the impact of SARS-CoV-2 infections on IEI patients with DNA repair disorders and summarizes susceptibility risk factors, pathogenic mechanisms, clinical manifestations and management strategies of COVID-19 in this special patient population.
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13
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Ni L, Li Z, Ren H, Kong L, Chen X, Xiong M, Zhang X, Ning B, Li J. Berberine inhibits non-small cell lung cancer cell growth through repressing DNA repair and replication rather than through apoptosis. Clin Exp Pharmacol Physiol 2021; 49:134-144. [PMID: 34448246 DOI: 10.1111/1440-1681.13582] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 08/11/2021] [Accepted: 08/24/2021] [Indexed: 12/16/2022]
Abstract
At present, there are still many problems in the treatment of lung cancer, such as high cost, side effects and low quality of life. The advantages of traditional Chinese medicine (TCM) in the treatment of lung cancer are reflected. Berberine has been increasingly popular in colorectal cancer treatment, but little is known about its bioactivity against non-small cell lung cancer (NSCLC). Cell proliferation, cell apoptosis, cDNA microarray, gene and protein expression, and NSCLC transplanted tumour growth were performed. Berberine suppressed NSCLC cell proliferation and colony formation in vitro and inhibited NSCLC tumour growth in subcutaneously transplanted tumour lung tumour models, leading to prolonged survival of tumour-bearing mice. However, berberine did not induce the cleavage of Caspase 3 and PARP1, and could not induce apoptosis in all NSCLC cells. Moreover, 646 genes were differentially expressed upon berberine administration, which were involved in seven signal pathways, such as DNA replication. In cDNA microarray, berberine downregulated the expression of RRM1, RRM2, LIG1, POLE2 that involving DNA repair and replication. Our findings demonstrate that berberine inhibits NSCLC cells growth through repressing DNA repair and replication rather than through apoptosis. Berberine could be used as a promising therapeutic candidate for NSCLC patients.
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Affiliation(s)
- Lulu Ni
- Department of Basic Medicine, Jiangnan University, Wuxi, China
| | - Zhongjie Li
- Department of Basic Medicine, Jiangnan University, Wuxi, China
| | - Hongli Ren
- The Institute of Science, Technology and Humanities, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Lingzhong Kong
- Department of Rehabilitation Acupuncture Medicine, Bozhou People's Hospital, Bozhou, China
| | - Xu Chen
- Department of Basic Medicine, Jiangnan University, Wuxi, China
| | - Mengrui Xiong
- Department of Basic Medicine, Jiangnan University, Wuxi, China
| | - Xiuqin Zhang
- Department of Respiratory Medicine, Affiliated Hospital of Jiangnan University, Wuxi, China
| | - Bingbing Ning
- Department of Cardiology, Shanghai Municipal Hospital of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Jiangan Li
- Department of Emergency, Wuxi No 2 People's Hospital, Wuxi, China
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14
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Lu J, Pan C, Fan W, Liu W, Zhao H, Li D, Wang S, Hu L, He B, Qian K, Qin R, Ruan J, Lin Q, Lü S, Cui P. A Chromosome-level Assembly of A Wild Castor Genome Provides New Insights into the Adaptive Evolution in A Tropical Desert. GENOMICS PROTEOMICS & BIOINFORMATICS 2021; 20:42-59. [PMID: 34339842 PMCID: PMC9510866 DOI: 10.1016/j.gpb.2021.04.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 04/03/2021] [Accepted: 04/12/2021] [Indexed: 02/01/2023]
Abstract
Wild castor grows in the high-altitude tropical desert of the African Plateau, a region known for high ultraviolet radiation, strong light, and extremely dry condition. To investigate the potential genetic basis of adaptation to both highland and tropical deserts, we generated a chromosome-level genome sequence assembly of the wild castor accession WT05, with a genome size of 316 Mb, a scaffold N50 of 31.93 Mb, and a contig N50 of 8.96 Mb, respectively. Compared with cultivated castor and other Euphorbiaceae species, the wild castor exhibits positive selection and gene family expansion for genes involved in DNA repair, photosynthesis, and abiotic stress responses. Genetic variations associated with positive selection were identified in several key genes, such as LIG1, DDB2, and RECG1, involved in nucleotide excision repair. Moreover, a study of genomic diversity among wild and cultivated accessions revealed genomic regions containing selection signatures associated with the adaptation to extreme environments. The identification of the genes and alleles with selection signatures provides insights into the genetic mechanisms underlying the adaptation of wild castor to the high-altitude tropical desert and would facilitate direct improvement of modern castor varieties.
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Affiliation(s)
- Jianjun Lu
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Cheng Pan
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
| | - Wei Fan
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Wanfei Liu
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Huayan Zhao
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 434200, China
| | - Donghai Li
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Sen Wang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Lianlian Hu
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Bing He
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Kun Qian
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Rui Qin
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Jue Ruan
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Qiang Lin
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China.
| | - Shiyou Lü
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 434200, China.
| | - Peng Cui
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China.
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15
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Kumamoto S, Nishiyama A, Chiba Y, Miyashita R, Konishi C, Azuma Y, Nakanishi M. HPF1-dependent PARP activation promotes LIG3-XRCC1-mediated backup pathway of Okazaki fragment ligation. Nucleic Acids Res 2021; 49:5003-5016. [PMID: 33872376 PMCID: PMC8136790 DOI: 10.1093/nar/gkab269] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 03/29/2021] [Accepted: 04/01/2021] [Indexed: 12/20/2022] Open
Abstract
DNA ligase 1 (LIG1) is known as the major DNA ligase responsible for Okazaki fragment joining. Recent studies have implicated LIG3 complexed with XRCC1 as an alternative player in Okazaki fragment joining in cases where LIG1 is not functional, although the underlying mechanisms are largely unknown. Here, using a cell-free system derived from Xenopus egg extracts, we demonstrated the essential role of PARP1-HPF1 in LIG3-dependent Okazaki fragment joining. We found that Okazaki fragments were eventually ligated even in the absence of LIG1, employing in its place LIG3-XRCC1, which was recruited onto chromatin. Concomitantly, LIG1 deficiency induces ADP-ribosylation of histone H3 in a PARP1-HPF1-dependent manner. The depletion of PARP1 or HPF1 resulted in a failure to recruit LIG3 onto chromatin and a subsequent failure in Okazaki fragment joining in LIG1-depleted extracts. Importantly, Okazaki fragments were not ligated at all when LIG1 and XRCC1 were co-depleted. Our results suggest that a unique form of ADP-ribosylation signaling promotes the recruitment of LIG3 on chromatin and its mediation of Okazaki fragment joining as a backup system for LIG1 perturbation.
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Affiliation(s)
- Soichiro Kumamoto
- Division of Cancer Cell Biology, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Atsuya Nishiyama
- Division of Cancer Cell Biology, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Yoshie Chiba
- Division of Cancer Cell Biology, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Ryota Miyashita
- Division of Cancer Cell Biology, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Chieko Konishi
- Division of Cancer Cell Biology, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Yoshiaki Azuma
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS 66045, USA
| | - Makoto Nakanishi
- Division of Cancer Cell Biology, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
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16
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Strubbe S, De Bruyne M, Pannicke U, Beyls E, Vandekerckhove B, Leclercq G, De Baere E, Bordon V, Vral A, Schwarz K, Haerynck F, Taghon T. A Novel Non-Coding Variant in DCLRE1C Results in Deregulated Splicing and Induces SCID Through the Generation of a Truncated ARTEMIS Protein That Fails to Support V(D)J Recombination and DNA Damage Repair. Front Immunol 2021; 12:674226. [PMID: 34220820 PMCID: PMC8248492 DOI: 10.3389/fimmu.2021.674226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 06/03/2021] [Indexed: 11/13/2022] Open
Abstract
Severe Combined Immune Deficiency (SCID) is a primary deficiency of the immune system in which opportunistic and recurring infections are often fatal during neonatal or infant life. SCID is caused by an increasing number of genetic defects that induce an abrogation of T lymphocyte development or function in which B and NK cells might be affected as well. Because of the increased availability and usage of next-generation sequencing (NGS), many novel variants in SCID genes are being identified and cause a heterogeneous disease spectrum. However, the molecular and functional implications of these new variants, of which some are non-coding, are often not characterized in detail. Using targeted NGS, we identified a novel homozygous c.465-1G>C splice acceptor site variant in the DCLRE1C gene in a T-B-NK+ SCID patient and fully characterized the molecular and functional impact. By performing a minigene splicing reporter assay, we revealed deregulated splicing of the DCLRE1C transcript since a cryptic splice acceptor in exon 7 was employed. This induced a frameshift and the generation of a p.Arg155Serfs*15 premature termination codon (PTC) within all DCLRE1C splice variants, resulting in the absence of full-length ARTEMIS protein. Consistently, a V(D)J recombination assay and a G0 micronucleus assay demonstrated the inability of the predicted mutant ARTEMIS protein to perform V(D)J recombination and DNA damage repair, respectively. Together, these experiments molecularly and functionally clarify how a newly identified c.465-1G>C variant in the DCLRE1C gene is responsible for inducing SCID. In a clinical context, this demonstrates how the experimental validation of new gene variants, that are identified by NGS, can facilitate the diagnosis of SCID which can be vital for implementing appropriate therapies.
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Affiliation(s)
- Steven Strubbe
- Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | | | - Ulrich Pannicke
- The Institute for Transfusion Medicine, University of Ulm, Ulm, Germany
| | - Elien Beyls
- Department of Human Structure and Repair, Ghent University, Ghent, Belgium
| | - Bart Vandekerckhove
- Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Georges Leclercq
- Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Elfride De Baere
- Center for Medical Genetics Ghent (CMGG), Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Victoria Bordon
- Department of Internal Medicine and Pediatrics, Division of Pediatric Hemato-Oncology and Stem Cell Transplantation, Ghent University Hospital, Ghent, Belgium
| | - Anne Vral
- Department of Human Structure and Repair, Ghent University, Ghent, Belgium
| | - Klaus Schwarz
- The Institute for Transfusion Medicine, University of Ulm, Ulm, Germany
- Institute for Clinical Transfusion Medicine and Immunogenetics Ulm, Germa Red Cross Blood Service Baden-Württemberg – Hessen, Ulm, Germany
| | - Filomeen Haerynck
- Primary Immunodeficiency Research Lab, Jeffrey Modell Diagnosis and Research Center, Ghent University Hospital, Ghent, Belgium
- Department of Internal Medicine and Pediatrics, Division of Pediatric Immunology and Pulmonology, Ghent University Hospital, Ghent, Belgium
| | - Tom Taghon
- Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
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17
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Jurkiw TJ, Tumbale PP, Schellenberg MJ, Cunningham-Rundles C, Williams RS, O’Brien PJ. LIG1 syndrome mutations remodel a cooperative network of ligand binding interactions to compromise ligation efficiency. Nucleic Acids Res 2021; 49:1619-1630. [PMID: 33444456 PMCID: PMC7897520 DOI: 10.1093/nar/gkaa1297] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 12/28/2020] [Accepted: 01/06/2021] [Indexed: 11/14/2022] Open
Abstract
Human DNA ligase I (LIG1) is the main replicative ligase and it also seals DNA breaks to complete DNA repair and recombination pathways. Immune compromised patients harbor hypomorphic LIG1 alleles encoding substitutions of conserved arginine residues, R771W and R641L, that compromise LIG1 activity through poorly defined mechanisms. To understand the molecular basis of LIG1 syndrome mutations, we determined high resolution X-ray structures and performed systematic biochemical characterization of LIG1 mutants using steady-state and pre-steady state kinetic approaches. Our results unveil a cooperative network of plastic DNA-LIG1 interactions that connect DNA substrate engagement with productive binding of Mg2+ cofactors for catalysis. LIG1 syndrome mutations destabilize this network, compromising Mg2+ binding affinity, decreasing ligation efficiency, and leading to elevated abortive ligation that may underlie the disease pathology. These findings provide novel insights into the fundamental mechanism by which DNA ligases engage with a nicked DNA substrate, and they suggest that disease pathology of LIG1 syndrome could be modulated by Mg2+ levels.
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Affiliation(s)
- Thomas J Jurkiw
- Department of Biological Chemistry, University of Michigan School of Medicine, Ann Arbor, MI, 48109, USA
| | - Percy P Tumbale
- Structural Cell Biology group, Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, US National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC, 27709, USA
| | - Matthew J Schellenberg
- Structural Cell Biology group, Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, US National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC, 27709, USA
| | - Charlotte Cunningham-Rundles
- Division of Clinical Immunology, Departments of Medicine and Pediatrics, and Graduate School of Biomedical Sciences, Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - R Scott Williams
- Structural Cell Biology group, Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, US National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC, 27709, USA
| | - Patrick J O’Brien
- Department of Biological Chemistry, University of Michigan School of Medicine, Ann Arbor, MI, 48109, USA
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18
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Abstract
DNA mismatch repair (MMR) is a highly conserved genome stabilizing pathway that corrects DNA replication errors, limits chromosomal rearrangements, and mediates the cellular response to many types of DNA damage. Counterintuitively, MMR is also involved in the generation of mutations, as evidenced by its role in causing somatic triplet repeat expansion in Huntington’s disease (HD) and other neurodegenerative disorders. In this review, we discuss the current state of mechanistic knowledge of MMR and review the roles of key enzymes in this pathway. We also present the evidence for mutagenic function of MMR in CAG repeat expansion and consider mechanistic hypotheses that have been proposed. Understanding the role of MMR in CAG expansion may shed light on potential avenues for therapeutic intervention in HD.
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Affiliation(s)
- Ravi R Iyer
- CHDI Management/CHDI Foundation, Princeton, NJ, USA
| | - Anna Pluciennik
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA, USA
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19
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Tomkinson AE, Naila T, Khattri Bhandari S. Altered DNA ligase activity in human disease. Mutagenesis 2021; 35:51-60. [PMID: 31630206 DOI: 10.1093/mutage/gez026] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 09/09/2019] [Indexed: 12/18/2022] Open
Abstract
The joining of interruptions in the phosphodiester backbone of DNA is critical to maintain genome stability. These breaks, which are generated as part of normal DNA transactions, such as DNA replication, V(D)J recombination and meiotic recombination as well as directly by DNA damage or due to DNA damage removal, are ultimately sealed by one of three human DNA ligases. DNA ligases I, III and IV each function in the nucleus whereas DNA ligase III is the sole enzyme in mitochondria. While the identification of specific protein partners and the phenotypes caused either by genetic or chemical inactivation have provided insights into the cellular functions of the DNA ligases and evidence for significant functional overlap in nuclear DNA replication and repair, different results have been obtained with mouse and human cells, indicating species-specific differences in the relative contributions of the DNA ligases. Inherited mutations in the human LIG1 and LIG4 genes that result in the generation of polypeptides with partial activity have been identified as the causative factors in rare DNA ligase deficiency syndromes that share a common clinical symptom, immunodeficiency. In the case of DNA ligase IV, the immunodeficiency is due to a defect in V(D)J recombination whereas the cause of the immunodeficiency due to DNA ligase I deficiency is not known. Overexpression of each of the DNA ligases has been observed in cancers. For DNA ligase I, this reflects increased proliferation. Elevated levels of DNA ligase III indicate an increased dependence on an alternative non-homologous end-joining pathway for the repair of DNA double-strand breaks whereas elevated level of DNA ligase IV confer radioresistance due to increased repair of DNA double-strand breaks by the major non-homologous end-joining pathway. Efforts to determine the potential of DNA ligase inhibitors as cancer therapeutics are on-going in preclinical cancer models.
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Affiliation(s)
- Alan E Tomkinson
- Departments of Internal Medicine and Molecular Genetics and Microbiology, and the University of New Mexico Comprehensive Cancer Center, University of New Mexico, Albuquerque, NM, USA
| | - Tasmin Naila
- Departments of Internal Medicine and Molecular Genetics and Microbiology, and the University of New Mexico Comprehensive Cancer Center, University of New Mexico, Albuquerque, NM, USA
| | - Seema Khattri Bhandari
- Departments of Internal Medicine and Molecular Genetics and Microbiology, and the University of New Mexico Comprehensive Cancer Center, University of New Mexico, Albuquerque, NM, USA
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20
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Tang Q, Kamble P, Çağlayan M. DNA ligase I variants fail in the ligation of mutagenic repair intermediates with mismatches and oxidative DNA damage. Mutagenesis 2020; 35:391-404. [PMID: 32914844 PMCID: PMC7846189 DOI: 10.1093/mutage/geaa023] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 08/10/2020] [Indexed: 01/26/2023] Open
Abstract
DNA ligase I (LIG1) joins DNA strand breaks during DNA replication and repair transactions and contributes to genome integrity. The mutations (P529L, E566K, R641L and R771W) in LIG1 gene are described in patients with LIG1-deficiency syndrome that exhibit immunodeficiency. LIG1 senses 3'-DNA ends with a mismatch or oxidative DNA base inserted by a repair DNA polymerase. However, the ligation efficiency of the LIG1 variants for DNA polymerase-promoted mutagenesis products with 3'-DNA mismatches or 8-oxo-2'-deoxyguanosine (8-oxodG) remains undefined. Here, we report that R641L and R771W fail in the ligation of nicked DNA with 3'-8-oxodG, leading to an accumulation of 5'-AMP-DNA intermediates in vitro. Moreover, we found that the presence of all possible 12 non-canonical base pairs variously impacts the ligation efficiency by P529L and R771W depending on the architecture at the DNA end, whereas E566K exhibits no activity against all substrates tested. Our results contribute to the understanding of the substrate specificity and mismatch discrimination of LIG1 for mutagenic repair intermediates and the effect of non-synonymous mutations on ligase fidelity.
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Affiliation(s)
- Qun Tang
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL, USA
| | - Pradnya Kamble
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL, USA
| | - Melike Çağlayan
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL, USA
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21
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Silva JMF, Jones A, Sibson K, Bibi S, Jeggo P, Woodbine L, Ahsan G, Gilmour KC, Rao K, Chiesa R, Lucchini G, Veys P, Worth A, Amrolia PJ. Haematopoietic Stem Cell Transplantation for DNA Ligase 1 Deficiency. J Clin Immunol 2020; 41:238-242. [PMID: 33025376 DOI: 10.1007/s10875-020-00871-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 09/16/2020] [Indexed: 10/23/2022]
Affiliation(s)
- Juliana M F Silva
- Department of Bone Marrow Transplantation, Great Ormond Street Hospital for Children NHS Trust, London, UK
| | - Alison Jones
- Department of Immunology, Camelia Botnar Laboratories, Great Ormond Street Hospital NHS Trust, London, UK
| | - Keith Sibson
- Department of Haematology, Great Ormond Street Hospital NHS Trust, London, UK
| | - Shahnaz Bibi
- Regional Molecular Genetics Laboratory, Great Ormond Street Hospital NHS Trust, London, UK
| | - Penny Jeggo
- Genome Damage and Stability Centre, University of Sussex, Science Park Road, Falmer, Brighton, BN19RQ, UK
| | - Lisa Woodbine
- Genome Damage and Stability Centre, University of Sussex, Science Park Road, Falmer, Brighton, BN19RQ, UK
| | - Gulrukh Ahsan
- Department of Immunology, Camelia Botnar Laboratories, Great Ormond Street Hospital NHS Trust, London, UK
| | - Kimberly C Gilmour
- Department of Immunology, Camelia Botnar Laboratories, Great Ormond Street Hospital NHS Trust, London, UK
| | - Kanchan Rao
- Department of Bone Marrow Transplantation, Great Ormond Street Hospital for Children NHS Trust, London, UK
| | - Robert Chiesa
- Department of Bone Marrow Transplantation, Great Ormond Street Hospital for Children NHS Trust, London, UK
| | - Giovanna Lucchini
- Department of Bone Marrow Transplantation, Great Ormond Street Hospital for Children NHS Trust, London, UK
| | - Paul Veys
- Department of Bone Marrow Transplantation, Great Ormond Street Hospital for Children NHS Trust, London, UK
| | - Austen Worth
- Department of Bone Marrow Transplantation, Great Ormond Street Hospital for Children NHS Trust, London, UK.,Molecular Immunology Unit, Institute of Child Health, University College London, London, UK
| | - Persis J Amrolia
- Department of Bone Marrow Transplantation, Great Ormond Street Hospital for Children NHS Trust, London, UK.
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22
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Song Y, Jin D, Chen J, Luo Z, Chen G, Yang Y, Liu X. Identification of an immune-related long non-coding RNA signature and nomogram as prognostic target for muscle-invasive bladder cancer. Aging (Albany NY) 2020; 12:12051-12073. [PMID: 32579540 PMCID: PMC7343518 DOI: 10.18632/aging.103369] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 05/01/2020] [Indexed: 12/24/2022]
Abstract
To identify an immune-related prognostic signature based on long non-coding RNAs (lncRNAs) and find immunotherapeutic targets for bladder urothelial carcinoma, we downloaded RNA-sequencing data from The Cancer Genome Atlas (TCGA) dataset. Functional enrichment analysis demonstrated bladder urothelial carcinoma was related to immune-related functions. We obtained 332 immune-related genes and 262 lncRNAs targeting immune-related genes. We constructed a signature based on eight lncRNAs in training cohort. Patients were classified as high-risk and low-risk according to signature risk score. High-risk patients had poor overall survival compared with low-risk patients (P < 0.001). Multivariate Cox regression suggested the signature was an independent prognostic indicator. The findings were further validated in testing, entire TCGA and external validation cohorts. Gene set enrichment analysis indicated significant enrichment of immune-related phenotype in high-risk group. Immunohistochemistry and online analyses validated the functions of 4 key immune-related genes (LIG1, TBX1, CTSG and CXCL12) in bladder urothelial carcinoma. Nomogram proved to be a good classifier for muscle-invasive bladder cancer through combining the signature. In conclusion, our immune-related prognostic signature and nomogram provided prognostic indicators and potential immunotherapeutic targets for muscle-invasive bladder cancer.
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Affiliation(s)
- Yuxuan Song
- Department of Urology, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Donghui Jin
- Department of Cardiothoracic Surgery, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Jingyi Chen
- Department of Gastroenterology and Institute of Clinical Molecular Biology, Peking University People's Hospital, Beijing 100044, China
| | - Zhiwen Luo
- Department of Hepatobiliary Surgery, National Cancer Center, National Clinical Research Center for Cancer, Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Guangyuan Chen
- The Second Clinical Medical School, Nanchang University, Nanchang 330006, Jiangxi, China
| | - Yongjiao Yang
- Department of Urology, The Second Hospital of Tianjin Medical University, Tianjin 300211, China
| | - Xiaoqiang Liu
- Department of Urology, Tianjin Medical University General Hospital, Tianjin 300052, China
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23
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Stratigopoulou M, van Dam TP, Guikema JEJ. Base Excision Repair in the Immune System: Small DNA Lesions With Big Consequences. Front Immunol 2020; 11:1084. [PMID: 32547565 PMCID: PMC7272602 DOI: 10.3389/fimmu.2020.01084] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 05/05/2020] [Indexed: 12/13/2022] Open
Abstract
The integrity of the genome is under constant threat of environmental and endogenous agents that cause DNA damage. Endogenous damage is particularly pervasive, occurring at an estimated rate of 10,000–30,000 per cell/per day, and mostly involves chemical DNA base lesions caused by oxidation, depurination, alkylation, and deamination. The base excision repair (BER) pathway is primary responsible for removing and repairing these small base lesions that would otherwise lead to mutations or DNA breaks during replication. Next to preventing DNA mutations and damage, the BER pathway is also involved in mutagenic processes in B cells during immunoglobulin (Ig) class switch recombination (CSR) and somatic hypermutation (SHM), which are instigated by uracil (U) lesions derived from activation-induced cytidine deaminase (AID) activity. BER is required for the processing of AID-induced lesions into DNA double strand breaks (DSB) that are required for CSR, and is of pivotal importance for determining the mutagenic outcome of uracil lesions during SHM. Although uracils are generally efficiently repaired by error-free BER, this process is surprisingly error-prone at the Ig loci in proliferating B cells. Breakdown of this high-fidelity process outside of the Ig loci has been linked to mutations observed in B-cell tumors and DNA breaks and chromosomal translocations in activated B cells. Next to its role in preventing cancer, BER has also been implicated in immune tolerance. Several defects in BER components have been associated with autoimmune diseases, and animal models have shown that BER defects can cause autoimmunity in a B-cell intrinsic and extrinsic fashion. In this review we discuss the contribution of BER to genomic integrity in the context of immune receptor diversification, cancer and autoimmune diseases.
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Affiliation(s)
- Maria Stratigopoulou
- Department of Pathology, Lymphoma and Myeloma Center Amsterdam (LYMMCARE), Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Tijmen P van Dam
- Department of Pathology, Lymphoma and Myeloma Center Amsterdam (LYMMCARE), Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Jeroen E J Guikema
- Department of Pathology, Lymphoma and Myeloma Center Amsterdam (LYMMCARE), Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
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24
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Tangye SG, Al-Herz W, Bousfiha A, Chatila T, Cunningham-Rundles C, Etzioni A, Franco JL, Holland SM, Klein C, Morio T, Ochs HD, Oksenhendler E, Picard C, Puck J, Torgerson TR, Casanova JL, Sullivan KE. Human Inborn Errors of Immunity: 2019 Update on the Classification from the International Union of Immunological Societies Expert Committee. J Clin Immunol 2020; 40:24-64. [PMID: 31953710 PMCID: PMC7082301 DOI: 10.1007/s10875-019-00737-x] [Citation(s) in RCA: 699] [Impact Index Per Article: 174.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 12/18/2019] [Indexed: 12/26/2022]
Abstract
We report the updated classification of Inborn Errors of Immunity/Primary Immunodeficiencies, compiled by the International Union of Immunological Societies Expert Committee. This report documents the key clinical and laboratory features of 430 inborn errors of immunity, including 64 gene defects that have either been discovered in the past 2 years since the previous update (published January 2018) or were characterized earlier but have since been confirmed or expanded upon in subsequent studies. The application of next-generation sequencing continues to expedite the rapid identification of novel gene defects, rare or common; broaden the immunological and clinical phenotypes of conditions arising from known gene defects and even known variants; and implement gene-specific therapies. These advances are contributing to greater understanding of the molecular, cellular, and immunological mechanisms of disease, thereby enhancing immunological knowledge while improving the management of patients and their families. This report serves as a valuable resource for the molecular diagnosis of individuals with heritable immunological disorders and also for the scientific dissection of cellular and molecular mechanisms underlying inborn errors of immunity and related human diseases.
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Affiliation(s)
- Stuart G Tangye
- Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW, 2010, Australia.
- Faculty of Medicine, St Vincent's Clinical School, UNSW, Sydney, NSW, Australia.
| | - Waleed Al-Herz
- Department of Pediatrics, Faculty of Medicine, Kuwait University, Kuwait City, Kuwait
| | - Aziz Bousfiha
- King Hassan II University, Laboratoire d'Immunologie Clinique, d'Inflammation et d'Allergy LICIA at Faculty of Medicine and Pharmacy, Clinical Immunology Unit, Pediatric Infectiouse Disease Department, Children's Hospital, Ibn Rochd University Hospital, Casablanca, Morocco
| | - Talal Chatila
- Division of Immunology, Children's Hospital Boston, Boston, MA, USA
| | | | - Amos Etzioni
- Ruth's Children's Hospital-Technion, Haifa, Israel
| | - Jose Luis Franco
- Grupo de Inmunodeficiencias Primarias, Facultad de Medicina, Universidad de Antioquia UdeA, Medellin, Colombia
| | - Steven M Holland
- Laboratory of Clinical Immunology & Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Christoph Klein
- Dr von Hauner Children's Hospital, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Tomohiro Morio
- Department of Pediatrics and Developmental Biology, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Hans D Ochs
- Department of Pediatrics, University of Washington and Seattle Children's Research Institute, Seattle, WA, USA
| | - Eric Oksenhendler
- Department of Clinical Immunology, Hôpital Saint-Louis, APHP, University Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Capucine Picard
- Study Center for Primary Immunodeficiencies, Necker Hospital for Sick Children, APHP, Paris, France
- Paris University, Laboratory of Lymphocyte Activation and Susceptibility to EBV, INSERM UMR1163, Imagine Institute, Necker Hospital for Sick Children, Paris, France
| | - Jennifer Puck
- Department of Pediatrics, University of California San Francisco and UCSF Benioff Children's Hospital, San Francisco, CA, USA
| | - Troy R Torgerson
- Department of Pediatrics, University of Washington and Seattle Children's Research Institute, Seattle, WA, USA
| | - Jean-Laurent Casanova
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
- Howard Hughes Medical Institute, New York, NY, USA
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR1163, Imagine Institute, Necker Hospital for Sick Children, Paris University, Paris, France
- Pediatric Hematology-Immunology Unit, Necker Hospital for Sick Children, Assistance Publique-Hôpitaux de Paris (APHP), Paris, France
| | - Kathleen E Sullivan
- Division of Allergy Immunology, Department of Pediatrics, The Children's Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
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25
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Tumbale PP, Jurkiw TJ, Schellenberg MJ, Riccio AA, O'Brien PJ, Williams RS. Two-tiered enforcement of high-fidelity DNA ligation. Nat Commun 2019; 10:5431. [PMID: 31780661 PMCID: PMC6882888 DOI: 10.1038/s41467-019-13478-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 11/05/2019] [Indexed: 01/07/2023] Open
Abstract
DNA ligases catalyze the joining of DNA strands to complete DNA replication, recombination and repair transactions. To protect the integrity of the genome, DNA ligase 1 (LIG1) discriminates against DNA junctions harboring mutagenic 3'-DNA mismatches or oxidative DNA damage, but how such high-fidelity ligation is enforced is unknown. Here, X-ray structures and kinetic analyses of LIG1 complexes with undamaged and oxidatively damaged DNA unveil that LIG1 employs Mg2+-reinforced DNA binding to validate DNA base pairing during the adenylyl transfer and nick-sealing ligation reaction steps. Our results support a model whereby LIG1 fidelity is governed by a high-fidelity (HiFi) interface between LIG1, Mg2+, and the DNA substrate that tunes the enzyme to release pro-mutagenic DNA nicks. In a second tier of protection, LIG1 activity is surveilled by Aprataxin (APTX), which suppresses mutagenic and abortive ligation at sites of oxidative DNA damage.
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Affiliation(s)
- Percy P Tumbale
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, US National Institutes of Health, Department of Health and Human Services, 111 TW Alexander Drive, Research Triangle Park, NC, 27709, USA
| | - Thomas J Jurkiw
- Biological Chemistry, University of Michigan, 1150 W Medical Center Drive Ann Arbor, Ann Arbor, MI, 48109, USA
| | - Matthew J Schellenberg
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, US National Institutes of Health, Department of Health and Human Services, 111 TW Alexander Drive, Research Triangle Park, NC, 27709, USA
| | - Amanda A Riccio
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, US National Institutes of Health, Department of Health and Human Services, 111 TW Alexander Drive, Research Triangle Park, NC, 27709, USA
| | - Patrick J O'Brien
- Biological Chemistry, University of Michigan, 1150 W Medical Center Drive Ann Arbor, Ann Arbor, MI, 48109, USA.
| | - R Scott Williams
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, US National Institutes of Health, Department of Health and Human Services, 111 TW Alexander Drive, Research Triangle Park, NC, 27709, USA.
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