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Malashetty V, Au A, Chavez J, Hanna M, Chu J, Penna J, Cortes P. The DNA binding domain and the C-terminal region of DNA Ligase IV specify its role in V(D)J recombination. PLoS One 2023; 18:e0282236. [PMID: 36827388 PMCID: PMC9956705 DOI: 10.1371/journal.pone.0282236] [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: 10/12/2022] [Accepted: 02/09/2023] [Indexed: 02/26/2023] Open
Abstract
DNA Ligase IV is responsible for the repair of DNA double-strand breaks (DSB), including DSBs that are generated during V(D)J recombination. Like other DNA ligases, Ligase IV contains a catalytic core with three subdomains-the DNA binding (DBD), the nucleotidyltransferase (NTD), and the oligonucleotide/oligosaccharide-fold subdomain (OBD). Ligase IV also has a unique C-terminal region that includes two BRCT domains, a nuclear localization signal sequence and a stretch of amino acid that participate in its interaction with XRCC4. Out of the three mammalian ligases, Ligase IV is the only ligase that participates in and is required for V(D)J recombination. Identification of the minimal domains within DNA Ligase IV that contribute to V(D)J recombination has remained unresolved. The interaction of the Ligase IV DNA binding domain with Artemis, and the interaction of its C-terminal region with XRCC4, suggest that both of these regions that also interact with the Ku70/80 heterodimer are important and might be sufficient for mediating participation of DNA Ligase IV in V(D)J recombination. This hypothesis was investigated by generating chimeric ligase proteins by swapping domains, and testing their ability to rescue V(D)J recombination in Ligase IV-deficient cells. We demonstrate that a fusion protein containing Ligase I NTD and OBDs flanked by DNA Ligase IV DBD and C-terminal region is sufficient to support V(D)J recombination. This chimeric protein, which we named Ligase 37, complemented formation of coding and signal joints. Coding joints generated with Ligase 37 were shorter than those observed with wild type DNA Ligase IV. The shorter length was due to increased nucleotide deletions and decreased nucleotide insertions. Additionally, overexpression of Ligase 37 in a mouse pro-B cell line supported a shift towards shorter coding joints. Our findings demonstrate that the ability of DNA Ligase IV to participate in V(D)J recombination is in large part mediated by its DBD and C-terminal region.
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Affiliation(s)
- Vidyasagar Malashetty
- Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Audrey Au
- Department of Molecular, Cellular and Biomedical Sciences, City University of New York School of Medicine, City College of New York, New York, NY, United States of America
| | - Jose Chavez
- Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Mary Hanna
- Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Jennifer Chu
- Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Jesse Penna
- Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Patricia Cortes
- Department of Molecular, Cellular and Biomedical Sciences, City University of New York School of Medicine, City College of New York, New York, NY, United States of America
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Wang M, Zhang L, Chang W, Zhang Y. The crosstalk between the gut microbiota and tumor immunity: Implications for cancer progression and treatment outcomes. Front Immunol 2023; 13:1096551. [PMID: 36726985 PMCID: PMC9885097 DOI: 10.3389/fimmu.2022.1096551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Accepted: 12/28/2022] [Indexed: 01/18/2023] Open
Abstract
The gastrointestinal tract is inhabited by trillions of commensal microorganisms that constitute the gut microbiota. As a main metabolic organ, the gut microbiota has co-evolved in a symbiotic relationship with its host, contributing to physiological homeostasis. Recent advances have provided mechanistic insights into the dual role of the gut microbiota in cancer pathogenesis. Particularly, compelling evidence indicates that the gut microbiota exerts regulatory effects on the host immune system to fight against cancer development. Some microbiota-derived metabolites have been suggested as potential activators of antitumor immunity. On the contrary, the disequilibrium of intestinal microbial communities, a condition termed dysbiosis, can induce cancer development. The altered gut microbiota reprograms the hostile tumor microenvironment (TME), thus allowing cancer cells to avoid immunosurvelliance. Furthermore, the gut microbiota has been associated with the effects and complications of cancer therapy given its prominent immunoregulatory properties. Therapeutic measures that aim to manipulate the interplay between the gut microbiota and tumor immunity may bring new breakthroughs in cancer treatment. Herein, we provide a comprehensive update on the evidence for the implication of the gut microbiota in immune-oncology and discuss the fundamental mechanisms underlying the influence of intestinal microbial communities on systemic cancer therapy, in order to provide important clues toward improving treatment outcomes in cancer patients.
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Watanabe G, Lieber MR. Dynamics of the Artemis and DNA-PKcs Complex in the Repair of Double-Strand Breaks. J Mol Biol 2022; 434:167858. [PMID: 36270581 PMCID: PMC9940633 DOI: 10.1016/j.jmb.2022.167858] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 10/11/2022] [Accepted: 10/11/2022] [Indexed: 11/05/2022]
Abstract
Pathologic chromosome breaks occur in human dividing cells ∼10 times per day, and physiologic breaks occur in each lymphoid cell many additional times per day. Nonhomologous DNA end joining (NHEJ) is the major pathway for the repair of all of these double-strand breaks (DSBs) during most of the cell cycle. Nearly all broken DNA ends require trimming before they can be suitable for joining by ligation. Artemis is the major nuclease for this purpose. Artemis is tightly regulated by one of the largest protein kinases, which tethers Artemis to its surface. This kinase is called DNA-dependent protein kinase catalytic subunit (or DNA-PKcs) because it is only active when it encounters a broken DNA end. With this activation, DNA-PKcs permits the Artemis catalytic domain to enter a large cavity in the center of DNA-PKcs. Given this remarkably tight supervision of Artemis by DNA-PKcs, it is an appropriate time to ask what we know about the Artemis:DNA-PKcs complex, as we integrate recent structural information with the biochemistry of the complex and how this relates to other NHEJ proteins and to V(D)J recombination in the immune system.
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Affiliation(s)
- Go Watanabe
- Department of Pathology, Department of Biochemistry & Molecular Biology, Department of Molecular Microbiology & Immunology, and Section of Molecular & Computational Biology, USC Norris Comprehensive Cancer Center, University of Southern California Keck School of Medicine, 1441 Eastlake Ave, Rm. 5428, Los Angeles, CA 90089, USA
| | - Michael R Lieber
- Department of Pathology, Department of Biochemistry & Molecular Biology, Department of Molecular Microbiology & Immunology, and Section of Molecular & Computational Biology, USC Norris Comprehensive Cancer Center, University of Southern California Keck School of Medicine, 1441 Eastlake Ave, Rm. 5428, Los Angeles, CA 90089, USA.
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Taylor JA, Hutchinson MA, Gearhart PJ, Maul RW. Antibodies in action: the role of humoral immunity in the fight against atherosclerosis. Immun Ageing 2022; 19:59. [PMID: 36461105 PMCID: PMC9717479 DOI: 10.1186/s12979-022-00316-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 11/21/2022] [Indexed: 12/03/2022]
Abstract
The sequestering of oxidation-modified low-density lipoprotein by macrophages results in the accumulation of fatty deposits within the walls of arteries. Necrosis of these cells causes a release of intercellular epitopes and the activation of the adaptive immune system, which we predict leads to robust autoantibody production. T cells produce cytokines that act in the plaque environment and further stimulate B cell antibody production. B cells in atherosclerosis meanwhile have a mixed role based on subclass. The current model is that B-1 cells produce protective IgM antibodies in response to oxidation-specific epitopes that work to control plaque formation, while follicular B-2 cells produce class-switched antibodies (IgG, IgA, and IgE) which exacerbate the disease. Over the course of this review, we discuss further the validation of these protective antibodies while evaluating the current dogma regarding class-switched antibodies in atherosclerosis. There are several contradictory findings regarding the involvement of class-switched antibodies in the disease. We hypothesize that this is due to antigen-specificity, and not simply isotype, being important, and that a closer evaluation of these antibodies' targets should be conducted. We propose that specific antibodies may have therapeutical potential in preventing and controlling plaque development within a clinical setting.
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Affiliation(s)
- Joshua A. Taylor
- grid.419475.a0000 0000 9372 4913Laboratory of Molecular Biology and Immunology, National Institute on Aging, NIH, Baltimore, MD USA ,grid.21107.350000 0001 2171 9311Graduate Program in Immunology, Johns Hopkins University School of Medicine, Baltimore, MD USA
| | - Mark A. Hutchinson
- grid.419475.a0000 0000 9372 4913Laboratory of Molecular Biology and Immunology, National Institute on Aging, NIH, Baltimore, MD USA
| | - Patricia J. Gearhart
- grid.419475.a0000 0000 9372 4913Laboratory of Molecular Biology and Immunology, National Institute on Aging, NIH, Baltimore, MD USA
| | - Robert W. Maul
- grid.419475.a0000 0000 9372 4913Laboratory of Molecular Biology and Immunology, National Institute on Aging, NIH, Baltimore, MD USA
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Yang X, Saha S, Yang W, Neuman KC, Pommier Y. Structural and biochemical basis for DNA and RNA catalysis by human Topoisomerase 3β. Nat Commun 2022; 13:4656. [PMID: 35945419 PMCID: PMC9363430 DOI: 10.1038/s41467-022-32221-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 07/21/2022] [Indexed: 11/09/2022] Open
Abstract
In metazoans, topoisomerase 3β (TOP3B) regulates R-loop dynamics and mRNA translation, which are critical for genome stability, neurodevelopment and normal aging. As a Type IA topoisomerase, TOP3B acts by general acid-base catalysis to break and rejoin single-stranded DNA. Passage of a second DNA strand through the transient break permits dissipation of hypernegative DNA supercoiling and catenation/knotting. Additionally, hsTOP3B was recently demonstrated as the human RNA topoisomerase, required for normal neurodevelopment and proposed to be a potential anti-viral target upon RNA virus infection. Here we elucidate the biochemical mechanisms of human TOP3B. We delineate the roles of divalent metal ions, and of a conserved Lysine residue (K10) in the differential catalysis of DNA and RNA. We also demonstrate that three regulatory factors fine-tune the catalytic performance of TOP3B: the TOP3B C-terminal tail, its protein partner TDRD3, and the sequence of its DNA/RNA substrates.
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Affiliation(s)
- Xi Yang
- Developmental Therapeutics Branch & Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Sourav Saha
- Developmental Therapeutics Branch & Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Wei Yang
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, MD, 20892, USA
| | - Keir C Neuman
- Laboratory of Single Molecule Biophysics, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Yves Pommier
- Developmental Therapeutics Branch & Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA.
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Structural insights into the evolution of the RAG recombinase. Nat Rev Immunol 2022; 22:353-370. [PMID: 34675378 DOI: 10.1038/s41577-021-00628-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/09/2021] [Indexed: 11/09/2022]
Abstract
Adaptive immunity in jawed vertebrates relies on the assembly of antigen receptor genes by the recombination activating gene 1 (RAG1)-RAG2 (collectively RAG) recombinase in a reaction known as V(D)J recombination. Extensive biochemical and structural evidence indicates that RAG and V(D)J recombination evolved from the components of a RAG-like (RAGL) transposable element through a process known as transposon molecular domestication. This Review describes recent advances in our understanding of the functional and structural transitions that occurred during RAG evolution. We use the structures of RAG and RAGL enzymes to trace the evolutionary adaptations that yielded a RAG recombinase with exquisitely regulated cleavage activity and a multilayered array of mechanisms to suppress transposition. We describe how changes in modes of DNA binding, alterations in the dynamics of protein-DNA complexes, single amino acid mutations and a modular design likely enabled RAG family enzymes to survive and spread in the genomes of eukaryotes. These advances highlight the insight that can be gained from viewing evolution of vertebrate immunity through the lens of comparative genome analyses coupled with structural biology and biochemistry.
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Almeida MV, Vernaz G, Putman AL, Miska EA. Taming transposable elements in vertebrates: from epigenetic silencing to domestication. Trends Genet 2022; 38:529-553. [DOI: 10.1016/j.tig.2022.02.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 02/14/2022] [Accepted: 02/15/2022] [Indexed: 12/20/2022]
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Ye Z, Shi Y, Lees-Miller SP, Tainer JA. Function and Molecular Mechanism of the DNA Damage Response in Immunity and Cancer Immunotherapy. Front Immunol 2021; 12:797880. [PMID: 34970273 PMCID: PMC8712645 DOI: 10.3389/fimmu.2021.797880] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 11/15/2021] [Indexed: 12/21/2022] Open
Abstract
The DNA damage response (DDR) is an organized network of multiple interwoven components evolved to repair damaged DNA and maintain genome fidelity. Conceptually the DDR includes damage sensors, transducer kinases, and effectors to maintain genomic stability and accurate transmission of genetic information. We have recently gained a substantially improved molecular and mechanistic understanding of how DDR components are interconnected to inflammatory and immune responses to stress. DDR shapes both innate and adaptive immune pathways: (i) in the context of innate immunity, DDR components mainly enhance cytosolic DNA sensing and its downstream STimulator of INterferon Genes (STING)-dependent signaling; (ii) in the context of adaptive immunity, the DDR is needed for the assembly and diversification of antigen receptor genes that is requisite for T and B lymphocyte development. Imbalances between DNA damage and repair impair tissue homeostasis and lead to replication and transcription stress, mutation accumulation, and even cell death. These impacts from DDR defects can then drive tumorigenesis, secretion of inflammatory cytokines, and aberrant immune responses. Yet, DDR deficiency or inhibition can also directly enhance innate immune responses. Furthermore, DDR defects plus the higher mutation load in tumor cells synergistically produce primarily tumor-specific neoantigens, which are powerfully targeted in cancer immunotherapy by employing immune checkpoint inhibitors to amplify immune responses. Thus, elucidating DDR-immune response interplay may provide critical connections for harnessing immunomodulatory effects plus targeted inhibition to improve efficacy of radiation and chemotherapies, of immune checkpoint blockade, and of combined therapeutic strategies.
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Affiliation(s)
- Zu Ye
- Department of Molecular and Cellular Oncology, and Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Yin Shi
- Department of Immunology, Zhejiang University School of Medicine, Hangzhou, China
- Division of Pediatrics, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Susan P. Lees-Miller
- Department of Biochemistry and Molecular Biology, Robson DNA Science Centre, Charbonneau Cancer Institute, University of Calgary, Calgary, AB, Canada
| | - John A. Tainer
- Department of Molecular and Cellular Oncology, and Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
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