1
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Kaminski AM, Chiruvella KK, Ramsden DA, Bebenek K, Kunkel TA, Pedersen LC. DNA polymerase λ Loop1 variant yields unexpected gain-of-function capabilities in nonhomologous end-joining. DNA Repair (Amst) 2024; 136:103645. [PMID: 38428373 PMCID: PMC11078337 DOI: 10.1016/j.dnarep.2024.103645] [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: 11/29/2023] [Revised: 01/26/2024] [Accepted: 01/31/2024] [Indexed: 03/03/2024]
Abstract
DNA polymerases lambda (Polλ) and mu (Polμ) are X-Family polymerases that participate in DNA double-strand break (DSB) repair by the nonhomologous end-joining pathway (NHEJ). Both polymerases direct synthesis from one DSB end, using template derived from a second DSB end. In this way, they promote the NHEJ ligation step and minimize the sequence loss normally associated with this pathway. The two polymerases differ in cognate substrate, as Polλ is preferred when synthesis must be primed from a base-paired DSB end, while Polμ is required when synthesis must be primed from an unpaired DSB end. We generated a Polλ variant (PolλKGET) that retained canonical Polλ activity on a paired end-albeit with reduced incorporation fidelity. We recently discovered that the variant had unexpectedly acquired the activity previously unique to Polμ-synthesis from an unpaired primer terminus. Though the sidechains of the Loop1 region make no contact with the DNA substrate, PolλKGET Loop1 amino acid sequence is surprisingly essential for its unique activity during NHEJ. Taken together, these results underscore that the Loop1 region plays distinct roles in different Family X polymerases.
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Affiliation(s)
- Andrea M Kaminski
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, 111 TW Alexander Dr., Bldg 101, Research Triangle Park, NC 27709, USA
| | - Kishore K Chiruvella
- Department of Biochemistry and Biophysics, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Dale A Ramsden
- Department of Biochemistry and Biophysics, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Katarzyna Bebenek
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, 111 TW Alexander Dr., Bldg 101, Research Triangle Park, NC 27709, USA
| | - Thomas A Kunkel
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, 111 TW Alexander Dr., Bldg 101, Research Triangle Park, NC 27709, USA
| | - Lars C Pedersen
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, 111 TW Alexander Dr., Bldg 101, Research Triangle Park, NC 27709, USA.
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2
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Jamaleddine H, Rogers D, Perreault G, Postat J, Patel D, Mandl JN, Khadra A. Chronic infection control relies on T cells with lower foreign antigen binding strength generated by N-nucleotide diversity. PLoS Biol 2024; 22:e3002465. [PMID: 38300945 PMCID: PMC10833529 DOI: 10.1371/journal.pbio.3002465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 12/08/2023] [Indexed: 02/03/2024] Open
Abstract
The breadth of pathogens to which T cells can respond is determined by the T cell receptors (TCRs) present in an individual's repertoire. Although more than 90% of the sequence diversity among TCRs is generated by terminal deoxynucleotidyl transferase (TdT)-mediated N-nucleotide addition during V(D)J recombination, the benefit of TdT-altered TCRs remains unclear. Here, we computationally and experimentally investigated whether TCRs with higher N-nucleotide diversity via TdT make distinct contributions to acute or chronic pathogen control specifically through the inclusion of TCRs with lower antigen binding strengths (i.e., lower reactivity to peptide-major histocompatibility complex (pMHC)). When T cells with high pMHC reactivity have a greater propensity to become functionally exhausted than those of low pMHC reactivity, our computational model predicts a shift toward T cells with low pMHC reactivity over time during chronic, but not acute, infections. This TCR-affinity shift is critical, as the elimination of T cells with lower pMHC reactivity in silico substantially increased the time to clear a chronic infection, while acute infection control remained largely unchanged. Corroborating an affinity-centric benefit for TCR diversification via TdT, we found evidence that TdT-deficient TCR repertoires possess fewer T cells with weaker pMHC binding strengths in vivo and showed that TdT-deficient mice infected with a chronic, but not an acute, viral pathogen led to protracted viral clearance. In contrast, in the case of a chronic fungal pathogen where T cells fail to clear the infection, both our computational model and experimental data showed that TdT-diversified TCR repertoires conferred no additional protection to the hosts. Taken together, our in silico and in vivo data suggest that TdT-mediated TCR diversity is of particular benefit for the eventual resolution of prolonged pathogen replication through the inclusion of TCRs with lower foreign antigen binding strengths.
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Affiliation(s)
| | - Dakota Rogers
- Department of Physiology, McGill University, Montreal, Quebec, Canada
- McGill University Research Centre on Complex Traits, Montreal, Quebec, Canada
| | - Geneviève Perreault
- McGill University Research Centre on Complex Traits, Montreal, Quebec, Canada
| | - Jérémy Postat
- Department of Physiology, McGill University, Montreal, Quebec, Canada
- McGill University Research Centre on Complex Traits, Montreal, Quebec, Canada
| | - Dhanesh Patel
- Department of Physiology, McGill University, Montreal, Quebec, Canada
- McGill University Research Centre on Complex Traits, Montreal, Quebec, Canada
| | - Judith N. Mandl
- Department of Physiology, McGill University, Montreal, Quebec, Canada
- McGill University Research Centre on Complex Traits, Montreal, Quebec, Canada
- Department of Microbiology and Immunology, McGill University, Montreal, Quebec, Canada
| | - Anmar Khadra
- Department of Physiology, McGill University, Montreal, Quebec, Canada
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3
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Textor J, Buytenhuijs F, Rogers D, Gauthier ÈM, Sultan S, Wortel IMN, Kalies K, Fähnrich A, Pagel R, Melichar HJ, Westermann J, Mandl JN. Machine learning analysis of the T cell receptor repertoire identifies sequence features of self-reactivity. Cell Syst 2023; 14:1059-1073.e5. [PMID: 38061355 DOI: 10.1016/j.cels.2023.11.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Revised: 09/01/2023] [Accepted: 11/09/2023] [Indexed: 12/23/2023]
Abstract
The T cell receptor (TCR) determines specificity and affinity for both foreign and self-peptides presented by the major histocompatibility complex (MHC). Although the strength of TCR interactions with self-pMHC impacts T cell function, it has been challenging to identify TCR sequence features that predict T cell fate. To discern patterns distinguishing TCRs from naive CD4+ T cells with low versus high self-reactivity, we used data from 42 mice to train a machine learning (ML) algorithm that identifies population-level differences between TCRβ sequence sets. This approach revealed that weakly self-reactive T cell populations were enriched for longer CDR3β regions and acidic amino acids. We tested our ML predictions of self-reactivity using retrogenic mice with fixed TCRβ sequences. Extrapolating our analyses to independent datasets, we predicted high self-reactivity for regulatory T cells and slightly reduced self-reactivity for T cells responding to chronic infections. Our analyses suggest a potential trade-off between TCR repertoire diversity and self-reactivity. A record of this paper's transparent peer review process is included in the supplemental information.
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Affiliation(s)
- Johannes Textor
- Data Science Group, Institute for Computing and Information Sciences, Radboud University, Nijmegen 6525 EC, the Netherlands; Medical BioSciences, Radboudumc, Nijmegen 6525 GA, the Netherlands.
| | - Franka Buytenhuijs
- Data Science Group, Institute for Computing and Information Sciences, Radboud University, Nijmegen 6525 EC, the Netherlands
| | - Dakota Rogers
- Department of Physiology, McGill University, Montreal, QC H3G 0B1, Canada; McGill Research Centre on Complex Traits, McGill University, Montreal, QC H3G 0B1, Canada
| | - Ève Mallet Gauthier
- Immunology-Oncology Unit, Maisonneuve-Rosemont Hospital Research Center, Montreal, QC H1T 2M4, Canada; Department of Microbiology, Infectious Diseases, and Immunology, Université de Montréal, Montréal, QC H3T 1J4, Canada
| | - Shabaz Sultan
- Data Science Group, Institute for Computing and Information Sciences, Radboud University, Nijmegen 6525 EC, the Netherlands; Medical BioSciences, Radboudumc, Nijmegen 6525 GA, the Netherlands
| | - Inge M N Wortel
- Data Science Group, Institute for Computing and Information Sciences, Radboud University, Nijmegen 6525 EC, the Netherlands; Medical BioSciences, Radboudumc, Nijmegen 6525 GA, the Netherlands
| | - Kathrin Kalies
- Institut für Anatomie, Universität zu Lübeck, 23562 Lübeck, Germany
| | - Anke Fähnrich
- Institut für Anatomie, Universität zu Lübeck, 23562 Lübeck, Germany
| | - René Pagel
- Institut für Anatomie, Universität zu Lübeck, 23562 Lübeck, Germany
| | - Heather J Melichar
- Immunology-Oncology Unit, Maisonneuve-Rosemont Hospital Research Center, Montreal, QC H1T 2M4, Canada; Department of Medicine, Université de Montréal, Montréal, QC H1T 2M4, Canada; Department of Microbiology & Immunology, McGill University, Montreal, QC H3A 1A3, Canada; Rosalind and Morris Goodman Cancer Institute, McGill University, Montreal, QC H3A 1A3, Canada
| | | | - Judith N Mandl
- Department of Physiology, McGill University, Montreal, QC H3G 0B1, Canada; Department of Microbiology & Immunology, McGill University, Montreal, QC H3A 1A3, Canada; McGill Research Centre on Complex Traits, McGill University, Montreal, QC H3G 0B1, Canada.
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4
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Del Pozo-Yauner L, Herrera GA, Perez Carreon JI, Turbat-Herrera EA, Rodriguez-Alvarez FJ, Ruiz Zamora RA. Role of the mechanisms for antibody repertoire diversification in monoclonal light chain deposition disorders: when a friend becomes foe. Front Immunol 2023; 14:1203425. [PMID: 37520549 PMCID: PMC10374031 DOI: 10.3389/fimmu.2023.1203425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 06/20/2023] [Indexed: 08/01/2023] Open
Abstract
The adaptive immune system of jawed vertebrates generates a highly diverse repertoire of antibodies to meet the antigenic challenges of a constantly evolving biological ecosystem. Most of the diversity is generated by two mechanisms: V(D)J gene recombination and somatic hypermutation (SHM). SHM introduces changes in the variable domain of antibodies, mostly in the regions that form the paratope, yielding antibodies with higher antigen binding affinity. However, antigen recognition is only possible if the antibody folds into a stable functional conformation. Therefore, a key force determining the survival of B cell clones undergoing somatic hypermutation is the ability of the mutated heavy and light chains to efficiently fold and assemble into a functional antibody. The antibody is the structural context where the selection of the somatic mutations occurs, and where both the heavy and light chains benefit from protective mechanisms that counteract the potentially deleterious impact of the changes. However, in patients with monoclonal gammopathies, the proliferating plasma cell clone may overproduce the light chain, which is then secreted into the bloodstream. This places the light chain out of the protective context provided by the quaternary structure of the antibody, increasing the risk of misfolding and aggregation due to destabilizing somatic mutations. Light chain-derived (AL) amyloidosis, light chain deposition disease (LCDD), Fanconi syndrome, and myeloma (cast) nephropathy are a diverse group of diseases derived from the pathologic aggregation of light chains, in which somatic mutations are recognized to play a role. In this review, we address the mechanisms by which somatic mutations promote the misfolding and pathological aggregation of the light chains, with an emphasis on AL amyloidosis. We also analyze the contribution of the variable domain (VL) gene segments and somatic mutations on light chain cytotoxicity, organ tropism, and structure of the AL fibrils. Finally, we analyze the most recent advances in the development of computational algorithms to predict the role of somatic mutations in the cardiotoxicity of amyloidogenic light chains and discuss the challenges and perspectives that this approach faces.
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Affiliation(s)
- Luis Del Pozo-Yauner
- Department of Pathology, University of South Alabama-College of Medicine, Mobile, AL, United States
| | - Guillermo A. Herrera
- Department of Pathology, University of South Alabama-College of Medicine, Mobile, AL, United States
| | | | - Elba A. Turbat-Herrera
- Department of Pathology, University of South Alabama-College of Medicine, Mobile, AL, United States
- Mitchell Cancer Institute, University of South Alabama-College of Medicine, Mobile, AL, United States
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5
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Xiao H, Wang S, Tang Y, Li S, Jiang Y, Yang Y, Zhang Y, Han Y, Wu X, Zheng L, Li Y, Gao Y. Absence of terminal deoxynucleotidyl transferase expression in T-ALL/LBL accumulates chromosomal abnormalities to induce drug resistance. Int J Cancer 2023; 152:2383-2395. [PMID: 36757202 DOI: 10.1002/ijc.34465] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Revised: 01/21/2023] [Accepted: 01/30/2023] [Indexed: 02/10/2023]
Abstract
T-acute lymphoblastic leukemia/lymphoma (T-ALL/LBL) is a malignant neoplasm of immature lymphoblasts. Terminal deoxynucleotidyl transferase (TDT) is a template-independent DNA polymerase that plays an essential role in generating diversity for immunoglobulin genes. T-ALL/LBL patients with TDT- have a worse prognosis. However, how TDT- promotes the disease progression of T-ALL/LBL remains unknown. Here we analyzed the prognosis of T-ALL/LBL patients in Shanghai Children's Medical Center (SCMC) and confirmed that TDT- patients had a higher rate of recurrence and remission failure and worse outcomes. Cellular experiments demonstrated that TDT was involved in DNA damage repair. TDT knockout delayed DNA repair, arrested the cell cycle and decreased apoptosis to induce the accumulation of chromosomal abnormalities and tolerance to abnormal karyotypes. Our study demonstrated that the poor outcomes in TDT- T-ALL/LBL might be due to the drug resistance (VP16 and MTX) induced by chromosomal abnormalities. Our findings revealed novel functions and mechanisms of TDT in T-ALL/LBL and supported that hematopoietic stem cell transplantation (HSCT) might be a better choice for these patients.
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Affiliation(s)
- Hui Xiao
- Department of Hematology & Oncology, Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, National Health Committee Key Laboratory of Pediatric Hematology & Oncology, Shanghai, China
| | - Siqi Wang
- Department of Hematology & Oncology, Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, National Health Committee Key Laboratory of Pediatric Hematology & Oncology, Shanghai, China
| | - Yuejia Tang
- Department of Hematology & Oncology, Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, National Health Committee Key Laboratory of Pediatric Hematology & Oncology, Shanghai, China
| | - Shanshan Li
- Department of Hematology & Oncology, Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, National Health Committee Key Laboratory of Pediatric Hematology & Oncology, Shanghai, China
| | - Yufeng Jiang
- Department of Hematology & Oncology, Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, National Health Committee Key Laboratory of Pediatric Hematology & Oncology, Shanghai, China
| | - Yi Yang
- Department of Hematology & Oncology, Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, National Health Committee Key Laboratory of Pediatric Hematology & Oncology, Shanghai, China
| | - Yinwen Zhang
- Department of Hematology & Oncology, Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, National Health Committee Key Laboratory of Pediatric Hematology & Oncology, Shanghai, China
| | - Yali Han
- Department of Hematology & Oncology, Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, National Health Committee Key Laboratory of Pediatric Hematology & Oncology, Shanghai, China
| | - Xiaoyu Wu
- Department of Hematology & Oncology, Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, National Health Committee Key Laboratory of Pediatric Hematology & Oncology, Shanghai, China
| | - Liang Zheng
- Department of Hematology & Oncology, Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, National Health Committee Key Laboratory of Pediatric Hematology & Oncology, Shanghai, China
| | - Yanxin Li
- Department of Hematology & Oncology, Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, National Health Committee Key Laboratory of Pediatric Hematology & Oncology, Shanghai, China
| | - Yijin Gao
- Department of Hematology & Oncology, Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, National Health Committee Key Laboratory of Pediatric Hematology & Oncology, Shanghai, China
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6
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Kaminski AM, Chiruvella KK, Ramsden DA, Bebenek K, Kunkel TA, Pedersen LC. Analysis of diverse double-strand break synapsis with Polλ reveals basis for unique substrate specificity in nonhomologous end-joining. Nat Commun 2022; 13:3806. [PMID: 35778389 PMCID: PMC9249759 DOI: 10.1038/s41467-022-31278-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 06/10/2022] [Indexed: 01/02/2023] Open
Abstract
DNA double-strand breaks (DSBs) threaten genomic stability, since their persistence can lead to loss of critical genetic information, chromosomal translocations or rearrangements, and cell death. DSBs can be repaired through the nonhomologous end-joining pathway (NHEJ), which processes and ligates DNA ends efficiently to prevent or minimize sequence loss. Polymerase λ (Polλ), one of the Family X polymerases, fills sequence gaps of DSB substrates with a strict specificity for a base-paired primer terminus. There is little information regarding Polλ's approach to engaging such substrates. We used in vitro polymerization and cell-based NHEJ assays to explore the contributions of conserved loop regions toward DSB substrate specificity and utilization. In addition, we present multiple crystal structures of Polλ in synapsis with varying biologically relevant DSB end configurations, revealing how key structural features and hydrogen bonding networks work in concert to stabilize these tenuous, potentially cytotoxic DNA lesions during NHEJ.
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Affiliation(s)
- Andrea M Kaminski
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, 111 TW Alexander Dr., Bldg. 101, Research Triangle Park, NC, 27709, USA
| | - Kishore K Chiruvella
- Department of Biochemistry and Biophysics, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Dale A Ramsden
- Department of Biochemistry and Biophysics, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Katarzyna Bebenek
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, 111 TW Alexander Dr., Bldg. 101, Research Triangle Park, NC, 27709, USA.
| | - Thomas A Kunkel
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, 111 TW Alexander Dr., Bldg. 101, Research Triangle Park, NC, 27709, USA
| | - Lars C Pedersen
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, 111 TW Alexander Dr., Bldg. 101, Research Triangle Park, NC, 27709, USA
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7
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Stutz R, Meyer C, Kaiser E, Goedicke-Fritz S, Schroeder HW, Bals R, Haertel C, Rogosch T, Kerzel S, Zemlin M. Attenuated asthma phenotype in mice with a fetal-like antigen receptor repertoire. Sci Rep 2021; 11:14199. [PMID: 34244568 PMCID: PMC8270943 DOI: 10.1038/s41598-021-93553-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 06/21/2021] [Indexed: 11/09/2022] Open
Abstract
We hypothesized that the scarcity of N-nucleotides might contribute to the inability of the neonate to mount a robust allergic immune response. To test this, we used terminal deoxyribunucleotidyl Transferase deficient (TdT-/-) mice, which express "fetal-like" T cell receptor and immunoglobulin repertoires with largely germline-encoded CDR3 regions. Intraperitoneal sensitization was followed by aerosol provocation with either PBS or the allergen OVA in both TdT-/- mice and wild-type mice to develop allergic respiratory inflammation. The effects of this procedure were investigated by lung function test, immunological analysis of serum and brochoalveolar lavage. The local TH2 cytokine milieu was significantly attenuated in TdT-/- mice. Within this group, the induction of total IgE levels was also significantly reduced after sensitization. TdT-/- mice showed a tendency toward reduced eosinophilic inflow into the bronchial tubes, which was associated with the elimination of respiratory hyperreactivity. In conclusion, in a murine model of allergic airway inflammation, the expression of fetal-like antigen receptors was associated with potent indications of a reduced ability to mount an asthma phenotype. This underlines the importance of somatically-generated antigen-receptor repertoire diversity in type one allergic immune responses and suggests that the fetus may be protected from allergic responses, at least in part, by controlling N addition.
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Affiliation(s)
- Regine Stutz
- Department of General Pediatrics and Neonatology, Saarland University Medical School, Homburg, Germany
| | - Christopher Meyer
- Department of General Pediatrics and Neonatology, Saarland University Medical School, Homburg, Germany
| | - Elisabeth Kaiser
- Department of General Pediatrics and Neonatology, Saarland University Medical School, Homburg, Germany
| | - Sybelle Goedicke-Fritz
- Department of General Pediatrics and Neonatology, Saarland University Medical School, Homburg, Germany.,Department of Pediatrics, Philipps-University Marburg, Marburg, Germany
| | - Harry W Schroeder
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Robert Bals
- Department of Internal Medicine V-Pulmonology, Allergology and Critical Care Medicine, Saarland University, Saarland University Medical School, Homburg, Germany
| | - Christoph Haertel
- Department of Pediatrics, Würzburg University Medical Center, Würzburg, Germany
| | - Tobias Rogosch
- Department of Pediatrics, Philipps-University Marburg, Marburg, Germany
| | - Sebastian Kerzel
- Department of Pediatrics, Philipps-University Marburg, Marburg, Germany.,Department of Pediatric Pneumology and Allergy, University Children's Hospital Regensburg, Campus St. Hedwig, Regensburg, Germany
| | - Michael Zemlin
- Department of General Pediatrics and Neonatology, Saarland University Medical School, Homburg, Germany. .,Department of Pediatrics, Philipps-University Marburg, Marburg, Germany.
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8
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Kaminski AM, Pryor JM, Ramsden DA, Kunkel TA, Pedersen LC, Bebenek K. Structural snapshots of human DNA polymerase μ engaged on a DNA double-strand break. Nat Commun 2020; 11:4784. [PMID: 32963245 PMCID: PMC7508851 DOI: 10.1038/s41467-020-18506-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 08/17/2020] [Indexed: 01/07/2023] Open
Abstract
Genomic integrity is threatened by cytotoxic DNA double-strand breaks (DSBs), which must be resolved efficiently to prevent sequence loss, chromosomal rearrangements/translocations, or cell death. Polymerase μ (Polμ) participates in DSB repair via the nonhomologous end-joining (NHEJ) pathway, by filling small sequence gaps in broken ends to create substrates ultimately ligatable by DNA Ligase IV. Here we present structures of human Polμ engaging a DSB substrate. Synapsis is mediated solely by Polμ, facilitated by single-nucleotide homology at the break site, wherein both ends of the discontinuous template strand are stabilized by a hydrogen bonding network. The active site in the quaternary Pol μ complex is poised for catalysis and nucleotide incoporation proceeds in crystallo. These structures demonstrate that Polμ may address complementary DSB substrates during NHEJ in a manner indistinguishable from single-strand breaks.
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Affiliation(s)
- Andrea M. Kaminski
- grid.94365.3d0000 0001 2297 5165Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, 111 TW Alexander Dr., Bldg. 101/Rm F338, Research Triangle Park, NC 27709 USA
| | - John M. Pryor
- grid.10698.360000000122483208Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, 32-046 Lineberger Comprehensive Cancer Center, 450 West Dr., CB 7295, Chapel Hill, NC 27599 USA
| | - Dale A. Ramsden
- grid.10698.360000000122483208Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, 32-046 Lineberger Comprehensive Cancer Center, 450 West Dr., CB 7295, Chapel Hill, NC 27599 USA
| | - Thomas A. Kunkel
- grid.94365.3d0000 0001 2297 5165Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, 111 TW Alexander Dr., Bldg. 101/Rm F338, Research Triangle Park, NC 27709 USA
| | - Lars C. Pedersen
- grid.94365.3d0000 0001 2297 5165Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, 111 TW Alexander Dr., Bldg. 101/Rm F338, Research Triangle Park, NC 27709 USA
| | - Katarzyna Bebenek
- grid.94365.3d0000 0001 2297 5165Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, 111 TW Alexander Dr., Bldg. 101/Rm F338, Research Triangle Park, NC 27709 USA
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9
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Abstract
Neonatal CD4+ and CD8+ T cells have historically been characterized as immature or defective. However, recent studies prompt a reinterpretation of the functions of neonatal T cells. Rather than a population of cells always falling short of expectations set by their adult counterparts, neonatal T cells are gaining recognition as a distinct population of lymphocytes well suited for the rapidly changing environment in early life. In this review, I will highlight new evidence indicating that neonatal T cells are not inert or less potent versions of adult T cells but instead are a broadly reactive layer of T cells poised to quickly develop into regulatory or effector cells, depending on the needs of the host. In this way, neonatal T cells are well adapted to provide fast-acting immune protection against foreign pathogens, while also sustaining tolerance to self-antigens.
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Affiliation(s)
- Brian D Rudd
- Department of Microbiology and Immunology, Cornell University, Ithaca, New York 14853, USA;
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10
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Carneiro-Sampaio M, Moreira-Filho CA, Bando SY, Demengeot J, Coutinho A. Intrauterine IPEX. Front Pediatr 2020; 8:599283. [PMID: 33330291 PMCID: PMC7714920 DOI: 10.3389/fped.2020.599283] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 10/26/2020] [Indexed: 01/18/2023] Open
Abstract
IPEX is one of the few Inborn Errors of Immunity that may manifest in the fetal period, and its intrauterine forms certainly represent the earliest human autoimmune diseases. Here, we review the clinical, histopathologic, and genetic findings from 21 individuals in 11 unrelated families, with nine different mutations, described as cases of intrauterine IPEX. Recurrent male fetal death (multigenerational in five families) due to hydrops in the midsemester of pregnancy was the commonest presentation (13/21). Noteworthy, in the affected families, there were only fetal- or perinatal-onset cases, with no affected individuals presenting milder forms with later-life manifestation. Most alive births were preterm (5/6). Skin desquamation and intrauterine growth restriction were observed in part of the cases. Fetal ultrasonography showed hyperechoic bowel or dilated bowel loops in the five cases with available imaging data. Histopathology showed multi-visceral infiltrates with T lymphocytes and other cells, including eosinophils, the pancreas being affected in most of the cases (11/21) and as early as at 18 weeks of gestational age. Regarding the nine FOXP3 mutations found in these cases, six determine protein truncation and three predictably impair protein function. Having found distinct presentations for the same FOXP3 mutation in different families, we resorted to the mouse system and showed that the scurfy mutation also shows divergent severity of phenotype and age of death in C57BL/6 and BALB/c backgrounds. We also reviewed age-of-onset data from other monogenic Tregopathies leading to IPEX-like phenotypes. In monogenic IPEX-like syndromes, the intrauterine onset was only observed in two kindreds with IL2RB mutations, with two stillbirths and two premature neonates who did not survive. In conclusion, intrauterine IPEX cases seem to constitute a particular IPEX subgroup, certainly with the most severe clinical presentation, although no strict mutation-phenotype correlations could be drawn for these cases.
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Affiliation(s)
- Magda Carneiro-Sampaio
- Laboratory of Medical Investigation (LIM-36, HCFMUSP), Department of Pediatrics, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Carlos Alberto Moreira-Filho
- Laboratory of Medical Investigation (LIM-36, HCFMUSP), Department of Pediatrics, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Silvia Yumi Bando
- Laboratory of Medical Investigation (LIM-36, HCFMUSP), Department of Pediatrics, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
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11
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Green MR, Sambrook J. Rapid Amplification of Sequences from the 5' Ends of mRNAs: 5'-RACE. Cold Spring Harb Protoc 2019; 2019:2019/5/pdb.prot095208. [PMID: 31043556 DOI: 10.1101/pdb.prot095208] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Isolating a full-length clone of cDNA provides certainty that the entire protein-coding sequence of the mRNA has been identified and allows the 5' end of the mRNA to be precisely mapped onto the genomic DNA sequence. Unfortunately, partial clones that lack sequences corresponding to the 5' end of the target mRNA occur commonly in cDNA libraries. Rapid amplification of cDNA ends (RACE) provides a means to overcome this obstacle by amplifying the 5'-terminal sequences of cDNA. This technique differs from conventional polymerase chain reaction in that it only requires knowledge of a small region of sequence within either the target RNA or in a partial clone of cDNA. In the first step of 5'-RACE, extension of the primer by reverse transcriptase yields single-stranded cDNAs complementary to the 5' regions of the mRNA. In the second step, a homopolymeric tail or a primer-adaptor is added to the 3' ends of the cDNAs. This generates a primer-binding site upstream of the unknown 5'-sequence of the target mRNA. Finally, synthesis of the second cDNA strand and amplification of the resulting double-stranded cDNAs is performed using the gene-specific primer and the upstream primer. The double-stranded products of the final stage are purified and cloned into a vector for sequencing analysis and subsequent manipulation.
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12
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Transcriptome analysis of immune genes in peripheral blood mononuclear cells of young foals and adult horses. PLoS One 2018; 13:e0202646. [PMID: 30183726 PMCID: PMC6124769 DOI: 10.1371/journal.pone.0202646] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 08/07/2018] [Indexed: 12/14/2022] Open
Abstract
During the neonatal period, the ability to generate immune effector and memory responses to vaccines or pathogens is often questioned. This study was undertaken to obtain a global view of the natural differences in the expression of immune genes early in life. Our hypothesis was that transcriptome analyses of peripheral blood mononuclear cells (PBMCs) of foals (on day 1 and day 42 after birth) and adult horses would show differential gene expression profiles that characterize natural immune processes. Gene ontology enrichment analysis provided assessment of biological processes affected by age, and a list of 897 genes with ≥2 fold higher (p<0.01) expression in day 42 when compared to day 1 foal samples. Up-regulated genes included B cell and T cell receptor diversity genes; DNA replication enzymes; natural killer cell receptors; granzyme B and perforin; complement receptors; immunomodulatory receptors; cell adhesion molecules; and cytokines/chemokines and their receptors. The list of 1,383 genes that had higher (p<0.01) expression on day 1 when compared to day 42 foal samples was populated by genes with roles in innate immunity such as antimicrobial proteins; pathogen recognition receptors; cytokines/chemokines and their receptors; cell adhesion molecules; co-stimulatory molecules; and T cell receptor delta chain. Within the 742 genes with increased expression between day 42 foal and adult samples, B cell immunity was the main biological process (p = 2.4E-04). Novel data on markedly low (p<0.0001) TLR3 gene expression, and high (p≤0.01) expression of IL27, IL13RA1, IREM-1, SIRL-1, and SIRPα on day 1 compared to day 42 foal samples point out potential mechanisms of increased susceptibility to pathogens in early life. The results portray a progression from innate immune gene expression predominance early in life to adaptive immune gene expression increasing with age with a putative overlay of immune suppressing genes in the neonatal phase. These results provide insight to the unique attributes of the equine neonatal and young immune system, and offer many avenues of future investigation.
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13
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Fontaine M, Vogel I, Van Eycke YR, Galuppo A, Ajouaou Y, Decaestecker C, Kassiotis G, Moser M, Leo O. Regulatory T cells constrain the TCR repertoire of antigen-stimulated conventional CD4 T cells. EMBO J 2018; 37:398-412. [PMID: 29263148 PMCID: PMC5793804 DOI: 10.15252/embj.201796881] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Revised: 11/17/2017] [Accepted: 11/27/2017] [Indexed: 01/22/2023] Open
Abstract
To analyze the potential role of Tregs in controlling the TCR repertoire breadth to a non-self-antigen, a TCRβ transgenic mouse model (EF4.1) expressing a limited, yet polyclonal naïve T-cell repertoire was used. The response of EF4.1 mice to an I-Ab-associated epitope of the F-MuLV envelope protein is dominated by clones expressing a Vα2 gene segment, thus allowing a comprehensive analysis of the TCRα repertoire in a relatively large cohort of mice. Control and Treg-depleted EF4.1 mice were immunized, and the extent of the Vα2-bearing, antigen-specific TCR repertoire was characterized by high-throughput sequencing and spectratyping analysis. In addition to increased clonal expansion and acquisition of effector functions, Treg depletion led to the expression of a more diverse TCR repertoire comprising several private clonotypes rarely observed in control mice or in the pre-immune repertoire. Injection of anti-CD86 antibodies in vivo led to a strong reduction in TCR diversity, suggesting that Tregs may influence TCR repertoire diversity by modulating costimulatory molecule availability. Collectively, these studies illustrate an additional mechanism whereby Tregs control the immune response to non-self-antigens.
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MESH Headings
- Animals
- Antibodies, Viral/immunology
- B7-2 Antigen/immunology
- Cells, Cultured
- Friend murine leukemia virus/immunology
- Lymphocyte Depletion
- Mice
- Mice, Inbred C57BL
- Mice, Transgenic
- Receptors, Antigen, T-Cell, alpha-beta/genetics
- Receptors, Antigen, T-Cell, alpha-beta/immunology
- T-Lymphocytes, Regulatory/immunology
- Viral Envelope Proteins/immunology
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Affiliation(s)
- Martina Fontaine
- Laboratoire d'Immunobiologie, Université Libre de Bruxelles (ULB), Gosselies, Belgium
| | - Isabel Vogel
- Laboratoire d'Immunobiologie, Université Libre de Bruxelles (ULB), Gosselies, Belgium
| | - Yves-Rémi Van Eycke
- DIAPath, Center for Microscopy and Molecular Imaging, Université Libre de Bruxelles (ULB), Gosselies, Belgium
- Laboratories of Image, Signal processing & Acoustics Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Adrien Galuppo
- Laboratoire d'Immunobiologie, Université Libre de Bruxelles (ULB), Gosselies, Belgium
| | - Yousra Ajouaou
- Laboratoire d'Immunobiologie, Université Libre de Bruxelles (ULB), Gosselies, Belgium
| | - Christine Decaestecker
- DIAPath, Center for Microscopy and Molecular Imaging, Université Libre de Bruxelles (ULB), Gosselies, Belgium
- Laboratories of Image, Signal processing & Acoustics Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - George Kassiotis
- Retroviral Immunology, The Francis Crick Institute, London, UK
- Department of Medicine Faculty of Medicine, Imperial College London London, UK
| | - Muriel Moser
- Laboratoire d'Immunobiologie, Université Libre de Bruxelles (ULB), Gosselies, Belgium
| | - Oberdan Leo
- Laboratoire d'Immunobiologie, Université Libre de Bruxelles (ULB), Gosselies, Belgium
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14
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Chen X, Poncette L, Blankenstein T. Human TCR-MHC coevolution after divergence from mice includes increased nontemplate-encoded CDR3 diversity. J Exp Med 2017; 214:3417-3433. [PMID: 28835417 PMCID: PMC5679170 DOI: 10.1084/jem.20161784] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Revised: 06/19/2017] [Accepted: 07/19/2017] [Indexed: 12/14/2022] Open
Abstract
Chen et al. demonstrate that human MHC selects a larger human TCR repertoire than mouse MHC. They show how humans optimized TCR diversity and suggest that CDR3 length adjusts for different V segment–MHC affinity. For thymic selection and responses to pathogens, T cells interact through their αβ T cell receptor (TCR) with peptide–major histocompatibility complex (MHC) molecules on antigen-presenting cells. How the diverse TCRs interact with a multitude of MHC molecules is unresolved. It is also unclear how humans generate larger TCR repertoires than mice do. We compared the TCR repertoire of CD4 T cells selected from a single mouse or human MHC class II (MHC II) in mice containing the human TCR gene loci. Human MHC II yielded greater thymic output and a more diverse TCR repertoire. The complementarity determining region 3 (CDR3) length adjusted for different inherent V-segment affinities to MHC II. Humans evolved with greater nontemplate-encoded CDR3 diversity than did mice. Our data, which demonstrate human TCR–MHC coevolution after divergence from rodents, explain the greater T cell diversity in humans and suggest a mechanism for ensuring that any V–J gene combination can be selected by a single MHC II.
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Affiliation(s)
- Xiaojing Chen
- Max-Delbrück-Center for Molecular Medicine, Berlin, Germany.,Charité Campus Buch, Institute of Immunology, Berlin, Germany
| | - Lucia Poncette
- Max-Delbrück-Center for Molecular Medicine, Berlin, Germany
| | - Thomas Blankenstein
- Max-Delbrück-Center for Molecular Medicine, Berlin, Germany .,Charité Campus Buch, Institute of Immunology, Berlin, Germany.,Berlin Institute of Health, Berlin, Germany
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15
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Jamsen JA, Beard WA, Pedersen LC, Shock DD, Moon AF, Krahn JM, Bebenek K, Kunkel TA, Wilson SH. Time-lapse crystallography snapshots of a double-strand break repair polymerase in action. Nat Commun 2017; 8:253. [PMID: 28811466 PMCID: PMC5557891 DOI: 10.1038/s41467-017-00271-7] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Accepted: 06/15/2017] [Indexed: 11/08/2022] Open
Abstract
DNA polymerase (pol) μ is a DNA-dependent polymerase that incorporates nucleotides during gap-filling synthesis in the non-homologous end-joining pathway of double-strand break repair. Here we report time-lapse X-ray crystallography snapshots of catalytic events during gap-filling DNA synthesis by pol μ. Unique catalytic intermediates and active site conformational changes that underlie catalysis are uncovered, and a transient third (product) metal ion is observed in the product state. The product manganese coordinates phosphate oxygens of the inserted nucleotide and PPi. The product metal is not observed during DNA synthesis in the presence of magnesium. Kinetic analyses indicate that manganese increases the rate constant for deoxynucleoside 5'-triphosphate insertion compared to magnesium. The likely product stabilization role of the manganese product metal in pol μ is discussed. These observations provide insight on structural attributes of this X-family double-strand break repair polymerase that impact its biological function in genome maintenance.DNA polymerase (pol) μ functions in DNA double-strand break repair. Here the authors use time-lapse X-ray crystallography to capture the states of pol µ during the conversion from pre-catalytic to product complex and observe a third transiently bound metal ion in the product state.
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Affiliation(s)
- Joonas A Jamsen
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, 27709, USA
| | - William A Beard
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, 27709, USA
| | - Lars C Pedersen
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, 27709, USA
| | - David D Shock
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, 27709, USA
| | - Andrea F Moon
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, 27709, USA
| | - Juno M Krahn
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, 27709, USA
| | - Katarzyna Bebenek
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, 27709, USA
| | - Thomas A Kunkel
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, 27709, USA
| | - Samuel H Wilson
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, 27709, USA.
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16
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Müller V, de Boer RJ, Bonhoeffer S, Szathmáry E. An evolutionary perspective on the systems of adaptive immunity. Biol Rev Camb Philos Soc 2017; 93:505-528. [PMID: 28745003 DOI: 10.1111/brv.12355] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Revised: 06/28/2017] [Accepted: 06/30/2017] [Indexed: 12/22/2022]
Abstract
We propose an evolutionary perspective to classify and characterize the diverse systems of adaptive immunity that have been discovered across all major domains of life. We put forward a new function-based classification according to the way information is acquired by the immune systems: Darwinian immunity (currently known from, but not necessarily limited to, vertebrates) relies on the Darwinian process of clonal selection to 'learn' by cumulative trial-and-error feedback; Lamarckian immunity uses templated targeting (guided adaptation) to internalize heritable information on potential threats; finally, shotgun immunity operates through somatic mechanisms of variable targeting without feedback. We argue that the origin of Darwinian (but not Lamarckian or shotgun) immunity represents a radical innovation in the evolution of individuality and complexity, and propose to add it to the list of major evolutionary transitions. While transitions to higher-level units entail the suppression of selection at lower levels, Darwinian immunity re-opens cell-level selection within the multicellular organism, under the control of mechanisms that direct, rather than suppress, cell-level evolution for the benefit of the individual. From a conceptual point of view, the origin of Darwinian immunity can be regarded as the most radical transition in the history of life, in which evolution by natural selection has literally re-invented itself. Furthermore, the combination of clonal selection and somatic receptor diversity enabled a transition from limited to practically unlimited capacity to store information about the antigenic environment. The origin of Darwinian immunity therefore comprises both a transition in individuality and the emergence of a new information system - the two hallmarks of major evolutionary transitions. Finally, we present an evolutionary scenario for the origin of Darwinian immunity in vertebrates. We propose a revival of the concept of the 'Big Bang' of vertebrate immunity, arguing that its origin involved a 'difficult' (i.e. low-probability) evolutionary transition that might have occurred only once, in a common ancestor of all vertebrates. In contrast to the original concept, we argue that the limiting innovation was not the generation of somatic diversity, but the regulatory circuitry needed for the safe operation of amplifiable immune responses with somatically acquired targeting. Regulatory complexity increased abruptly by genomic duplications at the root of the vertebrate lineage, creating a rare opportunity to establish such circuitry. We discuss the selection forces that might have acted at the origin of the transition, and in the subsequent stepwise evolution leading to the modern immune systems of extant vertebrates.
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Affiliation(s)
- Viktor Müller
- Parmenides Center for the Conceptual Foundations of Science, 82049 Pullach/Munich, Germany.,Department of Plant Systematics, Ecology and Theoretical Biology, Institute of Biology, Eötvös Loránd University, 1117 Budapest, Hungary.,Evolutionary Systems Research Group, MTA Centre for Ecological Research, 8237 Tihany, Hungary
| | - Rob J de Boer
- Theoretical Biology, Department of Biology, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Sebastian Bonhoeffer
- Institute of Integrative Biology, Department of Environmental Systems Science, ETH Zurich, 8092 Zurich, Switzerland
| | - Eörs Szathmáry
- Parmenides Center for the Conceptual Foundations of Science, 82049 Pullach/Munich, Germany.,Department of Plant Systematics, Ecology and Theoretical Biology, Institute of Biology, Eötvös Loránd University, 1117 Budapest, Hungary.,Evolutionary Systems Research Group, MTA Centre for Ecological Research, 8237 Tihany, Hungary
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17
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Dong M, Artusa P, Kelly SA, Fournier M, Baldwin TA, Mandl JN, Melichar HJ. Alterations in the Thymic Selection Threshold Skew the Self-Reactivity of the TCR Repertoire in Neonates. THE JOURNAL OF IMMUNOLOGY 2017; 199:965-973. [PMID: 28659353 DOI: 10.4049/jimmunol.1602137] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 06/02/2017] [Indexed: 12/19/2022]
Abstract
Neonatal and adult T cells differ in their effector functions. Although it is known that cell-intrinsic differences in mature T cells contribute to this phenomenon, the factors involved remain unclear. Given emerging evidence that the binding strength of a TCR for self-peptide presented by MHC (self-pMHC) impacts T cell function, we sought to determine whether altered thymic selection influences the self-reactivity of the TCR repertoire during ontogeny. We found that conventional and regulatory T cell subsets in the thymus of neonates and young mice expressed higher levels of cell surface CD5, a surrogate marker for TCR avidity for self-pMHC, as compared with their adult counterparts, and this difference in self-reactivity was independent of the germline bias of the neonatal TCR repertoire. The increased binding strength of the TCR repertoire for self-pMHC in neonates was not solely due to reported defects in clonal deletion. Rather, our data suggest that thymic selection is altered in young mice such that thymocytes bearing TCRs with low affinity for self-peptide are not efficiently selected into the neonatal repertoire, and stronger TCR signals accompany both conventional and regulatory T cell selection. Importantly, the distinct levels of T cell self-reactivity reflect physiologically relevant differences based on the preferential expansion of T cells from young mice to fill a lymphopenic environment. Therefore, differences in thymic selection in young versus adult mice skew the TCR repertoire, and the relatively higher self-reactivity of the T cell pool may contribute to the distinct immune responses observed in neonates.
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Affiliation(s)
- Mengqi Dong
- Maisonneuve-Rosemont Hospital Research Center, Montreal, Quebec H1T 2M4, Canada.,Department of Microbiology, Infectious Diseases, and Immunology, University of Montreal, Montreal, Quebec H3T 1J4, Canada
| | - Patricio Artusa
- Department of Physiology and McGill Research Centre for Complex Traits, McGill University, Montreal, Quebec H3G 1Y6, Canada
| | - Stephanie A Kelly
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta T6G 2E1, Canada; and
| | - Marilaine Fournier
- Maisonneuve-Rosemont Hospital Research Center, Montreal, Quebec H1T 2M4, Canada
| | - Troy A Baldwin
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta T6G 2E1, Canada; and
| | - Judith N Mandl
- Department of Physiology and McGill Research Centre for Complex Traits, McGill University, Montreal, Quebec H3G 1Y6, Canada
| | - Heather J Melichar
- Maisonneuve-Rosemont Hospital Research Center, Montreal, Quebec H1T 2M4, Canada; .,Department of Medicine, University of Montreal, Montreal, Quebec H3T 1J4, Canada
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18
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Li KP, Fähnrich A, Roy E, Cuda CM, Grimes HL, Perlman HR, Kalies K, Hildeman DA. Temporal Expression of Bim Limits the Development of Agonist-Selected Thymocytes and Skews Their TCRβ Repertoire. THE JOURNAL OF IMMUNOLOGY 2016; 198:257-269. [PMID: 27852740 DOI: 10.4049/jimmunol.1601200] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Accepted: 10/25/2016] [Indexed: 12/11/2022]
Abstract
CD8αα TCRαβ+ intestinal intraepithelial lymphocytes play a critical role in promoting intestinal homeostasis, although mechanisms controlling their development and peripheral homeostasis remain unclear. In this study, we examined the spatiotemporal role of Bim in the thymic selection of CD8αα precursors and the fate of these cells in the periphery. We found that T cell-specific expression of Bim during early/cortical, but not late/medullary, thymic development controls the agonist selection of CD8αα precursors and limits their private TCRβ repertoire. During this process, agonist-selected double-positive cells lose CD4/8 coreceptor expression and masquerade as double-negative (DN) TCRαβhi thymocytes. Although these DN thymocytes fail to re-express coreceptors after OP9-DL1 culture, they eventually mature and accumulate in the spleen where TCR and IL-15/STAT5 signaling promotes their conversion to CD8αα cells and their expression of gut-homing receptors. Adoptive transfer of splenic DN cells gives rise to CD8αα cells in the gut, establishing their precursor relationship in vivo. Interestingly, Bim does not restrict the IL-15-driven maturation of CD8αα cells that is critical for intestinal homeostasis. Thus, we found a temporal and tissue-specific role for Bim in limiting thymic agonist selection of CD8αα precursors and their TCRβ repertoire, but not in the maintenance of CD8αα intraepithelial lymphocytes in the intestine.
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Affiliation(s)
- Kun-Po Li
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229.,Department of Pediatrics, University of Cincinnati, Cincinnati, OH 45257
| | - Anke Fähnrich
- Institute for Anatomy, University of Lübeck, 23538 Lübeck, Germany; and
| | - Eron Roy
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229.,Department of Pediatrics, University of Cincinnati, Cincinnati, OH 45257
| | - Carla M Cuda
- Rheumatology Division, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611
| | - H Leighton Grimes
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229.,Department of Pediatrics, University of Cincinnati, Cincinnati, OH 45257
| | - Harris R Perlman
- Rheumatology Division, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611
| | - Kathrin Kalies
- Institute for Anatomy, University of Lübeck, 23538 Lübeck, Germany; and
| | - David A Hildeman
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229; .,Department of Pediatrics, University of Cincinnati, Cincinnati, OH 45257
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19
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Nelson RW, Rajpal MN, Jenkins MK. The Neonatal CD4+ T Cell Response to a Single Epitope Varies in Genetically Identical Mice. THE JOURNAL OF IMMUNOLOGY 2015; 195:2115-21. [PMID: 26179899 DOI: 10.4049/jimmunol.1500405] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Accepted: 06/19/2015] [Indexed: 01/16/2023]
Abstract
Neonatal infection is a major cause of morbidity and mortality worldwide. Increased susceptibility to infection in the neonate is attributed in part to defects in T cell-mediated immunity. A peptide:MHC class II tetramer-based cell enrichment method was used to test this hypothesis at the level of a single epitope. We found that naive T cells with TCRs specific for the 2W:I-A(b) epitope were present in the thymuses of 1-d-old CD57BL/6 mice but were barely detectable in the spleen, likely because each mouse contained very few total splenic CD4(+) T cells. By day 7 of life, however, the total number of splenic CD4(+) T cells increased dramatically and the frequency of 2W:I-A(b)-specific naive T cells reached that of adult mice. Injection of 2W peptide in CFA into 1-d-old mice generated a 2W:I-A(b)-specific effector cell population that peaked later than in adult mice and showed more animal-to-animal variation. Similarly, 2W:I-A(b)-specific naive T cells in different neonatal mice varied significantly in generation of Th1, Th2, and follicular Th cells compared with adult mice. These results suggest that delayed effector cell expansion and stochastic variability in effector cell generation due to an initially small naive repertoire contribute to defective peptide:MHC class II-specific immunity in neonates.
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Affiliation(s)
- Ryan W Nelson
- Department of Microbiology and Immunology, Center for Immunology, University of Minnesota Medical School, Minneapolis, MN 55455; and
| | - Miriam N Rajpal
- Department of Pediatrics, Center for Immunology, University of Minnesota Medical School, Minneapolis, MN 55455
| | - Marc K Jenkins
- Department of Microbiology and Immunology, Center for Immunology, University of Minnesota Medical School, Minneapolis, MN 55455; and
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20
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Kang J, Malhotra N. Transcription factor networks directing the development, function, and evolution of innate lymphoid effectors. Annu Rev Immunol 2015; 33:505-38. [PMID: 25650177 PMCID: PMC4674156 DOI: 10.1146/annurev-immunol-032414-112025] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Mammalian lymphoid immunity is mediated by fast and slow responders to pathogens. Fast innate lymphocytes are active within hours after infections in mucosal tissues. Slow adaptive lymphocytes are conventional T and B cells with clonal antigen receptors that function days after pathogen exposure. A transcription factor (TF) regulatory network guiding early T cell development is at the core of effector function diversification in all innate lymphocytes, and the kinetics of immune responses is set by developmental programming. Operational units within the innate lymphoid system are not classified by the types of pathogen-sensing machineries but rather by discrete effector functions programmed by regulatory TF networks. Based on the evolutionary history of TFs of the regulatory networks, fast effectors likely arose earlier in the evolution of animals to fortify body barriers, and in mammals they often develop in fetal ontogeny prior to the establishment of fully competent adaptive immunity.
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Affiliation(s)
- Joonsoo Kang
- Department of Pathology, University of Massachusetts Medical School, Worcester, Massachusetts 01655;
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21
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Liljavirta J, Niku M, Pessa-Morikawa T, Ekman A, Iivanainen A. Expansion of the preimmune antibody repertoire by junctional diversity in Bos taurus. PLoS One 2014; 9:e99808. [PMID: 24926997 PMCID: PMC4057420 DOI: 10.1371/journal.pone.0099808] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Accepted: 05/19/2014] [Indexed: 12/15/2022] Open
Abstract
Cattle have a limited range of immunoglobulin genes which are further diversified by antigen independent somatic hypermutation in fetuses. Junctional diversity generated during somatic recombination contributes to antibody diversity but its relative significance has not been comprehensively studied. We have investigated the importance of terminal deoxynucleotidyl transferase (TdT) -mediated junctional diversity to the bovine immunoglobulin repertoire. We also searched for new bovine heavy chain diversity (IGHD) genes as the information of the germline sequences is essential to define the junctional boundaries between gene segments. New heavy chain variable genes (IGHV) were explored to address the gene usage in the fetal recombinations. Our bioinformatics search revealed five new IGHD genes, which included the longest IGHD reported so far, 154 bp. By genomic sequencing we found 26 new IGHV sequences that represent potentially new IGHV genes or allelic variants. Sequence analysis of immunoglobulin heavy chain cDNA libraries of fetal bone marrow, ileum and spleen showed 0 to 36 nontemplated N-nucleotide additions between variable, diversity and joining genes. A maximum of 8 N nucleotides were also identified in the light chains. The junctional base profile was biased towards A and T nucleotide additions (64% in heavy chain VD, 52% in heavy chain DJ and 61% in light chain VJ junctions) in contrast to the high G/C content which is usually observed in mice. Sequence analysis also revealed extensive exonuclease activity, providing additional diversity. B-lymphocyte specific TdT expression was detected in bovine fetal bone marrow by reverse transcription-qPCR and immunofluorescence. These results suggest that TdT-mediated junctional diversity and exonuclease activity contribute significantly to the size of the cattle preimmune antibody repertoire already in the fetal period.
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Affiliation(s)
- Jenni Liljavirta
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
| | - Mikael Niku
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
| | | | - Anna Ekman
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
| | - Antti Iivanainen
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
- * E-mail:
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22
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The BRCT domain and the specific loop 1 of human Polμ are targets of Cdk2/cyclin A phosphorylation. DNA Repair (Amst) 2013; 12:824-34. [DOI: 10.1016/j.dnarep.2013.07.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Revised: 07/01/2013] [Accepted: 07/18/2013] [Indexed: 12/18/2022]
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23
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Mold JE, Anderson CC. A discussion of immune tolerance and the layered immune system hypothesis. CHIMERISM 2013; 4:62-70. [PMID: 23723085 DOI: 10.4161/chim.24914] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Affiliation(s)
- Jeff E Mold
- Department of Cell and Molecular Biology; Karolinska Institutet; Stockholm, Sweden
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24
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Alt FW, Zhang Y, Meng FL, Guo C, Schwer B. Mechanisms of programmed DNA lesions and genomic instability in the immune system. Cell 2013; 152:417-29. [PMID: 23374339 PMCID: PMC4382911 DOI: 10.1016/j.cell.2013.01.007] [Citation(s) in RCA: 345] [Impact Index Per Article: 31.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2012] [Indexed: 12/15/2022]
Abstract
Chromosomal translocations involving antigen receptor loci are common in lymphoid malignancies. Translocations require DNA double-strand breaks (DSBs) at two chromosomal sites, their physical juxtaposition, and their fusion by end-joining. Ability of lymphocytes to generate diverse repertoires of antigen receptors and effector antibodies derives from programmed genomic alterations that produce DSBs. We discuss these lymphocyte-specific processes, with a focus on mechanisms that provide requisite DSB target specificity and mechanisms that suppress DSB translocation. We also discuss recent work that provides new insights into DSB repair pathways and the influences of three-dimensional genome organization on physiological processes and cancer genomes.
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Affiliation(s)
- Frederick W Alt
- Departments of Genetics and Pediatrics, Harvard Medical School, Boston, MA 02115, USA.
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25
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Delacôte F, Perez C, Guyot V, Duhamel M, Rochon C, Ollivier N, Macmaster R, Silva GH, Pâques F, Daboussi F, Duchateau P. High frequency targeted mutagenesis using engineered endonucleases and DNA-end processing enzymes. PLoS One 2013; 8:e53217. [PMID: 23359797 PMCID: PMC3554739 DOI: 10.1371/journal.pone.0053217] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2012] [Accepted: 11/26/2012] [Indexed: 12/13/2022] Open
Abstract
Targeting DNA double-strand breaks is a powerful strategy for gene inactivation applications. Without the use of a repair plasmid, targeted mutagenesis can be achieved through Non-Homologous End joining (NHEJ) pathways. However, many of the DNA breaks produced by engineered nucleases may be subject to precise re-ligation without loss of genetic information and thus are likely to be unproductive. In this study, we combined engineered endonucleases and DNA-end processing enzymes to increase the efficiency of targeted mutagenesis, providing a robust and efficient method to (i) greatly improve targeted mutagenesis frequency up to 30-fold, and; (ii) control the nature of mutagenic events using meganucleases in conjunction with DNA-end processing enzymes in human primary cells.
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26
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Hogg M, Sauer-Eriksson AE, Johansson E. Promiscuous DNA synthesis by human DNA polymerase θ. Nucleic Acids Res 2012; 40:2611-22. [PMID: 22135286 PMCID: PMC3315306 DOI: 10.1093/nar/gkr1102] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2011] [Revised: 11/03/2011] [Accepted: 11/04/2011] [Indexed: 12/15/2022] Open
Abstract
The biological role of human DNA polymerase θ (POLQ) is not yet clearly defined, but it has been proposed to participate in several cellular processes based on its translesion synthesis capabilities. POLQ is a low-fidelity polymerase capable of efficient bypass of blocking lesions such as abasic sites and thymine glycols as well as extension of mismatched primer termini. Here, we show that POLQ possesses a DNA polymerase activity that appears to be template independent and allows efficient extension of single-stranded DNA as well as duplex DNA with either protruding or multiply mismatched 3'-OH termini. We hypothesize that this DNA synthesis activity is related to the proposed role for POLQ in the repair or tolerance of double-strand breaks.
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Affiliation(s)
- Matthew Hogg
- Department of Medical Biochemistry and Biophysics and Department of Chemistry, Umeå University, SE-901 87 Umeå, Sweden
| | - A. Elisabeth Sauer-Eriksson
- Department of Medical Biochemistry and Biophysics and Department of Chemistry, Umeå University, SE-901 87 Umeå, Sweden
| | - Erik Johansson
- Department of Medical Biochemistry and Biophysics and Department of Chemistry, Umeå University, SE-901 87 Umeå, Sweden
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27
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Immunoglobulin from Antarctic fish species of Rajidae family. Mar Genomics 2012; 5:35-41. [DOI: 10.1016/j.margen.2011.09.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2011] [Revised: 09/06/2011] [Accepted: 09/07/2011] [Indexed: 11/17/2022]
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28
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Xie P. A model for the dynamics of mammalian family X DNA polymerases. J Theor Biol 2011; 277:111-22. [PMID: 21377475 DOI: 10.1016/j.jtbi.2011.02.018] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2010] [Revised: 12/22/2010] [Accepted: 02/22/2011] [Indexed: 11/28/2022]
Abstract
Based on available structural studies, a model is presented for polymerization dynamics of mammalian family X DNA polymerases, including polymerases β, λ, μ, and terminal deoxynucleotidyl transferase (TdT). Using the model, distinct polymerization activities and processivities of the four polymerases acting on different forms of DNA substrate are analyzed and studied theoretically. A "gradient" of template dependence of polymerases β, λ, μ, and TdT is well explained. The much higher occurrence frequencies of the -1 frameshift DNA synthesis by pols λ and μ than that by pol β are well explained. The theoretical results on the polymerization processivities are also in agreement with the available experimental data.
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Affiliation(s)
- Ping Xie
- Key Laboratory of Soft Matter Physics and Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China.
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29
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Mao H, Graziano JJ, Chase TMA, Bentley CA, Bazirgan OA, Reddy NP, Song BD, Smider VV. Spatially addressed combinatorial protein libraries for recombinant antibody discovery and optimization. Nat Biotechnol 2010; 28:1195-202. [PMID: 20972421 DOI: 10.1038/nbt.1694] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2010] [Accepted: 09/27/2010] [Indexed: 12/21/2022]
Abstract
Antibody discovery typically uses hybridoma- or display-based selection approaches, which lack the advantages of directly screening spatially addressed compound libraries as in small-molecule discovery. Here we apply the latter strategy to antibody discovery, using a library of ∼10,000 human germline antibody Fabs created by de novo DNA synthesis and automated protein expression and purification. In multiplexed screening assays, we obtained specific hits against seven of nine antigens. Using sequence-activity relationships and iterative mutagenesis, we optimized the binding affinities of two hits to the low nanomolar range. The matured Fabs showed full and partial antagonism activities in cell-based assays. Thus, protein drug leads can be discovered using surprisingly small libraries of proteins with known sequences, questioning the requirement for billions of members in an antibody discovery library. This methodology also provides sequence, expression and specificity information at the first step of the discovery process, and could enable novel antibody discovery in functional screens.
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30
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Schelonka RL, Ivanov II, Vale AM, Szymanska E, Zemlin M, Gartland GL, Schroeder HW. The CDR-H3 repertoire from TdT-deficient adult bone marrow is a close, but not exact, homologue of the CDR-H3 repertoire from perinatal liver. THE JOURNAL OF IMMUNOLOGY 2010; 185:6075-84. [PMID: 20956348 DOI: 10.4049/jimmunol.1001419] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Compared with adult bone marrow (BM), the composition of the perinatal liver CDR-3 of the Ig H chain (CDR-H3) repertoire is marked by a paucity of N nucleotides and by enrichment for use of J(H) proximal DQ52 and D(H) proximal V(H) and J(H) gene segments. To test the extent to which these differences reflect limited perinatal TdT activity versus differences in the fetal/adult environment, we used the Hardy scheme to sort fractions B-F B lineage cells from TdT-deficient BALB/c adult BM. V(H)7183-containing VDJCμ transcripts from these cells were amplified, cloned, sequenced, and compared with transcripts from wild-type perinatal liver and adult BM. The pattern of V(H)DJ(H) usage in TdT-deficient BM largely matched that of TdT-sufficient adult cells. What minor differences were detected in the pro-B cell stage tended to diminish with B cell maturation, suggesting strong environmental or Ag-driven pressure to achieve a specific range of V(H)DJ(H) usage regardless of the extent of N nucleotide addition. However, although the patterns of V(H)DJ(H) usage in the TdT-deficient B lineage cells paralleled that of wild-type adult cells, the length distribution, global amino acid composition, and charge distribution of the CDR-H3 repertoire proved to be a close, although not exact, homologue of the CDR-H3 repertoire first expressed by late pre-B cells in the TdT-insufficient perinatal liver. Thus, although differing in V(H) content, TdT-deficient mice appear to represent a good, although not perfect, model for testing the role of perinatal CDR-H3 limitations on late B cell development and Ab responses.
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Affiliation(s)
- Robert L Schelonka
- Department of Pediatrics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
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31
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Montaudouin C, Boucontet L, Mailhé-Lembezat MP, Mariotti-Ferrandiz ME, Louise A, Six A, Freitas AA, Garcia S. Endogenous TCR recombination in TCR Tg single RAG-deficient mice uncovered by robust in vivo T cell activation and selection. PLoS One 2010; 5:e10238. [PMID: 20454452 PMCID: PMC2861594 DOI: 10.1371/journal.pone.0010238] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2009] [Accepted: 03/23/2010] [Indexed: 12/16/2022] Open
Abstract
Recombination activating gene (RAG)-deficient TCR (T Cell Receptor) Tg (transgenic) mice are routinely used as sources of monoclonal T cells. We found that after the transfer of T cells from a RAG-2-deficient 5CC7 TCR Tg mice into allogeneic hosts we recovered a population of T cells expressing diverse alphabeta-TCRs. In fact, in the thymus and spleen of the 5CC7 RAG-2-deficient donor mice, we detected rare T cells expressing non-Tg TCR chains. Similar observations were obtained using T cells from two other TCR transgenic strains, namely RAG-2-deficient aHY and RAG-1-deficient OT-1 mice. The sequences of the endogenous TCR transcripts suggested that gene recombination could occur, albeit quite inefficiently, in the RAG-deficient mice we used. In agreement, we evidenced rare TCR Valpha and Vbeta-chain transcripts in non-Tg RAG-2-deficient mice. Since in these non-Tg RAG-deficient mice no mature T cells could ever be found, our findings suggested a role for the TCR Tg in rescuing rare recombined endogenous chains. Robust T-cell activation by the allogeneic environment favored the selection and expansion of the rare cells expressing endogenous TCRs. Potential mechanisms involved in the recombination of the endogenous TCR chains in the different strains of RAG-deficient mice used, and in particular the possibility of RAG-1 hypomorphism due to an incomplete knocking out procedure, are discussed. Our findings have important experimental implications for studies using TCR-Tg RAG-deficient cells as monoclonal T cell populations.
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Affiliation(s)
- Caroline Montaudouin
- Unité de Biologie des Populations Lymphocytaires, Département d'Immunologie, Institut Pasteur, Centre National de Recherche Scientifique-Unité de Recherche Associée 1961, Paris, France
| | - Laurent Boucontet
- Unité du Développement des Lymphocytes, Département d'Immunologie, Institut Pasteur, Institut National de la Santé et de la Recherche Médicale U668, Paris, France
| | - Marie-Pierre Mailhé-Lembezat
- Unité de Biologie des Populations Lymphocytaires, Département d'Immunologie, Institut Pasteur, Centre National de Recherche Scientifique-Unité de Recherche Associée 1961, Paris, France
| | - Maria-Encarnita Mariotti-Ferrandiz
- Unité de Physiopathologie des Infections, Département d'Immunologie, Institut Pasteur, Centre National de Recherche Scientifique-Unité de Recherche Associée 1961, Paris, France
| | - Anne Louise
- Plate-forme de Cytométrie, Département d'Immunologie, Institut Pasteur, Paris, France
| | - Adrien Six
- Unité de Physiopathologie des Infections, Département d'Immunologie, Institut Pasteur, Centre National de Recherche Scientifique-Unité de Recherche Associée 1961, Paris, France
| | - Antonio A. Freitas
- Unité de Biologie des Populations Lymphocytaires, Département d'Immunologie, Institut Pasteur, Centre National de Recherche Scientifique-Unité de Recherche Associée 1961, Paris, France
- * E-mail: (AAF); (SG)
| | - Sylvie Garcia
- Unité de Biologie des Populations Lymphocytaires, Département d'Immunologie, Institut Pasteur, Centre National de Recherche Scientifique-Unité de Recherche Associée 1961, Paris, France
- * E-mail: (AAF); (SG)
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Haeryfar SMM, Hickman HD, Irvine KR, Tscharke DC, Bennink JR, Yewdell JW. Terminal deoxynucleotidyl transferase establishes and broadens antiviral CD8+ T cell immunodominance hierarchies. THE JOURNAL OF IMMUNOLOGY 2008; 181:649-59. [PMID: 18566432 DOI: 10.4049/jimmunol.181.1.649] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The action of TdT on mouse TCR genes accounts for approximately 90% of T cell repertoire diversity. We report that in TdT-/- mice, total T(CD8+) responses to influenza and vaccinia viruses are reduced by approximately 30% relative to wild-type mice. We find that T(CD8+) responses to three subdominant influenza virus determinants are reduced to background values in TdT-/- mice while responses to three immunodominant determinants undergo a major reshuffling. A similar reshuffling occurs in T(CD8+) responses to immunodominant vaccinia virus determinants, and is clearly based on broad differences in TCR family usage and CDR3 length between wild-type and TdT-/- mice. These findings demonstrate that TdT plays a critical role in the magnitude and breadth of anti-viral T(CD8+) responses toward individual determinants and suggests that germline TCR repertoire bias toward the most dominant determinants is a major factor in establishing immunodominance hierarchies.
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Affiliation(s)
- S M Mansour Haeryfar
- Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
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33
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Petrovic Berglund J, Petrovc Berglund J, Mariotti-Ferrandiz E, Rosmaraki E, Hall H, Cazenave PA, Six A, Höglund P. TCR repertoire dynamics in the pancreatic lymph nodes of non-obese diabetic (NOD) mice at the time of disease initiation. Mol Immunol 2008; 45:3059-64. [PMID: 18471883 DOI: 10.1016/j.molimm.2008.03.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2008] [Revised: 03/17/2008] [Accepted: 03/19/2008] [Indexed: 11/17/2022]
Abstract
Mouse T-cell development is unfinished at birth and continues during the first month of life, when T cells exit from the thymus and colonize secondary hematopoietic organs to build up a peripheral T-cell repertoire. T-cell responses against beta-cell-derived autoantigens are initiated in the pancreatic lymph nodes (PLN) of non-obese diabetic (NOD) mice during the same time period. We hypothesized that the combined effect of T-cell development and T-cell activation against tissue-specific antigens would create unique TCR repertoires in two different lymph node stations in NOD mice. To test this hypothesis, we determined the length distribution of the third complementarity-determining region (CDR3) of the TCR in the PLN and the inguinal lymph nodes (ILN) of 10, 14, 18 and 22-day-old NOD females. The analysis of all the BV genes revealed significant perturbations of the repertoire between days 10 and 22 but with no statistical differences between the PLN and ILN repertoires. In contrast, when a set of BV chains were amplified using BJ-specific primers, several unique TCR perturbations were observed in the PLN compared to the ILN. We propose that the TCR repertoire in peripheral lymph nodes of NOD mice develops dynamically between 10 and 22 days of age as a result of a developmental process. On top of that development, the local environment may fine-tune that repertoire, possibly by means of stimulation of T cells by tissue-specific antigens presented by local APC.
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Affiliation(s)
- Jelena Petrovic Berglund
- Department of Microbiology Tumor and Cell Biology, Karolinska Institutet, Box 280, S-171 77 Stockholm, Sweden
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Cherrier M, D'Andon MF, Rougeon F, Doyen N. Identification of a new cis-regulatory element of the terminal deoxynucleotidyl transferase gene in the 5' region of the murine locus. Mol Immunol 2007; 45:1009-17. [PMID: 17854898 DOI: 10.1016/j.molimm.2007.07.027] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2007] [Revised: 07/26/2007] [Accepted: 07/27/2007] [Indexed: 10/22/2022]
Abstract
Terminal deoxynucleotidyl transferase (TdT) expression is controlled at the transcriptional level, however, the TdT core promoter combining D, D', an initiator (Inr) and downstream basal elements (DBE) does not recapitulate the whole complex regulation of TdT expression. We hypothesized that important cis-regulatory elements of the gene are located outside of the TdT promoter. In an attempt to identify these elements, we performed DNase I hypersensitivity assays over 24kb including a 10kb region located upstream of the transcription start site (+1) and a 14kb region spanning exons and introns I to VI. Hypersensitive sites (HS) HS1 and HS2 were localized 8.5 and 8kb upstream of the transcription start site, respectively, and were exclusively detected in TdT+ cell types. HS3, HS4 and HS5 were mapped at positions -7, -3.4 and -3kb, respectively, and detected in both TdT negative and positive cells. HS6, HS7 and HS8 were detected immediately upstream of the TdT promoter. HS10 and HS11 were localized in the first and third intron of the gene. Luciferase reporter assays revealed that HS1, HS2 and HS3 synergize with the TdT promoter to activate transcription in a TdT+ pre-T cell line but not in a TdT+ pro-B cell line. In summary novel cis-regulatory elements have been identified in the 5' region of the TdT locus that synergize with the promoter to activate gene expression and our results suggest these elements may be more active in T cells.
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Affiliation(s)
- Marie Cherrier
- Développement des tissus lymphoïdes, Institut Pasteur, 25 rue du Docteur Roux, 75724 Paris Cedex 15, France.
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35
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Beetz S, Diekhoff D, Steiner LA. Characterization of terminal deoxynucleotidyl transferase and polymerase mu in zebrafish. Immunogenetics 2007; 59:735-44. [PMID: 17701034 DOI: 10.1007/s00251-007-0241-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2006] [Accepted: 06/27/2007] [Indexed: 11/30/2022]
Abstract
Terminal deoxynucleotidyl transferase (TdT) contributes to the junctional diversity of immunoglobulin and T-cell receptors by incorporating nucleotides in a template-independent manner. A closely related enzyme, polymerase mu (polmu), a template-directed polymerase, plays a role in general end-joining double-strand break repair. We cloned zebrafish TdT and polmu and found them to be 43% identical in amino acid sequence. Comparisons with sequences of other species revealed conserved residues typical for TdT in the zebrafish sequence that support the template independence of this enzyme. Some but not all of these features were identified in zebrafish polmu. In adult fish, TdT expression was most prominent in thymus, pro- and mesonephros, the primary lymphoid organs in teleost fish and in spleen, intestine, and the tissue around the intestine. Polmu expression was detected not only in pro- and mesonephros, the major sites for B-lymphocyte development, but also in ovary and testis and in all tissue preparations to a low extent. TdT expression starts at 4 dpf and increases thereafter. Polmu is expressed at all times to a similar extent. In situ studies showed a strong expression of TdT and polmicro in the thymic cortex of 8-week-old fish. The characterization of zebrafish TdT and polmu provide new insights in fish lymphopoiesis and addresses the importance and evolution of TdT and polmu themselves.
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Affiliation(s)
- Susann Beetz
- Biology Department, Massachusetts Institute of Technology, Cambridge, MA, USA.
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36
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Moon AF, Garcia-Diaz M, Batra VK, Beard WA, Bebenek K, Kunkel TA, Wilson SH, Pedersen LC. The X family portrait: structural insights into biological functions of X family polymerases. DNA Repair (Amst) 2007; 6:1709-25. [PMID: 17631059 PMCID: PMC2128704 DOI: 10.1016/j.dnarep.2007.05.009] [Citation(s) in RCA: 143] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2007] [Accepted: 05/22/2007] [Indexed: 11/19/2022]
Abstract
The mammalian family X DNA polymerases (DNA polymerases beta, lambda, mu, and TdT) contribute to base excision repair and double-strand break repair by virtue of their ability to fill short gaps in DNA. Structural information now exists for all four of these enzymes, making this the first mammalian polymerase family whose structural portrait is complete. Here we consider how distinctive structural features of these enzymes contribute to their biological functions in vivo.
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Affiliation(s)
- Andrea F. Moon
- Laboratory of Structural Biology, National Institute of Environmental Health Sciences. 111 T.W. Alexander Drive, MD F3-09, Research Triangle Park, North Carolina 27709
| | - Miguel Garcia-Diaz
- Laboratory of Structural Biology, National Institute of Environmental Health Sciences. 111 T.W. Alexander Drive, MD F3-09, Research Triangle Park, North Carolina 27709
- Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences. 111 T.W. Alexander Drive, MD F3-09, Research Triangle Park, North Carolina 27709
| | - Vinod K. Batra
- Laboratory of Structural Biology, National Institute of Environmental Health Sciences. 111 T.W. Alexander Drive, MD F3-09, Research Triangle Park, North Carolina 27709
| | - William A. Beard
- Laboratory of Structural Biology, National Institute of Environmental Health Sciences. 111 T.W. Alexander Drive, MD F3-09, Research Triangle Park, North Carolina 27709
| | - Katarzyna Bebenek
- Laboratory of Structural Biology, National Institute of Environmental Health Sciences. 111 T.W. Alexander Drive, MD F3-09, Research Triangle Park, North Carolina 27709
- Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences. 111 T.W. Alexander Drive, MD F3-09, Research Triangle Park, North Carolina 27709
| | - Thomas A. Kunkel
- Laboratory of Structural Biology, National Institute of Environmental Health Sciences. 111 T.W. Alexander Drive, MD F3-09, Research Triangle Park, North Carolina 27709
- Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences. 111 T.W. Alexander Drive, MD F3-09, Research Triangle Park, North Carolina 27709
| | - Samuel H. Wilson
- Laboratory of Structural Biology, National Institute of Environmental Health Sciences. 111 T.W. Alexander Drive, MD F3-09, Research Triangle Park, North Carolina 27709
| | - Lars C. Pedersen
- Laboratory of Structural Biology, National Institute of Environmental Health Sciences. 111 T.W. Alexander Drive, MD F3-09, Research Triangle Park, North Carolina 27709
- *Corresponding author: Phone: 919-541-0444; Fax: 919-541-7880;
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37
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Nguyen HH, Zemlin M, Ivanov II, Andrasi J, Zemlin C, Vu HL, Schelonka R, Schroeder HW, Mestecky J. Heterosubtypic immunity to influenza A virus infection requires a properly diversified antibody repertoire. J Virol 2007; 81:9331-8. [PMID: 17567700 PMCID: PMC1951409 DOI: 10.1128/jvi.00751-07] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Heterosubtypic immunity (HSI) is defined as cross-protection to infection with an influenza A virus serotype other than the one used for primary infection. Although HSI has been thought to be mediated by serotype cross-reactive cytotoxic T lymphocytes (CTL) that recognize conserved epitopes of structural proteins, recent studies suggest that antibodies (Abs) may make a significant contribution. In this study, we provide further evidence for the role of Abs in HSI using transgenic mice lacking terminal deoxyribonucleotidyltransferase (TdT), which adds N nucleotides to V-D and D-J junctions of the complementary determining region 3 (CDR3) (TdT(-/-)) and mice with altered Ab repertoires due to replacement of the complete locus of heavy chain diversity segments (D(H)) with an altered D(H) segment (namely, Delta D-iD). Both types of mice failed to generate complete HSI, although they were able to mount protective immunity to a homologous challenge. Lower levels of virus-specific antibodies along with more severely impaired HSI were observed in TdT(-/-) mice compared to those in Delta D-iD mice, while CTL activity remained unchanged in both types of mice. These findings indicate that a properly diversified antibody repertoire is required for HSI and that N addition by TdT is a more effective mechanism in the induction of a properly diversified antibody repertoire and, therefore, complete HSI. The results suggest that the diversity of the antibody repertoire as determined by the composition of the D region of HCDR3 and by N addition are among the mechanisms selected for in evolution to create a favorable environment to resolve infections with mutated viruses.
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MESH Headings
- Animals
- Antibodies, Viral/immunology
- Body Weight
- Cross Reactions
- DNA Nucleotidylexotransferase/deficiency
- Disease Models, Animal
- Humans
- Immunoglobulin Heavy Chains/genetics
- Influenza A virus/immunology
- Influenza, Human/immunology
- Mice
- Mice, Inbred BALB C
- Mice, Inbred C57BL
- Mice, Knockout
- Mice, Transgenic
- Receptors, Antigen, T-Cell/immunology
- Sequence Deletion
- Survival Analysis
- T-Lymphocyte Subsets/immunology
- T-Lymphocytes, Cytotoxic/immunology
- T-Lymphocytes, Helper-Inducer/immunology
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Affiliation(s)
- Huan H Nguyen
- Department of Microbiology, The University of Alabama at Birmingham, Birmingham, Alabama 35294-2170, USA.
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38
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Fazilleau N, Delarasse C, Motta I, Fillatreau S, Gougeon ML, Kourilsky P, Pham-Dinh D, Kanellopoulos JM. T cell repertoire diversity is required for relapses in myelin oligodendrocyte glycoprotein-induced experimental autoimmune encephalomyelitis. THE JOURNAL OF IMMUNOLOGY 2007; 178:4865-75. [PMID: 17404267 DOI: 10.4049/jimmunol.178.8.4865] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Comparison of TCRalphabeta repertoires of myelin oligodendrocyte glycoprotein (MOG)-specific T lymphocytes in C57BL/6 and TdT-deficient littermates (TdT(-/-)) generated during experimental autoimmune encephalomyelitis (EAE) highlights a link between a diversified TCRalphabeta repertoire and EAE relapses. At the onset of the disease, the EAE-severity is identical in TdT(+/-) and TdT(-/-) mice and the neuropathologic public MOG-specific T cell repertoires express closely similar public Valpha-Jalpha and Vbeta-Jbeta rearrangements in both strains. However, whereas TdT(+/+) and TdT(+/-) mice undergo successive EAE relapses, TdT(-/-) mice recover definitively and the lack of relapses does not stem from dominant regulatory mechanisms. During the first relapse of the disease in TdT(+/-) mice, new public Valpha-Jalpha and Vbeta-Jbeta rearrangements emerge that are distinct from those detected at the onset of the disease. Most of these rearrangements contain N additions and are found in CNS-infiltrating T lymphocytes. Furthermore, CD4(+) T splenocytes bearing these rearrangements proliferate to the immunodominant epitope of MOG and not to other immunodominant epitopes of proteolipid protein and myelin basic protein autoantigens, excluding epitope spreading to these myelin proteins. Thus, in addition to epitope spreading, a novel mechanism involving TCRalphabeta repertoire diversification contributes to autoimmune progression.
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Affiliation(s)
- Nicolas Fazilleau
- Institut National de la Santé et de la Recherche Médicale, Unité 277, Institut Pasteur, Paris, France
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39
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Moon AF, Garcia-Diaz M, Bebenek K, Davis BJ, Zhong X, Ramsden DA, Kunkel TA, Pedersen LC. Structural insight into the substrate specificity of DNA Polymerase mu. Nat Struct Mol Biol 2006; 14:45-53. [PMID: 17159995 DOI: 10.1038/nsmb1180] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2006] [Accepted: 11/10/2006] [Indexed: 11/08/2022]
Abstract
DNA polymerase mu (Pol mu) is a family X enzyme with unique substrate specificity that contributes to its specialized role in nonhomologous DNA end joining (NHEJ). To investigate Pol mu's unusual substrate specificity, we describe the 2.4 A crystal structure of the polymerase domain of murine Pol mu bound to gapped DNA with a correct dNTP at the active site. This structure reveals substrate interactions with side chains in Pol mu that differ from other family X members. For example, a single amino acid substitution, H329A, has little effect on template-dependent synthesis by Pol mu from a paired primer terminus, but it reduces both template-independent and template-dependent synthesis during NHEJ of intermediates whose 3' ends lack complementary template strand nucleotides. These results provide insight into the substrate specificity and differing functions of four closely related mammalian family X DNA polymerases.
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Affiliation(s)
- Andrea F Moon
- Laboratory of Structural Biology, National Institute of Environmental Health Sciences (National Institutes of Health, US Department of Health and Human Services), 111 T.W. Alexander Drive, MD F3-09, Research Triangle Park, North Carolina 27709, USA
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40
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Abstract
The specificities of lymphocytes for antigen are generated by a quasi-random process of gene rearrangement that often results in non-functional or autoreactive antigen receptors. Regulation of lymphocyte specificities involves not only the elimination of cells that display 'unsuitable' receptors for antigen but also the active genetic correction of these receptors by secondary recombination of the DNA. As I discuss here, an important mechanism for the genetic correction of antigen receptors is ongoing recombination, which leads to receptor editing. Receptor editing is probably an adaptation that is necessitated by the high probability of receptor autoreactivity. In both B cells and T cells, the genes that encode the two chains of the antigen receptor seem to be specialized to promote, on the one hand, the generation of diverse specificities and, on the other hand, the regulation of these specificities through efficient editing.
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Affiliation(s)
- David Nemazee
- Department of Immunology, The Scripps Research Institute, Mail Drop IMM-29, 10550 North Torrey Pines Road, La Jolla, California 92037, USA.
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41
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Abstract
Unicellular eukaryotes primarily employ self/nonself discrimination to avoid self-mating, whereas multicellular organisms also use self/nonself discrimination in immune defense. Recent advances in understanding self/nonself discrimination in eukaryotes shed new light on the emergence of the most sophisticated self/nonself discrimination system known, the antigen receptors employed in the adaptive immune system.
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Affiliation(s)
- Thomas Boehm
- Department of Developmental Immunology, Max-Planck Institute of Immunobiology, Freiburg, Germany.
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42
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Garcia-Diaz M, Bebenek K, Gao G, Pedersen LC, London RE, Kunkel TA. Structure–function studies of DNA polymerase lambda. DNA Repair (Amst) 2005; 4:1358-67. [PMID: 16213194 DOI: 10.1016/j.dnarep.2005.09.001] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
DNA polymerase lambda is a member of the X family of polymerases that is implicated in non-homologous end-joining of double-strand breaks in DNA and in base excision repair of DNA damage. To better understand the roles of DNA polymerase lambda in these repair pathways, here we review its structure and biochemical properties, with emphasis on its gap-filling polymerization activity, its dRP lyase activity and its unusual DNA synthetic (in)fidelity.
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Affiliation(s)
- Miguel Garcia-Diaz
- Laboratory of Structural Biology and Laboratory of Molecular Genetics NIEHS, NIH, DHHS, Research Triangle Park, NC 27709, USA
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43
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Pitcher RS, Tonkin LM, Green AJ, Doherty AJ. Domain structure of a NHEJ DNA repair ligase from Mycobacterium tuberculosis. J Mol Biol 2005; 351:531-44. [PMID: 16023671 DOI: 10.1016/j.jmb.2005.06.038] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2005] [Revised: 06/15/2005] [Accepted: 06/15/2005] [Indexed: 11/17/2022]
Abstract
A prokaryotic non-homologous end-joining (NHEJ) system for the repair of DNA double-strand breaks (DSBs), composed of a Ku homodimer (Mt-Ku) and a multidomain multifunctional ATP-dependent DNA ligase (Mt-Lig), has been described recently in Mycobacterium tuberculosis. Mt-Lig exhibits polymerase and nuclease activity in addition to DNA ligation activity. These functions were ascribed to putative polymerase, nuclease and ligase domains that together constitute a monomeric protein. Here, the separate polymerase, nuclease and ligase domains of Mt-Lig were cloned individually, over-expressed and the soluble proteins purified to homogeneity. The polymerase domain demonstrated DNA-dependent RNA primase activity, catalysing the synthesis of unprimed oligoribonucleotides on single-stranded DNA templates. The polymerase domain can also extend DNA in a template-dependent manner. This activity was eliminated when the catalytic aspartate residues were replaced with alanine. The ligase domain catalysed the sealing of nicked double-stranded DNA designed to mimic a DSB, consistent with the role of Mt-Lig in NHEJ. Deletion of the active-site lysine residue prevented the formation of an adenylated ligase complex and consequently thwarted ligation. The nuclease domain did not function independently as a 3'-5' exonuclease. DNA-binding assays revealed that both the polymerase and ligase domains bind DNA in vitro, the latter with considerably higher affinity. Mt-Ku directly stimulated the polymerase and nuclease activities of Mt-Lig. The polymerase domain bound Mt-Ku in vitro, suggesting it may recruit Mt-Lig to Ku-bound DNA in vivo. Consistent with these data, Mt-Ku stimulated the primer extension activity of the polymerase domain, suggestive of a functional interaction relevant to NHEJ-mediated DSB repair processes.
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Affiliation(s)
- Robert S Pitcher
- Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton BN1 9RQ, UK
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Nick McElhinny SA, Havener JM, Garcia-Diaz M, Juárez R, Bebenek K, Kee BL, Blanco L, Kunkel TA, Ramsden DA. A Gradient of Template Dependence Defines Distinct Biological Roles for Family X Polymerases in Nonhomologous End Joining. Mol Cell 2005; 19:357-66. [PMID: 16061182 DOI: 10.1016/j.molcel.2005.06.012] [Citation(s) in RCA: 254] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2004] [Revised: 04/22/2005] [Accepted: 06/10/2005] [Indexed: 01/13/2023]
Abstract
Three Pol X family members have been linked to nonhomologous end joining (NHEJ) in mammals. Template-independent TdT promotes diversity during NHEJ-dependent repair of V(D)J recombination intermediates, but the roles of the template-dependent polymerases mu and lambda in NHEJ remain unclear. We show here that pol mu and pol lambda are similarly recruited by NHEJ factors to fill gaps when ends have partially complementary overhangs, suggesting equivalent roles promoting accuracy in NHEJ. However, only pol mu promotes accuracy during immunoglobulin kappa recombination. This distinctive in vivo role correlates with the TdT-like ability of pol mu, but not pol lambda, to act when primer termini lack complementary bases in the template strand. However, unlike TdT, synthesis by pol mu in this context is primarily instructed by a template from another DNA molecule. This apparent gradient of template dependence is largely attributable to a small structural element that is present but different in all three polymerases.
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Affiliation(s)
- Stephanie A Nick McElhinny
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
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45
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Nick McElhinny SA, Ramsden DA. Sibling rivalry: competition between Pol X family members in V(D)J recombination and general double strand break repair. Immunol Rev 2005; 200:156-64. [PMID: 15242403 DOI: 10.1111/j.0105-2896.2004.00160.x] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The nonhomologous end-joining pathway is a major means for repairing double-strand breaks (DSBs) in all mitotic cell types. This repair pathway is also the only efficient means for resolving DSB intermediates in V(D)J recombination, a lymphocyte-specific genome rearrangement required for assembly of antigen receptors. A role for polymerases in end-joining has been well established. They are a major factor in determining the character of repair junctions but, in contrast to 'core' end-joining factors, typically appear to have a subtle impact on the efficiency of end-joining. Recent work implicates several members of the Pol X family in end-joining and suggests surprising complexity in the control of how these different polymerases are employed in this pathway.
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Affiliation(s)
- Stephanie A Nick McElhinny
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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46
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Thai TH, Kearney JF. Isoforms of terminal deoxynucleotidyltransferase: developmental aspects and function. Adv Immunol 2005; 86:113-36. [PMID: 15705420 DOI: 10.1016/s0065-2776(04)86003-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The immune system develops in a series of programmed developmental stages. Although recombination-activating gene (RAG) and nonhomologous end-joining (NHEJ) proteins are indispensable in the generation of immunoglobulins and T-cell receptors (TCRs), most CDR3 diversity is contributed by nontemplated addition of nucleotides catalyzed by the nuclear enzyme terminal deoxynucleotidyltransferase (TdT) and most nucleotide deletion is performed by exonucleases at V(D)J joins. Increasing TdT expression continuing into adult life results in N region addition and diversification of the T and B cell repertoires. In several species including mice and humans, there are multiple isoforms of TdT resulting from alternative mRNA splicing. The short form (TdTS) produces N additions during TCR and B-cell receptor (BCR) gene rearrangements. Other long isoforms, TdTL1 and TdTL2, have 3' --> 5' exonuclease activity. The two forms of TdT therefore have distinct and opposite functions in lymphocyte development. The enzymatic activities of the splice variants of TdT play an essential role in the diversification of lymphocyte repertoires by modifying the composition and length of the gene segments involved in the production of antibodies and T-cell receptors.
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Affiliation(s)
- To-Ha Thai
- Division of Developmental and Clinical Immunology, Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35204, USA
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47
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Abstract
Gene regulation by short RNAs is a ubiquitous and important mode of control. MicroRNAs are short, single-strand RNAs that bind with partial complementarity to the 3' untranslated region of several genes to silence their expression. This expanding class of endogenous short RNAs are evolutionarily conserved and participate in control of development and cell-specific gene function. Several of these microRNAs have been cloned uniquely from mammalian lymphocytes suggesting specialized roles in lymphocyte development and function. In addition, several genes linked to RNAi in lower eukaryotes have mammalian homologs with specialized roles in adaptive immunity. For example, in worms, the nonsense-mediated decay (NMD) and RNAi pathways appear to be intricately linked. NMD plays a key role in regulating antigen-receptor expression in lymphocytes and there are mammalian homologs for factors identified in worms that appear to be common in both RNAi and NMD pathways. On the other hand, RNA editing and RNAi have an inverse relationship and RNA editing has an important role in viral immunity. These observations indicate unique roles for dsRNAs in the mammalian immune system.
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Affiliation(s)
- Dipanjan Chowdhury
- Center for Blood Research and Department of Pediatrics, Harvard Medical School, Boston, Massachusetts 02115, USA
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48
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Fleurant M, Changchien L, Chen CT, Flajnik MF, Hsu E. Shark Ig Light Chain Junctions Are as Diverse as in Heavy Chains. THE JOURNAL OF IMMUNOLOGY 2004; 173:5574-82. [PMID: 15494507 DOI: 10.4049/jimmunol.173.9.5574] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
We have characterized a small family of four genes encoding one of the three nurse shark Ig L chain isotypes, called NS5. All NS5 cDNA sequences are encoded by three loci, of which two are organized as conventional clusters, each consisting of a V and J gene segment that can recombine and one C region exon; the third contains a germline-joined VJ in-frame and the fourth locus is a pseudogene. This is the second nurse shark L chain type where both germline-joined and split V-J organizations have been found. Since there are only two rearranging Ig loci, it was possible for the first time to examine junctional diversity in defined fish Ig genes, comparing productive vs nonproductive rearrangements. N region addition was found to be considerably more extensive in length and in frequency than any other vertebrate L chain so far reported and rivals that in H chain. We put forth the speculation that the unprecedented efficiency of N region addition (87-93% of NS5 sequences) may be a result not only of simultaneous H and L chain rearrangement in the shark but also of processing events that afford greater accessibility of the V or J gene coding ends to terminal deoxynucleotidyltransferase.
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Affiliation(s)
- Marshall Fleurant
- Department of Physiology and Pharmacology, State University of New York Health Science Center, Brooklyn, NY 11203, USA
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49
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Thai TH, Kearney JF. Distinct and opposite activities of human terminal deoxynucleotidyltransferase splice variants. THE JOURNAL OF IMMUNOLOGY 2004; 173:4009-19. [PMID: 15356150 DOI: 10.4049/jimmunol.173.6.4009] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Evidence for potential human TdT (hTdT) isoforms derived from hTdT genomic sequences led us to identify the short isoform (hTdTS), as well as mature long transcripts containing exon XII (hTdTL1) and another including exon VII (hTdTL2) in lymphoid cells. Normal B and T lymphocytes express exclusively hTdTS and hTdTL2, whereas hTdTL1 expression appears to be restricted to transformed lymphoid cell lines. In in vitro recombination and primer assays, both long isoforms were shown to have 3'-->5' exonuclease activity. Overexpression of hTdTS or hTdTL2 greatly reduced the efficiency of recombination, which was reverted to normal levels by the simultaneous expression of both enzymes. Therefore, alternative splicing may prevent the adverse effects of unchecked elongation or diminution of coding ends during V(D)J recombination, thus affecting the survival of a B or T cell precursor during receptor gene rearrangements. Finally, the newly discovered hTdT isoforms should be considered in future screening of human leukemias.
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Affiliation(s)
- To-Ha Thai
- Division of Developmental and Clinical Immunology, University of Alabama, Birmingham 35294, USA
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50
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Repasky JAE, Corbett E, Boboila C, Schatz DG. Mutational analysis of terminal deoxynucleotidyltransferase-mediated N-nucleotide addition in V(D)J recombination. THE JOURNAL OF IMMUNOLOGY 2004; 172:5478-88. [PMID: 15100289 DOI: 10.4049/jimmunol.172.9.5478] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The addition of nontemplated (N) nucleotides to coding ends in V(D)J recombination is the result of the action of a unique DNA polymerase, TdT. Although N-nucleotide addition by TdT plays a critical role in the generation of a diverse repertoire of Ag receptor genes, the mechanism by which TdT acts remains unclear. We conducted a structure-function analysis of the murine TdT protein to determine the roles of individual structural motifs that have been implicated in protein-protein and protein-DNA interactions important for TdT function in vivo. This analysis demonstrates that the N-terminal portion of TdT, including the BRCA-1 C-terminal (BRCT) domain, is not required for TdT activity, although the BRCT domain clearly contributes quantitatively to N-nucleotide addition activity. The second helix-hairpin-helix domain of TdT, but not the first, is required for activity. Deletional analysis also suggested that the entire C-terminal region of TdT is necessary for N-nucleotide addition in vivo. The long isoform of TdT was found to reduce N-nucleotide addition by the short form of TdT, but did not increase nucleotide deletion from coding ends in either human or rodent nonlymphoid cells. We consider these results in light of the recently reported structure of the catalytic region of TdT.
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Affiliation(s)
- Jamie A E Repasky
- Howard Hughes Medical Institute, Section of Immunobiology, Yale University School of Medicine, New Haven, CT 06510, USA
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