1
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Funck T, Barnkob MB, Holm N, Ohm-Laursen L, Mehlum CS, Möller S, Barington T. Nucleotide Composition of Human Ig Nontemplated Regions Depends on Trimming of the Flanking Gene Segments, and Terminal Deoxynucleotidyl Transferase Favors Adding Cytosine, Not Guanosine, in Most VDJ Rearrangements. THE JOURNAL OF IMMUNOLOGY 2018; 201:1765-1774. [PMID: 30097530 DOI: 10.4049/jimmunol.1800100] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Accepted: 07/05/2018] [Indexed: 01/12/2023]
Abstract
The formation of nontemplated (N) regions during Ig gene rearrangement is a major contributor to Ab diversity. To gain insights into the mechanisms behind this, we studied the nucleotide composition of N regions within 29,962 unique human VHDJH rearrangements and 8728 unique human DJH rearrangements containing exactly one identifiable D gene segment and thus two N regions, N1 and N2. We found a distinct decreasing content of cytosine (C) and increasing content of guanine (G) across each N region, suggesting that N regions are typically generated by concatenation of two 3' overhangs synthesized by addition of nucleoside triphosphates with a preference for dCTP. This challenges the general assumption that the terminal deoxynucleotidyl transferase favors dGTP in vivo. Furthermore, we found that the G and C gradients depended strongly on whether the germline gene segments were trimmed or not. Our data show that C-enriched N addition preferentially happens at trimmed 3' ends of VH, D, and JH gene segments, indicating a dependency of the transferase mechanism upon the nuclease mechanism.
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Affiliation(s)
- Tina Funck
- Department of Clinical Biochemistry, Zealand University Hospital, Roskilde 4000, Denmark.,Department of Clinical Immunology, Odense University Hospital, Odense 5000, Denmark
| | - Mike Bogetofte Barnkob
- Department of Clinical Immunology, Odense University Hospital, Odense 5000, Denmark.,Medical Research Council Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxfordshire OX3 9DS, United Kingdom
| | - Nanna Holm
- Department of Clinical Immunology, Odense University Hospital, Odense 5000, Denmark
| | - Line Ohm-Laursen
- Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical Biosciences, King's College London, London SE1 1UL, United Kingdom
| | - Camilla Slot Mehlum
- Department of Otorhinolaryngology-Head and Neck Surgery, Odense University Hospital, Odense 5000, Denmark
| | - Sören Möller
- OPEN, Odense Patient Data Explorative Network, Odense University Hospital, Odense 5000, Denmark; and.,Clinical Department, University of Southern Denmark, Odense 5000, Denmark
| | - Torben Barington
- Department of Clinical Immunology, Odense University Hospital, Odense 5000, Denmark; .,Clinical Department, University of Southern Denmark, Odense 5000, Denmark
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2
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Jensen MA, Davis RW. Template-Independent Enzymatic Oligonucleotide Synthesis (TiEOS): Its History, Prospects, and Challenges. Biochemistry 2018. [PMID: 29533604 DOI: 10.1021/acs.biochem.7b00937] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
There is a growing demand for sustainable methods in research and development, where instead of hazardous chemicals, an aqueous medium is chosen to perform biological reactions. In this Perspective, we examine the history and current methodology of using enzymes to generate artificial single-stranded DNA. By using traditional solid-phase phosphoramidite chemistry as a metric, we also explore criteria for the method of template-independent enzymatic oligonucleotide synthesis (TiEOS). As its key component, we delve into the biology of one of the most enigmatic enzymes, terminal deoxynucleotidyl transferase (TdT). As TdT is found to exponentially increase antigen receptor diversity in the vertebrate immune system by adding nucleotides in a template-free manner, researchers have exploited this function as an alternative to the phosphoramidite synthesis method. Though TdT is currently the preferred enzyme for TiEOS, its random nucleotide incorporation presents a barrier in synthesis automation. Taking a closer look at the TiEOS cycle, particularly the coupling step, we find it is comprised of additions > n+1 and deletions. By tapping into the physical and biochemical properties of TdT, we strive to further elucidate its mercurial behavior and offer ways to better optimize TiEOS for production-grade oligonucleotide synthesis.
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Affiliation(s)
- Michael A Jensen
- Stanford Genome Technology Center, Department of Biochemistry , Stanford University , Palo Alto , California 94304 , United States
| | - Ronald W Davis
- Stanford Genome Technology Center, Department of Biochemistry , Stanford University , Palo Alto , California 94304 , United States.,Department of Genetics , Stanford University , Palo Alto , California 94304 , United States
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3
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Quách TD, Hopkins TJ, Holodick NE, Vuyyuru R, Manser T, Bayer RL, Rothstein TL. Human B-1 and B-2 B Cells Develop from Lin-CD34+CD38lo Stem Cells. THE JOURNAL OF IMMUNOLOGY 2016; 197:3950-3958. [PMID: 27815443 DOI: 10.4049/jimmunol.1600630] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Accepted: 09/14/2016] [Indexed: 12/24/2022]
Abstract
The B-1 B cell population is an important bridge between innate and adaptive immunity primarily because B-1 cells produce natural Ab. Murine B-1 and B-2 cells arise from distinct progenitors; however, in humans, in part because it has been difficult to discriminate between them phenotypically, efforts to pinpoint the developmental origins of human B-1 and B-2 cells have lagged. To characterize progenitors of human B-1 and B-2 cells, we separated cord blood and bone marrow Lin-CD34+ hematopoietic stem cells into Lin-CD34+CD38lo and Lin-CD34+CD38hi populations. We found that transplanted Lin-CD34+CD38lo cells, but not Lin-CD34+CD38hi cells, generated a CD19+ B cell population after transfer into immunodeficient NOD.Cg-Prkdcscid Il2rgtm1wjl/SxJ neonates. The emergent CD19+ B cell population was found in spleen, bone marrow, and peritoneal cavity of humanized mice and included distinct populations displaying the B-1 or the B-2 cell phenotype. Engrafted splenic B-1 cells exhibited a mature phenotype, as evidenced by low-to-intermediate expression levels of CD24 and CD38. The engrafted B-1 cell population expressed a VH-DH-JH composition similar to cord blood B-1 cells, including frequent use of VH4-34 (8 versus 10%, respectively). Among patients with hematologic malignancies who underwent hematopoietic stem cell transplantation, B-1 cells were found in the circulation as early as 8 wk posttransplantation. Altogether, our data demonstrate that human B-1 and B-2 cells develop from a Lin-CD34+CD38lo stem cell population, and engrafted B-1 cells in humanized mice exhibit an Ig-usage pattern comparable to B-1 cells in cord blood.
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Affiliation(s)
- Tâm D Quách
- Center for Oncology and Cell Biology, The Feinstein Institute for Medical Research, Manhasset, NY 11030
| | - Thomas J Hopkins
- Center for Oncology and Cell Biology, The Feinstein Institute for Medical Research, Manhasset, NY 11030
| | - Nichol E Holodick
- Center for Oncology and Cell Biology, The Feinstein Institute for Medical Research, Manhasset, NY 11030
| | - Raja Vuyyuru
- Department of Microbiology and Immunology, Thomas Jefferson University, Philadelphia, PA 19107
| | - Tim Manser
- Department of Microbiology and Immunology, Thomas Jefferson University, Philadelphia, PA 19107
| | - Ruthee-Lu Bayer
- Monter Cancer Center, North Shore University Hospital, Northwell Health, Lake Success, NY 11042; and
| | - Thomas L Rothstein
- Center for Oncology and Cell Biology, The Feinstein Institute for Medical Research, Manhasset, NY 11030; .,Hofstra-Northwell Health School of Medicine, Hempstead, NY 11549
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4
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Bryson S, Thomson CA, Risnes LF, Dasgupta S, Smith K, Schrader JW, Pai EF. Structures of Preferred Human IgV Genes-Based Protective Antibodies Identify How Conserved Residues Contact Diverse Antigens and Assign Source of Specificity to CDR3 Loop Variation. THE JOURNAL OF IMMUNOLOGY 2016; 196:4723-30. [PMID: 27183571 DOI: 10.4049/jimmunol.1402890] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Accepted: 04/01/2016] [Indexed: 11/19/2022]
Abstract
The human Ab response to certain pathogens is oligoclonal, with preferred IgV genes being used more frequently than others. A pair of such preferred genes, IGVK3-11 and IGVH3-30, contributes to the generation of protective Abs directed against the 23F serotype of the pneumonococcal capsular polysaccharide of Streptococcus pneumoniae and against the AD-2S1 peptide of the gB membrane protein of human CMV. Structural analyses of Fab fragments of mAbs 023.102 and pn132p2C05 in complex with portions of the 23F polysaccharide revealed five germline-encoded residues in contact with the key component, l-rhamnose. In the case of the AD-2S1 peptide, the KE5 Fab fragment complex identified nine germline-encoded contact residues. Two of these germline-encoded residues, Arg91L and Trp94L, contact both the l-rhamnose and the AD-2S1 peptide. Comparison of the respective paratopes that bind to carbohydrate and protein reveals that stochastic diversity in both CDR3 loops alone almost exclusively accounts for their divergent specificity. Combined evolutionary pressure by human CMV and the 23F serotype of S. pneumoniae acted on the IGVK3-11 and IGVH3-30 genes as demonstrated by the multiple germline-encoded amino acids that contact both l-rhamnose and AD-2S1 peptide.
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Affiliation(s)
- Steve Bryson
- Princess Margaret Cancer Centre, Toronto, Ontario M5G 1L7, Canada; Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Christy A Thomson
- Biomedical Research Centre, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Louise F Risnes
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Somnath Dasgupta
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
| | - Kenneth Smith
- Oklahoma Medical Research Foundation, Oklahoma City, OK 73104
| | - John W Schrader
- Biomedical Research Centre, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Emil F Pai
- Princess Margaret Cancer Centre, Toronto, Ontario M5G 1L7, Canada; Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada; Department of Medical Biophysics, University of Toronto, Toronto, Ontario M5S 1A8, Canada; and Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5G 1L7, Canada
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5
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Quách TD, Rodríguez-Zhurbenko N, Hopkins TJ, Guo X, Hernández AM, Li W, Rothstein TL. Distinctions among Circulating Antibody-Secreting Cell Populations, Including B-1 Cells, in Human Adult Peripheral Blood. THE JOURNAL OF IMMUNOLOGY 2016; 196:1060-9. [PMID: 26740107 DOI: 10.4049/jimmunol.1501843] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Accepted: 12/01/2015] [Indexed: 11/19/2022]
Abstract
Human Ab-secreting cell (ASC) populations in circulation are not well studied. In addition to B-1 (CD20(+)CD27(+)CD38(lo/int)CD43(+)) cell and conventional plasmablast (PB) (CD20-CD27(hi)CD38(hi)) cell populations, in this study, we identified a novel B cell population termed 20(+)38(hi) B cells (CD20(+)CD27(hi)CD38(hi)) that spontaneously secretes Ab. At steady-state, 20(+)38(hi) B cells are distinct from PBs on the basis of CD20 expression, amount of Ab production, frequency of mutation, and diversity of BCR repertoire. However, cytokine treatment of 20(+)38(hi) B cells induces loss of CD20 and acquisition of CD138, suggesting that 20(+)38(hi) B cells are precursors to PBs or pre-PBs. We then evaluated similarities and differences among CD20(+)CD27(+)CD38(lo/int)CD43(+) B-1 cells, CD20(+)CD27(hi)CD38(hi) 20(+)38(hi) B cells, CD20(-)CD27(hi)CD38(hi) PBs, and CD20(+)CD27(+)CD38(lo/int)CD43(-) memory B cells. We found that B-1 cells differ from 20(+)38(hi) B cells and PBs in a number of ways, including Ag expression, morphological appearance, transcriptional profiling, Ab skewing, Ab repertoire, and secretory response to stimulation. In terms of gene expression, B-1 cells align more closely with memory B cells than with 20(+)38(hi) B cells or PBs, but differ in that memory B cells do not express Ab secretion-related genes. We found that B-1 cell Abs use Vh4-34, which is often associated with autoreactivity, 3- to 6-fold more often than other B cell populations. Along with selective production of IgM anti-phosphoryl choline, these data suggest that human B-1 cells might be preferentially selected for autoreactivity/natural specificity. In summary, our results indicate that human healthy adult peripheral blood at steady-state consists of three distinct ASC populations.
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Affiliation(s)
- Tâm D Quách
- Center for Oncology and Cell Biology, The Feinstein Institute for Medical Research, Manhasset, NY 11030
| | - Nely Rodríguez-Zhurbenko
- Center for Oncology and Cell Biology, The Feinstein Institute for Medical Research, Manhasset, NY 11030; Tumor Immunology Direction, Center for Molecular Immunology, Havana 11600, Cuba; and
| | - Thomas J Hopkins
- Center for Oncology and Cell Biology, The Feinstein Institute for Medical Research, Manhasset, NY 11030
| | - Xiaoti Guo
- Center for Oncology and Cell Biology, The Feinstein Institute for Medical Research, Manhasset, NY 11030
| | - Ana María Hernández
- Center for Oncology and Cell Biology, The Feinstein Institute for Medical Research, Manhasset, NY 11030; Tumor Immunology Direction, Center for Molecular Immunology, Havana 11600, Cuba; and
| | - Wentian Li
- Robert S. Boas Center for Genomics and Human Genetics, The Feinstein Institute for Medical Research, Manhasset, NY 11030
| | - Thomas L Rothstein
- Center for Oncology and Cell Biology, The Feinstein Institute for Medical Research, Manhasset, NY 11030;
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6
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Troshchynsky A, Dzneladze I, Chen L, Sheng Y, Saridakis V, Wu GE. Functional analyses of polymorphic variants of human terminal deoxynucleotidyl transferase. Genes Immun 2015; 16:388-98. [PMID: 26043173 DOI: 10.1038/gene.2015.19] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2015] [Revised: 04/19/2015] [Accepted: 04/23/2015] [Indexed: 12/11/2022]
Abstract
Human terminal deoxynucleotidyl transferase (hTdT) is a DNA polymerase that functions to generate diversity in the adaptive immune system. Here, we focus on the function of naturally occurring single-nucleotide polymorphisms (SNPs) of hTdT to evaluate their role in genetic-generated immune variation. The data demonstrate that the genetic variations generated by the hTdT SNPs will vary the human immune repertoire and thus its responses. Human TdT catalyzes template-independent addition of nucleotides (N-additions) during coding joint formation in V(D)J recombination. Its activity is crucial to the diversity of the antigen receptors of B and T lymphocytes. We used in vitro polymerase assays and in vivo human cell V(D)J recombination assays to evaluate the activity and the N-addition levels of six natural (SNP) variants of hTdT. In vitro, the variants differed from wild-type hTdT in polymerization ability with four having significantly lower activity. In vivo, the presence of TdT varied both the efficiency of recombination and N-addition, with two variants generating coding joints with significantly fewer N-additions. Although likely heterozygous, individuals possessing these genetic changes may have less diverse B- and T-cell receptors that would particularly effect individuals prone to adaptive immune disorders, including autoimmunity.
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Affiliation(s)
- A Troshchynsky
- Department of Biology, York University, Toronto, Ontario, Canada
| | - I Dzneladze
- Department of Biology, York University, Toronto, Ontario, Canada
| | - L Chen
- School of Kinesiology and Health Science, York University, Toronto, Ontario, Canada
| | - Y Sheng
- Department of Biology, York University, Toronto, Ontario, Canada
| | - V Saridakis
- Department of Biology, York University, Toronto, Ontario, Canada
| | - G E Wu
- Department of Biology, York University, Toronto, Ontario, Canada.,School of Kinesiology and Health Science, York University, Toronto, Ontario, Canada.,School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
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7
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Affiliation(s)
- Thomas L. Rothstein
- Center for Oncology and Cell Biology, The Feinstein Institute for Medical Research; and the Hofstra North Shore-LIJ School of Medicine; Manhasset New York
| | - Tam D. Quach
- Center for Oncology and Cell Biology, The Feinstein Institute for Medical Research; and the Hofstra North Shore-LIJ School of Medicine; Manhasset New York
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8
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Structures of the Leishmania infantum polymerase beta. DNA Repair (Amst) 2014; 18:1-9. [PMID: 24666693 DOI: 10.1016/j.dnarep.2014.03.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2014] [Revised: 02/28/2014] [Accepted: 03/01/2014] [Indexed: 11/21/2022]
Abstract
Protozoans of the genus Leishmania, the pathogenic agent causing leishmaniasis, encode the family X DNA polymerase Li Pol β. Here, we report the first crystal structures of Li Pol β. Our pre- and post-catalytic structures show that the polymerase adopts the common family X DNA polymerase fold. However, in contrast to other family X DNA polymerases, the dNTP-induced conformational changes in Li Pol β are much more subtle. Moreover, pre- and post-catalytic structures reveal that Li Pol β interacts with the template strand through a nonconserved, variable region known as loop3. Li Pol β Δloop3 mutants display a higher catalytic rate, catalytic efficiency and overall error rates with respect to WT Li Pol β. These results further demonstrate the subtle structural variability that exists within this family of enzymes and provides insight into how this variability underlies the substantial functional differences among their members.
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9
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Schelonka RL, Ivanov II, Vale AM, Dimmitt RA, Khaled M, Schroeder HW. Absence of N addition facilitates B cell development, but impairs immune responses. Immunogenetics 2011; 63:599-609. [PMID: 21660592 PMCID: PMC3181008 DOI: 10.1007/s00251-011-0543-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2010] [Accepted: 05/24/2011] [Indexed: 12/02/2022]
Abstract
The programmed, stepwise acquisition of immunocompetence that marks the development of the fetal immune response proceeds during a period when both T cell receptor and immunoglobulin (Ig) repertoires exhibit reduced junctional diversity due to physiologic terminal deoxynucleotidyl transferase (TdT) insufficiency. To test the effect of N addition on humoral responses, we transplanted bone marrow from TdT-deficient (TdT(-/-)) and wild-type (TdT(+/+)) BALB/c mice into recombination activation gene 1-deficient BALB/c hosts. Mice transplanted with TdT(-/-) cells exhibited diminished humoral responses to the T-independent antigens α-1-dextran and (2,4,6-trinitrophenyl) hapten conjugated to AminoEthylCarboxymethyl-FICOLL, to the T-dependent antigens NP(19)CGG and hen egg lysozyme, and to Enterobacter cloacae, a commensal bacteria that can become an opportunistic pathogen in immature and immunocompromised hosts. An exception to this pattern of reduction was the T-independent anti-phosphorylcholine response to Streptococcus pneumoniae, which is normally dominated by the N-deficient T15 idiotype. Most of the humoral immune responses in the recipients of TdT(-/-) bone marrow were impaired, yet population of the blood with B and T cells occurred more rapidly. To further test the effect of N-deficiency on B cell and T cell population growth, transplanted TdT-sufficient and -deficient BALB/c IgM(a) and congenic TdT-sufficient CB17 IgM(b) bone marrow were placed in competition. TdT(-/-) cells demonstrated an advantage in populating the bone marrow, the spleen, and the peritoneal cavity. TdT deficiency, which characterizes fetal lymphocytes, thus appears to facilitate filling both central and peripheral lymphoid compartments, but at the cost of altered responses to a broad set of antigens.
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Affiliation(s)
- Robert L. Schelonka
- Department of Pediatrics, University of Alabama at Birmingham, Birmingham, AL 35294 USA
- Present Address: Oregon Health and Science University, Portland, OR 97239 USA
| | - Ivaylo I. Ivanov
- Department of Microbiology, University of Alabama at Birmingham, Shelby Building 401, 1530 3rd Avenue South, Birmingham, AL 35294-2182 USA
- Present Address: Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY 10032 USA
| | - Andre M. Vale
- Department of Medicine, University of Alabama at Birmingham, Shelby Building 401, 1530 3rd Avenue South, Birmingham, AL 35294-2182 USA
| | - Reed A. Dimmitt
- Department of Pediatrics, University of Alabama at Birmingham, Birmingham, AL 35294 USA
| | - Mahnaz Khaled
- Department of Pediatrics, University of Alabama at Birmingham, Birmingham, AL 35294 USA
| | - Harry W. Schroeder
- Department of Microbiology, University of Alabama at Birmingham, Shelby Building 401, 1530 3rd Avenue South, Birmingham, AL 35294-2182 USA
- Department of Medicine, University of Alabama at Birmingham, Shelby Building 401, 1530 3rd Avenue South, Birmingham, AL 35294-2182 USA
- Department of Genetics, University of Alabama at Birmingham, Shelby Building 401, 1530 3rd Avenue South, Birmingham, AL 35294-2182 USA
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10
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Mahmoud TI, Kearney JF. Terminal deoxynucleotidyl transferase is required for an optimal response to the polysaccharide α-1,3 dextran. THE JOURNAL OF IMMUNOLOGY 2009; 184:851-8. [PMID: 20018621 DOI: 10.4049/jimmunol.0902791] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
An understanding of Ab responses to polysaccharides associated with pathogenic microorganisms is of importance for improving vaccine design, especially in neonates that respond poorly to these types of Ags. In this study, we have investigated the role of the lymphoid-specific enzyme TdT in generating B cell clones responsive to alpha-1,3 dextran (DEX). TdT is a DNA polymerase that plays a major role in generating diversity of lymphocyte AgRs during V(D)J recombination. In this study, we show that the DEX-specific Ab response is lower, and the dominant DEX-specific J558 idiotype (Id) is not detected in TdT(-/-) mice when compared with wild-type (WT) BALB/c mice. Nucleotide sequencing of H chain CDR3s of DEX-specific plasmablasts, sorted postimmunization, showed that TdT(-/-) mice generate a lower frequency of the predominant adult molecularly determined clone J558. Complementation of TdT expression in TdT(-/-) mice by early forced expression of the short splice variant of TdT-restored WT proportions of J558 Id+ clones and also abrogated the development of the minor M104E Id+ clones. J558 Id V(D)J rearrangements are detected as early as 7 d after birth in IgM-negative B cell precursors in the liver and spleen of WT and TdT-transgenic mice but not in TdT(-/-) mice. These data show that TdT is essential for the generation of the predominant higher-affinity DEX-responsive J558 clone.
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Affiliation(s)
- Tamer I Mahmoud
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
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11
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Motea EA, Berdis AJ. Terminal deoxynucleotidyl transferase: the story of a misguided DNA polymerase. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2009; 1804:1151-66. [PMID: 19596089 DOI: 10.1016/j.bbapap.2009.06.030] [Citation(s) in RCA: 158] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2009] [Revised: 06/27/2009] [Accepted: 06/30/2009] [Indexed: 01/06/2023]
Abstract
Nearly every DNA polymerase characterized to date exclusively catalyzes the incorporation of mononucleotides into a growing primer using a DNA or RNA template as a guide to direct each incorporation event. There is, however, one unique DNA polymerase designated terminal deoxynucleotidyl transferase that performs DNA synthesis using only single-stranded DNA as the nucleic acid substrate. In this chapter, we review the biological role of this enigmatic DNA polymerase and the biochemical mechanism for its ability to perform DNA synthesis in the absence of a templating strand. We compare and contrast the molecular events for template-independent DNA synthesis catalyzed by terminal deoxynucleotidyl transferase with other well-characterized DNA polymerases that perform template-dependent synthesis. This includes a quantitative inspection of how terminal deoxynucleotidyl transferase binds DNA and dNTP substrates, the possible involvement of a conformational change that precedes phosphoryl transfer, and kinetic steps that are associated with the release of products. These enzymatic steps are discussed within the context of the available structures of terminal deoxynucleotidyl transferase in the presence of DNA or nucleotide substrate. In addition, we discuss the ability of proteins involved in replication and recombination to regulate the activity of the terminal deoxynucleotidyl transferase. Finally, the biomedical role of this specialized DNA polymerase is discussed focusing on its involvement in cancer development and its use in biomedical applications such as labeling DNA for detecting apoptosis.
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Affiliation(s)
- Edward A Motea
- Department of Chemistry, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA
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12
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Germline V-genes sculpt the binding site of a family of antibodies neutralizing human cytomegalovirus. EMBO J 2008; 27:2592-602. [PMID: 18772881 DOI: 10.1038/emboj.2008.179] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2008] [Accepted: 08/13/2008] [Indexed: 12/31/2022] Open
Abstract
Immunoglobulin genes are generated somatically through specialized mechanisms resulting in a vast repertoire of antigen-binding sites. Despite the stochastic nature of these processes, the V-genes that encode most of the antigen-combining site are under positive evolutionary selection, raising the possibility that V-genes have been selected to encode key structural features of binding sites of protective antibodies against certain pathogens. Human, neutralizing antibodies to human cytomegalovirus that bind the AD-2S1 epitope on its gB envelope protein repeatedly use a pair of well-conserved, germline V-genes IGHV3-30 and IGKV3-11. Here, we present crystallographic, kinetic and thermodynamic analyses of the binding site of such an antibody and that of its primary immunoglobulin ancestor. These show that these germline V-genes encode key side chain contacts with the viral antigen and thereby dictate key structural features of the hypermutated, high-affinity neutralizing antibody. V-genes may thus encode an innate, protective immunological memory that targets vulnerable, invariant sites on multiple pathogens.
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13
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Abstract
To cope with an unpredictable variety of potential pathogenic insults, the immune system must generate an enormous diversity of recognition structures, and it does so by making stepwise modifications at key genetic loci in each lymphoid cell. These modifications proceed through the action of lymphoid-specific proteins acting together with the general DNA-repair machinery of the cell. Strikingly, these general mechanisms are usually diverted from their normal functions, being used in rather atypical ways in order to privilege diversity over accuracy. In this Review, we focus on the contribution of a set of DNA polymerases discovered in the past decade to these unique DNA transactions.
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14
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Fowler JD, Suo Z. Biochemical, structural, and physiological characterization of terminal deoxynucleotidyl transferase. Chem Rev 2007; 106:2092-110. [PMID: 16771444 DOI: 10.1021/cr040445w] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jason D Fowler
- Department of Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
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15
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Ohm-Laursen L, Nielsen M, Larsen SR, Barington T. No evidence for the use of DIR, D-D fusions, chromosome 15 open reading frames or VH replacement in the peripheral repertoire was found on application of an improved algorithm, JointML, to 6329 human immunoglobulin H rearrangements. Immunology 2006; 119:265-77. [PMID: 17005006 PMCID: PMC1782349 DOI: 10.1111/j.1365-2567.2006.02431.x] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Antibody diversity is created by imprecise joining of the variability (V), diversity (D) and joining (J) gene segments of the heavy and light chain loci. Analysis of rearrangements is complicated by somatic hypermutations and uncertainty concerning the sources of gene segments and the precise way in which they recombine. It has been suggested that D genes with irregular recombination signal sequences (DIR) and chromosome 15 open reading frames (OR15) can replace conventional D genes, that two D genes or inverted D genes may be used and that the repertoire can be further diversified by heavy chain V gene (VH) replacement. Safe conclusions require large, well-defined sequence samples and algorithms minimizing stochastic assignment of segments. Two computer programs were developed for analysis of heavy chain joints. JointHMM is a profile hidden Markow model, while JointML is a maximum-likelihood-based method taking the lengths of the joint and the mutational status of the VH gene into account. The programs were applied to a set of 6329 clonally unrelated rearrangements. A conventional D gene was found in 80% of unmutated sequences and 64% of mutated sequences, while D-gene assignment was kept below 5% in artificial (randomly permutated) rearrangements. No evidence for the use of DIR, OR15, multiple D genes or VH replacements was found, while inverted D genes were used in less than 1 per thousand of the sequences. JointML was shown to have a higher predictive performance for D-gene assignment in mutated and unmutated sequences than four other publicly available programs. An online version 1.0 of JointML is available at http://www.cbs.dtu.dk/services/VDJsolver.
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Affiliation(s)
- Line Ohm-Laursen
- Department of Clinical Immunology, Odense University HospitalOdense, Denmark
| | - Morten Nielsen
- Center for Biological Sequence Analysis, BioCentrum, Technical University of DenmarkLyngby, Denmark
| | - Stine R Larsen
- Department of Clinical Immunology, Odense University HospitalOdense, Denmark
| | - Torben Barington
- Department of Clinical Immunology, Odense University HospitalOdense, Denmark
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16
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Bertocci B, De Smet A, Weill JC, Reynaud CA. Nonoverlapping functions of DNA polymerases mu, lambda, and terminal deoxynucleotidyltransferase during immunoglobulin V(D)J recombination in vivo. Immunity 2006; 25:31-41. [PMID: 16860755 DOI: 10.1016/j.immuni.2006.04.013] [Citation(s) in RCA: 137] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2006] [Revised: 03/31/2006] [Accepted: 04/10/2006] [Indexed: 11/28/2022]
Abstract
DNA polymerases mu (pol mu), lambda (pol lambda), and terminal deoxynucleotidyltransferase (TdT) are enzymes of the pol X family that share homology in sequence and functional domain organization. We showed previously that pol mu participates in light chain but surprisingly not heavy chain gene rearrangement. We show here that immunoglobulin heavy chain junctions from pol lambda-deficient animals have shorter length with normal N-additions, thus indicating that pol lambda is recruited during heavy chain rearrangement at a step that precedes the action of TdT. In contrast to previous in vitro studies, analysis of animals with combined inactivation of these enzymes revealed no overlapping or compensatory activities for V(D)J recombination between pol mu, pol lambda, and TdT. This complex usage of polymerases with distinct catalytic specificities may correspond to the specific function that the third hypervariable region assumes for each immunoglobulin chain, with pol lambda maintaining a large heavy chain junctional heterogeneity and pol mu ensuring a restricted light chain junctional variability.
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Affiliation(s)
- Barbara Bertocci
- INSERM U783, Faculté de Médecine René Descartes, Site Necker-Enfants Malades, 156 rue de Vaugirard, 75730 Paris Cedex 15, France
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17
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Chen JM, Chuzhanova N, Stenson PD, Férec C, Cooper DN. Meta-analysis of gross insertions causing human genetic disease: novel mutational mechanisms and the role of replication slippage. Hum Mutat 2006; 25:207-21. [PMID: 15643617 DOI: 10.1002/humu.20133] [Citation(s) in RCA: 116] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Although gross insertions (>20 bp) comprise <1% of disease-causing mutations, they nevertheless represent an important category of pathological lesion. In an attempt to study these insertions in a systematic way, 158 gross insertions ranging in size between 21 bp and approximately 10 kb were identified using the Human Gene Mutation Database (www.hgmd.org). A careful meta-analytical study revealed extensive diversity in terms of the nature of the inserted DNA sequence and has provided new insights into the underlying mutational mechanisms. Some 70% of gross insertions were found to represent sequence duplications of different types (tandem, partial tandem, or complex). Although most of the tandem duplications were explicable by simple replication slippage, the three complex duplications appear to result from multiple slippage events. Some 11% of gross insertions were attributable to nonpolyglutamine repeat expansions (including octapeptide repeat expansions in the prion protein gene [PRNP] and polyalanine tract expansions) and evidence is presented to support the contention that these mutations are also caused by replication slippage rather than by unequal crossing over. Some 17% of gross insertions, all >or=276 bp in length, were found to be due to LINE-1 (L1) retrotransposition involving different types of element (L1 trans-driven Alu, L1 direct, and L1 trans-driven SVA). A second example of pathological mitochondrial-nuclear sequence transfer was identified in the USH1C gene but appears to arise via a novel mechanism, trans-replication slippage. Finally, evidence for another novel mechanism of human genetic disease, involving the possible capture of DNA oligonucleotides, is presented in the context of a 26-bp insertion into the ERCC6 gene.
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Affiliation(s)
- Jian-Min Chen
- INSERM (Institut National de la Santé et de la Recherche Médicale) U613-Génétique Moléculaire et Génétique Epidémiologique, Université de Bretagne Occidentale, Centre Hospitalier Universitaire, Brest, France.
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18
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Dudley DD, Chaudhuri J, Bassing CH, Alt FW. Mechanism and control of V(D)J recombination versus class switch recombination: similarities and differences. Adv Immunol 2006; 86:43-112. [PMID: 15705419 DOI: 10.1016/s0065-2776(04)86002-4] [Citation(s) in RCA: 214] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
V(D)J recombination is the process by which the variable region exons encoding the antigen recognition sites of receptors expressed on B and T lymphocytes are generated during early development via somatic assembly of component gene segments. In response to antigen, somatic hypermutation (SHM) and class switch recombination (CSR) induce further modifications of immunoglobulin genes in B cells. CSR changes the IgH constant region for an alternate set that confers distinct antibody effector functions. SHM introduces mutations, at a high rate, into variable region exons, ultimately allowing affinity maturation. All of these genomic alteration processes require tight regulatory control mechanisms, both to ensure development of a normal immune system and to prevent potentially oncogenic processes, such as translocations, caused by errors in the recombination/mutation processes. In this regard, transcription of substrate sequences plays a significant role in target specificity, and transcription is mechanistically coupled to CSR and SHM. However, there are many mechanistic differences in these reactions. V(D)J recombination proceeds via precise DNA cleavage initiated by the RAG proteins at short conserved signal sequences, whereas CSR and SHM are initiated over large target regions via activation-induced cytidine deaminase (AID)-mediated DNA deamination of transcribed target DNA. Yet, new evidence suggests that AID cofactors may help provide an additional layer of specificity for both SHM and CSR. Whereas repair of RAG-induced double-strand breaks (DSBs) involves the general nonhomologous end-joining DNA repair pathway, and CSR also depends on at least some of these factors, CSR requires induction of certain general DSB response factors, whereas V(D)J recombination does not. In this review, we compare and contrast V(D)J recombination and CSR, with particular emphasis on the role of the initiating enzymes and DNA repair proteins in these processes.
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Affiliation(s)
- Darryll D Dudley
- Howard Hughes Medical Institute, The Children's Hospital Boston, CBR Institute for Biomedical Research, and Harvard Medical School, Boston, MA 02115, USA
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19
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20
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Liu Y, Fan R, Zhou S, Yu Z, Zhang Z. Potential Contribution of VH Gene Replacement in Immunity and Disease. Ann N Y Acad Sci 2005; 1062:175-81. [PMID: 16461800 DOI: 10.1196/annals.1358.020] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
VH replacement occurs through RAG-mediated recombination between a cryptic recombination signal sequence (cRSS) presented in a rearranged VH gene and a 23-bp RSS from an upstream VH gene. VH replacement renews the entire VH coding region and extends the immunoglobulin heavy-chain (IgH) CDR3 regions preferentially with charged amino acids. VH replacement occurs in bone marrow-immature B cells and contributes significantly to the primary B-cell repertoire in humans. However, the biological significance of VH replacement is not clear. Our recent studies revealed elevated frequencies of VH replacement products in different autoimmune diseases, including rheumatoid arthritis, systemic lupus erythematosus, and Sjögren's syndrome. Moreover, elevated frequencies of VH replacement products were also found in patients with human immunodeficiency virus or hepatitis C virus infections. These results provide the first clue that VH replacement contributes to autoimmune disease and antiviral immunity, and they also suggest a potential link between viral infection and autoimmune disease.
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Affiliation(s)
- Yanwen Liu
- Division of Developmental and Clinical Immunology, University of Alabama at Birmingham, WTI378, 1824 6th Ave. S., Birmingham, AL 35294-3300, USA
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21
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Abstract
Epigenetic events that contribute to the assembly and maintenance of silent chromatin structures have been defined through genetic, molecular, and cytological studies in a variety of eukaryotic model organisms. However, the precise cascade of events responsible for converting a developmentally regulated gene from an active euchromatic state to a heritably silent heterochromatic state remains to be elucidated. To establish a molecular framework for studying this cascade, we examined the temporal order of events associated with silencing of the murine terminal transferase (Dntt) gene during thymocyte maturation. This article describes our findings in the context of current knowledge of gene silencing mechanisms.
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Affiliation(s)
- Ruey-Chyi Su
- Howard Hughes Medical Institute, Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, USA
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22
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McLean GR, Olsen OA, Watt IN, Rathanaswami P, Leslie KB, Babcook JS, Schrader JW. Recognition of human cytomegalovirus by human primary immunoglobulins identifies an innate foundation to an adaptive immune response. THE JOURNAL OF IMMUNOLOGY 2005; 174:4768-78. [PMID: 15814702 DOI: 10.4049/jimmunol.174.8.4768] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Most primates, including humans, are chronically infected with cospecifically evolved, potentially pathogenic CMV. Abs that bind a 10-aa linear epitope (antigenic determinant 2 site 1) within the extracellular domain of human CMV glycoprotein B neutralize viral infectivity. In this study, we show that genes generated by recombinations involving two well-conserved human germline V elements (IGHV3-30 and IGKV3-11), and IGHJ4, encode primary Ig molecules that bind glycoprotein B at this key epitope. These particular V(H), J(H), and V(kappa) genes enable humans to generate through recombination and N nucleotide addition, a useful frequency of primary Igs that efficiently target this critical site on human CMV and thus confer an innate foundation for a specific adaptive response to this pathogen.
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Affiliation(s)
- Gary R McLean
- The Biomedical Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
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23
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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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24
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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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25
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Link JM, Larson JE, Schroeder HW. Despite extensive similarity in germline DH and JH sequence, the adult Rhesus macaque CDR-H3 repertoire differs from human. Mol Immunol 2004; 42:943-55. [PMID: 15829286 DOI: 10.1016/j.molimm.2004.09.027] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2004] [Accepted: 09/21/2004] [Indexed: 11/28/2022]
Abstract
Rhesus macaques (Macaca mulatta) and chimpanzees (Pan troglodytes) are frequently used models for the study and treatment of human infectious diseases, including AIDS. Confidence in the equivalence to human of the humoral immune responses of these higher primates has grown as studies of immunoglobulin germline sequences have documented average identities of 90% or greater to human counterparts. The most variable component of the immunoglobulin heavy chain, complementarity determining region 3 (CDR-H3) is the product of somatic (junctional) as well as germline (combinatorial) mechanisms of diversity. Located at the center of the antigen binding site, CDR-H3 often exerts a dominant role in antibody specificity and affinity. To test whether similarity in germline DH and JH sequence would yield similarity in CDR-H3 composition in the expressed repertoire, we compared IgM CDR-H3 transcripts from Rhesus and chimpanzee blood to human. In fetal Rhesus, the range and mean of CDR-H3 lengths was similar to that observed in fetal human. However, the Rhesus repertoire of adult muCDR-H3 transcripts did not contain the longer hypervariable intervals that humans begin to express late in the second trimester of fetal life. Conversely, the adult chimpanzee repertoire included more long CDR-H3 structures than human. The differences between these adult repertoires reflected fine changes in N addition and terminal nucleotide loss. We conclude that the same mechanisms that refine and shape CDR-H3 diversity during ontogeny can also be used to fine tune and individualize species-specific antibody repertoires despite germline immunoglobulin sequence similarity.
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Affiliation(s)
- Jason M Link
- Division of Developmental and Clinical Immunology, Department of Microbiology, University of Alabama at Birmingham, AL 35294-3300, USA
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26
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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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27
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Abstract
First observed in mouse pre-B-cell lines and then in knock-in mice carrying self-reactive IgH transgenes, VH replacement has now been shown to contribute to the primary B-cell repertoire in humans. Through recombination-activating gene (RAG)-mediated recombination between a cryptic recombination signal sequence (RSS) present in almost all VH genes and the flanking 23 base pair RSS of an upstream VH gene, VH replacement renews the entire VH-coding region, while leaving behind a short stretch of nucleotides as a VH replacement footprint. In addition to extending the CDR3 region, the VH replacement footprints preferentially contribute charged amino acids. VH replacement rearrangement in immature B cells may either eliminate a self-reactive B-cell receptor or contribute to the generation of self-reactive antibodies. VH replacement may also rescue non-productive or dysfunctional VHDJH rearrangement in pro-B and pre-B cells. Conversely, VH replacement of a productive immunoglobulin H gene may generate non-productive VH replacement to disrupt or temporarily reverse the B-cell differentiation process. VH replacement can thus play a complex role in the generation of the primary B-cell repertoire.
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Affiliation(s)
- Zhixin Zhang
- Division of Developmental and Clinical Immunology, University of Alabama at Birmingham, Birmingham, AL 35294-3300, USA
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28
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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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29
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Morita M, Stamp G, Robins P, Dulic A, Rosewell I, Hrivnak G, Daly G, Lindahl T, Barnes DE. Gene-targeted mice lacking the Trex1 (DNase III) 3'-->5' DNA exonuclease develop inflammatory myocarditis. Mol Cell Biol 2004; 24:6719-27. [PMID: 15254239 PMCID: PMC444847 DOI: 10.1128/mcb.24.15.6719-6727.2004] [Citation(s) in RCA: 287] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
TREX1, originally designated DNase III, was isolated as a major nuclear DNA-specific 3'-->5' exonuclease that is widely distributed in both proliferating and nonproliferating mammalian tissues. The cognate cDNA shows homology to the editing subunit of the Escherichia coli replicative DNA polymerase III holoenzyme and encodes an exonuclease which was able to serve a DNA-editing function in vitro, promoting rejoining of a 3' mismatched residue in a reconstituted DNA base excision repair system. Here we report the generation of gene-targeted Trex1(-/-) mice. The null mice are viable and do not show the increase in spontaneous mutation frequency or cancer incidence that would be predicted if Trex1 served an obligatory role of editing mismatched 3' termini generated during DNA repair or DNA replication in vivo. Unexpectedly, Trex1(-/-) mice exhibit a dramatically reduced survival and develop inflammatory myocarditis leading to progressive, often dilated, cardiomyopathy and circulatory failure.
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Affiliation(s)
- Masashi Morita
- Cancer Research UK, London Research Institute, Clare Hall Laboratories, South Mimms, Hertfordshire EN6 3LD, United Kingdom
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30
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Doyen N, Boulé JB, Rougeon F, Papanicolaou C. Evidence that the long murine terminal deoxynucleotidyltransferase isoform plays no role in the control of V(D)J junctional diversity. THE JOURNAL OF IMMUNOLOGY 2004; 172:6764-7. [PMID: 15153493 DOI: 10.4049/jimmunol.172.11.6764] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Two TdT isoforms have been found in the mouse. The short isoform is known to add N regions to gene segment junctions during V(D)J recombination, but the role of the long (TdTL) isoform is controversial. We have shown that TdTL, although endowed with terminal transferase activity, is thermally unstable and unable to add N regions in vivo. In this study, we demonstrate that TdTL is devoid of 3'-5' exonuclease activity, and provide an analysis of nucleotide deletion and addition patterns in large series of V(D)J coding joins, arguing against a role of TdTL in the control of junctional diversity in Igs and TCRs.
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Affiliation(s)
- Noëlle Doyen
- Unité de Génétique et Biochimie du Développement, Unité de Recherche Associée Centre National de la Recherche Scientifique 2581, Institut Pasteur, Paris, France
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31
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Ramadan K, Shevelev IV, Maga G, Hübscher U. De novo DNA synthesis by human DNA polymerase lambda, DNA polymerase mu and terminal deoxyribonucleotidyl transferase. J Mol Biol 2004; 339:395-404. [PMID: 15136041 DOI: 10.1016/j.jmb.2004.03.056] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2004] [Revised: 03/18/2004] [Accepted: 03/19/2004] [Indexed: 11/23/2022]
Abstract
DNA polymerases (pols) catalyse the synthesis of DNA. This reaction requires a primer-template DNA in order to grow from the 3'OH end of the primer along the template. On the other hand terminal deoxyribonucleotidyl transferase (TdT) catalyses the addition of nucleotides at the 3'OH end of a DNA strand, without the need of a template. Pol lambda and pol micro are ubiquitous enzymes, possess both DNA polymerase and terminal deoxyribonucleotidyl transferase activities and belong to pol X family, together with pol beta and TdT. Here we show that pol lambda, pol micro and TdT, all possess the ability to synthesise in vitro short fragments of DNA in the absence of a primer-template or even a primer or a template in the reaction. The DNA synthesised de novo by pol lambda, pol micro and TdT appears to have an unusual structure. Furthermore we found that the amino acid Phe506 of pol lambda is essential for the de novo synthesis. This novel catalytic activity might be related to the proposed functions of these three pol X family members in DNA repair and DNA recombination.
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Affiliation(s)
- Kristijan Ramadan
- Institute of Veterinary Biochemistry and Molecular Biology, University of Zürich-Irchel, Winterthurerstrasse 190, CH-8057, Zürich, Switzerland
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32
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Sawchuk DJ, Mansilla-Soto J, Alarcon C, Singha NC, Langen H, Bianchi ME, Lees-Miller SP, Nussenzweig MC, Cortes P. Ku70/Ku80 and DNA-dependent Protein Kinase Catalytic Subunit Modulate RAG-mediated Cleavage. J Biol Chem 2004; 279:29821-31. [PMID: 15123719 DOI: 10.1074/jbc.m403706200] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The 12/23 rule is a critical step for regulation of V(D)J recombination. To date, only the RAG proteins and high mobility group protein 1 or 2 have been implicated in 12/23 regulation. Through protein fractionation and biochemical experiments, we find that Ku70/Ku80 and DNA-dependent protein kinase catalytic subunit (DNA-PKcs) modulate RAG-mediated cleavage. Modulation of cleavage by Ku70/80 and DNA-PKcs results in preferential inhibition of 12/12 and 23/23 DNA cleavage, thus increasing 12/23 rule specificity. This observation indicates that DNA repair factors, Ku70/80 and DNA-PKcs, might be present upstream of the DNA cleavage events and not recruited downstream as is currently thought, assigning new nonrepair functions to the DNA-dependent protein kinase.
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Affiliation(s)
- Dennis J Sawchuk
- Laboratory of Molecular Immunology and Howard Hughes Medical Institute, The Rockefeller University, New York, New York 10021, USA
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33
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Golub R, André S, Hassanin A, Affaticati P, Larijani M, Fellah JS. Early expression of two TdT isoforms in the hematopoietic system of the Mexican axolotl. Implications for the evolutionary origin of the N-nucleotide addition. Immunogenetics 2004; 56:204-13. [PMID: 15146297 DOI: 10.1007/s00251-004-0681-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2003] [Revised: 04/20/2004] [Indexed: 11/28/2022]
Abstract
Nontemplate (N)-nucleotide addition by the terminal dideoxynucleotidyl transferase (TdT) at the junctions of rearranging V( D) J gene segments greatly contribute to antigen-receptor diversity. TdT has been identified in several vertebrate species, where it is highly conserved. We report here the isolation of two forms of TdT mRNA in an amphibian, the Mexican axolotl. The isoform TdT1 shares all of the conserved structural motifs required for TdT activity and displays an average of 50-58% similarity at the amino acid level with TdT of other species. The second axolotl TdT variant ( TdT2) differs from TdT1 by a 57-amino acid deletion located between amino acids 165-222 of TdT1, including the first helix-hairpin-helix DNA-binding motif. During ontogeny, TdT products are first detected in the head of 6-week-old larvae and further in the head and trunk of 8-month-old larvae. These developmental stages correspond to the first detection of RAG1 and antigen-receptor (TCRbeta and IgHmicro) products in axolotl larvae. Our results suggest that in contrast to mammalian development, N diversity occurs early in axolotl development to diversify the primary repertoire. Phylogenetic analyses reveal that TdT and DNA polymerase mu(Pol mu) genes are closely related, and that both enzymes were already present in the common ancestor of jawed vertebrates.
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Affiliation(s)
- Rachel Golub
- Unité du Développement des Lymphocytes, CNRS URA 1961 Institut Pasteur, 25-28 rue du Docteur Roux, 75724, Paris Cedex 15, France
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Rumfelt LL, Lohr RL, Dooley H, Flajnik MF. Diversity and repertoire of IgW and IgM VH families in the newborn nurse shark. BMC Immunol 2004; 5:8. [PMID: 15132758 PMCID: PMC420240 DOI: 10.1186/1471-2172-5-8] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2004] [Accepted: 05/06/2004] [Indexed: 11/10/2022] Open
Abstract
Background Adult cartilaginous fish express three immunoglobulin (Ig) isotypes, IgM, IgNAR and IgW. Newborn nurse sharks, Ginglymostoma cirratum, produce 19S (multimeric) IgM and monomeric/dimeric IgM1gj, a germline-joined, IgM-related VH, and very low amounts of 7S (monomeric) IgM and IgNAR proteins. Newborn IgNAR VH mRNAs are diverse in the complementarity-determining region 3 (CDR3) with non-templated nucleotide (N-region) addition, which suggests that, unlike in many other vertebrates, terminal deoxynucleotidyl transferase (TdT) expressed at birth is functional. IgW is present in the lungfish, a bony fish sharing a common ancestor with sharks 460 million years ago, implying that the IgW VH family is as old as the IgM VH family. This nurse shark study examined the IgM and IgW VH repertoire from birth through adult life, and analyzed the phylogenetic relationships of these gene families. Results IgM and IgW VH cDNA clones isolated from newborn nurse shark primary and secondary lymphoid tissues had highly diverse and unique CDR3 with N-region addition and VDJ gene rearrangement, implicating functional TdT and RAG gene activity. Despite the clear presence of N-region additions, newborn CDR3 were significantly shorter than those of adults. The IgM clones are all included in a conventional VH family that can be classified into five discrete groups, none of which is orthologous to IgM VH genes in other elasmobranchs. In addition, a novel divergent VH family was orthologous to a published monotypic VH horn shark family. IgW VH genes have diverged sufficiently to form three families. IgM and IgW VH serine codons using the potential somatic hypermutation hotspot sequence occur mainly in VH framework 1 (FR1) and CDR1. Phylogenetic analysis of cartilaginous fish and lungfish IgM and IgW demonstrated they form two major ancient gene groups; furthermore, these VH genes generally diversify (duplicate and diverge) within a species. Conclusion As in ratfish, sandbar and horn sharks, most nurse shark IgM VH genes are from one family with multiple, heterogeneous loci. Their IgW VH genes have diversified, forming at least three families. The neonatal shark Ig VH CDR3 repertoire, diversified via N-region addition, is shorter than the adult VDJ junction, suggesting one means of postnatal repertoire diversification is expression of longer CDR3 junctions.
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Affiliation(s)
- Lynn L Rumfelt
- Department of Microbiology and Immunology, University of Miami School of Medicine, Miami, FL 33101 USA
- Department of Immunology, University of Toronto, Sunnybrook & Women's College Health Sciences Centre, 2075 Bayview Avenue, Toronto, Ontario M4N 3M5 Canada
| | - Rebecca L Lohr
- Department of Microbiology and Immunology, University of Maryland School of Medicine, 655 W. Baltimore St., Rm. BRB-13009, Baltimore, MD 21201 USA
| | - Helen Dooley
- Department of Microbiology and Immunology, University of Maryland School of Medicine, 655 W. Baltimore St., Rm. BRB-13009, Baltimore, MD 21201 USA
| | - Martin F Flajnik
- Department of Microbiology and Immunology, University of Miami School of Medicine, Miami, FL 33101 USA
- Department of Microbiology and Immunology, University of Maryland School of Medicine, 655 W. Baltimore St., Rm. BRB-13009, Baltimore, MD 21201 USA
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Sandor Z, Calicchio ML, Sargent RG, Roth DB, Wilson JH. Distinct requirements for Ku in N nucleotide addition at V(D)J- and non-V(D)J-generated double-strand breaks. Nucleic Acids Res 2004; 32:1866-73. [PMID: 15047854 PMCID: PMC390357 DOI: 10.1093/nar/gkh502] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2004] [Revised: 03/03/2004] [Accepted: 03/03/2004] [Indexed: 12/18/2022] Open
Abstract
Loss or addition of nucleotides at junctions generated by V(D)J recombination significantly expands the antigen-receptor repertoire. Addition of nontemplated (N) nucleotides is carried out by terminal deoxynucleotidyl transferase (TdT), whose only known physiological role is to create diversity at V(D)J junctions during lymphocyte development. Although purified TdT can act at free DNA ends, its ability to add nucleotides (i.e. form N regions) at coding joints appears to depend on the nonhomologous end-joining factor Ku80. Because the DNA ends generated during V(D)J rearrangements remain associated with the RAG proteins after cleavage, TdT might be targeted for N region addition through interactions with RAG proteins or with Ku80 during remodeling of the post-cleavage complex. Such regulated access would help to prevent TdT from acting at other types of broken ends and degrading the fidelity of end joining. To test this hypothesis, we measured TdT's ability to add nucleotides to endonuclease-induced chromosomal and extrachromosomal breaks. In both cases TdT added nucleotides efficiently to the cleaved DNA ends. Strikingly, the frequency of N regions at non-V(D)J-generated ends was not dependent on Ku80. Thus our results suggest that Ku80 is required to allow TdT access to RAG post-cleavage complexes, providing support for the hypothesis that Ku is involved in disassembling or remodeling the post-cleavage complex. We also found that N regions were abnormally long in the absence of Ku80, indicating that Ku80 may regulate TdT's activity at DNA ends in vivo.
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Affiliation(s)
- Zoltan Sandor
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
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Abstract
Cells have high-fidelity polymerases whose task is to accurately replicate the genome, and low-fidelity polymerases with specialized functions. Although some of these low-fidelity polymerases are exceptional in their ability to replicate damaged DNA and restore the undamaged sequence, they are error prone on undamaged DNA. In fact, these error-prone polymerases are sometimes used in circumstances where the capacity to make errors has a selective advantage. The mutagenic potential of the error-prone polymerases requires that their expression, activity, and access to undamaged DNA templates be regulated. Here we review these specialized polymerases with an emphasis on their biological roles.
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Affiliation(s)
- Alison J Rattray
- Gene Regulation and Chromosome Biology Laboratory, NCI-Frederick, National Cancer Institute, National Institutes of Health, Frederick, Maryland 21702, USA.
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Bartl S, Miracle AL, Rumfelt LL, Kepler TB, Mochon E, Litman GW, Flajnik MF. Terminal deoxynucleotidyl transferases from elasmobranchs reveal structural conservation within vertebrates. Immunogenetics 2003; 55:594-604. [PMID: 14579105 DOI: 10.1007/s00251-003-0608-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2003] [Revised: 08/25/2003] [Indexed: 01/21/2023]
Abstract
The DNA polymerase (pol) X family is an ancient group of enzymes that function in DNA replication and repair (pol beta), translesion synthesis (pol lambda and pol micro) and terminal addition of non-templated nucleotides. This latter terminal deoxynucleotidyl transferase (TdT) activity performs the unique function of providing diversity at coding joins of immunoglobulin and T-cell receptor genes. The first isolated full-length TdT genes from shark and skate are reported here. Comparisons with the three-dimensional structure of mouse TdT indicate structural similarity with elasmobranch orthologues that supports both a template-independent mode of replication and a lack of strong nucleotide bias. The vertebrate TdTs appear more closely related to pol micro and fungal polymerases than to pol lambda and pol beta. Thus, unlike other molecules of adaptive immunity, TdT is a member of an ancient gene family with a clear gene phylogeny and a high degree of similarity, which implies the existence of TdT ancestors in jawless fishes and invertebrates.
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Affiliation(s)
- Simona Bartl
- Moss Landing Marine Laboratories, 8272 Moss Landing Road, CA 95039, Moss Landing, USA.
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Bertocci B, De Smet A, Berek C, Weill JC, Reynaud CA. Immunoglobulin kappa light chain gene rearrangement is impaired in mice deficient for DNA polymerase mu. Immunity 2003; 19:203-11. [PMID: 12932354 DOI: 10.1016/s1074-7613(03)00203-6] [Citation(s) in RCA: 116] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
DNA polymerase mu (pol mu) is a template-dependent polymerase closely related to the lymphoid-specific enzyme terminal deoxynucleotidyl transferase (TdT). We report here the phenotype of pol mu-deficient mice. Such animals display an abnormal B cell differentiation, with a specific alteration in the IgM- to IgM+ transition in bone marrow. In all mice, Ig light chain gene rearrangement is impaired at the level of the Vkappa-Jkappa and Vlambda-Jlambda junctions, which show extensive nibbling of both coding extremities. These alterations lead to a profound defect in the peripheral B cell compartment which, although variable between animals, results in an average 40% reduction in the splenic B cell fraction. Pol mu appears, therefore, as a key element contributing to the relative homogeneity in size of light chain CDR3 and taking part in Ig gene rearrangement at a stage where TdT is no longer expressed.
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Affiliation(s)
- Barbara Bertocci
- Institut National Français de Recherche Médicale U373, Faculté de Médecine Necker-Enfants Malades, 156 rue de Vaugirard, 75730 Paris 15, France
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