101
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Faili A, Aoufouchi S, Flatter E, Guéranger Q, Reynaud CA, Weill JC. Induction of somatic hypermutation in immunoglobulin genes is dependent on DNA polymerase iota. Nature 2002; 419:944-7. [PMID: 12410315 DOI: 10.1038/nature01117] [Citation(s) in RCA: 156] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2002] [Accepted: 08/20/2002] [Indexed: 11/09/2022]
Abstract
Somatic hypermutation of immunoglobulin genes is a unique, targeted, adaptive process. While B cells are engaged in germinal centres in T-dependent responses, single base substitutions are introduced in the expressed Vh/Vl genes to allow the selection of mutants with a higher affinity for the immunizing antigen. Almost every possible DNA transaction has been proposed to explain this process, but each of these models includes an error-prone DNA synthesis step that introduces the mutations. The Y family of DNA polymerases--pol eta, pol iota, pol kappa and rev1--are specialized for copying DNA lesions and have high rates of error when copying a normal DNA template. By performing gene inactivation in a Burkitt's lymphoma cell line inducible for hypermutation, we show here that somatic hypermutation is dependent on DNA polymerase iota.
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Affiliation(s)
- Ahmad Faili
- INSERM U373, Faculté de Médecine Necker-Enfants Malades, 156 rue de Vaugirard, 75730, Paris Cedex 15, France
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102
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Abstract
Somatic hypermutation and switch recombination of immunoglobulin genes require the activity of the activation-induced deaminase, AID. Recent studies of mice deficient for the uracil-DNA glycosylase UNG, which removes U from DNA, suggest that AID catalyses the deamination of dC to dU during antibody diversification.
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Affiliation(s)
- Ursula Storb
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL 60637, USA
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103
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104
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Faili A, Aoufouchi S, Guéranger Q, Zober C, Léon A, Bertocci B, Weill JC, Reynaud CA. AID-dependent somatic hypermutation occurs as a DNA single-strand event in the BL2 cell line. Nat Immunol 2002; 3:815-21. [PMID: 12145648 DOI: 10.1038/ni826] [Citation(s) in RCA: 147] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Immunoglobulin (Ig) gene hypermutation can be induced in the BL2 Burkitt's lymphoma cell line by IgM cross-linking and coculture with normal or transformed T helper clones. We describe here a T cell#150;independent in vitro induction assay, by which hypermutation is induced in BL2 cells through simultaneous aggregation of three surface receptors: IgM, CD19 and CD21. The mutations arise as a post-transcriptional event within 90 min. They are stably introduced in the G1 phase of the cell cycle, occurring in one of the two variable gene DNA strands, and eventually become fixed by replication in one of the daughter cells. Inactivation of AID (activation-induced cytidine deaminase) by homologous recombination in BL2 cells completely inhibits the process, thus validating this induction procedure as a model for the in vivo mechanism.
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Affiliation(s)
- Ahmad Faili
- INSERM U373, Faculté de Médecine Necker-Enfants Malades, Paris, France
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105
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Affiliation(s)
- Alberto Martin
- Department of Cell Biology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Chanin 403, Bronx, New York 10461, USA.
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106
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Pavlov YI, Rogozin IB, Galkin AP, Aksenova AY, Hanaoka F, Rada C, Kunkel TA. Correlation of somatic hypermutation specificity and A-T base pair substitution errors by DNA polymerase eta during copying of a mouse immunoglobulin kappa light chain transgene. Proc Natl Acad Sci U S A 2002; 99:9954-9. [PMID: 12119399 PMCID: PMC126606 DOI: 10.1073/pnas.152126799] [Citation(s) in RCA: 102] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
To test the hypothesis that inaccurate DNA synthesis by mammalian DNA polymerase eta (pol eta) contributes to somatic hypermutation (SHM) of Ig genes, we measured the error specificity of mouse pol eta during synthesis of each strand of a mouse Ig kappa light chain transgene. We then compared the results to the base substitution specificity of SHM of this same gene in the mouse. The in vitro and in vivo base substitution spectra shared a number of common features. A highly significant correlation was observed for overall substitutions at A-T pairs but not for substitutions at G-C pairs. Sixteen mutational hotspots at A-T pairs observed in vivo were also found in spectra generated by mouse pol eta in vitro. The correlation was strongest for errors made by pol eta during synthesis of the non-transcribed strand, but it was also observed for synthesis of the transcribed strand. These facts, and the distribution of substitutions generated in vivo, support the hypothesis that pol eta contributes to SHM of Ig genes at A-T pairs via short patches of low fidelity DNA synthesis of both strands, but with a preference for the non-transcribed strand.
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Affiliation(s)
- Youri I Pavlov
- Laboratories of Molecular Genetics and Structural Biology, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA.
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107
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Abstract
The majority of both spontaneous and DNA damage-induced mutations in eukaryotes result from replication processes in which DNA polymerase zeta (Polzeta) and Rev1 protein (Rev1p) play major roles. Understanding these roles is likely to provide information relevant to the origin of genetic diseases, such as cancer, and may provide new insights for their prevention. DNA Polzeta also appears to be involved in the somatic hypermutability that occurs during development of the immune response. The results from a variety of genetic and enzymological investigations have started to delineate the cellular roles of these enzymes, but a number of important issues have not yet been resolved and much remains to be learned. Questions concerning the possible existence of other subunits to these enzymes, of their possible association with one another or with other proteins, of the nature of their enzymatic activities and of the relative roles played by these and other DNA polymerases in the bypass of different kinds of DNA damage, require further investigation. Finally, very little is known about the way these enzymes are regulated and brought into play when needed.
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Affiliation(s)
- Christopher W Lawrence
- Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA
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108
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Honjo T, Kinoshita K, Muramatsu M. Molecular mechanism of class switch recombination: linkage with somatic hypermutation. Annu Rev Immunol 2002; 20:165-96. [PMID: 11861601 DOI: 10.1146/annurev.immunol.20.090501.112049] [Citation(s) in RCA: 481] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Class switch recombination (CSR) and somatic hypermutation (SHM) have been considered to be mediated by different molecular mechanisms because both target DNAs and DNA modification products are quite distinct. However, involvement of activation-induced cytidine deaminase (AID) in both CSR and SHM has revealed that the two genetic alteration mechanisms are surprisingly similar. Accumulating data led us to propose the following scenario: AID is likely to be an RNA editing enzyme that modifies an unknown pre-mRNA to generate mRNA encoding a nicking endonuclease specific to the stem-loop structure. Transcription of the S and V regions, which contain palindromic sequences, leads to transient denaturation, forming the stem-loop structure that is cleaved by the AID-regulated endonuclease. Cleaved single-strand tails will be processed by error-prone DNA polymerase-mediated gap-filling or exonuclease-mediated resection. Mismatched bases will be corrected or fixed by mismatch repair enzymes. CSR ends are then ligated by the NHEJ system while SHM nicks are repaired by another ligation system.
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Affiliation(s)
- Tasuku Honjo
- Department of Medical Chemistry, Graduate School of Medicine, Kyoto University, Yoshida, Sakyo-ku, Kyoto 606-8501, Japan.
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109
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Bertocci B, De Smet A, Flatter E, Dahan A, Bories JC, Landreau C, Weill JC, Reynaud CA. Cutting edge: DNA polymerases mu and lambda are dispensable for Ig gene hypermutation. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2002; 168:3702-6. [PMID: 11937519 DOI: 10.4049/jimmunol.168.8.3702] [Citation(s) in RCA: 114] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Mutations arising in Ig V genes during an immune response are most likely introduced by one or several error-prone DNA polymerases. Many of the recently described nonreplicative DNA polymerases have an intrinsic fidelity compatible with such an activity, the strongest candidates being polymerase (pol) eta, pol iota, pol zeta, and pol mu. We report in this work that mice inactivated for either of the two polymerases related to pol beta (i.e., pol mu and pol lambda) are viable and fertile and display a normal hypermutation pattern.
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Affiliation(s)
- Barbara Bertocci
- Institut National de la Santé et de la Recherche Médicale, Unité 373, Faculté de Médecine Necker-Enfants Malades, Paris, France
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110
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Abstract
Immunoglobulin hypermutation provides the structural correlate for the affinity maturation of the antibody response. Characteristic modalities of this mechanism include a preponderance of point-mutations with prevalence of transitions over transversions, and the mutational hotspot RGYW sequence. Recent evidence suggests a mechanism whereby DNA-breaks induce error-prone DNA synthesis in immunoglobulin V(D)J regions by error-prone DNA polymerases. The nature of the targeting mechanism and the trans-factors effecting such breaks and their repair remain to be determined.
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Affiliation(s)
- Marilyn Diaz
- Department of Immunology, Imm16, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Paolo Casali
- Division of Molecular Immunology, C-410, Cornell University Weill Medical College, 1300 York Avenue, New York, NY 10021, USA
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111
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Abstract
Organisms control the specificity and frequency with which they mutate via their complement of proteins. The mismatch repair (MMR) proteins correct errors after they are made. The DNA polymerases of the cell determine the response to damaged DNA which has not been repaired by excision. Polymerase action can be considered as consisting of three main steps: addition of a base, proofreading of the added nucleotide and elongation. Each of these steps is kinetically complex and can be modulated. The modulation accounts for different behaviors of organisms in response to stress. The recent findings of DNA polymerases with properties appropriate for dealing with damaged DNA may help to account for the phenomenon of spontaneous mutation and for the hypermutability associated with immunoglobulin maturation and carcinogenesis.
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Affiliation(s)
- Bernard S Strauss
- Department of Molecular Genetics and Cell Biology, The University of Chicago, 920 East 58th Street, Chicago, IL 60637, USA.
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112
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Rogozin IB, Kunkel TA, Pavlov YI. Double-strand breaks in DNA during somatic hypermutation of Ig genes: cause or consequence? Trends Immunol 2002; 23:12-3. [PMID: 11801448 DOI: 10.1016/s1471-4906(01)02112-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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113
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Michael N, Martin TE, Nicolae D, Kim N, Padjen K, Zhan P, Nguyen H, Pinkert C, Storb U. Effects of sequence and structure on the hypermutability of immunoglobulin genes. Immunity 2002; 16:123-34. [PMID: 11825571 DOI: 10.1016/s1074-7613(02)00261-3] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Somatic hypermutation (SHM) is investigated in related immunoglobulin transgenes that differ in a short artificial sequence designed to vary the content of hotspot motifs and the potential to form RNA or DNA secondary structures. Mutability depends on hotspots, not secondary structure. Hotspot motifs predict about 50% of the mutations; the rest are in neutral and coldspots. Clusters of mutations and the sequential addition of mutations found in cell pedigrees suggest epigenetic attributes of SHM. Sometime in SHM, an essential factor seems to become limiting. Particular error-prone DNA polymerases appear to create mutations in hotspots on the top and bottom DNA strands throughout the target and the SHM process. One transgene is superhypermutable in all regions, suggesting the presence of a cis-element that enhances SHM.
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Affiliation(s)
- Nancy Michael
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL 60637, USA
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114
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Gearhart PJ, Wood RD. Emerging links between hypermutation of antibody genes and DNA polymerases. Nat Rev Immunol 2001; 1:187-92. [PMID: 11905827 DOI: 10.1038/35105009] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Substantial antibody variability is created when nucleotide substitutions are introduced into immunoglobulin variable genes by a controlled process of hypermutation. Evidence points to a mechanism involving DNA repair events at sites of targeted breaks. In vertebrate cells, there are many recently identified DNA polymerases that inaccurately copy templates. Some of these are candidates for enzymes that introduce base changes during hypermutation. Recent research has focused on possible roles for DNA polymerases zeta (POLZ), eta (POLH), iota (POLI), and mu (POLM) in the process.
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Affiliation(s)
- P J Gearhart
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, Baltimore, Maryland 21224, USA.
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115
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Longo NS, Lipsky PE. Somatic hypermutation in human B cell subsets. SPRINGER SEMINARS IN IMMUNOPATHOLOGY 2001; 23:367-85. [PMID: 11826615 DOI: 10.1007/s281-001-8165-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- N S Longo
- National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892, USA
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116
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117
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118
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Diaz M, Flajnik MF, Klinman N. Evolution and the molecular basis of somatic hypermutation of antigen receptor genes. Philos Trans R Soc Lond B Biol Sci 2001; 356:67-72. [PMID: 11205333 PMCID: PMC1087693 DOI: 10.1098/rstb.2000.0750] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Somatic hypermutation of immunoglobulin genes occurs in many vertebrates including sharks, frogs, camels, humans and mice. Similarities among species reveal a common mechanism and these include the AGC/T sequence hot spot, preponderance of base substitutions, a bias towards transitions and strand bias. There are some differences among species, however, that may unveil layers of the mechanism. These include a G:C bias in frog and shark IgM but not in nurse shark antigen receptor (NAR), a high frequency of doublets in NAR hypermutation, and the co-occurrence of somatic hypermutation with gene conversion in some species. Here we argue that some of the similarities and differences among species are best explained by error-prone DNA synthesis by the translesion synthesis DNA polymerase zeta (Pol zeta) and, as suggested by others, induction of DNA synthesis by DNA breaks in antigen receptor variable genes. Finally, targeting of the variable genes is probably obtained via transcription-related elements, and it is the targeting phase of somatic hypermutation that is the most likely to reveal molecules unique to adaptive immunity.
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Affiliation(s)
- M Diaz
- Department of Immunology, The Scripps Research Institute, La Jolla, CA 92037, USA.
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