1
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Amin W, Nishio S, Honjo T, Kobayashi M. Necessity of HuR/ELAVL1 for the activation-induced cytidine deaminase-dependent decrease in topoisomerase 1 in antibody diversification. Int Immunol 2023; 35:361-375. [PMID: 37086201 DOI: 10.1093/intimm/dxad011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Accepted: 04/17/2023] [Indexed: 04/23/2023] Open
Abstract
Activation-induced cytidine deaminase (AID)-dependent DNA cleavage is the initial event of antibody gene-diversification processes such as class switch recombination (CSR) and somatic hypermutation (SHM). We previously reported the requirement of an AID-dependent decrease of topoisomerase 1 (Top1) for efficient DNA cleavage, but the underlying molecular mechanism has remained elusive. This study focuses on HuR/ELAVL1, a protein that binds to AU-rich elements in RNA. HuR-knockout (KO) CH12 cells derived from murine B lymphoma cells were found to have lower CSR and hypermutation efficiencies due to decreased AID-dependent DNA cleavage levels. The HuR-KO CH12 cells do not show impairment in cell cycles and Myc expression, which have been reported in HuR-reduced spleen B cells. Furthermore, drugs that scavenge reactive oxygen species (ROS) do not rescue the lower CSR in HuR-KO CH12 cells, meaning that ROS or decreased c-Myc protein amount is not the reason for the deficiencies of CSR and hypermutation in HuR-KO CH12 cells. We show that HuR binds to Top1 mRNA and that complete deletion of HuR abolishes AID-dependent repression of Top1 protein synthesis in CH12 cells. Additionally, reduction of CSR to IgG3 in HuR-KO cells is rescued by knockdown of Top1, indicating that elimination of the AID-dependent Top1 decrease is the cause of the inefficiency of DNA cleavage, CSR and hypermutation in HuR-KO cells. These results show that HuR is required for initiation of antibody diversification and acquired immunity through the regulation of AID-dependent DNA cleavage by repressing Top1 protein synthesis.
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Affiliation(s)
- Wajid Amin
- Department of Immunology and Genomic Medicine, Center for Cancer Immunotherapy and Immunobiology, Graduate School of Medicine, Kyoto University, 606-8501, Kyoto, Japan
| | - Shoki Nishio
- Department of Immunology and Genomic Medicine, Center for Cancer Immunotherapy and Immunobiology, Graduate School of Medicine, Kyoto University, 606-8501, Kyoto, Japan
| | - Tasuku Honjo
- Department of Immunology and Genomic Medicine, Center for Cancer Immunotherapy and Immunobiology, Graduate School of Medicine, Kyoto University, 606-8501, Kyoto, Japan
| | - Maki Kobayashi
- Department of Immunology and Genomic Medicine, Center for Cancer Immunotherapy and Immunobiology, Graduate School of Medicine, Kyoto University, 606-8501, Kyoto, Japan
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2
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de Krijger I, Boersma V, Jacobs JJL. REV7: Jack of many trades. Trends Cell Biol 2021; 31:686-701. [PMID: 33962851 DOI: 10.1016/j.tcb.2021.04.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 03/23/2021] [Accepted: 04/08/2021] [Indexed: 01/01/2023]
Abstract
The HORMA domain protein REV7, also known as MAD2L2, interacts with a variety of proteins and thereby contributes to the establishment of different complexes. With doing so, REV7 impacts a diverse range of cellular processes and gained increasing interest as more of its activities became uncovered. REV7 has important roles in translesion synthesis and mitotic progression, and acts as a central component in the recently discovered shieldin complex that operates in DNA double-strand break repair. Here we discuss the roles of REV7 in its various complexes, focusing on its activity in genome integrity maintenance. Moreover, we will describe current insights on REV7 structural features that allow it to be such a versatile protein.
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Affiliation(s)
- Inge de Krijger
- Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
| | - Vera Boersma
- Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
| | - Jacqueline J L Jacobs
- Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands.
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3
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Martin SK, Tomida J, Wood RD. Disruption of DNA polymerase ζ engages an innate immune response. Cell Rep 2021; 34:108775. [PMID: 33626348 PMCID: PMC7990024 DOI: 10.1016/j.celrep.2021.108775] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 12/22/2020] [Accepted: 01/29/2021] [Indexed: 01/07/2023] Open
Abstract
In mammalian cells, specialized DNA polymerase ζ (pol ζ) contributes to genomic stability during normal DNA replication. Disruption of the catalytic subunit Rev3l is toxic and results in constitutive chromosome damage, including micronuclei. As manifestations of this genomic stress are unknown, we examined the transcriptome of pol ζ-defective cells by RNA sequencing (RNA-seq). Expression of 1,117 transcripts is altered by ≥4-fold in Rev3l-disrupted cells, with a pattern consistent with an induction of an innate immune response. Increased expression of interferon-stimulated genes at the mRNA and protein levels in pol ζ-defective cells is driven by the cyclic guanosine monophosphate-adenosine monophosphate synthase (cGAS)-signaling partner stimulator of interferon genes (STING) pathway. Expression of key interferon-stimulated chemokines is elevated in basal epithelial mouse skin cells with a disruption of Rev3l. These results indicate that the disruption of pol ζ may simultaneously increase sensitivity to genotoxins and potentially engage parts of the innate immune response, which could add an additional benefit to targeting pol ζ in cancer therapies.
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Affiliation(s)
- Sara K Martin
- Department of Epigenetics & Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX 78507, USA; The University of Texas MD Anderson Cancer Center, UT Health Graduate School of Biomedical Sciences, Houston, TX, USA
| | - Junya Tomida
- Department of Epigenetics & Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX 78507, USA
| | - Richard D Wood
- Department of Epigenetics & Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX 78507, USA; The University of Texas MD Anderson Cancer Center, UT Health Graduate School of Biomedical Sciences, Houston, TX, USA.
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4
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Ishii Y, Takasu S, Grúz P, Masumura K, Ogawa K, Nohmi T, Umemura T. The role of DNA polymerase ζ in benzo[a]pyrene-induced mutagenesis in the mouse lung. Mutagenesis 2021; 36:155-164. [PMID: 33544859 DOI: 10.1093/mutage/geab007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 02/02/2021] [Indexed: 11/12/2022] Open
Abstract
DNA polymerase zeta (Polζ) is a heterotetramer composed of the catalytic subunit Rev3l, Rev7 and two subunits of Polδ (PolD2/Pol31 and PolD3/Pol32), and this polymerase exerts translesion DNA synthesis (TLS) in yeast. Because Rev3l knockout results in embryonic lethality in mice, the functions of Polζ need further investigation in vivo. Then, we noted the two facts that substitution of leucine 979 of yeast Rev3l with methionine reduces Polζ replication fidelity and that reporter gene transgenic rodents are able to provide the detailed mutation status. Here, we established gpt delta mouse knocked in the constructed gene encoding methionine instead of leucine at residue 2610 of Rev3l (Rev3l L2610M gpt delta mice), to clarify the role of Polζ in TLS of chemical-induced bulky DNA adducts in vivo. Eight-week-old gpt delta mice and Rev3l L2610M gpt delta mice were treated with benzo[a]pyrene (BaP) at 0, 40, 80, or 160 mg/kg via single intraperitoneal injection. At necropsy 31 days after treatment, lungs were collected for reporter gene mutation assays. Although the gpt mutant frequency was significantly increased by BaP in both mouse genotypes, it was three times higher in Rev3l L2610M gpt delta than gpt delta mice after treatment with 160 mg/kg BaP. The frequencies of G:C base substitutions and characteristic complex mutations were significantly increased in Rev3l L2610M gpt delta mice compared with gpt delta mice. The BaP dose-response relationship suggested that Polζ plays a central role in TLS when protective mechanisms against BaP mutagenesis, such as error-free TLS, are saturated. Overall, Polζ may incorporate incorrect nucleotides at the sites opposite to BaP-modified guanines and extend short DNA sequences from the resultant terminal mismatches only when DNA is heavily damaged.
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Affiliation(s)
- Yuji Ishii
- Division of Pathology, National Institute of Health Sciences, Tonomachi, Kawasaki-shi, Kawasaki-ku, Kanagawa, Japan
| | - Shinji Takasu
- Division of Pathology, National Institute of Health Sciences, Tonomachi, Kawasaki-shi, Kawasaki-ku, Kanagawa, Japan
| | - Petr Grúz
- Division of Genetics and Mutagenesis, National Institute of Health Sciences, Tonomachi, Kawasaki-shi, Kawasaki-ku, Kanagawa, Japan
| | - Kenichi Masumura
- Division of Genetics and Mutagenesis, National Institute of Health Sciences, Tonomachi, Kawasaki-shi, Kawasaki-ku, Kanagawa, Japan
| | - Kumiko Ogawa
- Division of Pathology, National Institute of Health Sciences, Tonomachi, Kawasaki-shi, Kawasaki-ku, Kanagawa, Japan
| | - Takehiko Nohmi
- Division of Pathology, National Institute of Health Sciences, Tonomachi, Kawasaki-shi, Kawasaki-ku, Kanagawa, Japan
| | - Takashi Umemura
- Division of Pathology, National Institute of Health Sciences, Tonomachi, Kawasaki-shi, Kawasaki-ku, Kanagawa, Japan
- Faculty of Animal Health Technology, Yamazaki University of Animal Health Technology, Minami-osawa, Hachihoji, Tokyo, Japan
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5
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Suzuki T, Sassa A, Grúz P, Gupta RC, Johnson F, Adachi N, Nohmi T. Error-prone bypass patch by a low-fidelity variant of DNA polymerase zeta in human cells. DNA Repair (Amst) 2021; 100:103052. [PMID: 33607474 DOI: 10.1016/j.dnarep.2021.103052] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 01/16/2021] [Accepted: 01/20/2021] [Indexed: 11/15/2022]
Abstract
DNA polymerase ζ (Pol ζ) is a specialized Pol that is involved in translesion DNA synthesis (TLS), in particular, in the extension of primer DNA after bypassing DNA lesions. Previously, we established human cells that express a variant form of Pol ζ with an amino acid change of leucine 2618 to methionine (L2618M) in the catalytic subunit REV3L (DNA Repair, 45, 34-43, 2016). This amino acid change made the cells more sensitive to the mutagenicity of benzo[a]pyrene diol epoxide (BPDE). In this study, we embedded BPDE-N2-guanine at a defined position in the supF gene on the shuttle plasmid and introduced it to REV3 L2618M cells or the wild-type (WT) cells to examine how far Pol ζ L2618M extends the primer DNA after bypassing the lesion. The adduct induced primarily G to T and G to C at the adducted site in both cell lines, but generated additional sequence changes such as base substitutions, deletions and additions in the extension patch much more often in REV3 L2618M cells than in the WT cells. Mutations in the extension patch in REV3 L2618M cells occurred most often within 10 bps from the adducted site. Then, the number of mutations gradually decreased and no mutations were observed between 30 and 40 bps from the lesion. We concluded that human Pol ζ L2618M and perhaps WT Pol ζ extend the primer DNA up to approximately 30 bps from the lesion in vivo. The possibility of involvement of Pol ζ L2618M in the insertion step of TLS is discussed.
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Affiliation(s)
- Tetsuya Suzuki
- Division of Genetics and Mutagenesis, National Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki-ku, Kawasaki-shi, Kanagawa, 210-9501, Japan.
| | - Akira Sassa
- Division of Genetics and Mutagenesis, National Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki-ku, Kawasaki-shi, Kanagawa, 210-9501, Japan
| | - Petr Grúz
- Division of Genetics and Mutagenesis, National Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki-ku, Kawasaki-shi, Kanagawa, 210-9501, Japan
| | - Ramesh C Gupta
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, New York, 11794-3400, NY, United States
| | - Francis Johnson
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, New York, 11794-3400, NY, United States
| | - Noritaka Adachi
- Graduate School of Nanobioscience, Yokohama City University, 22-2 Seto, Kanazawa-ku, Yokohama, Kanagawa, 236-0027, Japan
| | - Takehiko Nohmi
- Division of Genetics and Mutagenesis, National Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki-ku, Kawasaki-shi, Kanagawa, 210-9501, Japan
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6
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Yang D, Sun Y, Chen J, Zhang Y, Fan S, Huang M, Xie X, Cai Y, Shang Y, Gui T, Sun L, Hu J, Dong J, Yeap LS, Wang X, Xiao W, Meng FL. REV7 is required for processing AID initiated DNA lesions in activated B cells. Nat Commun 2020; 11:2812. [PMID: 32499490 PMCID: PMC7272641 DOI: 10.1038/s41467-020-16632-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 05/13/2020] [Indexed: 01/10/2023] Open
Abstract
Activation-induced cytidine deaminase (AID) initiates both antibody class switch recombination (CSR) and somatic hypermutation (SHM) in antibody diversification. DNA double-strand break response (DSBR) factors promote rearrangement in CSR, while translesion synthesis (TLS) polymerases generate mutations in SHM. REV7, a component of TLS polymerase zeta, is also a downstream effector of 53BP1-RIF1 DSBR pathway. Here, we study the multi-functions of REV7 and find that REV7 is required for the B cell survival upon AID-deamination, which is independent of its roles in DSBR, G2/M transition or REV1-mediated TLS. The cell death in REV7-deficient activated B cells can be fully rescued by AID-deficiency in vivo. We further identify that REV7-depedent TLS across UNG-processed apurinic/apyrimidinic sites is required for cell survival upon AID/APOBEC deamination. This study dissects the multiple roles of Rev7 in antibody diversification, and discovers that TLS is not only required for sequence diversification but also B cell survival upon AID-initiated lesions. REV7 has emerged as a critical regulator of DNA double-strand breaks repair. Here, the authors show that REV7 is crucial for both antibody class switch recombination and somatic hypermutation in activated B cells, in addition to their survival upon AID-deamination.
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Affiliation(s)
- Dingpeng Yang
- State Key Laboratory of Molecular Biology, Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, 200031, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ying Sun
- College of Life Sciences, Capital Normal University, Beijing, 100048, China
| | - Jingjing Chen
- Department of Immunology, State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu, 211166, China
| | - Ying Zhang
- State Key Laboratory of Molecular Biology, Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Shuangshuang Fan
- State Key Laboratory of Molecular Biology, Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Min Huang
- State Key Laboratory of Molecular Biology, Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, 200031, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xia Xie
- State Key Laboratory of Molecular Biology, Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, 200031, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yanni Cai
- State Key Laboratory of Molecular Biology, Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Yafang Shang
- State Key Laboratory of Molecular Biology, Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, 200031, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Tuantuan Gui
- Department of Immunology and Microbiology, Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Liming Sun
- State Key Laboratory of Molecular Biology, Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, 200031, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jiazhi Hu
- The MOE Key Laboratory of Cell Proliferation and Differentiation, Genome Editing Research Center, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
| | - Junchao Dong
- Department of Immunology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China
| | - Leng-Siew Yeap
- Department of Immunology and Microbiology, Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Xiaoming Wang
- Department of Immunology, State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, Jiangsu, 211166, China
| | - Wei Xiao
- College of Life Sciences, Capital Normal University, Beijing, 100048, China
| | - Fei-Long Meng
- State Key Laboratory of Molecular Biology, Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, 200031, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China.
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7
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RNA-binding motifs of hnRNP K are critical for induction of antibody diversification by activation-induced cytidine deaminase. Proc Natl Acad Sci U S A 2020; 117:11624-11635. [PMID: 32385154 DOI: 10.1073/pnas.1921115117] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Activation-induced cytidine deaminase (AID) is the key enzyme for class switch recombination (CSR) and somatic hypermutation (SHM) to generate antibody memory. Previously, heterogeneous nuclear ribonucleoprotein K (hnRNP K) was shown to be required for AID-dependent DNA breaks. Here, we defined the function of major RNA-binding motifs of hnRNP K, GXXGs and RGGs in the K-homology (KH) and the K-protein-interaction (KI) domains, respectively. Mutation of GXXG, RGG, or both impaired CSR, SHM, and cMyc/IgH translocation equally, showing that these motifs were necessary for AID-dependent DNA breaks. AID-hnRNP K interaction is dependent on RNA; hence, mutation of these RNA-binding motifs abolished the interaction with AID, as expected. Some of the polypyrimidine sequence-carrying prototypical hnRNP K-binding RNAs, which participate in DNA breaks or repair bound to hnRNP K in a GXXG and RGG motif-dependent manner. Mutation of the GXXG and RGG motifs decreased nuclear retention of hnRNP K. Together with the previous finding that nuclear localization of AID is necessary for its function, lower nuclear retention of these mutants may worsen their functional deficiency, which is also caused by their decreased RNA-binding capacity. In summary, hnRNP K contributed to AID-dependent DNA breaks with all of its major RNA-binding motifs.
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8
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Islam H, Kobayashi M, Honjo T. Apurinic/apyrimidinic endonuclease 1 (APE1) is dispensable for activation-induced cytidine deaminase (AID)-dependent somatic hypermutation in the immunoglobulin gene. Int Immunol 2020; 31:543-554. [PMID: 30877298 DOI: 10.1093/intimm/dxz028] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2018] [Accepted: 03/14/2019] [Indexed: 12/13/2022] Open
Abstract
Activation-induced cytidine deaminase (AID) initiates DNA breakage in the variable (V) and switch (S) regions of the immunoglobulin gene, which results in somatic hypermutation (SHM) and class switch recombination (CSR), respectively. Apurinic/apyrimidinic endonuclease 1 (APE1) has been shown to be important for CSR, and is supposed to cleave at abasic sites when AID-dependently deaminated cytidine is removed by uracil DNA glycosylase. However, APE1 is unexpectedly dispensable for SHM in the S region and translocation between immunoglobulin heavy chain (IgH) and c-myc genes in the mouse B lymphoma cell line, CH12F3-2A. This suggested that APE1 is not involved in AID-dependent DNA breakage, but rather, in DNA repair. In order to investigate detailed molecular mechanisms underlying APE1's involvement in CSR and SHM, we measured apurinic/apyrimidinic (AP) sites via aldehyde reactive probe labeling. Results indicated that the frequencies of AP sites in the S regions were not different between APE1-/-/-CH12F3-2A and wild-type CH12F3-2A cells. To carry out similar experiments in SHM of the V region, we generated an APE1 knockout (APE1-/-) human Burkitt's lymphoma cell line, and compared SHM between APE1-proficient and -deficient BL2 lymphoma cells. SHM frequencies in the V regions of APE1-/-BL2 and APE1-proficient cells were also similar. Taken together, we showed that AID does not induce AP sites in the S region of the IgH gene, and that APE1 is not necessary for SHM in the V and S regions; however, it is required for DNA repair following DNA breakage in CSR.
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Affiliation(s)
- Helena Islam
- Immunology and Genomic Medicine, Graduate School of Medicine, Kyoto University, Yoshida-Konoe cho, Sakyo-ku, Kyoto, Japan
| | - Maki Kobayashi
- Immunology and Genomic Medicine, Graduate School of Medicine, Kyoto University, Yoshida-Konoe cho, Sakyo-ku, Kyoto, Japan
| | - Tasuku Honjo
- Immunology and Genomic Medicine, Graduate School of Medicine, Kyoto University, Yoshida-Konoe cho, Sakyo-ku, Kyoto, Japan
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9
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Martin SK, Wood RD. DNA polymerase ζ in DNA replication and repair. Nucleic Acids Res 2019; 47:8348-8361. [PMID: 31410467 PMCID: PMC6895278 DOI: 10.1093/nar/gkz705] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 07/24/2019] [Accepted: 08/08/2019] [Indexed: 12/22/2022] Open
Abstract
Here, we survey the diverse functions of DNA polymerase ζ (pol ζ) in eukaryotes. In mammalian cells, REV3L (3130 residues) is the largest catalytic subunit of the DNA polymerases. The orthologous subunit in yeast is Rev3p. Pol ζ also includes REV7 subunits (encoded by Rev7 in yeast and MAD2L2 in mammalian cells) and two subunits shared with the replicative DNA polymerase, pol δ. Pol ζ is used in response to circumstances that stall DNA replication forks in both yeast and mammalian cells. The best-examined situation is translesion synthesis at sites of covalent DNA lesions such as UV radiation-induced photoproducts. We also highlight recent evidence that uncovers various roles of pol ζ that extend beyond translesion synthesis. For instance, pol ζ is also employed when the replisome operates sub-optimally or at difficult-to-replicate DNA sequences. Pol ζ also participates in repair by microhomology mediated break-induced replication. A rev3 deletion is tolerated in yeast but Rev3l disruption results in embryonic lethality in mice. Inactivation of mammalian Rev3l results in genomic instability and invokes cell death and senescence programs. Targeting of pol ζ function may be a useful strategy in cancer therapy, although chromosomal instability associated with pol ζ deficiency must be considered.
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Affiliation(s)
- Sara K Martin
- Department of Epigenetics & Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX, USA and The University of Texas MD Anderson Cancer Center UT Health Graduate School of Biomedical Sciences
| | - Richard D Wood
- Department of Epigenetics & Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX, USA and The University of Texas MD Anderson Cancer Center UT Health Graduate School of Biomedical Sciences
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10
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Lange SS, Bhetawal S, Reh S, Powell KL, Kusewitt DF, Wood RD. DNA polymerase ζ deficiency causes impaired wound healing and stress-induced skin pigmentation. Life Sci Alliance 2018; 1. [PMID: 30046772 PMCID: PMC6055517 DOI: 10.26508/lsa.201800048] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Mice harboring DNA polymerase ζ–defective keratinocytes are shown to have a defect in wound healing and a striking p53-dependent migration of melanocytes to the skin following UV radiation or wounding. DNA polymerase ζ (pol ζ) is well established as a specialized enzyme important for DNA damage tolerance, facilitating DNA synthesis past lesions caused by radiation or chemical damage. We report that disruption of Rev3l (encoding the catalytic subunit of pol ζ) in mouse epidermis leads to a defect in proliferation that impairs cutaneous wound healing. A striking increase in epidermal skin pigmentation accompanied both wound healing and UV irradiation in these mice. This was a consequence of stress-induced migration of Rev3l-proficient melanocytes to the Rev3l-defective epidermis. We found that this pigmentation corresponded with p53 activation in keratinocytes and was absent in p53-negative areas of the epidermis. Expression of the kit ligand (Kitl) gene, a p53-controlled mediator of keratinocyte to melanocyte signaling, was enhanced during wound healing or following UV irradiation. This study extends the function of pol ζ to the process of proliferation during wound healing. Rev3l-deficient epidermis may be a useful mouse model system for examining communication between damaged keratinocytes and melanocytes, including signaling relevant to human disease.
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Affiliation(s)
- Sabine S Lange
- Department of Epigenetics & Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, and the Graduate School of Biomedical Sciences at Houston, Smithville, Texas, P.O. Box 389, Smithville, TX, 78957, USA
| | - Sarita Bhetawal
- Department of Epigenetics & Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, and the Graduate School of Biomedical Sciences at Houston, Smithville, Texas, P.O. Box 389, Smithville, TX, 78957, USA
| | - Shelley Reh
- Department of Epigenetics & Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, and the Graduate School of Biomedical Sciences at Houston, Smithville, Texas, P.O. Box 389, Smithville, TX, 78957, USA
| | - Katherine Leslie Powell
- Department of Epigenetics & Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, and the Graduate School of Biomedical Sciences at Houston, Smithville, Texas, P.O. Box 389, Smithville, TX, 78957, USA
| | - Donna F Kusewitt
- Department of Epigenetics & Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, and the Graduate School of Biomedical Sciences at Houston, Smithville, Texas, P.O. Box 389, Smithville, TX, 78957, USA
| | - Richard D Wood
- Department of Epigenetics & Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, and the Graduate School of Biomedical Sciences at Houston, Smithville, Texas, P.O. Box 389, Smithville, TX, 78957, USA
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11
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Haakenson JK, Huang R, Smider VV. Diversity in the Cow Ultralong CDR H3 Antibody Repertoire. Front Immunol 2018; 9:1262. [PMID: 29915599 PMCID: PMC5994613 DOI: 10.3389/fimmu.2018.01262] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2018] [Accepted: 05/18/2018] [Indexed: 01/26/2023] Open
Abstract
Typical antibodies found in humans and mice usually have short CDR H3s and generally flat binding surfaces. However, cows possess a subset of antibodies with ultralong CDR H3s that can range up to 70 amino acids and form a unique “stalk and knob” structure, with the knob protruding far out of the antibody surface, where it has the potential to bind antigens with concave epitopes. Activation-induced cytidine deaminase (AID) has a proven role in diversifying antibody repertoires in humoral immunity, and it has been found to induce somatic hypermutation in bovine immunoglobulin genes both before and after contact with antigen. Due to limited use of variable and diversity genes in the V(D)J recombination events that produce ultralong CDR H3 antibodies in cows, the diversity in the bovine ultralong antibody repertoire has been proposed to rely on AID-induced mutations targeted to the IGHD8-2 gene that encodes the entire knob region. In this review, we discuss the genetics, structures, and diversity of bovine ultralong antibodies, as well as the role of AID in creating a diverse antibody repertoire.
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Affiliation(s)
- Jeremy K Haakenson
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, United States
| | - Ruiqi Huang
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, United States
| | - Vaughn V Smider
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, United States
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12
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Quinet A, Lerner LK, Martins DJ, Menck CFM. Filling gaps in translesion DNA synthesis in human cells. MUTATION RESEARCH-GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS 2018; 836:127-142. [PMID: 30442338 DOI: 10.1016/j.mrgentox.2018.02.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Accepted: 02/21/2018] [Indexed: 01/06/2023]
Abstract
During DNA replication, forks may encounter unrepaired lesions that hamper DNA synthesis. Cells have universal strategies to promote damage bypass allowing cells to survive. DNA damage tolerance can be performed upon template switch or by specialized DNA polymerases, known as translesion (TLS) polymerases. Human cells count on more than eleven TLS polymerases and this work reviews the functions of some of these enzymes: Rev1, Pol η, Pol ι, Pol κ, Pol θ and Pol ζ. The mechanisms of damage bypass vary according to the lesion, as well as to the TLS polymerases available, and may occur directly at the fork during replication. Alternatively, the lesion may be skipped, leaving a single-stranded DNA gap that will be replicated later. Details of the participation of these enzymes are revised for the replication of damaged template. TLS polymerases also have functions in other cellular processes. These include involvement in somatic hypermutation in immunoglobulin genes, direct participation in recombination and repair processes, and contributing to replicating noncanonical DNA structures. The importance of DNA damage replication to cell survival is supported by recent discoveries that certain genes encoding TLS polymerases are induced in response to DNA damaging agents, protecting cells from a subsequent challenge to DNA replication. We retrace the findings on these genotoxic (adaptive) responses of human cells and show the common aspects with the SOS responses in bacteria. Paradoxically, although TLS of DNA damage is normally an error prone mechanism, in general it protects from carcinogenesis, as evidenced by increased tumorigenesis in xeroderma pigmentosum variant patients, who are deficient in Pol η. As these TLS polymerases also promote cell survival, they constitute an important mechanism by which cancer cells acquire resistance to genotoxic chemotherapy. Therefore, the TLS polymerases are new potential targets for improving therapy against tumors.
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Affiliation(s)
- Annabel Quinet
- Saint Louis University School of Medicine, St. Louis, MO, United States.
| | - Leticia K Lerner
- MRC Laboratory of Molecular Biology,Francis Crick Avenue, Cambridge CB2 0QH, UK.
| | - Davi J Martins
- Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Carlos F M Menck
- Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil.
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13
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Thientosapol ES, Sharbeen G, Lau KKE, Bosnjak D, Durack T, Stevanovski I, Weninger W, Jolly CJ. Proximity to AGCT sequences dictates MMR-independent versus MMR-dependent mechanisms for AID-induced mutation via UNG2. Nucleic Acids Res 2017; 45:3146-3157. [PMID: 28039326 PMCID: PMC5389528 DOI: 10.1093/nar/gkw1300] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 12/16/2016] [Indexed: 11/30/2022] Open
Abstract
AID deaminates C to U in either strand of Ig genes, exclusively producing C:G/G:C to T:A/A:T transition mutations if U is left unrepaired. Error-prone processing by UNG2 or mismatch repair diversifies mutation, predominantly at C:G or A:T base pairs, respectively. Here, we show that transversions at C:G base pairs occur by two distinct processing pathways that are dictated by sequence context. Within and near AGCT mutation hotspots, transversion mutation at C:G was driven by UNG2 without requirement for mismatch repair. Deaminations in AGCT were refractive both to processing by UNG2 and to high-fidelity base excision repair (BER) downstream of UNG2, regardless of mismatch repair activity. We propose that AGCT sequences resist faithful BER because they bind BER-inhibitory protein(s) and/or because hemi-deaminated AGCT motifs innately form a BER-resistant DNA structure. Distal to AGCT sequences, transversions at G were largely co-dependent on UNG2 and mismatch repair. We propose that AGCT-distal transversions are produced when apyrimidinic sites are exposed in mismatch excision patches, because completion of mismatch repair would require bypass of these sites.
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Affiliation(s)
- Eddy Sanchai Thientosapol
- Centenary Institute, Royal Prince Alfred Hospital, Camperdown NSW 2050, and Sydney Medical School, The University of Sydney, Sydney NSW 2006, Australia
| | - George Sharbeen
- Centenary Institute, Royal Prince Alfred Hospital, Camperdown NSW 2050, and Sydney Medical School, The University of Sydney, Sydney NSW 2006, Australia
| | - K K Edwin Lau
- Centenary Institute, Royal Prince Alfred Hospital, Camperdown NSW 2050, and Sydney Medical School, The University of Sydney, Sydney NSW 2006, Australia
| | - Daniel Bosnjak
- Centenary Institute, Royal Prince Alfred Hospital, Camperdown NSW 2050, and Sydney Medical School, The University of Sydney, Sydney NSW 2006, Australia
| | - Timothy Durack
- Centenary Institute, Royal Prince Alfred Hospital, Camperdown NSW 2050, and Sydney Medical School, The University of Sydney, Sydney NSW 2006, Australia
| | - Igor Stevanovski
- Centenary Institute, Royal Prince Alfred Hospital, Camperdown NSW 2050, and Sydney Medical School, The University of Sydney, Sydney NSW 2006, Australia
| | - Wolfgang Weninger
- Centenary Institute, Royal Prince Alfred Hospital, Camperdown NSW 2050, and Sydney Medical School, The University of Sydney, Sydney NSW 2006, Australia
| | - Christopher J Jolly
- Centenary Institute, Royal Prince Alfred Hospital, Camperdown NSW 2050, and Sydney Medical School, The University of Sydney, Sydney NSW 2006, Australia
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14
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Verkoczy L, Alt FW, Tian M. Human Ig knockin mice to study the development and regulation of HIV-1 broadly neutralizing antibodies. Immunol Rev 2017; 275:89-107. [PMID: 28133799 DOI: 10.1111/imr.12505] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
A major challenge for HIV-1 vaccine research is developing a successful immunization approach for inducing broadly neutralizing antibodies (bnAbs). A key shortcoming in meeting this challenge has been the lack of animal models capable of identifying impediments limiting bnAb induction and ranking vaccine strategies for their ability to promote bnAb development. Since 2010, immunoglobulin knockin (KI) technology, involving inserting functional rearranged human variable exons into the mouse IgH and IgL loci has been used to express bnAbs in mice. This approach has allowed immune tolerance mechanisms limiting bnAb production to be elucidated and strategies to overcome such limitations to be evaluated. From these studies, along with the wealth of knowledge afforded by analyses of recombinant Ig-based bnAb structures, it became apparent that key functional features of bnAbs often are problematic for their elicitation in mice by classic vaccine paradigms, necessitating more iterative testing of new vaccine concepts. In this regard, bnAb KI models expressing deduced precursor V(D)J rearrangements of mature bnAbs or unrearranged germline V, D, J segments (that can be assembled into variable region exons that encode bnAb precursors), have been engineered to evaluate novel immunogens/regimens for effectiveness in driving bnAb responses. One promising approach emerging from such studies is the ability of sequentially administered, modified immunogens (designed to bind progressively more mature bnAb precursors) to initiate affinity maturation. Here, we review insights gained from bnAb KI studies regarding the regulation and induction of bnAbs, and discuss new Ig KI methodologies to manipulate the production and/or expression of bnAbs in vivo, to further facilitate vaccine-guided bnAb induction studies.
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Affiliation(s)
- Laurent Verkoczy
- Departments of Medicine and Pathology, Duke University Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Frederick W Alt
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children's Hospital and Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Ming Tian
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children's Hospital and Department of Genetics, Harvard Medical School, Boston, MA, USA
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15
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Verkoczy L. Humanized Immunoglobulin Mice: Models for HIV Vaccine Testing and Studying the Broadly Neutralizing Antibody Problem. Adv Immunol 2017; 134:235-352. [PMID: 28413022 PMCID: PMC5914178 DOI: 10.1016/bs.ai.2017.01.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
A vaccine that can effectively prevent HIV-1 transmission remains paramount to ending the HIV pandemic, but to do so, will likely need to induce broadly neutralizing antibody (bnAb) responses. A major technical hurdle toward achieving this goal has been a shortage of animal models with the ability to systematically pinpoint roadblocks to bnAb induction and to rank vaccine strategies based on their ability to stimulate bnAb development. Over the past 6 years, immunoglobulin (Ig) knock-in (KI) technology has been leveraged to express bnAbs in mice, an approach that has enabled elucidation of various B-cell tolerance mechanisms limiting bnAb production and evaluation of strategies to circumvent such processes. From these studies, in conjunction with the wealth of information recently obtained regarding the evolutionary pathways and paratopes/epitopes of multiple bnAbs, it has become clear that the very features of bnAbs desired for their function will be problematic to elicit by traditional vaccine paradigms, necessitating more iterative testing of new vaccine concepts. To meet this need, novel bnAb KI models have now been engineered to express either inferred prerearranged V(D)J exons (or unrearranged germline V, D, or J segments that can be assembled into functional rearranged V(D)J exons) encoding predecessors of mature bnAbs. One encouraging approach that has materialized from studies using such newer models is sequential administration of immunogens designed to bind progressively more mature bnAb predecessors. In this review, insights into the regulation and induction of bnAbs based on the use of KI models will be discussed, as will new Ig KI approaches for higher-throughput production and/or altering expression of bnAbs in vivo, so as to further enable vaccine-guided bnAb induction studies.
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Affiliation(s)
- Laurent Verkoczy
- Duke University Human Vaccine Institute, Duke University School of Medicine, Durham, NC, United States.
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16
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Shimizu T, Tateishi S, Tanoue Y, Azuma T, Ohmori H. Somatic hypermutation of immunoglobulin genes in Rad18 knockout mice. DNA Repair (Amst) 2016; 50:54-60. [PMID: 28082021 DOI: 10.1016/j.dnarep.2016.12.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Revised: 12/24/2016] [Accepted: 12/27/2016] [Indexed: 10/20/2022]
Abstract
Somatic hypermutation (SHM) of immunoglobulin (Ig) genes is triggered by the activity of activation-induced cytidine deaminase (AID). AID induces DNA lesions in variable regions of Ig genes, and error-prone DNA repair mechanisms initiated in response to these lesions introduce the mutations that characterize SHM. Error-prone DNA repair in SHM is proposed to be mediated by low-fidelity DNA polymerases such as those that mediate trans-lesion synthesis (TLS); however, the mechanism by which these enzymes are recruited to AID-induced lesions remains unclear. Proliferating cell nuclear antigen (PCNA), the sliding clamp for multiple DNA polymerases, undergoes Rad6/Rad18-dependent ubiquitination in response to DNA damage. Ubiquitinated PCNA promotes the replacement of the replicative DNA polymerase stalled at the site of a DNA lesion with a TLS polymerase. To examine the potential role of Rad18-dependent PCNA ubiquitination in SHM, we analyzed Ig gene mutations in Rad18 knockout (KO) mice immunized with T cell-dependent antigens. We found that SHM in Rad18 KO mice was similar to wild-type mice, suggesting that Rad18 is dispensable for SHM. However, residual levels of ubiquitinated PCNA were observed in Rad18 KO cells, indicating that Rad18-independent PCNA ubiquitination might play a role in SHM.
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Affiliation(s)
- Takeyuki Shimizu
- Department of Immunology, Kochi Medical School, Kochi University, Oko-cho Kohasu, Nankoku, Kochi 783-8505, Japan.
| | - Satoshi Tateishi
- Institute of Molecular Embryology and Genetics, Kumamoto University, Honjo 2-2-1, Chuo-ku, Kumamoto 860-0811, Japan
| | - Yuki Tanoue
- Institute of Molecular Embryology and Genetics, Kumamoto University, Honjo 2-2-1, Chuo-ku, Kumamoto 860-0811, Japan
| | - Takachika Azuma
- Research Institute for Biological Sciences (RIBS), Tokyo University of Science, Yamazaki 2669, Noda, Chiba 278-0022, Japan
| | - Haruo Ohmori
- Departments of Gene Information Analysis, Institute for Virus Research, Kyoto University, Shogoin Kawara-cho 53, Sakyo-ku, Kyoto 606-8507, Japan
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17
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IJspeert H, van Schouwenburg PA, van Zessen D, Pico-Knijnenburg I, Driessen GJ, Stubbs AP, van der Burg M. Evaluation of the Antigen-Experienced B-Cell Receptor Repertoire in Healthy Children and Adults. Front Immunol 2016; 7:410. [PMID: 27799928 PMCID: PMC5066086 DOI: 10.3389/fimmu.2016.00410] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 09/22/2016] [Indexed: 12/03/2022] Open
Abstract
Upon antigen recognition via their B cell receptor (BR), B cells migrate to the germinal center where they undergo somatic hypermutation (SHM) to increase their affinity for the antigen, and class switch recombination (CSR) to change the effector function of the secreted antibodies. These steps are essential to create an antigen-experienced BR repertoire that efficiently protects the body against pathogens. At the same time, the BR repertoire should be selected to protect against responses to self-antigen or harmless antigens. Insights into the processes of SHM, selection, and CSR can be obtained by studying the antigen-experienced BR repertoire. Currently, a large reference data set of healthy children and adults, which ranges from neonates to the elderly, is not available. In this study, we analyzed the antigen-experienced repertoire of 38 healthy donors (HD), ranging from cord blood to 74 years old, by sequencing IGA and IGG transcripts using next generation sequencing. This resulted in a large, freely available reference data set containing 412,890 IGA and IGG transcripts. We used this data set to study mutation levels, SHM patterns, antigenic selection, and CSR from birth to elderly HD. Only small differences were observed in SHM patterns, while the mutation levels increase in early childhood and stabilize at 6 years of age at around 7%. Furthermore, comparison of the antigen-experienced repertoire with sequences from the naive immune repertoire showed that features associated with autoimmunity such as long CDR3 length and IGHV4-34 usage are reduced in the antigen-experienced repertoire. Moreover, IGA2 and IGG2 usage was increased in HD in higher age categories, while IGG1 usage was decreased. In addition, we studied clonal relationship in the different samples. Clonally related sequences were found with different subclasses. Interestingly, we found transcripts with the same CDR1–CDR3 sequence, but different subclasses. Together, these data suggest that a single antigen can provoke a B-cell response with BR of different subclasses and that, during the course of an immune response, some B cells change their isotype without acquiring additional SHM or can directly switch to different isotypes.
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Affiliation(s)
- Hanna IJspeert
- Department of Immunology, Erasmus MC, University Medical Center Rotterdam , Rotterdam , Netherlands
| | | | - David van Zessen
- Department of Immunology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands; Department of Bioinformatics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Ingrid Pico-Knijnenburg
- Department of Immunology, Erasmus MC, University Medical Center Rotterdam , Rotterdam , Netherlands
| | - Gertjan J Driessen
- Department of Pediatrics, Erasmus MC-Sophia Children's Hospital, University Medical Center Rotterdam , Rotterdam , Netherlands
| | - Andrew P Stubbs
- Department of Bioinformatics, Erasmus MC, University Medical Center Rotterdam , Rotterdam , Netherlands
| | - Mirjam van der Burg
- Department of Immunology, Erasmus MC, University Medical Center Rotterdam , Rotterdam , Netherlands
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18
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Sensitivity of human cells expressing low-fidelity or weak-catalytic-activity variants of DNA polymerase ζ to genotoxic stresses. DNA Repair (Amst) 2016; 45:34-43. [DOI: 10.1016/j.dnarep.2016.06.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Revised: 05/13/2016] [Accepted: 06/04/2016] [Indexed: 01/22/2023]
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19
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Maul RW, MacCarthy T, Frank EG, Donigan KA, McLenigan MP, Yang W, Saribasak H, Huston DE, Lange SS, Woodgate R, Gearhart PJ. DNA polymerase ι functions in the generation of tandem mutations during somatic hypermutation of antibody genes. J Exp Med 2016; 213:1675-83. [PMID: 27455952 PMCID: PMC4995076 DOI: 10.1084/jem.20151227] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Accepted: 06/01/2016] [Indexed: 11/04/2022] Open
Abstract
DNA polymerase ι (Pol ι) is an attractive candidate for somatic hypermutation in antibody genes because of its low fidelity. To identify a role for Pol ι, we analyzed mutations in two strains of mice with deficiencies in the enzyme: 129 mice with negligible expression of truncated Pol ι, and knock-in mice that express full-length Pol ι that is catalytically inactive. Both strains had normal frequencies and spectra of mutations in the variable region, indicating that loss of Pol ι did not change overall mutagenesis. We next examined if Pol ι affected tandem mutations generated by another error-prone polymerase, Pol ζ. The frequency of contiguous mutations was analyzed using a novel computational model to determine if they occur during a single DNA transaction or during two independent events. Analyses of 2,000 mutations from both strains indicated that Pol ι-compromised mice lost the tandem signature, whereas C57BL/6 mice accumulated significant amounts of double mutations. The results support a model where Pol ι occasionally accesses the replication fork to generate a first mutation, and Pol ζ extends the mismatch with a second mutation.
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Affiliation(s)
- Robert W Maul
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224
| | - Thomas MacCarthy
- Department of Applied Mathematics and Statistics, State University of New York, Stony Brook, NY 11794
| | - Ekaterina G Frank
- Laboratory of Genomic Integrity, National Institute of Child Health and Human Development, National Institutes of Health, Rockville, MD 20850
| | - Katherine A Donigan
- Laboratory of Genomic Integrity, National Institute of Child Health and Human Development, National Institutes of Health, Rockville, MD 20850
| | - Mary P McLenigan
- Laboratory of Genomic Integrity, National Institute of Child Health and Human Development, National Institutes of Health, Rockville, MD 20850
| | - William Yang
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224
| | - Huseyin Saribasak
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224
| | - Donald E Huston
- Laboratory of Genomic Integrity, National Institute of Child Health and Human Development, National Institutes of Health, Rockville, MD 20850
| | - Sabine S Lange
- Department of Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center Science Park, Smithville, TX 78957
| | - Roger Woodgate
- Laboratory of Genomic Integrity, National Institute of Child Health and Human Development, National Institutes of Health, Rockville, MD 20850
| | - Patricia J Gearhart
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224
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20
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Fritzen R, Delbos F, De Smet A, Palancade B, Canman CE, Aoufouchi S, Weill JC, Reynaud CA, Storck S. A single aspartate mutation in the conserved catalytic site of Rev3L generates a hypomorphic phenotype in vivo and in vitro. DNA Repair (Amst) 2016; 46:37-46. [PMID: 27481099 DOI: 10.1016/j.dnarep.2016.07.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Revised: 07/20/2016] [Accepted: 07/21/2016] [Indexed: 12/29/2022]
Abstract
Rev3, the catalytic subunit of yeast DNA polymerase ζ, is required for UV resistance and UV-induced mutagenesis, while its mammalian ortholog, REV3L, plays further vital roles in cell proliferation and embryonic development. To assess the contribution of REV3L catalytic activity to its in vivo function, we generated mutant mouse strains in which one or two Ala residues were substituted to the Asp of the invariant catalytic YGDTDS motif. The simultaneous mutation of both Asp (ATA) phenocopies the Rev3l knockout, which proves that the catalytic activity is mandatory for the vital functions of Rev3L, as reported recently. Surprisingly, although the mutation of the first Asp severely impairs the enzymatic activity of other B-family DNA polymerases, the corresponding mutation of Rev3 (ATD) is hypomorphic in yeast and mouse, as it does not affect viability and proliferation and moderately impacts UVC-induced cell death and mutagenesis. Interestingly, Rev3l hypomorphic mutant mice display a distinct, albeit modest, alteration of the immunoglobulin gene mutation spectrum at G-C base pairs, further documenting its role in this process.
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Affiliation(s)
- Rémi Fritzen
- Institut Necker-Enfants Malades, INSERM U1151-CNRS UMR 8253, Faculté de Médecine Paris Descartes, Université Paris Descartes, Sorbonne Paris Cité, Paris, France.
| | - Frédéric Delbos
- Institut Necker-Enfants Malades, INSERM U1151-CNRS UMR 8253, Faculté de Médecine Paris Descartes, Université Paris Descartes, Sorbonne Paris Cité, Paris, France.
| | - Annie De Smet
- Institut Necker-Enfants Malades, INSERM U1151-CNRS UMR 8253, Faculté de Médecine Paris Descartes, Université Paris Descartes, Sorbonne Paris Cité, Paris, France.
| | - Benoît Palancade
- Institut Jacques Monod, CNRS UMR 7592, Université Paris Diderot, Sorbonne Paris Cité, Paris, France.
| | | | - Said Aoufouchi
- Institut Gustave Roussy, CNRS UMR 8200, Villejuif, and Université Paris-Sud, Orsay, France.
| | - Jean-Claude Weill
- Institut Necker-Enfants Malades, INSERM U1151-CNRS UMR 8253, Faculté de Médecine Paris Descartes, Université Paris Descartes, Sorbonne Paris Cité, Paris, France.
| | - Claude-Agnès Reynaud
- Institut Necker-Enfants Malades, INSERM U1151-CNRS UMR 8253, Faculté de Médecine Paris Descartes, Université Paris Descartes, Sorbonne Paris Cité, Paris, France.
| | - Sébastien Storck
- Institut Necker-Enfants Malades, INSERM U1151-CNRS UMR 8253, Faculté de Médecine Paris Descartes, Université Paris Descartes, Sorbonne Paris Cité, Paris, France.
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21
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Zanotti KJ, Gearhart PJ. Antibody diversification caused by disrupted mismatch repair and promiscuous DNA polymerases. DNA Repair (Amst) 2016; 38:110-116. [PMID: 26719140 PMCID: PMC4740194 DOI: 10.1016/j.dnarep.2015.11.011] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Accepted: 11/30/2015] [Indexed: 10/25/2022]
Abstract
The enzyme activation-induced deaminase (AID) targets the immunoglobulin loci in activated B cells and creates DNA mutations in the antigen-binding variable region and DNA breaks in the switch region through processes known, respectively, as somatic hypermutation and class switch recombination. AID deaminates cytosine to uracil in DNA to create a U:G mismatch. During somatic hypermutation, the MutSα complex binds to the mismatch, and the error-prone DNA polymerase η generates mutations at A and T bases. During class switch recombination, both MutSα and MutLα complexes bind to the mismatch, resulting in double-strand break formation and end-joining. This review is centered on the mechanisms of how the MMR pathway is commandeered by B cells to generate antibody diversity.
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Affiliation(s)
- Kimberly J Zanotti
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Patricia J Gearhart
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA.
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22
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Kamiya H, Kurokawa M, Makino T, Kobayashi M, Matsuoka I. Induction of action-at-a-distance mutagenesis by 8-oxo-7,8-dihydroguanine in DNA pol λ-knockdown cells. Genes Environ 2015; 37:10. [PMID: 27350807 PMCID: PMC4918004 DOI: 10.1186/s41021-015-0015-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Accepted: 07/09/2015] [Indexed: 11/13/2022] Open
Abstract
Introduction In DNA, 8-oxo-7,8-dihydroguanine (GO, 8-hydroxyguanine) is one of the most pivotal oxidatively damaged bases and induces G:C → T:A transversion mutations. DNA polymerase λ preferentially inserts dCTP opposite GOin vitro, and this error-free bypass function is considered to be important after A base removal from GO:A pairs by the MUTYH DNA glycosylase. To examine the effects of reduced levels of DNA polymerase λ on the GO-induced mutations, the polymerase was knocked-down in human U2OS cells, and a shuttle plasmid DNA containing a GO:C pair at position 122 in the supF gene was transfected into the cells. The plasmid DNA replicated in the cells was introduced into an Escherichia coli indicator strain, to measure the supF mutant frequency. Results The knockdown of DNA polymerase λ significantly enhanced the mutant frequency of the GO plasmid DNA. Contrary to our expectations, the knockdown did not promote the targeted G:C → T:A transversion. Instead, substitution mutations at G:C sites other than position 122 were enhanced in the cells. Conclusions These results suggested that the knockdown of DNA polymerase λ induced action-at-a-distance mutagenesis in human cells when the GO:C pair was present in the DNA.
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Affiliation(s)
- Hiroyuki Kamiya
- Graduate School of Science and Engineering, Ehime University, 2-5 Bunkyo-cho, Matsuyama, 790-8577 Japan ; Graduate School of Biomedical and Health Sciences, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima 734-8553 Japan ; College of Pharmaceutical Sciences, Matsuyama University, 4-2 Bunkyo-cho, Matsuyama, 790-8578 Japan
| | - Masahiro Kurokawa
- Graduate School of Science and Engineering, Ehime University, 2-5 Bunkyo-cho, Matsuyama, 790-8577 Japan
| | - Tetsuaki Makino
- Graduate School of Science and Engineering, Ehime University, 2-5 Bunkyo-cho, Matsuyama, 790-8577 Japan ; Graduate School of Biomedical and Health Sciences, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima 734-8553 Japan
| | - Miwako Kobayashi
- College of Pharmaceutical Sciences, Matsuyama University, 4-2 Bunkyo-cho, Matsuyama, 790-8578 Japan
| | - Ichiro Matsuoka
- College of Pharmaceutical Sciences, Matsuyama University, 4-2 Bunkyo-cho, Matsuyama, 790-8578 Japan
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23
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Kamiya H, Yamazaki D, Nakamura E, Makino T, Kobayashi M, Matsuoka I, Harashima H. Action-at-a-Distance Mutagenesis Induced by Oxidized Guanine in Werner Syndrome Protein-Reduced Human Cells. Chem Res Toxicol 2015; 28:621-8. [DOI: 10.1021/tx500418m] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Hiroyuki Kamiya
- Faculty
of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan
- Graduate
School of Science and Engineering, Ehime University, 2-5 Bunkyo-cho, Matsuyama 790-8577, Japan
- College
of Pharmaceutical Sciences, Matsuyama University, 4-2 Bunkyo-cho, Matsuyama 790-8578, Japan
- Graduate
School of Biomedical and Health Sciences, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima 734-8553, Japan
| | - Daiki Yamazaki
- Faculty
of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan
| | - Eri Nakamura
- Graduate
School of Science and Engineering, Ehime University, 2-5 Bunkyo-cho, Matsuyama 790-8577, Japan
| | - Tetsuaki Makino
- Graduate
School of Science and Engineering, Ehime University, 2-5 Bunkyo-cho, Matsuyama 790-8577, Japan
- Graduate
School of Biomedical and Health Sciences, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima 734-8553, Japan
| | - Miwako Kobayashi
- College
of Pharmaceutical Sciences, Matsuyama University, 4-2 Bunkyo-cho, Matsuyama 790-8578, Japan
| | - Ichiro Matsuoka
- College
of Pharmaceutical Sciences, Matsuyama University, 4-2 Bunkyo-cho, Matsuyama 790-8578, Japan
| | - Hideyoshi Harashima
- Faculty
of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan
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24
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Autoreactivity in HIV-1 broadly neutralizing antibodies: implications for their function and induction by vaccination. Curr Opin HIV AIDS 2014; 9:224-34. [PMID: 24714565 DOI: 10.1097/coh.0000000000000049] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
PURPOSE OF REVIEW This review discusses progress in understanding the impact of immune tolerance on inducing broadly neutralizing antibodies (bnAbs), and how such knowledge can be incorporated into novel immunization approaches. RECENT FINDINGS Over 120 bnAbs have now been isolated, all of which bear unusual features associated with host tolerance controls, but paradoxically may also be required for their function. Evidence that poly/autoreactivity of membrane proximal external region bnAbs can invoke such controls has been demonstrated by knock-in technology, highlighting its potential for studying the impact of tolerance in the generation of bnAb lineages to distinct HIV-1 envelope targets. The requirement for extensive affinity maturation in developing neutralization breadth/potency during infection is being examined, and similar studies in the setting of immunization will be aided by testing novel vaccine approaches in knock-in models that either selectively express reverted V(D)J rearrangements, or unrearranged germline segments, from which bnAb lineages originate. SUMMARY It is increasingly apparent that immune tolerance, sometimes invoked by self-reactivity that overlaps with bnAb epitope specificity, adds to a formidable set of roadblocks impeding bnAb induction. The path to an effective HIV-1 vaccine may thus benefit from a deeper understanding of host controls, including categorizing those that are unique or common at distinct bnAb targets, and ranking those most feasible to overcome by immunization. Ultimately, such emerging information will be critical to incorporate into new vaccine approaches that can be tested in human trials.
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25
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APE1 is dispensable for S-region cleavage but required for its repair in class switch recombination. Proc Natl Acad Sci U S A 2014; 111:17242-7. [PMID: 25404348 DOI: 10.1073/pnas.1420221111] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Activation-induced cytidine deaminase (AID) is essential for antibody diversification, namely somatic hypermutation (SHM) and class switch recombination (CSR). The deficiency of apurinic/apyrimidinic endonuclease 1 (Ape1) in CH12F3-2A B cells reduces CSR to ∼20% of wild-type cells, whereas the effect of APE1 loss on SHM has not been examined. Here we show that, although APE1's endonuclease activity is important for CSR, it is dispensable for SHM as well as IgH/c-myc translocation. Importantly, APE1 deficiency did not show any defect in AID-induced S-region break formation, but blocked both the recruitment of repair protein Ku80 to the S region and the synapse formation between Sμ and Sα. Knockdown of end-processing factors such as meiotic recombination 11 homolog (MRE11) and carboxy-terminal binding protein (CtBP)-interacting protein (CtIP) further reduced the remaining CSR in Ape1-null CH12F3-2A cells. Together, our results show that APE1 is dispensable for SHM and AID-induced DNA breaks and may function as a DNA end-processing enzyme to facilitate the joining of broken ends during CSR.
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26
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Abstract
About 2% of human genetic polymorphisms have been hypothesized to arise via multinucleotide mutations (MNMs), complex events that generate SNPs at multiple sites in a single generation. MNMs have the potential to accelerate the pace at which single genes evolve and to confound studies of demography and selection that assume all SNPs arise independently. In this paper, we examine clustered mutations that are segregating in a set of 1092 human genomes, demonstrating that the signature of MNM becomes enriched as large numbers of individuals are sampled. We estimate the percentage of linked SNP pairs that were generated by simultaneous mutation as a function of the distance between affected sites and show that MNMs exhibit a high percentage of transversions relative to transitions, findings that are reproducible in data from multiple sequencing platforms and cannot be attributed to sequencing error. Among tandem mutations that occur simultaneously at adjacent sites, we find an especially skewed distribution of ancestral and derived alleles, with GC → AA, GA → TT, and their reverse complements making up 27% of the total. These mutations have been previously shown to dominate the spectrum of the error-prone polymerase Pol ζ, suggesting that low-fidelity DNA replication by Pol ζ is at least partly responsible for the MNMs that are segregating in the human population. We develop statistical estimates of MNM prevalence that can be used to correct phylogenetic and population genetic inferences for the presence of complex mutations.
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Affiliation(s)
- Kelley Harris
- Department of Mathematics, University of California Berkeley, Berkeley, California 94703, USA;
| | - Rasmus Nielsen
- Department of Integrative Biology, University of California Berkeley, Berkeley, California 94703, USA; Department of Statistics, University of California Berkeley, Berkeley, California 94703, USA; Center for Bioinformatics, University of Copenhagen, 2200 Copenhagen, Denmark
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27
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Yousif AS, Stanlie A, Begum NA, Honjo T. Opinion: uracil DNA glycosylase (UNG) plays distinct and non-canonical roles in somatic hypermutation and class switch recombination. Int Immunol 2014; 26:575-8. [PMID: 24994819 DOI: 10.1093/intimm/dxu071] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Activation-induced cytidine deaminase (AID) is essential to class switch recombination (CSR) and somatic hypermutation (SHM). Uracil DNA glycosylase (UNG), a member of the base excision repair complex, is required for CSR. The role of UNG in CSR and SHM is extremely controversial. AID deficiency in mice abolishes both CSR and SHM, while UNG-deficient mice have drastically reduced CSR but augmented SHM raising a possibility of differential functions of UNG in CSR and SHM. Interestingly, UNG has been associated with a CSR-specific repair adapter protein Brd4, which interacts with acetyl histone 4, γH2AX and 53BP1 to promote non-homologous end joining during CSR. A non-canonical scaffold function of UNG, but not the catalytic activity, can be attributed to the recruitment of essential repair proteins associated with the error-free repair during SHM, and the end joining during CSR.
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Affiliation(s)
- Ashraf S Yousif
- Department of Immunology and Genomic Medicine, Graduate School of Medicine, Kyoto University, Yoshida, Sakyo-ku, Kyoto 606-8501, Japan
| | - Andre Stanlie
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Nasim A Begum
- Department of Immunology and Genomic Medicine, Graduate School of Medicine, Kyoto University, Yoshida, Sakyo-ku, Kyoto 606-8501, Japan
| | - Tasuku Honjo
- Department of Immunology and Genomic Medicine, Graduate School of Medicine, Kyoto University, Yoshida, Sakyo-ku, Kyoto 606-8501, Japan
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28
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Differential regulation of S-region hypermutation and class-switch recombination by noncanonical functions of uracil DNA glycosylase. Proc Natl Acad Sci U S A 2014; 111:E1016-24. [PMID: 24591630 DOI: 10.1073/pnas.1402391111] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Activation-induced cytidine deaminase (AID) is essential to class-switch recombination (CSR) and somatic hypermutation (SHM) in both V region SHM and S region SHM (s-SHM). Uracil DNA glycosylase (UNG), a member of the base excision repair (BER) complex, is required for CSR. Strikingly, however, UNG deficiency causes augmentation of SHM, suggesting involvement of distinct functions of UNG in SHM and CSR. Here, we show that noncanonical scaffold functions of UNG regulate s-SHM negatively and CSR positively. The s-SHM suppressive function of UNG is attributed to the recruitment of faithful BER components at the cleaved DNA locus, with competition against error-prone polymerases. By contrast, the CSR-promoting function of UNG enhances AID-dependent S-S synapse formation by recruiting p53-binding protein 1 and DNA-dependent protein kinase, catalytic subunit. Several loss-of-catalysis mutants of UNG discriminated CSR-promoting activity from s-SHM suppressive activity. Taken together, the noncanonical function of UNG regulates the steps after AID-induced DNA cleavage: error-prone repair suppression in s-SHM and end-joining promotion in CSR.
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29
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Human Pol ζ purified with accessory subunits is active in translesion DNA synthesis and complements Pol η in cisplatin bypass. Proc Natl Acad Sci U S A 2014; 111:2954-9. [PMID: 24449906 DOI: 10.1073/pnas.1324001111] [Citation(s) in RCA: 144] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
DNA polymerase ζ (Pol ζ) is a eukaryotic B-family DNA polymerase that specializes in translesion synthesis and is essential for normal embryogenesis. At a minimum, Pol ζ consists of a catalytic subunit Rev3 and an accessory subunit Rev7. Mammalian Rev3 contains >3,000 residues and is twice as large as the yeast homolog. To date, no vertebrate Pol ζ has been purified for biochemical characterization. Here we report purification of a series of human Rev3 deletion constructs expressed in HEK293 cells and identification of a minimally catalytically active human Pol ζ variant. With a tagged form of an active Pol ζ variant, we isolated two additional accessory subunits of human Pol ζ, PolD2 and PolD3. The purified four-subunit Pol ζ4 (Rev3-Rev7-PolD2-PolD3) is much more efficient and more processive at bypassing a 1,2-intrastrand d(GpG)-cisplatin cross-link than the two-subunit Pol ζ2 (Rev3-Rev7). We show that complete bypass of cisplatin lesions requires Pol η to insert dCTP opposite the 3' guanine and Pol ζ4 to extend the primers.
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30
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Khalaj M, Abbasi A, Yamanishi H, Akiyama K, Wakitani S, Kikuchi S, Hirose M, Yuzuriha M, Magari M, Degheidy HA, Abe K, Ogura A, Hashimoto H, Kunieda T. A missense mutation in Rev7 disrupts formation of Polζ, impairing mouse development and repair of genotoxic agent-induced DNA lesions. J Biol Chem 2013; 289:3811-24. [PMID: 24356953 DOI: 10.1074/jbc.m113.514752] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Repro22 is a mutant mouse produced via N-ethyl-N-nitrosourea-induced mutagenesis that shows sterility with germ cell depletion caused by defective proliferation of primordial germ cells, decreased body weight, and partial lethality during embryonic development. Using a positional cloning strategy, we identified a missense mutation in Rev7/Mad2l2 (Rev7(C70R)) and confirmed that the mutation is the cause of the defects in repro22 mice through transgenic rescue with normal Rev7. Rev7/Mad2l2 encodes a subunit of DNA polymerase ζ (Polζ), 1 of 10 translesion DNA synthesis polymerases known in mammals. The mutant REV7 did not interact with REV3, the catalytic subunit of Polζ. Rev7(C70R/C70R) cells showed decreased proliferation, increased apoptosis, and arrest in S phase with extensive γH2AX foci in nuclei that indicated accumulation of DNA damage after treatment with the genotoxic agent mitomycin C. The Rev7(C70R) mutation does not affect the mitotic spindle assembly checkpoint. These results demonstrated that Rev7 is essential in resolving the replication stalls caused by DNA damage during S phase. We concluded that Rev7 is required for primordial germ cell proliferation and embryonic viability and development through the translesion DNA synthesis activity of Polζ preserving DNA integrity during cell proliferation, which is required in highly proliferating embryonic cells.
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Affiliation(s)
- Maryam Khalaj
- From the Graduate School of Natural Science and Technology and
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31
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Dual role for mammalian DNA polymerase ζ in maintaining genome stability and proliferative responses. Proc Natl Acad Sci U S A 2013; 110:E687-96. [PMID: 23386725 DOI: 10.1073/pnas.1217425110] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
DNA polymerase ζ (polζ) is critical for bypass of DNA damage and the associated mutagenesis, but also has unique functions in mammals. It is required for embryonic development and for viability of hematopoietic cells, but, paradoxically, skin epithelia appear to survive polζ deletion. We wished to determine whether polζ functions in a tissue-specific manner and how polζ status influences skin tumorigenesis. Mice were produced in which Rev3L (the catalytic subunit of polζ) was deleted in tissues expressing keratin 5. Efficient epidermal deletion of Rev3L was tolerated but led to skin and hair abnormalities, accompanied by evidence of DNA breaks. Unchallenged mice developed tumors in keratin 5-expressing tissues with age, consistent with the chromosomal instability accompanying a polζ defect. Unexpectedly, mice with the Rev3L deletion were much more sensitive to UVB radiation than mice defective in other DNA repair genes. Following irradiation, polζ-defective mice failed to mount skin-regenerative responses and responded to stress by mobilizing melanocytes to the epidermis. However, they did not develop skin tumors after chronic UVB irradiation. To determine the proliferative potential of polζ-deficient skin epithelia, keratinocytes were isolated and examined. These keratinocytes harbored chromosomal gaps and breaks and exhibited a striking proliferation defect. These results can be unified by a model in which slowly dividing cells accumulate replication-associated DNA breaks but otherwise survive Rev3L deletion, but functional polζ is essential for responses requiring rapid proliferation, both in cell culture and in vivo. The results reveal a biological role for mammalian polζ in tolerating DNA damage and enabling proliferative responses in vivo.
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32
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Stone JE, Lujan SA, Kunkel TA. DNA polymerase zeta generates clustered mutations during bypass of endogenous DNA lesions in Saccharomyces cerevisiae. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2012; 53:777-786. [PMID: 22965922 PMCID: PMC3678557 DOI: 10.1002/em.21728] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2012] [Revised: 07/15/2012] [Accepted: 07/25/2012] [Indexed: 06/01/2023]
Abstract
Multiple sequence changes that are simultaneously introduced in a single DNA transaction have a higher probability of altering gene function than do single base substitutions. DNA polymerase zeta (Pol ζ) has been shown to introduce such clustered mutations under specific selective and/or DNA damage-producing conditions. In this study, a forward mutation assay was used to determine the specificity of spontaneous mutations generated in Saccharomyces cerevisiae when either wild-type Pol ζ or a mutator Pol ζ variant (rev3-L979F) bypasses endogenous lesions. Mutagenesis in strains proficient for nucleotide excision repair (NER) was compared to mutagenesis in NER-deficient strains that retain unrepaired endogenous DNA lesions in the genome. Compared to NER-proficient strains, NER-deficient rad14Δ strains have elevated mutation rates that depend on Pol ζ. Rates are most strongly elevated for tandem base pair substitutions and clusters of multiple, closely spaced mutations. Both types of mutations depend on Pol ζ, but not on Pol η. Rates of each are further elevated in yeast strains bearing the rev3-979F allele. The results indicate that when Pol ζ performs mutagenic bypass of endogenous, helix-distorting lesions, it catalyzes a short track of processive, error-prone synthesis. We discuss the implications of this unique catalytic property of Pol ζ to its evolutionary conservation and possibly to multistage carcinogenesis.
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Affiliation(s)
| | | | - Thomas A. Kunkel
- Correspondence to: Laboratory of Molecular Genetics and Laboratory of Structural Biology, National Institute of Environmental Health Sciences, NIH, DHHS, Research Triangle Park, NC 27709.
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