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Bello A, Hirth G, Voigt S, Tepper S, Jungnickel B. Mechanism and regulation of secondary immunoglobulin diversification. Cell Cycle 2023; 22:2070-2087. [PMID: 37909747 PMCID: PMC10761156 DOI: 10.1080/15384101.2023.2275397] [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: 05/04/2023] [Accepted: 10/20/2023] [Indexed: 11/03/2023] Open
Abstract
Secondary immunoglobulin diversification by somatic hypermutation and class switch recombination in B cells is instrumental for an adequate adaptive humoral immune response. These genetic events may, however, also introduce aberrations into other cellular genes and thereby cause B cell malignancies. While the basic mechanism of somatic hypermutation and class switch recombination is now well understood, their regulation and in particular the mechanism of their specific targeting to immunoglobulin genes is still rather mysterious. In this review, we summarize the current knowledge on the mechanism and regulation of secondary immunoglobulin diversification and discuss known mechanisms of physiological targeting to immunoglobulin genes and mistargeting to other cellular genes. We summarize open questions in the field and provide an outlook on future research.
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Affiliation(s)
- Amanda Bello
- Institute of Biochemistry and Biophysics, Faculty of Biological Sciences, Friedrich Schiller University, Jena, Germany
| | - Gianna Hirth
- Institute of Biochemistry and Biophysics, Faculty of Biological Sciences, Friedrich Schiller University, Jena, Germany
| | - Stefanie Voigt
- Institute of Biochemistry and Biophysics, Faculty of Biological Sciences, Friedrich Schiller University, Jena, Germany
| | - Sandra Tepper
- Institute of Biochemistry and Biophysics, Faculty of Biological Sciences, Friedrich Schiller University, Jena, Germany
| | - Berit Jungnickel
- Institute of Biochemistry and Biophysics, Faculty of Biological Sciences, Friedrich Schiller University, Jena, Germany
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Ho YC, Ku CS, Tsai SS, Shiu JL, Jiang YZ, Miriam HE, Zhang HW, Chen YT, Chiu WT, Chang SB, Shen CH, Myung K, Chi P, Liaw H. PARP1 recruits DNA translocases to restrain DNA replication and facilitate DNA repair. PLoS Genet 2022; 18:e1010545. [PMID: 36512630 PMCID: PMC9794062 DOI: 10.1371/journal.pgen.1010545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 12/27/2022] [Accepted: 11/26/2022] [Indexed: 12/15/2022] Open
Abstract
Replication fork reversal which restrains DNA replication progression is an important protective mechanism in response to replication stress. PARP1 is recruited to stalled forks to restrain DNA replication. However, PARP1 has no helicase activity, and the mechanism through which PARP1 participates in DNA replication restraint remains unclear. Here, we found novel protein-protein interactions between PARP1 and DNA translocases, including HLTF, SHPRH, ZRANB3, and SMARCAL1, with HLTF showing the strongest interaction among these DNA translocases. Although HLTF and SHPRH share structural and functional similarity, it remains unclear whether SHPRH contains DNA translocase activity. We further identified the ability of SHPRH to restrain DNA replication upon replication stress, indicating that SHPRH itself could be a DNA translocase or a helper to facilitate DNA translocation. Although hydroxyurea (HU) and MMS induce different types of replication stress, they both induce common DNA replication restraint mechanisms independent of intra-S phase activation. Our results suggest that the PARP1 facilitates DNA translocase recruitment to damaged forks, preventing fork collapse and facilitating DNA repair.
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Affiliation(s)
- Yen-Chih Ho
- Department of Life Sciences, National Cheng Kung University, Tainan City, Taiwan
| | - Chen-Syun Ku
- Department of Life Sciences, National Cheng Kung University, Tainan City, Taiwan
| | - Siang-Sheng Tsai
- Department of Life Sciences, National Cheng Kung University, Tainan City, Taiwan
| | - Jia-Lin Shiu
- Department of Life Sciences, National Cheng Kung University, Tainan City, Taiwan
| | - Yi-Zhen Jiang
- Institute of Biochemical Sciences, National Taiwan University, Taipei City, Taiwan
| | - Hui Emmanuela Miriam
- Department of Life Sciences, National Cheng Kung University, Tainan City, Taiwan
| | - Han-Wen Zhang
- Department of Life Sciences, National Cheng Kung University, Tainan City, Taiwan
| | - Yen-Tzu Chen
- Department of Public Health & Institute of Environmental and Occupational Health Sciences, College of Public Health, National Taiwan University, Taipei City, Taiwan
| | - Wen-Tai Chiu
- Department of Biomedical Engineering, National Cheng Kung University, Tainan City, Taiwan
| | - Song-Bin Chang
- Department of Life Sciences, National Cheng Kung University, Tainan City, Taiwan
| | - Che-Hung Shen
- National Institute of Cancer Research, National Health Research Institutes, Tainan City, Taiwan
| | - Kyungjae Myung
- IBS Center for Genomic Integrity, UNIST-gil 50, Ulsan, Republic of Korea
| | - Peter Chi
- Institute of Biochemical Sciences, National Taiwan University, Taipei City, Taiwan
- Institute of Biological Chemistry, Academia Sinica, Taipei City, Taiwan
| | - Hungjiun Liaw
- Department of Life Sciences, National Cheng Kung University, Tainan City, Taiwan
- * E-mail:
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Haynes BM, Cunningham K, Shekhar MPV. RAD6 inhibition enhances paclitaxel sensitivity of triple negative breast cancer cells by aggravating mitotic spindle damage. BMC Cancer 2022; 22:1073. [PMID: 36258187 PMCID: PMC9578210 DOI: 10.1186/s12885-022-10119-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 09/22/2022] [Indexed: 11/28/2022] Open
Abstract
Background Paclitaxel (PTX), a first-line therapy for triple negative breast cancers (TNBC) induces anti-tumor activity by microtubule stabilization and inhibition of cell division. Its dose-limiting toxicity and short half-life, however, pose clinical challenges underscoring the need for strategies that increase its efficiency. RAD6, a E2 ubiquitin conjugating enzyme, is associated with centrosomes at all phases of cell cycle. Constitutive overexpression of the RAD6B homolog in normal breast cells induces centrosome amplification and multipolar spindle formation, indicating its importance in centrosome regulation. Methods TNBC centrosome numbers were scored by pericentrin immunostaining. PTX sensitivities and interactions with SMI#9, a RAD6-selective small molecule inhibitor, on TNBC cell survival were analyzed by MTT and colony forming assays and an isogenic MDA-MB-468 TNBC model of PTX resistance. The molecular mechanisms underlying PTX and SMI#9 induced cytotoxicity were determined by flow cytometry, immunoblot analysis of cyclin B1 and microtubule associated protein TAU, and dual immunofluorescence staining of TAU and α-tubulin. Results Our data show aberrant centrosome numbers and that PTX sensitivities are not correlated with TNBC BRCA1 status. Combining PTX with SMI#9 synergistically enhances PTX sensitivities of BRCA1 wild-type and mutant TNBC cells. Whereas SMI#9/PTX combination treatment increased cyclin B1 levels in MDA-MB-468 cells, it induced cyclin B1 loss in HCC1937 cells with accumulation of reproductively dead giant cells, a characteristic of mitotic catastrophe. Cell cycle analysis revealed drug-induced accumulation of tetraploid cells in S and G2/M phases, and robust increases in cells with 4 N DNA content in HCC1937 cells. TAU overexpression is associated with reduced PTX efficacy. Among the six TAU isoforms, both SMI#9 and PTX downregulated 1N3R TAU in MDA-MB-468 and HCC1937 cells, suggesting a common mechanism of 1N3R regulation. Dual TAU and α-tubulin immunostaining showed that SMI#9 induces monopolar mitotic spindles. Using the isogenic model of PTX resistance, we show that SMI#9 treatment restores PTX sensitivity. Conclusions These data support a common mechanism of microtubule regulation by SMI#9 and PTX and suggest that combining PTX with RAD6 inhibitor may be beneficial for increasing TNBC sensitivities to PTX and alleviating toxicity. This study demonstrates a new role for RAD6 in regulating microtubule dynamics. Supplementary Information The online version contains supplementary material available at 10.1186/s12885-022-10119-z.
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Affiliation(s)
- Brittany M Haynes
- Karmanos Cancer Institute, 4100 John R Street, Detroit, MI, 48201, USA.,Department of Oncology, Wayne State University School of Medicine, 421 E. Canfield Avenue, Detroit, MI, 48201, USA.,Present address: Office of Policy Communications, and Education, National Center for Advancing Translational Sciences, Besthesda, USA
| | - Kristen Cunningham
- Karmanos Cancer Institute, 4100 John R Street, Detroit, MI, 48201, USA.,Department of Oncology, Wayne State University School of Medicine, 421 E. Canfield Avenue, Detroit, MI, 48201, USA
| | - Malathy P V Shekhar
- Karmanos Cancer Institute, 4100 John R Street, Detroit, MI, 48201, USA. .,Department of Oncology, Wayne State University School of Medicine, 421 E. Canfield Avenue, Detroit, MI, 48201, USA. .,Department of Pathology, Wayne State University School of Medicine, 421 E. Canfield Avenue, Detroit, MI, 48201, USA.
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4
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Shiu JL, Wu CK, Chang SB, Sun YJ, Chen YJ, Lai CC, Chiu WT, Chang WT, Myung K, Su WP, Liaw H. The HLTF-PARP1 interaction in the progression and stability of damaged replication forks caused by methyl methanesulfonate. Oncogenesis 2020; 9:104. [PMID: 33281189 PMCID: PMC7719709 DOI: 10.1038/s41389-020-00289-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 11/04/2020] [Accepted: 11/17/2020] [Indexed: 11/27/2022] Open
Abstract
Human HLTF participates in the lesion-bypass mechanism through the fork reversal structure, known as template switching of post-replication repair. However, the mechanism by which HLTF promotes the replication progression and fork stability of damaged forks remains unclear. Here, we identify a novel protein–protein interaction between HLTF and PARP1. The depletion of HLTF and PARP1 increases chromosome breaks, further reduces the length of replication tracks, and concomitantly increases the number of stalled forks after methyl methanesulfonate treatment according to a DNA fiber analysis. The progression of replication also depends on BARD1 in the presence of MMS treatment. By combining 5-ethynyl-2′-deoxyuridine with a proximity ligation assay, we revealed that the HLTF, PARP1, and BRCA1/BARD1/RAD51 proteins were initially recruited to damaged forks. However, prolonged stalling of damaged forks results in fork collapse. HLTF and PCNA dissociate from the collapsed forks, with increased accumulation of PARP1 and BRCA1/BARD1/RAD51 at the collapsed forks. Our results reveal that HLTF together with PARP1 and BARD1 participates in the stabilization of damaged forks, and the PARP1–BARD1 interaction is further involved in the repair of collapse forks.
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Affiliation(s)
- Jia-Lin Shiu
- Department of Life Sciences, National Cheng Kung University, No.1 University Road, Tainan City, 701, Taiwan
| | - Cheng-Kuei Wu
- Institute of Clinical Medicine, College of Medicine, National Cheng Kung University, No.138, Sheng Li Road, Tainan City, 704, Taiwan
| | - Song-Bin Chang
- Department of Life Sciences, National Cheng Kung University, No.1 University Road, Tainan City, 701, Taiwan
| | - Yan-Jhih Sun
- Department of Life Sciences, National Cheng Kung University, No.1 University Road, Tainan City, 701, Taiwan
| | - Yen-Ju Chen
- Department of Life Sciences, National Cheng Kung University, No.1 University Road, Tainan City, 701, Taiwan
| | - Chien-Chen Lai
- Institute of Molecular Biology, College of Life Science, National Chung Hsing University, No.145 Xingda Rd. South Dist., Taichung City, Taiwan
| | - Wen-Tai Chiu
- Department of Biomedical Engineering, National Cheng Kung University, Tainan City, Taiwan
| | - Wen-Tsan Chang
- Department of Biochemistry and Molecular Biology, College of Medicine, National Cheng Kung University, Tainan City, Taiwan
| | - Kyungjae Myung
- IBS Center for Genomic Integrity, UNIST-gil 50, Ulsan, 689-798, Republic of Korea
| | - Wen-Pin Su
- Institute of Clinical Medicine, College of Medicine, National Cheng Kung University, No.138, Sheng Li Road, Tainan City, 704, Taiwan. .,Departments of Oncology and Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan City, 704, Taiwan.
| | - Hungjiun Liaw
- Department of Life Sciences, National Cheng Kung University, No.1 University Road, Tainan City, 701, Taiwan.
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A Genome-Wide Screen for Genes Affecting Spontaneous Direct-Repeat Recombination in Saccharomyces cerevisiae. G3-GENES GENOMES GENETICS 2020; 10:1853-1867. [PMID: 32265288 PMCID: PMC7263696 DOI: 10.1534/g3.120.401137] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Homologous recombination is an important mechanism for genome integrity maintenance, and several homologous recombination genes are mutated in various cancers and cancer-prone syndromes. However, since in some cases homologous recombination can lead to mutagenic outcomes, this pathway must be tightly regulated, and mitotic hyper-recombination is a hallmark of genomic instability. We performed two screens in Saccharomyces cerevisiae for genes that, when deleted, cause hyper-recombination between direct repeats. One was performed with the classical patch and replica-plating method. The other was performed with a high-throughput replica-pinning technique that was designed to detect low-frequency events. This approach allowed us to validate the high-throughput replica-pinning methodology independently of the replicative aging context in which it was developed. Furthermore, by combining the two approaches, we were able to identify and validate 35 genes whose deletion causes elevated spontaneous direct-repeat recombination. Among these are mismatch repair genes, the Sgs1-Top3-Rmi1 complex, the RNase H2 complex, genes involved in the oxidative stress response, and a number of other DNA replication, repair and recombination genes. Since several of our hits are evolutionarily conserved, and repeated elements constitute a significant fraction of mammalian genomes, our work might be relevant for understanding genome integrity maintenance in humans.
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Haynes B, Gajan A, Nangia-Makker P, Shekhar MP. RAD6B is a major mediator of triple negative breast cancer cisplatin resistance: Regulation of translesion synthesis/Fanconi anemia crosstalk and BRCA1 independence. Biochim Biophys Acta Mol Basis Dis 2019; 1866:165561. [PMID: 31639439 DOI: 10.1016/j.bbadis.2019.165561] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 08/26/2019] [Accepted: 09/16/2019] [Indexed: 12/20/2022]
Abstract
Triple negative breast cancer (TNBC) is an aggressive breast cancer subtype with few therapy options besides chemotherapy. Although platinum-based drugs have shown initial activity in BRCA1-mutated TNBCs, chemoresistance remains a challenge. Here we show that RAD6B (UBE2B), a principal mediator of translesion synthesis (TLS), is overexpressed in BRCA1 wild-type and mutant TNBCs, and RAD6B overexpression correlates with poor survival. Pretreatment with a RAD6-selective inhibitor, SMI#9, enhanced cisplatin chemosensitivity of BRCA1 wild-type and mutant TNBCs. SMI#9 attenuated cisplatin-induced PCNA monoubiquitination (TLS marker), FANCD2 (Fanconi anemia (FA) activation marker), and TLS polymerase POL η. SMI#9-induced decreases in γH2AX levels were associated with concomitant inhibition of H2AX monoubiquitination, suggesting a key role for RAD6 in modulating cisplatin-induced γH2AX via H2AX monoubiquitination. Concordantly, SMI#9 inhibited γH2AX, POL η and FANCD2 foci formation. RAD51 foci formation was unaffected by SMI#9, however, its recruitment to double-strand breaks was inhibited. Using the DR-GFP-based assay, we showed that RAD6B silencing or SMI#9 treatment impairs homologous recombination (HR) in HR-proficient cells. DNA fiber assays confirmed that restart of cisplatin-stalled replicating forks is inhibited by SMI#9 in both BRCA1 wild-type and mutant TNBC cells. Consistent with the in vitro data, SMI#9 and cisplatin combination treatment inhibited BRCA1 wild-type and mutant TNBC growth as compared to controls. These RAD6B activities are unaffected by BRCA1 status of TNBCs suggesting that the RAD6B function in TLS/FA crosstalk could occur in HR-dependent and independent modes. Collectively, these data implicate RAD6 as an important therapeutic target for TNBCs irrespective of their BRCA1 status.
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Affiliation(s)
- Brittany Haynes
- Karmanos Cancer Institute, 421 E. Canfield Avenue, Detroit, MI 48201, USA; Department of Oncology, Wayne State University School of Medicine, 421 E. Canfield Avenue, Detroit, MI 48201, USA
| | - Ambikai Gajan
- Karmanos Cancer Institute, 421 E. Canfield Avenue, Detroit, MI 48201, USA; Department of Oncology, Wayne State University School of Medicine, 421 E. Canfield Avenue, Detroit, MI 48201, USA
| | - Pratima Nangia-Makker
- Karmanos Cancer Institute, 421 E. Canfield Avenue, Detroit, MI 48201, USA; Department of Oncology, Wayne State University School of Medicine, 421 E. Canfield Avenue, Detroit, MI 48201, USA
| | - Malathy P Shekhar
- Karmanos Cancer Institute, 421 E. Canfield Avenue, Detroit, MI 48201, USA; Department of Oncology, Wayne State University School of Medicine, 421 E. Canfield Avenue, Detroit, MI 48201, USA; Department of Pathology, Wayne State University School of Medicine, 421 E. Canfield Avenue, Detroit, MI 48201, USA.
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7
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Pilzecker B, Jacobs H. Mutating for Good: DNA Damage Responses During Somatic Hypermutation. Front Immunol 2019; 10:438. [PMID: 30915081 PMCID: PMC6423074 DOI: 10.3389/fimmu.2019.00438] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 02/19/2019] [Indexed: 11/13/2022] Open
Abstract
Somatic hypermutation (SHM) of immunoglobulin (Ig) genes plays a key role in antibody mediated immunity. SHM in B cells provides the molecular basis for affinity maturation of antibodies. In this way SHM is key in optimizing antibody dependent immune responses. SHM is initiated by targeting the Activation-Induced Cytidine Deaminase (AID) to rearranged V(D)J and switch regions of Ig genes. The mutation rate of this programmed mutagenesis is ~10-3 base pairs per generation, a million-fold higher than the non-AID targeted genome of B cells. AID is a processive enzyme that binds single-stranded DNA and deaminates cytosines in DNA. Cytosine deamination generates highly mutagenic deoxy-uracil (U) in the DNA of both strands of the Ig loci. Mutagenic processing of the U by the DNA damage response generates the entire spectrum of base substitutions characterizing SHM at and around the initial U lesion. Starting from the U as a primary lesion, currently five mutagenic DNA damage response pathways have been identified in generating a well-defined SHM spectrum of C/G transitions, C/G transversions, and A/T mutations around this initial lesion. These pathways include (1) replication opposite template U generates transitions at C/G, (2) UNG2-dependent translesion synthesis (TLS) generates transversions at C/G, (3) a hybrid pathway comprising non-canonical mismatch repair (ncMMR) and UNG2-dependent TLS generates transversions at C/G, (4) ncMMR generates mutations at A/T, and (5) UNG2- and PCNA Ubiquitination (PCNA-Ub)-dependent mutations at A/T. Furthermore, specific strand-biases of SHM spectra arise as a consequence of a biased AID targeting, ncMMR, and anti-mutagenic repriming. Here, we review mammalian SHM with special focus on the mutagenic DNA damage response pathways involved in processing AID induced Us, the origin of characteristic strand biases, and relevance of the cell cycle.
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Affiliation(s)
| | - Heinz Jacobs
- Division of Tumor Biology & Immunology, The Netherlands Cancer Institute, Amsterdam, Netherlands
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8
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Meza Gutierrez F, Simsek D, Mizrak A, Deutschbauer A, Braberg H, Johnson J, Xu J, Shales M, Nguyen M, Tamse-Kuehn R, Palm C, Steinmetz LM, Krogan NJ, Toczyski DP. Genetic analysis reveals functions of atypical polyubiquitin chains. eLife 2018; 7:42955. [PMID: 30547882 PMCID: PMC6305200 DOI: 10.7554/elife.42955] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Accepted: 11/30/2018] [Indexed: 12/27/2022] Open
Abstract
Although polyubiquitin chains linked through all lysines of ubiquitin exist, specific functions are well-established only for lysine-48 and lysine-63 linkages in Saccharomyces cerevisiae. To uncover pathways regulated by distinct linkages, genetic interactions between a gene deletion library and a panel of lysine-to-arginine ubiquitin mutants were systematically identified. The K11R mutant had strong genetic interactions with threonine biosynthetic genes. Consistently, we found that K11R mutants import threonine poorly. The K11R mutant also exhibited a strong genetic interaction with a subunit of the anaphase-promoting complex (APC), suggesting a role in cell cycle regulation. K11-linkages are important for vertebrate APC function, but this was not previously described in yeast. We show that the yeast APC also modifies substrates with K11-linkages in vitro, and that those chains contribute to normal APC-substrate turnover in vivo. This study reveals comprehensive genetic interactomes of polyubiquitin chains and characterizes the role of K11-chains in two biological pathways.
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Affiliation(s)
- Fernando Meza Gutierrez
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States
| | | | - Arda Mizrak
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States
| | | | - Hannes Braberg
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, United States
| | - Jeffrey Johnson
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, United States
| | - Jiewei Xu
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, United States
| | - Michael Shales
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, United States
| | - Michelle Nguyen
- Stanford Genome Technology Center, Stanford University, Stanford, United States
| | - Raquel Tamse-Kuehn
- Stanford Genome Technology Center, Stanford University, Stanford, United States
| | - Curt Palm
- Stanford Genome Technology Center, Stanford University, Stanford, United States
| | - Lars M Steinmetz
- Stanford Genome Technology Center, Stanford University, Stanford, United States
| | - Nevan J Krogan
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, United States
| | - David P Toczyski
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States
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9
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Hsu SH, Chen SH, Kuo CC, Chang JY. Ubiquitin-conjugating enzyme E2 B regulates the ubiquitination of O 6-methylguanine-DNA methyltransferase and BCNU sensitivity in human nasopharyngeal carcinoma cells. Biochem Pharmacol 2018; 158:327-338. [PMID: 30449727 DOI: 10.1016/j.bcp.2018.10.029] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 10/25/2018] [Indexed: 02/06/2023]
Abstract
O6-Methylguanine-DNA methyltransferase (MGMT) is a DNA repair enzyme that removes the alkyl groups from the O6 position of guanine and is then degraded via ubiquitin-mediated degradation. Previous studies indicated that 1,3-bis(2-chloroethyl)-1-nitrosourea (BCNU) facilitates the ubiquitination and degradation of MGMT in several types of cancer cells. However, the underlying mechanism of MGMT ubiquitination remains unclear. In this study, we demonstrated for the first time that ubiquitin-conjugating enzyme E2 B (UBE2B) is a novel regulator of MGMT ubiquitination mediated by BCNU in nasopharyngeal carcinoma (NPC) cells. The E3 ubiquitin ligase RAD18, a partner of UBE2B, is also involved in BCNU-mediated MGMT ubiquitination. Overexpression/knockdown of UBE2B enhanced/reduced BCNU-mediated MGMT ubiquitination. Surprisingly, UBE2B knockdown significantly increased BCNU cytotoxicity in NPC cells. Therefore, loss of UBE2B seems to disrupt ubiquitin-mediated degradation of alkylated MGMT. We found that UBE2B knockdown reduced MGMT activity, suggesting that loss of UBE2B leads to the accumulation of deactivated MGMT and suppresses MGMT protein turnover in BCNU-treated cells. These findings indicate that UBE2B modulates sensitivity to BCNU in NPC cells by regulating MGMT ubiquitination.
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Affiliation(s)
- Shih-Han Hsu
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan; National Institute of Cancer Research, National Health Research Institutes, Tainan, Taiwan
| | - Shang-Hung Chen
- National Institute of Cancer Research, National Health Research Institutes, Tainan, Taiwan; Division of Hematology/Oncology, Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Ching-Chuan Kuo
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Zhunan, Taiwan
| | - Jang-Yang Chang
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan; National Institute of Cancer Research, National Health Research Institutes, Tainan, Taiwan; Division of Hematology/Oncology, Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan.
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10
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Rai SK, Sangesland M, Lee M, Esnault C, Cui Y, Chatterjee AG, Levin HL. Host factors that promote retrotransposon integration are similar in distantly related eukaryotes. PLoS Genet 2017; 13:e1006775. [PMID: 29232693 PMCID: PMC5741268 DOI: 10.1371/journal.pgen.1006775] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Revised: 12/22/2017] [Accepted: 11/07/2017] [Indexed: 12/14/2022] Open
Abstract
Retroviruses and Long Terminal Repeat (LTR)-retrotransposons have distinct patterns of integration sites. The oncogenic potential of retrovirus-based vectors used in gene therapy is dependent on the selection of integration sites associated with promoters. The LTR-retrotransposon Tf1 of Schizosaccharomyces pombe is studied as a model for oncogenic retroviruses because it integrates into the promoters of stress response genes. Although integrases (INs) encoded by retroviruses and LTR-retrotransposons are responsible for catalyzing the insertion of cDNA into the host genome, it is thought that distinct host factors are required for the efficiency and specificity of integration. We tested this hypothesis with a genome-wide screen of host factors that promote Tf1 integration. By combining an assay for transposition with a genetic assay that measures cDNA recombination we could identify factors that contribute differentially to integration. We utilized this assay to test a collection of 3,004 S. pombe strains with single gene deletions. Using these screens and immunoblot measures of Tf1 proteins, we identified a total of 61 genes that promote integration. The candidate integration factors participate in a range of processes including nuclear transport, transcription, mRNA processing, vesicle transport, chromatin structure and DNA repair. Two candidates, Rhp18 and the NineTeen complex were tested in two-hybrid assays and were found to interact with Tf1 IN. Surprisingly, a number of pathways we identified were found previously to promote integration of the LTR-retrotransposons Ty1 and Ty3 in Saccharomyces cerevisiae, indicating the contribution of host factors to integration are common in distantly related organisms. The DNA repair factors are of particular interest because they may identify the pathways that repair the single stranded gaps flanking the sites of strand transfer following integration of LTR retroelements. Retroviruses and retrotransposons are genetic elements that propagate by integrating into chromosomes of eukaryotic cells. Genetic disorders are being treated with retrovirus-based vectors that integrate corrective genes into the chromosomes of patients. Unfortunately, the vectors can alter expression of adjacent genes and depending on the position of integration, cancer genes can be induced. It is therefore essential that we understand how integration sites are selected. Interestingly, different retroviruses and retrotransposons have different profiles of integration sites. While specific proteins have been identified that select target sites, it’s not known what other cellular factors promote integration. In this paper, we report a comprehensive screen of host factors that promote LTR-retrotransposon integration in the widely-studied yeast, Schizosaccharomyces pombe. Unexpectedly, we found a wide range of pathways and host factors participate in integration. And importantly, we found the cellular processes that promote integration relative to recombination in S. pombe are the same that drive integration of LTR-retrotransposons in the distantly related yeast Saccharomyces cerevisiae. This suggests a specific set of cellular pathways are responsible for integration in a wide range of eukaryotic hosts.
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Affiliation(s)
- Sudhir Kumar Rai
- Section on Eukaryotic Transposable Elements, Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health (NIH), Bethesda, Maryland, United States of America
| | - Maya Sangesland
- Section on Eukaryotic Transposable Elements, Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health (NIH), Bethesda, Maryland, United States of America
| | - Michael Lee
- Section on Eukaryotic Transposable Elements, Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health (NIH), Bethesda, Maryland, United States of America
| | - Caroline Esnault
- Section on Eukaryotic Transposable Elements, Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health (NIH), Bethesda, Maryland, United States of America
| | - Yujin Cui
- Section on Eukaryotic Transposable Elements, Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health (NIH), Bethesda, Maryland, United States of America
| | - Atreyi Ghatak Chatterjee
- Section on Eukaryotic Transposable Elements, Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health (NIH), Bethesda, Maryland, United States of America
| | - Henry L. Levin
- Section on Eukaryotic Transposable Elements, Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health (NIH), Bethesda, Maryland, United States of America
- * E-mail:
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11
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Zilio N, Eifler-Olivi K, Ulrich HD. Functions of SUMO in the Maintenance of Genome Stability. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 963:51-87. [PMID: 28197906 DOI: 10.1007/978-3-319-50044-7_4] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Like in most other areas of cellular metabolism, the functions of the ubiquitin-like modifier SUMO in the maintenance of genome stability are manifold and varied. Perturbations of global sumoylation causes a wide spectrum of phenotypes associated with defects in DNA maintenance, such as hypersensitivity to DNA-damaging agents, gross chromosomal rearrangements and loss of entire chromosomes. Consistent with these observations, many key factors involved in various DNA repair pathways have been identified as SUMO substrates. However, establishing a functional connection between a given SUMO target, the cognate SUMO ligase and a relevant phenotype has remained a challenge, mainly because of the difficulties involved in identifying important modification sites and downstream effectors that specifically recognize the target in its sumoylated state. This review will give an overview over the major pathways of DNA repair and genome maintenance influenced by the SUMO system and discuss selected examples of SUMO's actions in these pathways where the biological consequences of the modification have been elucidated.
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Affiliation(s)
- Nicola Zilio
- Institute of Molecular Biology (IMB), Ackermannweg 4, D-55128, Mainz, Germany
| | | | - Helle D Ulrich
- Institute of Molecular Biology (IMB), Ackermannweg 4, D-55128, Mainz, Germany.
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12
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Sanders MA, Haynes B, Nangia-Makker P, Polin LA, Shekhar MP. Pharmacological targeting of RAD6 enzyme-mediated translesion synthesis overcomes resistance to platinum-based drugs. J Biol Chem 2017; 292:10347-10363. [PMID: 28490629 DOI: 10.1074/jbc.m117.792192] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Revised: 05/08/2017] [Indexed: 12/13/2022] Open
Abstract
Platinum drug-induced cross-link repair requires the concerted activities of translesion synthesis (TLS), Fanconi anemia (FA), and homologous recombination repair pathways. The E2 ubiquitin-conjugating enzyme RAD6 is essential for TLS. Here, we show that RAD6 plays a universal role in platinum-based drug tolerance. Using a novel RAD6-selective small-molecule inhibitor (SMI#9) targeting the RAD6 catalytic site, we demonstrate that SMI#9 potentiates the sensitivities of cancer cells with innate or acquired cisplatin or oxaliplatin resistance. 5-Iododeoxyuridine/5-chlorodeoxyuridine pulse-labeling experiments showed that RAD6 is necessary for overcoming cisplatin-induced replication fork stalling, as replication-restart was impaired in both SMI#9-pretreated and RAD6B-silenced cells. Consistent with the role of RAD6/TLS in late-S phase, SMI#9-induced DNA replication inhibition occurred preferentially in mid/late-S phase. The compromised DNA repair and chemosensitization induced by SMI#9 or RAD6B depletion were associated with decreased platinum drug-induced proliferating cell nuclear antigen (PCNA) and FANCD2 monoubiquitinations (surrogate markers of TLS and FA pathway activation, respectively) and with attenuated FANCD2, RAD6, γH2AX, and POL η foci formation and cisplatin-adduct removal. SMI#9 pretreatment synergistically increased cisplatin inhibition of MDA-MB-231 triple-negative breast cancer cell proliferation and tumor growth. Using an isogenic HCT116 colon cancer model of oxaliplatin resistance, we further show that γH2AX and monoubiquitinated PCNA and FANCD2 are constitutively up-regulated in oxaliplatin-resistant HCT116 (HCT116-OxR) cells and that γH2AX, PCNA, and FANCD2 monoubiquitinations are induced by oxaliplatin in parental HCT116 cells. SMI#9 pretreatment sensitized HCT116-OxR cells to oxaliplatin. These data deepen insights into the vital role of RAD6/TLS in platinum drug tolerance and reveal clinical benefits of targeting RAD6 with SMI#9 for managing chemoresistant cancers.
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Affiliation(s)
- Matthew A Sanders
- From the Karmanos Cancer Institute and.,the Departments of Oncology and
| | - Brittany Haynes
- From the Karmanos Cancer Institute and.,the Departments of Oncology and
| | - Pratima Nangia-Makker
- From the Karmanos Cancer Institute and.,Pathology, Wayne State University School of Medicine, Detroit, Michigan 48201
| | - Lisa A Polin
- From the Karmanos Cancer Institute and.,the Departments of Oncology and
| | - Malathy P Shekhar
- From the Karmanos Cancer Institute and .,the Departments of Oncology and.,Pathology, Wayne State University School of Medicine, Detroit, Michigan 48201
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13
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Chu TQ, Li R, Shao MH, Ye JY, Han BH. RAD18 polymorphisms are associated with platinum-based chemotherapy toxicity in Chinese patients with non-small cell lung cancer. Acta Pharmacol Sin 2016; 37:1490-1498. [PMID: 27665847 DOI: 10.1038/aps.2016.100] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Accepted: 07/29/2016] [Indexed: 12/15/2022] Open
Abstract
AIM Although targeted therapy is very efficient for lung cancer, traditional platinum-based chemotherapies are still the principal strategy in the absence of positive biomarkers. The aim of the present study is to evaluate the contribution of RAD18 polymorphisms to platinum-chemotherapy response and its potential side effects in Chinese patients with non-small cell lung cancer (NSCLC). METHODS A total of 1021 Chinese patients with histological diagnosis of advanced NSCLC were enrolled. Treatment responses were classified into 4 categories (complete response, partial response, stable disease and progressive disease). Gastrointestinal and hematological toxicity incidences were assessed twice a week during the first-line treatment. Ten RAD18 SNPs were genotyped. A logistic regression model was utilized to analyze the associations between RAD18 SNPs and treatment response or toxicity. RESULTS Among the 10 SNPs tested, none was significantly correlated with the treatment response in a combined cohort. For gastrointestinal toxicity incidences, rs586014 was significantly associated with an increased risk of grade 3 or 4 gastrointestinal toxicity in non-smokers and in the combined cohort; rs654448 and rs618784 were significantly associated with gastrointestinal toxicity in non-smokers; rs6763823 was significantly associated with gastrointestinal toxicity in smokers. For hematological toxicity incidences, rs586014, rs654448 and rs618784 were significantly associated with hematologic toxicity in non-smokers; rs6763823 and rs9880051 were significantly associated with leukocytopenia in smokers. CONCLUSION RAD18 polymorphisms are correlated with the side effects of platinum-chemotherapy in Chinese patients with advanced NSCLC.
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14
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Kobbe D, Kahles A, Walter M, Klemm T, Mannuss A, Knoll A, Focke M, Puchta H. AtRAD5A is a DNA translocase harboring a HIRAN domain which confers binding to branched DNA structures and is required for DNA repair in vivo. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 88:521-530. [PMID: 27458713 DOI: 10.1111/tpj.13283] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Revised: 07/20/2016] [Accepted: 07/22/2016] [Indexed: 05/26/2023]
Abstract
DNA lesions such as crosslinks represent obstacles for the replication machinery. Nonetheless, replication can proceed via the DNA damage tolerance pathway also known as postreplicative repair pathway. SNF2 ATPase Rad5 homologs, such as RAD5A of the model plant Arabidopsis thaliana, are important for the error-free mode of this pathway. We able to demonstrate before, that RAD5A is a key factor in the repair of DNA crosslinks in Arabidopsis. Here, we show by in vitro analysis that AtRAD5A protein is a DNA translocase able to catalyse fork regression. Interestingly, replication forks with a gap in the leading strand are processed best, in line with its suggested function. Furthermore AtRAD5A catalyses branch migration of a Holliday junction and is furthermore not impaired by the DNA binding of a model protein, which is indicative of its ability to displace other proteins. Rad5 homologs possess HIRAN (Hip116, Rad5; N-terminal) domains. By biochemical analysis we were able to demonstrate that the HIRAN domain variant from Arabidopsis RAD5A mediates structure selective DNA binding without the necessity for a free 3'OH group as has been shown to be required for binding of HIRAN domains in a mammalian RAD5 homolog. The biological importance of the HIRAN domain in AtRAD5A is demonstrated by our result that it is required for its function in DNA crosslink repair in vivo.
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Affiliation(s)
- Daniela Kobbe
- Botanical Institute II, Karlsruhe Institute of Technology (KIT), Karlsruhe, 76131, Germany
| | - Andy Kahles
- Botanical Institute II, Karlsruhe Institute of Technology (KIT), Karlsruhe, 76131, Germany
| | - Maria Walter
- Botanical Institute II, Karlsruhe Institute of Technology (KIT), Karlsruhe, 76131, Germany
| | - Tobias Klemm
- Botanical Institute II, Karlsruhe Institute of Technology (KIT), Karlsruhe, 76131, Germany
| | - Anja Mannuss
- Botanical Institute II, Karlsruhe Institute of Technology (KIT), Karlsruhe, 76131, Germany
| | - Alexander Knoll
- Botanical Institute II, Karlsruhe Institute of Technology (KIT), Karlsruhe, 76131, Germany
| | - Manfred Focke
- Botanical Institute II, Karlsruhe Institute of Technology (KIT), Karlsruhe, 76131, Germany
| | - Holger Puchta
- Botanical Institute II, Karlsruhe Institute of Technology (KIT), Karlsruhe, 76131, Germany
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15
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Abstract
Annexin A1 (ANXA1) is a Ca(2+)-regulated phospholipid-binding protein involved in various cell processes. ANXA1 was initially widely studied in inflammation resolution, but its overexpression was later reported in a large number of cancers. Further in-depth investigations have revealed that this protein could have many roles in cancer progression and act at different levels (from cancer initiation to metastasis). This is partly due to the location of ANXA1 in different cell compartments. ANXA1 can be nuclear, cytoplasmic and/or membrane associated. This last location allows ANXA1 to be proteolytically cleaved and/or to become accessible to its cognate partners, the formyl-peptide receptors. Indeed, in some cancers, ANXA1 is found at the cell surface, where it stimulates formyl-peptide receptors to trigger oncogenic pathways. In the present review, we look at the different locations of ANXA1 and their association with the deregulated pathways often observed in cancers. We have specifically detailed the non-classic pathways of ANXA1 externalization, the significance of its cleavage and the role of the ANXA1-formyl-peptide receptor complex in cancer progression.
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16
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Su WP, Hsu SH, Wu CK, Chang SB, Lin YJ, Yang WB, Hung JJ, Chiu WT, Tzeng SF, Tseng YL, Chang JY, Su WC, Liaw H. Chronic treatment with cisplatin induces replication-dependent sister chromatid recombination to confer cisplatin-resistant phenotype in nasopharyngeal carcinoma. Oncotarget 2015; 5:6323-37. [PMID: 25051366 PMCID: PMC4171633 DOI: 10.18632/oncotarget.2210] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Cisplatin can cause intrastrand and interstrand crosslinks between purine bases and is a chemotherapeutic drug widely used to treat cancer. However, the major barrier to the efficacy of the treatment is drug resistance. Homologous recombination (HR) plays a central role in restoring stalled forks caused by DNA lesions. Here, we report that chronic treatment with cisplatin induces HR to confer cisplatin resistance in nasopharyngeal carcinoma (NPC) cells. A high frequency of sister chromatid exchanges (SCE) occurs in the cisplatin-resistant NPC cells. In addition, several genes in the Fanconi anemia (FA) and template switching (TS) pathways show elevated expression. Significantly, depletion of HR gene BRCA1, TS gene UBC13, or FA gene FANCD2 suppresses SCE and causes cells to accumulate in the S phase, concomitantly with high γH2AX foci formation in the presence of low-dose cisplatin. Consistent with this result, depletion of several genes in the HR, TS, or FA pathway sensitizes the cisplatin-resistant NPC cells to cisplatin. Our results suggest that the enhanced HR, in coordination with the FA and TS pathways, underlies the cisplatin resistance. Targeting the HR, TS, or FA pathways could be a potential therapeutic strategy for treating cisplatin-resistant cancer.
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Affiliation(s)
- Wen-Pin Su
- Departments of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University; Graduate Institutes of Clinical Medicine, College of Medicine, National Cheng Kung University
| | - Sen-Huei Hsu
- Department of Life Sciences, National Cheng Kung University, No.1 University Road, Tainan City 701, Taiwan; These authors contributed equally to this work
| | - Cheng-Kuei Wu
- Department of Life Sciences, National Cheng Kung University, No.1 University Road, Tainan City 701, Taiwan; These authors contributed equally to this work
| | - Song-Bin Chang
- Department of Life Sciences, National Cheng Kung University, No.1 University Road, Tainan City 701, Taiwan
| | - Yi-Ju Lin
- Department of Life Sciences, National Cheng Kung University, No.1 University Road, Tainan City 701, Taiwan
| | - Wen-Bin Yang
- Institute of Bioinformatics and Biosignal Transduction, National Cheng Kung University
| | - Jan-Jong Hung
- Institute of Bioinformatics and Biosignal Transduction, National Cheng Kung University
| | - Wen-Tai Chiu
- Department of Biomedical Engineering, National Cheng Kung University
| | - Shun-Fen Tzeng
- Department of Life Sciences, National Cheng Kung University, No.1 University Road, Tainan City 701, Taiwan
| | - Yau-Lin Tseng
- Surgery, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University
| | - Jang-Yang Chang
- Departments of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University; National Institute of Cancer Research, National Health Research Institutes, Taiwan
| | - Wu-Chou Su
- Cancer Center, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University
| | - Hungjiun Liaw
- Department of Life Sciences, National Cheng Kung University, No.1 University Road, Tainan City 701, Taiwan
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Pijuan J, María C, Herrero E, Bellí G. Impaired mitochondrial Fe-S cluster biogenesis activates the DNA damage response through different signaling mediators. J Cell Sci 2015; 128:4653-65. [DOI: 10.1242/jcs.178046] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Accepted: 11/05/2015] [Indexed: 01/13/2023] Open
Abstract
Fe-S cluster biogenesis machinery is required for multiple DNA metabolism processes. In this work we show that defects at different stages of the mitochondrial Fe-S cluster assembly machinery (ISC) result in increased spontaneous mutation rate and hyperrecombination, accompanied by an increment in Rad52-associated DNA repair foci and a higher phosphorylated state of γH2A histone, altogether supporting the presence of constitutive DNA lesions. Furthermore, ISC assembly machinery deficiency elicits a DNA damage response that upregulates ribonucleotide reductase activity by promoting the reduction of Sml1 levels and the cytosolic redistribution of Rnr2/4 enzyme subunits. Depending on the impaired stage of the ISC machinery, different signaling pathway mediators contribute to such response, converging in Dun1. Thus, cells lacking Grx5 glutaredoxin, which are compromised at the core ISC system, show Mec1/Rad53-independent Dun1 activation, whereas both Mec1 and Chk1 are required when the non-core ISC member Iba57 is absent. Grx5-less cells exhibit a strong dependence on the error-free post-replication repair and the homologous recombination pathways, demonstrating that a DNA damage response is required to be activated upon ISC impairment to preserve cell viability.
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Affiliation(s)
- Jordi Pijuan
- Department of Basic Medical Sciences, IRBLleida, University of Lleida, 25198 Lleida, Spain
| | - Carlos María
- Department of Basic Medical Sciences, IRBLleida, University of Lleida, 25198 Lleida, Spain
| | - Enrique Herrero
- Department of Basic Medical Sciences, IRBLleida, University of Lleida, 25198 Lleida, Spain
| | - Gemma Bellí
- Department of Basic Medical Sciences, IRBLleida, University of Lleida, 25198 Lleida, Spain
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18
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Haynes B, Saadat N, Myung B, Shekhar MPV. Crosstalk between translesion synthesis, Fanconi anemia network, and homologous recombination repair pathways in interstrand DNA crosslink repair and development of chemoresistance. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2014; 763:258-66. [PMID: 25795124 DOI: 10.1016/j.mrrev.2014.11.005] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Revised: 11/10/2014] [Accepted: 11/11/2014] [Indexed: 12/12/2022]
Abstract
Bifunctional alkylating and platinum based drugs are chemotherapeutic agents used to treat cancer. These agents induce DNA adducts via formation of intrastrand or interstrand (ICL) DNA crosslinks, and DNA lesions of the ICL type are particularly toxic as they block DNA replication and/or DNA transcription. However, the therapeutic efficacies of these drugs are frequently limited due to the cancer cell's enhanced ability to repair and tolerate these toxic DNA lesions. This ability to tolerate and survive the DNA damage is accomplished by a set of specialized low fidelity DNA polymerases called translesion synthesis (TLS) polymerases since high fidelity DNA polymerases are unable to replicate the damaged DNA template. TLS is a crucial initial step in ICL repair as it synthesizes DNA across the lesion thus preparing the damaged DNA template for repair by the homologous recombination (HR) pathway and Fanconi anemia (FA) network, processes critical for ICL repair. Here we review the molecular features and functional roles of TLS polymerases, discuss the collaborative interactions and cross-regulation of the TLS DNA damage tolerance pathway, the FA network and the BRCA-dependent HRR pathway, and the impact of TLS hyperactivation on development of chemoresistance. Finally, since TLS hyperactivation results from overexpression of Rad6/Rad18 ubiquitinating enzymes (fundamental components of the TLS pathway), increased PCNA ubiquitination, and/or increased recruitment of TLS polymerases, the potential benefits of selectively targeting critical components of the TLS pathway for enhancing anti-cancer therapeutic efficacy and curtailing chemotherapy-induced mutagenesis are also discussed.
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Affiliation(s)
- Brittany Haynes
- Department of Oncology, Wayne State University, 110 East Warren Avenue, Detroit, MI 48201, United States; Karmanos Cancer Institute, Wayne State University, 110 East Warren Avenue, Detroit, MI 48201, United States
| | - Nadia Saadat
- Department of Oncology, Wayne State University, 110 East Warren Avenue, Detroit, MI 48201, United States; Karmanos Cancer Institute, Wayne State University, 110 East Warren Avenue, Detroit, MI 48201, United States
| | - Brian Myung
- Karmanos Cancer Institute, Wayne State University, 110 East Warren Avenue, Detroit, MI 48201, United States
| | - Malathy P V Shekhar
- Department of Oncology, Wayne State University, 110 East Warren Avenue, Detroit, MI 48201, United States; Karmanos Cancer Institute, Wayne State University, 110 East Warren Avenue, Detroit, MI 48201, United States; Department of Pathology, Wayne State University, 110 East Warren Avenue, Detroit, MI 48201, United States.
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19
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Hirata F, Harada T, Corcoran GB, Hirata A. Dietary flavonoids bind to mono-ubiquitinated annexin A1 in nuclei, and inhibit chemical induced mutagenesis. Mutat Res 2014; 759:29-36. [PMID: 24269256 DOI: 10.1016/j.mrfmmm.2013.11.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2013] [Accepted: 11/09/2013] [Indexed: 06/02/2023]
Abstract
In order to investigate the mechanisms of anti-mutagenic action by dietary flavonoids, we investigated if they inhibit mutation of the thymidine kinase (tk) gene in L5178Ytk(±) lymphoma cells. Silibinin, quercetin and genistein suppressed mutation of the tk gene induced in L5178Ytk(±) lymphoma cells by methyl methanesulfonate (MMS) and As(3+). Flavone and flavonol were less effective. To establish that mutation of the tk gene in L5178Ytk(±) lymphoma cells by MMS and As(3+) is mediated through mono-ubiquitinated annexin A1, L5178Ytk(±) lymphoma cells were treated with annexin A1 anti-sense oligonucleotide. The treatment reduced mRNA as well as protein levels of annexin A1, and suppressed mutation of the tk gene. Nuclear extracts from L5178Ytk(±) lymphoma cells catalyzed translesion DNA synthesis with an oligonucleotide template containing 8-oxo-guanosine in an annexin A1 dependent manner. This translesion DNA synthesis was inhibited by the anti-mutagenic flavonoids, silibinin, quercetin and genistein, in a concentration dependent manner, but only slightly by flavone and flavonol. Because these observations implicate involvement of annexin A1 in mutagenesis, we examined if flavonoids suppress nuclear annexin A1 helicase activity. Silibinin, quercetin and genistein inhibited ssDNA binding, DNA chain annealing and DNA unwinding activities of purified nuclear mono-ubiquitinated annexin A1. Flavone and flavonol were ineffective. The apparent direct binding of anti-mutagenic flavonoids to the annexin A1 molecule was supported by fluorescence quenching. Taken together, these findings illustrate that nuclear annexin A1 may be a novel and productive target protein of prevention for DNA damage induced gene mutation, ultimately conferring cancer chemoprevention.
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Affiliation(s)
- Fusao Hirata
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, Detroit, MI, United States.
| | - Takasuke Harada
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, Detroit, MI, United States
| | - George B Corcoran
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, Detroit, MI, United States
| | - Aiko Hirata
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, Detroit, MI, United States
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20
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Haruta N, Kubota Y, Hishida T. Chronic low-dose ultraviolet-induced mutagenesis in nucleotide excision repair-deficient cells. Nucleic Acids Res 2012; 40:8406-15. [PMID: 22743272 PMCID: PMC3458537 DOI: 10.1093/nar/gks580] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
UV radiation induces two major types of DNA lesions, cyclobutane pyrimidine dimers (CPDs) and 6-4 pyrimidine–pyrimidine photoproducts, which are both primarily repaired by nucleotide excision repair (NER). Here, we investigated how chronic low-dose UV (CLUV)-induced mutagenesis occurs in rad14Δ NER-deficient yeast cells, which lack the yeast orthologue of human xeroderma pigmentosum A (XPA). The results show that rad14Δ cells have a marked increase in CLUV-induced mutations, most of which are C→T transitions in the template strand for transcription. Unexpectedly, many of the CLUV-induced C→T mutations in rad14Δ cells are dependent on translesion synthesis (TLS) DNA polymerase η, encoded by RAD30, despite its previously established role in error-free TLS. Furthermore, we demonstrate that deamination of cytosine-containing CPDs contributes to CLUV-induced mutagenesis. Taken together, these results uncover a novel role for Polη in the induction of C→T transitions through deamination of cytosine-containing CPDs in CLUV-exposed NER deficient cells. More generally, our data suggest that Polη can act as both an error-free and a mutagenic DNA polymerase, depending on whether the NER pathway is available to efficiently repair damaged templates.
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Affiliation(s)
- Nami Haruta
- Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
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21
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Williams HL, Gottesman ME, Gautier J. Replication-independent repair of DNA interstrand crosslinks. Mol Cell 2012; 47:140-7. [PMID: 22658724 DOI: 10.1016/j.molcel.2012.05.001] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2011] [Revised: 03/19/2012] [Accepted: 04/17/2012] [Indexed: 12/24/2022]
Abstract
DNA interstrand crosslinks (ICLs) are cytotoxic lesions that covalently link opposite strands of the DNA helix and block DNA unwinding. ICLs are repaired during and outside S phase, and replication-independent ICL repair (RIR) is critical to maintain genomic integrity and to allow transcription in nondividing or slowly dividing cells. Here, we show that the Y family DNA polymerase kappa (Pol κ) is essential for RIR of a site-specific ICL lesion in Xenopus egg extracts, and that both its catalytic activity and UBZ domains are required for this function. We also demonstrate a requirement for PCNA and its modification on lysine 164. Finally, we show that Pol κ participates in ICL repair in mammalian cells, particularly in G0. Our results identify key components of the RIR pathway and begin to unravel its mechanism.
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Affiliation(s)
- Hannah L Williams
- Institute for Cancer Genetics, Department of Genetics and Development, Columbia University, New York, NY 10032, USA
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22
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Human RAD18 interacts with ubiquitylated chromatin components and facilitates RAD9 recruitment to DNA double strand breaks. PLoS One 2011; 6:e23155. [PMID: 21858012 PMCID: PMC3157352 DOI: 10.1371/journal.pone.0023155] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2010] [Accepted: 07/13/2011] [Indexed: 11/19/2022] Open
Abstract
RAD18 is an ubiquitin ligase involved in replicative damage bypass and DNA double-strand break (DSB) repair processes. We found that RPA is required for the dynamic pattern of RAD18 localization during the cell cycle, and for accumulation of RAD18 at sites of γ-irradiation-induced DNA damage. In addition, RAD18 colocalizes with chromatin-associated conjugated ubiquitin and ubiquitylated H2A throughout the cell cycle and following irradiation. This localization pattern depends on the presence of an intact, ubiquitin-binding Zinc finger domain. Using a biochemical approach, we show that RAD18 directly binds to ubiquitylated H2A and several other unknown ubiquitylated chromatin components. This interaction also depends on the RAD18 Zinc finger, and increases upon the induction of DSBs by γ-irradiation. Intriguingly, RAD18 does not always colocalize with regions that show enhanced H2A ubiquitylation. In human female primary fibroblasts, where one of the two X chromosomes is inactivated to equalize X-chromosomal gene expression between male (XY) and female (XX) cells, this inactive X is enriched for ubiquitylated H2A, but only rarely accumulates RAD18. This indicates that the binding of RAD18 to ubiquitylated H2A is context-dependent. Regarding the functional relevance of RAD18 localization at DSBs, we found that RAD18 is required for recruitment of RAD9, one of the components of the 9-1-1 checkpoint complex, to these sites. Recruitment of RAD9 requires the functions of the RING and Zinc finger domains of RAD18. Together, our data indicate that association of RAD18 with DSBs through ubiquitylated H2A and other ubiquitylated chromatin components allows recruitment of RAD9, which may function directly in DSB repair, independent of downstream activation of the checkpoint kinases CHK1 and CHK2.
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24
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Wong RPC, Lin H, Khosravi S, Piche B, Jafarnejad SM, Chen DWC, Li G. Tumour suppressor ING1b maintains genomic stability upon replication stress. Nucleic Acids Res 2011; 39:3632-42. [PMID: 21227930 PMCID: PMC3089469 DOI: 10.1093/nar/gkq1337] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The lesion bypass pathway, which is regulated by monoubiquitination of proliferating cell nuclear antigen (PCNA), is essential for resolving replication stalling due to DNA lesions. This process is important for preventing genomic instability and cancer development. Previously, it was shown that cells deficient in tumour suppressor p33ING1 (ING1b) are hypersensitive to DNA damaging agents via unknown mechanism. In this study, we demonstrated a novel tumour suppressive function of ING1b in preserving genomic stability upon replication stress through regulating PCNA monoubiquitination. We found that ING1b knockdown cells are more sensitive to UV due to defects in recovering from UV-induced replication blockage, leading to enhanced genomic instability. We revealed that ING1b is required for the E3 ligase Rad18-mediated PCNA monoubiquitination in lesion bypass. Interestingly, ING1b-mediated PCNA monoubiquitination is associated with the regulation of histone H4 acetylation. Results indicate that chromatin remodelling contributes to the stabilization of stalled replication fork and to the regulation of PCNA monoubiquitination during lesion bypass.
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Affiliation(s)
| | | | | | | | | | | | - Gang Li
- *To whom correspondence should be addressed. Tel: +1 604 875 5826; Fax: +1 604 875 4497;
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DNA repair defects sensitize cells to anticodon nuclease yeast killer toxins. Mol Genet Genomics 2010; 285:185-95. [PMID: 21188417 DOI: 10.1007/s00438-010-0597-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2010] [Accepted: 12/11/2010] [Indexed: 12/21/2022]
Abstract
Killer toxins from Kluyveromyces lactis (zymocin) and Pichia acaciae (PaT) were found to disable translation in target cells by virtue of anticodon nuclease (ACNase) activities on tRNA(Glu) and tRNA(Gln), respectively. Surprisingly, however, ACNase exposure does not only impair translation, but also affects genome integrity and concomitantly DNA damage occurs. Previously, it was shown that homologous recombination protects cells from ACNase toxicity. Here, we have analyzed whether other DNA repair pathways are functional in conferring ACNase resistance as well. In addition to HR, base excision repair (BER) and postreplication repair (PRR) promote clear resistance to either, PaT and zymocin. Comparative toxin sensitivity analysis of BER mutants revealed that its ACNase protective function is due to the endonucleases acting on apurinic (AP) sites, whereas none of the known DNA glycosylases is involved. Because PaT and zymocin require the presence of the ELP3/TRM9-dependent wobble uridine modification 5-methoxy-carbonyl-methyl (mcm(5)) for tRNA cleavage, we analyzed toxin response in DNA repair mutants additionally lacking such tRNA modifications. ACNase resistance caused by elp3 or trm9 mutations was found to rescue hypersensitivity of DNA repair defects, consistent with DNA damage to occur as a consequence of tRNA cleavage. The obtained genetic evidence promises to reveal new aspects into the mechanism linking translational fidelity and genome surveillance.
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Serrentino ME, Catalfo A, Angelin AR, de Guidi G, Sage E. Photosensitization induced by the antibacterial fluoroquinolone Rufloxacin leads to mutagenesis in yeast. Mutat Res 2010; 692:34-41. [PMID: 20696178 DOI: 10.1016/j.mrfmmm.2010.07.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2010] [Revised: 07/20/2010] [Accepted: 07/30/2010] [Indexed: 05/29/2023]
Abstract
Rufloxacin (RFX) is an antibacterial fluoroquinolone that exhibits UVA photosensitization properties. Photosensitization reactions lead to the formation of oxidative damage, mainly via singlet oxygen. Here we explore the phototoxic and photomutagenic potency of RFX using a panel of yeast (Saccharomyces cerevisiae) mutants affected in different DNA repair pathways. Yeast mutants provide a sensitive tool to identify the photodamage and the DNA repair pathways that cope with it. Cell viability test at increasing dose of UVA shows that both the DNA repair deficient and wild type cells are equally sensitive to RFX-induced photosensitization, demonstrating that phototoxic effect is not due to DNA injury. Photomutagenicity of RFX is evaluated by measuring the frequency of forward Can(R) mutations. The mutation induction is low in wild type cells. A high increase in mutation frequency is observed in strains affected in Ogg1 gene, compared to wild type and other base excision repair deficient strains. The mutation spectrum photomediated by RFX in wild type cells reveals a bias in favour of GC>TA transversions, whereas transition and frameshift mutations are less represented. Altogether data demonstrates that 8-oxo-7,8-dihydroguanine (8-oxoGua) is by far the major DNA damage produced by RFX photosensitization, leading to mutagenesis. We also explore the role played by DNA mismatch repair, translesion synthesis and post-replication repair in the prevention of mutagenic effects due to RFX exposure. In addition, we show that most of RFX photodegradation products are not mutagenic. This study defines the phototoxic and photomutagenic properties of antibacterial RFX and point out possible unwanted side effects in skin under sunlight.
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Conde F, Ontoso D, Acosta I, Gallego-Sánchez A, Bueno A, San-Segundo PA. Regulation of tolerance to DNA alkylating damage by Dot1 and Rad53 in Saccharomyces cerevisiae. DNA Repair (Amst) 2010; 9:1038-49. [PMID: 20674515 DOI: 10.1016/j.dnarep.2010.07.003] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2010] [Revised: 06/24/2010] [Accepted: 07/05/2010] [Indexed: 10/19/2022]
Abstract
To maintain genomic integrity cells have to respond properly to a variety of exogenous and endogenous factors that produce genome injuries and interfere with DNA replication. DNA integrity checkpoints coordinate this response by slowing cell cycle progression to provide time for the cell to repair the damage, stabilizing replication forks and stimulating DNA repair to restore the original DNA sequence and structure. In addition, there are also mechanisms of damage tolerance, such as translesion synthesis (TLS), which are important for survival after DNA damage. TLS allows replication to continue without removing the damage, but results in a higher frequency of mutagenesis. Here, we investigate the functional contribution of the Dot1 histone methyltransferase and the Rad53 checkpoint kinase to TLS regulation in Saccharomyces cerevisiae. We demonstrate that the Dot1-dependent status of H3K79 methylation modulates the resistance to the alkylating agent MMS, which depends on PCNA ubiquitylation at lysine 164. Strikingkly, either the absence of DOT1, which prevents full activation of Rad53, or the expression of an HA-tagged version of RAD53, which produces low amounts of the kinase, confer increased MMS resistance. However, the dot1Δ rad53-HA double mutant is hypersensitive to MMS and shows barely detectable amounts of activated kinase. Furthermore, moderate overexpression of RAD53 partially suppresses the MMS resistance of dot1Δ. In addition, we show that MMS-treated dot1Δ and rad53-HA cells display increased number of chromosome-associated Rev1 foci. We propose that threshold levels of Rad53 activity exquisitely modulate the tolerance to alkylating damage at least by controlling the abundance of the key TLS factor Rev1 bound to chromatin.
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Affiliation(s)
- Francisco Conde
- Instituto de Microbiología Bioquímica, Consejo Superior de Investigaciones Científicas and University of Salamanca, 37007 Salamanca, Spain
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Bermúdez-López M, Ceschia A, de Piccoli G, Colomina N, Pasero P, Aragón L, Torres-Rosell J. The Smc5/6 complex is required for dissolution of DNA-mediated sister chromatid linkages. Nucleic Acids Res 2010; 38:6502-12. [PMID: 20571088 PMCID: PMC2965248 DOI: 10.1093/nar/gkq546] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Mitotic chromosome segregation requires the removal of physical connections between sister chromatids. In addition to cohesin and topological entrapments, sister chromatid separation can be prevented by the presence of chromosome junctions or ongoing DNA replication. We will collectively refer to them as DNA-mediated linkages. Although this type of structures has been documented in different DNA replication and repair mutants, there is no known essential mechanism ensuring their timely removal before mitosis. Here, we show that the dissolution of these connections is an active process that requires the Smc5/6 complex, together with Mms21, its associated SUMO-ligase. Failure to remove DNA-mediated linkages causes gross chromosome missegregation in anaphase. Moreover, we show that Smc5/6 is capable to dissolve them in metaphase-arrested cells, thus restoring chromosome resolution and segregation. We propose that Smc5/6 has an essential role in the removal of DNA-mediated linkages to prevent chromosome missegregation and aneuploidy.
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Affiliation(s)
- Marcelino Bermúdez-López
- IRBLLEIDA, Department of Ciències Mèdiques Bàsiques, Facultat de Medicina, Universitat de Lleida, 25008 Lleida, Spain
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Davies AA, Neiss A, Ulrich HD. Ubiquitylation of the 9-1-1 Checkpoint Clamp Is Independent of Rad6-Rad18 and DNA Damage. Cell 2010; 141:1080-7. [DOI: 10.1016/j.cell.2010.04.039] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2009] [Revised: 02/09/2010] [Accepted: 04/08/2010] [Indexed: 12/30/2022]
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Choi K, Szakal B, Chen YH, Branzei D, Zhao X. The Smc5/6 complex and Esc2 influence multiple replication-associated recombination processes in Saccharomyces cerevisiae. Mol Biol Cell 2010; 21:2306-14. [PMID: 20444977 PMCID: PMC2893993 DOI: 10.1091/mbc.e10-01-0050] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
This work shows that Mph1, Mms2, and the Shu complex function in distinct pathways in replication-associated recombinational repair and that the Smc5/6 complex and Esc2 prevent the accumulation of toxic recombination intermediates generated in these pathways. Replication-associated recombinational repair is important for genome duplication and cell survival under DNA damage conditions. Several nonclassical recombination factors have been implicated in this process, but their functional relationships are not clear. Here, we show that three of these factors, Mph1, Mms2, and the Shu complex, can act independently to promote the formation of recombination intermediates during impaired replication. However, their functions become detrimental when cells lack the Smc5/6 complex or Esc2. We show that mph1Δ, mms2Δ, and shu1Δ suppress the sensitivity to the replication-blocking agent methylmethane sulfonate (MMS) in smc6 mutants, with double deletions conferring stronger suppression. These deletion mutations also rescue the MMS sensitivity of esc2Δ cells. In addition, two-dimensional gel analysis demonstrates that mph1Δ, mms2Δ, and shu1Δ each reduce the level of recombination intermediates in an smc6 mutant when cells replicate in the presence of MMS, and that double deletions lead to a greater reduction. Our work thus suggests that Mph1, Mms2, and the Shu complex can function in distinct pathways in replication-associated recombinational repair and that the Smc5/6 complex and Esc2 prevent the accumulation of toxic recombination intermediates generated in these processes.
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Affiliation(s)
- Koyi Choi
- Molecular Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
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Hirata F, Thibodeau LM, Hirata A. Ubiquitination and SUMOylation of annexin A1 and helicase activity. Biochim Biophys Acta Gen Subj 2010; 1800:899-905. [PMID: 20359522 DOI: 10.1016/j.bbagen.2010.03.020] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2009] [Revised: 03/22/2010] [Accepted: 03/24/2010] [Indexed: 10/19/2022]
Abstract
BACKGROUND While annexin A1 in nuclei is proposed to be involved in cell transformation, its functions remain poorly understood. Since annexin A1 has the consensus motif, ¹⁶⁰LKRD, for SUMOylation as well as Ks, acceptors for ubiquitination that regulates localization and functions of proteins, we investigated SUMOylation and ubiquitination of annexin A1. METHODS SUMOylation and ubiquitination of bovine annexin A1 were biochemically tested in vitro by purified proteins, and were confirmed by cell experiments with L5178 lymphoma cells. Effects of the modifications on DNA helicase activity were measured by ssDNA binding activity and by dsDNA unwinding activity. RESULTS SUMOylation of annexin A1 was catalyzed by Ubc9, while its ubiquitination was by Rad6-Rad 18. Ubiquitinated annexin A1 had higher affinity for damaged DNA, and promoted in vitro translesion DNA synthesis by Pol ß. In mouse lymphoma L5178Y tk(+/-) cells, levels of SUMOylated annexin A1 decreased by DNA damaging agents, MMS or As³, whereas those of ubiquitinated annexin A1 increased under the same conditions. CONCLUSION These observations suggest but do not necessarily prove that ubiquitinated annexin A1 in nuclei may be involved in DNA damage response, while SUMOylated annexin A1 functions in proliferation-differentiation. SIGNIFICANCE Ubiquitination of annexin A1 may play an important role in mutagenesis, an initial step of cell transformation.
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Affiliation(s)
- Fusao Hirata
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, Detroit, MI 48202, USA.
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Ertongur I, Tomi NS, Kutzera A, Fischer-Burkart S, Jungnickel B. Ubc13 dosage is critical for immunoglobulin gene conversion and gene targeting in vertebrate cells. Nucleic Acids Res 2010; 38:4701-7. [PMID: 20223767 PMCID: PMC2919702 DOI: 10.1093/nar/gkq154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
In contrast to lower eukaryotes, most vertebrate cells are characterized by a moderate efficiency of homologous recombination (HR) and limited feasibility of targeted genetic modifications. As a notable exception, the chicken DT40 B cell line is distinguished by efficient homology-mediated repair of DNA lesions during Ig gene conversion, and also shows exceptionally high gene-targeting efficiencies. The molecular basis of these phenomena is elusive. Here we show that the activity levels of Ubc13, the E2 enzyme responsible for non-canonical K63-linked polyubiquitination, are critical for high efficiency of Ig gene conversion and gene targeting in DT40. Ubc13(+/-) cells show substantially lower homology-mediated repair, yet do not display changes in somatic hypermutation, overall DNA repair or cell proliferation. Our results suggest that modulation of the activity of K63-linked polyubiquitination may be used to customize HR efficiencies in vertebrate cells.
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Affiliation(s)
- Isin Ertongur
- Institute of Clinical Molecular Biology, Helmholtz Center Munich, German Research Center for Environmental Health, Munich, Germany
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Panico ER, Ede C, Schildmann M, Schürer KA, Kramer W. Genetic evidence for a role of Saccharomyces cerevisiae Mph1 in recombinational DNA repair under replicative stress. Yeast 2010; 27:11-27. [PMID: 19918932 DOI: 10.1002/yea.1727] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
In yeast as in human, DNA helicases play critical roles in assisting replication fork progression. The Saccharomyces cerevisiae MPH1 gene, homologue of human FANCM, has been involved in homologous recombination and DNA repair. We describe a synthetic growth defect of an mph1 deletion if combined with an srs2 deletion that can result-depending on the genetic background-in synthetic lethality. The lethality is suppressed by mutations in homologous recombination (rad51, rad52, rad55, rad57) and in the DNA damage checkpoint (rad9, rad24, rad17). Importantly, rad54 and mph1, epistatic for damage sensitivity, are subadditive for spontaneous mutator phenotype. Therefore, Mph1 could be placed at the Rad51-mediated strand invasion process, with a function distinct from Rad54. Moreover, siz1 mutation is viable with mph1 and additive for DNA damage sensitivity. mph1 srs2 double mutants, isolated in a background where they are viable, are synergistically sensitive to DNA damage. Moderate overexpression of SGS1 partially suppresses this sensitivity. Finally, we observe an epistatic relationship in terms of sensitivity to camptothecin of mms4 or mus81 to mph1. Overall, our results support a role of Mph1 in assisting replication progression. We propose two models for the resumption of DNA synthesis under replicative stress where Mph1 is placed at the sister chromatid interaction step.
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Affiliation(s)
- Evandro Rocco Panico
- Department of Molecular Genetics and Preparative Molecular Biology, Institute for Microbiology and Genetics, University of Göttingen, D-37077 Göttingen, Germany.
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MacKay C, Toth R, Rouse J. Biochemical characterisation of the SWI/SNF family member HLTF. Biochem Biophys Res Commun 2009; 390:187-91. [DOI: 10.1016/j.bbrc.2009.08.151] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2009] [Accepted: 08/24/2009] [Indexed: 10/20/2022]
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Abstract
The six Saccharomyces cerevisiae SLX genes were identified in a screen for factors required for the viability of cells lacking Sgs1, a member of the RecQ helicase family involved in processing stalled replisomes and in the maintenance of genome stability. The six SLX gene products form three distinct heterodimeric complexes, and all three have catalytic activity. Slx3-Slx2 (also known as Mus81-Mms4) and Slx1-Slx4 are both heterodimeric endonucleases with a marked specificity for branched replication fork-like DNA species, whereas Slx5-Slx8 is a SUMO (small ubiquitin-related modifier)-targeted E3 ubiquitin ligase. All three complexes play important, but distinct, roles in different aspects of the cellular response to DNA damage and perturbed DNA replication. Slx4 interacts physically not only with Slx1, but also with Rad1-Rad10 [XPF (xeroderma pigmentosum complementation group F)-ERCC1 (excision repair cross-complementing 1) in humans], another structure-specific endonuclease that participates in the repair of UV-induced DNA damage and in a subpathway of recombinational DNA DSB (double-strand break) repair. Curiously, Slx4 is essential for repair of DSBs by Rad1-Rad10, but is not required for repair of UV damage. Slx4 also promotes cellular resistance to DNA-alkylating agents that block the progression of replisomes during DNA replication, by facilitating the error-free mode of lesion bypass. This does not require Slx1 or Rad1-Rad10, and so Slx4 has several distinct roles in protecting genome stability. In the present article, I provide an overview of our current understanding of the cellular roles of the Slx proteins, paying particular attention to the advances that have been made in understanding the cellular roles of Slx4. In particular, protein-protein interactions and underlying molecular mechanisms are discussed and I draw attention to the many questions that have yet to be answered.
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Abstract
Cancer is caused by genetic changes that often arise following failure to accurately replicate the DNA. PCNA (proliferating-cell nuclear antigen) forms a ring around the DNA to facilitate and control DNA replication. Emerging evidence suggests that PCNA is at the very heart of many essential cellular processes, such as DNA replication, repair of DNA damage, chromatin structure maintenance, chromosome segregation and cell-cycle progression. Progression of the DNA replication forks can be blocked by DNA lesions, formed either by endogenous damage or by exogenous agents, for instance anticancer drugs. Cellular response often results in change of PCNA function triggered either by specific post-translational modification of PCNA (i.e. ubiquitylation) or by exchange of its interaction partners. This puts PCNA in a central position in determining the fate of the replication fork. In the present article, we review PCNA modifications and interaction partners, and how those influence the course of events at replication forks, which ultimately determines both tumour progression as well as the outcome of anticancer treatment.
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The Saccharomyces cerevisiae Rad6 postreplication repair and Siz1/Srs2 homologous recombination-inhibiting pathways process DNA damage that arises in asf1 mutants. Mol Cell Biol 2009; 29:5226-37. [PMID: 19635810 DOI: 10.1128/mcb.00894-09] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The Asf1 and Rad6 pathways have been implicated in a number of common processes such as suppression of gross chromosomal rearrangements (GCRs), DNA repair, modification of chromatin, and proper checkpoint functions. We examined the relationship between Asf1 and different gene products implicated in postreplication repair (PRR) pathways in the suppression of GCRs, checkpoint function, sensitivity to hydroxyurea (HU) and methyl methanesulfonate (MMS), and ubiquitination of proliferating cell nuclear antigen (PCNA). We found that defects in Rad6 PRR pathway and Siz1/Srs2 homologous recombination suppression (HRS) pathway genes suppressed the increased GCR rates seen in asf1 mutants, which was independent of translesion bypass polymerases but showed an increased dependency on Dun1. Combining an asf1 deletion with different PRR mutations resulted in a synergistic increase in sensitivity to chronic HU and MMS treatment; however, these double mutants were not checkpoint defective, since they were capable of recovering from acute treatment with HU. Interestingly, we found that Asf1 and Rad6 cooperate in ubiquitination of PCNA, indicating that Rad6 and Asf1 function in parallel pathways that ubiquitinate PCNA. Our results show that ASF1 probably contributes to the maintenance of genome stability through multiple mechanisms, some of which involve the PRR and HRS pathways.
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Monkhorst K, de Hoon B, Jonkers I, Mulugeta Achame E, Monkhorst W, Hoogerbrugge J, Rentmeester E, Westerhoff HV, Grosveld F, Grootegoed JA, Gribnau J. The probability to initiate X chromosome inactivation is determined by the X to autosomal ratio and X chromosome specific allelic properties. PLoS One 2009; 4:e5616. [PMID: 19440388 PMCID: PMC2680018 DOI: 10.1371/journal.pone.0005616] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2008] [Accepted: 04/15/2009] [Indexed: 11/26/2022] Open
Abstract
Background In female mammalian cells, random X chromosome inactivation (XCI) equalizes the dosage of X-encoded gene products to that in male cells. XCI is a stochastic process, in which each X chromosome has a probability to be inactivated. To obtain more insight in the factors setting up this probability, we studied the role of the X to autosome (X∶A) ratio in initiation of XCI, and have used the experimental data in a computer simulation model to study the cellular population dynamics of XCI. Methodology/Principal Findings To obtain more insight in the role of the X∶A ratio in initiation of XCI, we generated triploid mouse ES cells by fusion of haploid round spermatids with diploid female and male ES cells. These fusion experiments resulted in only XXY triploid ES cells. XYY and XXX ES lines were absent, suggesting cell death related either to insufficient X-chromosomal gene dosage (XYY) or to inheritance of an epigenetically modified X chromosome (XXX). Analysis of active (Xa) and inactive (Xi) X chromosomes in the obtained triploid XXY lines indicated that the initiation frequency of XCI is low, resulting in a mixed population of XaXiY and XaXaY cells, in which the XaXiY cells have a small proliferative advantage. This result, and findings on XCI in diploid and tetraploid ES cell lines with different X∶A ratios, provides evidence that the X∶A ratio determines the probability for a given X chromosome to be inactivated. Furthermore, we found that the kinetics of the XCI process can be simulated using a probability for an X chromosome to be inactivated that is proportional to the X∶A ratio. These simulation studies re-emphasize our hypothesis that the probability is a function of the concentration of an X-encoded activator of XCI, and of X chromosome specific allelic properties determining the threshold for this activator. Conclusions The present findings reveal that the probability for an X chromosome to be inactivated is proportional to the X∶A ratio. This finding supports the presence of an X-encoded activator of the XCI process.
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Affiliation(s)
- Kim Monkhorst
- Department of Reproduction and Development, Erasmus MC, University Medical Center, Rotterdam, the Netherlands
- Department of Cell Biology, Erasmus MC, University Medical Center, Rotterdam, the Netherlands
| | - Bas de Hoon
- Department of Reproduction and Development, Erasmus MC, University Medical Center, Rotterdam, the Netherlands
| | - Iris Jonkers
- Department of Reproduction and Development, Erasmus MC, University Medical Center, Rotterdam, the Netherlands
- Department of Cell Biology, Erasmus MC, University Medical Center, Rotterdam, the Netherlands
| | - Eskeatnaf Mulugeta Achame
- Department of Reproduction and Development, Erasmus MC, University Medical Center, Rotterdam, the Netherlands
| | | | - Jos Hoogerbrugge
- Department of Reproduction and Development, Erasmus MC, University Medical Center, Rotterdam, the Netherlands
| | - Eveline Rentmeester
- Department of Reproduction and Development, Erasmus MC, University Medical Center, Rotterdam, the Netherlands
| | - Hans V. Westerhoff
- Department of Molecular Cell Physiology, Free University Amsterdam, Amsterdam, the Netherlands
- Manchester Centre for Integrative Systems Biology, Manchester, United Kingdom
| | - Frank Grosveld
- Department of Cell Biology, Erasmus MC, University Medical Center, Rotterdam, the Netherlands
| | - J. Anton Grootegoed
- Department of Reproduction and Development, Erasmus MC, University Medical Center, Rotterdam, the Netherlands
| | - Joost Gribnau
- Department of Reproduction and Development, Erasmus MC, University Medical Center, Rotterdam, the Netherlands
- * E-mail:
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van der Kemp PA, de Padula M, Burguiere-Slezak G, Ulrich HD, Boiteux S. PCNA monoubiquitylation and DNA polymerase eta ubiquitin-binding domain are required to prevent 8-oxoguanine-induced mutagenesis in Saccharomyces cerevisiae. Nucleic Acids Res 2009; 37:2549-59. [PMID: 19264809 PMCID: PMC2677869 DOI: 10.1093/nar/gkp105] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
7,8-Dihydro-8-oxoguanine (8-oxoG) is an abundant and mutagenic DNA lesion. In Saccharomyces cerevisiae, the 8-oxoG DNA N-glycosylase (Ogg1) acts as the primary defense against 8-oxoG. Here, we present evidence for cooperation between Rad18-Rad6-dependent monoubiquitylation of PCNA at K164, the damage-tolerant DNA polymerase eta and the mismatch repair system (MMR) to prevent 8-oxoG-induced mutagenesis. Preventing PCNA modification at lysine 164 (pol30-K164R) results in a dramatic increase in GC to TA mutations due to endogenous 8-oxoG in Ogg1-deficient cells. In contrast, deletion of RAD5 or SIZ1 has little effect implying that the modification of PCNA relevant for preventing 8-oxoG-induced mutagenesis is monoubiquitin as opposed to polyubiquitin or SUMO. We also report that the ubiquitin-binding domain (UBZ) of Pol eta is essential to prevent 8-oxoG-induced mutagenesis but only in conjunction with a functional PCNA-binding domain (PIP). We propose that PCNA is ubiquitylated during the repair synthesis reaction after the MMR-dependent excision of adenine incorporated opposite to 8-oxoG. Monoubiquitylation of PCNA would favor the recruitment of Pol eta thereby allowing error-free incorporation of dCMP opposite to 8-oxoG. This study suggests that Pol eta and the post-replication repair (PRR) machinery can also prevent mutagenesis at DNA lesions that do not stall replication forks.
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Affiliation(s)
- Patricia Auffret van der Kemp
- CEA, iRCM, UMR217 CNRS Radiobiologie Moléculaire et Cellulaire, 18 route du Panorama, BP6, 92265-Fontenay aux Roses, France
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Waters LS, Minesinger BK, Wiltrout ME, D'Souza S, Woodruff RV, Walker GC. Eukaryotic translesion polymerases and their roles and regulation in DNA damage tolerance. Microbiol Mol Biol Rev 2009; 73:134-54. [PMID: 19258535 PMCID: PMC2650891 DOI: 10.1128/mmbr.00034-08] [Citation(s) in RCA: 440] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
DNA repair and DNA damage tolerance machineries are crucial to overcome the vast array of DNA damage that a cell encounters during its lifetime. In this review, we summarize the current state of knowledge about the eukaryotic DNA damage tolerance pathway translesion synthesis (TLS), a process in which specialized DNA polymerases replicate across from DNA lesions. TLS aids in resistance to DNA damage, presumably by restarting stalled replication forks or filling in gaps that remain in the genome due to the presence of DNA lesions. One consequence of this process is the potential risk of introducing mutations. Given the role of these translesion polymerases in mutagenesis, we discuss the significant regulatory mechanisms that control the five known eukaryotic translesion polymerases: Rev1, Pol zeta, Pol kappa, Pol eta, and Pol iota.
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Affiliation(s)
- Lauren S Waters
- Department of Biology, Massachusetts Institute of Technology, Building 68, Room 653, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
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Control of histone methylation and genome stability by PTIP. EMBO Rep 2009; 10:239-45. [PMID: 19229280 DOI: 10.1038/embor.2009.21] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2008] [Accepted: 01/27/2009] [Indexed: 11/08/2022] Open
Abstract
PTIP regulates gene transcription by controlling the methylation of histone H3, and also has important roles in cellular responses to DNA damage or to perturbed DNA replication. The available data suggest that the functions of PTIP in transcription and preserving genome stability might be independent and mediated by functionally distinct cellular pools of PTIP. Although considerable progress has been made in understanding how PTIP influences transcription, a coherent picture of how it protects cells from DNA damage at the molecular level has yet to emerge. Here, we describe recent progress made in understanding the cellular roles of PTIP and the relevance of PTIP-interacting proteins, as well as the questions that have yet to be answered.
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Inagaki A, van Cappellen WA, van der Laan R, Houtsmuller AB, Hoeijmakers JH, Grootegoed JA, Baarends WM. Dynamic localization of human RAD18 during the cell cycle and a functional connection with DNA double-strand break repair. DNA Repair (Amst) 2009; 8:190-201. [DOI: 10.1016/j.dnarep.2008.10.008] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2008] [Revised: 09/16/2008] [Accepted: 10/06/2008] [Indexed: 11/25/2022]
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Two proteolytic pathways regulate DNA repair by cotargeting the Mgt1 alkylguanine transferase. Proc Natl Acad Sci U S A 2009; 106:2142-7. [PMID: 19164530 DOI: 10.1073/pnas.0812316106] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
O(6)-methylguanine (O(6)meG) and related modifications of guanine in double-stranded DNA are functionally severe lesions that can be produced by many alkylating agents, including N-methyl-N'-nitro-N-nitrosoguanidine (MNNG), a potent carcinogen. O(6)meG is repaired through its demethylation by the O(6)-alkylguanine-DNA alkyltransferase (AGT). This protein is called Mgmt (or MGMT) in mammals and Mgt1 in the yeast Saccharomyces cerevisiae. AGT proteins remove methyl and other alkyl groups from an alkylated O(6) in guanine by transferring the adduct to an active-site cysteine residue. The resulting S-alkyl-Cys of AGT is not restored back to Cys, so repair proteins of this kind can act only once. We report here that S. cerevisiae Mgt1 is cotargeted for degradation, through a degron near its N terminus, by 2 ubiquitin-mediated proteolytic systems, the Ubr1/Rad6-dependent N-end rule pathway and the Ufd4/Ubc4-dependent ubiquitin fusion degradation (UFD) pathway. The cotargeting of Mgt1 by these pathways is synergistic, in that it increases not only the yield of polyubiquitylated Mgt1, but also the processivity of polyubiquitylation. The N-end rule and UFD pathways comediate both the constitutive and MNNG-accelerated degradation of Mgt1. Yeast cells lacking the Ubr1 and Ufd4 ubiquitin ligases were hyperresistant to MNNG but hypersensitive to the toxicity of overexpressed Mgt1. We consider ramifications of this discovery for the control of DNA repair and mechanisms of substrate targeting by the ubiquitin system.
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RAD6-RAD18-RAD5-pathway-dependent tolerance to chronic low-dose ultraviolet light. Nature 2008; 457:612-5. [PMID: 19079240 DOI: 10.1038/nature07580] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2008] [Accepted: 10/24/2008] [Indexed: 12/21/2022]
Abstract
In nature, organisms are exposed to chronic low-dose ultraviolet light (CLUV) as opposed to the acute high doses common to laboratory experiments. Analysis of the cellular response to acute high-dose exposure has delineated the importance of direct DNA repair by the nucleotide excision repair pathway and for checkpoint-induced cell cycle arrest in promoting cell survival. Here we examine the response of yeast cells to CLUV and identify a key role for the RAD6-RAD18-RAD5 error-free postreplication repair (RAD6 error-free PRR) pathway in promoting cell growth and survival. We show that loss of the RAD6 error-free PRR pathway results in DNA-damage-checkpoint-induced G2 arrest in CLUV-exposed cells, whereas wild-type and nucleotide-excision-repair-deficient cells are largely unaffected. Cell cycle arrest in the absence of the RAD6 error-free PRR pathway was not caused by a repair defect or by the accumulation of ultraviolet-induced photoproducts. Notably, we observed increased replication protein A (RPA)- and Rad52-yellow fluorescent protein foci in the CLUV-exposed rad18Delta cells and demonstrated that Rad52-mediated homologous recombination is required for the viability of the rad18Delta cells after release from CLUV-induced G2 arrest. These and other data presented suggest that, in response to environmental levels of ultraviolet exposure, the RAD6 error-free PRR pathway promotes replication of damaged templates without the generation of extensive single-stranded DNA regions. Thus, the error-free PRR pathway is specifically important during chronic low-dose ultraviolet exposure to prevent counter-productive DNA checkpoint activation and allow cells to proliferate normally.
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Rego MA, Kolling FW, Howlett NG. The Fanconi anemia protein interaction network: casting a wide net. Mutat Res 2008; 668:27-41. [PMID: 19101576 DOI: 10.1016/j.mrfmmm.2008.11.018] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2008] [Revised: 11/16/2008] [Accepted: 11/25/2008] [Indexed: 11/26/2022]
Abstract
It has long been hypothesized that a defect in the repair of damaged DNA is central to the etiology of Fanconi anemia (FA). Indeed, an increased sensitivity of FA patient-derived cells to the lethal effects of various forms of DNA damaging agents was described over three decades ago [A.J. Fornace, Jr., J.B. Little, R.R. Weichselbaum, DNA repair in a Fanconi's anemia fibroblast cell strain, Biochim. Biophys. Acta 561 (1979) 99-109; Y. Fujiwara, M. Tatsumi, Repair of mitomycin C damage to DNA in mammalian cells and its impairment in Fanconi's anemia cells, Biochem. Biophys. Res. Commun. 66 (1975) 592-598; A.J. Rainbow, M. Howes, Defective repair of ultraviolet- and gamma-ray-damaged DNA in Fanconi's anaemia, Int. J. Radiat. Biol. Relat. Stud. Phys. Chem. Med. 31 (1977) 191-195]. Furthermore, the cytological hallmark of FA, the DNA crosslink-induced radial chromosome formation, exemplifies an innate impairment in the repair of these particularly cytotoxic DNA lesions [A.D. Auerbach, Fanconi anemia diagnosis and the diepoxybutane (DEB) test, Exp. Hematol. 21 (1993) 731-733]. Precisely defining the collective role of the FA proteins in DNA repair, however, continues to be one of the most enigmatic and challenging questions in the FA field. The first six identified FA proteins (A, C, E, F, G, and D2) harbored no recognizable enzymatic features, precluding association with a specific metabolic process. Consequently, our knowledge of the role of the FA proteins in the DNA damage response has been gleaned primarily through biochemical association studies with non-FA proteins. Here, we provide a chronological discourse of the major FA protein interaction network discoveries, with particular emphasis on the DNA damage response, that have defined our current understanding of the molecular basis of FA.
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Affiliation(s)
- Meghan A Rego
- Department of Cell and Molecular Biology, University of Rhode Island, 115 Morrill Hall, 45 Lower College Road, Kingston, RI 02881, USA
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Knizewski L, Ginalski K, Jerzmanowski A. Snf2 proteins in plants: gene silencing and beyond. TRENDS IN PLANT SCIENCE 2008; 13:557-65. [PMID: 18786849 DOI: 10.1016/j.tplants.2008.08.004] [Citation(s) in RCA: 77] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2008] [Revised: 08/05/2008] [Accepted: 08/05/2008] [Indexed: 05/17/2023]
Abstract
Proteins belonging to the conserved and diversified Snf2 family provide the ATP-driven motor subunits for remodelling systems, which control the accessibility of chromatin DNA. The 41 proteins of this family encoded in the Arabidopsis genome fall into 19 distinct subfamilies. Although most of the plant Snf2 proteins studied so far retain the functional specialization of their yeast and animal homologues, some have been adapted for functions occurring only in plants. We present a comprehensive in silico characterization of the domain architecture of the complete set of Arabidopsis Snf2 proteins. In combination with recent data on the molecular mechanisms underlying the functions of some yeast and animal homologues, this offers an insight into the different roles of Snf2 proteins in plants.
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Affiliation(s)
- Lukasz Knizewski
- Laboratory of Bioinformatics and Bioengineering, Interdisciplinary Center for Mathematical and Computational Modelling, University of Warsaw, Warsaw, Poland
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Moertl S, Karras GI, Wismüller T, Ahne F, Eckardt-Schupp F. Regulation of double-stranded DNA gap repair by the RAD6 pathway. DNA Repair (Amst) 2008; 7:1893-906. [PMID: 18722556 DOI: 10.1016/j.dnarep.2008.07.016] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2007] [Revised: 07/23/2008] [Accepted: 07/24/2008] [Indexed: 12/01/2022]
Abstract
The RAD6 pathway allows replication across DNA lesions by either an error-prone or error-free mode. Error-prone replication involves translesion polymerases and requires monoubiquitylation at lysine (K) 164 of PCNA by the Rad6 and Rad18 enzymes. By contrast, the error-free bypass is triggered by modification of PCNA by K63-linked polyubiquitin chains, a reaction that requires in addition to Rad6 and Rad18 the enzymes Rad5 and Ubc13-Mms2. Here, we show that the RAD6 pathway is also critical for controlling repair pathways that act on DNA double-strand breaks. By using gapped plasmids as substrates, we found that repair in wild-type cells proceeds almost exclusively by homology-dependent repair (HDR) using chromosomal DNA as a template, whereas non-homologous end-joining (NHEJ) is suppressed. In contrast, in cells deficient in PCNA polyubiquitylation, plasmid repair occurs largely by NHEJ. Mutant cells that are completely deficient in PCNA ubiquitylation, repair plasmids by HDR similar to wild-type cells. These findings are consistent with a model in which unmodified PCNA supports HDR, whereas PCNA monoubiquitylation diverts repair to NHEJ, which is suppressed by PCNA polyubiquitylation. More generally, our data suggest that the balance between HDR and NHEJ pathways is crucially controlled by genes of the RAD6 pathway through modifications of PCNA.
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Affiliation(s)
- Simone Moertl
- Institute for Radiobiology, Helmholtz Centre Munich-German Research Centre for Environmental Health, Ingolstaedter Landstrasse 1, Neuherberg, Germany.
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Szyjka SJ, Aparicio JG, Viggiani CJ, Knott S, Xu W, Tavaré S, Aparicio OM. Rad53 regulates replication fork restart after DNA damage in Saccharomyces cerevisiae. Genes Dev 2008; 22:1906-20. [PMID: 18628397 DOI: 10.1101/gad.1660408] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Replication fork stalling at a DNA lesion generates a damage signal that activates the Rad53 kinase, which plays a vital role in survival by stabilizing stalled replication forks. However, evidence that Rad53 directly modulates the activity of replication forks has been lacking, and the nature of fork stabilization has remained unclear. Recently, cells lacking the Psy2-Pph3 phosphatase were shown to be defective in dephosphorylation of Rad53 as well as replication fork restart after DNA damage, suggesting a mechanistic link between Rad53 deactivation and fork restart. To test this possibility we examined the progression of replication forks in methyl-methanesulfonate (MMS)-damaged cells, under different conditions of Rad53 activity. Hyperactivity of Rad53 in pph3Delta cells slows fork progression in MMS, whereas deactivation of Rad53, through expression of dominant-negative Rad53-KD, is sufficient to allow fork restart during recovery. Furthermore, combined deletion of PPH3 and PTC2, a second, unrelated Rad53 phosphatase, results in complete replication fork arrest and lethality in MMS, demonstrating that Rad53 deactivation is a key mechanism controlling fork restart. We propose a model for regulation of replication fork progression through damaged DNA involving a cycle of Rad53 activation and deactivation that coordinates replication restart with DNA repair.
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Affiliation(s)
- Shawn J Szyjka
- Molecular and Computational Biology Program, University of Southern California, Los Angeles, California 90089, USA
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Polyubiquitination of proliferating cell nuclear antigen by HLTF and SHPRH prevents genomic instability from stalled replication forks. Proc Natl Acad Sci U S A 2008; 105:12411-6. [PMID: 18719106 DOI: 10.1073/pnas.0805685105] [Citation(s) in RCA: 213] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Chronic stalling of DNA replication forks caused by DNA damage can lead to genomic instability. Cells have evolved lesion bypass pathways such as postreplication repair (PRR) to resolve these arrested forks. In yeast, one branch of PRR involves proliferating cell nuclear antigen (PCNA) polyubiquitination mediated by the Rad5-Ubc13-Mms2 complex that allows bypass of DNA lesion by a template-switching mechanism. Previously, we identified human SHPRH as a functional homologue of yeast Rad5 and revealed the existence of RAD5-like pathway in human cells. Here we report the identification of HLTF as a second RAD5 homologue in human cells. HLTF, like SHPRH, shares a unique domain architecture with Rad5 and promotes lysine 63-linked polyubiquitination of PCNA. Similar to yeast Rad5, HLTF is able to interact with UBC13 and PCNA, as well as SHPRH; and the reduction of either SHPRH or HLTF expression enhances spontaneous mutagenesis. Moreover, Hltf-deficient mouse embryonic fibroblasts show elevated chromosome breaks and fusions after methyl methane sulfonate treatment. Our results suggest that HLTF and SHPRH are functional homologues of yeast Rad5 that cooperatively mediate PCNA polyubiquitination and maintain genomic stability.
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Parker JL, Bucceri A, Davies AA, Heidrich K, Windecker H, Ulrich HD. SUMO modification of PCNA is controlled by DNA. EMBO J 2008; 27:2422-31. [PMID: 18701921 PMCID: PMC2518684 DOI: 10.1038/emboj.2008.162] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2008] [Accepted: 07/25/2008] [Indexed: 11/24/2022] Open
Abstract
Post-translational modification by the ubiquitin-like protein SUMO is often regulated by cellular signals that restrict the modification to appropriate situations. Nevertheless, many SUMO-specific ligases do not exhibit much target specificity, and—compared with the diversity of sumoylation substrates—their number is limited. This raises the question of how SUMO conjugation is controlled in vivo. We report here an unexpected mechanism by which sumoylation of the replication clamp protein, PCNA, from budding yeast is effectively coupled to S phase. We find that loading of PCNA onto DNA is a prerequisite for sumoylation in vivo and greatly stimulates modification in vitro. To our surprise, however, DNA binding by the ligase Siz1, responsible for PCNA sumoylation, is not strictly required. Instead, the stimulatory effect of DNA on conjugation is mainly attributable to DNA binding of PCNA itself. These findings imply a change in the properties of PCNA upon loading that enhances its capacity to be sumoylated.
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Affiliation(s)
- Joanne L Parker
- Cancer Research UK London Research Institute, Clare Hall Laboratories, South Mimms, UK
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