1
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Bhachoo JS, Garvin AJ. SUMO and the DNA damage response. Biochem Soc Trans 2024; 52:773-792. [PMID: 38629643 PMCID: PMC11088926 DOI: 10.1042/bst20230862] [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: 12/08/2023] [Revised: 03/20/2024] [Accepted: 03/25/2024] [Indexed: 04/25/2024]
Abstract
The preservation of genome integrity requires specialised DNA damage repair (DDR) signalling pathways to respond to each type of DNA damage. A key feature of DDR is the integration of numerous post-translational modification signals with DNA repair factors. These modifications influence DDR factor recruitment to damaged DNA, activity, protein-protein interactions, and ultimately eviction to enable access for subsequent repair factors or termination of DDR signalling. SUMO1-3 (small ubiquitin-like modifier 1-3) conjugation has gained much recent attention. The SUMO-modified proteome is enriched with DNA repair factors. Here we provide a snapshot of our current understanding of how SUMO signalling impacts the major DNA repair pathways in mammalian cells. We highlight repeating themes of SUMO signalling used throughout DNA repair pathways including the assembly of protein complexes, competition with ubiquitin to promote DDR factor stability and ubiquitin-dependent degradation or extraction of SUMOylated DDR factors. As SUMO 'addiction' in cancer cells is protective to genomic integrity, targeting components of the SUMO machinery to potentiate DNA damaging therapy or exacerbate existing DNA repair defects is a promising area of study.
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Affiliation(s)
- Jai S. Bhachoo
- SUMO Biology Lab, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, West Yorkshire LS2 9JT, U.K
| | - Alexander J. Garvin
- SUMO Biology Lab, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, West Yorkshire LS2 9JT, U.K
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2
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Cho T, Hoeg L, Setiaputra D, Durocher D. NFATC2IP is a mediator of SUMO-dependent genome integrity. Genes Dev 2024; 38:233-252. [PMID: 38503515 PMCID: PMC11065178 DOI: 10.1101/gad.350914.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 03/04/2024] [Indexed: 03/21/2024]
Abstract
The post-translational modification of proteins by SUMO is crucial for cellular viability and mammalian development in part due to the contribution of SUMOylation to genome duplication and repair. To investigate the mechanisms underpinning the essential function of SUMO, we undertook a genome-scale CRISPR/Cas9 screen probing the response to SUMOylation inhibition. This effort identified 130 genes whose disruption reduces or enhances the toxicity of TAK-981, a clinical-stage inhibitor of the SUMO E1-activating enzyme. Among the strongest hits, we validated and characterized NFATC2IP, an evolutionarily conserved protein related to the fungal Esc2 and Rad60 proteins that harbors tandem SUMO-like domains. Cells lacking NFATC2IP are viable but are hypersensitive to SUMO E1 inhibition, likely due to the accumulation of mitotic chromosome bridges and micronuclei. NFATC2IP primarily acts in interphase and associates with nascent DNA, suggesting a role in the postreplicative resolution of replication or recombination intermediates. Mechanistically, NFATC2IP interacts with the SMC5/6 complex and UBC9, the SUMO E2, via its first and second SUMO-like domains, respectively. AlphaFold-Multimer modeling suggests that NFATC2IP positions and activates the UBC9-NSMCE2 complex, the SUMO E3 ligase associated with SMC5/SMC6. We conclude that NFATC2IP is a key mediator of SUMO-dependent genomic integrity that collaborates with the SMC5/6 complex.
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Affiliation(s)
- Tiffany Cho
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Lisa Hoeg
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada
| | - Dheva Setiaputra
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Daniel Durocher
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada;
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
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3
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Zhao S, Xu Z, Niu X, Cao C, Gu Y, Wang H, Lu Q, Wu Z, Li L, Du J, Liao M. The role of SUMO specific peptidase 3 in secondary inflammation of ischemic stroke in mice. Biochim Biophys Acta Mol Basis Dis 2024; 1870:167104. [PMID: 38437993 DOI: 10.1016/j.bbadis.2024.167104] [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: 09/26/2023] [Revised: 01/06/2024] [Accepted: 02/22/2024] [Indexed: 03/06/2024]
Abstract
Ischemic stroke is the main cause of death and disability, and microglia play a crucial role in the pathophysiology of hypoxic ischemic brain injury. We found that SENP3 is highly expressed in the early stages of ischemic stroke in both in vivo and in vitro mouse models, and may be related to the deSUMOylation of the key kinase MKK7 in the TLR4/p-JNK signaling pathway. Knocking down SENP3 can inhibit the deSUMOylation of MKK7, thereby inhibiting the activation of the TLR4/p-JNK signaling pathway in an in vitro stroke model. Proteomic analysis showed that SENP3 undergoes phosphorylation at the T429 site after ischemic stroke. Computer simulation predictions show a significant enhancement of the interaction between pT429-SENP3 and MKK7, which has been confirmed through experiments on the interaction of biological macromolecules (SPR). The mitochondrial metabolic abnormalities caused by energy abnormalities in the early stages of stroke provide a good explanation for the phosphorylation of SENP3. Therefore, we used the mitochondrial complex inhibitor TTFA to reverse demonstrate that the phosphorylation of SENP3 comes from the large amount of adenosine triphosphate produced by mitochondrial abnormal metabolism caused by early oxygen glucose deficiency. Finally, proteomic analysis indicates that a significant amount of oxidative phosphorylation does occur in the early stages of stroke. In summary, targeted regulation of SENP3 phosphorylation to affect the deSUMOylation of MKK7 may inhibit secondary inflammation in ischemic stroke.
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Affiliation(s)
- Siyuan Zhao
- Institute of Neuroscience, School of Basic Medicine, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Zeting Xu
- Institute of Neuroscience, School of Basic Medicine, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Xueyuan Niu
- Institute of Neuroscience, School of Basic Medicine, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Cong Cao
- Institute of Neuroscience, School of Basic Medicine, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Yanlan Gu
- Institute of Neuroscience, School of Basic Medicine, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Hong Wang
- Institute of Neuroscience, School of Basic Medicine, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Qiuxia Lu
- Institute of Neuroscience, School of Basic Medicine, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Ziniu Wu
- Institute of Neuroscience, School of Basic Medicine, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Liangqiong Li
- Institute of Neuroscience, School of Basic Medicine, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Juanjuan Du
- Institute of Neuroscience, School of Basic Medicine, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Min Liao
- Institute of Neuroscience, School of Basic Medicine, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China.
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4
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Schwarz SD, Xu J, Gunasekera K, Schürmann D, Vågbø CB, Ferrari E, Slupphaug G, Hottiger MO, Schär P, Steinacher R. Covalent PARylation of DNA base excision repair proteins regulates DNA demethylation. Nat Commun 2024; 15:184. [PMID: 38167803 PMCID: PMC10762122 DOI: 10.1038/s41467-023-44209-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 12/04/2023] [Indexed: 01/05/2024] Open
Abstract
The intracellular ATP-ribosyltransferases PARP1 and PARP2, contribute to DNA base excision repair (BER) and DNA demethylation and have been implicated in epigenetic programming in early mammalian development. Recently, proteomic analyses identified BER proteins to be covalently poly-ADP-ribosylated by PARPs. The role of this posttranslational modification in the BER process is unknown. Here, we show that PARP1 senses AP-sites and SSBs generated during TET-TDG mediated active DNA demethylation and covalently attaches PAR to each BER protein engaged. Covalent PARylation dissociates BER proteins from DNA, which accelerates the completion of the repair process. Consistently, inhibition of PARylation in mESC resulted both in reduced locus-specific TET-TDG-targeted DNA demethylation, and in reduced general repair of random DNA damage. Our findings establish a critical function of covalent protein PARylation in coordinating molecular processes associated with dynamic DNA methylation.
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Affiliation(s)
- Simon D Schwarz
- Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Jianming Xu
- Department of Biomedicine, University of Basel, Basel, Switzerland
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland
| | - Kapila Gunasekera
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland
| | - David Schürmann
- Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Cathrine B Vågbø
- Proteomics and Modomics Experimental Core Facility (PROMEC), Norwegian University of Science and Technology and St. Olavs Hospital, Trondheim, Norway
| | - Elena Ferrari
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland
| | - Geir Slupphaug
- Proteomics and Modomics Experimental Core Facility (PROMEC), Norwegian University of Science and Technology and St. Olavs Hospital, Trondheim, Norway
| | - Michael O Hottiger
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland
| | - Primo Schär
- Department of Biomedicine, University of Basel, Basel, Switzerland.
| | - Roland Steinacher
- Department of Biomedicine, University of Basel, Basel, Switzerland.
- Institute of Molecular Health Sciences, ETH Zurich, Zurich, Switzerland.
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5
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Lobanova Y, Filonova G, Kaplun D, Zhigalova N, Prokhortchouk E, Zhenilo S. TRIM28 regulates transcriptional activity of methyl-DNA binding protein Kaiso by SUMOylation. Biochimie 2023; 206:73-80. [PMID: 36252888 DOI: 10.1016/j.biochi.2022.10.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 09/12/2022] [Accepted: 10/11/2022] [Indexed: 11/16/2022]
Abstract
Kaiso is a methyl DNA binding transcriptional factor involved in cell cycle control, WNT signaling, colon inflammation, and cancer progression. Recently, it was shown that SUMOylation dynamically modulates the transcriptional activity of Kaiso. However, factors involved in SUMOylation of Kaiso are unknown. Here we show that TRIM28 enhances SUMOylation of Kaiso leading to a decreased methyl-dependent repression ability. TRIM28 is a scaffold protein that regulates transcription and posttranslational modifications of factors involved in cell cycle progression, DNA damage, and viral gene expression. It has SUMO and ubiquitin E3 ligase activity. Here, we defined the domains involved in Kaiso-TRIM28 interaction. The RBCC domain of TRIM28 interacts with the BTB/POZ domain and the zinc fingers of Kaiso. The PHD-bromodomain of TRIM28 is sufficient for the interaction with zinc fingers of Kaiso. Additionally, we found that Kaiso enhances SUMOylation of TRIM28. Altogether our data suggest self-enhancement of SUMOylation of both Kaiso and TRIM28 that affects transcriptional activity of Kaiso.
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Affiliation(s)
- Y Lobanova
- Sckryabin Institute of Bioengineering, Federal Research Centre «Fundamentals of Biotechnology» RAS, pr. 60 let Oktyabrya, 7-1, 117312, Moscow, Russia
| | - G Filonova
- Sckryabin Institute of Bioengineering, Federal Research Centre «Fundamentals of Biotechnology» RAS, pr. 60 let Oktyabrya, 7-1, 117312, Moscow, Russia
| | - D Kaplun
- Sckryabin Institute of Bioengineering, Federal Research Centre «Fundamentals of Biotechnology» RAS, pr. 60 let Oktyabrya, 7-1, 117312, Moscow, Russia; Institute of Gene Biology RAS, 34/5 Vavilova Street, 119334 Moscow, Russia
| | - N Zhigalova
- Sckryabin Institute of Bioengineering, Federal Research Centre «Fundamentals of Biotechnology» RAS, pr. 60 let Oktyabrya, 7-1, 117312, Moscow, Russia
| | - E Prokhortchouk
- Sckryabin Institute of Bioengineering, Federal Research Centre «Fundamentals of Biotechnology» RAS, pr. 60 let Oktyabrya, 7-1, 117312, Moscow, Russia; Institute of Gene Biology RAS, 34/5 Vavilova Street, 119334 Moscow, Russia
| | - S Zhenilo
- Sckryabin Institute of Bioengineering, Federal Research Centre «Fundamentals of Biotechnology» RAS, pr. 60 let Oktyabrya, 7-1, 117312, Moscow, Russia; Institute of Gene Biology RAS, 34/5 Vavilova Street, 119334 Moscow, Russia.
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6
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Mai RT, Chao CH, Chang YW, Kao YC, Cheng Y, Hsu HY, Su YY, Wang CY, Lai BY. Sumoylation participates in the regulation of YB-1-mediated mismatch repair deficiency and alkylator tolerance. Am J Cancer Res 2022; 12:5462-5483. [PMID: 36628281 PMCID: PMC9827092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Accepted: 11/27/2022] [Indexed: 01/12/2023] Open
Abstract
Numerous reports indicate that enhanced expression of Y-box binding protein-1 (YB-1) in tumor cells is strongly associated with tumorigenesis, aggressiveness, drug resistance, as well as poor prognosis in several types of cancers, and YB-1 is considered to be an oncogene. The molecular mechanism contributing to the regulation of the biological activities of YB-1 remains obscure. Sumoylation, a post-translational modification involving the covalent conjugation of small ubiquitin-like modifier (SUMO) proteins to a target protein, plays key roles in the modulation of protein functions. In this study, our results revealed that YB-1 is sumoylated and that Lys26 is a critical residue for YB-1 sumoylation. Moreover, YB-1 was found to directly interact with SUMO proteins, and disruption of the SUMO-interacting motif (SIM) of YB-1 not only interfered with this interaction but also diminished YB-1 sumoylation. The subcellular localization, protein stability, and transcriptional regulatory activity of YB-1 were not significantly affected by sumoylation. However, decreased sumoylation disrupted the interaction between YB-1 and PCNA as well as YB-1-mediated inhibition of the MutSα/PCNA interaction and MutSα mismatch binding activity, indicating a functional role of YB-1 sumoylation in inducing DNA mismatch repair (MMR) deficiency and spontaneous mutations. The MMR machinery also recognizes alkylator-modified DNA adducts to signal for cell death. We further demonstrated that YB-1 sumoylation is crucial for the inhibition of SN1-type alkylator MNNG-induced cytotoxicity, G2/M-phase arrest, apoptosis, and the MMR-dependent DNA damage response. Collectively, these results provide molecular explanations for the impact of YB-1 sumoylation on MMR deficiency and alkylator tolerance, which may provide insight for designing therapeutic strategies for malignancies and alkylator-resistant cancers associated with YB-1 overexpression.
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Affiliation(s)
- Ru-Tsun Mai
- Department of Biological Science and Technology, College of Biological Science and Technology, National Yang Ming Chiao Tung UniversityHsinchu 300, Taiwan,Center for Intelligent Drug Systems and Smart Bio-devices (IDS2B), National Yang Ming Chiao Tung UniversityHsinchu 300, Taiwan
| | - Chi-Hong Chao
- Department of Biological Science and Technology, College of Biological Science and Technology, National Yang Ming Chiao Tung UniversityHsinchu 300, Taiwan,Institute of Molecular Medicine and Bioengineering, College of Biological Science and Technology, National Yang Ming Chiao Tung UniversityHsinchu 300, Taiwan,Center for Intelligent Drug Systems and Smart Bio-devices (IDS2B), National Yang Ming Chiao Tung UniversityHsinchu 300, Taiwan
| | - Yao-Wen Chang
- Institute of Biochemistry and Molecular Biology, School of Life Sciences, National Yang Ming Chiao Tung UniversityTaipei 112, Taiwan
| | - Yu-Ching Kao
- Department of Biological Science and Technology, College of Biological Science and Technology, National Yang Ming Chiao Tung UniversityHsinchu 300, Taiwan,Center for Intelligent Drug Systems and Smart Bio-devices (IDS2B), National Yang Ming Chiao Tung UniversityHsinchu 300, Taiwan
| | - Yi Cheng
- Institute of Molecular Medicine and Bioengineering, College of Biological Science and Technology, National Yang Ming Chiao Tung UniversityHsinchu 300, Taiwan,Center for Intelligent Drug Systems and Smart Bio-devices (IDS2B), National Yang Ming Chiao Tung UniversityHsinchu 300, Taiwan
| | - Hsiang-Yu Hsu
- Institute of Molecular Medicine and Bioengineering, College of Biological Science and Technology, National Yang Ming Chiao Tung UniversityHsinchu 300, Taiwan,Center for Intelligent Drug Systems and Smart Bio-devices (IDS2B), National Yang Ming Chiao Tung UniversityHsinchu 300, Taiwan
| | - Yi-Yuan Su
- Department of Biological Science and Technology, College of Biological Science and Technology, National Yang Ming Chiao Tung UniversityHsinchu 300, Taiwan,Center for Intelligent Drug Systems and Smart Bio-devices (IDS2B), National Yang Ming Chiao Tung UniversityHsinchu 300, Taiwan
| | - Chen-Yun Wang
- Institute of Molecular Medicine and Bioengineering, College of Biological Science and Technology, National Yang Ming Chiao Tung UniversityHsinchu 300, Taiwan,Center for Intelligent Drug Systems and Smart Bio-devices (IDS2B), National Yang Ming Chiao Tung UniversityHsinchu 300, Taiwan
| | - Bo-Ying Lai
- Institute of Biochemistry and Molecular Biology, School of Life Sciences, National Yang Ming Chiao Tung UniversityTaipei 112, Taiwan
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7
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Tarantino ME, Delaney S. Kinetic Analysis of the Effect of N-Terminal Acetylation on Thymine DNA Glycosylase. Biochemistry 2022; 61:895-908. [PMID: 35436101 PMCID: PMC9117521 DOI: 10.1021/acs.biochem.1c00823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Thymine DNA glycosylase (TDG) is tasked with initiating DNA base excision repair by recognizing and removing T, U, the chemotherapeutic 5-fluorouracil (5-FU), and many other oxidized and halogenated pyrimidine bases. TDG contains a long, unstructured N-terminus that contains four known sites of acetylation: lysine (K) residues 59, 83, 84, and 87. Here, K to glutamine (Q) mutants are used as acetyl-lysine (AcK) analogues to probe the effect of N-terminal acetylation on the kinetics of TDG. We find that mimicking acetylation affects neither the maximal single-turnover rate kmax nor the turnover rate kTO, indicating that the steps after initial binding, through chemistry and product release, are not affected. Under subsaturating conditions, however, acetylation changes the processing of U substrates. Subtle differences among AcK analogues are revealed with 5-FU in single-stranded DNA. We propose that the subtleties observed among the AcK analogues may be amplified on the genomic scale, leading to regulation of TDG activity. N-terminal acetylation, though, may also play a structural, rather than kinetic role in vivo.
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Affiliation(s)
- Mary E. Tarantino
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI 02912, United States
| | - Sarah Delaney
- Department of Chemistry, Brown University, Providence, RI 02912, United States
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8
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Liu X, Xu B, Yang J, He L, Zhang Z, Cheng X, Yu H, Liu X, Jin T, Peng Y, Huang Y, Xia L, Wang Y, Wu J, Wu X, Liu S, Shan L, Yang X, Sun L, Liang J, Zhang Y, Shang Y. UHRF2 commissions the completion of DNA demethylation through allosteric activation by 5hmC and K33-linked ubiquitination of XRCC1. Mol Cell 2021; 81:2960-2974.e7. [PMID: 34111398 DOI: 10.1016/j.molcel.2021.05.022] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 03/12/2021] [Accepted: 05/15/2021] [Indexed: 12/12/2022]
Abstract
The transition of oxidized 5-methylcytosine (5mC) intermediates into the base excision repair (BER) pipeline to complete DNA demethylation remains enigmatic. We report here that UHRF2, the only paralog of UHRF1 in mammals that fails to rescue Uhrf1-/- phenotype, is physically and functionally associated with BER complex. We show that UHRF2 is allosterically activated by 5-hydroxymethylcytosine (5hmC) and acts as a ubiquitin E3 ligase to catalyze K33-linked polyubiquitination of XRCC1. This nonproteolytic action stimulates XRCC1's interaction with the ubiquitin binding domain-bearing RAD23B, leading to the incorporation of TDG into BER complex. Integrative epigenomic analysis in mouse embryonic stem cells reveals that Uhrf2-fostered TDG-RAD23B-BER complex is functionally linked to the completion of DNA demethylation at active promoters and that Uhrf2 ablation impedes DNA demethylation on latent enhancers that undergo poised-to-active transition during neuronal commitment. Together, these observations highlight an essentiality of 5hmC-switched UHRF2 E3 ligase activity in commissioning the accomplishment of active DNA demethylation.
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Affiliation(s)
- Xiaoping Liu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Health Science Center, Beijing 100191, China
| | - Bosen Xu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Health Science Center, Beijing 100191, China
| | - Jianguo Yang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Health Science Center, Beijing 100191, China
| | - Lin He
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Health Science Center, Beijing 100191, China
| | - Zihan Zhang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Health Science Center, Beijing 100191, China
| | - Xiao Cheng
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Health Science Center, Beijing 100191, China
| | - Huajing Yu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Health Science Center, Beijing 100191, China
| | - Xujun Liu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Health Science Center, Beijing 100191, China
| | - Tong Jin
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Health Science Center, Beijing 100191, China
| | - Yani Peng
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Health Science Center, Beijing 100191, China
| | - Yunchao Huang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Health Science Center, Beijing 100191, China
| | - Lu Xia
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Health Science Center, Beijing 100191, China
| | - Yue Wang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Health Science Center, Beijing 100191, China; Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou 311121, China; Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing 100069, China
| | - Jiajing Wu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing 100069, China
| | - Xiaodi Wu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing 100069, China
| | - Shumeng Liu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing 100069, China
| | - Lin Shan
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing 100069, China
| | - Xiaohan Yang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Health Science Center, Beijing 100191, China
| | - Luyang Sun
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Health Science Center, Beijing 100191, China
| | - Jing Liang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Health Science Center, Beijing 100191, China
| | - Yu Zhang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Health Science Center, Beijing 100191, China.
| | - Yongfeng Shang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Health Science Center, Beijing 100191, China; Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou 311121, China; Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing 100069, China.
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9
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Hans F, Senarisoy M, Bhaskar Naidu C, Timmins J. Focus on DNA Glycosylases-A Set of Tightly Regulated Enzymes with a High Potential as Anticancer Drug Targets. Int J Mol Sci 2020; 21:ijms21239226. [PMID: 33287345 PMCID: PMC7730500 DOI: 10.3390/ijms21239226] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Accepted: 12/01/2020] [Indexed: 12/25/2022] Open
Abstract
Cancer is the second leading cause of death with tens of millions of people diagnosed with cancer every year around the world. Most radio- and chemotherapies aim to eliminate cancer cells, notably by causing severe damage to the DNA. However, efficient repair of such damage represents a common mechanism of resistance to initially effective cytotoxic agents. Thus, development of new generation anticancer drugs that target DNA repair pathways, and more particularly the base excision repair (BER) pathway that is responsible for removal of damaged bases, is of growing interest. The BER pathway is initiated by a set of enzymes known as DNA glycosylases. Unlike several downstream BER enzymes, DNA glycosylases have so far received little attention and the development of specific inhibitors of these enzymes has been lagging. Yet, dysregulation of DNA glycosylases is also known to play a central role in numerous cancers and at different stages of the disease, and thus inhibiting DNA glycosylases is now considered a valid strategy to eliminate cancer cells. This review provides a detailed overview of the activities of DNA glycosylases in normal and cancer cells, their modes of regulation, and their potential as anticancer drug targets.
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10
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The Function of SUMOylation and Its Role in the Development of Cancer Cells under Stress Conditions: A Systematic Review. Stem Cells Int 2020; 2020:8835714. [PMID: 33273928 PMCID: PMC7683158 DOI: 10.1155/2020/8835714] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Revised: 10/17/2020] [Accepted: 10/22/2020] [Indexed: 02/06/2023] Open
Abstract
Malignant tumors still pose serious threats to human health due to their high morbidity and mortality. Recurrence and metastasis are the most important factors affecting patient prognosis. Chemotherapeutic drugs and radiation used to treat these tumors mainly interfere with tumor metabolism, destroy DNA integrity, and inhibit protein synthesis. The upregulation of small ubiquitin-like modifier (SUMO) is a prevalent posttranslational modification (PTM) in various cancers and plays a critical role in tumor development. The dysregulation of SUMOylation can protect cancer cells from stresses exerted by external or internal stimuli. SUMOylation is a dynamic process finely regulated by SUMOylation enzymes and proteases to maintain a balance between SUMOylation and deSUMOylation. An increasing number of studies have reported that SUMOylation imbalance may contribute to cancer development, including metastasis, angiogenesis, invasion, and proliferation. High level of SUMOylation is required for cancer cells to survive internal or external stresses. Downregulation of SUMOylation may inhibit the development of cancer, making it an important potential clinical therapeutic target. Some studies have already begun to treat tumors by inhibiting the expression of SUMOylation family members, including SUMO E1 or E2. The tumor cells become more aggressive under internal and external stresses. The prevention of tumor development, metastasis, recurrence, and radiochemotherapy resistance by attenuating SUMOylation requires further exploration. This review focused on SUMOylation in tumor cells to discuss its effects on tumor suppressor proteins and oncoproteins as well as classical tumor pathways to identify new insights for cancer clinical therapy.
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11
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The Role of Posttranslational Modifications in DNA Repair. BIOMED RESEARCH INTERNATIONAL 2020. [DOI: 10.1155/2020/7493902] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The human body is a complex structure of cells, which are exposed to many types of stress. Cells must utilize various mechanisms to protect their DNA from damage caused by metabolic and external sources to maintain genomic integrity and homeostasis and to prevent the development of cancer. DNA damage inevitably occurs regardless of physiological or abnormal conditions. In response to DNA damage, signaling pathways are activated to repair the damaged DNA or to induce cell apoptosis. During the process, posttranslational modifications (PTMs) can be used to modulate enzymatic activities and regulate protein stability, protein localization, and protein-protein interactions. Thus, PTMs in DNA repair should be studied. In this review, we will focus on the current understanding of the phosphorylation, poly(ADP-ribosyl)ation, ubiquitination, SUMOylation, acetylation, and methylation of six typical PTMs and summarize PTMs of the key proteins in DNA repair, providing important insight into the role of PTMs in the maintenance of genome stability and contributing to reveal new and selective therapeutic approaches to target cancers.
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12
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Bangalore DM, Heil HS, Mehringer CF, Hirsch L, Hemmen K, Heinze KG, Tessmer I. Automated AFM analysis of DNA bending reveals initial lesion sensing strategies of DNA glycosylases. Sci Rep 2020; 10:15484. [PMID: 32968112 PMCID: PMC7511397 DOI: 10.1038/s41598-020-72102-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 08/25/2020] [Indexed: 12/31/2022] Open
Abstract
Base excision repair is the dominant DNA repair pathway of chemical modifications such as deamination, oxidation, or alkylation of DNA bases, which endanger genome integrity due to their high mutagenic potential. Detection and excision of these base lesions is achieved by DNA glycosylases. To investigate the remarkably high efficiency in target site search and recognition by these enzymes, we applied single molecule atomic force microscopy (AFM) imaging to a range of glycosylases with structurally different target lesions. Using a novel, automated, unbiased, high-throughput analysis approach, we were able to resolve subtly different conformational states of these glycosylases during DNA lesion search. Our results lend support to a model of enhanced lesion search efficiency through initial lesion detection based on altered mechanical properties at lesions. Furthermore, its enhanced sensitivity and easy applicability also to other systems recommend our novel analysis tool for investigations of diverse, fundamental biological interactions.
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Affiliation(s)
- Disha M Bangalore
- Rudolf Virchow Center for Experimental Biomedicine, University of Würzburg, Josef-Schneider-Strasse 2, 97080, Würzburg, Germany
| | - Hannah S Heil
- Rudolf Virchow Center for Experimental Biomedicine, University of Würzburg, Josef-Schneider-Strasse 2, 97080, Würzburg, Germany
| | - Christian F Mehringer
- Rudolf Virchow Center for Experimental Biomedicine, University of Würzburg, Josef-Schneider-Strasse 2, 97080, Würzburg, Germany
| | - Lisa Hirsch
- Rudolf Virchow Center for Experimental Biomedicine, University of Würzburg, Josef-Schneider-Strasse 2, 97080, Würzburg, Germany
| | - Katherina Hemmen
- Rudolf Virchow Center for Experimental Biomedicine, University of Würzburg, Josef-Schneider-Strasse 2, 97080, Würzburg, Germany
| | - Katrin G Heinze
- Rudolf Virchow Center for Experimental Biomedicine, University of Würzburg, Josef-Schneider-Strasse 2, 97080, Würzburg, Germany.
| | - Ingrid Tessmer
- Rudolf Virchow Center for Experimental Biomedicine, University of Würzburg, Josef-Schneider-Strasse 2, 97080, Würzburg, Germany.
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13
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Reading Targeted DNA Damage in the Active Demethylation Pathway: Role of Accessory Domains of Eukaryotic AP Endonucleases and Thymine-DNA Glycosylases. J Mol Biol 2020:S0022-2836(19)30720-X. [DOI: 10.1016/j.jmb.2019.12.020] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 11/24/2019] [Accepted: 12/05/2019] [Indexed: 01/07/2023]
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14
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Koliadenko V, Wilanowski T. Additional functions of selected proteins involved in DNA repair. Free Radic Biol Med 2020; 146:1-15. [PMID: 31639437 DOI: 10.1016/j.freeradbiomed.2019.10.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 10/16/2019] [Accepted: 10/16/2019] [Indexed: 12/30/2022]
Abstract
Protein moonlighting is a phenomenon in which a single polypeptide chain can perform a number of different unrelated functions. Here we present our analysis of moonlighting in the case of selected DNA repair proteins which include G:T mismatch-specific thymine DNA glycosylase (TDG), methyl-CpG-binding domain protein 4 (MBD4), apurinic/apyrimidinic endonuclease 1 (APE1), AlkB homologs, poly (ADP-ribose) polymerase 1 (PARP-1) and single-strand selective monofunctional uracil DNA glycosylase 1 (SMUG1). Most of their additional functions are not accidental and clear patterns are emerging. Participation in RNA metabolism is not surprising as bases occurring in RNA are the same or very similar to those in DNA. Other common additional function involves regulation of transcription. This is not unexpected as these proteins bind to specific DNA regions for DNA repair, hence they can also be recruited to regulate transcription. Participation in demethylation and replication of DNA appears logical as well. Some of the multifunctional DNA repair proteins play major roles in many diseases, including cancer. However, their moonlighting might prove a major difficulty in the development of new therapies because it will not be trivial to target a single protein function without affecting its other functions that are not related to the disease.
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Affiliation(s)
- Vlada Koliadenko
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Ilji Miecznikowa 1, 02-096, Warsaw, Poland
| | - Tomasz Wilanowski
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Ilji Miecznikowa 1, 02-096, Warsaw, Poland.
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15
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Sannai M, Doneddu V, Giri V, Seeholzer S, Nicolas E, Yip SC, Bassi MR, Mancuso P, Cortellino S, Cigliano A, Lurie R, Ding H, Chernoff J, Sobol RW, Yen TJ, Bagella L, Bellacosa A. Modification of the base excision repair enzyme MBD4 by the small ubiquitin-like molecule SUMO1. DNA Repair (Amst) 2019; 82:102687. [PMID: 31476572 PMCID: PMC6785017 DOI: 10.1016/j.dnarep.2019.102687] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Revised: 07/21/2019] [Accepted: 08/08/2019] [Indexed: 10/26/2022]
Abstract
The base excision repair DNA N-glycosylase MBD4 (also known as MED1), an interactor of the DNA mismatch repair protein MLH1, plays a central role in the maintenance of genomic stability of CpG sites by removing thymine and uracil from G:T and G:U mismatches, respectively. MBD4 is also involved in DNA damage response and transcriptional regulation. The interaction with other proteins is likely critical for understanding MBD4 functions. To identify novel proteins that interact with MBD4, we used tandem affinity purification (TAP) from HEK-293 cells. The MBD4-TAP fusion and its co-associated proteins were purified sequentially on IgG and calmodulin affinity columns; the final eluate was shown to contain MLH1 by western blotting, and MBD4-associated proteins were identified by mass spectrometry. Bands with molecular weight higher than that expected for MBD4 (˜66 kD) yielded peptides corresponding to MBD4 itself and the small ubiquitin-like molecule-1 (SUMO1), suggesting that MBD4 is sumoylated in vivo. MBD4 sumoylation was validated by co-immunoprecipitation in HEK-293 and MCF7 cells, and by an in vitrosumoylation assay. Sequence and mutation analysis identified three main sumoylation sites: MBD4 is sumoylated preferentially on K137, with additional sumoylation at K215 and K377. Patterns of MBD4 sumoylation were altered, in a DNA damage-specific way, by the anti-metabolite 5-fluorouracil, the alkylating agent N-Methyl-N-nitrosourea and the crosslinking agent cisplatin. MCF7 extract expressing sumoylated MBD4 displays higher thymine glycosylase activity than the unmodified species. Of the 67 MBD4 missense mutations reported in The Cancer Genome Atlas, 14 (20.9%) map near sumoylation sites. These results indicate that MBD4 is sumoylated in vivo in a DNA damage-specific manner, and suggest that sumoylation serves to regulate its repair activity and could be compromised in cancer. This study expands the role played by sumoylation in fine-tuning DNA damage response and repair.
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Affiliation(s)
- Mara Sannai
- Cancer Epigenetics and Cancer Biology Programs, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
| | - Valentina Doneddu
- Cancer Epigenetics and Cancer Biology Programs, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA; Department of Biomedical Sciences, University of Sassari, Sassari, 07100, Italy
| | - Veda Giri
- Cancer Epigenetics and Cancer Biology Programs, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
| | - Steven Seeholzer
- Proteomics Core, The Children's Hospital of Philadelphia, Philadelphia PA, 19104, USA
| | - Emmanuelle Nicolas
- Cancer Epigenetics and Cancer Biology Programs, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
| | - Shu-Chin Yip
- Cancer Biology Programs, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
| | - Maria Rosaria Bassi
- Cancer Epigenetics and Cancer Biology Programs, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
| | - Pietro Mancuso
- Cancer Epigenetics and Cancer Biology Programs, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
| | - Salvatore Cortellino
- Cancer Epigenetics and Cancer Biology Programs, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
| | - Antonio Cigliano
- Cancer Epigenetics and Cancer Biology Programs, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
| | - Rebecca Lurie
- Cancer Epigenetics and Cancer Biology Programs, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
| | - Hua Ding
- Proteomics Core, The Children's Hospital of Philadelphia, Philadelphia PA, 19104, USA
| | - Jonathan Chernoff
- Cancer Biology Programs, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
| | - Robert W Sobol
- Department of Oncologic Sciences, Mitchell Cancer Institute, University of South Alabama, Mobile, AL 36604, USA
| | - Timothy J Yen
- Cancer Biology Programs, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
| | - Luigi Bagella
- Department of Biomedical Sciences, University of Sassari, Sassari, 07100, Italy; Sbarro Institute for Cancer Research and Molecular Medicine, Center for Biotechnology, College of Science and Technology, Temple University, Philadelphia, PA, 19122, USA
| | - Alfonso Bellacosa
- Cancer Epigenetics and Cancer Biology Programs, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA.
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16
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Coey CT, Drohat AC. Defining the impact of sumoylation on substrate binding and catalysis by thymine DNA glycosylase. Nucleic Acids Res 2019; 46:5159-5170. [PMID: 29660017 PMCID: PMC6007377 DOI: 10.1093/nar/gky278] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 04/04/2018] [Indexed: 01/22/2023] Open
Abstract
Thymine DNA glycosylase (TDG) excises thymine from mutagenic G·T mispairs generated by deamination of 5-methylcytosine (mC) and it removes two mC derivatives, 5−formylcytosine (fC) and 5−carboxylcytosine (caC), in a multistep pathway for DNA demethylation. TDG is modified by small ubiquitin-like modifier (SUMO) proteins, but the impact of sumoylation on TDG activity is poorly defined and the functions of TDG sumoylation remain unclear. We determined the effect of TDG sumoylation, by SUMO-1 or SUMO-2, on substrate binding and catalytic parameters. Single turnover experiments reveal that sumoylation dramatically impairs TDG base-excision activity, such that G·T activity is reduced by ≥45-fold and fC and caC are excised slowly, with a reaction half-life of ≥9 min (37°C). Fluorescence anisotropy studies reveal that unmodified TDG binds tightly to G·fC and G·caC substrates, with dissociation constants in the low nanomolar range. While sumoylation of TDG weakens substrate binding, the residual affinity is substantial and is comparable to that of biochemically-characterized readers of fC and caC. Our findings raise the possibility that sumoylation enables TDG to function, at least transiently, as reader of fC and caC. Notably, sumoylation could potentially facilitate TDG recruitment of other proteins, including transcription factors or epigenetic regulators, to these sites in DNA.
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Affiliation(s)
- Christopher T Coey
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Alexander C Drohat
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD 21201, USA.,Molecular and Structural Biology Program, University of Maryland Marlene and Stewart Greenebaum Comprehensive Cancer Center, Baltimore, MD 21201, USA
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17
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Boldinova EO, Khairullin RF, Makarova AV, Zharkov DO. Isoforms of Base Excision Repair Enzymes Produced by Alternative Splicing. Int J Mol Sci 2019; 20:ijms20133279. [PMID: 31277343 PMCID: PMC6651865 DOI: 10.3390/ijms20133279] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 06/29/2019] [Accepted: 07/02/2019] [Indexed: 02/07/2023] Open
Abstract
Transcripts of many enzymes involved in base excision repair (BER) undergo extensive alternative splicing, but functions of the corresponding alternative splice variants remain largely unexplored. In this review, we cover the studies describing the common alternatively spliced isoforms and disease-associated variants of DNA glycosylases, AP-endonuclease 1, and DNA polymerase beta. We also discuss the roles of alternative splicing in the regulation of their expression, catalytic activities, and intracellular transport.
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Affiliation(s)
| | - Rafil F Khairullin
- Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, 9 Parizhskoy Kommuny Str., 420012 Kazan, Russia
| | - Alena V Makarova
- RAS Institute of Molecular Genetics, 2 Kurchatova Sq., 123182 Moscow, Russia.
| | - Dmitry O Zharkov
- Novosibirsk State University, 1 Pirogova St., 630090 Novosibirsk, Russia.
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., 630090 Novosibirsk, Russia.
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18
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Sarre A, Stelter M, Rollo F, De Bonis S, Seck A, Hognon C, Ravanat JL, Monari A, Dehez F, Moe E, Timmins J. The three Endonuclease III variants of Deinococcus radiodurans possess distinct and complementary DNA repair activities. DNA Repair (Amst) 2019; 78:45-59. [DOI: 10.1016/j.dnarep.2019.03.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 03/26/2019] [Accepted: 03/27/2019] [Indexed: 11/26/2022]
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19
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Ma CH, Su BY, Maciaszek A, Fan HF, Guga P, Jayaram M. A Flp-SUMO hybrid recombinase reveals multi-layered copy number control of a selfish DNA element through post-translational modification. PLoS Genet 2019; 15:e1008193. [PMID: 31242181 PMCID: PMC6594588 DOI: 10.1371/journal.pgen.1008193] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Accepted: 05/13/2019] [Indexed: 12/30/2022] Open
Abstract
Mechanisms for highly efficient chromosome-associated equal segregation, and for maintenance of steady state copy number, are at the heart of the evolutionary success of the 2-micron plasmid as a stable multi-copy extra-chromosomal selfish DNA element present in the yeast nucleus. The Flp site-specific recombination system housed by the plasmid, which is central to plasmid copy number maintenance, is regulated at multiple levels. Transcription of the FLP gene is fine-tuned by the repressor function of the plasmid-coded partitioning proteins Rep1 and Rep2 and their antagonist Raf1, which is also plasmid-coded. In addition, the Flp protein is regulated by the host's post-translational modification machinery. Utilizing a Flp-SUMO fusion protein, which functionally mimics naturally sumoylated Flp, we demonstrate that the modification signals ubiquitination of Flp, followed by its proteasome-mediated degradation. Furthermore, reduced binding affinity and cooperativity of the modified Flp decrease its association with the plasmid FRT (Flp recombination target) sites, and/or increase its dissociation from them. The resulting attenuation of strand cleavage and recombination events safeguards against runaway increase in plasmid copy number, which is deleterious to the host-and indirectly-to the plasmid. These results have broader relevance to potential mechanisms by which selfish genomes minimize fitness conflicts with host genomes by holding in check the extra genetic load they pose.
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Affiliation(s)
- Chien-Hui Ma
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, United States of America
| | - Bo-Yu Su
- Department of Life Sciences and Institute of Genome Sciences, Biophotonics and Molecular Imaging Research Center, National Yang-Ming University, Taipei City, Taiwan
| | - Anna Maciaszek
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Department of Bioorganic Chemistry, Lodz, Poland
| | - Hsiu-Fang Fan
- Department of Life Sciences and Institute of Genome Sciences, Biophotonics and Molecular Imaging Research Center, National Yang-Ming University, Taipei City, Taiwan
| | - Piotr Guga
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Department of Bioorganic Chemistry, Lodz, Poland
| | - Makkuni Jayaram
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, United States of America
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20
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Liu SY, Ma YL, Hsu WL, Chiou HY, Lee EHY. Protein inhibitor of activated STAT1 Ser 503 phosphorylation-mediated Elk-1 SUMOylation promotes neuronal survival in APP/PS1 mice. Br J Pharmacol 2019; 176:1793-1810. [PMID: 30849179 DOI: 10.1111/bph.14656] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 01/29/2019] [Accepted: 02/10/2019] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND AND PURPOSE Protein inhibitor of activated STAT1 (PIAS1) is phosphorylated by IKKα at Ser90 in a PIAS1 E3 ligase activity-dependent manner. Whether PIAS1 is also phosphorylated at other residues and the functional significance of these additional phosphorylation events are not known. The transcription factor Elk-1 remains SUMOylated under basal conditions, but the role of Elk-1 SUMOylation in brain is unknown. Here, we examined the functional significance of PIAS1-mediated Elk-1 SUMOylation in Alzheimer's disease (AD) using the APP/PS1 mouse model of AD and amyloid β (Aβ) microinjections in vivo. EXPERIMENTAL APPROACH Novel phosphorylation site(s) on PIAS1 were identified by LC-MS/MS, and MAPK/ERK-mediated phosphorylation of Elk-1 demonstrated using in vitro kinase assays. Elk-1 SUMOylation by PIAS1 in brain was determined using in vitro SUMOylation assays. Apoptosis in hippocampus was assessed by measuring GADD45α expression by western blotting, and apoptosis of hippocampal neurons in APP/PS1 mice was assessed by TUNEL assay. KEY RESULTS Using LC-MS/MS, we identified a novel MAPK/ERK-mediated phosphorylation site on PIAS1 at Ser503 and showed this phosphorylation determines PIAS1 E3 ligase activity. In rat brain, Elk-1 was SUMOylated by PIAS1, which decreased Elk-1 phosphorylation and down-regulated GADD45α expression. Moreover, lentiviral-mediated transduction of Elk-1-SUMO1 reduced the number of hippocampal apoptotic neurons in APP/PS1 mice. CONCLUSIONS AND IMPLICATIONS MAPK/ERK-mediated phosphorylation of PIAS1 at Ser503 determines PIAS1 E3 ligase activity. Moreover, PIAS1 mediates SUMOylation of Elk-1, which functions as an endogenous defence mechanism against Aβ toxicity in vivo. Targeting Elk-1 SUMOylation could be considered a novel therapeutic strategy against AD.
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Affiliation(s)
- Shau-Yu Liu
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Yun-Li Ma
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Wei-Lun Hsu
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Hsin-Ying Chiou
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan.,Division of Endocrinology and Metabolism, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| | - Eminy H Y Lee
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
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21
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Hu C, Jiang X. The SUMO-specific protease family regulates cancer cell radiosensitivity. Biomed Pharmacother 2019; 109:66-70. [DOI: 10.1016/j.biopha.2018.10.071] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Revised: 10/12/2018] [Accepted: 10/12/2018] [Indexed: 12/21/2022] Open
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22
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Endutkin AV, Yudkina AV, Sidorenko VS, Zharkov DO. Transient protein-protein complexes in base excision repair. J Biomol Struct Dyn 2018; 37:4407-4418. [PMID: 30488779 DOI: 10.1080/07391102.2018.1553741] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Transient protein-protein complexes are of great importance for organizing multiple enzymatic reactions into productive reaction pathways. Base excision repair (BER), a process of critical importance for maintaining genome stability against a plethora of DNA-damaging factors, involves several enzymes, including DNA glycosylases, AP endonucleases, DNA polymerases, DNA ligases and accessory proteins acting sequentially on the same damaged site in DNA. Rather than being assembled into one stable multisubunit complex, these enzymes pass the repair intermediates between them in a highly coordinated manner. In this review, we discuss the nature and the role of transient complexes arising during BER as deduced from structural and kinetic data. Almost all of the transient complexes are DNA-mediated, although some may also exist in solution and strengthen under specific conditions. The best-studied example, the interactions between DNA glycosylases and AP endonucleases, is discussed in more detail to provide a framework for distinguishing between stable and transient complexes based on the kinetic data. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Anton V Endutkin
- SB RAS Institute of Chemical Biology and Fundamental Medicine , Novosibirsk , Russia.,Novosibirsk State University , Novosibirsk , Russia.,Podalirius Ltd. , Novosibirsk , Russia
| | - Anna V Yudkina
- SB RAS Institute of Chemical Biology and Fundamental Medicine , Novosibirsk , Russia.,Novosibirsk State University , Novosibirsk , Russia
| | - Viktoriya S Sidorenko
- Department of Pharmacological Sciences, Stony Brook University , Stony Brook , NY , USA
| | - Dmitry O Zharkov
- SB RAS Institute of Chemical Biology and Fundamental Medicine , Novosibirsk , Russia.,Novosibirsk State University , Novosibirsk , Russia
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23
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Steinacher R, Barekati Z, Botev P, Kuśnierczyk A, Slupphaug G, Schär P. SUMOylation coordinates BERosome assembly in active DNA demethylation during cell differentiation. EMBO J 2018; 38:embj.201899242. [PMID: 30523148 DOI: 10.15252/embj.201899242] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Revised: 11/05/2018] [Accepted: 11/09/2018] [Indexed: 11/09/2022] Open
Abstract
During active DNA demethylation, 5-methylcytosine (5mC) is oxidized by TET proteins to 5-formyl-/5-carboxylcytosine (5fC/5caC) for replacement by unmethylated C by TDG-initiated DNA base excision repair (BER). Base excision generates fragile abasic sites (AP-sites) in DNA and has to be coordinated with subsequent repair steps to limit accumulation of genome destabilizing secondary DNA lesions. Here, we show that 5fC/5caC is generated at a high rate in genomes of differentiating mouse embryonic stem cells and that SUMOylation and the BER protein XRCC1 play critical roles in orchestrating TDG-initiated BER of these lesions. SUMOylation of XRCC1 facilitates physical interaction with TDG and promotes the assembly of a TDG-BER core complex. Within this TDG-BERosome, SUMO is transferred from XRCC1 and coupled to the SUMO acceptor lysine in TDG, promoting its dissociation while assuring the engagement of the BER machinery to complete demethylation. Although well-studied, the biological importance of TDG SUMOylation has remained obscure. Here, we demonstrate that SUMOylation of TDG suppresses DNA strand-break accumulation and toxicity to PARP inhibition in differentiating mESCs and is essential for neural lineage commitment.
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Affiliation(s)
| | - Zeinab Barekati
- Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Petar Botev
- Institute of Molecular Biology, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Anna Kuśnierczyk
- Department of Cancer Research and Molecular Medicine, Proteomics and Metabolomics Core Facility, PROMEC, Norwegian University of Science and Technology, Trondheim, Norway
| | - Geir Slupphaug
- Department of Cancer Research and Molecular Medicine, Proteomics and Metabolomics Core Facility, PROMEC, Norwegian University of Science and Technology, Trondheim, Norway
| | - Primo Schär
- Department of Biomedicine, University of Basel, Basel, Switzerland
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24
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Augustine RC, Vierstra RD. SUMOylation: re-wiring the plant nucleus during stress and development. CURRENT OPINION IN PLANT BIOLOGY 2018; 45:143-154. [PMID: 30014889 DOI: 10.1016/j.pbi.2018.06.006] [Citation(s) in RCA: 85] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Revised: 06/11/2018] [Accepted: 06/25/2018] [Indexed: 05/08/2023]
Abstract
Conjugation of small ubiquitin-related modifier (SUMO) to intracellular proteins provides a dynamic regulatory mechanism that enables plants to rapidly defend against environmental challenges. SUMOylation of mostly nuclear proteins is among the fastest stress responses observed but precisely how this post-translational modification provides stress resilience remains unclear. Here, we describe the plant SUMO system and its expanding target catalog, which implicates this modification in DNA repair, chromatin modification/remodeling, transcriptional activation/repression, epigenetics, and RNA metabolism, with a likely outcome being extensive nuclear re-wiring to withstand stress. In parallel, studies have linked SUMO to developmental programs such as gametogenesis and gene silencing. The accumulating data support the notion that SUMOylation substantially influences the transcriptional and epigenetic landscapes to promote stress tolerance and developmental progression.
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Affiliation(s)
- Robert C Augustine
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Richard D Vierstra
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA.
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25
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Tarantino ME, Dow BJ, Drohat AC, Delaney S. Nucleosomes and the three glycosylases: High, medium, and low levels of excision by the uracil DNA glycosylase superfamily. DNA Repair (Amst) 2018; 72:56-63. [PMID: 30268365 DOI: 10.1016/j.dnarep.2018.09.008] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2018] [Revised: 09/16/2018] [Accepted: 09/17/2018] [Indexed: 01/19/2023]
Abstract
Human cells express the UDG superfamily of glycosylases, which excise uracil (U) from the genome. The three members of this structural superfamily are uracil DNA glycosylase (UNG/UDG), single-strand selective monofunctional uracil DNA glycosylase (SMUG1), and thymine DNA glycosylase (TDG). We previously reported that UDG is efficient at removing U from DNA packaged into nucleosome core particles (NCP) and is minimally affected by the histone proteins when acting on an outward-facing U in the dyad region. In an effort to determine whether this high activity is a general property of the UDG superfamily of glycosylases, we compare the activity of UDG, SMUG1, and TDG on a U:G wobble base pair using NCP assembled from Xenopus laevis histones and the Widom 601 positioning sequence. We found that while UDG is highly active, SMUG1 is severely inhibited on NCP and this inhibition is independent of sequence context. Here we also provide the first report of TDG activity on an NCP, and found that TDG has an intermediate level of activity in excision of U and is severely inhibited in its excision of T. These results are discussed in the context of cellular roles for each of these enzymes.
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Affiliation(s)
- Mary E Tarantino
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI, 02912, United States
| | - Blaine J Dow
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD, 21201, United States
| | - Alexander C Drohat
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD, 21201, United States; University of Maryland Marlene and Stewart Greenebaum Cancer Center, Baltimore, MD, 21201, United States
| | - Sarah Delaney
- Department of Chemistry, Brown University, Providence, RI, 02912, United States.
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26
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Emadi-Baygi M, Sedighi R, Nourbakhsh N, Nikpour P. Pseudogenes in gastric cancer pathogenesis: a review article. Brief Funct Genomics 2018; 16:348-360. [PMID: 28459995 DOI: 10.1093/bfgp/elx004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Cancer burden rises globally at an alarming pace. According to GLOBOCAN 2012, gastric cancer (GC) is regarded as the fifth most common malignancy in the world. Being twice as high in men as in women, GC is the third leading cause of cancer mortality in both sexes globally. Being labeled as 'junk DNA', pseudogenes were considered as nonfunctional 'trash', which contribute nothing to survival of the organism; therefore, a number of strategies have been developed to circumvent their accidental detection. Recent progresses have confirmed that pseudogenes can have broad and multifaceted spectrum of activities in human cancers in general and GC in particular. Furthermore, the mentioned functions are parental gene-dependent and/or -independent. Therefore, pseudogenes can be regarded as the emerging class of elaborate modulators of gene expression involved in pathogenesis of human cancers including gastric adenocarcinoma.
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27
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Pawale VS, Yadav P, Roy RP. Facile One-Step Assembly of Bona Fide SUMO Conjugates by Chemoenzymatic Ligation. Chembiochem 2018; 19:1137-1141. [PMID: 29575440 DOI: 10.1002/cbic.201800090] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Indexed: 12/14/2022]
Abstract
The post-translational conjugation of the small ubiquitin-like modifiers (SUMOs) to target proteins occurs through a complex machinery that involves sequential action of at least three enzymes. SUMOylation performs crucial regulatory functions in several cellular processes. The availability of well-defined SUMO conjugates is necessary for untangling the mechanism of SUMOylation. However, assembly of homogeneous SUMO conjugates represents a challenge because of the multi-step synthesis involved and the unwieldiness of the reconstituted biosynthetic systems. Here we describe a simple one-step chemoenzymatic strategy for conjugating engineered SUMO (eSUMO) proteins to a prefabricated isopeptide-linked SUMO target peptide. Notably, the eSUMOs were efficiently recognized by the enzymes of the SUMOylation machinery and the SUMO conjugates served as bona fide substrates for DeSUMOylating enzymes.
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Affiliation(s)
- Vijaykumar S Pawale
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Prity Yadav
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Rajendra P Roy
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, 110067, India
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28
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Spallotta F, Cencioni C, Atlante S, Garella D, Cocco M, Mori M, Mastrocola R, Kuenne C, Guenther S, Nanni S, Azzimato V, Zukunft S, Kornberger A, Sürün D, Schnütgen F, von Melchner H, Di Stilo A, Aragno M, Braspenning M, van Criekinge W, De Blasio MJ, Ritchie RH, Zaccagnini G, Martelli F, Farsetti A, Fleming I, Braun T, Beiras-Fernandez A, Botta B, Collino M, Bertinaria M, Zeiher AM, Gaetano C. Stable Oxidative Cytosine Modifications Accumulate in Cardiac Mesenchymal Cells From Type2 Diabetes Patients. Circ Res 2018; 122:31-46. [DOI: 10.1161/circresaha.117.311300] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/06/2017] [Revised: 11/10/2017] [Accepted: 11/16/2017] [Indexed: 12/17/2022]
Abstract
Rationale:
Human cardiac mesenchymal cells (CMSCs) are a therapeutically relevant primary cell population. Diabetes mellitus compromises CMSC function as consequence of metabolic alterations and incorporation of stable epigenetic changes.
Objective:
To investigate the role of α-ketoglutarate (αKG) in the epimetabolic control of DNA demethylation in CMSCs.
Methods and Results:
Quantitative global analysis, methylated and hydroxymethylated DNA sequencing, and gene-specific GC methylation detection revealed an accumulation of 5-methylcytosine, 5-hydroxymethylcytosine, and 5-formylcytosine in the genomic DNA of human CMSCs isolated from diabetic donors. Whole heart genomic DNA analysis revealed iterative oxidative cytosine modification accumulation in mice exposed to high-fat diet (HFD), injected with streptozotocin, or both in combination (streptozotocin/HFD). In this context, untargeted and targeted metabolomics indicated an intracellular reduction of αKG synthesis in diabetic CMSCs and in the whole heart of HFD mice. This observation was paralleled by a compromised TDG (thymine DNA glycosylase) and TET1 (ten–eleven translocation protein 1) association and function with TET1 relocating out of the nucleus. Molecular dynamics and mutational analyses showed that αKG binds TDG on Arg275 providing an enzymatic allosteric activation. As a consequence, the enzyme significantly increased its capacity to remove G/T nucleotide mismatches or 5-formylcytosine. Accordingly, an exogenous source of αKG restored the DNA demethylation cycle by promoting TDG function, TET1 nuclear localization, and TET/TDG association. TDG inactivation by CRISPR/Cas9 knockout or TET/TDG siRNA knockdown induced 5-formylcytosine accumulation, thus partially mimicking the diabetic epigenetic landscape in cells of nondiabetic origin. The novel compound (S)-2-[(2,6-dichlorobenzoyl)amino]succinic acid (AA6), identified as an inhibitor of αKG dehydrogenase, increased the αKG level in diabetic CMSCs and in the heart of HFD and streptozotocin mice eliciting, in HFD, DNA demethylation, glucose uptake, and insulin response.
Conclusions:
Restoring the epimetabolic control of DNA demethylation cycle promises beneficial effects on cells compromised by environmental metabolic changes.
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Affiliation(s)
- Francesco Spallotta
- From the Goethe University, Frankfurt am Main, Germany (F. Spallotta, C.C., S.A., S.Z., D.S., F. Schnütgen, H.v.M., A.F., I.F., A.M.Z., C.G.); University of Turin, Torino, Italy (D.G., M. Cocco, R.M., A.D.S., M.A., M. Collino, M. Bertinaria); Istituto Italiano di Tecnologia CLNS@Sapienza Rome, Italy (M.M.); Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany (C.K., S.G., T.B.); Università Cattolica del Sacro Cuore, Rome, Italy (S.N.); Karolinska Institutet, Huddinge, Sweden (V.A
| | - Chiara Cencioni
- From the Goethe University, Frankfurt am Main, Germany (F. Spallotta, C.C., S.A., S.Z., D.S., F. Schnütgen, H.v.M., A.F., I.F., A.M.Z., C.G.); University of Turin, Torino, Italy (D.G., M. Cocco, R.M., A.D.S., M.A., M. Collino, M. Bertinaria); Istituto Italiano di Tecnologia CLNS@Sapienza Rome, Italy (M.M.); Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany (C.K., S.G., T.B.); Università Cattolica del Sacro Cuore, Rome, Italy (S.N.); Karolinska Institutet, Huddinge, Sweden (V.A
| | - Sandra Atlante
- From the Goethe University, Frankfurt am Main, Germany (F. Spallotta, C.C., S.A., S.Z., D.S., F. Schnütgen, H.v.M., A.F., I.F., A.M.Z., C.G.); University of Turin, Torino, Italy (D.G., M. Cocco, R.M., A.D.S., M.A., M. Collino, M. Bertinaria); Istituto Italiano di Tecnologia CLNS@Sapienza Rome, Italy (M.M.); Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany (C.K., S.G., T.B.); Università Cattolica del Sacro Cuore, Rome, Italy (S.N.); Karolinska Institutet, Huddinge, Sweden (V.A
| | - Davide Garella
- From the Goethe University, Frankfurt am Main, Germany (F. Spallotta, C.C., S.A., S.Z., D.S., F. Schnütgen, H.v.M., A.F., I.F., A.M.Z., C.G.); University of Turin, Torino, Italy (D.G., M. Cocco, R.M., A.D.S., M.A., M. Collino, M. Bertinaria); Istituto Italiano di Tecnologia CLNS@Sapienza Rome, Italy (M.M.); Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany (C.K., S.G., T.B.); Università Cattolica del Sacro Cuore, Rome, Italy (S.N.); Karolinska Institutet, Huddinge, Sweden (V.A
| | - Mattia Cocco
- From the Goethe University, Frankfurt am Main, Germany (F. Spallotta, C.C., S.A., S.Z., D.S., F. Schnütgen, H.v.M., A.F., I.F., A.M.Z., C.G.); University of Turin, Torino, Italy (D.G., M. Cocco, R.M., A.D.S., M.A., M. Collino, M. Bertinaria); Istituto Italiano di Tecnologia CLNS@Sapienza Rome, Italy (M.M.); Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany (C.K., S.G., T.B.); Università Cattolica del Sacro Cuore, Rome, Italy (S.N.); Karolinska Institutet, Huddinge, Sweden (V.A
| | - Mattia Mori
- From the Goethe University, Frankfurt am Main, Germany (F. Spallotta, C.C., S.A., S.Z., D.S., F. Schnütgen, H.v.M., A.F., I.F., A.M.Z., C.G.); University of Turin, Torino, Italy (D.G., M. Cocco, R.M., A.D.S., M.A., M. Collino, M. Bertinaria); Istituto Italiano di Tecnologia CLNS@Sapienza Rome, Italy (M.M.); Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany (C.K., S.G., T.B.); Università Cattolica del Sacro Cuore, Rome, Italy (S.N.); Karolinska Institutet, Huddinge, Sweden (V.A
| | - Raffaella Mastrocola
- From the Goethe University, Frankfurt am Main, Germany (F. Spallotta, C.C., S.A., S.Z., D.S., F. Schnütgen, H.v.M., A.F., I.F., A.M.Z., C.G.); University of Turin, Torino, Italy (D.G., M. Cocco, R.M., A.D.S., M.A., M. Collino, M. Bertinaria); Istituto Italiano di Tecnologia CLNS@Sapienza Rome, Italy (M.M.); Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany (C.K., S.G., T.B.); Università Cattolica del Sacro Cuore, Rome, Italy (S.N.); Karolinska Institutet, Huddinge, Sweden (V.A
| | - Carsten Kuenne
- From the Goethe University, Frankfurt am Main, Germany (F. Spallotta, C.C., S.A., S.Z., D.S., F. Schnütgen, H.v.M., A.F., I.F., A.M.Z., C.G.); University of Turin, Torino, Italy (D.G., M. Cocco, R.M., A.D.S., M.A., M. Collino, M. Bertinaria); Istituto Italiano di Tecnologia CLNS@Sapienza Rome, Italy (M.M.); Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany (C.K., S.G., T.B.); Università Cattolica del Sacro Cuore, Rome, Italy (S.N.); Karolinska Institutet, Huddinge, Sweden (V.A
| | - Stefan Guenther
- From the Goethe University, Frankfurt am Main, Germany (F. Spallotta, C.C., S.A., S.Z., D.S., F. Schnütgen, H.v.M., A.F., I.F., A.M.Z., C.G.); University of Turin, Torino, Italy (D.G., M. Cocco, R.M., A.D.S., M.A., M. Collino, M. Bertinaria); Istituto Italiano di Tecnologia CLNS@Sapienza Rome, Italy (M.M.); Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany (C.K., S.G., T.B.); Università Cattolica del Sacro Cuore, Rome, Italy (S.N.); Karolinska Institutet, Huddinge, Sweden (V.A
| | - Simona Nanni
- From the Goethe University, Frankfurt am Main, Germany (F. Spallotta, C.C., S.A., S.Z., D.S., F. Schnütgen, H.v.M., A.F., I.F., A.M.Z., C.G.); University of Turin, Torino, Italy (D.G., M. Cocco, R.M., A.D.S., M.A., M. Collino, M. Bertinaria); Istituto Italiano di Tecnologia CLNS@Sapienza Rome, Italy (M.M.); Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany (C.K., S.G., T.B.); Università Cattolica del Sacro Cuore, Rome, Italy (S.N.); Karolinska Institutet, Huddinge, Sweden (V.A
| | - Valerio Azzimato
- From the Goethe University, Frankfurt am Main, Germany (F. Spallotta, C.C., S.A., S.Z., D.S., F. Schnütgen, H.v.M., A.F., I.F., A.M.Z., C.G.); University of Turin, Torino, Italy (D.G., M. Cocco, R.M., A.D.S., M.A., M. Collino, M. Bertinaria); Istituto Italiano di Tecnologia CLNS@Sapienza Rome, Italy (M.M.); Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany (C.K., S.G., T.B.); Università Cattolica del Sacro Cuore, Rome, Italy (S.N.); Karolinska Institutet, Huddinge, Sweden (V.A
| | - Sven Zukunft
- From the Goethe University, Frankfurt am Main, Germany (F. Spallotta, C.C., S.A., S.Z., D.S., F. Schnütgen, H.v.M., A.F., I.F., A.M.Z., C.G.); University of Turin, Torino, Italy (D.G., M. Cocco, R.M., A.D.S., M.A., M. Collino, M. Bertinaria); Istituto Italiano di Tecnologia CLNS@Sapienza Rome, Italy (M.M.); Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany (C.K., S.G., T.B.); Università Cattolica del Sacro Cuore, Rome, Italy (S.N.); Karolinska Institutet, Huddinge, Sweden (V.A
| | - Angela Kornberger
- From the Goethe University, Frankfurt am Main, Germany (F. Spallotta, C.C., S.A., S.Z., D.S., F. Schnütgen, H.v.M., A.F., I.F., A.M.Z., C.G.); University of Turin, Torino, Italy (D.G., M. Cocco, R.M., A.D.S., M.A., M. Collino, M. Bertinaria); Istituto Italiano di Tecnologia CLNS@Sapienza Rome, Italy (M.M.); Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany (C.K., S.G., T.B.); Università Cattolica del Sacro Cuore, Rome, Italy (S.N.); Karolinska Institutet, Huddinge, Sweden (V.A
| | - Duran Sürün
- From the Goethe University, Frankfurt am Main, Germany (F. Spallotta, C.C., S.A., S.Z., D.S., F. Schnütgen, H.v.M., A.F., I.F., A.M.Z., C.G.); University of Turin, Torino, Italy (D.G., M. Cocco, R.M., A.D.S., M.A., M. Collino, M. Bertinaria); Istituto Italiano di Tecnologia CLNS@Sapienza Rome, Italy (M.M.); Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany (C.K., S.G., T.B.); Università Cattolica del Sacro Cuore, Rome, Italy (S.N.); Karolinska Institutet, Huddinge, Sweden (V.A
| | - Frank Schnütgen
- From the Goethe University, Frankfurt am Main, Germany (F. Spallotta, C.C., S.A., S.Z., D.S., F. Schnütgen, H.v.M., A.F., I.F., A.M.Z., C.G.); University of Turin, Torino, Italy (D.G., M. Cocco, R.M., A.D.S., M.A., M. Collino, M. Bertinaria); Istituto Italiano di Tecnologia CLNS@Sapienza Rome, Italy (M.M.); Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany (C.K., S.G., T.B.); Università Cattolica del Sacro Cuore, Rome, Italy (S.N.); Karolinska Institutet, Huddinge, Sweden (V.A
| | - Harald von Melchner
- From the Goethe University, Frankfurt am Main, Germany (F. Spallotta, C.C., S.A., S.Z., D.S., F. Schnütgen, H.v.M., A.F., I.F., A.M.Z., C.G.); University of Turin, Torino, Italy (D.G., M. Cocco, R.M., A.D.S., M.A., M. Collino, M. Bertinaria); Istituto Italiano di Tecnologia CLNS@Sapienza Rome, Italy (M.M.); Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany (C.K., S.G., T.B.); Università Cattolica del Sacro Cuore, Rome, Italy (S.N.); Karolinska Institutet, Huddinge, Sweden (V.A
| | - Antonella Di Stilo
- From the Goethe University, Frankfurt am Main, Germany (F. Spallotta, C.C., S.A., S.Z., D.S., F. Schnütgen, H.v.M., A.F., I.F., A.M.Z., C.G.); University of Turin, Torino, Italy (D.G., M. Cocco, R.M., A.D.S., M.A., M. Collino, M. Bertinaria); Istituto Italiano di Tecnologia CLNS@Sapienza Rome, Italy (M.M.); Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany (C.K., S.G., T.B.); Università Cattolica del Sacro Cuore, Rome, Italy (S.N.); Karolinska Institutet, Huddinge, Sweden (V.A
| | - Manuela Aragno
- From the Goethe University, Frankfurt am Main, Germany (F. Spallotta, C.C., S.A., S.Z., D.S., F. Schnütgen, H.v.M., A.F., I.F., A.M.Z., C.G.); University of Turin, Torino, Italy (D.G., M. Cocco, R.M., A.D.S., M.A., M. Collino, M. Bertinaria); Istituto Italiano di Tecnologia CLNS@Sapienza Rome, Italy (M.M.); Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany (C.K., S.G., T.B.); Università Cattolica del Sacro Cuore, Rome, Italy (S.N.); Karolinska Institutet, Huddinge, Sweden (V.A
| | - Maarten Braspenning
- From the Goethe University, Frankfurt am Main, Germany (F. Spallotta, C.C., S.A., S.Z., D.S., F. Schnütgen, H.v.M., A.F., I.F., A.M.Z., C.G.); University of Turin, Torino, Italy (D.G., M. Cocco, R.M., A.D.S., M.A., M. Collino, M. Bertinaria); Istituto Italiano di Tecnologia CLNS@Sapienza Rome, Italy (M.M.); Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany (C.K., S.G., T.B.); Università Cattolica del Sacro Cuore, Rome, Italy (S.N.); Karolinska Institutet, Huddinge, Sweden (V.A
| | - Wim van Criekinge
- From the Goethe University, Frankfurt am Main, Germany (F. Spallotta, C.C., S.A., S.Z., D.S., F. Schnütgen, H.v.M., A.F., I.F., A.M.Z., C.G.); University of Turin, Torino, Italy (D.G., M. Cocco, R.M., A.D.S., M.A., M. Collino, M. Bertinaria); Istituto Italiano di Tecnologia CLNS@Sapienza Rome, Italy (M.M.); Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany (C.K., S.G., T.B.); Università Cattolica del Sacro Cuore, Rome, Italy (S.N.); Karolinska Institutet, Huddinge, Sweden (V.A
| | - Miles J. De Blasio
- From the Goethe University, Frankfurt am Main, Germany (F. Spallotta, C.C., S.A., S.Z., D.S., F. Schnütgen, H.v.M., A.F., I.F., A.M.Z., C.G.); University of Turin, Torino, Italy (D.G., M. Cocco, R.M., A.D.S., M.A., M. Collino, M. Bertinaria); Istituto Italiano di Tecnologia CLNS@Sapienza Rome, Italy (M.M.); Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany (C.K., S.G., T.B.); Università Cattolica del Sacro Cuore, Rome, Italy (S.N.); Karolinska Institutet, Huddinge, Sweden (V.A
| | - Rebecca H. Ritchie
- From the Goethe University, Frankfurt am Main, Germany (F. Spallotta, C.C., S.A., S.Z., D.S., F. Schnütgen, H.v.M., A.F., I.F., A.M.Z., C.G.); University of Turin, Torino, Italy (D.G., M. Cocco, R.M., A.D.S., M.A., M. Collino, M. Bertinaria); Istituto Italiano di Tecnologia CLNS@Sapienza Rome, Italy (M.M.); Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany (C.K., S.G., T.B.); Università Cattolica del Sacro Cuore, Rome, Italy (S.N.); Karolinska Institutet, Huddinge, Sweden (V.A
| | - Germana Zaccagnini
- From the Goethe University, Frankfurt am Main, Germany (F. Spallotta, C.C., S.A., S.Z., D.S., F. Schnütgen, H.v.M., A.F., I.F., A.M.Z., C.G.); University of Turin, Torino, Italy (D.G., M. Cocco, R.M., A.D.S., M.A., M. Collino, M. Bertinaria); Istituto Italiano di Tecnologia CLNS@Sapienza Rome, Italy (M.M.); Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany (C.K., S.G., T.B.); Università Cattolica del Sacro Cuore, Rome, Italy (S.N.); Karolinska Institutet, Huddinge, Sweden (V.A
| | - Fabio Martelli
- From the Goethe University, Frankfurt am Main, Germany (F. Spallotta, C.C., S.A., S.Z., D.S., F. Schnütgen, H.v.M., A.F., I.F., A.M.Z., C.G.); University of Turin, Torino, Italy (D.G., M. Cocco, R.M., A.D.S., M.A., M. Collino, M. Bertinaria); Istituto Italiano di Tecnologia CLNS@Sapienza Rome, Italy (M.M.); Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany (C.K., S.G., T.B.); Università Cattolica del Sacro Cuore, Rome, Italy (S.N.); Karolinska Institutet, Huddinge, Sweden (V.A
| | - Antonella Farsetti
- From the Goethe University, Frankfurt am Main, Germany (F. Spallotta, C.C., S.A., S.Z., D.S., F. Schnütgen, H.v.M., A.F., I.F., A.M.Z., C.G.); University of Turin, Torino, Italy (D.G., M. Cocco, R.M., A.D.S., M.A., M. Collino, M. Bertinaria); Istituto Italiano di Tecnologia CLNS@Sapienza Rome, Italy (M.M.); Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany (C.K., S.G., T.B.); Università Cattolica del Sacro Cuore, Rome, Italy (S.N.); Karolinska Institutet, Huddinge, Sweden (V.A
| | - Ingrid Fleming
- From the Goethe University, Frankfurt am Main, Germany (F. Spallotta, C.C., S.A., S.Z., D.S., F. Schnütgen, H.v.M., A.F., I.F., A.M.Z., C.G.); University of Turin, Torino, Italy (D.G., M. Cocco, R.M., A.D.S., M.A., M. Collino, M. Bertinaria); Istituto Italiano di Tecnologia CLNS@Sapienza Rome, Italy (M.M.); Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany (C.K., S.G., T.B.); Università Cattolica del Sacro Cuore, Rome, Italy (S.N.); Karolinska Institutet, Huddinge, Sweden (V.A
| | - Thomas Braun
- From the Goethe University, Frankfurt am Main, Germany (F. Spallotta, C.C., S.A., S.Z., D.S., F. Schnütgen, H.v.M., A.F., I.F., A.M.Z., C.G.); University of Turin, Torino, Italy (D.G., M. Cocco, R.M., A.D.S., M.A., M. Collino, M. Bertinaria); Istituto Italiano di Tecnologia CLNS@Sapienza Rome, Italy (M.M.); Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany (C.K., S.G., T.B.); Università Cattolica del Sacro Cuore, Rome, Italy (S.N.); Karolinska Institutet, Huddinge, Sweden (V.A
| | - Andres Beiras-Fernandez
- From the Goethe University, Frankfurt am Main, Germany (F. Spallotta, C.C., S.A., S.Z., D.S., F. Schnütgen, H.v.M., A.F., I.F., A.M.Z., C.G.); University of Turin, Torino, Italy (D.G., M. Cocco, R.M., A.D.S., M.A., M. Collino, M. Bertinaria); Istituto Italiano di Tecnologia CLNS@Sapienza Rome, Italy (M.M.); Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany (C.K., S.G., T.B.); Università Cattolica del Sacro Cuore, Rome, Italy (S.N.); Karolinska Institutet, Huddinge, Sweden (V.A
| | - Bruno Botta
- From the Goethe University, Frankfurt am Main, Germany (F. Spallotta, C.C., S.A., S.Z., D.S., F. Schnütgen, H.v.M., A.F., I.F., A.M.Z., C.G.); University of Turin, Torino, Italy (D.G., M. Cocco, R.M., A.D.S., M.A., M. Collino, M. Bertinaria); Istituto Italiano di Tecnologia CLNS@Sapienza Rome, Italy (M.M.); Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany (C.K., S.G., T.B.); Università Cattolica del Sacro Cuore, Rome, Italy (S.N.); Karolinska Institutet, Huddinge, Sweden (V.A
| | - Massimo Collino
- From the Goethe University, Frankfurt am Main, Germany (F. Spallotta, C.C., S.A., S.Z., D.S., F. Schnütgen, H.v.M., A.F., I.F., A.M.Z., C.G.); University of Turin, Torino, Italy (D.G., M. Cocco, R.M., A.D.S., M.A., M. Collino, M. Bertinaria); Istituto Italiano di Tecnologia CLNS@Sapienza Rome, Italy (M.M.); Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany (C.K., S.G., T.B.); Università Cattolica del Sacro Cuore, Rome, Italy (S.N.); Karolinska Institutet, Huddinge, Sweden (V.A
| | - Massimo Bertinaria
- From the Goethe University, Frankfurt am Main, Germany (F. Spallotta, C.C., S.A., S.Z., D.S., F. Schnütgen, H.v.M., A.F., I.F., A.M.Z., C.G.); University of Turin, Torino, Italy (D.G., M. Cocco, R.M., A.D.S., M.A., M. Collino, M. Bertinaria); Istituto Italiano di Tecnologia CLNS@Sapienza Rome, Italy (M.M.); Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany (C.K., S.G., T.B.); Università Cattolica del Sacro Cuore, Rome, Italy (S.N.); Karolinska Institutet, Huddinge, Sweden (V.A
| | - Andreas M. Zeiher
- From the Goethe University, Frankfurt am Main, Germany (F. Spallotta, C.C., S.A., S.Z., D.S., F. Schnütgen, H.v.M., A.F., I.F., A.M.Z., C.G.); University of Turin, Torino, Italy (D.G., M. Cocco, R.M., A.D.S., M.A., M. Collino, M. Bertinaria); Istituto Italiano di Tecnologia CLNS@Sapienza Rome, Italy (M.M.); Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany (C.K., S.G., T.B.); Università Cattolica del Sacro Cuore, Rome, Italy (S.N.); Karolinska Institutet, Huddinge, Sweden (V.A
| | - Carlo Gaetano
- From the Goethe University, Frankfurt am Main, Germany (F. Spallotta, C.C., S.A., S.Z., D.S., F. Schnütgen, H.v.M., A.F., I.F., A.M.Z., C.G.); University of Turin, Torino, Italy (D.G., M. Cocco, R.M., A.D.S., M.A., M. Collino, M. Bertinaria); Istituto Italiano di Tecnologia CLNS@Sapienza Rome, Italy (M.M.); Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany (C.K., S.G., T.B.); Università Cattolica del Sacro Cuore, Rome, Italy (S.N.); Karolinska Institutet, Huddinge, Sweden (V.A
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29
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Garvin AJ, Morris JR. SUMO, a small, but powerful, regulator of double-strand break repair. Philos Trans R Soc Lond B Biol Sci 2017; 372:20160281. [PMID: 28847818 PMCID: PMC5577459 DOI: 10.1098/rstb.2016.0281] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/05/2017] [Indexed: 12/11/2022] Open
Abstract
The response to a DNA double-stranded break in mammalian cells is a process of sensing and signalling the lesion. It results in halting the cell cycle and local transcription and in the mediation of the DNA repair process itself. The response is launched through a series of post-translational modification signalling events coordinated by phosphorylation and ubiquitination. More recently modifications of proteins by Small Ubiquitin-like MOdifier (SUMO) isoforms have also been found to be key to coordination of the response (Morris et al. 2009 Nature462, 886-890 (doi:10.1038/nature08593); Galanty et al. 2009 Nature462, 935-939 (doi:10.1038/nature08657)). However our understanding of the role of SUMOylation is slight compared with our growing knowledge of how ubiquitin drives signal amplification and key chromatin interactions. In this review we consider our current knowledge of how SUMO isoforms, SUMO conjugation machinery, SUMO proteases and SUMO-interacting proteins contribute to directing altered chromatin states and to repair-protein kinetics at a double-stranded DNA lesion in mammalian cells. We also consider the gaps in our understanding.This article is part of the themed issue 'Chromatin modifiers and remodellers in DNA repair and signalling'.
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Affiliation(s)
- Alexander J Garvin
- Birmingham Centre for Genome Biology and Institute of Cancer and Genomic Sciences, Medical and Dental School, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Joanna R Morris
- Birmingham Centre for Genome Biology and Institute of Cancer and Genomic Sciences, Medical and Dental School, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
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30
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Ho JJ, Cattoglio C, McSwiggen DT, Tjian R, Fong YW. Regulation of DNA demethylation by the XPC DNA repair complex in somatic and pluripotent stem cells. Genes Dev 2017; 31:830-844. [PMID: 28512237 PMCID: PMC5435894 DOI: 10.1101/gad.295741.116] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2017] [Accepted: 04/14/2017] [Indexed: 12/19/2022]
Abstract
In this study, Ho et al. research the mechanism by which TDG-dependent DNA demethylation occurs in a rapid and site-specific manner. Their findings demonstrate two distinct but complementary mechanisms by which XPC influences gene regulation by coordinating efficient TDG-mediated DNA demethylation along with active transcription during somatic cell reprogramming. Faithful resetting of the epigenetic memory of a somatic cell to a pluripotent state during cellular reprogramming requires DNA methylation to silence somatic gene expression and dynamic DNA demethylation to activate pluripotency gene transcription. The removal of methylated cytosines requires the base excision repair enzyme TDG, but the mechanism by which TDG-dependent DNA demethylation occurs in a rapid and site-specific manner remains unclear. Here we show that the XPC DNA repair complex is a potent accelerator of global and locus-specific DNA demethylation in somatic and pluripotent stem cells. XPC cooperates with TDG genome-wide to stimulate the turnover of essential intermediates by overcoming slow TDG–abasic product dissociation during active DNA demethylation. We further establish that DNA demethylation induced by XPC expression in somatic cells overcomes an early epigenetic barrier in cellular reprogramming and facilitates the generation of more robust induced pluripotent stem cells, characterized by enhanced pluripotency-associated gene expression and self-renewal capacity. Taken together with our previous studies establishing the XPC complex as a transcriptional coactivator, our findings underscore two distinct but complementary mechanisms by which XPC influences gene regulation by coordinating efficient TDG-mediated DNA demethylation along with active transcription during somatic cell reprogramming.
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Affiliation(s)
- Jaclyn J Ho
- Department of Molecular and Cell Biology, Li Ka Shing Center for Biomedical and Health Sciences, California Institute for Regenerative Medicine Center of Excellence, University of California at Berkeley, Berkeley, California 94720, USA.,Howard Hughes Medical Institute, Berkeley, California 94720, USA
| | - Claudia Cattoglio
- Department of Molecular and Cell Biology, Li Ka Shing Center for Biomedical and Health Sciences, California Institute for Regenerative Medicine Center of Excellence, University of California at Berkeley, Berkeley, California 94720, USA.,Howard Hughes Medical Institute, Berkeley, California 94720, USA
| | - David T McSwiggen
- Department of Molecular and Cell Biology, Li Ka Shing Center for Biomedical and Health Sciences, California Institute for Regenerative Medicine Center of Excellence, University of California at Berkeley, Berkeley, California 94720, USA
| | - Robert Tjian
- Department of Molecular and Cell Biology, Li Ka Shing Center for Biomedical and Health Sciences, California Institute for Regenerative Medicine Center of Excellence, University of California at Berkeley, Berkeley, California 94720, USA.,Howard Hughes Medical Institute, Berkeley, California 94720, USA
| | - Yick W Fong
- Brigham Regenerative Medicine Center, Cardiovascular Division, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Cambridge, Massachusetts 02115, USA.,Harvard Stem Cell Institute, Cambridge, Massachusetts 02138, USA
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31
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Haak DC, Fukao T, Grene R, Hua Z, Ivanov R, Perrella G, Li S. Multilevel Regulation of Abiotic Stress Responses in Plants. FRONTIERS IN PLANT SCIENCE 2017; 8:1564. [PMID: 29033955 PMCID: PMC5627039 DOI: 10.3389/fpls.2017.01564] [Citation(s) in RCA: 97] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 08/28/2017] [Indexed: 05/18/2023]
Abstract
The sessile lifestyle of plants requires them to cope with stresses in situ. Plants overcome abiotic stresses by altering structure/morphology, and in some extreme conditions, by compressing the life cycle to survive the stresses in the form of seeds. Genetic and molecular studies have uncovered complex regulatory processes that coordinate stress adaptation and tolerance in plants, which are integrated at various levels. Investigating natural variation in stress responses has provided important insights into the evolutionary processes that shape the integrated regulation of adaptation and tolerance. This review primarily focuses on the current understanding of how transcriptional, post-transcriptional, post-translational, and epigenetic processes along with genetic variation orchestrate stress responses in plants. We also discuss the current and future development of computational tools to identify biologically meaningful factors from high dimensional, genome-scale data and construct the signaling networks consisting of these components.
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Affiliation(s)
- David C. Haak
- Department of Plant Pathology, Physiology, and Weed Science, Virginia Tech, BlacksburgVA, United States
| | - Takeshi Fukao
- Department of Crop and Soil Environmental Sciences, Virginia Tech, BlacksburgVA, United States
| | - Ruth Grene
- Department of Plant Pathology, Physiology, and Weed Science, Virginia Tech, BlacksburgVA, United States
| | - Zhihua Hua
- Department of Environmental and Plant Biology, Interdisciplinary Program in Molecular and Cellular Biology, Ohio University, AthensOH, United States
| | - Rumen Ivanov
- Institut für Botanik, Heinrich-Heine-Universität DüsseldorfDüsseldorf, Germany
| | - Giorgio Perrella
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of GlasgowGlasgow, United Kingdom
| | - Song Li
- Department of Crop and Soil Environmental Sciences, Virginia Tech, BlacksburgVA, United States
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32
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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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33
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Lee JS, Choi HJ, Baek SH. Sumoylation and Its Contribution to Cancer. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 963:283-298. [PMID: 28197919 DOI: 10.1007/978-3-319-50044-7_17] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Post-translational modifications play an important role in regulating protein activity by altering their functions. Sumoylation is a highly dynamic process which is tightly regulated by a fine balance between conjugating and deconjugating enzyme activities. It affects intracellular localization and their interaction with their binding partners, thereby changing gene expression. Consequently, these changes in turn affect signaling mechanisms that regulate many cellular functions, such as cell growth, proliferation, apoptosis , DNA repair , and cell survival. It is becoming apparent that deregulation in the SUMO pathway contributes to oncogenic transformation by affecting sumoylation/desumoylation of many oncoproteins and tumor suppressors. Loss of balance between sumoylation and desumoylation has been reported in a number of studies in a variety of disease types including cancer. This chapter summarizes the mechanisms and functions of the deregulated SUMO pathway affecting oncogenes and tumor suppressor genes.
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Affiliation(s)
- Jason S Lee
- Department of Biological Sciences, Seoul National University, Seoul, 151-742, South Korea
| | - Hee June Choi
- Department of Biological Sciences, Seoul National University, Seoul, 151-742, South Korea
| | - Sung Hee Baek
- Department of Biological Sciences, Seoul National University, Seoul, 151-742, South Korea.
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34
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Slyvka A, Mierzejewska K, Bochtler M. Nei-like 1 (NEIL1) excises 5-carboxylcytosine directly and stimulates TDG-mediated 5-formyl and 5-carboxylcytosine excision. Sci Rep 2017; 7:9001. [PMID: 28827588 PMCID: PMC5566547 DOI: 10.1038/s41598-017-07458-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Accepted: 06/26/2017] [Indexed: 01/01/2023] Open
Abstract
Thymine DNA glycosylase (TDG) and Nei-like 1 (NEIL1) have both been implicated in the base excision repair step of active DNA demethylation. The robust glycosylase activity of TDG on DNA substrates containing 5-formylcytosine (5fC) or 5-carboxylcytosine (5caC) is universally accepted, but the mode of action of NEIL1 is still debated. Based on genetic experiments, it has been suggested that NEIL1 acts redundantly with TDG and excises 5fC and 5caC directly. However, this result has been disputed, and it was suggested instead that NEIL1 is recruited by the monofunctional TDG for the 2′-deoxyribose excision step. Using purified human NEIL1 and its catalytically impaired P2T and E3Q variants as controls, we detect NEIL1 activity on 5caC, but not a 5fC containing dsDNA substrate. We confirm direct NEIL1 TDG binding and NEIL1 mediated 2′-deoxyribose excision downstream of TDG glycosylase activity. NEIL1 acts not only downstream of TDG, but also enhances TDG activity on 5fC or 5caC containing DNA. NEIL1 mediated enhancement of the TDG glycosylase activity is substrate specific and does not occur for dsDNA with a T/G mismatch.
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Affiliation(s)
- Anton Slyvka
- International Institute of Molecular and Cell Biology, Trojdena 4, 02-109, Warsaw, Poland
| | - Karolina Mierzejewska
- International Institute of Molecular and Cell Biology, Trojdena 4, 02-109, Warsaw, Poland
| | - Matthias Bochtler
- International Institute of Molecular and Cell Biology, Trojdena 4, 02-109, Warsaw, Poland. .,Polish Academy of Sciences, Institute of Biochemistry and Biophysics, Pawinskiego 5a, 02-106, Warsaw, Poland.
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35
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Wang Z, Zhu WG, Xu X. Ubiquitin-like modifications in the DNA damage response. Mutat Res 2017; 803-805:56-75. [PMID: 28734548 DOI: 10.1016/j.mrfmmm.2017.07.001] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Revised: 06/03/2017] [Accepted: 07/03/2017] [Indexed: 12/14/2022]
Abstract
Genomic DNA is damaged at an extremely high frequency by both endogenous and environmental factors. An improper response to DNA damage can lead to genome instability, accelerate the aging process and ultimately cause various human diseases, including cancers and neurodegenerative disorders. The mechanisms that underlie the cellular DNA damage response (DDR) are complex and are regulated at many levels, including at the level of post-translational modification (PTM). Since the discovery of ubiquitin in 1975 and ubiquitylation as a form of PTM in the early 1980s, a number of ubiquitin-like modifiers (UBLs) have been identified, including small ubiquitin-like modifiers (SUMOs), neural precursor cell expressed, developmentally down-regulated 8 (NEDD8), interferon-stimulated gene 15 (ISG15), human leukocyte antigen (HLA)-F adjacent transcript 10 (FAT10), ubiquitin-fold modifier 1 (UFRM1), URM1 ubiquitin-related modifier-1 (URM1), autophagy-related protein 12 (ATG12), autophagy-related protein 8 (ATG8), fan ubiquitin-like protein 1 (FUB1) and histone mono-ubiquitylation 1 (HUB1). All of these modifiers have known roles in the cellular response to various forms of stress, and delineating their underlying molecular mechanisms and functions is fundamental in enhancing our understanding of human disease and longevity. To date, however, the molecular mechanisms and functions of these UBLs in the DDR remain largely unknown. This review summarizes the current status of PTMs by UBLs in the DDR and their implication in cancer diagnosis, therapy and drug discovery.
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Affiliation(s)
- Zhifeng Wang
- Guangdong Key Laboratory of Genome Stability & Disease Prevention, Shenzhen University School of Medicine, Shenzhen, Guangdong 518060, China
| | - Wei-Guo Zhu
- Guangdong Key Laboratory of Genome Stability & Disease Prevention, Shenzhen University School of Medicine, Shenzhen, Guangdong 518060, China
| | - Xingzhi Xu
- Guangdong Key Laboratory of Genome Stability & Disease Prevention, Shenzhen University School of Medicine, Shenzhen, Guangdong 518060, China; Beijing Key Laboratory of DNA Damage Response, Capital Normal University College of Life Sciences, Beijing 100048, China.
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36
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Limpose KL, Corbett AH, Doetsch PW. BERing the burden of damage: Pathway crosstalk and posttranslational modification of base excision repair proteins regulate DNA damage management. DNA Repair (Amst) 2017. [PMID: 28629773 DOI: 10.1016/j.dnarep.2017.06.007] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
DNA base damage and non-coding apurinic/apyrimidinic (AP) sites are ubiquitous types of damage that must be efficiently repaired to prevent mutations. These damages can occur in both the nuclear and mitochondrial genomes. Base excision repair (BER) is the frontline pathway for identifying and excising damaged DNA bases in both of these cellular compartments. Recent advances demonstrate that BER does not operate as an isolated pathway but rather dynamically interacts with components of other DNA repair pathways to modulate and coordinate BER functions. We define the coordination and interaction between DNA repair pathways as pathway crosstalk. Numerous BER proteins are modified and regulated by post-translational modifications (PTMs), and PTMs could influence pathway crosstalk. Here, we present recent advances on BER/DNA repair pathway crosstalk describing specific examples and also highlight regulation of BER components through PTMs. We have organized and reported functional interactions and documented PTMs for BER proteins into a consolidated summary table. We further propose the concept of DNA repair hubs that coordinate DNA repair pathway crosstalk to identify central protein targets that could play a role in designing future drug targets.
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Affiliation(s)
- Kristin L Limpose
- Graduate Program in Cancer Biology, Emory University, Atlanta, GA, 30322, United States
| | - Anita H Corbett
- Department of Biology, Emory University, Atlanta, GA, 30322, United States; Winship Cancer Institute, Emory University, Atlanta, GA 30322, United States.
| | - Paul W Doetsch
- Graduate Program in Cancer Biology, Emory University, Atlanta, GA, 30322, United States; Department of Radiation Oncology, Emory University School of Medicine, Atlanta, GA, 30322, United States; Winship Cancer Institute, Emory University, Atlanta, GA 30322, United States; Department of Biochemistry, Emory University, Atlanta, GA, 30322, United States.
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37
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Esadze A, Rodriguez G, Cravens SL, Stivers JT. AP-Endonuclease 1 Accelerates Turnover of Human 8-Oxoguanine DNA Glycosylase by Preventing Retrograde Binding to the Abasic-Site Product. Biochemistry 2017; 56:1974-1986. [PMID: 28345889 DOI: 10.1021/acs.biochem.7b00017] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
A major product of oxidative DNA damage is 8-oxoguanine. In humans, 8-oxoguanine DNA glycosylase (hOGG1) facilitates removal of these lesions, producing an abasic (AP) site in the DNA that is subsequently incised by AP-endonuclease 1 (APE1). APE1 stimulates turnover of several glycosylases by accelerating rate-limiting product release. However, there have been conflicting accounts of whether hOGG1 follows a similar mechanism. In pre-steady-state kinetic measurements, we found that addition of APE1 had no effect on the rapid burst phase of 8-oxoguanine excision by hOGG1 but accelerated steady-state turnover (kcat) by ∼10-fold. The stimulation by APE1 required divalent cations, could be detected under multiple-turnover conditions using limiting concentrations of APE1, did not require flanking DNA surrounding the hOGG1 lesion site, and occurred efficiently even when the first 49 residues of APE1's N-terminus had been deleted. Stimulation by APE1 does not involve relief from product inhibition because thymine DNA glycosylase, an enzyme that binds more tightly to AP sites than hOGG1 does, could not effectively substitute for APE1. A stimulation mechanism involving stable protein-protein interactions between free APE1 and hOGG1, or the DNA-bound forms, was excluded using protein cross-linking assays. The combined results indicate a mechanism whereby dynamic excursions of hOGG1 from the AP site allow APE1 to invade the site and rapidly incise the phosphate backbone. This mechanism, which allows APE1 to access the AP site without forming specific interactions with the glycosylase, is a simple and elegant solution to passing along unstable intermediates in base excision repair.
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Affiliation(s)
- Alexandre Esadze
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine , 725 North Wolfe Street, Baltimore, Maryland 21205-2185, United States
| | - Gaddiel Rodriguez
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine , 725 North Wolfe Street, Baltimore, Maryland 21205-2185, United States
| | - Shannen L Cravens
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine , 725 North Wolfe Street, Baltimore, Maryland 21205-2185, United States
| | - James T Stivers
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine , 725 North Wolfe Street, Baltimore, Maryland 21205-2185, United States
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38
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Nakamura T, Murakami K, Tada H, Uehara Y, Nogami J, Maehara K, Ohkawa Y, Saitoh H, Nishitani H, Ono T, Nishi R, Yokoi M, Sakai W, Sugasawa K. Thymine DNA glycosylase modulates DNA damage response and gene expression by base excision repair-dependent and independent mechanisms. Genes Cells 2017; 22:392-405. [PMID: 28318075 DOI: 10.1111/gtc.12481] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Accepted: 02/01/2017] [Indexed: 02/04/2023]
Abstract
Thymine DNA glycosylase (TDG) is a base excision repair (BER) enzyme, which is implicated in correction of deamination-induced DNA mismatches, the DNA demethylation process and regulation of gene expression. Because of these pivotal roles associated, it is crucial to elucidate how the TDG functions are appropriately regulated in vivo. Here, we present evidence that the TDG protein undergoes degradation upon various types of DNA damage, including ultraviolet light (UV). The UV-induced degradation of TDG was dependent on proficiency in nucleotide excision repair and on CRL4CDT2 -mediated ubiquitination that requires a physical interaction between TDG and DNA polymerase clamp PCNA. Using the Tdg-deficient mouse embryonic fibroblasts, we found that ectopic expression of TDG compromised cellular survival after UV irradiation and repair of UV-induced DNA lesions. These negative effects on cellular UV responses were alleviated by introducing mutations in TDG that impaired its BER function. The expression of TDG induced a large-scale alteration in the gene expression profile independently of its DNA glycosylase activity, whereas a subset of genes was affected by the catalytic activity of TDG. Our results indicate the presence of BER-dependent and BER-independent functions of TDG, which are involved in regulation of cellular DNA damage responses and gene expression patterns.
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Affiliation(s)
- Tomohumi Nakamura
- Biosignal Research Center, Kobe University, Kobe, 657-8501, Japan.,Graduate School of Science, Kobe University, Kobe, 657-8501, Japan
| | - Kouichi Murakami
- Biosignal Research Center, Kobe University, Kobe, 657-8501, Japan.,Graduate School of Science, Kobe University, Kobe, 657-8501, Japan
| | - Haruto Tada
- Biosignal Research Center, Kobe University, Kobe, 657-8501, Japan.,Graduate School of Science, Kobe University, Kobe, 657-8501, Japan
| | - Yoshihiko Uehara
- Tohoku University Graduate School of Medicine, Sendai, 980-8575, Japan
| | - Jumpei Nogami
- Medical Institute of Bioregulation, Kyushu University, Fukuoka, 812-0054, Japan
| | - Kazumitsu Maehara
- Medical Institute of Bioregulation, Kyushu University, Fukuoka, 812-0054, Japan
| | - Yasuyuki Ohkawa
- Medical Institute of Bioregulation, Kyushu University, Fukuoka, 812-0054, Japan
| | - Hisato Saitoh
- Faculty of Advanced Science and Technology, Kumamoto University, Kumamoto, 860-8555, Japan
| | - Hideo Nishitani
- Graduate School of Life Science, University of Hyogo, Kamigori, 678-1297, Japan
| | - Tetsuya Ono
- Tohoku University Graduate School of Medicine, Sendai, 980-8575, Japan
| | - Ryotaro Nishi
- Biosignal Research Center, Kobe University, Kobe, 657-8501, Japan
| | - Masayuki Yokoi
- Biosignal Research Center, Kobe University, Kobe, 657-8501, Japan.,Graduate School of Science, Kobe University, Kobe, 657-8501, Japan
| | - Wataru Sakai
- Biosignal Research Center, Kobe University, Kobe, 657-8501, Japan.,Graduate School of Science, Kobe University, Kobe, 657-8501, Japan
| | - Kaoru Sugasawa
- Biosignal Research Center, Kobe University, Kobe, 657-8501, Japan.,Graduate School of Science, Kobe University, Kobe, 657-8501, Japan
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39
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Dustrude ET, Perez-Miller S, François-Moutal L, Moutal A, Khanna M, Khanna R. A single structurally conserved SUMOylation site in CRMP2 controls NaV1.7 function. Channels (Austin) 2017; 11:316-328. [PMID: 28277940 DOI: 10.1080/19336950.2017.1299838] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The neuronal collapsin response mediator protein 2 (CRMP2) undergoes several posttranslational modifications that codify its functions. Most recently, CRMP2 SUMOylation (addition of small ubiquitin like modifier (SUMO)) was identified as a key regulatory step within a modification program that codes for CRMP2 interaction with, and trafficking of, voltage-gated sodium channel NaV1.7. In this paper, we illustrate the utility of combining sequence alignment within protein families with structural analysis to identify, from several putative SUMOylation sites, those that are most likely to be biologically relevant. Co-opting this principle to CRMP2, we demonstrate that, of 3 sites predicted to be SUMOylated in CRMP2, only the lysine 374 site is a SUMOylation client. A reduction in NaV1.7 currents was the corollary of the loss of CRMP2 SUMOylation at this site. A 1.78-Å-resolution crystal structure of mouse CRMP2 was solved using X-ray crystallography, revealing lysine 374 as buried within the CRMP2 tetramer interface but exposed in the monomer. Since CRMP2 SUMOylation is dependent on phosphorylation, we postulate that this state forces CRMP2 toward a monomer, exposing the SUMO site and consequently, resulting in constitutive regulation of NaV1.7.
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Affiliation(s)
- Erik Thomas Dustrude
- a Department of Pharmacology, College of Medicine , University of Arizona , Tucson , AZ , USA
| | - Samantha Perez-Miller
- a Department of Pharmacology, College of Medicine , University of Arizona , Tucson , AZ , USA
| | - Liberty François-Moutal
- a Department of Pharmacology, College of Medicine , University of Arizona , Tucson , AZ , USA
| | - Aubin Moutal
- a Department of Pharmacology, College of Medicine , University of Arizona , Tucson , AZ , USA
| | - May Khanna
- a Department of Pharmacology, College of Medicine , University of Arizona , Tucson , AZ , USA
| | - Rajesh Khanna
- a Department of Pharmacology, College of Medicine , University of Arizona , Tucson , AZ , USA.,b Department of Anesthesiology, College of Medicine , University of Arizona , Tucson , AZ , USA.,c Neuroscience Graduate Interdisciplinary Program, College of Medicine , University of Arizona , Tucson , AZ , USA
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40
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Abstract
DNA methylation plays important roles in development and disease. Yet, only recently has the dynamic nature of this epigenetic mark via oxidation and DNA repair-mediated demethylation been recognized. A major conceptual challenge to the model that DNA methylation is reversible is the risk of genomic instability, which may come with widespread DNA repair activity. Here, we focus on recent advances in mechanisms of TET-TDG mediated demethylation and cellular strategies that avoid genomic instability. We highlight the recently discovered involvement of NEIL DNA glycosylases, which cooperate with TDG in oxidative demethylation to accelerate substrate turnover and promote the organized handover of harmful repair intermediates to maintain genome stability.
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Affiliation(s)
| | - Christof Niehrs
- Institute of Molecular Biology (IMB), Mainz, Germany.,Division of Molecular Embryology, German Cancer Research Center-Zentrum für Molekulare Biologie der Universität Heidelberg (DKFZ-ZMBH) Alliance, Heidelberg, Germany
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41
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Swartzlander DB, McPherson AJ, Powers HR, Limpose KL, Kuiper EG, Degtyareva NP, Corbett AH, Doetsch PW. Identification of SUMO modification sites in the base excision repair protein, Ntg1. DNA Repair (Amst) 2016; 48:51-62. [PMID: 27839712 DOI: 10.1016/j.dnarep.2016.10.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Revised: 10/25/2016] [Accepted: 10/27/2016] [Indexed: 12/19/2022]
Abstract
DNA damaging agents are a constant threat to genomes in both the nucleus and the mitochondria. To combat this threat, a suite of DNA repair pathways cooperate to repair numerous types of DNA damage. If left unrepaired, these damages can result in the accumulation of mutations which can lead to deleterious consequences including cancer and neurodegenerative disorders. The base excision repair (BER) pathway is highly conserved from bacteria to humans and is primarily responsible for the removal and subsequent repair of toxic and mutagenic oxidative DNA lesions. Although the biochemical steps that occur in the BER pathway have been well defined, little is known about how the BER machinery is regulated. The budding yeast, Saccharomyces cerevisiae is a powerful model system to biochemically and genetically dissect BER. BER is initiated by DNA N-glycosylases, such as S. cerevisiae Ntg1. Previous work demonstrates that Ntg1 is post-translationally modified by SUMO in response to oxidative DNA damage suggesting that this modification could modulate the function of Ntg1. In this study, we mapped the specific sites of SUMO modification within Ntg1 and identified the enzymes responsible for sumoylating/desumoylating Ntg1. Using a non-sumoylatable version of Ntg1, ntg1ΔSUMO, we performed an initial assessment of the functional impact of Ntg1 SUMO modification in the cellular response to DNA damage. Finally, we demonstrate that, similar to Ntg1, the human homologue of Ntg1, NTHL1, can also be SUMO-modified in response to oxidative stress. Our results suggest that SUMO modification of BER proteins could be a conserved mechanism to coordinate cellular responses to DNA damage.
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Affiliation(s)
- Daniel B Swartzlander
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, United States; Graduate Program in Genetics and Molecular Biology, Emory University School of Medicine, Atlanta, GA 30322, United States
| | - Annie J McPherson
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, United States; Graduate Program in Genetics and Molecular Biology, Emory University School of Medicine, Atlanta, GA 30322, United States
| | - Harry R Powers
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, United States
| | - Kristin L Limpose
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, United States; Graduate Program in Cancer Biology, Emory University School of Medicine, Atlanta, GA 30322, United States
| | - Emily G Kuiper
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, United States; Graduate Program in Biochemistry, Cell and Developmental Biology, Emory University School of Medicine, Atlanta, GA 30322, United States
| | - Natalya P Degtyareva
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, United States; Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA 30322, United States
| | - Anita H Corbett
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, United States; Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA 30322, United States.
| | - Paul W Doetsch
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, United States; Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA 30322, United States; Department of Radiation Oncology, Emory University School of Medicine, Atlanta, GA 30322, United States; Department of Hematology and Medical Oncology Emory University School of Medicine, Atlanta, GA 30322, United States.
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42
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Jin C, Qin T, Barton MC, Jelinek J, Issa JPJ. Minimal role of base excision repair in TET-induced global DNA demethylation in HEK293T cells. Epigenetics 2016; 10:1006-13. [PMID: 26440216 DOI: 10.1080/15592294.2015.1091145] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Abstract
Oxidation of 5-methylcytosine by TET family proteins can induce DNA replication-dependent (passive) DNA demethylation and base excision repair (BER)-based (active) DNA demethylation. The balance of active vs. passive TET-induced demethylation remains incompletely determined. In the context of large scale DNA demethylation, active demethylation may require massive induction of the DNA repair machinery and thus compromise genome stability. To study this issue, we constructed a tetracycline-controlled TET-induced global DNA demethylation system in HEK293T cells. Upon TET overexpression, we observed induction of DNA damage and activation of a DNA damage response; however, BER genes are not upregulated to promote DNA repair. Depletion of TDG (thymine DNA glycosylase) or APEX1 (apurinic/apyrimidinic endonuclease 1), two key BER enzymes, enhances rather than impairs global DNA demethylation, which can be explained by stimulated proliferation. By contrast, growth arrest dramatically blocks TET-induced global DNA demethylation. Thus, in the context of TET-induction in HEK293T cells, the DNA replication-dependent passive mechanism functions as the predominant pathway for global DNA demethylation. In the same context, BER-based active demethylation is markedly restricted by limited BER upregulation, thus potentially preventing a disastrous DNA damage response to extensive active DNA demethylation.
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Affiliation(s)
- Chunlei Jin
- a Fels Institute for Cancer Research and Molecular Biology; Temple University ; Philadelphia , PA USA.,b Department of Epigenetics and Molecular Carcinogenesis ; The University of Texas MD Anderson Cancer Center ; Houston , TX USA
| | - Taichun Qin
- c Department of Cancer Biology ; The University of Texas MD Anderson Cancer Center ; Houston , TX USA
| | - Michelle Craig Barton
- b Department of Epigenetics and Molecular Carcinogenesis ; The University of Texas MD Anderson Cancer Center ; Houston , TX USA
| | - Jaroslav Jelinek
- a Fels Institute for Cancer Research and Molecular Biology; Temple University ; Philadelphia , PA USA
| | - Jean-Pierre J Issa
- a Fels Institute for Cancer Research and Molecular Biology; Temple University ; Philadelphia , PA USA
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43
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Coey CT, Malik SS, Pidugu LS, Varney KM, Pozharski E, Drohat AC. Structural basis of damage recognition by thymine DNA glycosylase: Key roles for N-terminal residues. Nucleic Acids Res 2016; 44:10248-10258. [PMID: 27580719 PMCID: PMC5137436 DOI: 10.1093/nar/gkw768] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Revised: 08/20/2016] [Accepted: 08/22/2016] [Indexed: 11/13/2022] Open
Abstract
Thymine DNA Glycosylase (TDG) is a base excision repair enzyme functioning in DNA repair and epigenetic regulation. TDG removes thymine from mutagenic G·T mispairs arising from deamination of 5-methylcytosine (mC), and it processes other deamination-derived lesions including uracil (U). Essential for DNA demethylation, TDG excises 5-formylcytosine and 5-carboxylcytosine, derivatives of mC generated by Tet (ten-eleven translocation) enzymes. Here, we report structural and functional studies of TDG82-308, a new construct containing 29 more N-terminal residues than TDG111-308, the construct used for previous structures of DNA-bound TDG. Crystal structures and NMR experiments demonstrate that most of these N-terminal residues are disordered, for substrate- or product-bound TDG82-308 Nevertheless, G·T substrate affinity and glycosylase activity of TDG82-308 greatly exceeds that of TDG111-308 and is equivalent to full-length TDG. We report the first high-resolution structures of TDG in an enzyme-substrate complex, for G·U bound to TDG82-308 (1.54 Å) and TDG111-308 (1.71 Å), revealing new enzyme-substrate contacts, direct and water-mediated. We also report a structure of the TDG82-308 product complex (1.70 Å). TDG82-308 forms unique enzyme-DNA interactions, supporting its value for structure-function studies. The results advance understanding of how TDG recognizes and removes modified bases from DNA, particularly those resulting from deamination.
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Affiliation(s)
- Christopher T Coey
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Shuja S Malik
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Lakshmi S Pidugu
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Kristen M Varney
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD 21201, USA.,University of Maryland Marlene and Stewart Greenebaum Cancer Center, Baltimore, MD 21201, USA.,Center for Biomolecular Therapeutics, Institute for Bioscience and Biotechnology Research, Rockville, MD 20850, USA
| | - Edwin Pozharski
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD 21201, USA .,University of Maryland Marlene and Stewart Greenebaum Cancer Center, Baltimore, MD 21201, USA.,Center for Biomolecular Therapeutics, Institute for Bioscience and Biotechnology Research, Rockville, MD 20850, USA
| | - Alexander C Drohat
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD 21201, USA .,University of Maryland Marlene and Stewart Greenebaum Cancer Center, Baltimore, MD 21201, USA
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44
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Drohat AC, Coey CT. Role of Base Excision "Repair" Enzymes in Erasing Epigenetic Marks from DNA. Chem Rev 2016; 116:12711-12729. [PMID: 27501078 DOI: 10.1021/acs.chemrev.6b00191] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Base excision repair (BER) is one of several DNA repair pathways found in all three domains of life. BER counters the mutagenic and cytotoxic effects of damage that occurs continuously to the nitrogenous bases in DNA, and its critical role in maintaining genomic integrity is well established. However, BER also performs essential functions in processes other than DNA repair, where it acts on naturally modified bases in DNA. A prominent example is the central role of BER in mediating active DNA demethylation, a multistep process that erases the epigenetic mark 5-methylcytosine (5mC), and derivatives thereof, converting them back to cytosine. Herein, we review recent advances in the understanding of how BER mediates this critical component of epigenetic regulation in plants and animals.
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Affiliation(s)
- Alexander C Drohat
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine , Baltimore, Maryland 21201, United States
| | - Christopher T Coey
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine , Baltimore, Maryland 21201, United States
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45
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Abstract
Small ubiquitin-like modifiers (SUMOs) are essential for the regulation of several cellular processes and are potential therapeutic targets owing to their involvement in diseases such as cancer and Alzheimer disease. In the past decade, we have witnessed a rapid expansion of proteomic approaches for identifying sumoylated proteins, with recent advances in detecting site-specific sumoylation. In this Analysis, we combined all human SUMO proteomics data currently available into one cohesive database. We provide proteomic evidence for sumoylation of 3,617 proteins at 7,327 sumoylation sites, and insight into SUMO group modification by clustering the sumoylated proteins into functional networks. The data support sumoylation being a frequent protein modification (on par with other major protein modifications) with multiple nuclear functions, including in transcription, mRNA processing, DNA replication and the DNA-damage response.
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46
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Sridharan V, Azuma Y. SUMO-interacting motifs (SIMs) in Polo-like kinase 1-interacting checkpoint helicase (PICH) ensure proper chromosome segregation during mitosis. Cell Cycle 2016; 15:2135-2144. [PMID: 27230136 DOI: 10.1080/15384101.2016.1191713] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Polo-like kinase 1 (Plk1)-interacting checkpoint helicase (PICH) localizes at the centromere and is critical for proper chromosome segregation during mitosis. However, the precise molecular mechanism of PICH's centromeric localization and function at the centromere is not yet fully understood. Recently, using Xenopus egg extract assays, we showed that PICH is a promiscuous SUMO binding protein. To further determine the molecular consequence of PICH/SUMO interaction on PICH function, we identified 3 SUMO-interacting motifs (SIMs) on PICH and generated a SIM-deficient PICH mutant. Using the conditional expression of PICH in cells, we found distinct roles of PICH SIMs during mitosis. Although all SIMs are dispensable for PICH's localization on ultrafine anaphase DNA bridges, only SIM3 (third SIM, close to the C-terminus end of PICH) is critical for its centromeric localization. Intriguingly, the other 2 SIMs function in chromatin bridge prevention. With these results, we propose a novel SUMO-dependent regulation of PICH's function on mitotic centromeres.
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Affiliation(s)
- Vinidhra Sridharan
- a Department of Molecular Biosciences , University of Kansas , Lawrence , KS , USA
| | - Yoshiaki Azuma
- a Department of Molecular Biosciences , University of Kansas , Lawrence , KS , USA
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47
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Franz A, Ackermann L, Hoppe T. Ring of Change: CDC48/p97 Drives Protein Dynamics at Chromatin. Front Genet 2016; 7:73. [PMID: 27200082 PMCID: PMC4853748 DOI: 10.3389/fgene.2016.00073] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 04/16/2016] [Indexed: 12/31/2022] Open
Abstract
The dynamic composition of proteins associated with nuclear DNA is a fundamental property of chromosome biology. In the chromatin compartment dedicated protein complexes govern the accurate synthesis and repair of the genomic information and define the state of DNA compaction in vital cellular processes such as chromosome segregation or transcription. Unscheduled or faulty association of protein complexes with DNA has detrimental consequences on genome integrity. Consequently, the association of protein complexes with DNA is remarkably dynamic and can respond rapidly to cellular signaling events, which requires tight spatiotemporal control. In this context, the ring-like AAA+ ATPase CDC48/p97 emerges as a key regulator of protein complexes that are marked with ubiquitin or SUMO. Mechanistically, CDC48/p97 functions as a segregase facilitating the extraction of substrate proteins from the chromatin. As such, CDC48/p97 drives molecular reactions either by directed disassembly or rearrangement of chromatin-bound protein complexes. The importance of this mechanism is reflected by human pathologies linked to p97 mutations, including neurodegenerative disorders, oncogenesis, and premature aging. This review focuses on the recent insights into molecular mechanisms that determine CDC48/p97 function in the chromatin environment, which is particularly relevant for cancer and aging research.
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Affiliation(s)
- André Franz
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, Institute for Genetics, University of Cologne Cologne, Germany
| | - Leena Ackermann
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, Institute for Genetics, University of Cologne Cologne, Germany
| | - Thorsten Hoppe
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, Institute for Genetics, University of Cologne Cologne, Germany
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48
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Abstract
Base excision repair (BER) is an essential DNA repair pathway involved in the maintenance of genome stability and thus in the prevention of human diseases, such as premature aging, neurodegenerative diseases, and cancer. Protein posttranslational modifications (PTMs), including acetylation, methylation, phosphorylation, SUMOylation, and ubiquitylation, have emerged as important contributors in controlling cellular BER protein levels, enzymatic activities, protein-protein interactions, and protein cellular localization. These PTMs therefore play key roles in regulating the BER pathway and are consequently crucial for coordinating an efficient cellular DNA damage response. In this review, we summarize the presently available data on characterized PTMs of key BER proteins, the functional consequences of these modifications at the protein level, and also the impact on BER in vitro and in vivo.
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49
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Weber AR, Krawczyk C, Robertson AB, Kuśnierczyk A, Vågbø CB, Schuermann D, Klungland A, Schär P. Biochemical reconstitution of TET1-TDG-BER-dependent active DNA demethylation reveals a highly coordinated mechanism. Nat Commun 2016; 7:10806. [PMID: 26932196 PMCID: PMC4778062 DOI: 10.1038/ncomms10806] [Citation(s) in RCA: 145] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Accepted: 01/22/2016] [Indexed: 12/18/2022] Open
Abstract
Cytosine methylation in CpG dinucleotides is an epigenetic DNA modification dynamically established and maintained by DNA methyltransferases and demethylases. Molecular mechanisms of active DNA demethylation began to surface only recently with the discovery of the 5-methylcytosine (5mC)-directed hydroxylase and base excision activities of ten–eleven translocation (TET) proteins and thymine DNA glycosylase (TDG). This implicated a pathway operating through oxidation of 5mC by TET proteins, which generates substrates for TDG-dependent base excision repair (BER) that then replaces 5mC with C. Yet, direct evidence for a productive coupling of TET with BER has never been presented. Here we show that TET1 and TDG physically interact to oxidize and excise 5mC, and proof by biochemical reconstitution that the TET–TDG–BER system is capable of productive DNA demethylation. We show that the mechanism assures a sequential demethylation of symmetrically methylated CpGs, thereby avoiding DNA double-strand break formation but contributing to the mutability of methylated CpGs. Cytosine methylation is a dynamic DNA modification with the involvement of the base excision repair pathway suspected to be involved in demethylation. Here the authors show that TET1 and TDG interact to target modified bases and coordinate BER to avoid double strand breaks.
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Affiliation(s)
- Alain R Weber
- Department of Biomedicine, University of Basel, Mattenstrasse 28, Basel CH-4058, Switzerland
| | - Claudia Krawczyk
- Department of Biomedicine, University of Basel, Mattenstrasse 28, Basel CH-4058, Switzerland
| | - Adam B Robertson
- Department of Molecular Microbiology, Oslo University Hospital, Rikshospitalet, NO-0372 Oslo, Norway
| | - Anna Kuśnierczyk
- Proteomics and Metabolomics Core Facility, PROMEC, Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, NO-7489 Trondheim, Norway
| | - Cathrine B Vågbø
- Proteomics and Metabolomics Core Facility, PROMEC, Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, NO-7489 Trondheim, Norway
| | - David Schuermann
- Department of Biomedicine, University of Basel, Mattenstrasse 28, Basel CH-4058, Switzerland
| | - Arne Klungland
- Department of Molecular Microbiology, Oslo University Hospital, Rikshospitalet, NO-0372 Oslo, Norway
| | - Primo Schär
- Department of Biomedicine, University of Basel, Mattenstrasse 28, Basel CH-4058, Switzerland
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50
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McLaughlin D, Coey CT, Yang WC, Drohat AC, Matunis MJ. Characterizing Requirements for Small Ubiquitin-like Modifier (SUMO) Modification and Binding on Base Excision Repair Activity of Thymine-DNA Glycosylase in Vivo. J Biol Chem 2016; 291:9014-24. [PMID: 26917720 DOI: 10.1074/jbc.m115.706325] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Indexed: 12/12/2022] Open
Abstract
Thymine-DNA glycosylase (TDG) plays critical roles in DNA base excision repair and DNA demethylation. It has been proposed, based on structural studies and in vitro biochemistry, that sumoylation is required for efficient TDG enzymatic turnover following base excision. However, whether sumoylation is required for TDG activity in vivo has not previously been tested. We have developed an in vivo assay for TDG activity that takes advantage of its recently discovered role in DNA demethylation and selective recognition and repair of 5-carboxylcytosine. Using this assay, we investigated the role of sumoylation in regulating TDG activity through the use of TDG mutants defective for sumoylation and Small Ubiquitin-like Modifier (SUMO) binding and by altering TDG sumoylation through SUMO and SUMO protease overexpression experiments. Our findings indicate that sumoylation and SUMO binding are not essential for TDG-mediated excision and repair of 5-carboxylcytosine bases. Moreover, in vitro assays revealed that apurinic/apyrimidinic nuclease 1 provides nearly maximum stimulation of TDG processing of G·caC substrates. Thus, under our assay conditions, apurinic/apyrimidinic nuclease 1-mediated stimulation or other mechanisms sufficiently alleviate TDG product inhibition and promote its enzymatic turnover in vivo.
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Affiliation(s)
- Dylan McLaughlin
- From the Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland 21205 and
| | - Christopher T Coey
- the Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, Maryland 21201
| | - Wei-Chih Yang
- From the Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland 21205 and
| | - Alexander C Drohat
- the Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, Maryland 21201
| | - Michael J Matunis
- From the Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland 21205 and
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