1
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Zhao H, Han Y, Zhou P, Guan H, Gao S. Protein lysine crotonylation in cellular processions and disease associations. Genes Dis 2024; 11:101060. [PMID: 38957707 PMCID: PMC11217610 DOI: 10.1016/j.gendis.2023.06.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Revised: 05/05/2023] [Accepted: 06/27/2023] [Indexed: 07/04/2024] Open
Abstract
Protein lysine crotonylation (Kcr) is one conserved form of posttranslational modifications of proteins, which plays an important role in a series of cellular physiological and pathological processes. Lysine ε-amino groups are the primary sites of such modification, resulting in four-carbon planar lysine crotonylation that is structurally and functionally distinct from the acetylation of these residues. High levels of Kcr modifications have been identified on both histone and non-histone proteins. The present review offers an update on the research progression regarding protein Kcr modifications in biomedical contexts and provides a discussion of the mechanisms whereby Kcr modification governs a range of biological processes. In addition, given the importance of protein Kcr modification in disease onset and progression, the potential viability of Kcr regulators as therapeutic targets is elucidated.
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Affiliation(s)
- Hongling Zhao
- Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - Yang Han
- Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - Pingkun Zhou
- Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - Hua Guan
- Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - Shanshan Gao
- Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing 100850, China
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2
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Jordan MR, Oakley GG, Mayo LD, Balakrishnan L, Turchi JJ. The effect of replication protein A inhibition and post-translational modification on ATR kinase signaling. Sci Rep 2024; 14:19791. [PMID: 39187637 PMCID: PMC11347632 DOI: 10.1038/s41598-024-70589-y] [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: 06/12/2024] [Accepted: 08/19/2024] [Indexed: 08/28/2024] Open
Abstract
The ATR kinase responds to elevated levels of single-stranded DNA (ssDNA) to activate the G2/M checkpoint, regulate origin utilization, preserve fork stability, and allow DNA repair to ensure genome integrity. The intrinsic replication stress in cancer cells makes this pathway an attractive therapeutic target. The ssDNA that drives ATR signaling is sensed by the ssDNA-binding protein replication protein A (RPA), which acts as a platform for ATRIP recruitment and subsequent ATR activation by TopBP1. We have developed chemical RPA inhibitors (RPAi) that block RPA-ssDNA interactions (RPA-DBi) and RPA protein-protein interactions (RPA-PPIi); both activities are required for ATR activation. Here, we biochemically reconstitute the ATR kinase signaling pathway and demonstrate that RPA-DBi and RPA-PPIi abrogate ATR-dependent phosphorylation of target proteins with selectivity advantages over active site ATR inhibitors. We demonstrate that RPA post-translational modifications (PTMs) impact ATR kinase activation but do not alter sensitivity to RPAi. Specifically, phosphorylation of RPA32 and TopBP1 stimulate, while RPA70 acetylation does not affect ATR phosphorylation of target proteins. Collectively, this work reveals the RPAi mechanism of action to inhibit ATR signaling that can be regulated by RPA PTMs and offers insight into the anti-cancer activity of ATR pathway-targeted cancer therapeutics.
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Affiliation(s)
- Matthew R Jordan
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, 64202, USA
| | - Greg G Oakley
- Department of Oral Biology, University of Nebraska Medical Center, Lincoln, NE, 68583, USA
| | - Lindsey D Mayo
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Lata Balakrishnan
- Department of Biology, School of Science, Indiana University Indianapolis, Indianapolis, IN, 46202, USA
| | - John J Turchi
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, 64202, USA.
- NERx Biosciences Inc., Indianapolis, IN, 46202, USA.
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3
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Jordan MR, Oakley GG, Mayo LD, Balakrishnan L, Turchi JJ. The Effect of Replication Protein A Inhibition and Post-Translational Modification on ATR Kinase Signaling. RESEARCH SQUARE 2024:rs.3.rs-4570504. [PMID: 39108493 PMCID: PMC11302688 DOI: 10.21203/rs.3.rs-4570504/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 08/11/2024]
Abstract
The ATR kinase responds to elevated levels of single-stranded DNA (ssDNA) to activate the G2/M checkpoint, regulate origin utilization, preserve fork stability, and allow DNA repair towards ensuring genome integrity. The intrinsic replication stress in cancer cells makes this pathway an attractive therapeutic target. The ssDNA that drives ATR signaling is sensed by the ssDNA-binding protein replication protein A (RPA), which acts as a platform for ATRIP recruitment and subsequent ATR activation by TopBP1. We have developed chemical RPA inhibitors (RPAi) that block RPA-ssDNA interactions, termed RPA-DBi, and RPA protein-protein interactions, termed RPA-PPIi; both activities are required for ATR activation. Here, we employ a biochemically reconstituted ATR kinase signaling pathway and demonstrate that both RPA-DBi and RPA-PPIi abrogate ATR-dependent phosphorylation of downstream target proteins. We demonstrate that RPA post-translational modifications (PTMs) impact ATR kinase activation but do not alter sensitivity to RPAi. Specifically, phosphorylation of RPA32 and TopBP1 stimulate, while RPA70 acetylation has no effect on ATR phosphorylation of target proteins. Collectively, this work reveals the RPAi mechanism of action to inhibit ATR signaling that can be regulated by RPA PTMs and offers insight into the anti-cancer activity of ATR pathway targeted cancer therapeutics.
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Giovannini S, Weibel L, Schittek B, Sinnberg T, Schaller M, Lemberg C, Fehrenbacher B, Biesemeier A, Nordin R, Ivanova I, Kurz B, Svilenska T, Berger C, Bourquin JP, Kulik A, Fassihi H, Lehmann A, Sarkany R, Kobert N, van Toorn M, Marteijn JA, French LE, Rocken M, Vermeulen W, Kamenisch Y, Berneburg M. Skin cancer induction by the antimycotic drug voriconazole is caused by impaired DNA damage detection due to chromatin compaction. J Invest Dermatol 2024:S0022-202X(24)01920-1. [PMID: 39047967 DOI: 10.1016/j.jid.2024.03.050] [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: 06/21/2023] [Revised: 03/16/2024] [Accepted: 03/20/2024] [Indexed: 07/27/2024]
Abstract
Phototoxicity and skin cancer are severe adverse effects of the anti-fungal drug Voriconazole (VOR). These adverse effects resemble those seen in xeroderma pigmentosum (XP), caused by defective DNA nucleotide excision repair (NER), and we show that VOR decreases NER capacity. We show that VOR treatment does not perturb the expression of NER, or other DNA damage-related genes, but that VOR localizes to heterochromatin, in complexes containing histone acetyltransferase GCN5. Impairment of GCN5 binding to histone H3 reduced acetylation of H3, restricting damage-dependent chromatin unfolding, thereby reducing NER initiation. Restoration of H3 histone acetylation using histone deacetylase inhibitors (HDACi), rescued VOR-induced NER repression, thus offering a preventive therapeutic option. These findings underline the importance of DNA damage-dependent chromatin remodeling as an important prerequisite of functional DNA repair.
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Affiliation(s)
- Sara Giovannini
- Department of Dermatology, University Regensburg, Franz-Josef-Strauss-Allee 11, D-93053 Regensburg, Germany; Department of Dermatology, Eberhard Karls University, Liebermeisterstrasse 25, 72076 Tuebingen, Germany
| | - Lisa Weibel
- Department of Pediatric Dermatology and Children's Research Center, University Children's Hospital Zurich, Switzerland
| | - Birgit Schittek
- Department of Dermatology, Eberhard Karls University, Liebermeisterstrasse 25, 72076 Tuebingen, Germany
| | - Tobias Sinnberg
- Department of Dermatology, Eberhard Karls University, Liebermeisterstrasse 25, 72076 Tuebingen, Germany; Department of Dermatology, Venereology and Allergology, Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Martin Schaller
- Department of Dermatology, Eberhard Karls University, Liebermeisterstrasse 25, 72076 Tuebingen, Germany
| | - Christina Lemberg
- Section of Immunology, Vetsuisse Faculty, University of Zurich, Winterthurerstr. 266a, Zurich, Switzerland
| | - Birgit Fehrenbacher
- Department of Dermatology, Eberhard Karls University, Liebermeisterstrasse 25, 72076 Tuebingen, Germany
| | - Antje Biesemeier
- Division of Experimental Vitreoretinal Surgery and Core Facility for Electron Microscopy, Center for Ophthalmology, Schleichstr. 12/1, 72076 Tuebingen, Germany; Luxembourg Institute of Science and Technology (LIST), MRT - Materials Research and Technology Department, 41, rue du Brill, L-4422 Belvaux, Luxembourg
| | - Renate Nordin
- Department of Dermatology, Eberhard Karls University, Liebermeisterstrasse 25, 72076 Tuebingen, Germany
| | - Irina Ivanova
- Department of Dermatology, University Regensburg, Franz-Josef-Strauss-Allee 11, D-93053 Regensburg, Germany
| | - Bernadett Kurz
- Department of Dermatology, University Regensburg, Franz-Josef-Strauss-Allee 11, D-93053 Regensburg, Germany
| | - Teodora Svilenska
- Department of Dermatology, University Regensburg, Franz-Josef-Strauss-Allee 11, D-93053 Regensburg, Germany
| | - Christoph Berger
- Division of Infectious Diseases and Children's Research Center, University Children's Hospital Zurich, Switzerland
| | - Jean-Pierre Bourquin
- Department of Pediatric Oncology and Children's Research Center, University Children's Hospital Zurich, Switzerland
| | - Andreas Kulik
- Interfaculty Institute of Microbiology and Infection Medicine, Eberhard Karls University, Auf der Morgenstelle 28, 72076 Tuebingen, Germany
| | - Hiva Fassihi
- Guy's and St Thomas' NHS Trust, Guy's Hospital Great Maze Pond London SE1 9RT, UK
| | - Alan Lehmann
- Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton BN1 9RQ, UK
| | - Robert Sarkany
- Guy's and St Thomas' NHS Trust, Guy's Hospital Great Maze Pond London SE1 9RT, UK
| | - Nikita Kobert
- ICB Institute for Chemical and Bioengineering, ETH Zurich, Switzerland
| | - Marvin van Toorn
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Jurgen A Marteijn
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Lars E French
- Department of Dermatology and Allergy, University Hospital, Ludwig Maximilan University Munich, Munich, Germany; Dr. Philip Frost, Department of Dermatology and Cutaneous Surgery, University of Miami Miller School of Medicine, Miami, FL
| | - Martin Rocken
- Department of Dermatology, Eberhard Karls University, Liebermeisterstrasse 25, 72076 Tuebingen, Germany
| | - Wim Vermeulen
- Department of Molecular Genetics, Oncode Institute, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - York Kamenisch
- Department of Dermatology, University Regensburg, Franz-Josef-Strauss-Allee 11, D-93053 Regensburg, Germany; Department of Dermatology, Eberhard Karls University, Liebermeisterstrasse 25, 72076 Tuebingen, Germany
| | - Mark Berneburg
- Department of Dermatology, University Regensburg, Franz-Josef-Strauss-Allee 11, D-93053 Regensburg, Germany.
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5
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Fousek-Schuller VJ, Borgstahl GEO. The Intriguing Mystery of RPA Phosphorylation in DNA Double-Strand Break Repair. Genes (Basel) 2024; 15:167. [PMID: 38397158 PMCID: PMC10888239 DOI: 10.3390/genes15020167] [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: 12/20/2023] [Revised: 01/23/2024] [Accepted: 01/25/2024] [Indexed: 02/25/2024] Open
Abstract
Human Replication Protein A (RPA) was historically discovered as one of the six components needed to reconstitute simian virus 40 DNA replication from purified components. RPA is now known to be involved in all DNA metabolism pathways that involve single-stranded DNA (ssDNA). Heterotrimeric RPA comprises several domains connected by flexible linkers and is heavily regulated by post-translational modifications (PTMs). The structure of RPA has been challenging to obtain. Various structural methods have been applied, but a complete understanding of RPA's flexible structure, its function, and how it is regulated by PTMs has yet to be obtained. This review will summarize recent literature concerning how RPA is phosphorylated in the cell cycle, the structural analysis of RPA, DNA and protein interactions involving RPA, and how PTMs regulate RPA activity and complex formation in double-strand break repair. There are many holes in our understanding of this research area. We will conclude with perspectives for future research on how RPA PTMs control double-strand break repair in the cell cycle.
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Affiliation(s)
| | - Gloria E. O. Borgstahl
- Eppley Institute for Research in Cancer & Allied Diseases, UNMC, Omaha, NE 68198-6805, USA
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6
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Xiao Y, Jiang Z, Zhang M, Zhang X, Gan Q, Yang Y, Wu P, Feng X, Ni J, Dong X, She Q, Huang Q, Shen Y. The canonical single-stranded DNA-binding protein is not an essential replication factor but an RNA chaperon in Saccharolobus islandicus. iScience 2023; 26:108389. [PMID: 38034349 PMCID: PMC10684826 DOI: 10.1016/j.isci.2023.108389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 08/28/2023] [Accepted: 11/01/2023] [Indexed: 12/02/2023] Open
Abstract
Single-stranded DNA-binding proteins (SSBs) have been regarded as indispensable replication factors. Herein, we report that the genes encoding the canonical SSB (SisSSB) and the non-canonical SSB (SisDBP) in Saccharolobus islandicus REY15A are not essential for cell viability. Interestingly, at a lower temperature (55°C), the protein level of SisSSB increases and the growth of ΔSisssb and ΔSisssbΔSisdbp is retarded. SisSSB exhibits melting activity on dsRNA and DNA/RNA hybrid in vitro and is able to melt RNA hairpin in Escherichia coli. Furthermore, the core SisSSB domain is able to complement the absence of cold-shock proteins in E. coli. Importantly, these activities are conserved in the canonical SSBs from Crenarchaeota species that lack bacterial Csp homologs. Overall, our study has clarified the function of the archaeal canonical SSBs which do not function as a DNA-processing factor, but play a role in the processes requiring melting of dsRNA or DNA/RNA hybrid.
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Affiliation(s)
- Yuanxi Xiao
- CRISPR and Archaea Biology Research Center, State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao 266237, China
| | - Zhichao Jiang
- CRISPR and Archaea Biology Research Center, State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao 266237, China
| | - Mengqi Zhang
- CRISPR and Archaea Biology Research Center, State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao 266237, China
| | - Xuemei Zhang
- CRISPR and Archaea Biology Research Center, State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao 266237, China
| | - Qi Gan
- CRISPR and Archaea Biology Research Center, State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao 266237, China
| | - Yunfeng Yang
- CRISPR and Archaea Biology Research Center, State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao 266237, China
| | - Pengju Wu
- CRISPR and Archaea Biology Research Center, State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao 266237, China
| | - Xu Feng
- CRISPR and Archaea Biology Research Center, State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao 266237, China
| | - Jinfeng Ni
- CRISPR and Archaea Biology Research Center, State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao 266237, China
| | - Xiuzhu Dong
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Qunxin She
- CRISPR and Archaea Biology Research Center, State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao 266237, China
| | - Qihong Huang
- CRISPR and Archaea Biology Research Center, State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao 266237, China
| | - Yulong Shen
- CRISPR and Archaea Biology Research Center, State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao 266237, China
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7
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Qiu L, Xu W, Lu X, Chen F, Chen Y, Tian Y, Zhu Q, Liu X, Wang Y, Pei XH, Xu X, Zhang J, Zhu WG. The HDAC6-RNF168 axis regulates H2A/H2A.X ubiquitination to enable double-strand break repair. Nucleic Acids Res 2023; 51:9166-9182. [PMID: 37503842 PMCID: PMC10516627 DOI: 10.1093/nar/gkad631] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 06/24/2023] [Accepted: 07/17/2023] [Indexed: 07/29/2023] Open
Abstract
Histone deacetylase 6 (HDAC6) mediates DNA damage signaling by regulating the mismatch repair and nucleotide excision repair pathways. Whether HDAC6 also mediates DNA double-strand break (DSB) repair is unclear. Here, we report that HDAC6 negatively regulates DSB repair in an enzyme activity-independent manner. In unstressed cells, HDAC6 interacts with H2A/H2A.X to prevent its interaction with the E3 ligase RNF168. Upon sensing DSBs, RNF168 rapidly ubiquitinates HDAC6 at lysine 116, leading to HDAC6 proteasomal degradation and a restored interaction between RNF168 and H2A/H2A.X. H2A/H2A.X is ubiquitinated by RNF168, precipitating the recruitment of DSB repair factors (including 53BP1 and BRCA1) to chromatin and subsequent DNA repair. These findings reveal novel regulatory machinery based on an HDAC6-RNF168 axis that regulates the H2A/H2A.X ubiquitination status. Interfering with this axis might be leveraged to disrupt a key mechanism of cancer cell resistance to genotoxic damage and form a potential therapeutic strategy for cancer.
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Affiliation(s)
- Lingyu Qiu
- International Cancer Center, Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Marshall Laboratory of Biomedical Engineering, Department of Biochemistry and Molecular Biology, Shenzhen University Medical School, Shenzhen 518055, China
| | - Wenchao Xu
- International Cancer Center, Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Marshall Laboratory of Biomedical Engineering, Department of Biochemistry and Molecular Biology, Shenzhen University Medical School, Shenzhen 518055, China
| | - Xiaopeng Lu
- International Cancer Center, Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Marshall Laboratory of Biomedical Engineering, Department of Biochemistry and Molecular Biology, Shenzhen University Medical School, Shenzhen 518055, China
| | - Feng Chen
- International Cancer Center, Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Marshall Laboratory of Biomedical Engineering, Department of Biochemistry and Molecular Biology, Shenzhen University Medical School, Shenzhen 518055, China
| | - Yongcan Chen
- International Cancer Center, Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Marshall Laboratory of Biomedical Engineering, Department of Biochemistry and Molecular Biology, Shenzhen University Medical School, Shenzhen 518055, China
| | - Yuan Tian
- International Cancer Center, Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Marshall Laboratory of Biomedical Engineering, Department of Biochemistry and Molecular Biology, Shenzhen University Medical School, Shenzhen 518055, China
| | - Qian Zhu
- International Cancer Center, Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Marshall Laboratory of Biomedical Engineering, Department of Biochemistry and Molecular Biology, Shenzhen University Medical School, Shenzhen 518055, China
| | - Xiangyu Liu
- International Cancer Center, Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Marshall Laboratory of Biomedical Engineering, Department of Biochemistry and Molecular Biology, Shenzhen University Medical School, Shenzhen 518055, China
| | - Yongqing Wang
- Division of Rheumatology and Immunology, University of Toledo Medical Center, 3120 Glendale Avenue, Toledo 43614, OH, USA
| | - Xin-Hai Pei
- Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Marshall Laboratory of Biomedical Engineering, Department of Anatomy and Histology, Shenzhen University Medical School, Shenzhen 518055, China
| | - Xingzhi Xu
- International Cancer Center, Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Marshall Laboratory of Biomedical Engineering, Department of Cell Biology and Medical Genetics, Shenzhen University Medical School, Shenzhen 518055, China
| | - Jun Zhang
- International Cancer Center, Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Marshall Laboratory of Biomedical Engineering, Department of Biochemistry and Molecular Biology, Shenzhen University Medical School, Shenzhen 518055, China
| | - Wei-Guo Zhu
- International Cancer Center, Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Marshall Laboratory of Biomedical Engineering, Department of Biochemistry and Molecular Biology, Shenzhen University Medical School, Shenzhen 518055, China
- School of Basic Medical Sciences, Wannan Medical College, Wuhu, Anhui 241002, China
- Department of Biochemistry and Biophysics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
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8
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Huang F, Luo X, Ou Y, Gao Z, Tang Q, Chu Z, Zhu X, He Y. Control of histone demethylation by nuclear-localized α-ketoglutarate dehydrogenase. Science 2023; 381:eadf8822. [PMID: 37440635 DOI: 10.1126/science.adf8822] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 05/19/2023] [Indexed: 07/15/2023]
Abstract
Methylations on nucleosomal histones play fundamental roles in regulating eukaryotic transcription. Jumonji C domain-containing histone demethylases (JMJs) dynamically control the level of histone methylations. However, how JMJ activity is generally regulated is unknown. We found that the tricarboxylic acid cycle-associated enzyme α-ketoglutarate (α-KG) dehydrogenase (KGDH) entered the nucleus, where it interacted with various JMJs to regulate α-KG-dependent histone demethylations by JMJs, and thus controlled genome-wide gene expression in plants. We show that nuclear targeting is regulated by environmental signals and that KGDH is enriched at thousands of loci in Arabidopsis thaliana. Chromatin-bound KGDH catalyzes α-KG decarboxylation and thus may limit its local availability to KGDH-coupled JMJs, inhibiting histone demethylation. Thus, our results uncover a regulatory mechanism for histone demethylations by JMJs.
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Affiliation(s)
- Fei Huang
- National Key Laboratory of Wheat Improvement, Peking-Tsinghua Center for Life Sciences, School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences (CAS), Shanghai 201602, China
| | - Xiao Luo
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences (CAS), Shanghai 201602, China
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Shandong 261325, China
| | - Yang Ou
- National Key Laboratory of Wheat Improvement, Peking-Tsinghua Center for Life Sciences, School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences (CAS), Shanghai 201602, China
| | - Zhaoxu Gao
- National Key Laboratory of Wheat Improvement, Peking-Tsinghua Center for Life Sciences, School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
| | - Qiming Tang
- National Key Laboratory for Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, CAS, Shanghai, 200032, China
| | - Zhenzhen Chu
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences (CAS), Shanghai 201602, China
| | - Xinguang Zhu
- National Key Laboratory for Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, CAS, Shanghai, 200032, China
| | - Yuehui He
- National Key Laboratory of Wheat Improvement, Peking-Tsinghua Center for Life Sciences, School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
- Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences (CAS), Shanghai 201602, China
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Shandong 261325, China
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9
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Gan X, Zhang Y, Jiang D, Shi J, Zhao H, Xie C, Wang Y, Xu J, Zhang X, Cai G, Wang H, Huang J, Chen X. Proper RPA acetylation promotes accurate DNA replication and repair. Nucleic Acids Res 2023; 51:5565-5583. [PMID: 37140030 PMCID: PMC10287905 DOI: 10.1093/nar/gkad291] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Revised: 04/06/2023] [Accepted: 04/12/2023] [Indexed: 05/05/2023] Open
Abstract
The single-stranded DNA (ssDNA) binding protein complex RPA plays a critical role in promoting DNA replication and multiple DNA repair pathways. However, how RPA is regulated to achieve its functions precisely in these processes remains elusive. Here, we found that proper acetylation and deacetylation of RPA are required to regulate RPA function in promoting high-fidelity DNA replication and repair. We show that yeast RPA is acetylated on multiple conserved lysines by the acetyltransferase NuA4 upon DNA damage. Mimicking constitutive RPA acetylation or blocking its acetylation causes spontaneous mutations with the signature of micro-homology-mediated large deletions or insertions. In parallel, improper RPA acetylation/deacetylation impairs DNA double-strand break (DSB) repair by the accurate gene conversion or break-induced replication while increasing the error-prone repair by single-strand annealing or alternative end joining. Mechanistically, we show that proper acetylation and deacetylation of RPA ensure its normal nuclear localization and ssDNA binding ability. Importantly, mutation of the equivalent residues in human RPA1 also impairs RPA binding on ssDNA, leading to attenuated RAD51 loading and homologous recombination repair. Thus, timely RPA acetylation and deacetylation likely represent a conserved mechanism promoting high-fidelity replication and repair while discriminating the error-prone repair mechanisms in eukaryotes.
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Affiliation(s)
- Xiaoli Gan
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Frontier Science Centre of Immunology and Metabolism, Wuhan University, Wuhan, Hubei 430072, China
| | - Yueyue Zhang
- The First Affiliated Hospital of USTC, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230001, China
| | - Donghao Jiang
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Frontier Science Centre of Immunology and Metabolism, Wuhan University, Wuhan, Hubei 430072, China
| | - Jingyao Shi
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Frontier Science Centre of Immunology and Metabolism, Wuhan University, Wuhan, Hubei 430072, China
| | - Han Zhao
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Frontier Science Centre of Immunology and Metabolism, Wuhan University, Wuhan, Hubei 430072, China
| | - Chengyu Xie
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Frontier Science Centre of Immunology and Metabolism, Wuhan University, Wuhan, Hubei 430072, China
| | - Yanyan Wang
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Frontier Science Centre of Immunology and Metabolism, Wuhan University, Wuhan, Hubei 430072, China
| | - Jingyan Xu
- Department of Hematology, Nanjing Drum Tower Hospital, the Affiliated Hospital of Nanjing University Medical School, Nanjing, China
| | - Xinghua Zhang
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Frontier Science Centre of Immunology and Metabolism, Wuhan University, Wuhan, Hubei 430072, China
| | - Gang Cai
- The First Affiliated Hospital of USTC, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230001, China
| | - Hailong Wang
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Jun Huang
- The MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Xuefeng Chen
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Frontier Science Centre of Immunology and Metabolism, Wuhan University, Wuhan, Hubei 430072, China
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10
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Pinto ÉSM, Krause MJ, Dorn M, Feltes BC. The nucleotide excision repair proteins through the lens of molecular dynamics simulations. DNA Repair (Amst) 2023; 127:103510. [PMID: 37148846 DOI: 10.1016/j.dnarep.2023.103510] [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: 10/26/2022] [Revised: 04/07/2023] [Accepted: 04/23/2023] [Indexed: 05/08/2023]
Abstract
Mutations that affect the proteins responsible for the nucleotide excision repair (NER) pathway can lead to diseases such as xeroderma pigmentosum, trichothiodystrophy, Cockayne syndrome, and Cerebro-oculo-facio-skeletal syndrome. Hence, understanding their molecular behavior is needed to elucidate these diseases' phenotypes and how the NER pathway is organized and coordinated. Molecular dynamics techniques enable the study of different protein conformations, adaptable to any research question, shedding light on the dynamics of biomolecules. However, as important as they are, molecular dynamics studies focused on DNA repair pathways are still becoming more widespread. Currently, there are no review articles compiling the advancements made in molecular dynamics approaches applied to NER and discussing: (i) how this technique is currently employed in the field of DNA repair, focusing on NER proteins; (ii) which technical setups are being employed, their strengths and limitations; (iii) which insights or information are they providing to understand the NER pathway or NER-associated proteins; (iv) which open questions would be suited for this technique to answer; and (v) where can we go from here. These questions become even more crucial considering the numerous 3D structures published regarding the NER pathway's proteins in recent years. In this work, we tackle each one of these questions, revising and critically discussing the results published in the context of the NER pathway.
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Affiliation(s)
| | - Mathias J Krause
- Institute for Applied and Numerical Mathematics, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Márcio Dorn
- Center for Biotechnology, Federal University of Rio Grande do Sul, RS, Brazil; Institute of Informatics, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil; National Institute of Science and Technology - Forensic Science, Porto Alegre, RS, Brazil
| | - Bruno César Feltes
- Institute of Informatics, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil
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11
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Krasikova YS, Lavrik OI, Rechkunova NI. The XPA Protein-Life under Precise Control. Cells 2022; 11:cells11233723. [PMID: 36496984 PMCID: PMC9739396 DOI: 10.3390/cells11233723] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 11/15/2022] [Accepted: 11/16/2022] [Indexed: 11/24/2022] Open
Abstract
Nucleotide excision repair (NER) is a central DNA repair pathway responsible for removing a wide variety of DNA-distorting lesions from the genome. The highly choreographed cascade of core NER reactions requires more than 30 polypeptides. The xeroderma pigmentosum group A (XPA) protein plays an essential role in the NER process. XPA interacts with almost all NER participants and organizes the correct NER repair complex. In the absence of XPA's scaffolding function, no repair process occurs. In this review, we briefly summarize our current knowledge about the XPA protein structure and analyze the formation of contact with its protein partners during NER complex assembling. We focus on different ways of regulation of the XPA protein's activity and expression and pay special attention to the network of post-translational modifications. We also discuss the data that is not in line with the currently accepted hypothesis about the functioning of the XPA protein.
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Affiliation(s)
- Yuliya S. Krasikova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Olga I. Lavrik
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Nadejda I. Rechkunova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
- Correspondence:
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12
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Hu C, Wallace N. Beta HPV Deregulates Double-Strand Break Repair. Viruses 2022; 14:v14050948. [PMID: 35632690 PMCID: PMC9146468 DOI: 10.3390/v14050948] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 04/27/2022] [Accepted: 04/28/2022] [Indexed: 02/04/2023] Open
Abstract
Beta human papillomavirus (beta HPV) infections are common in adults. Certain types of beta HPVs are associated with nonmelanoma skin cancer (NMSC) in immunocompromised individuals. However, whether beta HPV infections promote NMSC in the immunocompetent population is unclear. They have been hypothesized to increase genomic instability stemming from ultraviolet light exposure by disrupting DNA damage responses. Implicit in this hypothesis is that the virus encodes one or more proteins that impair DNA repair signaling. Fluorescence-based reporters, next-generation sequencing, and animal models have been used to test this primarily in cells expressing beta HPV E6/E7. Of the two, beta HPV E6 appears to have the greatest ability to increase UV mutagenesis, by attenuating two major double-strand break (DSB) repair pathways, homologous recombination, and non-homologous end-joining. Here, we review this dysregulation of DSB repair and emerging approaches that can be used to further these efforts.
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13
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Li W, Jones K, Burke TJ, Hossain MA, Lariscy L. Epigenetic Regulation of Nucleotide Excision Repair. Front Cell Dev Biol 2022; 10:847051. [PMID: 35465333 PMCID: PMC9023881 DOI: 10.3389/fcell.2022.847051] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2022] [Accepted: 03/24/2022] [Indexed: 12/30/2022] Open
Abstract
Genomic DNA is constantly attacked by a plethora of DNA damaging agents both from endogenous and exogenous sources. Nucleotide excision repair (NER) is the most versatile repair pathway that recognizes and removes a wide range of bulky and/or helix-distorting DNA lesions. Even though the molecular mechanism of NER is well studied through in vitro system, the NER process inside the cell is more complicated because the genomic DNA in eukaryotes is tightly packaged into chromosomes and compacted into a nucleus. Epigenetic modifications regulate gene activity and expression without changing the DNA sequence. The dynamics of epigenetic regulation play a crucial role during the in vivo NER process. In this review, we summarize recent advances in our understanding of the epigenetic regulation of NER.
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14
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Feltes BC. Every protagonist has a sidekick: Structural aspects of human xeroderma pigmentosum-binding proteins in nucleotide excision repair. Protein Sci 2021; 30:2187-2205. [PMID: 34420242 DOI: 10.1002/pro.4173] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 08/13/2021] [Accepted: 08/17/2021] [Indexed: 12/30/2022]
Abstract
The seven xeroderma pigmentosum proteins (XPps), XPA-XPG, coordinate the nucleotide excision repair (NER) pathway, promoting the excision of DNA lesions caused by exposition to ionizing radiation, majorly from ultraviolet light. Significant efforts are made to investigate NER since mutations in any of the seven XPps may cause the xeroderma pigmentosum and trichothiodystrophy diseases. However, these proteins collaborate with other pivotal players in all known NER steps to accurately exert their purposes. Therefore, in the old and ever-evolving field of DNA repair, it is imperative to reexamine and describe their structures to understand NER properly. This work provides an up-to-date review of the protein structural aspects of the closest partners that directly interact and influence XPps: RAD23B, CETN2, DDB1, RPA (RPA70, 32, and 14), p8 (GTF2H5), and ERCC1. Structurally and functionally vital domains, regions, and critical residues are reexamined, providing structural lessons and perspectives about these indispensable proteins in the NER and other DNA repair pathways. By gathering all data related to the major human xeroderma pigmentosum-interacting proteins, this review will aid newcomers on the subject and guide structural and functional future studies.
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Affiliation(s)
- Bruno César Feltes
- Department of Theoretical Informatics, Institute of Informatics, Department of Theoretical Informatics, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
- Department of Genetics, Institute of Bioscience, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
- Department of Biophysics, Institute of Bioscience, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
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15
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Cheng X, Côté V, Côté J. NuA4 and SAGA acetyltransferase complexes cooperate for repair of DNA breaks by homologous recombination. PLoS Genet 2021; 17:e1009459. [PMID: 34228704 PMCID: PMC8284799 DOI: 10.1371/journal.pgen.1009459] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 07/16/2021] [Accepted: 06/21/2021] [Indexed: 12/30/2022] Open
Abstract
Chromatin modifying complexes play important yet not fully defined roles in DNA repair processes. The essential NuA4 histone acetyltransferase (HAT) complex is recruited to double-strand break (DSB) sites and spreads along with DNA end resection. As predicted, NuA4 acetylates surrounding nucleosomes upon DSB induction and defects in its activity correlate with altered DNA end resection and Rad51 recombinase recruitment. Importantly, we show that NuA4 is also recruited to the donor sequence during recombination along with increased H4 acetylation, indicating a direct role during strand invasion/D-loop formation after resection. We found that NuA4 cooperates locally with another HAT, the SAGA complex, during DSB repair as their combined action is essential for DNA end resection to occur. This cooperation of NuA4 and SAGA is required for recruitment of ATP-dependent chromatin remodelers, targeted acetylation of repair factors and homologous recombination. Our work reveals a multifaceted and conserved cooperation mechanism between acetyltransferase complexes to allow repair of DNA breaks by homologous recombination. DNA double-strand breaks (DSBs) are among the most dangerous types of DNA lesions as they can produce genomic instability that leads to cancer and genetic diseases. It is therefore crucial to understand the precise molecular mechanisms used by cells to detect and repair this type of damages. Homologous recombination using sister chromatid as template is the most accurate pathway to repair these breaks but has to occur within the context of the DNA compacted structure in chromosomes. Here, we show that two enzymes, NuA4 and SAGA, that acetylate the structural components of chromosomes in the vicinity of the DNA breaks are together essential for recombination-mediated repair to occur. We found that they are recruited at an early step after damage detection and their action allows subsequent remodeling of local structural organisation by other enzymes, providing DNA access to the recombination machinery. These results highlight the cooperation of enzymes for a same goal, providing robustness in the repair process as only the loss of both leads to major defects.
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Affiliation(s)
- Xue Cheng
- St-Patrick Research Group in Basic Oncology, Laval University Cancer Research Center, Oncology Division of CHU de Québec-Université Laval Research Center, Quebec City, Canada
| | - Valérie Côté
- St-Patrick Research Group in Basic Oncology, Laval University Cancer Research Center, Oncology Division of CHU de Québec-Université Laval Research Center, Quebec City, Canada
| | - Jacques Côté
- St-Patrick Research Group in Basic Oncology, Laval University Cancer Research Center, Oncology Division of CHU de Québec-Université Laval Research Center, Quebec City, Canada
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16
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Hou JY, Zhou L, Li JL, Wang DP, Cao JM. Emerging roles of non-histone protein crotonylation in biomedicine. Cell Biosci 2021; 11:101. [PMID: 34059135 PMCID: PMC8166067 DOI: 10.1186/s13578-021-00616-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 05/22/2021] [Indexed: 12/25/2022] Open
Abstract
Crotonylation of proteins is a newly found type of post-translational modifications (PTMs) which occurs leadingly on the lysine residue, namely, lysine crotonylation (Kcr). Kcr is conserved and is regulated by a series of enzymes and co-enzymes including lysine crotonyltransferase (writer), lysine decrotonylase (eraser), certain YEATS proteins (reader), and crotonyl-coenzyme A (donor). Histone Kcr has been substantially studied since 2011, but the Kcr of non-histone proteins is just an emerging field since its finding in 2017. Recent advances in the identification and quantification of non-histone protein Kcr by mass spectrometry have increased our understanding of Kcr. In this review, we summarized the main proteomic characteristics of non-histone protein Kcr and discussed its biological functions, including gene transcription, DNA damage response, enzymes regulation, metabolic pathways, cell cycle, and localization of heterochromatin in cells. We further proposed the performance of non-histone protein Kcr in diseases and the prospect of Kcr manipulators as potential therapeutic candidates in the diseases.
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Affiliation(s)
- Jia-Yi Hou
- Key Laboratory of Cellular Physiology At Shanxi Medical University, Ministry of Education, Key Laboratory of Cellular Physiology of Shanxi Province, and the Department of Physiology, Shanxi Medical University, Taiyuan, China.,Department of Clinical Laboratory, Shanxi Provincial Academy of Traditional Chinese Medicine, Taiyuan, China
| | - Lan Zhou
- Key Laboratory of Cellular Physiology At Shanxi Medical University, Ministry of Education, Key Laboratory of Cellular Physiology of Shanxi Province, and the Department of Physiology, Shanxi Medical University, Taiyuan, China
| | - Jia-Lei Li
- Key Laboratory of Cellular Physiology At Shanxi Medical University, Ministry of Education, Key Laboratory of Cellular Physiology of Shanxi Province, and the Department of Physiology, Shanxi Medical University, Taiyuan, China
| | - De-Ping Wang
- Key Laboratory of Cellular Physiology At Shanxi Medical University, Ministry of Education, Key Laboratory of Cellular Physiology of Shanxi Province, and the Department of Physiology, Shanxi Medical University, Taiyuan, China
| | - Ji-Min Cao
- Key Laboratory of Cellular Physiology At Shanxi Medical University, Ministry of Education, Key Laboratory of Cellular Physiology of Shanxi Province, and the Department of Physiology, Shanxi Medical University, Taiyuan, China.
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17
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Aguado-Barrera ME, Martínez-Calvo L, Fernández-Tajes J, Calvo-Crespo P, Taboada-Valladares B, Lobato-Busto R, Gómez-Caamaño A, Vega A. Validation of Polymorphisms Associated with the Risk of Radiation-Induced Oesophagitis in an Independent Cohort of Non-Small-Cell Lung Cancer Patients. Cancers (Basel) 2021; 13:cancers13061447. [PMID: 33810047 PMCID: PMC8004670 DOI: 10.3390/cancers13061447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 03/12/2021] [Accepted: 03/17/2021] [Indexed: 11/16/2022] Open
Abstract
Simple Summary Genetic variants identified in association with radiation therapy side effects in non-small-cell lung cancer patients require an independent validation. Therefore, the aim of our study was to replicate, in an independent cohort, the analyses of previously published studies associating single-nucleotide polymorphisms with radiation-induced oesophagitis. Following the original models, 2 of the 18 variants associated with radiation-induced oesophagitis in non-small-cell lung cancer patients were confirmed. Furthermore, we meta-analysed our cohort together with those of the reference studies. Twelve variants located in genes of inflammation and DNA double-strand break repair pathways remained associated with oesophagitis. These variants could be included in models for clinical prediction of radiation-induced oesophagitis to evaluate their performance. Abstract Several studies have identified single-nucleotide polymorphisms (SNPs) associated with adverse effects in non-small-cell lung cancer (NSCLC) patients treated with radiation therapy. Here, using an independent cohort, we aimed to validate the reported associations. We selected 23 SNPs in 17 genes previously associated with radiation-induced oesophagitis for validation in a cohort of 178 Spanish NSCLC patients. Of them, 18 SNPs were finally analysed, following the methods described in the original published studies. Two SNPs replicated their association with radiation-induced oesophagitis (rs7165790 located in the BLM gene: odds ratio (OR) = 0.16, 95% CI = 0.04–0.65, p-value = 0.010; rs4772468 at FGF14: OR = 4.36, 95% CI = 1.15–16.46, p-value = 0.029). The SNP rs2868371 at HSPB1 was also validated but displayed an opposite effect to the formerly described (OR = 3.72; 95% CI = 1.49–9.25; p-value = 0.004). Additionally, we tested a meta-analytic approach including our results and the previous datasets reported in the referenced publications. Twelve SNPs (including the two previously validated) retained their statistically significant association with radiation-induced oesophagitis. This study strengthens the role of inflammation and DNA double-strand break repair pathways in the risk prediction of developing radiation-induced oesophagitis in NSCLC patients. The validated variants are good candidates to be evaluated in risk prediction models for patient stratification based on their radiation susceptibility.
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Affiliation(s)
- Miguel E. Aguado-Barrera
- Grupo Genética en Cáncer y Enfermedades Raras, Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), Fundación Pública Galega de Medicina Xenómica (FPGMX), 15706 Santiago de Compostela, A Coruña, Spain; (M.E.A.-B.); (L.M.-C.); (J.F.-T.)
| | - Laura Martínez-Calvo
- Grupo Genética en Cáncer y Enfermedades Raras, Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), Fundación Pública Galega de Medicina Xenómica (FPGMX), 15706 Santiago de Compostela, A Coruña, Spain; (M.E.A.-B.); (L.M.-C.); (J.F.-T.)
| | - Juan Fernández-Tajes
- Grupo Genética en Cáncer y Enfermedades Raras, Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), Fundación Pública Galega de Medicina Xenómica (FPGMX), 15706 Santiago de Compostela, A Coruña, Spain; (M.E.A.-B.); (L.M.-C.); (J.F.-T.)
| | - Patricia Calvo-Crespo
- Department of Radiation Oncology Hospital Clínico Universitario de Santiago de Compostela, Servizo Galego de Saúde (SERGAS), Grupo Genética en Cáncer y Enfermedades Raras, Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), 15706 Santiago de Compostela, A Coruña, Spain; (P.C.-C.); (B.T.-V.)
| | - Begoña Taboada-Valladares
- Department of Radiation Oncology Hospital Clínico Universitario de Santiago de Compostela, Servizo Galego de Saúde (SERGAS), Grupo Genética en Cáncer y Enfermedades Raras, Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), 15706 Santiago de Compostela, A Coruña, Spain; (P.C.-C.); (B.T.-V.)
| | - Ramón Lobato-Busto
- Department of Medical Physics Hospital Clínico Universitario de Santiago de Compostela Servizo Galego de Saúde (SERGAS), 15706 Santiago de Compostela, A Coruña, Spain;
| | - Antonio Gómez-Caamaño
- Department of Radiation Oncology, Hospital Clínico Universitario de Santiago de Compostela, Servizo Galego de Saúde (SERGAS), 15706 Santiago de Compostela, A Coruña, Spain;
| | - Ana Vega
- Grupo Genética en Cáncer y Enfermedades Raras, Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), Fundación Pública Galega de Medicina Xenómica (FPGMX), Biomedical Network on Rare Diseases (CIBERER), 15706 Santiago de Compostela, A Coruña, Spain
- Correspondence: ; Tel.: +34-981-95-51-94
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18
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Li S, Shi B, Liu X, An HX. Acetylation and Deacetylation of DNA Repair Proteins in Cancers. Front Oncol 2020; 10:573502. [PMID: 33194676 PMCID: PMC7642810 DOI: 10.3389/fonc.2020.573502] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 09/17/2020] [Indexed: 12/12/2022] Open
Abstract
Hundreds of DNA repair proteins coordinate together to remove the diverse damages for ensuring the genomic integrity and stability. The repair system is an extensive network mainly encompassing cell cycle arrest, chromatin remodeling, various repair pathways, and new DNA fragment synthesis. Acetylation on DNA repair proteins is a dynamic epigenetic modification orchestrated by lysine acetyltransferases (HATs) and lysine deacetylases (HDACs), which dramatically affects the protein functions through multiple mechanisms, such as regulation of DNA binding ability, protein activity, post-translational modification (PTM) crosstalk, and protein–protein interaction. Accumulating evidence has indicated that the aberrant acetylation of DNA repair proteins contributes to the dysfunction of DNA repair ability, the pathogenesis and progress of cancer, as well as the chemosensitivity of cancer cells. In the present scenario, targeting epigenetic therapy is being considered as a promising method at par with the conventional cancer therapeutic strategies. This present article provides an overview of the recent progress in the functions and mechanisms of acetylation on DNA repair proteins involved in five major repair pathways, which warrants the possibility of regulating acetylation on repair proteins as a therapeutic target in cancers.
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Affiliation(s)
- Shiqin Li
- Department of Medical Oncology, Xiang'an Hospital of Xiamen University, Xiamen, China
| | - Bingbing Shi
- Department of Medical Oncology, Xiang'an Hospital of Xiamen University, Xiamen, China
| | - Xinli Liu
- Department of Medical Oncology, Xiang'an Hospital of Xiamen University, Xiamen, China
| | - Han-Xiang An
- Department of Medical Oncology, Xiang'an Hospital of Xiamen University, Xiamen, China
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19
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Caldwell CC, Spies M. Dynamic elements of replication protein A at the crossroads of DNA replication, recombination, and repair. Crit Rev Biochem Mol Biol 2020; 55:482-507. [PMID: 32856505 PMCID: PMC7821911 DOI: 10.1080/10409238.2020.1813070] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 08/18/2020] [Accepted: 08/18/2020] [Indexed: 01/19/2023]
Abstract
The heterotrimeric eukaryotic Replication protein A (RPA) is a master regulator of numerous DNA metabolic processes. For a long time, it has been viewed as an inert protector of ssDNA and a platform for assembly of various genome maintenance and signaling machines. Later, the modular organization of the RPA DNA binding domains suggested a possibility for dynamic interaction with ssDNA. This modular organization has inspired several models for the RPA-ssDNA interaction that aimed to explain how RPA, the high-affinity ssDNA binding protein, is replaced by the downstream players in DNA replication, recombination, and repair that bind ssDNA with much lower affinity. Recent studies, and in particular single-molecule observations of RPA-ssDNA interactions, led to the development of a new model for the ssDNA handoff from RPA to a specific downstream factor where not only stability and structural rearrangements but also RPA conformational dynamics guide the ssDNA handoff. Here we will review the current knowledge of the RPA structure, its dynamic interaction with ssDNA, and how RPA conformational dynamics may be influenced by posttranslational modification and proteins that interact with RPA, as well as how RPA dynamics may be harnessed in cellular decision making.
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Affiliation(s)
- Colleen C. Caldwell
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA 52242
| | - Maria Spies
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA 52242
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20
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Dueva R, Iliakis G. Replication protein A: a multifunctional protein with roles in DNA replication, repair and beyond. NAR Cancer 2020; 2:zcaa022. [PMID: 34316690 PMCID: PMC8210275 DOI: 10.1093/narcan/zcaa022] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 08/23/2020] [Accepted: 08/27/2020] [Indexed: 02/07/2023] Open
Abstract
Single-stranded DNA (ssDNA) forms continuously during DNA replication and is an important intermediate during recombination-mediated repair of damaged DNA. Replication protein A (RPA) is the major eukaryotic ssDNA-binding protein. As such, RPA protects the transiently formed ssDNA from nucleolytic degradation and serves as a physical platform for the recruitment of DNA damage response factors. Prominent and well-studied RPA-interacting partners are the tumor suppressor protein p53, the RAD51 recombinase and the ATR-interacting proteins ATRIP and ETAA1. RPA interactions are also documented with the helicases BLM, WRN and SMARCAL1/HARP, as well as the nucleotide excision repair proteins XPA, XPG and XPF–ERCC1. Besides its well-studied roles in DNA replication (restart) and repair, accumulating evidence shows that RPA is engaged in DNA activities in a broader biological context, including nucleosome assembly on nascent chromatin, regulation of gene expression, telomere maintenance and numerous other aspects of nucleic acid metabolism. In addition, novel RPA inhibitors show promising effects in cancer treatment, as single agents or in combination with chemotherapeutics. Since the biochemical properties of RPA and its roles in DNA repair have been extensively reviewed, here we focus on recent discoveries describing several non-canonical functions.
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Affiliation(s)
- Rositsa Dueva
- Institute of Medical Radiation Biology, University of Duisburg-Essen Medical School, 45122 Essen, Germany
| | - George Iliakis
- Institute of Medical Radiation Biology, University of Duisburg-Essen Medical School, 45122 Essen, Germany
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21
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PCAF-Mediated Histone Acetylation Promotes Replication Fork Degradation by MRE11 and EXO1 in BRCA-Deficient Cells. Mol Cell 2020; 80:327-344.e8. [PMID: 32966758 DOI: 10.1016/j.molcel.2020.08.018] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 07/22/2020] [Accepted: 08/26/2020] [Indexed: 12/12/2022]
Abstract
Stabilization of stalled replication forks is a prominent mechanism of PARP (Poly(ADP-ribose) Polymerase) inhibitor (PARPi) resistance in BRCA-deficient tumors. Epigenetic mechanisms of replication fork stability are emerging but remain poorly understood. Here, we report the histone acetyltransferase PCAF (p300/CBP-associated) as a fork-associated protein that promotes fork degradation in BRCA-deficient cells by acetylating H4K8 at stalled replication forks, which recruits MRE11 and EXO1. A H4K8ac binding domain within MRE11/EXO1 is required for their recruitment to stalled forks. Low PCAF levels, which we identify in a subset of BRCA2-deficient tumors, stabilize stalled forks, resulting in PARPi resistance in BRCA-deficient cells. Furthermore, PCAF activity is tightly regulated by ATR (ataxia telangiectasia and Rad3-related), which phosphorylates PCAF on serine 264 (S264) to limit its association and activity at stalled forks. Our results reveal PCAF and histone acetylation as critical regulators of fork stability and PARPi responses in BRCA-deficient cells, which provides key insights into targeting BRCA-deficient tumors and identifying epigenetic modulators of chemotherapeutic responses.
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22
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Duan S, Han X, Akbari M, Croteau DL, Rasmussen LJ, Bohr VA. Interaction between RECQL4 and OGG1 promotes repair of oxidative base lesion 8-oxoG and is regulated by SIRT1 deacetylase. Nucleic Acids Res 2020; 48:6530-6546. [PMID: 32432680 PMCID: PMC7337523 DOI: 10.1093/nar/gkaa392] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 04/14/2020] [Accepted: 05/04/2020] [Indexed: 12/17/2022] Open
Abstract
OGG1 initiated base excision repair (BER) is the major pathway for repair of oxidative DNA base damage 8-oxoguanine (8-oxoG). Here, we report that RECQL4 DNA helicase, deficient in the cancer-prone and premature aging Rothmund-Thomson syndrome, physically and functionally interacts with OGG1. RECQL4 promotes catalytic activity of OGG1 and RECQL4 deficiency results in defective 8-oxoG repair and increased genomic 8-oxoG. Furthermore, we show that acute oxidative stress leads to increased RECQL4 acetylation and its interaction with OGG1. The NAD+-dependent protein SIRT1 deacetylates RECQL4 in vitro and in cells thereby controlling the interaction between OGG1 and RECQL4 after DNA repair and maintaining RECQL4 in a low acetylated state. Collectively, we find that RECQL4 is involved in 8-oxoG repair through interaction with OGG1, and that SIRT1 indirectly modulates BER of 8-oxoG by controlling RECQL4–OGG1 interaction.
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Affiliation(s)
- Shunlei Duan
- Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Xuerui Han
- Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Mansour Akbari
- Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Deborah L Croteau
- Laboratory of Molecular Gerontology, National Institute on Aging, 251 Bayview Blvd, Baltimore, MD, 21224, USA
| | - Lene Juel Rasmussen
- Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Vilhelm A Bohr
- Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, DK-2200 Copenhagen, Denmark.,Laboratory of Molecular Gerontology, National Institute on Aging, 251 Bayview Blvd, Baltimore, MD, 21224, USA
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23
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Li S, Zhou M, Ze K, Sun X, Zhao C, Li Z, Lu H, Jiao Y, Wang T, Li S, Hua L, Cai H, Li X. Protective role of histone deacetylase 4 from ultraviolet radiation-induced DNA lesions. Mol Carcinog 2020; 59:1292-1301. [PMID: 32924161 DOI: 10.1002/mc.23257] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 08/29/2020] [Accepted: 08/29/2020] [Indexed: 01/22/2023]
Abstract
Ultraviolet B (UVB) exposure is a core factor that leads to skin disease or carcinogenesis through the insufficient repair of DNA lesions. UVB-induced DNA lesions are mainly removed by the nucleotide excision repair (NER) mechanism. The expression of histone deacetylase 4 (HDAC4) is altered in the skin upon UVB exposure, indicating its possible implication in UVB-induced DNA lesions repair. Here, we investigated the role of HDAC4 in the NER removal of the main classes of UVB-induced DNA lesions consisting of cyclobutane pyrimidine dimers and pyrimidine (6-4) pyrimidone photoproducts (6-4PPs). We found that UVB irradiation increased HDAC4 expression at both the mRNA and protein levels. HDAC4 interacted with NER factor XPC, which played an important role in effectively removing the UVB-induced DNA lesions. This study provides an understanding of the HDAC4 function in DNA repair, which will allow the development of efficient strategies to protect the skin from UVR-induced diseases.
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Affiliation(s)
- Shanshan Li
- Department of Forensic Medicine, Xuzhou Medical University, Xuzhou, Jiangsu, China.,Jiangsu Medical Engineering, Research Center of Gene Detection, Xuzhou, Jiangsu, China
| | - Mi Zhou
- Department of Dermatology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Kan Ze
- Department of Dermatology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Xiaoying Sun
- Institute of Dermatology, Shanghai Academy of Traditional Chinese Medicine, Shanghai, China
| | - Chunming Zhao
- Department of Human Anatomy, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Zhouru Li
- Department of Forensic Medicine, Xuzhou Medical University, Xuzhou, Jiangsu, China.,Jiangsu Medical Engineering, Research Center of Gene Detection, Xuzhou, Jiangsu, China
| | - Haiyang Lu
- Department of General Surgery, Shaanxi Sengong Hospital, Xi'an, Shaanxi, China
| | - Ying Jiao
- Department of Respiratory Medicine, Wenjiang District People's Hospital, Chengdu, China
| | - Tianyang Wang
- Department of Computer Science and Information Technology, Austin Peay State University, Clarksville, Tennessee, USA
| | - Su Li
- Department of Dermatology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Liang Hua
- Department of Dermatology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Hongxing Cai
- Department of Forensic Medicine, Xuzhou Medical University, Xuzhou, Jiangsu, China.,Jiangsu Medical Engineering, Research Center of Gene Detection, Xuzhou, Jiangsu, China
| | - Xin Li
- Department of Dermatology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China.,Institute of Dermatology, Shanghai Academy of Traditional Chinese Medicine, Shanghai, China
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24
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Ononye OE, Sausen CW, Balakrishnan L, Bochman ML. Lysine acetylation regulates the activity of nuclear Pif1. J Biol Chem 2020; 295:15482-15497. [PMID: 32878983 DOI: 10.1074/jbc.ra120.015164] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 08/28/2020] [Indexed: 12/16/2022] Open
Abstract
In Saccharomyces cerevisiae, the Pif1 helicase functions in both nuclear and mitochondrial DNA replication and repair processes, preferentially unwinding RNA:DNA hybrids and resolving G-quadruplex structures. We sought to determine how the various activities of Pif1 are regulated in vivo Here, we report lysine acetylation of nuclear Pif1 and demonstrate that it influences both Pif1's cellular roles and core biochemical activities. Using Pif1 overexpression toxicity assays, we determined that the acetyltransferase NuA4 and deacetylase Rpd3 are primarily responsible for the dynamic acetylation of nuclear Pif1. MS analysis revealed that Pif1 was modified in several domains throughout the protein's sequence on the N terminus (Lys-118 and Lys-129), helicase domain (Lys-525, Lys-639, and Lys-725), and C terminus (Lys-800). Acetylation of Pif1 exacerbated its overexpression toxicity phenotype, which was alleviated upon deletion of its N terminus. Biochemical assays demonstrated that acetylation of Pif1 stimulated its helicase, ATPase, and DNA-binding activities, whereas maintaining its substrate preferences. Limited proteolysis assays indicate that acetylation of Pif1 induces a conformational change that may account for its altered enzymatic properties. We propose that acetylation is involved in regulating of Pif1 activities, influencing a multitude of DNA transactions vital to the maintenance of genome integrity.
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Affiliation(s)
- Onyekachi E Ononye
- Department of Biology, School of Science, Indiana University, Purdue University Indianapolis, Indianapolis, Indiana, USA
| | - Christopher W Sausen
- Molecular and Cellular Biochemistry Department, Indiana University, Bloomington, Indiana, USA
| | - Lata Balakrishnan
- Department of Biology, School of Science, Indiana University, Purdue University Indianapolis, Indianapolis, Indiana, USA.
| | - Matthew L Bochman
- Molecular and Cellular Biochemistry Department, Indiana University, Bloomington, Indiana, USA.
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25
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Non-histone protein acetylation by the evolutionarily conserved GCN5 and PCAF acetyltransferases. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2020; 1864:194608. [PMID: 32711095 DOI: 10.1016/j.bbagrm.2020.194608] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Revised: 07/13/2020] [Accepted: 07/15/2020] [Indexed: 01/08/2023]
Abstract
GCN5, conserved from yeast to humans, and the vertebrate specific PCAF, are lysine acetyltransferase enzymes found in large protein complexes. Both enzymes have well documented roles in the histone acetylation and the concomitant regulation of transcription. However, these enzymes also acetylate non-histone substrates to impact diverse aspects of cell physiology. Here, I review our current understanding of non-histone acetylation by GCN5 and PCAF across eukaryotes, from target identification to molecular mechanism and regulation. I focus mainly on budding yeast, where Gcn5 was first discovered, and mammalian systems, where the bulk of non-histone substrates have been characterized. I end the review by defining critical caveats and open questions that apply to all models.
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26
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Nishimoto K, Niida H, Uchida C, Ohhata T, Kitagawa K, Motegi A, Suda T, Kitagawa M. HDAC3 Is Required for XPC Recruitment and Nucleotide Excision Repair of DNA Damage Induced by UV Irradiation. Mol Cancer Res 2020; 18:1367-1378. [DOI: 10.1158/1541-7786.mcr-20-0214] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 04/30/2020] [Accepted: 06/05/2020] [Indexed: 11/16/2022]
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27
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Rose E, Carvalho JL, Hecht M. Mechanisms of DNA repair in Trypanosoma cruzi: What do we know so far? DNA Repair (Amst) 2020; 91-92:102873. [PMID: 32505694 DOI: 10.1016/j.dnarep.2020.102873] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 03/27/2020] [Accepted: 05/22/2020] [Indexed: 12/13/2022]
Abstract
Trypanosoma cruzi is the etiological agent of Chagas Disease, which affects 6-7 million people worldwide. Since the early stages of infection and throughout its life cycle, the parasite is exposed to several genotoxic agents. Furthermore, DNA damage is also part of the mechanism of action of at least a few trypanocidal drugs, including Benznidazole. Thus, it is paramount for the parasite to count on an efficient DNA repair machinery to guarantee genome integrity and survival. The present work provides an up-to-date review of both the conserved and peculiar DNA repair mechanisms described in T. cruzi against oxidative stress, ultraviolet and ionizing radiation, DNA adduct-inducing agents, and Benznidazole. The comprehension of the DNA repair mechanisms of the parasite may shed light on the parasite evolution and possibly pave the way for the development of novel and more effective trypanocidal drugs.
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Affiliation(s)
- Ester Rose
- Interdisciplinary Laboratory of Biosciences, Faculty of Medicine, University of Brasília, Brasília, Brazil.
| | - Juliana Lott Carvalho
- Interdisciplinary Laboratory of Biosciences, Faculty of Medicine, University of Brasília, Brasília, Brazil; Genomic Sciences and Biotechnology Program, Catholic University of Brasília, Brasília, Brazil
| | - Mariana Hecht
- Interdisciplinary Laboratory of Biosciences, Faculty of Medicine, University of Brasília, Brasília, Brazil
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28
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Lu YF, Xu XP, Lu XP, Zhu Q, Liu G, Bao YT, Wen H, Li YL, Gu W, Zhu WG. SIRT7 activates p53 by enhancing PCAF-mediated MDM2 degradation to arrest the cell cycle. Oncogene 2020; 39:4650-4665. [PMID: 32404984 PMCID: PMC7286819 DOI: 10.1038/s41388-020-1305-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Revised: 04/09/2020] [Accepted: 04/16/2020] [Indexed: 02/04/2023]
Abstract
Sirtuin 7 (SIRT7), an NAD+-dependent deacetylase, plays vital roles in energy sensing, but the underlying mechanisms of action remain less clear. Here, we report that SIRT7 is required for p53-dependent cell-cycle arrest during glucose deprivation. We show that SIRT7 directly interacts with p300/CBP-associated factor (PCAF) and the affinity for this interaction increases during glucose deprivation. Upon binding, SIRT7 deacetylates PCAF at lysine 720 (K720), which augments PCAF binding to murine double minute (MDM2), the p53 E3 ubiquitin ligase, leading to accelerated MDM2 degradation. This effect results in upregulated expression of the cell-cycle inhibitor, p21Waf1/Cip1, which further leads to cell-cycle arrest and decreased cell viability. These data highlight the importance of the SIRT7–PCAF interaction in regulating p53 activity and cell-cycle progression during conditions of glucose deprivation. This axis may represent a new avenue to design effective therapeutics based on tumor starvation.
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Affiliation(s)
- Ya-Fei Lu
- Guangdong Key Laboratory of Genome Instability and Human Disease, Shenzhen University International Cancer Center, Department of Biochemistry and Molecular Biology, Shenzhen University School of Medicine, Shenzhen, 518055, China
| | - Xiao-Peng Xu
- Guangdong Key Laboratory of Genome Instability and Human Disease, Shenzhen University International Cancer Center, Department of Biochemistry and Molecular Biology, Shenzhen University School of Medicine, Shenzhen, 518055, China
| | - Xiao-Peng Lu
- Guangdong Key Laboratory of Genome Instability and Human Disease, Shenzhen University International Cancer Center, Department of Biochemistry and Molecular Biology, Shenzhen University School of Medicine, Shenzhen, 518055, China
| | - Qian Zhu
- Guangdong Key Laboratory of Genome Instability and Human Disease, Shenzhen University International Cancer Center, Department of Biochemistry and Molecular Biology, Shenzhen University School of Medicine, Shenzhen, 518055, China
| | - Ge Liu
- Guangdong Key Laboratory of Genome Instability and Human Disease, Shenzhen University International Cancer Center, Department of Biochemistry and Molecular Biology, Shenzhen University School of Medicine, Shenzhen, 518055, China
| | - Yan-Tao Bao
- Guangdong Key Laboratory of Genome Instability and Human Disease, Shenzhen University International Cancer Center, Department of Biochemistry and Molecular Biology, Shenzhen University School of Medicine, Shenzhen, 518055, China
| | - He Wen
- Guangdong Key Laboratory of Genome Instability and Human Disease, Shenzhen University International Cancer Center, Department of Biochemistry and Molecular Biology, Shenzhen University School of Medicine, Shenzhen, 518055, China
| | - Ying-Lu Li
- Institute for Cancer Genetics, College of Physicians and Surgeons, Columbia University, New York, NY, 10032, USA.
| | - Wei Gu
- Institute for Cancer Genetics, College of Physicians and Surgeons, Columbia University, New York, NY, 10032, USA
| | - Wei-Guo Zhu
- Guangdong Key Laboratory of Genome Instability and Human Disease, Shenzhen University International Cancer Center, Department of Biochemistry and Molecular Biology, Shenzhen University School of Medicine, Shenzhen, 518055, China. .,Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China. .,Peking University-Tsinghua University Center for Life Sciences, Beijing, 100871, China.
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29
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Yu H, Bu C, Liu Y, Gong T, Liu X, Liu S, Peng X, Zhang W, Peng Y, Yang J, He L, Zhang Y, Yi X, Yang X, Sun L, Shang Y, Cheng Z, Liang J. Global crotonylome reveals CDYL-regulated RPA1 crotonylation in homologous recombination-mediated DNA repair. SCIENCE ADVANCES 2020; 6:eaay4697. [PMID: 32201722 PMCID: PMC7069697 DOI: 10.1126/sciadv.aay4697] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2019] [Accepted: 12/17/2019] [Indexed: 05/15/2023]
Abstract
Previously, we reported that chromodomain Y-like (CDYL) acts as a crotonyl-coenzyme A hydratase and negatively regulates histone crotonylation (Kcr). However, the global CDYL-regulated crotonylome remains unclear. Here, we report a large-scale proteomics analysis for protein Kcr. We identify 14,311 Kcr sites across 3734 proteins in HeLa cells, providing by far the largest crotonylome dataset. We show that depletion of CDYL alters crotonylome landscape affecting diverse cellular pathways. Specifically, CDYL negatively regulated Kcr of RPA1, and mutation of the Kcr sites of RPA1 impaired its interaction with single-stranded DNA and/or with components of resection machinery, supporting a key role of RPA1 Kcr in homologous recombination DNA repair. Together, our study indicates that protein crotonylation has important implication in various pathophysiological processes.
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Affiliation(s)
- Huajing Yu
- Department of Biochemistry and Biophysics, School of Basic Medical Sciences, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Chen Bu
- Jingjie PTM BioLab (Hangzhou) Co. Ltd., Hangzhou 310018, China
| | - Yuncheng Liu
- Department of Biochemistry and Biophysics, School of Basic Medical Sciences, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Tianyu Gong
- Department of Biochemistry and Biophysics, School of Basic Medical Sciences, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Xiaoping Liu
- Department of Biochemistry and Biophysics, School of Basic Medical Sciences, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Shumeng Liu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing 100069, China
| | - Xiaojun Peng
- Jingjie PTM BioLab (Hangzhou) Co. Ltd., Hangzhou 310018, China
| | - Wenting Zhang
- Department of Biochemistry and Biophysics, School of Basic Medical Sciences, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Yani Peng
- Department of Biochemistry and Biophysics, School of Basic Medical Sciences, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Jianguo Yang
- Department of Biochemistry and Biophysics, School of Basic Medical Sciences, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Lin He
- Department of Biochemistry and Biophysics, School of Basic Medical Sciences, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Yu Zhang
- Department of Biochemistry and Biophysics, School of Basic Medical Sciences, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Xia Yi
- Department of Biochemistry and Biophysics, School of Basic Medical Sciences, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Xiaohan Yang
- Department of Biochemistry and Biophysics, School of Basic Medical Sciences, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Luyang Sun
- Department of Biochemistry and Biophysics, School of Basic Medical Sciences, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Yongfeng Shang
- Department of Biochemistry and Biophysics, School of Basic Medical Sciences, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Capital Medical University, Beijing 100069, China
| | - Zhongyi Cheng
- Jingjie PTM BioLab (Hangzhou) Co. Ltd., Hangzhou 310018, China
- Corresponding author. (J.L.); (Z.C.)
| | - Jing Liang
- Department of Biochemistry and Biophysics, School of Basic Medical Sciences, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
- Corresponding author. (J.L.); (Z.C.)
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30
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Moser B, Basílio J, Gotzmann J, Brachner A, Foisner R. Comparative Interactome Analysis of Emerin, MAN1 and LEM2 Reveals a Unique Role for LEM2 in Nucleotide Excision Repair. Cells 2020; 9:cells9020463. [PMID: 32085595 PMCID: PMC7072835 DOI: 10.3390/cells9020463] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 02/06/2020] [Accepted: 02/11/2020] [Indexed: 12/19/2022] Open
Abstract
LAP2-Emerin-MAN1 (LEM) domain-containing proteins represent an abundant group of inner nuclear membrane proteins involved in diverse nuclear functions, but their functional redundancies remain unclear. Here, using the biotinylation-dependent proximity approach, we report proteome-wide comparative interactome analysis of the two structurally related LEM proteins MAN1 (LEMD3) and LEM2 (LEMD2), and the more distantly related emerin (EMD). While over 60% of the relatively small group of MAN1 and emerin interactors were also found in the LEM2 interactome, the latter included a large number of candidates (>85%) unique for LEM2. The interacting partners unique for emerin support and provide further insight into the previously reported role of emerin in centrosome positioning, and the MAN1-specific interactors suggest a role of MAN1 in ribonucleoprotein complex assembly. Interestingly, the LEM2-specific interactome contained several proteins of the nucleotide excision repair pathway. Accordingly, LEM2-depleted cells, but not MAN1- and emerin-depleted cells, showed impaired proliferation following ultraviolet-C (UV-C) irradiation and prolonged accumulation of γH2AX, similar to cells deficient in the nucleotide excision repair protein DNA damage-binding protein 1 (DDB1). These findings indicate impaired DNA damage repair in LEM2-depleted cells. Overall, this interactome study identifies new potential interaction partners of emerin, MAN1 and particularly LEM2, and describes a novel potential involvement of LEM2 in nucleotide excision repair at the nuclear periphery.
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Affiliation(s)
- Bernhard Moser
- Max Perutz Labs, Center of Medical Biochemistry, Medical University of Vienna, Vienna Biocenter (VBC), 1030 Vienna, Austria; (B.M.); (J.G.)
- Department of Vascular Biology and Thrombosis Research, Center for Physiology and Pharmacology, Medical University of Vienna, 1090 Vienna, Austria
| | - José Basílio
- Department of Vascular Biology and Thrombosis Research, Center for Physiology and Pharmacology, Medical University of Vienna, 1090 Vienna, Austria
| | - Josef Gotzmann
- Max Perutz Labs, Center of Medical Biochemistry, Medical University of Vienna, Vienna Biocenter (VBC), 1030 Vienna, Austria; (B.M.); (J.G.)
| | - Andreas Brachner
- Max Perutz Labs, Center of Medical Biochemistry, Medical University of Vienna, Vienna Biocenter (VBC), 1030 Vienna, Austria; (B.M.); (J.G.)
- Correspondence: (A.B.); (R.F.)
| | - Roland Foisner
- Max Perutz Labs, Center of Medical Biochemistry, Medical University of Vienna, Vienna Biocenter (VBC), 1030 Vienna, Austria; (B.M.); (J.G.)
- Correspondence: (A.B.); (R.F.)
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31
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Acetylation of XPF by TIP60 facilitates XPF-ERCC1 complex assembly and activation. Nat Commun 2020; 11:786. [PMID: 32034146 PMCID: PMC7005904 DOI: 10.1038/s41467-020-14564-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 01/17/2020] [Indexed: 01/27/2023] Open
Abstract
The XPF-ERCC1 heterodimer is a structure-specific endonuclease that is essential for nucleotide excision repair (NER) and interstrand crosslink (ICL) repair in mammalian cells. However, whether and how XPF binding to ERCC1 is regulated has not yet been established. Here, we show that TIP60, also known as KAT5, a haplo-insufficient tumor suppressor, directly acetylates XPF at Lys911 following UV irradiation or treatment with mitomycin C and that this acetylation is required for XPF-ERCC1 complex assembly and subsequent activation. Mechanistically, acetylation of XPF at Lys911 disrupts the Glu907-Lys911 salt bridge, thereby leading to exposure of a previously unidentified second binding site for ERCC1. Accordingly, loss of XPF acetylation impairs the damage-induced XPF-ERCC1 interaction, resulting in defects in both NER and ICL repair. Our results not only reveal a mechanism that regulates XPF-ERCC1 complex assembly and activation, but also provide important insight into the role of TIP60 in the maintenance of genome stability. The XPF-ERCC1 heterodimer is an endonuclease involved in nucleotide excision (NER) and interstrand crosslink (ICL) repair in mammalian cells. Here, the authors provide insights into its regulation by revealing that TIP60 regulates XPF-ERCC1 complex assembly and activation.
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32
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Wang Y, Huang Y, Liu J, Zhang J, Xu M, You Z, Peng C, Gong Z, Liu W. Acetyltransferase GCN5 regulates autophagy and lysosome biogenesis by targeting TFEB. EMBO Rep 2020; 21:e48335. [PMID: 31750630 PMCID: PMC6945067 DOI: 10.15252/embr.201948335] [Citation(s) in RCA: 86] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Revised: 10/04/2019] [Accepted: 10/28/2019] [Indexed: 12/20/2022] Open
Abstract
Accumulating evidence highlights the role of histone acetyltransferase GCN5 in the regulation of cell metabolism in metazoans. Here, we report that GCN5 is a negative regulator of autophagy, a lysosome-dependent catabolic mechanism. In animal cells and Drosophila, GCN5 inhibits the biogenesis of autophagosomes and lysosomes by targeting TFEB, the master transcription factor for autophagy- and lysosome-related gene expression. We show that GCN5 is a specific TFEB acetyltransferase, and acetylation by GCN5 results in the decrease in TFEB transcriptional activity. Induction of autophagy inactivates GCN5, accompanied by reduced TFEB acetylation and increased lysosome formation. We further demonstrate that acetylation at K274 and K279 disrupts the dimerization of TFEB and the binding of TFEB to its target gene promoters. In a Tau-based neurodegenerative Drosophila model, deletion of dGcn5 improves the clearance of Tau protein aggregates and ameliorates the neurodegenerative phenotypes. Together, our results reveal GCN5 as a novel conserved TFEB regulator, and the regulatory mechanisms may be involved in autophagy- and lysosome-related physiological and pathological processes.
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Affiliation(s)
- Yusha Wang
- Department of Biochemistry and Department of Cardiology of the Second Affiliated HospitalZhejiang University School of MedicineHangzhouChina
| | - Yewei Huang
- Department of Biochemistry and Department of Cardiology of the Second Affiliated HospitalZhejiang University School of MedicineHangzhouChina
| | - Jiaqi Liu
- Department of Biochemistry and Department of Cardiology of the Second Affiliated HospitalZhejiang University School of MedicineHangzhouChina
| | - Jinna Zhang
- Department of Biochemistry and Department of Cardiology of the Second Affiliated HospitalZhejiang University School of MedicineHangzhouChina
| | - Mingming Xu
- Department of Biochemistry and Department of Cardiology of the Second Affiliated HospitalZhejiang University School of MedicineHangzhouChina
| | - Zhiyuan You
- Department of Biochemistry and Department of Cardiology of the Second Affiliated HospitalZhejiang University School of MedicineHangzhouChina
| | - Chao Peng
- National Center for Protein Science ShanghaiInstitute of Biochemistry and Cell BiologyShanghai Institutes of Biological SciencesChinese Academy of SciencesShanghaiChina
| | - Zhefeng Gong
- Department of NeurobiologyKey Laboratory of Medical Neurobiology of the Ministry of Health of ChinaZhejiang University School of MedicineHangzhouChina
| | - Wei Liu
- Department of Biochemistry and Department of Cardiology of the Second Affiliated HospitalZhejiang University School of MedicineHangzhouChina
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious DiseaseFirst Affiliated HospitalZhejiang University School of MedicineHangzhouChina
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33
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Rechkunova NI, Maltseva EA, Lavrik OI. Post-translational Modifications of Nucleotide Excision Repair Proteins and Their Role in the DNA Repair. BIOCHEMISTRY (MOSCOW) 2019; 84:1008-1020. [PMID: 31693460 DOI: 10.1134/s0006297919090037] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Nucleotide excision repair (NER) is one of the major DNA repair pathways aimed at maintaining genome stability. Correction of DNA damage by the NER system is a multistage process that proceeds with the formation of multiple DNA-protein and protein-protein intermediate complexes and requires precise coordination and regulation. NER proteins undergo post-translational modifications, such as ubiquitination, sumoylation, phosphorylation, acetylation, and poly(ADP-ribosyl)ation. These modifications affect the interaction of NER factors with DNA and other proteins and thus regulate either their recruitment into the complexes or dissociation from these complexes at certain stages of DNA repair, as well as modulate the functional activity of NER proteins and control the process of DNA repair in general. Here, we review the data on the post-translational modifications of NER factors and their effects on DNA repair. Protein poly(ADP-ribosyl)ation catalyzed by poly(ADP-ribose) polymerase 1 and its impact on NER are discussed in detail, since such analysis has not been done before.
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Affiliation(s)
- N I Rechkunova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia. .,Novosibirsk State University, Novosibirsk, 630090, Russia
| | - E A Maltseva
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia
| | - O I Lavrik
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia.,Novosibirsk State University, Novosibirsk, 630090, Russia
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Current role of mammalian sirtuins in DNA repair. DNA Repair (Amst) 2019; 80:85-92. [DOI: 10.1016/j.dnarep.2019.06.009] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 06/29/2019] [Indexed: 01/20/2023]
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Jarrett SG, Carter KM, Bautista RM, He D, Wang C, D'Orazio JA. Sirtuin 1-mediated deacetylation of XPA DNA repair protein enhances its interaction with ATR protein and promotes cAMP-induced DNA repair of UV damage. J Biol Chem 2018; 293:19025-19037. [PMID: 30327428 DOI: 10.1074/jbc.ra118.003940] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 10/12/2018] [Indexed: 12/31/2022] Open
Abstract
Blunted melanocortin 1 receptor (MC1R) signaling promotes melanocyte genomic instability in part by attenuating cAMP-mediated DNA repair responses, particularly nucleotide excision repair (NER), which recognizes and clears mutagenic photodamage. cAMP-enhanced NER is mediated by interactions between the ataxia telangiectasia-mutated and Rad3-related (ATR) and xeroderma pigmentosum complementation group A (XPA) proteins. We now report a critical role for sirtuin 1 (SIRT1) in regulating ATR-mediated phosphorylation of XPA. SIRT1 deacetylates XPA at residues Lys-63, Lys-67, and Lys-215 to promote interactions with ATR. Mutant XPA containing acetylation mimetics at residues Lys-63, Lys-67, and Lys-215 exhibit blunted UV-dependent ATR-XPA interactions even in the presence of cAMP signals. ATR-mediated phosphorylation of XPA on Ser-196 enhances cAMP-mediated optimization of NER and is promoted by SIRT1-mediated deacetylation of XPA on Lys-63, Lys-67, and Lys-215. Interference with ATR-mediated XPA phosphorylation at Ser-196 by persistent acetylation of XPA at Lys-63, Lys-67, and Lys-215 delays repair of UV-induced DNA damage and attenuates cAMP-enhanced NER. Our study identifies a regulatory ATR-SIRT1-XPA axis in cAMP-mediated regulation melanocyte genomic stability, involving SIRT1-mediated deacetylation (Lys-63, Lys-67, and Lys-215) and ATR-dependent phosphorylation (Ser-196) post-translational modifications of the core NER factor XPA.
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Affiliation(s)
- Stuart G Jarrett
- From the Markey Cancer Center and .,the Departments of Toxicology and Cancer Biology
| | | | | | - Daheng He
- From the Markey Cancer Center and.,Biostatistics and Bioinformatics, and
| | - Chi Wang
- From the Markey Cancer Center and.,Biostatistics and Bioinformatics, and
| | - John A D'Orazio
- From the Markey Cancer Center and .,the Departments of Toxicology and Cancer Biology.,Pediatrics, University of Kentucky College of Medicine, Lexington, Kentucky 40536
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Chakravarti D, Hazra TK. Feeling Stressed under the Sun? RPA1 Acetylation to the Rescue. Cell Rep 2018; 20:1995-1996. [PMID: 28854353 DOI: 10.1016/j.celrep.2017.08.045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Nucleotide excision repair (NER) requires replication protein A (RPA), among others, to respond to DNA damaging agents. In this issue of Cell Reports, He et al. (2017) and Zhao et al. (2017) show acetylation of RPA1 regulates the UV-induced DNA damage response.
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Affiliation(s)
- Debabrata Chakravarti
- Department of Obstetrics and Gynecology and Department of Pharmacology, Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.
| | - Tapas K Hazra
- Department of Internal Medicine, University of Texas Medical Branch, Galveston, TX, USA
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37
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Bondy-Chorney E, Denoncourt A, Sai Y, Downey M. Nonhistone targets of KAT2A and KAT2B implicated in cancer biology 1. Biochem Cell Biol 2018; 97:30-45. [PMID: 29671337 DOI: 10.1139/bcb-2017-0297] [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] [Indexed: 12/16/2022] Open
Abstract
Lysine acetylation is a critical post-translation modification that can impact a protein's localization, stability, and function. Originally thought to only occur on histones, we now know thousands of nonhistone proteins are also acetylated. In conjunction with many other proteins, lysine acetyltransferases (KATs) are incorporated into large protein complexes that carry out these modifications. In this review we focus on the contribution of two KATs, KAT2A and KAT2B, and their potential roles in the development and progression of cancer. Systems biology demands that we take a broad look at protein function rather than focusing on individual pathways or targets. As such, in this review we examine KAT2A/2B-directed nonhistone protein acetylations in cancer in the context of the 10 "Hallmarks of Cancer", as defined by Hanahan and Weinberg. By focusing on specific examples of KAT2A/2B-directed acetylations with well-defined mechanisms or strong links to a cancer phenotype, we aim to reinforce the complex role that these enzymes play in cancer biology.
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Affiliation(s)
- Emma Bondy-Chorney
- Department of Cellular and Molecular Medicine and Ottawa Institute of Systems Biology, 451 Smyth Rd., Ottawa, ON KIH 8M5, Canada.,Department of Cellular and Molecular Medicine and Ottawa Institute of Systems Biology, 451 Smyth Rd., Ottawa, ON KIH 8M5, Canada
| | - Alix Denoncourt
- Department of Cellular and Molecular Medicine and Ottawa Institute of Systems Biology, 451 Smyth Rd., Ottawa, ON KIH 8M5, Canada.,Department of Cellular and Molecular Medicine and Ottawa Institute of Systems Biology, 451 Smyth Rd., Ottawa, ON KIH 8M5, Canada
| | - Yuka Sai
- Department of Cellular and Molecular Medicine and Ottawa Institute of Systems Biology, 451 Smyth Rd., Ottawa, ON KIH 8M5, Canada.,Department of Cellular and Molecular Medicine and Ottawa Institute of Systems Biology, 451 Smyth Rd., Ottawa, ON KIH 8M5, Canada
| | - Michael Downey
- Department of Cellular and Molecular Medicine and Ottawa Institute of Systems Biology, 451 Smyth Rd., Ottawa, ON KIH 8M5, Canada.,Department of Cellular and Molecular Medicine and Ottawa Institute of Systems Biology, 451 Smyth Rd., Ottawa, ON KIH 8M5, Canada
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Zhao M, Geng R, Guo X, Yuan R, Zhou X, Zhong Y, Huo Y, Zhou M, Shen Q, Li Y, Zhu W, Wang J. PCAF/GCN5-Mediated Acetylation of RPA1 Promotes Nucleotide Excision Repair. Cell Rep 2017; 20:1997-2009. [DOI: 10.1016/j.celrep.2017.08.015] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Revised: 06/21/2017] [Accepted: 07/14/2017] [Indexed: 12/14/2022] Open
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39
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Wang Y, Luo J. Acetylation of BLM protein regulates its function in response to DNA damage. RSC Adv 2017. [DOI: 10.1039/c7ra06666j] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
This study first revealed the acetylation of the BLM protein and studied this regulatory process in the DNA damage response.
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Affiliation(s)
- Yankun Wang
- Department of Medical Genetics
- Peking University Health Science Center
- Beijing
- China
| | - Jianyuan Luo
- Department of Medical Genetics
- Peking University Health Science Center
- Beijing
- China
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