1
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Ma R, Xu X. Deciphering the role of post-translational modifications in fanconi anemia proteins and their influence on tumorigenesis. Cancer Gene Ther 2024; 31:1113-1123. [PMID: 38879655 DOI: 10.1038/s41417-024-00797-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 06/01/2024] [Accepted: 06/04/2024] [Indexed: 08/17/2024]
Abstract
Fanconi anemia (FA) is an autosomal or X-linked human disease, characterized by bone marrow failure, cancer susceptibility and various developmental abnormalities. So far, at least 22 FA genes (FANCA-W) have been identified. Germline inactivation of any one of these FA genes causes FA symptoms. Proteins encoded by FA genes are involved in the Fanconi anemia pathway, which is known for its roles in DNA inter-strand crosslinks (ICLs) repair. Besides, its roles in genome maintenance upon replication stress has also been reported. Post-translational modifications (PTMs) of FA proteins, particularly phosphorylation and ubiquitination, emerge as critical determinants in the activation of the FA pathway during ICL repair or replication stress response. Consequent inactivation of the FA pathway engenders heightened chromosomal instability, thereby constituting a genetic susceptibility conducive to cancer predisposition and the exacerbation of tumorigenesis. In this review, we have combined recent structural analysis of FA proteins and summarized knowledge on the functions of different PTMs in regulating FA pathways, and discuss potential contributions stemming from mutations at PTMs to the genesis and progression of tumorigenesis.
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Affiliation(s)
- Rui Ma
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, Hubei, 430062, China
| | - Xinlin Xu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, Hubei, 430062, China.
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2
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Das JK, Banskota N, Candia J, Griswold ME, Orenduff M, de Cabo R, Corcoran DL, Das SK, De S, Huffman KM, Kraus VB, Kraus WE, Martin C, Racette SB, Redman LM, Schilling B, Belsky D, Ferrucci L. Calorie restriction modulates the transcription of genes related to stress response and longevity in human muscle: The CALERIE study. Aging Cell 2023; 22:e13963. [PMID: 37823711 PMCID: PMC10726900 DOI: 10.1111/acel.13963] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 07/28/2023] [Accepted: 08/01/2023] [Indexed: 10/13/2023] Open
Abstract
The lifespan extension induced by 40% caloric restriction (CR) in rodents is accompanied by postponement of disease, preservation of function, and increased stress resistance. Whether CR elicits the same physiological and molecular responses in humans remains mostly unexplored. In the CALERIE study, 12% CR for 2 years in healthy humans induced minor losses of muscle mass (leg lean mass) without changes of muscle strength, but mechanisms for muscle quality preservation remained unclear. We performed high-depth RNA-Seq (387-618 million paired reads) on human vastus lateralis muscle biopsies collected from the CALERIE participants at baseline, 12- and 24-month follow-up from the 90 CALERIE participants randomized to CR and "ad libitum" control. Using linear mixed effect model, we identified protein-coding genes and splicing variants whose expression was significantly changed in the CR group compared to controls, including genes related to proteostasis, circadian rhythm regulation, DNA repair, mitochondrial biogenesis, mRNA processing/splicing, FOXO3 metabolism, apoptosis, and inflammation. Changes in some of these biological pathways mediated part of the positive effect of CR on muscle quality. Differentially expressed splicing variants were associated with change in pathways shown to be affected by CR in model organisms. Two years of sustained CR in humans positively affected skeletal muscle quality, and impacted gene expression and splicing profiles of biological pathways affected by CR in model organisms, suggesting that attainable levels of CR in a lifestyle intervention can benefit muscle health in humans.
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Affiliation(s)
- Jayanta Kumar Das
- Longitudinal Studies Section, Translation Gerontology BranchNational Institute on Aging, National Institutes of HealthBaltimoreMarylandUSA
| | - Nirad Banskota
- Computational Biology and Genomics CoreNational Institute on Aging, National Institutes of HealthBaltimoreMarylandUSA
| | - Julián Candia
- Longitudinal Studies Section, Translation Gerontology BranchNational Institute on Aging, National Institutes of HealthBaltimoreMarylandUSA
| | | | - Melissa Orenduff
- Duke Molecular Physiology Institute and Department of MedicineDuke University School of MedicineDurhamNorth CarolinaUSA
| | - Rafael de Cabo
- Translation Gerontology Branch, National Institute on AgingNational Institutes of HealthBaltimoreMarylandUSA
| | - David L. Corcoran
- Department of GeneticsUniversity of North Carolina at Chapel HillChapel HillNorth CarolinaUSA
| | - Sai Krupa Das
- Energy Metabolism, Jean Mayer USDA Human Nutrition Research Center on AgingTufts UniversityBostonMassachusettsUSA
| | - Supriyo De
- Computational Biology and Genomics CoreNational Institute on Aging, National Institutes of HealthBaltimoreMarylandUSA
| | - Kim Marie Huffman
- Duke Molecular Physiology Institute and Department of MedicineDuke University School of MedicineDurhamNorth CarolinaUSA
| | - Virginia B. Kraus
- Duke Molecular Physiology Institute and Department of MedicineDuke University School of MedicineDurhamNorth CarolinaUSA
| | - William E. Kraus
- Duke Molecular Physiology Institute and Department of MedicineDuke University School of MedicineDurhamNorth CarolinaUSA
| | - Corby K. Martin
- Pennington Biomedical Research CenterLouisiana State UniversityBaton RougeLouisianaUSA
| | - Susan B. Racette
- College of Health SolutionsArizona State UniversityPhoenixArizonaUSA
| | - Leanne M. Redman
- Pennington Biomedical Research CenterLouisiana State UniversityBaton RougeLouisianaUSA
| | | | - Daniel W. Belsky
- Department of Epidemiology & Butler Columbia Aging CenterColumbia University Mailman School of Public HealthNew York CityNew YorkUSA
| | - Luigi Ferrucci
- Longitudinal Studies Section, Translation Gerontology BranchNational Institute on Aging, National Institutes of HealthBaltimoreMarylandUSA
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3
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Jing J, Wu N, Xu W, Wang Y, Pawlowski WP, He Y. An F-box protein ACOZ1 functions in crossover formation by ensuring proper chromosome compaction during maize meiosis. THE NEW PHYTOLOGIST 2022; 235:157-172. [PMID: 35322878 DOI: 10.1111/nph.18116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 03/09/2022] [Indexed: 06/14/2023]
Abstract
Meiosis is an essential reproductive process to create new genetic variation. During early meiosis, higher order chromosome organization creates a platform for meiotic processes to ensure the accuracy of recombination and chromosome segregation. However, little is known about the regulatory mechanisms underlying dynamic chromosome organization in plant meiosis. Here, we describe abnormal chromosome organization in zygotene1 (ACOZ1), which encodes a canonical F-box protein in maize. In acoz1 mutant meiocytes, chromosomes maintain a leptotene-like state and never compact to a zygotene-like configuration. Telomere bouquet formation and homologous pairing are also distorted and installation of synaptonemal complex ZYP1 protein is slightly defective. Loading of early recombination proteins RAD51 and DMC1 is unaffected, indicating that ACOZ1 is not required for double strand break formation or repair. However, crossover formation is severely disturbed. The ACOZ1 protein localizes on the boundary of chromatin, rather directly to chromosomes. Furthermore, we identified that ACOZ1 interacts with SKP1 through its C-terminus, revealing that it acts as a subunit of the SCF E3 ubiquitin/SUMO ligase complex. Overall, our results suggest that ACOZ1 functions independently from the core meiotic recombination pathway to influence crossover formation by controlling chromosome compaction during maize meiosis.
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Affiliation(s)
- Juli Jing
- MOE Key Laboratory of Crop Heterosis and Utilization, National Maize Improvement Center of China, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100094, China
| | - Nan Wu
- MOE Key Laboratory of Crop Heterosis and Utilization, National Maize Improvement Center of China, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100094, China
| | - Wanyue Xu
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Yingxiang Wang
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | | | - Yan He
- MOE Key Laboratory of Crop Heterosis and Utilization, National Maize Improvement Center of China, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100094, China
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4
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He L, Lomberk G. Collateral Victim or Rescue Worker?-The Role of Histone Methyltransferases in DNA Damage Repair and Their Targeting for Therapeutic Opportunities in Cancer. Front Cell Dev Biol 2021; 9:735107. [PMID: 34869318 PMCID: PMC8636273 DOI: 10.3389/fcell.2021.735107] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 10/01/2021] [Indexed: 01/25/2023] Open
Abstract
Disrupted DNA damage signaling greatly threatens cell integrity and plays significant roles in cancer. With recent advances in understanding the human genome and gene regulation in the context of DNA damage, chromatin biology, specifically biology of histone post-translational modifications (PTMs), has emerged as a popular field of study with great promise for cancer therapeutics. Here, we discuss how key histone methylation pathways contribute to DNA damage repair and impact tumorigenesis within this context, as well as the potential for their targeting as part of therapeutic strategies in cancer.
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Affiliation(s)
- Lishu He
- Department of Pharmacology and Toxicology, Medical College of Wisconsin, Milwaukee, WI, United States,Division of Research, Department of Surgery, Medical College of Wisconsin, Milwaukee, WI, United States,Genomic Sciences and Precision Medicine Center, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Gwen Lomberk
- Department of Pharmacology and Toxicology, Medical College of Wisconsin, Milwaukee, WI, United States,Division of Research, Department of Surgery, Medical College of Wisconsin, Milwaukee, WI, United States,Genomic Sciences and Precision Medicine Center, Medical College of Wisconsin, Milwaukee, WI, United States,LaBahn Pancreatic Cancer Program, Medical College of Wisconsin, Milwaukee, WI, United States,*Correspondence: Gwen Lomberk,
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5
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Non-canonical function of DGCR8 in DNA double-strand break repair signaling and tumor radioresistance. Nat Commun 2021; 12:4033. [PMID: 34188037 PMCID: PMC8242032 DOI: 10.1038/s41467-021-24298-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 06/11/2021] [Indexed: 12/21/2022] Open
Abstract
In response to DNA double-strand breaks (DSBs), repair proteins are recruited to the damaged sites. Ubiquitin signaling plays a critical role in coordinating protein recruitment during the DNA damage response. Here, we find that the microRNA biogenesis factor DGCR8 promotes tumor resistance to X-ray radiation independently of its Drosha-binding ability. Upon radiation, the kinase ATM and the deubiquitinase USP51 mediate the activation and stabilization of DGCR8 through phosphorylation and deubiquitination. Specifically, radiation-induced ATM-dependent phosphorylation of DGCR8 at serine 677 facilitates USP51 to bind, deubiquitinate, and stabilize DGCR8, which leads to the recruitment of DGCR8 and DGCR8’s binding partner RNF168 to MDC1 and RNF8 at DSBs. This, in turn, promotes ubiquitination of histone H2A, repair of DSBs, and radioresistance. Altogether, these findings reveal the non-canonical function of DGCR8 in DSB repair and suggest that radiation treatment may result in therapy-induced tumor radioresistance through ATM- and USP51-mediated activation and upregulation of DGCR8. The molecular mechanisms underlying cancer cell radioresistance need to be elucidated. In this study, the authors show that the microRNA biogenesis factor DGCR8 is stabilized by USP51 and ATM upon irradiation and by consequence it promotes the repair of DNA double-strand breaks and radioresistance by recruiting RNF168 to sites of damage.
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6
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Liu G, Lim D, Cai Z, Ding W, Tian Z, Dong C, Zhang F, Guo G, Wang X, Zhou P, Feng Z. The Valproate Mediates Radio-Bidirectional Regulation Through RFWD3-Dependent Ubiquitination on Rad51. Front Oncol 2021; 11:646256. [PMID: 33842359 PMCID: PMC8029989 DOI: 10.3389/fonc.2021.646256] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2020] [Accepted: 03/08/2021] [Indexed: 12/23/2022] Open
Abstract
Ionizing radiation (IR) can induce DNA double-strand breaks (DSBs) in tumor cells during radiotherapy (RT), but the efficiency of RT is limited because of the toxicity to normal cells. Locating an adjuvant treatment to alleviate damage in normal cells while sensitizing tumor cells to IR has attracted much attention. Here, using the 7,12-dimethylbenz[α]anthracene (DMBA)-induced malignant transformed MCF10A cells, we found that valproate (VPA), a histone deacetylase inhibitor (HDACi), radiosensitized transformed cells while alleviated IR-induced damage in normal cells at a safe dose (0.5 mM). We further demonstrated the decrease of homologous recombination (HR)-associated Rad51 in the transformed cells was related to the increase of its ubiquitination regulated by E3 ligase RFWD3 for the radiosensitization, which was opposite to normal cells, indicating that RFWD3-dependent ubiquitination on Rad51 was involved in the VPA-mediated radio-bidirectional effect. Through DMBA-transformed breast cancer rat model, VPA at 200 mg/kg radiosensitized tumor tissue cells by increasing RFWD3 and inhibited Rad51, while radioprotected normal tissue cells by decreasing RFWD3 and enhanced Rad51. In addition, we found high-level Rad51 was associated with tumorigenesis and poor prognosis in breast cancer patients. Our findings uncovered RFWD3-dependent Rad51 ubiquitination was the novel mechanism of VPA-mediated radio-bidirectional effect, VPA is a potential adjuvant treatment for tumor RT.
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Affiliation(s)
- Guochao Liu
- Department of Occupational Health and Occupational Medicine, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - David Lim
- School of Health Sciences, Western Sydney University, Campbelltown, NSW, Australia
- College of Medicine and Public Health, Flinders University, Bedford Park, SA, Australia
| | - Zuchao Cai
- Department of Occupational Health and Occupational Medicine, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Wenwen Ding
- Department of Occupational Health and Occupational Medicine, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Zhujun Tian
- Department of Occupational Health and Occupational Medicine, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Chao Dong
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Fengmei Zhang
- Department of Occupational Health and Occupational Medicine, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Gongshe Guo
- Department of Medicine, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Xiaowei Wang
- Department of Radiation Oncology, Washington University, School of Medicine, St. Louis, MO, United States
| | - Pingkun Zhou
- Beijing Key Laboratory for Radiobiology, Department of Radiation Biology, Beijing Institute of Radiation Medicine, AMMS, Beijing, China
| | - Zhihui Feng
- Department of Occupational Health and Occupational Medicine, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, China
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7
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Pfeiffer A, Herzog LK, Luijsterburg MS, Shah RG, Rother MB, Stoy H, Kühbacher U, van Attikum H, Shah GM, Dantuma NP. Poly(ADP-ribosyl)ation temporally confines SUMO-dependent ataxin-3 recruitment to control DNA double-strand break repair. J Cell Sci 2021; 134:jcs.247809. [PMID: 33408245 DOI: 10.1242/jcs.247809] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 12/17/2020] [Indexed: 12/16/2022] Open
Abstract
DNA damage-induced SUMOylation serves as a signal for two antagonizing proteins that both stimulate repair of DNA double-strand breaks (DSBs). Here, we demonstrate that the SUMO-dependent recruitment of the deubiquitylating enzyme ataxin-3 to DSBs, unlike recruitment of the ubiquitin ligase RNF4, additionally depends on poly [ADP-ribose] polymerase 1 (PARP1)-mediated poly(ADP-ribosyl)ation (PARylation). The co-dependence of ataxin-3 recruitment on PARylation and SUMOylation temporally confines ataxin-3 to DSBs immediately after occurrence of DNA damage. We propose that this mechanism ensures that ataxin-3 prevents the premature removal of DNA repair proteins only during the early phase of the DSB response and does not interfere with the subsequent timely displacement of DNA repair proteins by RNF4. Thus, our data show that PARylation differentially regulates SUMO-dependent recruitment of ataxin-3 and RNF4 to DSBs, explaining how both proteins can play a stimulatory role at DSBs despite their opposing activities.
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Affiliation(s)
- Annika Pfeiffer
- Department of Cell and Molecular Biology, Karolinska Institutet, Biomedicum, Solnavägen 9, 17165 Stockholm, Sweden
| | - Laura K Herzog
- Department of Cell and Molecular Biology, Karolinska Institutet, Biomedicum, Solnavägen 9, 17165 Stockholm, Sweden
| | - Martijn S Luijsterburg
- Department of Human Genetics, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, The Netherlands
| | - Rashmi G Shah
- Laboratory for Skin Cancer Research, CHU-Q: University Hospital Research Centre of Quebec (CHUL site) and Laval University, Quebec City (QC) G1V 4G2, Canada
| | - Magdalena B Rother
- Department of Human Genetics, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, The Netherlands
| | - Henriette Stoy
- Department of Cell and Molecular Biology, Karolinska Institutet, Biomedicum, Solnavägen 9, 17165 Stockholm, Sweden
| | - Ulrike Kühbacher
- Department of Cell and Molecular Biology, Karolinska Institutet, Biomedicum, Solnavägen 9, 17165 Stockholm, Sweden
| | - Haico van Attikum
- Department of Human Genetics, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, The Netherlands
| | - Girish M Shah
- Laboratory for Skin Cancer Research, CHU-Q: University Hospital Research Centre of Quebec (CHUL site) and Laval University, Quebec City (QC) G1V 4G2, Canada
| | - Nico P Dantuma
- Department of Cell and Molecular Biology, Karolinska Institutet, Biomedicum, Solnavägen 9, 17165 Stockholm, Sweden
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8
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Zhang F, Gong Z. Regulation of DNA double-strand break repair pathway choice: a new focus on 53BP1. J Zhejiang Univ Sci B 2021; 22:38-46. [PMID: 33448186 DOI: 10.1631/jzus.b2000306] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Maintenance of cellular homeostasis and genome integrity is a critical responsibility of DNA double-strand break (DSB) signaling. P53-binding protein 1 (53BP1) plays a critical role in coordinating the DSB repair pathway choice and promotes the non-homologous end-joining (NHEJ)-mediated DSB repair pathway that rejoins DSB ends. New insights have been gained into a basic molecular mechanism that is involved in 53BP1 recruitment to the DNA lesion and how 53BP1 then recruits the DNA break-responsive effectors that promote NHEJ-mediated DSB repair while inhibiting homologous recombination (HR) signaling. This review focuses on the up- and downstream pathways of 53BP1 and how 53BP1 promotes NHEJ-mediated DSB repair, which in turn promotes the sensitivity of poly(ADP-ribose) polymerase inhibitor (PARPi) in BRCA1-deficient cancers and consequently provides an avenue for improving cancer therapy strategies.
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Affiliation(s)
- Fan Zhang
- Department of Cancer Biology, Cleveland Clinic Lerner Research Institute, Cleveland, OH 44195, USA
| | - Zihua Gong
- Department of Cancer Biology, Cleveland Clinic Lerner Research Institute, Cleveland, OH 44195, USA.
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9
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Guo Z, Wang S, Xie Y, Han Y, Hu S, Guan H, Xie D, Bai C, Liu X, Gu Y, Zhou PK, Ma T. HUWE1-dependent DNA-PKcs neddylation modulates its autophosphorylation in DNA damage response. Cell Death Dis 2020; 11:400. [PMID: 32457294 PMCID: PMC7250858 DOI: 10.1038/s41419-020-2611-0] [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: 02/11/2020] [Revised: 05/07/2020] [Accepted: 05/11/2020] [Indexed: 02/07/2023]
Abstract
DNA-dependent protein kinase catalytic subunit (DNA-PKcs) is the core component of DNA-PK complex in the non-homologous end-joining (NHEJ) repair of DNA double-strand breaks, and its activity is strictly controlled by DNA-PKcs phosphorylation. The ubiquitin-like protein, NEDD8 is involved in regulation of DNA damage response, but it remains mysterious whether and how NEDD8-related neddylation affects DNA-PKcs and the NHEJ process. Here, we show that DNA-PKcs is poly-neddylated at its kinase domain. The neddylation E2-conjugating enzyme UBE2M and E3 ligase HUWE1 (HECT, UBA, and WWE domain containing E3 ubiquitin protein ligase 1) are responsible for the DNA-PKcs neddylation. Moreover, inhibition of HUWE1-dependent DNA-PKcs neddylation impairs DNA-PKcs autophosphorylation at Ser2056. Finally, depletion of HUWE1-dependent DNA-PKcs neddylation reduces the efficiency of NHEJ. These studies provide insights how neddylation modulates the activity of NHEJ core complex.
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Affiliation(s)
- Zongpei Guo
- Department of Radiation Toxicology and Oncology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing, 100850, P. R. China
| | - Shaozheng Wang
- Department of Radiation Toxicology and Oncology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing, 100850, P. R. China
| | - Ying Xie
- Department of Radiation Toxicology and Oncology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing, 100850, P. R. China
| | - Yang Han
- Department of Radiation Toxicology and Oncology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing, 100850, P. R. China.,Institute for Environmental Medicine and Radiation Hygiene, School of Public Health, University of South China, Hengyang, Hunan Province, 421001, P. R. China
| | - Sai Hu
- Department of Radiation Toxicology and Oncology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing, 100850, P. R. China.,Institute for Environmental Medicine and Radiation Hygiene, School of Public Health, University of South China, Hengyang, Hunan Province, 421001, P. R. China
| | - Hua Guan
- Department of Radiation Toxicology and Oncology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing, 100850, P. R. China
| | - Dafei Xie
- Department of Radiation Toxicology and Oncology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing, 100850, P. R. China
| | - Chenjun Bai
- Department of Radiation Toxicology and Oncology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing, 100850, P. R. China
| | - Xiaodan Liu
- Department of Radiation Toxicology and Oncology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing, 100850, P. R. China
| | - Yongqing Gu
- Department of Radiation Toxicology and Oncology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing, 100850, P. R. China
| | - Ping-Kun Zhou
- Department of Radiation Toxicology and Oncology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing, 100850, P. R. China. .,Institute for Environmental Medicine and Radiation Hygiene, School of Public Health, University of South China, Hengyang, Hunan Province, 421001, P. R. China.
| | - Teng Ma
- Department of Radiation Toxicology and Oncology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing, 100850, P. R. China. .,Department of Cellular and Molecular Biology, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, 101149, P. R. China.
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10
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Qiu F, Liu L, Lin Y, Yang Z, Qiu F. Corilagin Inhibits Esophageal Squamous Cell Carcinoma by Inducing DNA Damage and Down-Regulation of RNF8. Anticancer Agents Med Chem 2020; 19:1021-1028. [PMID: 30848215 DOI: 10.2174/1871520619666190307120811] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 01/22/2019] [Accepted: 02/19/2019] [Indexed: 12/18/2022]
Abstract
BACKGROUND Esophageal squamous cell carcinoma (ESCC), the most prevalent histologic subtype of esophageal cancer, is an aggressive malignancy with poor prognosis and a high incidence in the East. Corilagin, an active component present in Phyllanthus niruri L., has been shown to suppress tumor growth in various cancers. However, the effects of corilagin on ESCC and the mechanisms for its tumor suppressive function remain unknown. METHODS Cell proliferation was measured by Cell Counting Kit-8 assay and colony formation assays. Annexin V/PI double-staining was performed to assess cell apoptosis. Immunofluorescence staining and western blotting were used to evaluate the protein expression. A xenograft mice model was used to assess the in vivo antitumor effects of corilagin alone or in combination with cisplatin. RESULTS We for the first time showed that corilagin was effectively able to inhibit ESCC cell proliferation and induce cell apoptosis. Additionally, our results validated its antitumor effects in vivo using a xenograft mouse model. Mechanistically, we found that corilagin caused significant DNA damage in ESCC cells. We found that corilagin could significantly attenuate the expression of the E3 ubiquitin ligase RING finger protein 8 (RNF8) through ubiquitin-proteasome pathway, leading to the inability of DNA damage repair response and eventually causing cell apoptosis. Furthermore, we also showed that corilagin substantially enhanced the antitumor effects of chemotherapy drug cisplatin both in vitro and in vivo. CONCLUSION Our results not only provided novel and previously unrecognized evidences for corilagin-induced tumor suppression through inducing DNA damage and targeting RNF8 in ESCC, but also highlighted that corilagin might serve as an adjunctive treatment to conventional chemotherapeutic drugs in ESCC patients.
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Affiliation(s)
- Fanghua Qiu
- Department of Infection Control, Guangzhou Hospital of Traditional Chinese Medicine, Guangzhou 510130, China
| | - Lifang Liu
- Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Yu Lin
- Department of Clinical Laboratory, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510120, China
| | - Zetian Yang
- Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Feng Qiu
- Department of General Practice Center, Nanhai Hospital of Southern Medical University, Foshan 528244, China
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11
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Mota MBS, Carvalho MA, Monteiro ANA, Mesquita RD. DNA damage response and repair in perspective: Aedes aegypti, Drosophila melanogaster and Homo sapiens. Parasit Vectors 2019; 12:533. [PMID: 31711518 PMCID: PMC6849265 DOI: 10.1186/s13071-019-3792-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Accepted: 11/05/2019] [Indexed: 01/18/2023] Open
Abstract
Background The maintenance of genomic integrity is the responsibility of a complex network, denominated the DNA damage response (DDR), which controls the lesion detection and DNA repair. The main repair pathways are base excision repair (BER), nucleotide excision repair (NER), mismatch repair (MMR), homologous recombination repair (HR) and non-homologous end joining repair (NHEJ). They correct double-strand breaks (DSB), single-strand breaks, mismatches and others, or when the damage is quite extensive and repair insufficient, apoptosis is activated. Methods In this study we used the BLAST reciprocal best-hit methodology to search for DDR orthologs proteins in Aedes aegypti. We also provided a comparison between Ae. aegypti, D. melanogaster and human DDR network. Results Our analysis revealed the presence of ATR and ATM signaling, including the H2AX ortholog, in Ae. aegypti. Key DDR proteins (orthologs to RAD51, Ku and MRN complexes, XP-components, MutS and MutL) were also identified in this insect. Other proteins were not identified in both Ae. aegypti and D. melanogaster, including BRCA1 and its partners from BRCA1-A complex, TP53BP1, PALB2, POLk, CSA, CSB and POLβ. In humans, their absence affects DSB signaling, HR and sub-pathways of NER and BER. Seven orthologs not known in D. melanogaster were found in Ae. aegypti (RNF168, RIF1, WRN, RAD54B, RMI1, DNAPKcs, ARTEMIS). Conclusions The presence of key DDR proteins in Ae. aegypti suggests that the main DDR pathways are functional in this insect, and the identification of proteins not known in D. melanogaster can help fill gaps in the DDR network. The mapping of the DDR network in Ae. aegypti can support mosquito biology studies and inform genetic manipulation approaches applied to this vector.
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Affiliation(s)
- Maria Beatriz S Mota
- Departamento de Bioquímica, Instituto de Química, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Marcelo Alex Carvalho
- Instituto Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil.,Instituto Nacional de Câncer, Divisão de Pesquisa Clínica, Rio de Janeiro, RJ, Brazil
| | - Alvaro N A Monteiro
- Cancer Epidemiology Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Rafael D Mesquita
- Departamento de Bioquímica, Instituto de Química, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil. .,Instituto Nacional de Ciência e Tecnologia em Entomologia Molecular, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil.
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12
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Felipe-Medina N, Gómez-H L, Condezo YB, Sanchez-Martín M, Barbero JL, Ramos I, Llano E, Pendás AM. Ubiquitin-specific protease 26 (USP26) is not essential for mouse gametogenesis and fertility. Chromosoma 2019; 128:237-247. [PMID: 30887115 DOI: 10.1007/s00412-019-00697-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 02/18/2019] [Accepted: 02/22/2019] [Indexed: 12/19/2022]
Abstract
Ubiquitin-specific protease 26 (USP26) is a deubiquitylating enzyme belonging to the USPs family with a transcription pattern restricted to the male germline. Since protein ubiquitination is an essential regulatory mechanism during meiosis, many efforts have been focused on elucidating the function of USP26 and its relationship with fertility. During the last decade, several studies have reported the presence of different polymorphisms in USP26 in patients with non-obstructive azoospermia (NOA) or severe oligozoospermia suggesting that this gene may be associated with human infertility. However, other studies have revealed the presence of these and novel polymorphisms, including nonsense mutations, in men with normal spermatogenesis as well. Thus, the results remain controversial and its function is unknown. In the present study, we describe the in vivo functional analysis of mice lacking USP26. The phenotypic analysis of two different Usp26-null mutants showed no overt-phenotype with both males and females being fertile. Cytological analysis of spermatocytes showed no defects in synapsis, chromosome dynamics, DNA repair, or recombination. Histopathological analysis revealed a normal distribution and number of the different cell types in both male and female mice. Finally, normal counts were observed in fertility assessments. These results represent the first in vivo evidence showing that USP26 is not essential for mouse gametogenesis.
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Affiliation(s)
- Natalia Felipe-Medina
- Molecular Mechanisms Program, Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer (CSIC-Universidad de Salamanca), 37007, Salamanca, Spain
| | - Laura Gómez-H
- Molecular Mechanisms Program, Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer (CSIC-Universidad de Salamanca), 37007, Salamanca, Spain
| | - Yazmine B Condezo
- Molecular Mechanisms Program, Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer (CSIC-Universidad de Salamanca), 37007, Salamanca, Spain
| | - Manuel Sanchez-Martín
- Departamento de Medicina, Universidad de Salamanca, Salamanca, 37007, Spain
- Transgenic Facility, Nucleus platform, Universidad de Salamanca, Salamanca, 37007, Spain
| | - José Luis Barbero
- Departamento de Biología Celular y Molecular, Centro de Investigaciones Biológicas (CSIC), Madrid, 28040, Spain
| | - Isabel Ramos
- Molecular Mechanisms Program, Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer (CSIC-Universidad de Salamanca), 37007, Salamanca, Spain
| | - Elena Llano
- Molecular Mechanisms Program, Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer (CSIC-Universidad de Salamanca), 37007, Salamanca, Spain
- Departamento de Fisiología y Farmacología, Universidad de Salamanca, Salamanca, 37007, Spain
| | - Alberto M Pendás
- Molecular Mechanisms Program, Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer (CSIC-Universidad de Salamanca), 37007, Salamanca, Spain.
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13
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53BP1: A key player of DNA damage response with critical functions in cancer. DNA Repair (Amst) 2019; 73:110-119. [DOI: 10.1016/j.dnarep.2018.11.008] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2018] [Revised: 11/18/2018] [Accepted: 11/19/2018] [Indexed: 02/06/2023]
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14
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Halim VA, García-Santisteban I, Warmerdam DO, van den Broek B, Heck AJR, Mohammed S, Medema RH. Doxorubicin-induced DNA Damage Causes Extensive Ubiquitination of Ribosomal Proteins Associated with a Decrease in Protein Translation. Mol Cell Proteomics 2018; 17:2297-2308. [PMID: 29438997 PMCID: PMC6283304 DOI: 10.1074/mcp.ra118.000652] [Citation(s) in RCA: 18] [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: 02/06/2018] [Indexed: 11/06/2022] Open
Abstract
Protein posttranslational modifications (PTMs) play a central role in the DNA damage response. In particular, protein phosphorylation and ubiquitination have been shown to be essential in the signaling cascade that coordinates break repair with cell cycle progression. Here, we performed whole-cell quantitative proteomics to identify global changes in protein ubiquitination that are induced by DNA double-strand breaks. In total, we quantified more than 9,400 ubiquitin sites and found that the relative abundance of ∼10% of these sites was altered in response to DNA double-strand breaks. Interestingly, a large proportion of ribosomal proteins, including those from the 40S as well as the 60S subunit, were ubiquitinated in response to DNA damage. In parallel, we discovered that DNA damage leads to the inhibition of ribosome function. Taken together, these data uncover the ribosome as a major target of the DNA damage response.
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Affiliation(s)
- Vincentius A Halim
- Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CH Utrecht, The Netherlands; Netherlands Proteomics Centre, 3584 CH Utrecht, The Netherlands; Division of Cell Biology and Cancer Genomics Center, Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | - Iraia García-Santisteban
- Division of Cell Biology and Cancer Genomics Center, Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands; Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Daniel O Warmerdam
- Division of Cell Biology and Cancer Genomics Center, Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands; European Research Institute for the Biology of Ageing, University Medical Center Groningen, 9713 AV Groningen, The Netherlands
| | - Bram van den Broek
- Division of Cell Biology and Cancer Genomics Center, Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CH Utrecht, The Netherlands; Netherlands Proteomics Centre, 3584 CH Utrecht, The Netherlands
| | - Shabaz Mohammed
- Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CH Utrecht, The Netherlands; Netherlands Proteomics Centre, 3584 CH Utrecht, The Netherlands; Department of Biochemistry, University of Oxford, OX13TA Oxford, United Kingdom; Chemistry Research Laboratory, Department of Chemistry, University of Oxford, OX13TA Oxford, United Kingdom
| | - René H Medema
- Division of Cell Biology and Cancer Genomics Center, Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands.
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15
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The Role for the DSB Response Pathway in Regulating Chromosome Translocations. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1044:65-87. [PMID: 29956292 DOI: 10.1007/978-981-13-0593-1_6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
In response to DNA double strand breaks (DSB), mammalian cells activate the DNA Damage Response (DDR), a network of factors that coordinate their detection, signaling and repair. Central to this network is the ATM kinase and its substrates at chromatin surrounding DSBs H2AX, MDC1 and 53BP1. In humans, germline inactivation of ATM causes Ataxia Telangiectasia (A-T), an autosomal recessive syndrome of increased proneness to hematological malignancies driven by clonal chromosomal translocations. Studies of cancers arising in A-T patients and in genetically engineered mouse models (GEMM) deficient for ATM and its substrates have revealed complex, multilayered roles for ATM in translocation suppression and identified functional redundancies between ATM and its substrates in this context. "Programmed" DSBs at antigen receptor loci in developing lymphocytes employ ubiquitous DDR factors for signaling and repair and have been particularly useful for mechanistic studies because they are region-specific and can be monitored in vitro and in vivo. In this context, murine thymocytes deficient for ATM recapitulate the molecular events that lead to transformation in T cells from A-T patients and provide a widely used model to study the mechanisms that suppress RAG recombinase-dependent translocations. Similarly, analyses of the fate of Activation induced Cytidine Deaminase (AID)-dependent DSBs during mature B cell Class Switch Recombination (CSR) have defined the genetic requirements for end-joining and translocation suppression in this setting. Moreover, a unique role for 53BP1 in the promotion of synapsis of distant DSBs has emerged from these studies.
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16
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Wang J, Yuan Z, Cui Y, Xie R, Yang G, Kassab MA, Wang M, Ma Y, Wu C, Yu X, Liu X. Molecular basis for the inhibition of the methyl-lysine binding function of 53BP1 by TIRR. Nat Commun 2018; 9:2689. [PMID: 30002377 PMCID: PMC6043480 DOI: 10.1038/s41467-018-05174-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2018] [Accepted: 06/14/2018] [Indexed: 11/09/2022] Open
Abstract
53BP1 performs essential functions in DNA double-strand break (DSB) repair and it was recently reported that Tudor interacting repair regulator (TIRR) negatively regulates 53BP1 during DSB repair. Here, we present the crystal structure of the 53BP1 tandem Tudor domain (TTD) in complex with TIRR. Our results show that three loops from TIRR interact with 53BP1 TTD and mask the methylated lysine-binding pocket in TTD. Thus, TIRR competes with histone H4K20 methylation for 53BP1 binding. We map key interaction residues in 53BP1 TTD and TIRR, whose mutation abolishes complex formation. Moreover, TIRR suppresses the relocation of 53BP1 to DNA lesions and 53BP1-dependent DNA damage repair. Finally, despite the high-sequence homology between TIRR and NUDT16, NUDT16 does not directly interact with 53BP1 due to the absence of key residues required for binding. Taken together, our study provides insights into the molecular mechanism underlying TIRR-mediated suppression of 53BP1-dependent DNA damage repair.
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Affiliation(s)
- Jiaxu Wang
- College of Life Sciences, Hebei University, Baoding, 071000, Hebei, China
| | - Zenglin Yuan
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, 250100, Shandong, China
| | - Yaqi Cui
- College of Life Sciences, Hebei University, Baoding, 071000, Hebei, China
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope, 1500 East Duarte Road, Duarte, CA, 91010, USA
| | - Rong Xie
- College of Life Sciences, Hebei University, Baoding, 071000, Hebei, China
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope, 1500 East Duarte Road, Duarte, CA, 91010, USA
| | - Guang Yang
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope, 1500 East Duarte Road, Duarte, CA, 91010, USA
| | - Muzaffer A Kassab
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope, 1500 East Duarte Road, Duarte, CA, 91010, USA
| | - Mengxi Wang
- College of Life Sciences, Hebei University, Baoding, 071000, Hebei, China
| | - Yinliang Ma
- College of Life Sciences, Hebei University, Baoding, 071000, Hebei, China
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope, 1500 East Duarte Road, Duarte, CA, 91010, USA
| | - Chen Wu
- College of Life Sciences, Hebei University, Baoding, 071000, Hebei, China
| | - Xiaochun Yu
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope, 1500 East Duarte Road, Duarte, CA, 91010, USA.
| | - Xiuhua Liu
- College of Life Sciences, Hebei University, Baoding, 071000, Hebei, China.
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17
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Role of RNF20 in cancer development and progression - a comprehensive review. Biosci Rep 2018; 38:BSR20171287. [PMID: 29934362 PMCID: PMC6043722 DOI: 10.1042/bsr20171287] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Revised: 06/20/2018] [Accepted: 06/22/2018] [Indexed: 02/06/2023] Open
Abstract
Evolving strategies to counter cancer initiation and progression rely on the identification of novel therapeutic targets that exploit the aberrant genetic changes driving oncogenesis. Several chromatin associated enzymes have been shown to influence post-translational modification (PTM) in DNA, histones, and non-histone proteins. Any deregulation of this core group of enzymes often leads to cancer development. Ubiquitylation of histone H2B in mammalian cells was identified over three decades ago. An exciting really interesting new gene (RING) family of E3 ubiquitin ligases, known as RNF20 and RNF40, monoubiquitinates histone H2A at K119 or H2B at K120, is known to function in transcriptional elongation, DNA double-strand break (DSB) repair processes, maintenance of chromatin differentiation, and exerting tumor suppressor activity. RNF20 is somatically altered in breast, lung, prostate cancer, clear cell renal cell carcinoma (ccRCC), and mixed lineage leukemia, and its reduced expression is a key factor in initiating genome instability; and it also functions as one of the significant driving factors of oncogenesis. Loss of RNF20/40 and H2B monoubiquitination (H2Bub1) is found in several cancers and is linked to an aggressive phenotype, and is also an indicator of poor prognosis. In this review, we summarized the current knowledge of RNF20 in chronic inflammation-driven cancers, DNA DSBs, and apoptosis, and its impact on chromatin structure beyond the single nucleosome level.
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18
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Nowsheen S, Aziz K, Aziz A, Deng M, Qin B, Luo K, Jeganathan KB, Zhang H, Liu T, Yu J, Deng Y, Yuan J, Ding W, van Deursen JM, Lou Z. L3MBTL2 orchestrates ubiquitin signalling by dictating the sequential recruitment of RNF8 and RNF168 after DNA damage. Nat Cell Biol 2018; 20:455-464. [PMID: 29581593 PMCID: PMC6083879 DOI: 10.1038/s41556-018-0071-x] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Accepted: 02/22/2018] [Indexed: 12/12/2022]
Abstract
Cells respond to cytotoxic DNA double-strand breaks (DSBs) by recruiting DNA repair proteins to the damaged site. This recruitment is dependent on ubiquitylation of adjacent chromatin areas by E3 ubiquitin ligases such as RNF8 and RNF168, which are recruited sequentially to the DSBs. However, it is unclear what dictates the sequential order and recruits RNF168 to the DNA lesion. Here, we reveal that L3MBTL2 (lethal(3)malignant brain tumour-like protein 2) is the missing link between RNF8 and RNF168. We found that L3MBTL2 is recruited by MDC1 and subsequently ubiquitylated by RNF8. Ubiquitylated L3MBTL2, in turn, facilitates recruitment of RNF168 to the DNA lesion and promotes DNA DSB repair. These results identify L3MBTL2 as a key target of RNF8 following DNA damage and demonstrates how the DNA damage response pathway is orchestrated by ubiquitin signalling.
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Affiliation(s)
- Somaira Nowsheen
- Mayo Medical Scientist Training Program, Mayo Clinic School of Medicine and Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic, Rochester, MN, USA
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA
| | - Khaled Aziz
- Mayo Medical Scientist Training Program, Mayo Clinic School of Medicine and Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic, Rochester, MN, USA
| | - Asef Aziz
- Department of Pediatrics and Adolescent Medicine, Mayo Clinic, Rochester, MN, USA
| | - Min Deng
- Department of Oncology, Mayo Clinic, Rochester, MN, USA
| | - Bo Qin
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA
- Department of Oncology, Mayo Clinic, Rochester, MN, USA
| | - Kuntian Luo
- Department of Oncology, Mayo Clinic, Rochester, MN, USA
| | - Karthik B Jeganathan
- Department of Pediatrics and Adolescent Medicine, Mayo Clinic, Rochester, MN, USA
| | - Henan Zhang
- Department of Hematology, Mayo Clinic, Rochester, MN, USA
| | - Tongzheng Liu
- Department of Oncology, Mayo Clinic, Rochester, MN, USA
- Institute of Tumor Pharmacology, Jinan University, Guangzhou, China
| | - Jia Yu
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA
| | - Yibin Deng
- Laboratory of Cancer Genetics, The University of Minnesota Hormel Institute, Austin, MN, USA
| | - Jian Yuan
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA
- Research Center for Translational Medicine, East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Wei Ding
- Department of Hematology, Mayo Clinic, Rochester, MN, USA
| | - Jan M van Deursen
- Department of Pediatrics and Adolescent Medicine, Mayo Clinic, Rochester, MN, USA
| | - Zhenkun Lou
- Department of Oncology, Mayo Clinic, Rochester, MN, USA.
- Research Center for Translational Medicine, East Hospital, Tongji University School of Medicine, Shanghai, China.
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19
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DNA damage-induced histone H1 ubiquitylation is mediated by HUWE1 and stimulates the RNF8-RNF168 pathway. Sci Rep 2017; 7:15353. [PMID: 29127375 PMCID: PMC5681673 DOI: 10.1038/s41598-017-15194-y] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Accepted: 10/16/2017] [Indexed: 01/08/2023] Open
Abstract
The DNA damage response (DDR), comprising distinct repair and signalling pathways, safeguards genomic integrity. Protein ubiquitylation is an important regulatory mechanism of the DDR. To study its role in the UV-induced DDR, we characterized changes in protein ubiquitylation following DNA damage using quantitative di-Gly proteomics. Interestingly, we identified multiple sites of histone H1 that are ubiquitylated upon UV-damage. We show that UV-dependent histone H1 ubiquitylation at multiple lysines is mediated by the E3-ligase HUWE1. Recently, it was shown that poly-ubiquitylated histone H1 is an important signalling intermediate in the double strand break response. This poly-ubiquitylation is dependent on RNF8 and Ubc13 which extend pre-existing ubiquitin modifications to K63-linked chains. Here we demonstrate that HUWE1 depleted cells showed reduced recruitment of RNF168 and 53BP1 to sites of DNA damage, two factors downstream of RNF8 mediated histone H1 poly-ubiquitylation, while recruitment of MDC1, which act upstream of histone H1 ubiquitylation, was not affected. Our data show that histone H1 is a prominent target for ubiquitylation after UV-induced DNA damage. Our data are in line with a model in which HUWE1 primes histone H1 with ubiquitin to allow ubiquitin chain elongation by RNF8, thereby stimulating the RNF8-RNF168 mediated DDR.
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20
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Lee JH, Park SJ, Hariharasudhan G, Kim MJ, Jung SM, Jeong SY, Chang IY, Kim C, Kim E, Yu J, Bae S, You HJ. ID3 regulates the MDC1-mediated DNA damage response in order to maintain genome stability. Nat Commun 2017; 8:903. [PMID: 29026069 PMCID: PMC5638908 DOI: 10.1038/s41467-017-01051-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 08/14/2017] [Indexed: 01/01/2023] Open
Abstract
MDC1 plays a critical role in the DNA damage response (DDR) by interacting directly with several factors including γ-H2AX. However, the mechanism by which MDC1 is recruited to damaged sites remains elusive. Here, we show that MDC1 interacts with a helix–loop–helix (HLH)-containing protein called inhibitor of DNA-binding 3 (ID3). In response to double-strand breaks (DSBs) in the genome, ATM phosphorylates ID3 at serine 65 within the HLH motif, and this modification allows a direct interaction with MDC1. Moreover, depletion of ID3 results in impaired formation of ionizing radiation (IR)-induced MDC1 foci, suppression of γ-H2AX-bound MDC1, impaired DSB repair, cellular hypersensitivity to IR, and genomic instability. Disruption of the MDC1–ID3 interaction prevents accumulation of MDC1 at sites of DSBs and suppresses DSB repair. Thus, our study uncovers an ID3-dependent mechanism of recruitment of MDC1 to DNA damage sites and suggests that the ID3–MDC1 interaction is crucial for DDR. MDC1 is a key component of the DNA damage response and interacts with several factors such as γ-H2AX. Here the authors show that MDC1 interacts with ID3, facilitating MDC1 recruitment to sites of damage and repair of breaks.
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Affiliation(s)
- Jung-Hee Lee
- Laboratory of Genomic Instability and Cancer Therapeutics, Cancer Mutation Research Center, Chosun University School of medicine, Gwangju, 501-759, Republic of Korea. .,Department of Cellular and Molecular Medicine, Chosun University School of medicine, Gwangju, 501-759, Republic of Korea.
| | - Seon-Joo Park
- Laboratory of Genomic Instability and Cancer Therapeutics, Cancer Mutation Research Center, Chosun University School of medicine, Gwangju, 501-759, Republic of Korea.,Department of Premedical Sciences, Chosun University School of medicine, Gwangju, 501-759, Republic of Korea
| | - Gurusamy Hariharasudhan
- Laboratory of Genomic Instability and Cancer Therapeutics, Cancer Mutation Research Center, Chosun University School of medicine, Gwangju, 501-759, Republic of Korea
| | - Min-Ji Kim
- Laboratory of Genomic Instability and Cancer Therapeutics, Cancer Mutation Research Center, Chosun University School of medicine, Gwangju, 501-759, Republic of Korea
| | - Sung Mi Jung
- Laboratory of Genomic Instability and Cancer Therapeutics, Cancer Mutation Research Center, Chosun University School of medicine, Gwangju, 501-759, Republic of Korea
| | - Seo-Yeon Jeong
- Laboratory of Genomic Instability and Cancer Therapeutics, Cancer Mutation Research Center, Chosun University School of medicine, Gwangju, 501-759, Republic of Korea.,Department of Cellular and Molecular Medicine, Chosun University School of medicine, Gwangju, 501-759, Republic of Korea
| | - In-Youb Chang
- Department of Anatomy, Chosun University School of medicine, Gwangju, 501-759, Republic of Korea
| | - Cheolhee Kim
- College of Pharmacy, Chosun University, 375 Seosuk-dong, Gwangju, 501-759, Republic of Korea
| | - Eunae Kim
- College of Pharmacy, Chosun University, 375 Seosuk-dong, Gwangju, 501-759, Republic of Korea
| | - Jihyeon Yu
- Department of Chemistry, Hanyang University, Seoul, 04763, Republic of Korea
| | - Sangsu Bae
- Department of Chemistry, Hanyang University, Seoul, 04763, Republic of Korea
| | - Ho Jin You
- Laboratory of Genomic Instability and Cancer Therapeutics, Cancer Mutation Research Center, Chosun University School of medicine, Gwangju, 501-759, Republic of Korea. .,Department of Pharmacology, Chosun University School of medicine, Gwangju, 501-759, Republic of Korea.
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21
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van den Boom J, Wolf M, Weimann L, Schulze N, Li F, Kaschani F, Riemer A, Zierhut C, Kaiser M, Iliakis G, Funabiki H, Meyer H. VCP/p97 Extracts Sterically Trapped Ku70/80 Rings from DNA in Double-Strand Break Repair. Mol Cell 2017; 64:189-198. [PMID: 27716483 DOI: 10.1016/j.molcel.2016.08.037] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Revised: 07/18/2016] [Accepted: 08/30/2016] [Indexed: 02/07/2023]
Abstract
During DNA double-strand break (DSB) repair, the ring-shaped Ku70/80 complex becomes trapped on DNA and needs to be actively extracted, but it has remained unclear what provides the required energy. By means of reconstitution of DSB repair on beads, we demonstrate here that DNA-locked Ku rings are released by the AAA-ATPase p97. To achieve this, p97 requires ATP hydrolysis, cooperates with the Ufd1-Npl4 ubiquitin-adaptor complex, and specifically targets Ku80 that is modified by K48-linked ubiquitin chains. In U2OS cells, chemical inhibition of p97 or siRNA-mediated depletion of p97 or its adapters impairs Ku80 removal after non-homologous end joining of DSBs. Moreover, this inhibition attenuates early steps in homologous recombination, consistent with p97-driven Ku release also affecting repair pathway choice. Thus, our data answer a central question regarding regulation of Ku in DSB repair and illustrate the ability of p97 to segregate even tightly bound protein complexes for release from DNA.
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Affiliation(s)
- Johannes van den Boom
- Molecular Biology I, Faculty of Biology, University of Duisburg-Essen, 45117 Essen, Germany
| | - Markus Wolf
- Molecular Biology I, Faculty of Biology, University of Duisburg-Essen, 45117 Essen, Germany
| | - Lena Weimann
- Molecular Biology I, Faculty of Biology, University of Duisburg-Essen, 45117 Essen, Germany
| | - Nina Schulze
- ICCE, Faculty of Biology, University of Duisburg-Essen, 45117 Essen, Germany
| | - Fanghua Li
- Institute of Medical Radiation Biology, Medical School, University of Duisburg-Essen, 45122 Essen, Germany
| | - Farnusch Kaschani
- Chemical Proteomics, Faculty of Biology, University of Duisburg-Essen, 45117 Essen, Germany
| | - Anne Riemer
- Molecular Biology I, Faculty of Biology, University of Duisburg-Essen, 45117 Essen, Germany
| | - Christian Zierhut
- Laboratory of Chromosome and Cell Biology, The Rockefeller University, New York, NY 10065, USA
| | - Markus Kaiser
- Chemical Proteomics, Faculty of Biology, University of Duisburg-Essen, 45117 Essen, Germany
| | - George Iliakis
- Institute of Medical Radiation Biology, Medical School, University of Duisburg-Essen, 45122 Essen, Germany
| | - Hironori Funabiki
- Laboratory of Chromosome and Cell Biology, The Rockefeller University, New York, NY 10065, USA
| | - Hemmo Meyer
- Molecular Biology I, Faculty of Biology, University of Duisburg-Essen, 45117 Essen, Germany.
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22
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Abstract
Cellular chromosomal DNA is the principal target through which ionising radiation exerts it diverse biological effects. This chapter summarises the relevant DNA damage signalling and repair pathways used by normal and tumour cells in response to irradiation. Strategies for tumour radiosensitisation are reviewed which exploit tumour-specific DNA repair deficiencies or signalling pathway addictions, with a special focus on growth factor signalling, PARP, cancer stem cells, cell cycle checkpoints and DNA replication. This chapter concludes with a discussion of DNA repair-related candidate biomarkers of tumour response which are of crucial importance for implementing precision medicine in radiation oncology.
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Schwertman P, Bekker-Jensen S, Mailand N. Regulation of DNA double-strand break repair by ubiquitin and ubiquitin-like modifiers. Nat Rev Mol Cell Biol 2017; 17:379-94. [PMID: 27211488 DOI: 10.1038/nrm.2016.58] [Citation(s) in RCA: 265] [Impact Index Per Article: 37.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
DNA double-strand breaks (DSBs) are highly cytotoxic DNA lesions. The swift recognition and faithful repair of such damage is crucial for the maintenance of genomic stability, as well as for cell and organismal fitness. Signalling by ubiquitin, SUMO and other ubiquitin-like modifiers (UBLs) orchestrates and regulates cellular responses to DSBs at multiple levels, often involving extensive crosstalk between these modifications. Recent findings have revealed compelling insights into the complex mechanisms by which ubiquitin and UBLs regulate protein interactions with DSB sites to promote accurate lesion repair and protection of genome integrity in mammalian cells. These advances offer new therapeutic opportunities for diseases linked to genetic instability.
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Affiliation(s)
- Petra Schwertman
- Ubiquitin Signaling Group, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Simon Bekker-Jensen
- Ubiquitin Signaling Group, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Niels Mailand
- Ubiquitin Signaling Group, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
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24
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Nie M, Moser BA, Nakamura TM, Boddy MN. SUMO-targeted ubiquitin ligase activity can either suppress or promote genome instability, depending on the nature of the DNA lesion. PLoS Genet 2017; 13:e1006776. [PMID: 28475613 PMCID: PMC5438191 DOI: 10.1371/journal.pgen.1006776] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Revised: 05/19/2017] [Accepted: 04/24/2017] [Indexed: 11/19/2022] Open
Abstract
The posttranslational modifiers SUMO and ubiquitin critically regulate the DNA damage response (DDR). Important crosstalk between these modifiers at DNA lesions is mediated by the SUMO-targeted ubiquitin ligase (STUbL), which ubiquitinates SUMO chains to generate SUMO-ubiquitin hybrids. These SUMO-ubiquitin hybrids attract DDR proteins able to bind both modifiers, and/or are degraded at the proteasome. Despite these insights, specific roles for SUMO chains and STUbL in the DDR remain poorly defined. Notably, fission yeast defective in SUMO chain formation exhibit near wild-type resistance to genotoxins and moreover, have a greatly reduced dependency on STUbL activity for DNA repair. Based on these and other data, we propose that a critical role of STUbL is to antagonize DDR-inhibitory SUMO chain formation at DNA lesions. In this regard, we identify a SUMO-binding Swi2/Snf2 translocase called Rrp2 (ScUls1) as a mediator of the DDR defects in STUbL mutant cells. Therefore, in support of our proposal, SUMO chains attract activities that can antagonize STUbL and other DNA repair factors. Finally, we find that Taz1TRF1/TRF2-deficiency triggers extensive telomeric poly-SUMOylation. In this setting STUbL, together with its cofactor Cdc48p97, actually promotes genomic instability caused by the aberrant processing of taz1Δ telomeres by DNA repair factors. In summary, depending on the nature of the initiating DNA lesion, STUbL activity can either be beneficial or harmful. Since its discovery in 2007, SUMO-targeted ubiquitin ligase (STUbL) activity has been identified as a key regulator of diverse cellular processes such as DNA repair, mitosis and DNA replication. In each of these processes, STUbL has been shown to promote the chromatin extraction and/or degradation of SUMO chain modified proteins. However, it remains unclear whether STUbL acts as part of a "programmed" cascade to remove specific proteins, or antagonizes localized SUMO chain formation that otherwise impedes each process. Here we determine that SUMO chains, the major recruitment signal for STUbL, are largely dispensable for genotoxin resistance in fission yeast. Moreover, when SUMO chain formation is compromised, the need for STUbL activity in DNA repair is strongly reduced. These results indicate a primary role for STUbL in antagonizing localized SUMO chain formation. Interestingly, we also find that STUbL activity can be toxic at certain genomic lesions that induce extensive local SUMOylation. For example, STUbL promotes the chromosome instability and cell death caused by deprotected telomeres following Taz1TRF1/2 deletion. Together, our data suggest that STUbL limits DNA repair-inhibitory SUMO chain formation, and depending on the nature of the genomic lesion, can either suppress or cause genome instability.
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Affiliation(s)
- Minghua Nie
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, United States of America
| | - Bettina A. Moser
- Department of Biochemistry and Molecular Genetics, College of Medicine, University of Illinois at Chicago, Chicago, IL, United States of America
| | - Toru M. Nakamura
- Department of Biochemistry and Molecular Genetics, College of Medicine, University of Illinois at Chicago, Chicago, IL, United States of America
| | - Michael N. Boddy
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, United States of America
- * E-mail:
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25
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Kuo CY, Li X, Stark JM, Shih HM, Ann DK. RNF4 regulates DNA double-strand break repair in a cell cycle-dependent manner. Cell Cycle 2016; 15:787-98. [PMID: 26766492 PMCID: PMC4845925 DOI: 10.1080/15384101.2016.1138184] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
Both RNF4 and KAP1 play critical roles in the response to DNA double-strand breaks (DSBs), but the functional interplay of RNF4 and KAP1 in regulating DNA damage response remains unclear. We have previously demonstrated the recruitment and degradation of KAP1 by RNF4 require the phosphorylation of Ser824 (pS824) and SUMOylation of KAP1. In this report, we show the retention of DSB-induced pS824-KAP1 foci and RNF4 abundance are inversely correlated as cell cycle progresses. Following irradiation, pS824-KAP1 foci predominantly appear in the cyclin A (-) cells, whereas RNF4 level is suppressed in the G0-/G1-phases and then accumulates during S-/G2-phases. Notably, 53BP1 foci, but not BRCA1 foci, co-exist with pS824-KAP1 foci. Depletion of KAP1 yields opposite effect on the dynamics of 53BP1 and BRCA1 loading, favoring homologous recombination repair. In addition, we identify p97 is present in the RNF4-KAP1 interacting complex and the inhibition of p97 renders MCF7 breast cancer cells relatively more sensitive to DNA damage. Collectively, these findings suggest that combined effect of dynamic recruitment of RNF4 to KAP1 regulates the relative occupancy of 53BP1 and BRCA1 at DSB sites to direct DSB repair in a cell cycle-dependent manner.
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Affiliation(s)
- Ching-Ying Kuo
- a Department of Molecular Pharmacology , Beckman Research Institute, City of Hope , Duarte , CA , USA.,b Irell & Manella Graduate School of Biological Sciences, Beckman Research Institute , City of Hope, Duarte , CA , USA
| | - Xu Li
- a Department of Molecular Pharmacology , Beckman Research Institute, City of Hope , Duarte , CA , USA
| | - Jeremy M Stark
- b Irell & Manella Graduate School of Biological Sciences, Beckman Research Institute , City of Hope, Duarte , CA , USA.,c Department of Radiation Biology , Beckman Research Institute , City of Hope, Duarte , CA , USA
| | - Hsiu-Ming Shih
- d Institute of Biomedical Sciences, Academia Sinica , Taipei , Taiwan , Republic of China
| | - David K Ann
- a Department of Molecular Pharmacology , Beckman Research Institute, City of Hope , Duarte , CA , USA.,b Irell & Manella Graduate School of Biological Sciences, Beckman Research Institute , City of Hope, Duarte , CA , USA
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26
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Xu Z, Song Z, Li G, Tu H, Liu W, Liu Y, Wang P, Wang Y, Cui X, Liu C, Shang Y, de Rooij DG, Gao F, Li W. H2B ubiquitination regulates meiotic recombination by promoting chromatin relaxation. Nucleic Acids Res 2016; 44:9681-9697. [PMID: 27431324 PMCID: PMC5175339 DOI: 10.1093/nar/gkw652] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2016] [Accepted: 07/11/2016] [Indexed: 12/22/2022] Open
Abstract
Meiotic recombination is essential for fertility in most sexually reproducing species, but the molecular mechanisms underlying this process remain poorly understood in mammals. Here, we show that RNF20-mediated H2B ubiquitination is required for meiotic recombination. A germ cell-specific knockout of the H2B ubiquitination E3 ligase RNF20 results in complete male infertility. The Stra8-Rnf20−/− spermatocytes arrest at the pachytene stage because of impaired programmed double-strand break (DSB) repair. Further investigations reveal that the depletion of RNF20 in the germ cells affects chromatin relaxation, thus preventing programmed DSB repair factors from being recruited to proper positions on the chromatin. The gametogenetic defects of the H2B ubiquitination deficient cells could be partially rescued by forced chromatin relaxation. Taken together, our results demonstrate that RNF20/Bre1p-mediated H2B ubiquitination regulates meiotic recombination by promoting chromatin relaxation, and suggest an old drug may provide a new way to treat some oligo- or azoospermia patients with chromatin relaxation disorders.
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Affiliation(s)
- Zhiliang Xu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.,University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Zhenhua Song
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.,University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Guoping Li
- The Key Laboratory of Geriatrics, Beijing Hospital and Beijing Institute of Geriatrics, Ministry of Health, Beijing 100730, China
| | - Huayu Tu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.,University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Weixiao Liu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yujiao Liu
- College of Marine Life, Ocean University of China, Qingdao 266003, China
| | - Pan Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yuanting Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.,University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Xiuhong Cui
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Chao Liu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.,University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Yongliang Shang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.,University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Dirk G de Rooij
- Reproductive Biology Group, Division of Developmental Biology, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, 3584 Utrecht, the Netherlands
| | - Fei Gao
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Wei Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
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27
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Cipolla L, Maffia A, Bertoletti F, Sabbioneda S. The Regulation of DNA Damage Tolerance by Ubiquitin and Ubiquitin-Like Modifiers. Front Genet 2016; 7:105. [PMID: 27379156 PMCID: PMC4904029 DOI: 10.3389/fgene.2016.00105] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Accepted: 05/25/2016] [Indexed: 11/13/2022] Open
Abstract
DNA replication is an extremely complex process that needs to be executed in a highly accurate manner in order to propagate the genome. This task requires the coordination of a number of enzymatic activities and it is fragile and prone to arrest after DNA damage. DNA damage tolerance provides a last line of defense that allows completion of DNA replication in the presence of an unrepaired template. One of such mechanisms is called post-replication repair (PRR) and it is used by the cells to bypass highly distorted templates caused by damaged bases. PRR is extremely important for the cellular life and performs the bypass of the damage both in an error-free and in an error-prone manner. In light of these two possible outcomes, PRR needs to be tightly controlled in order to prevent the accumulation of mutations leading ultimately to genome instability. Post-translational modifications of PRR proteins provide the framework for this regulation with ubiquitylation and SUMOylation playing a pivotal role in choosing which pathway to activate, thus controlling the different outcomes of damage bypass. The proliferating cell nuclear antigen (PCNA), the DNA clamp for replicative polymerases, plays a central role in the regulation of damage tolerance and its modification by ubiquitin, and SUMO controls both the error-free and error-prone branches of PRR. Furthermore, a significant number of polymerases are involved in the bypass of DNA damage possess domains that can bind post-translational modifications and they are themselves target for ubiquitylation. In this review, we will focus on how ubiquitin and ubiquitin-like modifications can regulate the DNA damage tolerance systems and how they control the recruitment of different proteins to the replication fork.
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Affiliation(s)
- Lina Cipolla
- Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche, Pavia Italia
| | - Antonio Maffia
- Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche, Pavia Italia
| | - Federica Bertoletti
- Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche, Pavia Italia
| | - Simone Sabbioneda
- Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche, Pavia Italia
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28
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Franz A, Ackermann L, Hoppe T. Ring of Change: CDC48/p97 Drives Protein Dynamics at Chromatin. Front Genet 2016; 7:73. [PMID: 27200082 PMCID: PMC4853748 DOI: 10.3389/fgene.2016.00073] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 04/16/2016] [Indexed: 12/31/2022] Open
Abstract
The dynamic composition of proteins associated with nuclear DNA is a fundamental property of chromosome biology. In the chromatin compartment dedicated protein complexes govern the accurate synthesis and repair of the genomic information and define the state of DNA compaction in vital cellular processes such as chromosome segregation or transcription. Unscheduled or faulty association of protein complexes with DNA has detrimental consequences on genome integrity. Consequently, the association of protein complexes with DNA is remarkably dynamic and can respond rapidly to cellular signaling events, which requires tight spatiotemporal control. In this context, the ring-like AAA+ ATPase CDC48/p97 emerges as a key regulator of protein complexes that are marked with ubiquitin or SUMO. Mechanistically, CDC48/p97 functions as a segregase facilitating the extraction of substrate proteins from the chromatin. As such, CDC48/p97 drives molecular reactions either by directed disassembly or rearrangement of chromatin-bound protein complexes. The importance of this mechanism is reflected by human pathologies linked to p97 mutations, including neurodegenerative disorders, oncogenesis, and premature aging. This review focuses on the recent insights into molecular mechanisms that determine CDC48/p97 function in the chromatin environment, which is particularly relevant for cancer and aging research.
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Affiliation(s)
- André Franz
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, Institute for Genetics, University of Cologne Cologne, Germany
| | - Leena Ackermann
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, Institute for Genetics, University of Cologne Cologne, Germany
| | - Thorsten Hoppe
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, Institute for Genetics, University of Cologne Cologne, Germany
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29
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Lenart P, Krejci L. Reprint of "DNA, the central molecule of aging". Mutat Res 2016; 788:25-31. [PMID: 27133220 DOI: 10.1016/j.mrfmmm.2016.04.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Revised: 01/16/2016] [Accepted: 01/30/2016] [Indexed: 01/05/2023]
Abstract
Understanding the molecular mechanism of aging could have enormous medical implications. Despite a century of research, however, there is no universally accepted theory regarding the molecular basis of aging. On the other hand, there is plentiful evidence suggesting that DNA constitutes the central molecule in this process. Here, we review the roles of chromatin structure, DNA damage, and shortening of telomeres in aging and propose a hypothesis for how their interplay leads to aging phenotypes.
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Affiliation(s)
- Peter Lenart
- Department of Biology, Masaryk University, Brno, Czech Republic
| | - Lumir Krejci
- Department of Biology, Masaryk University, Brno, Czech Republic; International Clinical Research Center, Center for Biomolecular and Cellular Engineering, St. Anne's University Hospital Brno, Brno, Czech Republic; National Centre for Biomolecular Research, Masaryk University, Brno, Czech Republic.
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30
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Pellegrino S, Altmeyer M. Interplay between Ubiquitin, SUMO, and Poly(ADP-Ribose) in the Cellular Response to Genotoxic Stress. Front Genet 2016; 7:63. [PMID: 27148359 PMCID: PMC4835507 DOI: 10.3389/fgene.2016.00063] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2016] [Accepted: 04/04/2016] [Indexed: 01/13/2023] Open
Abstract
Cells employ a complex network of molecular pathways to cope with endogenous and exogenous genotoxic stress. This multilayered response ensures that genomic lesions are efficiently detected and faithfully repaired in order to safeguard genome integrity. The molecular choreography at sites of DNA damage relies heavily on post-translational modifications (PTMs). Protein modifications with ubiquitin and the small ubiquitin-like modifier SUMO have recently emerged as important regulatory means to coordinate DNA damage signaling and repair. Both ubiquitylation and SUMOylation can lead to extensive chain-like protein modifications, a feature that is shared with yet another DNA damage-induced PTM, the modification of proteins with poly(ADP-ribose) (PAR). Chains of ubiquitin, SUMO, and PAR all contribute to the multi-protein assemblies found at sites of DNA damage and regulate their spatio-temporal dynamics. Here, we review recent advancements in our understanding of how ubiquitin, SUMO, and PAR coordinate the DNA damage response and highlight emerging examples of an intricate interplay between these chain-like modifications during the cellular response to genotoxic stress.
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Affiliation(s)
| | - Matthias Altmeyer
- Department of Molecular Mechanisms of Disease, University of ZurichZürich, Switzerland
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31
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Dantuma NP, Pfeiffer A. Real Estate in the DNA Damage Response: Ubiquitin and SUMO Ligases Home in on DNA Double-Strand Breaks. Front Genet 2016; 7:58. [PMID: 27148355 PMCID: PMC4826866 DOI: 10.3389/fgene.2016.00058] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Accepted: 03/26/2016] [Indexed: 11/13/2022] Open
Abstract
Ubiquitin and the ubiquitin-like modifier SUMO are intimately connected with the cellular response to various types of DNA damage. A striking feature is the local accumulation of these proteinaceous post-translational modifications in the direct vicinity to DNA double-strand breaks, which plays a critical role in the formation of ionizing radiation-induced foci. The functional significance of these modifications is the coordinated recruitment and removal of proteins involved in DNA damage signaling and repair in a timely manner. The central orchestrators of these processes are the ubiquitin and SUMO ligases that are responsible for accurately tagging a broad array of chromatin and chromatin-associated proteins thereby changing their behavior or destination. Despite many differences in the mode of action of these enzymes, they share some striking features that are of direct relevance for their function in the DNA damage response. In this review, we outline the molecular mechanisms that are responsible for the recruitment of ubiquitin and SUMO ligases and discuss the importance of chromatin proximity in this process.
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Affiliation(s)
- Nico P Dantuma
- Department of Cell and Molecular Biology, Karolinska Institutet Stockholm, Sweden
| | - Annika Pfeiffer
- Department of Cell and Molecular Biology, Karolinska Institutet Stockholm, Sweden
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32
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DNA, the central molecule of aging. Mutat Res 2016; 786:1-7. [PMID: 26871429 DOI: 10.1016/j.mrfmmm.2016.01.007] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Revised: 01/16/2016] [Accepted: 01/30/2016] [Indexed: 02/07/2023]
Abstract
Understanding the molecular mechanism of aging could have enormous medical implications. Despite a century of research, however, there is no universally accepted theory regarding the molecular basis of aging. On the other hand, there is plentiful evidence suggesting that DNA constitutes the central molecule in this process. Here, we review the roles of chromatin structure, DNA damage, and shortening of telomeres in aging and propose a hypothesis for how their interplay leads to aging phenotypes.
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33
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RFWD3-Dependent Ubiquitination of RPA Regulates Repair at Stalled Replication Forks. Mol Cell 2016; 60:280-93. [PMID: 26474068 DOI: 10.1016/j.molcel.2015.09.011] [Citation(s) in RCA: 100] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Revised: 08/02/2015] [Accepted: 09/10/2015] [Indexed: 02/07/2023]
Abstract
We have used quantitative proteomics to profile ubiquitination in the DNA damage response (DDR). We demonstrate that RPA, which functions as a protein scaffold in the replication stress response, is multiply ubiquitinated upon replication fork stalling. Ubiquitination of RPA occurs on chromatin, involves sites outside its DNA binding channel, does not cause proteasomal degradation, and increases under conditions of fork collapse, suggesting a role in repair at stalled forks. We demonstrate that the E3 ligase RFWD3 mediates RPA ubiquitination. RFWD3 is necessary for replication fork restart, normal repair kinetics during replication stress, and homologous recombination (HR) at stalled replication forks. Mutational analysis suggests that multisite ubiquitination of the entire RPA complex is responsible for repair at stalled forks. Multisite protein group sumoylation is known to promote HR in yeast. Our findings reveal a similar requirement for multisite protein group ubiquitination during HR at stalled forks in mammalian cells.
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34
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Liu C, Srihari S, Lal S, Gautier B, Simpson PT, Khanna KK, Ragan MA, Lê Cao KA. Personalised pathway analysis reveals association between DNA repair pathway dysregulation and chromosomal instability in sporadic breast cancer. Mol Oncol 2016; 10:179-93. [PMID: 26456802 PMCID: PMC5528935 DOI: 10.1016/j.molonc.2015.09.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Revised: 08/19/2015] [Accepted: 09/04/2015] [Indexed: 01/05/2023] Open
Abstract
The Homologous Recombination (HR) pathway is crucial for the repair of DNA double-strand breaks (DSBs) generated during DNA replication. Defects in HR repair have been linked to the initiation and development of a wide variety of human malignancies, and exploited in chemical, radiological and targeted therapies. In this study, we performed a personalised pathway analysis independently for four large sporadic breast cancer cohorts to investigate the status of HR pathway dysregulation in individual sporadic breast tumours, its association with HR repair deficiency and its impact on tumour characteristics. Specifically, we first manually curated a list of HR genes according to our recent review on this pathway (Liu et al., 2014), and then applied a personalised pathway analysis method named Pathifier (Drier et al., 2013) on the expression levels of the curated genes to obtain an HR score quantifying HR pathway dysregulation in individual tumours. Based on the score, we observed a great diversity in HR dysregulation between and within gene expression-based breast cancer subtypes, and by using two published HR-defect signatures, we found HR pathway dysregulation reflects HR repair deficiency. Furthermore, we identified a novel association between HR pathway dysregulation and chromosomal instability (CIN) in sporadic breast cancer. Although CIN has long been considered as a hallmark of most solid tumours, with recent extensive studies highlighting its importance in tumour evolution and drug resistance, the molecular basis of CIN in sporadic cancers remains poorly understood. Our results imply that HR pathway dysregulation might contribute to CIN in sporadic breast cancer.
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Affiliation(s)
- Chao Liu
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD 4067, Australia
| | - Sriganesh Srihari
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD 4067, Australia
| | - Samir Lal
- The University of Queensland, UQ Centre for Clinical Research, Herston, QLD 4029, Australia
| | - Benoît Gautier
- University of Queensland Diamantina Institute, Translational Research Institute, Woolloongabba, QLD 4102, Australia
| | - Peter T Simpson
- The University of Queensland, UQ Centre for Clinical Research, Herston, QLD 4029, Australia; School of Medicine, The University of Queensland, Herston, QLD 4006, Australia
| | - Kum Kum Khanna
- QIMR-Berghofer Medical Research Institute, Herston, Brisbane, QLD 4029, Australia
| | - Mark A Ragan
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD 4067, Australia.
| | - Kim-Anh Lê Cao
- University of Queensland Diamantina Institute, Translational Research Institute, Woolloongabba, QLD 4102, Australia.
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35
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Dantuma NP, van Attikum H. Spatiotemporal regulation of posttranslational modifications in the DNA damage response. EMBO J 2015; 35:6-23. [PMID: 26628622 DOI: 10.15252/embj.201592595] [Citation(s) in RCA: 154] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 11/06/2015] [Indexed: 11/09/2022] Open
Abstract
A timely and accurate cellular response to DNA damage requires tight regulation of the action of DNA damage response (DDR) proteins at lesions. A multitude of posttranslational modifications (PTMs) of chromatin and chromatin-associated proteins coordinates the recruitment of critical proteins that dictate the appropriate DNA repair pathway and enable the actual repair of lesions. Phosphorylation, ubiquitylation, SUMOylation, neddylation, poly(ADP-ribosyl)ation, acetylation, and methylation are among the DNA damage-induced PTMs that have taken center stage as important DDR regulators. Redundant and multivalent interactions of DDR proteins with PTMs may not only be a means to facilitate efficient relocalization, but also a feature that allows high temporal and spatial resolution of protein recruitment to, and extraction from, DNA damage sites. In this review, we will focus on the complex interplay between such PTMs, and discuss the importance of their interconnectivity in coding DNA lesions and maintaining the integrity of the genome.
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Affiliation(s)
- Nico P Dantuma
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Haico van Attikum
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
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36
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Lavin MF, Kozlov S, Gatei M, Kijas AW. ATM-Dependent Phosphorylation of All Three Members of the MRN Complex: From Sensor to Adaptor. Biomolecules 2015; 5:2877-902. [PMID: 26512707 PMCID: PMC4693261 DOI: 10.3390/biom5042877] [Citation(s) in RCA: 103] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Revised: 10/14/2015] [Accepted: 10/16/2015] [Indexed: 11/16/2022] Open
Abstract
The recognition, signalling and repair of DNA double strand breaks (DSB) involves the participation of a multitude of proteins and post-translational events that ensure maintenance of genome integrity. Amongst the proteins involved are several which when mutated give rise to genetic disorders characterised by chromosomal abnormalities, cancer predisposition, neurodegeneration and other pathologies. ATM (mutated in ataxia-telangiectasia (A-T) and members of the Mre11/Rad50/Nbs1 (MRN complex) play key roles in this process. The MRN complex rapidly recognises and locates to DNA DSB where it acts to recruit and assist in ATM activation. ATM, in the company of several other DNA damage response proteins, in turn phosphorylates all three members of the MRN complex to initiate downstream signalling. While ATM has hundreds of substrates, members of the MRN complex play a pivotal role in mediating the downstream signalling events that give rise to cell cycle control, DNA repair and ultimately cell survival or apoptosis. Here we focus on the interplay between ATM and the MRN complex in initiating signaling of breaks and more specifically on the adaptor role of the MRN complex in mediating ATM signalling to downstream substrates to control different cellular processes.
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Affiliation(s)
- Martin F Lavin
- UQ Centre for Clinical Research, The University of Queensland, Brisbane, QLD 4029, Australia.
| | - Sergei Kozlov
- UQ Centre for Clinical Research, The University of Queensland, Brisbane, QLD 4029, Australia.
| | - Magtouf Gatei
- UQ Centre for Clinical Research, The University of Queensland, Brisbane, QLD 4029, Australia.
| | - Amanda W Kijas
- UQ Centre for Clinical Research, The University of Queensland, Brisbane, QLD 4029, Australia.
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37
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Eifler K, Vertegaal ACO. Mapping the SUMOylated landscape. FEBS J 2015; 282:3669-80. [PMID: 26185901 PMCID: PMC4869838 DOI: 10.1111/febs.13378] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Revised: 06/15/2015] [Accepted: 07/14/2015] [Indexed: 12/26/2022]
Abstract
SUMOylation is a post‐translational modification that regulates a multitude of cellular processes, including replication, cell‐cycle progression, protein transport and the DNA damage response. Similar to ubiquitin, SUMO (small ubiquitin‐like modifier) is covalently attached to target proteins in a reversible process via an enzymatic cascade. SUMOylation is essential for nearly all eukaryotic organisms, and deregulation of the SUMO system is associated with human diseases such as cancer and neurodegenerative diseases. Therefore, it is of great interest to understand the regulation and dynamics of this post‐translational modification. Within the last decade, mass spectrometry analyses of SUMO proteomes have overcome several obstacles, greatly expanding the number of known SUMO target proteins. In this review, we briefly outline the basic concepts of the SUMO system, and discuss the potential of proteomic approaches to decipher SUMOylation patterns in order to understand the role of SUMO in health and disease.
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Affiliation(s)
- Karolin Eifler
- Department of Molecular Cell Biology, Leiden University Medical Center, Leiden, The Netherlands
| | - Alfred C O Vertegaal
- Department of Molecular Cell Biology, Leiden University Medical Center, Leiden, The Netherlands
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38
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Elia AEH, Boardman AP, Wang DC, Huttlin EL, Everley RA, Dephoure N, Zhou C, Koren I, Gygi SP, Elledge SJ. Quantitative Proteomic Atlas of Ubiquitination and Acetylation in the DNA Damage Response. Mol Cell 2015; 59:867-81. [PMID: 26051181 DOI: 10.1016/j.molcel.2015.05.006] [Citation(s) in RCA: 249] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Revised: 03/17/2015] [Accepted: 04/29/2015] [Indexed: 01/06/2023]
Abstract
Execution of the DNA damage response (DDR) relies upon a dynamic array of protein modifications. Using quantitative proteomics, we have globally profiled ubiquitination, acetylation, and phosphorylation in response to UV and ionizing radiation. To improve acetylation site profiling, we developed the strategy FACET-IP. Our datasets of 33,500 ubiquitination and 16,740 acetylation sites provide valuable insight into DDR remodeling of the proteome. We find that K6- and K33-linked polyubiquitination undergo bulk increases in response to DNA damage, raising the possibility that these linkages are largely dedicated to DDR function. We also show that Cullin-RING ligases mediate 10% of DNA damage-induced ubiquitination events and that EXO1 is an SCF-Cyclin F substrate in the response to UV radiation. Our extensive datasets uncover additional regulated sites on known DDR players such as PCNA and identify previously unknown DDR targets such as CENPs, underscoring the broad impact of the DDR on cellular physiology.
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Affiliation(s)
- Andrew E H Elia
- Department of Genetics, Harvard Medical School; Division of Genetics, Brigham and Women's Hospital; Howard Hughes Medical Institute, Boston, MA 02115, USA; Department of Radiation Oncology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Alexander P Boardman
- Department of Genetics, Harvard Medical School; Division of Genetics, Brigham and Women's Hospital; Howard Hughes Medical Institute, Boston, MA 02115, USA; Department of Radiation Oncology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - David C Wang
- Department of Genetics, Harvard Medical School; Division of Genetics, Brigham and Women's Hospital; Howard Hughes Medical Institute, Boston, MA 02115, USA; Department of Radiation Oncology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Edward L Huttlin
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Robert A Everley
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Noah Dephoure
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Chunshui Zhou
- Department of Genetics, Harvard Medical School; Division of Genetics, Brigham and Women's Hospital; Howard Hughes Medical Institute, Boston, MA 02115, USA
| | - Itay Koren
- Department of Genetics, Harvard Medical School; Division of Genetics, Brigham and Women's Hospital; Howard Hughes Medical Institute, Boston, MA 02115, USA
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Stephen J Elledge
- Department of Genetics, Harvard Medical School; Division of Genetics, Brigham and Women's Hospital; Howard Hughes Medical Institute, Boston, MA 02115, USA.
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39
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Sarangi P, Zhao X. SUMO-mediated regulation of DNA damage repair and responses. Trends Biochem Sci 2015; 40:233-42. [PMID: 25778614 DOI: 10.1016/j.tibs.2015.02.006] [Citation(s) in RCA: 104] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Revised: 02/17/2015] [Accepted: 02/17/2015] [Indexed: 12/21/2022]
Abstract
Sumoylation has important roles during DNA damage repair and responses. Recent broad-scope and substrate-based studies have shed light on the regulation and significance of sumoylation during these processes. An emerging paradigm is that sumoylation of many DNA metabolism proteins is controlled by DNA engagement. Such 'on-site modification' can explain low substrate modification levels and has important implications in sumoylation mechanisms and effects. New studies also suggest that sumoylation can regulate a process through an ensemble effect or via major substrates. Additionally, we describe new trends in the functional effects of sumoylation, such as bi-directional changes in biomolecule binding and multilevel coordination with other modifications. These emerging themes and models will stimulate our thinking and research in sumoylation and genome maintenance.
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Affiliation(s)
- Prabha Sarangi
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Programs in Biochemistry, Cell, and Molecular Biology, Weill Graduate School of Medical Sciences of Cornell University, New York, NY 10021, USA
| | - Xiaolan Zhao
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
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40
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Xie J, Kim H, Moreau LA, Puhalla S, Garber J, Al Abo M, Takeda S, D'Andrea AD. RNF4-mediated polyubiquitination regulates the Fanconi anemia/BRCA pathway. J Clin Invest 2015; 125:1523-32. [PMID: 25751062 DOI: 10.1172/jci79325] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Accepted: 01/20/2015] [Indexed: 12/13/2022] Open
Abstract
The Fanconi anemia/BRCA (FA/BRCA) pathway is a DNA repair pathway that is required for excision of DNA interstrand cross-links. The 17 known FA proteins, along with several FA-associated proteins (FAAPs), cooperate in this pathway to detect, unhook, and excise DNA cross-links and to subsequently repair the double-strand breaks generated in the process. In the current study, we identified a patient with FA with a point mutation in FANCA, which encodes a mutant FANCA protein (FANCAI939S). FANCAI939S failed to bind to the FAAP20 subunit of the FA core complex, leading to decreased stability. Loss of FAAP20 binding exposed a SUMOylation site on FANCA at amino acid residue K921, resulting in E2 SUMO-conjugating enzyme UBC9-mediated SUMOylation, RING finger protein 4-mediated (RNF4-mediated) polyubiquitination, and proteasome-mediated degradation of FANCA. Mutation of the SUMOylation site of FANCA rescued the expression of the mutant protein. Wild-type FANCA was also subject to SUMOylation, RNF4-mediated polyubiquitination, and degradation, suggesting that regulated release of FAAP20 from FANCA is a critical step in the normal FA pathway. Consistent with this model, cells lacking RNF4 exhibited interstrand cross-linker hypersensitivity, and the gene encoding RNF4 was epistatic with the other genes encoding members of the FA/BRCA pathway. Together, the results from our study underscore the importance of analyzing unique patient-derived mutations for dissecting complex DNA repair processes.
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41
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Jaiswal H, Lindqvist A. Bystander communication and cell cycle decisions after DNA damage. Front Genet 2015; 6:63. [PMID: 25774166 PMCID: PMC4343024 DOI: 10.3389/fgene.2015.00063] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Accepted: 02/08/2015] [Indexed: 01/07/2023] Open
Abstract
The DNA damage response (DDR) has two main goals, to repair the damaged DNA and to communicate the presence of damaged DNA. This communication allows the adaptation of cellular behavior to minimize the risk associated with DNA damage. In particular, cell cycle progression must be adapted after a DNA-damaging insult, and cells either pause or terminally exit the cell cycle during a DDR. As cells can accumulate mutations after a DDR due to error-prone DNA repair, terminal cell cycle exit may prevent malignant transformation. The tumor suppressor p53 plays a key role in promoting terminal cell cycle exit. Interestingly, p53 has been implicated in communication of a stress response to surrounding cells, known as the bystander response. Recently, surrounding cells have also been shown to affect the damaged cell, suggesting the presence of intercellular feedback loops. How such feedback may affect terminal cell cycle exit remains unclear, but its presence calls for caution in evaluating cellular outcome without controlling the cellular surrounding. In addition, such feedback may contribute to how the cellular environment affects malignant transformation after DNA damage.
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Affiliation(s)
- Himjyot Jaiswal
- Department of Cell and Molecular Biology, Karolinska Institutet , Stockholm, Sweden
| | - Arne Lindqvist
- Department of Cell and Molecular Biology, Karolinska Institutet , Stockholm, Sweden
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42
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SUMOylation is developmentally regulated and required for cell pairing during conjugation in Tetrahymena thermophila. EUKARYOTIC CELL 2014; 14:170-81. [PMID: 25527524 DOI: 10.1128/ec.00252-14] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The covalent attachment of small ubiquitin-like modifier (SUMO) to target proteins regulates numerous nuclear events in eukaryotes, including transcription, mitosis and meiosis, and DNA repair. Despite extensive interest in nuclear pathways within the field of ciliate molecular biology, there have been no investigations of the SUMO pathway in Tetrahymena. The developmental program of sexual reproduction of this organism includes cell pairing, micronuclear meiosis, and the formation of a new somatic macronucleus. We identified the Tetrahymena thermophila SMT3 (SUMO) and UBA2 (SUMO-activating enzyme) genes and demonstrated that the corresponding green fluorescent protein (GFP) tagged gene products are found predominantly in the somatic macronucleus during vegetative growth. Use of an anti-Smt3p antibody to perform immunoblot assays with whole-cell lysates during conjugation revealed a large increase in SUMOylation that peaked during formation of the new macronucleus. Immunofluorescence using the same antibody showed that the increase was localized primarily within the new macronucleus. To initiate functional analysis of the SUMO pathway, we created germ line knockout cell lines for both the SMT3 and UBA2 genes and found both are essential for cell viability. Conditional Smt3p and Uba2p cell lines were constructed by incorporation of the cadmium-inducible metallothionein promoter. Withdrawal of cadmium resulted in reduced cell growth and increased sensitivity to DNA-damaging agents. Interestingly, Smt3p and Uba2p conditional cell lines were unable to pair during sexual reproduction in the absence of cadmium, consistent with a function early in conjugation. Our studies are consistent with multiple roles for SUMOylation in Tetrahymena, including a dynamic regulation associated with the sexual life cycle.
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Yuan J, Luo K, Deng M, Li Y, Yin P, Gao B, Fang Y, Wu P, Liu T, Lou Z. HERC2-USP20 axis regulates DNA damage checkpoint through Claspin. Nucleic Acids Res 2014; 42:13110-21. [PMID: 25355518 PMCID: PMC4245938 DOI: 10.1093/nar/gku1034] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2014] [Revised: 09/23/2014] [Accepted: 10/12/2014] [Indexed: 12/26/2022] Open
Abstract
The DNA damage response triggers cell-cycle checkpoints, DNA repair and apoptosis using multiple post-translational modifications as molecular switches. However, how ubiquitination regulates ATR signaling in response to replication stress and single-strand break is still unclear. Here, we identified the deubiquitination enzyme (DUB) USP20 as a pivotal regulator of ATR-related DDR pathway. Through screening a panel of DUBs, we identified USP20 as critical for replication stress response. USP20 is phosphorylated by ATR, resulting in disassociation of the E3 ubiquitin ligase HERC2 from USP20 and USP20 stabilization. USP20 in turn deubiquitinates and stabilizes Claspin and enhances the activation of ATR-Chk1 signaling. These findings reveal USP20 to be a novel regulator of ATR-dependent DNA damage signaling.
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Affiliation(s)
- Jian Yuan
- Research Center for Translational Medicine, East Hospital, Tongji University School of Medicine, No. 150 Jimo Road, Shanghai 200120, China Key Laboratory of Arrhythmia, Ministry of Education, East Hospital, Tongji University School of Medicine, No. 150 Jimo Road, Shanghai 200120, China
| | - Kuntian Luo
- Research Center for Translational Medicine, East Hospital, Tongji University School of Medicine, No. 150 Jimo Road, Shanghai 200120, China Key Laboratory of Arrhythmia, Ministry of Education, East Hospital, Tongji University School of Medicine, No. 150 Jimo Road, Shanghai 200120, China
| | - Min Deng
- Division of Oncology Research, Department of Oncology, Mayo Clinic, 200 1st St. SW, Rochester, MN 55905, USA
| | - Yunhui Li
- Research Center for Translational Medicine, East Hospital, Tongji University School of Medicine, No. 150 Jimo Road, Shanghai 200120, China Key Laboratory of Arrhythmia, Ministry of Education, East Hospital, Tongji University School of Medicine, No. 150 Jimo Road, Shanghai 200120, China
| | - Ping Yin
- Division of Oncology Research, Department of Oncology, Mayo Clinic, 200 1st St. SW, Rochester, MN 55905, USA
| | - Bowen Gao
- Division of Oncology Research, Department of Oncology, Mayo Clinic, 200 1st St. SW, Rochester, MN 55905, USA
| | - Yuan Fang
- Division of Oncology Research, Department of Oncology, Mayo Clinic, 200 1st St. SW, Rochester, MN 55905, USA
| | - Puqiang Wu
- Division of Oncology Research, Department of Oncology, Mayo Clinic, 200 1st St. SW, Rochester, MN 55905, USA
| | - Tongzheng Liu
- Research Center for Translational Medicine, East Hospital, Tongji University School of Medicine, No. 150 Jimo Road, Shanghai 200120, China Key Laboratory of Arrhythmia, Ministry of Education, East Hospital, Tongji University School of Medicine, No. 150 Jimo Road, Shanghai 200120, China Division of Oncology Research, Department of Oncology, Mayo Clinic, 200 1st St. SW, Rochester, MN 55905, USA
| | - Zhenkun Lou
- Division of Oncology Research, Department of Oncology, Mayo Clinic, 200 1st St. SW, Rochester, MN 55905, USA
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44
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Samba-Louaka A, Pereira JM, Nahori MA, Villiers V, Deriano L, Hamon MA, Cossart P. Listeria monocytogenes dampens the DNA damage response. PLoS Pathog 2014; 10:e1004470. [PMID: 25340842 PMCID: PMC4207825 DOI: 10.1371/journal.ppat.1004470] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Accepted: 09/14/2014] [Indexed: 12/17/2022] Open
Abstract
The DNA damage response (DDR) is an essential signaling pathway that detects DNA lesions, which constantly occur upon either endogenous or exogenous assaults, and maintains genetic integrity. An infection by an invading pathogen is one such assault, but how bacteria impact the cellular DDR is poorly documented. Here, we report that infection with Listeria monocytogenes induces host DNA breaks. Strikingly, the signature response to these breaks is only moderately activated. We uncover the role of the listerial toxin listeriolysin O (LLO) in blocking the signaling response to DNA breaks through degradation of the sensor Mre11. Knocking out or inactivating proteins involved in the DDR promotes bacterial replication showing the importance of this mechanism for the control of infection. Together, our data highlight that bacterial dampening of the DDR is critical for a successful listerial infection. In eukaryotic cells both normal metabolic activities and environmental factors such as UV radiation can cause DNA lesions or mutations. The ability of a cell to restore integrity to its genome is vital, and depends on a signaling cascade called the DNA damage response (DDR) that both senses and responds to the assaults. Bacterial infection is one such assault, but its effect on the DDR of the invaded cell remains elusive. Here we used the bacterial pathogen Listeria monocytogenes to study its effect on host DNA damage and its impact on the DDR. Our results show that although Listeria is able to induce DNA damage, the ensuing response is surprisingly low, demonstrating that this bacterium is able to dampen the DDR. We have also shown that the listerial toxin listeriolysin O (LLO) is responsible for the observed block in the DDR. In fact, we find that LLO induces protein degradation of the main DNA damage sensor, Mre11, thereby blocking downstream signaling. Furthermore, we have studied the impact of mutating the DDR on the infectious process and find that it negatively regulates infection with Listeria. In conclusion, our findings reveal that dampening of the DDR is crucial for a productive infection.
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Affiliation(s)
- Ascel Samba-Louaka
- Institut Pasteur, Unité des interactions Bactéries-Cellules, Paris, France
- The French National Institute of Health and Medical Research (Inserm), Paris, France
- The French National Institute for Agricultural Research (INRA), Paris, France
| | - Jorge M. Pereira
- Institut Pasteur, Unité des interactions Bactéries-Cellules, Paris, France
- The French National Institute of Health and Medical Research (Inserm), Paris, France
- The French National Institute for Agricultural Research (INRA), Paris, France
| | - Marie-Anne Nahori
- Institut Pasteur, Unité des interactions Bactéries-Cellules, Paris, France
- The French National Institute of Health and Medical Research (Inserm), Paris, France
- The French National Institute for Agricultural Research (INRA), Paris, France
| | - Veronique Villiers
- Institut Pasteur, Unité des interactions Bactéries-Cellules, Paris, France
- The French National Institute of Health and Medical Research (Inserm), Paris, France
- The French National Institute for Agricultural Research (INRA), Paris, France
| | - Ludovic Deriano
- Institut Pasteur, Laboratoire développement Lymphocytaire et Oncogénèse, Paris, France
- Centre National de la Recherche Scientifique (CNRS) Paris, France
| | - Mélanie A. Hamon
- Institut Pasteur, Unité des interactions Bactéries-Cellules, Paris, France
- The French National Institute of Health and Medical Research (Inserm), Paris, France
- The French National Institute for Agricultural Research (INRA), Paris, France
- * E-mail: (MAH); (PC)
| | - Pascale Cossart
- Institut Pasteur, Unité des interactions Bactéries-Cellules, Paris, France
- The French National Institute of Health and Medical Research (Inserm), Paris, France
- The French National Institute for Agricultural Research (INRA), Paris, France
- * E-mail: (MAH); (PC)
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45
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Regulation of 53BP1 protein stability by RNF8 and RNF168 is important for efficient DNA double-strand break repair. PLoS One 2014; 9:e110522. [PMID: 25337968 PMCID: PMC4206297 DOI: 10.1371/journal.pone.0110522] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Accepted: 09/23/2014] [Indexed: 11/19/2022] Open
Abstract
53BP1 regulates DNA double-strand break (DSB) repair. In functional assays for specific DSB repair pathways, we found that 53BP1 was important in the conservative non-homologous end-joining (C-NHEJ) pathway, and this activity was dependent upon RNF8 and RNF168. We observed that 53BP1 protein was diffusely abundant in nuclei, and upon ionizing radiation, 53BP1 was everywhere degraded except at DNA damage sites. Depletion of RNF8 or RNF168 blocked the degradation of the diffusely localized nuclear 53BP1, and ionizing radiation induced foci (IRIF) did not form. Furthermore, when 53BP1 degradation was inhibited, a subset of 53BP1 was bound to DNA damage sites but bulk, unbound 53BP1 remained in the nucleoplasm, and localization of its downstream effector RIF1 at DSBs was abolished. Our data suggest a novel mechanism for responding to DSB that upon ionizing radiation, 53BP1 was divided into two populations, ensuring functional DSB repair: damage site-bound 53BP1 whose binding signal is known to be generated by RNF8 and RNF168; and unbound bulk 53BP1 whose ensuing degradation is regulated by RNF8 and RNF168.
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46
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The ubiquitin ligases RNF8 and RNF168 display rapid but distinct dynamics at DNA repair foci in living cells. Int J Biochem Cell Biol 2014; 57:27-34. [PMID: 25304081 DOI: 10.1016/j.biocel.2014.09.027] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2014] [Revised: 09/25/2014] [Accepted: 09/30/2014] [Indexed: 01/15/2023]
Abstract
Rapid assembly of DNA damage response (DDR) proteins at nuclear "repair" foci is a hallmark response of ionizing radiation (IR)-treated cells. The ubiquitin E3 ligases RNF8 and RNF168 are critical for foci formation, and here we aim to determine their dynamic mobility and abundance at individual foci in living cells. To this end, YFP-tagged RNF8 and RNF168 were expressed at physiological levels in MCF-7 cells, then analyzed by fluorescence recovery after photobleaching (FRAP) assays, nuclear retention measurement, and virus-like particles (VLPs)-based quantification. The results showed that RNF8 and RNF168 were both highly dynamic at IR-induced foci. Intriguingly, RNF8 displayed remarkably faster in vivo association/dissociation rates than RNF168, and RNF8-positive IR-foci were less resistant to detergent extraction. In addition, copy number assay revealed that RNF168 was two-fold more abundant than RNF8 at foci. Collectively, we show for the first time that RNF8 moves on-and-off nuclear DNA repair foci more than six-fold as quickly as RNF168. The faster kinetics of RNF8 recruitment explains why RNF8 is generally observed at DNA-breaks prior to RNF168. Moreover, our finding that RNF8 is less abundant than RNF168 identifies RNF8 as a rate-limiting determinant of focal repair complex assembly.
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47
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Dantuma NP, Acs K, Luijsterburg MS. Should I stay or should I go: VCP/p97-mediated chromatin extraction in the DNA damage response. Exp Cell Res 2014; 329:9-17. [PMID: 25169698 DOI: 10.1016/j.yexcr.2014.08.025] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Revised: 08/11/2014] [Accepted: 08/18/2014] [Indexed: 10/24/2022]
Abstract
The ordered assembly of DNA repair factors on chromatin has been studied in great detail, whereas we are only beginning to realize that selective extraction of proteins from chromatin plays a central role in the DNA damage response. Interestingly, the protein modifier ubiquitin not only regulates the well-documented recruitment of repair proteins, but also governs the temporally and spatially controlled extraction of proteins from DNA lesions. The facilitator of protein extraction is the ubiquitin-dependent ATPase valosin-containing protein (VCP)/p97 complex, which, through its segregase activity, directly extracts ubiquitylated proteins from chromatin. In this review, we summarize recent studies that uncovered this important role of VCP/p97 in the cellular response to genomic insults and discuss how ubiquitin regulates two intuitively counteracting activities at sites of DNA damage.
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Affiliation(s)
- Nico P Dantuma
- Department of Cell and Molecular Biology, Karolinska Institutet, von Eulers väg 3, S-17177 Stockholm, Sweden.
| | - Klara Acs
- Department of Cell and Molecular Biology, Karolinska Institutet, von Eulers väg 3, S-17177 Stockholm, Sweden
| | - Martijn S Luijsterburg
- Department of Human Genetics, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, The Netherlands.
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48
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Marchiani S, Tamburrino L, Ricci B, Nosi D, Cambi M, Piomboni P, Belmonte G, Forti G, Muratori M, Baldi E. SUMO1 in human sperm: new targets, role in motility and morphology and relationship with DNA damage. Reproduction 2014; 148:453-67. [PMID: 25118297 DOI: 10.1530/rep-14-0173] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
In studies carried out previously, we demonstrated that small ubiquitin-like modifier 1 (SUMO1) is associated with poor sperm motility when evaluated with a protocol that reveals mostly SUMO1-ylated live sperm. Recently, with another protocol, it has been demonstrated that SUMO is expressed in most sperm and is related to poor morphology and motility, suggesting that sumoylation may have multiple roles depending on its localisation and targets. We show herein, by confocal microscopy and co-immunoprecipitation, that dynamin-related protein 1 (DRP1), Ran GTPase-activating protein 1 (RanGAP1) and Topoisomerase IIα, SUMO1 targets in somatic and/or germ cells, are SUMO1-ylated in mature human spermatozoa. DRP1 co-localises with SUMO1 in the mid-piece, whereas RanGAP1 and Topoisomerase IIα in the post-acrosomal region of the head. Both SUMO1 expression and co-localisation with the three proteins were significantly higher in morphologically abnormal sperm, suggesting that sumoylation represents a marker of defective sperm. DRP1 sumoylation at the mid-piece level was higher in the sperm of asthenospermic men. As in somatic cells, DRP1 sumoylation is associated with mitochondrial alterations, this protein may represent the link between SUMO and poor motility. As SUMO pathways are involved in responses to DNA damage, another aim of our study was to investigate the relationship between sumoylation and sperm DNA fragmentation (SDF). By flow cytometry, we demonstrated that SUMO1-ylation and SDF are correlated (r=0.4, P<0.02, n=37) and most sumoylated sperm shows DNA damage in co-localisation analysis. When SDF was induced by stressful conditions (freezing and thawing and oxidative stress), SUMO1-ylation increased. Following freezing and thawing, SUMO1-Topoisomerase IIα co-localisation and co-immunoprecipitation increased, suggesting an involvement in the formation/repair of DNA breakage.
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Affiliation(s)
- S Marchiani
- Department of BiomedicalExperimental and Clinical Sciences, Center of Excellence DeNotheDepartment of Experimental and Clinical MedicineUniversity of Florence, Viale Pieraccini 6, I-50139 Florence, ItalyDepartments of Molecular and Developmental MedicineMedicalSurgical and Neurological Sciences, University of Siena, 53100 Siena, Italy
| | - L Tamburrino
- Department of BiomedicalExperimental and Clinical Sciences, Center of Excellence DeNotheDepartment of Experimental and Clinical MedicineUniversity of Florence, Viale Pieraccini 6, I-50139 Florence, ItalyDepartments of Molecular and Developmental MedicineMedicalSurgical and Neurological Sciences, University of Siena, 53100 Siena, Italy
| | - B Ricci
- Department of BiomedicalExperimental and Clinical Sciences, Center of Excellence DeNotheDepartment of Experimental and Clinical MedicineUniversity of Florence, Viale Pieraccini 6, I-50139 Florence, ItalyDepartments of Molecular and Developmental MedicineMedicalSurgical and Neurological Sciences, University of Siena, 53100 Siena, Italy
| | - D Nosi
- Department of BiomedicalExperimental and Clinical Sciences, Center of Excellence DeNotheDepartment of Experimental and Clinical MedicineUniversity of Florence, Viale Pieraccini 6, I-50139 Florence, ItalyDepartments of Molecular and Developmental MedicineMedicalSurgical and Neurological Sciences, University of Siena, 53100 Siena, Italy
| | - M Cambi
- Department of BiomedicalExperimental and Clinical Sciences, Center of Excellence DeNotheDepartment of Experimental and Clinical MedicineUniversity of Florence, Viale Pieraccini 6, I-50139 Florence, ItalyDepartments of Molecular and Developmental MedicineMedicalSurgical and Neurological Sciences, University of Siena, 53100 Siena, Italy
| | - P Piomboni
- Department of BiomedicalExperimental and Clinical Sciences, Center of Excellence DeNotheDepartment of Experimental and Clinical MedicineUniversity of Florence, Viale Pieraccini 6, I-50139 Florence, ItalyDepartments of Molecular and Developmental MedicineMedicalSurgical and Neurological Sciences, University of Siena, 53100 Siena, Italy
| | - G Belmonte
- Department of BiomedicalExperimental and Clinical Sciences, Center of Excellence DeNotheDepartment of Experimental and Clinical MedicineUniversity of Florence, Viale Pieraccini 6, I-50139 Florence, ItalyDepartments of Molecular and Developmental MedicineMedicalSurgical and Neurological Sciences, University of Siena, 53100 Siena, Italy
| | - G Forti
- Department of BiomedicalExperimental and Clinical Sciences, Center of Excellence DeNotheDepartment of Experimental and Clinical MedicineUniversity of Florence, Viale Pieraccini 6, I-50139 Florence, ItalyDepartments of Molecular and Developmental MedicineMedicalSurgical and Neurological Sciences, University of Siena, 53100 Siena, Italy
| | - M Muratori
- Department of BiomedicalExperimental and Clinical Sciences, Center of Excellence DeNotheDepartment of Experimental and Clinical MedicineUniversity of Florence, Viale Pieraccini 6, I-50139 Florence, ItalyDepartments of Molecular and Developmental MedicineMedicalSurgical and Neurological Sciences, University of Siena, 53100 Siena, Italy
| | - E Baldi
- Department of BiomedicalExperimental and Clinical Sciences, Center of Excellence DeNotheDepartment of Experimental and Clinical MedicineUniversity of Florence, Viale Pieraccini 6, I-50139 Florence, ItalyDepartments of Molecular and Developmental MedicineMedicalSurgical and Neurological Sciences, University of Siena, 53100 Siena, Italy
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Ulrich HD. Two-way communications between ubiquitin-like modifiers and DNA. Nat Struct Mol Biol 2014; 21:317-24. [PMID: 24699080 DOI: 10.1038/nsmb.2805] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2013] [Accepted: 02/28/2014] [Indexed: 12/18/2022]
Abstract
Many aspects of nucleic acid metabolism, such as DNA replication, repair and transcription, are regulated by the post-translational modifiers ubiquitin and SUMO. Not surprisingly, DNA itself plays an integral part in determining the modification of most chromatin-associated targets. Conversely, ubiquitination or SUMOylation of a protein can impinge on its DNA-binding properties. This review describes mechanistic principles governing the mutual interactions between DNA and ubiquitin or SUMO.
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Groocock LM, Nie M, Prudden J, Moiani D, Wang T, Cheltsov A, Rambo RP, Arvai AS, Hitomi C, Tainer JA, Luger K, Perry JJP, Lazzerini-Denchi E, Boddy MN. RNF4 interacts with both SUMO and nucleosomes to promote the DNA damage response. EMBO Rep 2014; 15:601-8. [PMID: 24714598 DOI: 10.1002/embr.201338369] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
The post-translational modification of DNA repair and checkpoint proteins by ubiquitin and small ubiquitin-like modifier (SUMO) critically orchestrates the DNA damage response (DDR). The ubiquitin ligase RNF4 integrates signaling by SUMO and ubiquitin, through its selective recognition and ubiquitination of SUMO-modified proteins. Here, we define a key new determinant for target discrimination by RNF4, in addition to interaction with SUMO. We identify a nucleosome-targeting motif within the RNF4 RING domain that can bind DNA and thereby enables RNF4 to selectively ubiquitinate nucleosomal histones. Furthermore, RNF4 nucleosome-targeting is crucially required for the repair of TRF2-depleted dysfunctional telomeres by 53BP1-mediated non-homologous end joining.
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Affiliation(s)
- Lynda M Groocock
- Department of Cell and Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA
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