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Cybulla E, Wallace S, Meroni A, Jackson J, Agashe S, Tennakoon M, Limbu M, Quinet A, Lomonosova E, Noia H, Tirman S, Wood M, Lemacon D, Fuh K, Zou L, Vindigni A. A RAD18-UBC13-PALB2-RNF168 axis mediates replication fork recovery in BRCA1-deficient cancer cells. Nucleic Acids Res 2024; 52:8861-8879. [PMID: 38943334 PMCID: PMC11347138 DOI: 10.1093/nar/gkae563] [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: 02/07/2024] [Revised: 05/24/2024] [Accepted: 06/21/2024] [Indexed: 07/01/2024] Open
Abstract
BRCA1/2 proteins function in genome stability by promoting repair of double-stranded DNA breaks through homologous recombination and by protecting stalled replication forks from nucleolytic degradation. In BRCA1/2-deficient cancer cells, extensively degraded replication forks can be rescued through distinct fork recovery mechanisms that also promote cell survival. Here, we identified a novel pathway mediated by the E3 ubiquitin ligase RAD18, the E2-conjugating enzyme UBC13, the recombination factor PALB2, the E3 ubiquitin ligase RNF168 and PCNA ubiquitination that promotes fork recovery in BRCA1- but not BRCA2-deficient cells. We show that this pathway does not promote fork recovery by preventing replication fork reversal and degradation in BRCA1-deficient cells. We propose a mechanism whereby the RAD18-UBC13-PALB2-RNF168 axis facilitates resumption of DNA synthesis by promoting re-annealing of the complementary single-stranded template strands of the extensively degraded forks, thereby allowing re-establishment of a functional replication fork. We also provide preliminary evidence for the potential clinical relevance of this novel fork recovery pathway in BRCA1-mutated cancers, as RAD18 is over-expressed in BRCA1-deficient cancers, and RAD18 loss compromises cell viability in BRCA1-deficient cancer cells.
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Affiliation(s)
- Emily Cybulla
- Division of Oncology, Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO 63104, USA
| | - Sierra Wallace
- Division of Oncology, Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Alice Meroni
- Division of Oncology, Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Jessica Jackson
- Division of Oncology, Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Sumedha Agashe
- Division of Oncology, Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Mithila Tennakoon
- Division of Oncology, Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Mangsi Limbu
- Division of Oncology, Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Annabel Quinet
- Division of Oncology, Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Elena Lomonosova
- Department of Obstetrics and Gynecology, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Hollie Noia
- Department of Obstetrics and Gynecology, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Stephanie Tirman
- Division of Oncology, Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Matthew Wood
- Division of Oncology, Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Delphine Lemacon
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO 63104, USA
| | - Katherine Fuh
- Division of Gynecologic Oncology, Department of Ob/Gyn and Reproductive Sciences, University of California San Francisco, San Francisco, CA 94143, USA
| | - Lee Zou
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC 27708, USA
| | - Alessandro Vindigni
- Division of Oncology, Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA
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Mao P, Feng Z, Liu Y, Zhang K, Zhao G, Lei Z, Di T, Zhang H. The Role of Ubiquitination in Osteosarcoma Development and Therapies. Biomolecules 2024; 14:791. [PMID: 39062505 PMCID: PMC11274928 DOI: 10.3390/biom14070791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Revised: 06/20/2024] [Accepted: 06/28/2024] [Indexed: 07/28/2024] Open
Abstract
The ubiquitin-proteasome system (UPS) maintains intracellular protein homeostasis and cellular function by regulating various biological processes. Ubiquitination, a common post-translational modification, plays a crucial role in the regulation of protein degradation, signal transduction, and other physiological and pathological processes, and is involved in the pathogenesis of various cancers, including osteosarcoma. Osteosarcoma, the most common primary malignant bone tumor, is characterized by high metastatic potential and poor prognosis. It is a refractory bone disease, and the main treatment modalities are surgery combined with chemotherapy. Increasing evidence suggests a close association between UPS abnormalities and the progression of osteosarcoma. Due to the complexity and pleiotropy of the ubiquitination system, each step in the ubiquitination process can be targeted by drugs. In recent years, research and development of inhibitors targeting the ubiquitin system have increased gradually, showing great potential for clinical application. This article reviews the role of the ubiquitination system in the development and treatment of osteosarcoma, as well as research progress, with the hope of improving the therapeutic effects and prognosis of osteosarcoma patients by targeting effective molecules in the ubiquitination system.
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Affiliation(s)
- Peng Mao
- Department of Orthopedics, Lanzhou University Second Hospital, Second Clinical School, Lanzhou University, Lanzhou 730030, China
- Key Laboratory of Orthopaedics of Gansu Province, Lanzhou University, Lanzhou 730030, China
| | - Zuxi Feng
- Department of Hematology, Lanzhou University Second Hospital, Lanzhou 730030, China
| | - Yong Liu
- Department of Orthopedics, Lanzhou University Second Hospital, Second Clinical School, Lanzhou University, Lanzhou 730030, China
- Key Laboratory of Orthopaedics of Gansu Province, Lanzhou University, Lanzhou 730030, China
| | - Kai Zhang
- Department of Orthopedics, Lanzhou University Second Hospital, Second Clinical School, Lanzhou University, Lanzhou 730030, China
- Key Laboratory of Orthopaedics of Gansu Province, Lanzhou University, Lanzhou 730030, China
| | - Guanghai Zhao
- Department of Orthopedics, Lanzhou University Second Hospital, Second Clinical School, Lanzhou University, Lanzhou 730030, China
- Key Laboratory of Orthopaedics of Gansu Province, Lanzhou University, Lanzhou 730030, China
| | - Zeyuan Lei
- Department of Orthopedics, Lanzhou University Second Hospital, Second Clinical School, Lanzhou University, Lanzhou 730030, China
- Key Laboratory of Orthopaedics of Gansu Province, Lanzhou University, Lanzhou 730030, China
| | - Tianning Di
- Department of Orthopedics, Lanzhou University Second Hospital, Second Clinical School, Lanzhou University, Lanzhou 730030, China
| | - Haihong Zhang
- Department of Orthopedics, Lanzhou University Second Hospital, Second Clinical School, Lanzhou University, Lanzhou 730030, China
- Key Laboratory of Orthopaedics of Gansu Province, Lanzhou University, Lanzhou 730030, China
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Muggiolu G, Torfeh E, Simon M, Devès G, Seznec H, Barberet P. Recruitment Kinetics of XRCC1 and RNF8 Following MeV Proton and α-Particle Micro-Irradiation. BIOLOGY 2023; 12:921. [PMID: 37508352 PMCID: PMC10376363 DOI: 10.3390/biology12070921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 06/19/2023] [Accepted: 06/20/2023] [Indexed: 07/30/2023]
Abstract
Time-lapse fluorescence imaging coupled to micro-irradiation devices provides information on the kinetics of DNA repair protein accumulation, from a few seconds to several minutes after irradiation. Charged-particle microbeams are valuable tools for such studies since they provide a way to selectively irradiate micrometric areas within a cell nucleus, control the dose and the micro-dosimetric quantities by means of advanced detection systems and Monte Carlo simulations and monitor the early cell response by means of beamline microscopy. We used the charged-particle microbeam installed at the AIFIRA facility to perform micro-irradiation experiments and measure the recruitment kinetics of two proteins involved in DNA signaling and repair pathways following exposure to protons and α-particles. We developed and validated image acquisition and processing methods to enable a systematic study of the recruitment kinetics of GFP-XRCC1 and GFP-RNF8. We show that XRCC1 is recruited to DNA damage sites a few seconds after irradiation as a function of the total deposited energy and quite independently of the particle LET. RNF8 is recruited to DNA damage sites a few minutes after irradiation and its recruitment kinetics depends on the particle LET.
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Affiliation(s)
| | - Eva Torfeh
- University Bordeaux, CNRS, LP2I, UMR 5797, 33170 Gradignan, France
| | - Marina Simon
- University Bordeaux, CNRS, LP2I, UMR 5797, 33170 Gradignan, France
| | - Guillaume Devès
- University Bordeaux, CNRS, LP2I, UMR 5797, 33170 Gradignan, France
| | - Hervé Seznec
- University Bordeaux, CNRS, LP2I, UMR 5797, 33170 Gradignan, France
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Koo SY, Park EJ, Noh HJ, Jo SM, Ko BK, Shin HJ, Lee CW. Ubiquitination Links DNA Damage and Repair Signaling to Cancer Metabolism. Int J Mol Sci 2023; 24:ijms24098441. [PMID: 37176148 PMCID: PMC10179089 DOI: 10.3390/ijms24098441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 05/04/2023] [Accepted: 05/05/2023] [Indexed: 05/15/2023] Open
Abstract
Changes in the DNA damage response (DDR) and cellular metabolism are two important factors that allow cancer cells to proliferate. DDR is a set of events in which DNA damage is recognized, DNA repair factors are recruited to the site of damage, the lesion is repaired, and cellular responses associated with the damage are processed. In cancer, DDR is commonly dysregulated, and the enzymes associated with DDR are prone to changes in ubiquitination. Additionally, cellular metabolism, especially glycolysis, is upregulated in cancer cells, and enzymes in this metabolic pathway are modulated by ubiquitination. The ubiquitin-proteasome system (UPS), particularly E3 ligases, act as a bridge between cellular metabolism and DDR since they regulate the enzymes associated with the two processes. Hence, the E3 ligases with high substrate specificity are considered potential therapeutic targets for treating cancer. A number of small molecule inhibitors designed to target different components of the UPS have been developed, and several have been tested in clinical trials for human use. In this review, we discuss the role of ubiquitination on overall cellular metabolism and DDR and confirm the link between them through the E3 ligases NEDD4, APC/CCDH1, FBXW7, and Pellino1. In addition, we present an overview of the clinically important small molecule inhibitors and implications for their practical use.
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Affiliation(s)
- Seo-Young Koo
- Department of Molecular Cell Biology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Suwon 16419, Republic of Korea
| | - Eun-Ji Park
- Department of Molecular Cell Biology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Suwon 16419, Republic of Korea
| | - Hyun-Ji Noh
- Department of Molecular Cell Biology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Suwon 16419, Republic of Korea
| | - Su-Mi Jo
- Department of Molecular Cell Biology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Suwon 16419, Republic of Korea
| | - Bo-Kyoung Ko
- Department of Molecular Cell Biology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Suwon 16419, Republic of Korea
| | - Hyun-Jin Shin
- Team of Radiation Convergence Research, Korea Institute of Radiological & Medical Sciences, Seoul 01812, Republic of Korea
| | - Chang-Woo Lee
- Department of Molecular Cell Biology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Suwon 16419, Republic of Korea
- SKKU Institute for Convergence, Sungkyunkwan University, Suwon 16419, Republic of Korea
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5
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Chen YN, Shih CY, Guo SL, Liu CY, Shen MH, Chang SC, Ku WC, Huang CC, Huang CJ. Potential prognostic and predictive value of UBE2N, IMPDH1, DYNC1LI1 and HRASLS2 in colorectal cancer stool specimens. Biomed Rep 2023; 18:22. [PMID: 36846616 PMCID: PMC9945078 DOI: 10.3892/br.2023.1604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 12/20/2022] [Indexed: 02/10/2023] Open
Abstract
Colorectal cancer (CRC) is the most common gastrointestinal malignancy worldwide. The poor specificity and sensitivity of the fecal occult blood test has prompted the development of CRC-related genetic markers for CRC screening and treatment. Gene expression profiles in stool specimens are effective, sensitive and clinically applicable. Herein, a novel advantage of using cells shed from the colon is presented for cost-effective CRC screening. Molecular panels were generated through a series of leave-one-out cross-validation and discriminant analyses. A logistic regression model following reverse transcription-quantitative polymerase chain reaction (RT-qPCR) and immunohistochemistry was used to validate a specific panel for CRC prediction. The panel, consisting of ubiquitin-conjugating enzyme E2 N (UBE2N), inosine monophosphate dehydrogenase 1 (IMPDH1), dynein cytoplasmic 1 light intermediate chain 1 (DYNC1LI1) and phospholipase A and acyltransferase 2 (HRASLS2), accurately recognized patients with CRC and could thus be further investigated as a potential prognostic and predictive biomarker for CRC. UBE2N, IMPDH1 and DYNC1LI1 expression levels were upregulated and HRASLS2 expression was downregulated in CRC tissues. The predictive power of the panel was 96.6% [95% confidence interval (CI), 88.1-99.6%] sensitivity and 89.7% (95% CI, 72.6-97.8%) specificity at a predicted cut-off value at 0.540, suggesting that this four-gene panel testing of stool specimens can faithfully mirror the state of the colon. On the whole, the present study demonstrates that screening for CRC or cancer detection in stool specimens collected non-invasively does not require the inclusion of an excessive number of genes, and colonic defects can be identified via the detection of an aberrant protein in the mucosa or submucosa.
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Affiliation(s)
- Yu-Nung Chen
- Division of Colorectal Surgery, Department of Surgery, Cathay General Hospital, Taipei 10630, Taiwan, R.O.C
| | - Cheng-Yen Shih
- Division of Gastroenterology, Department of Internal Medicine, Sijhih Cathay General Hospital, New Taipei 22174, Taiwan, R.O.C
| | - Shu-Lin Guo
- School of Medicine, College of Medicine, Fu Jen Catholic University, New Taipei 24205, Taiwan, R.O.C.,Department of Anesthesiology, Cathay General Hospital, Taipei 10630, Taiwan, R.O.C,Department of Anesthesiology, Tri-Service General Hospital and National Defense Medical Center, Taipei 11490, Taiwan, R.O.C
| | - Chih-Yi Liu
- School of Medicine, College of Medicine, Fu Jen Catholic University, New Taipei 24205, Taiwan, R.O.C.,Division of Pathology, Sijhih Cathay General Hospital, New Taipei City 22174, Taiwan, R.O.C
| | - Ming-Hung Shen
- School of Medicine, College of Medicine, Fu Jen Catholic University, New Taipei 24205, Taiwan, R.O.C.,Department of Surgery, Fu Jen Catholic University Hospital, New Taipei 24352, Taiwan, R.O.C.,PhD Program in Nutrition and Food Science, College of Medicine, Fu Jen Catholic University, New Taipei 24205, Taiwan, R.O.C
| | - Shih-Chang Chang
- Division of Colorectal Surgery, Department of Surgery, Cathay General Hospital, Taipei 10630, Taiwan, R.O.C
| | - Wei-Chi Ku
- School of Medicine, College of Medicine, Fu Jen Catholic University, New Taipei 24205, Taiwan, R.O.C
| | - Chi-Cheng Huang
- Comprehensive Breast Health Center, Department of Surgery, Taipei Veterans General Hospital, Taipei 11217, Taiwan, R.O.C.,Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, Taipei 10090, Taiwan, R.O.C.,Correspondence to: Dr Chi-Cheng Huang, Comprehensive Breast Health Center, Department of Surgery, Taipei Veterans General Hospital, No. 201, Section 2, Shipai Road, Taipei 11217, Taiwan, R.O.C.
| | - Chi-Jung Huang
- Department of Medical Research, Cathay General Hospital, Taipei 10630, Taiwan, R.O.C.,Department of Biochemistry, National Defense Medical Center, Taipei 11490, Taiwan, R.O.C.,Correspondence to: Dr Chi-Cheng Huang, Comprehensive Breast Health Center, Department of Surgery, Taipei Veterans General Hospital, No. 201, Section 2, Shipai Road, Taipei 11217, Taiwan, R.O.C.
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Yin X, Liu Q, Liu F, Tian X, Yan T, Han J, Jiang S. Emerging Roles of Non-proteolytic Ubiquitination in Tumorigenesis. Front Cell Dev Biol 2022; 10:944460. [PMID: 35874839 PMCID: PMC9298949 DOI: 10.3389/fcell.2022.944460] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Accepted: 06/15/2022] [Indexed: 12/13/2022] Open
Abstract
Ubiquitination is a critical type of protein post-translational modification playing an essential role in many cellular processes. To date, more than eight types of ubiquitination exist, all of which are involved in distinct cellular processes based on their structural differences. Studies have indicated that activation of the ubiquitination pathway is tightly connected with inflammation-related diseases as well as cancer, especially in the non-proteolytic canonical pathway, highlighting the vital roles of ubiquitination in metabolic programming. Studies relating degradable ubiquitination through lys48 or lys11-linked pathways to cellular signaling have been well-characterized. However, emerging evidence shows that non-degradable ubiquitination (linked to lys6, lys27, lys29, lys33, lys63, and Met1) remains to be defined. In this review, we summarize the non-proteolytic ubiquitination involved in tumorigenesis and related signaling pathways, with the aim of providing a reference for future exploration of ubiquitination and the potential targets for cancer therapies.
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Affiliation(s)
- Xiu Yin
- Clinical Medical Laboratory Center, Jining First People's Hospital, Jining Medical University, Jining, China
| | - Qingbin Liu
- Clinical Medical Laboratory Center, Jining First People's Hospital, Jining Medical University, Jining, China
| | - Fen Liu
- Clinical Medical Laboratory Center, Jining First People's Hospital, Jining Medical University, Jining, China
| | - Xinchen Tian
- Clinical Medical Laboratory Center, Jining First People's Hospital, Jining Medical University, Jining, China.,Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Tinghao Yan
- Clinical Medical Laboratory Center, Jining First People's Hospital, Jining Medical University, Jining, China.,Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Jie Han
- Department of Thyroid and Breast Surgery, Jining First People's Hospital, Jining Medical University, Jining, China
| | - Shulong Jiang
- Clinical Medical Laboratory Center, Jining First People's Hospital, Jining Medical University, Jining, China
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Habu T, Harada KH. UBC13 is an RNF213-associated E2 ubiquitin-conjugating enzyme, and Lysine 63-linked ubiquitination by the RNF213-UBC13 axis is responsible for angiogenic activity. FASEB Bioadv 2021; 3:243-258. [PMID: 33842849 PMCID: PMC8019261 DOI: 10.1096/fba.2019-00092] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 12/26/2020] [Accepted: 12/30/2020] [Indexed: 12/13/2022] Open
Abstract
Moyamoya disease (MMD) is a cryptogenic vascular disorder in the intracranial arteries. RING protein 213 (RNF213) is the susceptibility gene for MMD, and encodes a RING domain and a Walker motif. Herein, we identified UBC13 (UBE2N) as an E2 ubiquitin‐conjugating enzyme for RNF213 E3 ubiquitin ligase by yeast two‐hybrid screening with a fragment containing RNF213 RING domain as bait, and the immunocomplex of RNF213‐UBC13 was detected in vivo. Analysis of the ubiquitin chain on RNF213 by monitoring autoubiquitination showed that RNF213 was autoubiquitinated in a K63 chain fashion, but not in a K48 chain fashion. Finally, this RNF213 ubiquitination in a UBC13‐dependent manner was required for cell mobility and invasion activity for HUVEC cells in UBC13 knock‐down and ubiquitination‐dead RNF213 mutant expressing experiments. These findings demonstrated that RNF213 is a K63‐linked E3 ubiquitin ligase, and UBC13 is responsible for RNF213 dependent ubiquitination. The RNF213‐UBC13 axis may be associated with angiogenic activity and MMD.
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Affiliation(s)
- Toshiyuki Habu
- Department of Food Sciences and Nutrition School of Food Sciences and Nutrition Mukogawa Women's University Nishinomiya Hyogo Japan
| | - Kouji H Harada
- Department of Health and Environmental Sciences Kyoto University Graduate School of Medicine Kyoto Japan
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8
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Panigrahi R, Glover JNM. Structural insights into DNA double-strand break signaling. Biochem J 2021; 478:135-156. [PMID: 33439989 DOI: 10.1042/bcj20200066] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 12/10/2020] [Accepted: 12/15/2020] [Indexed: 12/14/2022]
Abstract
Genomic integrity is most threatened by double-strand breaks, which, if left unrepaired, lead to carcinogenesis or cell death. The cell generates a network of protein-protein signaling interactions that emanate from the DNA damage which are now recognized as a rich basis for anti-cancer therapy development. Deciphering the structures of signaling proteins has been an uphill task owing to their large size and complex domain organization. Recent advances in mammalian protein expression/purification and cryo-EM-based structure determination have led to significant progress in our understanding of these large multidomain proteins. This review is an overview of the structural principles that underlie some of the key signaling proteins that function at the double-strand break site. We also discuss some plausible ideas that could be considered for future structural approaches to visualize and build a more complete understanding of protein dynamics at the break site.
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Affiliation(s)
- Rashmi Panigrahi
- Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - J N Mark Glover
- Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
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9
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Zhu Q, Chen J, Pan P, Lin F, Zhang X. UBE2N Regulates Paclitaxel Sensitivity of Ovarian Cancer via Fos/P53 Axis. Onco Targets Ther 2020; 13:12751-12761. [PMID: 33363381 PMCID: PMC7751838 DOI: 10.2147/ott.s271164] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 11/10/2020] [Indexed: 01/10/2023] Open
Abstract
Background Chemo-resistance is still considered one of the key factors in the mortality of ovarian cancer. In this work, we found that ubiquitin-conjugating enzyme E2 N (UBE2N) is downregulated in paclitaxel-resistant ovarian cancer cells. It suggests UBE2N to be critical in the regulation of paclitaxel sensitivity in ovarian cancer. Materials and Methods Ovarian cancer cells with stably overexpressed UBE2N were injected into nude mice to assess tumor growth and paclitaxel sensitivity in vivo. The MTT assay was applied to observe the effect of UBE2N expression on paclitaxel sensitivity. A real-time PCR array, specific for human cancer drug resistance, was used to examine the potential downstream target genes of UBE2N. The expression of UBE2N and potential downstream target genes was determined by Western blotting. The analysis of Gene Ontology and protein–protein interactions of these differentially expressed genes (DEGs) was performed using online tools. To evaluate the prognostic value of hub genes expression for ovarian cancer patients treated with paclitaxel, we applied the online survival analysis tool. Results Overexpressed UBE2N enhanced the paclitaxel sensitivity of ovarian cancer cells in vitro and in vivo. Thirteen upregulated DEGs and 11 downregulated DEGs were identified when we knockdown UBE2N. Meanwhile, 9 hub genes with a high degree of connectivity were selected. Only Fos proto-oncogene, AP-1 transcription factor subunit (Fos), was overexpressed upon decreasing UBE2N levels, indicating a poor outcome for patients treated with paclitaxel. Moreover, reduced UBE2N could increase Fos expression and reduce P53. Furthermore, reversed regulation of Fos and P53 based on UBE2N reduction could reverse paclitaxel sensitivity, respectively. Conclusion Our study suggests that UBE2N could be used as a therapeutic agent for paclitaxel-resistant ovarian cancer through Fos/P53 pathway. Further studies are needed to elucidate the specific mechanism.
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Affiliation(s)
- Qiuyuan Zhu
- Department of Gynecology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325000, People's Republic of China
| | - Jieyuan Chen
- Department of Gynecology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325000, People's Republic of China
| | - Peipei Pan
- Department of Gynecology and Obstetrics, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325000, People's Republic of China
| | - Feng Lin
- Department of Gynecology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325000, People's Republic of China
| | - Xu Zhang
- Department of Gynecology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325000, People's Republic of China
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Sun J, Zhu Z, Li W, Shen M, Cao C, Sun Q, Guo Z, Liu L, Wu D. UBE2T-regulated H2AX monoubiquitination induces hepatocellular carcinoma radioresistance by facilitating CHK1 activation. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2020; 39:222. [PMID: 33087136 PMCID: PMC7576867 DOI: 10.1186/s13046-020-01734-4] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 10/13/2020] [Indexed: 02/08/2023]
Abstract
Background Radioresistance is the major obstacle in radiation therapy (RT) for hepatocellular carcinoma (HCC). Dysregulation of DNA damage response (DDR), which includes DNA repair and cell cycle checkpoints activation, leads to radioresistance and limits radiotherapy efficacy in HCC patients. However, the underlying mechanism have not been clearly understood. Methods We obtained 7 pairs of HCC tissues and corresponding non-tumor tissues, and UBE2T was identified as one of the most upregulated genes. The radioresistant role of UBE2T was examined by colony formation assays in vitro and xenograft tumor models in vivo. Comet assay, cell cycle flow cytometry and γH2AX foci measurement were used to investigate the mechanism by which UBE2T mediating DDR. Chromatin fractionation and immunofluorescence staining were used to assess cell cycle checkpoint kinase 1(CHK1) activation. Finally, we analyzed clinical data from HCC patients to verify the function of UBE2T. Results Here, we found that ubiquitin-conjugating enzyme E2T (UBE2T) was upregulated in HCC tissues, and the HCC patients with higher UBE2T levels exhibited poorer outcomes. Functional studies indicated that UBE2T increased HCC radioresistance in vitro and in vivo. Mechanistically, UBE2T-RNF8, was identified as the E2-E3 pair, physically bonded with and monoubiquitinated histone variant H2AX/γH2AX upon radiation exposure. UBE2T-regulated H2AX/γH2AX monoubiquitination facilitated phosphorylation of CHK1 for activation and CHK1 release from the chromatin to cytosol for degradation. The interruption of UBE2T-mediated monoubiquitination on H2AX/γH2AX, including E2-enzyme-deficient mutation (C86A) of UBE2T and monoubiquitination-site-deficient mutation (K119/120R) of H2AX, cannot effectively activate CHK1. Moreover, genetical and pharmacological inhibition of CHK1 impaired the radioresistant role of UBE2T in HCC. Furthermore, clinical data suggested that the HCC patients with higher UBE2T levels exhibited worse response to radiotherapy. Conclusion Our results revealed a novel role of UBE2T-mediated H2AX/γH2AX monoubiquitination on facilitating cell cycle arrest activation to provide sufficient time for radiation-induced DNA repair, thus conferring HCC radioresistance. This study indicated that disrupting UBE2T-H2AX-CHK1 pathway maybe a promising potential strategy to overcome HCC radioresistance. Supplementary information Supplementary information accompanies this paper at 10.1186/s13046-020-01734-4.
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Affiliation(s)
- Jingyuan Sun
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Zhenru Zhu
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Wenwen Li
- Hepatology Unit and Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Mengying Shen
- Hepatology Unit and Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Chuanhui Cao
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Qingcan Sun
- Hepatology Unit and Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Zeqin Guo
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Li Liu
- Hepatology Unit and Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China.
| | - Dehua Wu
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China.
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11
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Singh AN, Oehler J, Torrecilla I, Kilgas S, Li S, Vaz B, Guérillon C, Fielden J, Hernandez‐Carralero E, Cabrera E, Tullis IDC, Meerang M, Barber PR, Freire R, Parsons J, Vojnovic B, Kiltie AE, Mailand N, Ramadan K. The p97-Ataxin 3 complex regulates homeostasis of the DNA damage response E3 ubiquitin ligase RNF8. EMBO J 2019; 38:e102361. [PMID: 31613024 PMCID: PMC6826192 DOI: 10.15252/embj.2019102361] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 09/16/2019] [Accepted: 09/19/2019] [Indexed: 12/31/2022] Open
Abstract
The E3 ubiquitin ligase RNF8 (RING finger protein 8) is a pivotal enzyme for DNA repair. However, RNF8 hyper-accumulation is tumour-promoting and positively correlates with genome instability, cancer cell invasion, metastasis and poor patient prognosis. Very little is known about the mechanisms regulating RNF8 homeostasis to preserve genome stability. Here, we identify the cellular machinery, composed of the p97/VCP ubiquitin-dependent unfoldase/segregase and the Ataxin 3 (ATX3) deubiquitinase, which together form a physical and functional complex with RNF8 to regulate its proteasome-dependent homeostasis under physiological conditions. Under genotoxic stress, when RNF8 is rapidly recruited to sites of DNA lesions, the p97-ATX3 machinery stimulates the extraction of RNF8 from chromatin to balance DNA repair pathway choice and promote cell survival after ionising radiation (IR). Inactivation of the p97-ATX3 complex affects the non-homologous end joining DNA repair pathway and hypersensitises human cancer cells to IR. We propose that the p97-ATX3 complex is the essential machinery for regulation of RNF8 homeostasis under both physiological and genotoxic conditions and that targeting ATX3 may be a promising strategy to radio-sensitise BRCA-deficient cancers.
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Affiliation(s)
- Abhay Narayan Singh
- Department of OncologyCancer Research UK/Medical Research Council Oxford Institute for Radiation OncologyUniversity of OxfordOxfordUK
| | - Judith Oehler
- Department of OncologyCancer Research UK/Medical Research Council Oxford Institute for Radiation OncologyUniversity of OxfordOxfordUK
- Present address:
Department of BiochemistryUniversity of OxfordOxfordUK
| | - Ignacio Torrecilla
- Department of OncologyCancer Research UK/Medical Research Council Oxford Institute for Radiation OncologyUniversity of OxfordOxfordUK
| | - Susan Kilgas
- Department of OncologyCancer Research UK/Medical Research Council Oxford Institute for Radiation OncologyUniversity of OxfordOxfordUK
| | - Shudong Li
- Department of OncologyCancer Research UK/Medical Research Council Oxford Institute for Radiation OncologyUniversity of OxfordOxfordUK
| | - Bruno Vaz
- Department of OncologyCancer Research UK/Medical Research Council Oxford Institute for Radiation OncologyUniversity of OxfordOxfordUK
| | - Claire Guérillon
- Novo Nordisk Foundation Center for Protein ResearchUniversity of CopenhagenCopenhagenDenmark
| | - John Fielden
- Department of OncologyCancer Research UK/Medical Research Council Oxford Institute for Radiation OncologyUniversity of OxfordOxfordUK
| | - Esperanza Hernandez‐Carralero
- Unidad de InvestigaciónHospital Universitario de CanariasLa LagunaSpain
- Instituto de Tecnologías BiomédicasUniversidad de La LagunaLa LagunaSpain
| | - Elisa Cabrera
- Unidad de InvestigaciónHospital Universitario de CanariasLa LagunaSpain
- Instituto de Tecnologías BiomédicasUniversidad de La LagunaLa LagunaSpain
| | - Iain DC Tullis
- Department of OncologyCancer Research UK/Medical Research Council Oxford Institute for Radiation OncologyUniversity of OxfordOxfordUK
| | - Mayura Meerang
- Institute of Pharmacology and Toxicology‐Vetsuisse FacultyUniversity of ZurichZurichSwitzerland
- Present address:
Department of Thoracic SurgeryUniversity Hospital ZurichZurichSwitzerland
| | - Paul R Barber
- Department of OncologyCancer Research UK/Medical Research Council Oxford Institute for Radiation OncologyUniversity of OxfordOxfordUK
| | - Raimundo Freire
- Unidad de InvestigaciónHospital Universitario de CanariasLa LagunaSpain
- Instituto de Tecnologías BiomédicasUniversidad de La LagunaLa LagunaSpain
- Universidad Fernando Pessoa CanariasSanta Maria de GuiaSpain
| | - Jason Parsons
- Department of Molecular and Clinical Cancer MedicineCancer Research CentreUniversity of LiverpoolLiverpoolUK
| | - Borivoj Vojnovic
- Department of OncologyCancer Research UK/Medical Research Council Oxford Institute for Radiation OncologyUniversity of OxfordOxfordUK
| | - Anne E Kiltie
- Department of OncologyCancer Research UK/Medical Research Council Oxford Institute for Radiation OncologyUniversity of OxfordOxfordUK
| | - Niels Mailand
- Novo Nordisk Foundation Center for Protein ResearchUniversity of CopenhagenCopenhagenDenmark
| | - Kristijan Ramadan
- Department of OncologyCancer Research UK/Medical Research Council Oxford Institute for Radiation OncologyUniversity of OxfordOxfordUK
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12
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Gundogdu M, Walden H. Structural basis of generic versus specific E2-RING E3 interactions in protein ubiquitination. Protein Sci 2019; 28:1758-1770. [PMID: 31340062 DOI: 10.1002/pro.3690] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 07/11/2019] [Accepted: 07/11/2019] [Indexed: 12/21/2022]
Abstract
Protein ubiquitination is a fundamental regulatory component in eukaryotic cell biology, where a cascade of ubiquitin activating (E1), conjugating (E2), and ligating (E3) enzymes assemble distinct ubiquitin signals on target proteins. E2s specify the type of ubiquitin signal generated, while E3s associate with the E2~Ub conjugate and select the substrate for ubiquitination. Thus, producing the right ubiquitin signal on the right target requires the right E2-E3 pair. The question of how over 600 E3s evolved to discriminate between 38 structurally related E2s has therefore been an area of intensive research, and with over 50 E2-E3 complex structures generated to date, the answer is beginning to emerge. The following review discusses the structural basis of generic E2-RING E3 interactions, contrasted with emerging themes that reveal how specificity can be achieved.
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Affiliation(s)
- Mehmet Gundogdu
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Helen Walden
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
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13
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Zhou Y, Millott R, Kim HJ, Peng S, Edwards RA, Skene-Arnold T, Hammel M, Lees-Miller SP, Tainer JA, Holmes CFB, Glover JNM. Flexible Tethering of ASPP Proteins Facilitates PP-1c Catalysis. Structure 2019; 27:1485-1496.e4. [PMID: 31402222 DOI: 10.1016/j.str.2019.07.012] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 06/14/2019] [Accepted: 07/22/2019] [Indexed: 12/15/2022]
Abstract
ASPP (apoptosis-stimulating proteins of p53) proteins bind PP-1c (protein phosphatase 1) and regulate p53 impacting cancer cell growth and apoptosis. Here we determine the crystal structure of the oncogenic ASPP protein, iASPP, bound to PP-1c. The structure reveals a 1:1 complex that relies on interactions of the iASPP SILK and RVxF motifs with PP-1c, plus interactions of the PP-1c PxxPxR motif with the iASPP SH3 domain. Small-angle X-ray scattering analyses suggest that the crystal structure undergoes slow interconversion with more extended conformations in solution. We show that iASPP, and the tumor suppressor ASPP2, enhance the catalytic activity of PP-1c against the small-molecule substrate, pNPP as well as p53. The combined results suggest that PxxPxR binding to iASPP SH3 domain is critical for complex formation, and that the modular ASPP-PP-1c interface provides dynamic flexibility that enables functional binding and dephosphorylation of p53 and other diverse protein substrates.
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Affiliation(s)
- Yeyun Zhou
- Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Robyn Millott
- Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Hyeong Jin Kim
- Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Shiyun Peng
- Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Ross A Edwards
- Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Tamara Skene-Arnold
- Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Michal Hammel
- Molecular Biophysics & Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Susan P Lees-Miller
- Department of Biochemistry and Molecular Biology, Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, AB, Canada
| | - John A Tainer
- Molecular Biophysics & Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Department of Molecular and Cellular Oncology, The University of Texas M. D. Anderson Cancer Center, Houston, TX 77030, USA
| | - Charles F B Holmes
- Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2H7, Canada.
| | - J N Mark Glover
- Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2H7, Canada.
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14
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Jones WM, Davis AG, Wilson RH, Elliott KL, Sumner I. A conserved asparagine in a ubiquitin-conjugating enzyme positions the substrate for nucleophilic attack. J Comput Chem 2019; 40:1969-1977. [PMID: 31070815 DOI: 10.1002/jcc.25852] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 02/26/2019] [Accepted: 04/14/2019] [Indexed: 01/30/2023]
Abstract
The mechanism used by the ubiquitin-conjugating enzyme, Ubc13, to catalyze ubiquitination is probed with three computational techniques: Born-Oppenheimer molecular dynamics, single point quantum mechanics/molecular mechanics energies, and classical molecular dynamics. These simulations support a long-held hypothesis and show that Ubc13-catalyzed ubiquitination uses a stepwise, nucleophilic attack mechanism. Furthermore, they show that the first step-the formation of a tetrahedral, zwitterionic intermediate-is rate limiting. However, these simulations contradict another popular hypothesis that supposes that the negative charge on the intermediate is stabilized by a highly conserved asparagine (Asn79 in Ubc13). Instead, calculated reaction profiles of the N79A mutant illustrate how charge stabilization actually increases the barrier to product formation. Finally, an alternate role for Asn79 is suggested by simulations of wild-type, N79A, N79D, and H77A Ubc13: it stabilizes the motion of the electrophile prior to the reaction, positioning it for nucleophilic attack. © 2019 Wiley Periodicals, Inc.
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Affiliation(s)
- Walker M Jones
- Department of Chemistry and Biochemistry, James Madison University, Harrisonburg, Virginia, 22807
| | - Aaron G Davis
- Department of Chemistry and Biochemistry, James Madison University, Harrisonburg, Virginia, 22807
| | - R Hunter Wilson
- Department of Chemistry and Biochemistry, James Madison University, Harrisonburg, Virginia, 22807
| | - Katherine L Elliott
- Department of Chemistry and Biochemistry, James Madison University, Harrisonburg, Virginia, 22807
| | - Isaiah Sumner
- Department of Chemistry and Biochemistry, James Madison University, Harrisonburg, Virginia, 22807
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15
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Wilson MD, Durocher D. Reading chromatin signatures after DNA double-strand breaks. Philos Trans R Soc Lond B Biol Sci 2018; 372:rstb.2016.0280. [PMID: 28847817 DOI: 10.1098/rstb.2016.0280] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/18/2017] [Indexed: 12/14/2022] Open
Abstract
DNA double-strand breaks (DSBs) are DNA lesions that must be accurately repaired in order to preserve genomic integrity and cellular viability. The response to DSBs reshapes the local chromatin environment and is largely orchestrated by the deposition, removal and detection of a complex set of chromatin-associated post-translational modifications. In particular, the nucleosome acts as a central signalling hub and landing platform in this process by organizing the recruitment of repair and signalling factors, while at the same time coordinating repair with other DNA-based cellular processes. While current research has provided a descriptive overview of which histone marks affect DSB repair, we are only beginning to understand how these marks are interpreted to foster an efficient DSB response. Here we review how the modified chromatin surrounding DSBs is read, with a focus on the insights gleaned from structural and biochemical studies.This article is part of the themed issue 'Chromatin modifiers and remodellers in DNA repair and signalling'.
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Affiliation(s)
- Marcus D Wilson
- Macromolecular Machines Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Daniel Durocher
- The Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, Ontario, Canada M5G 1X5.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada M5S 3E1
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16
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Torrecilla I, Oehler J, Ramadan K. The role of ubiquitin-dependent segregase p97 (VCP or Cdc48) in chromatin dynamics after DNA double strand breaks. Philos Trans R Soc Lond B Biol Sci 2018; 372:rstb.2016.0282. [PMID: 28847819 PMCID: PMC5577460 DOI: 10.1098/rstb.2016.0282] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/24/2017] [Indexed: 12/27/2022] Open
Abstract
DNA double strand breaks (DSBs) are the most cytotoxic DNA lesions and, if not repaired, lead to chromosomal rearrangement, genomic instability and cell death. Cells have evolved a complex network of DNA repair and signalling molecules which promptly detect and repair DSBs, commonly known as the DNA damage response (DDR). The DDR is orchestrated by various post-translational modifications such as phosphorylation, methylation, ubiquitination or SUMOylation. As DSBs are located in complex chromatin structures, the repair of DSBs is engineered at two levels: (i) at sites of broken DNA and (ii) at chromatin structures that surround DNA lesions. Thus, DNA repair and chromatin remodelling machineries must work together to efficiently repair DSBs. Here, we summarize the current knowledge of the ubiquitin-dependent molecular unfoldase/segregase p97 (VCP in vertebrates and Cdc48 in worms and lower eukaryotes) in DSB repair. We identify p97 as an essential factor that regulates DSB repair. p97-dependent extraction of ubiquitinated substrates mediates spatio-temporal protein turnover at and around the sites of DSBs, thus orchestrating chromatin remodelling and DSB repair. As p97 is a druggable target, p97 inhibition in the context of DDR has great potential for cancer therapy, as shown for other DDR components such as PARP, ATR and CHK1.This article is part of the themed issue 'Chromatin modifiers and remodellers in DNA repair and signalling'.
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Affiliation(s)
- Ignacio Torrecilla
- Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Judith Oehler
- Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Kristijan Ramadan
- Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Roosevelt Drive, Oxford OX3 7DQ, UK
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17
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Zhao Y, Long MJC, Wang Y, Zhang S, Aye Y. Ube2V2 Is a Rosetta Stone Bridging Redox and Ubiquitin Codes, Coordinating DNA Damage Responses. ACS CENTRAL SCIENCE 2018; 4. [PMID: 29532025 PMCID: PMC5833000 DOI: 10.1021/acscentsci.7b00556] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Posttranslational modifications (PTMs) are the lingua franca of cellular communication. Most PTMs are enzyme-orchestrated. However, the reemergence of electrophilic drugs has ushered mining of unconventional/non-enzyme-catalyzed electrophile-signaling pathways. Despite the latest impetus toward harnessing kinetically and functionally privileged cysteines for electrophilic drug design, identifying these sensors remains challenging. Herein, we designed "G-REX"-a technique that allows controlled release of reactive electrophiles in vivo. Mitigating toxicity/off-target effects associated with uncontrolled bolus exposure, G-REX tagged first-responding innate cysteines that bind electrophiles under true kcat/Km conditions. G-REX identified two allosteric ubiquitin-conjugating proteins-Ube2V1/Ube2V2-sharing a novel privileged-sensor-cysteine. This non-enzyme-catalyzed-PTM triggered responses specific to each protein. Thus, G-REX is an unbiased method to identify novel functional cysteines. Contrasting conventional active-site/off-active-site cysteine-modifications that regulate target activity, modification of Ube2V2 allosterically hyperactivated its enzymatically active binding-partner Ube2N, promoting K63-linked client ubiquitination and stimulating H2AX-dependent DNA damage response. This work establishes Ube2V2 as a Rosetta-stone bridging redox and ubiquitin codes to guard genome integrity.
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Affiliation(s)
- Yi Zhao
- Department of Chemistry & Chemical Biology and Proteomics and Mass Spectrometry
Facility, Institute of Biotechnology, Cornell
University, Ithaca, New York 14850, United States
| | - Marcus J. C. Long
- Department of Chemistry & Chemical Biology and Proteomics and Mass Spectrometry
Facility, Institute of Biotechnology, Cornell
University, Ithaca, New York 14850, United States
| | - Yiran Wang
- Department of Chemistry & Chemical Biology and Proteomics and Mass Spectrometry
Facility, Institute of Biotechnology, Cornell
University, Ithaca, New York 14850, United States
| | - Sheng Zhang
- Department of Chemistry & Chemical Biology and Proteomics and Mass Spectrometry
Facility, Institute of Biotechnology, Cornell
University, Ithaca, New York 14850, United States
| | - Yimon Aye
- Department of Chemistry & Chemical Biology and Proteomics and Mass Spectrometry
Facility, Institute of Biotechnology, Cornell
University, Ithaca, New York 14850, United States
- Department
of Biochemistry, Weill Cornell Medicine, New York, New York 10065, United States
- E-mail:
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18
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Sheppard EC, Morrish RB, Dillon MJ, Leyland R, Chahwan R. Epigenomic Modifications Mediating Antibody Maturation. Front Immunol 2018. [PMID: 29535729 PMCID: PMC5834911 DOI: 10.3389/fimmu.2018.00355] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Epigenetic modifications, such as histone modifications, DNA methylation status, and non-coding RNAs (ncRNA), all contribute to antibody maturation during somatic hypermutation (SHM) and class-switch recombination (CSR). Histone modifications alter the chromatin landscape and, together with DNA primary and tertiary structures, they help recruit Activation-Induced Cytidine Deaminase (AID) to the immunoglobulin (Ig) locus. AID is a potent DNA mutator, which catalyzes cytosine-to-uracil deamination on single-stranded DNA to create U:G mismatches. It has been shown that alternate chromatin modifications, in concert with ncRNAs and potentially DNA methylation, regulate AID recruitment and stabilize DNA repair factors. We, hereby, assess the combination of these distinct modifications and discuss how they contribute to initiating differential DNA repair pathways at the Ig locus, which ultimately leads to enhanced antibody–antigen binding affinity (SHM) or antibody isotype switching (CSR). We will also highlight how misregulation of epigenomic regulation during DNA repair can compromise antibody development and lead to a number of immunological syndromes and cancer.
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Affiliation(s)
- Emily C Sheppard
- Living Systems Institute, University of Exeter, Exeter, United Kingdom
| | | | - Michael J Dillon
- Living Systems Institute, University of Exeter, Exeter, United Kingdom
| | | | - Richard Chahwan
- Living Systems Institute, University of Exeter, Exeter, United Kingdom
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19
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Hodge CD, Spyracopoulos L, Glover JNM. Ubc13: the Lys63 ubiquitin chain building machine. Oncotarget 2018; 7:64471-64504. [PMID: 27486774 PMCID: PMC5325457 DOI: 10.18632/oncotarget.10948] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 07/19/2016] [Indexed: 12/25/2022] Open
Abstract
Ubc13 is an ubiquitin E2 conjugating enzyme that participates with many different E3 ligases to form lysine 63-linked (Lys63) ubiquitin chains that are critical to signaling in inflammatory and DNA damage response pathways. Recent studies have suggested Ubc13 as a potential therapeutic target for intervention in various human diseases including several different cancers, alleviation of anti-cancer drug resistance, chronic inflammation, and viral infections. Understanding a potential therapeutic target from different angles is important to assess its usefulness and potential pitfalls. Here we present a global review of Ubc13 from its structure, function, and cellular activities, to its natural and chemical inhibition. The aim of this article is to review the literature that directly implicates Ubc13 in a biological function, and to integrate structural and mechanistic insights into the larger role of this critical E2 enzyme. We discuss observations of multiple Ubc13 structures that suggest a novel mechanism for activation of Ubc13 that involves conformational change of the active site loop.
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Affiliation(s)
- Curtis D Hodge
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Leo Spyracopoulos
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada
| | - J N Mark Glover
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada
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20
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The inhibition of UBC13 expression and blockage of the DNMT1-CHFR-Aurora A pathway contribute to paclitaxel resistance in ovarian cancer. Cell Death Dis 2018; 9:93. [PMID: 29367628 PMCID: PMC5833742 DOI: 10.1038/s41419-017-0137-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Revised: 09/03/2017] [Accepted: 11/08/2017] [Indexed: 12/14/2022]
Abstract
Paclitaxel is widely used as a first-line chemotherapeutic drug for patients with ovarian cancer and other solid cancers, but drug resistance occurs frequently, resulting in ovarian cancer still presenting as the highest lethality among all gynecological tumors. Here, using DIGE quantitative proteomics, we identified UBC13 as down-regulated in paclitaxel-resistant ovarian cancer cells, and it was further revealed by immunohistochemical staining that UBC13 low-expression was associated with poorer prognosis and shorter survival of the patients. Through gene function experiments, we found that paclitaxel exposure induced UBC13 down-regulation, and the enforced change in UBC13 expression altered the sensitivity to paclitaxel. Meanwhile, the reduction of UBC13 increased DNMT1 levels by attenuating its ubiquitination, and the up-regulated DNMT1 enhanced the CHFR promoter DNA methylation levels, leading to a reduction of CHFR expression, and an increased in the levels of Aurora A. Our findings revealed a novel function for UBC13 in regulating paclitaxel sensitivity through a DNMT1-CHFR-Aurora A pathway in ovarian cancer cells. UBC13 could potentially be employed as a therapeutic molecular drug for reversing paclitaxel resistance in ovarian cancer patients.
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21
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Streich FC, Lima CD. Strategies to Trap Enzyme-Substrate Complexes that Mimic Michaelis Intermediates During E3-Mediated Ubiquitin-Like Protein Ligation. Methods Mol Biol 2018; 1844:169-196. [PMID: 30242710 DOI: 10.1007/978-1-4939-8706-1_12] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Most cellular functions rely on pathways that catalyze posttranslational modification of cellular proteins by ubiquitin (Ub) and ubiquitin-like (Ubl) proteins. Like other posttranslational modifications that require distinct writers, readers, and erasers during signaling, Ub/Ubl pathways employ distinct enzymes that catalyze Ub/Ubl attachment, Ub/Ubl recognition, and Ub/Ubl removal. Ubl protein conjugation typically relies on parallel but distinct enzymatic cascades catalyzed by an E1-activating enzyme, an E2 carrier protein, and an E3 ubiquitin-like protein ligase. One major class of E3, with ca. 600 members, harbors RING or the RING-like SP-RING or Ubox domains. These RING/RING-like domains bind and activate the E2-Ubl thioester by stabilizing a conformation that is optimal for nucleophilic attack by the side chain residue (typically lysine) on the substrate. These RING/RING-like domains typically function together with other domains or protein complexes that often serve to recruit particular substrates. How these RING/RING-like E3 domains function to activate the E2-Ubl thioester while engaged with substrate remains poorly understood. We describe a strategy to generate and purify a unique E2Ubc9-UblSUMO thioester mimetic that can be cross-linked to the SubstratePCNA at Lys164, a conjugation site that is only observed in the presence of E3Siz1. We describe two techniques to cross-link the E2Ubc9-UblSUMO thioester mimetic active site to the site of modification on PCNA and the subsequent purification of these complexes. Finally, we describe the reconstitution and purification of the E2Ubc9-UblSUMO-PCNA complex with the E3Siz1 and purification that enabled its crystallization and structure determination. We think this technique can be extended to other E2-Ubl-substrate/E3 complexes to better probe the function and specificity of RING-based E3 Ubl ligases.
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Affiliation(s)
- Frederick C Streich
- Structural Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY, USA
| | - Christopher D Lima
- Structural Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY, USA.
- Howard Hughes Medical Institute, 1275 York Ave, New York, NY, USA.
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22
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Complementary uses of small angle X-ray scattering and X-ray crystallography. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1865:1623-1630. [PMID: 28743534 DOI: 10.1016/j.bbapap.2017.07.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Revised: 07/10/2017] [Accepted: 07/20/2017] [Indexed: 12/11/2022]
Abstract
Most proteins function within networks and, therefore, protein interactions are central to protein function. Although stable macromolecular machines have been extensively studied, dynamic protein interactions remain poorly understood. Small-angle X-ray scattering probes the size, shape and dynamics of proteins in solution at low resolution and can be used to study samples in a large range of molecular weights. Therefore, it has emerged as a powerful technique to study the structure and dynamics of biomolecular systems and bridge fragmented information obtained using high-resolution techniques. Here we review how small-angle X-ray scattering can be combined with other structural biology techniques to study protein dynamics. This article is part of a Special Issue entitled: Biophysics in Canada, edited by Lewis Kay, John Baenziger, Albert Berghuis and Peter Tieleman.
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23
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Tainer JA. Uncovering the secrets of protein interactions with the DNA enforcing genomic stability. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2017; 127:89-92. [PMID: 28709479 DOI: 10.1016/j.pbiomolbio.2017.07.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- John A Tainer
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Holcombe Blvd., Houston, TX 77030, United States; SIBYLS, Advanced Light Source, Lawrence Berkeley National Lab, United States. http://bl1231.als.lbl.gov
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Lee BL, Singh A, Mark Glover JN, Hendzel MJ, Spyracopoulos L. Molecular Basis for K63-Linked Ubiquitination Processes in Double-Strand DNA Break Repair: A Focus on Kinetics and Dynamics. J Mol Biol 2017; 429:3409-3429. [PMID: 28587922 DOI: 10.1016/j.jmb.2017.05.029] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Revised: 05/20/2017] [Accepted: 05/30/2017] [Indexed: 11/18/2022]
Abstract
Cells are exposed to thousands of DNA damage events on a daily basis. This damage must be repaired to preserve genetic information and prevent development of disease. The most deleterious damage is a double-strand break (DSB), which is detected and repaired by mechanisms known as non-homologous end-joining (NHEJ) and homologous recombination (HR), which are components of the DNA damage response system. NHEJ is an error-prone first line of defense, whereas HR invokes error-free repair and is the focus of this review. The functions of the protein components of HR-driven DNA repair are regulated by the coordinated action of post-translational modifications including lysine acetylation, phosphorylation, ubiquitination, and SUMOylation. The latter two mechanisms are fundamental for recognition of DSBs and reorganizing chromatin to facilitate repair. We focus on the structures and molecular mechanisms for the protein components underlying synthesis, recognition, and cleavage of K63-linked ubiquitin chains, which are abundant at damage sites and obligatory for DSB repair. The forward flux of the K63-linked ubiquitination cascade is driven by the combined activity of E1 enzyme, the heterodimeric E2 Mms2-Ubc13, and its cognate E3 ligases RNF8 and RNF168, which is balanced through the binding and cleavage of chains by the deubiquitinase BRCC36, and the proteasome, and through the binding of chains by recognition modules on repair proteins such as RAP80. We highlight a number of aspects regarding our current understanding for the role of kinetics and dynamics in determining the function of the enzymes and chain recognition modules that drive K63 ubiquitination.
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Affiliation(s)
- Brian L Lee
- Department of Biochemistry, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Anamika Singh
- Department of Biochemistry, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - J N Mark Glover
- Department of Biochemistry, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Michael J Hendzel
- Department of Oncology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada; Department of Cell Biology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
| | - Leo Spyracopoulos
- Department of Biochemistry, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada.
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Brosey CA, Ahmed Z, Lees-Miller SP, Tainer JA. What Combined Measurements From Structures and Imaging Tell Us About DNA Damage Responses. Methods Enzymol 2017; 592:417-455. [PMID: 28668129 DOI: 10.1016/bs.mie.2017.04.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
DNA damage outcomes depend upon the efficiency and fidelity of DNA damage responses (DDRs) for different cells and damage. As such, DDRs represent tightly regulated prototypical systems for linking nanoscale biomolecular structure and assembly to the biology of genomic regulation and cell signaling. However, the dynamic and multifunctional nature of DDR assemblies can render elusive the correlation between the structures of DDR factors and specific biological disruptions to the DDR when these structures are altered. In this chapter, we discuss concepts and strategies for combining structural, biophysical, and imaging techniques to investigate DDR recognition and regulation, and thus bridge sequence-level structural biochemistry to quantitative biological outcomes visualized in cells. We focus on representative DDR responses from PARP/PARG/AIF damage signaling in DNA single-strand break repair and nonhomologous end joining complexes in double-strand break repair. Methods with exemplary experimental results are considered with a focus on strategies for probing flexibility, conformational changes, and assembly processes that shape a predictive understanding of DDR mechanisms in a cellular context. Integration of structural and imaging measurements promises to provide foundational knowledge to rationally control and optimize DNA damage outcomes for synthetic lethality and for immune activation with resulting insights for biology and cancer interventions.
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Affiliation(s)
- Chris A Brosey
- The University of Texas, M.D. Anderson Cancer Center, Houston, TX, United States
| | - Zamal Ahmed
- The University of Texas, M.D. Anderson Cancer Center, Houston, TX, United States
| | - Susan P Lees-Miller
- Robson DNA Science Centre, Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, AB, Canada.
| | - John A Tainer
- The University of Texas, M.D. Anderson Cancer Center, Houston, TX, United States; Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, United States.
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Boubriak II, Malhas AN, Drozdz MM, Pytowski L, Vaux DJ. Stress-induced release of Oct-1 from the nuclear envelope is mediated by JNK phosphorylation of lamin B1. PLoS One 2017; 12:e0177990. [PMID: 28542436 PMCID: PMC5443517 DOI: 10.1371/journal.pone.0177990] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Accepted: 05/06/2017] [Indexed: 02/08/2023] Open
Abstract
The nuclear lamina can bind and sequester transcription factors (TFs), a function lost if the lamina is abnormal, with missing or mutant lamin proteins. We now show that TF sequestration is not all-or-nothing, but a dynamic physiological response to external signals. We show that the binding of the ubiquitous TF, Oct-1, to lamin B1 was reversed under conditions of cellular stress caused, inter alia, by the chemical methylating agent methylmethanesulfonate (MMS). A search for lamin B1 post-translational modifications that might mediate changes in Oct-1 binding using kinase inhibitors uncovered a role for c-Jun N-terminal kinase (JNK). Phosphoproteomic and site-directed mutagenesis analyses of lamin B1 isolated from control and MMS-treated nuclei identified T575 as a JNK site phosphorylated after stress. A new phospho-T575 specific anti-peptide antibody confirmed increased interphase cellular T575 phosphorylation after cell exposure to certain stress conditions, enabling us to conclude that lamin B1 acts as an interphase kinase target, releasing Oct-1 to execute a protective response to stress.
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Affiliation(s)
- Ivan I. Boubriak
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Ashraf N. Malhas
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Marek M. Drozdz
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Lior Pytowski
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - David J. Vaux
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
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Abstract
Ubiquitin-like proteins (Ubl's) are conjugated to target proteins or lipids to regulate their activity, stability, subcellular localization, or macromolecular interactions. Similar to ubiquitin, conjugation is achieved through a cascade of activities that are catalyzed by E1 activating enzymes, E2 conjugating enzymes, and E3 ligases. In this review, we will summarize structural and mechanistic details of enzymes and protein cofactors that participate in Ubl conjugation cascades. Precisely, we will focus on conjugation machinery in the SUMO, NEDD8, ATG8, ATG12, URM1, UFM1, FAT10, and ISG15 pathways while referring to the ubiquitin pathway to highlight common or contrasting themes. We will also review various strategies used to trap intermediates during Ubl activation and conjugation.
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Affiliation(s)
- Laurent Cappadocia
- Structural Biology Program, Sloan Kettering Institute , New York, New York 10021, United States
| | - Christopher D Lima
- Structural Biology Program, Sloan Kettering Institute , New York, New York 10021, United States.,Howard Hughes Medical Institute, Sloan Kettering Institute , New York, New York 10021, United States
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