1
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Kawamura A, Yoshida S, Yoshida K. The diverse functions of DYRK2 in response to cellular stress. Histol Histopathol 2024; 39:1427-1434. [PMID: 38656683 DOI: 10.14670/hh-18-744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
To maintain microenvironmental and cellular homeostasis, cells respond to multiple stresses by activating characteristic cellular mechanisms consisting of receptors, signal transducers, and effectors. Dysfunction of these mechanisms can trigger multiple human diseases as well as cancers. Dual-specificity tyrosine-regulated kinases (DYRKs) are members of the CMGC group and are evolutionarily conserved from yeast to mammals. Previous studies revealed that DYRK2 has important roles in the regulation of the cell cycle and survival in cancer cells. On the other hand, recent studies show that DYRK2 also exhibits significant functions in multiple cellular stress responses and in maintaining cellular homeostasis. Hence, the further elucidation of mechanisms underlying DYRK2's diverse responses to various stresses helps to promote the advancement of innovative clinical therapies and pharmacological drugs. This review summarizes the molecular mechanisms of DYRK2, particularly focusing on cellular stress responses.
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Affiliation(s)
- Akira Kawamura
- Department of Biochemistry, The Jikei University School of Medicine, Tokyo, Japan
| | - Saishu Yoshida
- Department of Biochemistry, The Jikei University School of Medicine, Tokyo, Japan
| | - Kiyotsugu Yoshida
- Department of Biochemistry, The Jikei University School of Medicine, Tokyo, Japan.
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2
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Gill JK, Shaw GS. Using Förster Resonance Energy Transfer (FRET) to Understand the Ubiquitination Landscape. Chembiochem 2024; 25:e202400193. [PMID: 38632088 DOI: 10.1002/cbic.202400193] [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: 03/01/2024] [Revised: 04/15/2024] [Accepted: 04/17/2024] [Indexed: 04/19/2024]
Abstract
Förster resonance energy transfer (FRET) is a fluorescence technique that allows quantitative measurement of protein interactions, kinetics and dynamics. This review covers the use of FRET to study the structures and mechanisms of ubiquitination and related proteins. We survey FRET assays that have been developed where donor and acceptor fluorophores are placed on E1, E2 or E3 enzymes and ubiquitin (Ub) to monitor steady-state and real-time transfer of Ub through the ubiquitination cascade. Specialized FRET probes placed on Ub and Ub-like proteins have been developed to monitor Ub removal by deubiquitinating enzymes (DUBs) that result in a loss of a FRET signal upon cleavage of the FRET probes. FRET has also been used to understand conformational changes in large complexes such as multimeric E3 ligases and the proteasome, frequently using sophisticated single molecule methods. Overall, FRET is a powerful tool to help unravel the intricacies of the complex ubiquitination system.
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Affiliation(s)
- Jashanjot Kaur Gill
- Department of Biochemistry, University of Western Ontario, London, Ontario, Canada, N6A5C1
| | - Gary S Shaw
- Department of Biochemistry, University of Western Ontario, London, Ontario, Canada, N6A5C1
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3
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Wang D, Zhao J, Yang X, Ji Y, Yu J, Li Z, Shi Y, Guo J, Zhou J, Hou L, Liu J. E3 ligase RNF2 inhibits porcine circovirus type 3 replication by targeting its capsid protein for ubiquitination-dependent degradation. J Virol 2024; 98:e0022324. [PMID: 39046246 PMCID: PMC11334428 DOI: 10.1128/jvi.00223-24] [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: 02/01/2024] [Accepted: 06/21/2024] [Indexed: 07/25/2024] Open
Abstract
Porcine circovirus type 3 (PCV3) is closely associated with various diseases, such as the porcine dermatitis, nephropathy syndrome, and multisystemic clinicopathological diseases. PCV3-associated diseases are increasingly recognized as severe diseases in the global swine industry. Ring finger protein 2 (RNF2), an E3 ubiquitin ligase exclusively located in the nucleus, contributes to various biological processes. This ligase interacts with the PCV3 Cap. However, its role in PCV3 replication remains unclear. This study confirmed that the nuclear localization signal domain of the Cap and the RNF2 N-terminal RING domain facilitate the interaction between the Cap and RNF2. Furthermore, RNF2 promoted the binding of K48-linked polyubiquitination chains to lysine at positions 139 and 140 (K139 and K140) of the PCV3 Cap, thereby degrading the Cap. RNF2 knockdown and overexpression increased or decreased PCV3 replication, respectively. Moreover, the RING domain-deleted RNF2 mutant eliminated the RNF2-induced degradation of the PCV3 Cap and RNF2-mediated inhibition of viral replication. This indicates that both processes were associated with its E3 ligase activity. Our findings demonstrate that RNF2 can interact with and degrade the PCV3 Cap via its N-terminal RING domain in a ubiquitination-dependent manner, thereby inhibiting PCV3 replication.IMPORTANCEPorcine circovirus type 3 is a recently described pathogen that is prevalent worldwide, causing substantial economic losses to the swine industry. However, the mechanisms through which host proteins regulate its replication remain unclear. Here, we demonstrate that ring finger protein 2 inhibits porcine circovirus type 3 replication by interacting with and degrading the Cap of this pathogen in a ubiquitination-dependent manner, requiring its N-terminal RING domain. Ring finger protein 2-mediated degradation of the Cap relies on its E3 ligase activity and the simultaneous existence of K139 and K140 within the Cap. These findings reveal the mechanism by which this protein interacts with and degrades the Cap to inhibit porcine circovirus type 3 replication. This consequently provides novel insights into porcine circovirus type 3 pathogenesis and facilitates the development of preventative measures against this pathogen.
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Affiliation(s)
- Dedong Wang
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| | - Jie Zhao
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| | - Xiaoyu Yang
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| | - Ying Ji
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| | - Ju Yu
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
| | - Zhaoyang Li
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| | - Yongyan Shi
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| | - Jinshuo Guo
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| | - Jianwei Zhou
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| | - Lei Hou
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| | - Jue Liu
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
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4
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Dos Santos K, Bartocci A, Gillet N, Denis-Quanquin S, Roux A, Lin E, Xu Z, Finizola R, Chedozeau P, Chen X, Caradeuc C, Baudin M, Bertho G, Riobé F, Maury O, Dumont E, Giraud N. One touch is all it takes: the supramolecular interaction between ubiquitin and lanthanide complexes revisited by paramagnetic NMR and molecular dynamics. Phys Chem Chem Phys 2024; 26:14573-14581. [PMID: 38722087 DOI: 10.1039/d4cp00463a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/23/2024]
Abstract
The supramolecular interaction between lanthanide complexes and proteins is at the heart of numerous chemical and biological studies. Some of these complexes have demonstrated remarkable interaction properties with proteins or peptides in solution and in the crystalline state. Here we have used the paramagnetism of lanthanide ions to characterize the affinity of two lanthanide complexes for ubiquitin. As the interaction process is dynamic, the acquired NMR data only reflect the time average of the different steps. We have used molecular dynamics (MD) simulations to get a deeper insight into the detailed interaction scenario at the microsecond scale. This NMR/MD approach enabled us to establish that the tris-dipicolinate complex interacts specifically with arginines and lysines, while the crystallophore explores the protein surface through weak interactions with carboxylates. These observations shed new light on the dynamic interaction properties of these complexes, which will ultimately enable us to propose a crystallization mechanism.
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Affiliation(s)
- Karen Dos Santos
- Université Paris Cité, Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, UMR CNRS 8601, Paris, France.
| | - Alessio Bartocci
- Department of Physics, University of Trento, Via Sommarive 14, I-38123 Trento, Italy
- INFN-TIFPA, Trento Institute for Fundamental Physics and Applications, Via Sommarive 14, I-38123 Trento, Italy
- Institut de Chimie de Strasbourg, UMR 7177, CNRS, Université de Strasbourg, Strasbourg Cedex 67083, France
| | - Natacha Gillet
- Univ. Lyon, ENS de Lyon, CNRS UMR 5182, Université Claude Bernard Lyon 1, Laboratoire de Chimie, F69342, Lyon, France
| | - Sandrine Denis-Quanquin
- Univ. Lyon, ENS de Lyon, CNRS UMR 5182, Université Claude Bernard Lyon 1, Laboratoire de Chimie, F69342, Lyon, France
| | - Amandine Roux
- Univ. Lyon, ENS de Lyon, CNRS UMR 5182, Université Claude Bernard Lyon 1, Laboratoire de Chimie, F69342, Lyon, France
- Polyvalan SAS, Lyon, France
| | - Eugene Lin
- Université Paris Cité, Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, UMR CNRS 8601, Paris, France.
| | - Zeren Xu
- Université Paris Cité, Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, UMR CNRS 8601, Paris, France.
| | - Raphael Finizola
- Univ. Lyon, ENS de Lyon, CNRS UMR 5182, Université Claude Bernard Lyon 1, Laboratoire de Chimie, F69342, Lyon, France
| | - Pauline Chedozeau
- Université Paris Cité, Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, UMR CNRS 8601, Paris, France.
| | - Xi Chen
- Université Paris Cité, Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, UMR CNRS 8601, Paris, France.
| | - Cédric Caradeuc
- Université Paris Cité, Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, UMR CNRS 8601, Paris, France.
| | - Mathieu Baudin
- Université Paris Cité, Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, UMR CNRS 8601, Paris, France.
- Laboratoire des Biomolécules, LBM, Département de chimie, École Normale Supérieure, PSL Université, Sorbonne Université 45 Rue d'Ulm, 75005 Paris, France
| | - Gildas Bertho
- Université Paris Cité, Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, UMR CNRS 8601, Paris, France.
| | - François Riobé
- Univ. Bordeaux CNRS, Bordeaux INP, ICMCB UMR 5026, F-33600 Pessac, France
| | - Olivier Maury
- INFN-TIFPA, Trento Institute for Fundamental Physics and Applications, Via Sommarive 14, I-38123 Trento, Italy
| | - Elise Dumont
- Université Côte d'Azur, CNRS, Institut de Chimie de Nice, UMR 7272, 06108 Nice, France.
- Institut Universitaire de France, 5 rue Descartes, 75005 Paris, France
| | - Nicolas Giraud
- Université Paris Cité, Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, UMR CNRS 8601, Paris, France.
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5
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Tessier TM, Chowdhury A, Stekel Z, Fux J, Sartori MA, Teyra J, Jarvik N, Chung J, Kurinov I, Sicheri F, Sidhu SS, Singer AU, Zhang W. Structural and functional validation of a highly specific Smurf2 inhibitor. Protein Sci 2024; 33:e4885. [PMID: 38147466 PMCID: PMC10823456 DOI: 10.1002/pro.4885] [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: 08/31/2023] [Revised: 12/20/2023] [Accepted: 12/21/2023] [Indexed: 12/28/2023]
Abstract
Smurf1 and Smurf2 are two closely related member of the HECT (homologous to E6AP carboxy terminus) E3 ubiquitin ligase family and play important roles in the regulation of various cellular processes. Both were initially identified to regulate transforming growth factor-β and bone morphogenetic protein signaling pathways through regulating Smad protein stability and are now implicated in various pathological processes. Generally, E3 ligases, of which over 800 exist in humans, are ideal targets for inhibition as they determine substrate specificity; however, there are few inhibitors with the ability to precisely target a particular E3 ligase of interest. In this work, we explored a panel of ubiquitin variants (UbVs) that were previously identified to bind Smurf1 or Smurf2. In vitro binding and ubiquitination assays identified a highly specific Smurf2 inhibitor, UbV S2.4, which was able to inhibit ligase activity with high potency in the low nanomolar range. Orthologous cellular assays further demonstrated high specificity of UbV S2.4 toward Smurf2 and no cross-reactivity toward Smurf1. Structural analysis of UbV S2.4 in complex with Smurf2 revealed its mechanism of inhibition was through targeting the E2 binding site. In summary, we investigated several protein-based inhibitors of Smurf1 and Smurf2 and identified a highly specific Smurf2 inhibitor that disrupts the E2-E3 protein interaction interface.
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Affiliation(s)
- Tanner M. Tessier
- Department of Molecular and Cellular BiologyUniversity of GuelphGuelphOntarioCanada
| | - Arvid Chowdhury
- Department of Molecular GeneticsUniversity of TorontoTorontoOntarioCanada
| | - Zane Stekel
- Department of Molecular and Cellular BiologyUniversity of GuelphGuelphOntarioCanada
| | - Julia Fux
- Department of Molecular and Cellular BiologyUniversity of GuelphGuelphOntarioCanada
| | | | | | - Nick Jarvik
- Department of PharmacyUniversity of WaterlooKitchenerOntarioCanada
| | - Jacky Chung
- Department of PharmacyUniversity of WaterlooKitchenerOntarioCanada
| | - Igor Kurinov
- NE‐CAT, Department of Chemistry and Chemical BiologyCornell UniversityArgonneIllinoisUSA
| | - Frank Sicheri
- Lunenfeld‐Tanenbaum Research Institute, Mount Sinai HospitalTorontoOntarioCanada
| | - Sachdev S. Sidhu
- Department of PharmacyUniversity of WaterlooKitchenerOntarioCanada
| | - Alex U. Singer
- Department of PharmacyUniversity of WaterlooKitchenerOntarioCanada
| | - Wei Zhang
- Department of Molecular and Cellular BiologyUniversity of GuelphGuelphOntarioCanada
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6
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Wang S, Tian X, Zhou Y, Xie J, Gao M, Zhong Y, Zhang C, Yu K, Bai L, Qin Q, Zhong B, Lin D, Feng P, Lan K, Zhang J. Non-canonical regulation of the reactivation of an oncogenic herpesvirus by the OTUD4-USP7 deubiquitinases. PLoS Pathog 2024; 20:e1011943. [PMID: 38215174 PMCID: PMC10810452 DOI: 10.1371/journal.ppat.1011943] [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: 09/26/2023] [Revised: 01/25/2024] [Accepted: 01/03/2024] [Indexed: 01/14/2024] Open
Abstract
Deubiquitinases (DUBs) remove ubiquitin from substrates and play crucial roles in diverse biological processes. However, our understanding of deubiquitination in viral replication remains limited. Employing an oncogenic human herpesvirus Kaposi's sarcoma-associated herpesvirus (KSHV) to probe the role of protein deubiquitination, we found that Ovarian tumor family deubiquitinase 4 (OTUD4) promotes KSHV reactivation. OTUD4 interacts with the replication and transcription activator (K-RTA), a key transcription factor that controls KSHV reactivation, and enhances K-RTA stability by promoting its deubiquitination. Notably, the DUB activity of OTUD4 is not required for K-RTA stabilization; instead, OTUD4 functions as an adaptor protein to recruit another DUB, USP7, to deubiquitinate K-RTA and facilitate KSHV lytic reactivation. Our study has revealed a novel mechanism whereby KSHV hijacks OTUD4-USP7 deubiquitinases to promote lytic reactivation, which could be potentially harnessed for the development of new antiviral therapies.
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Affiliation(s)
- Shaowei Wang
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, State Key Laboratory of Virology, Medical Research Institute, Wuhan University, Wuhan, China
- Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, China
- Hubei Key Laboratory of Tumor Biological Behaviors, Hubei Province Cancer Clinical Study Center, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Xuezhang Tian
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, State Key Laboratory of Virology, Medical Research Institute, Wuhan University, Wuhan, China
- Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, China
| | - Yaru Zhou
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, State Key Laboratory of Virology, Medical Research Institute, Wuhan University, Wuhan, China
- Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, China
| | - Jun Xie
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, State Key Laboratory of Virology, Medical Research Institute, Wuhan University, Wuhan, China
- Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, China
| | - Ming Gao
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, State Key Laboratory of Virology, Medical Research Institute, Wuhan University, Wuhan, China
- Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, China
| | - Yunhong Zhong
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, State Key Laboratory of Virology, Medical Research Institute, Wuhan University, Wuhan, China
- Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, China
| | - Chuchu Zhang
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, State Key Laboratory of Virology, Medical Research Institute, Wuhan University, Wuhan, China
- Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, China
| | - Keying Yu
- Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, China
- Department of Gastrointestinal Surgery, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, China
| | - Lei Bai
- State Key Laboratory of Virology, School of Life Sciences, Wuhan University, Wuhan, China
| | - Qingsong Qin
- Laboratory of Human Virology and Oncology, Shantou University Medical College, Shantou, China
| | - Bo Zhong
- Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, China
- Department of Gastrointestinal Surgery, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, China
| | - Dandan Lin
- Cancer Center, Renmin Hospital of Wuhan University, Wuhan University, Wuhan, China
| | - Pinghui Feng
- Section of Infection and Immunity, Herman Ostrow School of Dentistry, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, California, United States of America
| | - Ke Lan
- Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, China
- State Key Laboratory of Virology, School of Life Sciences, Wuhan University, Wuhan, China
| | - Junjie Zhang
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, State Key Laboratory of Virology, Medical Research Institute, Wuhan University, Wuhan, China
- Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, China
- Hubei Key Laboratory of Tumor Biological Behaviors, Hubei Province Cancer Clinical Study Center, Zhongnan Hospital of Wuhan University, Wuhan, China
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7
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Wang D, Hou L, Ji Y, Xie J, Zhao J, Zhu N, Yang X, Zhou J, Cui Y, Guo J, Feng X, Liu J. Ubiquitination-dependent degradation of nucleolin mediated by porcine circovirus type 3 capsid protein. J Virol 2023; 97:e0089423. [PMID: 38032196 PMCID: PMC10734473 DOI: 10.1128/jvi.00894-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 09/27/2023] [Indexed: 12/01/2023] Open
Abstract
IMPORTANCE Porcine circovirus type 3 (PCV3) is an emerging pathogen that causes multisystem disease in pigs and poses a severe threat to the swine industry. However, the mechanisms of how PCV3 uses host proteins to regulate its own life cycle are not well understood. In this study, we found that PCV3 capsid protein interacts with nucleolin and degrades it. Degradation of nucleolin by the PCV3 capsid protein requires recruitment of the enzyme RNF34, which is transported to the nucleolus from the cytoplasm in the presence of the PCV3 capsid protein. Nucleolin also decreases PCV3 replication by promoting the release of interferon β. These findings clarify the mechanism by which nucleolin modulates PCV3 replication in cells, thereby facilitating to provide an important strategy for preventing and controlling PCV3 infection.
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Affiliation(s)
- Dedong Wang
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| | - Lei Hou
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| | - Ying Ji
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| | - Jiali Xie
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| | - Jie Zhao
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| | - Ning Zhu
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| | - Xiaoyu Yang
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| | - Jianwei Zhou
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| | - Yongqiu Cui
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| | - Jinshuo Guo
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| | - Xufei Feng
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| | - Jue Liu
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
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8
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Abstract
Ubiquitination is an essential regulator of most, if not all, signalling pathways, and defects in cellular signalling are central to cancer initiation, progression and, eventually, metastasis. The attachment of ubiquitin signals by E3 ubiquitin ligases is directly opposed by the action of approximately 100 deubiquitinating enzymes (DUBs) in humans. Together, DUBs and E3 ligases coordinate ubiquitin signalling by providing selectivity for different substrates and/or ubiquitin signals. The balance between ubiquitination and deubiquitination is exquisitely controlled to ensure properly coordinated proteostasis and response to cellular stimuli and stressors. Not surprisingly, then, DUBs have been associated with all hallmarks of cancer. These relationships are often complex and multifaceted, highlighted by the implication of multiple DUBs in certain hallmarks and by the impact of individual DUBs on multiple cancer-associated pathways, sometimes with contrasting cancer-promoting and cancer-inhibiting activities, depending on context and tumour type. Although it is still understudied, the ever-growing knowledge of DUB function in cancer physiology will eventually identify DUBs that warrant specific inhibition or activation, both of which are now feasible. An integrated appreciation of the physiological consequences of DUB modulation in relevant cancer models will eventually lead to the identification of patient populations that will most likely benefit from DUB-targeted therapies.
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Affiliation(s)
- Grant Dewson
- Ubiquitin Signalling Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia.
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia.
| | - Pieter J A Eichhorn
- Curtin Medical School, Curtin University, Perth, Western Australia, Australia.
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.
| | - David Komander
- Ubiquitin Signalling Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia.
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia.
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9
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Silva ARR, Silva PV, Soares AR, González-Alcaraz MN, van Gestel CAM, Roelofs D, Moura G, Soares AMVM, Loureiro S. Daphnia magna Multigeneration Exposure to Carbendazim: Gene Transcription Responses. TOXICS 2023; 11:918. [PMID: 37999570 PMCID: PMC10674461 DOI: 10.3390/toxics11110918] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 10/30/2023] [Accepted: 11/07/2023] [Indexed: 11/25/2023]
Abstract
The world population is experiencing colossal growth and thus demand for food, leading to an increase in the use of pesticides. Persistent pesticide contamination, such as carbendazim, remains a pressing environmental concern, with potentially long-term impacts on aquatic ecosystems. In the present study, Daphnia magna was exposed to carbendazim (5 µg L-1) for 12 generations, with the aim of assessing gene transcription alterations induced by carbendazim (using a D. magna custom microarray). The results showed that carbendazim caused changes in genes involved in the response to stress, DNA replication/repair, neurotransmission, ATP production, and lipid and carbohydrate metabolism at concentrations already found in the environment. These outcomes support the results of previous studies, in which carbendazim induced genotoxic effects and reproduction impairment (increasing the number of aborted eggs with the decreasing number of neonates produced). The exposure of daphnids to carbendazim did not cause a stable change in gene transcription between generations, with more genes being differentially expressed in the F0 generation than in the F12 generation. This could show some possible daphnid acclimation after 12 generations and is aligned with previous multigenerational studies where few ecotoxicological effects at the individual and populational levels and other subcellular level effects (e.g., biochemical biomarkers) were found.
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Affiliation(s)
- Ana Rita R. Silva
- Centre for Environmental and Marine Studies (CESAM) & Department of Biology, University of Aveiro, 3810-193 Aveiro, Portugal; (P.V.S.); (A.M.V.M.S.); (S.L.)
| | - Patrícia V. Silva
- Centre for Environmental and Marine Studies (CESAM) & Department of Biology, University of Aveiro, 3810-193 Aveiro, Portugal; (P.V.S.); (A.M.V.M.S.); (S.L.)
| | - Ana Raquel Soares
- Department of Medical Sciences & Institute for Biomedicine (iBiMED), University of Aveiro, 3810-193 Aveiro, Portugal; (A.R.S.); (G.M.)
| | - M. Nazaret González-Alcaraz
- Department of Agricultural Engineering of the E.T.S.I.A., Technical University of Cartagena, 30203 Cartagena, Spain;
| | - Cornelis A. M. van Gestel
- Amsterdam Institute for Life and Environment (A-LIFE), Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands; (C.A.M.v.G.); (D.R.)
| | - Dick Roelofs
- Amsterdam Institute for Life and Environment (A-LIFE), Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands; (C.A.M.v.G.); (D.R.)
- Keygene N.V., Agro Business Park 90, 6708 PW Wageningen, The Netherlands
| | - Gabriela Moura
- Department of Medical Sciences & Institute for Biomedicine (iBiMED), University of Aveiro, 3810-193 Aveiro, Portugal; (A.R.S.); (G.M.)
| | - Amadeu M. V. M. Soares
- Centre for Environmental and Marine Studies (CESAM) & Department of Biology, University of Aveiro, 3810-193 Aveiro, Portugal; (P.V.S.); (A.M.V.M.S.); (S.L.)
| | - Susana Loureiro
- Centre for Environmental and Marine Studies (CESAM) & Department of Biology, University of Aveiro, 3810-193 Aveiro, Portugal; (P.V.S.); (A.M.V.M.S.); (S.L.)
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10
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Wu X, Zhou X, Wang S, Mao G. DNA damage response(DDR): a link between cellular senescence and human cytomegalovirus. Virol J 2023; 20:250. [PMID: 37915066 PMCID: PMC10621139 DOI: 10.1186/s12985-023-02203-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 10/04/2023] [Indexed: 11/03/2023] Open
Abstract
The DNA damage response (DDR) is a signaling cascade that is triggered by DNA damage, involving the halting of cell cycle progression and repair. It is a key event leading to senescence, which is characterized by irreversible cell cycle arrest and the senescence-associated secretory phenotype (SASP) that includes the expression of inflammatory cytokines. Human cytomegalovirus (HCMV) is a ubiquitous pathogen that plays an important role in the senescence process. It has been established that DDR is necessary for HCMV to replicate effectively. This paper reviews the relationship between DDR, cellular senescence, and HCMV, providing new sights for virus-induced senescence (VIS).
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Affiliation(s)
- Xinna Wu
- Affiliated Zhejiang Hospital, Zhejiang University School of Medicine, Hangzhou, 310030, China
| | - Xuqiang Zhou
- College of Life Science, Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Sanying Wang
- Zhejiang Provincial Key Lab of Geriatrics & Geriatrics Institute of Zhejiang Province, Department of Geriatrics, Zhejiang Hospital, Hangzhou, 310030, China.
| | - Genxiang Mao
- Affiliated Zhejiang Hospital, Zhejiang University School of Medicine, Hangzhou, 310030, China.
- Zhejiang Provincial Key Lab of Geriatrics & Geriatrics Institute of Zhejiang Province, Department of Geriatrics, Zhejiang Hospital, Hangzhou, 310030, China.
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11
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Wang X, Xu X, Wang Z. The Post-Translational Role of UFMylation in Physiology and Disease. Cells 2023; 12:2543. [PMID: 37947621 PMCID: PMC10648299 DOI: 10.3390/cells12212543] [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: 08/30/2023] [Revised: 10/13/2023] [Accepted: 10/20/2023] [Indexed: 11/12/2023] Open
Abstract
Ubiquitin-fold modifier 1 (UFM1) is a newly identified ubiquitin-like protein that has been conserved during the evolution of multicellular organisms. In a similar manner to ubiquitin, UFM1 can become covalently linked to the lysine residue of a substrate via a dedicated enzymatic cascade. Although a limited number of substrates have been identified so far, UFM1 modification (UFMylation) has been demonstrated to play a vital role in a variety of cellular activities, including mammalian development, ribosome biogenesis, the DNA damage response, endoplasmic reticulum stress responses, immune responses, and tumorigenesis. In this review, we summarize what is known about the UFM1 enzymatic cascade and its biological functions, and discuss its recently identified substrates. We also explore the pathological role of UFMylation in human disease and the corresponding potential therapeutic targets and strategies.
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Affiliation(s)
| | - Xingzhi Xu
- Guangdong Key Laboratory for Genome Stability & Disease Prevention and Carson International Cancer Center, Marshall Laboratory of Biomedical Engineering, Shenzhen University Medical School, Shenzhen 518060, China;
| | - Zhifeng Wang
- Guangdong Key Laboratory for Genome Stability & Disease Prevention and Carson International Cancer Center, Marshall Laboratory of Biomedical Engineering, Shenzhen University Medical School, Shenzhen 518060, China;
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12
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Wu C, Shi W, Zhang S. ZEB1 promotes DNA homologous recombination repair and contributes to the 5-Fluorouracil resistance in colorectal cancer. Am J Cancer Res 2023; 13:4101-4114. [PMID: 37818077 PMCID: PMC10560938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 08/06/2023] [Indexed: 10/12/2023] Open
Abstract
Chemotherapy resistance represents a significant obstacle in clinical practice of colorectal cancer (CRC). In this study we aim to clarify the underlying mechanism of chemotherapy resistance mediated by ZEB1 in CRC. shRNA-mediated repression of ZEB1 induced DNA damage in SW480 and RKO cells. Ectopic expression of ZEB1 suppressed the DNA damage caused by ZEB1 knocking down in SW480 and RKO cells. In addition, ZEB1 directly targeted several DNA damage response (DDR) factors including NBS1, RNF8 and RNF168, and thereby the homologous recombination (HR) repair is mediated by ZEB1 via NBS1, RNF8 and RNF168 in CRC cells. Furthermore, ZEB1 maintained chromosome stability in CRC cells. By inducing NBS1, RNF8 and RNF168, ZEB1 is capable of promoting the 5-Fluorouracil (5-FU) resistance in CRC cells via enhancing the DDR signaling and DNA repair. The high expression of ZEB1, NBS1, RNF8 and RNF168 is associated with chemotherapy resistance in primary CRC patients. In conclusion, ZEB1 directly induces the expression of NBS1, RNF8 and RNF168, and thereby enhances DNA HR repair in CRC. The ZEB1-mediated DNA repair contributes to the 5-FU resistance in CRC.
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Affiliation(s)
- Chao Wu
- Klinikum rechts der Isar, Technical University of MunichMunich, Germany
| | - Wenjing Shi
- Department of Clinical Laboratory, The International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong UniversityShanghai, China
- Shanghai Key Laboratory of Embryo Original DiseasesShanghai, China
- Shanghai Municipal Key Clinical SpecialityShanghai, China
- Experimental and Molecular Pathology, Institute of Pathology, Ludwig-Maximilians-UniversityMunich, Germany
| | - Sen Zhang
- Department of General Surgery, Ruijin Hospital, School of Medicine, Shanghai Jiao Tong UniversityShanghai, China
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13
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Jian Y, Chen X, Sun K, Liu Z, Cheng D, Cao J, Liu J, Cheng X, Wu L, Zhang F, Luo Y, Hahn M, Ma Z, Yin Y. SUMOylation regulates pre-mRNA splicing to overcome DNA damage in fungi. THE NEW PHYTOLOGIST 2023; 237:2298-2315. [PMID: 36539920 DOI: 10.1111/nph.18692] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 12/09/2022] [Indexed: 06/17/2023]
Abstract
Pathogenic fungi are subject to DNA damage stress derived from host immune responses during infection. Small ubiquitin-like modifier (SUMO) modification and precursor (pre)-mRNA splicing are both involved in DNA damage response (DDR). However, the mechanisms of how SUMOylation and splicing coordinated in DDR remain largely unknown. Combining with biochemical analysis, RNA-Seq method, and biological analysis, we report that SUMO pathway participates in DDR and virulence in Fusarium graminearum, a causal agent of Fusarium head blight of cereal crops world-wide. Interestingly, a key transcription factor FgSR is SUMOylated upon DNA damage stress. SUMOylation regulates FgSR nuclear-cytoplasmic partitioning and its phosphorylation by FgMec1, and promotes its interaction with chromatin remodeling complex SWI/SNF for activating the expression of DDR-related genes. Moreover, the SWI/SNF complex was found to further recruit splicing-related NineTeen Complex, subsequently modulates pre-mRNA splicing during DDR. Our findings reveal a novel function of SUMOylation in DDR by regulating a transcription factor to orchestrate gene expression and pre-mRNA splicing to overcome DNA damage during the infection of F. graminearum, which advances the understanding of the delicate regulation of DDR by SUMOylation in pathogenic fungi, and extends the knowledge of cooperation of SUMOylation and pre-mRNA splicing in DDR in eukaryotes.
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Affiliation(s)
- Yunqing Jian
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China
| | - Xia Chen
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China
| | - Kewei Sun
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China
| | - Zunyong Liu
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China
| | - Danni Cheng
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China
| | - Jie Cao
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Hangzhou, 310058, China
| | - Jianzhao Liu
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Hangzhou, 310058, China
| | - Xiaofei Cheng
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region of Chinese Education Ministry, College of Agriculture, Northeast Agricultural University, Harbin, 150030, China
| | - Liang Wu
- Institute of Crop Science, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China
| | - Feng Zhang
- Key Laboratory of Pesticide, College of Plant Protection, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yuming Luo
- Jiangsu Key Laboratory for Eco-Agricultural Biotechnology around Hongze Lake, Jiangsu Collaborative Innovation Center of Regional Modern Agriculture and Environmental Protection, Huaiyin Normal University, Huai'an, 223300, China
| | - Matthias Hahn
- Department of Biology, University of Kaiserslautern, PO Box 3049, 67653, Kaiserslautern, Germany
| | - Zhonghua Ma
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China
| | - Yanni Yin
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China
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14
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Xu Y, Wang H, Sahu SK, Li L, Liang H, Günther G, Wong GKS, Melkonian B, Melkonian M, Liu H, Wang S. Chromosome-level genome of Pedinomonas minor (Chlorophyta) unveils adaptations to abiotic stress in a rapidly fluctuating environment. THE NEW PHYTOLOGIST 2022; 235:1409-1425. [PMID: 35560066 DOI: 10.1111/nph.18220] [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: 03/14/2022] [Accepted: 05/04/2022] [Indexed: 06/15/2023]
Abstract
The Pedinophyceae (Viridiplantae) comprise a class of small uniflagellate algae with a pivotal position in the phylogeny of the Chlorophyta as the sister group of the 'core chlorophytes'. We present a chromosome-level genome assembly of the freshwater type species of the class, Pedinomonas minor. We sequenced the genome using Pacbio, Illumina and Hi-C technologies, performed comparative analyses of genome and gene family evolution, and analyzed the transcriptome under various abiotic stresses. Although the genome is relatively small (55 Mb), it shares many traits with core chlorophytes including number of introns and protein-coding genes, messenger RNA (mRNA) lengths, and abundance of transposable elements. Pedinomonas minor is only bounded by the plasma membrane, thriving in temporary habitats that frequently dry out. Gene family innovations and expansions and transcriptomic responses to abiotic stresses have shed light on adaptations of P. minor to its fluctuating environment. Horizontal gene transfers from bacteria and fungi have possibly contributed to the evolution of some of these traits. We identified a putative endogenization site of a nucleocytoplasmic large DNA virus and hypothesized that endogenous viral elements donated foreign genes to the host genome, their spread enhanced by transposable elements, located at gene boundaries in several of the expanded gene families.
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Affiliation(s)
- Yan Xu
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 10049, China
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Hongli Wang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 10049, China
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Sunil Kumar Sahu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Linzhou Li
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, 2800, Denmark
| | - Hongping Liang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 10049, China
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Gerd Günther
- Private Laboratory, Knittkuhler Str. 61, Düsseldorf, 40629, Germany
| | - Gane Ka-Shu Wong
- Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E9, Canada
- Department of Medicine, University of Alberta, Edmonton, AB, T6G 2E9, Canada
| | - Barbara Melkonian
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, 50829, Germany
| | - Michael Melkonian
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, 50829, Germany
| | - Huan Liu
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 10049, China
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Sibo Wang
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518083, China
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15
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Wang W, Yan T, Guo X, Cai H, Liang C, Huang L, Wang Y, Ma P, Qi S. KAP1 phosphorylation promotes the survival of neural stem cells after ischemia/reperfusion by maintaining the stability of PCNA. Stem Cell Res Ther 2022; 13:290. [PMID: 35799276 PMCID: PMC9264526 DOI: 10.1186/s13287-022-02962-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 04/17/2022] [Indexed: 11/28/2022] Open
Abstract
Aims To explore the function of phosphorylation of KAP1 (p-KAP1) at the serine-824 site (S824) in the proliferation and apoptosis of endogenous neural stem cells (NSCs) after cerebral ischemic/reperfusion (I/R). Methods The apoptosis and proliferation of C17.2 cells transfected with the p-KAP1-expression plasmids and the expression of proliferation cell nuclear antigen (PCNA) and p-KAP1 were detected by immunofluorescence and Western blotting after the Oxygen Glucose deprivation/reperfusion model (OGD/R). The interaction of p-KAP1 and CUL4A with PCNA was analyzed by immunoprecipitation. In the rats MCAO model, we performed the adeno-associated virus (AAV) 2/9 gene delivery of p-KAP1 mutants to verify the proliferation of endogenous NSCs and the colocalization of PCNA and CUL4A by immunofluorescence. Results The level of p-KAP1 was significantly down-regulated in the stroke model in vivo and in vitro. Simulated p-KAP1(S824) significantly increased the proliferation of C17.2 cells and the expression of PCNA after OGD/R. Simulated p-KAP1(S824) enhanced the binding of p-KAP1 and PCNA and decreased the interaction between PCNA and CUL4A in C17.2 cells subjected to OGD/R. The AAV2/9-mediated p-KAP1(S824) increased endogenous NSCs proliferation, PCNA expression, p-KAP1 binding to PCNA, and improved neurological function in the rat MCAO model. Conclusions Our findings confirmed that simulated p-KAP1(S824) improved the survival and proliferation of endogenous NSCs. The underlying mechanism is that highly expressed p-KAP1(S824) promotes binding to PCNA, and inhibits the binding of CUL4A to PCNA. This reduced CUL4A-mediated ubiquitination degradation to increase the stability of PCNA and promote the survival and proliferation of NSCs. Supplementary Information The online version contains supplementary material available at 10.1186/s13287-022-02962-5.
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Affiliation(s)
- Wan Wang
- School of Medical Technology, Xuzhou Key Laboratory of Laboratory Diagnostics, Xuzhou Medical University, Xuzhou, 221004, China.,Department of Laboratory Medicine, Affiliated Hospital of Xuzhou Medical University, Xuzhou, 221002, China
| | - Tianqing Yan
- School of Medical Technology, Xuzhou Key Laboratory of Laboratory Diagnostics, Xuzhou Medical University, Xuzhou, 221004, China
| | - Xinjian Guo
- School of Medical Technology, Xuzhou Key Laboratory of Laboratory Diagnostics, Xuzhou Medical University, Xuzhou, 221004, China
| | - Heng Cai
- School of Medical Technology, Xuzhou Key Laboratory of Laboratory Diagnostics, Xuzhou Medical University, Xuzhou, 221004, China
| | - Chang Liang
- School of Basic Medical Science, Xuzhou Medical University, Xuzhou, 221004, China
| | - Linyan Huang
- School of Medical Technology, Xuzhou Key Laboratory of Laboratory Diagnostics, Xuzhou Medical University, Xuzhou, 221004, China
| | - Yanling Wang
- School of Medical Technology, Xuzhou Key Laboratory of Laboratory Diagnostics, Xuzhou Medical University, Xuzhou, 221004, China
| | - Ping Ma
- School of Medical Technology, Xuzhou Key Laboratory of Laboratory Diagnostics, Xuzhou Medical University, Xuzhou, 221004, China. .,Department of Laboratory Medicine, Affiliated Hospital of Xuzhou Medical University, Xuzhou, 221002, China.
| | - Suhua Qi
- School of Medical Technology, Xuzhou Key Laboratory of Laboratory Diagnostics, Xuzhou Medical University, Xuzhou, 221004, China. .,Pharmacology College, Xuzhou Medical University, Xuzhou, 221004, China.
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16
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Kelliher J, Ghosal G, Leung JWC. New answers to the old RIDDLE: RNF168 and the DNA damage response pathway. FEBS J 2022; 289:2467-2480. [PMID: 33797206 PMCID: PMC8486888 DOI: 10.1111/febs.15857] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 03/12/2021] [Accepted: 03/31/2021] [Indexed: 12/31/2022]
Abstract
The chromatin-based DNA damage response pathway is tightly orchestrated by histone post-translational modifications, including histone H2A ubiquitination. Ubiquitination plays an integral role in regulating cellular processes including DNA damage signaling and repair. The ubiquitin E3 ligase RNF168 is essential in assembling a cohort of DNA repair proteins at the damaged chromatin via its enzymatic activity. RNF168 ubiquitinates histone H2A(X) at the N terminus and generates a specific docking scaffold for ubiquitin-binding motif-containing proteins. The regulation of RNF168 at damaged chromatin and the mechanistic implication in the recruitment of DNA repair proteins to the damaged sites remain an area of active investigation. Here, we review the function and regulation of RNF168 in the context of ubiquitin-mediated DNA damage signaling and repair. We will also discuss the unanswered questions that require further investigation and how understanding RNF168 targeting specificity could benefit the therapeutic development for cancer treatment.
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Affiliation(s)
- Jessica Kelliher
- Department of Radiation Oncology, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR 72205, United States
| | - Gargi Ghosal
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198, United States,To whom correspondence should be addressed: and
| | - Justin Wai Chung Leung
- Department of Radiation Oncology, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR 72205, United States,To whom correspondence should be addressed: and
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17
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Hu C, Wallace N. Beta HPV Deregulates Double-Strand Break Repair. Viruses 2022; 14:948. [PMID: 35632690 PMCID: PMC9146468 DOI: 10.3390/v14050948] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 04/27/2022] [Accepted: 04/28/2022] [Indexed: 02/04/2023] Open
Abstract
Beta human papillomavirus (beta HPV) infections are common in adults. Certain types of beta HPVs are associated with nonmelanoma skin cancer (NMSC) in immunocompromised individuals. However, whether beta HPV infections promote NMSC in the immunocompetent population is unclear. They have been hypothesized to increase genomic instability stemming from ultraviolet light exposure by disrupting DNA damage responses. Implicit in this hypothesis is that the virus encodes one or more proteins that impair DNA repair signaling. Fluorescence-based reporters, next-generation sequencing, and animal models have been used to test this primarily in cells expressing beta HPV E6/E7. Of the two, beta HPV E6 appears to have the greatest ability to increase UV mutagenesis, by attenuating two major double-strand break (DSB) repair pathways, homologous recombination, and non-homologous end-joining. Here, we review this dysregulation of DSB repair and emerging approaches that can be used to further these efforts.
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Affiliation(s)
| | - Nicholas Wallace
- Division of Biology, Kansas State University, Manhattan, KS 66506, USA;
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18
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Swift ML, Azizkhan-Clifford J. DNA damage-induced sumoylation of Sp1 induces its interaction with RNF4 and degradation in S phase to remove 53BP1 from DSBs and permit HR. DNA Repair (Amst) 2022; 111:103289. [DOI: 10.1016/j.dnarep.2022.103289] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 01/26/2022] [Accepted: 01/29/2022] [Indexed: 02/06/2023]
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19
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Choi SH, Cho K, Kim ES, Yoo HY. Proline-serine-threonine-repeat region of MDC1 mediates Chk1 phosphorylation and the DNA double-strand break repair. Int J Biochem Cell Biol 2021; 143:106152. [PMID: 34974185 DOI: 10.1016/j.biocel.2021.106152] [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: 09/10/2021] [Revised: 12/27/2021] [Accepted: 12/28/2021] [Indexed: 11/29/2022]
Abstract
MDC1, a mediator of DNA damage response, recruits other repair proteins on double-strand break (DSB) sites. MDC1 is necessary for activating checkpoint kinases Chk1 and Chk2. It is unclear whether Chk1 interacts with MDC1. MDC1 also comprises many discrete domains. The role of the proline-serine-threonine (PST)-repeat domain of MDC1 in the DNA damage response is unclear. Here, we showed that MDC1 directly binds Chk1 through this PST-repeat region. Phosphorylation of Chk1 by ionizing radiation (IR) also required this PST-repeat domain. Degradation of intact MDC1 was accelerated depending on the PST-repeat domain after IR exposure. In the IR damage response, the PST-repeat-deleted MDC1 levels remained elevated with slow degradation. This abnormal regulation of MDC1 was F-box- and WD40 repeat-containing 7 (FBXW7)-dependent. The mutation of lysine 1413 within the PST-repeat of MDC1 deregulated MDC1 with or without damage. K1413R mutant and PST-deleted MDC1 displayed reduced ability to repair the damaged genome post-IR exposure. These results provide that the PST domain of MDC1 is involved in Chk1 and DNA repair activation. The findings suggest new insights into how MDC1 connects the checkpoint and DNA repair in the DNA damage response.
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Affiliation(s)
- Seung Ho Choi
- Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences and Technology, Sungkyunkwan University, Seoul 06355, Korea; Samsung Biomedical Research Institute, Research Institute for Future Medicine, Samsung Medical Center, Seoul 06355, Korea
| | - Kyoungjoo Cho
- Department of Life Science, College of Fusion Science, Kyonggi University, Suwon 16227, Korea
| | - Eun Seon Kim
- Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences and Technology, Sungkyunkwan University, Seoul 06355, Korea; Samsung Biomedical Research Institute, Research Institute for Future Medicine, Samsung Medical Center, Seoul 06355, Korea
| | - Hae Yong Yoo
- Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences and Technology, Sungkyunkwan University, Seoul 06355, Korea; Samsung Biomedical Research Institute, Research Institute for Future Medicine, Samsung Medical Center, Seoul 06355, Korea.
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20
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Di Genova A, Nardocci G, Maldonado-Agurto R, Hodar C, Valdivieso C, Morales P, Gajardo F, Marina R, Gutiérrez RA, Orellana A, Cambiazo V, González M, Glavic A, Mendez MA, Maass A, Allende ML, Montecino MA. Genome sequencing and transcriptomic analysis of the Andean killifish Orestias ascotanensis reveals adaptation to high-altitude aquatic life. Genomics 2021; 114:305-315. [PMID: 34954349 DOI: 10.1016/j.ygeno.2021.12.018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 11/26/2021] [Accepted: 12/17/2021] [Indexed: 12/21/2022]
Abstract
Orestias ascotanensis (Cyprinodontidae) is a teleost pupfish endemic to springs feeding into the Ascotan saltpan in the Chilean Altiplano (3,700 m.a.s.l.) and represents an opportunity to study adaptations to high-altitude aquatic environments. We have de novo assembled the genome of O. ascotanensis at high coverage. Comparative analysis of the O. ascotanensis genome showed an overall process of contraction, including loss of genes related to G-protein signaling, chemotaxis and signal transduction, while there was expansion of gene families associated with microtubule-based movement and protein ubiquitination. We identified 818 genes under positive selection, many of which are involved in DNA repair. Additionally, we identified novel and conserved microRNAs expressed in O. ascotanensis and its closely-related species, Orestias gloriae. Our analysis suggests that positive selection and expansion of genes that preserve genome stability are a potential adaptive mechanism to cope with the increased solar UV radiation to which high-altitude animals are exposed to.
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Affiliation(s)
- Alex Di Genova
- FONDAP Center for Genome Regulation, Santiago, Chile; Center for Mathematical Modeling, Department of Mathematical Engineering, Faculty of Physical and Mathematical Sciences, Universidad de Chile and IRL CNRS, 2807 Santiago, Chile
| | - Gino Nardocci
- FONDAP Center for Genome Regulation, Santiago, Chile; Institute of Biomedical Sciences, Faculty of Medicine and Faculty of Life Sciences, Universidad Andres Bello, Santiago, Chile
| | - Rodrigo Maldonado-Agurto
- FONDAP Center for Genome Regulation, Santiago, Chile; Institute of Biomedical Sciences, Faculty of Medicine and Faculty of Life Sciences, Universidad Andres Bello, Santiago, Chile
| | - Christian Hodar
- FONDAP Center for Genome Regulation, Santiago, Chile; Institute of Nutrition and Food Technology, Universidad de Chile, Santiago, Chile
| | - Camilo Valdivieso
- FONDAP Center for Genome Regulation, Santiago, Chile; Faculty of Sciences, Universidad de Chile, Santiago, Chile
| | - Pamela Morales
- FONDAP Center for Genome Regulation, Santiago, Chile; Faculty of Sciences, Universidad de Chile, Santiago, Chile
| | - Felipe Gajardo
- FONDAP Center for Genome Regulation, Santiago, Chile; Faculty of Sciences, Universidad de Chile, Santiago, Chile
| | - Raquel Marina
- FONDAP Center for Genome Regulation, Santiago, Chile; Institute of Biomedical Sciences, Faculty of Medicine and Faculty of Life Sciences, Universidad Andres Bello, Santiago, Chile
| | - Rodrigo A Gutiérrez
- FONDAP Center for Genome Regulation, Santiago, Chile; Department of Molecular Genetics and Microbiology, Pontificia Universidad Catolica de Chile, Santiago, Chile
| | - Ariel Orellana
- FONDAP Center for Genome Regulation, Santiago, Chile; Center of Plant Biotechnology, Universidad Andres Bello, Santiago, Chile
| | - Veronica Cambiazo
- FONDAP Center for Genome Regulation, Santiago, Chile; Institute of Nutrition and Food Technology, Universidad de Chile, Santiago, Chile
| | - Mauricio González
- FONDAP Center for Genome Regulation, Santiago, Chile; Institute of Nutrition and Food Technology, Universidad de Chile, Santiago, Chile
| | - Alvaro Glavic
- FONDAP Center for Genome Regulation, Santiago, Chile; Faculty of Sciences, Universidad de Chile, Santiago, Chile
| | - Marco A Mendez
- FONDAP Center for Genome Regulation, Santiago, Chile; Faculty of Sciences, Universidad de Chile, Santiago, Chile; Center of Applied Ecology and Sustainability (CAPES), Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Chile; Institute of Ecology and Biodiversity, Chile
| | - Alejandro Maass
- FONDAP Center for Genome Regulation, Santiago, Chile; Center for Mathematical Modeling, Department of Mathematical Engineering, Faculty of Physical and Mathematical Sciences, Universidad de Chile and IRL CNRS, 2807 Santiago, Chile
| | - Miguel L Allende
- FONDAP Center for Genome Regulation, Santiago, Chile; Faculty of Sciences, Universidad de Chile, Santiago, Chile.
| | - Martin A Montecino
- FONDAP Center for Genome Regulation, Santiago, Chile; Institute of Biomedical Sciences, Faculty of Medicine and Faculty of Life Sciences, Universidad Andres Bello, Santiago, Chile.
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21
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Wan Q, Chen Q, Cai D, Zhao Y, Wu X. OTUB2 Promotes Homologous Recombination Repair Through Stimulating Rad51 Expression in Endometrial Cancer. Cell Transplant 2021; 29:963689720931433. [PMID: 32830515 PMCID: PMC7563931 DOI: 10.1177/0963689720931433] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Genetic instability, raised from dysregulation of DNA repair, is involved in tumor development. OTUB2 (ovarian tumor domain protease domain-containing ubiquitin aldehyde-binding protein 2), which is responsible for DNA double-strand break (DSB), is implicated in carcinogenesis of various tumors. The effect of OTUB2 on endometrial cancer progression was then investigated. First, OTUB2 was found to be upregulated in endometrial cancer tissues and cell lines, and was closely associated with overall survival of endometrial cancer patients. Cell Counting Kit-8 and flow cytometry assay results revealed that overexpression of OTUB2 enhanced cell viability of endometrial cancer cells, while knockdown of OTUB2 inhibited cell viability. Moreover, as demonstrated by promoting cell viability and suppression of cell apoptosis, cisplatin-induced cell damage was reversed by OTUB2. Mechanistically, OTUB2 could activate Yes-associated protein/transcriptional co-activator with PDZ-binding motif (TAZ) to promote homologous recombination repair via depletion of γH2AX (phosphorylation of histone H2AX) and accumulation of Rad51. In vivo xenograft model also showed that silence of OTUB2 suppressed the growth of endometrial cancer and increased tumor sensitivity to antitumor drugs. In conclusion, OTUB2 promoted homologous recombination repair in endometrial cancer via YAP/TAZ-mediated Rad51 expression, providing a potential therapeutic target for endometrial cancer.
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Affiliation(s)
- Qiuyuan Wan
- Department of Obstetrics and Gynecology, the Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an City, Shaanxi Province, PR China
| | - Qing Chen
- Department of Obstetrics and Gynecology, the Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an City, Shaanxi Province, PR China
| | - Dongge Cai
- Department of Obstetrics and Gynecology, the Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an City, Shaanxi Province, PR China
| | - Yan Zhao
- Department of Obstetrics and Gynecology, the Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an City, Shaanxi Province, PR China
| | - Xiaoling Wu
- Department of Obstetrics and Gynecology, the Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an City, Shaanxi Province, PR China
- Xiaoling Wu, Department of Obstetrics and Gynecology, the Second Affiliated Hospital of Xi’an Jiaotong University, No. 157 Xiwu Road, Xi’an City, Shaanxi Province, PR China.
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22
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Blount JR, Johnson SL, Todi SV. Unanchored Ubiquitin Chains, Revisited. Front Cell Dev Biol 2020; 8:582361. [PMID: 33195227 PMCID: PMC7659471 DOI: 10.3389/fcell.2020.582361] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 09/15/2020] [Indexed: 12/20/2022] Open
Abstract
The small modifier protein, ubiquitin, holds a special place in eukaryotic biology because of its myriad post-translational effects that control normal cellular processes and are implicated in various diseases. By being covalently conjugated onto other proteins, ubiquitin changes their interaction landscape - fostering new interactions as well as inhibiting others - and ultimately deciding the fate of its substrates and controlling pathways that span most cell physiology. Ubiquitin can be attached onto other proteins as a monomer or as a poly-ubiquitin chain of diverse structural topologies. Among the types of poly-ubiquitin species generated are ones detached from another substrate - comprising solely ubiquitin as their constituent - referred to as unanchored, or free chains. Considered to be toxic byproducts, these species have recently emerged to have specific physiological functions in immune pathways and during cell stress. Free chains also do not appear to be detrimental to multi-cellular organisms; they can be active members of the ubiquitination process, rather than corollary species awaiting disassembly into mono-ubiquitin. Here, we summarize past and recent studies on unanchored ubiquitin chains, paying special attention to their emerging roles as second messengers in several signaling pathways. These investigations paint complex and flexible outcomes for free ubiquitin chains, and present a revised model of unanchored poly-ubiquitin biology that is in need of additional investigation.
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Affiliation(s)
- Jessica R Blount
- Department of Pharmacology, Wayne State University School of Medicine, Detroit, MI, United States
| | - Sean L Johnson
- Department of Pharmacology, Wayne State University School of Medicine, Detroit, MI, United States
| | - Sokol V Todi
- Department of Pharmacology, Wayne State University School of Medicine, Detroit, MI, United States.,Department of Neurology, Wayne State University School of Medicine, Detroit, MI, United States
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23
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Li L, Bai J, Fan H, Yan J, Li S, Jiang P. E2 ubiquitin-conjugating enzyme UBE2L6 promotes Senecavirus A proliferation by stabilizing the viral RNA polymerase. PLoS Pathog 2020; 16:e1008970. [PMID: 33104725 PMCID: PMC7588118 DOI: 10.1371/journal.ppat.1008970] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 09/08/2020] [Indexed: 12/29/2022] Open
Abstract
Senecavirus A (SVA), discovered in 2002, is an emerging pathogen of swine that has since been reported in numerous pork producing countries. To date, the mechanism of SVA replication remains poorly understood. In this study, utilizing iTRAQ analysis we found that UBE2L6, an E2 ubiquitin-conjugating enzyme, is up-regulated in SVA-infected BHK-21 cells, and that its overexpression promotes SVA replication. We determined that UBE2L6 interacts with, and ubiquitinates the RNA-dependent RNA polymerase of SVA, (the 3D protein) and this ubiquitination serves to inhibit the degradation of 3D. UBE2L6-mediated ubiquitination of 3D requires a cystine at residue 86 in UBE2L6, and lysines at residues 169 and 321 in 3D. Virus with mutations in 3D (rK169R and rK321R) exhibited significantly decreased replication compared to wild type SVA and the repaired viruses, rK169R(R) and rK321R(R). These data indicate that UBE2L6, the enzyme, targets the 3D polymerase, the substrate, during SVA infection to facilitate replication. Senecavirus A (SVA) is a newly emerging pathogen causing swine idiopathic vesicular disease and epidemic transient neonatal losses. Infections have been reported in many pork producing countries, yet the mechanism of SVA replication remains poorly understood. In this study, we found that UBE2L6, an E2 ubiquitin-conjugating enzyme, is up-regulated in SVA-infected BHK-21 cells. The viral RNA dependent RNA polymerase (RdRp) 3D is ubiquitinated by UBE2L6, and the lysines at residues 169 and 321 of 3D are the required ubiquitination sites. The level of replication of recombinant viruses harboring ubiquitination-deficient 3D was significantly decreased compared to parental SVA. Our data demonstrate that UBE2L6 ubiquitinates SVA 3D, thereby facilitating SVA infection. These results may make it possible to identify novel targets for disease treatment.
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Affiliation(s)
- Liang Li
- Key Laboratory of Animal Diseases Diagnostic and Immunology, Ministry of Agriculture, MOE International Joint Collaborative Research Laboratory for Animal Health & Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Juan Bai
- Key Laboratory of Animal Diseases Diagnostic and Immunology, Ministry of Agriculture, MOE International Joint Collaborative Research Laboratory for Animal Health & Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China
- * E-mail: (JB); (PJ)
| | - Hui Fan
- Key Laboratory of Animal Diseases Diagnostic and Immunology, Ministry of Agriculture, MOE International Joint Collaborative Research Laboratory for Animal Health & Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Junfang Yan
- Key Laboratory of Animal Diseases Diagnostic and Immunology, Ministry of Agriculture, MOE International Joint Collaborative Research Laboratory for Animal Health & Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Shihai Li
- Key Laboratory of Animal Diseases Diagnostic and Immunology, Ministry of Agriculture, MOE International Joint Collaborative Research Laboratory for Animal Health & Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Ping Jiang
- Key Laboratory of Animal Diseases Diagnostic and Immunology, Ministry of Agriculture, MOE International Joint Collaborative Research Laboratory for Animal Health & Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China
- * E-mail: (JB); (PJ)
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24
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Bi Y, Cui D, Xiong X, Zhao Y. The characteristics and roles of β-TrCP1/2 in carcinogenesis. FEBS J 2020; 288:3351-3374. [PMID: 33021036 DOI: 10.1111/febs.15585] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 09/02/2020] [Accepted: 10/01/2020] [Indexed: 12/11/2022]
Abstract
β-transducin repeat-containing protein (β-TrCP), one of the well-characterized F-box proteins, acts as a substrate receptor and constitutes an active SCFβ-TrCP E3 ligase with a scaffold protein CUL1, a RING protein RBX1, and an adaptor protein SKP1. β-TrCP plays a critical role in the regulation of various physiological and pathological processes, including signal transduction, cell cycle progression, cell migration, DNA damage response, and tumorigenesis, by governing burgeoning amounts of key regulators for ubiquitination and proteasomal degradation. Given that a variety of β-TrCP substrates are well-known oncoproteins and tumor suppressors, and dysregulation of β-TrCP is frequently identified in human cancers, β-TrCP plays a vital role in carcinogenesis. In this review, we first briefly introduce the characteristics of β-TrCP1, β-TrCP2, and SCFβ-TrCP ubiquitin ligase, and then discuss SCFβ-TrCP ubiquitin ligase regulated biological processes by targeting its substrates for degradation. Moreover, we summarize the regulation of β-TrCP1 and β-TrCP2 at multiple layers and further discuss the various roles of β-TrCP1 and β-TrCP2 in human cancer, functioning as either an oncoprotein or a tumor suppressor in a manner dependent of cellular context. Finally, we provide novel insights for future perspectives on the potential of targeting β-TrCP1 and β-TrCP2 for cancer therapy.
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Affiliation(s)
- Yanli Bi
- Key Laboratory of Combined Multi-Organ Transplantation, Ministry of Public Health, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, China
| | - Danrui Cui
- Key Laboratory of Combined Multi-Organ Transplantation, Ministry of Public Health, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, China
| | - Xiufang Xiong
- Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, China.,Cancer Institute of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yongchao Zhao
- Key Laboratory of Combined Multi-Organ Transplantation, Ministry of Public Health, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, China
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25
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Wu R, Liu W, Sun Y, Shen C, Guo J, Zhao J, Mao G, Li Y, Du G. Nanoscale insight into chromatin remodeling and DNA repair complex in HeLa cells after ionizing radiation. DNA Repair (Amst) 2020; 96:102974. [PMID: 32998084 DOI: 10.1016/j.dnarep.2020.102974] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 09/08/2020] [Accepted: 09/09/2020] [Indexed: 10/23/2022]
Abstract
The dynamic structure of nuclear chromatin and its regulation in the formation of repair complex is essential in DNA damage response and repair. Using single molecule localization microscopy STORM this work discovered that the nuclear chromatin organization was relaxed from 200 to 400 nm thick irregular frame and remodeled to dispersed sub-100 nm structure in HeLa cells after X-ray irradiation. The DSB repair factors (γ-H2AX, MDC1, 53BP1) showed distribution as microscale-colocalized and nanoscale interlaced substructure in the DSB repair complex. The dual-color nanoscopic imaging of γ-H2AX and chromatin at the DSB sites suggest that DNA damage response and repair cascade are chromatin structure-dependent and also partly dependent on the distance to the DSB sites. The sub-100 nm structure of fibers and nanoclusters of the relaxed nuclear chromatin and the DSB repair factors highly resembled the cross-section view of chromatin organization. These data demonstrated the polymorphic and dynamic behavior of the chromatin organization in vivo, and provided nanoscale insight into the interplay between chromatin remodeling and DNA damage response and DNA repair.
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Affiliation(s)
- Ruqun Wu
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, 730000, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wenjing Liu
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, 730000, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yujie Sun
- BIOPIC, Peking University, Beijing, 100871, China
| | - Cheng Shen
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jinlong Guo
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, 730000, China
| | - Jing Zhao
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Guangbo Mao
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yaning Li
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, 730000, China
| | - Guanghua Du
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, 730000, China.
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26
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LeBlanc N, Mallette E, Zhang W. Targeted modulation of E3 ligases using engineered ubiquitin variants. FEBS J 2020; 288:2143-2165. [PMID: 32867007 DOI: 10.1111/febs.15536] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 08/17/2020] [Accepted: 08/21/2020] [Indexed: 12/11/2022]
Abstract
Ubiquitination plays an essential role in signal transduction to regulate most if not all cellular processes. Among the enzymes that are involved in the ubiquitin (Ub) signaling cascade, tremendous efforts have been focused on elucidating the roles of E3 Ub ligases as they determine the complexity and specificity of ubiquitination. Not surprisingly, the malfunction of E3 ligases is directly implicated in many human diseases, including cancer. Therefore, there is an urgent need to develop potent and specific molecules to modulate E3 ligase activity as intracellular probes for target validation and as pharmacological agents in preclinical research. Unfortunately, the progress has been hampered by the dynamic regulation mechanisms for different types of E3 ligases. Here, we summarize the progress of using protein engineering to develop Ub variant (UbV) inhibitors for all major families of E3 ligases and UbV activators for homologous with E6-associated protein C terminus E3s and homodimeric RING E3s. We believe that this provides a general strategy and a valuable toolkit for the research community to inhibit or activate E3 ligases and these synthetic molecules have important implications in exploring protein degradation for drug discovery.
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Affiliation(s)
- Nicole LeBlanc
- Department of Molecular and Cellular Biology, College of Biological Science, University of Guelph, Guelph, ON, Canada
| | - Evan Mallette
- Department of Molecular and Cellular Biology, College of Biological Science, University of Guelph, Guelph, ON, Canada
| | - Wei Zhang
- Department of Molecular and Cellular Biology, College of Biological Science, University of Guelph, Guelph, ON, Canada.,CIFAR Azrieli Global Scholars Program, Canadian Institute for Advanced Research, Toronto, ON, Canada
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27
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Antao AM, Tyagi A, Kim KS, Ramakrishna S. Advances in Deubiquitinating Enzyme Inhibition and Applications in Cancer Therapeutics. Cancers (Basel) 2020; 12:E1579. [PMID: 32549302 PMCID: PMC7352412 DOI: 10.3390/cancers12061579] [Citation(s) in RCA: 86] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 06/07/2020] [Accepted: 06/11/2020] [Indexed: 12/11/2022] Open
Abstract
Since the discovery of the ubiquitin proteasome system (UPS), the roles of ubiquitinating and deubiquitinating enzymes (DUBs) have been widely elucidated. The ubiquitination of proteins regulates many aspects of cellular functions such as protein degradation and localization, and also modifies protein-protein interactions. DUBs cleave the attached ubiquitin moieties from substrates and thereby reverse the process of ubiquitination. The dysregulation of these two paramount pathways has been implicated in numerous diseases, including cancer. Attempts are being made to identify inhibitors of ubiquitin E3 ligases and DUBs that potentially have clinical implications in cancer, making them an important target in the pharmaceutical industry. Therefore, studies in medicine are currently focused on the pharmacological disruption of DUB activity as a rationale to specifically target cancer-causing protein aberrations. Here, we briefly discuss the pathophysiological and physiological roles of DUBs in key cancer-related pathways. We also discuss the clinical applications of promising DUB inhibitors that may contribute to the development of DUBs as key therapeutic targets in the future.
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Affiliation(s)
- Ainsley Mike Antao
- Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul 04763, Korea; (A.M.A.); (A.T.)
| | - Apoorvi Tyagi
- Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul 04763, Korea; (A.M.A.); (A.T.)
| | - Kye-Seong Kim
- Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul 04763, Korea; (A.M.A.); (A.T.)
- College of Medicine, Hanyang University, Seoul 04763, Korea
| | - Suresh Ramakrishna
- Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul 04763, Korea; (A.M.A.); (A.T.)
- College of Medicine, Hanyang University, Seoul 04763, Korea
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28
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Ren S, Ur Rehman Z, Gao B, Yang Z, Zhou J, Meng C, Song C, Nair V, Sun Y, Ding C. ATM-mediated DNA double-strand break response facilitated oncolytic Newcastle disease virus replication and promoted syncytium formation in tumor cells. PLoS Pathog 2020; 16:e1008514. [PMID: 32479542 PMCID: PMC7263568 DOI: 10.1371/journal.ppat.1008514] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Accepted: 04/03/2020] [Indexed: 12/25/2022] Open
Abstract
Deoxyribonucleic acid (DNA) damage response (DDR) is the fundamental cellular response for maintaining genomic integrity and suppressing tumorigenesis. The activation of ataxia telangiectasia-mutated (ATM) kinase is central to DNA double-strand break (DSB) for maintaining host-genome integrity in mammalian cells. Oncolytic Newcastle disease virus (NDV) can selectively replicate in tumor cells; however, its influence on the genome integrity of tumor cells is not well-elucidated. Here, we found that membrane fusion and NDV infection triggered DSBs in tumor cells. The late replication and membrane fusion of NDV mechanistically activated the ATM-mediated DSB pathway via the ATM-Chk2 axis, as evidenced by the hallmarks of DSBs, i.e., auto-phosphorylated ATM and phosphorylated H2AX and Chk2. Immunofluorescence data showed that multifaceted ATM-controlled phosphorylation markedly induced the formation of pan-nuclear punctum foci in response to NDV infection and F-HN co-expression. Specific drug-inhibitory experiments on ATM kinase activity further suggested that ATM-mediated DSBs facilitated NDV replication and membrane fusion. We confirmed that the Mre11-RAD50-NBS1 (MRN) complex sensed the DSB signal activation triggered by NDV infection and membrane fusion. The pharmacological inhibition of MRN activity also significantly inhibited intracellular and extracellular NDV replication and syncytia formation. Collectively, these data identified for the first time a direct link between the membrane fusion induced by virus infection and DDR pathways, thereby providing new insights into the efficient replication of oncolytic NDV in tumor cells.
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Affiliation(s)
- Shanhui Ren
- Department of Avian Infectious Diseases, Shanghai Veterinary Research Institute. Chinese Academy of Agricultural Science, Shanghai, P.R. China
| | - Zaib Ur Rehman
- Department of Avian Infectious Diseases, Shanghai Veterinary Research Institute. Chinese Academy of Agricultural Science, Shanghai, P.R. China
| | - Bo Gao
- Department of Avian Infectious Diseases, Shanghai Veterinary Research Institute. Chinese Academy of Agricultural Science, Shanghai, P.R. China
| | - Zengqi Yang
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, P.R. China
| | - Jiyong Zhou
- Key Laboratory of Animal Virology of Ministry of Agriculture, Department of Veterinary Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Chunchun Meng
- Department of Avian Infectious Diseases, Shanghai Veterinary Research Institute. Chinese Academy of Agricultural Science, Shanghai, P.R. China
| | - Cuiping Song
- Department of Avian Infectious Diseases, Shanghai Veterinary Research Institute. Chinese Academy of Agricultural Science, Shanghai, P.R. China
| | - Venugopal Nair
- Avian Oncogenic viruses group, UK-China Centre of Excellence on Avian Disease Research, The Pirbright Institute, Pirbright, Guildford, Surrey, United Kingdom
| | - Yingjie Sun
- Department of Avian Infectious Diseases, Shanghai Veterinary Research Institute. Chinese Academy of Agricultural Science, Shanghai, P.R. China
| | - Chan Ding
- Department of Avian Infectious Diseases, Shanghai Veterinary Research Institute. Chinese Academy of Agricultural Science, Shanghai, P.R. China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Disease and Zoonoses, Yangzhou University, Yangzhou, Jiangsu, P.R. China
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29
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Kovaleva TF, Maksimova NS, Pchelin PV, Pershin VI, Tkachenko NM, Gainullin MR, Mukhina IV. A New Cofilin-Dependent Mechanism for the Regulation of Brain Mitochondria Biogenesis and Degradation. Sovrem Tekhnologii Med 2020; 12:6-13. [PMID: 34513032 PMCID: PMC8353704 DOI: 10.17691/stm2020.12.1.01] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2019] [Indexed: 11/14/2022] Open
Abstract
The aim Was to study the role of post-translational modifications of cofilin in the regulation of respiration and autophagy in murine brain mitochondria.
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Affiliation(s)
- T F Kovaleva
- Senior Researcher, Molecular and Cellular Technologies Department, Institute of Fundamental Medicine, Privolzhsky Research Medical University, 10/1 Minin and Pozharsky Square, Nizhny Novgorod, 603005, Russia
| | - N S Maksimova
- PhD Student, Junior Researcher, Molecular and Cellular Technologies Department, Institute of Fundamental Medicine, Privolzhsky Research Medical University, 10/1 Minin and Pozharsky Square, Nizhny Novgorod, 603005, Russia
| | - P V Pchelin
- Laboratory Assistant, Molecular and Cellular Technologies Department, Institute of Fundamental Medicine, Privolzhsky Research Medical University, 10/1 Minin and Pozharsky Square, Nizhny Novgorod, 603005, Russia
| | - V I Pershin
- Laboratory Assistant, Molecular and Cellular Technologies Department, Institute of Fundamental Medicine, Privolzhsky Research Medical University, 10/1 Minin and Pozharsky Square, Nizhny Novgorod, 603005, Russia
| | - N M Tkachenko
- Junior Researcher, Molecular and Cellular Technologies Department, Institute of Fundamental Medicine, Privolzhsky Research Medical University, 10/1 Minin and Pozharsky Square, Nizhny Novgorod, 603005, Russia
| | - M R Gainullin
- Senior Researcher, Molecular and Cellular Technologies Department, Institute of Fundamental Medicine, Privolzhsky Research Medical University, 10/1 Minin and Pozharsky Square, Nizhny Novgorod, 603005, Russia, Researcher, Norwegian PSC Research Center, Department of Transplantation Medicine, Division of Surgery, Inflammatory Diseases and Transplantation, Oslo University Hospital Rikshospitalet, P.O. Box 4950, Nydalen, Oslo, 0424, Norway, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, P.O. Box 1171, Blindern, Oslo, 0318, Norway
| | - I V Mukhina
- Professor, Director of the Institute of Fundamental Medicine, Privolzhsky Research Medical University, 10/1 Minin and Pozharsky Square, Nizhny Novgorod, 603005, Russia, Head of the Department of Normal Physiology named after N.Y. Belenkov, Privolzhsky Research Medical University, 10/1 Minin and Pozharsky Square, Nizhny Novgorod, 603005, Russia, Professor, Department of Neurotechnologies, Institute of Biology and Biomedicine, National Research Lobachevsky State University of Nizhni Novgorod, 23 Prospekt Gagarina, Nizhny Novgorod, 603950, Russia
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30
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Innes CL, Hesse JE, Morales AJ, Helmink BA, Schurman SH, Sleckman BP, Paules RS. DNA damage responses in murine Pre-B cells with genetic deficiencies in damage response genes. Cell Cycle 2020; 19:67-83. [PMID: 31757180 PMCID: PMC6927727 DOI: 10.1080/15384101.2019.1693118] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Revised: 10/29/2019] [Accepted: 11/07/2019] [Indexed: 01/11/2023] Open
Abstract
DNA damage can be generated in multiple ways from genotoxic and physiologic sources. Genotoxic damage is known to disrupt cellular functions and is lethal if not repaired properly. We compare the transcriptional programs activated in response to genotoxic DNA damage induced by ionizing radiation (IR) in abl pre-B cells from mice deficient in DNA damage response (DDR) genes Atm, Mre11, Mdc1, H2ax, 53bp1, and DNA-PKcs. We identified a core IR-specific transcriptional response that occurs in abl pre-B cells from WT mice and compared the response of the other genotypes to the WT response. We also identified genotype specific responses and compared those to each other. The WT response includes many processes involved in lymphocyte development and immune response, as well as responses associated with the molecular mechanisms of cancer, such as TP53 signaling. As expected, there is a range of similarity in transcriptional profiles in comparison to WT cells, with Atm-/- cells being the most different from the core WT DDR and Mre11 hypomorph (Mre11A/A) cells also very dissimilar to WT and other genotypes. For example, NF-kB-related signaling and CD40 signaling are deficient in both Atm-/- and Mre11A/A cells, but present in all other genotypes. In contrast, IR-induced TP53 signaling is seen in the Mre11A/A cells, while these responses are not seen in the Atm-/- cells. By examining the similarities and differences in the signaling pathways in response to IR when specific genes are absent, our results further illustrate the contribution of each gene to the DDR. The microarray gene expression data discussed in this paper have been deposited in NCBI's Gene Expression Omnibus (GEO) (http://www.ncbi.nlm.nih.gov/geo/) and are accessible under accession number GSE116388.
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Affiliation(s)
- Cynthia L. Innes
- Environmental Stress and Cancer Group, Division of Intramural Research, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - Jill E. Hesse
- Environmental Stress and Cancer Group, Division of Intramural Research, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - Abigail J. Morales
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Beth A. Helmink
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Shepherd H. Schurman
- Clinical Research Branch, Division of Intramural Research, National Institute of Environmental Health Sciences, Research Triangle Park, Durham, NC, USA
| | - Barry P. Sleckman
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Richard S. Paules
- Environmental Stress and Cancer Group, Division of Intramural Research, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
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31
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Pérez-Benavente B, Nasresfahani AF, Farràs R. Ubiquitin-Regulated Cell Proliferation and Cancer. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1233:3-28. [PMID: 32274751 DOI: 10.1007/978-3-030-38266-7_1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Ubiquitin ligases (E3) play a crucial role in the regulation of different cellular processes such as proliferation and differentiation via recognition, interaction, and ubiquitination of key cellular proteins in a spatial and temporal regulated manner. The type of ubiquitin chain formed determines the fate of the substrates. The ubiquitinated substrates can be degraded by the proteasome, display altered subcellular localization, or can suffer modifications on their interaction with functional protein complexes. Deregulation of E3 activities is frequently found in various human pathologies, including cancer. The illegitimated or accelerated degradation of oncosuppressive proteins or, inversely, the abnormally high accumulation of oncoproteins, contributes to cell proliferation and transformation. Anomalies in protein abundance may be related to mutations that alter the direct or indirect recognition of proteins by the E3 enzymes or alterations in the level of expression or activity of ubiquitin ligases. Through a few examples, we illustrate here the complexity and diversity of the molecular mechanisms related to protein ubiquitination involved in cell cycle regulation. We will discuss the role of ubiquitin-dependent degradation mediated by the proteasome, the role of non-proteolytic ubiquitination during cell cycle progression, and the consequences of this deregulation on cellular transformation. Finally, we will highlight the novel opportunities that arise from these studies for therapeutic intervention.
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Affiliation(s)
| | | | - Rosa Farràs
- Oncogenic Signaling Laboratory, Centro de Investigación Príncipe Felipe, Valencia, Spain.
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32
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Yang Y, Yang C, Li T, Yu S, Gan T, Hu J, Cui J, Zheng X. The Deubiquitinase USP38 Promotes NHEJ Repair through Regulation of HDAC1 Activity and Regulates Cancer Cell Response to Genotoxic Insults. Cancer Res 2019; 80:719-731. [PMID: 31874856 DOI: 10.1158/0008-5472.can-19-2149] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 10/16/2019] [Accepted: 12/13/2019] [Indexed: 11/16/2022]
Abstract
The DNA damage response (DDR) is essential for maintaining genome integrity. Mounting evidence reveals that protein modifications play vital roles in the DDR. Here, we show that USP38 is involved in the DDR by regulating the activity of HDAC1. In response to DNA damage, USP38 interacted with HDAC1 and specifically removed the K63-linked ubiquitin chain promoting the deacetylase activity of HDAC1. As a result, HDAC1 was able to deacetylate H3K56. USP38 deletion resulted in persistent focal accumulation of nonhomologous end joining (NHEJ) factors at DNA damage sites and impaired NHEJ efficiency, causing genome instability and sensitizing cancer cells to genotoxic insults. Knockout of USP38 rendered mice hypersensitive to irradiation and shortened survival. In addition, USP38 was expressed at low levels in certain types of cancers including renal cell carcinoma, indicating dysregulation of USP38 expression contributes to genomic instability and may lead to tumorigenesis. In summary, this study identifies a critical role of USP38 in modulating genome integrity and cancer cell resistance to genotoxic insults by deubiquitinating HDAC1 and regulating its deacetylation activity. SIGNIFICANCE: This study demonstrates that USP38 regulates genome stability and mediates cancer cell resistance to DNA-damaging therapy, providing insight into tumorigenesis and implicating USP38 as a potential target for cancer diagnosis.
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Affiliation(s)
- Yongfeng Yang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China.,Department of Biochemistry and Molecular Biology, School of Life Sciences, Peking University, Beijing, China
| | - Chuanzhen Yang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China.,Department of Biochemistry and Molecular Biology, School of Life Sciences, Peking University, Beijing, China
| | - Tingting Li
- State Key Laboratory of Proteomics, National Center of Biomedical Analysis, Institute of Basic Medical Sciences, Beijing, China
| | - Shuyu Yu
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China.,Department of Biochemistry and Molecular Biology, School of Life Sciences, Peking University, Beijing, China
| | - Tingting Gan
- Department of Cell Biology, School of Life Sciences, Peking University, Beijing, China
| | - Jiazhi Hu
- Department of Cell Biology, School of Life Sciences, Peking University, Beijing, China
| | - Jun Cui
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China.,Collaborative Innovation Center of Cancer Medicine, Sun Yat-sen University, Guangzhou, China
| | - Xiaofeng Zheng
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China. .,Department of Biochemistry and Molecular Biology, School of Life Sciences, Peking University, Beijing, China
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33
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Chaugule VK, Arkinson C, Rennie ML, Kämäräinen O, Toth R, Walden H. Allosteric mechanism for site-specific ubiquitination of FANCD2. Nat Chem Biol 2019; 16:291-301. [PMID: 31873223 PMCID: PMC7035956 DOI: 10.1038/s41589-019-0426-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 11/05/2019] [Indexed: 01/31/2023]
Abstract
DNA damage repair is implemented by proteins that are coordinated by specialised molecular signals. One such signal in the Fanconi Anemia (FA) DNA-interstrand crosslink repair pathway is the site-specific monoubiquitination of FANCD2 and FANCI. The signal is mediated by a multi-protein FA core complex (FA-CC) however, the mechanics for precise ubiquitination remain elusive. We show that FANCL, the RING-bearing module in FA-CC, allosterically activates its cognate E2 Ube2T to drive site-specific FANCD2 ubiquitination. Unlike typical RING E3 ligases, FANCL catalyses ubiquitination by rewiring Ube2T’s intra-residue network to influence the active site. Consequently, a basic triad unique to Ube2T engages a structured acidic patch near the target lysine on FANCD2. This three-dimensional complementarity, between the E2 active site and substrate surface, induced by FANCL is central to site-specific monoubiquitination in the FA pathway. Furthermore, the allosteric network of Ube2T can be engineered to enhance FANCL catalysed FANCD2-FANCI di-monoubiquitination without compromising site-specificity.
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Affiliation(s)
- Viduth K Chaugule
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK. .,MRC Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences, University of Dundee, Dundee, UK.
| | - Connor Arkinson
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK.,MRC Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences, University of Dundee, Dundee, UK
| | - Martin L Rennie
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Outi Kämäräinen
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Rachel Toth
- MRC Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences, University of Dundee, Dundee, UK
| | - Helen Walden
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK. .,MRC Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences, University of Dundee, Dundee, UK.
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34
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Systematic analysis of alterations in the ubiquitin proteolysis system reveals its contribution to driver mutations in cancer. ACTA ACUST UNITED AC 2019; 1:122-135. [DOI: 10.1038/s43018-019-0001-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 10/11/2019] [Indexed: 12/21/2022]
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35
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Imai J, Koganezawa Y, Tuzuki H, Ishikawa I, Sakai T. An optical and non-invasive method to detect the accumulation of ubiquitin chains. Cell Biol Int 2019; 43:1393-1406. [PMID: 31136031 DOI: 10.1002/cbin.11186] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 05/25/2019] [Indexed: 01/24/2023]
Abstract
The accumulations of excess amounts of polyubiquitinated proteins are cytotoxic and frequently observed in pathologic tissue from patients of neurodegenerative diseases. Therefore, optical and non-invasive methods to detect the increase of the amounts of polyubiquitinated proteins in living cells is a promising strategy to find out symptoms and environmental cause of neurodegenerative diseases, also for identifying compounds that could inhibit gathering of polyubiquitinated proteins. Therefore, we generated a pair of fluorescent protein [Azamigreen (Azg) and Kusabiraorange (Kuo)] tagged ubiquitin on its N-terminus (Azg-Ub and Kuo-Ub) and developed an Azg/Kuo-based Fluorescence Resonance Energy Transfer (FRET) assay to estimate the amount of polyubiquitin chains in vitro and in vivo. The FRET intensity was attenuated in the presence of ubiquitin-activating enzyme inhibitor, PYR-41, indicating that both fluorescent ubiquitin is incorporated into ubiquitin chains likewise normal ubiquitin. The FRET intensity was enhanced by the addition of the proteasome inhibitor, MG-132, and was reduced in the presence of the autophagy activator Rapamycin, designating that ubiquitin chains with fluorescent ubiquitin act as the degradation signal equally with normal ubiquitin chains. In summary, the above optical methods provide powerful research tools to estimate the amounts of polyubiquitin chains in vitro and in vivo, especially non-invasively in living cells.
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Affiliation(s)
- Jun Imai
- Laboratory of Physiological Chemistry, Faculty of Pharmacy, Takasaki University of Health and Welfare, 60 Nakaorui-machi, Takasaki-shi, Gunma, 370-0033, Japan
| | - Yuuta Koganezawa
- Laboratory of Physiological Chemistry, Faculty of Pharmacy, Takasaki University of Health and Welfare, 60 Nakaorui-machi, Takasaki-shi, Gunma, 370-0033, Japan
| | - Haruka Tuzuki
- Laboratory of Physiological Chemistry, Faculty of Pharmacy, Takasaki University of Health and Welfare, 60 Nakaorui-machi, Takasaki-shi, Gunma, 370-0033, Japan
| | - Ikumi Ishikawa
- Laboratory of Physiological Chemistry, Faculty of Pharmacy, Takasaki University of Health and Welfare, 60 Nakaorui-machi, Takasaki-shi, Gunma, 370-0033, Japan
| | - Takahiro Sakai
- Laboratory of Physiological Chemistry, Faculty of Pharmacy, Takasaki University of Health and Welfare, 60 Nakaorui-machi, Takasaki-shi, Gunma, 370-0033, Japan
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36
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Salamun SG, Sitz J, De La Cruz-Herrera CF, Yockteng-Melgar J, Marcon E, Greenblatt J, Fradet-Turcotte A, Frappier L. The Epstein-Barr Virus BMRF1 Protein Activates Transcription and Inhibits the DNA Damage Response by Binding NuRD. J Virol 2019; 93:e01070-19. [PMID: 31462557 PMCID: PMC6819917 DOI: 10.1128/jvi.01070-19] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 08/16/2019] [Indexed: 02/08/2023] Open
Abstract
The BMRF1 protein of Epstein-Barr virus (EBV) has multiple roles in viral lytic infection, including serving as the DNA polymerase processivity factor, activating transcription from several EBV promoters and inhibiting the host DNA damage response to double-stranded DNA breaks (DSBs). Using affinity purification coupled to mass spectrometry, we identified the nucleosome remodeling and deacetylation (NuRD) complex as the top interactor of BMRF1. We further found that NuRD components localize with BMRF1 at viral replication compartments and that this interaction occurs through the BMRF1 C-terminal region previously shown to mediate transcriptional activation. We identified an RBBP4 binding motif within this region that can interact with both RBBP4 and MTA2 components of the NuRD complex and showed that point mutation of this motif abrogates NuRD binding as well as the ability of BMRF1 to activate transcription from the BDLF3 and BLLF1 EBV promoters. In addition to its role in transcriptional regulation, NuRD has been shown to contribute to DSB signaling in enabling recruitment of RNF168 ubiquitin ligase and subsequent ubiquitylation at the break. We showed that BMRF1 inhibited RNF168 recruitment and ubiquitylation at DSBs and that this inhibition was at least partly relieved by loss of the NuRD interaction. The results reveal a mechanism by which BMRF1 activates transcription and inhibits DSB signaling and a novel role for NuRD in transcriptional activation in EBV.IMPORTANCE The Epstein-Barr virus (EBV) BMRF1 protein is critical for EBV infection, playing key roles in viral genome replication, activation of EBV genes, and inhibition of host DNA damage responses (DDRs). Here we show that BMRF1 targets the cellular nucleosome remodeling and deacetylation (NuRD) complex, using a motif in the BMRF1 transcriptional activation sequence. Mutation of this motif disrupts the ability of BMRF1 to activate transcription and interfere with DDRs, showing the importance of the NuRD interaction for BMRF1 functions. BMRF1 was shown to act at the same step in the DDR as NuRD, suggesting that it interferes with NuRD function.
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Affiliation(s)
- Samuel G Salamun
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Justine Sitz
- Cancer Research Center and CHU de Québec Research Center-Hôtel-Dieu de Québec, Université Laval, Québec, Canada
| | | | - Jaime Yockteng-Melgar
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
- Facultad de ciencias de la vida, Escuela Superior Politécnica del Litoral, Guayaquil, Ecuador
| | - Edyta Marcon
- Donnelly Centre, University of Toronto, Toronto, Canada
| | - Jack Greenblatt
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
- Donnelly Centre, University of Toronto, Toronto, Canada
| | - Amelie Fradet-Turcotte
- Cancer Research Center and CHU de Québec Research Center-Hôtel-Dieu de Québec, Université Laval, Québec, Canada
| | - Lori Frappier
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
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Yoshida S, Yoshida K. Multiple functions of DYRK2 in cancer and tissue development. FEBS Lett 2019; 593:2953-2965. [PMID: 31505048 DOI: 10.1002/1873-3468.13601] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 08/27/2019] [Accepted: 09/02/2019] [Indexed: 01/09/2023]
Abstract
Dual-specificity tyrosine-regulated kinases (DYRKs) are evolutionarily conserved from yeast to mammals. Accumulating studies have revealed that DYRKs have important roles in regulation of the cell cycle and survival. DYRK2, a member of the class II DYRK family protein, is a key regulator of p53, and phosphorylates it at Ser46 to induce apoptosis in response to DNA damage. Moreover, recent studies have uncovered that DYRK2 regulates G1/S transition, epithelial-mesenchymal-transition, and stemness in human cancer cells. DYRK2 also appears to have roles in tissue development in lower eukaryotes. Thus, the elucidation of mechanisms for DYRK2 during mammalian tissue development will promote the understanding of cell differentiation, tissue homeostasis, and congenital diseases as well as cancer. In this review, we discuss the roles of DYRK2 in tumor cells. Moreover, we focus on DYRK2-dependent developmental mechanisms in several species including fly (Drosophila), worm (Caenorhabditis elegans), zebrafish (Danio rerio), and mammals.
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Affiliation(s)
- Saishu Yoshida
- Department of Biochemistry, The Jikei University School of Medicine, Tokyo, Japan
| | - Kiyotsugu Yoshida
- Department of Biochemistry, The Jikei University School of Medicine, Tokyo, Japan
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38
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Zalzman M, Meltzer WA, Portney BA, Brown RA, Gupta A. The Role of Ubiquitination and SUMOylation in Telomere Biology. Curr Issues Mol Biol 2019; 35:85-98. [PMID: 31422934 DOI: 10.21775/cimb.035.085] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Telomeres are a unique structure of DNA repeats covered by proteins at the ends of the chromosomes that protect the coding regions of the genome and function as a biological clock. They require a tight regulation of the factors covering and protecting their structure, as they are shortened with each cell division to limit the ability of cells to replicate uncontrollably. Additionally, they protect the chromosome ends from DNA damage responses and thereby, prevent genomic instability. Telomere dysfunction can lead to chromosomal abnormalities and cancer. Therefore, dysregulation of any of the factors that regulate the integrity of the telomeres will have implications to chromosomal stability, replicative lifespan and may lead to cell transformation. This review will cover the main factors participating in the normal function of the telomeres and how these are regulated by the ubiquitin and SUMO systems. Accumulating evidence indicate that the ubiquitin and SUMO pathways are significant regulators of the shelterin complex and other chromatin modifiers, which are important for telomere structure integrity. Furthermore, the crosstalk between these two pathways has been reported in telomeric DNA repair. A better understanding of the factors contributing to telomere biology, and how they are regulated, is important for the design of new strategies for cancer therapies and regenerative medicine.
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Affiliation(s)
- Michal Zalzman
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - W Alex Meltzer
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Benjamin A Portney
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Robert A Brown
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Aditi Gupta
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD, USA
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39
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Allegra A, Innao V, Allegra AG, Pugliese M, Di Salvo E, Ventura-Spagnolo E, Musolino C, Gangemi S. Lymphocyte Subsets and Inflammatory Cytokines of Monoclonal Gammopathy of Undetermined Significance and Multiple Myeloma. Int J Mol Sci 2019; 20:ijms20112822. [PMID: 31185596 PMCID: PMC6600674 DOI: 10.3390/ijms20112822] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 05/29/2019] [Accepted: 06/08/2019] [Indexed: 01/10/2023] Open
Abstract
Almost all multiple myeloma (MM) cases have been demonstrated to be linked to earlier monoclonal gammopathy of undetermined significance (MGUS). Nevertheless, there are no identified characteristics in the diagnosis of MGUS that have been helpful in differentiating subjects whose cancer may progress to a malignant situation. Regarding malignancy, the role of lymphocyte subsets and cytokines at the beginning of neoplastic diseases is now incontestable. In this review, we have concentrated our attention on the equilibrium between the diverse lymphocyte subsets and the cytokine system and summarized the current state of knowledge, providing an overview of the condition of the entire system in MGUS and MM. In an age where the therapy of neoplastic monoclonal gammopathies largely relies on drugs capable of acting on the immune system (immunomodulants, immunological checkpoint inhibitors, CAR-T), detailed knowledge of the the differences existing in benign and neoplastic forms of gammopathy is the main foundation for the adequate and optimal use of new drugs.
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Affiliation(s)
- Alessandro Allegra
- Division of Hematology, Department of Human Pathology in Adulthood and Childhood "Gaetano Barresi", University of Messina, 98125 Messina, Italy.
| | - Vanessa Innao
- Division of Hematology, Department of Human Pathology in Adulthood and Childhood "Gaetano Barresi", University of Messina, 98125 Messina, Italy.
| | - Andrea Gaetano Allegra
- Division of Hematology, Department of Human Pathology in Adulthood and Childhood "Gaetano Barresi", University of Messina, 98125 Messina, Italy.
| | - Marta Pugliese
- Division of Hematology, Department of Human Pathology in Adulthood and Childhood "Gaetano Barresi", University of Messina, 98125 Messina, Italy.
| | - Eleonora Di Salvo
- National Research Council of Italy (CNR)-Institute of Applied Science and Intelligent System (ISASI), 98164 Messina, Italy.
| | - Elvira Ventura-Spagnolo
- Legal Medicine Section, Department for Health Promotion and Mother-Child Care, University of Palermo, 90127 Palermo, Italy.
| | - Caterina Musolino
- Division of Hematology, Department of Human Pathology in Adulthood and Childhood "Gaetano Barresi", University of Messina, 98125 Messina, Italy.
| | - Sebastiano Gangemi
- School and Division of Allergy and Clinical Immunology, Department of Clinical and Experimental Medicine, University Hospital "G. Martino", Via Consolare Valeria SNC, 98125 Messina, Italy.
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40
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Abstract
Infections by DNA viruses including, Epstein–Barr virus (EBV), typically induce cellular DNA damage responses (DDR), in particular double-stranded break signaling. To avoid apoptosis associated with constitutive DDR signaling, downstream steps of this pathway must be inactivated. EBV has developed multiple ways of disabling the DDR using several different viral proteins expressed at various stages of EBV infection. Here the interplay between EBV and host DDRs is discussed at each stage of EBV infection, along with the EBV proteins and miRNAs that are known to interfere with DDR signaling. The newly discovered APOBEC editing of EBV DNA and protection from this mutation is also discussed.
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Affiliation(s)
- Lori Frappier
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
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41
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Zhang W, Sidhu SS. Generating Intracellular Modulators of E3 Ligases and Deubiquitinases from Phage-Displayed Ubiquitin Variant Libraries. Methods Mol Biol 2019; 1844:101-119. [PMID: 30242706 DOI: 10.1007/978-1-4939-8706-1_8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Ubiquitination is a posttranslational protein modification pathway regulating diverse cellular processes that are implicated in numerous human diseases. However, targeting the enzymes in the ubiquitination cascade potently and selectively remains a major challenge. Recently we devised a methodology to generate ubiquitin-based modulators for E3 ligases and deubiquitinases, enzymes that control the specificity of protein ubiquitination and deubiquitination, respectively. Here, we describe methods to generate libraries of ubiquitin variants and perform phage display selections to isolate high-affinity binders for target proteins. Importantly, the strategy introduced here can be applied to other small protein domains mediating protein-protein interactions to engineer tools for target validation and potential therapeutic development.
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Affiliation(s)
- Wei Zhang
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada.
| | - Sachdev S Sidhu
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada. .,Banting and Best Department of Medical Research, University of Toronto, Toronto, ON, Canada. .,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.
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42
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USP39 regulates DNA damage response and chemo-radiation resistance by deubiquitinating and stabilizing CHK2. Cancer Lett 2019; 449:114-124. [PMID: 30771428 DOI: 10.1016/j.canlet.2019.02.015] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 02/07/2019] [Accepted: 02/10/2019] [Indexed: 11/23/2022]
Abstract
The serine/threonine kinase, CHK2 (checkpoint kinase 2), is a key mediator in DNA damage response and a tumor suppressor, which is implicated in promoting cell cycle arrest, apoptosis and DNA repair. Accumulating evidence suggests that these functions are primarily exerted through phosphorylation downstream factors such as p53 and BRCA1. Recent studies have shown that ubiquitination is an important mode of regulation of CHK2. However, it remains largely unclear whether deubiquitinases participate in regulation of CHK2. Here, we report that a deubiquitinase, USP39, is a new regulator of CHK2. Mechanistically, USP39 deubiquitinates and stabilizes CHK2, which in turn enhances CHK2 stability. Short hairpin RNA (shRNA) mediated knockdown of USP39 led to deregulate CHK2, which resulted in compromising the DNA damage-induced G2/M checkpoint, decreasing apoptosis, and conferring cancer cells resistance to chemotherapy drugs and radiation treatment. Collectively, we identify USP39 as a novel regulator of CHK2 in the DNA damage response.
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43
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Abstract
In higher eukaryotes, DNA damage repair response pathways are orchestrated by several molecular signals including ubiquitination. In particular the repair of DNA interstrand crosslinks, toxic to transcription and replication processes, involve the activation of the Fanconi anemia repair pathway. At the heart of this pathway lies the monoubiquitination of FANCD2 and FANCI proteins, which triggers the recruitment of DNA repair factors. A major road block in our understanding of this fundamental repair pathway arises from the challenge with generating sufficient quantities of site-specifically monoubiquitinated FANCD2 and FANCI proteins to enable mechanistic and molecular studies. Current in vitro methods rely on the purification of a large (~0.8MDa), multiprotein E3 complex that can only partially monoubiquitinate a FANCD2-FANCI-DNA complex. In this chapter, we describe detailed protocols for the preparation of homogeneously and natively monoubiquitinated FANCD2 and FANCI proteins in isolation. The method relies on the use of a minimal E3 module and an engineered E2 variant that together drive site-specific ubiquitination of the isolated substrates, without the requirement of DNA cofactors. Using the enzymatic approach, we also demonstrate how added functionalities such as a fluorescently labeled ubiquitin can be conjugated on the FANCD2 and FANCI substrates, thus enabling multiple downstream applications.
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Reilly NM, Yard BD, Pittman DL. Homologous Recombination-Mediated DNA Repair and Implications for Clinical Treatment of Repair Defective Cancers. Methods Mol Biol 2019; 1999:3-29. [PMID: 31127567 DOI: 10.1007/978-1-4939-9500-4_1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Double-strand DNA breaks (DSBs) are generated by ionizing radiation and as intermediates during the processing of DNA, such as repair of interstrand cross-links and collapsed replication forks. These potentially deleterious DSBs are repaired primarily by the homologous recombination (HR) and nonhomologous end joining (NHEJ) DNA repair pathways. HR utilizes a homologous template to accurately restore damaged DNA, whereas NHEJ utilizes microhomology to join breaks in close proximity. The pathway available for DSB repair is dependent upon the cell cycle stage; for example, HR primarily functions during the S/G2 stages while NHEJ can repair DSBs at any cell cycle stage. Posttranslational modifications (PTMs) promote activity of specific pathways and subpathways through enzyme activation and precisely timed protein recruitment and degradation. This chapter provides an overview of PTMs occurring during DSB repair. In addition, clinical phenotypes associated with HR-defective cancers, such as mutational signatures used to predict response to poly(ADP-ribose) polymerase inhibitors, are discussed. Understanding these processes will provide insight into mechanisms of genome maintenance and likely identify targets and new avenues for therapeutic interventions.
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Affiliation(s)
- Nicole M Reilly
- Fondazione Piemontese per la Ricerca sul Cancro ONLUS, Candiolo, Italy
| | - Brian D Yard
- Department of Translational Hematology and Oncology Research, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Douglas L Pittman
- Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina, Columbia, SC, USA.
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45
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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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46
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Fournier LA, Kumar A, Stirling PC. Chromatin as a Platform for Modulating the Replication Stress Response. Genes (Basel) 2018; 9:genes9120622. [PMID: 30544989 PMCID: PMC6316668 DOI: 10.3390/genes9120622] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 12/03/2018] [Accepted: 12/04/2018] [Indexed: 02/06/2023] Open
Abstract
Eukaryotic DNA replication occurs in the context of chromatin. Recent years have seen major advances in our understanding of histone supply, histone recycling and nascent histone incorporation during replication. Furthermore, much is now known about the roles of histone remodellers and post-translational modifications in replication. It has also become clear that nucleosome dynamics during replication play critical roles in genome maintenance and that chromatin modifiers are important for preventing DNA replication stress. An understanding of how cells deploy specific nucleosome modifiers, chaperones and remodellers directly at sites of replication fork stalling has been building more slowly. Here we will specifically discuss recent advances in understanding how chromatin composition contribute to replication fork stability and restart.
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Affiliation(s)
| | - Arun Kumar
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, BC V5Z 1L3, Canada.
| | - Peter C Stirling
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, BC V5Z 1L3, Canada.
- Department of Medical Genetics, University of British Columbia, Vancouver, BC V5Z 1L3, Canada.
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47
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Whitcomb EA, Tsai YC, Basappa J, Liu K, Le Feuvre AK, Weissman AM, Taylor A. Stabilization of p27 Kip1/CDKN1B by UBCH7/UBE2L3 catalyzed ubiquitinylation: a new paradigm in cell-cycle control. FASEB J 2018; 33:1235-1247. [PMID: 30113882 DOI: 10.1096/fj.201800960r] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Ubiquitinylation drives many cellular processes by targeting proteins for proteasomal degradation. Ubiquitin conjugation enzymes promote ubiquitinylation and, thus, degradation of protein substrates. Ubiquitinylation is a well-known posttranslational modification controlling cell-cycle transitions and levels or/and activation levels of ubiquitin-conjugating enzymes change during development and cell cycle. Progression through the cell cycle is tightly controlled by CDK inhibitors such as p27Kip1. Here we show that, in contrast to promoting its degradation, the ubiquitin-conjugating enzyme UBCH7/UBE2L3 specifically protects p27Kip1 from degradation. Overexpression of UBCH7/UBE2L3 stabilizes p27Kip1 and delays the G1-to-S transition, while depletion of UBCH7/UBE2L3 increases turnover of p27Kip1. Levels of p21Cip1/Waf1, p57Kip2, cyclin A and cyclin E, all of which are also involved in regulating the G1/S transition are not affected by UBCH7/UBE2L3 depletion. The effect of UBCH7/UBE2L3 on p27Kip1 is not due to alteration of the levels of any of the ubiquitin ligases known to ubiquitinylate p27Kip1. Rather, UBCH7/UBE2L3 catalyzes the conjugation of heterotypic ubiquitin chains on p27Kip1 that are proteolytically incompetent. These data reveal new controls and concepts about the ubiquitin proteasome system in which a ubiquitin-conjugating enzyme selectively inhibits and may even protect, rather than promote degradation of a crucial cell-cycle regulatory molecule.-Whitcomb, E. A., Tsai, Y. C., Basappa, J., Liu, K., Le Feuvre, A. K., Weissman, A. M., Taylor, A. Stabilization of p27Kip1/CDKN1B by UBCH7/UBE2L3 catalyzed ubiquitinylation: a new paradigm in cell-cycle control.
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Affiliation(s)
- Elizabeth A Whitcomb
- Laboratory for Nutrition and Vision Research Jean Mayer-U.S. Department of Agriculture (JM-USDA) Human Nutrition Research Center on Aging, Tufts University, Boston, Massachusetts, USA
| | - Yien Che Tsai
- Laboratory of Protein Dynamics and Signaling, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, USA
| | - Johnvesly Basappa
- Laboratory for Nutrition and Vision Research Jean Mayer-U.S. Department of Agriculture (JM-USDA) Human Nutrition Research Center on Aging, Tufts University, Boston, Massachusetts, USA
| | - Ke Liu
- Laboratory for Nutrition and Vision Research Jean Mayer-U.S. Department of Agriculture (JM-USDA) Human Nutrition Research Center on Aging, Tufts University, Boston, Massachusetts, USA
| | - Aurélie K Le Feuvre
- Laboratory for Nutrition and Vision Research Jean Mayer-U.S. Department of Agriculture (JM-USDA) Human Nutrition Research Center on Aging, Tufts University, Boston, Massachusetts, USA
| | - Allan M Weissman
- Laboratory of Protein Dynamics and Signaling, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, USA
| | - Allen Taylor
- Laboratory for Nutrition and Vision Research Jean Mayer-U.S. Department of Agriculture (JM-USDA) Human Nutrition Research Center on Aging, Tufts University, Boston, Massachusetts, USA
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48
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Liu J, Pan L. Structural bases of the assembly, recognition and disassembly of linear ubiquitin chain. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2018; 1865:1410-1422. [PMID: 29981772 DOI: 10.1016/j.bbamcr.2018.07.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Revised: 06/25/2018] [Accepted: 07/03/2018] [Indexed: 12/31/2022]
Abstract
Linear ubiquitin chain is a latest discovered type of poly-ubiquitin chain that is broadly involved in innate immune and inflammatory pathways. Dysfunctions in its assembly, recognition or disassembly are intimately related with numerous immunodeficiency or autoimmune diseases. Our understanding of the molecular mechanism for linear ubiquitin chain formation, recognition and disassembly has being significantly evolved in recent years, with particular contribution from the biochemical and structural characterizations of related proteins. Here, we focus on the relevant proteins for the synthesis, recognition and digestion of linear ubiquitin chain, and review recent findings to summarize currently known molecular mechanism from a perspective of structural biology.
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Affiliation(s)
- Jianping Liu
- State Key Laboratory of Bioorganic and Natural Products Chemistry, University of Chinese Academy of Sciences, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, People's Republic of China
| | - Lifeng Pan
- State Key Laboratory of Bioorganic and Natural Products Chemistry, University of Chinese Academy of Sciences, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, People's Republic of China; Collaborative Innovation Center of Chemistry for Life Sciences, University of Chinese Academy of Sciences, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, People's Republic of China.
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49
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Preclinical evaluation of the selective small-molecule UBA1 inhibitor, TAK-243, in acute myeloid leukemia. Leukemia 2018; 33:37-51. [DOI: 10.1038/s41375-018-0167-0] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 04/06/2018] [Accepted: 05/02/2018] [Indexed: 02/07/2023]
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50
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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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