1
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Park HB, Baek KH. Current and future directions of USP7 interactome in cancer study. Biochim Biophys Acta Rev Cancer 2023; 1878:188992. [PMID: 37775071 DOI: 10.1016/j.bbcan.2023.188992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 09/14/2023] [Accepted: 09/23/2023] [Indexed: 10/01/2023]
Abstract
The ubiquitin-proteasome system (UPS) is an essential protein quality controller for regulating protein homeostasis and autophagy. Ubiquitination is a protein modification process that involves the binding of one or more ubiquitins to substrates through a series of enzymatic processes. These include ubiquitin-activating enzymes (E1), ubiquitin-conjugating enzymes (E2), and ubiquitin ligases (E3). Conversely, deubiquitination is a reverse process that removes ubiquitin from substrates via deubiquitinating enzymes (DUBs). Dysregulation of ubiquitination-related enzymes can lead to various human diseases, including cancer, through the modulation of protein ubiquitination. The most structurally and functionally studied DUB is the ubiquitin-specific protease 7 (USP7). Both the TRAF and UBL domains of USP7 are known to bind to the [P/A/E]-X-X-S or K-X-X-X-K motif of substrates. USP7 has been shown to be involved in cancer pathogenesis by binding with numerous substrates. Recently, a novel substrate of USP7 was discovered through a systemic analysis of its binding motif. This review summarizes the currently discovered substrates and cellular functions of USP7 in cancer and suggests putative substrates of USP7 through a comprehensive systemic analysis.
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Affiliation(s)
- Hong-Beom Park
- Department of Convergence, CHA University, Gyeonggi-Do 13488, Republic of Korea
| | - Kwang-Hyun Baek
- Department of Convergence, CHA University, Gyeonggi-Do 13488, Republic of Korea; International Ubiquitin Center(,) CHA University, Gyeonggi-Do 13488, Republic of Korea.
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2
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Zou X, Yu H, Li Q. Genome-wide identification and transcriptome-based expression profiling of E2 gene family: Implication for potential roles in gonad development of Crassostrea gigas. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2023; 47:101108. [PMID: 37418813 DOI: 10.1016/j.cbd.2023.101108] [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: 06/02/2023] [Revised: 06/27/2023] [Accepted: 06/27/2023] [Indexed: 07/09/2023]
Abstract
In this study, we investigated the role of E2 ubiquitin conjugating enzymes (E2) in the Pacific oyster Crassostrea gigas, with a focus on their involvement in gonad development. We identified 34 E2 genes clustered into nine subgroups and 24 subfamilies. The gene structure and intron-exon location were conserved within the same subfamily, but motif variation suggested functional diversity. Tissue transcriptome analyses revealed that most E2 genes were broadly expressed, with UBE2CL showing specific expression in the female gonad. Expression profiling of E2 genes during early embryo-larvae development stages suggested that five E2 genes were highly expressed in early embryo development, indicating their involvement in cell division processes. Furthermore, by profiling the expression of E2 genes in different gonadal developmental stages, we observed a gradual increase in expression for four genes during gametogenesis, with significantly higher expression in the female gonad at the maturation stage. Similarly, five E2 genes displayed elevated expression levels in the male gonad at the maturation stage, indicating their crucial roles in gonadal development and gametogenesis. Our study provides valuable insights into the potential functions of the E2 gene family in C. gigas, shedding light on the molecular mechanisms underlying gonad development in oysters.
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Affiliation(s)
- Xiaoyu Zou
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Qingdao 266003, China
| | - Hong Yu
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Qingdao 266003, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China.
| | - Qi Li
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Qingdao 266003, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China; Laboratory of Tropical Marine Germplasm Resources and Breeding Engineering, Sanya Oceanographic Institution, Ocean University of China, Sanya 572000, China
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3
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Zhao Y, Huang X, Zhu D, Wei M, Luo J, Yu S, Tian Y, Zheng X. Deubiquitinase OTUD6A promotes breast cancer progression by increasing TopBP1 stability and rendering tumor cells resistant to DNA-damaging therapy. Cell Death Differ 2022; 29:2531-2544. [PMID: 35768646 PMCID: PMC9751275 DOI: 10.1038/s41418-022-01036-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 06/14/2022] [Accepted: 06/15/2022] [Indexed: 01/31/2023] Open
Abstract
The DNA damage response (DDR) is critical for maintaining cellular homeostasis and genome integrity. Mounting evidence has shown that posttranslational protein modifications play vital roles in the DDR. In this study, we showed that deubiquitinase OTUD6A is involved in the DDR and is important for maintaining genomic stability. Mechanistically, in response to DNA damage, the abundance of OTUD6A was increased; meanwhile, PP2A interacted with OTUD6A and dephosphorylated OTUD6A at sites S70/71/74, which promoted nuclear localization of OTUD6A. Subsequently, OTUD6A was recruited to the damage site, where it interacted with TopBP1 and blocked the interaction between TopBP1 and its ubiquitin E3 ligase UBR5, decreasing K48-linked polyubiquitination and increasing the stability of TopBP1. OTUD6A depletion impaired CHK1 S345 phosphorylation and blocked cell cycle progression under DNA replication stress. Consistently, knockout of OTUD6A rendered mice hypersensitive to irradiation, shortened survival, and inhibited tumor growth by regulating TopBP1 in xenografted nude mice. Moreover, OTUD6A is expressed at high levels in breast cancer, and OTUD6A overexpression promotes cell proliferation, migration and invasion, indicating that dysregulation of OTUD6A expression contributes to genomic instability and is associated with tumor development. In summary, this study demonstrates that OTUD6A plays a critical role in promoting tumor cell resistance to chemoradiotherapy by deubiquitinating and stabilizing TopBP1.
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Affiliation(s)
- Yan Zhao
- 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
| | - Xinping Huang
- 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
| | - Dan Zhu
- 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
| | - Min Wei
- 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
| | - Jiechen Luo
- 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
| | - 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
| | - Yonglu Tian
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, State Key Laboratory of Membrane Biology, School of Life Sciences, Peking University, Beijing, 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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4
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Baile F, Gómez-Zambrano Á, Calonje M. Roles of Polycomb complexes in regulating gene expression and chromatin structure in plants. PLANT COMMUNICATIONS 2022; 3:100267. [PMID: 35059633 PMCID: PMC8760139 DOI: 10.1016/j.xplc.2021.100267] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 11/09/2021] [Accepted: 11/23/2021] [Indexed: 05/16/2023]
Abstract
The evolutionary conserved Polycomb Group (PcG) repressive system comprises two central protein complexes, PcG repressive complex 1 (PRC1) and PRC2. These complexes, through the incorporation of histone modifications on chromatin, have an essential role in the normal development of eukaryotes. In recent years, a significant effort has been made to characterize these complexes in the different kingdoms, and despite there being remarkable functional and mechanistic conservation, some key molecular principles have diverged. In this review, we discuss current views on the function of plant PcG complexes. We compare the composition of PcG complexes between animals and plants, highlight the role of recently identified plant PcG accessory proteins, and discuss newly revealed roles of known PcG partners. We also examine the mechanisms by which the repression is achieved and how these complexes are recruited to target genes. Finally, we consider the possible role of some plant PcG proteins in mediating local and long-range chromatin interactions and, thus, shaping chromatin 3D architecture.
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Affiliation(s)
- Fernando Baile
- Institute of Plant Biochemistry and Photosynthesis (IBVF-CSIC-US), Avenida Américo Vespucio 49, 41092 Seville, Spain
| | - Ángeles Gómez-Zambrano
- Institute of Plant Biochemistry and Photosynthesis (IBVF-CSIC-US), Avenida Américo Vespucio 49, 41092 Seville, Spain
| | - Myriam Calonje
- Institute of Plant Biochemistry and Photosynthesis (IBVF-CSIC-US), Avenida Américo Vespucio 49, 41092 Seville, Spain
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5
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Gupta R, Jha A, Ambasta RK, Kumar P. Regulatory mechanism of cyclins and cyclin-dependent kinases in post-mitotic neuronal cell division. Life Sci 2021; 285:120006. [PMID: 34606852 DOI: 10.1016/j.lfs.2021.120006] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 09/24/2021] [Accepted: 09/25/2021] [Indexed: 12/18/2022]
Abstract
Neurodegenerative diseases (NDDs) are the most common life-threatening disease of the central nervous system and it cause the progressive loss of neuronal cells. The exact mechanism of the disease's progression is not clear and thus line of treatment for NDDs is a baffling issue. During the progression of NDDs, oxidative stress and DNA damage play an important regulatory function, and ultimately induces neurodegeneration. Recently, aberrant cell cycle events have been demonstrated in the progression of different NDDs. However, the pertinent role of signaling mechanism, for instance, post-translational modifications, oxidative stress, DNA damage response pathway, JNK/p38 MAPK, MEK/ERK cascade, actively participated in the aberrant cell cycle reentry induced neuronal cell death. Mounting evidence has demonstrated that aberrant cell cycle re-entry is a major contributing factor in the pathogenesis of NDDs rather than a secondary phenomenon. In the brain of AD patients with mild cognitive impairment, post miotic cell division can be seen in the early stage of the disease. However, in the brain of PD patients, response to various neurotoxic signals, the cell cycle re-entry has been observed that causes neuronal apoptosis. On contrary, the contributing factors that leads to the induction of cell cycle events in mature neurons in HD and ALS brain pathology is remain unclear. Various pharmacological drugs have been developed to reduce the pathogenesis of NDDs, but they are still not helpful in eliminating the cause of these NDDs.
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Affiliation(s)
- Rohan Gupta
- Molecular Neuroscience and Functional Genomics Laboratory, Delhi Technological University (Formerly Delhi College of Engineering), India
| | - Ankita Jha
- Molecular Neuroscience and Functional Genomics Laboratory, Delhi Technological University (Formerly Delhi College of Engineering), India
| | - Rashmi K Ambasta
- Molecular Neuroscience and Functional Genomics Laboratory, Delhi Technological University (Formerly Delhi College of Engineering), India
| | - Pravir Kumar
- Molecular Neuroscience and Functional Genomics Laboratory, Delhi Technological University (Formerly Delhi College of Engineering), India.
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6
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Ge J, Yu W, Li J, Ma H, Wang P, Zhou Y, Wang Y, Zhang J, Shi G. USP16 regulates castration-resistant prostate cancer cell proliferation by deubiquitinating and stablizing c-Myc. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2021; 40:59. [PMID: 33546726 PMCID: PMC7866668 DOI: 10.1186/s13046-021-01843-8] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 01/13/2021] [Indexed: 12/14/2022]
Abstract
Background c-Myc, a well-established oncogene, plays an important role in the initiation and progression of various cancers, including prostate cancer. However, its mechanism in cancer cell remains largely unknown and whether there exist a deubiquitinase targeting c-Myc also remains elusive. Methods Bioinformatic analysis and shRNA screening methods were used to identify potential deubiquitinases that correlate with c-Myc gene signature. Cell proliferation and viability were measured by Cell-Counting-Kit 8 and colony formation assays. A mouse xenograft model of PC3 cells was established to confirm the function of USP16 in vivo. The interaction between USP16 and c-Myc protein was assessed by co-immunoprecipitation and protein co-localization assays. Immunohistochemistry staining was performed to detect the expression of USP16, Ki67, and c-Myc in xenograft tissues and clinical tumour tissues. Furthermore, the correlation between USP16 and c-Myc was confirmed by RNA sequencing. Results Functional analyses identified USP16, known as a deubiquitinase, was strongly correlated with the c-Myc gene signature. Depletion of USP16 was shown to significantly suppress the growth of PCa cells both in vitro and in vivo. Co-immunoprecipitation and ubiquitination assays confirmed that USP16 served as a novel deubiquitinase of c-Myc and overexpression of c-Myc significantly rescued the effects of USP16 disruption. Immunohistochemistry staining and RNA-seq tactics were further used to confirm the positive correlation between USP16 and c-Myc expression. Expression of USP16 in human PCa tissues was higher than that seen in normal prostate tissues and its high expression was found associated with poor prognosis. Conclusions USP16 serves as a novel deubiquitinase of c-Myc. Downregulation of USP16 markedly suppressed PCa cell growth both in vitro and in vivo. USP16 regulates PCa cell proliferation by deubiquitinating and stabilizing c-Myc, making it a potential therapeutic candidate for the treatment of PCa. Supplementary Information The online version contains supplementary material available at 10.1186/s13046-021-01843-8.
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Affiliation(s)
- Jianchao Ge
- Department of Urology, The Fifth People's Hospital of Shanghai, Fudan University, No. 801, Heqing Road,Minhang District, Shanghai, 200240, People's Republic of China
| | - Wandong Yu
- Department of Urology, The Fifth People's Hospital of Shanghai, Fudan University, No. 801, Heqing Road,Minhang District, Shanghai, 200240, People's Republic of China
| | - Junhong Li
- Department of Urology, The Fifth People's Hospital of Shanghai, Fudan University, No. 801, Heqing Road,Minhang District, Shanghai, 200240, People's Republic of China
| | - Hangbin Ma
- Department of Urology, The Fifth People's Hospital of Shanghai, Fudan University, No. 801, Heqing Road,Minhang District, Shanghai, 200240, People's Republic of China
| | - Pengyu Wang
- Department of Urology, The Fifth People's Hospital of Shanghai, Fudan University, No. 801, Heqing Road,Minhang District, Shanghai, 200240, People's Republic of China
| | - Yinghao Zhou
- Department of Urology, The Fifth People's Hospital of Shanghai, Fudan University, No. 801, Heqing Road,Minhang District, Shanghai, 200240, People's Republic of China
| | - Yang Wang
- Department of Urology, The Fifth People's Hospital of Shanghai, Fudan University, No. 801, Heqing Road,Minhang District, Shanghai, 200240, People's Republic of China
| | - Jun Zhang
- Department of Urology, The Fifth People's Hospital of Shanghai, Fudan University, No. 801, Heqing Road,Minhang District, Shanghai, 200240, People's Republic of China.
| | - Guowei Shi
- Department of Urology, The Fifth People's Hospital of Shanghai, Fudan University, No. 801, Heqing Road,Minhang District, Shanghai, 200240, People's Republic of China.
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7
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Mustofa MK, Tanoue Y, Chirifu M, Shimasaki T, Tateishi C, Nakamura T, Tateishi S. RAD18 mediates DNA double-strand break-induced ubiquitination of chromatin protein. J Biochem 2021; 170:33-40. [PMID: 33508099 DOI: 10.1093/jb/mvab010] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 01/04/2021] [Indexed: 11/14/2022] Open
Affiliation(s)
- Md Kawsar Mustofa
- Department of Cell Maintenance, Institute of Molecular Embryology and Genetics, Kumamoto University, 2-2-1 Honjo Chuoku, Kumamoto, 860-0811, Japan
| | - Yuki Tanoue
- Department of Cell Maintenance, Institute of Molecular Embryology and Genetics, Kumamoto University, 2-2-1 Honjo Chuoku, Kumamoto, 860-0811, Japan.,Yuki Tanoue, The Chemo-Sero-Therapeutic Research Institute (KAKETSUKEN), 4-7 Hanabatacho Chuoku, Kumamoto, 860-0806, Japan
| | - Mami Chirifu
- Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oehonmachi, Chuoku, Kumamoto, 862-0973, Japan
| | - Tatsuya Shimasaki
- Isotope science, IRDA, Kumamoto University, Kumamoto University, 2-2-1 Honjo Chuoku, Kumamoto, 860-0811, Japan
| | - Chie Tateishi
- Department of Cell Maintenance, Institute of Molecular Embryology and Genetics, Kumamoto University, 2-2-1 Honjo Chuoku, Kumamoto, 860-0811, Japan
| | - Teruya Nakamura
- Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oehonmachi, Chuoku, Kumamoto, 862-0973, Japan.,Priority Organization for Innovation and Excellence, Kumamoto University, 5-1 Oehonmachi, Chuoku, Kumamoto, 862-0973, Japan
| | - Satoshi Tateishi
- Department of Cell Maintenance, Institute of Molecular Embryology and Genetics, Kumamoto University, 2-2-1 Honjo Chuoku, Kumamoto, 860-0811, Japan
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8
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Zhong L, Zhang Y, Li M, Song Y, Liu D, Yang X, Yang D, Qu H, Lai L, Wang Q, Chen Z. E3 ligase FBXW7 restricts M2-like tumor-associated macrophage polarization by targeting c-Myc. Aging (Albany NY) 2020; 12:24394-24423. [PMID: 33260160 PMCID: PMC7762499 DOI: 10.18632/aging.202293] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 09/24/2020] [Indexed: 06/12/2023]
Abstract
FBXW7 functions as an E3 ubiquitin ligase to mediate oncoprotein degradation via the ubiquitin-proteasome system in cancer cells, effectively inhibiting the growth and survival of tumor cells. However, little is known about the functions of FBXW7 in macrophages and the tumor immune microenvironment. In this study, we find that FBXW7 suppresses M2-like tumor-associated macrophage (TAM) polarization to limit tumor progression. We identified a significant increase in the proportion of M2-like TAMs and aggravated tumor growth in mice with myeloid FBXW7 deficiency by subcutaneous inoculation with Lewis lung carcinoma cells (LLCs). When stimulated with LLCs supernatant in vitro, FBXW7-knockout macrophages displayed increased M2 macrophage polarization and enhanced ability of supporting cancer cells growth. In mechanism, we confirmed that FBXW7 inhibited M2-like TAM polarization by mediating c-Myc degradation via the ubiquitin-proteasome system. These findings highlight the role of FBXW7 in M2-like TAM polarization and provide new insights into the potential targets for cancer immunotherapies.
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Affiliation(s)
- Lijia Zhong
- Department of Pulmonology, The Children’s Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou 310052, China
| | - Yuanyuan Zhang
- Department of Pulmonology, The Children’s Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou 310052, China
| | - Mengyao Li
- Department of Pulmonology, The Children’s Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou 310052, China
| | - Yinjing Song
- Sir Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, China
| | - Danhui Liu
- Institute of Immunology, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Xin Yang
- Department of Pulmonology, The Children’s Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou 310052, China
| | - Dehua Yang
- Department of Pulmonology, The Children’s Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou 310052, China
| | - Hao Qu
- Department of Orthopedic Surgery, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou 310009, China
| | - Lihua Lai
- Institute of Immunology, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Qingqing Wang
- Institute of Immunology, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Zhimin Chen
- Department of Pulmonology, The Children’s Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou 310052, China
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9
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Zang W, Zheng X. Structure and functions of cellular redox sensor HSCARG/NMRAL1, a linkage among redox status, innate immunity, DNA damage response, and cancer. Free Radic Biol Med 2020; 160:768-774. [PMID: 32950687 PMCID: PMC7497778 DOI: 10.1016/j.freeradbiomed.2020.09.016] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 08/31/2020] [Accepted: 09/11/2020] [Indexed: 01/05/2023]
Abstract
NmrA-like proteins are NAD(P) (H) interacting molecules whose structures are similar to that of short-chain dehydrogenases. In this review, we focus on an NADP(H) sensor, HSCARG (also named NMRAL1), which is a NmrA-like protein that is widely present in mammals, and provide a comprehensive overview of the current knowledge of its structure and physiological functions. HSCARG selectively binds to the reduced form of type II coenzyme NADPH via its Rossmann fold domain. In response to reduction of intracellular NADPH concentration, HSCARG transforms from homodimer to monomer and exhibits enhanced interactions with its binding partners. In the cytoplasm, HSCARG negatively regulates innate immunity through impairing the activities of NF-κB and RLR pathways. Besides, HSCARG regulates redox homeostasis via suppression of ROS and NO generation. Intensive and persistent oxidative stress leads to translocation of HSCARG from the cytoplasm to the nucleus, where it regulates the DNA damage response. Taken together, HSCARG functions as a linkage between cellular redox status and other signaling pathways and fine-tunes cellular response to redox changes.
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Affiliation(s)
- Weicheng Zang
- 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
| | - 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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10
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Li J, Wang R, Jin J, Han M, Chen Z, Gao Y, Hu X, Zhu H, Gao H, Lu K, Shao Y, Lyu C, Lai W, Li P, Hu G, Li J, Li D, Wang H, Wu Q, Wong J. USP7 negatively controls global DNA methylation by attenuating ubiquitinated histone-dependent DNMT1 recruitment. Cell Discov 2020; 6:58. [PMID: 32884836 PMCID: PMC7445300 DOI: 10.1038/s41421-020-00188-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 05/27/2020] [Indexed: 11/08/2022] Open
Abstract
Previous studies have implicated an essential role for UHRF1-mediated histone H3 ubiquitination in recruiting DNMT1 to replication sites for DNA maintenance methylation during S phase of the cell cycle. However, the regulatory mechanism on UHRF1-mediated histone ubiquitination is not clear. Here we present evidence that UHRF1 and USP7 oppositely control ubiquitination of histones H3 and H2B in S phase of the cell cycle and that DNMT1 binds both ubiquitinated H3 and H2B. USP7 knockout markedly increased the levels of ubiquitinated H3 and H2B in S phase, the association of DNMT1 with replication sites and importantly, led to a progressive increase of global DNA methylation shown with increased cell passages. Using DNMT3A/DNMT3B/USP7 triple knockout cells and various DNA methylation analyses, we demonstrated that USP7 knockout led to an overall elevation of DNA methylation levels. Mechanistic study demonstrated that USP7 suppresses DNMT1 recruitment and DNA methylation through its deubiquitinase activity and the interaction with DNMT1. Altogether our study provides evidence that USP7 is a negative regulator of global DNA methylation and that USP7 protects the genome from excessive DNA methylation by attenuating histone ubiquitination-dependent DNMT1 recruitment.
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Affiliation(s)
- Jialun Li
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241 China
- Joint Center for Translational Medicine, Fengxian District Central Hospital, 6600th Nanfeng Road, Fengxian District, Shanghai, 201499 China
| | - Ruiping Wang
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241 China
| | - Jianyu Jin
- College of Education, Wenzhou University, Wenzhou, Zhejiang 325035 China
| | - Mengmeng Han
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241 China
| | - Zhaosu Chen
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241 China
| | - Yingying Gao
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241 China
| | - Xueli Hu
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241 China
| | - Haijun Zhu
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241 China
| | - Huifang Gao
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241 China
| | - Kongbin Lu
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241 China
| | - Yanjiao Shao
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241 China
| | - Cong Lyu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085 China
| | - Weiyi Lai
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085 China
| | - Pishun Li
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, RTP, Durham, NC 27709 USA
| | - Guang Hu
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, RTP, Durham, NC 27709 USA
| | - Jiwen Li
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241 China
| | - Dali Li
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241 China
| | - Hailin Wang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085 China
| | - Qihan Wu
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241 China
- Key Laboratory of Reproduction Regulation of NPFPC, SIPPR, IRD, Fudan University, Shanghai, 200032 China
| | - Jiemin Wong
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241 China
- Joint Center for Translational Medicine, Fengxian District Central Hospital, 6600th Nanfeng Road, Fengxian District, Shanghai, 201499 China
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Gutierrez-Diaz BT, Gu W, Ntziachristos P. Deubiquitinases: Pro-oncogenic Activity and Therapeutic Targeting in Blood Malignancies. Trends Immunol 2020; 41:327-340. [PMID: 32139316 PMCID: PMC7258259 DOI: 10.1016/j.it.2020.02.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 02/10/2020] [Accepted: 02/10/2020] [Indexed: 12/18/2022]
Abstract
Deubiquitinases are enzymes that remove ubiquitin moieties from the vast majority of cellular proteins, controlling their stability, interactions, and localization. The expression and activity of deubiquitinases are critical for physiology and can go awry in various diseases, including cancer. Based on recent findings in human blood cancers, we discuss the functions of selected deubiquitinases in acute leukemia and efforts to target these enzymes with the aim of blocking leukemia growth and improving disease outcomes. We focus on the emergence of the newest generation of preclinical inhibitors by discussing their modes of inhibition and their effects on leukemia biology.
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Affiliation(s)
- Blanca T Gutierrez-Diaz
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, 303 E. Superior Street, Chicago, IL 60611, USA
| | - Wei Gu
- Institute for Cancer Genetics, Department of Pathology and Cell Biology, and Herbert Irving Comprehensive Cancer Center, College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Panagiotis Ntziachristos
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, 303 E. Superior Street, Chicago, IL 60611, USA; Simpson Querrey Center for Epigenetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA; Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.
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12
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Cellular redox sensor HSCARG negatively regulates the translesion synthesis pathway and exacerbates mammary tumorigenesis. Proc Natl Acad Sci U S A 2019; 116:25624-25633. [PMID: 31796584 DOI: 10.1073/pnas.1910250116] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
The translesion synthesis (TLS) pathway is a double-edged sword in terms of genome integrity. Deficiency in TLS leads to generation of DNA double strand break (DSB) during replication stress, while excessive activation of the TLS pathway increases the risk of point mutation. Here we demonstrate that HSCARG, a cellular redox sensor, directly interacts with the key protein PCNA in the TLS pathway. HSCARG enhances the interaction between PCNA and the deubiquitinase complex USP1/UAF1 and inhibits the monoubiquitination of PCNA, thereby impairing the recruitment of Y-family polymerases and increasing cell sensitivity to stimuli that trigger replication fork blockades. In response to oxidative stress, disaggregation of HSCARG dimers into monomers and the nuclear transport of HSCARG activate the regulatory function of HSCARG in the TLS pathway. Moreover, HSCARG, which is highly expressed in breast carcinoma, promotes the accumulation of DSBs and mutations. HSCARG knockout PyMT transgenic mice exhibit delayed mammary tumorigenesis compared with that in HSCARG wild-type or heterozygous PyMT mice. Taken together, these findings expand our understanding of TLS regulatory mechanisms and establish a link between the cellular redox status and the DNA damage response (DDR).
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13
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Jones RM, Melton PE, Pinese M, Rea AJ, Ingley E, Ballinger ML, Wood DJ, Thomas DM, Moses EK. Identification of novel sarcoma risk genes using a two-stage genome wide DNA sequencing strategy in cancer cluster families and population case and control cohorts. BMC MEDICAL GENETICS 2019; 20:69. [PMID: 31053105 PMCID: PMC6499942 DOI: 10.1186/s12881-019-0808-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 04/16/2019] [Indexed: 12/26/2022]
Abstract
Background Although familial clustering of cancers is relatively common, only a small proportion of familial cancer risk can be explained by known cancer predisposition genes. Methods In this study we employed a two-stage approach to identify candidate sarcoma risk genes. First, we conducted whole exome sequencing in three multigenerational cancer families ascertained through a sarcoma proband (n = 19) in order to prioritize candidate genes for validation in an independent case-control cohort of sarcoma patients using family-based association and segregation analysis. The second stage employed a burden analysis of rare variants within prioritized candidate genes identified from stage one in 560 sarcoma cases and 1144 healthy ageing controls, for which whole genome sequence was available. Results Variants from eight genes were identified in stage one. Following gene-based burden testing and after correction for multiple testing, two of these genes, ABCB5 and C16orf96, were determined to show statistically significant association with cancer. The ABCB5 gene was found to have a higher burden of putative regulatory variants (OR = 4.9, p-value = 0.007, q-value = 0.04) based on allele counts in sarcoma cases compared to controls. C16orf96, was found to have a significantly lower burden (OR = 0.58, p-value = 0.0004, q-value = 0.003) of regulatory variants in controls compared to sarcoma cases. Conclusions Based on these genetic association data we propose that ABCB5 and C16orf96 are novel candidate risk genes for sarcoma. Although neither of these two genes have been previously associated with sarcoma, ABCB5 has been shown to share clinical drug resistance associations with melanoma and leukaemia and C16orf96 shares regulatory elements with genes that are involved with TNF-alpha mediated apoptosis in a p53/TP53-dependent manner. Future genetic studies in other family and population cohorts will be required for further validation of these novel findings. Electronic supplementary material The online version of this article (10.1186/s12881-019-0808-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Rachel M Jones
- The Curtin UWA Centre for Genetic Origins of Health and Disease, Faculty of Health Sciences, Curtin University and Faculty of Health and Medical Sciences, M409 The University of Western Australia, 35 Stirling Hwy, Crawley, 6009, Western Australia.,Medical School, Faculty of Health and Medical Sciences, University of Western Australia, Crawley, Australia
| | - Phillip E Melton
- The Curtin UWA Centre for Genetic Origins of Health and Disease, Faculty of Health Sciences, Curtin University and Faculty of Health and Medical Sciences, M409 The University of Western Australia, 35 Stirling Hwy, Crawley, 6009, Western Australia.,School of Pharmacy and Biomedical Sciences, Faculty of Health Sciences, Curtin University, Bentley, Western Australia
| | - Mark Pinese
- Cancer Division, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Alexander J Rea
- The Curtin UWA Centre for Genetic Origins of Health and Disease, Faculty of Health Sciences, Curtin University and Faculty of Health and Medical Sciences, M409 The University of Western Australia, 35 Stirling Hwy, Crawley, 6009, Western Australia
| | - Evan Ingley
- School of Veterinary and Life Sciences, Murdoch University, Murdoch, Australia.,Harry Perkins Institute of Medical Research, Murdoch, Western Australia.,The Centre for Medical Research, The University of Western Australia, Crawley, Australia
| | - Mandy L Ballinger
- Cancer Division, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | | | - David J Wood
- Medical School, Faculty of Health and Medical Sciences, University of Western Australia, Crawley, Australia
| | - David M Thomas
- Cancer Division, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Eric K Moses
- The Curtin UWA Centre for Genetic Origins of Health and Disease, Faculty of Health Sciences, Curtin University and Faculty of Health and Medical Sciences, M409 The University of Western Australia, 35 Stirling Hwy, Crawley, 6009, Western Australia. .,School of Pharmacy and Biomedical Sciences, Faculty of Health Sciences, Curtin University, Bentley, Western Australia. .,School of Biomedical Sciences, Faculty of Health and Medical Sciences, The University of Western Australia, Crawley, Australia.
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14
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Rawat R, Starczynowski DT, Ntziachristos P. Nuclear deubiquitination in the spotlight: the multifaceted nature of USP7 biology in disease. Curr Opin Cell Biol 2019; 58:85-94. [PMID: 30897496 DOI: 10.1016/j.ceb.2019.02.008] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2018] [Revised: 01/23/2019] [Accepted: 02/20/2019] [Indexed: 12/11/2022]
Abstract
Ubiquitination is a versatile and tightly regulated post-translational protein modification with many distinct outcomes affecting protein stability, localization, interactions, and activity. Ubiquitin chain linkages anchored on substrates can be further modified by additional post-translational modifications, including phosphorylation and SUMOylation. Deubiquitinases (DUBs) reverse these ubiquitin marks with matched levels of precision. Over hundred known DUBs regulate a wide variety of cellular events. In this review, we focus on ubiquitin-specific protease 7 (USP7, also known as herpesvirus-associated ubiquitin-specific protease, or HAUSP) as one of the best studied, disease-associated DUBs. By highlighting the functions of USP7, particularly in the nucleus, and the emergence of the newest generation of USP7 inhibitors, we illustrate the importance of individual DUBs in the nucleus, and the therapeutic prospects of DUB targeting in human disease.
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Affiliation(s)
- Radhika Rawat
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, 303 E. Superior Street, Chicago, IL 60611, USA
| | - Daniel T Starczynowski
- Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH; Department of Cancer Biology, University of Cincinnati, Cincinnati, OH
| | - Panagiotis Ntziachristos
- Simpson Querrey Center for Epigenetics; Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL.
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15
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Yang C, Zang W, Tang Z, Ji Y, Xu R, Yang Y, Luo A, Hu B, Zhang Z, Liu Z, Zheng X. A20/TNFAIP3 Regulates the DNA Damage Response and Mediates Tumor Cell Resistance to DNA-Damaging Therapy. Cancer Res 2017; 78:1069-1082. [DOI: 10.1158/0008-5472.can-17-2143] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Revised: 11/02/2017] [Accepted: 12/01/2017] [Indexed: 11/16/2022]
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16
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Dong X, Guan J, Zheng C, Zheng X. The herpes simplex virus 1 UL36USP deubiquitinase suppresses DNA repair in host cells via deubiquitination of proliferating cell nuclear antigen. J Biol Chem 2017; 292:8472-8483. [PMID: 28348081 DOI: 10.1074/jbc.m117.778076] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2017] [Revised: 03/24/2017] [Indexed: 12/18/2022] Open
Abstract
Herpes simplex virus 1 (HSV-1) infection manipulates distinct host DNA-damage responses to facilitate virus proliferation, but the molecular mechanisms remain to be elucidated. One possible HSV-1 target might be DNA damage-tolerance mechanisms, such as the translesion synthesis (TLS) pathway. In TLS, proliferating cell nuclear antigen (PCNA) is monoubiquitinated in response to DNA damage-caused replication fork stalling. Ubiquitinated PCNA then facilitates the error-prone DNA polymerase η (polη)-mediated TLS, allowing the fork to bypass damaged sites. Because of the involvement of PCNA ubiquitination in DNA-damage repair, we hypothesized that the function of PCNA might be altered by HSV-1. Here we show that PCNA is a substrate of the HSV-1 deubiquitinase UL36USP, which has previously been shown to be involved mainly in virus uptake and maturation. In HSV-1-infected cells, viral infection-associated UL36USP consistently reduced PCNA ubiquitination. The deubiquitination of PCNA inhibited the formation of polη foci and also increased cell sensitivity to DNA-damage agents. Moreover, the catalytically inactive mutant UL36C40A failed to deubiquitinate PCNA. Of note, the levels of virus marker genes increased strikingly in cells infected with wild-type HSV-1, but only moderately in UL36C40A mutant virus-infected cells, indicating that the UL36USP deubiquitinating activity supports HSV-1 virus replication during infection. These findings suggest a role of UL36USP in the DNA damage-response pathway.
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Affiliation(s)
- Xiaodong Dong
- State Key Lab of Protein and Plant Gene Research; Department of Biochemistry and Molecular Biology, School of Life Sciences, Peking University, Beijing 100871, China
| | - Junhong Guan
- State Key Lab of Protein and Plant Gene Research; Department of Biochemistry and Molecular Biology, School of Life Sciences, Peking University, Beijing 100871, China
| | - Chunfu Zheng
- Institutes of Biology and Medical Sciences, Soochow University, Suzhou 215123, China; Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Alberta T2N 1N4, Canada
| | - Xiaofeng Zheng
- State Key Lab of Protein and Plant Gene Research; Department of Biochemistry and Molecular Biology, School of Life Sciences, Peking University, Beijing 100871, China.
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17
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Shaw S, Le Cocq K, Paszkiewicz K, Moore K, Winsbury R, de Torres Zabala M, Studholme DJ, Salmon D, Thornton CR, Grant MR. Transcriptional reprogramming underpins enhanced plant growth promotion by the biocontrol fungus Trichoderma hamatum GD12 during antagonistic interactions with Sclerotinia sclerotiorum in soil. MOLECULAR PLANT PATHOLOGY 2016; 17:1425-1441. [PMID: 27187266 PMCID: PMC6638342 DOI: 10.1111/mpp.12429] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The free-living soil fungus Trichoderma hamatum strain GD12 is notable amongst Trichoderma strains in both controlling plant diseases and stimulating plant growth, a property enhanced during its antagonistic interactions with pathogens in soil. These attributes, alongside its markedly expanded genome and proteome compared with other biocontrol and plant growth-promoting Trichoderma strains, imply a rich potential for sustainable alternatives to synthetic pesticides and fertilizers for the control of plant disease and for increasing yields. The purpose of this study was to investigate the transcriptional responses of GD12 underpinning its biocontrol and plant growth promotion capabilities during antagonistic interactions with the pathogen Sclerotinia sclerotiorum in soil. Using an extensive mRNA-seq study capturing different time points during the pathogen-antagonist interaction in soil, we show that dynamic and biphasic signatures in the GD12 transcriptome underpin its biocontrol and plant (lettuce) growth-promoting activities. Functional predictions of differentially expressed genes demonstrate the enrichment of transcripts encoding proteins involved in transportation and oxidation-reduction reactions during both processes and an over-representation of siderophores. We identify a biphasic response during biocontrol characterized by a significant induction of transcripts encoding small-secreted cysteine-rich proteins, secondary metabolite-producing gene clusters and genes unique to GD12. These data support the hypothesis that Sclerotinia biocontrol is mediated by the synthesis and secretion of antifungal compounds and that GD12's unique reservoir of uncharacterized genes is actively recruited during the effective biological control of a plurivorous plant pathogen.
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Affiliation(s)
- Sophie Shaw
- Biosciences, College of Life and Environmental SciencesUniversity of ExeterGeoffrey Pope Building, Stocker RoadExeterEX4 4QDUK
- Centre for Genome Enabled Biology and MedicineUniversity of Aberdeen23 St. Machar DriveOld AberdeenAB24 3RYUK
| | - Kate Le Cocq
- Biosciences, College of Life and Environmental SciencesUniversity of ExeterGeoffrey Pope Building, Stocker RoadExeterEX4 4QDUK
- Sustainable Soils and Grassland Systems DepartmentRothamsted ResearchNorth WykeOkehamptonEX20 2SBUK
| | - Konrad Paszkiewicz
- Biosciences, College of Life and Environmental SciencesUniversity of ExeterGeoffrey Pope Building, Stocker RoadExeterEX4 4QDUK
| | - Karen Moore
- Biosciences, College of Life and Environmental SciencesUniversity of ExeterGeoffrey Pope Building, Stocker RoadExeterEX4 4QDUK
| | - Rebecca Winsbury
- Biosciences, College of Life and Environmental SciencesUniversity of ExeterGeoffrey Pope Building, Stocker RoadExeterEX4 4QDUK
- Department of Biological ChemistryJohn Innes CentreNorwich Research ParkNorwichNR4 7UHUK
| | - Marta de Torres Zabala
- Biosciences, College of Life and Environmental SciencesUniversity of ExeterGeoffrey Pope Building, Stocker RoadExeterEX4 4QDUK
| | - David J. Studholme
- Biosciences, College of Life and Environmental SciencesUniversity of ExeterGeoffrey Pope Building, Stocker RoadExeterEX4 4QDUK
| | - Deborah Salmon
- Biosciences, College of Life and Environmental SciencesUniversity of ExeterGeoffrey Pope Building, Stocker RoadExeterEX4 4QDUK
| | - Christopher R. Thornton
- Biosciences, College of Life and Environmental SciencesUniversity of ExeterGeoffrey Pope Building, Stocker RoadExeterEX4 4QDUK
| | - Murray R. Grant
- Biosciences, College of Life and Environmental SciencesUniversity of ExeterGeoffrey Pope Building, Stocker RoadExeterEX4 4QDUK
- School of Life Sciences, Gibbet Hill CampusUniversity of WarwickCoventryCV4 7ALUK
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18
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Lim KH, Song MH, Baek KH. Decision for cell fate: deubiquitinating enzymes in cell cycle checkpoint. Cell Mol Life Sci 2016; 73:1439-55. [PMID: 26762302 PMCID: PMC11108577 DOI: 10.1007/s00018-015-2129-2] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2015] [Revised: 12/03/2015] [Accepted: 12/30/2015] [Indexed: 09/29/2022]
Abstract
All organs consisting of single cells are consistently maintaining homeostasis in response to stimuli such as free oxygen, DNA damage, inflammation, and microorganisms. The cell cycle of all mammalian cells is regulated by protein expression in the right phase to respond to proliferation and apoptosis signals. Post-translational modifications (PTMs) of proteins by several protein-editing enzymes are associated with cell cycle regulation by their enzymatic functions. Ubiquitination, one of the PTMs, is also strongly related to cell cycle regulation by protein degradation or signal transduction. The importance of deubiquitinating enzymes (DUBs), which have a reversible function for ubiquitination, has recently suggested that the function of DUBs is also important for determining the fate of proteins during cell cycle processing. This article reviews and summarizes the diverse roles of DUBs, including DNA damage, cell cycle processing, and regulation of histone proteins, and also suggests the possibility for therapeutic targets.
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Affiliation(s)
- Key-Hwan Lim
- Department of Biomedical Science, CHA University, 335 Pangyo-Ro, Bundang-Gu, Seongnam-Si, Gyeonggi-Do, 463-400, Republic of Korea
| | - Myoung-Hyun Song
- Department of Biomedical Science, CHA University, 335 Pangyo-Ro, Bundang-Gu, Seongnam-Si, Gyeonggi-Do, 463-400, Republic of Korea
| | - Kwang-Hyun Baek
- Department of Biomedical Science, CHA University, 335 Pangyo-Ro, Bundang-Gu, Seongnam-Si, Gyeonggi-Do, 463-400, Republic of Korea.
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19
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Dolbniak M, Kimmel M, Smieja J. Modeling epigenetic regulation of PRC1 protein accumulation in the cell cycle. Biol Direct 2015; 10:62. [PMID: 26458878 PMCID: PMC4603771 DOI: 10.1186/s13062-015-0078-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Accepted: 09/02/2015] [Indexed: 12/18/2022] Open
Abstract
Background Epigenetic regulation contributes to many important processes in biological cells. Examples include developmental processes, differentiation and maturation of stem cells, evolution of malignancy and other. Cell cycle regulation has been subject of mathematical modeling by a number of authors that resulted in many interesting models and application of analytic techniques ranging from stochastic processes to partial differential equations and to integral, functional and operator equations. In this paper we address the question of how the regulation of protein contents influences the long-term dynamics of the population. To accomplish this, we follow the philosophy of a 1984 model by Kimmel et al., but adjust the details to fit the experimental data on protein PRC1 from a more recent paper. Results We built a model of cell cycle dynamics of the PRC1 and fitted it to the data made available by Cohen and his co-authors. We have run the model for a large number of cell generations, recording the PRC1 contents in all cells of the resulting pedigree, at constant time intervals. During cell division the PRC1 is unequally divided between daughter cells. The picture emerging from simulations of Data set 1 is that of a very well-tuned regulatory circuit that provides a stable distribution of PRC1 contents and interdivision times. Data set 2 seems qualitatively different, with more variation in cell cycle duration. Conclusions The main question we address is whether the regulatory feedbacks deduced from single cell cycle data provide epigenetic regulation of cell characteristics in long run. PRC1 is a good candidate because of its role in setting timing of division. Findings of the current paper include tight regulation of the cell cycle (particularly the timing of the cell cycle) even that PRC1 is only one of the players in cell dynamics. Understanding that association, even close, does not necessarily imply causation, we consider this an interesting and important result. Reviewers This article was reviewed by Ollivier Hyrien, Anna Marciniak-Czochra and Alberto d’Onofrio.
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Affiliation(s)
- Marzena Dolbniak
- Systems Engineering Group, Silesian University of Technology, Akademicka 16, 44-100, Gliwice, Poland.
| | - Marek Kimmel
- Systems Engineering Group, Silesian University of Technology, Akademicka 16, 44-100, Gliwice, Poland. .,Departments of Statistics and Bioengineering, Rice University, MS 138, 6100 Main, Houston, TX, 77005, USA.
| | - Jaroslaw Smieja
- Systems Engineering Group, Silesian University of Technology, Akademicka 16, 44-100, Gliwice, Poland.
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Chemical proteomics reveals a γH2AX-53BP1 interaction in the DNA damage response. Nat Chem Biol 2015; 11:807-14. [PMID: 26344695 PMCID: PMC4589150 DOI: 10.1038/nchembio.1908] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Accepted: 08/12/2015] [Indexed: 11/16/2022]
Abstract
DNA double-strand break repair involves phosphorylation of histone variant H2AX (‘γH2AX’), which accumulates in foci at sites of damage. In current models, the recruitment of multiple DNA repair proteins to γH2AX foci depends mainly on recognition of this ‘mark’ by a single protein, MDC1. However, DNA repair proteins accumulate at γH2AX sites without MDC1, suggesting that other ‘readers’ exist. Here, we use a quantitative chemical proteomics approach to profile direct, phospho-selective γH2AX binders in native proteomes. We identify γH2AX binders, including the DNA repair mediator, 53BP1, which we show recognizes γH2AX through its BRCT domains. Furthermore, we investigate targeting of wild-type 53BP1 or a mutant form deficient in γH2AX binding, to chromosomal breaks resulting from endogenous and exogenous DNA damage. Our results show how direct recognition of γH2AX modulates protein localization at DNA damage sites, and suggest how specific chromatin ‘mark’-‘reader’ interactions contribute to essential mechanisms ensuring genome stability.
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Abstract
USP7 is a protein deubiquitinase with an essential role in development. Here, we provide evidence that USP7 regulates the activity of Polycomb repressive complex 1 (PRC1) in coordination with SCML2. There are six versions of PRC1 defined by the association of one of the PCGF homologues (PCGF1 to PCGF6) with the common catalytic subunit RING1B. First, we show that SCML2, a Polycomb group protein that associates with PRC1.2 (containing PCGF2/MEL18) and PRC1.4 (containing PCGF4/BMI1), modulates the localization of USP7 and bridges USP7 with PRC1.4, allowing for the stabilization of BMI1. Chromatin immunoprecipitation (ChIP) experiments demonstrate that USP7 is found at SCML2 and BMI1 target genes. Second, inhibition of USP7 leads to a reduction in the level of ubiquitinated histone H2A (H2Aub), the catalytic product of PRC1 and key for its repressive activity. USP7 regulates the posttranslational status of RING1B and BMI1, a specific component of PRC1.4. Thus, not only does USP7 stabilize PRC1 components, its catalytic activity is also necessary to maintain a functional PRC1, thereby ensuring appropriate levels of repressive H2Aub.
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Stabilization of ATF5 by TAK1-Nemo-like kinase critically regulates the interleukin-1β-stimulated C/EBP signaling pathway. Mol Cell Biol 2014; 35:778-88. [PMID: 25512613 DOI: 10.1128/mcb.01228-14] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Interleukin-1β (IL-1β) is a key proinflammatory cytokine that initiates several signaling cascades, including those involving CCAAT/enhancer binding proteins (C/EBPs). The mechanism by which IL-1β propagates a signal that activates C/EBP has remained elusive. Nemo-like kinase (NLK) is a mitogen-activated protein kinase (MAPK)-like kinase associated with many pathways and phenotypes that are not yet well understood. Using a luciferase reporter screen, we found that IL-1β-induced C/EBP activation was positively regulated by NLK. Overexpression of NLK activated C/EBP and potentiated IL-1β-triggered C/EBP activation, whereas knockdown or knockout of NLK had the opposite effect. NLK interacted with activating transcription factor 5 (ATF5) and inhibited the proteasome-dependent degradation of ATF5 in a kinase-independent manner. Consistently, NLK deficiency resulted in decreased levels of ATF5. NLK cooperated with ATF5 to activate C/EBP, whereas NLK could not activate C/EBP upon knockdown of ATF5. Moreover, TAK1, a downstream effector of IL-1β that acts upstream of NLK, mimicked the ability of NLK to stabilize ATF5 and activate C/EBP. Thus, our findings reveal the TAK1-NLK pathway as a novel regulator of basal or IL-1β-triggered C/EBP activation though stabilization of ATF5.
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