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Rong Q, Xi Z, Guo D, Xu W, Zhang L, Wu Q. Regulation of ubiquitination and antiviral activity of Cactin by deubiquitinase Usp14 in Drosophila. J Virol 2024; 98:e0017724. [PMID: 38563731 PMCID: PMC11092352 DOI: 10.1128/jvi.00177-24] [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: 01/25/2024] [Accepted: 03/10/2024] [Indexed: 04/04/2024] Open
Abstract
Cactin, a highly conserved protein, plays a crucial role in various physiological processes in eukaryotes, including innate immunity. Recently, the function of Cactin in the innate immunity of Drosophila has been explored, revealing that Cactin regulates a non-canonical signaling pathway associated with the Toll and Imd pathways via the Cactin-Deaf1 axis. In addition, Cactin exhibits specific antiviral activity against the Drosophila C virus (DCV) in Drosophila, with an unknown mechanism. During DCV infection, it has been confirmed that the protein level and antiviral activity of Cactin are regulated by ubiquitination. However, the precise ubiquitination and deubiquitination mechanisms of Cactin in Drosophila remain unexplored. In this study, we identified ubiquitin-specific protease 14 (Usp14) as a major deubiquitinase for Cactin through comprehensive deubiquitinase screening. Our results demonstrate that Usp14 interacts with the C_Cactus domain of Cactin via its USP domain. Usp14 efficiently removes K48- and K63-linked polyubiquitin chains from Cactin, thereby preventing its degradation through the ubiquitin-proteasome pathway. Usp14 significantly inhibits DCV replication in Drosophila cells by stabilizing Cactin. Moreover, Usp14-deficient fruit flies exhibit increased susceptibility to DCV infection compared to wild-type flies. Collectively, our findings reveal the regulation of ubiquitination and antiviral activity of Cactin by the deubiquitinase Usp14, providing valuable insights into the modulation of Cactin-mediated antiviral activity in Drosophila.IMPORTANCEViral infections pose a severe threat to human health, marked by high pathogenicity and mortality rates. Innate antiviral pathways, such as Toll, Imd, and JAK-STAT, are generally conserved across insects and mammals. Recently, the multi-functionality of Cactin in innate immunity has been identified in Drosophila. In addition to regulating a non-canonical signaling pathway through the Cactin-Deaf1 axis, Cactin exhibits specialized antiviral activity against the Drosophila C virus (DCV) with an unknown mechanism. A previous study emphasized the significance of the Cactin level, regulated by the ubiquitin-proteasome pathway, in modulating antiviral signaling. However, the regulatory mechanisms governing Cactin remain unexplored. In this study, we demonstrate that Usp14 stabilizes Cactin by preventing its ubiquitination and subsequent degradation. Furthermore, Usp14 plays a crucial role in regulating the antiviral function mediated by Cactin. Therefore, our findings elucidate the regulatory mechanism of Cactin in Drosophila, offering a potential target for the prevention and treatment of viral infections.
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Affiliation(s)
- Qiqi Rong
- Department of Pharmacy, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
- Key Laboratory of Anhui Province for Emerging and Reemerging Infectious Diseases, University of Science and Technology of China, Hefei, China
| | - Zhichong Xi
- Department of Pharmacy, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Dongyang Guo
- Department of Pharmacy, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
- Key Laboratory of Anhui Province for Emerging and Reemerging Infectious Diseases, University of Science and Technology of China, Hefei, China
| | - Wen Xu
- Department of Pharmacy, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
- Anhui Provincial Key Laboratory of Precision Pharmaceutical Preparations and Clinical Pharmacy, Hefei, Anhui, China
| | - Liqin Zhang
- Department of Pharmacy, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
- Department of Immunology and Pathogen Biology, School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou, China
| | - Qingfa Wu
- Department of Pharmacy, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
- Division of Molecular Medicine, CAS Key Laboratory of Innate Immunity and Chronic Disease, University of Science and Technology of China, Hefei, Anhui, China
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2
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Li P, Zhang Z, Xiao G, Zhao Z, He K, Yang X, Pan Q, Mi G, Jia Z, Yan J, Chen F, Yuan L. Genomic basis determining root system architecture in maize. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:102. [PMID: 38607439 DOI: 10.1007/s00122-024-04606-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Accepted: 03/21/2024] [Indexed: 04/13/2024]
Abstract
KEY MESSAGE A total of 389 and 344 QTLs were identified by GWAS and QTL mapping explaining accumulatively 32.2-65.0% and 23.7-63.4% of phenotypic variation for 14 shoot-borne root traits using more than 1300 individuals across multiple field trails. Efficient nutrient and water acquisition from soils depends on the root system architecture (RSA). However, the genetic determinants underlying RSA in maize remain largely unexplored. In this study, we conducted a comprehensive genetic analysis for 14 shoot-borne root traits using 513 inbred lines and 800 individuals from four recombinant inbred line (RIL) populations at the mature stage across multiple field trails. Our analysis revealed substantial phenotypic variation for these 14 root traits, with a total of 389 and 344 QTLs identified through genome-wide association analysis (GWAS) and linkage analysis, respectively. These QTLs collectively explained 32.2-65.0% and 23.7-63.4% of the trait variation within each population. Several a priori candidate genes involved in auxin and cytokinin signaling pathways, such as IAA26, ARF2, LBD37 and CKX3, were found to co-localize with these loci. In addition, a total of 69 transcription factors (TFs) from 27 TF families (MYB, NAC, bZIP, bHLH and WRKY) were found for shoot-borne root traits. A total of 19 genes including PIN3, LBD15, IAA32, IAA38 and ARR12 and 19 GWAS signals were overlapped with selective sweeps. Further, significant additive effects were found for root traits, and pyramiding the favorable alleles could enhance maize root development. These findings could contribute to understand the genetic basis of root development and evolution, and provided an important genetic resource for the genetic improvement of root traits in maize.
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Affiliation(s)
- Pengcheng Li
- State Key Laboratory of Nutrient Use and Management, College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, China Agricultural University, Beijing, 100193, China
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou, 225009, China
| | - Zhihai Zhang
- State Key Laboratory of Nutrient Use and Management, College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, China Agricultural University, Beijing, 100193, China
| | - Gui Xiao
- State Key Laboratory of Nutrient Use and Management, College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, China Agricultural University, Beijing, 100193, China
| | - Zheng Zhao
- State Key Laboratory of Nutrient Use and Management, College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, China Agricultural University, Beijing, 100193, China
| | - Kunhui He
- State Key Laboratory of Nutrient Use and Management, College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, China Agricultural University, Beijing, 100193, China
| | - Xiaohong Yang
- National Maize Improvement Center of China, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Qingchun Pan
- State Key Laboratory of Nutrient Use and Management, College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, China Agricultural University, Beijing, 100193, China
- Key Lab of Plant-Soil Interaction, MOE, Center for Resources, Environment and Food Security, College Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, China
| | - Guohua Mi
- State Key Laboratory of Nutrient Use and Management, College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, China Agricultural University, Beijing, 100193, China
- Key Lab of Plant-Soil Interaction, MOE, Center for Resources, Environment and Food Security, College Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, China
| | - Zhongtao Jia
- State Key Laboratory of Nutrient Use and Management, College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, China Agricultural University, Beijing, 100193, China
- Key Lab of Plant-Soil Interaction, MOE, Center for Resources, Environment and Food Security, College Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, China
| | - Jianbing Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Fanjun Chen
- State Key Laboratory of Nutrient Use and Management, College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, China Agricultural University, Beijing, 100193, China.
- Key Lab of Plant-Soil Interaction, MOE, Center for Resources, Environment and Food Security, College Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, China.
| | - Lixing Yuan
- State Key Laboratory of Nutrient Use and Management, College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, China Agricultural University, Beijing, 100193, China.
- Key Lab of Plant-Soil Interaction, MOE, Center for Resources, Environment and Food Security, College Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, China.
- Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, 100193, China.
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Wu S, Hu C, Zhu C, Fan Y, Zhou J, Xia X, Shi K, Zhou Y, Foyer CH, Yu J. The MYC2-PUB22-JAZ4 module plays a crucial role in jasmonate signaling in tomato. MOLECULAR PLANT 2024; 17:598-613. [PMID: 38341757 DOI: 10.1016/j.molp.2024.02.006] [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: 08/03/2023] [Revised: 12/06/2023] [Accepted: 02/06/2024] [Indexed: 02/13/2024]
Abstract
Jasmonates (JAs), a class of lipid-derived stress hormones, play a crucial role across an array of plant physiological processes and stress responses. Although JA signaling is thought to rely predominantly on the degradation of specific JAZ proteins by SCFCOI1, it remains unclear whether other pathways are involved in the regulation of JAZ protein stability. Here, we report that PUB22, a plant U-box type E3 ubiquitin ligase, plays a critical role in the regulation of plant resistance against Helicoverpa armigera and other JA responses in tomato. Whereas COI1 physically interacts with JAZ1/2/5/7, PUB22 physically interacts with JAZ1/3/4/6. PUB22 ubiquitinates JAZ4 to promote its degradation via the 26S proteasome pathway. Importantly, we observed that pub22 mutants showreduced resistance to H. armigera, whereas jaz4 single mutants and jaz1 jaz3 jaz4 jaz6 quadruple mutants have enhanced resistance. The hypersensitivity of pub22 mutants to herbivores could be partially rescued by JAZ4 mutation. Moreover, we found that expression of PUB22 can be transcriptionally activated by MYC2, thus forming a positive feedback circuit in JA signaling. We noticed that the PUB22-JAZ4 module also regulates other JA responses, including defense against B. cinerea, inhibition of root elongation, and anthocyanin accumulation. Taken together, these results indicate that PUB22 plays a crucial role in plant growth and defense responses, together with COI1-regulated JA signaling, by targeting specific JAZs.
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Affiliation(s)
- Shaofang Wu
- Department of Horticulture, Zijingang Campus, Zhejiang University, Hangzhou 310058, China
| | - Chaoyi Hu
- Department of Horticulture, Zijingang Campus, Zhejiang University, Hangzhou 310058, China; Hainan Institute, Zhejiang University, Yazhou Bay Science and Technology City, Sanya 572025, China
| | - Changan Zhu
- Department of Horticulture, Zijingang Campus, Zhejiang University, Hangzhou 310058, China
| | - Yanfen Fan
- Department of Horticulture, Zijingang Campus, Zhejiang University, Hangzhou 310058, China; College of Horticulture, Northwest Agriculture & Forestry University, Xianyang 712100, China
| | - Jie Zhou
- Department of Horticulture, Zijingang Campus, Zhejiang University, Hangzhou 310058, China
| | - Xiaojia Xia
- Department of Horticulture, Zijingang Campus, Zhejiang University, Hangzhou 310058, China
| | - Kai Shi
- Department of Horticulture, Zijingang Campus, Zhejiang University, Hangzhou 310058, China
| | - Yanhong Zhou
- Department of Horticulture, Zijingang Campus, Zhejiang University, Hangzhou 310058, China
| | - Christine H Foyer
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Edgbaston B15 2TT, UK
| | - Jingquan Yu
- Department of Horticulture, Zijingang Campus, Zhejiang University, Hangzhou 310058, China; Hainan Institute, Zhejiang University, Yazhou Bay Science and Technology City, Sanya 572025, China; Key Laboratory of Horticultural Plants Growth and Development, Agricultural Ministry of China, Zhejiang University, Hangzhou 310058, China.
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4
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Fry M. The discovery of archaea: from observed anomaly to consequential restructuring of the phylogenetic tree. HISTORY AND PHILOSOPHY OF THE LIFE SCIENCES 2024; 46:16. [PMID: 38530473 DOI: 10.1007/s40656-024-00616-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 02/14/2024] [Indexed: 03/28/2024]
Abstract
Observational and experimental discoveries of new factual entities such as objects, systems, or processes, are major contributors to some advances in the life sciences. Yet, whereas discovery of theories was extensively deliberated by philosophers of science, very little philosophical attention was paid to the discovery of factual entities. This paper examines historical and philosophical aspects of the experimental discovery by Carl Woese of archaea, prokaryotes that comprise one of the three principal domains of the phylogenetic tree. Borrowing Kuhn's terminology, this discovery of a major biological entity was made during a 'normal science' project of building molecular taxonomy for prokaryotes. Unexpectedly, however, an observed anomaly instigated the discovery of archaea. Substantiation of the existence of the new archaeal entity and consequent reconstruction of the phylogenetic tree prompted replacement of a long-held model of a prokarya and eukarya bipartite tree of life by a new model of a tripartite tree comprising of bacteria, archaea, and eukarya. This paper explores the history and philosophical implications of the progression of Woese's project from normal science to anomaly-instigated model-changing discovery. It is also shown that the consequential discoveries of RNA splicing and of ribozymes were similarly prompted by unexpected irregularities during normal science activities. It is thus submitted that some discoveries of factual biological entities are triggered by unforeseen observational or experimental anomalies.
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Affiliation(s)
- Michael Fry
- Department of Biochemistry, Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Efron St., Bat Galim, POB 9649, Haifa, 31096, Israel.
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5
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Li H, Ma YP, Wang HL, Tian CJ, Guo YX, Zhang HB, Liu XM, Liu PF. Establishment of a prognosis predictive model for liver cancer based on expression of genes involved in the ubiquitin-proteasome pathway. World J Clin Oncol 2024; 15:434-446. [PMID: 38576590 PMCID: PMC10989257 DOI: 10.5306/wjco.v15.i3.434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 12/27/2023] [Accepted: 02/05/2024] [Indexed: 03/22/2024] Open
Abstract
BACKGROUND The ubiquitin-proteasome pathway (UPP) has been proven to play important roles in cancer. AIM To investigate the prognostic significance of genes involved in the UPP and develop a predictive model for liver cancer based on the expression of these genes. METHODS In this study, UPP-related E1, E2, E3, deubiquitylating enzyme, and proteasome gene sets were obtained from the Kyoto Encyclopedia of Genes and Genomes (KEGG) database, aiming to screen the prognostic genes using univariate and multivariate regression analysis and develop a prognosis predictive model based on the Cancer Genome Atlas liver cancer cases. RESULTS Five genes (including autophagy related 10, proteasome 20S subunit alpha 8, proteasome 20S subunit beta 2, ubiquitin specific peptidase 17 like family member 2, and ubiquitin specific peptidase 8) were proven significantly correlated with prognosis and used to develop a prognosis predictive model for liver cancer. Among training, validation, and Gene Expression Omnibus sets, the overall survival differed significantly between the high-risk and low-risk groups. The expression of the five genes was significantly associated with immunocyte infiltration, tumor stage, and postoperative recurrence. A total of 111 differentially expressed genes (DEGs) were identified between the high-risk and low-risk groups and they were enriched in 20 and 5 gene ontology and KEGG pathways. Cell division cycle 20, Kelch repeat and BTB domain containing 11, and DDB1 and CUL4 associated factor 4 like 2 were the DEGs in the E3 gene set that correlated with survival. CONCLUSION We have constructed a prognosis predictive model in patients with liver cancer, which contains five genes that associate with immunocyte infiltration, tumor stage, and postoperative recurrence.
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Affiliation(s)
- Hua Li
- Department of Endoscopy, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy of Tianjin, Tianjin’s Clinical Research Center for Cancer, Tianjin 300060, China
| | - Yi-Po Ma
- Department of Critical Care Medicine, Dingzhou City People’s Hospital, Dingzhou 073000, Hebei Province, China
| | - Hai-Long Wang
- Department of Oncology, Tianjin Academy of Traditional Chinese Medicine Affiliated Hospital, Tianjin 300120, China
| | - Cai-Juan Tian
- Tianjin Marvel Medical Laboratory, Tianjin Marvelbio Technology Co., Ltd, Tianjin 300180, China
| | - Yi-Xian Guo
- Department of Intelligent Technology, Tianjin Yunquan Intelligent Technology Co., Ltd, Tianjin 300381, China
| | - Hong-Bo Zhang
- Tianjin Marvel Medical Laboratory, Tianjin Marvelbio Technology Co., Ltd, Tianjin 300180, China
| | - Xiao-Min Liu
- Department of Oncology, Tianjin Huanhu Hospital, Tianjin 300350, China
| | - Peng-Fei Liu
- Department of Oncology, Tianjin Academy of Traditional Chinese Medicine Affiliated Hospital, Tianjin 300120, China
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6
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Yu H, Zhang J, Liu J, Pan R, Wang Y, Jin X, Ahmed RZ, Zheng Y. TBBPA rather than its main derivatives enhanced growth of endometrial cancer via p53 ubiquitination. J Environ Sci (China) 2024; 137:82-95. [PMID: 37980057 DOI: 10.1016/j.jes.2022.12.030] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 12/21/2022] [Accepted: 12/25/2022] [Indexed: 11/20/2023]
Abstract
Tetrabromobisphenol A (TBBPA) and its derivatives widely exist in various environments and biota. Although the available data indicate that TBBPA exposure is highly associated with the increased incidence of endometrial cancer (EC), the effects of TBBPA and its main derivatives on EC proliferation and the involved crucial mechanism remain unclear. The present study aimed to investigate the effects of TBBPA and its derivatives under environmental concentrations on the proliferation of EC, and the crucial mechanism on the progression of EC caused by bromine flame retardants exposure. In this research, TBBPA and two of the most common TBBPA derivatives including TBBPA bis (2-hydroxyethyl ether) (TBBPA-BHEE) and TBBPA bis (dibromopropyl ether) (TBBPA-BDBPE) were screened for their capacities in induced EC proliferation and explored the related mechanism by in vitro cell culture model and in vivo mice model. Under environmental concentrations, TBBPA promoted the proliferation of EC, the main derivatives of TBBPA (TBBPA-BHEE and TBBPA-BDBPE) did not present the similar facilitation effects. The ubiquitination degradation of p53 was crucial in TBBPA induced EC proliferation, which resulted in the increase of downstream cell cycle and decrease of apoptosis. The further molecular docking result suggested the high affinity between TBBPA and ubiquitinated proteasome. This finding revealed the effects of TBBPA and its derivatives on EC proliferation, thus providing novel insights into the underlying mechanisms of TBBPA-caused EC.
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Affiliation(s)
- Hongyan Yu
- Department of Occupational Health and Environmental Health, School of Public Health, Qingdao University, Qingdao 266071, China
| | - Jingxu Zhang
- Department of Occupational Health and Environmental Health, School of Public Health, Qingdao University, Qingdao 266071, China
| | - Jing Liu
- Department of Occupational Health and Environmental Health, School of Public Health, Qingdao University, Qingdao 266071, China
| | - Ruonan Pan
- Department of Occupational Health and Environmental Health, School of Public Health, Qingdao University, Qingdao 266071, China
| | - Yu Wang
- Department of Occupational Health and Environmental Health, School of Public Health, Qingdao University, Qingdao 266071, China
| | - Xiaoting Jin
- Department of Occupational Health and Environmental Health, School of Public Health, Qingdao University, Qingdao 266071, China.
| | - Rifat Zubair Ahmed
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; Department of Genetics, University of Karachi, Karachi 75270, Pakistan
| | - Yuxin Zheng
- Department of Occupational Health and Environmental Health, School of Public Health, Qingdao University, Qingdao 266071, China
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7
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Ma Y, Huang L, Zhang Z, Yang P, Chen Q, Zeng X, Tan F, Wang C, Ruan X, Liao X. CD36 promotes tubular ferroptosis by regulating the ubiquitination of FSP1 in acute kidney injury. Genes Dis 2024; 11:449-463. [PMID: 37588197 PMCID: PMC10425750 DOI: 10.1016/j.gendis.2022.12.003] [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: 09/12/2022] [Revised: 11/20/2022] [Accepted: 12/01/2022] [Indexed: 01/05/2023] Open
Abstract
Reactive oxidative species (ROS) production-driven ferroptosis plays a role in acute kidney injury (AKI). However, its exact molecular mechanism is poorly understood. Scavenger receptor CD36 has important roles in oxidizing lipids, lipid accumulation, metabolic syndrome, and insulin resistance in chronic kidney disease, but its roles remain unexplored in AKI. The present study investigated the role and mechanism of CD36 in regulating proximal tubular cell ferroptosis and AKI. The expression of CD36 was found to be significantly up-regulated in AKI renal tissues and correlated with renal function, which might serve as an independent biomarker for AKI patients. Moreover, in adult mice subjected to AKI, deletion of CD36 (CD36-/-) induced tubular cell ROS accumulation, ferroptosis activation, and renal injury. Mechanistically, combining LC-MS/MS, co-IP, and ubiquitination analyses revealed that CD36 could specifically bind to ferroptosis suppressor protein 1 (FSP1) and regulate its ubiquitination at sites K16 and K24, leading to FSP1 degradation and progression of ferroptosis in AKI. The present results emphasize a novel mechanism of CD36 in cisplatin-induced AKI. The discovery of the special CD36 roles in promoting ferroptosis and AKI development by regulating the ubiquitination of FSP1 in proximal tubular cells may be potential therapeutic targets for AKI. Moreover, CD36 may play a key role in the progression of AKI. Therefore, targeting CD36 may provide a promising treatment option for AKI.
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Affiliation(s)
- Yixin Ma
- Department of Nephrology, The Second Affiliated Hospital, Chongqing Medical University, Chongqing 400010, China
| | - Lili Huang
- Department of Nephrology, The Second Affiliated Hospital, Chongqing Medical University, Chongqing 400010, China
| | - Zheng Zhang
- Department of Nephrology, The Second Affiliated Hospital, Chongqing Medical University, Chongqing 400010, China
- Department of Cell Biology and Genetics, Chongqing Medical University, Chongqing 400016, China
| | - Pengfei Yang
- Department of Nephrology, The Second Affiliated Hospital, Chongqing Medical University, Chongqing 400010, China
| | - Qingsong Chen
- Department of Nephrology, The Second Affiliated Hospital, Chongqing Medical University, Chongqing 400010, China
| | - Xujia Zeng
- Department of Nephrology, The Second Affiliated Hospital, Chongqing Medical University, Chongqing 400010, China
| | - Fangyan Tan
- Department of Nephrology, The Second Affiliated Hospital, Chongqing Medical University, Chongqing 400010, China
| | - Chunxia Wang
- Department of Nephrology, The Second Affiliated Hospital, Chongqing Medical University, Chongqing 400010, China
| | - Xiongzhong Ruan
- Centre for Nephrology, Royal Free and University College Medical School, University College London, Royal Free Campus, Rowland Hill Street, London NW3 2PF, United Kingdom
- Centre for Lipid Research, Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, Chongqing Medical University, Chongqing 400016, China
- Kuanren Laboratory of Translational Lipidology, Centre for Lipid Research, Second Affiliated Hospital of Chongqing Medical University, Chongqing 400010, China
| | - Xiaohui Liao
- Department of Nephrology, The Second Affiliated Hospital, Chongqing Medical University, Chongqing 400010, China
- Kuanren Laboratory of Translational Lipidology, Centre for Lipid Research, Second Affiliated Hospital of Chongqing Medical University, Chongqing 400010, China
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8
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Zhang D, Zhang X, Liu Z, Ma X, Li H, Shen M, Chen J, Liu H. Diosmin Promotes Myogenesis via Activating the Akt/FOXO1 Pathway to Facilitate the Proliferation of C2C12 Myoblasts. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:19705-19716. [PMID: 38029323 PMCID: PMC10723065 DOI: 10.1021/acs.jafc.3c04828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 11/09/2023] [Accepted: 11/15/2023] [Indexed: 12/01/2023]
Abstract
Our previous study with artificial intelligence (AI)-assisted screening found that diosmin, a natural flavonoid extracted from citrus, may affect myoblast proliferation and differentiation. At present, few studies have been conducted regarding the biological function of diosmin in muscle cells. Here, using molecular biological techniques, we found that diosmin elevated the proliferation ability of C2C12 myoblasts via activating the Akt/FOXO1 pathway to promote FOXO1 nuclear export, thus repressing p27 protein expression, increasing CDK2, CDK4, and cyclin D1 and cyclin E1 protein expression and accelerating cell cycle transformation, which contributed to myogenesis. Moreover, diosmin suppressed differentiation of C2C12 myoblasts by delaying the terminal exit of the cell cycle in early differentiated myoblasts and inhibiting autophagic flux in mature myotubes. Furthermore, diosmin promoted myogenesis by activating the Akt/FOXO1 pathway to facilitate myoblast proliferation, which had a positive biological effect on the repair of muscle injury. This study revealed the effect and mechanism of diosmin on skeletal muscle cells and simultaneously provided a new candidate drug for the treatment of myopathy.
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Affiliation(s)
- Dingding Zhang
- Department of Animal
Genetics,
Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Xuan Zhang
- Department of Animal
Genetics,
Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhaojun Liu
- Department of Animal
Genetics,
Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiangfei Ma
- Department of Animal
Genetics,
Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Hongmin Li
- Department of Animal
Genetics,
Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Ming Shen
- Department of Animal
Genetics,
Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Jie Chen
- Department of Animal
Genetics,
Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Honglin Liu
- Department of Animal
Genetics,
Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
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9
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Ma Q, Feng Y, Luo S, Cheng L, Tong W, Lu X, Li Y, Zhang P. The aquaporin MePIP2;7 improves MeMGT9-mediated Mg 2 + acquisition in cassava. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:2349-2367. [PMID: 37548108 DOI: 10.1111/jipb.13552] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 08/03/2023] [Indexed: 08/08/2023]
Abstract
Aquaporins are important transmembrane water transport proteins which transport water and several neutral molecules. However, how aquaporins are involved in the synergistic transport of Mg2+ and water remains poorly understood. Here, we found that the cassava aquaporin MePIP2;7 was involved in Mg2+ transport through interaction with MeMGT9, a lower affinity magnesium transporter protein. Knockdown of MePIP2;7 in cassava led to magnesium deficiency in basal mature leaves with chlorosis and necrotic spots on their edges and starch over-accumulation. Mg2+ content was significantly decreased in leaves and roots of MePIP2;7-RNA interference (PIP-Ri) plants grown in both field and Mg2+ -free hydroponic solution. Xenopus oocyte injection analysis verified that MePIP2;7 possessed the ability to transport water only and MeMGT9 was responsible for Mg2+ efflux. More importantly, MePIP2;7 improved the transportability of Mg2+ via MeMGT9 as verified using the CM66 mutant complementation assay and Xenopus oocytes expressing system. Yeast two-hybrid, bimolecular fluorescence complementation, co-localization, and co-immunoprecipitation assays demonstrated the direct protein-protein interaction between MePIP2;7 and MeMGT9 in vivo. Mg2+ flux was significantly elevated in MePIP2;7-overexpressing lines in hydroponic solution through non-invasive micro-test technique analysis. Under Mg2+ -free condition, the retarded growth of PIP-Ri transgenic plants could be recovered with Mg2+ supplementation. Taken together, our results demonstrated the synergistic effect of the MePIP2;7 and MeMGT9 interaction in regulating water and Mg2+ absorption and transport in cassava.
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Affiliation(s)
- Qiuxiang Ma
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Yancai Feng
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shu Luo
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lu Cheng
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Weijing Tong
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xinlu Lu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Youzhi Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/College of Life Science and Technology, Guangxi University, Nanning, 530004, China
| | - Peng Zhang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
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10
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Zhou H, Tan W, Shi S. DeepGpgs: a novel deep learning framework for predicting arginine methylation sites combined with Gaussian prior and gated self-attention mechanism. Brief Bioinform 2023; 24:7000314. [PMID: 36694944 DOI: 10.1093/bib/bbad018] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 12/26/2022] [Accepted: 01/04/2023] [Indexed: 01/26/2023] Open
Abstract
Protein arginine methylation is an important posttranslational modification (PTM) associated with protein functional diversity and pathological conditions including cancer. Identification of methylation binding sites facilitates a better understanding of the molecular function of proteins. Recent developments in the field of deep neural networks have led to a proliferation of deep learning-based methylation identification studies because of their fast and accurate prediction. In this paper, we propose DeepGpgs, an advanced deep learning model incorporating Gaussian prior and gated attention mechanism. We introduce a residual network channel to extract the evolutionary information of proteins. Then we combine the adaptive embedding with bidirectional long short-term memory networks to form a context-shared encoder layer. A gated multi-head attention mechanism is followed to obtain the global information about the sequence. A Gaussian prior is injected into the sequence to assist in predicting PTMs. We also propose a weighted joint loss function to alleviate the false negative problem. We empirically show that DeepGpgs improves Matthews correlation coefficient by 6.3% on the arginine methylation independent test set compared with the existing state-of-the-art methylation site prediction methods. Furthermore, DeepGpgs has good robustness in phosphorylation site prediction of SARS-CoV-2, which indicates that DeepGpgs has good transferability and the potential to be extended to other modification sites prediction. The open-source code and data of the DeepGpgs can be obtained from https://github.com/saizhou1/DeepGpgs.
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Affiliation(s)
- Haiwei Zhou
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai 200433, China
| | - Wenxi Tan
- School of Mathematical Sciences, Fudan University, Shanghai 200433, China
| | - Shaoping Shi
- Department of Mathematics, School of Mathematics and Computer Sciences, Nanchang University, Nanchang 330031, China
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11
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Lu C, Lu P, Gong L, Zhu LJ, An Y, Wang Y. Rational design and development of novel NAE inhibitors for the treatment of pancreatic cancer. Med Chem Res 2023. [DOI: 10.1007/s00044-022-02979-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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12
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Dutta S, Smith MD. Detection of Protein-Protein Interactions Utilizing the Split-Ubiquitin Membrane-Based Yeast Two-Hybrid System. Methods Mol Biol 2023; 2690:37-57. [PMID: 37450135 DOI: 10.1007/978-1-0716-3327-4_4] [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] [Indexed: 07/18/2023]
Abstract
Identifying the interactors of a protein is a key step in understanding its possible cellular function(s). Among the various methods that can be used to study protein-protein interactions (PPIs), the yeast two-hybrid (Y2H) assay is one of the most standardized, sensitive, and cost-effective in vivo methods available. The most commonly used GAL4-based Y2H system utilizes the yeast transcription factor GAL4 to detect interactions between soluble proteins. By virtue of involving a transcription factor, the protein-protein interactions occur in the nucleus. The split-ubiquitin Y2H system offers an alternative to the traditional GAL4-based Y2H system and takes advantage of the reconstitution of split-ubiquitin in the cytosol to identify interactions between two proteins. Moreover, new membranous and soluble interacting partner(s) can be identified by screening a target protein against proteins produced from a cDNA library using this system.
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Affiliation(s)
- Siddhartha Dutta
- Department of Microbiology and Biotechnology, Sister Nivedita University, Kolkata, West Bengal, India
| | - Matthew D Smith
- Department of Biology, Wilfrid Laurier University, Waterloo, ON, Canada.
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13
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ITCH deficiency clinical phenotype expansion and mitochondrial dysfunction. Mol Genet Metab Rep 2022; 33:100932. [PMID: 36338154 PMCID: PMC9634006 DOI: 10.1016/j.ymgmr.2022.100932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Revised: 10/20/2022] [Accepted: 10/22/2022] [Indexed: 11/07/2022] Open
Abstract
Autoimmune Disease, Multisystem, with Facial Dysmorphism (ADMFD) is an autosomal recessive disorder due to pathogenic variants in the ITCH gene. It is characterized by failure to thrive, dysmorphic facial features, developmental delay, and systemic autoimmunity that can manifest variably with autoimmune hepatitis, thyroiditis, and enteropathy, among other organ manifestations. It was originally described in 10 consanguineous Old Order Amish patients, and more recently in two patients of White British and Black German ethnicities. While the role of ITCH protein in apoptosis and inflammation has previously been characterized, a defect in cellular bioenergetics has not yet been reported in ITCH deficiency. Here we present a Caucasian female originally evaluated for possible mitochondrial respiratory chain deficiency, who ultimately was found to have two novel variants in ITCH with absence of ITCH protein in patient derived fibroblasts. Clinical studies of patient muscle showed mitochondrial DNA copy number of 57% compared to controls. Functional studies in skin fibroblasts revealed decreased activity of mitochondrial fatty acid oxidation and oxidative phosphorylation, and decreased overall ATP production. Our findings confirm mitochondrial energy dysfunction in a patient with ITCH deficiency offering the opportunity to assess alternative therapeutic options.
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14
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Paul D, Kales SC, Cornwell JA, Afifi MM, Rai G, Zakharov A, Simeonov A, Cappell SD. Revealing β-TrCP activity dynamics in live cells with a genetically encoded biosensor. Nat Commun 2022; 13:6364. [PMID: 36289220 PMCID: PMC9606124 DOI: 10.1038/s41467-022-33762-3] [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: 05/06/2022] [Accepted: 09/30/2022] [Indexed: 12/25/2022] Open
Abstract
The F-box protein beta-transducin repeat containing protein (β-TrCP) acts as a substrate adapter for the SCF E3 ubiquitin ligase complex, plays a crucial role in cell physiology, and is often deregulated in many types of cancers. Here, we develop a fluorescent biosensor to quantitatively measure β-TrCP activity in live, single cells in real-time. We find β-TrCP remains constitutively active throughout the cell cycle and functions to maintain discreet steady-state levels of its substrates. We find no correlation between expression levels of β-TrCP and β-TrCP activity, indicating post-transcriptional regulation. A high throughput screen of small-molecules using our reporter identifies receptor-tyrosine kinase signaling as a key axis for regulating β-TrCP activity by inhibiting binding between β-TrCP and the core SCF complex. Our study introduces a method to monitor β-TrCP activity in live cells and identifies a key signaling network that regulates β-TrCP activity throughout the cell cycle.
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Affiliation(s)
- Debasish Paul
- grid.48336.3a0000 0004 1936 8075Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892 USA
| | - Stephen C. Kales
- grid.94365.3d0000 0001 2297 5165National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD 20850 USA
| | - James A. Cornwell
- grid.48336.3a0000 0004 1936 8075Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892 USA
| | - Marwa M. Afifi
- grid.48336.3a0000 0004 1936 8075Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892 USA
| | - Ganesha Rai
- grid.94365.3d0000 0001 2297 5165National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD 20850 USA
| | - Alexey Zakharov
- grid.94365.3d0000 0001 2297 5165National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD 20850 USA
| | - Anton Simeonov
- grid.94365.3d0000 0001 2297 5165National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD 20850 USA
| | - Steven D. Cappell
- grid.48336.3a0000 0004 1936 8075Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892 USA
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15
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Osana S, Kitajima Y, Naoki S, Takada H, Murayama K, Kano Y, Nagatomi R. Little involvement of recycled-amino acids from proteasomal proteolysis in de novo protein synthesis. Biochem Biophys Res Commun 2022; 634:40-47. [DOI: 10.1016/j.bbrc.2022.09.113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Accepted: 09/28/2022] [Indexed: 11/27/2022]
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16
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Oliveira RI, Guedes RA, Salvador JAR. Highlights in USP7 inhibitors for cancer treatment. Front Chem 2022; 10:1005727. [PMID: 36186590 PMCID: PMC9520255 DOI: 10.3389/fchem.2022.1005727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 08/22/2022] [Indexed: 11/13/2022] Open
Abstract
Ubiquitin-specific protease 7 (USP7) is a member of one of the most largely studied families of deubiquitylating enzymes. It plays a key role modulating the levels of multiple proteins, including tumor suppressors, transcription factors, epigenetic modulators, DNA repair proteins, and regulators of the immune response. The abnormal expression of USP7 is found in various malignant tumors and a high expression signature generally indicates poor tumor prognosis. This suggests USP7 as a promising prognostic and druggable target for cancer therapy. Nonetheless, no approved drugs targeting USP7 have already entered clinical trials. Therefore, the development of potent and selective USP7 inhibitors still requires intensive research and development efforts before the pre-clinical benefits translate into the clinic. This mini review systematically summarizes the role of USP7 as a drug target for cancer therapeutics, as well as the scaffolds, activities, and binding modes of some of the most representative small molecule USP7 inhibitors reported in the scientific literature. To wind up, development challenges and potential combination therapies using USP7 inhibitors for less tractable tumors are also disclosed.
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Affiliation(s)
- Rita I. Oliveira
- Laboratory of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Coimbra, Coimbra, Portugal
- Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
| | - Romina A. Guedes
- Laboratory of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Coimbra, Coimbra, Portugal
- Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
| | - Jorge A. R. Salvador
- Laboratory of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Coimbra, Coimbra, Portugal
- Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
- *Correspondence: Jorge A. R. Salvador,
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17
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Yang W, Li X, Jiang G, Long Y, Li H, Yu S, Zhao H, Liu J. Crotonylation versus acetylation in petunia corollas with reduced acetyl-CoA due to PaACL silencing. PHYSIOLOGIA PLANTARUM 2022; 174:e13794. [PMID: 36193016 DOI: 10.1111/ppl.13794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 09/08/2022] [Accepted: 09/29/2022] [Indexed: 06/16/2023]
Abstract
Protein acetylation and crotonylation are important posttranslational modifications of lysine. In animal cells, the correlation of acetylation and crotonylation has been well characterized and the lysines of some proteins are acetylated or crotonylated depending on the relative concentrations of acetyl-CoA and crotonyl-CoA. However, in plants, the correlation of acetylation and crotonylation and the effects of the relative intracellular concentrations of crotonyl-CoA and acetyl-CoA on protein crotonylation and acetylation are not well known. In our previous study, PaACL silencing changed the content of acetyl-CoA in petunia (Petunia hybrida) corollas, and the effect of PaACL silencing on the global acetylation proteome in petunia was analyzed. In the present study, we found that PaACL silencing did not significantly alter the content of crotonyl-CoA. We performed a global crotonylation proteome analysis of the corollas of PaACL-silenced and control petunia plants; we found that protein crotonylation was closely related to protein acetylation and that proteins with more crotonylation sites often had more acetylation sites. Crotonylated proteins and acetylated proteins were enriched in many common Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. However, PaACL silencing resulted in different KEGG pathway enrichments of proteins with different levels of crotonylation sites and acetylation sites. PaACLB1-B2 silencing did not led to changes in the opposite direction in crotonylation and acetylation levels at the same lysine site in cytoplasmic proteins, which indicated that cytoplasmic lysine acetylation and crotonylation might not depend on the relative concentrations of acetyl-CoA and crotonyl-CoA. Moreover, the global crotonylome and acetylome were weakly positively correlated in the corollas of PaACL-silenced and control plants.
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Affiliation(s)
- Weiyuan Yang
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Xin Li
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Guiyun Jiang
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Yu Long
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Hui Li
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Shujun Yu
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Huina Zhao
- College of Horticulture, South China Agricultural University, Guangzhou, China
- College of Landscape Architecture and Art, Henan Agricultural University, Zhengzhou, China
| | - Juanxu Liu
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
- College of Horticulture, South China Agricultural University, Guangzhou, China
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18
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Mini-review: Recent advances in post-translational modification site prediction based on deep learning. Comput Struct Biotechnol J 2022; 20:3522-3532. [PMID: 35860402 PMCID: PMC9284371 DOI: 10.1016/j.csbj.2022.06.045] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 06/21/2022] [Accepted: 06/21/2022] [Indexed: 11/23/2022] Open
Abstract
Post-translational modifications (PTMs) are closely linked to numerous diseases, playing a significant role in regulating protein structures, activities, and functions. Therefore, the identification of PTMs is crucial for understanding the mechanisms of cell biology and diseases therapy. Compared to traditional machine learning methods, the deep learning approaches for PTM prediction provide accurate and rapid screening, guiding the downstream wet experiments to leverage the screened information for focused studies. In this paper, we reviewed the recent works in deep learning to identify phosphorylation, acetylation, ubiquitination, and other PTM types. In addition, we summarized PTM databases and discussed future directions with critical insights.
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Key Words
- AAindex, Amino acid index
- ATP, Adenosine triphosphate
- AUC, Area under curve
- Ac, Acetylation
- BE, Binary encoding
- BLOSUM, Blocks substitution matrix
- Bi-LSTM, Bidirectional LSTM
- CKSAAP, Composition of k-spaced amino acid Pairs
- CNN, Convolutional neural network
- CNNOH, CNN with the one-hot encoding
- CNNWE, CNN with the word-embedding encoding
- CNNrgb, CNN red green blue
- CV, Cross-validation
- DC-CNN, Densely connected convolutional neural network
- DL, Deep learning
- DNNs, Deep neural networks
- Deep learning
- E. coli, Escherichia coli
- EBGW, Encoding based on grouped weight
- EGAAC, Enhanced grouped amino acids content
- IG, Information gain
- K, Lysine
- KNN, k nearest neighbor
- LASSO, Least absolute shrinkage and selection operator
- LSTM, Long short-term memory
- LSTMWE, LSTM with the word-embedding encoding
- M.musculus, Mus musculus
- MDC, Modular densely connected convolutional networks
- MDCAN, Multilane dense convolutional attention network
- ML, Machine learning
- MLP, Multilayer perceptron
- MMI, Multivariate mutual information
- Machine learning
- Mass spectrometry
- NMBroto, Normalized Moreau-Broto autocorrelation
- P, Proline
- PSP, PhosphoSitePlus
- PSSM, Position-specific scoring matrix
- PTM, Post-translational modifications
- Ph, Phosphorylation
- Post-translational modification
- Prediction
- PseAAC, Pseudo-amino acid composition
- R, Arginine
- RF, Random forest
- RNN, Recurrent neural network
- ROC, Receiver operating characteristic
- S, Serine
- S. typhimurium, Salmonella typhimurium
- S.cerevisiae, Saccharomyces cerevisiae
- SE, Squeeze and excitation
- SEV, Split to Equal Validation
- ST, Source and target
- SUMO, Small ubiquitin-like modifier
- SVM, Support vector machines
- T, Threonine
- Ub, Ubiquitination
- Y, Tyrosine
- ZSL, Zero-shot learning
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Zhou W, Dong G, Gao G, He Z, Xu J, Aziz S, Ma L, Zhao W. Evaluation of HZX-960, a novel DCN1-UBC12 interaction inhibitor, as a potential antifibrotic compound for liver fibrosis. Biochem Cell Biol 2022; 100:309-324. [PMID: 35544948 DOI: 10.1139/bcb-2021-0585] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Liver fibrosis is a very common health problem and currently lacks effective treatments. Cullin ring E3 ligases (CRLs) regulate the turnover of ~20% of mammalian cell proteins. Neddylation, the process by which NEDD8 is covalently attached to cullin proteins through sequential enzymatic reactions, is critical for the activation of CRLs and was recently found to be elevated in liver fibrosis. NEDD8-activating enzyme E1-specific inhibition led to the reduced liver damage characterized by decreased apoptosis, inflammation and fibrosis. However, the relevance of a co-E3 ligase, DCN1, in liver fibrosis remains unclear. Here, a novel and potent DCN1-UBC12 interaction inhibitor HZX-960 was discovered with an IC50 value of 9.37nM, which could inhibit the neddylation of cullin3. Importantly, we identified that HZX-960 treatment could attenuate TGFβ-induced liver fibrotic responses by reducing the deposition of collagen I and α-SMA, and upregulating cellular NRF2, HO-1 and NQO1 level in two hepatic stellate cell lines. Additionally, DCN1 was shown to be unregulated in CCl4-induced mice liver tissue, and liver fibrotic signaling in mice was reduced by HZX-960. Therefore, our data demonstrated that HZX-960 possessed anti-liver fibrosis ability, and DCN1 may be a potential therapeutic target for liver fibrosis treatment.
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Affiliation(s)
- Wenjuan Zhou
- Zhengzhou University, 12636, school of pharmacy, Zhengzhou, Henan, China.,Oslo University Hospital, 155272, Department of Pathology, Oslo, Norway;
| | - Guanjun Dong
- Zhengzhou University, 12636, school of pharmacy, Zhnezhou, China;
| | - Ge Gao
- Zhengzhou University, 12636, school of pharmacy, Zhengzhou, Henan, China;
| | - Zhangxu He
- Zhengzhou University, 12636, school of pharmacy, Zhengzhou, Henan, China;
| | - Jiale Xu
- Zhengzhou University, 12636, school of pharmacy, Zhengzhou, Henan, China;
| | - Shireen Aziz
- Zhengzhou University, 12636, Zhengzhou, Henan, China;
| | - Liying Ma
- Zhengzhou University, 12636, school of pharmacy, Zhengzhou, Henan, China;
| | - Wen Zhao
- Zhengzhou University, 12636, school of pharmacy, Zhengzhou, Henan, China;
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20
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Ubiquitin-specific protease 35 (USP35) mediates cisplatin-induced apoptosis by stabilizing BIRC3 in non-small cell lung cancer. J Transl Med 2022; 102:524-533. [PMID: 35022505 DOI: 10.1038/s41374-021-00725-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Revised: 12/10/2021] [Accepted: 12/14/2021] [Indexed: 12/23/2022] Open
Abstract
Ubiquitin-specific protease 35 (USP35) is a member of the ubiquitin-specific protease family (USP), which influences the progression of multiple cancers by deubiquitinating a variety of substrates. In recent years, the specific role of USP35 was begun to be understood. In this study, we investigated the role and underlying molecular mechanisms of USP35 in chemoresistance of non-small cell lung cancer (NSCLC) to cisplatin. Depletion of USP35 increased the sensitivity of NSCLC to cisplatin-induced apoptosis. We screened and identified a potential substrate of USP35, baculoviral IAP repeat containing 3 (BIRC3). Overexpression of USP35 in H460 cells increased the abundance of BIRC3, while USP35 knockdown in Anip973 cells decreased BIRC3 abundance. Notably, USP35 directly interacted with and stabilized BIRC3 through lys48-mediated polyubiquitination via its deubiquitinating enzyme activity. USP35 alleviated cisplatin-induced cell apoptosis by regulating BIRC3 levels in NSCLC cells. Moreover, a significant positive correlation between USP35 and BIRC3 protein expression levels was observed in human NSCLC tissues. Taken together, USP35 plays a vital role in resistance to cisplatin-induced cell death through the overexpression of BIRC3. USP35 might be a potentially novel therapeutic target in human NSCLC.
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21
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Yu Z, Wei X, Liu L, Sun H, Fang T, Wang L, Li Y, Sui W, Wang K, He Y, Zhao Y, Huang W, An G, Meng F, Huang C, Yu T, Anderson KC, Cheng T, Qiu L, Hao M. Indirubin-3'-monoxime acts as proteasome inhibitor: Therapeutic application in multiple myeloma. EBioMedicine 2022; 78:103950. [PMID: 35344764 PMCID: PMC8958548 DOI: 10.1016/j.ebiom.2022.103950] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 02/26/2022] [Accepted: 03/07/2022] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Multiple myeloma (MM) is still an incurable malignancy of plasma cells. Proteasome inhibitors (PIs) work as the backbone agent and have greatly improved the outcome in majority of newly diagnosed patients with myeloma. However, drug resistance remains the major obstacle causing treatment failure in clinical practice. Here, we investigated the effects of Indirubin-3'-monoxime (I3MO), one of the derivatives of Indirubin, in the treatment of MM. METHODS MM patient primary samples and human cell lines were examined. I3MO effects on myeloma treatment and the underling molecular mechanisms were investigated via in vivo and in vitro study. FINDINGS Our results demonstrated the anti-MM activity of I3MO in both drug- sensitive and -resistance MM cells. I3MO sensitizes MM cells to bortezomib-induced apoptosis. Mechanistically, I3MO acts as a multifaceted regulator of cell death, which induced DNA damage, cell cycle arrest, and abrogates NF-κB activation. I3MO efficiently down-regulated USP7 expression, promoted NEK2 degradation, and suppressed NF-κB signaling in MM. Our study reported that I3MO directly bound with and caused the down-regulation of PA28γ (PSME3), and PA200 (PSME4), the proteasome activators. Knockdown of PSME3 or PSME4 caused the inhibition of proteasome capacity and the overload of paraprotein, which sensitizes MM cells to bortezomib-mediated growth arrest. Clinical data demonstrated that PSME3 and PSME4 are over-expressed in relapsed/refractory MM (RRMM) and associated with inferior outcome. INTERPRETATION Altogether, our study indicates that I3MO is agent triggering proteasome inhibition and represents a promising therapeutic strategy to improve patient outcome in MM. FUNDINGS A full list of funding can be found in the acknowledgements.
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Affiliation(s)
- Zhen Yu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Hai he Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, PR China
| | - Xiaojing Wei
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Hai he Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, PR China
| | - Lanting Liu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Hai he Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, PR China
| | - Hao Sun
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Hai he Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, PR China
| | - Teng Fang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Hai he Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, PR China
| | - Lu Wang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Hai he Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, PR China
| | - Ying Li
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Hai he Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, PR China
| | - Weiwei Sui
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Hai he Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, PR China
| | - Kefei Wang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Hai he Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, PR China
| | - Yi He
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Hai he Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, PR China
| | - Yaozhong Zhao
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Hai he Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, PR China
| | - Wenyang Huang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Hai he Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, PR China
| | - Gang An
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Hai he Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, PR China
| | - Fancui Meng
- Tianjin Key Laboratory of Molecular Design and Drug Discovery, Tianjin Institute of Pharmaceutical Research, Tianjin 300301, PR China; State Key Laboratory of Drug Delivery Technology and Pharmacokinetics, Tianjin Institute of Pharmaceutical Research, Tianjin 300301, PR China
| | - Changjiang Huang
- Tianjin Key Laboratory of Molecular Design and Drug Discovery, Tianjin Institute of Pharmaceutical Research, Tianjin 300301, PR China; State Key Laboratory of Drug Delivery Technology and Pharmacokinetics, Tianjin Institute of Pharmaceutical Research, Tianjin 300301, PR China
| | - Tengteng Yu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Hai he Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, PR China
| | - Kenneth C Anderson
- LeBow Institute for Myeloma Therapeutics and Jerome Lipper Center for Multiple Myeloma Center, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Tao Cheng
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Hai he Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, PR China
| | - Lugui Qiu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Hai he Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, PR China.
| | - Mu Hao
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Hai he Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, PR China.
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22
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Gong L, Lu P, Lu C, Li M, Wan H, Wang Y. Design, Synthesis and Biological Evaluation of Coumarin Derivatives as NEDD8 Activating Enzyme Inhibitors in Pancreatic Cancer Cells. Med Chem 2022; 18:679-693. [PMID: 34895126 DOI: 10.2174/1573406418666211210163817] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 10/01/2021] [Accepted: 10/01/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND NEDD8 (neural precursor cell expressed developmentally downregulated protein 8) is one of the ubiquitin-like proteins which is activated by the NEDD8 activating enzyme (NAE). The overexpressed NAE can cause a variety of diseases such as numerous cancer types and inflammatory diseases. The selective inhibition of NAE could mediate the rate of ubiquitination and the subsequent degradation of proteins associated with cancer so as to achieve the purpose of treatment. OBJECTIVE In this article, we decided to study the synthesis and screening of coumarin scaffold derivatives against cancer cell lines, specifically the human pancreatic cancer cell line BxPC-3. METHODS Twenty-four targeted compounds were synthesized, and their anti-proliferative activity against three cancer cell lines, cytotoxicity against three normal cell lines through CCK-8 and MTT assay were evaluated to screen out the candidate compound. Then the target was further confirmed by both enzyme and cell-based experiments, as well as cell apoptosis research. RESULTS Several new 4-position substituted coumarin derivatives (12a~x) were synthesized and most of them exhibit antiproliferative activity in three cancer cell lines. A series of experiments were performed to identify the best candidate compound 12v. This compound displayed the highest potency against BxPC-3 with an IC50 value of 0.28 μM. It can also inhibit NAE activity in enzyme and cellbased assay, and induce CRLs-mediated accumulation of the substrate and apoptosis in BxPC-3 cells. Meanwhile, it exhibited relatively low toxicity in three normal cells. CONCLUSION Based on these results, we found that compound 12v inhibited NAE activity in enzyme and cell-based systems and induced apoptosis in BxPC-3 cells. Additionally, it also had a low toxicity. These results suggested that 12v may be promising lead compounds for the development of new anticancer drugs.
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Affiliation(s)
- Lei Gong
- School of Pharmaceutical Sciences, Nanjing Technical University, No. 5 Xinmofan Road, Nanjing 210009, People's Republic of China
| | - Peng Lu
- School of Pharmaceutical Sciences, Nanjing Technical University, No. 5 Xinmofan Road, Nanjing 210009, People's Republic of China
| | - Cheng Lu
- School of Pharmaceutical Sciences, Nanjing Technical University, No. 5 Xinmofan Road, Nanjing 210009, People's Republic of China
| | - Mengli Li
- School of Pharmaceutical Sciences, Nanjing Technical University, No. 5 Xinmofan Road, Nanjing 210009, People's Republic of China
| | - Huiyang Wan
- School of Pharmaceutical Sciences, Nanjing Technical University, No. 5 Xinmofan Road, Nanjing 210009, People's Republic of China
| | - Yubin Wang
- School of Pharmaceutical Sciences, Nanjing Technical University, No. 5 Xinmofan Road, Nanjing 210009, People's Republic of China
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23
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Exercise as a Peripheral Circadian Clock Resynchronizer in Vascular and Skeletal Muscle Aging. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:ijerph182412949. [PMID: 34948558 PMCID: PMC8702158 DOI: 10.3390/ijerph182412949] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 11/30/2021] [Accepted: 12/02/2021] [Indexed: 12/25/2022]
Abstract
Aging is characterized by several progressive physiological changes, including changes in the circadian rhythm. Circadian rhythms influence behavior, physiology, and metabolic processes in order to maintain homeostasis; they also influence the function of endothelial cells, smooth muscle cells, and immune cells in the vessel wall. A clock misalignment could favor vascular damage and indirectly also affect skeletal muscle function. In this review, we focus on the dysregulation of circadian rhythm due to aging and its relationship with skeletal muscle changes and vascular health as possible risk factors for the development of sarcopenia, as well as the role of physical exercise as a potential modulator of these processes.
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24
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Liu X, Song L, Zhang H, Lin Y, Shen X, Guo J, Su M, Shi G, Wang Z, Lu G. Rice ubiquitin-conjugating enzyme OsUBC26 is essential for immunity to the blast fungus Magnaporthe oryzae. MOLECULAR PLANT PATHOLOGY 2021; 22:1613-1623. [PMID: 34459564 PMCID: PMC8578843 DOI: 10.1111/mpp.13132] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Revised: 07/17/2021] [Accepted: 08/11/2021] [Indexed: 06/13/2023]
Abstract
The functions of ubiquitin-conjugating enzymes (E2) in plant immunity are not well understood. In this study, OsUBC26, a rice ubiquitin-conjugating enzyme, was characterized in the defence against Magnaporthe oryzae. The expression of OsUBC26 was induced by M. oryzae inoculation and methyl jasmonate treatment. Both RNA interference lines and CRISPR/Cas9 null mutants of OsUBC26 reduced rice resistance to M. oryzae. WRKY45 was down-regulated in OsUBC26 null mutants. In vitro E2 activity assay indicated that OsUBC26 is an active ubiquitin-conjugating enzyme. Yeast two-hybrid assays using OsUBC26 as bait identified the RING-type E3 ligase UCIP2 as an interacting protein. Coimmunoprecipitation assays confirmed the interaction between OsUBC26 and UCIP2. The CRISPR/Cas9 mutants of UCIP2 also showed compromised resistance to M. oryzae. Yeast two-hybrid screening using UCIP2 as bait revealed that APIP6 is a binding partner of UCIP2. Moreover, OsUBC26 working with APIP6 ubiquitinateds AvrPiz-t, an avirulence effector of M. oryzae, and OsUBC26 null mutation impaired the proteasome degradation of AvrPiz-t in rice cells. In summary, OsUBC26 plays important roles in rice disease resistance by regulating WRKY45 expression and working with E3 ligases such as APIP6 to counteract the effector protein AvrPiz-t from M. oryzae.
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Affiliation(s)
- Xin Liu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan CropsKey Laboratory of Biopesticide and Chemistry BiologyMinistry of EducationFujian Agriculture and Forestry UniversityFuzhouChina
| | - Linlin Song
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan CropsKey Laboratory of Biopesticide and Chemistry BiologyMinistry of EducationFujian Agriculture and Forestry UniversityFuzhouChina
| | - Heng Zhang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan CropsKey Laboratory of Biopesticide and Chemistry BiologyMinistry of EducationFujian Agriculture and Forestry UniversityFuzhouChina
| | - Yijuan Lin
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan CropsKey Laboratory of Biopesticide and Chemistry BiologyMinistry of EducationFujian Agriculture and Forestry UniversityFuzhouChina
| | - Xiaolei Shen
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan CropsKey Laboratory of Biopesticide and Chemistry BiologyMinistry of EducationFujian Agriculture and Forestry UniversityFuzhouChina
| | - Jiayuan Guo
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan CropsKey Laboratory of Biopesticide and Chemistry BiologyMinistry of EducationFujian Agriculture and Forestry UniversityFuzhouChina
| | - Meiling Su
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan CropsKey Laboratory of Biopesticide and Chemistry BiologyMinistry of EducationFujian Agriculture and Forestry UniversityFuzhouChina
| | - Gaosheng Shi
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan CropsKey Laboratory of Biopesticide and Chemistry BiologyMinistry of EducationFujian Agriculture and Forestry UniversityFuzhouChina
| | - Zonghua Wang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan CropsKey Laboratory of Biopesticide and Chemistry BiologyMinistry of EducationFujian Agriculture and Forestry UniversityFuzhouChina
| | - Guo‐Dong Lu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan CropsKey Laboratory of Biopesticide and Chemistry BiologyMinistry of EducationFujian Agriculture and Forestry UniversityFuzhouChina
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25
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Aksenova AY, Zhuk AS, Lada AG, Zotova IV, Stepchenkova EI, Kostroma II, Gritsaev SV, Pavlov YI. Genome Instability in Multiple Myeloma: Facts and Factors. Cancers (Basel) 2021; 13:5949. [PMID: 34885058 PMCID: PMC8656811 DOI: 10.3390/cancers13235949] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 10/20/2021] [Accepted: 11/22/2021] [Indexed: 02/06/2023] Open
Abstract
Multiple myeloma (MM) is a malignant neoplasm of terminally differentiated immunoglobulin-producing B lymphocytes called plasma cells. MM is the second most common hematologic malignancy, and it poses a heavy economic and social burden because it remains incurable and confers a profound disability to patients. Despite current progress in MM treatment, the disease invariably recurs, even after the transplantation of autologous hematopoietic stem cells (ASCT). Biological processes leading to a pathological myeloma clone and the mechanisms of further evolution of the disease are far from complete understanding. Genetically, MM is a complex disease that demonstrates a high level of heterogeneity. Myeloma genomes carry numerous genetic changes, including structural genome variations and chromosomal gains and losses, and these changes occur in combinations with point mutations affecting various cellular pathways, including genome maintenance. MM genome instability in its extreme is manifested in mutation kataegis and complex genomic rearrangements: chromothripsis, templated insertions, and chromoplexy. Chemotherapeutic agents used to treat MM add another level of complexity because many of them exacerbate genome instability. Genome abnormalities are driver events and deciphering their mechanisms will help understand the causes of MM and play a pivotal role in developing new therapies.
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Affiliation(s)
- Anna Y. Aksenova
- Laboratory of Amyloid Biology, St. Petersburg State University, 199034 St. Petersburg, Russia
| | - Anna S. Zhuk
- International Laboratory “Computer Technologies”, ITMO University, 197101 St. Petersburg, Russia;
| | - Artem G. Lada
- Department of Microbiology and Molecular Genetics, University of California, Davis, CA 95616, USA;
| | - Irina V. Zotova
- Department of Genetics and Biotechnology, St. Petersburg State University, 199034 St. Petersburg, Russia; (I.V.Z.); (E.I.S.)
- Vavilov Institute of General Genetics, St. Petersburg Branch, Russian Academy of Sciences, 199034 St. Petersburg, Russia
| | - Elena I. Stepchenkova
- Department of Genetics and Biotechnology, St. Petersburg State University, 199034 St. Petersburg, Russia; (I.V.Z.); (E.I.S.)
- Vavilov Institute of General Genetics, St. Petersburg Branch, Russian Academy of Sciences, 199034 St. Petersburg, Russia
| | - Ivan I. Kostroma
- Russian Research Institute of Hematology and Transfusiology, 191024 St. Petersburg, Russia; (I.I.K.); (S.V.G.)
| | - Sergey V. Gritsaev
- Russian Research Institute of Hematology and Transfusiology, 191024 St. Petersburg, Russia; (I.I.K.); (S.V.G.)
| | - Youri I. Pavlov
- Eppley Institute for Research in Cancer, Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA
- Departments of Biochemistry and Molecular Biology, Microbiology and Pathology, Genetics Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198, USA
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26
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Over Fifty Years of Life, Death, and Cannibalism: A Historical Recollection of Apoptosis and Autophagy. Int J Mol Sci 2021; 22:ijms222212466. [PMID: 34830349 PMCID: PMC8618802 DOI: 10.3390/ijms222212466] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 11/02/2021] [Accepted: 11/03/2021] [Indexed: 01/18/2023] Open
Abstract
Research in biomedical sciences has changed dramatically over the past fifty years. There is no doubt that the discovery of apoptosis and autophagy as two highly synchronized and regulated mechanisms in cellular homeostasis are among the most important discoveries in these decades. Along with the advancement in molecular biology, identifying the genetic players in apoptosis and autophagy has shed light on our understanding of their function in physiological and pathological conditions. In this review, we first describe the history of key discoveries in apoptosis with a molecular insight and continue with apoptosis pathways and their regulation. We touch upon the role of apoptosis in human health and its malfunction in several diseases. We discuss the path to the morphological and molecular discovery of autophagy. Moreover, we dive deep into the precise regulation of autophagy and recent findings from basic research to clinical applications of autophagy modulation in human health and illnesses and the available therapies for many diseases caused by impaired autophagy. We conclude with the exciting crosstalk between apoptosis and autophagy, from the early discoveries to recent findings.
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27
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Yang K, Yuan MY, Liu Y, Guo CL, Liu TX, Zhang YJ, Chu D. First evidence for thermal tolerance benefits of the bacterial symbiont Cardinium in an invasive whitefly, Bemisia tabaci. PEST MANAGEMENT SCIENCE 2021; 77:5021-5031. [PMID: 34216527 DOI: 10.1002/ps.6543] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 07/03/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUD Cardinium symbiont is a maternally inherited bacterial endosymbiont and widely spreads in arthropods including Bemisia tabaci (Hemiptera: Aleyrodidae). However, the potential role of Cardinium played in the biology of their hosts is largely unknown. In two genetic lines (i.e. LS and SG lines) of B. tabaci MED, collected from different locations in China, we tested the effects of Cardinium on the performance of the host whitefly under a constant high temperature (31 °C) using the age-stage two-sex life table method, and explored the genes influenced by Cardinium-infection by RNA-sequencing. RESULTS We found that Cardinium did provide protection of B. tabaci against heat stress under 31 °C. However, there was a significant connection between Cardinium-infection and whitefly genetic backgrounds. Performance revealed that Cardinium infection can increase the longevity of both female and male adults and oviposition periods in both lines, but it also conferred benefits of fecundity and pre-adult period to LS line. Additionally, the population parameters such as intrinsic rate of increase (r), finite rate of increase (λ) and mean generation time (T) demonstrated that Cardinium infection conferred fitness benefits to LS line but not to SG line. Transcriptome analysis indicated that several genes related to homeostasis and metamorphosis such as ubiquitin-related genes were highly expressed in Cardinium-infected B. tabaci. CONCLUSION The research provided the first evidence that Cardinium can increase the thermal tolerance of whitefly, which may be associated with host genetic background.
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Affiliation(s)
- Kun Yang
- Key Lab of Integrated Crop Pest Management of Shandong Province, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, China
| | - Meng-Ying Yuan
- Key Lab of Integrated Crop Pest Management of Shandong Province, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, China
| | - Ying Liu
- Key Lab of Integrated Crop Pest Management of Shandong Province, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, China
| | - Chen-Liang Guo
- Key Lab of Integrated Crop Pest Management of Shandong Province, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, China
| | - Tong-Xian Liu
- Key Lab of Integrated Crop Pest Management of Shandong Province, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, China
| | - You-Jun Zhang
- Department of Plant Protection, Institute of Vegetables and Flowers, |Chinese Academy of Agricultural Sciences, Beijing, China
| | - Dong Chu
- Key Lab of Integrated Crop Pest Management of Shandong Province, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, China
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28
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Wang X, Best S, Danilov AV. Neddylation and anti-tumor immunity. Oncotarget 2021; 12:2227-2230. [PMID: 34676055 PMCID: PMC8522835 DOI: 10.18632/oncotarget.28019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 06/21/2021] [Indexed: 02/06/2023] Open
Abstract
Contrary to chemotherapy, novel targeted therapies are associated with diverse immunomodulatory effects. Nedd8 is a small ubiquitin-like modifier that is involved in regulation of protein degradation. Neddylation is a promising target in cancer. Pevonedistat, a small molecule inhibitor of the Nedd8-activating enzyme, demonstrates pre-clinical activity in multiple tumor types. Recent studies have revealed that neddylation is important in immunity. We and others have shown that interfering with neddylation causes downstream immunomodulatory effects potentially leading to enhanced anti-tumor immunity. Thus, Nedd8 is a promising target in immuno-oncology.
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Affiliation(s)
- Xiaoguang Wang
- Department of Hematology and Hematopoietic Stem Cell Transplant, City of Hope National Medical Center, Duarte, CA, USA
| | - Scott Best
- Molecular and Cellular Biology, University of Washington, Seattle, WA, USA
| | - Alexey V Danilov
- Department of Hematology and Hematopoietic Stem Cell Transplant, City of Hope National Medical Center, Duarte, CA, USA
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29
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Loh D, Reiter RJ. Melatonin: Regulation of Biomolecular Condensates in Neurodegenerative Disorders. Antioxidants (Basel) 2021; 10:1483. [PMID: 34573116 PMCID: PMC8465482 DOI: 10.3390/antiox10091483] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 09/10/2021] [Accepted: 09/13/2021] [Indexed: 12/12/2022] Open
Abstract
Biomolecular condensates are membraneless organelles (MLOs) that form dynamic, chemically distinct subcellular compartments organizing macromolecules such as proteins, RNA, and DNA in unicellular prokaryotic bacteria and complex eukaryotic cells. Separated from surrounding environments, MLOs in the nucleoplasm, cytoplasm, and mitochondria assemble by liquid-liquid phase separation (LLPS) into transient, non-static, liquid-like droplets that regulate essential molecular functions. LLPS is primarily controlled by post-translational modifications (PTMs) that fine-tune the balance between attractive and repulsive charge states and/or binding motifs of proteins. Aberrant phase separation due to dysregulated membrane lipid rafts and/or PTMs, as well as the absence of adequate hydrotropic small molecules such as ATP, or the presence of specific RNA proteins can cause pathological protein aggregation in neurodegenerative disorders. Melatonin may exert a dominant influence over phase separation in biomolecular condensates by optimizing membrane and MLO interdependent reactions through stabilizing lipid raft domains, reducing line tension, and maintaining negative membrane curvature and fluidity. As a potent antioxidant, melatonin protects cardiolipin and other membrane lipids from peroxidation cascades, supporting protein trafficking, signaling, ion channel activities, and ATPase functionality during condensate coacervation or dissolution. Melatonin may even control condensate LLPS through PTM and balance mRNA- and RNA-binding protein composition by regulating N6-methyladenosine (m6A) modifications. There is currently a lack of pharmaceuticals targeting neurodegenerative disorders via the regulation of phase separation. The potential of melatonin in the modulation of biomolecular condensate in the attenuation of aberrant condensate aggregation in neurodegenerative disorders is discussed in this review.
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Affiliation(s)
- Doris Loh
- Independent Researcher, Marble Falls, TX 78654, USA
| | - Russel J. Reiter
- Department of Cellular and Structural Biology, UT Health Science Center, San Antonio, TX 78229, USA
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30
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Nomura Y, Nakano M, Woo Sung H, Han M, Pandey D. Inhibition of HDAC6 Activity Protects Against Endothelial Dysfunction and Atherogenesis in vivo: A Role for HDAC6 Neddylation. Front Physiol 2021; 12:675724. [PMID: 34220539 PMCID: PMC8245780 DOI: 10.3389/fphys.2021.675724] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 05/14/2021] [Indexed: 12/22/2022] Open
Abstract
We previously reported that histone deacetylase 6 (HDAC6) has an important role in endothelial cell (EC) function in vitro. However, whether HDAC6 plays a role in atherogenesis in vivo and the mechanism(s) that control HDAC6 activity/expression in response to atherogenic stimuli are unclear. The goals of this study were to determine whether HDAC6 inhibitor tubacin attenuates atherogenesis and to elucidate specific molecular mechanism(s) that regulate endothelial HDAC6 expression/activity. We evaluated whether administration of tubacin attenuated or reversed the endothelial dysfunction and atherosclerosis induced in mice by a single intraperitoneal injection of adeno-associated viruses encoding liver-target PCSK9 gain-of-function mutant followed by a high fat diet (HFD) for 18 weeks. Tubacin significantly blunted PCSK9-induced increases in pulse wave velocity (index of vascular stiffness and overall vascular health) that are also seen in atherogenic mice. Furthermore, tubacin protected vessels from defective vasorelaxation, as evaluated by acetylcholine-mediated relaxation using wire myograph. Plaque burden defined by Oil Red O staining was also found to be significantly less in mice that received tubacin than in those that received PCSK9 alone. Inhibition of the NEDDylation pathway with MLN4924, an inhibitor of NEDD8-activating enzyme 1 (NAE1), significantly increased HDAC6 activity in HAECs. Interestingly, HDAC6 expression remained unchanged. Further, HAECs exposed to the atherogenic stimulus oxidized low-density lipoprotein (OxLDL) exhibited enhanced HDAC6 activity, which was attenuated by pretreatment with MLN4924. The HDAC6 NEDDylation molecular pathway might regulate genes related to endothelial control of vasomotor tone, reactivity, and atherosclerosis. Tubacin may represent a novel pharmacologic intervention for atherogenesis and other vasculopathies.
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Affiliation(s)
- Yohei Nomura
- Department of Anesthesiology and Critical Care Medicine, Johns Hopkins University, Baltimore, MD, United States.,Department of Cardiovascular Surgery, Saitama Medical Center, Jichi Medical University, Saitama, Japan
| | - Mitsunori Nakano
- Department of Anesthesiology and Critical Care Medicine, Johns Hopkins University, Baltimore, MD, United States.,Department of Cardiovascular Surgery, Saitama Medical Center, Jichi Medical University, Saitama, Japan
| | - Hyun Woo Sung
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, United States
| | - Mingming Han
- Department of Anesthesiology and Critical Care Medicine, Johns Hopkins University, Baltimore, MD, United States.,Department of Anesthesiology, The First Affiliated Hospital of USTC, University of Science and Technology of China, Hefei, China
| | - Deepesh Pandey
- Department of Anesthesiology and Critical Care Medicine, Johns Hopkins University, Baltimore, MD, United States
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31
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Zhu L, Lu P, Gong L, Lu C, Li M, Wang Y. Design, Synthesis, and Biological Evaluation of 4-amino Substituted 2Hchromen- 2-one Derivatives as an NEDD8 Activating Enzyme Inhibitor in Pancreatic Cancer Cells. Med Chem 2021; 16:969-983. [PMID: 31880252 DOI: 10.2174/1573406416666191227121520] [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: 03/09/2019] [Revised: 12/10/2019] [Accepted: 12/10/2019] [Indexed: 11/22/2022]
Abstract
BACKGROUND NEDD8 activating enzyme (NAE) plays a critical role in various cellular functions in carcinomas. The selective inhibition of NAE could mediate the rate of ubiquitination and the subsequent degradation of proteins associated with cancer so as to achieve the purpose of treatment. OBJECTIVE In this article, we decided to study the synthesis and screening of 4-amino substituted 2H-chromen-2-one derivatives against cancer cell lines, specifically the human pancreatic cancer cell line BxPC-3. METHODS After synthesis of twenty targeted compounds, we evaluated their anti-proliferative activity against six cancer cell lines, cytotoxicity against three normal cell lines through MTT assay, and hemolysis to screen out the candidate compound, which was further conducted drug-like physical property measurement, target confirmation by enzyme-based experiment, cell apoptosis, and synergistic effect research. RESULTS Starting from intermediates 4 and 5, several new 4-amino substituted 2H-chromen-2-one derivatives (9-28) were synthesized and evaluated for their cell activities using six cancer cell lines. We performed tests of cytotoxicity, hemolysis, ATP-dependent NAE inhibition in the enzyme- based system, apoptosis, and synergistic effect in BxPC-3 cells against the best candidate compound 21. CONCLUSION Based on these results, we found that compound 21 inhibited NAE activity in an ATP-dependent manner in the enzyme-based system, induced apoptosis in BxPC-3 cells, and synergized with bortezomib on BxPC-3 cell growth inhibition. Additionally, it had low toxicity with reasonable Log P-value and water solubility.
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Affiliation(s)
- Lijuan Zhu
- School of Pharmaceutical Sciences, Nanjing Tech University, No. 5 Xinmofan Road, Nanjing 210009, China
| | - Peng Lu
- School of Pharmaceutical Sciences, Nanjing Tech University, No. 5 Xinmofan Road, Nanjing 210009, China
| | - Lei Gong
- School of Pharmaceutical Sciences, Nanjing Tech University, No. 5 Xinmofan Road, Nanjing 210009, China
| | - Cheng Lu
- School of Pharmaceutical Sciences, Nanjing Tech University, No. 5 Xinmofan Road, Nanjing 210009, China
| | - Mengli Li
- School of Pharmaceutical Sciences, Nanjing Tech University, No. 5 Xinmofan Road, Nanjing 210009, China
| | - Yubin Wang
- School of Pharmaceutical Sciences, Nanjing Tech University, No. 5 Xinmofan Road, Nanjing 210009, China
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Genome-wide analysis of RING-type E3 ligase family identifies potential candidates regulating high amylose starch biosynthesis in wheat (Triticum aestivum L.). Sci Rep 2021; 11:11461. [PMID: 34075092 PMCID: PMC8169666 DOI: 10.1038/s41598-021-90685-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 05/10/2021] [Indexed: 12/02/2022] Open
Abstract
In ubiquitin-mediated post-translational modifications, RING finger families are emerged as important E3 ligases in regulating biological processes. Amylose and amylopectin are two major constituents of starch in wheat seed endosperm. Studies have been found the beneficial effects of high amylose or resistant starch on health. The ubiquitin-mediated post-translational regulation of key enzymes for amylose/amylopectin biosynthesis (GBSSI and SBEII) is still unknown. In this study, the genome-wide analysis identified 1272 RING domains in 1255 proteins in wheat, which is not reported earlier. The identified RING domains classified into four groups—RING-H2, RING-HC, RING-v, RING-G, based on the amino acid residues (Cys, His) at metal ligand positions and the number of residues between them with the predominance of RING-H2 type. A total of 1238 RING protein genes were found to be distributed across all 21 wheat chromosomes. Among them, 1080 RING protein genes were identified to show whole genome/segmental duplication within the hexaploid wheat genome. In silico expression analysis using transcriptome data revealed 698 RING protein genes, having a possible role in seed development. Based on differential gene expression and correlation analysis of 36 RING protein genes in diverse (high and low) amylose mutants and parent, 10 potential RING protein genes found to be involved in high amylose biosynthesis and significantly associated with two starch biosynthesis genes; GBSSI and SBEIIa. Characterization of mutant lines using next-generation sequencing method identified unique mutations in 698 RING protein genes. This study signifies the putative role of RING-type E3 ligases in amylose biosynthesis and this information will be helpful for further functional validation and its role in other biological processes in wheat.
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Ruby CL, Major RJ, Hinrichsen RD. Regulation of tissue regeneration by the circadian clock. Eur J Neurosci 2021; 53:3576-3597. [PMID: 33893679 DOI: 10.1111/ejn.15244] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 03/31/2021] [Accepted: 04/16/2021] [Indexed: 12/12/2022]
Abstract
Circadian rhythms are regulated by a highly conserved transcriptional/translational feedback loop that maintains approximately 24-hr periodicity from cellular to organismal levels. Much research effort is being devoted to understanding how the outputs of the master clock affect peripheral oscillators, and in turn, numerous biological processes. Recent studies have revealed roles for circadian timing in the regulation of numerous cellular behaviours in support of complex tissue regeneration. One such role involves the interaction between the circadian clockwork and the cell cycle. The molecular mechanisms that control the cell cycle create a system of regulation that allows for high fidelity DNA synthesis, mitosis and apoptosis. In recent years, it has become clear that clock gene products are required for proper DNA synthesis and cell cycle progression, and conversely, elements of the cell cycle cascade feedback to influence molecular circadian timing mechanisms. It is through this crosstalk that the circadian system orchestrates stem cell proliferation, niche exit and control of the signalling pathways that govern differentiation and self-renewal. In this review, we discuss the evidence for circadian control of tissue homeostasis and repair and suggest new avenues for research.
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Affiliation(s)
- Christina L Ruby
- Department of Biology, Indiana University of Pennsylvania, Indiana, PA, USA
| | - Robert J Major
- Department of Biology, Indiana University of Pennsylvania, Indiana, PA, USA
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Selective inhibition of cullin 3 neddylation through covalent targeting DCN1 protects mice from acetaminophen-induced liver toxicity. Nat Commun 2021; 12:2621. [PMID: 33976147 PMCID: PMC8113459 DOI: 10.1038/s41467-021-22924-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 03/29/2021] [Indexed: 11/08/2022] Open
Abstract
Cullin-RING E3 ligases (CRLs) regulate the turnover of approximately 20% of mammalian cellular proteins. Neddylation of individual cullin proteins is essential for the activation of each CRL. We report herein the discovery of DI-1548 and DI-1859 as two potent, selective and covalent DCN1 inhibitors. These inhibitors selectively inhibit neddylation of cullin 3 in cells at low nanomolar concentrations and are 2-3 orders of magnitude more potent than our previously reported reversible DCN1 inhibitor. Mass spectrometric analysis and co-crystal structures reveal that these compounds employ a unique mechanism of covalent bond formation with DCN1. DI-1859 induces a robust increase of NRF2 protein, a CRL3 substrate, in mouse liver and effectively protects mice from acetaminophen-induced liver damage. Taken together, this study demonstrates the therapeutic potential of selective inhibition of cullin neddylation.
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Abstract
Ubiquitin (Ub) is one of the proteins that are highly conserved from yeast to humans. It is an essential core unit of the well-defined post-translational modification, called ubiquitination, which is involved in a variety of biological processes. In meta-zoans, Ub is encoded by two monoubiquitin genes and two polyubiquitin genes, in which a single Ub is fused to a ribosomal protein or Ub coding units are arranged in tandem repeats. In mice, polyubiquitin genes (Ubb and Ubc) play a pivotal role to meet the requirement of cellular Ub pools during embryonic development. In addition, expression levels of polyubiquitin genes are increased to adapt to environmental stimuli such as oxidative, heat-shock, and proteotoxic stress. Several researchers have reported about the perturbation of Ub pools through genetic alteration or exogenous Ub delivery using diverse model systems. To study Ub pool changes in a physiologically relevant manner, changing Ub pools via the regulation of endogenous polyubiquitin gene expression has recently been introduced. Furthermore, to understand the regulation of polyubiquitin gene expression more precisely, cis-acting elements and trans-acting factors, which are regulatory components of polyubiquitin genes, have been analyzed. In this review, we discuss how the role of polyu-biquitin genes has been studied during the past decade, es-pecially focusing on their regulation.
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Affiliation(s)
- Seung-Woo Han
- Department of Life Science, University of Seoul, Seoul 02504, Korea
| | - Byung-Kwon Jung
- Department of Life Science, University of Seoul, Seoul 02504, Korea
| | - Kwon-Yul Ryu
- Department of Life Science, University of Seoul, Seoul 02504, Korea
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36
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Xiong C, Zhou L, Tan J, Song S, Bao X, Zhang N, Ding H, Zhao J, He JX, Miao ZH, Zhang A. Development of Potent NEDD8-Activating Enzyme Inhibitors Bearing a Pyrimidotriazole Scaffold. J Med Chem 2021; 64:6161-6178. [PMID: 33857374 DOI: 10.1021/acs.jmedchem.1c00242] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The ubiquitin-like protein NEDD8 is a critical signaling molecule implicated in the functional maintenance and homeostasis of cells. Dysregulation of this process is involved in a variety of human diseases, including cancer. Therefore, NEDD8-activating enzyme E1 (NAE), the only activation enzyme of the neddylation pathway, has been an emergent anticancer target. In view of the single-agent modest response of the clinical NAE inhibitor, pevonedistat (compound 1, MLN4924), efforts on development of new inhibitors with both high potency and better safety profiles are urgently needed. Here, we report a structural hopping strategy by optimizing the central deazapurine framework and the solvent interaction region of compound 1, leading to compound 26 bearing a pyrimidotriazole scaffold. Compound 26 not only has compatible potency in the biochemical and cell assays but also possesses improved pharmacokinetic (PK) properties than compound 1. In vivo, compound 26 showed significant antitumor efficacy and good safety in xenograft models.
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Affiliation(s)
- Chaodong Xiong
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica (SIMM), Chinese Academy of Sciences, Shanghai 201203, China.,Pharm-X Center, School of Pharmacy, Shanghai Jiao Tong University, Shanghai 200240, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lina Zhou
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica (SIMM), Chinese Academy of Sciences, Shanghai 201203, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jing Tan
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica (SIMM), Chinese Academy of Sciences, Shanghai 201203, China.,Pharm-X Center, School of Pharmacy, Shanghai Jiao Tong University, Shanghai 200240, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shanshan Song
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica (SIMM), Chinese Academy of Sciences, Shanghai 201203, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xubin Bao
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica (SIMM), Chinese Academy of Sciences, Shanghai 201203, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ning Zhang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica (SIMM), Chinese Academy of Sciences, Shanghai 201203, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Huaqian Ding
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica (SIMM), Chinese Academy of Sciences, Shanghai 201203, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiannan Zhao
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica (SIMM), Chinese Academy of Sciences, Shanghai 201203, China.,Pharm-X Center, School of Pharmacy, Shanghai Jiao Tong University, Shanghai 200240, China.,School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Jin-Xue He
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica (SIMM), Chinese Academy of Sciences, Shanghai 201203, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ze-Hong Miao
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica (SIMM), Chinese Academy of Sciences, Shanghai 201203, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ao Zhang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica (SIMM), Chinese Academy of Sciences, Shanghai 201203, China.,Pharm-X Center, School of Pharmacy, Shanghai Jiao Tong University, Shanghai 200240, China.,University of Chinese Academy of Sciences, Beijing 100049, China.,Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, School of Pharmacy, Shanghai Jiao Tong University, Shanghai 200240, China.,State Key Laboratory of Esophageal Cancer Prevention and Treatment, Ministry of Education of China, Zhengzhou University, Zhengzhou 450001, China
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Usman B, Zhao N, Nawaz G, Qin B, Liu F, Liu Y, Li R. CRISPR/Cas9 Guided Mutagenesis of Grain Size 3 Confers Increased Rice ( Oryza sativa L.) Grain Length by Regulating Cysteine Proteinase Inhibitor and Ubiquitin-Related Proteins. Int J Mol Sci 2021; 22:ijms22063225. [PMID: 33810044 PMCID: PMC8004693 DOI: 10.3390/ijms22063225] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 03/19/2021] [Accepted: 03/20/2021] [Indexed: 12/21/2022] Open
Abstract
Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/CRISPR-associated protein (Cas9)-mediated genome editing has become an important way for molecular breeding in crop plants. To promote rice breeding, we edited the Grain Size 3 (GS3) gene for obtaining valuable and stable long-grain rice mutants. Furthermore, isobaric tags for the relative and absolute quantitation (iTRAQ)-based proteomic method were applied to determine the proteome-wide changes in the GS3 mutants compared with wild type (WT). Two target sites were designed to construct the vector, and the Agrobacterium-mediated method was used for rice transformation. Specific mutations were successfully introduced, and the grain length (GL) and 1000-grain weight (GWT) of the mutants were increased by 31.39% and 27.15%, respectively, compared with WT. The iTRAQ-based proteomic analysis revealed that a total of 31 proteins were differentially expressed in the GS3 mutants, including 20 up-regulated and 11 down-regulated proteins. Results showed that differentially expressed proteins (DEPs) were mainly related to cysteine synthase, cysteine proteinase inhibitor, vacuolar protein sorting-associated, ubiquitin, and DNA ligase. Furthermore, functional analysis revealed that DEPs were mostly enriched in cellular process, metabolic process, binding, transmembrane, structural, and catalytic activities. Pathway enrichment analysis revealed that DEPs were mainly involved in lipid metabolism and oxylipin biosynthesis. The protein-to-protein interaction (PPI) network found that proteins related to DNA damage-binding, ubiquitin-40S ribosomal, and cysteine proteinase inhibitor showed a higher degree of interaction. The homozygous mutant lines featured by stable inheritance and long-grain phenotype were obtained using the CRISPR/Cas9 system. This study provides a convenient and effective way of improving grain yield, which could significantly accelerate the breeding process of long-grain japonica parents and promote the development of high-yielding rice.
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Affiliation(s)
- Babar Usman
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning 530004, China; (B.U.); (N.Z.); (G.N.); (B.Q.); (F.L.)
| | - Neng Zhao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning 530004, China; (B.U.); (N.Z.); (G.N.); (B.Q.); (F.L.)
| | - Gul Nawaz
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning 530004, China; (B.U.); (N.Z.); (G.N.); (B.Q.); (F.L.)
| | - Baoxiang Qin
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning 530004, China; (B.U.); (N.Z.); (G.N.); (B.Q.); (F.L.)
| | - Fang Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning 530004, China; (B.U.); (N.Z.); (G.N.); (B.Q.); (F.L.)
| | - Yaoguang Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agricultural Bioresources, South China Agricultural University, Guangzhou 510642, China
- Correspondence: (Y.L.); (R.L.); Tel.: +86-20-8528-1908 (Y.L.); +86-136-0009-4135 (R.L.)
| | - Rongbai Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning 530004, China; (B.U.); (N.Z.); (G.N.); (B.Q.); (F.L.)
- Correspondence: (Y.L.); (R.L.); Tel.: +86-20-8528-1908 (Y.L.); +86-136-0009-4135 (R.L.)
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38
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Wan T, Li X, Li Y. The role of TRIM family proteins in autophagy, pyroptosis, and diabetes mellitus. Cell Biol Int 2021; 45:913-926. [PMID: 33438267 DOI: 10.1002/cbin.11550] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 01/06/2021] [Accepted: 01/10/2021] [Indexed: 01/22/2023]
Abstract
The ubiquitin-proteasome system, which is one of the systems for cell protein homeostasis and degradation, happens through the ordered and coordinated action of three types of enzymes, E1 ubiquitin-activating enzyme, E2 ubiquitin-carrier enzyme, E3 ubiquitin-protein ligase. Tripartite motif-containing (TRIM) family proteins are the richest subfamily of really interesting new gene E3 ubiquitin ligases, which play a critical role not only in many biological processes, including proliferation, apoptosis, pyroptosis, innate immunity, and autophagy, but also many diseases like cancer, diabetes mellitus, and neurodegenerative disease. Increasing evidence suggests that TRIM family proteins play a vital role in modulating autophagy, pyroptosis, and diabetes mellitus. The aim of this review is to discuss the role of TRIM proteins in the regulation of autophagy, pyroptosis, diabetes mellitus, and diabetic complications.
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Affiliation(s)
- Tingting Wan
- Department of Endocrinology, First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Xiudan Li
- Department of Endocrinology, First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Yanbo Li
- Department of Endocrinology, First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
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Chen X, Yang X, Mao F, Wei J, Xu Y, Li B, Zhu J, Ni S, Jia L, Li J. Development of novel benzimidazole-derived neddylation inhibitors for suppressing tumor growth invitro and invivo. Eur J Med Chem 2021; 210:112964. [PMID: 33129593 DOI: 10.1016/j.ejmech.2020.112964] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 09/21/2020] [Accepted: 10/19/2020] [Indexed: 01/22/2023]
Abstract
Ubiquitin-like protein neddylation is overactivated in various human cancers and correlates with disease progression, and targeting this pathway represents a valuable therapeutic strategy. Our previous work disclosed an antihypertensive agent, candesartan cilexetic (CDC), serves as a novel neddylation inhibitor for suppressing tumor growth by targeting Nedd8-activating enzyme (NAE). In this study, 42 benzimidazole derivatives were designed and synthesized based on lead compound CDC to improve the neddylation inhibition and anticancer efficacy. Optimal benzimidazole-derived 35 displayed superior neddylation inhibition in enzyme assay compared to CDC (IC50 = 5.51 μM vs 16.43 μM), along with promising target inhibitory activity and killing selectivity in cancer cell. The results of cellular mechanism research combined with tumor growth suppression in human lung cancer cell A549 in vivo, accompanied with docking model, revealed that 35 has the potential to be developed as a promising neddylation inhibitor for anticancer therapy.
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Affiliation(s)
- Xin Chen
- State Key Laboratory of Bioreactor Engineering, Shanghai Key Laboratory of New Drug Design, East China University of Science and Technology, 130 Mei Long Road, Shanghai, 200237, China
| | - Xi Yang
- Cancer Institute, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, 200032, China
| | - Fei Mao
- State Key Laboratory of Bioreactor Engineering, Shanghai Key Laboratory of New Drug Design, East China University of Science and Technology, 130 Mei Long Road, Shanghai, 200237, China
| | - Jinlian Wei
- State Key Laboratory of Bioreactor Engineering, Shanghai Key Laboratory of New Drug Design, East China University of Science and Technology, 130 Mei Long Road, Shanghai, 200237, China
| | - Yixiang Xu
- State Key Laboratory of Bioreactor Engineering, Shanghai Key Laboratory of New Drug Design, East China University of Science and Technology, 130 Mei Long Road, Shanghai, 200237, China
| | - Baoli Li
- State Key Laboratory of Bioreactor Engineering, Shanghai Key Laboratory of New Drug Design, East China University of Science and Technology, 130 Mei Long Road, Shanghai, 200237, China
| | - Jin Zhu
- State Key Laboratory of Bioreactor Engineering, Shanghai Key Laboratory of New Drug Design, East China University of Science and Technology, 130 Mei Long Road, Shanghai, 200237, China
| | - Shuaishuai Ni
- Cancer Institute, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, 200032, China.
| | - Lijun Jia
- Cancer Institute, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, 200032, China.
| | - Jian Li
- State Key Laboratory of Bioreactor Engineering, Shanghai Key Laboratory of New Drug Design, East China University of Science and Technology, 130 Mei Long Road, Shanghai, 200237, China; College of Pharmacy and Chemistry, Dali University, 5 Xue Ren Road, Dali, Yunnan, 671000, China; Frontiers Science Center for Materiobiology and Dynamic Chemistry, East China University of Science and Technology, 130 Mei Long Road, Shanghai, 200237, China.
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40
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Zhu L, Cheng H, Peng G, Wang S, Zhang Z, Ni E, Fu X, Zhuang C, Liu Z, Zhou H. Ubiquitinome Profiling Reveals the Landscape of Ubiquitination Regulation in Rice Young Panicles. GENOMICS PROTEOMICS & BIOINFORMATICS 2020; 18:305-320. [PMID: 33147495 PMCID: PMC7801245 DOI: 10.1016/j.gpb.2019.01.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 12/06/2018] [Accepted: 01/11/2019] [Indexed: 02/04/2023]
Abstract
Ubiquitination, an essential post-transcriptional modification (PTM), plays a vital role in nearly every biological process, including development and growth. Despite its functions in plant reproductive development, its targets in rice panicles remain unclear. In this study, we used proteome-wide profiling of lysine ubiquitination in rice (O. sativa ssp. indica) young panicles. We created the largest ubiquitinome dataset in rice to date, identifying 1638 lysine ubiquitination sites on 916 unique proteins. We detected three conserved ubiquitination motifs, noting that acidic glutamic acid (E) and aspartic acid (D) were most frequently present around ubiquitinated lysine. Enrichment analysis of Gene Ontology (GO) annotations and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways of these ubiquitinated proteins revealed that ubiquitination plays an important role in fundamental cellular processes in rice young panicles. Interestingly, enrichment analysis of protein domains indicated that ubiquitination was enriched on a variety of receptor-like kinases and cytoplasmic tyrosine and serine-threonine kinases. Furthermore, we analyzed the crosstalk between ubiquitination, acetylation, and succinylation, and constructed a potential protein interaction network within our rice ubiquitinome. Moreover, we identified ubiquitinated proteins related to pollen and grain development, indicating that ubiquitination may play a critical role in the physiological functions in young panicles. Taken together, we reported the most comprehensive lysine ubiquitinome in rice so far, and used it to reveal the functional role of lysine ubiquitination in rice young panicles.
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Affiliation(s)
- Liya Zhu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Instrumental Analysis and Research Center, Key Laboratory of Plant Functional Genomics and Biotechnology of Guangdong Provincial Higher Education Institutions College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Han Cheng
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China; School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China; College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Guoqing Peng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Instrumental Analysis and Research Center, Key Laboratory of Plant Functional Genomics and Biotechnology of Guangdong Provincial Higher Education Institutions College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Shuansuo Wang
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, National Centre for Plant Gene Research, Beijing 100101, China
| | - Zhiguo Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Instrumental Analysis and Research Center, Key Laboratory of Plant Functional Genomics and Biotechnology of Guangdong Provincial Higher Education Institutions College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Erdong Ni
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Instrumental Analysis and Research Center, Key Laboratory of Plant Functional Genomics and Biotechnology of Guangdong Provincial Higher Education Institutions College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Xiangdong Fu
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, National Centre for Plant Gene Research, Beijing 100101, China
| | - Chuxiong Zhuang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Instrumental Analysis and Research Center, Key Laboratory of Plant Functional Genomics and Biotechnology of Guangdong Provincial Higher Education Institutions College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Zexian Liu
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China; College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China.
| | - Hai Zhou
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Instrumental Analysis and Research Center, Key Laboratory of Plant Functional Genomics and Biotechnology of Guangdong Provincial Higher Education Institutions College of Life Sciences, South China Agricultural University, Guangzhou 510642, China.
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Kong D, Gu R, Zhang C, Yin R. Knockdown of hsa_circ_0059955 Induces Apoptosis and Cell Cycle Arrest in Nucleus Pulposus Cells via Inhibiting Itchy E3 Ubiquitin Protein Ligase. DRUG DESIGN DEVELOPMENT AND THERAPY 2020; 14:3951-3963. [PMID: 33061300 PMCID: PMC7526870 DOI: 10.2147/dddt.s253293] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 07/21/2020] [Indexed: 12/19/2022]
Abstract
Background Circular RNAs (circRNAs) play an important role in the progression of intervertebral disc (IVD) degeneration (IVDD). Using bioinformatics analysis, we have found that the expression of circRNA hsa_circ_0059955 was significantly downregulated in IVDD tissues. However, the relevant mechanism of hsa_circ_0059955 in the progression of IVDD remains unclear. Methods CCK-8 and flow cytometry assays were used to evaluate cell proliferation and apoptosis. In addition, Western blot assay was used to detect the expressions of ITCH, p73, CDK2 in nucleus pulposus (NP) cells. Moreover, a puncture-induced IVDD rat model was established to explore the role of hsa_circ_0059955 in IVDD. Results The level of hsa_circ_0059955 was significantly decreased in IVDD tissues from IVDD patients. Itchy E3 ubiquitin protein ligase (ITCH) is the host gene of hsa_circ_0059955, and downregulation of hsa_circ_0059955 significantly decreased the expression of ITCH in NP cells. In addition, downregulation of hsa_circ_0059955 markedly inhibited proliferation and induced apoptosis and cell cycle arrest in NP cells. Moreover, in vivo study illustrated that overexpression of hsa_circ_0059955 ameliorated IVDD in rats. Conclusion Downregulation of hsa_circ_0059955 could induce apoptosis and cell cycle arrest in NP cells in vitro, while overexpression of hsa_circ_0059955 attenuated the IVDD in a puncture-induced rat model in vivo. Therefore, hsa_circ_0059955 might serve as a therapeutic target for the treatment of IVDD.
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Affiliation(s)
- Daliang Kong
- Department of Orthopedics, China-Japan Union Hospital, Changchun, Jilin 130031, People's Republic of China
| | - Rui Gu
- Department of Orthopedics, China-Japan Union Hospital, Changchun, Jilin 130031, People's Republic of China
| | - Chengtao Zhang
- Department of Orthopedics, China-Japan Union Hospital, Changchun, Jilin 130031, People's Republic of China
| | - Ruofeng Yin
- Department of Orthopedics, China-Japan Union Hospital, Changchun, Jilin 130031, People's Republic of China
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42
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Sharma B, Taganna J. Genome-wide analysis of the U-box E3 ubiquitin ligase enzyme gene family in tomato. Sci Rep 2020; 10:9581. [PMID: 32533036 PMCID: PMC7293263 DOI: 10.1038/s41598-020-66553-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 05/18/2020] [Indexed: 12/15/2022] Open
Abstract
E3 ubiquitin ligases are a central modifier of plant signaling pathways that act through targeting proteins to the degradation pathway. U-box E3 ubiquitin ligases are a distinct class of E3 ligases that utilize intramolecular interactions for its scaffold stabilization. U-box E3 ubiquitin ligases are prevalent in plants in comparison to animals. However, the evolutionary aspects, genetic organizations, and functional fate of the U-box E3 gene family in plant development, especially in tomato is not well understood. In the present study, we have performed in-silico genome-wide analysis of the U-box E3 ubiquitin ligase gene family in Solanum lycopersicum. We have identified 62 U-box genes with U-box/Ub Fusion Degradation 2 (UFD2) domain. The chromosomal localization, phylogenetic analysis, gene structure, motifs, gene duplication, syntenic regions, promoter, physicochemical properties, and ontology were investigated. The U-box gene family showed significant conservation of the U-box domain throughout the gene family. Duplicated genes discerned noticeable functional transitions among duplicated genes. The gene expression profiles of U-box E3 family members show involvement in abiotic and biotic stress signaling as well as hormonal pathways. We found remarkable participation of the U-box gene family in the vegetative and reproductive tissue development. It is predicted to be actively regulating flowering time and endosperm formation. Our study provides a comprehensive picture of distribution, structural features, promoter elements, evolutionary relationship, and gene expression of the U-box gene family in the tomato. We predict the crucial participation of the U-box gene family in tomato plant development and stress responses.
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Affiliation(s)
- Bhaskar Sharma
- TERI School of Advanced Studies, 10 Institutional Area, Vasant Kunj, New Delhi, Delhi, 110070, India.
- School of Life and Environmental Sciences, Faculty of Science, Engineering, and Built Environment, Deakin University, Geelong, VIC-3220, Australia.
| | - Joemar Taganna
- SciBiz Informatics, 2/F Unit 3 CFI Building, Maharlika Highway, Brgy. Guindapunan, Palo, Leyte, 6501, Philippines
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Proteomic analysis identifies mechanism(s) of overcoming bortezomib resistance via targeting ubiquitin receptor Rpn13. Leukemia 2020; 35:550-561. [PMID: 32424294 DOI: 10.1038/s41375-020-0865-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 04/29/2020] [Accepted: 05/05/2020] [Indexed: 12/15/2022]
Abstract
Our prior study showed that inhibition of 19S proteasome-associated ubiquitin receptor Rpn13 can overcome bortezomib resistance in MM cells. Here, we performed proteomic analysis of Rpn13 inhibitor (RA190)-treated MM cells and identified an antioxidant enzyme superoxide dismutase (SOD1) as a mediator of Rpn13 signaling. SOD1 levels are higher in MM patient cells versus normal PBMCs; and importantly, SOD1 expression correlates with the progression of disease and shorter survival. Functional validation studies show that RA190-induced cytotoxicity in bortezomib-sensitive and -resistant MM cells is associated with decrease in SOD1 levels; conversely, forced expression of SOD1 inhibits RA190-induced cell death. Genetic knockdown and biochemical blockade of SOD1 with LCS-1 sensitizes bortezomib-resistant MM cells to bortezomib. SOD1 inhibitor LCS-1 decreases viability in MM cell lines and patient cells. LCS-1-induced cell death is associated with: (1) increase in superoxide and ROS levels; (2) activation of caspases, and p53/p21 signaling; (3) decrease in MCL-1, BCLxL, CDC2, cyclin-B1, and c-Myc; (4) ER stress response; and (5) inhibition of proteasome function. In animal model studies, LCS-1 inhibits xenografted bortezomib-resistant human MM cell growth and prolongs host survival. Our studies therefore show that targeting Rpn13 overcomes bortezomib resistance by decreasing cellular SOD1 levels, and provide the rationale for novel therapeutics targeting SOD1 to improve patient outcome in MM.
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Yu Q, Jiang Y, Sun Y. Anticancer drug discovery by targeting cullin neddylation. Acta Pharm Sin B 2020; 10:746-765. [PMID: 32528826 PMCID: PMC7276695 DOI: 10.1016/j.apsb.2019.09.005] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2019] [Revised: 08/17/2019] [Accepted: 09/11/2019] [Indexed: 12/15/2022] Open
Abstract
Protein neddylation is a post-translational modification which transfers the ubiquitin-like protein NEDD8 to a lysine residue of the target substrate through a three-step enzymatic cascade. The best-known substrates of neddylation are cullin family proteins, which are the core component of Cullin–RING E3 ubiquitin ligases (CRLs). Given that cullin neddylation is required for CRL activity, and CRLs control the turn-over of a variety of key signal proteins and are often abnormally activated in cancers, targeting neddylation becomes a promising approach for discovery of novel anti-cancer therapeutics. In the past decade, we have witnessed significant progress in the field of protein neddylation from preclinical target validation, to drug screening, then to the clinical trials of neddylation inhibitors. In this review, we first briefly introduced the nature of protein neddylation and the regulation of neddylation cascade, followed by a summary of all reported chemical inhibitors of neddylation enzymes. We then discussed the structure-based targeting of protein–protein interaction in neddylation cascade, and finally the available approaches for the discovery of new neddylation inhibitors. This review will provide a focused, up-to-date and yet comprehensive overview on the discovery effort of neddylation inhibitors.
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Key Words
- AMP, adenosine 5′-monophosphate
- Anticancer
- BLI, biolayer interferometry
- CETSA, cellular thermal shift assay
- Drug discovery
- FH, frequent hitters
- HTS, high-throughput screen
- High-throughput screening
- IP, immunoprecipitation
- ITC, isothermal titration calorimetry
- NAE, NEDD8 activating enzyme
- Neddylation
- PAINS, pan-assay interference compounds
- SAR, structure–activity relationship
- Small molecule inhibitors
- UBL, ubiquitin-like protein
- Ubiquitin–proteasome system
- Virtual screen
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The role of deubiquitinating enzymes in cancer drug resistance. Cancer Chemother Pharmacol 2020; 85:627-639. [PMID: 32146496 DOI: 10.1007/s00280-020-04046-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 02/19/2020] [Indexed: 12/18/2022]
Abstract
Drug resistance is a well-known phenomenon leading to a reduction in the effectiveness of pharmaceutical treatments. Resistance to chemotherapeutic agents can involve various intrinsic cellular processes including drug efflux, increased resistance to apoptosis, increased DNA damage repair capabilities in response to platinum salts or other DNA-damaging drugs, drug inactivation, drug target alteration, epithelial-mesenchymal transition (EMT), inherent cell heterogeneity, epigenetic effects, or any combination of these mechanisms. Deubiquitinating enzymes (DUBs) reverse ubiquitination of target proteins, maintaining a balance between ubiquitination and deubiquitination of proteins to maintain cell homeostasis. Increasing evidence supports an association of altered DUB activity with development of several cancers. Thus, DUBs are promising candidates for targeted drug development. In this review, we outline the involvement of DUBs, particularly ubiquitin-specific proteases, and their roles in drug resistance in different types of cancer. We also review potential small molecule DUB inhibitors that can be used as drugs for cancer treatment.
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Zhou H, Lu J, Yang CY, Sun Y, Wang S. Targeting DCN1-UBC12 Protein-Protein Interaction for Regulation of Neddylation Pathway. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1217:349-362. [PMID: 31898237 DOI: 10.1007/978-981-15-1025-0_20] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Protein neddylation is one type of posttranslational modifications that regulates the activity of the substrate proteins. Neddylation modification is catalyzed by NEDD8-activating enzyme (NAE, E1), NEDD8-conjugating enzyme (E2), and NEDD8 ligase (E3) to attach NEDD8, an ubiquitin-like molecule, to a lysine residue of a substrate protein. The best known neddylation substrates are cullin family members, which are scaffold components of cullin-RING ligases (CRLs), and cullin neddylation is required for activation of CRLs. In mammalian cells, there are one E1, two E2s (UBC12/UBE2M and UBE2F), and over a dozen E3s. MLN4924, the first-in-class small-molecule inhibitor of NAE, blocks the entire neddylation modification to inactivate activity of all CRLs. MLN4924 is currently in the Phase I/II clinical trials for anticancer application.In the last few years, targeting protein-protein interactions of the neddylation complexes has been pursued as a potential strategy to selectively inhibit the activity of individual CRL. Analysis of the co-crystal structures of DCN1, a co-E3 for neddylation, and its binding partners UBC12 (a neddylation E2) suggested that it may be amenable for the design of potent, small-molecule inhibitors. In this chapter, we will review the discovery of small-molecule inhibitors that block the interactions of DCN1 with UBC12 (hereafter called DCN1 inhibitors) from a number of laboratories, including ours, leading to selective inactivation of CRL-1 and/or CRL-3. We will also discuss potential therapeutic applications of these small-molecule inhibitors.
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Affiliation(s)
- Haibin Zhou
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Jianfeng Lu
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Chao-Yie Yang
- Department of Pharmaceutical Sciences, College of Pharmacy, The University of Tennessee Health Sciences Center, Memphis, TN, USA
| | - Yi Sun
- Division of Radiation and Cancer Biology, Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, USA
| | - Shaomeng Wang
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA. .,Department of Pharmacology, University of Michigan, Ann Arbor, MI, USA. .,Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI, USA.
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Lázaro DF, Outeiro TF. The Interplay Between Proteostasis Systems and Parkinson’s Disease. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1233:223-236. [DOI: 10.1007/978-3-030-38266-7_9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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Alam I, Cui DL, Batool K, Yang YQ, Lu YH. Comprehensive Genomic Survey, Characterization and Expression Analysis of the HECT Gene Family in Brassica rapa L. and Brassica oleracea L. Genes (Basel) 2019; 10:genes10050400. [PMID: 31137879 PMCID: PMC6562426 DOI: 10.3390/genes10050400] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2019] [Revised: 05/11/2019] [Accepted: 05/13/2019] [Indexed: 11/16/2022] Open
Abstract
The HECT-domain protein family is one of the most important classes of E3 ligases. While the roles of this family in human diseases have been intensively studied, the information for plant HECTs is limited. In the present study, we performed the identification of HECT genes in Brassica rapa and Brassica oleracea, followed by analysis of phylogeny, gene structure, additional domains, putative cis-regulatory elements, chromosomal location, synteny, and expression. Ten and 13 HECT genes were respectively identified in B. rapa and B. oleracea and then resolved into seven groups along with their Arabidopsis orthologs by phylogenetic analysis. This classification is well supported by analyses of gene structure, motif composition within the HECT domain and additional protein domains. Ka/Ks ratio analysis showed that these HECT genes primarily underwent purifying selection with varied selection pressures resulting in different rates of evolution. RNA-Seq data analysis showed that the overwhelming majority of them were constitutively expressed in all tested tissues. qRT-PCR based expression analysis of the 10 B. rapa HECT genes under salt and drought stress conditions showed that all of them were responsive to the two stress treatments, which was consistent with their promoter sequence analysis revealing the presence of an important number of phytohormone-responsive and stress-related cis-regulatory elements. Our study provides useful information and lays the foundation for further functional determination of each HECT gene across the Brassica species.
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Affiliation(s)
- Intikhab Alam
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Dong-Li Cui
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Khadija Batool
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Sciences, Key Lab of Biopesticides and Chemical Biology, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Yan-Qing Yang
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Yun-Hai Lu
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
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Sircar S, Parekh N. Meta-analysis of drought-tolerant genotypes in Oryza sativa: A network-based approach. PLoS One 2019; 14:e0216068. [PMID: 31059518 PMCID: PMC6502313 DOI: 10.1371/journal.pone.0216068] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Accepted: 04/12/2019] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Drought is a severe environmental stress. It is estimated that about 50% of the world rice production is affected mainly by drought. Apart from conventional breeding strategies to develop drought-tolerant crops, innovative computational approaches may provide insights into the underlying molecular mechanisms of stress response and identify drought-responsive markers. Here we propose a network-based computational approach involving a meta-analytic study of seven drought-tolerant rice genotypes under drought stress. RESULTS Co-expression networks enable large-scale analysis of gene-pair associations and tightly coupled clusters that may represent coordinated biological processes. Considering differentially expressed genes in the co-expressed modules and supplementing external information such as resistance/tolerance QTLs, transcription factors, network-based topological measures, we identify and prioritize drought-adaptive co-expressed gene modules and potential candidate genes. Using the candidate genes that are well-represented across the datasets as 'seed' genes, two drought-specific protein-protein interaction networks (PPINs) are constructed with up- and down-regulated genes. Cluster analysis of the up-regulated PPIN revealed ABA signalling pathway as a central process in drought response with a probable crosstalk with energy metabolic processes. Tightly coupled gene clusters representing up-regulation of core cellular respiratory processes and enhanced degradation of branched chain amino acids and cell wall metabolism are identified. Cluster analysis of down-regulated PPIN provides a snapshot of major processes associated with photosynthesis, growth, development and protein synthesis, most of which are shut down during drought. Differential regulation of phytohormones, e.g., jasmonic acid, cell wall metabolism, signalling and posttranslational modifications associated with biotic stress are elucidated. Functional characterization of topologically important, drought-responsive uncharacterized genes that may play a role in important processes such as ABA signalling, calcium signalling, photosynthesis and cell wall metabolism is discussed. Further transgenic studies on these genes may help in elucidating their biological role under stress conditions. CONCLUSION Currently, a large number of resources for rice functional genomics exist which are mostly underutilized by the scientific community. In this study, a computational approach integrating information from various resources such as gene co-expression networks, protein-protein interactions and pathway-level information is proposed to provide a systems-level view of complex drought-responsive processes across the drought-tolerant genotypes.
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Affiliation(s)
- Sanchari Sircar
- Centre for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad, India
| | - Nita Parekh
- Centre for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad, India
- * E-mail:
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50
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Song Y, Park PMC, Wu L, Ray A, Picaud S, Li D, Wimalasena VK, Du T, Filippakopoulos P, Anderson KC, Qi J, Chauhan D. Development and preclinical validation of a novel covalent ubiquitin receptor Rpn13 degrader in multiple myeloma. Leukemia 2019; 33:2685-2694. [PMID: 30962579 DOI: 10.1038/s41375-019-0467-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Accepted: 03/25/2019] [Indexed: 12/13/2022]
Abstract
Proteasome inhibition is an effective treatment for multiple myeloma (MM); however, targeting different components of the ubiquitin-proteasome system (UPS) remains elusive. Our RNA-interference studies identified proteasome-associated ubiquitin-receptor Rpn13 as a mediator of MM cell growth and survival. Here, we developed the first degrader of Rpn13, WL40, using a small-molecule-induced targeted protein degradation strategy to selectively degrade this component of the UPS. WL40 was synthesized by linking the Rpn13 covalent inhibitor RA190 with the cereblon (CRBN) binding ligand thalidomide. We show that WL40 binds to both Rpn13 and CRBN and triggers degradation of cellular Rpn13, and is therefore first-in-class in exploiting a covalent inhibitor for the development of degraders. Biochemical and cellular studies show that WL40-induced Rpn13 degradation is both CRBN E3 ligase- and Rpn13-dependent. Importantly, WL40 decreases viability in MM cell lines and patient MM cells, even those resistant to bortezomib. Mechanistically, WL40 interrupts Rpn13 function and activates caspase apoptotic cascade, ER stress response and p53/p21 signaling. In animal model studies, WL40 inhibits xenografted human MM cell growth and prolongs survival. Overall, our data show the development of the first UbR Rpn13 degrader with potent anti-MM activity, and provide proof of principle for the development of degraders targeting components of the UPS for therapeutic application.
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Affiliation(s)
- Yan Song
- LeBow Institute for Myeloma Therapeutics and Jerome Lipper Myeloma Center, Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Paul M C Park
- Department of Cancer Biology, Dana-Farber Cancer Institute, Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Lei Wu
- Department of Cancer Biology, Dana-Farber Cancer Institute, Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Arghya Ray
- LeBow Institute for Myeloma Therapeutics and Jerome Lipper Myeloma Center, Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | | | - Deyao Li
- Department of Cancer Biology, Dana-Farber Cancer Institute, Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Virangika K Wimalasena
- Department of Cancer Biology, Dana-Farber Cancer Institute, Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Ting Du
- LeBow Institute for Myeloma Therapeutics and Jerome Lipper Myeloma Center, Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | | | - Kenneth C Anderson
- LeBow Institute for Myeloma Therapeutics and Jerome Lipper Myeloma Center, Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.
| | - Jun Qi
- Department of Cancer Biology, Dana-Farber Cancer Institute, Department of Medicine, Harvard Medical School, Boston, MA, USA.
| | - Dharminder Chauhan
- LeBow Institute for Myeloma Therapeutics and Jerome Lipper Myeloma Center, Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.
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