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Li YD, Liu YC, Jiang YX, Namisy A, Chung WH, Sun YH, Chen SY. Analyzing genetic diversity in luffa and developing a Fusarium wilt-susceptible linked SNP marker through a single plant genome-wide association (sp-GWAS) study. BMC PLANT BIOLOGY 2024; 24:307. [PMID: 38644483 PMCID: PMC11034075 DOI: 10.1186/s12870-024-05022-7] [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: 08/15/2023] [Accepted: 04/15/2024] [Indexed: 04/23/2024]
Abstract
BACKGROUND Luffa (Luffa spp.) is an economically important crop of the Cucurbitaceae family, commonly known as sponge gourd or vegetable gourd. It is an annual cross-pollinated crop primarily found in the subtropical and tropical regions of Asia, Australia, Africa, and the Americas. Luffa serves not only as a vegetable but also exhibits medicinal properties, including anti-inflammatory, antidiabetic, and anticancer effects. Moreover, the fiber derived from luffa finds extensive applications in various fields such as biotechnology and construction. However, luffa Fusarium wilt poses a severe threat to its production, and existing control methods have proven ineffective in terms of cost-effectiveness and environmental considerations. Therefore, there is an urgent need to develop luffa varieties resistant to Fusarium wilt. Single-plant GWAS (sp-GWAS) has been demonstrated as a promising tool for the rapid and efficient identification of quantitative trait loci (QTLs) associated with target traits, as well as closely linked molecular markers. RESULTS In this study, a collection of 97 individuals from 73 luffa accessions including two major luffa species underwent single-plant GWAS to investigate luffa Fusarium wilt resistance. Utilizing the double digest restriction site associated DNA (ddRAD) method, a total of 8,919 high-quality single nucleotide polymorphisms (SNPs) were identified. The analysis revealed the potential for Fusarium wilt resistance in accessions from both luffa species. There are 6 QTLs identified from 3 traits, including the area under the disease progress curve (AUDPC), a putative disease-resistant QTL, was identified on the second chromosome of luffa. Within the region of linkage disequilibrium, a candidate gene homologous to LOC111009722, which encodes peroxidase 40 and is associated with disease resistance in Cucumis melo, was identified. Furthermore, to validate the applicability of the marker associated with resistance from sp-GWAS, an additional set of 21 individual luffa plants were tested, exhibiting 93.75% accuracy in detecting susceptible of luffa species L. aegyptiaca Mill. CONCLUSION In summary, these findings give a hint of genome position that may contribute to luffa wild resistance to Fusarium and can be utilized in the future luffa wilt resistant breeding programs aimed at developing wilt-resistant varieties by using the susceptible-linked SNP marker.
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Affiliation(s)
- Yun-Da Li
- Department of Agronomy, National Chung-Hsing University, Taichung, Taiwan
| | - Yu-Chi Liu
- Department of Agronomy, National Chung-Hsing University, Taichung, Taiwan
| | - Yu-Xuan Jiang
- Department of Agronomy, National Chung-Hsing University, Taichung, Taiwan
| | - Ahmed Namisy
- Department of Plant Pathology, National Chung-Hsing University, Taichung, Taiwan
| | - Wen-Hsin Chung
- Department of Plant Pathology, National Chung-Hsing University, Taichung, Taiwan
| | - Ying-Hsuan Sun
- Department of Forestry, National Chung-Hsing University, Taichung, Taiwan
| | - Shu-Yun Chen
- Department of Agronomy, National Chung-Hsing University, Taichung, Taiwan.
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Li W, Wang Z. Ubiquitination Process Mediates Prostate Cancer Development and Metastasis through Multiple Mechanisms. Cell Biochem Biophys 2024; 82:77-90. [PMID: 37847340 PMCID: PMC10866789 DOI: 10.1007/s12013-023-01156-x] [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: 01/07/2023] [Accepted: 07/30/2023] [Indexed: 10/18/2023]
Abstract
Prostate cancer (PCa) is a common malignant tumor in men, when the disease progresses to the advanced stage, most patients will develop distant metastasis and develop into castration-resistant prostate cancer (CRPC), resulting in increased mortality. Ubiquitination is a widespread protein post-translational modification process in the biological world, and it plays an important role in the development and transfer of PCa. E3 ubiquitin ligase plays an important role in the specific selection and role of substrates in the process of ubiquitination ligase. This review will briefly introduce the ubiquitination process and E3 ubiquitin ligase, focus on the recently discovered multiple mechanisms by which ubiquitination affects PCa development and metastasis, and a summary of the current emerging proteolysis-targeting chimeras (PROTAC) in the treatment of PCa.
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Affiliation(s)
- Wen Li
- Department of Immuno-Oncology, The Fourth Hospital of Hebei Medical University, Shijiazhuang, China
| | - Zhiyu Wang
- Department of Immuno-Oncology, The Fourth Hospital of Hebei Medical University, Shijiazhuang, China.
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Jin B, Li B, Qu J, Sun Y, Wang M, Yang C, Fan Y, Wang Y, Xu P, Sun H, Jiang B, Zhao B. Recruitment of ubiquitin E2 enzymes is determined jointly by the U-box domains and substrates of E3 ligases. FEBS Lett 2024; 598:702-715. [PMID: 38439679 DOI: 10.1002/1873-3468.14845] [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: 12/19/2023] [Revised: 01/29/2024] [Accepted: 02/09/2024] [Indexed: 03/06/2024]
Abstract
Ubiquitination is a cascade reaction involving E1, E2, and E3 enzymes. The orthogonal ubiquitin transfer (OUT) method has been previously established to identify potential substrates of E3 ligases. In this study, we verified the ubiquitination of five substrates mediated by the E3 ligases CHIP and E4B. To further explore the activity of U-box domains of E3 ligases, two mutants with the U-box domains interchanged between CHIP and E4B were generated. They exhibited a significantly reduced ubiquitination ability. Additionally, different E3s recruited similar E2 ubiquitin-conjugating enzymes when ubiquitinating the same substrates, highlighting that U-box domains determined the E2 recruitment, while the substrate determined the E2 selectivity. This study reveals the influence of substrates and U-box domains on E2 recruitment, providing a novel perspective on the function of U-box domains of E3 ligases.
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Affiliation(s)
- Bo Jin
- Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, and School of Pharmacy, Shanghai Jiao Tong University, China
| | - Bei Li
- Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, and School of Pharmacy, Shanghai Jiao Tong University, China
| | - Junyao Qu
- Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, and School of Pharmacy, Shanghai Jiao Tong University, China
| | - Yiheng Sun
- Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, and School of Pharmacy, Shanghai Jiao Tong University, China
| | - Mengran Wang
- Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, and School of Pharmacy, Shanghai Jiao Tong University, China
| | - Changjiang Yang
- Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, and School of Pharmacy, Shanghai Jiao Tong University, China
| | - Yuchen Fan
- Nanjing Institute of Measurement and Testing Technology, China
| | - Yanan Wang
- Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, and School of Pharmacy, Shanghai Jiao Tong University, China
| | - Peng Xu
- Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, and School of Pharmacy, Shanghai Jiao Tong University, China
| | - Haiying Sun
- Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, and School of Pharmacy, Shanghai Jiao Tong University, China
| | - Bo Jiang
- Department of Hand and Foot Surgery, The Second Affiliated Hospital of Soochow University, Suzhou, China
- State Key Laboratory of Radiation Medicine and Protection, Soochow University, Suzhou, China
| | - Bo Zhao
- Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, and School of Pharmacy, Shanghai Jiao Tong University, China
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Parolini F, Ataie Kachoie E, Leo G, Civiero L, Bubacco L, Arrigoni G, Munari F, Assfalg M, D'Onofrio M, Capaldi S. Site-Specific Ubiquitination of Tau Amyloids Promoted by the E3 Ligase CHIP. Angew Chem Int Ed Engl 2023; 62:e202310230. [PMID: 37878393 DOI: 10.1002/anie.202310230] [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: 07/18/2023] [Revised: 10/13/2023] [Accepted: 10/25/2023] [Indexed: 10/27/2023]
Abstract
Post-translational modifications of Tau are emerging as key players in determining the onset and progression of different tauopathies such as Alzheimer's disease, and are recognized to mediate the structural diversity of the disease-specific Tau amyloids. Here we show that the E3 ligase CHIP catalyzes the site-specific ubiquitination of Tau filaments both in vitro and in cellular models, proving that also Tau amyloid aggregates are direct substrate of PTMs. Transmission electron microscopy and mass spectrometry analysis on ubiquitin-modified Tau amyloids revealed that the conformation of the filaments restricts CHIP-mediated ubiquitination to specific positions of the repeat domain, while only minor alterations in the structure of the fibril core were inferred using seeding experiments in vitro and in a cell-based tauopathy model. Overexpression of CHIP significantly increased the ubiquitination of exogenous PHF, proving that the ligase can interact and modify Tau aggregates also in a complex cellular environment.
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Affiliation(s)
| | | | - Giulia Leo
- Department of Biotechnology, University of Verona, 37134, Verona, Italy
| | - Laura Civiero
- Department of Biology, University of Padova, 35121, Padova, Italy
- IRCCS San Camillo Hospital, 30126, Venice, Italy
| | - Luigi Bubacco
- Department of Biology, University of Padova, 35121, Padova, Italy
| | - Giorgio Arrigoni
- Department of Biomedical Sciences, University of Padova, 35131, Padova, Italy
- Proteomics Center, University of Padova and Azienda Ospedaliera di Padova, 35131, Padova, Italy
| | - Francesca Munari
- Department of Biotechnology, University of Verona, 37134, Verona, Italy
| | - Michael Assfalg
- Department of Biotechnology, University of Verona, 37134, Verona, Italy
| | | | - Stefano Capaldi
- Department of Biotechnology, University of Verona, 37134, Verona, Italy
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5
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Zhou Z, Zheng K, Zhou S, Yang Y, Chen J, Jin X. E3 ubiquitin ligases in nasopharyngeal carcinoma and implications for therapies. J Mol Med (Berl) 2023; 101:1543-1565. [PMID: 37796337 DOI: 10.1007/s00109-023-02376-7] [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: 11/08/2022] [Revised: 09/05/2023] [Accepted: 09/14/2023] [Indexed: 10/06/2023]
Abstract
Nasopharyngeal carcinoma (NPC) is one of the most common squamous cell carcinomas of the head and neck, and Epstein-Barr virus (EBV) infection is one of the pathogenic factors involved in the oncogenetic development and progression of NPC. E3 ligases, which are key members of the ubiquitin proteasome system (UPS), specifically recognize various oncogenic factors and tumor suppressors and contribute to determining their fate through ubiquitination. Several studies have demonstrated that E3 ligases are aberrantly expressed and mutated in NPC and that these changes are closely associated with the occurrence and progression of NPC. Herein, we aim to thoroughly review the specific action mechanisms by which E3 ligases participate in NPC signaling pathways and discuss their functional relationship with EBV. Moreover, we describe the current progress in and limitations for targeted therapies against E3 ligases in NPC. KEY MESSAGES: • E3 ubiquitin ligases, as members of the UPS system, determine the fate of their substrates and may act either as oncogenic or anti-tumorigenic factors in NPC. • Mutations or dysregulated expression of E3 ubiquitin ligases is closely related to the occurrence, development, and therapeutic sensitivity of NPC, as they play important roles in several signaling pathways affected by EBV infection. • As promising therapeutic targets, E3 ligases may open new avenues for treatment and for improving the prognosis of NPC patients.
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Affiliation(s)
- Zijian Zhou
- Department of Chemoradiotherapy, The Affiliated People's Hospital of Ningbo University, Ningbo, 315040, China
| | - Kaifeng Zheng
- Department of Chemoradiotherapy, The Affiliated People's Hospital of Ningbo University, Ningbo, 315040, China
| | - Shao Zhou
- Department of Otolaryngology-Head and Neck Surgery, The Affiliated People's Hospital of Ningbo University, Ningbo, 315040, China
| | - Youxiong Yang
- Department of Otolaryngology-Head and Neck Surgery, Ningbo Yinzhou Second Hospital, Ningbo, 315199, China.
| | - Jun Chen
- Department of Chemoradiotherapy, The Affiliated People's Hospital of Ningbo University, Ningbo, 315040, China.
| | - Xiaofeng Jin
- Department of Chemoradiotherapy, The Affiliated People's Hospital of Ningbo University, Ningbo, 315040, China.
- Department of Biochemistry and Molecular Biology, and Zhejiang Key Laboratory of Pathophysiology, Health Science Center of Ningbo University, Ningbo, 315211, China.
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6
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Dong Y, Chen Y, Ma G, Cao H. The role of E3 ubiquitin ligases in bone homeostasis and related diseases. Acta Pharm Sin B 2023; 13:3963-3987. [PMID: 37799379 PMCID: PMC10547920 DOI: 10.1016/j.apsb.2023.06.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 05/16/2023] [Accepted: 05/18/2023] [Indexed: 10/07/2023] Open
Abstract
The ubiquitin-proteasome system (UPS) dedicates to degrade intracellular proteins to modulate demic homeostasis and functions of organisms. These enzymatic cascades mark and modifies target proteins diversly through covalently binding ubiquitin molecules. In the UPS, E3 ubiquitin ligases are the crucial constituents by the advantage of recognizing and presenting proteins to proteasomes for proteolysis. As the major regulators of protein homeostasis, E3 ligases are indispensable to proper cell manners in diverse systems, and they are well described in physiological bone growth and bone metabolism. Pathologically, classic bone-related diseases such as metabolic bone diseases, arthritis, bone neoplasms and bone metastasis of the tumor, etc., were also depicted in a UPS-dependent manner. Therefore, skeletal system is versatilely regulated by UPS and it is worthy to summarize the underlying mechanism. Furthermore, based on the current status of treatment, normal or pathological osteogenesis and tumorigenesis elaborated in this review highlight the clinical significance of UPS research. As a strategy possibly remedies the limitations of UPS treatment, emerging PROTAC was described comprehensively to illustrate its potential in clinical application. Altogether, the purpose of this review aims to provide more evidence for exploiting novel therapeutic strategies based on UPS for bone associated diseases.
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Affiliation(s)
| | | | - Guixing Ma
- Department of Biochemistry, School of Medicine, Southern University of Science and Technology, Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, Key University Laboratory of Metabolism and Health of Guangdong, Shenzhen 518055, China
| | - Huiling Cao
- Department of Biochemistry, School of Medicine, Southern University of Science and Technology, Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, Key University Laboratory of Metabolism and Health of Guangdong, Shenzhen 518055, China
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Liu T, Chen J, Wu J, Du Q, Liu J, Tan S, Pan Y, Yao S. Role of the tripartite motif (TRIM) family in female genital neoplasms. Pathol Res Pract 2023; 250:154811. [PMID: 37713735 DOI: 10.1016/j.prp.2023.154811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 09/03/2023] [Accepted: 09/08/2023] [Indexed: 09/17/2023]
Abstract
The tripartite motif proteins (TRIMs) family represents a class of highly conservative proteins which play a large regulatory role in molecular processes. Recently, increasing evidence has demonstrated a role of TRIMs in female genital neoplasms. Our review thereby aimed to provide an overview of the biological involvement of TRIMs in female genital neoplasms, to provide a better understanding of its role in the development and progression of such diseases, and emphasize its potential as targeted cancer therapy. Overall, our review highlighted that the wide-ranging roles of TRIMs, in not only target protein ubiquitination, tumor migration and/or invasion, epithelial-mesenchymal transition, stemness, cell adhesion, proliferation, cell cycle regulation, and apoptosis, but also in influencing estrogenic, and chemotherapy response.
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Affiliation(s)
- Tianyu Liu
- Department of Obstetrics and Gynecology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China; Guangdong Provincial Clinical Research Center for Obstetrical and Gynecological Diseases, Guangzhou, Guangdong, China
| | - Jian Chen
- Department of Thyroid and Hernia Surgery, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Jinjie Wu
- Department of Colorectal Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Qiqiao Du
- Department of Obstetrics and Gynecology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China; Guangdong Provincial Clinical Research Center for Obstetrical and Gynecological Diseases, Guangzhou, Guangdong, China
| | - Junxiu Liu
- Department of Obstetrics and Gynecology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China; Guangdong Provincial Clinical Research Center for Obstetrical and Gynecological Diseases, Guangzhou, Guangdong, China
| | - Silu Tan
- Department of Obstetrics and Gynecology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China; Guangdong Provincial Clinical Research Center for Obstetrical and Gynecological Diseases, Guangzhou, Guangdong, China
| | - Yuwen Pan
- Department of Obstetrics and Gynecology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China; Guangdong Provincial Clinical Research Center for Obstetrical and Gynecological Diseases, Guangzhou, Guangdong, China
| | - Shuzhong Yao
- Department of Obstetrics and Gynecology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China; Guangdong Provincial Clinical Research Center for Obstetrical and Gynecological Diseases, Guangzhou, Guangdong, China.
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Fang S, Chen G, Wang Y, Ganti R, Chernova TA, Zhou L, Jacobs SE, Duong D, Kiyokawa H, Chernoff YO, Li M, Shcherbik N, Zhao B, Yin J. Profiling and verifying the substrates of E3 ubiquitin ligase Rsp5 in yeast cells. STAR Protoc 2023; 4:102489. [PMID: 37561636 PMCID: PMC10440593 DOI: 10.1016/j.xpro.2023.102489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 04/07/2023] [Accepted: 07/11/2023] [Indexed: 08/12/2023] Open
Abstract
Yeast is an essential model organism for studying protein ubiquitination pathways; however, identifying the direct substrates of E3 in the cell presents a challenge. Here, we present a protocol for using the orthogonal ubiquitin transfer (OUT) cascade to profile the substrate specificity of yeast E3 Rsp5. We describe steps for OUT profiling, proteomics analysis, in vitro and in cell ubiquitination, and stability assay. The protocol can be adapted for identifying and verifying the ubiquitination targets of other E3s in yeast. For complete details on the use and execution of this protocol, please refer to Wang et al.1.
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Affiliation(s)
- Shuai Fang
- Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, and School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China; Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303, USA
| | - Geng Chen
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303, USA; Kobilka Institute of Innovative Drug Discovery, School of Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen, Guangdong 518172, China
| | - Yiyang Wang
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303, USA; Department of Pathophysiology, School of Medicine, Jinan University, Guangzhou, Guangdong 510632, China
| | - Rakhee Ganti
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Tatiana A Chernova
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Li Zhou
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303, USA
| | - Savannah E Jacobs
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303, USA
| | - Duc Duong
- Integrated Proteomics Core, Emory University, Atlanta, GA 30322, USA
| | - Hiroaki Kiyokawa
- Department of Pharmacology, Northwestern University, Chicago, IL 60611, USA
| | - Yury O Chernoff
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Ming Li
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI 48019, USA
| | - Natalia Shcherbik
- Department of Cell Biology and Neuroscience, Rowan University School of Osteopathic Medicine, Stratford, NJ 08084, USA.
| | - Bo Zhao
- Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, and School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China.
| | - Jun Yin
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303, USA.
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Guo F, Ye Y, Zhu K, Lin S, Wang Y, Dong Z, Yao R, Li H, Wang W, Liao Z, Guo B, Yan X. Genetic Diversity, Population Structure, and Environmental Adaptation Signatures of Chinese Coastal Hard-Shell Mussel Mytilus coruscus Revealed by Whole-Genome Sequencing. Int J Mol Sci 2023; 24:13641. [PMID: 37686445 PMCID: PMC10488143 DOI: 10.3390/ijms241713641] [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: 07/21/2023] [Revised: 08/28/2023] [Accepted: 08/28/2023] [Indexed: 09/10/2023] Open
Abstract
The hard-shell mussel (Mytilus coruscus) is widespread in the temperate coastal areas of the northwest Pacific and holds a significant position in the shellfish aquaculture market in China. However, the natural resources of this species have been declining, and population genetic studies of M. coruscus are also lacking. In this study, we conducted whole-genome resequencing (WGR) of M. coruscus from eight different latitudes along the Chinese coast and identified a total of 25,859,986 single nucleotide polymorphism (SNP) markers. Our findings indicated that the genetic diversity of M. coruscus from the Zhoushan region was lower compared with populations from other regions. Furthermore, we observed that the evolutionary tree clustered into two primary branches, and the Zhangzhou (ZZ) population was in a separate branch. The ZZ population was partly isolated from populations in other regions, but the distribution of branches was not geographically homogeneous, and a nested pattern emerged, consistent with the population differentiation index (FST) results. To investigate the selection characteristics, we utilized the northern M. coruscus populations (Dalian and Qingdao) and the central populations (Zhoushan and Xiangshan) as reference populations and the southern ZZ population as the target population. Our selection scan analysis identified several genes associated with thermal responses, including Hsp70 and CYP450. These genes may play important roles in the adaptation of M. coruscus to different living environments. Overall, our study provides a comprehensive understanding of the genomic diversity of coastal M. coruscus in China and is a valuable resource for future studies on genetic breeding and the evolutionary adaptation of this species.
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Affiliation(s)
- Feng Guo
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan 316022, China; (F.G.); (Y.Y.); (S.L.); (H.L.)
| | - Yingying Ye
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan 316022, China; (F.G.); (Y.Y.); (S.L.); (H.L.)
| | - Kecheng Zhu
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China;
| | - Shuangrui Lin
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan 316022, China; (F.G.); (Y.Y.); (S.L.); (H.L.)
| | - Yuxia Wang
- Marine Science and Technology College, Zhejiang Ocean University, Zhoushan 316022, China; (Y.W.); (Z.D.); (R.Y.); (W.W.); (Z.L.)
| | - Zhenyu Dong
- Marine Science and Technology College, Zhejiang Ocean University, Zhoushan 316022, China; (Y.W.); (Z.D.); (R.Y.); (W.W.); (Z.L.)
| | - Ronghui Yao
- Marine Science and Technology College, Zhejiang Ocean University, Zhoushan 316022, China; (Y.W.); (Z.D.); (R.Y.); (W.W.); (Z.L.)
| | - Hongfei Li
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan 316022, China; (F.G.); (Y.Y.); (S.L.); (H.L.)
| | - Weifeng Wang
- Marine Science and Technology College, Zhejiang Ocean University, Zhoushan 316022, China; (Y.W.); (Z.D.); (R.Y.); (W.W.); (Z.L.)
| | - Zhi Liao
- Marine Science and Technology College, Zhejiang Ocean University, Zhoushan 316022, China; (Y.W.); (Z.D.); (R.Y.); (W.W.); (Z.L.)
| | - Baoying Guo
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan 316022, China; (F.G.); (Y.Y.); (S.L.); (H.L.)
- Marine Science and Technology College, Zhejiang Ocean University, Zhoushan 316022, China; (Y.W.); (Z.D.); (R.Y.); (W.W.); (Z.L.)
| | - Xiaojun Yan
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan 316022, China; (F.G.); (Y.Y.); (S.L.); (H.L.)
- Marine Science and Technology College, Zhejiang Ocean University, Zhoushan 316022, China; (Y.W.); (Z.D.); (R.Y.); (W.W.); (Z.L.)
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10
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Liu Y, Zhou H, Tang X. STUB1/CHIP: New insights in cancer and immunity. Biomed Pharmacother 2023; 165:115190. [PMID: 37506582 DOI: 10.1016/j.biopha.2023.115190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Revised: 07/12/2023] [Accepted: 07/18/2023] [Indexed: 07/30/2023] Open
Abstract
The STUB1 gene (STIP1 homology and U-box-containing protein 1), located at 16q13.3, encodes the CHIP (carboxyl terminus of Hsc70-interacting protein), an essential E3 ligase involved in protein quality control. CHIP comprises three domains: an N-terminal tetratricopeptide repeat (TPR) domain, a middle coiled-coil domain, and a C-terminal U-box domain. It functions as a co-chaperone for heat shock protein (HSP) via the TPR domain and as an E3 ligase, ubiquitinating substrates through its U-box domain. Numerous studies suggest that STUB1 plays a crucial role in various physiological process, such as aging, autophagy, and bone remodeling. Moreover, emerging evidence has shown that STUB1 can degrade oncoproteins to exert tumor-suppressive functions, and it has recently emerged as a novel player in tumor immunity. This review provides a comprehensive overview of STUB1's role in cancer, including its clinical significance, impact on tumor progression, dual roles, tumor stem cell-like properties, angiogenesis, drug resistance, and DNA repair. In addition, we explore STUB1's functions in immune cell differentiation and maturation, inflammation, autoimmunity, antiviral immune response, and tumor immunity. Collectively, STUB1 represents a promising and valuable therapeutic target in cancer and immunology.
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Affiliation(s)
- Yongshuo Liu
- Biomedical Pioneering Innovation Center (BIOPIC), Beijing Advanced Innovation Center for Genomics, Peking-Tsinghua Center for Life Sciences, Peking University Genome Editing Research Center, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China.
| | - Honghong Zhou
- Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiaolong Tang
- Biomedical Pioneering Innovation Center (BIOPIC), Beijing Advanced Innovation Center for Genomics, Peking-Tsinghua Center for Life Sciences, Peking University Genome Editing Research Center, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China.
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11
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Li S, Yao X, Zhang B, Tang H, Lu L. Genome-wide characterization of the U-box gene in Camellia sinensis and functional analysis in transgenic tobacco under abiotic stresses. Gene 2023; 865:147301. [PMID: 36813060 DOI: 10.1016/j.gene.2023.147301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 12/16/2022] [Accepted: 02/16/2023] [Indexed: 02/22/2023]
Abstract
Plants U-box genes are crucial for plant survival, and they extensively regulate plant growth, reproduction and development as well as coping with stress and other processes. In this study, we identified 92 CsU-box genes through genome-wide analysis in the tea plant (Camellia sinensis), all of them contained the conserved U-box domain and were divided into 5 groups, which supported by the further genes structure analysis. The expression profiles in eight tea plant tissues and under abiotic and hormone stresses were analyzed using the TPIA database. 7 CsU-box genes (CsU-box27/28/39/46/63/70/91) were selected to verify and analyze expression patterns under PEG-induced drought and heat stress in tea plant respectively, the qRT-PCR results showed consistent with transcriptome datasets; and the CsU-box39 were further heterologous expressed in tobacco to perform gene function analysis. Phenotypic analyses of overexpression transgenic tobacco seedlings and physiological experiments revealed that CsU-box39 positively regulated the plant response to drought stress. These results lay a solid foundation for studying the biological function of CsU-box, and will provide breeding strategy basis for tea plant breeders.
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Affiliation(s)
- Shiyu Li
- College of Tea Sciences, Guizhou University, Guiyang 550025, China
| | - Xinzhuan Yao
- College of Tea Sciences, Guizhou University, Guiyang 550025, China
| | - Baohui Zhang
- Institute of Agricultural Bioengineering/College of Life Sciences, Key Laboratory of Mountain Plant Resources Conservation and Germplasm Innovation, Ministry of Education, Collaborative Innovation Center for Mountain Ecology and Agricultural Bioengineering, Guiyang 550025, China
| | - Hu Tang
- College of Tea Sciences, Guizhou University, Guiyang 550025, China; Institute of Agricultural Bioengineering/College of Life Sciences, Key Laboratory of Mountain Plant Resources Conservation and Germplasm Innovation, Ministry of Education, Collaborative Innovation Center for Mountain Ecology and Agricultural Bioengineering, Guiyang 550025, China.
| | - Litang Lu
- College of Tea Sciences, Guizhou University, Guiyang 550025, China; Institute of Agricultural Bioengineering/College of Life Sciences, Key Laboratory of Mountain Plant Resources Conservation and Germplasm Innovation, Ministry of Education, Collaborative Innovation Center for Mountain Ecology and Agricultural Bioengineering, Guiyang 550025, China.
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12
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Kleissl L, Weinmüllner R, Lämmermann I, Dingelmaier-Hovorka R, Jafarmadar M, El Ghalbzouri A, Stary G, Grillari J, Dellago H. PRPF19 modulates morphology and growth behavior in a cell culture model of human skin. FRONTIERS IN AGING 2023; 4:1154005. [PMID: 37214773 PMCID: PMC10196211 DOI: 10.3389/fragi.2023.1154005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 04/11/2023] [Indexed: 05/24/2023]
Abstract
The skin provides one of the most visual aging transformations in humans, and premature aging as a consequence of oxidative stress and DNA damage is a frequently seen effect. Cells of the human skin are continuously exposed to endogenous and exogenous DNA damaging factors, which can cause DNA damage in all phases of the cell cycle. Increased levels of DNA damage and/or defective DNA repair can, therefore, accelerate the aging process and/or lead to age-related diseases like cancer. It is not yet clear if enhanced activity of DNA repair factors could increase the life or health span of human skin cells. In previous studies, we identified and characterized the human senescence evasion factor (SNEV)/pre-mRNA-processing factor (PRPF) 19 as a multitalented protein involved in mRNA splicing, DNA repair pathways and lifespan regulation. Here, we show that overexpression of PRPF19 in human dermal fibroblasts leads to a morphological change, reminiscent of juvenile, papillary fibroblasts, despite simultaneous expression of senescence markers. Moreover, conditioned media of this subpopulation showed a positive effect on keratinocyte repopulation of wounded areas. Taken together, these findings indicate that PRPF19 promotes cell viability and slows down the aging process in human skin.
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Affiliation(s)
- Lisa Kleissl
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Regina Weinmüllner
- Institute of Molecular Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
- Christian Doppler Laboratory for Biotechnology of Skin Aging, Vienna, Austria
| | - Ingo Lämmermann
- Institute of Molecular Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
- Christian Doppler Laboratory for Biotechnology of Skin Aging, Vienna, Austria
| | | | - Mohammad Jafarmadar
- Ludwig Boltzmann Institute for Traumatology in cooperation with AUVA, Vienna, Austria
| | | | - Georg Stary
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Johannes Grillari
- Institute of Molecular Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
- Ludwig Boltzmann Institute for Traumatology in cooperation with AUVA, Vienna, Austria
| | - Hanna Dellago
- Institute of Molecular Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
- Christian Doppler Laboratory for Biotechnology of Skin Aging, Vienna, Austria
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13
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Wang K, Li S, Chen L, Tian H, Chen C, Fu Y, Du H, Hu Z, Li R, Du Y, Li J, Zhao Q, Du C. E3 ubiquitin ligase OsPIE3 destabilises the B-lectin receptor-like kinase PID2 to control blast disease resistance in rice. THE NEW PHYTOLOGIST 2023; 237:1826-1842. [PMID: 36440499 DOI: 10.1111/nph.18637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 11/18/2022] [Indexed: 06/16/2023]
Abstract
Previous studies have reported that PID2, which encodes a B-lectin receptor-like kinase, is a key gene in the resistance of rice to Magnaporthe oryzae strain ZB15. However, the PID2-mediated downstream signalling events remain largely unknown. The U-box E3 ubiquitin ligase OsPIE3 (PID2-interacting E3) was isolated and confirmed to play key roles in PID2-mediated rice blast resistance. Yeast two-hybrid analysis showed that the armadillo repeat region of OsPIE3 is required for its interaction with PID2. Further investigation demonstrated that OsPIE3 can modify the subcellular localisation of PID2, thus promoting its nuclear recruitment from the plasma membrane for protein degradation in the ubiquitin-proteasome system. Site-directed mutagenesis of a conserved cysteine site (C230S) within the U-box domain of OsPIE3 reduces PID2 translocation and ubiquitination. Genetic analysis suggested that OsPIE3 loss-of-function mutants exhibited enhanced resistance to M. oryzae isolate ZB15, whereas mutants with overexpressed OsPIE3 exhibited reduced resistance. Furthermore, the OsPIE3/PID2-double mutant displayed a similar blast phenotype to that of the PID2 single mutant, suggesting that OsPIE3 is a negative regulator and functions along with PID2 in blast disease resistance. Our findings confirm that the E3 ubiquitin ligase OsPIE3 is necessary for PID2-mediated rice blast disease resistance regulation.
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Affiliation(s)
- Ke Wang
- Collaborative Innovation Center of Henan Grain Crops, Key Laboratory of Henan Rice Biology, Center for Crop Genome Engineering, College of Agronomy, Henan Agricultural University, Zhengzhou, 450046, China
| | - Shen Li
- Collaborative Innovation Center of Henan Grain Crops, Key Laboratory of Henan Rice Biology, Center for Crop Genome Engineering, College of Agronomy, Henan Agricultural University, Zhengzhou, 450046, China
| | - Longxin Chen
- Molecular Biology Laboratory, Zhengzhou Normal University, Zhengzhou, 450044, China
| | - Haoran Tian
- Collaborative Innovation Center of Henan Grain Crops, Key Laboratory of Henan Rice Biology, Center for Crop Genome Engineering, College of Agronomy, Henan Agricultural University, Zhengzhou, 450046, China
| | - Cong Chen
- Collaborative Innovation Center of Henan Grain Crops, Key Laboratory of Henan Rice Biology, Center for Crop Genome Engineering, College of Agronomy, Henan Agricultural University, Zhengzhou, 450046, China
| | - Yihan Fu
- Collaborative Innovation Center of Henan Grain Crops, Key Laboratory of Henan Rice Biology, Center for Crop Genome Engineering, College of Agronomy, Henan Agricultural University, Zhengzhou, 450046, China
| | - Haitao Du
- Collaborative Innovation Center of Henan Grain Crops, Key Laboratory of Henan Rice Biology, Center for Crop Genome Engineering, College of Agronomy, Henan Agricultural University, Zhengzhou, 450046, China
| | - Zheng Hu
- Collaborative Innovation Center of Henan Grain Crops, Key Laboratory of Henan Rice Biology, Center for Crop Genome Engineering, College of Agronomy, Henan Agricultural University, Zhengzhou, 450046, China
| | - Runting Li
- Molecular Biology Laboratory, Zhengzhou Normal University, Zhengzhou, 450044, China
| | - Yanxiu Du
- Collaborative Innovation Center of Henan Grain Crops, Key Laboratory of Henan Rice Biology, Center for Crop Genome Engineering, College of Agronomy, Henan Agricultural University, Zhengzhou, 450046, China
| | - Junzhou Li
- Collaborative Innovation Center of Henan Grain Crops, Key Laboratory of Henan Rice Biology, Center for Crop Genome Engineering, College of Agronomy, Henan Agricultural University, Zhengzhou, 450046, China
| | - Quanzhi Zhao
- Collaborative Innovation Center of Henan Grain Crops, Key Laboratory of Henan Rice Biology, Center for Crop Genome Engineering, College of Agronomy, Henan Agricultural University, Zhengzhou, 450046, China
- Rice Industrial Technology Research Institute, Guizhou University, Guiyang, 550025, China
| | - Changqing Du
- Collaborative Innovation Center of Henan Grain Crops, Key Laboratory of Henan Rice Biology, Center for Crop Genome Engineering, College of Agronomy, Henan Agricultural University, Zhengzhou, 450046, China
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14
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Sap KA, Geijtenbeek KW, Schipper-Krom S, Guler AT, Reits EA. Ubiquitin-modifying enzymes in Huntington's disease. Front Mol Biosci 2023; 10:1107323. [PMID: 36926679 PMCID: PMC10013475 DOI: 10.3389/fmolb.2023.1107323] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 01/16/2023] [Indexed: 02/10/2023] Open
Abstract
Huntington's disease (HD) is a neurodegenerative disorder caused by a CAG repeat expansion in the N-terminus of the HTT gene. The CAG repeat expansion translates into a polyglutamine expansion in the mutant HTT (mHTT) protein, resulting in intracellular aggregation and neurotoxicity. Lowering the mHTT protein by reducing synthesis or improving degradation would delay or prevent the onset of HD, and the ubiquitin-proteasome system (UPS) could be an important pathway to clear the mHTT proteins prior to aggregation. The UPS is not impaired in HD, and proteasomes can degrade mHTT entirely when HTT is targeted for degradation. However, the mHTT protein is differently ubiquitinated when compared to wild-type HTT (wtHTT), suggesting that the polyQ expansion affects interaction with (de) ubiquitinating enzymes and subsequent targeting for degradation. The soluble mHTT protein is associated with several ubiquitin-modifying enzymes, and various ubiquitin-modifying enzymes have been identified that are linked to Huntington's disease, either by improving mHTT turnover or affecting overall homeostasis. Here we describe their potential mechanism of action toward improved mHTT targeting towards the proteostasis machinery.
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Affiliation(s)
- Karen A Sap
- Department of Medical Biology, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Karlijne W Geijtenbeek
- Department of Medical Biology, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Sabine Schipper-Krom
- Department of Medical Biology, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Arzu Tugce Guler
- Department of Medical Biology, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Eric A Reits
- Department of Medical Biology, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
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15
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Shao X, Zhu J, Shi Y, Fang H, Chen J, Zhang Y, Wang J, Jian H, Lan S, Jiang F, Zhong F, Zhang Y, Cao C. Upregulated UBE4B expression correlates with poor prognosis and tumor immune infiltration in hepatocellular carcinoma. Aging (Albany NY) 2022; 14:9632-9646. [PMID: 36470669 PMCID: PMC9792214 DOI: 10.18632/aging.204414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 11/23/2022] [Indexed: 12/11/2022]
Abstract
BACKGROUND Hepatocellular carcinoma (HCC) is a major human health concern. Increasing evidence has demonstrated that ubiquitin ligase E4B (UBE4B) may be involved in the occurrence and development of various human cancers and may affect prognosis. However, the specific role and mechanism of UBE4B in HCC is unclear. METHODS A pan-cancer analysis of UBE4B expression, clinicopathological features, and prognosis was performed using bioinformatics techniques. Subsequently, the expression, prognosis, and correlation of UBE4B and its upstream miRNAs and lncRNAs were analyzed. We investigated the relationship between UBE4B expression and immune cell infiltration, immunomodulatory factors, and chemokines in HCC. The expression levels of UBE4B and its upstream lncRNAs (FGD5-AS1, LINC00858, and SNHG16) and miRNAs (hsa-miR-22-3p) were evaluated in HCC cell lines using qRT-PCR. RESULTS UBE4B expression increased in HCC and was correlated with a poor survival rate in patients with HCC. A ceRNA network was established to identify the UBE4B-hsa-miR-22-3p-FGD5-AS1/LINC00858/SNHG16 regulatory axis in HCC. UBE4B expression was significantly associated with immune cell infiltration, immunomodulators, chemokines, and their receptors in HCC. The mRNA expression of FGD5-AS1, LINC00858, SNHG16, and UBE4B was higher in the HCC cell lines (7721 and HepG2) than in the normal hepatocyte line (LO2), and the expression of hsa-miR-22-3p mRNA showed a decreasing trend. CONCLUSIONS Our findings showed that upregulation of UBE4B was associated with poor prognosis and tumor immune infiltration in HCC. These findings will aid in understanding the relevant functions of UBE4B and provide new strategies for drug development and exploration of prognosis-related biomarkers.
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Affiliation(s)
- Xuyang Shao
- Graduate School of Bengbu Medical College, Bengbu 233000, Anhui Province, China,Department of General Surgery, The Second Affiliated Hospital of Jiaxing University, Jiaxing 314000, Zhejiang Province, China
| | - Jun Zhu
- Department of Oncology, Fuyang Hospital of Anhui Medical University, Fuyang 236000, Anhui Province, China
| | - Yanlong Shi
- Hepatopancreatobiliary Center, The Second Affiliated Hospital of Nanjing Medical University, Nanjing 210003, Jiangsu Province, China
| | - Hanlu Fang
- Institute of Medical and Health Science of HeBMU, Hebei Medical University, Shijiazhuang 050017, Hebei Province, China
| | - Jingsi Chen
- Department of Intensive Care Unit, Fuyang Women and Children’s Hospital, Fuyang 236000, Anhui Province, China
| | - Yixiao Zhang
- The First Clinical College of Zhejiang Chinese Medical University, Hangzhou 310053, Zhejiang Province, China
| | - Jingyan Wang
- Department of Anesthesia, Shaoxing People’s Hospital, Shaoxing 312000, Zhejiang Province, China
| | - Haokun Jian
- School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang 453003, Henan Province, China
| | - Sheng Lan
- The Second Clinical College of Guangzhou Medical University, Guangzhou 510030, Guangdong Province, China
| | - Fei Jiang
- Department of General Surgery, Fuyang Hospital of Anhui Medical University, Fuyang 236000, Anhui Province, China
| | - Fei Zhong
- Department of Oncology, Fuyang Hospital of Anhui Medical University, Fuyang 236000, Anhui Province, China,Department of Oncology, The First Affiliated Hospital of Anhui Medical University, Hefei 230000, Anhui Province, China
| | - Yewei Zhang
- Hepatopancreatobiliary Center, The Second Affiliated Hospital of Nanjing Medical University, Nanjing 210003, Jiangsu Province, China
| | - Chenxi Cao
- Graduate School of Bengbu Medical College, Bengbu 233000, Anhui Province, China,Department of General Surgery, The Second Affiliated Hospital of Jiaxing University, Jiaxing 314000, Zhejiang Province, China
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16
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Bouron A, Fauvarque MO. Genome-wide analysis of genes encoding core components of the ubiquitin system during cerebral cortex development. Mol Brain 2022; 15:72. [PMID: 35974412 PMCID: PMC9380329 DOI: 10.1186/s13041-022-00958-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 08/02/2022] [Indexed: 11/21/2022] Open
Abstract
Ubiquitination involves three types of enzymes (E1, E2, and E3) that sequentially attach ubiquitin (Ub) to target proteins. This posttranslational modification controls key cellular processes, such as the degradation, endocytosis, subcellular localization and activity of proteins. Ubiquitination, which can be reversed by deubiquitinating enzymes (DUBs), plays important roles during brain development. Furthermore, deregulation of the Ub system is linked to the pathogenesis of various diseases, including neurodegenerative disorders. We used a publicly available RNA-seq database to perform an extensive genome-wide gene expression analysis of the core components of the ubiquitination machinery, covering Ub genes as well as E1, E2, E3 and DUB genes. The ubiquitination network was governed by only Uba1 and Ube2m, the predominant E1 and E2 genes, respectively; their expression was positively regulated during cortical formation. The principal genes encoding HECT (homologous to the E6-AP carboxyl terminus), RBR (RING-in-between-RING), and RING (really interesting new gene) E3 Ub ligases were also highly regulated. Pja1, Dtx3 (RING ligases) and Stub1 (U-box RING) were the most highly expressed E3 Ub ligase genes and displayed distinct developmental expression patterns. Moreover, more than 80 DUB genes were expressed during corticogenesis, with two prominent genes, Uch-l1 and Usp22, showing highly upregulated expression. Several components of the Ub system overexpressed in cancers were also highly expressed in the cerebral cortex under conditions not related to tumour formation or progression. Altogether, this work provides an in-depth overview of transcriptomic changes during embryonic formation of the cerebral cortex. The data also offer new insight into the characterization of the Ub system and may contribute to a better understanding of its involvement in the pathogenesis of neurodevelopmental disorders.
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Affiliation(s)
- Alexandre Bouron
- Université Grenoble Alpes, Inserm, CEA, UMR 1292, 38000, Grenoble, France. .,Genetics and Chemogenomics Lab, Building C3, CEA, 17 rue des Martyrs, 38054, Grenoble Cedex 9, France.
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17
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Wang DR, Zhang XW, Xu RR, Wang GL, You CX, An JP. Apple U-box-type E3 ubiquitin ligase MdPUB23 reduces cold-stress tolerance by degrading the cold-stress regulatory protein MdICE1. HORTICULTURE RESEARCH 2022; 9:uhac171. [PMID: 36247364 PMCID: PMC9557189 DOI: 10.1093/hr/uhac171] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 07/27/2022] [Indexed: 06/16/2023]
Abstract
Cold stress limits plant growth, geographical distribution, and crop yield. The MYC-type bHLH transcription factor ICE1 is recognized as the core positive regulator of the cold-stress response. However, how ICE1 protein levels are regulated remains to be further studied. In this study, we observed that a U-box-type E3 ubiquitin ligase, MdPUB23, positively regulated the cold-stress response in apple. The expression of MdPUB23 increased at both the transcriptional and post-translational levels in response to cold stress. Overexpression of MdPUB23 in transgenic apple enhanced sensitivity to cold stress. Further study showed that MdPUB23 directly interacted with MdICE1, promoting the ubiquitination-mediated degradation of the MdICE1 protein through the 26S-proteasome pathway and reducing the MdICE1-improved cold-stress tolerance in apple. Our results reveal that MdPUB23 regulates the cold-stress response by directly mediating the stability of the positive regulator MdICE1. The PUB23-ICE1 ubiquitination module may play a role in maintaining ICE1 protein homeostasis and preventing overreactions from causing damage to plants. The discovery of the ubiquitination regulatory pathway of ICE1 provides insights for the further exploration of plant cold-stress-response mechanisms.
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Affiliation(s)
| | | | - Rui-Rui Xu
- Key Laboratory of Biochemistry and Molecular Biology in Universities of Shandong, College of Biology and Oceanography, Weifang University, Weifang 261061, Shandong, China
| | - Gui-Luan Wang
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, 271018, Shandong, China
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18
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Zhao Y, Li J, Chen J, Ye M, Jin X. Functional roles of E3 ubiquitin ligases in prostate cancer. J Mol Med (Berl) 2022; 100:1125-1144. [PMID: 35816219 DOI: 10.1007/s00109-022-02229-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 06/20/2022] [Accepted: 06/22/2022] [Indexed: 12/16/2022]
Abstract
Prostate cancer (PCa) is a malignant epithelial tumor of the prostate gland with a high male cancer incidence. Numerous studies indicate that abnormal function of ubiquitin-proteasome system (UPS) is associated with the progression and metastasis of PCa. E3 ubiquitin ligases, key components of UPS, determine the specificity of substrates, and substantial advances of E3 ubiquitin ligases have been reached recently. Herein, we introduce the structures and functions of E3 ubiquitin ligases and summarize the mechanisms of E3 ubiquitin ligases-related PCa signaling pathways. In addition, some progresses in the development of inhibitors targeting E3 ubiquitin ligases are also included.
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Affiliation(s)
- Yiting Zhao
- Department of Oncology, The Affiliated Hospital of Medical School, Ningbo University, Ningbo, 315020, China.,Department of Biochemistry and Molecular Biology and Zhejiang Key Laboratory of Pathophysiology, Medical School of Ningbo University, Ningbo, 315211, China.,Department of Chemoradiotherapy, the Affiliated People's Hospital of Ningbo University, Ningbo, 315040, China
| | - Jinyun Li
- Department of Oncology, The Affiliated Hospital of Medical School, Ningbo University, Ningbo, 315020, China.,Department of Biochemistry and Molecular Biology and Zhejiang Key Laboratory of Pathophysiology, Medical School of Ningbo University, Ningbo, 315211, China
| | - Jun Chen
- Department of Chemoradiotherapy, the Affiliated People's Hospital of Ningbo University, Ningbo, 315040, China
| | - Meng Ye
- Department of Oncology, The Affiliated Hospital of Medical School, Ningbo University, Ningbo, 315020, China.,Department of Biochemistry and Molecular Biology and Zhejiang Key Laboratory of Pathophysiology, Medical School of Ningbo University, Ningbo, 315211, China
| | - Xiaofeng Jin
- Department of Oncology, The Affiliated Hospital of Medical School, Ningbo University, Ningbo, 315020, China. .,Department of Biochemistry and Molecular Biology and Zhejiang Key Laboratory of Pathophysiology, Medical School of Ningbo University, Ningbo, 315211, China.
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19
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Wang MX, Liuyu T, Zhang ZD. Multifaceted Roles of the E3 Ubiquitin Ligase RING Finger Protein 115 in Immunity and Diseases. Front Immunol 2022; 13:936579. [PMID: 35844553 PMCID: PMC9279554 DOI: 10.3389/fimmu.2022.936579] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 06/06/2022] [Indexed: 11/25/2022] Open
Abstract
Ubiquitination is a post-translational modification that plays essential roles in various physiological and pathological processes. Protein ubiquitination depends on E3 ubiquitin ligases that catalyze the conjugation of ubiquitin molecules on lysine residues of targeted substrates. RING finger protein 115 (RNF115), also known as breast cancer associated gene 2 (BCA2) and Rab7-interacting RING finger protein (Rabring7), has been identified as a highly expressed protein in breast cancer cells and tissues. Later, it has been demonstrated that RNF115 catalyzes ubiquitination of a series of proteins to modulate a number of signaling pathways, and thereby regulates viral infections, autoimmunity, cell proliferation and death and tumorigenesis. In this review, we introduce the identification, expression and activity regulation of RNF115, summarize the substrates and functions of RNF115 in different pathways, and discuss the roles of RNF115 as a biomarker or therapeutic target in diseases.
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Affiliation(s)
- Mei-Xia Wang
- The Executive Master of Business Administration (EMBA) Program, School of Management, Fudan University, Shanghai, China
| | - Tianzi Liuyu
- Department of Gastrointestinal Surgery, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Zhi-dong Zhang
- Department of Gastrointestinal Surgery, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan, China
- *Correspondence: Zhi-dong Zhang,
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20
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Wang T, Liu W, Wang C, Ma X, Akhtar MF, Li Y, Li L. MRKNs: Gene, Functions, and Role in Disease and Infection. Front Oncol 2022; 12:862206. [PMID: 35463379 PMCID: PMC9024132 DOI: 10.3389/fonc.2022.862206] [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: 02/14/2022] [Accepted: 03/17/2022] [Indexed: 11/26/2022] Open
Abstract
The makorin RING finger protein (MKRN) gene family encodes proteins (makorins) with a characteristic array of zinc-finger motifs present in a wide array from invertebrates to vertebrates. MKRNs (MKRN1, MKRN2, MKRN3, MKRN4) as RING finger E3 ligases that mediate substrate degradation are related with conserved RING finger domains that control multiple cellular components via the ubiquitin-proteasome system (UPS), including p53, p21, FADD, PTEN, p65, Nptx1, GLK, and some viral or bacterial proteins. MKRNs also served as diverse roles in disease, like MKRN1 in transcription regulation, metabolic disorders, and tumors; MKRN2 in testis physiology, neurogenesis, apoptosis, and mutation of MKRN2 regulation signals transduction, inflammatory responses, melanoma, and neuroblastoma; MKRN3 in central precocious puberty (CPP) therapy; and MKRN4 firstly reported as a novel E3 ligase instead of a pseudogene to contribute to systemic lupus erythematosus (SLE). Here, we systematically review advances in the gene’s expression, function, and role of MKRNs orthologs in disease and pathogens infection. Further, MKRNs can be considered targets for the host’s innate intracellular antiviral defenses and disease therapy.
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Affiliation(s)
- Tongtong Wang
- College of Agronomy, Liaocheng University, Liaocheng, China
| | - Wenqiang Liu
- College of Agronomy, Liaocheng University, Liaocheng, China
| | - Changfa Wang
- College of Agronomy, Liaocheng University, Liaocheng, China
| | - Xuelian Ma
- Veterinary Medicine, Xinjiang Agricultural University, Urumqi, China
| | | | - Yubao Li
- College of Agronomy, Liaocheng University, Liaocheng, China
- *Correspondence: Yubao Li, ; Liangliang Li,
| | - Liangliang Li
- College of Agronomy, Liaocheng University, Liaocheng, China
- *Correspondence: Yubao Li, ; Liangliang Li,
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21
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Wang S, Lv X, Zhang J, Chen D, Chen S, Fan G, Ma C, Wang Y. Roles of E3 Ubiquitin Ligases in Plant Responses to Abiotic Stresses. Int J Mol Sci 2022; 23:ijms23042308. [PMID: 35216424 PMCID: PMC8878164 DOI: 10.3390/ijms23042308] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 02/13/2022] [Accepted: 02/16/2022] [Indexed: 01/09/2023] Open
Abstract
Plants are frequently exposed to a variety of abiotic stresses, such as those caused by salt, drought, cold, and heat. All of these stressors can induce changes in the proteoforms, which make up the proteome of an organism. Of the many different proteoforms, protein ubiquitination has attracted a lot of attention because it is widely involved in the process of protein degradation; thus regulates many plants molecular processes, such as hormone signal transduction, to resist external stresses. Ubiquitin ligases are crucial in substrate recognition during this ubiquitin modification process. In this review, the molecular mechanisms of plant responses to abiotic stresses from the perspective of ubiquitin ligases have been described. This information is critical for a better understanding of plant molecular responses to abiotic stresses.
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Affiliation(s)
- Shuang Wang
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education, Heilongjiang University, Harbin 150080, China; (S.W.); (J.Z.)
| | - Xiaoyan Lv
- School of Life Science and Technology, Harbin Institute of Technology, Harbin 150080, China;
| | - Jialin Zhang
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education, Heilongjiang University, Harbin 150080, China; (S.W.); (J.Z.)
| | - Daniel Chen
- Judy Genshaft Honors College and College of Arts and Sciences, University of South Florida, Tampa, FL 33620, USA;
| | - Sixue Chen
- Plant Molecular and Cellular Biology Program, Department of Biology, Genetics Institude, University of Florida, Gainesville, FL 32610, USA;
| | - Guoquan Fan
- Industrial Crops Institute, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China;
| | - Chunquan Ma
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education, Heilongjiang University, Harbin 150080, China; (S.W.); (J.Z.)
- Correspondence: (C.M.); (Y.W.)
| | - Yuguang Wang
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education, Heilongjiang University, Harbin 150080, China; (S.W.); (J.Z.)
- Correspondence: (C.M.); (Y.W.)
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22
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Xie C, Long F, Li L, Li X, Ma M, Lu Z, Wu R, Zhang Y, Huang L, Chou J, Gong N, Hu G, Lin C. PTBP3 modulates P53 expression and promotes colorectal cancer cell proliferation by maintaining UBE4A mRNA stability. Cell Death Dis 2022; 13:128. [PMID: 35136024 PMCID: PMC8826374 DOI: 10.1038/s41419-022-04564-8] [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: 09/07/2021] [Revised: 12/27/2021] [Accepted: 01/17/2022] [Indexed: 11/22/2022]
Abstract
The RNA binding protein PTBP3 was recently reported to play a critical role in multiple cancers, and the molecular mechanisms involved RNA splicing, 3′ end processing and translation. However, the role of PTBP3 in colorectal cancer (CRC) remains poorly explored. Herein, PTBP3 was upregulated in CRC and associated with a poor prognosis. PTBP3 knockdown in colorectal cancer cell lines restricted CRC proliferative capacities in vitro and in vivo. Mechanistically, PTBP3 regulated the expression of the E3 ubiquitin ligase UBE4A by binding the 3′ UTR of its mRNA, preventing its degradation. UBE4A participated in P53 degradation, and PTBP3 knockdown in colorectal cancer cell lines showed increased P53 expression. UBE4A overexpression rescued PTBP3 knockdown-induced inhibition of CRC cell proliferation and P53 expression. Our results demonstrated that PTBP3 plays an essential role in CRC cell proliferation by stabilizing UBE4A to regulate P53 expression and may serve as a new prognostic biomarker and effective therapeutic target for CRC.
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23
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Kim JH, Kim MS, Kim DY, Amoah JN, Seo YW. Molecular Characterization of U-box E3 Ubiquitin Ligases (TaPUB2 and TaPUB3) Involved in the Positive Regulation of Drought Stress Response in Arabidopsis. Int J Mol Sci 2021; 22:13658. [PMID: 34948454 PMCID: PMC8704797 DOI: 10.3390/ijms222413658] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 12/16/2021] [Accepted: 12/18/2021] [Indexed: 12/25/2022] Open
Abstract
Plant U-box E3 ubiquitin ligase (PUB) is involved in various environmental stress conditions. However, the molecular mechanism of U-box proteins in response to abiotic stress in wheat remains unknown. In this study, two U-box E3 ligase genes (TaPUB2 and TaPUB3), which are highly expressed in response to adverse abiotic stresses, were isolated from common wheat, and their cellular functions were characterized under drought stress. Transient expression assay revealed that TaPUB2 was localized in the cytoplasm and Golgi apparatus, whereas TaPUB3 was expressed only in the Golgi apparatus in wheat protoplasts. Additionally, TaPUB2 and TaPUB3 underwent self-ubiquitination. Moreover, TaPUB2/TaPUB3 heterodimer was identified in yeast and the cytoplasm of wheat protoplasts using a pull-down assay and bimolecular fluorescence complementation analysis. Heterogeneous overexpression of TaPUB2 and TaPUB3 conferred tolerance to drought stress. Taken together, these results implied that the heterodimeric form of U-box E3 ubiquitin ligases (TaPUB2/TaPUB3) responded to abiotic stress and roles as a positive regulator of drought stress tolerance.
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Affiliation(s)
| | | | | | | | - Yong Weon Seo
- Department of Plant Biotechnology, Korea University, Seoul 02841, Korea; (J.H.K.); (M.S.K.); (D.Y.K.); (J.N.A.)
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24
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Huntingtin Ubiquitination Mechanisms and Novel Possible Therapies to Decrease the Toxic Effects of Mutated Huntingtin. J Pers Med 2021; 11:jpm11121309. [PMID: 34945781 PMCID: PMC8709430 DOI: 10.3390/jpm11121309] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 11/19/2021] [Accepted: 11/21/2021] [Indexed: 12/24/2022] Open
Abstract
Huntington Disease (HD) is a dominant, lethal neurodegenerative disorder caused by the abnormal expansion (>35 copies) of a CAG triplet located in exon 1 of the HTT gene encoding the huntingtin protein (Htt). Mutated Htt (mHtt) easily aggregates, thereby inducing ER stress that in turn leads to neuronal injury and apoptosis. Therefore, both the inhibition of mHtt aggregate formation and the acceleration of mHtt degradation represent attractive strategies to delay HD progression, and even for HD treatment. Here, we describe the mechanism underlying mHtt degradation by the ubiquitin–proteasome system (UPS), which has been shown to play a more important role than the autophagy–lysosomal pathway. In particular, we focus on E3 ligase proteins involved in the UPS and detail their structure–function relationships. In this framework, we discuss the possible exploitation of PROteolysis TArgeting Chimeras (PROTACs) for HD therapy. PROTACs are heterobifunctional small molecules that comprise two different ligands joined by an appropriate linker; one of the ligands is specific for a selected E3 ubiquitin ligase, the other ligand is able to recruit a target protein of interest, in this case mHtt. As a consequence of PROTAC binding, mHtt and the E3 ubiquitin ligase can be brought to a relative position that allows mHtt to be ubiquitinated and, ultimately, allows a reduction in the amount of mHtt in the cell.
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25
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Shen J, Fu B, Li Y, Wu Y, Sang H, Zhang H, Lin H, Liu H, Huang W. E3 Ubiquitin Ligase-Mediated Regulation of Osteoblast Differentiation and Bone Formation. Front Cell Dev Biol 2021; 9:706395. [PMID: 34513836 PMCID: PMC8430030 DOI: 10.3389/fcell.2021.706395] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 08/03/2021] [Indexed: 12/13/2022] Open
Abstract
The ubiquitin–proteasome system (UPS) is an essential pathway that regulates the homeostasis and function of intracellular proteins and is a crucial protein-degradation system in osteoblast differentiation and bone formation. Abnormal regulation of ubiquitination leads to osteoblast differentiation disorders, interfering with bone formation and ultimately leading to osteoporosis. E3 ubiquitin ligases (E3) promote addition of a ubiquitin moiety to substrate proteins, specifically recognizing the substrate and modulating tyrosine kinase receptors, signaling proteins, and transcription factors involved in the regulation of osteoblast proliferation, differentiation, survival, and bone formation. In this review, we summarize current progress in the understanding of the function and regulatory effects of E3 ligases on the transcription factors and signaling pathways that regulate osteoblast differentiation and bone formation. A deep understanding of E3 ligase-mediated regulation of osteoblast differentiation provides a scientific rationale for the discovery and development of novel E3-targeting therapeutic strategies for osteoporosis.
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Affiliation(s)
- Jianlin Shen
- Guangdong Innovation Platform for Translation of 3D Printing Application, Center for Orthopaedic Surgery, The Third Affiliated Hospital of Southern Medical University, Guangzhou, China.,Department of Orthopedics, Affiliated Hospital of Putian University, Putian, China
| | - Bowen Fu
- Guangdong Innovation Platform for Translation of 3D Printing Application, Center for Orthopaedic Surgery, The Third Affiliated Hospital of Southern Medical University, Guangzhou, China
| | - Yanfang Li
- Department of Pediatric Surgery, Affiliated Hospital of Putian University, Putian, China
| | - Yanjiao Wu
- Department of Orthopedics, Shunde Hospital of Southern Medical University, Guangzhou, China
| | - Hongxun Sang
- Department of Orthopedics, Shenzhen Hospital, Southern Medical University, Shenzhen, China
| | - Heshi Zhang
- Department of Vessel and Breast, Affiliated Traditional Chinese Medicine Hospital of Southwest Medical University, Luzhou, China
| | - Haibin Lin
- Department of Orthopedics, Affiliated Hospital of Putian University, Putian, China
| | - Huan Liu
- Department of Orthopedics, Affiliated Traditional Chinese Medicine Hospital, Southwest Medical University, Luzhou, China
| | - Wenhua Huang
- Guangdong Innovation Platform for Translation of 3D Printing Application, Center for Orthopaedic Surgery, The Third Affiliated Hospital of Southern Medical University, Guangzhou, China.,Guangdong Engineering Research Center for Translation of Medical 3D Printing Application, Guangdong Provincial Key Laboratory of Medical Biomechanics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China.,Orthopedic Center, Affiliated Hospital of Guangdong Medical University, Guangdong Medical University, Zhanjiang, China
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26
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Wang L, Sun X, He J, Liu Z. Functions and Molecular Mechanisms of Deltex Family Ubiquitin E3 Ligases in Development and Disease. Front Cell Dev Biol 2021; 9:706997. [PMID: 34513839 PMCID: PMC8424196 DOI: 10.3389/fcell.2021.706997] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Accepted: 08/05/2021] [Indexed: 12/14/2022] Open
Abstract
Ubiquitination is a posttranslational modification of proteins that significantly affects protein stability and function. The specificity of substrate recognition is determined by ubiquitin E3 ligase during ubiquitination. Human Deltex (DTX) protein family, which functions as ubiquitin E3 ligases, comprises five members, namely, DTX1, DTX2, DTX3, DTX3L, and DTX4. The characteristics and functional diversity of the DTX family proteins have attracted significant attention over the last decade. DTX proteins have several physiological and pathological roles and are closely associated with cell signal transduction, growth, differentiation, and apoptosis, as well as the occurrence and development of various tumors. Although they have been extensively studied in various species, data on structural features, biological functions, and potential mechanisms of action of the DTX family proteins remain limited. In this review, recent research progress on each member of the DTX family is summarized, providing insights into future research directions and potential strategies in disease diagnosis and therapy.
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Affiliation(s)
- Lidong Wang
- Department of General Surgery, Shengjing Hospital of China Medical University, Shenyang, China
| | - Xiaodan Sun
- Postdoctoral Research Workstation, Jilin Cancer Hospital, Changchun, China
| | - Jingni He
- Department of General Surgery, Shengjing Hospital of China Medical University, Shenyang, China
| | - Zhen Liu
- Department of General Surgery, Shengjing Hospital of China Medical University, Shenyang, China
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27
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Kumar S, Basu M, Ghosh MK. Chaperone-assisted E3 ligase CHIP: A double agent in cancer. Genes Dis 2021; 9:1521-1555. [PMID: 36157498 PMCID: PMC9485218 DOI: 10.1016/j.gendis.2021.08.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 08/06/2021] [Indexed: 12/11/2022] Open
Abstract
The carboxy-terminus of Hsp70-interacting protein (CHIP) is a ubiquitin ligase and co-chaperone belonging to Ubox family that plays a crucial role in the maintenance of cellular homeostasis by switching the equilibrium of the folding-refolding mechanism towards the proteasomal or lysosomal degradation pathway. It links molecular chaperones viz. HSC70, HSP70 and HSP90 with ubiquitin proteasome system (UPS), acting as a quality control system. CHIP contains charged domain in between N-terminal tetratricopeptide repeat (TPR) and C-terminal Ubox domain. TPR domain interacts with the aberrant client proteins via chaperones while Ubox domain facilitates the ubiquitin transfer to the client proteins for ubiquitination. Thus, CHIP is a classic molecule that executes ubiquitination for degradation of client proteins. Further, CHIP has been found to be indulged in cellular differentiation, proliferation, metastasis and tumorigenesis. Additionally, CHIP can play its dual role as a tumor suppressor as well as an oncogene in numerous malignancies, thus acting as a double agent. Here, in this review, we have reported almost all substrates of CHIP established till date and classified them according to the hallmarks of cancer. In addition, we discussed about its architectural alignment, tissue specific expression, sub-cellular localization, folding-refolding mechanisms of client proteins, E4 ligase activity, normal physiological roles, as well as involvement in various diseases and tumor biology. Further, we aim to discuss its importance in HSP90 inhibitors mediated cancer therapy. Thus, this report concludes that CHIP may be a promising and worthy drug target towards pharmaceutical industry for drug development.
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28
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Seo DH, Lee A, Yu SG, Cui LH, Min HJ, Lee SE, Cho NH, Kim S, Bae H, Kim WT. OsPUB41, a U-box E3 ubiquitin ligase, acts as a negative regulator of drought stress response in rice (Oryza Sativa L.). PLANT MOLECULAR BIOLOGY 2021; 106:463-477. [PMID: 34100185 DOI: 10.1007/s11103-021-01158-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 05/20/2021] [Indexed: 05/29/2023]
Abstract
OsPUB41 plays a negative role in drought stress response through the mediation of OsUBC25 and interacts with OsCLC6, suggesting a putative substrate. The notable expansion of Plant U-Box E3 ligases (PUB), compared with those in mammals, implies that PUB proteins have evolved to perform plant-specific functions. OsPUB41, a potential ortholog of CMPG1, was recently reported to regulate the cell wall degrading enzyme (CWDE)-induced innate immune response in rice. Here, we characterized the OsPUB41 gene, which encodes a dual-localized cytosolic and nuclear U-box E3 ligase in rice. OsPUB41 expression was specifically induced by dehydration among various abiotic stresses and abscisic acid (ABA) treatments. Furthermore, we revealed that the core U-box motif of OsPUB41 possesses the E3 ligase activity that can be activated by OsUBC25 in rice. The Ubi:RNAi-OsPUB41 knock-down and ospub41 suppression mutant plants exhibited enhanced tolerance to drought stress compared with the wild-type rice plants in terms of transpirational water loss, long-term dehydration response, and chlorophyll content. Moreover, the knock-down or suppression of the OsPUB41 gene did not cause adverse effect on rice yield-related traits. Yeast two-hybrid and an in vitro pull-down analyses revealed that OsCLC6, a chloride channel, is a putative substrate of OsPUB41. Overall, these results suggest that OsPUB41 acts as a negative regulator of dehydration conditions and interacts with OsCLC6, implying that it is a substrate of OsPUB41.
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Affiliation(s)
- Dong Hye Seo
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul, 03722, Republic of Korea.
| | - Andosung Lee
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul, 03722, Republic of Korea
| | - Seong Gwan Yu
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul, 03722, Republic of Korea
| | - Li Hua Cui
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul, 03722, Republic of Korea
| | - Hye Jo Min
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul, 03722, Republic of Korea
| | - Seung Eun Lee
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul, 03722, Republic of Korea
| | - Na Hyun Cho
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul, 03722, Republic of Korea
| | - Sojung Kim
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul, 03722, Republic of Korea
| | - Hansol Bae
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul, 03722, Republic of Korea
| | - Woo Taek Kim
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul, 03722, Republic of Korea.
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29
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Fan C, Su H, Liao Z, Su J, Yang C, Zhang Y, Su J. Teleost-Specific MxG, a Traitor in the Mx Family, Negatively Regulates Antiviral Responses by Targeting IPS-1 for Proteasomal Degradation and STING for Lysosomal Degradation. THE JOURNAL OF IMMUNOLOGY 2021; 207:281-295. [PMID: 34135063 DOI: 10.4049/jimmunol.2000555] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 04/29/2021] [Indexed: 11/19/2022]
Abstract
IFN-β promoter stimulator-1 (IPS-1)- and stimulator of IFN genes (STING)-mediated type I IFNs play a critical role in antiviral responses. Myxovirus resistance (Mx) proteins are pivotal components of the antiviral effectors induced by IFNs in many species. An unprecedented expansion of Mx genes has occurred in fish. However, the functions and mechanisms of Mx family members remain largely unknown in fish. In this study, we found that grass carp (Ctenopharyngodon idella) MxG, a teleost-specific Mx protein, is induced by IFNs and viruses, and it negatively regulates both IPS-1- and STING-mediated antiviral responses to facilitate grass carp reovirus, spring viremia of carp virus, and cyprinid herpesvirus-2 replication. MxG binds and degrades IPS-1 via the proteasomal pathway and STING through the lysosomal pathway, thereby negatively regulating IFN1 antiviral responses and NF-κB proinflammatory cytokines. MxG also suppresses the phosphorylation of STING IFN regulatory factor 3/7, and it subsequently downregulates IFN1 and NF-κB1 at the promoter, transcription, and protein levels. GTPase and GTPase effector domains of MxG contribute to the negative regulatory function. On the contrary, MxG knockdown weakens virus replication and cytopathic effect. Therefore, MxG can be an ISG molecule induced by IFNs and viruses, and degrade IPS-1 and STING proteins in a negative feedback manner to maintain homeostasis and avoid excessive immune responses after virus infection. To our knowledge, this is the first identification of a negative regulator in the Mx family, and our findings clarify a novel mechanism by which the IFN response is regulated.
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Affiliation(s)
- Chengjian Fan
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan, China.,Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, China
| | - Hang Su
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan, China
| | - Zhiwei Liao
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan, China
| | - Juanjuan Su
- Key Laboratory of Marine Drugs (Ministry of Education), Shandong Provincial Key Laboratory of Glycoscience and Glycoengineering, School of Medicine and Pharmacy, Ocean University of China, Qingdao, China; and
| | - Chunrong Yang
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Yongan Zhang
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan, China
| | - Jianguo Su
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan, China; .,Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, China
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30
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Inui N, Sakai S, Kitagawa M. Molecular Pathogenesis of Pulmonary Fibrosis, with Focus on Pathways Related to TGF-β and the Ubiquitin-Proteasome Pathway. Int J Mol Sci 2021; 22:6107. [PMID: 34198949 PMCID: PMC8201174 DOI: 10.3390/ijms22116107] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 05/27/2021] [Accepted: 06/02/2021] [Indexed: 02/07/2023] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is a progressive and fatal interstitial lung disease. During the past decade, novel pathogenic mechanisms of IPF have been elucidated that have shifted the concept of IPF from an inflammatory-driven to an epithelial-driven disease. Dysregulated repair responses induced by recurrent epithelial cell damage and excessive extracellular matrix accumulation result in pulmonary fibrosis. Although there is currently no curative therapy for IPF, two medications, pirfenidone and nintedanib, have been introduced based on understanding the pathogenesis of the disease. In this review, we discuss advances in understanding IPF pathogenesis, highlighting epithelial-mesenchymal transition (EMT), the ubiquitin-proteasome system, and endothelial cells. TGF-β is a central regulator involved in EMT and pulmonary fibrosis. HECT-, RING finger-, and U-box-type E3 ubiquitin ligases regulate TGF-β-Smad pathway-mediated EMT via the ubiquitin-proteasome pathway. p27 degradation mediated by the SCF-type E3 ligase, Skp2, contributes to the progression of pulmonary fibrosis by promotion of either mesenchymal fibroblast proliferation, EMT, or both. In addition to fibroblasts as key effector cells in myofibroblast differentiation and extracellular matrix deposition, endothelial cells also play a role in the processes of IPF. Endothelial cells can transform into myofibroblasts; therefore, endothelial-mesenchymal transition can be another source of myofibroblasts.
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Affiliation(s)
- Naoki Inui
- Department of Clinical Pharmacology and Therapeutics, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu, Shizuoka 431-3192, Japan
| | - Satoshi Sakai
- Department of Molecular Biology, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu, Shizuoka 431-3192, Japan;
| | - Masatoshi Kitagawa
- Department of Molecular Biology, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu, Shizuoka 431-3192, Japan;
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31
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Karre S, Kim S, Samira R, Balint‐Kurti P. The maize ZmMIEL1 E3 ligase and ZmMYB83 transcription factor proteins interact and regulate the hypersensitive defence response. MOLECULAR PLANT PATHOLOGY 2021; 22:694-709. [PMID: 33825303 PMCID: PMC8126188 DOI: 10.1111/mpp.13057] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 02/24/2021] [Accepted: 03/08/2021] [Indexed: 05/10/2023]
Abstract
The plant hypersensitive response (HR), a rapid cell death at the point of pathogenesis, is mediated by nucleotide-binding site, leucine-rich repeat (NLR) resistance proteins (R-proteins) that recognize the presence of specific pathogen-derived proteins. Rp1-D21 is an autoactive maize NLR R-protein that triggers HR spontaneously. We previously mapped loci associated with variation in the strength of HR induced by Rp1-D21. Here we identify the E3 ligase ZmMIEL1 as the causal gene at a chromosome 10 modifier locus. Transient ZmMIEL1 expression in Nicotiana benthamiana reduced HR induced by Rp1-D21, while suppression of ZmMIEL1 expression in maize carrying Rp1-D21 increased HR. ZmMIEL1 also suppressed HR induced by another autoactive NLR, the Arabidopsis R-protein RPM1D505V, in N. benthamiana. We demonstrated that ZmMIEL1 is a functional E3 ligase and that the effect of ZmMIEL1 was dependent on the proteasome but also that levels of Rp1-D21 and RPM1D505V were not reduced when coexpressed with ZmMIEL1 in the N. benthamiana system. By comparison to a similar system in Arabidopsis, we identify ZmMYB83 as a potential target of ZmMIEL1. Suppression of ZmMYB83 expression in maize lines carrying Rp1-D21 suppressed HR. Suppression of ZmMIEL1 expression caused an increase in ZmMYB83 transcript and protein levels in N. benthamiana and maize. Using coimmunoprecipitation and bimolecular fluorescence complementation assays, we demonstrated that ZmMIEL1 and ZmMYB83 physically interacted. Additionally, ZmMYB83 and ZmMIEL1 regulated the expression of a set of maize very long chain fatty acid (VLCFA) biosynthetic genes that may be involved in regulating HR.
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Affiliation(s)
- Shailesh Karre
- Department of Entomology and Plant PathologyNC State UniversityRaleighNorth CarolinaUSA
| | - Saet‐Byul Kim
- Department of Entomology and Plant PathologyNC State UniversityRaleighNorth CarolinaUSA
| | - Rozalynne Samira
- Department of Entomology and Plant PathologyNC State UniversityRaleighNorth CarolinaUSA
- Fiber and Biopolymer Research InstituteDepartment of Plant and Soil ScienceTexas Tech UniversityLubbockTexasUSA
| | - Peter Balint‐Kurti
- Department of Entomology and Plant PathologyNC State UniversityRaleighNorth CarolinaUSA
- Plant Science Research Unit USDA‐ARSRaleighNorth CarolinaUSA
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32
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Zhao G, Liu C, Wen X, Luan G, Xie L, Guo X. The translational values of TRIM family in pan-cancers: From functions and mechanisms to clinics. Pharmacol Ther 2021; 227:107881. [PMID: 33930453 DOI: 10.1016/j.pharmthera.2021.107881] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 04/21/2021] [Accepted: 04/22/2021] [Indexed: 02/08/2023]
Abstract
Cancer is the second leading cause of human death across the world. Tripartite motif (TRIM) family, with E3 ubiquitin ligase activities in majority of its members, is reported to be involved in multiple cellular processes and signaling pathways. TRIM proteins have critical effects in the regulation of biological behaviors of cancer cells. Here, we discussed the current understanding of the molecular mechanism of TRIM proteins regulation of cancer cells. We also comprehensively reviewed published studies on TRIM family members as oncogenes or tumor suppressors in the oncogenesis, development, and progression of a variety of types of human cancers. Finally, we highlighted that certain TRIM family members are potential molecular biomarkers for cancer diagnosis and prognosis, and potential therapeutic targets.
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Affiliation(s)
- Guo Zhao
- Department of Preventive Medicine, Institute of Biomedical Informatics, Bioinformatics Center, Henan Provincial Engineering Center for Tumor Molecular Medicine, School of Basic Medical Sciences, Henan University, Kaifeng 475004, China
| | - Chuan Liu
- Department of Preventive Medicine, Institute of Biomedical Informatics, Bioinformatics Center, Henan Provincial Engineering Center for Tumor Molecular Medicine, School of Basic Medical Sciences, Henan University, Kaifeng 475004, China
| | - Xin Wen
- Department of Preventive Medicine, Institute of Biomedical Informatics, Bioinformatics Center, Henan Provincial Engineering Center for Tumor Molecular Medicine, School of Basic Medical Sciences, Henan University, Kaifeng 475004, China
| | - Gan Luan
- Department of Mathematical Sciences, New Jersey Institute of Technology, Newark, NJ 07102, USA
| | - Longxiang Xie
- Department of Preventive Medicine, Institute of Biomedical Informatics, Bioinformatics Center, Henan Provincial Engineering Center for Tumor Molecular Medicine, School of Basic Medical Sciences, Henan University, Kaifeng 475004, China.
| | - Xiangqian Guo
- Department of Preventive Medicine, Institute of Biomedical Informatics, Bioinformatics Center, Henan Provincial Engineering Center for Tumor Molecular Medicine, School of Basic Medical Sciences, Henan University, Kaifeng 475004, China.
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Mathieu NA, Levin RH, Spratt DE. Exploring the Roles of HERC2 and the NEDD4L HECT E3 Ubiquitin Ligase Subfamily in p53 Signaling and the DNA Damage Response. Front Oncol 2021; 11:659049. [PMID: 33869064 PMCID: PMC8044464 DOI: 10.3389/fonc.2021.659049] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 03/16/2021] [Indexed: 12/27/2022] Open
Abstract
Cellular homeostasis is governed by the precise expression of genes that control the translation, localization, and termination of proteins. Oftentimes, environmental and biological factors can introduce mutations into the genetic framework of cells during their growth and division, and these genetic abnormalities can result in malignant transformations caused by protein malfunction. For example, p53 is a prominent tumor suppressor protein that is capable of undergoing more than 300 posttranslational modifications (PTMs) and is involved with controlling apoptotic signaling, transcription, and the DNA damage response (DDR). In this review, we focus on the molecular mechanisms and interactions that occur between p53, the HECT E3 ubiquitin ligases WWP1, SMURF1, HECW1 and HERC2, and other oncogenic proteins in the cell to explore how irregular HECT-p53 interactions can induce tumorigenesis.
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Affiliation(s)
- Nicholas A Mathieu
- Gustaf H. Carlson School of Chemistry and Biochemistry, Clark University, Worcester, MA, United States
| | - Rafael H Levin
- Gustaf H. Carlson School of Chemistry and Biochemistry, Clark University, Worcester, MA, United States
| | - Donald E Spratt
- Gustaf H. Carlson School of Chemistry and Biochemistry, Clark University, Worcester, MA, United States
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Pan M, Blattner C. Regulation of p53 by E3s. Cancers (Basel) 2021; 13:745. [PMID: 33670160 PMCID: PMC7916862 DOI: 10.3390/cancers13040745] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 01/15/2021] [Accepted: 02/05/2021] [Indexed: 12/18/2022] Open
Abstract
More than 40 years of research on p53 have given us tremendous knowledge about this protein. Today we know that p53 plays a role in different biological processes such as proliferation, invasion, pluripotency, metabolism, cell cycle control, ROS (reactive oxygen species) production, apoptosis, inflammation and autophagy. In the nucleus, p53 functions as a bona-fide transcription factor which activates and represses transcription of a number of target genes. In the cytoplasm, p53 can interact with proteins of the apoptotic machinery and by this also induces cell death. Despite being so important for the fate of the cell, expression levels of p53 are kept low in unstressed cells and the protein is largely inactive. The reason for the low expression level is that p53 is efficiently degraded by the ubiquitin-proteasome system and the vast inactivity of the tumor suppressor protein under normal growth conditions is due to the absence of activating and the presence of inactivating posttranslational modifications. E3s are important enzymes for these processes as they decorate p53 with ubiquitin and small ubiquitin-like proteins and by this control p53 degradation, stability and its subcellular localization. In this review, we provide an overview about E3s that target p53 and discuss the connection between p53, E3s and tumorigenesis.
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Affiliation(s)
| | - Christine Blattner
- Institute of Biological and Chemical Systems—Biological Information Processing, Karlsruhe Institute of Technology, PO-box 3640, 76021 Karlsruhe, Germany;
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Fei X, Shi Q, Qi Y, Wang S, Lei Y, Hu H, Liu Y, Yang T, Wei A. ZbAGL11, a class D MADS-box transcription factor of Zanthoxylum bungeanum, is involved in sporophytic apomixis. HORTICULTURE RESEARCH 2021; 8:23. [PMID: 33518706 PMCID: PMC7848008 DOI: 10.1038/s41438-020-00459-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 11/26/2020] [Accepted: 11/27/2020] [Indexed: 05/26/2023]
Abstract
Apomixis is a reproductive model that bypasses sexual reproduction, so it does not require the combination of paternal and maternal gametes but instead results in the production of offspring directly from maternal tissues. This reproductive mode results in the same genetic material in the mother and the offspring and has significant applications in agricultural breeding. Molecular and cytological methods were used to identify the reproductive type of Zanthoxylum bungeanum (ZB). Fluorescence detection of the amplified products of 12 pairs of polymorphic SSR primers showed consistent fluorescence signals for mother and offspring, indicating that no trait separation occurred during reproduction. In addition, the cytological observation results showed differentiation of ZB embryos (2n) from nucellar cells (2n) to form indefinite embryonic primordia and then form adventitious embryos (2n), indicating that the apomictic type of ZB is sporophytic apomixis. The MADS-box transcription factor ZbAGL11 was highly expressed during the critical period of nucellar embryo development in ZB. Unpollinated ZbAGL11-OE Arabidopsis produced fertile offspring and exhibited an apomictic phenotype. The overexpression of ZbAGL11 increased the callus induction rate of ZB tissue. In addition, the results of the yeast two-hybrid experiment showed that ZbAGL11 could interact with the ZbCYP450 and ZbCAD11 proteins. Our results demonstrate that ZbAGL11 can cause developmental disorders of Arabidopsis flower organs and result in apomixis-like phenotypes.
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Affiliation(s)
- Xitong Fei
- College of Forestry, Northwest Agriculture and Forestry University, Yangling, Shaanxi, China
- Research Centre for Engineering and Technology of Zanthoxylum State Forestry Administration, Yangling, Xianyang, 712100, China
| | - Qianqian Shi
- College of Forestry, Northwest Agriculture and Forestry University, Yangling, Shaanxi, China
| | - Yichen Qi
- College of Forestry, Northwest Agriculture and Forestry University, Yangling, Shaanxi, China
- Research Centre for Engineering and Technology of Zanthoxylum State Forestry Administration, Yangling, Xianyang, 712100, China
| | - Shujie Wang
- College of Forestry, Northwest Agriculture and Forestry University, Yangling, Shaanxi, China
- Research Centre for Engineering and Technology of Zanthoxylum State Forestry Administration, Yangling, Xianyang, 712100, China
| | - Yu Lei
- College of Forestry, Northwest Agriculture and Forestry University, Yangling, Shaanxi, China
- Research Centre for Engineering and Technology of Zanthoxylum State Forestry Administration, Yangling, Xianyang, 712100, China
| | - Haichao Hu
- College of Forestry, Northwest Agriculture and Forestry University, Yangling, Shaanxi, China
- Research Centre for Engineering and Technology of Zanthoxylum State Forestry Administration, Yangling, Xianyang, 712100, China
| | - Yulin Liu
- College of Forestry, Northwest Agriculture and Forestry University, Yangling, Shaanxi, China
- Research Centre for Engineering and Technology of Zanthoxylum State Forestry Administration, Yangling, Xianyang, 712100, China
| | - Tuxi Yang
- College of Forestry, Northwest Agriculture and Forestry University, Yangling, Shaanxi, China
- Research Centre for Engineering and Technology of Zanthoxylum State Forestry Administration, Yangling, Xianyang, 712100, China
| | - Anzhi Wei
- College of Forestry, Northwest Agriculture and Forestry University, Yangling, Shaanxi, China.
- Research Centre for Engineering and Technology of Zanthoxylum State Forestry Administration, Yangling, Xianyang, 712100, China.
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Price CT, Abu Kwaik Y. Evolution and Adaptation of Legionella pneumophila to Manipulate the Ubiquitination Machinery of Its Amoebae and Mammalian Hosts. Biomolecules 2021; 11:biom11010112. [PMID: 33467718 PMCID: PMC7830128 DOI: 10.3390/biom11010112] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 01/11/2021] [Accepted: 01/12/2021] [Indexed: 02/07/2023] Open
Abstract
The ubiquitin pathway is highly conserved across the eukaryotic domain of life and plays an essential role in a plethora of cellular processes. It is not surprising that many intracellular bacterial pathogens often target the essential host ubiquitin pathway. The intracellular bacterial pathogen Legionella pneumophila injects into the host cell cytosol multiple classes of classical and novel ubiquitin-modifying enzymes that modulate diverse ubiquitin-related processes in the host cell. Most of these pathogen-injected proteins, designated as effectors, mimic known E3-ubiquitin ligases through harboring F-box or U-box domains. The classical F-box effector, AnkB targets host proteins for K48-linked polyubiquitination, which leads to excessive proteasomal degradation that is required to generate adequate supplies of amino acids for metabolism of the pathogen. In contrast, the SidC and SdcA effectors share no structural similarity to known eukaryotic ligases despite having E3-ubiquitin ligase activity, suggesting that the number of E3-ligases in eukaryotes is under-represented. L. pneumophila also injects into the host many novel ubiquitin-modifying enzymes, which are the SidE family of effectors that catalyze phosphoribosyl-ubiquitination of serine residue of target proteins, independently of the canonical E1-2-3 enzymatic cascade. Interestingly, the environmental bacterium, L. pneumophila, has evolved within a diverse range of amoebal species, which serve as the natural hosts, while accidental transmission through contaminated aerosols can cause pneumonia in humans. Therefore, it is likely that the novel ubiquitin-modifying enzymes of L. pneumophila were acquired by the pathogen through interkingdom gene transfer from the diverse natural amoebal hosts. Furthermore, conservation of the ubiquitin pathway across eukaryotes has enabled these novel ubiquitin-modifying enzymes to function similarly in mammalian cells. Studies on the biological functions of these effectors are likely to reveal further novel ubiquitin biology and shed further lights on the evolution of ubiquitin.
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Affiliation(s)
- Christopher T.D. Price
- Department of Microbiology and Immunology, University of Louisville, Louisville, KY 40202, USA;
| | - Yousef Abu Kwaik
- Department of Microbiology and Immunology, University of Louisville, Louisville, KY 40202, USA;
- Center for Predictive Medicine, College of Medicine, University of Louisville, Louisville, KY 40202, USA
- Correspondence:
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Li J, Zhang Y, Gao Z, Xu X, Wang Y, Lin Y, Ye P, Huang T. Plant U-box E3 ligases PUB25 and PUB26 control organ growth in Arabidopsis. THE NEW PHYTOLOGIST 2021; 229:403-413. [PMID: 32810874 DOI: 10.1111/nph.16885] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 08/09/2020] [Indexed: 05/12/2023]
Abstract
Plant organs often grow into a genetically determined size and shape. How organ growth is finely regulated to achieve a well defined pattern is a fascinating, but largely unresolved, question in plant research. We utilised the Arabidopsis petal to study the genetic control of plant organ growth, and identify two closely related U-box E3 ligases PUB25 and PUB26 as important growth regulators by screening the targets of the petal-specific growth-promoting transcription factor RABBIT EARS (RBE). We showed that PUB25 is directly controlled by RBE in petal development in a spatial- and temporal-specific manner and acts as a major target to mediate RBE's function in petal growth. We also showed that PUB25 and PUB26 repress petal growth by restricting the period of cell proliferation, and their regulation appears to be independent of other plant E3 ligase genes implicated in growth control. PUB25 and PUB26 are among the first U-box E3 ligases shown to function in plant growth control. Furthermore, as they were also found to play a vital role in plant stress responses, PUB25 and PUB26 may act as a key hub to integrate developmental and environmental signals for balancing growth and defence in plants.
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Affiliation(s)
- Jing Li
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, Guangdong, 518071, China
| | - Yongxia Zhang
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, Guangdong, 518071, China
| | - Zhong Gao
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, Guangdong, 518071, China
| | - Xiumei Xu
- Key Laboratory of Plant Stress Biology, State Key Laboratory of Cotton Biology, College of Life Sciences, Henan University, Kaifeng, Henan, 475004, China
| | - Yanzhi Wang
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, Guangdong, 518071, China
| | - Yaoxi Lin
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, Guangdong, 518071, China
| | - Peiming Ye
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, Guangdong, 518071, China
| | - Tengbo Huang
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, Guangdong, 518071, China
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Feltrin RDS, Segatto ALA, de Souza TA, Schuch AP. Open gaps in the evolution of the eukaryotic nucleotide excision repair. DNA Repair (Amst) 2020; 95:102955. [DOI: 10.1016/j.dnarep.2020.102955] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 08/06/2020] [Accepted: 08/16/2020] [Indexed: 12/24/2022]
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Gori Savellini G, Bini L, Gagliardi A, Anichini G, Gandolfo C, Prathyumnan S, Cusi MG. Ubiquitin and Not Only Unfolded Domains Drives Toscana Virus Non-Structural NSs Protein Degradation. Viruses 2020; 12:E1153. [PMID: 33053780 PMCID: PMC7601456 DOI: 10.3390/v12101153] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 10/05/2020] [Accepted: 10/09/2020] [Indexed: 01/09/2023] Open
Abstract
The non-structural protein NSs of the Phenuiviridae family members appears to have a role in the host immunity escape. The stability of Toscana virus (TOSV) NSs protein was tested by a cycloheximide (CHX) chase approach on cells transfected with NSs deleted versions fused to a reporter gene. The presence of intrinsically disordered regions (IDRs) both at the C- and N-terminus appeared to affect the protein stability. Indeed, the NSsΔC and NSsΔN proteins were more stable than the wild-type NSs counterpart. Since TOSV NSs exerts its inhibitory function by triggering RIG-I for proteasomal degradation, the interaction of the ubiquitin system and TOSV NSs was further examined. Chase experiments with CHX and the proteasome inhibitor MG-132 demonstrated the involvement of the ubiquitin-proteasome system in controlling NSs protein amount expressed in the cells. The analysis of TOSV NSs by mass spectrometry allowed the direct identification of K104, K109, K154, K180, K244, K294, and K298 residues targeted for ubiquitination. Analysis of NSs K-mutants confirmed the presence and the important role of lysine residues located in the central and the C-terminal parts of the protein in controlling the NSs cellular level. Therefore, we directly demonstrated a new cellular pathway involved in controlling TOSV NSs fate and activity, and this opens the way to new investigations among more pathogenic viruses of the Phenuiviridae family.
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Affiliation(s)
- Gianni Gori Savellini
- Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy; (G.A.); (C.G.); (S.P.); (M.G.C.)
| | - Luca Bini
- Department of Life Sciences, University of Siena, 53100 Siena, Italy;
| | - Assunta Gagliardi
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Laboratory of Synthetic and Structural Vaccinology, 38122 Trento, Italy;
| | - Gabriele Anichini
- Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy; (G.A.); (C.G.); (S.P.); (M.G.C.)
| | - Claudia Gandolfo
- Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy; (G.A.); (C.G.); (S.P.); (M.G.C.)
- S. Maria delle Scotte Hospital, V.le Bracci, 1, 53100 Siena, Italy
| | - Shibily Prathyumnan
- Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy; (G.A.); (C.G.); (S.P.); (M.G.C.)
| | - Maria Grazia Cusi
- Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy; (G.A.); (C.G.); (S.P.); (M.G.C.)
- S. Maria delle Scotte Hospital, V.le Bracci, 1, 53100 Siena, Italy
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Abstract
Through coevolution with host cells, microorganisms have acquired mechanisms to avoid the detection by the host surveillance system and to use the cell's supplies to establish themselves. Indeed, certain pathogens have evolved proteins that imitate specific eukaryotic cell proteins, allowing them to manipulate host pathways, a phenomenon termed molecular mimicry. Bacterial "eukaryotic-like proteins" are a remarkable example of molecular mimicry. They are defined as proteins that strongly resemble eukaryotic proteins or that carry domains that are predominantly present in eukaryotes and that are generally absent from prokaryotes. The widest diversity of eukaryotic-like proteins known to date can be found in members of the bacterial genus Legionella, some of which cause a severe pneumonia in humans. The characterization of a number of these proteins shed light on their importance during infection. The subsequent identification of eukaryotic-like genes in the genomes of other amoeba-associated bacteria and bacterial symbionts suggested that eukaryotic-like proteins are a common means of bacterial evasion and communication, shaped by the continuous interactions between bacteria and their protozoan hosts. In this review, we discuss the concept of molecular mimicry using Legionella as an example and show that eukaryotic-like proteins effectively manipulate host cell pathways. The study of the function and evolution of such proteins is an exciting field of research that is leading us toward a better understanding of the complex world of bacterium-host interactions. Ultimately, this knowledge will teach us how host pathways are manipulated and how infections may possibly be tackled.
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Luh LM, Scheib U, Juenemann K, Wortmann L, Brands M, Cromm PM. Prey for the Proteasome: Targeted Protein Degradation-A Medicinal Chemist's Perspective. Angew Chem Int Ed Engl 2020; 59:15448-15466. [PMID: 32428344 PMCID: PMC7496094 DOI: 10.1002/anie.202004310] [Citation(s) in RCA: 79] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Indexed: 12/12/2022]
Abstract
Targeted protein degradation (TPD), the ability to control a proteins fate by triggering its degradation in a highly selective and effective manner, has created tremendous excitement in chemical biology and drug discovery within the past decades. The TPD field is spearheaded by small molecule induced protein degradation with molecular glues and proteolysis targeting chimeras (PROTACs) paving the way to expand the druggable space and to create a new paradigm in drug discovery. However, besides the therapeutic angle of TPD a plethora of novel techniques to modulate and control protein levels have been developed. This enables chemical biologists to better understand protein function and to discover and verify new therapeutic targets. This Review gives a comprehensive overview of chemical biology techniques inducing TPD. It explains the strengths and weaknesses of these methods in the context of drug discovery and discusses their future potential from a medicinal chemist's perspective.
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Affiliation(s)
- Laura M. Luh
- Research and DevelopmentPharmaceuticalsBayer AG13353BerlinGermany
| | - Ulrike Scheib
- Research and DevelopmentPharmaceuticalsBayer AG13353BerlinGermany
| | - Katrin Juenemann
- Research and DevelopmentPharmaceuticalsBayer AG13353BerlinGermany
| | - Lars Wortmann
- Research and DevelopmentPharmaceuticalsBayer AG13353BerlinGermany
| | - Michael Brands
- Research and DevelopmentPharmaceuticalsBayer AG13353BerlinGermany
| | - Philipp M. Cromm
- Research and DevelopmentPharmaceuticalsBayer AG13353BerlinGermany
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42
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Yoo YH, Jiang X, Jung KH. An Abiotic Stress Responsive U-Box E3 Ubiquitin Ligase Is Involved in OsGI-Mediating Diurnal Rhythm Regulating Mechanism. PLANTS 2020; 9:plants9091071. [PMID: 32825403 PMCID: PMC7569774 DOI: 10.3390/plants9091071] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 08/11/2020] [Accepted: 08/17/2020] [Indexed: 12/21/2022]
Abstract
The plant U-box (PUB) protein is the E3 ligase that plays roles in the degradation or post-translational modification of target proteins. In rice, 77 U-box proteins were identified and divided into eight classes according to the domain configuration. We performed a phylogenomic analysis by integrating microarray expression data under abiotic stress to the phylogenetic tree context. Real-time quantitative reverse transcription polymerase chain reaction (qRT-PCR) expression analyses identified that eight, twelve, and eight PUB family genes are associated with responses to drought, salinity, and cold stress, respectively. In total, 16 genes showed increased expression in response to three abiotic stresses. Among them, the expression of OsPUB2 in class II and OsPUB33, OsPUB39, and OsPUB41 in class III increased in all three abiotic stresses, indicating their involvement in multiple abiotic stress regulation. In addition, we identified the circadian rhythmic expression for three out of 16 genes responding to abiotic stress through meta-microarray expression data analysis. Among them, OsPUB4 is predicted to be involved in the rice GIGANTEA (OsGI)-mediating diurnal rhythm regulating mechanism. In the last, we constructed predicted protein-protein interaction networks associated with OsPUB4 and OsGI. Our analysis provides essential information to improve environmental stress tolerance mediated by the PUB family members in rice.
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Luh LM, Scheib U, Juenemann K, Wortmann L, Brands M, Cromm PM. Beute für das Proteasom: Gezielter Proteinabbau aus medizinalchemischer Perspektive. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202004310] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Laura M. Luh
- Research and Development Pharmaceuticals Bayer AG 13353 Berlin Germany
| | - Ulrike Scheib
- Research and Development Pharmaceuticals Bayer AG 13353 Berlin Germany
| | - Katrin Juenemann
- Research and Development Pharmaceuticals Bayer AG 13353 Berlin Germany
| | - Lars Wortmann
- Research and Development Pharmaceuticals Bayer AG 13353 Berlin Germany
| | - Michael Brands
- Research and Development Pharmaceuticals Bayer AG 13353 Berlin Germany
| | - Philipp M. Cromm
- Research and Development Pharmaceuticals Bayer AG 13353 Berlin Germany
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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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Zhao B, Tsai YC, Jin B, Wang B, Wang Y, Zhou H, Carpenter T, Weissman AM, Yin J. Protein Engineering in the Ubiquitin System: Tools for Discovery and Beyond. Pharmacol Rev 2020; 72:380-413. [PMID: 32107274 PMCID: PMC7047443 DOI: 10.1124/pr.118.015651] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Ubiquitin (UB) transfer cascades consisting of E1, E2, and E3 enzymes constitute a complex network that regulates a myriad of biologic processes by modifying protein substrates. Deubiquitinating enzymes (DUBs) reverse UB modifications or trim UB chains of diverse linkages. Additionally, many cellular proteins carry UB-binding domains (UBDs) that translate the signals encoded in UB chains to target proteins for degradation by proteasomes or in autophagosomes, as well as affect nonproteolytic outcomes such as kinase activation, DNA repair, and transcriptional regulation. Dysregulation of the UB transfer pathways and malfunctions of DUBs and UBDs play causative roles in the development of many diseases. A greater understanding of the mechanism of UB chain assembly and the signals encoded in UB chains should aid in our understanding of disease pathogenesis and guide the development of novel therapeutics. The recent flourish of protein-engineering approaches such as unnatural amino acid incorporation, protein semisynthesis by expressed protein ligation, and high throughput selection by phage and yeast cell surface display has generated designer proteins as powerful tools to interrogate cell signaling mediated by protein ubiquitination. In this study, we highlight recent achievements of protein engineering on mapping, probing, and manipulating UB transfer in the cell. SIGNIFICANCE STATEMENT: The post-translational modification of proteins with ubiquitin alters the fate and function of proteins in diverse ways. Protein engineering is fundamentally transforming research in this area, providing new mechanistic insights and allowing for the exploration of concepts that can potentially be applied to therapeutic intervention.
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Affiliation(s)
- Bo Zhao
- Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, and School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China (B.Z., B.J., B.W.); Department of Pathophysiology, School of Medicine, Jinan University, Guangzhou, China (Y.W.); Laboratory of Protein Dynamics and Signaling, Center for Cancer Research, National Cancer Institute, Frederick, Maryland (Y.C.T., A.M.W.); and Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia (Y.W., H.Z., T.C., J.Y.)
| | - Yien Che Tsai
- Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, and School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China (B.Z., B.J., B.W.); Department of Pathophysiology, School of Medicine, Jinan University, Guangzhou, China (Y.W.); Laboratory of Protein Dynamics and Signaling, Center for Cancer Research, National Cancer Institute, Frederick, Maryland (Y.C.T., A.M.W.); and Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia (Y.W., H.Z., T.C., J.Y.)
| | - Bo Jin
- Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, and School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China (B.Z., B.J., B.W.); Department of Pathophysiology, School of Medicine, Jinan University, Guangzhou, China (Y.W.); Laboratory of Protein Dynamics and Signaling, Center for Cancer Research, National Cancer Institute, Frederick, Maryland (Y.C.T., A.M.W.); and Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia (Y.W., H.Z., T.C., J.Y.)
| | - Bufan Wang
- Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, and School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China (B.Z., B.J., B.W.); Department of Pathophysiology, School of Medicine, Jinan University, Guangzhou, China (Y.W.); Laboratory of Protein Dynamics and Signaling, Center for Cancer Research, National Cancer Institute, Frederick, Maryland (Y.C.T., A.M.W.); and Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia (Y.W., H.Z., T.C., J.Y.)
| | - Yiyang Wang
- Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, and School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China (B.Z., B.J., B.W.); Department of Pathophysiology, School of Medicine, Jinan University, Guangzhou, China (Y.W.); Laboratory of Protein Dynamics and Signaling, Center for Cancer Research, National Cancer Institute, Frederick, Maryland (Y.C.T., A.M.W.); and Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia (Y.W., H.Z., T.C., J.Y.)
| | - Han Zhou
- Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, and School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China (B.Z., B.J., B.W.); Department of Pathophysiology, School of Medicine, Jinan University, Guangzhou, China (Y.W.); Laboratory of Protein Dynamics and Signaling, Center for Cancer Research, National Cancer Institute, Frederick, Maryland (Y.C.T., A.M.W.); and Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia (Y.W., H.Z., T.C., J.Y.)
| | - Tomaya Carpenter
- Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, and School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China (B.Z., B.J., B.W.); Department of Pathophysiology, School of Medicine, Jinan University, Guangzhou, China (Y.W.); Laboratory of Protein Dynamics and Signaling, Center for Cancer Research, National Cancer Institute, Frederick, Maryland (Y.C.T., A.M.W.); and Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia (Y.W., H.Z., T.C., J.Y.)
| | - Allan M Weissman
- Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, and School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China (B.Z., B.J., B.W.); Department of Pathophysiology, School of Medicine, Jinan University, Guangzhou, China (Y.W.); Laboratory of Protein Dynamics and Signaling, Center for Cancer Research, National Cancer Institute, Frederick, Maryland (Y.C.T., A.M.W.); and Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia (Y.W., H.Z., T.C., J.Y.)
| | - Jun Yin
- Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, and School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China (B.Z., B.J., B.W.); Department of Pathophysiology, School of Medicine, Jinan University, Guangzhou, China (Y.W.); Laboratory of Protein Dynamics and Signaling, Center for Cancer Research, National Cancer Institute, Frederick, Maryland (Y.C.T., A.M.W.); and Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia (Y.W., H.Z., T.C., J.Y.)
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Zuo Y, Chong BK, Jiang K, Finley D, Klenerman D, Ye Y. A General in Vitro Assay for Studying Enzymatic Activities of the Ubiquitin System. Biochemistry 2020; 59:851-861. [PMID: 31951392 DOI: 10.1021/acs.biochem.9b00602] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The ubiquitin (Ub) system regulates a wide range of cellular signaling pathways. Several hundred E1, E2, and E3 enzymes are together responsible for protein ubiquitination, thereby controlling cellular activities. Due to the numerous enzymes and processes involved, studies of ubiquitination activities have been challenging. We here report a novel Förster resonance energy transfer (FRET)-based assay for studying the in vitro kinetics of ubiquitination. FRET is established upon binding of fluorophore-labeled Ub to eGFP-tagged ZnUBP, a domain that exclusively binds unconjugated Ub. We name this assay the free Ub sensor system (FUSS). Using Uba1, UbcH5, and CHIP as model E1, E2, and E3 enzymes, respectively, we demonstrate that ubiquitination results in decreasing FRET efficiency, from which reaction rates can be determined. Further treatment with USP21, a deubiquitinase, leads to increased FRET efficiency, confirming the reversibility of the assay. We subsequently use this assay to show that increasing the concentration of CHIP or UbcH5 but not Uba1 enhances ubiquitination rates and develop a novel machine learning approach to model ubiquitination. The overall ubiquitination activity is also increased upon incubation with tau, a substrate of CHIP. Our data together demonstrate the versatile applications of a novel ubiquitination assay that does not require labeling of E1, E2, E3, or substrates and is thus likely compatible with any E1-E2-E3 combinations.
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Affiliation(s)
- Yukun Zuo
- Department of Chemistry , University of Cambridge , Cambridge CB2 1EW , U.K.,UK Dementia Research Institute at University of Cambridge , Cambridge CB2 0XY , U.K
| | - Boon Keat Chong
- Department of Chemistry , University of Cambridge , Cambridge CB2 1EW , U.K
| | - Kun Jiang
- Department of Chemistry , University of Cambridge , Cambridge CB2 1EW , U.K
| | - Daniel Finley
- Department of Cell Biology , Harvard Medical School , Boston , Massachusetts 02115 , United States
| | - David Klenerman
- Department of Chemistry , University of Cambridge , Cambridge CB2 1EW , U.K.,UK Dementia Research Institute at University of Cambridge , Cambridge CB2 0XY , U.K
| | - Yu Ye
- Department of Chemistry , University of Cambridge , Cambridge CB2 1EW , U.K.,Department of Cell Biology , Harvard Medical School , Boston , Massachusetts 02115 , United States.,Department of Brain Sciences, Division of Neuroscience , Imperial College London , London W12 0NN , U.K.,UK Dementia Research Institute at Imperial College London , London W12 0NN , U.K
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Li Q, Niu H, Xu K, Xu Q, Wang S, Liang X, Jiang Y, Niu J. GWAS for resistance against black point caused by Bipolaris sorokiniana in wheat. J Cereal Sci 2020. [DOI: 10.1016/j.jcs.2019.102859] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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48
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Targeting the ubiquitin-proteasome pathway to overcome anti-cancer drug resistance. Drug Resist Updat 2020; 48:100663. [DOI: 10.1016/j.drup.2019.100663] [Citation(s) in RCA: 101] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 11/01/2019] [Accepted: 11/03/2019] [Indexed: 02/07/2023]
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Liu H, Pfirrmann T. The Gid-complex: an emerging player in the ubiquitin ligase league. Biol Chem 2019; 400:1429-1441. [DOI: 10.1515/hsz-2019-0139] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 02/20/2019] [Indexed: 12/16/2022]
Abstract
Abstract
The Saccharomyces cerevisiae Gid-complex is a highly evolutionary conserved ubiquitin ligase with at least seven protein subunits. Here, we review our knowledge about the yeast Gid-complex as an important regulator of glucose metabolism, specifically targeting key enzymes of gluconeogenesis for degradation. Furthermore, we summarize existing data about the individual subunits, the topology and possible substrate recognition mechanisms and compare the striking similarities, but also differences, between the yeast complex and its vertebrate counterpart. Present data is summarized to give an overview about cellular processes regulated by the vertebrate GID-complex that range from cell cycle regulation, primary cilia function to the regulation of energy homeostasis. In conclusion, the vertebrate GID-complex evolved as a versatile ubiquitin ligase complex with functions beyond the regulation of glucose metabolism.
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Affiliation(s)
- Huaize Liu
- Martin Luther University Halle-Wittenberg , Institute of Physiological Chemistry , Hollystr. 1 , D-06114 Halle , Germany
| | - Thorsten Pfirrmann
- Martin Luther University Halle-Wittenberg , Institute of Physiological Chemistry , Hollystr. 1 , D-06114 Halle , Germany
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Structural and Functional Insights into Human Nuclear Cyclophilins. Biomolecules 2018; 8:biom8040161. [PMID: 30518120 PMCID: PMC6315705 DOI: 10.3390/biom8040161] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 11/21/2018] [Accepted: 11/22/2018] [Indexed: 02/05/2023] Open
Abstract
The peptidyl prolyl isomerases (PPI) of the cyclophilin type are distributed throughout human cells, including eight found solely in the nucleus. Nuclear cyclophilins are involved in complexes that regulate chromatin modification, transcription, and pre-mRNA splicing. This review collects what is known about the eight human nuclear cyclophilins: peptidyl prolyl isomerase H (PPIH), peptidyl prolyl isomerase E (PPIE), peptidyl prolyl isomerase-like 1 (PPIL1), peptidyl prolyl isomerase-like 2 (PPIL2), peptidyl prolyl isomerase-like 3 (PPIL3), peptidyl prolyl isomerase G (PPIG), spliceosome-associated protein CWC27 homolog (CWC27), and peptidyl prolyl isomerase domain and WD repeat-containing protein 1 (PPWD1). Each “spliceophilin” is evaluated in relation to the spliceosomal complex in which it has been studied, and current work studying the biological roles of these cyclophilins in the nucleus are discussed. The eight human splicing complexes available in the Protein Data Bank (PDB) are analyzed from the viewpoint of the human spliceophilins. Future directions in structural and cellular biology, and the importance of developing spliceophilin-specific inhibitors, are considered.
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