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Zhou X, Xu R, Wu Y, Zhou L, Xiang T. The role of proteasomes in tumorigenesis. Genes Dis 2024; 11:101070. [PMID: 38523673 PMCID: PMC10958230 DOI: 10.1016/j.gendis.2023.06.037] [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: 02/22/2023] [Revised: 05/10/2023] [Accepted: 06/27/2023] [Indexed: 03/26/2024] Open
Abstract
Protein homeostasis is the basis of normal life activities, and the proteasome family plays an extremely important function in this process. The proteasome 20S is a concentric circle structure with two α rings and two β rings overlapped. The proteasome 20S can perform both ATP-dependent and non-ATP-dependent ubiquitination proteasome degradation by binding to various subunits (such as 19S, 11S, and 200 PA), which is performed by its active subunit β1, β2, and β5. The proteasome can degrade misfolded, excess proteins to maintain homeostasis. At the same time, it can be utilized by tumors to degrade over-proliferate and unwanted proteins to support their growth. Proteasomes can affect the development of tumors from several aspects including tumor signaling pathways such as NF-κB and p53, cell cycle, immune regulation, and drug resistance. Proteasome-encoding genes have been found to be overexpressed in a variety of tumors, providing a potential novel target for cancer therapy. In addition, proteasome inhibitors such as bortezomib, carfilzomib, and ixazomib have been put into clinical application as the first-line treatment of multiple myeloma. More and more studies have shown that it also has different therapeutic effects in other tumors such as hepatocellular carcinoma, non-small cell lung cancer, glioblastoma, and neuroblastoma. However, proteasome inhibitors are not much effective due to their tolerance and singleness in other tumors. Therefore, further studies on their mechanisms of action and drug interactions are needed to investigate their therapeutic potential.
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Affiliation(s)
- Xiangyi Zhou
- Department of Oncology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
- Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized Treatment, Chongqing University Cancer Hospital, Chongqing 400030, China
| | - Ruqing Xu
- Department of Oncology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Yue Wu
- Department of Oncology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Li Zhou
- Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized Treatment, Chongqing University Cancer Hospital, Chongqing 400030, China
| | - Tingxiu Xiang
- Department of Oncology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
- Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized Treatment, Chongqing University Cancer Hospital, Chongqing 400030, China
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Luo D, Tang H, Tan L, Zhang L, Wang L, Cheng Q, Lei X, Wu J. lncRNA JPX Promotes Tumor Progression by Interacting with and Destabilizing YTHDF2 in Cutaneous Melanoma. Mol Cancer Res 2024; 22:524-537. [PMID: 38441563 DOI: 10.1158/1541-7786.mcr-23-0701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Revised: 01/18/2024] [Accepted: 03/01/2024] [Indexed: 06/05/2024]
Abstract
Aberrant long noncoding RNAs just proximal to Xist (lncRNA JPX) expression levels have been detected in multiple tumors. However, whether JPX is involved in melanoma progression remains unclear. Our study showed that JPX expression is significantly increased in melanoma tissues and cell lines. To clarify the effect of JPX on cutaneous melanoma, we successfully generated JPX-overexpressing or JPX-knockdown A375 and A2058 cells. CCK-8, colony formation EdU, Transwell, and cell-cycle phase assays were performed, and subcutaneously implanted tumor models were used to determine the function of JPX in cutaneous melanoma. The results showed that JPX knockdown reduced the proliferation and migration of malignant melanoma cells both in vitro and in vivo. To further elucidate the molecular mechanism of JPX-induced cutaneous melanoma deterioration, we performed RNA pull-down, RNA immunoprecipitation, coimmunoprecipitation, Western blot, and RNA-sequence analyses. JPX can directly interact with YTHDF2 and impede the protection of YTHDF2 from ubiquitin-specific protease 10 (USP10), which promotes its deubiquitination. Thus, JPX decreases protein stability and promotes the degradation of YTHDF2, thereby stabilizing BMP2 mRNA and activating AKT phosphorylation. Overall, our study revealed a novel effect of JPX on YTHDF2 ubiquitination, suggesting the possibility of blocking the JPX/USP10/YTHDF2/BMP2 axis as a prospective therapeutic approach for cutaneous melanoma. IMPLICATIONS This study highlights the ubiquitination effect of USP10 and JPX on YTHDF2 in cutaneous melanoma, and proposes that the JPX/USP10/YTHDF2/BMP2 axis may be a prospective therapeutic target for cutaneous melanoma.
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Affiliation(s)
- Dan Luo
- Department of Dermatology, Daping Hospital, Army Medical University, Chongqing, China
| | - Hui Tang
- Department of Dermatology, Daping Hospital, Army Medical University, Chongqing, China
| | - Liuchang Tan
- Department of Plastic and Cosmetic Surgery, Daping Hospital, Army Medical University, Chongqing, China
| | - Long Zhang
- Department of Dermatology, Daping Hospital, Army Medical University, Chongqing, China
| | - Lei Wang
- Department of Dermatology, Daping Hospital, Army Medical University, Chongqing, China
| | - Qionghui Cheng
- Department of Dermatology, Daping Hospital, Army Medical University, Chongqing, China
| | - Xia Lei
- Department of Dermatology, Daping Hospital, Army Medical University, Chongqing, China
| | - Jinjin Wu
- Department of Dermatology, Daping Hospital, Army Medical University, Chongqing, China
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Takeda Y, Ueki M, Matsuhiro J, Walinda E, Tanaka T, Yamada M, Fujita H, Takezaki S, Kobayashi I, Tamaki S, Nagata S, Miyake N, Matsumoto N, Osawa M, Yasumi T, Heike T, Ohtake F, Saito MK, Toguchida J, Takita J, Ariga T, Iwai K. A de novo dominant-negative variant is associated with OTULIN-related autoinflammatory syndrome. J Exp Med 2024; 221:e20231941. [PMID: 38652464 PMCID: PMC11040501 DOI: 10.1084/jem.20231941] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 02/21/2024] [Accepted: 03/15/2024] [Indexed: 04/25/2024] Open
Abstract
OTULIN-related autoinflammatory syndrome (ORAS), a severe autoinflammatory disease, is caused by biallelic pathogenic variants of OTULIN, a linear ubiquitin-specific deubiquitinating enzyme. Loss of OTULIN attenuates linear ubiquitination by inhibiting the linear ubiquitin chain assembly complex (LUBAC). Here, we report a patient who harbors two rare heterozygous variants of OTULIN (p.P152L and p.R306Q). We demonstrated accumulation of linear ubiquitin chains upon TNF stimulation and augmented TNF-induced cell death in mesenchymal stem cells differentiated from patient-derived iPS cells, which confirms that the patient has ORAS. However, although the de novo p.R306Q variant exhibits attenuated deubiquitination activity without reducing the amount of OTULIN, the deubiquitination activity of the p.P152L variant inherited from the mother was equivalent to that of the wild-type. Patient-derived MSCs in which the p.P152L variant was replaced with wild-type also exhibited augmented TNF-induced cell death and accumulation of linear chains. The finding that ORAS can be caused by a dominant-negative p.R306Q variant of OTULIN furthers our understanding of disease pathogenesis.
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Affiliation(s)
- Yukiko Takeda
- Department of Molecular and Cellular Physiology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Masahiro Ueki
- Department of Pediatrics, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, Sapporo, Japan
| | - Junpei Matsuhiro
- Department of Molecular and Cellular Physiology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Erik Walinda
- Department of Molecular and Cellular Physiology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Takayuki Tanaka
- Department of Pediatrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Masafumi Yamada
- Department of Pediatrics, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, Sapporo, Japan
- Department of Food and Human Wellness, Rakuno Gakuen University, Ebetsu, Japan
| | - Hiroaki Fujita
- Department of Molecular and Cellular Physiology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Shunichiro Takezaki
- Department of Pediatrics, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, Sapporo, Japan
| | - Ichiro Kobayashi
- Department of Pediatrics, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, Sapporo, Japan
| | - Sakura Tamaki
- Department of Regeneration Science and Engineering, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Sanae Nagata
- Department of Fundamental Cell Technology, Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan
| | - Noriko Miyake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
- Department of Human Genetics, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Mitsujiro Osawa
- Department of Clinical Application, Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan
| | - Takahiro Yasumi
- Department of Pediatrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Toshio Heike
- Department of Pediatrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Fumiaki Ohtake
- Institute for Advanced Life Sciences, Hoshi University, Tokyo, Japan
| | - Megumu K. Saito
- Department of Clinical Application, Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan
| | - Junya Toguchida
- Department of Regeneration Science and Engineering, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
- Department of Fundamental Cell Technology, Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan
| | - Junko Takita
- Department of Pediatrics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Tadashi Ariga
- Department of Pediatrics, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, Sapporo, Japan
| | - Kazuhiro Iwai
- Department of Molecular and Cellular Physiology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
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Opdensteinen P, Charudattan R, Hong JC, Rosskopf EN, Steinmetz NF. Biochemical and nanotechnological approaches to combat phytoparasitic nematodes. PLANT BIOTECHNOLOGY JOURNAL 2024. [PMID: 38831638 DOI: 10.1111/pbi.14359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 03/09/2024] [Accepted: 04/05/2024] [Indexed: 06/05/2024]
Abstract
The foundation of most food production systems underpinning global food security is the careful management of soil resources. Embedded in the concept of soil health is the impact of diverse soil-borne pests and pathogens, and phytoparasitic nematodes represent a particular challenge. Root-knot nematodes and cyst nematodes are severe threats to agriculture, accounting for annual yield losses of US$157 billion. The control of soil-borne phytoparasitic nematodes conventionally relies on the use of chemical nematicides, which can have adverse effects on the environment and human health due to their persistence in soil, plants, and water. Nematode-resistant plants offer a promising alternative, but genetic resistance is species-dependent, limited to a few crops, and breeding and deploying resistant cultivars often takes years. Novel approaches for the control of phytoparasitic nematodes are therefore required, those that specifically target these parasites in the ground whilst minimizing the impact on the environment, agricultural ecosystems, and human health. In addition to the development of next-generation, environmentally safer nematicides, promising biochemical strategies include the combination of RNA interference (RNAi) with nanomaterials that ensure the targeted delivery and controlled release of double-stranded RNA. Genome sequencing has identified more than 75 genes in root knot and cyst nematodes that have been targeted with RNAi so far. But despite encouraging results, the delivery of dsRNA to nematodes in the soil remains inefficient. In this review article, we describe the state-of-the-art RNAi approaches targeting phytoparasitic nematodes and consider the potential benefits of nanotechnology to improve dsRNA delivery.
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Affiliation(s)
- Patrick Opdensteinen
- Department of NanoEngineering, University of California, San Diego, La Jolla, California, USA
- Center for Nano-ImmunoEngineering, University of California, San Diego, La Jolla, California, USA
- Shu and K.C. Chien and Peter Farrell Collaboratory, University of California, San Diego, La Jolla, California, USA
| | | | - Jason C Hong
- USDA-ARS-U.S. Horticultural Research Laboratory, Fort Pierce, Florida, USA
| | - Erin N Rosskopf
- USDA-ARS-U.S. Horticultural Research Laboratory, Fort Pierce, Florida, USA
| | - Nicole F Steinmetz
- Department of NanoEngineering, University of California, San Diego, La Jolla, California, USA
- Center for Nano-ImmunoEngineering, University of California, San Diego, La Jolla, California, USA
- Shu and K.C. Chien and Peter Farrell Collaboratory, University of California, San Diego, La Jolla, California, USA
- Department of Bioengineering, University of California, San Diego, La Jolla, California, USA
- Department of Radiology, University of California, San Diego, La Jolla, California, USA
- Institute for Materials Discovery and Design, University of California, San Diego, La Jolla, California, USA
- Moores Cancer Center, University of California, San Diego, La Jolla, California, USA
- Center for Engineering in Cancer, Institute of Engineering in Medicine, University of California, San Diego, La Jolla, California, USA
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Shi Y, Fang N, Wu Y, Xu H, Ning A, Zhang W, Liu Y, Tao X, Chen Q, Tian T, Zhang L, Chu M, Cui J. NEDD4L mediates ITGB4 ubiquitination and degradation to suppress esophageal carcinoma progression. Cell Commun Signal 2024; 22:302. [PMID: 38831335 DOI: 10.1186/s12964-024-01685-9] [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: 02/05/2024] [Accepted: 05/27/2024] [Indexed: 06/05/2024] Open
Abstract
The ubiquitination-mediated protein degradation exerts a vital role in the progression of multiple tumors. NEDD4L, which belongs to the E3 ubiquitin ligase NEDD4 family, is related to tumor genesis, metastasis and drug resistance. However, the anti-tumor role of NEDD4L in esophageal carcinoma, and the potential specific recognition substrate remain unclear. Based on public esophageal carcinoma database and clinical sample data, it was discovered in this study that the expression of NEDD4L in esophageal carcinoma was apparently lower than that in atypical hyperplastic esophageal tissue and esophageal squamous epithelium. Besides, patients with high expression of NEDD4L in esophageal carcinoma tissue had longer progression-free survival than those with low expression. Experiments in vivo and in vitro also verified that NEDD4L suppressed the growth and metastasis of esophageal carcinoma. Based on co-immunoprecipitation and proteome analysis, the NEDD4L ubiquitination-degraded protein ITGB4 was obtained. In terms of the mechanism, the HECT domain of NEDD4L specifically bound to the Galx-β domain of ITGB4, which modified the K915 site of ITGB4 in an ubiquitination manner, and promoted the ubiquitination degradation of ITGB4, thus suppressing the malignant phenotype of esophageal carcinoma.
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Affiliation(s)
- Yijun Shi
- Department of Thoracic and Cardiovascular Surgery, The Affiliated People's Hospital of Jiangsu University, Zhenjiang, 212002, China
| | - Na Fang
- Department of Oncology, The Affiliated People's Hospital of Jiangsu University, Zhenjiang, 212002, China
| | - Yutong Wu
- Department of Epidemiology, School of Public Health, Nantong University, 9 Seyuan Road, Nantong, 226019, China
| | - Huiwen Xu
- Department of Epidemiology, School of Public Health, Nantong University, 9 Seyuan Road, Nantong, 226019, China
| | - Anhui Ning
- Department of Epidemiology, School of Public Health, Nantong University, 9 Seyuan Road, Nantong, 226019, China
| | - Wendi Zhang
- Department of Epidemiology, School of Public Health, Nantong University, 9 Seyuan Road, Nantong, 226019, China
| | - Yiran Liu
- Department of Epidemiology, School of Public Health, Nantong University, 9 Seyuan Road, Nantong, 226019, China
| | - Xiaobo Tao
- Department of Epidemiology, School of Public Health, Nantong University, 9 Seyuan Road, Nantong, 226019, China
| | - Qiong Chen
- Department of Epidemiology, School of Public Health, Nantong University, 9 Seyuan Road, Nantong, 226019, China
| | - Tian Tian
- Department of Epidemiology, School of Public Health, Nantong University, 9 Seyuan Road, Nantong, 226019, China
| | - Lei Zhang
- Department of Epidemiology, School of Public Health, Nantong University, 9 Seyuan Road, Nantong, 226019, China
| | - Minjie Chu
- Department of Epidemiology, School of Public Health, Nantong University, 9 Seyuan Road, Nantong, 226019, China.
| | - Jiahua Cui
- Department of Epidemiology, School of Public Health, Nantong University, 9 Seyuan Road, Nantong, 226019, China.
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China.
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Lu L, Jifu C, Xia J, Wang J. E3 ligases and DUBs target ferroptosis: A potential therapeutic strategy for neurodegenerative diseases. Biomed Pharmacother 2024; 175:116753. [PMID: 38761423 DOI: 10.1016/j.biopha.2024.116753] [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: 03/14/2024] [Revised: 04/30/2024] [Accepted: 05/10/2024] [Indexed: 05/20/2024] Open
Abstract
Ferroptosis is a form of cell death mediated by iron and lipid peroxidation (LPO). Recent studies have provided compelling evidence to support the involvement of ferroptosis in the pathogenesis of various neurodegenerative diseases (NDDs), such as Alzheimer's disease (AD), Parkinson's disease (PD). Therefore, understanding the mechanisms that regulate ferroptosis in NDDs may improve disease management. Ferroptosis is regulated by multiple mechanisms, and different degradation pathways, including autophagy and the ubiquitinproteasome system (UPS), orchestrate the complex ferroptosis response by directly or indirectly regulating iron accumulation or lipid peroxidation. Ubiquitination plays a crucial role as a protein posttranslational modification in driving ferroptosis. Notably, E3 ubiquitin ligases (E3s) and deubiquitinating enzymes (DUBs) are key enzymes in the ubiquitin system, and their dysregulation is closely linked to the progression of NDDs. A growing body of evidence highlights the role of ubiquitin system enzymes in regulating ferroptosis sensitivity. However, reports on the interaction between ferroptosis and ubiquitin signaling in NDDs are scarce. In this review, we first provide a brief overview of the biological processes and roles of the UPS, summarize the core molecular mechanisms and potential biological functions of ferroptosis, and explore the pathophysiological relevance and therapeutic implications of ferroptosis in NDDs. In addition, reviewing the roles of E3s and DUBs in regulating ferroptosis in NDDs aims to provide new insights and strategies for the treatment of NDDs. These include E3- and DUB-targeted drugs and ferroptosis inhibitors, which can be used to prevent and ameliorate the progression of NDDs.
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Affiliation(s)
- Linxia Lu
- College of Basic Medicine, Jiamusi University, Jiamusi 154007, People's Republic of China
| | - Cili Jifu
- College of Basic Medicine, Jiamusi University, Jiamusi 154007, People's Republic of China
| | - Jun Xia
- College of Basic Medicine, Jiamusi University, Jiamusi 154007, People's Republic of China
| | - Jingtao Wang
- College of Basic Medicine, Jiamusi University, Jiamusi 154007, People's Republic of China.
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Hu H, Ma J, Peng Y, Feng R, Luo C, Zhang M, Tao Z, Chen L, Zhang T, Chen W, Yin Q, Zhai J, Chen J, Yin A, Wang CC, Zhong M. Thrombospondin-1 Regulates Trophoblast Necroptosis via NEDD4-Mediated Ubiquitination of TAK1 in Preeclampsia. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2309002. [PMID: 38569496 DOI: 10.1002/advs.202309002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 03/05/2024] [Indexed: 04/05/2024]
Abstract
Preeclampsia (PE) is considered as a disease of placental origin. However, the specific mechanism of placental abnormalities remains elusive. This study identified thrombospondin-1 (THBS1) is downregulated in preeclamptic placentae and negatively correlated with blood pressure. Functional studies show that THBS1 knockdown inhibits proliferation, migration, and invasion and increases the cycle arrest and apoptosis rate of HTR8/SVneo cells. Importantly, THBS1 silencing induces necroptosis in HTR8/SVneo cells, accompanied by the release of damage-associated molecular patterns (DAMPs). Necroptosis inhibitors necrostatin-1 and GSK'872 restore the trophoblast survival while pan-caspase inhibitor Z-VAD-FMK has no effect. Mechanistically, the results show that THBS1 interacts with transforming growth factor B-activated kinase 1 (TAK1), which is a central modulator of necroptosis quiescence and affects its stability. Moreover, THBS1 silencing up-regulates the expression of neuronal precursor cell-expressed developmentally down-regulated 4 (NEDD4), which acts as an E3 ligase of TAK1 and catalyzes K48-linked ubiquitination of TAK1 in HTR8/SVneo cells. Besides, THBS1 attenuates PE phenotypes and improves the placental necroptosis in vivo. Taken together, the down-regulation of THBS1 destabilizes TAK1 by activating NEDD4-mediated, K48-linked TAK1 ubiquitination and promotes necroptosis and DAMPs release in trophoblast cells, thus participating in the pathogenesis of PE.
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Affiliation(s)
- Haoyue Hu
- Department of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, 510515, China
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, Guangdong, 510515, China
| | - Jing Ma
- Department of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, 510515, China
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, Guangdong, 510515, China
| | - You Peng
- Department of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, 510515, China
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, Guangdong, 510515, China
| | - Rixuan Feng
- School of Nursing, Southern Medical University, Guangzhou, Guangdong, 510515, China
| | - Chenling Luo
- School of Nursing, Southern Medical University, Guangzhou, Guangdong, 510515, China
| | - Minyi Zhang
- Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou, Guangdong, 510515, China
| | - Zixin Tao
- Department of Obstetrics and Gynecology, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, Guangdong, 510180, China
| | - Lu Chen
- Department of Obstetrics and Gynaecology;, Li Ka Shing Institute of Health Sciences;, School of Biomedical Sciences;, Chinese University of Hong Kong-Sichuan University Joint Laboratory in Reproductive Medicine; The Chinese University of Hong Kong, Hong Kong SAR, NT, China
| | - Tao Zhang
- Department of Obstetrics and Gynaecology;, Li Ka Shing Institute of Health Sciences;, School of Biomedical Sciences;, Chinese University of Hong Kong-Sichuan University Joint Laboratory in Reproductive Medicine; The Chinese University of Hong Kong, Hong Kong SAR, NT, China
| | - Wenqian Chen
- Department of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, 510515, China
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, Guangdong, 510515, China
| | - Qian Yin
- Department of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, 510515, China
| | - Jinguo Zhai
- School of Nursing, Southern Medical University, Guangzhou, Guangdong, 510515, China
| | - Jun Chen
- Department of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, 510515, China
| | - Ailan Yin
- Department of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, 510515, China
| | - Chi Chiu Wang
- Department of Obstetrics and Gynaecology;, Li Ka Shing Institute of Health Sciences;, School of Biomedical Sciences;, Chinese University of Hong Kong-Sichuan University Joint Laboratory in Reproductive Medicine; The Chinese University of Hong Kong, Hong Kong SAR, NT, China
| | - Mei Zhong
- Department of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, 510515, China
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Ma K, Xian W, Liu H, Shu R, Ge J, Luo ZQ, Liu X, Qiu J. Bacterial ubiquitin ligases hijack the host deubiquitinase OTUB1 to inhibit MTORC1 signaling and promote autophagy. Autophagy 2024:1-16. [PMID: 38818749 DOI: 10.1080/15548627.2024.2353492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 05/05/2024] [Indexed: 06/01/2024] Open
Abstract
Many bacterial pathogens have evolved effective strategies to interfere with the ubiquitination network to evade clearance by the innate immune system. Here, we report that OTUB1, one of the most abundant deubiquitinases (DUBs) in mammalian cells, is subjected to both canonical and noncanonical ubiquitination during Legionella pneumophila infection. The effectors SidC and SdcA catalyze OTUB1 ubiquitination at multiple lysine residues, resulting in its association with a Legionella-containing vacuole. Lysine ubiquitination by SidC and SdcA promotes interactions between OTUB1 and DEPTOR, an inhibitor of the MTORC1 pathway, thus suppressing MTORC1 signaling. The inhibition of MTORC1 leads to suppression of host protein synthesis and promotion of host macroautophagy/autophagy during L. pneumophila infection. In addition, members of the SidE family effectors (SidEs) induce phosphoribosyl (PR)-linked ubiquitination of OTUB1 at Ser16 and Ser18 and block its DUB activity. The levels of the lysine and serine ubiquitination of OTUB1 are further regulated by effectors that function to antagonize the activities of SidC, SdcA and SidEs, including Lem27, DupA, DupB, SidJ and SdjA. Our study reveals an effectors-mediated complicated mechanism in regulating the activity of a host DUB.Abbreviations: BafA1: bafilomycin A1; BMDMs: bone marrow-derived macrophages; DUB: deubiquitinase; Dot/Icm: defective for organelle trafficking/intracellular multiplication; DEPTOR: DEP domain containing MTOR interacting protein; GAPDH: glyceraldehyde-3-phosphate dehydrogenase; L. pneumophila: Legionella pneumophila; LCV: Legionella-containing vacuole; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; MOI: multiplicity of infection; MTORC1: mechanistic target of rapamycin kinase complex 1; OTUB1: OTU deubiquitinase, ubiquitin aldehyde binding 1; PR-Ub: phosphoribosyl (PR)-linked ubiquitin; PTM: posttranslational modification; SDS-PAGE: sodium dodecyl sulfate-polyacrylamide gel electrophoresis; SidEs: SidE family effectors; Ub: ubiquitin.
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Affiliation(s)
- Kelong Ma
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, College of Veterinary Medicine, Jilin University, Center for Pathogen Biology and Infectious Diseases, The First Hospital of Jilin University, Changchun, China
| | - Wei Xian
- Department of Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Hongtao Liu
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, College of Veterinary Medicine, Jilin University, Center for Pathogen Biology and Infectious Diseases, The First Hospital of Jilin University, Changchun, China
| | - Rundong Shu
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, College of Veterinary Medicine, Jilin University, Center for Pathogen Biology and Infectious Diseases, The First Hospital of Jilin University, Changchun, China
| | - Jinli Ge
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, College of Veterinary Medicine, Jilin University, Center for Pathogen Biology and Infectious Diseases, The First Hospital of Jilin University, Changchun, China
| | - Zhao-Qing Luo
- Purdue Institute for Inflammation, Immunology and Infectious Disease and Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Xiaoyun Liu
- Department of Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
- NHC Key Laboratory of Medical Immunology, Peking University, Beijing, China
| | - Jiazhang Qiu
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, College of Veterinary Medicine, Jilin University, Center for Pathogen Biology and Infectious Diseases, The First Hospital of Jilin University, Changchun, China
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9
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Yu Q, Ding J, Li S, Li Y. Autophagy in cancer immunotherapy: Perspective on immune evasion and cell death interactions. Cancer Lett 2024; 590:216856. [PMID: 38583651 DOI: 10.1016/j.canlet.2024.216856] [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: 03/04/2024] [Revised: 03/22/2024] [Accepted: 04/02/2024] [Indexed: 04/09/2024]
Abstract
Both the innate and adaptive immune systems work together to produce immunity. Cancer immunotherapy is a novel approach to tumor suppression that has arisen in response to the ineffectiveness of traditional treatments like radiation and chemotherapy. On the other hand, immune evasion can diminish immunotherapy's efficacy. There has been a lot of focus in recent years on autophagy and other underlying mechanisms that impact the possibility of cancer immunotherapy. The primary feature of autophagy is the synthesis of autophagosomes, which engulf cytoplasmic components and destroy them by lysosomal degradation. The planned cell death mechanism known as autophagy can have opposite effects on carcinogenesis, either increasing or decreasing it. It is autophagy's job to maintain the balance and proper functioning of immune cells like B cells, T cells, and others. In addition, autophagy controls whether macrophages adopt the immunomodulatory M1 or M2 phenotype. The ability of autophagy to control the innate and adaptive immune systems is noteworthy. Interleukins and chemokines are immunological checkpoint chemicals that autophagy regulates. Reducing antigen presentation to induce immunological tolerance is another mechanism by which autophagy promotes cancer survival. Therefore, targeting autophagy is of importance for enhancing potential of cancer immunotherapy.
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Affiliation(s)
- Qiang Yu
- Department of Digestive Surgery, Xijing Hospital, Air Force Medical University, Xi'an, 710032, China
| | - Jiajun Ding
- Department of Thyroid, Breast and Vascular Surgery, Xijing Hospital, Air Force Medical University, Xi'an, 710032, China
| | - Shisen Li
- Department of Digestive Surgery, Xijing Hospital, Air Force Medical University, Xi'an, 710032, China
| | - Yunlong Li
- Department of Digestive Surgery, Xijing Hospital, Air Force Medical University, Xi'an, 710032, China.
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10
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Li Y, Perez-Gil J, Lois LM, Varejão N, Reverter D. Broad-spectrum ubiquitin/ubiquitin-like deconjugation activity of the rhizobial effector NopD from Bradyrhizobium (sp. XS1150). Commun Biol 2024; 7:644. [PMID: 38802699 PMCID: PMC11130253 DOI: 10.1038/s42003-024-06344-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 05/16/2024] [Indexed: 05/29/2024] Open
Abstract
The post-translational modification of proteins by ubiquitin-like modifiers (UbLs), such as SUMO, ubiquitin, and Nedd8, regulates a vast array of cellular processes. Dedicated UbL deconjugating proteases families reverse these modifications. During bacterial infection, effector proteins, including deconjugating proteases, are released to disrupt host cell defenses and promote bacterial survival. NopD, an effector protein from rhizobia involved in legume nodule symbiosis, exhibits deSUMOylation activity and, unexpectedly, also deubiquitination and deNeddylation activities. Here, we present two crystal structures of Bradyrhizobium (sp. XS1150) NopD complexed with either Arabidopsis SUMO2 or ubiquitin at 1.50 Å and 1.94 Å resolution, respectively. Despite their low sequence similarity, SUMO and ubiquitin bind to a similar NopD interface, employing a unique loop insertion in the NopD sequence. In vitro binding and activity assays reveal specific residues that distinguish between deubiquitination and deSUMOylation. These unique multifaceted deconjugating activities against SUMO, ubiquitin, and Nedd8 exemplify an optimized bacterial protease that disrupts distinct UbL post-translational modifications during host cell infection.
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Affiliation(s)
- Ying Li
- Institut de Biotecnologia i de Biomedicina and Dept. de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain
- Qingdao University, 266071, Qingdao, China
| | - Jordi Perez-Gil
- Center for Research in Agricultural Genomics-CRAG, Edifici CRAG-Campus UAB, 08193, Bellaterra, Barcelona, Spain
- ARC Centre of Excellence in Synthetic Biology and Centre for Agriculture and the Bioeconomy, Queensland University of Technology, Brisbane, QLD, 4000, Australia
| | - L Maria Lois
- Center for Research in Agricultural Genomics-CRAG, Edifici CRAG-Campus UAB, 08193, Bellaterra, Barcelona, Spain
- Consejo Superior de Investigaciones Científicas (CSIC), Barcelona, Spain
| | - Nathalia Varejão
- Institut de Biotecnologia i de Biomedicina and Dept. de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain.
| | - David Reverter
- Institut de Biotecnologia i de Biomedicina and Dept. de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain.
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.
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11
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Li B, Adam Eichhorn PJ, Chng WJ. Targeting the ubiquitin pathway in lymphoid malignancies. Cancer Lett 2024; 594:216978. [PMID: 38795760 DOI: 10.1016/j.canlet.2024.216978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 05/14/2024] [Accepted: 05/18/2024] [Indexed: 05/28/2024]
Abstract
Ubiquitination and related cellular processes control a variety of aspects in human cell biology, and defects in these processes contribute to multiple illnesses. In recent decades, our knowledge about the pathological role of ubiquitination in lymphoid cancers and therapeutic strategies to target the modified ubiquitination system has evolved tremendously. Here we review the altered signalling mechanisms mediated by the aberrant expression of cancer-associated E2s/E3s and deubiquitinating enzymes (DUBs), which result in the hyperactivation of oncoproteins or the frequently allied downregulation of tumour suppressors. We discuss recent highlights pertaining to the several different therapeutic interventions which are currently being evaluated to effectively block abnormal ubiquitin-proteasome pathway and the use of heterobifunctional molecules which recruit the ubiquitination system to degrade or stabilize non-cognate substrates. This review aids in comprehension of ubiquitination aberrance in lymphoid cancers and current targeting strategies and elicits further investigations to deeply understand the link between cellular ubiquitination and lymphoid pathogenesis as well as to ameliorate corresponding treatment interventions.
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Affiliation(s)
- Boheng Li
- College of Pharmaceutical Sciences, Southwest University, Chongqing, China
| | - Pieter Johan Adam Eichhorn
- Curtin Health Innovation Research Institute, Faculty of Health Sciences, Curtin University, Bentley, Western Australia, Australia; Curtin Medical School, Faculty of Health Sciences, Curtin University, Bentley, Western Australia, Australia.
| | - Wee-Joo Chng
- Cancer Science Institute of Singapore, Singapore, Singapore; Department of Haematology-Oncology, National University Cancer Institute of Singapore, Singapore, Singapore; Department of Medicine, School of Medicine, National University of Singapore, Singapore, Singapore.
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12
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Delos Reyes AMV, Lux MC, Hann ZS, Ji C, Kochańczyk T, DiBello M, Lima CD, Tan DS. Design and Semisynthesis of Biselectrophile-Functionalized Ubiquitin Probes To Investigate Transthioesterification Reactions. Org Lett 2024. [PMID: 38781175 DOI: 10.1021/acs.orglett.4c01102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2024]
Abstract
Ubiquitin (Ub) regulates a wide array of cellular processes through post-translational modification of protein substrates. Ub is conjugated at its C-terminus to target proteins via an enzymatic cascade in which covalently bound Ub thioesters are transferred from E1 activating enzymes to E2 conjugating enzymes, and then to certain E3 protein ligases. These transthioesterification reactions proceed via transient tetrahedral intermediates. A variety of chemical strategies have been used to capture E1-Ub-E2 and E2-Ub-E3 mimics, but these introduce modifications that disrupt atomic spacing at the linkage point relative to the native tetrahedral intermediate. We have developed a biselectrophilic PSAN warhead that can be installed in place of the conserved C-terminal glycine in Ub and used to form ternary protein complexes linked via cyanomethyldithioacetals that closely mimic the native tetrahedral intermediates. Investigation of the reactivity of the warhead and substituted analogues led to an effective semisynthetic route to Ub-1-PSAN, which was used to form a ternary E1-Ub*-E2 complex as a mimic of the transthioesterification intermediate.
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Affiliation(s)
- Avelyn Mae V Delos Reyes
- Pharmacology Program, Weill Cornell Graduate School of Medical Sciences, Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States
- Chemical Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States
| | - Michaelyn C Lux
- Chemical Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States
- Tri-Institutional PhD Program in Chemical BiologyMemorial Sloan Kettering Cancer Center, New York, New York 10065, United States
| | - Zachary S Hann
- Tri-Institutional PhD Program in Chemical BiologyMemorial Sloan Kettering Cancer Center, New York, New York 10065, United States
- Structural Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States
| | - Cheng Ji
- Chemical Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States
| | - Tomasz Kochańczyk
- Structural Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States
| | - Mikaela DiBello
- Chemical Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States
- Gerstner Sloan Kettering Summer Undergraduate Research Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States
| | - Christopher D Lima
- Tri-Institutional PhD Program in Chemical BiologyMemorial Sloan Kettering Cancer Center, New York, New York 10065, United States
- Structural Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States
- Howard Hughes Medical Institute, 1275 York Avenue, New York, New York 10065, United States
| | - Derek S Tan
- Pharmacology Program, Weill Cornell Graduate School of Medical Sciences, Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States
- Chemical Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States
- Tri-Institutional PhD Program in Chemical BiologyMemorial Sloan Kettering Cancer Center, New York, New York 10065, United States
- Tri-Institutional Research Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States
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13
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Yu ZQ, Carmichael J, Collins GA, D'Agostino MD, Lessard M, Firth HV, Harijan P, Fry AE, Dean J, Zhang J, Kini U, Goldberg AL, Rubinsztein DC. PSMC5 insufficiency and P320R mutation impair proteasome function. Hum Mol Genet 2024:ddae085. [PMID: 38776958 DOI: 10.1093/hmg/ddae085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 05/03/2024] [Accepted: 05/08/2024] [Indexed: 05/25/2024] Open
Abstract
The ubiquitin-proteasome system mediates the degradation of a wide variety of proteins. Proteasome dysfunction is associated with neurodegenerative diseases and neurodevelopmental disorders in humans. Here we identified mutations in PSMC5, an AAA ATPase subunit of the proteasome 19S regulatory particle, in individuals with neurodevelopmental disorders, which were initially considered as variants of unknown significance. We have now found heterozygotes with the following mutations: P320R (6 individuals), R325W, Q160A, and one nonsense mutation at Q69. We focused on understanding the functional consequence of PSMC5 insufficiency and the P320R mutation in cells and found that both impair proteasome function and activate apoptosis. Interestingly, the P320R mutation impairs proteasome function by weakening the association between the 19S regulatory particle and the 20S core particle. Our study supports that proteasome dysfunction is the pathogenic cause of neurodevelopmental disorders in individuals carrying PSMC5 variants.
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Affiliation(s)
- Zhong-Qiu Yu
- Cambridge Institute for Medical Research, The Keith Peters Building, Department of Medical Genetics, University of Cambridge, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, United Kingdom
- UK Dementia Research Institute, University of Cambridge, The Keith Peters Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, United Kingdom
| | - Jenny Carmichael
- Department of Clinical Genetics, Cambridge University Hospitals NHS Foundation Trust, Box 134, Addenbrooke's Hospital, Cambridge CB2 0QQ, United Kingdom
| | - Galen A Collins
- Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, United States
- Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State University, 32 Creelman Street, Starkville MS 39762, United States
| | - Maria Daniela D'Agostino
- Division of Medical Genetics, Department of Specialised Medicine, McGill University Health Centre, 1001 Decarie Boulevard, Montreal, Quebec, H4A 3J1, Canada
- Care for Rare Canada Consortium, Children's Hospital of Eastern Ontario Research Institute, 401 Smyth Road, Ottawa, K1H 8L1, ON, Canada
| | - Mathieu Lessard
- Division of Medical Genetics, Department of Specialised Medicine, McGill University Health Centre, 1001 Decarie Boulevard, Montreal, Quebec, H4A 3J1, Canada
- Care for Rare Canada Consortium, Children's Hospital of Eastern Ontario Research Institute, 401 Smyth Road, Ottawa, K1H 8L1, ON, Canada
| | - Helen V Firth
- Department of Clinical Genetics, Cambridge University Hospitals NHS Foundation Trust, Box 134, Addenbrooke's Hospital, Cambridge CB2 0QQ, United Kingdom
| | - Pooja Harijan
- Department of Paediatric Neurosciences, Box 107, Child development centre, Addenbrooke's Hospital, Hills Road, Cambridge CB2 0QQ, United Kingdom
| | - Andrew E Fry
- All Wales Medical Genomics Service, University Hospital of Wales, Heath Park, Cardiff CF14 4XW, United Kingdom
- Division of Cancer and Genetics, Cardiff University, Heath Park, Cardiff CF14 4XN, United Kingdom
| | - John Dean
- The School of Medicine, Medical Sciences and Nutrition, Polwarth Building, University of Aberdeen, Aberdeen, AB25 2ZD, United Kingdom
| | - Jiuchun Zhang
- Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, United States
| | - Usha Kini
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford & Radcliffe Department of Medicine, University of Oxford, Windmill Road, Oxford, OX3 7HE, United Kingdom
| | - Alfred L Goldberg
- Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, United States
| | - David C Rubinsztein
- Cambridge Institute for Medical Research, The Keith Peters Building, Department of Medical Genetics, University of Cambridge, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, United Kingdom
- UK Dementia Research Institute, University of Cambridge, The Keith Peters Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, United Kingdom
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14
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Zhang J, Xue M, Huang J, He S, Zhu L, Zhao X, Wang B, Jiang T, Zhang Y, Miao C, Zhou G. Deficiency of UCHL1 results in insufficient decidualization accompanied by impaired dNK modulation and eventually miscarriage. J Transl Med 2024; 22:478. [PMID: 38769534 PMCID: PMC11103838 DOI: 10.1186/s12967-024-05253-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 04/29/2024] [Indexed: 05/22/2024] Open
Abstract
BACKGROUND Miscarriage is a frustrating complication of pregnancy that is common among women of reproductive age. Insufficient decidualization which not only impairs embryo implantation but disturbs fetomaternal immune-tolerance, has been widely regarded as a major cause of miscarriage; however, the underlying mechanisms resulting in decidual impairment are largely unknown. METHODS With informed consent, decidual tissue from patients with spontaneous abortion or normal pregnant women was collected to detect the expression profile of UCHL1. Human endometrial stromal cells (HESCs) were used to explore the roles of UCHL1 in decidualization and dNK modulation, as well as the mechanisms involved. C57/BL6 female mice (7-10 weeks old) were used to construct pregnancy model or artificially induced decidualization model to evaluate the effect of UCHL1 on mice decidualization and pregnancy outcome. RESULTS The Ubiquitin C-terminal hydrolase L1 (UCHL1), as a deubiquitinating enzyme, was significantly downregulated in decidua from patients with miscarriage, along with impaired decidualization and decreased dNKs. Blockage of UCHL1 led to insufficient decidualization and resultant decreased expression of cytokines CXCL12, IL-15, TGF-β which were critical for generation of decidual NK cells (dNKs), whereas UCHL1 overexpression enhanced decidualization accompanied by increase in dNKs. Mechanistically, the promotion of UCHL1 on decidualization was dependent on its deubiquitinating activity, and intervention of UCHL1 inhibited the activation of JAK2/STAT3 signaling pathway, resulting in aberrant decidualization and decreased production of cytokines associated with dNKs modulation. Furthermore, we found that inhibition of UCHL1 also disrupted the decidualization in mice and eventually caused adverse pregnancy outcome. CONCLUSIONS UCHL1 plays significant roles in decidualization and dNKs modulation during pregnancy in both humans and mice. Its deficiency indicates a poor pregnancy outcome due to defective decidualization, making UCHL1 a potential target for the diagnosis and treatment of miscarriage.
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Affiliation(s)
- Jie Zhang
- Department of Gastrointestinal Surgery, The Affiliated Changshu Hospital of Nantong University, 68 South Haiyu Road, Changshu, 215500, China
- Department of Anesthesiology, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai, 200032, China
| | - Mingxing Xue
- Institutes for Translational Medicine, Children's Hospital of Soochow University, Soochow University, Suzhou, China
- Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, China
| | - Jiefang Huang
- Institutes for Translational Medicine, Children's Hospital of Soochow University, Soochow University, Suzhou, China
- Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, China
| | - Shan He
- Institutes for Translational Medicine, Children's Hospital of Soochow University, Soochow University, Suzhou, China
| | - Lingqiao Zhu
- Institutes for Translational Medicine, Children's Hospital of Soochow University, Soochow University, Suzhou, China
| | - Xiaonan Zhao
- Institutes for Translational Medicine, Children's Hospital of Soochow University, Soochow University, Suzhou, China
| | - Bei Wang
- Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, China
| | - Tingwang Jiang
- Department of Gastrointestinal Surgery, The Affiliated Changshu Hospital of Nantong University, 68 South Haiyu Road, Changshu, 215500, China
| | - Yanyun Zhang
- Department of Gastrointestinal Surgery, The Affiliated Changshu Hospital of Nantong University, 68 South Haiyu Road, Changshu, 215500, China.
- Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, China.
| | - Changhong Miao
- Department of Anesthesiology, Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai, 200032, China.
| | - Guoqiang Zhou
- Department of Gastrointestinal Surgery, The Affiliated Changshu Hospital of Nantong University, 68 South Haiyu Road, Changshu, 215500, China.
- Gusu College, Nanjing Medical University, Nanjing, China.
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15
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Clausen L, Okarmus J, Voutsinos V, Meyer M, Lindorff-Larsen K, Hartmann-Petersen R. PRKN-linked familial Parkinson's disease: cellular and molecular mechanisms of disease-linked variants. Cell Mol Life Sci 2024; 81:223. [PMID: 38767677 PMCID: PMC11106057 DOI: 10.1007/s00018-024-05262-8] [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: 02/27/2024] [Revised: 04/25/2024] [Accepted: 05/02/2024] [Indexed: 05/22/2024]
Abstract
Parkinson's disease (PD) is a common and incurable neurodegenerative disorder that arises from the loss of dopaminergic neurons in the substantia nigra and is mainly characterized by progressive loss of motor function. Monogenic familial PD is associated with highly penetrant variants in specific genes, notably the PRKN gene, where homozygous or compound heterozygous loss-of-function variants predominate. PRKN encodes Parkin, an E3 ubiquitin-protein ligase important for protein ubiquitination and mitophagy of damaged mitochondria. Accordingly, Parkin plays a central role in mitochondrial quality control but is itself also subject to a strict protein quality control system that rapidly eliminates certain disease-linked Parkin variants. Here, we summarize the cellular and molecular functions of Parkin, highlighting the various mechanisms by which PRKN gene variants result in loss-of-function. We emphasize the importance of high-throughput assays and computational tools for the clinical classification of PRKN gene variants and how detailed insights into the pathogenic mechanisms of PRKN gene variants may impact the development of personalized therapeutics.
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Affiliation(s)
- Lene Clausen
- Department of Biology, Linderstrøm-Lang Centre for Protein Science, University of Copenhagen, 2200, Copenhagen, Denmark
| | - Justyna Okarmus
- Department of Neurobiology Research, Institute of Molecular Medicine, University of Southern Denmark, 5230, Odense, Denmark
| | - Vasileios Voutsinos
- Department of Biology, Linderstrøm-Lang Centre for Protein Science, University of Copenhagen, 2200, Copenhagen, Denmark
| | - Morten Meyer
- Department of Neurobiology Research, Institute of Molecular Medicine, University of Southern Denmark, 5230, Odense, Denmark
- Department of Neurology, Odense University Hospital, 5000, Odense, Denmark
- Department of Clinical Research, BRIDGE, Brain Research Inter Disciplinary Guided Excellence, University of Southern Denmark, 5230, Odense, Denmark
| | - Kresten Lindorff-Larsen
- Department of Biology, Linderstrøm-Lang Centre for Protein Science, University of Copenhagen, 2200, Copenhagen, Denmark
| | - Rasmus Hartmann-Petersen
- Department of Biology, Linderstrøm-Lang Centre for Protein Science, University of Copenhagen, 2200, Copenhagen, Denmark.
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16
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Xie Y, Shao F, Ji Y, Feng D, Wang L, Huang Z, Wu S, Sun F, Jiang H, Miyamoto A, Wang H, Zhang C. Network Analysis of Osteoarthritis Progression Using a Steiner Minimal Tree Algorithm. J Inflamm Res 2024; 17:3201-3209. [PMID: 38779430 PMCID: PMC11110812 DOI: 10.2147/jir.s438407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Accepted: 12/09/2023] [Indexed: 05/25/2024] Open
Abstract
Purpose To provide a comprehensive analysis of associated genes with osteoarthritis (OA). Here, we reported a network analysis of OA progression by using a Steiner minimal tree algorithm. Methods We collected the OA-related genes through screening the publications in MEDLINE. We performed functional analysis to analyze the associated biochemical pathways of the OA-related genes. Pathway crosstalk analysis was constructed to explore interactions of the enriched pathways. Steiner minimal tree algorithm was used to analyze molecular pathway networks. The average clustering coefficient was compared with the corresponding values of the Osteoarthritis-specific network. The new finding RNA was compared with former single-cell RNA-seq analysis results. Results A gene set with 177 members reported to be significantly associated with Osteoarthritis was collected from 187 studies. Functional enrichment analysis revealed a specific related-OA gene including skeletal system development, cytokine-mediated signaling pathway, inflammatory response, cartilage development, and extracellular matrix organization. We performed a pathway crosstalk analysis among the 72 significantly enriched pathways. A total of 151 of the 177 genes in the Osteoarthritis gene set were included in the human interactome network. There were 31 genes in the former single-cell RNA-seq analysis results. The CLU, ENO1, SRRM1, UBC, HMGB1, NR3C1, NOTCH2NL, and CBX5 have significantly increased expression in seven molecularly defined populations of OA cartilage. Conclusion The Steiner tree-based approach finds new biological molecules associated with OA genes.
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Affiliation(s)
- Yujie Xie
- Rehabilitation Medicine Department, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, People’s Republic of China
| | - Fanglin Shao
- Rehabilitation Medicine Department, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, People’s Republic of China
| | - Yuxiu Ji
- Rehabilitation Medicine Department, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, People’s Republic of China
| | - Dechao Feng
- Rehabilitation Medicine Department, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, People’s Republic of China
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, Sichuan, People’s Republic of China
| | - Ling Wang
- School of Information and Communication Engineering, University of Electronic Science and Technology, Chengdu, Sichuan, People’s Republic of China
| | - Zonghai Huang
- School of Information and Communication Engineering, University of Electronic Science and Technology, Chengdu, Sichuan, People’s Republic of China
| | - Shengjian Wu
- Rehabilitation Medicine Department, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, People’s Republic of China
| | - Fuhua Sun
- Rehabilitation Medicine Department, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, People’s Republic of China
| | - Hong Jiang
- Rehabilitation Medicine Department, Xichong County People’s hospital, Nanchong, Sichuan, People’s Republic of China
| | - Akira Miyamoto
- Faculty of Rehabilitation, Nishikyushu University, Kansaitama, Japan
| | - Haiming Wang
- Department of Rehabilitation Medicine, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, People’s Republic of China
| | - Chi Zhang
- Rehabilitation Medicine Department, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, People’s Republic of China
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17
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Uenaka E, Ojima K, Suzuki T, Kobayashi K, Muroya S, Nishimura T. Murf1 alters myosin replacement rates in cultured myotubes in a myosin isoform-dependent manner. In Vitro Cell Dev Biol Anim 2024:10.1007/s11626-024-00916-0. [PMID: 38758432 DOI: 10.1007/s11626-024-00916-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 04/23/2024] [Indexed: 05/18/2024]
Abstract
Skeletal muscle tissue increases or decreases its volume by synthesizing or degrading myofibrillar proteins. The ubiquitin-proteasome system plays a pivotal role during muscle atrophy, where muscle ring finger proteins (Murf) function as E3 ubiquitin ligases responsible for identifying and targeting substrates for degradation. Our previous study demonstrated that overexpression of Ozz, an E3 specific to embryonic myosin heavy chain (Myh3), precisely reduced the Myh3 replacement rate in the thick filaments of myotubes (E. Ichimura et al., Physiol Rep. 9:e15003, 2021). These findings strongly suggest that E3 plays a critical role in regulating myosin replacement. Here, we hypothesized that the Murf isoforms, which recognize Myhs as substrates, reduced the myosin replacement rates through the enhanced Myh degradation by Murfs. First, fluorescence recovery after a photobleaching experiment was conducted to assess whether Murf isoforms affected the GFP-Myh3 replacement. In contrast to Murf2 or Murf3 overexpression, Murf1 overexpression selectively facilitated the GFP-Myh3 myosin replacement. Next, to examine the effects of Murf1 overexpression on the replacement of myosin isoforms, Cherry-Murf1 was coexpressed with GFP-Myh1, GFP-Myh4, or GFP-Myh7 in myotubes. Intriguingly, Murf1 overexpression enhanced the myosin replacement of GFP-Myh4 but did not affect those of GFP-Myh1 or GFP-Myh7. Surprisingly, overexpression of Murf1 did not enhance the ubiquitination of proteins. These results indicate that Murf1 selectively regulated myosin replacement in a Myh isoform-dependent fashion, independent of enhanced ubiquitination. This suggests that Murf1 may have a role beyond functioning as a ubiquitin ligase E3 in thick filament myosin replacement.
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Affiliation(s)
- Emi Uenaka
- Research Faculty of Agriculture, Graduate School of Agriculture, Hokkaido University, 9 Kita, 9 Nishi, Sapporo, Hokkaido, 060-8589, Japan
- Space Environment and Energy Laboratories, Nippon Telegraph and Telephone Corporation, Musashino, Tokyo, 180-8585, Japan
| | - Koichi Ojima
- Muscle Biology Research Unit, Division of Animal Products Research, Institute of Livestock and Grassland Science, NARO, 2 Ikenodai, Tsukuba, Ibaraki, 305-0901, Japan
| | - Takahiro Suzuki
- Laboratory of Muscle and Meat Science, Department of Animal and Marine Bioresource Sciences, Faculty of Agriculture, Graduate School of Agriculture, Kyushu University, Motooka 744, Nishi-Ku, Fukuoka, 819-0395, Japan
| | - Ken Kobayashi
- Research Faculty of Agriculture, Graduate School of Agriculture, Hokkaido University, 9 Kita, 9 Nishi, Sapporo, Hokkaido, 060-8589, Japan
| | - Susumu Muroya
- Muscle Biology Research Unit, Division of Animal Products Research, Institute of Livestock and Grassland Science, NARO, 2 Ikenodai, Tsukuba, Ibaraki, 305-0901, Japan
- Laboratory of Meat Science and Production, Faculty of Veterinary Medicine, Kagoshima University, 1-21-24, Korimoto, Kagoshima, 890-0065, Japan
| | - Takanori Nishimura
- Research Faculty of Agriculture, Graduate School of Agriculture, Hokkaido University, 9 Kita, 9 Nishi, Sapporo, Hokkaido, 060-8589, Japan.
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18
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Xu H, Zhang LB, Luo YY, Wang L, Zhang YP, Chen PQ, Ba XY, Han J, Luo H. Synaptotagmins family affect glucose transport in retinal pigment epithelial cells through their ubiquitination-mediated degradation and glucose transporter-1 regulation. World J Diabetes 2024; 15:958-976. [PMID: 38766439 PMCID: PMC11099358 DOI: 10.4239/wjd.v15.i5.958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 01/22/2024] [Accepted: 03/11/2024] [Indexed: 05/10/2024] Open
Abstract
BACKGROUND Synaptotagmins (SYTs) are a family of 17 membrane transporters that function as calcium ion sensors during the release of Ca2+-dependent neurotransmitters and hormones. However, few studies have reported whether members of the SYT family play a role in glucose uptake in diabetic retinopathy (DR) through Ca2+/glucose transporter-1 (GLUT1) and the possible regulatory mechanism of SYTs. AIM To elucidate the role of the SYT family in the regulation of glucose transport in retinal pigment epithelial cells and explore its potential as a therapeutic target for the clinical management of DR. METHODS DR was induced by streptozotocin in C57BL/6J mice and by high glucose medium in human retinal pigment epithelial cells (ARPE-19). Bioinformatics analysis, reverse transcriptase-polymerase chain reaction, Western blot, flow cytometry, ELISA, HE staining, and TUNEL staining were used for analysis. RESULTS Six differentially expressed proteins (SYT2, SYT3, SYT4, SYT7, SYT11, and SYT13) were found between the DR and control groups, and SYT4 was highly expressed. Hyperglycemia induces SYT4 overexpression, manipulates Ca2+ influx to induce GLUT1 fusion with the plasma membrane, promotes abnormal expression of the glucose transporter GLUT1 and excessive glucose uptake, induces ARPE-19 cell apoptosis, and promotes DR progression. Parkin deficiency inhibits the proteasomal degradation of SYT4 in DR, resulting in SYT4 accumulation and enhanced GLUT1 fusion with the plasma membrane, and these effects were blocked by oe-Parkin treatment. Moreover, dysregulation of the myelin transcription factor 1 (Myt1)-induced transcription of SYT4 in DR further activated the SYT4-mediated stimulus-secretion coupling process, and this process was inhibited in the oe-MYT1-treated group. CONCLUSION Our study reveals the key role of SYT4 in regulating glucose transport in retinal pigment epithelial cells during the pathogenesis of DR and the underlying mechanism and suggests potential therapeutic targets for clinical DR.
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Affiliation(s)
- Hong Xu
- Department of Ophthalmology, The People’s Hospital of Chuxiong Yi Autonomous Prefecture & The Fourth Affiliated Hospital of Dali University, Chuxiong Yi Autonomous Prefecture 675000, Yunnan Province, China
| | - Li-Bo Zhang
- Department of Ophthalmology, The People’s Hospital of Chuxiong Yi Autonomous Prefecture & The Fourth Affiliated Hospital of Dali University, Chuxiong Yi Autonomous Prefecture 675000, Yunnan Province, China
| | - Yi-Yi Luo
- Precision Medicine Center of Chuxiong Yi Autonomous Prefecture, The People’s Hospital of Chuxiong Yi Autonomous Prefecture & The Fourth Affiliated Hospital of Dali University, Chuxiong Yi Autonomous Prefecture 675000, Yunnan Province, China
| | - Ling Wang
- Department of Endocrinology, The People’s Hospital of Chuxiong Yi Autonomous Prefecture & The Fourth Affiliated Hospital of Dali University, Chuxiong Yi Autonomous Prefecture 675000, Yunnan Province, China
| | - Ye-Pin Zhang
- Department of Pathology, The People’s Hospital of Chuxiong Yi Autonomous Prefecture & The Fourth Affiliated Hospital of Dali University, Chuxiong Yi Autonomous Prefecture 675000, Yunnan Province, China
| | - Pei-Qi Chen
- Department of Endocrinology, The People’s Hospital of Chuxiong Yi Autonomous Prefecture & The Fourth Affiliated Hospital of Dali University, Chuxiong Yi Autonomous Prefecture 675000, Yunnan Province, China
| | - Xue-Ying Ba
- Precision Medicine Center of Chuxiong Yi Autonomous Prefecture, The People’s Hospital of Chuxiong Yi Autonomous Prefecture & The Fourth Affiliated Hospital of Dali University, Chuxiong Yi Autonomous Prefecture 675000, Yunnan Province, China
| | - Jian Han
- Precision Medicine Center of Chuxiong Yi Autonomous Prefecture, The People’s Hospital of Chuxiong Yi Autonomous Prefecture & The Fourth Affiliated Hospital of Dali University, Chuxiong Yi Autonomous Prefecture 675000, Yunnan Province, China
| | - Heng Luo
- Department of Ophthalmology, The People’s Hospital of Chuxiong Yi Autonomous Prefecture & The Fourth Affiliated Hospital of Dali University, Chuxiong Yi Autonomous Prefecture 675000, Yunnan Province, China
- Precision Medicine Center of Chuxiong Yi Autonomous Prefecture, The People’s Hospital of Chuxiong Yi Autonomous Prefecture & The Fourth Affiliated Hospital of Dali University, Chuxiong Yi Autonomous Prefecture 675000, Yunnan Province, China
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19
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Rong Q, Xi Z, Guo D, Xu W, Zhang L, Wu Q. Regulation of ubiquitination and antiviral activity of Cactin by deubiquitinase Usp14 in Drosophila. J Virol 2024; 98:e0017724. [PMID: 38563731 PMCID: PMC11092352 DOI: 10.1128/jvi.00177-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 03/10/2024] [Indexed: 04/04/2024] Open
Abstract
Cactin, a highly conserved protein, plays a crucial role in various physiological processes in eukaryotes, including innate immunity. Recently, the function of Cactin in the innate immunity of Drosophila has been explored, revealing that Cactin regulates a non-canonical signaling pathway associated with the Toll and Imd pathways via the Cactin-Deaf1 axis. In addition, Cactin exhibits specific antiviral activity against the Drosophila C virus (DCV) in Drosophila, with an unknown mechanism. During DCV infection, it has been confirmed that the protein level and antiviral activity of Cactin are regulated by ubiquitination. However, the precise ubiquitination and deubiquitination mechanisms of Cactin in Drosophila remain unexplored. In this study, we identified ubiquitin-specific protease 14 (Usp14) as a major deubiquitinase for Cactin through comprehensive deubiquitinase screening. Our results demonstrate that Usp14 interacts with the C_Cactus domain of Cactin via its USP domain. Usp14 efficiently removes K48- and K63-linked polyubiquitin chains from Cactin, thereby preventing its degradation through the ubiquitin-proteasome pathway. Usp14 significantly inhibits DCV replication in Drosophila cells by stabilizing Cactin. Moreover, Usp14-deficient fruit flies exhibit increased susceptibility to DCV infection compared to wild-type flies. Collectively, our findings reveal the regulation of ubiquitination and antiviral activity of Cactin by the deubiquitinase Usp14, providing valuable insights into the modulation of Cactin-mediated antiviral activity in Drosophila.IMPORTANCEViral infections pose a severe threat to human health, marked by high pathogenicity and mortality rates. Innate antiviral pathways, such as Toll, Imd, and JAK-STAT, are generally conserved across insects and mammals. Recently, the multi-functionality of Cactin in innate immunity has been identified in Drosophila. In addition to regulating a non-canonical signaling pathway through the Cactin-Deaf1 axis, Cactin exhibits specialized antiviral activity against the Drosophila C virus (DCV) with an unknown mechanism. A previous study emphasized the significance of the Cactin level, regulated by the ubiquitin-proteasome pathway, in modulating antiviral signaling. However, the regulatory mechanisms governing Cactin remain unexplored. In this study, we demonstrate that Usp14 stabilizes Cactin by preventing its ubiquitination and subsequent degradation. Furthermore, Usp14 plays a crucial role in regulating the antiviral function mediated by Cactin. Therefore, our findings elucidate the regulatory mechanism of Cactin in Drosophila, offering a potential target for the prevention and treatment of viral infections.
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Affiliation(s)
- Qiqi Rong
- Department of Pharmacy, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
- Key Laboratory of Anhui Province for Emerging and Reemerging Infectious Diseases, University of Science and Technology of China, Hefei, China
| | - Zhichong Xi
- Department of Pharmacy, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Dongyang Guo
- Department of Pharmacy, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
- Key Laboratory of Anhui Province for Emerging and Reemerging Infectious Diseases, University of Science and Technology of China, Hefei, China
| | - Wen Xu
- Department of Pharmacy, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
- Anhui Provincial Key Laboratory of Precision Pharmaceutical Preparations and Clinical Pharmacy, Hefei, Anhui, China
| | - Liqin Zhang
- Department of Pharmacy, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
- Department of Immunology and Pathogen Biology, School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou, China
| | - Qingfa Wu
- Department of Pharmacy, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
- Division of Molecular Medicine, CAS Key Laboratory of Innate Immunity and Chronic Disease, University of Science and Technology of China, Hefei, Anhui, China
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20
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Jiao D, Sun H, Zhao X, Chen Y, Lv Z, Shi Q, Li Y, Wang C, Gao K. mTORC1/S6K1 signaling promotes sustained oncogenic translation through modulating CRL3 IBTK-mediated ubiquitination of eIF4A1 in cancer cells. eLife 2024; 12:RP92236. [PMID: 38738857 PMCID: PMC11090508 DOI: 10.7554/elife.92236] [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] [Indexed: 05/14/2024] Open
Abstract
Enhanced protein synthesis is a crucial molecular mechanism that allows cancer cells to survive, proliferate, metastasize, and develop resistance to anti-cancer treatments, and often arises as a consequence of increased signaling flux channeled to mRNA-bearing eukaryotic initiation factor 4F (eIF4F). However, the post-translational regulation of eIF4A1, an ATP-dependent RNA helicase and subunit of the eIF4F complex, is still poorly understood. Here, we demonstrate that IBTK, a substrate-binding adaptor of the Cullin 3-RING ubiquitin ligase (CRL3) complex, interacts with eIF4A1. The non-degradative ubiquitination of eIF4A1 catalyzed by the CRL3IBTK complex promotes cap-dependent translational initiation, nascent protein synthesis, oncogene expression, and cervical tumor cell growth both in vivo and in vitro. Moreover, we show that mTORC1 and S6K1, two key regulators of protein synthesis, directly phosphorylate IBTK to augment eIF4A1 ubiquitination and sustained oncogenic translation. This link between the CRL3IBTK complex and the mTORC1/S6K1 signaling pathway, which is frequently dysregulated in cancer, represents a promising target for anti-cancer therapies.
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Affiliation(s)
- Dongyue Jiao
- State Key Laboratory of Genetic Engineering, Shanghai Stomatological Hospital & School of Stomatology, MOE Engineering Research Center of Gene Technology, Shanghai Engineering Research Center of Industrial Microorganisms, School of Life Sciences, Fudan UniversityShanghaiChina
| | - Huiru Sun
- State Key Laboratory of Genetic Engineering, Shanghai Stomatological Hospital & School of Stomatology, MOE Engineering Research Center of Gene Technology, Shanghai Engineering Research Center of Industrial Microorganisms, School of Life Sciences, Fudan UniversityShanghaiChina
| | - Xiaying Zhao
- State Key Laboratory of Genetic Engineering, Shanghai Stomatological Hospital & School of Stomatology, MOE Engineering Research Center of Gene Technology, Shanghai Engineering Research Center of Industrial Microorganisms, School of Life Sciences, Fudan UniversityShanghaiChina
| | - Yingji Chen
- State Key Laboratory of Genetic Engineering, Shanghai Stomatological Hospital & School of Stomatology, MOE Engineering Research Center of Gene Technology, Shanghai Engineering Research Center of Industrial Microorganisms, School of Life Sciences, Fudan UniversityShanghaiChina
| | - Zeheng Lv
- Department of Clinical Laboratory, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji UniversityShanghaiChina
- Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji UniversityShanghaiChina
| | - Qing Shi
- State Key Laboratory of Genetic Engineering, Shanghai Stomatological Hospital & School of Stomatology, MOE Engineering Research Center of Gene Technology, Shanghai Engineering Research Center of Industrial Microorganisms, School of Life Sciences, Fudan UniversityShanghaiChina
| | - Yao Li
- State Key Laboratory of Genetic Engineering, Shanghai Stomatological Hospital & School of Stomatology, MOE Engineering Research Center of Gene Technology, Shanghai Engineering Research Center of Industrial Microorganisms, School of Life Sciences, Fudan UniversityShanghaiChina
| | - Chenji Wang
- State Key Laboratory of Genetic Engineering, Shanghai Stomatological Hospital & School of Stomatology, MOE Engineering Research Center of Gene Technology, Shanghai Engineering Research Center of Industrial Microorganisms, School of Life Sciences, Fudan UniversityShanghaiChina
| | - Kun Gao
- Department of Clinical Laboratory, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji UniversityShanghaiChina
- Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji UniversityShanghaiChina
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21
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Targa Dias Anastacio H, Matosin N, Ooi L. Familial Alzheimer's Disease Neurons Bearing Mutations in PSEN1 Display Increased Calcium Responses to AMPA as an Early Calcium Dysregulation Phenotype. Life (Basel) 2024; 14:625. [PMID: 38792645 PMCID: PMC11123496 DOI: 10.3390/life14050625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 04/18/2024] [Accepted: 05/08/2024] [Indexed: 05/26/2024] Open
Abstract
Familial Alzheimer's disease (FAD) can be caused by mutations in PSEN1 that encode presenilin-1, a component of the gamma-secretase complex that cleaves amyloid precursor protein. Alterations in calcium (Ca2+) homeostasis and glutamate signaling are implicated in the pathogenesis of FAD; however, it has been difficult to assess in humans whether or not these phenotypes are the result of amyloid or tau pathology. This study aimed to assess the early calcium and glutamate phenotypes of FAD by measuring the Ca2+ response of induced pluripotent stem cell (iPSC)-derived neurons bearing PSEN1 mutations to glutamate and the ionotropic glutamate receptor agonists NMDA, AMPA, and kainate compared to isogenic control and healthy lines. The data show that in early neurons, even in the absence of amyloid and tau phenotypes, FAD neurons exhibit increased Ca2+ responses to glutamate and AMPA, but not NMDA or kainate. Together, this suggests that PSEN1 mutations alter Ca2+ and glutamate signaling as an early phenotype of FAD.
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Affiliation(s)
- Helena Targa Dias Anastacio
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Northfields Avenue, Wollongong, NSW 2522, Australia;
| | - Natalie Matosin
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2050, Australia;
| | - Lezanne Ooi
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Northfields Avenue, Wollongong, NSW 2522, Australia;
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22
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Nuga O, Richardson K, Patel N, Wang X, Pagala V, Stephan A, Peng J, Demontis F, Todi SV. Linear ubiquitin chains remodel the proteome and influence the levels of hundreds of regulators in Drosophila. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.09.593206. [PMID: 38766269 PMCID: PMC11100727 DOI: 10.1101/2024.05.09.593206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Ubiquitin controls many cellular processes via its post-translational conjugation onto substrates. Its use is highly variable due to its ability to form poly-ubiquitin with various topologies. Among them, linear chains have emerged as important regulators of immune responses and protein degradation. Previous studies in Drosophila melanogaster found that expression of linear poly-ubiquitin that cannot be dismantled into single moieties leads to their own ubiquitination and degradation or, alternatively, to their conjugation onto proteins. However, it remains largely unknown which proteins are sensitive to linear poly-ubiquitin. To address this question, here we expanded the toolkit to modulate linear chains and conducted ultra-deep coverage proteomics from flies that express non-cleavable, linear chains comprising 2, 4, or 6 moieties. We found that these chains regulate shared and distinct cellular processes in Drosophila by impacting hundreds of proteins. Our results provide key insight into the proteome subsets and cellular pathways that are influenced by linear poly-ubiquitin with distinct lengths and suggest that the ubiquitin system is exceedingly pliable.
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23
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Lauinger L, Andronicos A, Flick K, Yu C, Durairaj G, Huang L, Kaiser P. Cadmium binding by the F-box domain induces p97-mediated SCF complex disassembly to activate stress response programs. Nat Commun 2024; 15:3894. [PMID: 38719837 PMCID: PMC11079001 DOI: 10.1038/s41467-024-48184-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 04/22/2024] [Indexed: 05/12/2024] Open
Abstract
The F-box domain is a highly conserved structural motif that defines the largest class of ubiquitin ligases, Skp1/Cullin1/F-box protein (SCF) complexes. The only known function of the F-box motif is to form the protein interaction surface with Skp1. Here we show that the F-box domain can function as an environmental sensor. We demonstrate that the F-box domain of Met30 is a cadmium sensor that blocks the activity of the SCFMet30 ubiquitin ligase during cadmium stress. Several highly conserved cysteine residues within the Met30 F-box contribute to binding of cadmium with a KD of 8 µM. Binding induces a conformational change that allows for Met30 autoubiquitylation, which in turn leads to recruitment of the segregase Cdc48/p97/VCP followed by active SCFMet30 disassembly. The resulting inactivation of SCFMet30 protects cells from cadmium stress. Our results show that F-box domains participate in regulation of SCF ligases beyond formation of the Skp1 binding interface.
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Affiliation(s)
- Linda Lauinger
- Department of Biological Chemistry, University of California, Irvine, Irvine, CA, 92697, USA.
| | - Anna Andronicos
- Department of Biological Chemistry, University of California, Irvine, Irvine, CA, 92697, USA
| | - Karin Flick
- Department of Biological Chemistry, University of California, Irvine, Irvine, CA, 92697, USA
| | - Clinton Yu
- Department of Physiology and Biophysics, University of California, Irvine, Irvine, CA, 92697, USA
| | - Geetha Durairaj
- Department of Biological Chemistry, University of California, Irvine, Irvine, CA, 92697, USA
| | - Lan Huang
- Department of Physiology and Biophysics, University of California, Irvine, Irvine, CA, 92697, USA
| | - Peter Kaiser
- Department of Biological Chemistry, University of California, Irvine, Irvine, CA, 92697, USA.
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24
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Akizuki Y, Kaypee S, Ohtake F, Ikeda F. The emerging roles of non-canonical ubiquitination in proteostasis and beyond. J Cell Biol 2024; 223:e202311171. [PMID: 38517379 PMCID: PMC10959754 DOI: 10.1083/jcb.202311171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 03/04/2024] [Accepted: 03/05/2024] [Indexed: 03/23/2024] Open
Abstract
Ubiquitin regulates various cellular functions by posttranslationally modifying substrates with diverse ubiquitin codes. Recent discoveries of new ubiquitin chain topologies, types of bonds, and non-protein substrates have substantially expanded the complexity of the ubiquitin code. Here, we describe the ubiquitin system covering the basic principles and recent discoveries related to mechanisms, technologies, and biological importance.
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Affiliation(s)
- Yoshino Akizuki
- Institute for Advanced Life Sciences, Hoshi University, Tokyo, Japan
| | - Stephanie Kaypee
- Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan
| | - Fumiaki Ohtake
- Institute for Advanced Life Sciences, Hoshi University, Tokyo, Japan
| | - Fumiyo Ikeda
- Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan
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25
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Jung JE, Ewing MA, Valentine SJ, Clemmer DE. Structural Insights into Linkage-Specific Ubiquitin Chains Using Ion Mobility Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:982-991. [PMID: 38597281 DOI: 10.1021/jasms.4c00019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/11/2024]
Abstract
The structural characterization and differentiation of four types of oligoubiquitin conjugates [linear (Met1)-, Lys11-, Lys48-, Lys63-linked di-, tri-, and tetraubiquitin chains] using ion mobility mass spectrometry are reported. A comparison of collision cross sections for the same linkage of di-, tri-, and tetraubiquitin chains shows differences in conformational elongation for higher charge states due to the interplay of linkage-derived structure and Coulombic repulsion. For di- and triubiquitin chains, this elongation results in a single narrow feature representing an elongated conformation type for multiple higher charge state species. In contrast, higher charge state tetraubiquitin species do not form a single conformer type as readily. A comparison of different linkages in tetraubiquitin chains reveals greater similarity in conformation type at lower charge states; with increasing charge state, the four linkage types diverge in the relative proportions of elongated conformer types with Met1- ≥ Lys11- > Lys63- > Lys48-linkage. These differences in conformational trends could be discussed with respect to biological functions of linkage-specific polyubiquitinated proteins.
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Affiliation(s)
- Ji Eun Jung
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405-7102, United States
- Forensic Chemistry Division, National Forensic Service, Wonju 26460, Korea
| | - Michael A Ewing
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405-7102, United States
- Roche Infomatics, F. Hoffman-La Roche AG, Basel, CH 4070, Switzerland
| | - Stephen J Valentine
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405-7102, United States
- Department of Chemistry, West Virginia University, Morgantown, West Virginia 26506, United States
| | - David E Clemmer
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405-7102, United States
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26
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Ri-Wen, Yang YH, Zhang TN, Liu CF, Yang N. Targeting epigenetic and post-translational modifications regulating pyroptosis for the treatment of inflammatory diseases. Pharmacol Res 2024; 203:107182. [PMID: 38614373 DOI: 10.1016/j.phrs.2024.107182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 04/09/2024] [Accepted: 04/10/2024] [Indexed: 04/15/2024]
Abstract
Inflammatory diseases, including infectious diseases, diabetes-related diseases, arthritis-related diseases, neurological diseases, digestive diseases, and tumor, continue to threaten human health and impose a significant financial burden despite advancements in clinical treatment. Pyroptosis, a pro-inflammatory programmed cell death pathway, plays an important role in the regulation of inflammation. Moderate pyroptosis contributes to the activation of native immunity, whereas excessive pyroptosis is associated with the occurrence and progression of inflammation. Pyroptosis is complicated and tightly controlled by various factors. Accumulating evidence has confirmed that epigenetic modifications and post-translational modifications (PTMs) play vital roles in the regulation of pyroptosis. Epigenetic modifications, which include DNA methylation and histone modifications (such as methylation and acetylation), and post-translational modifications (such as ubiquitination, phosphorylation, and acetylation) precisely manipulate gene expression and protein functions at the transcriptional and post-translational levels, respectively. In this review, we summarize the major pathways of pyroptosis and focus on the regulatory roles and mechanisms of epigenetic and post-translational modifications of pyroptotic components. We also illustrate these within pyroptosis-associated inflammatory diseases. In addition, we discuss the effects of novel therapeutic strategies targeting epigenetic and post-translational modifications on pyroptosis, and provide prospective insight into the regulation of pyroptosis for the treatment of inflammatory diseases.
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Affiliation(s)
- Ri-Wen
- Department of Pediatrics, Shengjing Hospital of China Medical University, Shenyang 110004, China
| | - Yu-Hang Yang
- Department of Pediatrics, Shengjing Hospital of China Medical University, Shenyang 110004, China
| | - Tie-Ning Zhang
- Department of Pediatrics, Shengjing Hospital of China Medical University, Shenyang 110004, China
| | - Chun-Feng Liu
- Department of Pediatrics, Shengjing Hospital of China Medical University, Shenyang 110004, China.
| | - Ni Yang
- Department of Pediatrics, Shengjing Hospital of China Medical University, Shenyang 110004, China.
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27
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Su H, Zhang Y, He Z, Yang Y, Ren Y, Cao W, Liu Y, Ren J, Wang Y, Wang G, Gong C, Hou J. Functional analysis of the ube3a response in Japanese flounder (Paralichthys olivaceus) to CSBV infection. FISH & SHELLFISH IMMUNOLOGY 2024; 148:109495. [PMID: 38461876 DOI: 10.1016/j.fsi.2024.109495] [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: 10/21/2023] [Revised: 02/17/2024] [Accepted: 03/07/2024] [Indexed: 03/12/2024]
Abstract
Ube3a is a member of the E3 ubiquitin ligase HECTc family, and its role has been established in neurodevelopmental disorders. However, studies on its role in Japanese flounder are scarce. Thus, in this study, the ube3a of Japanese flounder was cloned, and its role in conferring resistance against Chinook salmon bafnivirus (CSBV) was analyzed. Japanese flounder ube3a encoded a protein containing 834 amino acids. Interestingly, its homology with the Atlantic halibut was determined to be 94%. In addition, there were differential expressions of ube3a in different tissues of Japanese flounder, with the highest expression level observed in the fin, followed by the gills and skin (P ≤ 0.05). Subcellular localization analysis revealed that Ube3a is a cytoplasmic protein. We established an in vitro CSBV infection model using Japanese flounder gill cell line (FG). After ube3a overexpression, the viral load was significantly lower than that of the control group (P ≤ 0.05). Contrastingly, after incubation of FG cells with an E3 ubiquitin ligase inhibitor, the viral load was significantly higher than in the control group (P ≤ 0.01). Then, the expression levels of nf-κb, traf3, and tnf-α after incubation with an E3 ubiquitin ligase inhibitor were examined. The results demonstrated that ube3a may exerted a significant antiviral effect in Japanese flounder via the ubiquitination pathway.
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Affiliation(s)
- Huaxing Su
- Hebei Key Laboratory of the Bohai Sea Fish Germplasm Resources Conservation and Utilization, Beidaihe Central Experiment Station, Chinese Academy of Fishery Sciences, Qinhuangdao, 066100, China; Ocean College, Hebei Agricultural University, Qinhuangdao, 066009, China; Bohai Sea Fishery Research Center, Chinese Academy of Fishery Sciences, Qinhuangdao, 066100, China
| | - Yitong Zhang
- Hebei Key Laboratory of the Bohai Sea Fish Germplasm Resources Conservation and Utilization, Beidaihe Central Experiment Station, Chinese Academy of Fishery Sciences, Qinhuangdao, 066100, China; Bohai Sea Fishery Research Center, Chinese Academy of Fishery Sciences, Qinhuangdao, 066100, China
| | - Zhongwei He
- Hebei Key Laboratory of the Bohai Sea Fish Germplasm Resources Conservation and Utilization, Beidaihe Central Experiment Station, Chinese Academy of Fishery Sciences, Qinhuangdao, 066100, China; Bohai Sea Fishery Research Center, Chinese Academy of Fishery Sciences, Qinhuangdao, 066100, China
| | - Yucong Yang
- Hebei Key Laboratory of the Bohai Sea Fish Germplasm Resources Conservation and Utilization, Beidaihe Central Experiment Station, Chinese Academy of Fishery Sciences, Qinhuangdao, 066100, China; Bohai Sea Fishery Research Center, Chinese Academy of Fishery Sciences, Qinhuangdao, 066100, China
| | - Yuqin Ren
- Hebei Key Laboratory of the Bohai Sea Fish Germplasm Resources Conservation and Utilization, Beidaihe Central Experiment Station, Chinese Academy of Fishery Sciences, Qinhuangdao, 066100, China; Bohai Sea Fishery Research Center, Chinese Academy of Fishery Sciences, Qinhuangdao, 066100, China
| | - Wei Cao
- Hebei Key Laboratory of the Bohai Sea Fish Germplasm Resources Conservation and Utilization, Beidaihe Central Experiment Station, Chinese Academy of Fishery Sciences, Qinhuangdao, 066100, China; Bohai Sea Fishery Research Center, Chinese Academy of Fishery Sciences, Qinhuangdao, 066100, China
| | - Yufeng Liu
- Hebei Key Laboratory of the Bohai Sea Fish Germplasm Resources Conservation and Utilization, Beidaihe Central Experiment Station, Chinese Academy of Fishery Sciences, Qinhuangdao, 066100, China; Bohai Sea Fishery Research Center, Chinese Academy of Fishery Sciences, Qinhuangdao, 066100, China
| | - Jiangong Ren
- Hebei Key Laboratory of the Bohai Sea Fish Germplasm Resources Conservation and Utilization, Beidaihe Central Experiment Station, Chinese Academy of Fishery Sciences, Qinhuangdao, 066100, China; Bohai Sea Fishery Research Center, Chinese Academy of Fishery Sciences, Qinhuangdao, 066100, China
| | - Yufen Wang
- Hebei Key Laboratory of the Bohai Sea Fish Germplasm Resources Conservation and Utilization, Beidaihe Central Experiment Station, Chinese Academy of Fishery Sciences, Qinhuangdao, 066100, China; Bohai Sea Fishery Research Center, Chinese Academy of Fishery Sciences, Qinhuangdao, 066100, China
| | - Guixing Wang
- Hebei Key Laboratory of the Bohai Sea Fish Germplasm Resources Conservation and Utilization, Beidaihe Central Experiment Station, Chinese Academy of Fishery Sciences, Qinhuangdao, 066100, China; Bohai Sea Fishery Research Center, Chinese Academy of Fishery Sciences, Qinhuangdao, 066100, China
| | - Chunguang Gong
- Ocean College, Hebei Agricultural University, Qinhuangdao, 066009, China.
| | - Jilun Hou
- Hebei Key Laboratory of the Bohai Sea Fish Germplasm Resources Conservation and Utilization, Beidaihe Central Experiment Station, Chinese Academy of Fishery Sciences, Qinhuangdao, 066100, China; Bohai Sea Fishery Research Center, Chinese Academy of Fishery Sciences, Qinhuangdao, 066100, China.
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Li Z, Li J, Li Z, Song Y, Wang Y, Wang C, Yuan L, Xiao W, Wang J. Zebrafish mylipb attenuates antiviral innate immunity through two synergistic mechanisms targeting transcription factor irf3. PLoS Pathog 2024; 20:e1012227. [PMID: 38739631 PMCID: PMC11115282 DOI: 10.1371/journal.ppat.1012227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 05/23/2024] [Accepted: 04/26/2024] [Indexed: 05/16/2024] Open
Abstract
IFN regulatory factor 3 (IRF3) is the transcription factor crucial for the production of type I IFN in viral defence and inflammatory responses. The activity of IRF3 is strictly modulated by post-translational modifications (PTMs) to effectively protect the host from infection while avoiding excessive immunopathology. Here, we report that zebrafish myosin-regulated light chain interacting protein b (mylipb) inhibits virus-induced type I IFN production via two synergistic mechanisms: induction of autophagic degradation of irf3 and reduction of irf3 phosphorylation. In vivo, mylipb-null zebrafish exhibit reduced lethality and viral mRNA levels compared to controls. At the cellular level, overexpression of mylipb significantly reduces cellular antiviral capacity, and promotes viral proliferation. Mechanistically, mylipb associates with irf3 and targets Lys 352 to increase K6-linked polyubiquitination, dependent on its E3 ubiquitin ligase activity, leading to autophagic degradation of irf3. Meanwhile, mylipb acts as a decoy substrate for the phosphokinase tbk1 to attenuate irf3 phosphorylation and cellular antiviral responses independent of its enzymatic activity. These findings support a critical role for zebrafish mylipb in the limitation of antiviral innate immunity through two synergistic mechanisms targeting irf3.
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Affiliation(s)
- Zhi Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, China
| | - Jun Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ziyi Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yanan Song
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yanyi Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Chunling Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Le Yuan
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Wuhan Xiao
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
- Hubei Hongshan Laboratory, Wuhan, China
- The Innovation of Seed Design, Chinese Academy of Sciences, Wuhan, China
| | - Jing Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
- Hubei Hongshan Laboratory, Wuhan, China
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29
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Skowyra ML, Feng P, Rapoport TA. Towards solving the mystery of peroxisomal matrix protein import. Trends Cell Biol 2024; 34:388-405. [PMID: 37743160 PMCID: PMC10957506 DOI: 10.1016/j.tcb.2023.08.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 08/21/2023] [Accepted: 08/25/2023] [Indexed: 09/26/2023]
Abstract
Peroxisomes are vital metabolic organelles that import their lumenal (matrix) enzymes from the cytosol using mobile receptors. Surprisingly, the receptors can even import folded proteins, but the underlying mechanism has been a mystery. Recent results reveal how import receptors shuttle cargo into peroxisomes. The cargo-bound receptors move from the cytosol across the peroxisomal membrane completely into the matrix by a mechanism that resembles transport through the nuclear pore. The receptors then return to the cytosol through a separate retrotranslocation channel, leaving the cargo inside the organelle. This cycle concentrates imported proteins within peroxisomes, and the energy for cargo import is supplied by receptor export. Peroxisomal protein import thus fundamentally differs from other previously known mechanisms for translocating proteins across membranes.
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Affiliation(s)
- Michael L Skowyra
- Howard Hughes Medical Institute and Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
| | - Peiqiang Feng
- Howard Hughes Medical Institute and Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
| | - Tom A Rapoport
- Howard Hughes Medical Institute and Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA.
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30
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Mandal K, Tomar SK, Kumar Santra M. Decoding the ubiquitin language: Orchestrating transcription initiation and gene expression through chromatin remodelers and histones. Gene 2024; 904:148218. [PMID: 38307220 DOI: 10.1016/j.gene.2024.148218] [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: 10/20/2023] [Revised: 01/22/2024] [Accepted: 01/25/2024] [Indexed: 02/04/2024]
Abstract
Eukaryotic transcription is a finely orchestrated process and it is controlled by transcription factors as well as epigenetic regulators. Transcription factors and epigenetic regulators undergo different types of posttranslational modifications including ubiquitination to control transcription process. Ubiquitination, traditionally associated with protein degradation, has emerged as a crucial contributor to the regulation of chromatin structure through ubiquitination of histone and chromatin remodelers. Ubiquitination introduces new layers of intricacy to the regulation of transcription initiation through controlling the equilibrium between euchromatin and heterochromatin states. Nucleosome, the fundamental units of chromatin, spacing in euchromatin and heterochromatin states are regulated by histone modification and chromatin remodeling complexes. Chromatin remodeling complexes actively sculpt the chromatin architecture and thereby influence the transcriptional states of genes. Therefore, understanding the dynamic behavior of nucleosome spacing is critical as it impacts various cellular functions through controlling gene expression profiles. In this comprehensive review, we discussed the intricate interplay between ubiquitination and transcription initiation, and illuminated the underlying molecular mechanisms that occur in a variety of biological contexts. This exploration sheds light on the complex regulatory networks that govern eukaryotic transcription, providing important insights into the fine orchestration of gene expression and chromatin dynamics.
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Affiliation(s)
- Kartik Mandal
- Cancer Biology Division, National Centre for Cell Science, Ganeshkhind Road, Pune, Maharashtra 411007, India; Department of Biotechnology, Savitribai Phule Pune University, Ganeshkhind Road, Pune, Maharashtra 411007, India
| | - Shiva Kumar Tomar
- Cancer Biology Division, National Centre for Cell Science, Ganeshkhind Road, Pune, Maharashtra 411007, India; Department of Biotechnology, Savitribai Phule Pune University, Ganeshkhind Road, Pune, Maharashtra 411007, India
| | - Manas Kumar Santra
- Cancer Biology Division, National Centre for Cell Science, Ganeshkhind Road, Pune, Maharashtra 411007, India.
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31
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Kinger S, Jagtap YA, Kumar P, Choudhary A, Prasad A, Prajapati VK, Kumar A, Mehta G, Mishra A. Proteostasis in neurodegenerative diseases. Adv Clin Chem 2024; 121:270-333. [PMID: 38797543 DOI: 10.1016/bs.acc.2024.04.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Proteostasis is essential for normal function of proteins and vital for cellular health and survival. Proteostasis encompasses all stages in the "life" of a protein, that is, from translation to functional performance and, ultimately, to degradation. Proteins need native conformations for function and in the presence of multiple types of stress, their misfolding and aggregation can occur. A coordinated network of proteins is at the core of proteostasis in cells. Among these, chaperones are required for maintaining the integrity of protein conformations by preventing misfolding and aggregation and guide those with abnormal conformation to degradation. The ubiquitin-proteasome system (UPS) and autophagy are major cellular pathways for degrading proteins. Although failure or decreased functioning of components of this network can lead to proteotoxicity and disease, like neuron degenerative diseases, underlying factors are not completely understood. Accumulating misfolded and aggregated proteins are considered major pathomechanisms of neurodegeneration. In this chapter, we have described the components of three major branches required for proteostasis-chaperones, UPS and autophagy, the mechanistic basis of their function, and their potential for protection against various neurodegenerative conditions, like Alzheimer's, Parkinson's, and Huntington's disease. The modulation of various proteostasis network proteins, like chaperones, E3 ubiquitin ligases, proteasome, and autophagy-associated proteins as therapeutic targets by small molecules as well as new and unconventional approaches, shows promise.
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Affiliation(s)
- Sumit Kinger
- Cellular and Molecular Neurobiology Unit, Indian Institute of Technology Jodhpur, Rajasthan, India
| | - Yuvraj Anandrao Jagtap
- Cellular and Molecular Neurobiology Unit, Indian Institute of Technology Jodhpur, Rajasthan, India
| | - Prashant Kumar
- Cellular and Molecular Neurobiology Unit, Indian Institute of Technology Jodhpur, Rajasthan, India
| | - Akash Choudhary
- Cellular and Molecular Neurobiology Unit, Indian Institute of Technology Jodhpur, Rajasthan, India
| | - Amit Prasad
- School of Biosciences and Bioengineering, Indian Institute of Technology Mandi, Mandi, Himachal Pradesh, India
| | - Vijay Kumar Prajapati
- Department of Biochemistry, University of Delhi South Campus, Dhaula Kuan, New Delhi, India
| | - Amit Kumar
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol, Indore, Madhya Pradesh, India
| | - Gunjan Mehta
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Telangana, India
| | - Amit Mishra
- Cellular and Molecular Neurobiology Unit, Indian Institute of Technology Jodhpur, Rajasthan, India.
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32
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Tsai JM, Nowak RP, Ebert BL, Fischer ES. Targeted protein degradation: from mechanisms to clinic. Nat Rev Mol Cell Biol 2024:10.1038/s41580-024-00729-9. [PMID: 38684868 DOI: 10.1038/s41580-024-00729-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/21/2024] [Indexed: 05/02/2024]
Abstract
Targeted protein degradation refers to the use of small molecules to induce the selective degradation of proteins. In its most common form, this degradation is achieved through ligand-mediated neo-interactions between ubiquitin E3 ligases - the principal waste disposal machines of a cell - and the protein targets of interest, resulting in ubiquitylation and subsequent proteasomal degradation. Notable advances have been made in biological and mechanistic understanding of serendipitously discovered degraders. This improved understanding and novel chemistry has not only provided clinical proof of concept for targeted protein degradation but has also led to rapid growth of the field, with dozens of investigational drugs in active clinical trials. Two distinct classes of protein degradation therapeutics are being widely explored: bifunctional PROTACs and molecular glue degraders, both of which have their unique advantages and challenges. Here, we review the current landscape of targeted protein degradation approaches and how they have parallels in biological processes. We also outline the ongoing clinical exploration of novel degraders and provide some perspectives on the directions the field might take.
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Affiliation(s)
- Jonathan M Tsai
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Radosław P Nowak
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
- Institute of Structural Biology, Medical Faculty, University of Bonn, Bonn, Germany
| | - Benjamin L Ebert
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, MA, USA.
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Boston, MA, USA.
| | - Eric S Fischer
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA.
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33
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Morito D. Molecular structure and function of mysterin/RNF213. J Biochem 2024; 175:495-505. [PMID: 38378744 DOI: 10.1093/jb/mvae020] [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: 12/05/2023] [Revised: 01/19/2024] [Accepted: 01/24/2024] [Indexed: 02/22/2024] Open
Abstract
Mysterin is a large intracellular protein harboring a RING finger ubiquitin ligase domain and is also referred to as RING finger protein 213 (RNF213). The author performed the first molecular cloning of the mysterin gene as the final step in genetic exploration of cerebrovascular moyamoya disease (MMD) and initiated the next round of exploration to understand its molecular and cellular functions. Although much remains unknown, accumulating findings suggest that mysterin functions in cells by targeting massive intracellular structures, such as lipid droplets (LDs) and various invasive pathogens. In the latter case, mysterin appears to directly surround and ubiquitylate the surface of pathogens and stimulate cell-autonomous antimicrobial reactions, such as xenophagy and inflammatory response. To date, multiple mutations causing MMD have been identified within and near the RING finger domain of mysterin; however, their functional relevance remains largely unknown. Besides the RING finger, mysterin harbors a dynein-like ATPase core and an RZ finger, another ubiquitin ligase domain unique to mysterin, while functional exploration of these domains has also just commenced. In this review, the author attempts to summarize the core findings regarding the molecular structure and function of the mysterin protein, with an emphasis on the perspective of MMD research.
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Affiliation(s)
- Daisuke Morito
- Department of Biochemistry, Showa University School of Medicine, Hatanodai 1-5-8, Shinagawa, Tokyo 142-0064, Japan
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34
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van Wijk KJ, Adam Z. Does the polyubiquitination pathway operate inside intact chloroplasts to remove proteins? THE PLANT CELL 2024:koae104. [PMID: 38683741 DOI: 10.1093/plcell/koae104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 03/19/2024] [Indexed: 05/02/2024]
Affiliation(s)
- Klaas J van Wijk
- Section of Plant Biology, School of Integrative Plant Sciences (SIPS), Cornell University, Ithaca, NY 14853, USA
| | - Zach Adam
- Faculty of Agriculture, Institute of Plant Sciences, The Hebrew University of Jerusalem, Rehovot 76100, Israel
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35
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Wang Z, Fan F, Li Z, Ye F, Wang Q, Gao R, Qiu J, Lv Y, Lin M, Xu W, Luo C, Yu X. Structural insights into the functional mechanism of the ubiquitin ligase E6AP. Nat Commun 2024; 15:3531. [PMID: 38670961 PMCID: PMC11053172 DOI: 10.1038/s41467-024-47586-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 04/04/2024] [Indexed: 04/28/2024] Open
Abstract
E6AP dysfunction is associated with Angelman syndrome and Autism spectrum disorder. Additionally, the host E6AP is hijacked by the high-risk HPV E6 to aberrantly ubiquitinate the tumor suppressor p53, which is linked with development of multiple types of cancer, including most cervical cancers. Here we show that E6AP and the E6AP/E6 complex exist, respectively, as a monomer and a dimer of the E6AP/E6 protomer. The short α1-helix of E6AP transforms into a longer helical structure when in complex with E6. The extended α1-helices of the dimer intersect symmetrically and contribute to the dimerization. The two protomers sway around the crossed region of the two α1-helices to promote the attachment and detachment of substrates to the catalytic C-lobe of E6AP, thus facilitating ubiquitin transfer. These findings, complemented by mutagenesis analysis, suggest that the α1-helix, through conformational transformations, controls the transition between the inactive monomer and the active dimer of E6AP.
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Affiliation(s)
- Zhen Wang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Fengying Fan
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhihai Li
- University of Chinese Academy of Sciences, Beijing, 100049, China
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310024, China
| | - Fei Ye
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Qingxia Wang
- Cryo-Electron Microscopy Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Rongchao Gao
- Cryo-Electron Microscopy Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Jiaxuan Qiu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yixin Lv
- University of Chinese Academy of Sciences, Beijing, 100049, China
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310024, China
| | - Min Lin
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Wenwen Xu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Cheng Luo
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310024, China.
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan, 528437, China.
- Department of Pharmacy, Guiyang University of Traditional Chinese Medicine, South Dong Qing Road, Huaxi District, Guizhou, 550025, China.
| | - Xuekui Yu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Cryo-Electron Microscopy Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.
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36
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Tam S, Wear D, Morrone CD, Yu WH. The complexity of extracellular vesicles: Bridging the gap between cellular communication and neuropathology. J Neurochem 2024. [PMID: 38650384 DOI: 10.1111/jnc.16108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Revised: 03/12/2024] [Accepted: 03/31/2024] [Indexed: 04/25/2024]
Abstract
Brain-derived extracellular vesicles (EVs) serve a prominent role in maintaining homeostasis and contributing to pathology in health and disease. This review establishes a crucial link between physiological processes leading to EV biogenesis and their impacts on disease. EVs are involved in the clearance and transport of proteins and nucleic acids, responding to changes in cellular processes associated with neurodegeneration, including autophagic disruption, organellar dysfunction, aging, and other cell stresses. In neurodegenerative disorders (e.g., Alzheimer's disease, Parkinson's disease, etc.), EVs contribute to the spread of pathological proteins like amyloid β, tau, ɑ-synuclein, prions, and TDP-43, exacerbating neurodegeneration and accelerating disease progression. Despite evidence for both neuropathological and neuroprotective effects of EVs, the mechanistic switch between their physiological and pathological functions remains elusive, warranting further research into their involvement in neurodegenerative disease. Moreover, owing to their innate ability to traverse the blood-brain barrier and their ubiquitous nature, EVs emerge as promising candidates for novel diagnostic and therapeutic strategies. The review uniquely positions itself at the intersection of EV cell biology, neurophysiology, and neuropathology, offering insights into the diverse biological roles of EVs in health and disease.
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Affiliation(s)
- Stephanie Tam
- Brain Health Imaging Centre, Centre for Addiction and Mental Health, Toronto, Ontario, Canada
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario, Canada
| | - Darcy Wear
- Brain Health Imaging Centre, Centre for Addiction and Mental Health, Toronto, Ontario, Canada
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario, Canada
| | - Christopher D Morrone
- Brain Health Imaging Centre, Centre for Addiction and Mental Health, Toronto, Ontario, Canada
| | - Wai Haung Yu
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario, Canada
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37
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Zi G, Chen J, Peng Y, Wang Y, Peng B. Hyperthermia and cisplatin combination therapy promotes caspase-8 accumulation and activation to enhance apoptosis and pyroptosis in cancer cells. Int J Hyperthermia 2024; 41:2325489. [PMID: 38632954 DOI: 10.1080/02656736.2024.2325489] [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: 10/30/2023] [Accepted: 02/26/2024] [Indexed: 04/19/2024] Open
Abstract
BACKGROUND Hyperthermia can play a synergistic role with chemotherapy in combination therapy. Although the association between caspase activation, apoptosis, and pyroptosis have been published for both cisplatin (CDDP) and hyperthermia therapies independently, the interactions between these molecular pathways in combination therapy are unknown. The present study aimed to investigate the possible interactions between caspase 8 activation, apoptosis, and pyroptosis in combination therapy. METHODS Cells were treated with CDDP (15 µg/ml), followed by hyperthermia at optimized temperature (42.5 °C) in water-bath. After combination therapy, cell viability was analyzed by CCK-8, and cell death was analyzed by Annexin-V-FITC/PI and caspases activation. Immuno-staining and co-immuno-precipitation were used to examine the interaction between p62 and caspase-8. Pyroptosis was investigated by western blotting and transmission electron microscopy. E3 ligase Cullin 3 was knockdown by siRNA. In addition, caspase-8 activation was modulated by CRISPR-Cas9 gene-editing or pharmacological inhibition. RESULTS Combination therapy promoted K63-linked polyubiquitination of caspase-8 and cellular accumulation of caspase-8. In turn, polyubiquitinated caspase-8 interacted with p62 and led to the activation of caspase-3. Knockdown of the E3 ligase Cullin 3 by siRNA reduced caspase-8 polyubiquitination and activation. In addition, combination therapy induced release of the pore-forming N-terminus from gasdermins and promoted pyroptosis along with caspase-8 accumulation and activation. Knockdown of caspase-8 by CRISPR/Cas9 based gene editing reduced the sensitivity of tumor cells to apoptosis and pyroptosis. CONCLUSIONS Our study presented a novel mechanism in which hyperthermia synergized with chemotherapy in promoting apoptosis and pyroptosis in a caspase-8 dependent manner.
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Affiliation(s)
- Guanghui Zi
- College of Pharmacy, DaLi University, Dali, Yunan Province , China
| | - Jin Chen
- College of Pharmacy, DaLi University, Dali, Yunan Province , China
| | | | - Yue Wang
- College of Pharmacy, DaLi University, Dali, Yunan Province , China
| | - Baowei Peng
- College of Pharmacy, DaLi University, Dali, Yunan Province , China
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38
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Zhou K, Wang D, Du X, Feng X, Zhu X, Wang C. UBE2C enhances temozolomide resistance by regulating the expression of p53 to induce aerobic glycolysis in glioma. Acta Biochim Biophys Sin (Shanghai) 2024. [PMID: 38634120 DOI: 10.3724/abbs.2024033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/19/2024] Open
Abstract
UBE2C is overexpressed in gliomas, and its overexpression has been reported to be correlated with the drug resistance of gliomas to some extent. In this study, we explore the role of UBE2C in regulating temozolomide (TMZ) resistance in glioma and investigate the underlying mechanisms involved. Twenty normal brain tissues and 100 glioma tissues from 50 TMZ-resistant patients and 50 TMZ-sensitive patients are included in this study. TMZ-resistant cell lines are constructed to explore the role of UBE2C in regulating glioma cell viability and TMZ resistance. Our results show that both the mRNA and protein levels of UBE2C are significantly elevated in the brain tissues of glioma patients, especially in those of TMZ-resistant patients. Consistently, UBE2C expression is markedly upregulated in TMZ-resistant cell lines. Overexpression of UBE2C rescues glioma cells from TMZ-mediated apoptosis and enhances cell viability. In contrast, downregulation of UBE2C expression further enhances TMZ function, increases cell apoptosis and decreases cell viability. Mechanistically, UBE2C overexpression decreases p53 expression and enhances aerobic glycolysis level by increasing ATP level, lactate production, and glucose uptake. Downregulation of p53 level abolishes the role of UBE2C downregulation in inhibiting TMZ resistance and aerobic glycolysis in glioma cells. Moreover, an animal assay confirms that downregulation of UBE2C expression further suppresses tumor growth in the context of TMZ treatment. Collectively, this study reveals that downregulation of UBE2C expression enhances the sensitivity of glioma cells to TMZ by regulating the expression of p53 to inhibit aerobic glycolysis.
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Affiliation(s)
- Kun Zhou
- Department of Neurosurgery, the Jinyang Hospital Affiliated to Guizhou Medical University, Guiyang 550084, China
| | - Dexin Wang
- Department of Neurosurgery, the Jinyang Hospital Affiliated to Guizhou Medical University, Guiyang 550084, China
| | - Xiaolin Du
- Department of Neurosurgery, the Jinyang Hospital Affiliated to Guizhou Medical University, Guiyang 550084, China
| | - Xia Feng
- Department of Sleep Medicine, the Second People's Hospital of Guizhou Province, Guiyang 550084, China
| | - Xiaoxi Zhu
- Key Laboratory of Cell Engineering of Guizhou Province, Affiliated Hospital of Zunyi Medical University, Zunyi 563000, China
| | - Cheng Wang
- Department of Neurosurgery, the Jinyang Hospital Affiliated to Guizhou Medical University, Guiyang 550084, China
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Guo J, Shi Y, Jiang G, Zeng P, Wu Z, Wang D, Cui Y, Yang X, Zhou J, Feng X, Hou L, Liu J. SQSTM1 downregulates avian metapneumovirus subgroup C replication via mediating selective autophagic degradation of viral M2-2 protein. J Virol 2024; 98:e0005124. [PMID: 38466095 PMCID: PMC11019959 DOI: 10.1128/jvi.00051-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Accepted: 02/20/2024] [Indexed: 03/12/2024] Open
Abstract
Avian metapneumovirus subgroup C (aMPV/C), an important pathogen causing acute respiratory infection in chickens and turkeys, contributes to substantial economic losses in the poultry industry worldwide. aMPV/C has been reported to induce autophagy, which is beneficial to virus replication. Sequestosome 1 (SQSTM1/P62), a selective autophagic receptor, plays a crucial role in viral replication by clearing ubiquitinated proteins. However, the relationship between SQSTM1-mediated selective autophagy and aMPV/C replication is unclear. In this study, we found that the expression of SQSTM1 negatively regulates aMPV/C replication by reducing viral protein expression and viral titers. Further studies revealed that the interaction between SQSTM1 and aMPV/C M2-2 protein is mediated via the Phox and Bem1 (PB1) domain of the former, which recognizes a ubiquitinated lysine at position 67 of the M2-2 protein, and finally degrades M2-2 via SQSTM1-mediated selective autophagy. Collectively, our results reveal that SQSTM1 degrades M2-2 via a process of selective autophagy to suppress aMPV/C replication, thereby providing novel insights for the prevention and control of aMPV/C infection.IMPORTANCEThe selective autophagy plays an important role in virus replication. As an emerging pathogen of avian respiratory virus, clarification of the effect of SQSTM1, a selective autophagic receptor, on aMPV/C replication in host cells enables us to better understand the viral pathogenesis. Previous study showed that aMPV/C infection reduced the SQSTM1 expression accompanied by virus proliferation, but the specific regulatory mechanism between them was still unclear. In this study, we demonstrated for the first time that SQSTM1 recognizes the 67th amino acid of M2-2 protein by the interaction between them, followed by M2-2 degradation via the SQSTM1-mediated selective autophagy, and finally inhibits aMPV/C replication. This information supplies the mechanism by which SQSTM1 negatively regulates viral replication, and provides new insights for preventing and controlling aMPV/C infection.
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Affiliation(s)
- Jinshuo Guo
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| | - Yongyan Shi
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| | - Genghong Jiang
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| | - Penghui Zeng
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| | - Zhi Wu
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| | - Dedong Wang
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| | - Yongqiu Cui
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| | - Xiaoyu Yang
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| | - Jianwei Zhou
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| | - Xufei Feng
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| | - Lei Hou
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| | - Jue Liu
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
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Coene J, Wilms S, Verhelst SHL. Photopharmacology of Protease Inhibitors: Current Status and Perspectives. Chemistry 2024; 30:e202303999. [PMID: 38224181 DOI: 10.1002/chem.202303999] [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: 11/30/2023] [Revised: 01/10/2024] [Accepted: 01/15/2024] [Indexed: 01/16/2024]
Abstract
Proteases are involved in many essential biological processes. Dysregulation of their activity underlies a wide variety of human diseases. Photopharmacology, as applied on various classes of proteins, has the potential to assist protease research by enabling spatiotemporal control of protease activity. Moreover, it may be used to decrease side-effects of protease-targeting drugs. In this review, we discuss the current status of the chemical design of photoactivatable proteases inhibitors and their biological application. Additionally, we give insight into future possibilities for further development of this field of research.
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Affiliation(s)
- Jonathan Coene
- Department of Cellular and Molecular Medicine, KU Leuven - University of Leuven, Herestraat 49, box 901b, 3000, Leuven, Belgium
| | - Simon Wilms
- Department of Cellular and Molecular Medicine, KU Leuven - University of Leuven, Herestraat 49, box 901b, 3000, Leuven, Belgium
| | - Steven H L Verhelst
- Department of Cellular and Molecular Medicine, KU Leuven - University of Leuven, Herestraat 49, box 901b, 3000, Leuven, Belgium
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Hu J, Song S, Yu M, Yu Y, Ju Z, Wang Y, Cao X. Molecular dynamics simulation of the effect of temperature on the conformation of ubiquitin protein. J Mol Model 2024; 30:134. [PMID: 38625615 DOI: 10.1007/s00894-024-05928-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: 09/22/2023] [Accepted: 04/04/2024] [Indexed: 04/17/2024]
Abstract
CONTENT Ubiquitin, a ubiquitous small protein found in all living organisms, is crucial for tagging proteins earmarked for degradation and holds pivotal importance in biomedicine. Protein functionality is intricately linked to its structure. To comprehend the impact of diverse temperatures on ubiquitin protein structure, our study delved into the energy landscape, hydrogen bonding, and overall structural stability of ubiquitin protein at varying temperatures. Through meticulous analysis of root mean square deviation and root mean square fluctuation, we validated the robustness of the simulation conditions employed. Within our simulated system, the bonding energy and electrostatic potential energy exhibited linear augmentation, while the van der Waals energy demonstrated a linear decline. Additionally, our findings highlighted that the α-Helix secondary structure of the ubiquitin protein gradually transitions toward helix destabilization under high-temperature conditions. The secondary structure of ubiquitin protein experiences distinct changes under varying temperatures. The outcomes of our molecular simulations offer a theoretical framework that enhances our comprehension of how temperature impacts the structural stability of ubiquitin protein. These insights contribute not only to a deeper understanding of iniquity's behavior but also hold broader implications in the realm of biomedicine and beyond. METHODS All the MD simulations were performed using the GROMACS software with GROMOS96 force field and SPC for water. The ubiquitin protein was put in the center of a cubic box with a length of 8 nm, a setting that allowed > 0.8 nm in the minimal distance between the protein surface and the box wall. To remove the possible coordinate collision of the configurations, in the beginning, the steepest descent method was used until the maximum force between atoms was under 100 kJ/mol·nm with a 0.01 nm step size. Minimization was followed by 30 ps of position-restrained MD simulation. The protein was restrained to its initial position, and the solvent was freely equilibrated. The product phase was obtained with the whole system simulated for 10 ns without any restraint using an integral time step of 1 fs with different temperatures. The cutoff for short-range electronic interaction was set to 1.5 nm. The long-range interactions were treated with a particle-mesh Ewald (PME) method with a grid width of 1.2 nm.
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Affiliation(s)
- Junpeng Hu
- College of Chemical & Material Engineering, Quzhou University, Quzhou, 324000, Zhejiang, China
| | - Shanshan Song
- College of Chemical & Material Engineering, Quzhou University, Quzhou, 324000, Zhejiang, China
| | - Mengting Yu
- College of Chemical & Material Engineering, Quzhou University, Quzhou, 324000, Zhejiang, China
| | - Yihang Yu
- College of Chemical & Material Engineering, Quzhou University, Quzhou, 324000, Zhejiang, China
| | - Zhaoyang Ju
- College of Chemical & Material Engineering, Quzhou University, Quzhou, 324000, Zhejiang, China.
| | - Yufen Wang
- Zhejiang Qingke Environmental Technology Co, Ltd, 324004, QuzhouZhejiang, China
| | - Xiaoyong Cao
- Institute of Zhejiang University-Quzhou, Quzhou, 324003, Zhejiang, China.
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Liu Y, Yuan J, Zhang Y, Qin F, Bai X, Sun W, Chen T, Liu F, Zheng Y, Qi X, Zhao W, Liu B, Gao C. OTUD5 promotes the inflammatory immune response by enhancing MyD88 oligomerization and Myddosome formation. Cell Death Differ 2024:10.1038/s41418-024-01293-7. [PMID: 38605168 DOI: 10.1038/s41418-024-01293-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Revised: 03/23/2024] [Accepted: 04/02/2024] [Indexed: 04/13/2024] Open
Abstract
Myddosome is an oligomeric complex required for the transmission of inflammatory signals from TLR/IL1Rs and consists of MyD88 and IRAK family kinases. However, the molecular basis for the self-assemble of Myddosome proteins and regulation of intracellular signaling remains poorly understood. Here, we identify OTUD5 acts as an essential regulator for MyD88 oligomerization and Myddosome formation. OTUD5 directly interacts with MyD88 and cleaves its K11-linked polyubiquitin chains at Lys95, Lys231 and Lys250. This polyubiquitin cleavage enhances MyD88 oligomerization after LPS stimulation, which subsequently promotes the recruitment of downstream IRAK4 and IRAK2 to form Myddosome and the activation of NF-κB and MAPK signaling and production of inflammatory cytokines. Consistently, Otud5-deficient mice are less susceptible to LPS- and CLP-induced sepsis. Taken together, our findings reveal a positive regulatory role of OTUD5 in MyD88 oligomerization and Myddosome formation, which provides new sights into the treatment of inflammatory diseases.
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Affiliation(s)
- Yaxing Liu
- Key Laboratory of Infection and Immunity of Shandong Province & Key Laboratory for Experimental Teratology of Ministry of Education, Shandong University, Jinan, Shandong, 250012, P.R. China
- Department of Immunology, School of Basic Medical Sciences, Shandong University, Jinan, Shandong, 250012, P.R. China
| | - Jiahua Yuan
- Key Laboratory of Infection and Immunity of Shandong Province & Key Laboratory for Experimental Teratology of Ministry of Education, Shandong University, Jinan, Shandong, 250012, P.R. China
- Department of Immunology, School of Basic Medical Sciences, Shandong University, Jinan, Shandong, 250012, P.R. China
| | - Yuling Zhang
- Key Laboratory of Infection and Immunity of Shandong Province & Key Laboratory for Experimental Teratology of Ministry of Education, Shandong University, Jinan, Shandong, 250012, P.R. China
- Department of Immunology, School of Basic Medical Sciences, Shandong University, Jinan, Shandong, 250012, P.R. China
| | - Fei Qin
- Key Laboratory of Infection and Immunity of Shandong Province & Key Laboratory for Experimental Teratology of Ministry of Education, Shandong University, Jinan, Shandong, 250012, P.R. China
- Department of Immunology, School of Basic Medical Sciences, Shandong University, Jinan, Shandong, 250012, P.R. China
| | - Xuemei Bai
- Key Laboratory of Infection and Immunity of Shandong Province & Key Laboratory for Experimental Teratology of Ministry of Education, Shandong University, Jinan, Shandong, 250012, P.R. China
- Department of Immunology, School of Basic Medical Sciences, Shandong University, Jinan, Shandong, 250012, P.R. China
| | - Wanwei Sun
- Key Laboratory of Infection and Immunity of Shandong Province & Key Laboratory for Experimental Teratology of Ministry of Education, Shandong University, Jinan, Shandong, 250012, P.R. China
- Department of Immunology, School of Basic Medical Sciences, Shandong University, Jinan, Shandong, 250012, P.R. China
| | - Tian Chen
- Key Laboratory of Infection and Immunity of Shandong Province & Key Laboratory for Experimental Teratology of Ministry of Education, Shandong University, Jinan, Shandong, 250012, P.R. China
- Department of Pathogenic Biology, School of Basic Medical Sciences, Shandong University, Jinan, Shandong, 250012, P. R. China
| | - Feng Liu
- Key Laboratory of Infection and Immunity of Shandong Province & Key Laboratory for Experimental Teratology of Ministry of Education, Shandong University, Jinan, Shandong, 250012, P.R. China
- Department of Immunology, School of Basic Medical Sciences, Shandong University, Jinan, Shandong, 250012, P.R. China
| | - Yi Zheng
- Key Laboratory of Infection and Immunity of Shandong Province & Key Laboratory for Experimental Teratology of Ministry of Education, Shandong University, Jinan, Shandong, 250012, P.R. China
- Department of Immunology, School of Basic Medical Sciences, Shandong University, Jinan, Shandong, 250012, P.R. China
| | - Xiaopeng Qi
- Advanced Medical Research Institute, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, P. R. China
| | - Wei Zhao
- Key Laboratory of Infection and Immunity of Shandong Province & Key Laboratory for Experimental Teratology of Ministry of Education, Shandong University, Jinan, Shandong, 250012, P.R. China
- Department of Pathogenic Biology, School of Basic Medical Sciences, Shandong University, Jinan, Shandong, 250012, P. R. China
| | - Bingyu Liu
- Key Laboratory of Infection and Immunity of Shandong Province & Key Laboratory for Experimental Teratology of Ministry of Education, Shandong University, Jinan, Shandong, 250012, P.R. China.
- Department of Immunology, School of Basic Medical Sciences, Shandong University, Jinan, Shandong, 250012, P.R. China.
| | - Chengjiang Gao
- Key Laboratory of Infection and Immunity of Shandong Province & Key Laboratory for Experimental Teratology of Ministry of Education, Shandong University, Jinan, Shandong, 250012, P.R. China.
- Department of Immunology, School of Basic Medical Sciences, Shandong University, Jinan, Shandong, 250012, P.R. China.
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Patel RS, Pannala NM, Das C. Reading and Writing the Ubiquitin Code Using Genetic Code Expansion. Chembiochem 2024:e202400190. [PMID: 38588469 DOI: 10.1002/cbic.202400190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 04/04/2024] [Accepted: 04/08/2024] [Indexed: 04/10/2024]
Abstract
Deciphering ubiquitin proteoform signaling and its role in disease has been a long-standing challenge in the field. The effects of ubiquitin modifications, its relation to ubiquitin-related machineries, and its signaling output has been particularly limited by its reconstitution and means of characterization. Advances in genetic code expansion have contributed towards addressing these challenges by precision incorporation of unnatural amino acids through site selective codon suppression. This review discusses recent advances in studying the 'writers', 'readers', and 'erasers' of the ubiquitin code using genetic code expansion. Highlighting strategies towards genetically encoded protein ubiquitination, ubiquitin phosphorylation, acylation, and finally surveying ubiquitin interactions, we strive to bring attention to this unique approach towards addressing a widespread proteoform problem.
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Affiliation(s)
- Rishi S Patel
- Department of Chemistry, Purdue University, 560 Oval Dr., West Lafayette, IN 47907, USA
| | - Nipuni M Pannala
- Department of Chemistry, Purdue University, 560 Oval Dr., West Lafayette, IN 47907, USA
| | - Chittaranjan Das
- Department of Chemistry, Purdue University, 560 Oval Dr., West Lafayette, IN 47907, USA
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Fabijan A, Polis B, Zawadzka-Fabijan A, Korabiewska I, Zakrzewski K, Nowosławska E, Chojnacki M. Domains in Action: Understanding Ddi1's Diverse Functions in the Ubiquitin-Proteasome System. Int J Mol Sci 2024; 25:4080. [PMID: 38612889 PMCID: PMC11012796 DOI: 10.3390/ijms25074080] [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: 03/04/2024] [Revised: 04/01/2024] [Accepted: 04/03/2024] [Indexed: 04/14/2024] Open
Abstract
The ubiquitin-proteasome system (UPS) is a pivotal cellular mechanism responsible for the selective degradation of proteins, playing an essential role in proteostasis, protein quality control, and regulating various cellular processes, with ubiquitin marking proteins for degradation through a complex, multi-stage process. The shuttle proteins family is a very unique group of proteins that plays an important role in the ubiquitin-proteasome system. Ddi1, Dsk2, and Rad23 are shuttle factors that bind ubiquitinated substrates and deliver them to the 26S proteasome. Besides mediating the delivery of ubiquitinated proteins, they are also involved in many other biological processes. Ddi1, the least-studied shuttle protein, exhibits unique physicochemical properties that allow it to play non-canonical functions in the cells. It regulates cell cycle progression and response to proteasome inhibition and defines MAT type of yeast cells. The Ddi1 contains UBL and UBA domains, which are crucial for binding to proteasome receptors and ubiquitin respectively, but also an additional domain called RVP. Additionally, much evidence has been provided to question whether Ddi1 is a classical shuttle protein. For many years, the true nature of this protein remained unclear. Here, we highlight the recent discoveries, which shed new light on the structure and biological functions of the Ddi1 protein.
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Affiliation(s)
- Artur Fabijan
- Department of Neurosurgery, Polish-Mother’s Memorial Hospital Research Institute, 93-338 Lodz, Poland; (B.P.); (K.Z.); (E.N.)
| | - Bartosz Polis
- Department of Neurosurgery, Polish-Mother’s Memorial Hospital Research Institute, 93-338 Lodz, Poland; (B.P.); (K.Z.); (E.N.)
| | - Agnieszka Zawadzka-Fabijan
- Department of Rehabilitation Medicine, Faculty of Health Sciences, Medical University of Lodz, 90-419 Lodz, Poland;
| | - Izabela Korabiewska
- Department of Rehabilitation, Faculty of Dental Medicine, Medical University of Warsaw, 02-091 Warsaw, Poland;
| | - Krzysztof Zakrzewski
- Department of Neurosurgery, Polish-Mother’s Memorial Hospital Research Institute, 93-338 Lodz, Poland; (B.P.); (K.Z.); (E.N.)
| | - Emilia Nowosławska
- Department of Neurosurgery, Polish-Mother’s Memorial Hospital Research Institute, 93-338 Lodz, Poland; (B.P.); (K.Z.); (E.N.)
| | - Michał Chojnacki
- Department of Medical Biochemistry, Medical University of Lodz, 92-215 Lodz, Poland;
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Rutherford KA, McManus KJ. PROTACs: Current and Future Potential as a Precision Medicine Strategy to Combat Cancer. Mol Cancer Ther 2024; 23:454-463. [PMID: 38205881 PMCID: PMC10985480 DOI: 10.1158/1535-7163.mct-23-0747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 12/20/2023] [Accepted: 01/05/2024] [Indexed: 01/12/2024]
Abstract
Proteolysis targeting chimeras (PROTAC) are an emerging precision medicine strategy, which targets key proteins for proteolytic degradation to ultimately induce cancer cell killing. These hetero-bifunctional molecules hijack the ubiquitin proteasome system to selectively add polyubiquitin chains onto a specific protein target to induce proteolytic degradation. Importantly, PROTACs have the capacity to target virtually any intracellular and transmembrane protein for degradation, including oncoproteins previously considered undruggable, which strategically positions PROTACs at the crossroads of multiple cancer research areas. In this review, we present normal functions of the ubiquitin regulation proteins and describe the application of PROTACs to improve the efficacy of current broad-spectrum therapeutics. We subsequently present the potential for PROTACs to exploit specific cancer vulnerabilities through synthetic genetic approaches, which may expedite the development, translation, and utility of novel synthetic genetic therapies in cancer. Finally, we describe the challenges associated with PROTACs and the ongoing efforts to overcome these issues to streamline clinical translation. Ultimately, these efforts may lead to their routine clinical use, which is expected to revolutionize cancer treatment strategies, delay familial cancer onset, and ultimately improve the lives and outcomes of those living with cancer.
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Affiliation(s)
- Kailee A. Rutherford
- Paul Albrechtsen Research Institute CancerCare Manitoba, Winnipeg, Manitoba, Canada
- Department of Biochemistry and Medical Genetics, Rady Faculty of Health Sciencs, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Kirk J. McManus
- Paul Albrechtsen Research Institute CancerCare Manitoba, Winnipeg, Manitoba, Canada
- Department of Biochemistry and Medical Genetics, Rady Faculty of Health Sciencs, University of Manitoba, Winnipeg, Manitoba, Canada
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Eichbichler D, Bernecker C, Stengel F, Scheffner M. Phase separation promotes the activity of HECT E3 ligases-A word of caution. Proc Natl Acad Sci U S A 2024; 121:e2402551121. [PMID: 38527205 PMCID: PMC10998622 DOI: 10.1073/pnas.2402551121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/27/2024] Open
Affiliation(s)
| | | | - Florian Stengel
- Department of Biology, University of Konstanz, 78457Konstanz, Germany
| | - Martin Scheffner
- Department of Biology, University of Konstanz, 78457Konstanz, Germany
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Pepelnjak M, Rogawski R, Arkind G, Leushkin Y, Fainer I, Ben-Nissan G, Picotti P, Sharon M. Systematic identification of 20S proteasome substrates. Mol Syst Biol 2024; 20:403-427. [PMID: 38287148 PMCID: PMC10987551 DOI: 10.1038/s44320-024-00015-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 12/13/2023] [Accepted: 01/05/2024] [Indexed: 01/31/2024] Open
Abstract
For years, proteasomal degradation was predominantly attributed to the ubiquitin-26S proteasome pathway. However, it is now evident that the core 20S proteasome can independently target proteins for degradation. With approximately half of the cellular proteasomes comprising free 20S complexes, this degradation mechanism is not rare. Identifying 20S-specific substrates is challenging due to the dual-targeting of some proteins to either 20S or 26S proteasomes and the non-specificity of proteasome inhibitors. Consequently, knowledge of 20S proteasome substrates relies on limited hypothesis-driven studies. To comprehensively explore 20S proteasome substrates, we employed advanced mass spectrometry, along with biochemical and cellular analyses. This systematic approach revealed hundreds of 20S proteasome substrates, including proteins undergoing specific N- or C-terminal cleavage, possibly for regulation. Notably, these substrates were enriched in RNA- and DNA-binding proteins with intrinsically disordered regions, often found in the nucleus and stress granules. Under cellular stress, we observed reduced proteolytic activity in oxidized proteasomes, with oxidized protein substrates exhibiting higher structural disorder compared to unmodified proteins. Overall, our study illuminates the nature of 20S substrates, offering crucial insights into 20S proteasome biology.
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Affiliation(s)
- Monika Pepelnjak
- Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Rivkah Rogawski
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Galina Arkind
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Yegor Leushkin
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Irit Fainer
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Gili Ben-Nissan
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Paola Picotti
- Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, Zurich, Switzerland.
| | - Michal Sharon
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel.
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48
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Zheng C, Zhou J, Yuan X, Zheng E, Liu X, Cui W, Yan C, Wu Y, Ruan W, Yi K, Chen J, Wang X. Elevating plant immunity by translational regulation of a rice WRKY transcription factor. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:1033-1048. [PMID: 37997501 PMCID: PMC10955491 DOI: 10.1111/pbi.14243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 10/20/2023] [Accepted: 11/11/2023] [Indexed: 11/25/2023]
Abstract
Plants have intricate mechanisms that tailor their defence responses to pathogens. WRKY transcription factors play a pivotal role in plant immunity by regulating various defence signalling pathways. Many WRKY genes are transcriptionally activated upon pathogen attack, but how their functions are regulated after transcription remains elusive. Here, we show that OsWRKY7 functions as a crucial positive regulator of rice basal immunity against Xanthomonas oryzae pv. oryzae (Xoo). The activity of OsWRKY7 was regulated at both translational and post-translational levels. Two translational products of OsWRKY7 were generated by alternative initiation. The full-length OsWRKY7 protein is normally degraded by the ubiquitin-proteasome system but was accumulated following elicitor or pathogen treatment, whereas the alternate product initiated from the downstream in-frame start codon was stable. Both the full and alternate OsWRKY7 proteins have transcriptional activities in yeast and rice cells, and overexpression of each form enhanced resistance to Xoo infection. Furthermore, disruption of the main AUG in rice increased the endogenous translation of the alternate stabilized form of OsWRKY7 and enhanced bacterial blight resistance. This study provides insights into the coordination of alternative translation and protein stability in the regulation of plant growth and basal defence mediated by the OsWRKY7 transcription factor, and also suggests a promising strategy to breed disease-resistant rice by translation initiation control.
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Affiliation(s)
- Chao Zheng
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agroproducts, Ministry of Agriculture Key Laboratory for Plant Protection and Biotechnology, Zhejiang Provincial Key Laboratory of Plant Virology, Institute of Virology and BiotechnologyZhejiang Academy of Agricultural SciencesHangzhouP. R. China
- College of Plant ProtectionNorthwest A&F UniversityYanglingP.R. China
| | - Jie Zhou
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agroproducts, Ministry of Agriculture Key Laboratory for Plant Protection and Biotechnology, Zhejiang Provincial Key Laboratory of Plant Virology, Institute of Virology and BiotechnologyZhejiang Academy of Agricultural SciencesHangzhouP. R. China
| | - Xiaoya Yuan
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agroproducts, Ministry of Agriculture Key Laboratory for Plant Protection and Biotechnology, Zhejiang Provincial Key Laboratory of Plant Virology, Institute of Virology and BiotechnologyZhejiang Academy of Agricultural SciencesHangzhouP. R. China
- College of Plant ProtectionNorthwest A&F UniversityYanglingP.R. China
| | - Ersong Zheng
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agroproducts, Ministry of Agriculture Key Laboratory for Plant Protection and Biotechnology, Zhejiang Provincial Key Laboratory of Plant Virology, Institute of Virology and BiotechnologyZhejiang Academy of Agricultural SciencesHangzhouP. R. China
- College of Plant ProtectionNorthwest A&F UniversityYanglingP.R. China
| | - Xiuli Liu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agroproducts, Ministry of Agriculture Key Laboratory for Plant Protection and Biotechnology, Zhejiang Provincial Key Laboratory of Plant Virology, Institute of Virology and BiotechnologyZhejiang Academy of Agricultural SciencesHangzhouP. R. China
| | - Weijun Cui
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agroproducts, Ministry of Agriculture Key Laboratory for Plant Protection and Biotechnology, Zhejiang Provincial Key Laboratory of Plant Virology, Institute of Virology and BiotechnologyZhejiang Academy of Agricultural SciencesHangzhouP. R. China
| | - Chengqi Yan
- Institute of BiotechnologyNingbo Academy of Agricultural SciencesNingboP.R. China
| | - Yueyan Wu
- Zhejiang Wan Li UniversityNingboP.R. China
| | - Wenyuan Ruan
- Institute of Agricultural Resources and Regional PlanningChinese Academy of Agricultural SciencesBeijingChina
| | - Keke Yi
- Institute of Agricultural Resources and Regional PlanningChinese Academy of Agricultural SciencesBeijingChina
| | - Jianping Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agroproducts, Ministry of Agriculture Key Laboratory for Plant Protection and Biotechnology, Zhejiang Provincial Key Laboratory of Plant Virology, Institute of Virology and BiotechnologyZhejiang Academy of Agricultural SciencesHangzhouP. R. China
- Institute of Plant VirologyNingbo UniversityNingboP. R. China
| | - Xuming Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agroproducts, Ministry of Agriculture Key Laboratory for Plant Protection and Biotechnology, Zhejiang Provincial Key Laboratory of Plant Virology, Institute of Virology and BiotechnologyZhejiang Academy of Agricultural SciencesHangzhouP. R. China
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49
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Vela‐Rodríguez C, Yang C, Alanen HI, Eki R, Abbas TA, Maksimainen MM, Glumoff T, Duman R, Wagner A, Paschal BM, Lehtiö L. Oligomerization mediated by the D2 domain of DTX3L is critical for DTX3L-PARP9 reading function of mono-ADP-ribosylated androgen receptor. Protein Sci 2024; 33:e4945. [PMID: 38511494 PMCID: PMC10955461 DOI: 10.1002/pro.4945] [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: 11/30/2023] [Revised: 02/07/2024] [Accepted: 02/11/2024] [Indexed: 03/22/2024]
Abstract
Deltex proteins are a family of E3 ubiquitin ligases that encode C-terminal RING and DTC domains that mediate interactions with E2 ubiquitin-conjugating enzymes and recognize ubiquitination substrates. DTX3L is unique among the Deltex proteins based on its N-terminal domain architecture. The N-terminal D1 and D2 domains of DTX3L mediate homo-oligomerization, and the D3 domain interacts with PARP9, a protein that contains tandem macrodomains with ADP-ribose reader function. While DTX3L and PARP9 are known to heterodimerize, and assemble into a high molecular weight oligomeric complex, the nature of the oligomeric structure, including whether this contributes to the ADP-ribose reader function is unknown. Here, we report a crystal structure of the DTX3L N-terminal D2 domain and show that it forms a tetramer with, conveniently, D2 symmetry. We identified two interfaces in the structure: a major, conserved interface with a surface of 973 Å2 and a smaller one of 415 Å2. Using native mass spectrometry, we observed molecular species that correspond to monomers, dimers and tetramers of the D2 domain. Reconstitution of DTX3L knockout cells with a D1-D2 deletion mutant showed the domain is dispensable for DTX3L-PARP9 heterodimer formation, but necessary to assemble an oligomeric complex with efficient reader function for ADP-ribosylated androgen receptor. Our results suggest that homo-oligomerization of DTX3L is important for the DTX3L-PARP9 complex to read mono-ADP-ribosylation on a ligand-regulated transcription factor.
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Affiliation(s)
- Carlos Vela‐Rodríguez
- Faculty of Biochemistry and Molecular Medicine & Biocenter OuluUniversity of OuluOuluFinland
| | - Chunsong Yang
- Department of Biochemistry and Molecular GeneticsUniversity of VirginiaCharlottesvilleVirginiaUSA
| | - Heli I. Alanen
- Faculty of Biochemistry and Molecular Medicine & Biocenter OuluUniversity of OuluOuluFinland
| | - Rebeka Eki
- Department of Radiation OncologyUniversity of VirginiaCharlottesvilleVirginiaUSA
| | - Tarek A. Abbas
- Department of Radiation OncologyUniversity of VirginiaCharlottesvilleVirginiaUSA
| | - Mirko M. Maksimainen
- Faculty of Biochemistry and Molecular Medicine & Biocenter OuluUniversity of OuluOuluFinland
| | - Tuomo Glumoff
- Faculty of Biochemistry and Molecular Medicine & Biocenter OuluUniversity of OuluOuluFinland
| | - Ramona Duman
- Diamond Light Source, Harwell Science and Innovation CampusDidcotUK
| | - Armin Wagner
- Diamond Light Source, Harwell Science and Innovation CampusDidcotUK
| | - Bryce M. Paschal
- Department of Biochemistry and Molecular GeneticsUniversity of VirginiaCharlottesvilleVirginiaUSA
| | - Lari Lehtiö
- Faculty of Biochemistry and Molecular Medicine & Biocenter OuluUniversity of OuluOuluFinland
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50
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Zou Y, Zhang Y, Li M, Cao K, Song C, Zhang Z, Cai K, Geng D, Chen S, Wu Y, Zhang N, Sun G, Wang J, Zhang Y, Sun Y. Regulation of lipid metabolism by E3 ubiquitin ligases in lipid-associated metabolic diseases. Int J Biol Macromol 2024; 265:130961. [PMID: 38508558 DOI: 10.1016/j.ijbiomac.2024.130961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 03/10/2024] [Accepted: 03/15/2024] [Indexed: 03/22/2024]
Abstract
Previous studies have progressively elucidated the involvement of E3 ubiquitin (Ub) ligases in regulating lipid metabolism. Ubiquitination, facilitated by E3 Ub ligases, modifies critical enzymes in lipid metabolism, enabling them to respond to specific signals. In this review, we aim to present a comprehensive analysis of the role of E3 Ub ligases in lipid metabolism, which includes lipid synthesis and lipolysis, and their influence on cellular lipid homeostasis through the modulation of lipid uptake and efflux. Furthermore, it explores how the ubiquitination process governs the degradation or activation of pivotal enzymes, thereby regulating lipid metabolism at the transcriptional level. Perturbations in lipid metabolism have been implicated in various diseases, including hepatic lipid metabolism disorders, atherosclerosis, diabetes, and cancer. Therefore, this review focuses on the association between E3 Ub ligases and lipid metabolism in lipid-related diseases, highlighting enzymes critically involved in lipid synthesis and catabolism, transcriptional regulators, lipid uptake translocators, and transporters. Overall, this review aims to identify gaps in current knowledge, highlight areas requiring further research, offer potential targeted therapeutic approaches, and provide a comprehensive outlook on clinical conditions associated with lipid metabolic diseases.
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Affiliation(s)
- Yuanming Zou
- Department of Cardiology, the First Hospital of China Medical University, 155 Nanjing North Street, Heping District, Shenyang, 110001, Liaoning Province, People's Republic of China
| | - Ying Zhang
- Department of Cardiology, the First Hospital of China Medical University, 155 Nanjing North Street, Heping District, Shenyang, 110001, Liaoning Province, People's Republic of China; Institute of Health Sciences, China Medical University, 77 Puhe Road, Shenbei New District, Shenyang, 110001, Liaoning Province, People's Republic of China.
| | - Mohan Li
- Department of Cardiology, the First Hospital of China Medical University, 155 Nanjing North Street, Heping District, Shenyang, 110001, Liaoning Province, People's Republic of China
| | - Kexin Cao
- Department of Cardiology, the First Hospital of China Medical University, 155 Nanjing North Street, Heping District, Shenyang, 110001, Liaoning Province, People's Republic of China
| | - Chunyu Song
- Department of Cardiology, the First Hospital of China Medical University, 155 Nanjing North Street, Heping District, Shenyang, 110001, Liaoning Province, People's Republic of China
| | - Zhaobo Zhang
- Department of Cardiology, the First Hospital of China Medical University, 155 Nanjing North Street, Heping District, Shenyang, 110001, Liaoning Province, People's Republic of China
| | - Kexin Cai
- Department of Cardiology, the First Hospital of China Medical University, 155 Nanjing North Street, Heping District, Shenyang, 110001, Liaoning Province, People's Republic of China
| | - Danxi Geng
- Department of Cardiology, the First Hospital of China Medical University, 155 Nanjing North Street, Heping District, Shenyang, 110001, Liaoning Province, People's Republic of China
| | - Shuxian Chen
- Department of Cardiology, the First Hospital of China Medical University, 155 Nanjing North Street, Heping District, Shenyang, 110001, Liaoning Province, People's Republic of China
| | - Yanjiao Wu
- Department of Cardiology, the First Hospital of China Medical University, 155 Nanjing North Street, Heping District, Shenyang, 110001, Liaoning Province, People's Republic of China
| | - Naijin Zhang
- Department of Cardiology, the First Hospital of China Medical University, 155 Nanjing North Street, Heping District, Shenyang, 110001, Liaoning Province, People's Republic of China; Institute of Health Sciences, China Medical University, 77 Puhe Road, Shenbei New District, Shenyang, 110001, Liaoning Province, People's Republic of China; Key Laboratory of Reproductive and Genetic Medicine (China Medical University), National Health Commission, 77 Puhe Road, Shenbei New District, Shenyang, 110001, Liaoning Province, People's Republic of China
| | - Guozhe Sun
- Department of Cardiology, the First Hospital of China Medical University, 155 Nanjing North Street, Heping District, Shenyang, 110001, Liaoning Province, People's Republic of China.
| | - Jing Wang
- Department of Hematology, the First Hospital of China Medical University, 155 Nanjing North Street, Heping District, Shenyang, 110001, Liaoning Province, People's Republic of China.
| | - Yixiao Zhang
- Department of Urology Surgery, Shengjing Hospital of China Medical University, 36 Sanhao Street, Heping District, Shenyang, 110004, Liaoning Province, People's Republic of China.
| | - Yingxian Sun
- Department of Cardiology, the First Hospital of China Medical University, 155 Nanjing North Street, Heping District, Shenyang, 110001, Liaoning Province, People's Republic of China; Institute of Health Sciences, China Medical University, 77 Puhe Road, Shenbei New District, Shenyang, 110001, Liaoning Province, People's Republic of China; Key Laboratory of Environmental Stress and Chronic Disease Control and Prevention, Ministry of Education, China Medical University, 77 Puhe Road, Shenbei New District, Shenyang, 110001, Liaoning Province, People's Republic of China.
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