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Mei Q, Li M, Chen J, Yang J, Duan D, Yang J, Ma F, Mao K. Genome-wide analyses of Ariadne family genes reveal their involvement in abiotic stress responses in apple. Gene 2025; 935:149076. [PMID: 39505090 DOI: 10.1016/j.gene.2024.149076] [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: 08/13/2024] [Revised: 10/26/2024] [Accepted: 10/31/2024] [Indexed: 11/08/2024]
Abstract
E3 ligases are essential for ubiquitination and play a role in regulating various aspects of eukaryotic life. Ariadne (ARI) proteins, a subfamily of RBR (RING-between-RING) proteins, have been recognized as a new class of RING-finger E3 ligases. Recent research has shed light on their potential involvement in plants' responses to abiotic stress. However, comprehensive studies on ARI genes in apple (Malus domestica) are still lacking. This study identified ten MdARI genes in the apple genome, and examined intraspecific and interspecific collinearity to explore the evolutionary relationships of ARI family members. Phylogenetic analyses classified MdARIs into two subfamilies (A and B), and by integrating gene structure, conserved motifs, and sequence comparison results, subfamily B was further divided into two subgroups (I and II). Tissue expression analyses revealed varied expression patterns of MdARI genes in different tissues, and subcellular localization showed that MdARI1-1, MdARI1-2, and MdARI9-1 were located in the nucleus, while the other seven MdARIs were distributed throughout the cell. Analyses of promoter cis-elements and expression patterns under cold, salt, and drought treatments indicated the involvement of MdARIs in abiotic stress responses. Several proteins crucial to the plant stress response were predicted to be potential MdARIs-interacting proteins based on the protein interaction network. Additionally, the interaction between UBC11 (E2) and MdARI7-2 was confirmed by a yeast two-hybrid (Y2H) experiment, suggesting that MdARI7-2 may function as an E3. These findings will greatly benefit future research on the role and mechanisms of ARI proteins in apple stress response.
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Affiliation(s)
- Quanlin Mei
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Ming Li
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Jing Chen
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Jiaxin Yang
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Dingyue Duan
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Jie Yang
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Fengwang Ma
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China.
| | - Ke Mao
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China.
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2
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Nyenhuis DA, Watanabe SM, Tjandra N, Carter CA. Tsg101 mimicry of canonical E2 enzymes underlies its role in ubiquitin signaling. Proc Natl Acad Sci U S A 2025; 122:e2419542121. [PMID: 39739800 DOI: 10.1073/pnas.2419542121] [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: 09/24/2024] [Accepted: 11/26/2024] [Indexed: 01/02/2025] Open
Abstract
Tsg101 is a highly conserved protein best known as an early-functioning component of cellular ESCRT machinery participating in recognition, sorting, and trafficking of cellular cargo to various intracellular destinations. It shares sequence and structural homology to canonical ubiquitin-conjugating (E2) enzymes and is linked to diverse events regulated by Ub signaling. How it might fulfill these roles is unclear. Here, we show that Tsg101 E2 mimicry permits interactions with diverse ubiquitin ligating (E3) enzymes and underlies its multifunctional capabilities. Coexpression of Tsg101 with the E3 ligase NNedd4-2s protected the enzyme from degradation and, remarkably, other widely divergent ligases as well. Structural alignment with UbcH5, a canonical E2 enzyme, revealed that recognition at the E2-E3 interface, a region broadly conserved despite sequence and structural differences in both E2 and E3 enzymes, was critical for protection. Nevertheless, UbcH5 failed to protect NNedd4-2s, indicating that the UEV chaperone function is unique to the variant. Studies using Cy5-Ub-VME showed that Tsg101-mediated protection reduced accessibility to Cys residues in the ligase. Access to Tsg101 Ub-binding sites was critical: Rabeprazole, which interferes with Tsg101 Ub-binding, diminished E3 ligase protection. Thus, E2 mimicry permitting control of E3 ligase ubiquitin signaling underlies Tsg101's broad ability to participate in multiple cellular functions. The study provides mechanistic insight into how Tsg101, by partnering with diverse E3 ligases, can contribute to a broad range of cellular activities.
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Affiliation(s)
- David A Nyenhuis
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD 20982
| | - Susan M Watanabe
- Department of Microbiology and Immunology, Renaissance School of Medicine, Stony Brook University, Stony Brook, NY 11794-5222
| | - Nico Tjandra
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD 20982
| | - Carol A Carter
- Department of Microbiology and Immunology, Renaissance School of Medicine, Stony Brook University, Stony Brook, NY 11794-5222
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Zhang Q, Gu R, Dai Y, Chen J, Ye P, Zhu H, He W, Nie X. Molecular mechanisms of ubiquitination in wound healing. Biochem Pharmacol 2025; 231:116670. [PMID: 39613112 DOI: 10.1016/j.bcp.2024.116670] [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: 07/03/2024] [Revised: 11/02/2024] [Accepted: 11/25/2024] [Indexed: 12/01/2024]
Abstract
Wound healing is a complex biological process involving multiple cellular and molecular mechanisms. Ubiquitination, a crucial post-translational modification, plays a vital role in regulating various aspects of wound healing through protein modification and degradation. This review comprehensively examines the molecular mechanisms of ubiquitination in wound healing, focusing on its regulation of inflammatory responses, macrophage polarization, angiogenesis, and the activities of fibroblasts and keratinocytes. We discuss how ubiquitination modifies key signaling pathways, including TGF-β/Smad3, NF-κB, and HIF-α, which are essential for proper wound healing. Understanding these mechanisms provides insights into potential therapeutic strategies for treating impaired wound healing, particularly in conditions such as diabetes. The review highlights recent advances in understanding ubiquitination's role in wound healing and discusses future research directions for developing targeted therapeutic approaches.
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Affiliation(s)
- Qianbo Zhang
- College of Pharmacy, Zunyi Medical University, Zunyi 563006, PR China; Key Lab of the Basic Pharmacology of the Ministry of Education & Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi 563006, PR China.
| | - Rifang Gu
- College of Pharmacy, Zunyi Medical University, Zunyi 563006, PR China; School Medical Office, Zunyi Medical University, Zunyi 563006, PR China.
| | - Yuhe Dai
- College of Pharmacy, Zunyi Medical University, Zunyi 563006, PR China; Key Lab of the Basic Pharmacology of the Ministry of Education & Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi 563006, PR China.
| | - Jitao Chen
- College of Pharmacy, Zunyi Medical University, Zunyi 563006, PR China; Key Lab of the Basic Pharmacology of the Ministry of Education & Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi 563006, PR China.
| | - Penghui Ye
- College of Pharmacy, Zunyi Medical University, Zunyi 563006, PR China; Key Lab of the Basic Pharmacology of the Ministry of Education & Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi 563006, PR China.
| | - Huan Zhu
- College of Pharmacy, Zunyi Medical University, Zunyi 563006, PR China; Key Lab of the Basic Pharmacology of the Ministry of Education & Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi 563006, PR China.
| | - Wenping He
- College of Pharmacy, Zunyi Medical University, Zunyi 563006, PR China; Key Lab of the Basic Pharmacology of the Ministry of Education & Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi 563006, PR China.
| | - Xuqiang Nie
- College of Pharmacy, Zunyi Medical University, Zunyi 563006, PR China; Key Lab of the Basic Pharmacology of the Ministry of Education & Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi 563006, PR China.
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4
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Li T, Zheng C, Zhu H. A Guideline Strategy for Identifying Genes/Proteins Regulating Antiviral Innate Immunity. Methods Mol Biol 2025; 2854:1-7. [PMID: 39192112 DOI: 10.1007/978-1-0716-4108-8_1] [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: 08/29/2024]
Abstract
Antiviral innate immunity is a complicated system initiated by the induction of type I interferon (IFN-I) and downstream interferon-stimulated genes (ISGs) and is finely regulated by numerous positive and negative factors at different signaling adaptors. During this process, posttranslational modifications, especially ubiquitination, are the most common regulatory strategy used by the host to switch the antiviral innate signaling pathway and are mainly controlled by E3 ubiquitin ligases from different protein families. A comprehensive understanding of the regulatory mechanisms and a novel discovery of regulatory factors involved in the IFN-I signaling pathway are important for researchers to identify novel therapeutic targets against viral infectious diseases based on innate immunotherapy. In this section, we use the E3 ubiquitin ligase as an example to guide the identification of a protein belonging to the RING Finger (RNF) family that regulates the RIG-I-mediated IFN-I pathway through ubiquitination.
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Affiliation(s)
- Ting Li
- Basic Medical College of Gannan Medical University, Ganzhou, Jiangxi, China
| | - Chunfu Zheng
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, AB, Canada
| | - Huifang Zhu
- Basic Medical College of Gannan Medical University, Ganzhou, Jiangxi, China
- Institute of Children's Medical, First Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi, China
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Frey Y, Lungu C, Olayioye MA. Regulation and functions of the DLC family of RhoGAP proteins: Implications for development and cancer. Cell Signal 2025; 125:111505. [PMID: 39549821 DOI: 10.1016/j.cellsig.2024.111505] [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: 07/26/2024] [Revised: 10/18/2024] [Accepted: 11/05/2024] [Indexed: 11/18/2024]
Abstract
The DLC (Deleted in Liver Cancer) family of RhoGAP (Rho GTPase-activating) proteins has been extensively studied since the identification of the first family member nearly 30 years ago. Rho GTPase signaling is essential for various cellular processes, including cytoskeletal dynamics, cell migration, and proliferation. Members of the DLC family are key regulators of this signaling pathway, with well-established roles in development and carcinogenesis. Here, we provide a comprehensive review of research into DLC regulation and cellular functions over the last three decades. In particular, we summarize control mechanisms of DLC gene expression at both the transcriptional and post-transcriptional level. Additionally, recent advances in understanding the post-translational regulation of DLC proteins that allow for tuning of protein activity and localization are highlighted. This detailed overview will serve as resource for future studies aimed at further elucidating the complex regulatory mechanisms of DLC family proteins and exploring their potential as targets for therapeutic applications.
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Affiliation(s)
- Yannick Frey
- University of Stuttgart, Institute of Cell Biology and Immunology, Stuttgart, Germany; Medical University of Innsbruck, Institute of Pathophysiology, Innsbruck, Austria
| | - Cristiana Lungu
- University of Stuttgart, Institute of Cell Biology and Immunology, Stuttgart, Germany; University of Stuttgart, Stuttgart Research Center Systems Biology, Stuttgart, Germany
| | - Monilola A Olayioye
- University of Stuttgart, Institute of Cell Biology and Immunology, Stuttgart, Germany; University of Stuttgart, Stuttgart Research Center Systems Biology, Stuttgart, Germany.
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Yook S, Deewan A, Ziolkowski L, Lane S, Tohidifar P, Cheng MH, Singh V, Stasiewicz MJ, Rao CV, Jin YS. Engineering and evolution of Yarrowia lipolytica for producing lipids from lignocellulosic hydrolysates. BIORESOURCE TECHNOLOGY 2025; 416:131806. [PMID: 39536885 DOI: 10.1016/j.biortech.2024.131806] [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: 05/27/2024] [Revised: 09/09/2024] [Accepted: 11/10/2024] [Indexed: 11/16/2024]
Abstract
Yarrowia lipolytica, an oleaginous yeast, shows promise for industrial fermentation due to its robust acetyl-CoA flux and well-developed genetic engineering tools. However, its lack of an active xylose metabolism restricts the conversion of cellulosic sugars to valuable products. To address this, metabolic engineering, and adaptive laboratory evolution (ALE) were applied to the Y. lipolytica PO1f strain, resulting in an efficient xylose-assimilating strain (XEV). Whole-genome sequencing (WGS) of the XEV followed by reverse engineering revealed that the amplification of the heterologous oxidoreductase pathway and a mutation in the GTPase-activating protein gene (YALI0B12100g) might be the primary reasons for improved xylose assimilation in the XEV strain. When a sorghum hydrolysate was used, the XEV strain showed superior xylose consumption and lipid production compared to its parental strain (X123). This study advances our understanding of xylose metabolism in Y. lipolytica and proposes effective metabolic engineering strategies for optimizing lignocellulosic hydrolysates.
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Affiliation(s)
- Sangdo Yook
- Carl Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA; Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL, USA; DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Anshu Deewan
- Carl Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA; Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA; DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Leah Ziolkowski
- Carl Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA; Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Stephan Lane
- Carl Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA; Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL, USA; DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Payman Tohidifar
- Carl Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA; Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA; DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Ming-Hsun Cheng
- Carl Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA; Department of Agricultural and Biological Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA; DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Vijay Singh
- Carl Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA; Department of Agricultural and Biological Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA; DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Matthew J Stasiewicz
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Christopher V Rao
- Carl Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA; Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA; DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Yong-Su Jin
- Carl Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA; Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL, USA; DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois Urbana-Champaign, Urbana, IL, USA.
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Chen D, Jiang J, Zhang W, Li X, Ge Q, Liu X, Li X. Tripartite motif-containing protein 50 suppresses triple-negative breast cancer progression by regulating the epithelial-mesenchymal transition. Cancer Biol Ther 2024; 25:2427410. [PMID: 39538371 PMCID: PMC11572070 DOI: 10.1080/15384047.2024.2427410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Revised: 11/02/2024] [Accepted: 11/05/2024] [Indexed: 11/16/2024] Open
Abstract
BACKGROUND AND OBJECTIVES Tripartite motif-containing protein 50 (TRIM50) is a recently discovered E3 ubiquitin ligase that participates in tumor progression. TRIM50 is overexpressed in many cancers, although few studies focused on TRIM50's role in breast cancer. METHODS We overexpressed TRIM50 in triple-negative breast cancer cell lines using plasmid and found that TRIM50 upregulation markedly reduced breast cancer cell proliferation, clone formation, and migration, as well as promoted breast cancer cell apoptosis. Western blotting revealed that accumulated TRIM50 resulted in both mRNA and protein depletion of SNAI1, and partially attenuated the epithelial-mesenchymal transition (EMT) induced by SNAI1. RESULTS In this study, we demonstrate that TRIM50 is downregulated in human breast cancer and that its overexpression closely correlates with diminished invasion capacity in breast cancer, suggesting that TRIM50 may serve as a diagnostic marker and therapeutic target. CONCLUSION TRIM50 plays a key role in breast cancer proliferation and potentially serves as a prognostic and therapeutic target.
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Affiliation(s)
- Danxiang Chen
- Department of Oncology, Ningbo No. 2 Hospital, Ningbo, Zhejiang, PR China
- Department of Breast Surgery, Ningbo No. 2 Hospital, Ningbo, Zhejiang, China
| | - Jing Jiang
- Department of Oncology, Ningbo No. 2 Hospital, Ningbo, Zhejiang, PR China
- Department of Breast Surgery, Ningbo No. 2 Hospital, Ningbo, Zhejiang, China
| | - Wei Zhang
- Department of Oncology, Ningbo No. 2 Hospital, Ningbo, Zhejiang, PR China
- Department of Breast Surgery, Ningbo No. 2 Hospital, Ningbo, Zhejiang, China
| | - Xinlin Li
- Department of Oncology, Ningbo No. 2 Hospital, Ningbo, Zhejiang, PR China
- Department of Breast Surgery, Ningbo No. 2 Hospital, Ningbo, Zhejiang, China
| | - Qidong Ge
- Department of Oncology, Ningbo No. 2 Hospital, Ningbo, Zhejiang, PR China
- Department of Breast Surgery, Ningbo No. 2 Hospital, Ningbo, Zhejiang, China
| | - Xia Liu
- Department of Anesthesiology, Ningbo 1st Hospital, Ningbo, Zhejiang, China
| | - Xujun Li
- Department of Oncology, Ningbo No. 2 Hospital, Ningbo, Zhejiang, PR China
- Department of Breast Surgery, Ningbo No. 2 Hospital, Ningbo, Zhejiang, China
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Wong PF, Kamarul T. Targeting Ubiquitin-Proteasome System (UPS) in Treating Osteoarthritis. Eur J Pharmacol 2024:177237. [PMID: 39732357 DOI: 10.1016/j.ejphar.2024.177237] [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: 08/03/2024] [Revised: 11/21/2024] [Accepted: 12/23/2024] [Indexed: 12/30/2024]
Abstract
Despite osteoarthritis (OA) being recognised for over a century as a debilitating disease that affects millions, there are huge gaps in our understanding of the underlying pathophysiology that drives this disease. Present day studies that focussed on ubiquitination (Ub) and ubiquitylation-like (Ubl) modification related mechanisms have brought light into the possibility of attenuating OA development by targeting these specific proteins in chondrocytes. In the present review, we discuss recent advances in studies involving Ub ligases and deubiquitinating enzymes (DUBs) which are of importance in the development of OA, and may offer potential therapeutic strategies for OA. Such targets may involve attenuating proteases such as MMP1, 8, 13, 4 and several ADAMTS that are well known for their role in cartilage breakdown. Ligases such as E2 and E3 that are involved in extracellular matrix (ECM) degradation in OA and of their pathogenesis would be discussed. In addition to catabolic and degenerative downstream effects of Ub and DUBs in OA, inflammatory mechanisms most notably involving NF-κB signalling pathways regulated through Ub and using various targeting molecules would also be highlighted. Challenges, gaps and insights from clinical trials will provide valuable guidance for future investigations on targeting UPS as a therapeutic option for OA.
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Affiliation(s)
- Pooi-Fong Wong
- Department of Pharmacology, Faculty of Medicine, 50603 Kuala Lumpur.
| | - Tunku Kamarul
- National Orthopaedic Centre of Excellence in Research and Learning (NOCERAL), Department of Orthopaedic Surgery, Faculty of Medicine, University of Malaya, Kuala Lumpur 50603, Malaysia
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Cao S, Garcia SF, Shi H, James EI, Kito Y, Shi H, Mao H, Kaisari S, Rona G, Deng S, Goldberg HV, Ponce J, Ueberheide B, Lignitto L, Guttman M, Pagano M, Zheng N. Recognition of BACH1 quaternary structure degrons by two F-box proteins under oxidative stress. Cell 2024; 187:7568-7584.e22. [PMID: 39504958 DOI: 10.1016/j.cell.2024.10.012] [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: 10/12/2023] [Revised: 08/25/2024] [Accepted: 10/10/2024] [Indexed: 11/08/2024]
Abstract
Ubiquitin-dependent proteolysis regulates diverse cellular functions with high substrate specificity, which hinges on the ability of ubiquitin E3 ligases to decode the targets' degradation signals, i.e., degrons. Here, we show that BACH1, a transcription repressor of antioxidant response genes, features two distinct unconventional degrons encrypted in the quaternary structure of its homodimeric BTB domain. These two degrons are both functionalized by oxidative stress and are deciphered by two complementary E3s. FBXO22 recognizes a degron constructed by the BACH1 BTB domain dimer interface, which is unmasked from transcriptional co-repressors after oxidative stress releases BACH1 from chromatin. When this degron is impaired by oxidation, a second BACH1 degron manifested by its destabilized BTB dimer is probed by a pair of FBXL17 proteins that remodels the substrate into E3-bound monomers for ubiquitination. Our findings highlight the multidimensionality of protein degradation signals and the functional complementarity of different ubiquitin ligases targeting the same substrate.
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Affiliation(s)
- Shiyun Cao
- Department of Pharmacology, University of Washington, Box 357280, Seattle, WA 98195, USA; Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
| | - Sheena Faye Garcia
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, 10016, USA; Laura and Isaac Perlmutter Cancer Center, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Huigang Shi
- Department of Pharmacology, University of Washington, Box 357280, Seattle, WA 98195, USA; Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
| | - Ellie I James
- Department of Medicinal Chemistry, University of Washington, Seattle, WA 98195, USA; Molecular Engineering & Science Institute, University of Washington, Seattle, WA 98195, USA
| | - Yuki Kito
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, 10016, USA; Laura and Isaac Perlmutter Cancer Center, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Hui Shi
- Department of Pharmacology, University of Washington, Box 357280, Seattle, WA 98195, USA; Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
| | - Haibin Mao
- Department of Pharmacology, University of Washington, Box 357280, Seattle, WA 98195, USA; Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
| | - Sharon Kaisari
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, 10016, USA; Laura and Isaac Perlmutter Cancer Center, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Gergely Rona
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, 10016, USA; Laura and Isaac Perlmutter Cancer Center, New York University Grossman School of Medicine, New York, NY 10016, USA; Howard Hughes Medical Institute, New York University Grossman School of Medicine, New York, NY 10016, USA; Institute of Molecular Life Sciences, HUN-REN Research Centre for Natural Sciences, Budapest, Hungary
| | - Sophia Deng
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, 10016, USA; Laura and Isaac Perlmutter Cancer Center, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Hailey V Goldberg
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, 10016, USA; Laura and Isaac Perlmutter Cancer Center, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Jackeline Ponce
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, 10016, USA; Laura and Isaac Perlmutter Cancer Center, New York University Grossman School of Medicine, New York, NY 10016, USA; Proteomics Laboratory, Division of Advanced Research Technologies, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Beatrix Ueberheide
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, 10016, USA; Laura and Isaac Perlmutter Cancer Center, New York University Grossman School of Medicine, New York, NY 10016, USA; Proteomics Laboratory, Division of Advanced Research Technologies, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Luca Lignitto
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, 10016, USA; Laura and Isaac Perlmutter Cancer Center, New York University Grossman School of Medicine, New York, NY 10016, USA; Cancer Research Center of Marseille (CRCM), CNRS, Aix Marseille University, INSERM, Institut Paoli-Calmettes, Marseille, France
| | - Miklos Guttman
- Department of Medicinal Chemistry, University of Washington, Seattle, WA 98195, USA; Molecular Engineering & Science Institute, University of Washington, Seattle, WA 98195, USA
| | - Michele Pagano
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, 10016, USA; Laura and Isaac Perlmutter Cancer Center, New York University Grossman School of Medicine, New York, NY 10016, USA; Howard Hughes Medical Institute, New York University Grossman School of Medicine, New York, NY 10016, USA.
| | - Ning Zheng
- Department of Pharmacology, University of Washington, Box 357280, Seattle, WA 98195, USA; Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA.
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10
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Huang H, Zhu W, Huang B, Fu Z, Xiong Y, Cao D, Ye Y, Chang Q, Li W, Li L, Zhou H, Niu X, Zhang W. Structural insights into the biochemical mechanism of the E2/E3 hybrid enzyme UBE2O. Structure 2024:S0969-2126(24)00537-9. [PMID: 39740670 DOI: 10.1016/j.str.2024.12.002] [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: 11/12/2023] [Revised: 11/08/2024] [Accepted: 12/03/2024] [Indexed: 01/02/2025]
Abstract
The E2/E3 hybrid enzyme UBE2O plays important roles in key biological events, but its autoubiquitination mechanism remains largely unclear. In this study, we determined the crystal structures of full-length (FL) UBE2O from Trametes pubescens (tp) and its ubiquitin-conjugating (UBC) domain. The dimeric FL-tpUBE2O structure revealed interdomain interactions between the conserved regions (CR1-CR2) and UBC. The dimeric intermolecular and canonical ubiquitin/UBC interactions are mechanistically important for UBE2O functions in catalyzing the formation of free polyubiquitin chains and substrate ubiquitination. Beyond dimerization, autoubiquitination within the CR1-CR2 domain also regulates tpUBE2O activity. Additionally, we show that tpUBE2O catalyzes the formation of all seven types of polyubiquitin chains in vitro. The CR1-CR2/UBC and canonical ubiquitin/UBC interactions are important for the polyubiquitination of AMP-activated protein kinase α2 (AMPKα2) by human UBE2O (hUBE2O), which leads to tumorigenesis. These structural insights lay the groundwork for understanding UBE2O's mechanisms and developing structure-based therapeutics targeting UBE2O.
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Affiliation(s)
- Hao Huang
- State Key Laboratory of Chemical Oncogenomics, Laboratory of Structural Biology and Drug Discovery, Laboratory of Ubiquitination and Targeted Therapy, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China; Institute of Chemical Biology, Shenzhen Bay Laboratory, Shenzhen, Guangdong 518132, China.
| | - Wenning Zhu
- State Key Laboratory of Chemical Oncogenomics, Laboratory of Structural Biology and Drug Discovery, Laboratory of Ubiquitination and Targeted Therapy, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Bin Huang
- State Key Laboratory of Chemical Oncogenomics, Laboratory of Structural Biology and Drug Discovery, Laboratory of Ubiquitination and Targeted Therapy, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Ziyang Fu
- State Key Laboratory of Chemical Oncogenomics, Laboratory of Structural Biology and Drug Discovery, Laboratory of Ubiquitination and Targeted Therapy, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Yuxian Xiong
- State Key Laboratory of Chemical Oncogenomics, Laboratory of Structural Biology and Drug Discovery, Laboratory of Ubiquitination and Targeted Therapy, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Dan Cao
- State Key Laboratory of Chemical Oncogenomics, Laboratory of Structural Biology and Drug Discovery, Laboratory of Ubiquitination and Targeted Therapy, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Yuxin Ye
- State Key Laboratory of Chemical Oncogenomics, Laboratory of Structural Biology and Drug Discovery, Laboratory of Ubiquitination and Targeted Therapy, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Qing Chang
- Beijing Advanced Innovation Center for Structural Biology, Technology Center for Protein Research, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Wenqi Li
- Beijing Advanced Innovation Center for Structural Biology, Technology Center for Protein Research, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Long Li
- Institute of Chemical Biology, Shenzhen Bay Laboratory, Shenzhen, Guangdong 518132, China
| | - Huan Zhou
- Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, China
| | - Xiaogang Niu
- College of Chemistry and Molecular Engineering, Beijing Nuclear Magnetic Resonance Center, Peking University, Beijing 100871, China
| | - Wei Zhang
- Department of Molecular and Cellular Biology, College of Biological Science, University of Guelph, Guelph, ON, Canada
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11
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Tachibana S, Otaki Y, Watanabe T, Goto J, Ochi H, Tanaka T, Ono H, Yamaguchi R, Sato J, Takahashi H, Arimoto T, Goto K, Watanabe M. Diacylglycerol Kinase ζ Attenuates Doxorubicin-Induced Cardiotoxicity Through p53 Degradation. J Am Heart Assoc 2024:e035608. [PMID: 39719406 DOI: 10.1161/jaha.124.035608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/04/2024] [Accepted: 08/20/2024] [Indexed: 12/26/2024]
Abstract
BACKGROUND Doxorubicin-induced cardiotoxicity is still an important medical problem associated with a high mortality rate in cancer survivors. p53 plays a key role in doxorubicin-induced cardiotoxicity. Diacylglycerol kinase ζ (Dgkζ), a 130-kDa enzyme abundant in cardiomyocytes, regulates the p53 protein expression level in neurons. To elucidate the mechanism of doxorubicin-induced cardiotoxicity, we focused on the functional role of Dgkζ and its interaction with heat shock protein 70 (Hsp70)-related ubiquitin E3 ligases such as E6-associated protein (E6ap) and C-terminus of Hsp70-interacting protein. METHODS AND RESULTS Protein interactions of Dgkζ with Hsp70 and E6ap were confirmed by immunoprecipitation, but not C-terminus of Hsp70-interacting protein. We administered doxorubicin in cardiac-specific overexpression of Dgkζ transgenic (Dgkζ-Tg) mice and wild-type littermates. Dgkζ-Tg mice showed lower p53 protein expression levels, preserved cardiac function, and improved survival rates compared with wild-type littermates after doxorubicin administration. RNA sequence analysis of myocardial tissues from Dgkζ-Tg after doxorubicin stimulation identified Hspa1b encoding Hsp70 as the differentially expressed gene. Dgkζ overexpression increased proteasomal p53 degradation and attenuated cardiomyocyte apoptosis after doxorubicin stimulation in cardiomyocytes, which was reversed by knockdown of E6ap. Dgkζ interacted with E6ap through ankyrin-like repeats. The overexpression of mutant Dgkζ, lacking ankyrin-like repeats, failed to inhibit p53 protein expression after doxorubicin stimulation. In Dgkζ-overexpressing cardiomyocytes, expression levels of p53 and caspase-3 were increased by knockdown of the C-terminus of Hsp70-interacting protein. CONCLUSIONS We demonstrated for the first time that Dgkζ augments p53 ubiquitin-proteasome degradation and ameliorates doxorubicin-induced cardiotoxicity by interacting with Hsp70 and E3 ligases such as E6ap and C-terminus of Hsp70-interacting protein.
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Affiliation(s)
- Shingo Tachibana
- Department of Cardiology, Pulmonology, and Nephrology Yamagata University School of Medicine Yamagata Japan
| | - Yoichiro Otaki
- Department of Cardiology, Pulmonology, and Nephrology Yamagata University School of Medicine Yamagata Japan
| | - Tetsu Watanabe
- Department of Cardiology, Pulmonology, and Nephrology Yamagata University School of Medicine Yamagata Japan
| | - Jun Goto
- Department of Cardiology, Pulmonology, and Nephrology Yamagata University School of Medicine Yamagata Japan
| | - Haruki Ochi
- Institute for Promotion of Medical Science Research, Faculty of Medicine Yamagata University Yamagata Japan
| | - Toshiaki Tanaka
- Department of Anatomy and Cell Biology, School of Medicine Yamagata University Yamagata Japan
| | - Hiroe Ono
- Department of Cardiology, Pulmonology, and Nephrology Yamagata University School of Medicine Yamagata Japan
| | - Ryuhei Yamaguchi
- Department of Cardiology, Pulmonology, and Nephrology Yamagata University School of Medicine Yamagata Japan
| | - Junya Sato
- Department of Cardiology, Pulmonology, and Nephrology Yamagata University School of Medicine Yamagata Japan
| | - Hiroki Takahashi
- Department of Cardiology, Pulmonology, and Nephrology Yamagata University School of Medicine Yamagata Japan
| | - Takanori Arimoto
- Department of Cardiology, Pulmonology, and Nephrology Yamagata University School of Medicine Yamagata Japan
| | - Kaoru Goto
- Department of Anatomy and Cell Biology, School of Medicine Yamagata University Yamagata Japan
| | - Masafumi Watanabe
- Department of Cardiology, Pulmonology, and Nephrology Yamagata University School of Medicine Yamagata Japan
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12
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Gottfried Y, Lulu-Shimron C, Goldhirsh G, Fisher Y, Ziv T, Hoon DSB, Kravtsova-Ivantsiv Y, Ciechanover A. Vimentin is a ubiquitination and degradation substrate of the ubiquitin ligase KPC1. Biochem Biophys Res Commun 2024; 745:151231. [PMID: 39732122 DOI: 10.1016/j.bbrc.2024.151231] [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: 12/11/2024] [Accepted: 12/20/2024] [Indexed: 12/30/2024]
Abstract
The ubiquitin proteasome system (UPS), driven by ubiquitin as a degradation signal, eliminates, in a highly specific manner, 'abnormal' proteins and proteins that completed their function. This process involves a hierarchical cascade of E1, E2, and E3 enzymes. The E3 ubiquitin ligases, act as specific receptors that bind their cognate substrates. We have previously shown that the ubiquitin ligase KPC1 possesses a strong tumor-suppressive characteristic caused by the p50 subunit of the NF-κB transcription factor, which is generated by limited, KPC1-mediated processing of its p105 precursor. In this study, we identified vimentin as a novel substrate of the KPC1. We demonstrated that the ligase forms a complex with vimentin and modifies it by ubiquitination. Overexpression of KPC1 in HEK293T cells downregulates vimentin expression. Conversely, deletion of KPC1 in HAP1 cells results in upregulation of vimentin. Importantly, we revealed both in vitro and in a tumor model in mice that at least part of this effect is mediated through the downregulation of vimentin. Furthermore, in human clear cell renal cell carcinoma (ccRCC) samples, we found a negative correlation between KPC1 and vimentin expression. Overall, we demonstrate that the KPC1 ubiquitin E3 ligase downregulates vimentin expression, thereby reducing migration and tumorigenicity of cancer cells.
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Affiliation(s)
- Yossi Gottfried
- The Rappaport Faculty of Medicine and Research Institute, and the Rappaport Technion Integrated Cancer Center (R-TICC), Technion-Israel Institute of Technology, Haifa, 3109601, Israel
| | - Chen Lulu-Shimron
- The Rappaport Faculty of Medicine and Research Institute, and the Rappaport Technion Integrated Cancer Center (R-TICC), Technion-Israel Institute of Technology, Haifa, 3109601, Israel
| | - Gilad Goldhirsh
- The Rappaport Faculty of Medicine and Research Institute, and the Rappaport Technion Integrated Cancer Center (R-TICC), Technion-Israel Institute of Technology, Haifa, 3109601, Israel
| | - Yael Fisher
- Institue of Pathology, Rambam Health Care Campus, Haifa, 3109601, Israel
| | - Tamar Ziv
- Smoler Proteomics Center, Technion-Israel Institute of Technology, Haifa, 3200003, Israel
| | - Dave S B Hoon
- Department of Translational Molecular Medicine, Saint Johns Cancer Institute, PHS, Santa Monica, CA, 90025, USA
| | - Yelena Kravtsova-Ivantsiv
- The Rappaport Faculty of Medicine and Research Institute, and the Rappaport Technion Integrated Cancer Center (R-TICC), Technion-Israel Institute of Technology, Haifa, 3109601, Israel.
| | - Aaron Ciechanover
- The Rappaport Faculty of Medicine and Research Institute, and the Rappaport Technion Integrated Cancer Center (R-TICC), Technion-Israel Institute of Technology, Haifa, 3109601, Israel.
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13
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Johnson N, Qi B, Wen J, Du B, Banerjee S. KLHL24 associated cardiomyopathy: Gene function to clinical management. Gene 2024; 939:149185. [PMID: 39708934 DOI: 10.1016/j.gene.2024.149185] [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: 07/20/2024] [Revised: 10/26/2024] [Accepted: 12/17/2024] [Indexed: 12/23/2024]
Abstract
BACKGROUND KLHL24 (Kelch-like protein 24) is a significant component of the ubiquitin-proteasome system (UPS), involved in regulating protein turnover through targeted ubiquitination and degradation. Germline mutations in KLHL24 gene have been known to cause Epidermolysis Bullosa Simplex characterized by skin fragility but has recently been found to cause Cardiomyopathy. MAIN BODY Various cardiomyopathies, including hypertrophic cardiomyopathy and dilated cardiomyopathy, leading to abnormal protein degradation and affecting the stability and function of essential cardiac proteins which finally results into structural and functional abnormalities in cardiac muscle. In this review, in order to understand the disease association of germline mutations of KLHL24, we summarize all the studies performed with KLHL24 gene including studies from 2016 when KLHL24 was first identified to be associated with epidermolysis bullosa simplex till the recent studies in 2024 by using keywords such as KLHL24 gene, hypertrophic cardiomyopathy, dilated cardiomyopathy and epidermolysis bullosa simplex. Furthermore, we explored the proposed molecular mechanisms and pathophysiologies of KLHL24 associated diseases. Patients with KLHL24 mutations were usually presented with variable clinical symptoms. The main clinical presentations have been cutaneous lesions, cardiac symptoms associated with cardiomyopathies and there have been reports of skeletal muscle weakness and neurological symptoms as well. Current treatments focus on managing clinical symptoms and preventing complications through medications, lifestyle changes, and surgical interventions. In addition, researches have also been conducted cell culture based in vitro studies for reducing the clinical symptoms of KLHL24 associated diseases. However, currently there are no specific clinical trials going on regarding the therapeutic strategies among patients with KLHL24 mutations. Understanding the role of KLHL24 in cardiomyopathies is very important for developing targeted diagnostic approach with therapeutic strategies. CONCLUSION This review emphasizes the importance of KLHL24 mutations as a newly recognized cause of cardiomyopathy, paving the way for improved clinical diagnosis, targeted therapies, and ultimately, for better patient outcomes.
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Affiliation(s)
- Neil Johnson
- Department of Genetics, College of Basic Medical Sciences, Jilin University, Changchun, Jilin, 130021, China; Department of Cardiology, China-Japan Union Hospital of Jilin University, Norman Bethune Health Science Center, Changchun, China
| | - Baiyu Qi
- Department of Genetics, College of Basic Medical Sciences, Jilin University, Changchun, Jilin, 130021, China
| | - Jianping Wen
- Department of Genetics, College of Basic Medical Sciences, Jilin University, Changchun, Jilin, 130021, China
| | - Beibei Du
- Department of Cardiology, China-Japan Union Hospital of Jilin University, Norman Bethune Health Science Center, Changchun, China
| | - Santasree Banerjee
- Department of Genetics, College of Basic Medical Sciences, Jilin University, Changchun, Jilin, 130021, China.
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14
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Ma R, Liang S, Zeng W, Li J, Lai Y, Yang X, Diao F. Single-cell RNA sequencing reveals the important role of Dcaf17 in spermatogenesis of golden hamsters†. Biol Reprod 2024; 111:1326-1340. [PMID: 39239833 DOI: 10.1093/biolre/ioae132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 07/10/2024] [Accepted: 09/05/2024] [Indexed: 09/07/2024] Open
Abstract
Dcaf17, also known as DDB1- and CUL4-associated factor 17, is a member of the DCAF family and acts as the receptor for the CRL4 ubiquitin E3 ligase complex. Several previous studies have reported that mutations in Dcaf17 cause Woodhouse-Sakati syndrome, which results in oligoasthenoteratozoospermia and male infertility. As a model to explore the role of Dcaf17 in the male reproductive system, we created Dcaf17-deficient male golden hamsters using CRISPR-Cas9 technology; the results of which demonstrate that deletion of Dcaf17 led to abnormal spermatogenesis and infertility. To uncover the underlying molecular mechanisms involved, we conducted single cell Ribonucleic Acid sequencing analysis to evaluate the effect of Dcaf17 deficiency on transcriptional levels in spermatogenic cells during various stages of spermatogenesis. These data emphasize the significant regulatory role played by Dcaf17 in early spermatogenic cells, with many biological processes being affected, including spermatogenesis and protein degradation. Dysregulation of genes associated with these functions ultimately leads to abnormalities. In summary, our findings highlight the critical function of Dcaf17 in spermatogenesis and clarify the specific stage at which Dcaf17 exerts its effects, while simultaneously providing a novel animal model for the study of Dcaf17.
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Affiliation(s)
- Rongzhu Ma
- State Key Laboratory of Reproductive Medicine and Offspring Health, Clinical Center of Reproductive Medicine, First Affiliated Hospital, Nanjing Medical University, Jiangsu Province, China
| | - Shuang Liang
- State Key Laboratory of Reproductive Medicine and Offspring Health, Jiangsu Animal Experimental Center of Medicine and Pharmacy, Department of Cell Biology, Animal Core facility, Key Laboratory of Model Animal, Collaborative Innovation Center for Cardiovascular Disease Translational Medicine, National Vaccine Innovation Platform, Nanjing Medical University, Nanjing China
| | - Wentao Zeng
- State Key Laboratory of Reproductive Medicine and Offspring Health, Jiangsu Animal Experimental Center of Medicine and Pharmacy, Department of Cell Biology, Animal Core facility, Key Laboratory of Model Animal, Collaborative Innovation Center for Cardiovascular Disease Translational Medicine, National Vaccine Innovation Platform, Nanjing Medical University, Nanjing China
| | - Jianmin Li
- State Key Laboratory of Reproductive Medicine and Offspring Health, Jiangsu Animal Experimental Center of Medicine and Pharmacy, Department of Cell Biology, Animal Core facility, Key Laboratory of Model Animal, Collaborative Innovation Center for Cardiovascular Disease Translational Medicine, National Vaccine Innovation Platform, Nanjing Medical University, Nanjing China
| | - Yana Lai
- State Key Laboratory of Reproductive Medicine and Offspring Health, Jiangsu Animal Experimental Center of Medicine and Pharmacy, Department of Cell Biology, Animal Core facility, Key Laboratory of Model Animal, Collaborative Innovation Center for Cardiovascular Disease Translational Medicine, National Vaccine Innovation Platform, Nanjing Medical University, Nanjing China
| | - Xiaoyu Yang
- State Key Laboratory of Reproductive Medicine and Offspring Health, Clinical Center of Reproductive Medicine, First Affiliated Hospital, Nanjing Medical University, Jiangsu Province, China
| | - Feiyang Diao
- State Key Laboratory of Reproductive Medicine and Offspring Health, Clinical Center of Reproductive Medicine, First Affiliated Hospital, Nanjing Medical University, Jiangsu Province, China
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15
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Ambrozkiewicz MC, Lorenz S. Understanding ubiquitination in neurodevelopment by integrating insights across space and time. Nat Struct Mol Biol 2024:10.1038/s41594-024-01422-3. [PMID: 39633012 DOI: 10.1038/s41594-024-01422-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Accepted: 10/08/2024] [Indexed: 12/07/2024]
Abstract
Ubiquitination regulates a myriad of eukaryotic signaling cascades by modifying substrate proteins, thereby determining their functions and fates. In this perspective, we discuss current challenges in investigating the ubiquitin system in the developing brain. We foster the concept that ubiquitination pathways are spatiotemporally regulated and tightly intertwined with molecular and cellular transitions during neurogenesis and neural circuit assembly. Focusing on the neurologically highly relevant class of homologous to E6AP C-terminus (HECT) ubiquitin ligases, we propose cross-disciplinary translational approaches bridging state-of-the-art cell biology, proteomics, biochemistry, structural biology and neuroscience to dissect ubiquitination in neurodevelopment and its specific perturbations in brain diseases. We highlight that a comprehensive understanding of ubiquitin signaling in the brain may reveal new horizons in basic neuroscience and clinical applications.
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Affiliation(s)
- Mateusz C Ambrozkiewicz
- Institute of Cell Biology and Neurobiology, Research Group 'Proteostasis', Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Charitéplatz 1, Berlin, Germany.
| | - Sonja Lorenz
- Max Planck Institute for Multidisciplinary Sciences, Research Group 'Ubiquitin Signaling Specificity', Am Fassberg 11, Göttingen, Germany.
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16
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Pechmann S. Heterogeneous folding landscapes and predetermined breaking points within a protein family. Protein Sci 2024; 33:e5205. [PMID: 39555686 PMCID: PMC11571096 DOI: 10.1002/pro.5205] [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: 07/30/2024] [Revised: 10/16/2024] [Accepted: 10/17/2024] [Indexed: 11/19/2024]
Abstract
The accurate prediction of protein structures with artificial intelligence has been a spectacular success. Yet, how proteins fold into their native structures inside the cell remains incompletely understood. Of particular interest is to rationalize how proteins interact with the protein homeostasis network, an organism specific set of protein folding and quality control enzymes. Failure of protein homeostasis leads to widespread misfolding and aggregation, and thus neurodegeneration. Here, I present a comparative analysis of the folding of 16 single-domain proteins from the same organism across a protein family, the Saccharomyces cerevisiae small GTPases. Using computational modeling to directly probe protein folding dynamics, this work shows how near identical structures from the same folding environment can exhibit heterogeneous folding landscapes. Remarkably, yeast small GTPases are found to unfold along different pathways either via the N- or C-terminus initiated by structure-encoded predetermined breaking points. Degrons as recognition signals for ubiquitin-dependent degradation were systematically absent from the initial unfolding sites, as if to protect from too rapid degradation upon spontaneous unfolding or before completion of the folding. The presented results highlight a direct coordination of folding pathway and protein homeostasis interaction signals across a protein family. A deeper understanding of the interdependence of proteins with their folding environment will help to rationalize and combat diseases linked to protein misfolding and dysregulation. More generally, this work underlines the importance of understanding protein folding in the cellular context, and highlights valuable constraints towards a systems-level understanding of protein homeostasis.
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17
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Sun F, Hamada N, Montes C, Li Y, Meier ND, Walley JW, Dinesh‐Kumar SP, Shabek N. TurboID-based proteomic profiling reveals proxitome of ASK1 and CUL1 of the SCF ubiquitin ligase in plants. THE NEW PHYTOLOGIST 2024; 244:2127-2136. [PMID: 39081016 PMCID: PMC11579432 DOI: 10.1111/nph.20014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2024] [Accepted: 07/14/2024] [Indexed: 11/22/2024]
Affiliation(s)
- Fuai Sun
- Department of Plant Biology, College of Biological SciencesUniversity of California, DavisDavisCA95616USA
| | - Natalie Hamada
- Department of Plant Biology, College of Biological SciencesUniversity of California, DavisDavisCA95616USA
| | - Christian Montes
- Department of Plant Pathology, Entomology, and MicrobiologyIowa State UniversityAmesIA50011USA
| | - Yuanyuan Li
- Department of Plant Biology, College of Biological SciencesUniversity of California, DavisDavisCA95616USA
| | - Nathan D. Meier
- Department of Plant Biology, College of Biological SciencesUniversity of California, DavisDavisCA95616USA
| | - Justin W. Walley
- Department of Plant Pathology, Entomology, and MicrobiologyIowa State UniversityAmesIA50011USA
| | - Savithramma P. Dinesh‐Kumar
- Department of Plant Biology, College of Biological SciencesUniversity of California, DavisDavisCA95616USA
- The Genome CenterUniversity of California, DavisDavisCA95616USA
| | - Nitzan Shabek
- Department of Plant Biology, College of Biological SciencesUniversity of California, DavisDavisCA95616USA
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18
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Lim CJ, Seo HJ, Yin H, Cho NH, Yang HW, Park TH, Kim YJ, Kim WT, Seo DH. MpPUB9, a U-box E3 ubiquitin ligase, acts as a positive regulator by promoting the turnover of MpEXO70.1 under high salinity in Marchantia polymorpha. THE NEW PHYTOLOGIST 2024; 244:2343-2363. [PMID: 39387122 PMCID: PMC11579444 DOI: 10.1111/nph.20169] [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: 01/19/2024] [Accepted: 09/09/2024] [Indexed: 10/12/2024]
Abstract
Marchantia polymorpha, occupying a basal position in the monophyletic assemblage of land plants, displays a notable expansion of plant U-box (PUB) proteins compared with those in animals. We elucidated the roles of MpPUB9 in regulating salt stress tolerance in M. polymorpha. MpPUB9 expression was rapidly induced by high salinity and dehydration. MpPUB9 possessed an intact U-box domain in the N-terminus. MpPUB9-Citrine localized to punctate structures and was peripherally associated with microsomal membranes. Phenotypic analyses demonstrate that the hyponastic and epinastic thallus growth phenotypes, which were induced by the overexpression and suppression of MpPUB9, may provoke salt stress-resistant and -susceptible phenotypes, respectively. MpPUB9 was also found to directly interact with the exocyst protein MpEXO70.1, leading to its ubiquitination. Under high-salinity conditions, though the stability of MpPUB9 was dramatically increased, MpEXO70.1 showed slightly faster turnover rates. Transcriptome analyses showed that salt treatment and the overexpression of MpPUB9 co-upregulated the genes related to the modulation of H2O2 and cell wall organization. Overall, our results suggest that MpPUB9 plays a crucial role in the positive regulation of salt stress tolerance, resulting from its interaction with MpEXO70.1 and modulating turnover of the protein under high-salt conditions via the coordination of UPS with autophagy.
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Affiliation(s)
- Cheol Jin Lim
- Department of Systems Biology and Division of Life ScienceYonsei UniversitySeoul03722Korea
- Institute of Life Science and BiotechnologyYonsei UniversitySeoul03722Korea
| | - Hyeon Ji Seo
- Department of Systems Biology and Division of Life ScienceYonsei UniversitySeoul03722Korea
- Institute of Life Science and BiotechnologyYonsei UniversitySeoul03722Korea
| | - Haijing Yin
- Department of Systems Biology and Division of Life ScienceYonsei UniversitySeoul03722Korea
- Institute of Life Science and BiotechnologyYonsei UniversitySeoul03722Korea
| | - Na Hyun Cho
- Department of Systems Biology and Division of Life ScienceYonsei UniversitySeoul03722Korea
- Institute of Life Science and BiotechnologyYonsei UniversitySeoul03722Korea
| | - Hee Woong Yang
- Department of Systems Biology and Division of Life ScienceYonsei UniversitySeoul03722Korea
- Institute of Life Science and BiotechnologyYonsei UniversitySeoul03722Korea
| | - Tae Hyeon Park
- Department of Systems Biology and Division of Life ScienceYonsei UniversitySeoul03722Korea
- Institute of Life Science and BiotechnologyYonsei UniversitySeoul03722Korea
| | - Yun Ju Kim
- Department of Systems Biology and Division of Life ScienceYonsei UniversitySeoul03722Korea
- Institute of Life Science and BiotechnologyYonsei UniversitySeoul03722Korea
| | - Woo Taek Kim
- Department of Systems Biology and Division of Life ScienceYonsei UniversitySeoul03722Korea
- Institute of Life Science and BiotechnologyYonsei UniversitySeoul03722Korea
| | - Dong Hye Seo
- Department of Systems Biology and Division of Life ScienceYonsei UniversitySeoul03722Korea
- Institute of Life Science and BiotechnologyYonsei UniversitySeoul03722Korea
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19
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Swarnkar A, Leidner F, Rout AK, Ainatzi S, Schmidt CC, Becker S, Urlaub H, Griesinger C, Grubmüller H, Stein A. Determinants of chemoselectivity in ubiquitination by the J2 family of ubiquitin-conjugating enzymes. EMBO J 2024; 43:6705-6739. [PMID: 39533056 DOI: 10.1038/s44318-024-00301-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2024] [Revised: 10/29/2024] [Accepted: 10/31/2024] [Indexed: 11/16/2024] Open
Abstract
Ubiquitin-conjugating enzymes (E2) play a crucial role in the attachment of ubiquitin to proteins. Together with ubiquitin ligases (E3), they catalyze the transfer of ubiquitin (Ub) onto lysines with high chemoselectivity. A subfamily of E2s, including yeast Ubc6 and human Ube2J2, also mediates noncanonical modification of serines, but the structural determinants for this chemical versatility remain unknown. Using a combination of X-ray crystallography, molecular dynamics (MD) simulations, and reconstitution approaches, we have uncovered a two-layered mechanism that underlies this unique reactivity. A rearrangement of the Ubc6/Ube2J2 active site enhances the reactivity of the E2-Ub thioester, facilitating attack by weaker nucleophiles. Moreover, a conserved histidine in Ubc6/Ube2J2 activates a substrate serine by general base catalysis. Binding of RING-type E3 ligases further increases the serine selectivity inherent to Ubc6/Ube2J2, via an allosteric mechanism that requires specific positioning of the ubiquitin tail at the E2 active site. Our results elucidate how subtle structural modifications to the highly conserved E2 fold yield distinct enzymatic activity.
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Affiliation(s)
- Anuruti Swarnkar
- Research Group Membrane Protein Biochemistry, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077, Göttingen, Germany
| | - Florian Leidner
- Department of Theoretical and Computational Biophysics, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077, Göttingen, Germany
| | - Ashok K Rout
- Department of NMR-based Structural Biology, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077, Göttingen, Germany
- Institut für Chemie und Metabolomics, Universität zu Lübeck, 23562, Lübeck, Germany
| | - Sofia Ainatzi
- Research Group Bioanalytical Mass Spectrometry, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077, Göttingen, Germany
| | - Claudia C Schmidt
- Research Group Membrane Protein Biochemistry, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077, Göttingen, Germany
- ETH Zürich, Otto-Stern-Weg 3, 8093, Zürich, Switzerland
| | - Stefan Becker
- Department of NMR-based Structural Biology, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077, Göttingen, Germany
| | - Henning Urlaub
- Research Group Bioanalytical Mass Spectrometry, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077, Göttingen, Germany
| | - Christian Griesinger
- Department of NMR-based Structural Biology, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077, Göttingen, Germany
| | - Helmut Grubmüller
- Department of Theoretical and Computational Biophysics, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077, Göttingen, Germany
| | - Alexander Stein
- Research Group Membrane Protein Biochemistry, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077, Göttingen, Germany.
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20
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Gupta D, Shukla R, Mishra K. SUMO-targeted Ubiquitin Ligases as crucial mediators of protein homeostasis in Candida glabrata. PLoS Pathog 2024; 20:e1012742. [PMID: 39642165 DOI: 10.1371/journal.ppat.1012742] [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: 08/09/2024] [Revised: 12/18/2024] [Accepted: 11/11/2024] [Indexed: 12/08/2024] Open
Abstract
Candida glabrata is an opportunistic human pathogen, capable of causing severe systemic infections that are often resistant to standard antifungal treatments. To understand the importance of protein SUMOylation in the physiology and pathogenesis of C. glabrata, we earlier identified the components of SUMOylation pathway and demonstrated that the deSUMOylase CgUlp2 is essential for pathogenesis. In this work we show that the CgUlp2 is essential to maintain protein homeostasis via the SUMO-targeted ubiquitin ligase pathway. The dual loss of deSUMOylase and specific ubiquitin ligase, CgSlx8, results in heightened protein degradation, rendering the cells vulnerable to various stressors. This degradation affects crucial processes such as purine biosynthesis and compromises mitochondrial function in the mutants. Importantly, the absence of these ubiquitin ligases impedes the proliferation of C. glabrata in macrophages. These findings underscore the significance of SUMOylation and SUMO-mediated protein homeostasis as pivotal regulators of C. glabrata physiology and capacity to survive in host cells. Understanding these mechanisms could pave the way for the development of effective antifungal treatments.
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Affiliation(s)
- Dipika Gupta
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Renu Shukla
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Krishnaveni Mishra
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, India
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21
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Guo Z, Liu H, Zheng S, Qi K, Xie Z, Wang X, Hong Y, Cui Y, Liu X, Gu C, Zhang SL. The transcription factor PbbHLH164 is destabilized by PbRAD23C/D.1 and mediates ethylene biosynthesis during pear fruit ripening. J Adv Res 2024; 66:119-131. [PMID: 38190939 DOI: 10.1016/j.jare.2024.01.004] [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: 10/09/2023] [Revised: 12/17/2023] [Accepted: 01/05/2024] [Indexed: 01/10/2024] Open
Abstract
The phytohormone ethylene plays an important role in climacteric fruit ripening. However, the knowledge on molecular regulation of ethylene biosynthesis remains limited in pear fruit. Herein, a new basic helix-loop-helix transcription factor, PbbHLH164, was identified based on the transcriptome analysis of different developing and ripening fruits of two pear cultivars 'Sucui No. 1' and 'Cuiguan'. PbbHLH164 was more highly expressed in ripening fruit than in developing fruit and positively correlated with ethylene production in both cultivars. PbbHLH164 could directly bind to the promoter of 1-aminocyclopropane-1-carboxylate synthase, PbACS1b, to enhance the expression, leading to the increase of ethylene production and the acceleration of fruit ripening. Interestingly, PbbHLH164 physically interacted with an ubiquitin-like/ubiquitin-associated protein PbRAD23C/D.1, and the interaction of PbbHLH164 with PbRAD23C/D.1 attenuated the function of PbbHLH164 in enhancing the activity of the PbACS1b promoter. Notably, PbRAD23C/D.1 was involved in the degradation of PbbHLH164, and this degradation was inhibited by an ubiquitin proteasome inhibitor MG132. Different from PbbHLH164, PbRAD23C/D.1 was more highly expressed in developing fruit than in ripening fruit of both cultivars. These results suggest that the increase of ethylene production during pear fruit ripening results from the up-regulated expression of PbbHLH164 and the down-regulated expression of PbRAD23C/D.1. This information provided new insights into the molecular regulation of ethylene biosynthesis during fruit ripening.
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Affiliation(s)
- ZhiHua Guo
- Jiangsu Engineering Research Centre for Pear, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Hong Liu
- Jiangsu Engineering Research Centre for Pear, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - SiQi Zheng
- Jiangsu Engineering Research Centre for Pear, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - KaiJie Qi
- Jiangsu Engineering Research Centre for Pear, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - ZhiHua Xie
- Jiangsu Engineering Research Centre for Pear, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - XuePing Wang
- Jiangsu Engineering Research Centre for Pear, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - YeMei Hong
- Jiangsu Engineering Research Centre for Pear, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - YanBo Cui
- Nanjing Ningcui Biological Seed Company Limited, Nanjing, Jiangsu, China
| | - Xiaoxiang Liu
- Jiangsu Engineering Research Centre for Pear, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Chao Gu
- Jiangsu Engineering Research Centre for Pear, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China.
| | - Shao-Ling Zhang
- Jiangsu Engineering Research Centre for Pear, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China.
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22
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Zhu Q, Zhou H, Xie F. Regulation of ovarian cancer by protein post-translational modifications. Front Oncol 2024; 14:1437953. [PMID: 39678497 PMCID: PMC11638062 DOI: 10.3389/fonc.2024.1437953] [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: 05/24/2024] [Accepted: 11/12/2024] [Indexed: 12/17/2024] Open
Abstract
Ovarian cancer is one of the predominant gynecologic malignancies worldwide, ranking as the fifth leading cause of cancer-induced mortality among women globally. Post-translational modifications (PTMs) refer to the enzyme-catalyzed attachment of functional groups to proteins, thereby inducing structural and functional alterations. Recent evidence suggests that PTMs play multifaceted roles in the pathogenesis of ovarian cancer, influencing processes such as cell cycle, metabolism reprogramming, chemoresistance, and immune responses against cancer. Accordingly, a comprehensive understanding of the diverse PTMs in ovarian cancer is imperative for decoding the complex molecular mechanisms that drive cancer progression. This review discusses the latest developments in the study of protein PTMs in ovarian cancer and introduces pharmacological approaches that target these modifications as therapeutic strategies.
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Affiliation(s)
- Qiugang Zhu
- Department of Laboratory Medicine, Shangyu People’s Hospital of Shaoxing, Shaoxing University, Shaoxing, China
| | - Huimin Zhou
- Department of Laboratory Medicine, Wuxi Ninth People’s Hospital Affiliated to Soochow University, Wuxi, China
| | - Feiting Xie
- Zhejiang Key Laboratory of Precision Diagnosis and Therapy for Major Gynecological Diseases, Women’s Hospital, Zhejiang University School of Medicine, Hangzhou, China
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23
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Shi X, Shen L, Chen S, Liu M, Wang J, Wen X, Liu W, Mao L, Ding Y, Yu L, Xu J. Swine RNF5 positively regulates the antiviral activity of IFITM1 by mediating the degradation of ABHD16A. J Virol 2024:e0127724. [PMID: 39601593 DOI: 10.1128/jvi.01277-24] [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: 07/22/2024] [Accepted: 10/25/2024] [Indexed: 11/29/2024] Open
Abstract
Interferon-inducible transmembrane (IFITM) proteins are broad-spectrum antiviral factors that confer cellular resistance to virus invasion. α/β-Hydrolase domain-containing 16A (ABHD16A) has recently been identified as a novel depalmitoylase that can inhibit the antiviral activity of IFITM proteins by catalyzing the depalmitoyl reaction; this pattern may be crucial for the host to avoid damage caused by excessive immune response. However, it remains largely elusive about how host cells regulate the activity of ABHD16A. In the present study, we performed the AlphaFold2-based protein-protein interaction prediction and identified swine E3 ubiquitin ligase ring finger protein 5 (sRNF5) as a sABHD16A-interacting protein and negatively regulated the stability of sABHD16A. Using immunofluorescence and co-immunoprecipitation techniques, we uncovered that sRNF5 targeted sABHD16A for ubiquitination and degradation via the proteasomal pathway at residues K3 and K452. Furthermore, sABHD16A catalyzed the depalmitoylation of sIFITM1, which obstructed the antiviral function of sIFITM1, while sRNF5 caused ubiquitination of sABHD16A, which attenuated the depalmitoylation effect on sIFITM1, and consequently restored the antiviral activity of sIFITM1. Collectively, our findings demonstrate for the first time that sRNF5 positively regulates the antiviral function of sIFITM1 by mediating the degradation of sABHD16A, which expands the biological functions of RNF5 and ABHD16A in immune regulation. Moreover, our work highlights the well-designed interplay between RNF5, ABHD16A, and IFITM, which balances antiviral immune responses to avoid the disorders induced by excessive immune response. IMPORTANCE Interferon and interferon-stimulated genes play significant and protective roles in the host's defense against viral infection. IFITM family proteins, which can be strongly induced by interferon, have been identified as the first line of defense to prevent invasion of various viruses. Further analysis reveals the antiviral activity of IFITMs depends on palmitoylation/depalmitoylation. Recently, we reported that ABHD16A, as the first depalmitoylase of IFITMs, negatively regulated the antiviral activity of IFITMs. However, these raise crucial questions: how ABHD16A is regulated and remained in a balanced manner? Here, we show that swine RNF5 attenuates the negative regulation of sIFITM1 against virus invasion by modifying sABHD16A through ubiquitination and guiding sABHD16A for degradation. Thus, sRNF5-sABHD16A interplay plays an indispensable role in regulating immune response and avoiding the disorders induced by elevated interferon levels. Overall, our findings extend the upstream subtle regulatory molecular mechanism of IFITMs and provide potential targets for viral disease therapy.
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Affiliation(s)
- Xuemeng Shi
- College of Life Science, Zhengdong New District Longzi Lake Campus, Henan Agricultural University, Zhengzhou, Henan, China
| | - Lingyi Shen
- College of Life Science, Zhengdong New District Longzi Lake Campus, Henan Agricultural University, Zhengzhou, Henan, China
| | - Shuaiwu Chen
- College of Life Science, Zhengdong New District Longzi Lake Campus, Henan Agricultural University, Zhengzhou, Henan, China
| | - Mingyang Liu
- College of Life Science, Zhengdong New District Longzi Lake Campus, Henan Agricultural University, Zhengzhou, Henan, China
| | - Jingyi Wang
- College of Life Science, Zhengdong New District Longzi Lake Campus, Henan Agricultural University, Zhengzhou, Henan, China
| | - Xin Wen
- College of Life Science, Zhengdong New District Longzi Lake Campus, Henan Agricultural University, Zhengzhou, Henan, China
| | - Wei Liu
- College of Life Science, Zhengdong New District Longzi Lake Campus, Henan Agricultural University, Zhengzhou, Henan, China
| | - Lin Mao
- College of Life Science, Zhengdong New District Longzi Lake Campus, Henan Agricultural University, Zhengzhou, Henan, China
| | - Yunyun Ding
- College of Life Science, Zhengdong New District Longzi Lake Campus, Henan Agricultural University, Zhengzhou, Henan, China
| | - Li Yu
- College of Life Science, Zhengdong New District Longzi Lake Campus, Henan Agricultural University, Zhengzhou, Henan, China
| | - Jun Xu
- College of Life Science, Zhengdong New District Longzi Lake Campus, Henan Agricultural University, Zhengzhou, Henan, China
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24
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Mabanglo MF, Wilson B, Noureldin M, Kimani SW, Mamai A, Krausser C, González-Álvarez H, Srivastava S, Mohammed M, Hoffer L, Chan M, Avrumutsoae J, Li ASM, Hajian T, Tucker S, Green S, Szewczyk M, Barsyte-Lovejoy D, Santhakumar V, Ackloo S, Loppnau P, Li Y, Seitova A, Kiyota T, Wang JG, Privé GG, Kuntz DA, Patel B, Rathod V, Vala A, Rout B, Aman A, Poda G, Uehling D, Ramnauth J, Halabelian L, Marcellus R, Al-Awar R, Vedadi M. Crystal structures of DCAF1-PROTAC-WDR5 ternary complexes provide insight into DCAF1 substrate specificity. Nat Commun 2024; 15:10165. [PMID: 39580491 PMCID: PMC11585590 DOI: 10.1038/s41467-024-54500-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Accepted: 11/12/2024] [Indexed: 11/25/2024] Open
Abstract
Proteolysis-targeting chimeras (PROTACs) have been explored for the degradation of drug targets for more than two decades. However, only a handful of E3 ligase substrate receptors have been efficiently used. Downregulation and mutation of these receptors would reduce the effectiveness of such PROTACs. We recently developed potent ligands for DCAF1, a substrate receptor of EDVP and CUL4 E3 ligases. Here, we focus on DCAF1 toward the development of PROTACs for WDR5, a drug target in various cancers. We report four DCAF1-based PROTACs with endogenous and exogenous WDR5 degradation effects and high-resolution crystal structures of the ternary complexes of DCAF1-PROTAC-WDR5. The structures reveal detailed insights into the interaction of DCAF1 with various WDR5-PROTACs, indicating a significant role of DCAF1 loops in providing needed surface plasticity, and reflecting the mechanism by which DCAF1 functions as a substrate receptor for E3 ligases with diverse sets of substrates.
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Affiliation(s)
- Mark F Mabanglo
- Drug Discovery Program, Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Brian Wilson
- Drug Discovery Program, Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Mahmoud Noureldin
- Drug Discovery Program, Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Serah W Kimani
- Structural Genomics Consortium, University of Toronto, Toronto, ON, Canada
| | - Ahmed Mamai
- Drug Discovery Program, Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Chiara Krausser
- Drug Discovery Program, Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Héctor González-Álvarez
- Drug Discovery Program, Ontario Institute for Cancer Research, Toronto, ON, Canada
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON, Canada
| | - Smriti Srivastava
- Drug Discovery Program, Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Mohammed Mohammed
- Drug Discovery Program, Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Laurent Hoffer
- Drug Discovery Program, Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Manuel Chan
- Drug Discovery Program, Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Jamie Avrumutsoae
- Drug Discovery Program, Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Alice Shi Ming Li
- Drug Discovery Program, Ontario Institute for Cancer Research, Toronto, ON, Canada
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON, Canada
| | - Taraneh Hajian
- Drug Discovery Program, Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Sarah Tucker
- Drug Discovery Program, Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Stuart Green
- Structural Genomics Consortium, University of Toronto, Toronto, ON, Canada
| | - Magdalena Szewczyk
- Structural Genomics Consortium, University of Toronto, Toronto, ON, Canada
| | - Dalia Barsyte-Lovejoy
- Structural Genomics Consortium, University of Toronto, Toronto, ON, Canada
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON, Canada
| | | | - Suzanne Ackloo
- Structural Genomics Consortium, University of Toronto, Toronto, ON, Canada
| | - Peter Loppnau
- Structural Genomics Consortium, University of Toronto, Toronto, ON, Canada
| | - Yanjun Li
- Structural Genomics Consortium, University of Toronto, Toronto, ON, Canada
| | - Almagul Seitova
- Structural Genomics Consortium, University of Toronto, Toronto, ON, Canada
| | - Taira Kiyota
- Drug Discovery Program, Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Jue George Wang
- Drug Discovery Program, Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Gilbert G Privé
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Douglas A Kuntz
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Bhashant Patel
- Piramal Discovery Solutions, Pharmaceutical Special Economic Zone, Ahmedabad, Gujarat, India
| | - Vaibhavi Rathod
- Piramal Discovery Solutions, Pharmaceutical Special Economic Zone, Ahmedabad, Gujarat, India
| | - Anand Vala
- Piramal Discovery Solutions, Pharmaceutical Special Economic Zone, Ahmedabad, Gujarat, India
| | - Bhimsen Rout
- Piramal Discovery Solutions, Pharmaceutical Special Economic Zone, Ahmedabad, Gujarat, India
| | - Ahmed Aman
- Drug Discovery Program, Ontario Institute for Cancer Research, Toronto, ON, Canada
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON, Canada
| | - Gennady Poda
- Drug Discovery Program, Ontario Institute for Cancer Research, Toronto, ON, Canada
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, ON, Canada
| | - David Uehling
- Drug Discovery Program, Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Jailall Ramnauth
- Drug Discovery Program, Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Levon Halabelian
- Structural Genomics Consortium, University of Toronto, Toronto, ON, Canada
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON, Canada
| | - Richard Marcellus
- Drug Discovery Program, Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Rima Al-Awar
- Drug Discovery Program, Ontario Institute for Cancer Research, Toronto, ON, Canada.
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON, Canada.
- Department of Chemistry, University of Toronto, Toronto, ON, Canada.
| | - Masoud Vedadi
- Drug Discovery Program, Ontario Institute for Cancer Research, Toronto, ON, Canada.
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON, Canada.
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25
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Hao W, Lin F, Kong W, Shi H, Dong H, Guan Z, Liu G, Wang X, Wang L, Liu M, Jiang Y. Significant role and the underly mechanism of cullin-1 in chronic obstructive pulmonary disease. Open Med (Wars) 2024; 19:20241070. [PMID: 39588388 PMCID: PMC11587924 DOI: 10.1515/med-2024-1070] [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: 05/15/2024] [Revised: 09/14/2024] [Accepted: 09/28/2024] [Indexed: 11/27/2024] Open
Abstract
Background This study investigated the role and mechanisms of cullin-1 (CUL1) in chronic obstructive pulmonary disease (COPD). Methods Cigarette smoke extract (CSE)-treated mouse pulmonary microvascular endothelial cells (mPMECs) and cigarette smoke inhalation (CSI)-stimulated mice were used to construct in vitro and in vivo COPD models, respectively. CUL1 expression was assessed using reverse transcriptase-quantitative polymerase chain reaction, Western blotting, and immunohistochemistry. The 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide assay and flow cytometry were used to detect cell viability and apoptosis, respectively. We conducted an enzyme-linked immunosorbent assay on mPMECs and bronchoalveolar lavage fluid (BALF) to detect inflammatory factors. Reactive oxygen species, malondialdehyde, and superoxide dismutase were detected using the corresponding kits. The histological characteristics of the lung tissues were determined by hematoxylin and eosin staining. Results CUL1 expression was downregulated in COPD. CUL1 overexpression significantly promoted cell viability, reduced cell apoptosis, and inhibited inflammatory responses and oxidative stress in CSE-treated mPMECs. These changes were reversed by the p53 agonist nutlin-3. In addition, CUL1 overexpression significantly relieved COPD in mice, as confirmed by the reduced secretion of inflammatory factors in BALF, inhibited oxidative stress response, and improved lung function. Conclusion CUL1 plays a protective role in CSE-treated mPMECs and CSI-stimulated mice by inhibiting the p53 signaling pathway.
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Affiliation(s)
- Wenbo Hao
- Cardiothoracic Surgery, The Third Affiliated Hospital of Qiqihar Medical University, Qiqihar, 161006, China
| | - Fei Lin
- Endocrinology, The Third Affiliated Hospital of Qiqihar Medical University, Qiqihar, 161006, China
| | - Weili Kong
- Department of Respiratory and Critical Care Medicine, The Third Affiliated Hospital of Qiqihar Medical University, Qiqihar, 161006, China
| | - Hanbing Shi
- Department of Respiratory and Critical Care Medicine, The Third Affiliated Hospital of Qiqihar Medical University, Qiqihar, 161006, China
| | - Haiying Dong
- Pathology and Pathophysiology, Qiqihar Medical University, Qiqihar, 161006, China
| | - Zhanjiang Guan
- Intensive Care Unit, The Third Affiliated Hospital of Qiqihar Medical University, Qiqihar, 161006, China
| | - Guohua Liu
- Department of Respiratory and Critical Care Medicine, The Third Affiliated Hospital of Qiqihar Medical University, Qiqihar, 161006, China
| | - Xiao Wang
- Department of Respiratory and Critical Care Medicine, The Third Affiliated Hospital of Qiqihar Medical University, Qiqihar, 161006, China
| | - Li Wang
- Radiology Imaging Diagnosis Center, The Third Affiliated Hospital of Qiqihar Medical University, Qiqihar, 161006, China
| | - Moran Liu
- Test Center, The Third Affiliated Hospital of Qiqihar Medical University, Qiqihar, 161006, China
| | - Yunfei Jiang
- Department of Respiratory and Critical Care Medicine, The Third Affiliated Hospital of Qiqihar Medical University, No. 27 Taishun Street, Tiefeng District, Qiqihar, 161006, China
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26
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Sun L, Zhang H, Li Y. The E3 ligase HUWE1 interacts with ubiquitin non-covalently via key residues in the HECT domain. FEBS Lett 2024. [PMID: 39543712 DOI: 10.1002/1873-3468.15050] [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: 09/12/2024] [Revised: 10/06/2024] [Accepted: 10/15/2024] [Indexed: 11/17/2024]
Abstract
HUWE1, a HECT E3 ligase, is critical for processes like protein degradation and tumor development. Contrary to previous findings which suggested minimal non-covalent interactions between the HUWE1 HECT domain and ubiquitin, we identified a non-covalent interaction between the HUWE1 HECT N-lobe and ubiquitin using NMR spectroscopy, revealing a conserved ubiquitin-binding mode shared across HECT E3 ligases. Molecular dynamics simulations not only confirmed the stability of this interaction but also uncovered conformational changes in key residues, which likely influence binding affinity. Additionally, we highlighted the roles of both conserved and unique residues in ubiquitin binding. These findings advance our understanding of the interactions between the HUWE1 HECT domain and ubiquitin, and highlight potential targets for therapeutic intervention in the ubiquitin-proteasome pathway.
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Affiliation(s)
- Li Sun
- Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College and State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Huazhong University of Science and Technology, Wuhan, China
| | - Haoran Zhang
- Department of Infectious Disease, Tongji Hospital, Tongji Medical College and State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Huazhong University of Science and Technology, Wuhan, China
| | - Yan Li
- Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College and State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Huazhong University of Science and Technology, Wuhan, China
- Department of Pediatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Hubei Key Laboratory of Drug Target Research and Pharmacodynamic Evaluation, Wuhan, China
- Tongji-Rongcheng Center for Biomedicine, Huazhong University of Science and Technology, Wuhan, China
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27
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Xu Z, Lei Z, Peng S, Fu X, Xu Y, Pan G. Dysregulation of deubiquitinases in gastric cancer progression. Front Oncol 2024; 14:1456710. [PMID: 39605891 PMCID: PMC11598704 DOI: 10.3389/fonc.2024.1456710] [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: 06/29/2024] [Accepted: 10/24/2024] [Indexed: 11/29/2024] Open
Abstract
Gastric cancer (GC), characterized by a high incidence rate, poses significant clinical challenges owing to its poor prognosis despite advancements in diagnostic and therapeutic approaches. Therefore, a comprehensive understanding of the molecular mechanisms driving GC progression is crucial for identifying predictive markers and defining treatment targets. Deubiquitinating enzymes (DUBs), also called deubiquitinases, function as reverse transcriptases within the ubiquitin-proteasome system to counteract protein degradation. Recent findings suggest that DUB dysregulation could be a crucial factor in GC pathogenesis. In this review, we examined recent research findings on DUBs in the context of GC, elucidating their molecular characteristics, categorizations, and roles while also exploring the potential mechanisms underlying their dysregulation in GC. Furthermore, we assessed the therapeutic efficacy of DUB inhibitors in treating malignancies and evaluated the prevalence of aberrant DUB expression in GC.
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Affiliation(s)
| | | | | | | | | | - Guoqing Pan
- First Affiliated Hospital of Kunming Medical University, Department of Pathology, Kunming, China
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28
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Shen H, Kou Q, Shao L, Zhang J, Li F. E3 ubiquitin ligase HECW2: a promising target for tumour therapy. Cancer Cell Int 2024; 24:374. [PMID: 39529070 PMCID: PMC11556196 DOI: 10.1186/s12935-024-03563-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 11/06/2024] [Indexed: 11/16/2024] Open
Abstract
Ubiquitination is a prevalent post-translational modification that plays a crucial role in a wide range of pathophysiological processes, including cell proliferation, apoptosis, autophagy, immune response, and DNA damage repair. Among the enzymes involved in ubiquitination, E3 ubiquitin ligases are particularly significant, serving as key regulators of numerous diseases, including tumours. This review focuses on HECW2 (HECT, C2, and WW domain-containing E3 ubiquitin protein ligase 2, also known as NEDL2), providing a comprehensive overview of its interactors and its pathological roles in tumorous cancer and other diseases. The insights gained from this review may contribute to the development of novel treatment strategies for various diseases, particularly tumours.
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Affiliation(s)
- Hui Shen
- Medical College of Yan'an University, Yan'an University, Yan'an, 716000, China
| | - Qianrui Kou
- Medical College of Yan'an University, Yan'an University, Yan'an, 716000, China
| | - Linxin Shao
- Medical College of Yan'an University, Yan'an University, Yan'an, 716000, China
| | - Jing Zhang
- Medical College of Yan'an University, Yan'an University, Yan'an, 716000, China.
- Medical Research and Experimental Center, The Second Affiliated Hospital of Xi'an Medical University, Xi'an, Shaanxi Province, 710077, China.
| | - Fang Li
- Medical College of Yan'an University, Yan'an University, Yan'an, 716000, China.
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Huang S, Qin X, Fu S, Hu J, Jiang Z, Hu M, Zhang B, Liu J, Chen Y, Wang M, Liu X, Chen Z, Wang L. STAMBPL1/TRIM21 Balances AXL Stability Impacting Mesenchymal Phenotype and Immune Response in KIRC. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2405083. [PMID: 39527690 DOI: 10.1002/advs.202405083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2024] [Revised: 10/09/2024] [Indexed: 11/16/2024]
Abstract
Kidney renal clear cell carcinoma (KIRC) is recognized as an immunogenic tumor, and immunotherapy is incorporated into its treatment landscape for decades. The acquisition of a tumor mesenchymal phenotype through epithelial-to-mesenchymal transition (EMT) is associated with immune evasion and can contribute to immunotherapy resistance. Here, the involvement of STAM Binding Protein Like 1 (STAMBPL1) is reported in the development of mesenchymal and immune evasion phenotypes in KIRC cells. Mechanistically, STAMBPL1 elevated protein abundance and surface accumulation of TAM Receptor AXL through diminishing the TRIM21-mediated K63-linked ubiquitination and subsequent lysosomal degradation of AXL, thereby enhancing the expression of mesenchymal genes while suppressing chemokines CXCL9/10 and HLA/B/C. In addition, STAMBPL1 enhanced PD-L1 transcription via facilitating nuclear translocation of p65, and knockdown (KD) of STAMBPL1 augmented antitumor effects of PD-1 blockade. Furthermore, STAMBPL1 silencing and the tyrosine kinase inhibitor (TKI) sunitinib also exhibited a synergistic effect on the suppression of KIRC. Collectively, targeting the STAMBPL1/TRIM21/AXL axis can decrease mesenchymal phenotype and potentiate anti-tumor efficacy of cancer therapy.
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Affiliation(s)
- Shiyu Huang
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan, Hubei, 430060, China
- Institute of Urologic Disease, Renmin Hospital of Wuhan University, Wuhan, Hubei, 430060, China
| | - Xuke Qin
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan, Hubei, 430060, China
- Institute of Urologic Disease, Renmin Hospital of Wuhan University, Wuhan, Hubei, 430060, China
| | - Shujie Fu
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan, Hubei, 430060, China
- Institute of Urologic Disease, Renmin Hospital of Wuhan University, Wuhan, Hubei, 430060, China
| | - Juncheng Hu
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan, Hubei, 430060, China
- Institute of Urologic Disease, Renmin Hospital of Wuhan University, Wuhan, Hubei, 430060, China
| | - Zhengyu Jiang
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan, Hubei, 430060, China
- Institute of Urologic Disease, Renmin Hospital of Wuhan University, Wuhan, Hubei, 430060, China
| | - Min Hu
- Department of Cardiology, Renmin Hospital of Wuhan University, Wuhan, Hubei, 430060, China
| | - Banghua Zhang
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan, Hubei, 430060, China
- Institute of Urologic Disease, Renmin Hospital of Wuhan University, Wuhan, Hubei, 430060, China
- Hubei Key Laboratory of Digestive System Disease, Wuhan, 430060, China
| | - Jiachen Liu
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan, Hubei, 430060, China
- Institute of Urologic Disease, Renmin Hospital of Wuhan University, Wuhan, Hubei, 430060, China
- Central Laboratory, Renmin Hospital of Wuhan University, Wuhan, Hubei, 430060, China
| | - Yujie Chen
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan, Hubei, 430060, China
- Institute of Urologic Disease, Renmin Hospital of Wuhan University, Wuhan, Hubei, 430060, China
| | - Minghui Wang
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan, Hubei, 430060, China
- Institute of Urologic Disease, Renmin Hospital of Wuhan University, Wuhan, Hubei, 430060, China
| | - Xiuheng Liu
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan, Hubei, 430060, China
- Institute of Urologic Disease, Renmin Hospital of Wuhan University, Wuhan, Hubei, 430060, China
| | - Zhiyuan Chen
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan, Hubei, 430060, China
- Institute of Urologic Disease, Renmin Hospital of Wuhan University, Wuhan, Hubei, 430060, China
| | - Lei Wang
- Department of Urology, Renmin Hospital of Wuhan University, Wuhan, Hubei, 430060, China
- Institute of Urologic Disease, Renmin Hospital of Wuhan University, Wuhan, Hubei, 430060, China
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Tian S, Xu M, Geng X, Fang J, Xu H, Xue X, Hu H, Zhang Q, Yu D, Guo M, Zhang H, Lu J, Guo C, Wang Q, Liu S, Zhang W. Network Medicine-Based Strategy Identifies Maprotiline as a Repurposable Drug by Inhibiting PD-L1 Expression via Targeting SPOP in Cancer. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2410285. [PMID: 39499771 DOI: 10.1002/advs.202410285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2024] [Revised: 10/21/2024] [Indexed: 11/07/2024]
Abstract
Immune checkpoint inhibitors (ICIs) are drugs that inhibit immune checkpoint (ICP) molecules to restore the antitumor activity of immune cells and eliminate tumor cells. Due to the limitations and certain side effects of current ICIs, such as programmed death protein-1, programmed cell death-ligand 1, and cytotoxic T lymphocyte-associated antigen 4 (CTLA4) antibodies, there is an urgent need to find new drugs with ICP inhibitory effects. In this study, a network-based computational framework called multi-network algorithm-driven drug repositioning targeting ICP (Mnet-DRI) is developed to accurately repurpose novel ICIs from ≈3000 Food and Drug Administration-approved or investigational drugs. By applying Mnet-DRI to PD-L1, maprotiline (MAP), an antidepressant drug is repurposed, as a potential PD-L1 modifier for colorectal and lung cancers. Experimental validation revealed that MAP reduced PD-L1 expression by targeting E3 ubiquitin ligase speckle-type zinc finger structural protein (SPOP), and the combination of MAP and anti-CTLA4 in vivo significantly enhanced the antitumor effect, providing a new alternative for the clinical treatment of colorectal and lung cancer.
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Affiliation(s)
- Saisai Tian
- Department of Phytochemistry, School of Pharmacy, Second Military Medical University, Shanghai, 200433, China
| | - Mengting Xu
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Xiangxin Geng
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Jiansong Fang
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
| | - Hanchen Xu
- Institute of Digestive Diseases, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, 200032, China
| | - Xinying Xue
- Department of Respiratory and Critical Care, Emergency and Critical Care Medical Center, Beijing Shijitan Hospital, Capital Medical University, Beijing, 100038, China
| | - Hongmei Hu
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Qing Zhang
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Dianping Yu
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Mengmeng Guo
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Hongwei Zhang
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Jinyuan Lu
- Department of Phytochemistry, School of Pharmacy, Second Military Medical University, Shanghai, 200433, China
| | - Chengyang Guo
- Department of Phytochemistry, School of Pharmacy, Second Military Medical University, Shanghai, 200433, China
| | - Qun Wang
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Sanhong Liu
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Weidong Zhang
- Department of Phytochemistry, School of Pharmacy, Second Military Medical University, Shanghai, 200433, China
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100193, China
- The Research Center for Traditional Chinese Medicine, Shanghai Institute of Infectious Diseases and Biosafety, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
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Lin Y, Lin P, Lu Y, Zheng J, Zheng Y, Huang X, Zhao X, Cui L. Post-Translational Modifications of RNA-Modifying Proteins in Cellular Dynamics and Disease Progression. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2406318. [PMID: 39377984 PMCID: PMC11600222 DOI: 10.1002/advs.202406318] [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: 06/10/2024] [Revised: 09/02/2024] [Indexed: 11/28/2024]
Abstract
RNA-modifying proteins, classified as "writers," "erasers," and "readers," dynamically modulate RNA by adding, removing, or interpreting chemical groups, thereby influencing RNA stability, functionality, and interactions. To date, over 170 distinct RNA chemical modifications and more than 100 RNA-modifying enzymes have been identified, with ongoing research expanding these numbers. Although significant progress has been made in understanding RNA modification, the regulatory mechanisms that govern RNA-modifying proteins themselves remain insufficiently explored. Post-translational modifications (PTMs) such as phosphorylation, ubiquitination, and acetylation are crucial in modulating the function and behavior of these proteins. However, the full extent of PTM influence on RNA-modifying proteins and their role in disease development remains to be fully elucidated. This review addresses these gaps by offering a comprehensive analysis of the roles PTMs play in regulating RNA-modifying proteins. Mechanistic insights are provided into how these modifications alter biological processes, contribute to cellular function, and drive disease progression. In addition, the current research landscape is examined, highlighting the therapeutic potential of targeting PTMs on RNA-modifying proteins for precision medicine. By advancing understanding of these regulatory networks, this review seeks to facilitate the development of more effective therapeutic strategies and inspire future research in the critical area of PTMs in RNA-modifying proteins.
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Affiliation(s)
- Yunfan Lin
- Stomatological Hospital, School of StomatologySouthern Medical UniversityGuangzhouGuangdong510280China
| | - Pei Lin
- Stomatological Hospital, School of StomatologySouthern Medical UniversityGuangzhouGuangdong510280China
| | - Ye Lu
- Stomatological Hospital, School of StomatologySouthern Medical UniversityGuangzhouGuangdong510280China
| | - Jiarong Zheng
- Department of Dentistry, The First Affiliated HospitalSun Yat‐Sen UniversityGuangzhou510080China
| | - Yucheng Zheng
- Stomatological Hospital, School of StomatologySouthern Medical UniversityGuangzhouGuangdong510280China
| | - Xiangyu Huang
- Stomatological Hospital, School of StomatologySouthern Medical UniversityGuangzhouGuangdong510280China
| | - Xinyuan Zhao
- Stomatological Hospital, School of StomatologySouthern Medical UniversityGuangzhouGuangdong510280China
| | - Li Cui
- Stomatological Hospital, School of StomatologySouthern Medical UniversityGuangzhouGuangdong510280China
- School of DentistryUniversity of California, Los AngelesLos AngelesCA90095USA
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32
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Verma S, Ghatak A. Involvement of E3 Ubiquitin Ligases in Viral Infections of the Human Host. Viral Immunol 2024; 37:419-431. [PMID: 39469796 DOI: 10.1089/vim.2024.0068] [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: 10/30/2024] Open
Abstract
Viral infections are one of the principal causes of global primary health crises, with increased rate of infection and mortality demonstrated by the newer progeny of viruses. Viral invasion of the host involves utilization of various cellular machinery. Ubiquitination is one of a few central regulatory systems used by viruses for establishment of the infections in the host. Members of the ubiquitination system are involved in carrying out proteasomal degradation or functional modification of proteins in numerous cellular processes. E3 ubiquitin ligases play a major role in this system through recognition and recruitment of protein substrates and catalyzing the transfer of ubiquitin to these substrates. The versatility of ubiquitin ligases frequently makes them useful tools for the viruses, for either utilizing or degrading other cellular machineries, for carrying out their multiplication or inactivating the defensive strategies of the host. Therefore, these ligases are important targets for aiming at major pathways causing viral protein degradation or functional modification of the infection process. In this review, we have discussed the role and mechanism of different types of ubiquitin ligases in the context of infections of mainly human viruses, highlighting the viral proteins directly interacting with the ligases. Knowledge about these direct interactions is central in understanding the ubiquitin-dependent processes. This comprehensive account may also be beneficial for pharmaceutical exploration of E3 ligase-based broad-spectrum antiviral treatment.
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Affiliation(s)
- Suchanda Verma
- School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Deemed to be University, Bhubaneswar, India
| | - Archana Ghatak
- School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Deemed to be University, Bhubaneswar, India
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Jiang H, Miller BD, Viennet T, Kim H, Lee K, Arthanari H, Cole PA. Protein semisynthesis reveals plasticity in HECT E3 ubiquitin ligase mechanisms. Nat Chem 2024; 16:1894-1905. [PMID: 39030419 DOI: 10.1038/s41557-024-01576-z] [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: 04/08/2023] [Accepted: 06/11/2024] [Indexed: 07/21/2024]
Abstract
Lys ubiquitination is catalysed by E3 ubiquitin ligases and is central to the regulation of protein stability and cell signalling in normal and disease states. There are gaps in our understanding of E3 mechanisms, and here we use protein semisynthesis, chemical rescue, microscale thermophoresis and other biochemical approaches to dissect the role of catalytic base/acid function and conformational interconversion in HECT-domain E3 catalysis. We demonstrate that there is plasticity in the use of the terminal side chain or backbone carboxylate for proton transfer in HECT E3 ubiquitin ligase reactions, with yeast Rsp5 orthologues appearing to be possible evolutionary intermediates. We also show that the HECT-domain ubiquitin covalent intermediate appears to eject the E2 conjugating enzyme, promoting catalytic turnover. These findings provide key mechanistic insights into how protein ubiquitination occurs and provide a framework for understanding E3 functions and regulation.
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Affiliation(s)
- Hanjie Jiang
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Bryant D Miller
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Department of Human Biology, Sattler College, Boston, MA, USA
| | - Thibault Viennet
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana Farber Cancer Institute, Boston, MA, USA
| | - Hyojeon Kim
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Kwangwoon Lee
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Haribabu Arthanari
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana Farber Cancer Institute, Boston, MA, USA
| | - Philip A Cole
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA.
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.
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Dai C, Miao Y, Li Z, Liu Y, Liu J, Liu X, Tan S, Wu H, Xiao J, Zou J, Feng H. Black carp RNF135 enhances RIG-I-mediated antiviral signaling by facilitating its oligomerization. FISH & SHELLFISH IMMUNOLOGY 2024; 154:109987. [PMID: 39490911 DOI: 10.1016/j.fsi.2024.109987] [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: 07/02/2024] [Revised: 09/22/2024] [Accepted: 10/24/2024] [Indexed: 11/05/2024]
Abstract
RNF135, also known as RIPLET, plays a crucial role in facilitating RIG-I signaling in mammals. However, the function and regulatory mechanism of RNF135 in teleosts remain much to be elucidated. In this study, RNF135 homolog of black carp (bcRNF135) has been cloned and identified. The coding sequence (CDS) of bcRNF135 gene comprises 1221 nucleotides, encoding a protein of 407 amino acids. Immunoblotting (IB) and immunofluorescence (IF) assays identified that bcRNF135 is approximately 50 kDa and localized in the cytoplasm. qRT-PCR demonstrated that bcRNF135 mRNA levels were increased in host cells following SVCV infection and poly (I:C) stimulation. Co-expressed bcRNF135 obviously enhanced the induced transcription of IFN promoters by bcRIG-I in reporter assay, as well as improved bcRIG-I triggered antiviral response. Notably, bcRNF135 knockdown reduced the antiviral ability of host cells and increased virus replication. Co-immunoprecipitation (Co-IP) assays and IF assays confirmed that bcRNF135 interacted with bcRIG-I. Moreover, SDD-AGE revealed that bcRNF135 promotes the oligomerization of bcRIG-I, a process critical for RIG-I activation. Overall, our data conclude that bcRNF135 enhances bcRIG-I-mediated antiviral signaling by facilitating its ubiquitination and oligomerization, enriching our understanding of RIG-I regulation in teleost innate immunity.
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Affiliation(s)
- Chushan Dai
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, China
| | - Yujia Miao
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, China
| | - Zhan'ao Li
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, China
| | - Yumian Liu
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, China
| | - Ji Liu
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, China
| | - Xiaoyu Liu
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, China
| | - Shasha Tan
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, China
| | - Hui Wu
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, China
| | - Jun Xiao
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, China; Institute of Interdisciplinary Studies, Hunan Normal University, Changsha, 410081, China.
| | - Jun Zou
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, 201306, China
| | - Hao Feng
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, 410081, China; Institute of Interdisciplinary Studies, Hunan Normal University, Changsha, 410081, China.
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35
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Lee DH, Lee HJ, Yang G, Kim DY, Kim JU, Yook TH, Lee JH, Kim HJ. A novel treatment strategy targeting cellular pathways with natural products to alleviate sarcopenia. Phytother Res 2024; 38:5033-5051. [PMID: 39099170 DOI: 10.1002/ptr.8301] [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: 12/26/2023] [Revised: 07/08/2024] [Accepted: 07/12/2024] [Indexed: 08/06/2024]
Abstract
Sarcopenia is a condition marked by a significant reduction in muscle mass and strength, primarily due to the aging process, which critically impacts muscle protein dynamics, metabolic functions, and overall physical functionality. This condition leads to increased body fat and reduced daily activity, contributing to severe health issues and a lower quality of life among the elderly. Recognized in the ICD-10-CM only in 2016, sarcopenia lacks definitive treatment options despite its growing prevalence and substantial social and economic implications. Given the aging global population, addressing sarcopenia has become increasingly relevant and necessary. The primary causes include aging, cachexia, diabetes, and nutritional deficiencies, leading to imbalances in protein synthesis and degradation, mitochondrial dysfunction, and hormonal changes. Exercise remains the most effective intervention, but it is often impractical for individuals with limited mobility, and pharmacological options such as anabolic steroids and myostatin inhibitors are not FDA-approved and are still under investigation. This review is crucial as it examines the potential of natural products as a novel treatment strategy for sarcopenia, targeting multiple mechanisms involved in its pathogenesis. By exploring natural products' multi-targeted effects, this study aims to provide innovative and practical solutions for sarcopenia management. Therefore, this review indicates significant improvements in muscle mass and function with the use of specific natural compounds, suggesting promising alternatives for those unable to engage in regular physical activity.
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Affiliation(s)
- Da Hee Lee
- College of Korean Medicine, Woosuk University, Jeonju-si, Republic of Korea
| | - Hye Jin Lee
- College of Korean Medicine, Woosuk University, Jeonju-si, Republic of Korea
| | - Gabsik Yang
- College of Korean Medicine, Woosuk University, Jeonju-si, Republic of Korea
| | - Dae Yong Kim
- College of Korean Medicine, Woosuk University, Jeonju-si, Republic of Korea
| | - Jong Uk Kim
- College of Korean Medicine, Woosuk University, Jeonju-si, Republic of Korea
| | - Tae Han Yook
- College of Korean Medicine, Woosuk University, Jeonju-si, Republic of Korea
| | - Jun Ho Lee
- College of Korean Medicine, Woosuk University, Jeonju-si, Republic of Korea
- Da Capo Co., Ltd., Jeonju-si, Republic of Korea
| | - Hong Jun Kim
- College of Korean Medicine, Woosuk University, Jeonju-si, Republic of Korea
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Zhang SH, Zeng N, Xu JZ, Liu CQ, Xu MY, Sun JX, An Y, Zhong XY, Miao LT, Wang SG, Xia QD. Recent breakthroughs in innovative elements, multidimensional enhancements, derived technologies, and novel applications of PROTACs. Biomed Pharmacother 2024; 180:117584. [PMID: 39427546 DOI: 10.1016/j.biopha.2024.117584] [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: 08/06/2024] [Revised: 10/08/2024] [Accepted: 10/14/2024] [Indexed: 10/22/2024] Open
Abstract
Proteolysis Targeting Chimera (PROTAC) is an emerging and evolving technology based on targeted protein degradation (TPD). Small molecule PROTACs have shown great efficacy in degrading disease-specific proteins in preclinical and clinical studies, but also showed various limitations. In recent years, new technologies and advances in TPD have provided additional optimized strategies based on conventional PROTACs that can overcome the shortcomings of conventional PROTACs in terms of undruggable targets, bioavailability, tissue-specificity, spatiotemporal control, and degradation scope. In addition, some designs of special targeting chimeras and applications based on multidisciplinary science have shed light on novel therapeutic modalities and drug design. However, each improvement has its own advantages, disadvantages and application conditions. In this review, we summarize the exploration of PROTAC elements, depict a landscape of improvements and derived concepts of PROTACs, and expect to provide perspectives for technological innovations, combinations and applications in future targeting chimera design.
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Affiliation(s)
- Si-Han Zhang
- Department and Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, No. 1095 Jiefang Avenue, Wuhan 430030, China
| | - Na Zeng
- Department and Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, No. 1095 Jiefang Avenue, Wuhan 430030, China
| | - Jin-Zhou Xu
- Department and Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, No. 1095 Jiefang Avenue, Wuhan 430030, China
| | - Chen-Qian Liu
- Department and Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, No. 1095 Jiefang Avenue, Wuhan 430030, China
| | - Meng-Yao Xu
- Department and Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, No. 1095 Jiefang Avenue, Wuhan 430030, China
| | - Jian-Xuan Sun
- Department and Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, No. 1095 Jiefang Avenue, Wuhan 430030, China
| | - Ye An
- Department and Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, No. 1095 Jiefang Avenue, Wuhan 430030, China
| | - Xing-Yu Zhong
- Department and Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, No. 1095 Jiefang Avenue, Wuhan 430030, China
| | - Lin-Tao Miao
- Department and Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, No. 1095 Jiefang Avenue, Wuhan 430030, China
| | - Shao-Gang Wang
- Department and Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, No. 1095 Jiefang Avenue, Wuhan 430030, China.
| | - Qi-Dong Xia
- Department and Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, No. 1095 Jiefang Avenue, Wuhan 430030, China.
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Sun K, Zhi Y, Ren W, Li S, Zheng J, Gao L, Zhi K. Crosstalk between O-GlcNAcylation and ubiquitination: a novel strategy for overcoming cancer therapeutic resistance. Exp Hematol Oncol 2024; 13:107. [PMID: 39487556 PMCID: PMC11529444 DOI: 10.1186/s40164-024-00569-5] [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: 07/01/2024] [Accepted: 10/04/2024] [Indexed: 11/04/2024] Open
Abstract
Developing resistance to cancer treatments is a major challenge, often leading to disease recurrence and metastasis. Understanding the underlying mechanisms of therapeutic resistance is critical for developing effective strategies. O-GlcNAcylation, a post-translational modification that adds GlcNAc from the donor UDP-GlcNAc to serine and threonine residues of proteins, plays a crucial role in regulating protein function and cellular signaling, which are frequently dysregulated in cancer. Similarly, ubiquitination, which involves the attachment of ubiquitin to to proteins, is crucial for protein degradation, cell cycle control, and DNA repair. The interplay between O-GlcNAcylation and ubiquitination is associated with cancer progression and resistance to treatment. This review discusses recent discoveries regarding the roles of O-GlcNAcylation and ubiquitination in cancer resistance, their interactions, and potential mechanisms. It also explores how targeting these pathways may provide new opportunities to overcome cancer treatment resistance in cancer, offering fresh insights and directions for research and therapeutic development.
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Affiliation(s)
- Kai Sun
- Department of Oral and Maxillofacial Reconstruction, The Affiliated Hospital of Qingdao University, 1677 Wutaishan Road, Huangdao Distract, Qingdao, 266003, Shandong, China
- School of Stomatology, Qingdao University, Qingdao, 266003, China
| | - Yuan Zhi
- Department of Oral and Maxillofacial Reconstruction, The Affiliated Hospital of Qingdao University, 1677 Wutaishan Road, Huangdao Distract, Qingdao, 266003, Shandong, China
| | - Wenhao Ren
- Department of Oral and Maxillofacial Reconstruction, The Affiliated Hospital of Qingdao University, 1677 Wutaishan Road, Huangdao Distract, Qingdao, 266003, Shandong, China
- School of Stomatology, Qingdao University, Qingdao, 266003, China
- Department of Oral and Maxillofacial Surgery, The Affiliated Hospital of Qingdao University, 1677 Wutaishan Road, Huangdao Distract, Qingdao, 266003, Shandong, China
| | - Shaoming Li
- Department of Oral and Maxillofacial Reconstruction, The Affiliated Hospital of Qingdao University, 1677 Wutaishan Road, Huangdao Distract, Qingdao, 266003, Shandong, China
- School of Stomatology, Qingdao University, Qingdao, 266003, China
- Department of Oral and Maxillofacial Surgery, The Affiliated Hospital of Qingdao University, 1677 Wutaishan Road, Huangdao Distract, Qingdao, 266003, Shandong, China
| | - Jingjing Zheng
- School of Stomatology, Qingdao University, Qingdao, 266003, China
- Department of Endodontics, the Affiliated Hospital of Qingdao University, Qingdao, 266003, China
| | - Ling Gao
- Department of Oral and Maxillofacial Reconstruction, The Affiliated Hospital of Qingdao University, 1677 Wutaishan Road, Huangdao Distract, Qingdao, 266003, Shandong, China.
- School of Stomatology, Qingdao University, Qingdao, 266003, China.
- Key Lab of Oral Clinical Medicine, The Affiliated Hospital of Qingdao University, Qingdao, 266003, China.
- Department of Oral and Maxillofacial Surgery, The Affiliated Hospital of Qingdao University, 1677 Wutaishan Road, Huangdao Distract, Qingdao, 266003, Shandong, China.
| | - Keqian Zhi
- Department of Oral and Maxillofacial Reconstruction, The Affiliated Hospital of Qingdao University, 1677 Wutaishan Road, Huangdao Distract, Qingdao, 266003, Shandong, China.
- School of Stomatology, Qingdao University, Qingdao, 266003, China.
- Key Lab of Oral Clinical Medicine, The Affiliated Hospital of Qingdao University, Qingdao, 266003, China.
- Department of Oral and Maxillofacial Surgery, The Affiliated Hospital of Qingdao University, 1677 Wutaishan Road, Huangdao Distract, Qingdao, 266003, Shandong, China.
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Zeng C, Weng L, Song Y, Huang Y, Xiang W, Ye Z, Yu C, Lai Z, Song Y, Yang H, Zhang L, Liu B. N-butanol extract of Broussonetia papyrifera (L.) L'Hér. ex Vent root bark alleviates atopic dermatitis by targeting E3 ubiquitin ligase WWP1 to promote NLRP3 degradation. Biomed Pharmacother 2024; 180:117561. [PMID: 39405906 DOI: 10.1016/j.biopha.2024.117561] [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: 07/11/2024] [Revised: 09/22/2024] [Accepted: 10/08/2024] [Indexed: 11/14/2024] Open
Abstract
BACKGROUND Broussonetia papyrifera (L.) L'Hér. ex Vent (B. papyrifera) is a deciduous tree widely distributed in Asia. Previous studies have revealed that leaves of B. papyrifera ameliorated atopic dermatitis (AD)-like symptoms and inflammatory response. However, the impact and underlying mechanism of other parts of B. papyrifera on AD remain elusive. METHODS The AD mice induced by 1-Chloro-2,4-dinitrochlorobenzene were used to observe the histopathological alterations in the skin tissues using hematoxylin-eosin staining and toluidine blue staining techniques. Serum levels of inflammatory factors were quantified utilizing ELISA. Pyroptosis was analyzed by lactate dehydrogenase release and flow cytometry in human keratinocytes. The activation of Nod-like receptor protein 3 (NLRP3) inflammasome was analyzed by western blots. Furthermore, the mechanism underlying the inhibition of NLRP3 inflammasome by N-butanol extracts of B. papyrifera root bark (NE-BPRB) was investigated using cellular thermal shift assay and surface plasmon resonance techniques. RESULTS Treatment with NE-BPRB significantly ameliorated symptoms of AD mice and reduced serum levels of pro-inflammatory factors. NE-BPRB intervention exhibited inhibitory effects on NLRP3 inflammasome activation and pyroptosis in vitro and in vivo. NE-BPRB and its primary bioactive constituent chlorogenic acid (CA) promote the K48-linked ubiquitination of NLRP3, leading to its proteasomal degradation by binding WW domain containing E3 ubiquitin protein ligase 1 (WWP1). CONCLUSIONS The NE-BPRB and its primary bioactive constituent, CA, effectively inhibit the formation of the NLRP3 inflammasome and impede cell pyroptosis by promoting K48-linked ubiquitin-dependent proteasomal degradation of NLRP3 through binding to the E3 ubiquitin ligase WWP1, thereby resulting in improved AD.
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Affiliation(s)
- Cheng Zeng
- Key Specialty of Clinical Pharmacy, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou 510699, China; Center for Drug Research and Development, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Liangkun Weng
- Center for Drug Research and Development, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Yuanming Song
- Center for Drug Research and Development, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Yihang Huang
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Wenjing Xiang
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Zhiming Ye
- Center for Drug Research and Development, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Can Yu
- Center for Drug Research and Development, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Zixuan Lai
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Yuxuan Song
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Huiwen Yang
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou 510006, China.
| | - Luyong Zhang
- Center for Drug Research and Development, Guangdong Pharmaceutical University, Guangzhou 510006, China.
| | - Bing Liu
- School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou 510006, China; Key Specialty of Clinical Pharmacy, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou 510699, China.
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Sun X, Chen X, Wu B, Zhou L, Chen Y, Zheng S, Wang S, Liu Z. Clam Genome and Transcriptomes Provide Insights into Molecular Basis of Morphological Novelties and Adaptations in Mollusks. BIOLOGY 2024; 13:870. [PMID: 39596825 PMCID: PMC11592408 DOI: 10.3390/biology13110870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2024] [Revised: 10/17/2024] [Accepted: 10/23/2024] [Indexed: 11/29/2024]
Abstract
Bivalve mollusks, comprising animals enclosed in two shell valves, are well-adapted to benthic life in many intertidal zones. Clams have evolved the buried lifestyle, which depends on their unique soft tissue structure and their wedge-shaped muscular foot and long extendible siphons. However, molecular mechanisms of adaptative phenotype evolution remain largely unknown. In the present study, we obtain the high-quality chromosome-level genome of Manila clam R. philippinarum, an economically important marine bivalve in many coastal areas. The genome is constructed by the Hi-C assisted assembly, which yields 19 chromosomes with a total of 1.17 Gb and BUSCO integrity of 92.23%. The de novo assembled genome has a contig N50 length of 307.7 kb and scaffold N50 of 59.5 Mb. Gene family expansion analysis reveals that a total of 24 single-copy gene families have undergone the significant expansion or contraction, including E3 ubiquitin ligase and dynein heavy chain. The significant expansion of transposable elements has been also identified, including long terminal repeats (LTR) and non-LTR retrotransposons. The comparative transcriptomics among different clam tissues reveals that extracellular matrix (ECM) receptors and neuroactive ligand receptors may play the important roles in tissue structural support and neurotransmission during their infaunal life. These findings of gene family expansion and tissue-specific expression may reflect the unique soft tissue structure of clams, suggesting the evolution of lineage-specific morphological novelties. The high-quality genome and transcriptome data of R. philippinarum will not only facilitate the genetic studies on clams but will also provide valuable information on morphological novelties in mollusks.
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Affiliation(s)
- Xiujun Sun
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; (X.S.); (X.C.); (B.W.); (L.Z.); (S.Z.); (S.W.)
- Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory, Qingdao 266071, China
| | - Xi Chen
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; (X.S.); (X.C.); (B.W.); (L.Z.); (S.Z.); (S.W.)
- Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory, Qingdao 266071, China
| | - Biao Wu
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; (X.S.); (X.C.); (B.W.); (L.Z.); (S.Z.); (S.W.)
- Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory, Qingdao 266071, China
| | - Liqing Zhou
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; (X.S.); (X.C.); (B.W.); (L.Z.); (S.Z.); (S.W.)
- Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory, Qingdao 266071, China
| | - Yancui Chen
- Zhangzhou Aquatic Technology Promotion Station, Zhangzhou 363000, China;
| | - Sichen Zheng
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; (X.S.); (X.C.); (B.W.); (L.Z.); (S.Z.); (S.W.)
- Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory, Qingdao 266071, China
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai 201306, China
| | - Songlin Wang
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; (X.S.); (X.C.); (B.W.); (L.Z.); (S.Z.); (S.W.)
- Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory, Qingdao 266071, China
- College of Marine Science and Fisheries, Jiangsu Ocean University, Lianyungang 222005, China
| | - Zhihong Liu
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; (X.S.); (X.C.); (B.W.); (L.Z.); (S.Z.); (S.W.)
- Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory, Qingdao 266071, China
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Wu Y, Huang Z, Luo P, Xiang Z, Zhang M, Chen Z, Zhou Y, Li J. RNF2 promotes chondrosarcoma progression by regulating ubiquitination and degradation of CBX7. Cancer Metab 2024; 12:30. [PMID: 39456039 PMCID: PMC11520121 DOI: 10.1186/s40170-024-00359-x] [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: 05/09/2024] [Accepted: 10/16/2024] [Indexed: 10/28/2024] Open
Abstract
OBJECTIVE Chondrosarcoma (CHS) is resistant to conventional chemotherapy and radiotherapy and currently lacks effective treatment options when in advanced stages. Accordingly, this research investigated the mechanism of RNF2/CBX7 in CHS to drive the development of molecularly targeted drugs for CHS. METHODS RNF2 and CBX7 levels were detected in CHS cells and tissues. RNF2 and CBX7 expression was modulated through cell transfection to examine their effects on cell proliferation, apoptosis, migration, and angiogenesis. The correlation between RNF2 and CBX7 levels was determined, and the ubiquitination level of CBX7 was tested. Protein synthesis was blocked in RNF2-knockdown/overexpressing cells with CHX to assess the effect of RNF2 on CBX7 stability. JJ012 cells transfected with LV-sh-RNF2 were subcutaneously injected into nu/nu nude mice to ascertain the action of RNF2 in the growth and metastasis of CHS. RESULTS RNF2 was highly expressed in CHS cells and tissues. RNF2 knockdown curbed CHS cell proliferation, migration, and angiogenesis while promoting apoptosis. RNF2 knockdown in JJ012 cells upregulated CBX7 protein levels and reduced CBX7 ubiquitination, whilst RNF2 had no effect on CBX7 mRNA expression. CBX7 knockdown partially nullified the repressing effects of RNF2 knockdown on CHS cell proliferation, migration, and angiogenesis, and CBX7 overexpression partially abolished the promotional effects of RNF2 overexpression. LV-sh-RNF2 prominently restricted tumor growth and weight and declined lung metastatic nodules and Ki-67-positive cells in mice. CONCLUSION RNF2 fosters CHS progression by elevating CBX7 degradation via the ubiquitination pathway.
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Affiliation(s)
- Yue Wu
- Department of Orthopedics, Beijing Chaoyang Hospital, No.8 Gongti South Rd, Chaoyang District, Beijing, 100020, China
| | - Zheng Huang
- Department of Orthopedics, Huazhong University of Science and Technology Union Shenzhen Hospital, No. 89 Taoyuan Road, Nanshan District, Shenzhen City, 210009, Guangdong, China
| | - Ping Luo
- Department of Spinal Surgery, The Fourth Hospital of Changsha, Changsha Hospital of Hunan Normal University, No.70 Lushan Road, Yuelu District, Changsha, 410006, Hunan, China.
| | - Zhong Xiang
- Department of Spinal Surgery, The Fourth Hospital of Changsha, Changsha Hospital of Hunan Normal University, No.70 Lushan Road, Yuelu District, Changsha, 410006, Hunan, China
| | - Meng Zhang
- Department of Spinal Surgery, The Fourth Hospital of Changsha, Changsha Hospital of Hunan Normal University, No.70 Lushan Road, Yuelu District, Changsha, 410006, Hunan, China
| | - Zhiwu Chen
- Department of Spinal Surgery, The Fourth Hospital of Changsha, Changsha Hospital of Hunan Normal University, No.70 Lushan Road, Yuelu District, Changsha, 410006, Hunan, China
| | - Yalu Zhou
- Department of Spinal Surgery, The Fourth Hospital of Changsha, Changsha Hospital of Hunan Normal University, No.70 Lushan Road, Yuelu District, Changsha, 410006, Hunan, China
| | - Jiameng Li
- Department of Spinal Surgery, The Fourth Hospital of Changsha, Changsha Hospital of Hunan Normal University, No.70 Lushan Road, Yuelu District, Changsha, 410006, Hunan, China
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Wanka V, Fottner M, Cigler M, Lang K. Genetic Code Expansion Approaches to Decipher the Ubiquitin Code. Chem Rev 2024; 124:11544-11584. [PMID: 39311880 PMCID: PMC11503651 DOI: 10.1021/acs.chemrev.4c00375] [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: 05/17/2024] [Revised: 08/05/2024] [Accepted: 08/19/2024] [Indexed: 10/25/2024]
Abstract
The covalent attachment of Ub (ubiquitin) to target proteins (ubiquitylation) represents one of the most versatile PTMs (post-translational modifications) in eukaryotic cells. Substrate modifications range from a single Ub moiety being attached to a target protein to complex Ub chains that can also contain Ubls (Ub-like proteins). Ubiquitylation plays pivotal roles in most aspects of eukaryotic biology, and cells dedicate an orchestrated arsenal of enzymes to install, translate, and reverse these modifications. The entirety of this complex system is coined the Ub code. Deciphering the Ub code is challenging due to the difficulty in reconstituting enzymatic machineries and generating defined Ub/Ubl-protein conjugates. This Review provides a comprehensive overview of recent advances in using GCE (genetic code expansion) techniques to study the Ub code. We highlight strategies to site-specifically ubiquitylate target proteins and discuss their advantages and disadvantages, as well as their various applications. Additionally, we review the potential of small chemical PTMs targeting Ub/Ubls and present GCE-based approaches to study this additional layer of complexity. Furthermore, we explore methods that rely on GCE to develop tools to probe interactors of the Ub system and offer insights into how future GCE-based tools could help unravel the complexity of the Ub code.
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Affiliation(s)
- Vera Wanka
- Laboratory
for Organic Chemistry (LOC), Department of Chemistry and Applied Biosciences
(D-CHAB), ETH Zurich, Vladimir-Prelog-Weg 3, 8093 Zurich, Switzerland
| | - Maximilian Fottner
- Laboratory
for Organic Chemistry (LOC), Department of Chemistry and Applied Biosciences
(D-CHAB), ETH Zurich, Vladimir-Prelog-Weg 3, 8093 Zurich, Switzerland
| | - Marko Cigler
- Department
of Chemistry, Technical University of Munich, 85748 Garching, Germany
| | - Kathrin Lang
- Laboratory
for Organic Chemistry (LOC), Department of Chemistry and Applied Biosciences
(D-CHAB), ETH Zurich, Vladimir-Prelog-Weg 3, 8093 Zurich, Switzerland
- Department
of Chemistry, Technical University of Munich, 85748 Garching, Germany
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Xu X, Shi X, You X, Hao Z, Wang R, Wang M, He F, Peng S, Tao H, Liu Z, Wang J, Zhang C, Feng Q, Wu W, Wang GL, Ning Y. A pair of E3 ubiquitin ligases control immunity and flowering by targeting different ELF3 proteins in rice. Dev Cell 2024; 59:2731-2744.e4. [PMID: 39025063 DOI: 10.1016/j.devcel.2024.06.013] [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: 11/13/2023] [Revised: 04/19/2024] [Accepted: 06/19/2024] [Indexed: 07/20/2024]
Abstract
The ubiquitin-proteasome system (UPS) plays crucial roles in cellular processes including plant growth, development, and stress responses. In this study, we report that a pair of E3 ubiquitin ligases, AvrPiz-t-interaction protein 6 (APIP6) and IPA1-interaction protein 1 (IPI1), intricately target early flowering3 (ELF3) paralogous proteins to control rice immunity and flowering. APIP6 forms homo-oligomers or hetero-oligomers with IPI1. Both proteins interact with OsELF3-2, promoting its degradation to positively control resistance against the rice blast fungus (Magnaporthe oryzae). Intriguingly, overexpression of IPI1 in Nipponbare caused significantly late-flowering phenotypes similar to the oself3-1 mutant. Except for late flowering, oself3-1 enhances resistance against M. oryzae. IPI1 also interacts with and promotes the degradation of OsELF3-1, a paralog of OsELF3-2. Notably, IPI1 and APIP6 synergistically modulate OsELF3s degradation, finely tuning blast disease resistance by targeting OsELF3-2, while IPI1 controls both disease resistance and flowering by targeting OsELF3-1. This study unravels multiple functions for a pair of E3 ligases in rice.
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Affiliation(s)
- Xiao Xu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; Agro-Biotechnology and Ministry of Agriculture Key Laboratory of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Xuetao Shi
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Xiaoman You
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Zeyun Hao
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Ruyi Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Min Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Feng He
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Shasha Peng
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Hui Tao
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Zheng Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Jisong Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Chongyang Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Qin Feng
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; Department of Plant Pathology, The Ohio State University, Columbus, OH 43210, USA
| | - Weixun Wu
- China National Center for Rice Improvement and State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 311400, China
| | - Guo-Liang Wang
- Department of Plant Pathology, The Ohio State University, Columbus, OH 43210, USA
| | - Yuese Ning
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
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Jiaerken B, Liu W, Zheng J, Qu W, Wu Q, Ai Z. The SUMO Family: Mechanisms and Implications in Thyroid Cancer Pathogenesis and Therapy. Biomedicines 2024; 12:2408. [PMID: 39457720 PMCID: PMC11505470 DOI: 10.3390/biomedicines12102408] [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: 09/05/2024] [Revised: 10/12/2024] [Accepted: 10/17/2024] [Indexed: 10/28/2024] Open
Abstract
(1) Background: Small ubiquitin-like modifiers (SUMOs) are pivotal in post-translational modifications, influencing various cellular processes, such as protein localization, stability, and genome integrity. (2) Methods: This review explores the SUMO family, including its isoforms and catalytic cycle, highlighting their significance in regulating key biological functions in thyroid cancer. We discuss the multifaceted roles of SUMOylation in DNA repair mechanisms, protein stability, and the modulation of receptor activities, particularly in the context of thyroid cancer. (3) Results: The aberrant SUMOylation machinery contributes to tumorigenesis through altered gene expression and immune evasion mechanisms. Furthermore, we examine the therapeutic potential of targeting SUMOylation pathways in thyroid cancer treatment, emphasizing the need for further research to develop effective SUMOylation inhibitors. (4) Conclusions: By understanding the intricate roles of SUMOylation in cancer biology, we can pave the way for innovative therapeutic strategies to improve outcomes for patients with advanced tumors.
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Affiliation(s)
- Bahejuan Jiaerken
- Department of Surgery (Thyroid & Breast), Zhongshan Hospital, Fudan University, Shanghai 200032, China
- School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Wei Liu
- Department of Surgery (Thyroid & Breast), Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Jiaojiao Zheng
- Department of Surgery (Thyroid & Breast), Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Weifeng Qu
- Department of Surgery (Thyroid & Breast), Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Qiao Wu
- Department of Surgery (Thyroid & Breast), Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Zhilong Ai
- Department of Surgery (Thyroid & Breast), Zhongshan Hospital, Fudan University, Shanghai 200032, China
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Li X, Huang Y, Liu X, Zhang L, Wang X, Zhao F, Zou L, Wu K, Chen W, Qin Y, Zeng S, Li B, He Y, Song Y, Li Z, Fan J, Zhao M, Yi L, Ding H, Fan S, Chen J. Classical swine fever virus inhibits serine metabolism-mediated antiviral immunity by deacetylating modified PHGDH. mBio 2024; 15:e0209724. [PMID: 39207107 PMCID: PMC11481501 DOI: 10.1128/mbio.02097-24] [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: 07/16/2024] [Accepted: 08/05/2024] [Indexed: 09/04/2024] Open
Abstract
Classical swine fever virus (CSFV), an obligate intracellular pathogen, hijacks cellular metabolism to evade immune surveillance and facilitate its replication. The precise mechanisms by which CSFV modulates immune metabolism remain largely unknown. Our study reveals that CSFV infection disrupts serine metabolism, which plays a crucial role in antiviral immunity. Notably, we discovered that CSFV infection leads to the deacetylation of PHGDH, a key enzyme in serine metabolism, resulting in autophagic degradation. This deacetylation impairs PHGDH's enzymatic activity, reduces serine biosynthesis, weakens innate immunity, and promotes viral proliferation. Molecularly, CSFV infection induces the association of HDAC3 with PHGDH, leading to deacetylation at the K364 site. This modification attracts the E3 ubiquitin ligase RNF125, which facilitates the addition of K63-linked ubiquitin chains to PHGDH-K364R. Subsequently, PHGDH is targeted for lysosomal degradation by p62 and NDP52. Furthermore, the deacetylation of PHGDH disrupts its interaction with the NAD+ substrate, destabilizing the PHGDH-NAD complex, impeding the active site, and thereby inhibiting de novo serine synthesis. Additionally, our research indicates that deacetylated PHGDH suppresses the mitochondria-MAVS-IRF3 pathway through its regulatory effect on serine metabolism, leading to decreased IFN-β production and enhanced viral replication. Overall, our findings elucidate the complex interplay between CSFV and serine metabolism, revealing a novel aspect of viral immune evasion through the lens of immune metabolism. IMPORTANCE Classical swine fever (CSF) seriously restricts the healthy development of China's aquaculture industry, and the unclear pathogenic mechanism and pathogenesis of classical swine fever virus (CSFV) are the main obstacle to CSF prevention, control, and purification. Therefore, it is of great significance to explore the molecular mechanism of CSFV and host interplay, to search for the key signaling pathways and target molecules in the host that regulate the replication of CSFV infection, and to elucidate the mechanism of action of host immune dysfunction and immune escape due to CSFV infection for the development of novel CSFV vaccines and drugs. This study reveals the mechanism of serine metabolizing enzyme post-translational modifications and antiviral signaling proteins in the replication of CSFV and enriches the knowledge of CSFV infection and immune metabolism.
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Affiliation(s)
- Xiaowen Li
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Yaoyao Huang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Xueyi Liu
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Lihong Zhang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Xinyan Wang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Feifan Zhao
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Linke Zou
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Keke Wu
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Wenxian Chen
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Yuwei Qin
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Sen Zeng
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Bingke Li
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Yintao He
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Yiwan Song
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Zhaoyao Li
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Jindai Fan
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Mingqiu Zhao
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Lin Yi
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Hongxing Ding
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Shuangqi Fan
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Jinding Chen
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
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Jing F, Zhu L, Zhang J, Zhou X, Bai J, Li X, Zhang H, Li T. Multi-omics reveals lactylation-driven regulatory mechanisms promoting tumor progression in oral squamous cell carcinoma. Genome Biol 2024; 25:272. [PMID: 39407253 PMCID: PMC11476802 DOI: 10.1186/s13059-024-03383-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Accepted: 08/30/2024] [Indexed: 10/20/2024] Open
Abstract
BACKGROUND Lactylation, a post-translational modification, is increasingly recognized for its role in cancer progression. This study investigates its prevalence and impact in oral squamous cell carcinoma (OSCC). RESULTS Immunohistochemical staining of 81 OSCC cases shows lactylation levels correlate with malignancy grading. Proteomic analyses of six OSCC tissue pairs reveal 2765 lactylation sites on 1033 proteins, highlighting its extensive presence. These modifications influence metabolic processes, molecular synthesis, and transport. CAL27 cells are subjected to cleavage under targets and tagmentation assay for accessible-chromatin with high-throughput sequencing, and transcriptomic sequencing pre- and post-lactate treatment, with 217 genes upregulated due to lactylation. Chromatin immunoprecipitation-quantitative PCR and real-time fluorescence quantitative PCR confirm the regulatory role of lactylation at the K146 site of dexh-box helicase 9 (DHX9), a key factor in OSCC progression. CCK8, colony formation, scratch healing, and Transwell assays demonstrate that lactylation mitigates the inhibitory effect of DHX9 on OSCC, thereby promoting its occurrence and development. CONCLUSIONS Lactylation actively modulates gene expression in OSCC, with significant effects on chromatin structure and cellular processes. This study provides a foundation for developing targeted therapies against OSCC, leveraging the role of lactylation in disease pathogenesis.
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Affiliation(s)
- Fengyang Jing
- Department of Oral Pathology, Peking University School and Hospital of Stomatology, National Center of Stomatology, National Clinical Research Center for Oral Diseases, National Engineering Laboratory for Digital and Material Technology of Stomatology, Beijing Key Laboratory of Digital Stomatology, Research Center of Engineering and Technology for Computerized Dentistry Ministry of Health, NMPA Key Laboratory for Dental Materials, Beijing, 100081, China
- Research Unit of Precision Pathologic Diagnosis in Tumors of the Oral and Maxillofacial Regions, Chinese Academy of Medical Sciences (2019RU034), Beijing, 100081, China
| | - Lijing Zhu
- Department of Oral Pathology, Peking University School and Hospital of Stomatology, National Center of Stomatology, National Clinical Research Center for Oral Diseases, National Engineering Laboratory for Digital and Material Technology of Stomatology, Beijing Key Laboratory of Digital Stomatology, Research Center of Engineering and Technology for Computerized Dentistry Ministry of Health, NMPA Key Laboratory for Dental Materials, Beijing, 100081, China
- Research Unit of Precision Pathologic Diagnosis in Tumors of the Oral and Maxillofacial Regions, Chinese Academy of Medical Sciences (2019RU034), Beijing, 100081, China
| | - Jianyun Zhang
- Department of Oral Pathology, Peking University School and Hospital of Stomatology, National Center of Stomatology, National Clinical Research Center for Oral Diseases, National Engineering Laboratory for Digital and Material Technology of Stomatology, Beijing Key Laboratory of Digital Stomatology, Research Center of Engineering and Technology for Computerized Dentistry Ministry of Health, NMPA Key Laboratory for Dental Materials, Beijing, 100081, China
- Research Unit of Precision Pathologic Diagnosis in Tumors of the Oral and Maxillofacial Regions, Chinese Academy of Medical Sciences (2019RU034), Beijing, 100081, China
| | - Xuan Zhou
- Department of Oral Pathology, Peking University School and Hospital of Stomatology, National Center of Stomatology, National Clinical Research Center for Oral Diseases, National Engineering Laboratory for Digital and Material Technology of Stomatology, Beijing Key Laboratory of Digital Stomatology, Research Center of Engineering and Technology for Computerized Dentistry Ministry of Health, NMPA Key Laboratory for Dental Materials, Beijing, 100081, China
- Research Unit of Precision Pathologic Diagnosis in Tumors of the Oral and Maxillofacial Regions, Chinese Academy of Medical Sciences (2019RU034), Beijing, 100081, China
| | - Jiaying Bai
- Department of Oral Pathology, Peking University School and Hospital of Stomatology, National Center of Stomatology, National Clinical Research Center for Oral Diseases, National Engineering Laboratory for Digital and Material Technology of Stomatology, Beijing Key Laboratory of Digital Stomatology, Research Center of Engineering and Technology for Computerized Dentistry Ministry of Health, NMPA Key Laboratory for Dental Materials, Beijing, 100081, China
| | - Xuefen Li
- Central Laboratory, Peking University School and Hospital of Stomatology, Beijing, 100081, China
| | - Heyu Zhang
- Central Laboratory, Peking University School and Hospital of Stomatology, Beijing, 100081, China.
- Research Unit of Precision Pathologic Diagnosis in Tumors of the Oral and Maxillofacial Regions, Chinese Academy of Medical Sciences (2019RU034), Beijing, 100081, China.
| | - Tiejun Li
- Department of Oral Pathology, Peking University School and Hospital of Stomatology, National Center of Stomatology, National Clinical Research Center for Oral Diseases, National Engineering Laboratory for Digital and Material Technology of Stomatology, Beijing Key Laboratory of Digital Stomatology, Research Center of Engineering and Technology for Computerized Dentistry Ministry of Health, NMPA Key Laboratory for Dental Materials, Beijing, 100081, China.
- Research Unit of Precision Pathologic Diagnosis in Tumors of the Oral and Maxillofacial Regions, Chinese Academy of Medical Sciences (2019RU034), Beijing, 100081, China.
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Crowe C, Nakasone MA, Chandler S, Craigon C, Sathe G, Tatham MH, Makukhin N, Hay RT, Ciulli A. Mechanism of degrader-targeted protein ubiquitinability. SCIENCE ADVANCES 2024; 10:eado6492. [PMID: 39392888 PMCID: PMC11468923 DOI: 10.1126/sciadv.ado6492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Accepted: 09/09/2024] [Indexed: 10/13/2024]
Abstract
Small-molecule degraders of disease-driving proteins offer a clinically proven modality with enhanced therapeutic efficacy and potential to tackle previously undrugged targets. Stable and long-lived degrader-mediated ternary complexes drive fast and profound target degradation; however, the mechanisms by which they affect target ubiquitination remain elusive. Here, we show cryo-EM structures of the VHL Cullin 2 RING E3 ligase with the degrader MZ1 directing target protein Brd4BD2 toward UBE2R1-ubiquitin, and Lys456 at optimal positioning for nucleophilic attack. In vitro ubiquitination and mass spectrometry illuminate a patch of favorably ubiquitinable lysines on one face of Brd4BD2, with cellular degradation and ubiquitinomics confirming the importance of Lys456 and nearby Lys368/Lys445, identifying the "ubiquitination zone." Our results demonstrate the proficiency of MZ1 in positioning the substrate for catalysis, the favorability of Brd4BD2 for ubiquitination by UBE2R1, and the flexibility of CRL2 for capturing suboptimal lysines. We propose a model for ubiquitinability of degrader-recruited targets, providing a mechanistic blueprint for further rational drug design.
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Affiliation(s)
- Charlotte Crowe
- Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, 1 James Lindsay Place, Dundee DD1 5JJ, UK
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, James Black Centre, Dow Street, Dundee DD1 5EH, UK
| | - Mark A. Nakasone
- Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, 1 James Lindsay Place, Dundee DD1 5JJ, UK
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, James Black Centre, Dow Street, Dundee DD1 5EH, UK
| | - Sarah Chandler
- Division of Molecular, Cellular and Developmental Biology, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Conner Craigon
- Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, 1 James Lindsay Place, Dundee DD1 5JJ, UK
| | - Gajanan Sathe
- Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, 1 James Lindsay Place, Dundee DD1 5JJ, UK
| | - Michael H. Tatham
- Division of Molecular, Cellular and Developmental Biology, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Nikolai Makukhin
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, James Black Centre, Dow Street, Dundee DD1 5EH, UK
| | - Ronald T. Hay
- Division of Molecular, Cellular and Developmental Biology, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Alessio Ciulli
- Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, 1 James Lindsay Place, Dundee DD1 5JJ, UK
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, James Black Centre, Dow Street, Dundee DD1 5EH, UK
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Masuda S, Kurabayashi N, Nunokawa R, Otobe Y, Kozuka-Hata H, Oyama M, Shibata Y, Inoue JI, Koebis M, Aiba A, Yoshitane H, Fukada Y. TRAF7 determines circadian period through ubiquitination and degradation of DBP. Commun Biol 2024; 7:1280. [PMID: 39379486 PMCID: PMC11461874 DOI: 10.1038/s42003-024-07002-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: 11/09/2023] [Accepted: 10/01/2024] [Indexed: 10/10/2024] Open
Abstract
D-site binding protein, DBP, is a clock-controlled transcription factor and drives daily rhythms of physiological processes through the regulation of an array of genes harboring a DNA binding motif, D-box. DBP protein levels show a circadian oscillation with an extremely robust peak/trough ratio, but it is elusive how the temporal pattern is regulated by post-translational regulation. In this study, we show that DBP protein levels are down-regulated by the ubiquitin-proteasome pathway. Analysis using 19 dominant-negative forms of E2 enzymes have revealed that UBE2G1 and UBE2T mediate the degradation of DBP. A proteomic analysis of DBP-interacting proteins and database screening have identified Tumor necrosis factor Receptor-Associated Factor 7 (TRAF7), a RING-type E3 ligase, that forms a complex with UBE2G1 and/or UBE2T. Ubiquitination analysis have revealed that TRAF7 enhances K48-linked polyubiquitination of DBP in cultured cells. Overexpression of TRAF7 down-regulates DBP protein level, while knockdown of TRAF7 up-regulates DBP in cultured cells. Knockout of TRAF7 in NIH3T3 cells have revealed that TRAF7 mediates the time-of-the-day-dependent regulation of DBP levels. Furthermore, TRAF7 has a period-shortening effect on the cellular clock. Together, TRAF7 plays an important role in circadian clock oscillation through destabilization of DBP.
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Affiliation(s)
- Shusaku Masuda
- Department of Biological Sciences, School of Science, The University of Tokyo, Tokyo, Japan
| | - Nobuhiro Kurabayashi
- Circadiain Clock Project, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Rina Nunokawa
- Department of Biological Sciences, School of Science, The University of Tokyo, Tokyo, Japan
| | - Yuta Otobe
- Department of Biological Sciences, School of Science, The University of Tokyo, Tokyo, Japan
- Circadiain Clock Project, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Hiroko Kozuka-Hata
- Medical Proteomics Laboratory, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Masaaki Oyama
- Medical Proteomics Laboratory, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Yuri Shibata
- Division of Cellular and Molecular Biology, Department of Cancer Biology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Jun-Ichiro Inoue
- Medical Proteomics Laboratory, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Division of Cellular and Molecular Biology, Department of Cancer Biology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Michinori Koebis
- Laboratory of Animal Resources, Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Atsu Aiba
- Department of Biological Sciences, School of Science, The University of Tokyo, Tokyo, Japan
- Laboratory of Animal Resources, Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Hikari Yoshitane
- Department of Biological Sciences, School of Science, The University of Tokyo, Tokyo, Japan.
- Circadiain Clock Project, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan.
| | - Yoshitaka Fukada
- Department of Biological Sciences, School of Science, The University of Tokyo, Tokyo, Japan.
- Circadiain Clock Project, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan.
- Laboratory of Animal Resources, Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.
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Xiu W, Zhang Y, Tang D, Lee SH, Zeng R, Ye T, Li H, Lu Y, Qin C, Yang Y, Yan X, Wang X, Hu X, Chu M, Sun Z, Xu W. Inhibition of EREG/ErbB/ERK by Astragaloside IV reversed taxol-resistance of non-small cell lung cancer through attenuation of stemness via TGFβ and Hedgehog signal pathway. Cell Oncol (Dordr) 2024:10.1007/s13402-024-00999-7. [PMID: 39373858 DOI: 10.1007/s13402-024-00999-7] [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] [Accepted: 09/25/2024] [Indexed: 10/08/2024] Open
Abstract
PURPOSE Taxol is the first-line chemo-drug for advanced non-small cell lung cancer (NSCLC), but it frequently causes acquired resistance, which leads to the failure of treatment. Therefore, it is critical to screen and characterize the mechanism of the taxol-resistance reversal agent that could re-sensitize the resistant cancer cells to chemo-drug. METHOD The cell viability, sphere-forming and xenografts assay were used to evaluate the ability of ASIV to reverse taxol-resistance. Immunohistochemistry, cytokine application, small-interfering RNA, small molecule inhibitors, and RNA-seq approaches were applied to characterize the molecular mechanism of inhibition of epiregulin (EREG) and downstream signaling by ASIV to reverse taxol-resistance. RESULTS ASIV reversed taxol resistance through suppression of the stemness-associated genes of spheres in NSCLC. The mechanism exploration revealed that ASIV promoted the K48-linked polyubiquitination of EREG along with degradation. Moreover, EREG could be triggered by chemo-drug treatment. Consequently, EREG bound to the ErbB receptor and activated the ERK signal to regulate the expression of the stemness-associated genes. Inhibition of EREG/ErbB/ERK could reverse the taxol-resistance by inhibiting the stemness-associated genes. Finally, it was observed that TGFβ and Hedgehog signaling were downstream of EREG/ErbB/ERK, which could be targeted using inhibitors to reverse the taxol resistance of NSCLC. CONCLUSIONS These findings revealed that inhibition of EREG by ASIV reversed taxol-resistance through suppression of the stemness of NSCLC via EREG/ErbB/ERK-TGFβ, Hedgehog axis.
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Affiliation(s)
- Wenhao Xiu
- School of Integrative Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Yujia Zhang
- School of Integrative Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
- Department of Clinical Medicine, Suzhou Vocational Health College, Suzhou, Jiangsu, China
| | - Dongfang Tang
- Department of Thoracic Surgery, Huadong Hospital Affiliated to Fudan University, Shanghai, China
| | - Sau Har Lee
- School of Biosciences, Faculty of Health and Medical Sciences, Taylor's University, Subang Jaya, Selangor, Malaysia
| | - Rui Zeng
- School of Integrative Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Tingjie Ye
- School of Integrative Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Hua Li
- School of Integrative Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Yanlin Lu
- Department of Oncology and Institute of Traditional Chinese Medicine in Oncology, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Changtai Qin
- School of Integrative Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Yuxi Yang
- School of Integrative Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Xiaofeng Yan
- School of Integrative Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Xiaoling Wang
- School of Integrative Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Xudong Hu
- School of Integrative Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Maoquan Chu
- School of Life Science and Technology, Tongji University, Shanghai, China
| | - Zhumei Sun
- School of Integrative Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China.
| | - Wei Xu
- School of Integrative Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China.
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De Santis A, Grifagni D, Orsetti A, Lenci E, Rosato A, D’Onofrio M, Trabocchi A, Ciofi-Baffoni S, Cantini F, Calderone V. A Structural Investigation of the Interaction between a GC-376-Based Peptidomimetic PROTAC and Its Precursor with the Viral Main Protease of Coxsackievirus B3. Biomolecules 2024; 14:1260. [PMID: 39456193 PMCID: PMC11506516 DOI: 10.3390/biom14101260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2024] [Revised: 09/16/2024] [Accepted: 10/02/2024] [Indexed: 10/28/2024] Open
Abstract
The conservation of the main protease in viral genomes, combined with the absence of a homologous protease in humans, makes this enzyme family an ideal target for developing broad-spectrum antiviral drugs with minimized host toxicity. GC-376, a peptidomimetic 3CL protease inhibitor, has shown significant efficacy against coronaviruses. Recently, a GC-376-based PROTAC was developed to target and induce the proteasome-mediated degradation of the dimeric SARS-CoV-2 3CLPro protein. Extending this approach, the current study investigates the application of the GC-376 PROTAC to the 3CPro protease of enteroviruses, specifically characterizing its interaction with CVB3 3CPro through X-ray crystallography, NMR (Nuclear Magnetic Resonance) and biochemical techniques. The crystal structure of CVB3 3CPro bound to the GC-376 PROTAC precursor was obtained at 1.9 Å resolution. The crystallographic data show that there are some changes between the binding of CVB3 3CPro and SARS-CoV-2 3CLPro, but the overall similarity is strong (RMSD on C-alpha 0.3 Å). The most notable variation is the orientation of the benzyloxycarbonyl group of GC-376 with the S4 subsite of the proteases. NMR backbone assignment of CVB3 3CPro bound and unbound to the GC-376 PROTAC precursor (80% and 97%, respectively) was obtained. This information complemented the investigation, by NMR, of the interaction of CVB3 3CPro with the GC-376 PROTAC, and its precursor allows us to define that the GC-376 PROTAC binds to CVB3 3CPro in a mode very similar to that of the precursor. The NMR relaxation data indicate that a quench of dynamics of a large part of the protein backbone involving the substrate-binding site and surrounding regions occurs upon GC-376 PROTAC precursor binding. This suggests that the substrate cavity, by sampling different backbone conformations in the absence of the substrate, is able to select the suitable one necessary to covalently bind the substrate, this being the latter reaction, which is the fundamental step required to functionally activate the enzymatic reaction. The inhibition activity assay showed inhibition potency in the micromolar range for GC-376 PROTAC and its precursor. Overall, we can conclude that the GC-376 PROTAC fits well within the binding sites of both proteases, demonstrating its potential as a broad-spectrum antiviral agent.
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Affiliation(s)
- Alessia De Santis
- Magnetic Resonance Center CERM, University of Florence, Via Luigi Sacconi 6, Sesto Fiorentino, 50019 Florence, Italy; (A.D.S.); (D.G.); (A.O.); (A.R.); (S.C.-B.)
- Department of Chemistry, University of Florence, Via della Lastruccia 3-13, Sesto Fiorentino, 50019 Florence, Italy; (E.L.); (A.T.)
| | - Deborah Grifagni
- Magnetic Resonance Center CERM, University of Florence, Via Luigi Sacconi 6, Sesto Fiorentino, 50019 Florence, Italy; (A.D.S.); (D.G.); (A.O.); (A.R.); (S.C.-B.)
- Department of Chemistry, University of Florence, Via della Lastruccia 3-13, Sesto Fiorentino, 50019 Florence, Italy; (E.L.); (A.T.)
| | - Andrea Orsetti
- Magnetic Resonance Center CERM, University of Florence, Via Luigi Sacconi 6, Sesto Fiorentino, 50019 Florence, Italy; (A.D.S.); (D.G.); (A.O.); (A.R.); (S.C.-B.)
- Department of Chemistry, University of Florence, Via della Lastruccia 3-13, Sesto Fiorentino, 50019 Florence, Italy; (E.L.); (A.T.)
| | - Elena Lenci
- Department of Chemistry, University of Florence, Via della Lastruccia 3-13, Sesto Fiorentino, 50019 Florence, Italy; (E.L.); (A.T.)
| | - Antonio Rosato
- Magnetic Resonance Center CERM, University of Florence, Via Luigi Sacconi 6, Sesto Fiorentino, 50019 Florence, Italy; (A.D.S.); (D.G.); (A.O.); (A.R.); (S.C.-B.)
- Department of Chemistry, University of Florence, Via della Lastruccia 3-13, Sesto Fiorentino, 50019 Florence, Italy; (E.L.); (A.T.)
| | - Mariapina D’Onofrio
- Department of Biotechnology, University of Verona, Strada le Grazie 15, 37134 Verona, Italy;
| | - Andrea Trabocchi
- Department of Chemistry, University of Florence, Via della Lastruccia 3-13, Sesto Fiorentino, 50019 Florence, Italy; (E.L.); (A.T.)
| | - Simone Ciofi-Baffoni
- Magnetic Resonance Center CERM, University of Florence, Via Luigi Sacconi 6, Sesto Fiorentino, 50019 Florence, Italy; (A.D.S.); (D.G.); (A.O.); (A.R.); (S.C.-B.)
- Department of Chemistry, University of Florence, Via della Lastruccia 3-13, Sesto Fiorentino, 50019 Florence, Italy; (E.L.); (A.T.)
| | - Francesca Cantini
- Magnetic Resonance Center CERM, University of Florence, Via Luigi Sacconi 6, Sesto Fiorentino, 50019 Florence, Italy; (A.D.S.); (D.G.); (A.O.); (A.R.); (S.C.-B.)
- Department of Chemistry, University of Florence, Via della Lastruccia 3-13, Sesto Fiorentino, 50019 Florence, Italy; (E.L.); (A.T.)
| | - Vito Calderone
- Magnetic Resonance Center CERM, University of Florence, Via Luigi Sacconi 6, Sesto Fiorentino, 50019 Florence, Italy; (A.D.S.); (D.G.); (A.O.); (A.R.); (S.C.-B.)
- Department of Chemistry, University of Florence, Via della Lastruccia 3-13, Sesto Fiorentino, 50019 Florence, Italy; (E.L.); (A.T.)
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Kowalczyk J, Kłodawska K, Zych M, Burczyk J, Malec P. Ubiquitin-like and ubiquitinylated proteins associated with the maternal cell walls of Scenedesmus obliquus 633 as identified by immunochemistry and LC-MS/MS proteomics. PROTOPLASMA 2024:10.1007/s00709-024-01994-3. [PMID: 39365352 DOI: 10.1007/s00709-024-01994-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 09/23/2024] [Indexed: 10/05/2024]
Abstract
The cell walls of green algae Scenedesmus obliquus are complex, polymeric structures including an inner cellulose layer surrounded by an algaenan-containing trilaminar sheath. The process of autosporulation leads to the formation of sporangial (maternal) cell walls, which are released into the medium after sporangial autolysis. In this study, a fraction of maternal cell wall material (CWM) was isolated from the stationary phase cultures of Scenedesmus obliquus 633 and subjected to immunofluorescence microscopy using polyclonal anti-ubiquitin antibodies. The water-extracted polypeptide fraction from the maternal cell walls was then analyzed using immunoblotting and LC-MS/MS. An immunoanalysis showed the presence of several peptides reactive with polyclonal anti-ubiquitin serum, with apparent molecular masses of c. 12, 70, 120, 200, and > 250 kDa. Cell wall-associated peptides were identified on the basis of LC-MS/MS spectra across NCBI databases, including the Scenedesmaceae family (58 records), the Chlorophyceae class (37 records), and Chlamydomonas reinhardtii (18 records) corresponding to the signatures of 95 identified proteins. In particular, three signatures identified ubiquitin and ubiquitin-related proteins. In the maternal cell walls, immunoblotting analysis, immunofluorescence microscopy, and LC-MS/MS proteomics collectively demonstrated the presence of ubiquitin-like epitopes, ubiquitin-specific peptide signatures, and several putative ubiquitin conjugates of a higher molecular mass. These results support the presence of ubiquitin-like proteins in the extramembranous compartment of Scenedesmus obliquus 633 and suggest that protein ubiquitination plays a significant role in the formation and functional integrity of the maternal cell walls in green algae.
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Affiliation(s)
- Justyna Kowalczyk
- Department of Plant Physiology and Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387, Kraków, Poland
- Doctoral School of Exact and Natural Sciences, Jagiellonian University, 30-348, Kraków, Poland
| | - Kinga Kłodawska
- Department of Plant Physiology and Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387, Kraków, Poland
| | - Maria Zych
- Department of Pharmacognosy and Phytochemistry, Faculty of Pharmaceutical Sciences in Sosnowiec, Medical University of Silesia, Katowice, Jagiellońska 4, 41-200, Sosnowiec, Poland
| | - Jan Burczyk
- Department of Pharmacognosy and Phytochemistry, Faculty of Pharmaceutical Sciences in Sosnowiec, Medical University of Silesia, Katowice, Jagiellońska 4, 41-200, Sosnowiec, Poland
- Laboratory of Biotechnology, Puńcowska 74, 43-400, Cieszyn, Poland
| | - Przemysław Malec
- Department of Plant Physiology and Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387, Kraków, Poland.
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