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Huang Z, Nie Y, Huang Y, Liu L, Liu B. Elucidating the role of monoacetylphlorogulcinol in the pathogenicity of Pseudomonas 'gingeri' against Agaricus bisporus. PEST MANAGEMENT SCIENCE 2024; 80:3526-3539. [PMID: 38446123 DOI: 10.1002/ps.8057] [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: 12/02/2023] [Revised: 02/29/2024] [Accepted: 03/06/2024] [Indexed: 03/07/2024]
Abstract
BACKGROUND Agaricus bisporus is a globally important edible fungus. The occurrence of ginger blotch caused by Pseudomonas 'gingeri' during A. bisporus growth and post-harvest stages results in significant economic losses. The biotoxin monoacetylphloroglucinol (MAPG) produced by P. 'gingeri' is responsible for inducing ginger blotch on A. bisporus. However, the understanding of the toxic mechanisms of MAPG on A. bisporus remains limited, which hinders the precise control of ginger blotch disease in A. bisporus and the breeding of disease-resistant varieties. RESULTS Integrating transcriptomic, metabolomic, and physiological data revealed that MAPG led to an increase in intracellular superoxide anion (O2 -) levels and lipid peroxidation in A. bisporus. MAPG changed the cellular membrane composition of A. bisporus, causing to damage membrane permeability. MAPG inhibited the expression of genes associated with the 19s subunit of the proteasome, thereby impeding cellular waste degradation in A. bisporus. Unlike melanin, MAPG stimulated the synthesis of flavonoids in A. bisporus, which might explain the manifestation of ginger-colored symptoms rather than browning. Meanwhile, the glutathione metabolism pathway in A. bisporus played a pivotal role in counteracting the cytotoxic effects of MAPG. Additionally, enhanced catalase activity and up-regulation of defense-related genes, including cytochrome P450s, Major Facilitator Superfamily (MFS), and ABC transporters, were observed. CONCLUSION This study provides comprehensive insights into MAPG toxicity in A. bisporus and uncovers the detoxification strategies of A. bisporus against MAPG. The findings offer valuable evidence for precise control and breeding of resistant varieties against ginger blotch in A. bisporus. © 2024 Society of Chemical Industry.
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Affiliation(s)
- Zaixing Huang
- Institute of Applied Microbiology, College of Agriculture, Guangxi University, Nanning, China
| | - Yulu Nie
- Institute of Applied Microbiology, College of Agriculture, Guangxi University, Nanning, China
| | - Yiyun Huang
- Institute of Applied Microbiology, College of Agriculture, Guangxi University, Nanning, China
| | - Lizhen Liu
- Institute of Applied Microbiology, College of Agriculture, Guangxi University, Nanning, China
| | - Bin Liu
- Institute of Applied Microbiology, College of Agriculture, Guangxi University, Nanning, China
- Guangxi Key Laboratory for Agro-Environment and Agro-Product Safety, Nanning, China
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2
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Cascio P. PA28γ, the ring that makes tumors invisible to the immune system? Biochimie 2024:S0300-9084(24)00078-6. [PMID: 38631454 DOI: 10.1016/j.biochi.2024.04.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 03/29/2024] [Accepted: 04/12/2024] [Indexed: 04/19/2024]
Abstract
PA28γ is a proteasomal interactor whose main and most known function is to stimulate the hydrolytic activity of the 20 S proteasome independently of ubiquitin and ATP. Unlike its two paralogues, PA28α and PA28β, PA28γ is largely present in the nuclear compartment and plays pivotal functions in important pathways such as cellular division, apoptosis, neoplastic transformation, chromatin structure and organization, fertility, lipid metabolism, and DNA repair mechanisms. Although it is known that a substantial fraction of PA28γ is found in the cell in a free form (i.e. not associated with 20 S), almost all of the studies so far have focused on its ability to modulate proteasomal enzymatic activities. In this respect, the ability of PA28γ to strongly stimulate degradation of proteins, especially if intrinsically disordered and therefore devoid of three-dimensional tightly folded structure, appears to be the main molecular mechanism underlying its multiple biological effects. Initial studies, conducted more than 20 years ago, came to the conclusion that among the many biological functions of PA28γ, the immunological ones were rather limited and circumscribed. In this review, we focus on recent evidence showing that PA28γ fulfills significant functions in cell-mediated acquired immunity, with a particular role in attenuating MHC class I antigen presentation, especially in relation to neoplastic transformation and autoimmune diseases.
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Affiliation(s)
- Paolo Cascio
- Department of Veterinary Sciences, University of Turin, Largo P. Braccini 2, 10095, Grugliasco, Turin, Italy.
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3
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Sun H, Le S, Guo Z, Chen H. Exploring the free energy landscape of proteins using magnetic tweezers. Methods Enzymol 2024; 694:237-261. [PMID: 38492953 DOI: 10.1016/bs.mie.2023.12.008] [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: 03/18/2024]
Abstract
Proteins fold to their native states by searching through the free energy landscapes. As single-domain proteins are the basic building block of multiple-domain proteins or protein complexes composed of subunits, the free energy landscapes of single-domain proteins are of critical importance to understand the folding and unfolding processes of proteins. To explore the free energy landscapes of proteins over large conformational space, the stability of native structure is perturbed by biochemical or mechanical means, and the conformational transition process is measured. In single molecular manipulation experiments, stretching force is applied to proteins, and the folding and unfolding transitions are recorded by the extension time course. Due to the broad force range and long-time stability of magnetic tweezers, the free energy landscape over large conformational space can be obtained. In this article, we describe the magnetic tweezers instrument design, protein construct design and preparation, fluid chamber preparation, common-used measuring protocols including force-ramp and force-jump measurements, and data analysis methods to construct the free energy landscape. Single-domain cold shock protein is introduced as an example to build its free energy landscape by magnetic tweezers measurements.
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Affiliation(s)
- Hao Sun
- Center of Biomedical Physics, Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, P.R. China
| | - Shimin Le
- Department of Physics, Research Institute for Biomimetics and Soft Matter, Fujian Provincial Key Lab for Soft Functional Materials Research, Xiamen University, Xiamen, P.R. China
| | - Zilong Guo
- Center of Biomedical Physics, Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, P.R. China.
| | - Hu Chen
- Center of Biomedical Physics, Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, P.R. China; Department of Physics, Research Institute for Biomimetics and Soft Matter, Fujian Provincial Key Lab for Soft Functional Materials Research, Xiamen University, Xiamen, P.R. China.
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4
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Brat C, Huynh Phuoc HP, Awad O, Parmar BS, Hellmuth N, Heinicke U, Amr S, Grimmer J, Sürün D, Husnjak K, Carlsson M, Fahrer J, Bauer T, Krieg SC, Manolikakes G, Zacharowski K, Steinhilber D, Münch C, Maier TJ, Roos J. Endogenous anti-tumorigenic nitro-fatty acids inhibit the ubiquitin-proteasome system by directly targeting the 26S proteasome. Cell Chem Biol 2023; 30:1277-1294.e12. [PMID: 37473760 DOI: 10.1016/j.chembiol.2023.06.017] [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: 02/10/2022] [Revised: 04/11/2023] [Accepted: 06/16/2023] [Indexed: 07/22/2023]
Abstract
Nitro-fatty acids (NFAs) are endogenous lipid mediators causing a spectrum of anti-inflammatory effects by covalent modification of key proteins within inflammatory signaling pathways. Recent animal models of solid tumors have helped demonstrate their potential as anti-tumorigenic therapeutics. This study evaluated the anti-tumorigenic effects of NFAs in colon carcinoma cells and other solid and leukemic tumor cell lines. NFAs inhibited the ubiquitin-proteasome system (UPS) by directly targeting the 26S proteasome, leading to polyubiquitination and inhibition of the proteasome activities. UPS suppression induced the unfolded protein response, resulting in tumor cell death. The NFA-mediated effects were substantial, specific, and enduring, representing a unique mode of action for UPS suppression. This study provides mechanistic insights into the biological actions of NFAs as possible endogenous tumor-suppressive factors, indicating that NFAs might be key structures for designing a novel class of direct proteasome inhibitors.
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Affiliation(s)
- Camilla Brat
- Department of Anesthesia, Intensive Care Medicine and Pain Therapy, University Hospital Frankfurt, Goethe-University, Frankfurt/Main 60590 Hesse, Germany
| | - Hai Phong Huynh Phuoc
- Department Safety of Medicinal Products and Medical Devices, Paul-Ehrlich-Institute, Federal Institute for Vaccines and Biomedicines, Langen, 63225 Hesse, Germany
| | - Omar Awad
- Department Safety of Medicinal Products and Medical Devices, Paul-Ehrlich-Institute, Federal Institute for Vaccines and Biomedicines, Langen, 63225 Hesse, Germany
| | - Bhavesh S Parmar
- Institute of Biochemistry II, University Hospital Frankfurt, Goethe-University, Frankfurt/Main, 60590 Hesse, Germany
| | - Nadine Hellmuth
- Department of Anesthesia, Intensive Care Medicine and Pain Therapy, University Hospital Frankfurt, Goethe-University, Frankfurt/Main 60590 Hesse, Germany
| | - Ulrike Heinicke
- Department of Anesthesia, Intensive Care Medicine and Pain Therapy, University Hospital Frankfurt, Goethe-University, Frankfurt/Main 60590 Hesse, Germany
| | - Shady Amr
- Institute of Biochemistry II, University Hospital Frankfurt, Goethe-University, Frankfurt/Main, 60590 Hesse, Germany
| | - Jennifer Grimmer
- Department of Chemistry, RPTU Kaiserslautern-Landau, Kaiserslautern, 67663 Rhineland-Palatinate, Germany
| | - Duran Sürün
- Medical Systems Biology, Faculty of Medicine, TU Dresden, Dresden, 01307 Saxony, Germany
| | - Koraljka Husnjak
- Institute of Biochemistry II, University Hospital Frankfurt, Goethe-University, Frankfurt/Main, 60590 Hesse, Germany
| | - Max Carlsson
- Division of Food Chemistry and Toxicology, Department of Chemistry, RPTU Kaiserslautern-Landau, Kaiserslautern, 67663 Rhineland-Palatinate, Germany
| | - Jörg Fahrer
- Division of Food Chemistry and Toxicology, Department of Chemistry, RPTU Kaiserslautern-Landau, Kaiserslautern, 67663 Rhineland-Palatinate, Germany
| | - Tom Bauer
- Department Safety of Medicinal Products and Medical Devices, Paul-Ehrlich-Institute, Federal Institute for Vaccines and Biomedicines, Langen, 63225 Hesse, Germany
| | - Sara-Cathrin Krieg
- Department of Chemistry, RPTU Kaiserslautern-Landau, Kaiserslautern, 67663 Rhineland-Palatinate, Germany
| | - Georg Manolikakes
- Department of Chemistry, RPTU Kaiserslautern-Landau, Kaiserslautern, 67663 Rhineland-Palatinate, Germany
| | - Kai Zacharowski
- Department of Anesthesia, Intensive Care Medicine and Pain Therapy, University Hospital Frankfurt, Goethe-University, Frankfurt/Main 60590 Hesse, Germany
| | - Dieter Steinhilber
- Institute of Pharmaceutical Chemistry, Goethe-University, Frankfurt/Main, 60438 Hesse, Germany
| | - Christian Münch
- Institute of Biochemistry II, University Hospital Frankfurt, Goethe-University, Frankfurt/Main, 60590 Hesse, Germany
| | - Thorsten Jürgen Maier
- Department of Anesthesia, Intensive Care Medicine and Pain Therapy, University Hospital Frankfurt, Goethe-University, Frankfurt/Main 60590 Hesse, Germany; Department Safety of Medicinal Products and Medical Devices, Paul-Ehrlich-Institute, Federal Institute for Vaccines and Biomedicines, Langen, 63225 Hesse, Germany
| | - Jessica Roos
- Department of Anesthesia, Intensive Care Medicine and Pain Therapy, University Hospital Frankfurt, Goethe-University, Frankfurt/Main 60590 Hesse, Germany; Department Safety of Medicinal Products and Medical Devices, Paul-Ehrlich-Institute, Federal Institute for Vaccines and Biomedicines, Langen, 63225 Hesse, Germany.
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5
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Silhan J, Fajtova P, Bartosova J, Hurysz BM, Almaliti J, Miyamoto Y, Eckmann L, Gerwick WH, O’Donoghue AJ, Boura E. Structural elucidation of recombinant Trichomonas vaginalis 20S proteasome bound to covalent inhibitors. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.17.553660. [PMID: 37645851 PMCID: PMC10462138 DOI: 10.1101/2023.08.17.553660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Proteasomes are essential for protein homeostasis in mammalian cells1-4 and in protozoan parasites such as Trichomonas vaginalis (Tv).5 Tv and other protozoan 20S proteasomes have been validated as druggable targets.6-8 However, in the case of Tv 20S proteasome (Tv20S), biochemical and structural studies were impeded by low yields and purity of the native proteasome. We successfully made recombinant Tv20S by expressing all seven α and seven β subunits together with the Ump-1 chaperone in insect cells. We isolated recombinant proteasome and showed that it was biochemically indistinguishable from the native enzyme. We confirmed that the recombinant Tv20S is inhibited by the natural product marizomib (MZB)9 and the recently developed peptide inhibitor carmaphycin-17 (CP-17)8,10. Specifically, MZB binds to the β1, β2 and β5 subunits, while CP-17 binds the β2 and β5 subunits. Next, we obtained cryo-EM structures of Tv20S in complex with these covalent inhibitors at 2.8Å resolution. The structures revealed the overall fold of the Tv20S and the binding mode of MZB and CP-17. Our work explains the low specificity of MZB and higher specificity of CP-17 towards Tv20S as compared to human proteasome and provides the platform for the development of Tv20S inhibitors for treatment of trichomoniasis.
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Affiliation(s)
- Jan Silhan
- Institute of Organic Chemistry and Biochemistry AS CR, v.v.i., Flemingovo nam. 2., 166 10 Prague 6, Czech Republic
| | - Pavla Fajtova
- Institute of Organic Chemistry and Biochemistry AS CR, v.v.i., Flemingovo nam. 2., 166 10 Prague 6, Czech Republic
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, 92037, USA
| | - Jitka Bartosova
- Institute of Organic Chemistry and Biochemistry AS CR, v.v.i., Flemingovo nam. 2., 166 10 Prague 6, Czech Republic
| | - Brianna M. Hurysz
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, 92037, USA
| | - Jehad Almaliti
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, 92037, USA
| | - Yukiko Miyamoto
- Division of Gastroenterology, School of Medicine, University of California San Diego, La Jolla, CA, 92037, USA
| | - Lars Eckmann
- Division of Gastroenterology, School of Medicine, University of California San Diego, La Jolla, CA, 92037, USA
| | - William H. Gerwick
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, 92037, USA
| | - Anthony J. O’Donoghue
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, 92037, USA
- Center for Discovery and Innovation in Parasitic Diseases, Skaggs School of Pharmacy and pharmaceutical Sciences, University of California, San Diego, 9500 Gilman Dr., La Jolla, CA 92093, USA
| | - Evzen Boura
- Institute of Organic Chemistry and Biochemistry AS CR, v.v.i., Flemingovo nam. 2., 166 10 Prague 6, Czech Republic
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6
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Wang H, Zhou R, Xu F, Yang K, Zheng L, Zhao P, Shi G, Dai L, Xu C, Yu L, Li Z, Wang J, Wang J. Beyond canonical PROTAC: biological targeted protein degradation (bioTPD). Biomater Res 2023; 27:72. [PMID: 37480049 PMCID: PMC10362593 DOI: 10.1186/s40824-023-00385-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2023] [Accepted: 04/21/2023] [Indexed: 07/23/2023] Open
Abstract
Targeted protein degradation (TPD) is an emerging therapeutic strategy with the potential to modulate disease-associated proteins that have previously been considered undruggable, by employing the host destruction machinery. The exploration and discovery of cellular degradation pathways, including but not limited to proteasomes and lysosome pathways as well as their degraders, is an area of active research. Since the concept of proteolysis-targeting chimeras (PROTACs) was introduced in 2001, the paradigm of TPD has been greatly expanded and moved from academia to industry for clinical translation, with small-molecule TPD being particularly represented. As an indispensable part of TPD, biological TPD (bioTPD) technologies including peptide-, fusion protein-, antibody-, nucleic acid-based bioTPD and others have also emerged and undergone significant advancement in recent years, demonstrating unique and promising activities beyond those of conventional small-molecule TPD. In this review, we provide an overview of recent advances in bioTPD technologies, summarize their compositional features and potential applications, and briefly discuss their drawbacks. Moreover, we present some strategies to improve the delivery efficacy of bioTPD, addressing their challenges in further clinical development.
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Affiliation(s)
- Huifang Wang
- Shenzhen Institute of Respiratory Disease, Shenzhen Clinical Research Centre for Respirology, The Second Clinical Medical College, The First Affiliated Hospital, Shenzhen People's Hospital, Jinan University, Southern University of Science and Technology, Shenzhen, 518020, Guangdong, P. R. China
| | - Runhua Zhou
- School of Pharmaceutical Science, Southern Medical University, Guangzhou, 510515, P. R. China
| | - Fushan Xu
- The Second Clinical Medical College, The First Affiliated Hospital, Shenzhen People's Hospital, Jinan University, Southern University of Science and Technology, Shenzhen, 518020, Guangdong, P. R. China
| | - Kongjun Yang
- The Second Clinical Medical College, The First Affiliated Hospital, Shenzhen People's Hospital, Jinan University, Southern University of Science and Technology, Shenzhen, 518020, Guangdong, P. R. China
| | - Liuhai Zheng
- Shenzhen Institute of Respiratory Disease, Shenzhen Clinical Research Centre for Respirology, The Second Clinical Medical College, The First Affiliated Hospital, Shenzhen People's Hospital, Jinan University, Southern University of Science and Technology, Shenzhen, 518020, Guangdong, P. R. China
| | - Pan Zhao
- Shenzhen Institute of Respiratory Disease, Shenzhen Clinical Research Centre for Respirology, The Second Clinical Medical College, The First Affiliated Hospital, Shenzhen People's Hospital, Jinan University, Southern University of Science and Technology, Shenzhen, 518020, Guangdong, P. R. China
| | - Guangwei Shi
- School of Pharmaceutical Science, Southern Medical University, Guangzhou, 510515, P. R. China
| | - Lingyun Dai
- Shenzhen Institute of Respiratory Disease, Shenzhen Clinical Research Centre for Respirology, The Second Clinical Medical College, The First Affiliated Hospital, Shenzhen People's Hospital, Jinan University, Southern University of Science and Technology, Shenzhen, 518020, Guangdong, P. R. China
| | - Chengchao Xu
- Shenzhen Institute of Respiratory Disease, Shenzhen Clinical Research Centre for Respirology, The Second Clinical Medical College, The First Affiliated Hospital, Shenzhen People's Hospital, Jinan University, Southern University of Science and Technology, Shenzhen, 518020, Guangdong, P. R. China
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Artemisinin Research Center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, P. R. China
| | - Le Yu
- School of Pharmaceutical Science, Southern Medical University, Guangzhou, 510515, P. R. China.
| | - Zhijie Li
- Shenzhen Institute of Respiratory Disease, Shenzhen Clinical Research Centre for Respirology, The Second Clinical Medical College, The First Affiliated Hospital, Shenzhen People's Hospital, Jinan University, Southern University of Science and Technology, Shenzhen, 518020, Guangdong, P. R. China.
| | - Jianhong Wang
- Shenzhen Mental Health Center, Shenzhen Kangning Hospital, Shenzhen, 518020, Guangdong, P. R. China.
| | - Jigang Wang
- Shenzhen Institute of Respiratory Disease, Shenzhen Clinical Research Centre for Respirology, The Second Clinical Medical College, The First Affiliated Hospital, Shenzhen People's Hospital, Jinan University, Southern University of Science and Technology, Shenzhen, 518020, Guangdong, P. R. China.
- School of Pharmaceutical Science, Southern Medical University, Guangzhou, 510515, P. R. China.
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Artemisinin Research Center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, P. R. China.
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7
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Choi WH, Yun Y, Byun I, Kim S, Lee S, Sim J, Levi S, Park SH, Jun J, Kleifeld O, Kim KP, Han D, Chiba T, Seok C, Kwon YT, Glickman MH, Lee MJ. ECPAS/Ecm29-mediated 26S proteasome disassembly is an adaptive response to glucose starvation. Cell Rep 2023; 42:112701. [PMID: 37384533 DOI: 10.1016/j.celrep.2023.112701] [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: 08/29/2022] [Revised: 05/07/2023] [Accepted: 06/09/2023] [Indexed: 07/01/2023] Open
Abstract
The 26S proteasome comprises 20S catalytic and 19S regulatory complexes. Approximately half of the proteasomes in cells exist as free 20S complexes; however, our mechanistic understanding of what determines the ratio of 26S to 20S species remains incomplete. Here, we show that glucose starvation uncouples 26S holoenzymes into 20S and 19S subcomplexes. Subcomplex affinity purification and quantitative mass spectrometry reveal that Ecm29 proteasome adaptor and scaffold (ECPAS) mediates this structural remodeling. The loss of ECPAS abrogates 26S dissociation, reducing degradation of 20S proteasome substrates, including puromycylated polypeptides. In silico modeling suggests that ECPAS conformational changes commence the disassembly process. ECPAS is also essential for endoplasmic reticulum stress response and cell survival during glucose starvation. In vivo xenograft model analysis reveals elevated 20S proteasome levels in glucose-deprived tumors. Our results demonstrate that the 20S-19S disassembly is a mechanism adapting global proteolysis to physiological needs and countering proteotoxic stress.
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Affiliation(s)
- Won Hoon Choi
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul 03080, Korea
| | - Yejin Yun
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul 03080, Korea; Department of Biomedical Sciences, Seoul National University Graduate School, Seoul 03080, Korea
| | - Insuk Byun
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul 03080, Korea; Department of Biomedical Sciences, Seoul National University Graduate School, Seoul 03080, Korea
| | - Sumin Kim
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul 03080, Korea; Department of Biomedical Sciences, Seoul National University Graduate School, Seoul 03080, Korea
| | - Seho Lee
- Department of Chemistry, Seoul National University, Seoul 08826, Korea
| | - Jiho Sim
- Department of Chemistry, Seoul National University, Seoul 08826, Korea
| | - Shahar Levi
- Department of Biology, Technion-Israel Institute of Technology, Haifa 32000, Israel
| | - Seo Hyeong Park
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul 03080, Korea; Department of Biomedical Sciences, Seoul National University Graduate School, Seoul 03080, Korea
| | - Jeongmoo Jun
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul 03080, Korea
| | - Oded Kleifeld
- Department of Biology, Technion-Israel Institute of Technology, Haifa 32000, Israel
| | - Kwang Pyo Kim
- Department of Applied Chemistry, Institute of Natural Science, Global Center for Pharmaceutical Ingredient Materials, Kyung Hee University, Yongin 17104, Korea
| | - Dohyun Han
- Proteomics Core Facility, Biomedical Research Institute, Seoul National University Hospital, Seoul 03080, Korea
| | - Tomoki Chiba
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Ibaraki 305-8577, Japan
| | - Chaok Seok
- Department of Chemistry, Seoul National University, Seoul 08826, Korea
| | - Yong Tae Kwon
- Department of Biomedical Sciences, Seoul National University Graduate School, Seoul 03080, Korea; Ischemic/Hypoxic Disease Institute, Convergence Research Center for Dementia, Seoul National University College of Medicine, Seoul 03080, Korea
| | - Michael H Glickman
- Department of Biology, Technion-Israel Institute of Technology, Haifa 32000, Israel.
| | - Min Jae Lee
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul 03080, Korea; Department of Biomedical Sciences, Seoul National University Graduate School, Seoul 03080, Korea; Ischemic/Hypoxic Disease Institute, Convergence Research Center for Dementia, Seoul National University College of Medicine, Seoul 03080, Korea.
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8
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Krüger G, Kirkpatrick J, Mahieu E, Franzetti B, Gabel F, Carlomagno T. An NMR Study of a 300-kDa AAA+ Unfoldase. J Mol Biol 2023; 435:167997. [PMID: 37330287 DOI: 10.1016/j.jmb.2023.167997] [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: 11/07/2022] [Revised: 01/20/2023] [Accepted: 01/30/2023] [Indexed: 06/19/2023]
Abstract
AAA+ ATPases are ubiquitous hexameric unfoldases acting in cellular protein quality control. In complex with proteases, they form protein degradation machinery (the proteasome) in both archaea and eukaryotes. Here, we use solution-state NMR spectroscopy to determine the symmetry properties of the archaeal PAN AAA+ unfoldase and gain insights into its functional mechanism. PAN consists of three folded domains: the coiled-coil (CC), OB and ATPase domains. We find that full-length PAN assembles into a hexamer with C2 symmetry, and that this symmetry extends over the CC, OB and ATPase domains. The NMR data, collected in the absence of substrate, are incompatible with the spiral staircase structure observed in electron-microscopy studies of archaeal PAN in the presence of substrate and in electron-microscopy studies of eukaryotic unfoldases both in the presence and in the absence of substrate. Based on the C2 symmetry revealed by NMR spectroscopy in solution, we propose that archaeal ATPases are flexible enzymes, which can adopt distinct conformations in different conditions. This study reaffirms the importance of studying dynamic systems in solution.
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Affiliation(s)
- Georg Krüger
- Centre of Biomolecular Drug Research and Institute of Organic Chemistry, Leibniz University Hannover, Schneiderberg 38, 30167 Hannover, Germany
| | - John Kirkpatrick
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Emilie Mahieu
- Univ. Grenoble Alpes, CEA, CNRS, IBS, 71 avenue des Martyrs, F-38000 Grenoble, France
| | - Bruno Franzetti
- Univ. Grenoble Alpes, CEA, CNRS, IBS, 71 avenue des Martyrs, F-38000 Grenoble, France
| | - Frank Gabel
- Univ. Grenoble Alpes, CEA, CNRS, IBS, 71 avenue des Martyrs, F-38000 Grenoble, France
| | - Teresa Carlomagno
- Centre of Biomolecular Drug Research and Institute of Organic Chemistry, Leibniz University Hannover, Schneiderberg 38, 30167 Hannover, Germany; School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK; Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK.
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9
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Krüger G, Kirkpatrick J, Mahieu E, Franzetti B, Gabel F, Carlomagno T. A real-time analysis of GFP unfolding by the AAA+ unfoldase PAN. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2023; 350:107431. [PMID: 37058954 DOI: 10.1016/j.jmr.2023.107431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 03/27/2023] [Accepted: 03/30/2023] [Indexed: 05/10/2023]
Abstract
Protein quality control systems are essential to maintain a healthy proteome. They often consist of an unfoldase unit, typically an AAA+ ATPase, coupled with a protease unit. In all kingdoms of life, they function to eliminate misfolded proteins, and thus prevent that their aggregates do harm to the cell, and to rapidly regulate protein levels in the presence of environmental changes. Despite the huge progress made in the past two decades in understanding the mechanism of function of protein degradation systems, the fate of the substrate during the unfolding and proteolytic processes remains poorly understood. Here we exploit an NMR-based approach to monitor GFP processing by the archaeal PAN unfoldase and the PAN-20S degradation system in real time. We find that PAN-dependent unfolding of GFP does not involve the release of partially-folded GFP molecules resulting from futile unfolding attempts. In contrast, once stably engaged with PAN, GFP molecules are efficiently transferred to the proteolytic chamber of the 20S subunit, despite the only weak affinity of PAN for the 20S subunit in the absence of substrate. This is essential to guarantee that unfolded but not proteolyzed proteins are not released into solution, where they would form toxic aggregates. The results of our studies are in good agreement with previous results derived from real-time small-angle-neutron-scattering experiments and have the advantage of allowing the investigation of substrates and products at amino-acid resolution.
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Affiliation(s)
- Georg Krüger
- Institute of Organic Chemistry and Centre of Biomolecular Drug Design, Leibniz University Hannover, Schneiderberg 38, D-30167 Hannover, Germany
| | - John Kirkpatrick
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Edgbaston, B15 2TT Birmingham, United Kingdom
| | - Emilie Mahieu
- Univ. Grenoble Alpes, CEA, CNRS, IBS, 71 avenue des Martyrs, F-38000 Grenoble, France
| | - Bruno Franzetti
- Univ. Grenoble Alpes, CEA, CNRS, IBS, 71 avenue des Martyrs, F-38000 Grenoble, France
| | - Frank Gabel
- Univ. Grenoble Alpes, CEA, CNRS, IBS, 71 avenue des Martyrs, F-38000 Grenoble, France
| | - Teresa Carlomagno
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Edgbaston, B15 2TT Birmingham, United Kingdom.
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10
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Zhu H, Wang J, Zhang Q, Pan X, Zhang J. Novel strategies and promising opportunities for targeted protein degradation: An innovative therapeutic approach to overcome cancer resistance. Pharmacol Ther 2023; 244:108371. [PMID: 36871783 DOI: 10.1016/j.pharmthera.2023.108371] [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: 12/31/2022] [Revised: 02/23/2023] [Accepted: 02/28/2023] [Indexed: 03/07/2023]
Abstract
Targeted Protein Degradation is an emerging and rapidly developing technique for designing and treating new drugs. With the emergence of a promising class of pharmaceutical molecules, Heterobifunctional Proteolysis-targeting chimeras (PROTACs), TPD has become a powerful tool to completely tackle pathogenic proteins with traditional small molecule inhibitors. However, the conventional PROTACs have gradually exposed potential disadvantages of poor oral bioavailability and pharmacokinetic (PK) and absorption, distribution, metabolism, excretion, and toxicity (ADMET) characteristics due to their larger molecular weight and more complex structure than the conventional small-molecule inhibitors. Therefore, 20 years after the concept of PROTAC was proposed, more and more scientists are committed to developing new TPD technology to overcome its defects. And several new technologies and means have been explored based on "PROTAC" to target "undruggable proteins". Here, we aim to comprehensively summarize and profoundly analyze the research progress of targeted protein degradation based on PROTAC targeting the degradation of "undruggable" targets. In order to clarify the significance of emerging and highly effective strategies based PROTACs in the treatment of various diseases especially in overcoming drug resistance in cancer, we will focus on the molecular structure, action mechanism, design concepts, development advantages and challenges of these emerging methods(e.g., aptamer-PROTAC conjugates, antibody-PROTACs and folate-PROTACs).
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Affiliation(s)
- Huanjie Zhu
- School of Pharmacy, Health Science Center, Xi'an Jiaotong University, Xi'an 710061, China
| | - Jin Wang
- School of Pharmacy, Health Science Center, Xi'an Jiaotong University, Xi'an 710061, China
| | - Qingqing Zhang
- School of Pharmacy, Health Science Center, Xi'an Jiaotong University, Xi'an 710061, China
| | - Xiaoyan Pan
- School of Pharmacy, Health Science Center, Xi'an Jiaotong University, Xi'an 710061, China
| | - Jie Zhang
- School of Pharmacy, Health Science Center, Xi'an Jiaotong University, Xi'an 710061, China.
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11
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Mukherjee S, Mepperi J, Sahu P, Barman DK, Kotamarthi HC. Single-Molecule Optical Tweezers As a Tool for Delineating the Mechanisms of Protein-Processing Mechanoenzymes. ACS OMEGA 2023; 8:87-97. [PMID: 36643560 PMCID: PMC9835622 DOI: 10.1021/acsomega.2c06044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 12/06/2022] [Indexed: 06/17/2023]
Abstract
Mechanoenzymes convert chemical energy from the hydrolysis of nucleotide triphosphates to mechanical energy for carrying out cellular functions ranging from DNA unwinding to protein degradation. Protein-processing mechanoenzymes either remodel the protein structures or translocate them across cellular compartments in an energy-dependent manner. Optical-tweezer-based single-molecule force spectroscopy assays have divulged information on details of chemo-mechanical coupling, directed motion, as well as mechanical forces these enzymes are capable of generating. In this review, we introduce the working principles of optical tweezers as a single-molecule force spectroscopy tool and assays developed to decipher the properties such as unfolding kinetics, translocation velocities, and step sizes by protein remodeling mechanoenzymes. We focus on molecular motors involved in protein degradation and disaggregation, i.e., ClpXP, ClpAP, and ClpB, and insights provided by single-molecule assays on kinetics and stepping dynamics during protein unfolding and translocation. Cellular activities such as protein synthesis, folding, and translocation across membranes are also energy dependent, and the recent single-molecule studies decoding the role of mechanical forces on these processes have been discussed.
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12
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Alwahsh M, Farhat J, Talhouni S, Hamadneh L, Hergenröder R. Bortezomib advanced mechanisms of action in multiple myeloma, solid and liquid tumors along with its novel therapeutic applications. EXCLI JOURNAL 2023; 22:146-168. [PMID: 36998701 PMCID: PMC10043448 DOI: 10.17179/excli2022-5653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 01/12/2023] [Indexed: 04/01/2023]
Abstract
Bortezomib (BTZ) is a first-in-class reversible and selective proteasome inhibitor. It inhibits the ubiquitin proteasome pathway that leads to the degradation of many intracellular proteins. Initially, BTZ was FDA approved for the treatment of refractory or relapsed multiple myeloma (MM) in 2003. Later, its usage was approved for patients with previously untreated MM. In 2006, BTZ was approved for the treatment of relapsed or refractory Mantle Cell Lymphoma (MCL) and, in 2014, for previously untreated MCL. BTZ has been extensively studied either alone or in combination with other drugs for the treatment of different liquid tumors especially in MM. However, limited data evaluated the efficacy and safety of using BTZ in patients with solid tumors. In this review, we will discuss the advanced and novel mechanisms of action of BTZ documented in MM, solid tumors and liquid tumors. Moreover, we will shed the light on the newly discovered pharmacological effects of BTZ in other prevalent diseases.
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Affiliation(s)
- Mohammad Alwahsh
- Department of Pharmacy, Faculty of Pharmacy, Al-Zaytoonah University of Jordan, P.O. Box 130, Amman, 11733, Jordan
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., 44139 Dortmund, Germany
- Institute of Pathology and Medical Research Center (ZMF), University Medical Center Mannheim, Heidelberg University, 68167 Mannheim, Germany
- *To whom correspondence should be addressed: Mohammad Alwahsh, Department of Pharmacy, Faculty of Pharmacy, Al-Zaytoonah University of Jordan, P.O. Box 130, Amman, 11733, Jordan, E-mail:
| | - Joviana Farhat
- Department of Epidemiology and Population Health, College of Medicine and Health Sciences, Khalifa University, Abu Dhabi, PO Box 127788, United Arab Emirates
| | - Shahd Talhouni
- Department of Pharmacy, Faculty of Pharmacy, Al-Zaytoonah University of Jordan, P.O. Box 130, Amman, 11733, Jordan
| | - Lama Hamadneh
- Department of Pharmacy, Faculty of Pharmacy, Al-Zaytoonah University of Jordan, P.O. Box 130, Amman, 11733, Jordan
| | - Roland Hergenröder
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., 44139 Dortmund, Germany
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13
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Targeted protein degradation: mechanisms, strategies and application. Signal Transduct Target Ther 2022; 7:113. [PMID: 35379777 PMCID: PMC8977435 DOI: 10.1038/s41392-022-00966-4] [Citation(s) in RCA: 167] [Impact Index Per Article: 83.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 02/21/2022] [Accepted: 03/15/2022] [Indexed: 12/11/2022] Open
Abstract
Traditional drug discovery mainly focuses on direct regulation of protein activity. The development and application of protein activity modulators, particularly inhibitors, has been the mainstream in drug development. In recent years, PROteolysis TArgeting Chimeras (PROTAC) technology has emerged as one of the most promising approaches to remove specific disease-associated proteins by exploiting cells’ own destruction machinery. In addition to PROTAC, many different targeted protein degradation (TPD) strategies including, but not limited to, molecular glue, Lysosome-Targeting Chimaera (LYTAC), and Antibody-based PROTAC (AbTAC), are emerging. These technologies have not only greatly expanded the scope of TPD, but also provided fresh insights into drug discovery. Here, we summarize recent advances of major TPD technologies, discuss their potential applications, and hope to provide a prime for both biologists and chemists who are interested in this vibrant field.
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14
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Kudryashova TV, Dabral S, Nayakanti S, Ray A, Goncharov DA, Avolio T, Shen Y, Rode A, Pena A, Jiang L, Lin D, Baust J, Bachman TN, Graumann J, Ruppert C, Guenther A, Schmoranzer M, Grobs Y, Lemay SE, Tremblay E, Breuils-Bonnet S, Boucherat O, Mora AL, DeLisser H, Zhao J, Zhao Y, Bonnet S, Seeger W, Pullamsetti SS, Goncharova EA. Noncanonical HIPPO/MST Signaling via BUB3 and FOXO Drives Pulmonary Vascular Cell Growth and Survival. Circ Res 2022; 130:760-778. [PMID: 35124974 PMCID: PMC8897250 DOI: 10.1161/circresaha.121.319100] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
RATIONALE The MSTs (mammalian Ste20-like kinases) 1/2 are members of the HIPPO pathway that act as growth suppressors in adult proliferative diseases. Pulmonary arterial hypertension (PAH) manifests by increased proliferation and survival of pulmonary vascular cells in small PAs, pulmonary vascular remodeling, and the rise of pulmonary arterial pressure. The role of MST1/2 in PAH is currently unknown. OBJECTIVE To investigate the roles and mechanisms of the action of MST1 and MST2 in PAH. METHODS AND RESULTS Using early-passage pulmonary vascular cells from PAH and nondiseased lungs and mice with smooth muscle-specific tamoxifen-inducible Mst1/2 knockdown, we found that, in contrast to canonical antiproliferative/proapoptotic roles, MST1/2 act as proproliferative/prosurvival molecules in human PAH pulmonary arterial vascular smooth muscle cells and pulmonary arterial adventitial fibroblasts and support established pulmonary vascular remodeling and pulmonary hypertension in mice with SU5416/hypoxia-induced pulmonary hypertension. By using unbiased proteomic analysis, gain- and loss-of function approaches, and pharmacological inhibition of MST1/2 kinase activity by XMU-MP-1, we next evaluated mechanisms of regulation and function of MST1/2 in PAH pulmonary vascular cells. We found that, in PAH pulmonary arterial adventitial fibroblasts, the proproliferative function of MST1/2 is caused by IL-6-dependent MST1/2 overexpression, which induces PSMC6-dependent downregulation of forkhead homeobox type O 3 and hyperproliferation. In PAH pulmonary arterial vascular smooth muscle cells, MST1/2 acted via forming a disease-specific interaction with BUB3 and supported ECM (extracellular matrix)- and USP10-dependent BUB3 accumulation, upregulation of Akt-mTORC1, cell proliferation, and survival. Supporting our in vitro observations, smooth muscle-specific Mst1/2 knockdown halted upregulation of Akt-mTORC1 in small muscular PAs of mice with SU5416/hypoxia-induced pulmonary hypertension. CONCLUSIONS Together, this study describes a novel proproliferative/prosurvival role of MST1/2 in PAH pulmonary vasculature, provides a novel mechanistic link from MST1/2 via BUB3 and forkhead homeobox type O to the abnormal proliferation and survival of pulmonary arterial vascular smooth muscle cells and pulmonary arterial adventitial fibroblasts, remodeling and pulmonary hypertension, and suggests new target pathways for therapeutic intervention.
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Affiliation(s)
- Tatiana V. Kudryashova
- Lung Center, Division of Pulmonary, Critical Care and Sleep Medicine, University of California, Davis School of Medicine, Davis, CA, USA
- Pittsburgh Heart, Lung and Blood Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, PA, USA
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Swati Dabral
- Max Planck Institute for Heart and Lung Research, Department of Lung Development and Remodeling, Member of the German Center for Lung Research (DZL), Bad Nauheim, Germany
| | - Sreenath Nayakanti
- Max Planck Institute for Heart and Lung Research, Department of Lung Development and Remodeling, Member of the German Center for Lung Research (DZL), Bad Nauheim, Germany
| | - Arnab Ray
- Pittsburgh Heart, Lung and Blood Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, PA, USA
| | - Dmitry A. Goncharov
- Lung Center, Division of Pulmonary, Critical Care and Sleep Medicine, University of California, Davis School of Medicine, Davis, CA, USA
- Pittsburgh Heart, Lung and Blood Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, PA, USA
| | - Theodore Avolio
- Pittsburgh Heart, Lung and Blood Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, PA, USA
| | - Yuanjun Shen
- Lung Center, Division of Pulmonary, Critical Care and Sleep Medicine, University of California, Davis School of Medicine, Davis, CA, USA
- Pittsburgh Heart, Lung and Blood Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, PA, USA
| | - Analise Rode
- Pittsburgh Heart, Lung and Blood Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, PA, USA
| | - Andressa Pena
- Pittsburgh Heart, Lung and Blood Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, PA, USA
| | - Lifeng Jiang
- Lung Center, Division of Pulmonary, Critical Care and Sleep Medicine, University of California, Davis School of Medicine, Davis, CA, USA
| | - Derek Lin
- Lung Center, Division of Pulmonary, Critical Care and Sleep Medicine, University of California, Davis School of Medicine, Davis, CA, USA
| | - Jeffrey Baust
- Pittsburgh Heart, Lung and Blood Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, PA, USA
| | - Timothy N. Bachman
- Pittsburgh Heart, Lung and Blood Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, PA, USA
| | - Johannes Graumann
- Biomolecular Mass Spectrometry, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Clemens Ruppert
- Department of Internal Medicine, Member of the DZL, Member of CPI, Justus Liebig University, Giessen, 35392, Germany
| | - Andreas Guenther
- Department of Internal Medicine, Member of the DZL, Member of CPI, Justus Liebig University, Giessen, 35392, Germany
| | - Mario Schmoranzer
- Max Planck Institute for Heart and Lung Research, Department of Lung Development and Remodeling, Member of the German Center for Lung Research (DZL), Bad Nauheim, Germany
| | - Yann Grobs
- Department of Medicine, Faculty of Medicine, Université Laval, Quebec City, Canada
| | - Sarah Eve Lemay
- Department of Medicine, Faculty of Medicine, Université Laval, Quebec City, Canada
| | - Eve Tremblay
- Department of Medicine, Faculty of Medicine, Université Laval, Quebec City, Canada
| | | | - Olivier Boucherat
- Department of Medicine, Faculty of Medicine, Université Laval, Quebec City, Canada
| | - Ana L. Mora
- Pittsburgh Heart, Lung and Blood Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, PA, USA
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Horace DeLisser
- Department of Pathology and Laboratory Medicine, Pulmonary Vascular Disease Program, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Jing Zhao
- The Ohio State University College of Medicine, Columbus, OH, USA
| | - Yutong Zhao
- The Ohio State University College of Medicine, Columbus, OH, USA
| | - Sébastien Bonnet
- Department of Medicine, Faculty of Medicine, Université Laval, Quebec City, Canada
| | - Werner Seeger
- Max Planck Institute for Heart and Lung Research, Department of Lung Development and Remodeling, Member of the German Center for Lung Research (DZL), Bad Nauheim, Germany
- Department of Internal Medicine, Universities of Giessen and Marburg Lung Center (UGMLC), Institute for Lung Health (ILH), Cardio-Pulmonary Institute (CPI), Member of the DZL, Justus Liebig University, Giessen, Germany
| | - Soni S. Pullamsetti
- Max Planck Institute for Heart and Lung Research, Department of Lung Development and Remodeling, Member of the German Center for Lung Research (DZL), Bad Nauheim, Germany
- Department of Internal Medicine, Universities of Giessen and Marburg Lung Center (UGMLC), Institute for Lung Health (ILH), Cardio-Pulmonary Institute (CPI), Member of the DZL, Justus Liebig University, Giessen, Germany
| | - Elena A. Goncharova
- Lung Center, Division of Pulmonary, Critical Care and Sleep Medicine, University of California, Davis School of Medicine, Davis, CA, USA
- Pittsburgh Heart, Lung and Blood Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, PA, USA
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
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15
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The Function of Immunoproteasomes-An Immunologists' Perspective. Cells 2021; 10:cells10123360. [PMID: 34943869 PMCID: PMC8699091 DOI: 10.3390/cells10123360] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 11/23/2021] [Accepted: 11/25/2021] [Indexed: 01/02/2023] Open
Abstract
Proteasomes are responsible for intracellular proteolysis and play an important role in cellular protein homeostasis. Cells of the immune system assemble a specialized form of proteasomes, known as immunoproteasomes, in which the constitutive catalytic sites are replaced for cytokine-inducible homologues. While immunoproteasomes may fulfill all standard proteasome’ functions, they seem specially adapted for a role in MHC class I antigen processing and CD8+ T-cell activation. In this way, they may contribute to CD8+ T-cell-mediated control of intracellular infections, but also to the immunopathogenesis of autoimmune diseases. Starting at the discovery of its catalytic subunits in the genome, here, we review the observations shaping our current understanding of immunoproteasome function, and the consequential novel opportunities for immune intervention.
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16
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Sahu I, Mali SM, Sulkshane P, Xu C, Rozenberg A, Morag R, Sahoo MP, Singh SK, Ding Z, Wang Y, Day S, Cong Y, Kleifeld O, Brik A, Glickman MH. The 20S as a stand-alone proteasome in cells can degrade the ubiquitin tag. Nat Commun 2021; 12:6173. [PMID: 34702852 PMCID: PMC8548400 DOI: 10.1038/s41467-021-26427-0] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 10/04/2021] [Indexed: 12/13/2022] Open
Abstract
The proteasome, the primary protease for ubiquitin-dependent proteolysis in eukaryotes, is usually found as a mixture of 30S, 26S, and 20S complexes. These complexes have common catalytic sites, which makes it challenging to determine their distinctive roles in intracellular proteolysis. Here, we chemically synthesize a panel of homogenous ubiquitinated proteins, and use them to compare 20S and 26S proteasomes with respect to substrate selection and peptide-product generation. We show that 20S proteasomes can degrade the ubiquitin tag along with the conjugated substrate. Ubiquitin remnants on branched peptide products identified by LC-MS/MS, and flexibility in the 20S gate observed by cryo-EM, reflect the ability of the 20S proteasome to proteolyze an isopeptide-linked ubiquitin-conjugate. Peptidomics identifies proteasome-trapped ubiquitin-derived peptides and peptides of potential 20S substrates in Hi20S cells, hypoxic cells, and human failing-heart. Moreover, elevated levels of 20S proteasomes appear to contribute to cell survival under stress associated with damaged proteins.
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Affiliation(s)
- Indrajit Sahu
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, 32000, Israel
| | - Sachitanand M Mali
- Schulich faculty of Chemistry, Technion-Israel Institute of Technology, Haifa, 32000, Israel
| | - Prasad Sulkshane
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, 32000, Israel
| | - Cong Xu
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Andrey Rozenberg
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, 32000, Israel
| | - Roni Morag
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, 32000, Israel
| | | | - Sumeet K Singh
- Schulich faculty of Chemistry, Technion-Israel Institute of Technology, Haifa, 32000, Israel
| | - Zhanyu Ding
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Yifan Wang
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Sharleen Day
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Yao Cong
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, 200031, China
- Shanghai Science Research Center, Chinese Academy of Sciences, Shanghai, 201210, China
| | - Oded Kleifeld
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, 32000, Israel.
| | - Ashraf Brik
- Schulich faculty of Chemistry, Technion-Israel Institute of Technology, Haifa, 32000, Israel.
| | - Michael H Glickman
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, 32000, Israel.
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17
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Takashima M, Lalonde C, Olszanski LA, Zhao FQ. Localized and Systemic Inflammatory Mediators in a Murine Acute Mastitis Model. J Inflamm Res 2021; 14:4053-4067. [PMID: 34456581 PMCID: PMC8387587 DOI: 10.2147/jir.s313799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 07/08/2021] [Indexed: 11/28/2022] Open
Abstract
Introduction Milk depression is the major driver of economic loss due to mastitis in dairy animals. The aim of this study was to identify potential mediators of milk depression by investigating the local and systemic changes in gene expression or cytokine production during endotoxin challenge of the mammary gland in a mouse model. Methods The left and right sides of the 4th pair of mouse mammary glands were alternatively injected with either lipopolysaccharide (LPS, Escherichia coli 055: B5, 50 μL of 0.4 mg/mL) or sterile PBS through the teat meatus 3 days postpartum (n = 9). The 4th glands were individually collected 12 h after LPS injection and analyzed to identify gene expression changes by RNA sequencing and real-time PCR, and the plasma was collected before and after LPS challenge and analyzed to determine the levels of 32 cytokines. Results Transcriptome analysis showed that in addition to strong pro-inflammatory responses, which included granulocyte and monocyte migration and cytokine production and signaling, the LPS-treated glands exhibited strong ubiquitin-mediated and immune-mediated proteasome activation and an increase in nitric oxide-mediated oxidative stress. Furthermore, LPS induced a down-regulation in vesicle membrane, vesicle-mediated trafficking, and metabolic processes of amino acids and other organic molecules in the mammary gland. Of the 32 cytokines analyzed, the levels of 24 (mainly IL-6, G-CSF, MCP-1, RANTES, MIG, MIP-1b, KC, MIP-2, IP-10, and TNFα) were increased or tended to increase in the blood after LPS treatment, and only the levels of IL-9 were decreased. In the mammary gland after LPS challenge, the levels of IL-5, IL-6, IP-10, LIF, MCP-1, MIP-2, and TNFα were significantly increased, and the levels of INFΥ, IL-2, IL-4, IL-10, and IL-12 (p40) were decreased. Discussion These observations provide potential markers and targets for further studies on the prevention and treatment of gram-negative bacteria-induced mastitis.
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Affiliation(s)
- Miyuki Takashima
- Department of Animal and Veterinary Sciences, University of Vermont, Burlington, VT, 05405, USA.,Wakunaga Pharmaceutical Co. Ltd, Osaka, 532-0003, Japan
| | - Christian Lalonde
- Department of Animal and Veterinary Sciences, University of Vermont, Burlington, VT, 05405, USA
| | - Laura Ashley Olszanski
- Department of Animal and Veterinary Sciences, University of Vermont, Burlington, VT, 05405, USA
| | - Feng-Qi Zhao
- Department of Animal and Veterinary Sciences, University of Vermont, Burlington, VT, 05405, USA
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18
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Zhang J, Vancea AI, Shahul Hameed UF, Arold ST. Versatile control of the CDC48 segregase by the plant UBX-containing (PUX) proteins. Comput Struct Biotechnol J 2021; 19:3125-3132. [PMID: 34141135 PMCID: PMC8181520 DOI: 10.1016/j.csbj.2021.05.025] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 05/12/2021] [Accepted: 05/13/2021] [Indexed: 11/26/2022] Open
Abstract
In plants, AAA-adenosine triphosphatase (ATPase) Cell Division Control Protein 48 (CDC48) uses the force generated through ATP hydrolysis to pull, extract, and unfold ubiquitylated or sumoylated proteins from the membrane, chromatin, or protein complexes. The resulting changes in protein or RNA content are an important means for plants to control protein homeostasis and thereby adapt to shifting environmental conditions. The activity and targeting of CDC48 are controlled by adaptor proteins, of which the plant ubiquitin regulatory X (UBX) domain-containing (PUX) proteins constitute the largest family. Emerging knowledge on the structure and function of PUX proteins highlights that these proteins are versatile factors for plant homeostasis and adaptation that might inspire biotechnological applications.
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Affiliation(s)
- Junrui Zhang
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Biological and Environmental Science and Engineering (BESE), Thuwal 23955-6900, Saudi Arabia
| | - Alexandra I Vancea
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Biological and Environmental Science and Engineering (BESE), Thuwal 23955-6900, Saudi Arabia
| | - Umar F Shahul Hameed
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Biological and Environmental Science and Engineering (BESE), Thuwal 23955-6900, Saudi Arabia
| | - Stefan T Arold
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Biological and Environmental Science and Engineering (BESE), Thuwal 23955-6900, Saudi Arabia.,Centre de Biochimie Structurale, CNRS, INSERM, Université de Montpellier, 34090 Montpellier, France
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19
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Proteasome in action: substrate degradation by the 26S proteasome. Biochem Soc Trans 2021; 49:629-644. [PMID: 33729481 PMCID: PMC8106498 DOI: 10.1042/bst20200382] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 02/22/2021] [Accepted: 02/25/2021] [Indexed: 12/16/2022]
Abstract
Ubiquitination is the major criteria for the recognition of a substrate-protein by the 26S proteasome. Additionally, a disordered segment on the substrate — either intrinsic or induced — is critical for proteasome engagement. The proteasome is geared to interact with both of these substrate features and prepare it for degradation. To facilitate substrate accessibility, resting proteasomes are characterised by a peripheral distribution of ubiquitin receptors on the 19S regulatory particle (RP) and a wide-open lateral surface on the ATPase ring. In this substrate accepting state, the internal channel through the ATPase ring is discontinuous, thereby obstructing translocation of potential substrates. The binding of the conjugated ubiquitin to the ubiquitin receptors leads to contraction of the 19S RP. Next, the ATPases engage the substrate at a disordered segment, energetically unravel the polypeptide and translocate it towards the 20S catalytic core (CP). In this substrate engaged state, Rpn11 is repositioned at the pore of the ATPase channel to remove remaining ubiquitin modifications and accelerate translocation. C-termini of five of the six ATPases insert into corresponding lysine-pockets on the 20S α-ring to complete 20S CP gate opening. In the resulting substrate processing state, the ATPase channel is fully contiguous with the translocation channel into the 20S CP, where the substrate is proteolyzed. Complete degradation of a typical ubiquitin-conjugate takes place over a few tens of seconds while hydrolysing tens of ATP molecules in the process (50 kDa/∼50 s/∼80ATP). This article reviews recent insight into biochemical and structural features that underlie substrate recognition and processing by the 26S proteasome.
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20
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Cascio P. PA28γ: New Insights on an Ancient Proteasome Activator. Biomolecules 2021; 11:228. [PMID: 33562807 PMCID: PMC7915322 DOI: 10.3390/biom11020228] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2021] [Revised: 02/02/2021] [Accepted: 02/03/2021] [Indexed: 02/06/2023] Open
Abstract
PA28 (also known as 11S, REG or PSME) is a family of proteasome regulators whose members are widely present in many of the eukaryotic supergroups. In jawed vertebrates they are represented by three paralogs, PA28α, PA28β, and PA28γ, which assemble as heptameric hetero (PA28αβ) or homo (PA28γ) rings on one or both extremities of the 20S proteasome cylindrical structure. While they share high sequence and structural similarities, the three isoforms significantly differ in terms of their biochemical and biological properties. In fact, PA28α and PA28β seem to have appeared more recently and to have evolved very rapidly to perform new functions that are specifically aimed at optimizing the process of MHC class I antigen presentation. In line with this, PA28αβ favors release of peptide products by proteasomes and is particularly suited to support adaptive immune responses without, however, affecting hydrolysis rates of protein substrates. On the contrary, PA28γ seems to be a slow-evolving gene that is most similar to the common ancestor of the PA28 activators family, and very likely retains its original functions. Notably, PA28γ has a prevalent nuclear localization and is involved in the regulation of several essential cellular processes including cell growth and proliferation, apoptosis, chromatin structure and organization, and response to DNA damage. In striking contrast with the activity of PA28αβ, most of these diverse biological functions of PA28γ seem to depend on its ability to markedly enhance degradation rates of regulatory protein by 20S proteasome. The present review will focus on the molecular mechanisms and biochemical properties of PA28γ, which are likely to account for its various and complex biological functions and highlight the common features with the PA28αβ paralog.
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Affiliation(s)
- Paolo Cascio
- Department of Veterinary Sciences, University of Turin, Largo P. Braccini 2, 10095 Grugliasco, Italy
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21
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Chen SY, Zhang HP, Li J, Shi JH, Tang HW, Zhang Y, Zhang JK, Wen PH, Wang ZH, Shi XY, He YT, Hu BW, Yang H, Guo WZ, Zhang SJ. Tripartite Motif-Containing 27 Attenuates Liver Ischemia/Reperfusion Injury by Suppressing Transforming Growth Factor β-Activated Kinase 1 (TAK1) by TAK1 Binding Protein 2/3 Degradation. Hepatology 2021; 73:738-758. [PMID: 32343849 PMCID: PMC7898667 DOI: 10.1002/hep.31295] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 03/31/2020] [Accepted: 04/07/2020] [Indexed: 12/21/2022]
Abstract
BACKGROUND AND AIMS Hepatic ischemia-reperfusion (I/R) injury, which mainly involves inflammatory responses and apoptosis, is a common cause of organ dysfunction in liver transplantation (LT). As a critical mediator of inflammation and apoptosis in various cell types, the role of tripartite motif-containing (TRIM) 27 in hepatic I/R injury remains worthy of study. APPROACH AND RESULTS This study systemically evaluated the putative role of TRIM27/transforming growth factor β-activated kinase 1 (TAK1)/JNK (c-Jun N-terminal kinase)/p38 signaling in hepatic I/R injury. TRIM27 expression was significantly down-regulated in liver tissue from LT patients, mice subjected to hepatic I/R surgery, and hepatocytes challenged by hypoxia/reoxygenation (H/R) treatment. Subsequently, using global Trim27 knockout mice (Trim27-KO mice) and hepatocyte-specific Trim27 transgenic mice (Trim27-HTG mice), TRIM27 functions to ameliorate liver damage, reduce the inflammatory response, and prevent cell apoptosis. In parallel in vitro studies, activating TRIM27 also prevented H/R-induced hepatocyte inflammation and apoptosis. Mechanistically, TRIM27 constitutively interacted with the critical components, TAK1 and TAK1 binding protein 2/3 (TAB2/3), and promoted the degradation of TAB2/3, leading to inactivation of TAK1 and the subsequent suppression of downstream JNK/p38 signaling. CONCLUSIONS TRIM27 is a key regulator of hepatic I/R injury by mediating the degradation of TAB2/3 and suppression of downstream TAK1-JNK/p38 signaling. TRIM27 may be a promising approach to protect the liver against I/R-mediated hepatocellular damage in transplant recipients.
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Affiliation(s)
- San-Yang Chen
- Department of Hepatobiliary and Pancreatic SurgeryThe First Affiliated Hospital of Zhengzhou UniversityZhengzhouChina.,Henan Key Laboratory of Digestive Organ TransplantationZhengzhouChina.,Open and Key Laboratory of Hepatobiliary & Pancreatic Surgery and Digestive Organ Transplantation at Henan UniversitiesZhengzhouChina
| | - Hua-Peng Zhang
- Department of Hepatobiliary and Pancreatic SurgeryThe First Affiliated Hospital of Zhengzhou UniversityZhengzhouChina.,Henan Key Laboratory of Digestive Organ TransplantationZhengzhouChina.,Open and Key Laboratory of Hepatobiliary & Pancreatic Surgery and Digestive Organ Transplantation at Henan UniversitiesZhengzhouChina
| | - Jie Li
- Department of Hepatobiliary and Pancreatic SurgeryThe First Affiliated Hospital of Zhengzhou UniversityZhengzhouChina.,Henan Key Laboratory of Digestive Organ TransplantationZhengzhouChina.,Open and Key Laboratory of Hepatobiliary & Pancreatic Surgery and Digestive Organ Transplantation at Henan UniversitiesZhengzhouChina
| | - Ji-Hua Shi
- Department of Hepatobiliary and Pancreatic SurgeryThe First Affiliated Hospital of Zhengzhou UniversityZhengzhouChina.,Henan Key Laboratory of Digestive Organ TransplantationZhengzhouChina.,Open and Key Laboratory of Hepatobiliary & Pancreatic Surgery and Digestive Organ Transplantation at Henan UniversitiesZhengzhouChina
| | - Hong-Wei Tang
- Henan Key Laboratory of Digestive Organ TransplantationZhengzhouChina.,Open and Key Laboratory of Hepatobiliary & Pancreatic Surgery and Digestive Organ Transplantation at Henan UniversitiesZhengzhouChina
| | - Yi Zhang
- Department of SurgeryThe First Affiliated Hospital of Zhengzhou UniversityZhengzhouChina
| | - Jia-Kai Zhang
- Department of Hepatobiliary and Pancreatic SurgeryThe First Affiliated Hospital of Zhengzhou UniversityZhengzhouChina.,Henan Key Laboratory of Digestive Organ TransplantationZhengzhouChina.,Open and Key Laboratory of Hepatobiliary & Pancreatic Surgery and Digestive Organ Transplantation at Henan UniversitiesZhengzhouChina
| | - Pei-Hao Wen
- Department of Hepatobiliary and Pancreatic SurgeryThe First Affiliated Hospital of Zhengzhou UniversityZhengzhouChina.,Henan Key Laboratory of Digestive Organ TransplantationZhengzhouChina.,Open and Key Laboratory of Hepatobiliary & Pancreatic Surgery and Digestive Organ Transplantation at Henan UniversitiesZhengzhouChina
| | - Zhi-Hui Wang
- Department of Hepatobiliary and Pancreatic SurgeryThe First Affiliated Hospital of Zhengzhou UniversityZhengzhouChina.,Henan Key Laboratory of Digestive Organ TransplantationZhengzhouChina.,Open and Key Laboratory of Hepatobiliary & Pancreatic Surgery and Digestive Organ Transplantation at Henan UniversitiesZhengzhouChina
| | - Xiao-Yi Shi
- Department of Hepatobiliary and Pancreatic SurgeryThe First Affiliated Hospital of Zhengzhou UniversityZhengzhouChina.,Henan Key Laboratory of Digestive Organ TransplantationZhengzhouChina.,Open and Key Laboratory of Hepatobiliary & Pancreatic Surgery and Digestive Organ Transplantation at Henan UniversitiesZhengzhouChina
| | - Yu-Ting He
- Department of Hepatobiliary and Pancreatic SurgeryThe First Affiliated Hospital of Zhengzhou UniversityZhengzhouChina.,Henan Key Laboratory of Digestive Organ TransplantationZhengzhouChina.,Open and Key Laboratory of Hepatobiliary & Pancreatic Surgery and Digestive Organ Transplantation at Henan UniversitiesZhengzhouChina
| | - Bo-Wen Hu
- Department of Hepatobiliary and Pancreatic SurgeryThe First Affiliated Hospital of Zhengzhou UniversityZhengzhouChina.,Henan Key Laboratory of Digestive Organ TransplantationZhengzhouChina.,Open and Key Laboratory of Hepatobiliary & Pancreatic Surgery and Digestive Organ Transplantation at Henan UniversitiesZhengzhouChina
| | - Han Yang
- Department of Hepatobiliary and Pancreatic SurgeryThe First Affiliated Hospital of Zhengzhou UniversityZhengzhouChina.,Henan Key Laboratory of Digestive Organ TransplantationZhengzhouChina.,Open and Key Laboratory of Hepatobiliary & Pancreatic Surgery and Digestive Organ Transplantation at Henan UniversitiesZhengzhouChina
| | - Wen-Zhi Guo
- Department of Hepatobiliary and Pancreatic SurgeryThe First Affiliated Hospital of Zhengzhou UniversityZhengzhouChina.,Henan Key Laboratory of Digestive Organ TransplantationZhengzhouChina.,Open and Key Laboratory of Hepatobiliary & Pancreatic Surgery and Digestive Organ Transplantation at Henan UniversitiesZhengzhouChina
| | - Shui-Jun Zhang
- Department of Hepatobiliary and Pancreatic SurgeryThe First Affiliated Hospital of Zhengzhou UniversityZhengzhouChina.,Henan Key Laboratory of Digestive Organ TransplantationZhengzhouChina.,Open and Key Laboratory of Hepatobiliary & Pancreatic Surgery and Digestive Organ Transplantation at Henan UniversitiesZhengzhouChina
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22
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Structural Insights into Substrate Recognition and Processing by the 20S Proteasome. Biomolecules 2021; 11:biom11020148. [PMID: 33498876 PMCID: PMC7910952 DOI: 10.3390/biom11020148] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2021] [Revised: 01/18/2021] [Accepted: 01/21/2021] [Indexed: 12/12/2022] Open
Abstract
Four decades of proteasome research have yielded extensive information on ubiquitin-dependent proteolysis. The archetype of proteasomes is a 20S barrel-shaped complex that does not rely on ubiquitin as a degradation signal but can degrade substrates with a considerable unstructured stretch. Since roughly half of all proteasomes in most eukaryotic cells are free 20S complexes, ubiquitin-independent protein degradation may coexist with ubiquitin-dependent degradation by the highly regulated 26S proteasome. This article reviews recent advances in our understanding of the biochemical and structural features that underlie the proteolytic mechanism of 20S proteasomes. The two outer α-rings of 20S proteasomes provide a number of potential docking sites for loosely folded polypeptides. The binding of a substrate can induce asymmetric conformational changes, trigger gate opening, and initiate its own degradation through a protease-driven translocation mechanism. Consequently, the substrate translocates through two additional narrow apertures augmented by the β-catalytic active sites. The overall pulling force through the two annuli results in a protease-like unfolding of the substrate and subsequent proteolysis in the catalytic chamber. Although both proteasomes contain identical β-catalytic active sites, the differential translocation mechanisms yield distinct peptide products. Nonoverlapping substrate repertoires and product outcomes rationalize cohabitation of both proteasome complexes in cells.
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23
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Molecular and cellular dynamics of the 26S proteasome. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2020; 1869:140583. [PMID: 33321258 DOI: 10.1016/j.bbapap.2020.140583] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 12/07/2020] [Accepted: 12/09/2020] [Indexed: 01/16/2023]
Abstract
In eukaryotic cells, the ubiquitin-proteasome system serves to remove proteins that are either dysfunctional or no longer needed. The 26S proteasome is a 2.5 MDa multisubunit complex comprising the 20S core particle, where degradation is executed, and one or two regulatory particles which prepare substrates for degradation. Whereas the 20S core particles of several species had been studied extensively by X-ray crystallography, the 26S holocomplex structure had remained elusive for a long time. Recent advances in single-particle cryo-electron microscopy have changed the situation and provided atomic resolution models of this intriguing molecular machine and its dynamics. Besides, cryo-electron tomography enables structural studies in situ, providing molecular resolution images of macromolecules inside pristinely preserved cellular environments. This has greatly contributed to our understanding of proteasome dynamics in the context of cells.
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24
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Marshall RS, Gemperline DC, McLoughlin F, Book AJ, Hofmann K, Vierstra RD. An evolutionarily distinct chaperone promotes 20S proteasome α-ring assembly in plants. J Cell Sci 2020; 133:jcs249862. [PMID: 33033180 PMCID: PMC7657472 DOI: 10.1242/jcs.249862] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 09/21/2020] [Indexed: 11/20/2022] Open
Abstract
The core protease (CP) subcomplex of the 26S proteasome houses the proteolytic active sites and assumes a barrel shape comprised of four co-axially stacked heptameric rings formed by structurally related α- and β-subunits. CP biogenesis typically begins with the assembly of the α-ring, which then provides a template for β-subunit integration. In eukaryotes, α-ring assembly is partially mediated by two hetero-dimeric chaperones, termed Pba1-Pba2 (Add66) and Pba3-Pba4 (also known as Irc25-Poc4) in yeast. Pba1-Pba2 initially promotes orderly recruitment of the α-subunits through interactions between their C-terminal HbYX or HbF motifs and pockets at the α5-α6 and α6-α7 interfaces. Here, we identified PBAC5 as a fifth α-ring assembly chaperone in Arabidopsis that directly binds the Pba1 homolog PBAC1 to form a trimeric PBAC5-PBAC1-PBAC2 complex. PBAC5 harbors a HbYX motif that docks with a pocket between the α4 and α5 subunits during α-ring construction. Arabidopsis lacking PBAC5, PBAC1 and/or PBAC2 are hypersensitive to proteotoxic, salt and osmotic stresses, and display proteasome assembly defects. Remarkably, whereas PBAC5 is evolutionarily conserved among plants, sequence relatives are also dispersed within other kingdoms, including a scattered array of fungal, metazoan and oomycete species.
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Affiliation(s)
- Richard S Marshall
- Department of Biology, Washington University in St. Louis, 1 Brookings Drive, St. Louis, MO 63130, USA
- Department of Genetics, University of Wisconsin, 425 Henry Mall, Madison, WI 53706, USA
| | - David C Gemperline
- Department of Genetics, University of Wisconsin, 425 Henry Mall, Madison, WI 53706, USA
| | - Fionn McLoughlin
- Department of Biology, Washington University in St. Louis, 1 Brookings Drive, St. Louis, MO 63130, USA
| | - Adam J Book
- Department of Genetics, University of Wisconsin, 425 Henry Mall, Madison, WI 53706, USA
| | - Kay Hofmann
- Institute for Genetics, University of Cologne, Zülpicher Straße 47a, 50674 Cologne, Germany
| | - Richard D Vierstra
- Department of Biology, Washington University in St. Louis, 1 Brookings Drive, St. Louis, MO 63130, USA
- Department of Genetics, University of Wisconsin, 425 Henry Mall, Madison, WI 53706, USA
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25
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Matarredona L, Camacho M, Zafrilla B, Bonete MJ, Esclapez J. The Role of Stress Proteins in Haloarchaea and Their Adaptive Response to Environmental Shifts. Biomolecules 2020; 10:biom10101390. [PMID: 33003558 PMCID: PMC7601130 DOI: 10.3390/biom10101390] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 09/18/2020] [Accepted: 09/24/2020] [Indexed: 12/26/2022] Open
Abstract
Over the years, in order to survive in their natural environment, microbial communities have acquired adaptations to nonoptimal growth conditions. These shifts are usually related to stress conditions such as low/high solar radiation, extreme temperatures, oxidative stress, pH variations, changes in salinity, or a high concentration of heavy metals. In addition, climate change is resulting in these stress conditions becoming more significant due to the frequency and intensity of extreme weather events. The most relevant damaging effect of these stressors is protein denaturation. To cope with this effect, organisms have developed different mechanisms, wherein the stress genes play an important role in deciding which of them survive. Each organism has different responses that involve the activation of many genes and molecules as well as downregulation of other genes and pathways. Focused on salinity stress, the archaeal domain encompasses the most significant extremophiles living in high-salinity environments. To have the capacity to withstand this high salinity without losing protein structure and function, the microorganisms have distinct adaptations. The haloarchaeal stress response protects cells against abiotic stressors through the synthesis of stress proteins. This includes other heat shock stress proteins (Hsp), thermoprotectants, survival proteins, universal stress proteins, and multicellular structures. Gene and family stress proteins are highly conserved among members of the halophilic archaea and their study should continue in order to develop means to improve for biotechnological purposes. In this review, all the mechanisms to cope with stress response by haloarchaea are discussed from a global perspective, specifically focusing on the role played by universal stress proteins.
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26
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Mahieu E, Covès J, Krüger G, Martel A, Moulin M, Carl N, Härtlein M, Carlomagno T, Franzetti B, Gabel F. Observing Protein Degradation by the PAN-20S Proteasome by Time-Resolved Neutron Scattering. Biophys J 2020; 119:375-388. [PMID: 32640186 PMCID: PMC7376118 DOI: 10.1016/j.bpj.2020.06.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 06/05/2020] [Accepted: 06/09/2020] [Indexed: 12/21/2022] Open
Abstract
The proteasome is a key player of regulated protein degradation in all kingdoms of life. Although recent atomic structures have provided snapshots on a number of conformations, data on substrate states and populations during the active degradation process in solution remain scarce. Here, we use time-resolved small-angle neutron scattering of a deuterium-labeled GFPssrA substrate and an unlabeled archaeal PAN-20S system to obtain direct structural information on substrate states during ATP-driven unfolding and subsequent proteolysis in solution. We find that native GFPssrA structures are degraded in a biexponential process, which correlates strongly with ATP hydrolysis, the loss of fluorescence, and the buildup of small oligopeptide products. Our solution structural data support a model in which the substrate is directly translocated from PAN into the 20S proteolytic chamber, after a first, to our knowledge, successful unfolding process that represents a point of no return and thus prevents dissociation of the complex and the release of harmful, aggregation-prone products.
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Affiliation(s)
- Emilie Mahieu
- University Grenoble Alpes, CEA, CNRS, IBS, Grenoble, France
| | - Jacques Covès
- University Grenoble Alpes, CEA, CNRS, IBS, Grenoble, France
| | - Georg Krüger
- Leibniz University Hannover, Centre for Biomolecular Drug Research, Hannover, Germany
| | | | | | - Nico Carl
- Institut Laue-Langevin, Grenoble, France
| | | | - Teresa Carlomagno
- Leibniz University Hannover, Centre for Biomolecular Drug Research, Hannover, Germany; Group of Structural Chemistry, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | | | - Frank Gabel
- University Grenoble Alpes, CEA, CNRS, IBS, Grenoble, France; Institut Laue-Langevin, Grenoble, France.
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