1
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Chu S, Xie X, Payan C, Stochaj U. Valosin containing protein (VCP): initiator, modifier, and potential drug target for neurodegenerative diseases. Mol Neurodegener 2023; 18:52. [PMID: 37545006 PMCID: PMC10405438 DOI: 10.1186/s13024-023-00639-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 06/27/2023] [Indexed: 08/08/2023] Open
Abstract
The AAA+ ATPase valosin containing protein (VCP) is essential for cell and organ homeostasis, especially in cells of the nervous system. As part of a large network, VCP collaborates with many cofactors to ensure proteostasis under normal, stress, and disease conditions. A large number of mutations have revealed the importance of VCP for human health. In particular, VCP facilitates the dismantling of protein aggregates and the removal of dysfunctional organelles. These are critical events to prevent malfunction of the brain and other parts of the nervous system. In line with this idea, VCP mutants are linked to the onset and progression of neurodegeneration and other diseases. The intricate molecular mechanisms that connect VCP mutations to distinct brain pathologies continue to be uncovered. Emerging evidence supports the model that VCP controls cellular functions on multiple levels and in a cell type specific fashion. Accordingly, VCP mutants derail cellular homeostasis through several mechanisms that can instigate disease. Our review focuses on the association between VCP malfunction and neurodegeneration. We discuss the latest insights in the field, emphasize open questions, and speculate on the potential of VCP as a drug target for some of the most devastating forms of neurodegeneration.
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Affiliation(s)
- Siwei Chu
- Department of Physiology, McGill University, Montreal, HG3 1Y6, Canada
| | - Xinyi Xie
- Department of Physiology, McGill University, Montreal, HG3 1Y6, Canada
| | - Carla Payan
- Department of Physiology, McGill University, Montreal, HG3 1Y6, Canada
| | - Ursula Stochaj
- Department of Physiology, McGill University, Montreal, HG3 1Y6, Canada.
- Quantitative Life Sciences Program, McGill University, Montreal, Canada.
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2
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Zhang Y, Pan L, Zhang Y, Wang K, Wang L, Zhang H, Zhang J, Chen X. Understanding the Streptomyces albulus response to low-pH stress at the interface of physiology and transcriptomics. Appl Microbiol Biotechnol 2023; 107:2611-2626. [PMID: 36882645 DOI: 10.1007/s00253-023-12449-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 02/15/2023] [Accepted: 02/21/2023] [Indexed: 03/09/2023]
Abstract
Streptomyces albulus is a well-established cell factory for ε-poly-L-lysine (ε-PL) production. It has been reported that ε-PL biosynthesis is strictly regulated by pH and that ε-PL can accumulate at approximately pH 4.0, which is outside of the general pH range for natural product production by Streptomyces species. However, how S. albulus responds to low pH is not clear. In this study, we attempted to explore the response of S. albulus to low-pH stress at the physiological and global gene transcription levels. At the physiological level, S. albulus maintained intracellular pH homeostasis at ~pH 7.5, increased the unsaturated fatty acid ratio, extended the fatty acid chain length, enhanced ATP accumulation, increased H+-ATPase activity, and accumulated the basic amino acids L-lysine and L-arginine. At the global gene transcription level, carbohydrate metabolism, oxidative phosphorylation, macromolecule protection and repair, and the acid tolerance system were found to be involved in combating low-pH stress. Finally, we preliminarily evaluated the effect of the acid tolerance system and cell membrane fatty acid synthesis on low-pH tolerance via gene manipulation. This work provides new insight into the adaptation mechanism of Streptomyces to low-pH stress and a new opportunity for constructing robust S. albulus strains for ε-PL production. KEY POINTS: • S. albulus consistently remained pH i at ~7.4 regardless of the environmental pH. • S. albulus combats low-pH stress by modulating lipid composition of cell membrane. • Overexpression of cfa in S. albulus could improve low-pH tolerance and ɛ-PL titer.
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Affiliation(s)
- Yulin Zhang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi214122, Wuxi, Jiangsu, China
| | - Long Pan
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi214122, Wuxi, Jiangsu, China
- School of Biological Engineering, Henan University of Technology, Zhengzhou, 450001, China
| | - Yue Zhang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi214122, Wuxi, Jiangsu, China
| | - Kaifang Wang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi214122, Wuxi, Jiangsu, China
| | - Liang Wang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi214122, Wuxi, Jiangsu, China
| | - Hongjian Zhang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi214122, Wuxi, Jiangsu, China
| | - Jianhua Zhang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi214122, Wuxi, Jiangsu, China
| | - Xusheng Chen
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi214122, Wuxi, Jiangsu, China.
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3
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Scott DC, King MT, Baek K, Gee CT, Kalathur R, Li J, Purser N, Nourse A, Chai SC, Vaithiyalingam S, Chen T, Lee RE, Elledge SJ, Kleiger G, Schulman BA. E3 ligase autoinhibition by C-degron mimicry maintains C-degron substrate fidelity. Mol Cell 2023; 83:770-786.e9. [PMID: 36805027 PMCID: PMC10080726 DOI: 10.1016/j.molcel.2023.01.019] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 12/19/2022] [Accepted: 01/18/2023] [Indexed: 02/18/2023]
Abstract
E3 ligase recruitment of proteins containing terminal destabilizing motifs (degrons) is emerging as a major form of regulation. How those E3s discriminate bona fide substrates from other proteins with terminal degron-like sequences remains unclear. Here, we report that human KLHDC2, a CRL2 substrate receptor targeting C-terminal Gly-Gly degrons, is regulated through interconversion between two assemblies. In the self-inactivated homotetramer, KLHDC2's C-terminal Gly-Ser motif mimics a degron and engages the substrate-binding domain of another protomer. True substrates capture the monomeric CRL2KLHDC2, driving E3 activation by neddylation and subsequent substrate ubiquitylation. Non-substrates such as NEDD8 bind KLHDC2 with high affinity, but its slow on rate prevents productive association with CRL2KLHDC2. Without substrate, neddylated CRL2KLHDC2 assemblies are deactivated via distinct mechanisms: the monomer by deneddylation and the tetramer by auto-ubiquitylation. Thus, substrate specificity is amplified by KLHDC2 self-assembly acting like a molecular timer, where only bona fide substrates may bind before E3 ligase inactivation.
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Affiliation(s)
- Daniel C Scott
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.
| | - Moeko T King
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Kheewoong Baek
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Clifford T Gee
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Ravi Kalathur
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Protein Technologies Center, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jerry Li
- Department of Chemistry and Biochemistry, University of Nevada, Las Vegas, Las Vegas, NV, USA
| | - Nicholas Purser
- Department of Chemistry and Biochemistry, University of Nevada, Las Vegas, Las Vegas, NV, USA
| | - Amanda Nourse
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Protein Technologies Center, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Sergio C Chai
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Sivaraja Vaithiyalingam
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Protein Technologies Center, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Taosheng Chen
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Richard E Lee
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Stephen J Elledge
- Division of Genetics, Brigham and Women's Hospital, Howard Hughes Medical Institute, Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Gary Kleiger
- Department of Chemistry and Biochemistry, University of Nevada, Las Vegas, Las Vegas, NV, USA
| | - Brenda A Schulman
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
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Palomba T, Baroni M, Cross S, Cruciani G, Siragusa L. ELIOT: A platform to navigate the E3 pocketome and aid the design of new PROTACs. Chem Biol Drug Des 2023; 101:69-86. [PMID: 35857806 DOI: 10.1111/cbdd.14123] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 07/11/2022] [Accepted: 07/17/2022] [Indexed: 12/15/2022]
Abstract
Proteolysis-targeting chimeras (PROTACs) are novel therapeutics for the treatment of human disease. They exploit the enormous potential of the E3 ligases, a class of proteins that mark a target protein for degradation via the ubiquitin-proteasome system. Despite the existence of several E3 ligase-related databases, the choice of the functioning ligase is limited to only 1.6% of those available, probably due to the fragmentary understanding of their structures and their known ligands; in fact, none of the existing databases report detailed studies covering their 3D structure or their pockets. Here, we report ELIOT (E3 LIgase pocketOme navigaTor), an accurate and complete platform containing the E3 ligase pocketome to enable navigation and selection of new E3 ligases and new ligands for the design of new PROTACs. All E3 ligase pockets were characterized with innovative 3D descriptors including their PROTAC-ability score, and similarity analyses between E3 pockets are presented. Tissue specificity and their degree of involvement in patients with specific cancer types are also annotated for each E3 ligase, enabling appropriate selection for the design of a PROTAC with improved specificity. All data are available at https://eliot.moldiscovery.com.
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Affiliation(s)
- Tommaso Palomba
- Laboratory for Chemometrics and Molecular Modeling, Department of Chemistry, Biology, and Biotechnology, University of Perugia, Perugia, Italy
| | - Massimo Baroni
- Molecular Discovery Ltd., The Kinetic Centre, Hertfordshire, UK
| | - Simon Cross
- Molecular Discovery Ltd., The Kinetic Centre, Hertfordshire, UK
| | - Gabriele Cruciani
- Laboratory for Chemometrics and Molecular Modeling, Department of Chemistry, Biology, and Biotechnology, University of Perugia, Perugia, Italy
| | - Lydia Siragusa
- Molecular Discovery Ltd., The Kinetic Centre, Hertfordshire, UK.,Molecular Horizon Srl, Bettona, Italy
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5
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Masania J, Wijten P, Keipert S, Ost M, Klaus S, Rabbani N, Thornalley PJ. Decreased methylglyoxal-mediated protein glycation in the healthy aging mouse model of ectopic expression of UCP1 in skeletal muscle. Redox Biol 2022; 59:102574. [PMID: 36521306 PMCID: PMC9772855 DOI: 10.1016/j.redox.2022.102574] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 12/05/2022] [Accepted: 12/05/2022] [Indexed: 12/12/2022] Open
Abstract
Mice with ectopic expression of uncoupling protein-1 (UCP1) in skeletal muscle exhibit a healthy aging phenotype with increased longevity and resistance to impaired metabolic health. This may be achieved by decreasing protein glycation by the reactive metabolite, methylglyoxal (MG). We investigated protein glycation and oxidative damage in skeletal muscle of mice with UCP1 expression under control of the human skeletal actin promoter (HSA-mUCP1) at age 12 weeks (young) and 70 weeks (aged). We found both young and aged HSA-mUCP1 mice had decreased advanced glycation endproducts (AGEs) formed from MG, lysine-derived Nε(1-carboxyethyl)lysine (CEL) and arginine-derived hydroimidazolone, MG-H1, whereas protein glycation by glucose forming Nε-fructosyl-lysine (FL) was increased ca. 2-fold, compared to wildtype controls. There were related increases in FL-linked AGEs, Nε-carboxymethyl-lysine (CML) and 3-deoxylglucosone-derived hydroimidazolone 3DG-H, and minor changes in protein oxidative and nitration adducts. In aged HSA-mUCP1 mice, urinary MG-derived AGEs/FL ratio was decreased ca. 60% whereas there was no change in CML/FL ratio - a marker of oxidative damage. This suggests that, normalized for glycemic status, aged HSA-mUCP1 mice had a lower flux of whole body MG-derived AGE exposure compared to wildtype controls. Proteomics analysis of skeletal muscle revealed a shift to increased heat shock proteins and mechanoprotection and repair in HSA-mUCP1 mice. Decreased MG-derived AGE protein content in skeletal muscle of aged HSA-mUCP1 mice is therefore likely produced by increased proteolysis of MG-modified proteins and increased proteostasis surveillance of the skeletal muscle proteome. From this and previous transcriptomic studies, signaling involved in enhanced removal of MG-modified protein is likely increased HSPB1-directed HUWE1 ubiquitination through eIF2α-mediated, ATF5-induced increased expression of HSPB1. Decreased whole body exposure to MG-derived AGEs may be linked to increased weight specific physical activity of HSA-mUCP1 mice. Decreased formation and increased clearance of MG-derived AGEs may be associated with healthy aging in the HSA-mUCP1 mouse.
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Affiliation(s)
- Jinit Masania
- Clinical Sciences Research Laboratories, Warwick Medical School, University of Warwick, University Hospital, Coventry, CV2 2DX, UK
| | - Patrick Wijten
- Diabetes Research Center, Qatar Biomedical Research Institute, Hamad Bin Khalifa University, Qatar Foundation, P.O. Box 34110, Doha, Qatar
| | - Susanne Keipert
- Department of Physiology of Energy Metabolism, German Institute of Human Nutrition, Potsdam-Rehbruecke, 14558, Nuthetal, Germany
| | - Mario Ost
- Department of Physiology of Energy Metabolism, German Institute of Human Nutrition, Potsdam-Rehbruecke, 14558, Nuthetal, Germany
| | - Susanne Klaus
- Department of Physiology of Energy Metabolism, German Institute of Human Nutrition, Potsdam-Rehbruecke, 14558, Nuthetal, Germany,University of Potsdam, Institute of Nutrition Science, Potsdam-Rehbruecke, 14558, Nuthetal, Germany
| | - Naila Rabbani
- Department of Basic Medical Science, College of Medicine, QU Health, Qatar University, P.O. Box 2713, Doha, Qatar
| | - Paul J. Thornalley
- Clinical Sciences Research Laboratories, Warwick Medical School, University of Warwick, University Hospital, Coventry, CV2 2DX, UK,Diabetes Research Center, Qatar Biomedical Research Institute, Hamad Bin Khalifa University, Qatar Foundation, P.O. Box 34110, Doha, Qatar,Corresponding author. Diabetes Research Center, Qatar Biomedical Research Institute, Hamad Bin Khalifa University, Qatar Foundation, P.O. Box 34110, Doha, Qatar.
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6
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Koren I. The hidden (degron) truth behind the degradation of DHFR disease-associated variants. Structure 2022; 30:1219-1221. [PMID: 36055220 DOI: 10.1016/j.str.2022.08.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
In this issue of Structure, Kampmeyer et al. provide detailed mechanistic insights into how structural changes in disease-associated dihydrofolate reductase (DHFR) missense variants affect their cellular protein abundance and discuss implications for hereditary megaloblastic anemia disease.
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Affiliation(s)
- Itay Koren
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, 5290002, Israel.
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7
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Carroll EC, Marqusee S. Site-specific ubiquitination: Deconstructing the degradation tag. Curr Opin Struct Biol 2022; 73:102345. [PMID: 35247748 DOI: 10.1016/j.sbi.2022.102345] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 12/28/2021] [Accepted: 01/17/2022] [Indexed: 02/04/2023]
Abstract
Ubiquitin is a small eukaryotic protein so named for its cellular abundance and originally recognized for its role as the posttranslational modification (PTM) "tag" condemning substrates to degradation by the 26S proteasome. Since its discovery in the 1970s, protein ubiquitination has also been identified as a key regulatory feature in dozens of non-degradative cellular processes. This myriad of roles illustrates the versatility of ubiquitin as a PTM; however, understanding the cellular and molecular factors that enable discrimination between degradative versus non-degradative ubiquitination events has been a persistent challenge. Here, we discuss recent advances in uncovering how site-specificity - the exact residue that gets modified - modulates distinct protein fates and cellular outcomes with an emphasis on how ubiquitination site specificity regulates proteasomal degradation. We explore recent advances in structural biology, biophysics, and cell biology that have enabled a broader understanding of the role of ubiquitination in altering the dynamics of the target protein, including implications for the design of targeted protein degradation therapeutics.
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Affiliation(s)
- Emma C Carroll
- Institute for Neurodegenerative Diseases, University of California, San Francisco, San Francisco, CA, 94038, USA.
| | - Susan Marqusee
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, 94720, USA; QB3 Institute for Quantitative Biosciences, University of California Berkeley, Berkeley, CA, 94720, USA; Department of Chemistry, University of California Berkeley, Berkeley, CA, 94720, USA.
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8
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Mishra R, Bansal A, Mishra A. LISTERIN E3 Ubiquitin Ligase and Ribosome-Associated Quality Control (RQC) Mechanism. Mol Neurobiol 2021; 58:6593-6609. [PMID: 34590243 DOI: 10.1007/s12035-021-02564-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 09/12/2021] [Indexed: 01/09/2023]
Abstract
According to cellular demands, ribosomes synthesize and maintain the desired pool of proteins inside the cell. However, sometimes due to defects in ribosomal machinery and faulty mRNAs, these nascent polypeptides are constantly under threat to become non-functional. In such conditions, cells acquire the help of ribosome-associated quality control mechanisms (RQC) to eliminate such aberrant nascent proteins. The primary regulator of RQC is RING domain containing LISTERIN E3 ubiquitin ligase, which is associated with ribosomes and alleviates non-stop proteins-associated stress in cells. Mouse RING finger protein E3 ubiquitin ligase LISTERIN is crucial for embryonic development, and a loss in its function causes neurodegeneration. LISTERIN is overexpressed in the mouse brain and spinal cord regions, and its perturbed functions generate neurological and motor deficits, but the mechanism of the same is unclear. Overall, LISTERIN is crucial for brain health and brain development. The present article systematically describes the detailed nature, molecular functions, and cellular physiological characterization of LISTERIN E3 ubiquitin ligase. Improve comprehension of LISTERIN's neurological roles may uncover pathways linked with neurodegeneration, which in turn might elucidate a promising novel therapeutic intervention against human neurodegenerative diseases.
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Affiliation(s)
- Ribhav Mishra
- Cellular and Molecular Neurobiology Unit, Indian Institute of Technology Jodhpur, Karwar, Rajasthan, 342037, India
| | - Anurag Bansal
- Center for Converging Technologies, Jaipur, University of Rajasthan, Jaipur, 302001, India
| | - Amit Mishra
- Cellular and Molecular Neurobiology Unit, Indian Institute of Technology Jodhpur, Karwar, Rajasthan, 342037, India.
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Sabouri S, Liu M, Zhang S, Yao B, Soleimaninejad H, Baxter AA, Armendariz-Vidales G, Subedi P, Duan C, Lou X, Hogan CF, Heras B, Poon IKH, Hong Y. Construction of a Highly Sensitive Thiol-Reactive AIEgen-Peptide Conjugate for Monitoring Protein Unfolding and Aggregation in Cells. Adv Healthc Mater 2021; 10:e2101300. [PMID: 34655462 DOI: 10.1002/adhm.202101300] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 09/24/2021] [Indexed: 01/09/2023]
Abstract
Impairment of the protein quality control network leads to the accumulation of unfolded and aggregated proteins. Direct detection of unfolded protein accumulation in the cells may provide the possibility for early diagnosis of neurodegenerative diseases. Here a new platform based on a peptide-conjugated thiol-reactive aggregation-induced emission fluorogen (AIEgen), named MI-BTD-P (or D1), for labeling and tracking unfolded proteins in cells is reported. In vitro experiments with model proteins show that the non-fluorescent D1 only becomes highly fluorescent when reacted with the thiol group of free cysteine (Cys) residues on unfolded proteins but not glutathione or folded proteins with buried or surface exposed Cys. When the labeled unfolded proteins form aggregates, D1 fluorescence intensity is further increased, and fluorescence lifetime is prolonged. D1 is then used to measure unfolded protein loads in cells by flow cytometry and track the aggregate formation of the D1 labeled unfolded proteins using confocal microscopy. In combination with fluorescence lifetime imaging technique, the proteome at different folding statuses can be better differentiated, demonstrating the versatility of this new platform. The rational design of D1 demonstrates the outlook of incorporation of diverse functional groups to achieve maximal sensitivity and selectivity in biological samples.
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Affiliation(s)
- Soheila Sabouri
- Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria, 3086, Australia
| | - Mengjie Liu
- Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria, 3086, Australia
| | - Shouxiang Zhang
- Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria, 3086, Australia
| | - Bicheng Yao
- Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria, 3086, Australia
| | - Hamid Soleimaninejad
- Biological Optical Microscopy Platform (BOMP), The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Amy A Baxter
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria, 3086, Australia
| | - Georgina Armendariz-Vidales
- Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria, 3086, Australia
| | - Pramod Subedi
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria, 3086, Australia
| | - Chong Duan
- Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan, 4300078, China
| | - Xiaoding Lou
- Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan, 4300078, China
| | - Conor F Hogan
- Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria, 3086, Australia
| | - Begoña Heras
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria, 3086, Australia
| | - Ivan K H Poon
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria, 3086, Australia
| | - Yuning Hong
- Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria, 3086, Australia
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10
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Dias C, Nita E, Faktor J, Tynan AC, Hernychova L, Vojtesek B, Nylandsted J, Hupp TR, Kunath T, Ball KL. CHIP-dependent regulation of the actin cytoskeleton is linked to neuronal cell membrane integrity. iScience 2021; 24:102878. [PMID: 34401662 PMCID: PMC8350547 DOI: 10.1016/j.isci.2021.102878] [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: 11/20/2020] [Revised: 04/13/2021] [Accepted: 07/15/2021] [Indexed: 12/12/2022] Open
Abstract
CHIP is an E3-ubiquitin ligase that contributes to healthy aging and has been characterized as neuroprotective. To elucidate dominant CHIP-dependent changes in protein steady-state levels in a patient-derived human neuronal model, CHIP function was ablated using gene-editing and an unbiased proteomic analysis conducted to compare knock-out and wild-type isogenic induced pluripotent stem cell (iPSC)-derived cortical neurons. Rather than a broad effect on protein homeostasis, loss of CHIP function impacted on a focused cohort of proteins from actin cytoskeleton signaling and membrane integrity networks. In support of the proteomics, CHIP knockout cells had enhanced sensitivity to induced membrane damage. We conclude that the major readout of CHIP function in cortical neurons derived from iPSC of a patient with elevate α-synuclein, Parkinson's disease and dementia, is the modulation of substrates involved in maintaining cellular "health". Thus, regulation of the actin cytoskeletal and membrane integrity likely contributes to the neuroprotective function(s) of CHIP.
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Affiliation(s)
- Catarina Dias
- Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK
- Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, The University of Edinburgh, Edinburgh EH16 4UU, UK
| | - Erisa Nita
- Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Jakub Faktor
- Research Centre for Applied Molecular Oncology, Masaryk Memorial Cancer Institute, 656 53 Brno, Czech Republic
- University of Gdansk, International Centre for Cancer Vaccine Science, 80-822 Gdansk, Poland
| | - Ailish C. Tynan
- Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Lenka Hernychova
- Research Centre for Applied Molecular Oncology, Masaryk Memorial Cancer Institute, 656 53 Brno, Czech Republic
| | - Borivoj Vojtesek
- Research Centre for Applied Molecular Oncology, Masaryk Memorial Cancer Institute, 656 53 Brno, Czech Republic
| | - Jesper Nylandsted
- Membrane Integrity Group, Danish Cancer Society Research Center, Strandboulevarden 49, 2100, Copenhagen, Denmark
| | - Ted R. Hupp
- Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK
- University of Gdansk, International Centre for Cancer Vaccine Science, 80-822 Gdansk, Poland
| | - Tilo Kunath
- Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, The University of Edinburgh, Edinburgh EH16 4UU, UK
| | - Kathryn L. Ball
- Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK
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11
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Saffari-Chaleshtori J, Asadi-Samani M, Rasouli M, Shafiee SM. Autophagy and Ubiquitination as Two Major Players in Colorectal Cancer: A Review on Recent Patents. Recent Pat Anticancer Drug Discov 2021; 15:143-153. [PMID: 32603286 DOI: 10.2174/1574892815666200630103626] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 05/30/2020] [Accepted: 06/01/2020] [Indexed: 02/06/2023]
Abstract
BACKGROUND As one of the most commonly diagnosed cancers among men and women, Colorectal Cancer (CRC) leads to high rates of morbidity and mortality across the globe. Recent anti- CRC therapies are now targeting specific signaling pathways involved in colorectal carcinogenesis. Ubiquitin Proteasome System (UPS) and autophagy are two main protein quality control systems, which play major roles in the carcinogenesis of colorectal cancer. A balanced function of these two pathways is necessary for the regulation of cell proliferation and cell death. OBJECTIVE In this systematic review, we discuss the available evidence regarding the roles of autophagy and ubiquitination in progression and inhibition of CRC. METHODS The search terms "colorectal cancer" or "colon cancer" or "colorectal carcinoma" or "colon carcinoma" in combination with "ubiquitin proteasome" and "autophagy" were searched in PubMed, Web of Science, and Scopus databases, and also Google Patents (https://patents.google .com) from January 2000 to Feb 2020. RESULTS The most important factors involved in UPS and autophagy have been investigated. There are many important factors involved in UPS and autophagy but this systematic review shows the studies that have mostly focused on the role of ATG, 20s proteasome and mTOR in CRC, and the more important factors such as ATG8, FIP200, and TIGAR factors that are effective in the regulation of autophagy in CRC cells have not been yet investigated. CONCLUSION The most important factors involved in UPS and autophagy such as ATG, 20s proteasome and mTOR, ATG8, FIP200, and TIGAR can be considered in drug therapy for controlling or activating autophagy.
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Affiliation(s)
- Javad Saffari-Chaleshtori
- Clinical Biochemistry Research Center, Basic Health Sciences Institute, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Majid Asadi-Samani
- Cellular and Molecular Research Center, Basic Health Sciences Institute, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Maryam Rasouli
- Department of Biochemistry, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Sayed Mohammad Shafiee
- Department of Biochemistry, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
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12
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Abstract
Sustaining a healthy proteome is a lifelong challenge for each individual cell of an organism. However, protein homeostasis or proteostasis is constantly jeopardized since damaged proteins accumulate under proteotoxic stress that originates from ever-changing metabolic, environmental, and pathological conditions. Proteostasis is achieved via a conserved network of quality control pathways that orchestrate the biogenesis of correctly folded proteins, prevent proteins from misfolding, and remove potentially harmful proteins by selective degradation. Nevertheless, the proteostasis network has a limited capacity and its collapse deteriorates cellular functionality and organismal viability, causing metabolic, oncological, or neurodegenerative disorders. While cell-autonomous quality control mechanisms have been described intensely, recent work on Caenorhabditis elegans has demonstrated the systemic coordination of proteostasis between distinct tissues of an organism. These findings indicate the existence of intricately balanced proteostasis networks important for integration and maintenance of the organismal proteome, opening a new door to define novel therapeutic targets for protein aggregation diseases. Here, we provide an overview of individual protein quality control pathways and the systemic coordination between central proteostatic nodes. We further provide insights into the dynamic regulation of cellular and organismal proteostasis mechanisms that integrate environmental and metabolic changes. The use of C. elegans as a model has pioneered our understanding of conserved quality control mechanisms important to safeguard the organismal proteome in health and disease.
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13
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Dong S, Wei J, Bowser RK, Chen BB, Mallampalli RK, Miao J, Ye Q, Tran KC, Zhao Y, Zhao J. SCF FBXW17 E3 ubiquitin ligase regulates FBXL19 stability and cell migration. J Cell Biochem 2021; 122:326-334. [PMID: 33053230 PMCID: PMC7887023 DOI: 10.1002/jcb.29860] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 09/28/2020] [Accepted: 09/29/2020] [Indexed: 01/16/2023]
Abstract
The Skp1-Cul1-F-box protein (SCF) E3 ligase complex is one of the largest ubiquitin E3 ligase families. FBXL19, a F-box protein in SCFFBXL19 E3 ligase complex, regulates a variety of cellular responses including cell migration. We have shown that FBXL19 is not stable and its degradation is mediated by the ubiquitin-proteasome system, while the ubiquitin E3 ligase for FBXL19 ubiquitination and degradation has not been identified. In the study, we discovered that a new ubiquitin E3 ligase, SCFFBXW17 , ubiquitinates and induces FBXL19 degradation. Exogenous FBXW17 targets FBXL19 for its ubiquitination and degradation. Lysine 114 in FBXL19 is a potential ubiquitin acceptor site. Acetylation of FBXL19 attenuated SCFFBXW17 -mediated FBXL19 degradation. SCFFBXL19 E3 ligase reduced Rac1 levels and cell migration, while the effects were attenuated by exogenous FBXW17. Downregulation of FBXW17 attenuated lysophosphatidic acid-induced lamellipodia formation and Rac1 accumulation at migration leading edge. Taken together with our previous studies, FBXL19 is degraded by the ubiquitin-proteasome system and its site-specific ubiquitination is mediated by SCFFBXW17 E3 ligase, which promotes cell migration.
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Affiliation(s)
- Su Dong
- Department of Physiology and Cell Biology, Dorothy M. Davis
Heart and Lung Research Institute, The Ohio State University, Columbus, OH
| | - Jianxin Wei
- Department of Medicine, The University of Pittsburgh,
Pittsburgh, PA
| | - Rachel K. Bowser
- Department of Medicine, The University of Pittsburgh,
Pittsburgh, PA
| | - Bill B. Chen
- Department of Medicine, The University of Pittsburgh,
Pittsburgh, PA
| | - Rama K. Mallampalli
- Pulmonary, Critical Care & Sleep Medicine Division, The
Ohio State University, Columbus, OH
| | - Jiaxing Miao
- Department of Physiology and Cell Biology, Dorothy M. Davis
Heart and Lung Research Institute, The Ohio State University, Columbus, OH
| | - Qinmao Ye
- Department of Physiology and Cell Biology, Dorothy M. Davis
Heart and Lung Research Institute, The Ohio State University, Columbus, OH
| | - Kevin C. Tran
- Department of Physiology and Cell Biology, Dorothy M. Davis
Heart and Lung Research Institute, The Ohio State University, Columbus, OH
| | - Yutong Zhao
- Department of Physiology and Cell Biology, Dorothy M. Davis
Heart and Lung Research Institute, The Ohio State University, Columbus, OH,Pulmonary, Critical Care & Sleep Medicine Division, The
Ohio State University, Columbus, OH
| | - Jing Zhao
- Department of Physiology and Cell Biology, Dorothy M. Davis
Heart and Lung Research Institute, The Ohio State University, Columbus, OH,Pulmonary, Critical Care & Sleep Medicine Division, The
Ohio State University, Columbus, OH,Address correspondence to: Jing Zhao, MD, PhD,
Department of Physiology and Cell Biology, The Ohio State University, 333 10th
Avenue, Graves Hall 2166D, Columbus, OH, United States, 43065. Tel:
614-685-0024;
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14
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The dialogue between the ubiquitin-proteasome system and autophagy: Implications in ageing. Ageing Res Rev 2020; 64:101203. [PMID: 33130248 DOI: 10.1016/j.arr.2020.101203] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 10/09/2020] [Accepted: 10/25/2020] [Indexed: 02/06/2023]
Abstract
Dysregulated proteostasis is one of the hallmarks of ageing. Damaged proteins may impair cellular function and their accumulation may lead to tissue dysfunction and disease. This is why protective mechanisms to safeguard the cell proteome have evolved. These mechanisms consist of cellular machineries involved in protein quality control, including regulators of protein translation, folding, trafficking and degradation. In eukaryotic cells, protein degradation occurs via two main pathways: the ubiquitin-proteasome system (UPS) and the autophagy-lysosome pathway. Although distinct pathways, they are not isolated systems and have a complementary nature, as evidenced by recent studies. These findings raise the question of how autophagy and the proteasome crosstalk. In this review we address how the two degradation pathways impact each other, thereby adding a new layer of regulation to protein degradation. We also analyze the implications of the UPS and autophagy in ageing.
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15
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Tyagi A, Sarodaya N, Kaushal K, Chandrasekaran AP, Antao AM, Suresh B, Rhie BH, Kim KS, Ramakrishna S. E3 Ubiquitin Ligase APC/C Cdh1 Regulation of Phenylalanine Hydroxylase Stability and Function. Int J Mol Sci 2020; 21:E9076. [PMID: 33260674 PMCID: PMC7729981 DOI: 10.3390/ijms21239076] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 11/18/2020] [Accepted: 11/25/2020] [Indexed: 12/20/2022] Open
Abstract
Phenylketonuria (PKU) is an autosomal recessive metabolic disorder caused by the dysfunction of the enzyme phenylalanine hydroxylase (PAH). Alterations in the level of PAH leads to the toxic accumulation of phenylalanine in the blood and brain. Protein degradation mediated by ubiquitination is a principal cellular process for maintaining protein homeostasis. Therefore, it is important to identify the E3 ligases responsible for PAH turnover and proteostasis. Here, we report that anaphase-promoting complex/cyclosome-Cdh1 (APC/C)Cdh1 is an E3 ubiquitin ligase complex that interacts and promotes the polyubiquitination of PAH through the 26S proteasomal pathway. Cdh1 destabilizes and declines the half-life of PAH. In contrast, the CRISPR/Cas9-mediated knockout of Cdh1 stabilizes PAH expression and enhances phenylalanine metabolism. Additionally, our current study demonstrates the clinical relevance of PAH and Cdh1 correlation in hepatocellular carcinoma (HCC). Overall, we show that PAH is a prognostic marker for HCC and Cdh1 could be a potential therapeutic target to regulate PAH-mediated physiological and metabolic disorders.
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Affiliation(s)
- Apoorvi Tyagi
- Department of Biomedical Science, Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul 04763, Korea; (A.T.); (N.S.); (K.K.); (A.P.C.); (A.M.A.); ( (B.S.); (B.H.R.)
| | - Neha Sarodaya
- Department of Biomedical Science, Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul 04763, Korea; (A.T.); (N.S.); (K.K.); (A.P.C.); (A.M.A.); ( (B.S.); (B.H.R.)
| | - Kamini Kaushal
- Department of Biomedical Science, Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul 04763, Korea; (A.T.); (N.S.); (K.K.); (A.P.C.); (A.M.A.); ( (B.S.); (B.H.R.)
| | - Arun Pandian Chandrasekaran
- Department of Biomedical Science, Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul 04763, Korea; (A.T.); (N.S.); (K.K.); (A.P.C.); (A.M.A.); ( (B.S.); (B.H.R.)
| | - Ainsley Mike Antao
- Department of Biomedical Science, Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul 04763, Korea; (A.T.); (N.S.); (K.K.); (A.P.C.); (A.M.A.); ( (B.S.); (B.H.R.)
| | - Bharathi Suresh
- Department of Biomedical Science, Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul 04763, Korea; (A.T.); (N.S.); (K.K.); (A.P.C.); (A.M.A.); ( (B.S.); (B.H.R.)
| | - Byung Ho Rhie
- Department of Biomedical Science, Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul 04763, Korea; (A.T.); (N.S.); (K.K.); (A.P.C.); (A.M.A.); ( (B.S.); (B.H.R.)
| | - Kye Seong Kim
- Department of Biomedical Science, Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul 04763, Korea; (A.T.); (N.S.); (K.K.); (A.P.C.); (A.M.A.); ( (B.S.); (B.H.R.)
- College of Medicine, Hanyang University, Seoul 04763, Korea
| | - Suresh Ramakrishna
- Department of Biomedical Science, Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul 04763, Korea; (A.T.); (N.S.); (K.K.); (A.P.C.); (A.M.A.); ( (B.S.); (B.H.R.)
- College of Medicine, Hanyang University, Seoul 04763, Korea
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16
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Johnston HE, Samant RS. Alternative systems for misfolded protein clearance: life beyond the proteasome. FEBS J 2020; 288:4464-4487. [PMID: 33135311 DOI: 10.1111/febs.15617] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 10/15/2020] [Accepted: 10/30/2020] [Indexed: 12/18/2022]
Abstract
Protein misfolding is a major driver of ageing-associated frailty and disease pathology. Although all cells possess multiple, well-characterised protein quality control systems to mitigate the toxicity of misfolded proteins, how they are integrated to maintain protein homeostasis ('proteostasis') in health-and how their disintegration contributes to disease-is still an exciting and fast-paced area of research. Under physiological conditions, the predominant route for misfolded protein clearance involves ubiquitylation and proteasome-mediated degradation. When the capacity of this route is overwhelmed-as happens during conditions of acute environmental stress, or chronic ageing-related decline-alternative routes for protein quality control are activated. In this review, we summarise our current understanding of how proteasome-targeted misfolded proteins are retrafficked to alternative protein quality control routes such as juxta-nuclear sequestration and selective autophagy when the ubiquitin-proteasome system is compromised. We also discuss the molecular determinants of these alternative protein quality control systems, attempt to clarify distinctions between various cytoplasmic spatial quality control inclusion bodies (e.g., Q-bodies, p62 bodies, JUNQ, aggresomes, and aggresome-like induced structures 'ALIS'), and speculate on emerging concepts in the field that we hope will spur future research-with the potential to benefit the rational development of healthy ageing strategies.
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Affiliation(s)
| | - Rahul S Samant
- Signalling Programme, The Babraham Institute, Cambridge, UK
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17
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E3 Ubiquitin Ligase APC/C Cdh1 Negatively Regulates FAH Protein Stability by Promoting Its Polyubiquitination. Int J Mol Sci 2020; 21:ijms21228719. [PMID: 33218190 PMCID: PMC7699203 DOI: 10.3390/ijms21228719] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 11/13/2020] [Accepted: 11/16/2020] [Indexed: 12/15/2022] Open
Abstract
Fumarylacetoacetate hydrolase (FAH) is the last enzyme in the degradation pathway of the amino acids tyrosine and phenylalanine in mammals that catalyzes the hydrolysis of 4-fumarylacetoacetate into acetoacetate and fumarate. Mutations of the FAH gene are associated with hereditary tyrosinemia type I (HT1), resulting in reduced protein stability, misfolding, accelerated degradation and deficiency in functional proteins. Identifying E3 ligases, which are necessary for FAH protein stability and degradation, is essential. In this study, we demonstrated that the FAH protein level is elevated in liver cancer tissues compared to that in normal tissues. Further, we showed that the FAH protein undergoes 26S proteasomal degradation and its protein turnover is regulated by the anaphase-promoting complex/cyclosome-Cdh1 (APC/C)Cdh1 E3 ubiquitin ligase complex. APC/CCdh1 acts as a negative stabilizer of FAH protein by promoting FAH polyubiquitination and decreases the half-life of FAH protein. Thus, we envision that Cdh1 might be a key factor in the maintenance of FAH protein level to regulate FAH-mediated physiological functions.
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18
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Clausen L, Stein A, Grønbæk-Thygesen M, Nygaard L, Søltoft CL, Nielsen SV, Lisby M, Ravid T, Lindorff-Larsen K, Hartmann-Petersen R. Folliculin variants linked to Birt-Hogg-Dubé syndrome are targeted for proteasomal degradation. PLoS Genet 2020; 16:e1009187. [PMID: 33137092 PMCID: PMC7660926 DOI: 10.1371/journal.pgen.1009187] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 11/12/2020] [Accepted: 10/10/2020] [Indexed: 01/24/2023] Open
Abstract
Germline mutations in the folliculin (FLCN) tumor suppressor gene are linked to Birt-Hogg-Dubé (BHD) syndrome, a dominantly inherited genetic disease characterized by predisposition to fibrofolliculomas, lung cysts, and renal cancer. Most BHD-linked FLCN variants include large deletions and splice site aberrations predicted to cause loss of function. The mechanisms by which missense variants and short in-frame deletions in FLCN trigger disease are unknown. Here, we present an integrated computational and experimental study that reveals that the majority of such disease-causing FLCN variants cause loss of function due to proteasomal degradation of the encoded FLCN protein, rather than directly ablating FLCN function. Accordingly, several different single-site FLCN variants are present at strongly reduced levels in cells. In line with our finding that FLCN variants are protein quality control targets, several are also highly insoluble and fail to associate with the FLCN-binding partners FNIP1 and FNIP2. The lack of FLCN binding leads to rapid proteasomal degradation of FNIP1 and FNIP2. Half of the tested FLCN variants are mislocalized in cells, and one variant (ΔE510) forms perinuclear protein aggregates. A yeast-based stability screen revealed that the deubiquitylating enzyme Ubp15/USP7 and molecular chaperones regulate the turnover of the FLCN variants. Lowering the temperature led to a stabilization of two FLCN missense proteins, and for one (R362C), function was re-established at low temperature. In conclusion, we propose that most BHD-linked FLCN missense variants and small in-frame deletions operate by causing misfolding and degradation of the FLCN protein, and that stabilization and resulting restoration of function may hold therapeutic potential of certain disease-linked variants. Our computational saturation scan encompassing both missense variants and single site deletions in FLCN may allow classification of rare FLCN variants of uncertain clinical significance.
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Affiliation(s)
- Lene Clausen
- The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Amelie Stein
- The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Martin Grønbæk-Thygesen
- The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Lasse Nygaard
- The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Cecilie L. Søltoft
- The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Sofie V. Nielsen
- The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Michael Lisby
- The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Tommer Ravid
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Kresten Lindorff-Larsen
- The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Rasmus Hartmann-Petersen
- The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
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19
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CHIP ubiquitylates NOXA and induces its lysosomal degradation in response to DNA damage. Cell Death Dis 2020; 11:740. [PMID: 32913203 PMCID: PMC7484759 DOI: 10.1038/s41419-020-02923-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 07/29/2020] [Accepted: 07/30/2020] [Indexed: 02/06/2023]
Abstract
The BH3-only protein NOXA is a regulator of mitochondrial apoptosis by specifically antagonizing the anti-apoptotic protein MCL-1. Here we show that the E3 ubiquitin ligase CHIP controls NOXA stability after DNA damage. Our findings reveal that CHIP and MCL-1 are binding partners of NOXA and differentially define the fate of NOXA. Whereas NOXA is initially targeted to mitochondria upon MCL-1-binding, CHIP mediates ubiquitylation of cytosolic NOXA and promotes lysosomal degradation of NOXA, which is not bound by MCL-1. Our data indicate that MCL-1 defines NOXA abundance and its pro-apoptotic activity. Increased NOXA levels beyond this threshold are effectively removed by lysosomal protein degradation triggered via CHIP-mediated ubiquitylation. Together, these results shed new light on regulatory circuits controlling DNA damage response and identified the E3 ligase CHIP as a new molecular guardian, which restricts the cytosolic accumulation of NOXA upon genotoxic stress.
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20
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Sarodaya N, Suresh B, Kim KS, Ramakrishna S. Protein Degradation and the Pathologic Basis of Phenylketonuria and Hereditary Tyrosinemia. Int J Mol Sci 2020; 21:ijms21144996. [PMID: 32679806 PMCID: PMC7404301 DOI: 10.3390/ijms21144996] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 07/10/2020] [Accepted: 07/13/2020] [Indexed: 12/15/2022] Open
Abstract
A delicate intracellular balance among protein synthesis, folding, and degradation is essential to maintaining protein homeostasis or proteostasis, and it is challenged by genetic and environmental factors. Molecular chaperones and the ubiquitin proteasome system (UPS) play a vital role in proteostasis for normal cellular function. As part of protein quality control, molecular chaperones recognize misfolded proteins and assist in their refolding. Proteins that are beyond repair or refolding undergo degradation, which is largely mediated by the UPS. The importance of protein quality control is becoming ever clearer, but it can also be a disease-causing mechanism. Diseases such as phenylketonuria (PKU) and hereditary tyrosinemia-I (HT1) are caused due to mutations in PAH and FAH gene, resulting in reduced protein stability, misfolding, accelerated degradation, and deficiency in functional proteins. Misfolded or partially unfolded proteins do not necessarily lose their functional activity completely. Thus, partially functional proteins can be rescued from degradation by molecular chaperones and deubiquitinating enzymes (DUBs). Deubiquitination is an important mechanism of the UPS that can reverse the degradation of a substrate protein by covalently removing its attached ubiquitin molecule. In this review, we discuss the importance of molecular chaperones and DUBs in reducing the severity of PKU and HT1 by stabilizing and rescuing mutant proteins.
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Affiliation(s)
- Neha Sarodaya
- Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul 04763, Korea; (N.S.); (B.S.)
| | - Bharathi Suresh
- Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul 04763, Korea; (N.S.); (B.S.)
| | - Kye-Seong Kim
- Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul 04763, Korea; (N.S.); (B.S.)
- College of Medicine, Hanyang University, Seoul 04763, Korea
- Correspondence: (K.-S.K.); or (S.R.)
| | - Suresh Ramakrishna
- Graduate School of Biomedical Science and Engineering, Hanyang University, Seoul 04763, Korea; (N.S.); (B.S.)
- College of Medicine, Hanyang University, Seoul 04763, Korea
- Correspondence: (K.-S.K.); or (S.R.)
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21
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Fusella F, Seclì L, Cannata C, Brancaccio M. The one thousand and one chaperones of the NF-κB pathway. Cell Mol Life Sci 2020; 77:2275-2288. [PMID: 31811308 PMCID: PMC11104964 DOI: 10.1007/s00018-019-03402-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 11/04/2019] [Accepted: 11/26/2019] [Indexed: 12/16/2022]
Abstract
The NF-κB pathway represents a crucial signaling mechanism in sensing and integrating a multitude of environmental and intracellular stimuli and directing a coordinated response that from the cellular level may impact on the entire organism. A plethora of chaperone proteins work at multiple steps of the pathway, from membrane receptor activation to transcription factor binding to DNA. Indeed, chaperones are required to assist protein conformational changes, to assemble supramolecular complexes and to regulate protein ubiquitination, required for pathway activation. Some chaperones acquired a role as integral components of the signaling complexes, needed for signal progression. Here we describe the chaperones involved in the NF-κB pathway and their specific roles in the different contexts.
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Affiliation(s)
- Federica Fusella
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Turin, Italy
| | - Laura Seclì
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Turin, Italy
| | - Cristiana Cannata
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Turin, Italy
| | - Mara Brancaccio
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Turin, Italy.
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22
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Molecular Chaperones and Proteolytic Machineries Regulate Protein Homeostasis In Aging Cells. Cells 2020; 9:cells9051308. [PMID: 32456366 PMCID: PMC7291254 DOI: 10.3390/cells9051308] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 05/15/2020] [Accepted: 05/19/2020] [Indexed: 12/14/2022] Open
Abstract
Throughout their life cycles, cells are subject to a variety of stresses that lead to a compromise between cell death and survival. Survival is partially provided by the cell proteostasis network, which consists of molecular chaperones, a ubiquitin-proteasome system of degradation and autophagy. The cooperation of these systems impacts the correct function of protein synthesis/modification/transport machinery starting from the adaption of nascent polypeptides to cellular overcrowding until the utilization of damaged or needless proteins. Eventually, aging cells, in parallel to the accumulation of flawed proteins, gradually lose their proteostasis mechanisms, and this loss leads to the degeneration of large cellular masses and to number of age-associated pathologies and ultimately death. In this review, we describe the function of proteostasis mechanisms with an emphasis on the possible associations between them.
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23
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McGrail DJ, Garnett J, Yin J, Dai H, Shih DJH, Lam TNA, Li Y, Sun C, Li Y, Schmandt R, Wu JY, Hu L, Liang Y, Peng G, Jonasch E, Menter D, Yates MS, Kopetz S, Lu KH, Broaddus R, Mills GB, Sahni N, Lin SY. Proteome Instability Is a Therapeutic Vulnerability in Mismatch Repair-Deficient Cancer. Cancer Cell 2020; 37:371-386.e12. [PMID: 32109374 PMCID: PMC7337255 DOI: 10.1016/j.ccell.2020.01.011] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 11/22/2019] [Accepted: 01/30/2020] [Indexed: 12/30/2022]
Abstract
Deficient DNA mismatch repair (dMMR) induces a hypermutator phenotype that can lead to tumorigenesis; however, the functional impact of the high mutation burden resulting from this phenotype remains poorly explored. Here, we demonstrate that dMMR-induced destabilizing mutations lead to proteome instability in dMMR tumors, resulting in an abundance of misfolded protein aggregates. To compensate, dMMR cells utilize a Nedd8-mediated degradation pathway to facilitate clearance of misfolded proteins. Blockade of this Nedd8 clearance pathway with MLN4924 causes accumulation of misfolded protein aggregates, ultimately inducing immunogenic cell death in dMMR cancer cells. To leverage this immunogenic cell death, we combined MLN4924 treatment with PD1 inhibition and found the combination was synergistic, significantly improving efficacy over either treatment alone.
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Affiliation(s)
- Daniel J McGrail
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
| | - Jeannine Garnett
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jun Yin
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Hui Dai
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - David J H Shih
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Truong Nguyen Anh Lam
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yang Li
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Chaoyang Sun
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yongsheng Li
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Rosemarie Schmandt
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Ji Yuan Wu
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Limei Hu
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yulong Liang
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Guang Peng
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Eric Jonasch
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - David Menter
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Melinda S Yates
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Scott Kopetz
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Karen H Lu
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Russell Broaddus
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC, USA
| | - Gordon B Mills
- Knight Cancer Institute, Oregon Health and Science University, Portland, OR 97239, USA
| | - Nidhi Sahni
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Program in Quantitative and Computational Biosciences (QCB), Baylor College of Medicine, Houston, TX 77030, USA; Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA; Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
| | - Shiaw-Yih Lin
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
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24
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Joazeiro CAP. Mechanisms and functions of ribosome-associated protein quality control. Nat Rev Mol Cell Biol 2020; 20:368-383. [PMID: 30940912 DOI: 10.1038/s41580-019-0118-2] [Citation(s) in RCA: 243] [Impact Index Per Article: 60.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The stalling of ribosomes during protein synthesis results in the production of truncated polypeptides that can have deleterious effects on cells and therefore must be eliminated. In eukaryotes, this function is carried out by a dedicated surveillance mechanism known as ribosome-associated protein quality control (RQC). The E3 ubiquitin ligase Ltn1 (listerin in mammals) plays a key part in RQC by targeting the aberrant nascent polypeptides for proteasomal degradation. Consistent with having an important protein quality control function, mutations in listerin cause neurodegeneration in mice. Ltn1/listerin is part of the multisubunit RQC complex, and recent findings have revealed that the Rqc2 subunit of this complex catalyses the formation of carboxy-terminal alanine and threonine tails (CAT tails), which are extensions of nascent chains known to either facilitate substrate ubiquitylation and targeting for degradation or induce protein aggregation. RQC, originally described for quality control on ribosomes translating cytosolic proteins, is now known to also have a role on the surfaces of the endoplasmic reticulum and mitochondria. This Review describes our current knowledge on RQC mechanisms, highlighting key features of Ltn1/listerin action that provide a paradigm for understanding how E3 ligases operate in protein quality control in general, and discusses how defects in this pathway may compromise cellular function and lead to disease.
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Affiliation(s)
- Claudio A P Joazeiro
- Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg, Germany. .,Department of Molecular Medicine, Scripps Research, Jupiter, FL, USA.
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25
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Metzger MB, Scales JL, Dunklebarger MF, Loncarek J, Weissman AM. A protein quality control pathway at the mitochondrial outer membrane. eLife 2020; 9:51065. [PMID: 32118579 PMCID: PMC7136024 DOI: 10.7554/elife.51065] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Accepted: 03/01/2020] [Indexed: 12/27/2022] Open
Abstract
Maintaining the essential functions of mitochondria requires mechanisms to recognize and remove misfolded proteins. However, quality control (QC) pathways for misfolded mitochondrial proteins remain poorly defined. Here, we establish temperature-sensitive (ts-) peripheral mitochondrial outer membrane (MOM) proteins as novel model QC substrates in Saccharomyces cerevisiae. The ts- proteins sen2-1HAts and sam35-2HAts are degraded from the MOM by the ubiquitin-proteasome system. Ubiquitination of sen2-1HAts is mediated by the ubiquitin ligase (E3) Ubr1, while sam35-2HAts is ubiquitinated primarily by San1. Mitochondria-associated degradation (MAD) of both substrates requires the SSA family of Hsp70s and the Hsp40 Sis1, providing the first evidence for chaperone involvement in MAD. In addition to a role for the Cdc48-Npl4-Ufd1 AAA-ATPase complex, Doa1 and a mitochondrial pool of the transmembrane Cdc48 adaptor, Ubx2, are implicated in their degradation. This study reveals a unique QC pathway comprised of a combination of cytosolic and mitochondrial factors that distinguish it from other cellular QC pathways.
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Affiliation(s)
- Meredith B Metzger
- Laboratory of Protein Dynamics and Signaling, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, United States
| | - Jessica L Scales
- Laboratory of Protein Dynamics and Signaling, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, United States
| | - Mitchell F Dunklebarger
- Laboratory of Protein Dynamics and Signaling, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, United States
| | - Jadranka Loncarek
- Laboratory of Protein Dynamics and Signaling, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, United States
| | - Allan M Weissman
- Laboratory of Protein Dynamics and Signaling, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, United States
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26
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Abstract
Protein ubiquitylation is essential for the maintenance of cellular homeostasis. E3 ubiquitin ligases are key components of the enzymatic machinery catalyzing the attachment of ubiquitin to substrate proteins. Consequently, enzymatic dysfunction has been associated with medical conditions including cancer, diabetes, and cardiovascular and neurodegenerative disorders. To safeguard substrate selection and ubiquitylation, the activity of E3 ligases is tightly regulated by post-translational modifications including phosphorylation, sumoylation, and ubiquitylation, as well as binding of alternative adaptor molecules and cofactors. Recent structural studies identified homotypic and heterotypic interactions between E3 ligases, adding another layer of control for rapid adaptation to changing environmental and physiological conditions. Here, we discuss the regulation of E3 ligase activity by combinatorial oligomerization and summarize examples of associated ubiquitylation pathways and mechanisms.
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Affiliation(s)
- Vishnu Balaji
- Institute for Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Thorsten Hoppe
- Institute for Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany.,Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
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27
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Gorry M, Yoneyama T, Vujanovic L, Moss ML, Garlin MA, Miller MA, Herman J, Stabile LP, Vujanovic NL. Development of flow cytometry assays for measuring cell-membrane enzyme activity on individual cells. J Cancer 2020; 11:702-715. [PMID: 31942194 PMCID: PMC6959049 DOI: 10.7150/jca.30813] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2018] [Accepted: 09/12/2019] [Indexed: 02/06/2023] Open
Abstract
Background: Cell-membrane expressing enzymes such as ADAM (a disintegrin and metalloproteinase) superfamily members are thought to be key catalysts of vital cellular functions. To directly measure these enzymes and determine their association with particular cells and functions, individual-cell membrane-bound enzyme activity assays are required, but unavailable. Methods: We developed two such assays, using a fluorescence resonance energy transfer (FRET) peptide substrate (FPS) and flow cytometry. One assay measured live-cell natural processing of FPS and binding of its fluorescent product onto individual-cell membrane-bound enzymes. The other assay measured processing of specifically-bound and glutaraldehyde-crosslinked FPS, and consequent generation of its coupled fluorescent product onto individual-cell membrane-bound enzymes. Results: Confocal-microscopy imaging indicated that proteolytic processing of FPS selectively occurred on and labeled cell membrane of individual cells. The new assays measured specific increases of cell-associated FPS fluorescent product in substrate-concentration-, temperature- and time-dependent manners. A large proportion of processed FPS fluorescent products remained cell-associated after cell washing, indicating their binding to cell-membrane expressing enzymes. The assays measured higher levels of cell-associated FPS fluorescent product on wild-type than ADAM10-knockout mouse fibroblasts and on human monocytes than lymphocytes, which correlated with ADAM10 presence and expression levels on cell membrane, respectively. Furthermore, the enzyme activity assays could be combined with fluorescent anti-ADAM10 antibody staining to co-label and more directly associate enzyme activity and ADAM10 protein levels on cell membrane of individual cells. Conclusions: We report on two novel assays for measuring cell-membrane anchored enzyme activity on individual cells, and their potential use to directly study specific biology of cell-surface-expressing proteases.
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Affiliation(s)
- Michael Gorry
- University of Pittsburgh Cancer Institute, Pittsburgh, PA.,Department of Pathology, University of Pittsburgh.,VAPHS, Pittsburgh, PA
| | - Toshie Yoneyama
- University of Pittsburgh Cancer Institute, Pittsburgh, PA.,Department of Pathology, University of Pittsburgh.,VAPHS, Pittsburgh, PA
| | - Lazar Vujanovic
- University of Pittsburgh Cancer Institute, Pittsburgh, PA.,Department of Otolaryngology, University of Pittsburgh
| | | | - Michelle A Garlin
- Center for Systems Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA
| | - Miles A Miller
- Center for Systems Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA
| | - James Herman
- University of Pittsburgh Cancer Institute, Pittsburgh, PA.,Department of Medicine, University of Pittsburgh
| | - Laura P Stabile
- University of Pittsburgh Cancer Institute, Pittsburgh, PA.,Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA
| | - Nikola L Vujanovic
- University of Pittsburgh Cancer Institute, Pittsburgh, PA.,Department of Pathology, University of Pittsburgh.,Department of Immunology, University of Pittsburgh.,VAPHS, Pittsburgh, PA
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28
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Singh R, Gurao A, Rajesh C, Mishra SK, Rani S, Behl A, Kumar V, Kataria RS. Comparative modeling and mutual docking of structurally uncharacterized heat shock protein 70 and heat shock factor-1 proteins in water buffalo. Vet World 2019; 12:2036-2045. [PMID: 32095057 PMCID: PMC6989329 DOI: 10.14202/vetworld.2019.2036-2045] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 11/13/2019] [Indexed: 12/20/2022] Open
Abstract
Aim: In this study, a wide range of in silico investigation of Bubalus bubalis (BB) heat shock protein 70 (HSP70) and heat shock factor-1 (HSF1) has been performed, ranging from sequence evaluation among species to homology modeling along with their docking studies to decipher the interacting residues of both molecules. Materials and Methods: Protein sequences of BB HSP70 and HSF1 were retrieved from NCBI database in FASTA format. Primary and secondary structure prediction were computed using Expasy ProtParam server and Phyre2 server, respectively. TMHMM server was used to identify the transmembrane regions in HSP70. Multiple sequence alignment and comparative analysis of the protein was carried out using MAFFT and visualization was created using ESPript 3.0. Phylogenetic analysis was accomplished by COBALT. Interactions of HSP70 with other proteins were studied using STRING database. Modeller 9.18, RaptorX, Swiss-Modeller, Phyre2, and I-TASSER were utilized to design the three-dimensional structure of these proteins followed by refinement; energy minimization was accomplished using ModRefiner and SPDBV program. Stereochemical quality along with the accuracy of the predicted models and their visualization was observed by PROCHECK program of PDBsum and UCSF Chimera, respectively. ClusPro 2.0 server was accessed for the docking of the receptor protein with the ligand. Results: The lower value of Grand Average of Hydropathy indicates the more hydrophilic nature of HSP70 protein. Value of the instability index (II) classified the protein as stable. No transmembrane region was reported for HSP70 by TMHMM server. Phylogenetic analysis based on multiple sequence alignments (MSAs) by COBALT indicated more evolutionarily closeness of Bos indicus (BI) with Bos taurus as compared to BI and BB. STRING database clearly indicates the HSF1 as one of the interacting molecules among 10 interacting partners with HSP 70. The best hit of 3D model of HSP70 protein and HSF1 was retrieved from I-TASSER and Phyre2, respectively. Interacting residues and type of bonding between both the molecules which were docked by ClusPro 2.0 were decoded by PIC server. Hydrophobic interactions, protein-protein main-chain-side-chain hydrogen bonds, and protein-protein side-chain-side-chain hydrogen bonds were delineated in this study. Conclusion: This is the first-ever study on in silico interaction of HSP70 and HSF1 proteins in BB. Several bioinformatics web tools were utilized to study secondary structure along with comparative modeling, physicochemical properties, and protein-protein interaction. The various interacting amino acid residues of both proteins have been indicated in this study.
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Affiliation(s)
- Ravinder Singh
- ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, India.,Department of Biotechnology, Sri Guru Granth Sahib World University, Fatehgarh Sahib, Punjab, India
| | - Ankita Gurao
- Department of Veterinary Microbiology and Biotechnology, Rajasthan University of Veterinary and Animal Sciences, Bikaner, Rajasthan, India
| | - C Rajesh
- Department of Biotechnology, Sri Guru Granth Sahib World University, Fatehgarh Sahib, Punjab, India
| | - S K Mishra
- ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, India
| | - Saroj Rani
- Department of Agriculture, Maharishi Markandeshwar University, Ambala, Haryana, India
| | - Ankita Behl
- Department of Biotechnology, Guru Nanak Dev University, Amritsar, Punjab, India
| | - Vikash Kumar
- Department of Molecular Biology and Biochemistry, Guru Nanak Dev University, Amritsar, Punjab, India
| | - R S Kataria
- ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, India
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29
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Abstract
Nuclear proteins participate in diverse cellular processes, many of which are essential for cell survival and viability. To maintain optimal nuclear physiology, the cell employs the ubiquitin-proteasome system to eliminate damaged and misfolded proteins in the nucleus that could otherwise harm the cell. In this review, we highlight the current knowledge about the major ubiquitin-protein ligases involved in protein quality control degradation (PQCD) in the nucleus and how they orchestrate their functions to eliminate misfolded proteins in different nuclear subcompartments. Many human disorders are causally linked to protein misfolding in the nucleus, hence we discuss major concepts that still need to be clarified to better understand the basis of the nuclear misfolded proteins' toxic effects. Additionally, we touch upon potential strategies for manipulating nuclear PQCD pathways to ameliorate diseases associated with protein misfolding and aggregation in the nucleus.
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Affiliation(s)
- Charisma Enam
- Department of Pharmacology, University of Washington, Seattle, Washington 98195, USA; ,
| | - Yifat Geffen
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat-Ram, Jerusalem 91904, Israel; ,
| | - Tommer Ravid
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat-Ram, Jerusalem 91904, Israel; ,
| | - Richard G Gardner
- Department of Pharmacology, University of Washington, Seattle, Washington 98195, USA; ,
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30
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Early Stage Discovery and Validation of Pharmacological Chaperones for the Correction of Protein Misfolding Diseases. Methods Mol Biol 2019; 1873:279-292. [PMID: 30341617 DOI: 10.1007/978-1-4939-8820-4_18] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Pharmacological chaperones are small molecular weight molecules that bind specifically to protein targets and stabilize unstable and misfolded conformations. In particular, there is an increasing interest in the application of this type of compounds for the correction of genetic conformational disorders, which are caused by mutations leading to protein instability. The discovery of compounds with pharmacological chaperone ability is customarily initiated by a high-throughput screening of chemical libraries searching for stabilizing binders. However, there is no established consensus for the subsequent steps. Therefore, here, we introduce an example of a successful protocol directed to the discovery of pharmacological chaperones with potential for the therapeutic correction of phenylketonuria, a defect caused by mutations in the enzyme phenylalanine hydroxylase.
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31
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Fernández-Higuero JÁ, Betancor-Fernández I, Mesa-Torres N, Muga A, Salido E, Pey AL. Structural and functional insights on the roles of molecular chaperones in the mistargeting and aggregation phenotypes associated with primary hyperoxaluria type I. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2018; 114:119-152. [PMID: 30635080 DOI: 10.1016/bs.apcsb.2018.09.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
To carry out their biological function in cells, proteins must be folded and targeted to the appropriate subcellular location. These processes are controlled by a vast collection of interacting proteins collectively known as the protein homeostasis network, in which molecular chaperones play a prominent role. Protein homeostasis can be impaired by inherited mutations leading to genetic diseases. In this chapter, we focus on a particular disease, primary hyperoxaluria type 1 (PH1), in which disease-associated mutations exacerbate protein aggregation in the cell and mistarget the peroxisomal alanine:glyoxylate aminotransferase (AGT) protein to mitochondria, in part due to native state destabilization and enhanced interaction with Hsp60, 70 and 90 chaperone systems. After a general introduction of molecular chaperones and PH1, we review our current knowledge on the structural and energetic features of PH1-causing mutants that lead to these particular pathogenic mechanisms. From this perspective, and in the context of the key role of molecular chaperones in PH1 pathogenesis, we present and discuss current and future perspectives for pharmacological treatments for this disease.
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Affiliation(s)
- José Ángel Fernández-Higuero
- Biofisika Institute (CSIC, UPV/EHU) and Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Bilbao, Spain
| | - Isabel Betancor-Fernández
- Centre for Biomedical Research on Rare Diseases (CIBERER), Hospital Universitario de Canarias, ITB, University of La Laguna, Tenerife, Spain
| | - Noel Mesa-Torres
- Department of Physical Chemistry, University of Granada, Granada, Spain
| | - Arturo Muga
- Biofisika Institute (CSIC, UPV/EHU) and Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Bilbao, Spain
| | - Eduardo Salido
- Centre for Biomedical Research on Rare Diseases (CIBERER), Hospital Universitario de Canarias, ITB, University of La Laguna, Tenerife, Spain
| | - Angel L Pey
- Department of Physical Chemistry, University of Granada, Granada, Spain.
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32
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Balaji V, Pokrzywa W, Hoppe T. Ubiquitylation Pathways In Insulin Signaling and Organismal Homeostasis. Bioessays 2018; 40:e1700223. [PMID: 29611634 DOI: 10.1002/bies.201700223] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 02/26/2018] [Indexed: 12/26/2022]
Abstract
The insulin/insulin-like growth factor-1 (IGF-1) signaling (IIS) pathway is a pivotal genetic program regulating cell growth, tissue development, metabolic physiology, and longevity of multicellular organisms. IIS integrates a fine-tuned cascade of signaling events induced by insulin/IGF-1, which is precisely controlled by post-translational modifications. The ubiquitin/proteasome-system (UPS) influences the functionality of IIS through inducible ubiquitylation pathways that regulate internalization of the insulin/IGF-1 receptor, the stability of downstream insulin/IGF-1 signaling targets, and activity of nuclear receptors for control of gene expression. An age-related decline in UPS activity is often associated with an impairment of IIS, contributing to pathologies such as cancer, diabetes, cardiovascular, and neurodegenerative disorders. Recent findings identified a key role of diverse ubiquitin modifications in insulin signaling decisions, which governs dynamic adaption upon environmental and physiological changes. In this review, we discuss the mutual crosstalk between ubiquitin and insulin signaling pathways in the context of cellular and organismal homeostasis.
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Affiliation(s)
- Vishnu Balaji
- Institute for Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Joseph-Stelzmann Str. 26, 50931 Cologne, Germany
| | - Wojciech Pokrzywa
- Laboratory of Protein Metabolism in Development and Aging, International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Thorsten Hoppe
- Institute for Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Joseph-Stelzmann Str. 26, 50931 Cologne, Germany
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33
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Just W. Jerusalem Special Issue. FEBS Lett 2018; 591:2503-2504. [PMID: 28876461 DOI: 10.1002/1873-3468.12789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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34
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CHIPped balance of proteostasis and longevity. Oncotarget 2017; 8:96472-96473. [PMID: 29228542 PMCID: PMC5722494 DOI: 10.18632/oncotarget.22101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 10/24/2017] [Indexed: 11/25/2022] Open
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35
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Pokrzywa W, Lorenz R, Hoppe T. Chaperone-directed ubiquitylation maintains proteostasis at the expense of longevity. WORM 2017; 6:e1371403. [PMID: 28959501 PMCID: PMC5612283 DOI: 10.1080/21624054.2017.1371403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 08/18/2017] [Indexed: 11/24/2022]
Abstract
The integrity of the cellular proteome is supported by quality control networks, which govern protein synthesis, folding, and degradation. It is generally accepted that an age-related decline in protein homeostasis (proteostasis) contributes to protein aggregation diseases. However, the mechanistic principles underlying proteostasis imbalance and the impact on life expectancy are not well understood. We recently demonstrated that this interrelation is affected by chaperone-directed ubiquitylation, shifting the amount of the conserved DAF-2/insulin receptor both in Caenorhabditis elegans and Drosophila melanogaster. The ubiquitin ligase CHIP either targets the membrane bound insulin receptor or misfolded proteins for degradation, which depends on the cellular proteostasis status. Increased proteotoxicity triggers chaperone-assisted redirection of CHIP toward protein aggregates, limiting its capacity to degrade the insulin receptor and prevent premature aging. In light of these findings, we discuss a new concept for understanding the impact of proteome imbalance on longevity risk.
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Affiliation(s)
- Wojciech Pokrzywa
- Institute for Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany.,International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Robin Lorenz
- Institute for Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Thorsten Hoppe
- Institute for Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
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