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Tower J. Selectively advantageous instability in biotic and pre-biotic systems and implications for evolution and aging. FRONTIERS IN AGING 2024; 5:1376060. [PMID: 38818026 PMCID: PMC11137231 DOI: 10.3389/fragi.2024.1376060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 04/15/2024] [Indexed: 06/01/2024]
Abstract
Rules of biology typically involve conservation of resources. For example, common patterns such as hexagons and logarithmic spirals require minimal materials, and scaling laws involve conservation of energy. Here a relationship with the opposite theme is discussed, which is the selectively advantageous instability (SAI) of one or more components of a replicating system, such as the cell. By increasing the complexity of the system, SAI can have benefits in addition to the generation of energy or the mobilization of building blocks. SAI involves a potential cost to the replicating system for the materials and/or energy required to create the unstable component, and in some cases, the energy required for its active degradation. SAI is well-studied in cells. Short-lived transcription and signaling factors enable a rapid response to a changing environment, and turnover is critical for replacement of damaged macromolecules. The minimal gene set for a viable cell includes proteases and a nuclease, suggesting SAI is essential for life. SAI promotes genetic diversity in several ways. Toxin/antitoxin systems promote maintenance of genes, and SAI of mitochondria facilitates uniparental transmission. By creating two distinct states, subject to different selective pressures, SAI can maintain genetic diversity. SAI of components of synthetic replicators favors replicator cycling, promoting emergence of replicators with increased complexity. Both classical and recent computer modeling of replicators reveals SAI. SAI may be involved at additional levels of biological organization. In summary, SAI promotes replicator genetic diversity and reproductive fitness, and may promote aging through loss of resources and maintenance of deleterious alleles.
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Affiliation(s)
- John Tower
- Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, CA, United States
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2
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Abdelmoaty AAA, Zhang P, Lin W, Fan YJ, Ye SN, Xu JH. C0818, a novel curcumin derivative, induces ROS-dependent cytotoxicity in human hepatocellular carcinoma cells in vitro via disruption of Hsp90 function. Acta Pharmacol Sin 2022; 43:446-456. [PMID: 33824458 PMCID: PMC8792041 DOI: 10.1038/s41401-021-00642-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 03/08/2021] [Indexed: 02/03/2023] Open
Abstract
Heat shock protein 90 (Hsp90) is the most common molecular chaperone that controls the maturation of many oncoproteins critical in tumor development. Hsp90 has been considered as a promising target for cancer treatment, but the clinical significance of Hsp90 and the mechanisms of Hsp90 regulating the tumor-promoting effects in hepatocellular carcinoma (HCC) remain obscure. Previous studies have shown that curcumin, a polyphenol derived from the plant turmeric (Curcuma longa), inhibits tumor growth, which may provide an effective alternative therapy for HCC. Compared to curcumin, a novel derivative of curcumin, 3,5-(E)-Bis(3-methoxy-4-hydroxybenzal)-4-piperidinone hydrochloride (C0818) that is more potent in Hsp90 inhibition and antitumor activity. In this study, we investigated the effect of C0818 on HCC cells in vitro and its relation to Hsp90 inhibition. We showed that C0818 concentration-dependently inhibited the proliferation, the colony formation and induced apoptosis in HepG2 and Sk-Hep-1 cells. C0818 concentration-dependently inhibited DNA synthesis and induced G2/M phase arrest in HepG2 and Sk-Hep-1 cells. We further demonstrated that C0818 induced ROS- and caspase-dependent apoptosis in HCC cells through the mitochondrial-mediated pathway. C0818 induced the degradation of Hsp90 client proteins as RAS, C-Raf, P-C-Raf, Erk, P-ERK, MEK, P-MEK, Akt and P-Akt, which led to subsequent inhibition of the RAS/RAF/MEK/ERK and PI3K/AKT pathways. We revealed that C0818 could inhibit the binding of Hsp90 with its clients without affecting their transcription, which subsequently induced the degradation of Hsp90 clients by the proteasome rather than the lysosome. These results are of potential importance for elucidating a novel Hsp90 inhibitor targeting HCC.
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Affiliation(s)
- Ahmed Attia Ahmed Abdelmoaty
- Department of Pharmacology, School of Pharmacy, Fujian Provincial Key Laboratory of Natural Medicine Pharmacology, Fujian Medical University, Fuzhou, 350122, China
| | - Ping Zhang
- Department of Pharmacology, School of Pharmacy, Fujian Provincial Key Laboratory of Natural Medicine Pharmacology, Fujian Medical University, Fuzhou, 350122, China
| | - Wen Lin
- The First Affiliated Hospital of Fujian Medical University, Fuzhou, 350004, China
| | - Ying-Juan Fan
- Department of Pharmacology, School of Pharmacy, Fujian Provincial Key Laboratory of Natural Medicine Pharmacology, Fujian Medical University, Fuzhou, 350122, China
| | - Sheng-Nan Ye
- The First Affiliated Hospital of Fujian Medical University, Fuzhou, 350004, China.
| | - Jian-Hua Xu
- Department of Pharmacology, School of Pharmacy, Fujian Provincial Key Laboratory of Natural Medicine Pharmacology, Fujian Medical University, Fuzhou, 350122, China.
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3
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Chargui A, Belaid A, Ndiaye PD, Imbert V, Samson M, Guigonis JM, Tauc M, Peyron JF, Poujeol P, Brest P, Hofman P, Mograbi B. The Carcinogen Cadmium Activates Lysine 63 (K63)-Linked Ubiquitin-Dependent Signaling and Inhibits Selective Autophagy. Cancers (Basel) 2021; 13:2490. [PMID: 34065348 PMCID: PMC8161291 DOI: 10.3390/cancers13102490] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 05/11/2021] [Indexed: 01/18/2023] Open
Abstract
Signaling, proliferation, and inflammation are dependent on K63-linked ubiquitination-conjugation of a chain of ubiquitin molecules linked via lysine 63. However, very little information is currently available about how K63-linked ubiquitination is subverted in cancer. The present study provides, for the first time, evidence that cadmium (Cd), a widespread environmental carcinogen, is a potent activator of K63-linked ubiquitination, independently of oxidative damage, activation of ubiquitin ligase, or proteasome impairment. We show that Cd induces the formation of protein aggregates that sequester and inactivate cylindromatosis (CYLD) and selective autophagy, two tumor suppressors that deubiquitinate and degrade K63-ubiquitinated proteins, respectively. The aggregates are constituted of substrates of selective autophagy-SQSTM1, K63-ubiquitinated proteins, and mitochondria. These protein aggregates also cluster double-membrane remnants, which suggests an impairment in autophagosome maturation. However, failure to eliminate these selective cargos is not due to alterations in the general autophagy process, as degradation of long-lived proteins occurs normally. We propose that the simultaneous disruption of CYLD and selective autophagy by Cd feeds a vicious cycle that further amplifies K63-linked ubiquitination and downstream activation of the NF-κB pathway, processes that support cancer progression. These novel findings link together impairment of selective autophagy, K63-linked ubiquitination, and carcinogenesis.
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Affiliation(s)
- Abderrahman Chargui
- Université Côte d’Azur, Institute of Research on Cancer and Aging in Nice (IRCAN), Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), Fédération Hospitalo-Universitaire (FHU) OncoAge, Centre Antoine Lacassagne, F-06189 Nice, France; (A.C.); (A.B.); (P.D.N.); (P.B.); (P.H.)
- Higher School of Agriculture of Kef, University Jendouba, Le Kef and Laboratory of Histology, Embryology and Cell Biology, Faculty of Medicine Tunis, 7110 Le Kef, Tunisia
| | - Amine Belaid
- Université Côte d’Azur, Institute of Research on Cancer and Aging in Nice (IRCAN), Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), Fédération Hospitalo-Universitaire (FHU) OncoAge, Centre Antoine Lacassagne, F-06189 Nice, France; (A.C.); (A.B.); (P.D.N.); (P.B.); (P.H.)
| | - Papa Diogop Ndiaye
- Université Côte d’Azur, Institute of Research on Cancer and Aging in Nice (IRCAN), Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), Fédération Hospitalo-Universitaire (FHU) OncoAge, Centre Antoine Lacassagne, F-06189 Nice, France; (A.C.); (A.B.); (P.D.N.); (P.B.); (P.H.)
| | - Véronique Imbert
- Université Côte d’Azur, Centre Méditerranéen de Médecine Moléculaire (C3M), Institut National de la Santé et de la Recherche Médicale (INSERM), F-06204 Nice, France; (V.I.); (J.-F.P.)
| | - Michel Samson
- Université Côte d’Azur, Laboratory Transporter in Imaging and Radiotherapy in Oncology (TIRO), Direction de la Recherche Fondamentale (DRF), Institut des sciences du vivant Fréderic Joliot, Commissariat à l’Energie Atomique et aux énergies alternatives (CEA), F-06107 Nice, France; (M.S.); (J.-M.G.)
| | - Jean-Marie Guigonis
- Université Côte d’Azur, Laboratory Transporter in Imaging and Radiotherapy in Oncology (TIRO), Direction de la Recherche Fondamentale (DRF), Institut des sciences du vivant Fréderic Joliot, Commissariat à l’Energie Atomique et aux énergies alternatives (CEA), F-06107 Nice, France; (M.S.); (J.-M.G.)
| | - Michel Tauc
- Université Côte d’Azur, Laboratoire de Physiomédecine Moléculaire, LP2M, Labex ICST, Centre National de la Recherche Scientifique (CNRS), F-06107 Nice, France; (M.T.); (P.P.)
| | - Jean-François Peyron
- Université Côte d’Azur, Centre Méditerranéen de Médecine Moléculaire (C3M), Institut National de la Santé et de la Recherche Médicale (INSERM), F-06204 Nice, France; (V.I.); (J.-F.P.)
| | - Philippe Poujeol
- Université Côte d’Azur, Laboratoire de Physiomédecine Moléculaire, LP2M, Labex ICST, Centre National de la Recherche Scientifique (CNRS), F-06107 Nice, France; (M.T.); (P.P.)
| | - Patrick Brest
- Université Côte d’Azur, Institute of Research on Cancer and Aging in Nice (IRCAN), Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), Fédération Hospitalo-Universitaire (FHU) OncoAge, Centre Antoine Lacassagne, F-06189 Nice, France; (A.C.); (A.B.); (P.D.N.); (P.B.); (P.H.)
| | - Paul Hofman
- Université Côte d’Azur, Institute of Research on Cancer and Aging in Nice (IRCAN), Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), Fédération Hospitalo-Universitaire (FHU) OncoAge, Centre Antoine Lacassagne, F-06189 Nice, France; (A.C.); (A.B.); (P.D.N.); (P.B.); (P.H.)
- Université Côte d’Azur, Laboratory of Clinical and Experimental Pathology, FHU OncoAge, Hospital-Integrated Biobank (BB-0033-00025), Centre Hospitalier Universitaire (CHU) de Nice, F-06001 Nice, France
| | - Baharia Mograbi
- Université Côte d’Azur, Institute of Research on Cancer and Aging in Nice (IRCAN), Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), Fédération Hospitalo-Universitaire (FHU) OncoAge, Centre Antoine Lacassagne, F-06189 Nice, France; (A.C.); (A.B.); (P.D.N.); (P.B.); (P.H.)
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Qu T, Calabrese P, Singhavi P, Tower J. Incorporating antagonistic pleiotropy into models for molecular replicators. Biosystems 2020; 201:104333. [PMID: 33359635 DOI: 10.1016/j.biosystems.2020.104333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Revised: 12/17/2020] [Accepted: 12/17/2020] [Indexed: 11/15/2022]
Abstract
In modern cells, chromosomal genes composed of DNA encode multi-subunit protein/RNA complexes that catalyze the replication of the chromosome and cell. One prevailing theory for the origin of life posits an early stage involving self-replicating macromolecules called replicators, which can be considered genes capable of self-replication. One prevailing theory for the genetics of aging in humans and other organisms is antagonistic pleiotropy, which posits that a gene can be beneficial in one context, and detrimental in another context. We previously reported that the conceptual simplicity of molecular replicators facilitates the generation of two simple models involving antagonistic pleiotropy. Here a third model is proposed, and each of the three models is presented with improved definition of the time variable. Computer simulations were used to calculate the proliferation of a hypothetical two-subunit replicator (AB), when one of the two subunits (B) exhibits antagonistic pleiotropy, leading to an advantage for B to be unstable. In model 1, instability of B yields free A subunits, which in turn stimulate the activity of other AB replicators. In model 2, B is lost and sometimes replaced by a more active mutant form, B'. In model 3, B becomes damaged and loses activity, and its instability allows it to be replaced by a new B. For each model, conditions were identified where instability of B was detrimental, and where instability of B was beneficial. The results are consistent with the hypothesis that antagonistic pleiotropy can promote molecular instability and system complexity, and provide further support for a model linking aging and evolution.
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Affiliation(s)
- Tianjiao Qu
- Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA
| | - Peter Calabrese
- Quantitative and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA
| | - Pratik Singhavi
- Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA
| | - John Tower
- Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA.
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5
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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: 44] [Impact Index Per Article: 11.0] [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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6
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Protein folding vs. COVID-19 and the Mediterranean diet. BIO-ALGORITHMS AND MED-SYSTEMS 2020. [DOI: 10.1515/bams-2020-0029] [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
Abstract
The experience of the ongoing pandemic gives rise to a variety of questions, touching – among others – upon its biological aspects. Among the most often raised issues is why the situation has deteriorated to such a degree in the Mediterranean basin and the American eastern seaboard. This work identifies possible links between the protein folding process and the aforementioned epidemic. Given the circumstances, it should be regarded as a popular science article.
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7
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Mori Y, Yoshida Y, Satoh A, Moriya H. Development of an experimental method of systematically estimating protein expression limits in HEK293 cells. Sci Rep 2020; 10:4798. [PMID: 32179769 PMCID: PMC7075890 DOI: 10.1038/s41598-020-61646-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 02/28/2020] [Indexed: 11/25/2022] Open
Abstract
Protein overexpression sometimes causes cellular defects, although the underlying mechanism is still unknown. A protein's expression limit, which triggers cellular defects, is a useful indication of the underlying mechanism. In this study, we developed an experimental method of estimating the expression limits of target proteins in the human embryonic kidney cell line HEK293 by measuring the proteins' expression levels in cells that survived after the high-copy introduction of plasmid DNA by which the proteins were expressed under a strong cytomegalovirus promoter. The expression limits of nonfluorescent target proteins were indirectly estimated by measuring the levels of green fluorescent protein (GFP) connected to the target proteins with the self-cleaving sequence P2A. The expression limit of a model GFP was ~5.0% of the total protein, and sustained GFP overexpression caused cell death. The expression limits of GFPs with mitochondria-targeting signals and endoplasmic reticulum localization signals were 1.6% and 0.38%, respectively. The expression limits of four proteins involved in vesicular trafficking were far lower compared to a red fluorescent protein. The protein expression limit estimation method developed will be valuable for defining toxic proteins and consequences of protein overexpression.
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Affiliation(s)
- Yoshihiro Mori
- Graduate School of Natural Science and Technology, Okayama University, Okayama, Japan
| | - Yuki Yoshida
- Sony Computer Science Laboratories, Tokyo, Japan
| | - Ayano Satoh
- Graduate School of Interdisciplinary Science and Engineering in Health Systems, Okayama University, Okayama, Japan
| | - Hisao Moriya
- Research Core for Interdisciplinary Sciences, Okayama University, Okayama, Japan.
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan.
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8
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Luhr M, Sætre F, Engedal N. The Long-lived Protein Degradation Assay: an Efficient Method for Quantitative Determination of the Autophagic Flux of Endogenous Proteins in Adherent Cell Lines. Bio Protoc 2018; 8:e2836. [PMID: 34286043 DOI: 10.21769/bioprotoc.2836] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Revised: 04/17/2018] [Accepted: 04/20/2018] [Indexed: 12/25/2022] Open
Abstract
Autophagy is a key player in the maintenance of cellular homeostasis in eukaryotes, and numerous diseases, including cancer and neurodegenerative disorders, are associated with alterations in autophagy. The interest for studying autophagy has grown intensely in the last two decades, and so has the arsenal of methods utilised to study this highly dynamic and complex process. Changes in the expression and/or localisation of autophagy-related proteins are frequently assessed by Western blot and various microscopy techniques. Such analyses may be indicative of alterations in autophagy-related processes and informative about the specific marker being investigated. However, since these proteins are part of the autophagic machinery, and not autophagic cargo, they cannot be used to draw conclusions regarding autophagic cargo flux. Here, we provide a protocol to quantitatively assess bulk autophagic flux by employing the long-lived protein degradation assay. Our procedure, which traces the degradation of 14C valine-labelled proteins, is simple and quick, allows for processing of a relatively large number of samples in parallel, and can in principle be used with any adherent cell line. Most importantly, it enables quantitative measurements of endogenous cargo flux through the autophagic pathway. As such, it is one of the gold standards for studying autophagic activity.
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Affiliation(s)
- Morten Luhr
- The Autophagy Team, Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, Oslo, Norway
| | - Frank Sætre
- The Autophagy Team, Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, Oslo, Norway
| | - Nikolai Engedal
- The Autophagy Team, Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, Oslo, Norway
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9
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Mishra R, Upadhyay A, Prajapati VK, Mishra A. Proteasome-mediated proteostasis: Novel medicinal and pharmacological strategies for diseases. Med Res Rev 2018; 38:1916-1973. [DOI: 10.1002/med.21502] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2017] [Revised: 03/13/2018] [Accepted: 04/04/2018] [Indexed: 02/06/2023]
Affiliation(s)
- Ribhav Mishra
- Cellular and Molecular Neurobiology Unit; Indian Institute of Technology Jodhpur; Rajasthan India
| | - Arun Upadhyay
- Cellular and Molecular Neurobiology Unit; Indian Institute of Technology Jodhpur; Rajasthan India
| | - Vijay Kumar Prajapati
- Department of Biochemistry; School of Life Sciences; Central University of Rajasthan; Rajasthan India
| | - Amit Mishra
- Cellular and Molecular Neurobiology Unit; Indian Institute of Technology Jodhpur; Rajasthan India
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10
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Yang J, Wu W, Wen J, Ye H, Luo H, Bai P, Tang M, Wang F, Zheng L, Yang S, Li W, Peng A, Yang L, Wan L, Chen L. Liposomal honokiol induced lysosomal degradation of Hsp90 client proteins and protective autophagy in both gefitinib-sensitive and gefitinib-resistant NSCLC cells. Biomaterials 2017; 141:188-198. [DOI: 10.1016/j.biomaterials.2017.07.002] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Revised: 06/30/2017] [Accepted: 07/02/2017] [Indexed: 12/19/2022]
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11
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Tundo GR, Sbardella D, Ciaccio C, Grasso G, Gioia M, Coletta A, Polticelli F, Di Pierro D, Milardi D, Van Endert P, Marini S, Coletta M. Multiple functions of insulin-degrading enzyme: a metabolic crosslight? Crit Rev Biochem Mol Biol 2017. [PMID: 28635330 DOI: 10.1080/10409238.2017.1337707] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Insulin-degrading enzyme (IDE) is a ubiquitous zinc peptidase of the inverzincin family, which has been initially discovered as the enzyme responsible for insulin catabolism; therefore, its involvement in the onset of diabetes has been largely investigated. However, further studies on IDE unraveled its ability to degrade several other polypeptides, such as β-amyloid, amylin, and glucagon, envisaging the possible implication of IDE dys-regulation in the "aggregopathies" and, in particular, in neurodegenerative diseases. Over the last decade, a novel scenario on IDE biology has emerged, pointing out a multi-functional role of this enzyme in several basic cellular processes. In particular, latest advances indicate that IDE behaves as a heat shock protein and modulates the ubiquitin-proteasome system, suggesting a major implication in proteins turnover and cell homeostasis. In addition, recent observations have highlighted that the regulation of glucose metabolism by IDE is not merely based on its largely proposed role in the degradation of insulin in vivo. There is increasing evidence that improper IDE function, regulation, or trafficking might contribute to the etiology of metabolic diseases. In addition, the enzymatic activity of IDE is affected by metals levels, thus suggesting a role also in the metal homeostasis (metallostasis), which is thought to be tightly linked to the malfunction of the "quality control" machinery of the cell. Focusing on the physiological role of IDE, we will address a comprehensive vision of the very complex scenario in which IDE takes part, outlining its crucial role in interconnecting several relevant cellular processes.
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Affiliation(s)
- Grazia R Tundo
- a Department of Clinical Sciences and Translation Medicine , University of Roma Tor Vergata , Roma , Italy.,b CIRCMSB , Bari , Italy
| | - Diego Sbardella
- a Department of Clinical Sciences and Translation Medicine , University of Roma Tor Vergata , Roma , Italy.,b CIRCMSB , Bari , Italy.,c Center for TeleInfrastructures, University of Roma Tor Vergata , Roma , Italy
| | - Chiara Ciaccio
- a Department of Clinical Sciences and Translation Medicine , University of Roma Tor Vergata , Roma , Italy.,b CIRCMSB , Bari , Italy
| | - Giuseppe Grasso
- d Department of Chemistry , University of Catania , Catania , Italy.,e CNR IBB , Catania , Italy
| | - Magda Gioia
- a Department of Clinical Sciences and Translation Medicine , University of Roma Tor Vergata , Roma , Italy.,b CIRCMSB , Bari , Italy
| | - Andrea Coletta
- f Department of Chemistry , University of Aarhus , Aarhus , Denmark
| | | | - Donato Di Pierro
- a Department of Clinical Sciences and Translation Medicine , University of Roma Tor Vergata , Roma , Italy.,b CIRCMSB , Bari , Italy
| | | | - Peter Van Endert
- h Université Paris Descartes, INSERM, U1151, CNRS , Paris , France
| | - Stefano Marini
- a Department of Clinical Sciences and Translation Medicine , University of Roma Tor Vergata , Roma , Italy.,b CIRCMSB , Bari , Italy.,c Center for TeleInfrastructures, University of Roma Tor Vergata , Roma , Italy
| | - Massimo Coletta
- a Department of Clinical Sciences and Translation Medicine , University of Roma Tor Vergata , Roma , Italy.,b CIRCMSB , Bari , Italy.,c Center for TeleInfrastructures, University of Roma Tor Vergata , Roma , Italy
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12
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Song C, Mitter SK, Qi X, Beli E, Rao HV, Ding J, Ip CS, Gu H, Akin D, Dunn WA, Bowes Rickman C, Lewin AS, Grant MB, Boulton ME. Oxidative stress-mediated NFκB phosphorylation upregulates p62/SQSTM1 and promotes retinal pigmented epithelial cell survival through increased autophagy. PLoS One 2017; 12:e0171940. [PMID: 28222108 PMCID: PMC5319799 DOI: 10.1371/journal.pone.0171940] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Accepted: 01/27/2017] [Indexed: 12/16/2022] Open
Abstract
p62 is a scaffolding adaptor implicated in the clearance of protein aggregates by autophagy. Reactive oxygen species (ROS) can either stimulate or inhibit NFκB-mediated gene expression influencing cellular fate. We studied the effect of hydrogen peroxide (H2O2)-mediated oxidative stress and NFκB signaling on p62 expression in the retinal pigment epithelium (RPE) and investigated its role in regulation of autophagy and RPE survival against oxidative damage. Cultured human RPE cell line ARPE-19 and primary human adult and fetal RPE cells were exposed to H2O2-induced oxidative stress. The human apolipoprotein E4 targeted-replacement (APOE4) mouse model of AMD was used to study expression of p62 and other autophagy proteins in the retina. p62, NFκB p65 (total, phosphorylated, nuclear and cytoplasmic) and ATG10 expression was assessed by mRNA and protein analyses. Cellular ROS and mitochondrial superoxide were measured by CM-H2DCFDA and MitoSOX staining respectively. Mitochondrial viability was determined using MTT activity. qPCR-array system was used to investigate autophagic genes affected by p62. Nuclear and cytoplasmic levels of NFκB p65 were evaluated after cellular fractionation by Western blotting. We report that p62 is up-regulated in RPE cells under H2O2-induced oxidative stress and promotes autophagic activity. Depletion of endogenous p62 reduces autophagy by downregulation of ATG10 rendering RPE more susceptible to oxidative damage. NFκB p65 phosphorylation at Ser-536 was found to be critical for p62 upregulation in response to oxidative stress. Proteasome inhibition by H2O2 causes p62-NFκB signaling as antioxidant pre-treatment reversed p62 expression and p65 phosphorylation when RPE was challenged by H2O2 but not when by Lactacystin. p62 protein but not RNA levels are elevated in APOE4-HFC AMD mouse model, suggesting reduction of autophagic flux in disease conditions. Our findings suggest that p62 is necessary for RPE cytoprotection under oxidative stress and functions, in part, by modulating ATG10 expression. NFκB p65 activity may be a critical upstream initiator of p62 expression in RPE cells under oxidative stress.
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Affiliation(s)
- Chunjuan Song
- Department of Anatomy and Cell Biology, University of Florida, Gainesville, Florida, United States of America
| | - Sayak K Mitter
- Department of Ophthalmology, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
| | - Xiaoping Qi
- Department of Ophthalmology, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
| | - Eleni Beli
- Department of Ophthalmology, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
| | - Haripriya V Rao
- Department of Anatomy and Cell Biology, University of Florida, Gainesville, Florida, United States of America
| | - Jindong Ding
- Departments of Ophthalmology and Cell Biology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Colin S Ip
- Department of Ophthalmology, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
| | - Hongmei Gu
- Department of Ophthalmology, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
| | - Debra Akin
- Department of Anatomy and Cell Biology, University of Florida, Gainesville, Florida, United States of America
| | - William A Dunn
- Department of Anatomy and Cell Biology, University of Florida, Gainesville, Florida, United States of America
| | - Catherine Bowes Rickman
- Departments of Ophthalmology and Cell Biology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Alfred S Lewin
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, Florida, United States of America
| | - Maria B Grant
- Department of Ophthalmology, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
| | - Michael E Boulton
- Department of Ophthalmology, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
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Cohen-Kaplan V, Livneh I, Avni N, Cohen-Rosenzweig C, Ciechanover A. The ubiquitin-proteasome system and autophagy: Coordinated and independent activities. Int J Biochem Cell Biol 2016; 79:403-418. [DOI: 10.1016/j.biocel.2016.07.019] [Citation(s) in RCA: 113] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Revised: 07/13/2016] [Accepted: 07/18/2016] [Indexed: 01/10/2023]
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Cecarini V, Bonfili L, Cuccioloni M, Mozzicafreddo M, Angeletti M, Keller JN, Eleuteri AM. The fine-tuning of proteolytic pathways in Alzheimer's disease. Cell Mol Life Sci 2016; 73:3433-51. [PMID: 27120560 PMCID: PMC11108445 DOI: 10.1007/s00018-016-2238-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Revised: 03/31/2016] [Accepted: 04/21/2016] [Indexed: 11/28/2022]
Abstract
Several integrated proteolytic systems contribute to the maintenance of cellular homeostasis through the continuous removal of misfolded, aggregated or oxidized proteins and damaged organelles. Among these systems, the proteasome and autophagy play the major role in protein quality control, which is a fundamental issue in non-proliferative cells such as neurons. Disturbances in the functionality of these two pathways are frequently observed in neurodegenerative diseases, like Alzheimer's disease, and reflect the accumulation of protease-resistant, deleterious protein aggregates. In this review, we explored the sophisticated crosstalk between the ubiquitin-proteasome system and autophagy in the removal of the harmful structures that characterize Alzheimer's disease neurons. We also dissected the role of the numerous shuttle factors and chaperones that, directly or indirectly interacting with ubiquitin and LC3, are used for cargo selection and delivery to one pathway or the other.
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Affiliation(s)
- Valentina Cecarini
- Department of Biosciences and Veterinary Medicine, School of Biosciences and Veterinary Medicine, University of Camerino, Via Gentile III da Varano, 62032, Camerino, Italy.
| | - Laura Bonfili
- Department of Biosciences and Veterinary Medicine, School of Biosciences and Veterinary Medicine, University of Camerino, Via Gentile III da Varano, 62032, Camerino, Italy
| | - Massimiliano Cuccioloni
- Department of Biosciences and Veterinary Medicine, School of Biosciences and Veterinary Medicine, University of Camerino, Via Gentile III da Varano, 62032, Camerino, Italy
| | - Matteo Mozzicafreddo
- Department of Biosciences and Veterinary Medicine, School of Biosciences and Veterinary Medicine, University of Camerino, Via Gentile III da Varano, 62032, Camerino, Italy
| | - Mauro Angeletti
- Department of Biosciences and Veterinary Medicine, School of Biosciences and Veterinary Medicine, University of Camerino, Via Gentile III da Varano, 62032, Camerino, Italy
| | - Jeffrey N Keller
- Pennington Biomedical Research Centre, Louisiana State University System, Baton Rouge, LA, 70808, USA
| | - Anna Maria Eleuteri
- Department of Biosciences and Veterinary Medicine, School of Biosciences and Veterinary Medicine, University of Camerino, Via Gentile III da Varano, 62032, Camerino, Italy
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15
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Nepveu-Traversy MÉ, Demogines A, Fricke T, Plourde MB, Riopel K, Veillette M, Diaz-Griffero F, Sawyer SL, Berthoux L. A putative SUMO interacting motif in the B30.2/SPRY domain of rhesus macaque TRIM5α important for NF-κB/AP-1 signaling and HIV-1 restriction. Heliyon 2016; 2:e00056. [PMID: 27441239 PMCID: PMC4945854 DOI: 10.1016/j.heliyon.2015.e00056] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Revised: 11/26/2015] [Accepted: 12/11/2015] [Indexed: 12/28/2022] Open
Abstract
TRIM5α from the rhesus macaque (TRIM5αRh) is a restriction factor that shows strong activity against HIV-1. TRIM5αRh binds specifically to HIV-1 capsid (CA) through its B30.2/PRYSPRY domain shortly after entry of the virus into the cytoplasm. Recently, three putative SUMO interacting motifs (SIMs) have been identified in the PRYSPRY domain of human and macaque TRIM5α. However, structural modeling of this domain suggested that two of them were buried in the hydrophobic core of the protein, implying that interaction with SUMO was implausible, while the third one was not relevant to restriction. In light of these results, we re-analyzed the TRIM5αRh PRYSPRY sequence and identified an additional putative SIM ((435)VIIC(438)) which we named SIM4. This motif is exposed at the surface of the PRYSPRY domain, allowing potential interactions with SUMO or SUMOylated proteins. Introducing a double mutation in SIM4 (V435K, I436K) did not alter stability, unlike mutations in SIM1. SIM4-mutated TRIM5αRh failed to bind HIV-1CA and lost the ability to restrict this virus. Accordingly, SIM4 undergoes significant variation among primates and substituting this motif with naturally occurring SIM4 variants affected HIV-1 restriction by TRIM5αRh, suggesting a direct role in capsid recognition. Interestingly, SIM4-mutated TRIM5αRh also failed to activate NF-κB and AP-1-mediated transcription. Although there is no direct evidence that SIM4 is involved in direct interaction with SUMO or a SUMOylated protein, mutating this motif strongly reduced co-localization of TRIM5αRh with SUMO-1 and with PML, a SUMOylated nuclear protein. In conclusion, this new putative SIM is crucial for both direct interaction with incoming capsids and for NF-κB/AP-1 signaling. We speculate that the latter function is mediated by interactions of SIM4 with a SUMOylated protein involved in the NF-κB/AP-1 signaling pathways.
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Affiliation(s)
- Marie-Édith Nepveu-Traversy
- Laboratory of Retrovirology, Department of Medical Biology and BioMed Research Group, Université du Québec à Trois-Rivières. 3351 Boulevard des Forges, CP500, Trois-Rivières, QC, G9A 5H7, Canada
| | - Ann Demogines
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Thomas Fricke
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Mélodie B. Plourde
- Laboratory of Retrovirology, Department of Medical Biology and BioMed Research Group, Université du Québec à Trois-Rivières. 3351 Boulevard des Forges, CP500, Trois-Rivières, QC, G9A 5H7, Canada
| | - Kathleen Riopel
- Laboratory of Retrovirology, Department of Medical Biology and BioMed Research Group, Université du Québec à Trois-Rivières. 3351 Boulevard des Forges, CP500, Trois-Rivières, QC, G9A 5H7, Canada
| | - Maxime Veillette
- Laboratory of Retrovirology, Department of Medical Biology and BioMed Research Group, Université du Québec à Trois-Rivières. 3351 Boulevard des Forges, CP500, Trois-Rivières, QC, G9A 5H7, Canada
| | - Felipe Diaz-Griffero
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Sara L. Sawyer
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
- Department of Molecular, Cellular, and Developmental Biology and the BioFrontiers Institute, University of Colorado Boulder, Boulder, CO, USA
| | - Lionel Berthoux
- Laboratory of Retrovirology, Department of Medical Biology and BioMed Research Group, Université du Québec à Trois-Rivières. 3351 Boulevard des Forges, CP500, Trois-Rivières, QC, G9A 5H7, Canada
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16
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Romá-Mateo C, Aguado C, García-Giménez JL, Knecht E, Sanz P, Pallardó FV. Oxidative stress, a new hallmark in the pathophysiology of Lafora progressive myoclonus epilepsy. Free Radic Biol Med 2015; 88:30-41. [PMID: 25680286 DOI: 10.1016/j.freeradbiomed.2015.01.034] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Revised: 01/16/2015] [Accepted: 01/28/2015] [Indexed: 12/12/2022]
Abstract
Lafora disease (LD; OMIM 254780, ORPHA501) is a devastating neurodegenerative disorder characterized by the presence of glycogen-like intracellular inclusions called Lafora bodies and caused, in most cases, by mutations in either the EPM2A or the EPM2B gene, encoding respectively laforin, a phosphatase with dual specificity that is involved in the dephosphorylation of glycogen, and malin, an E3-ubiquitin ligase involved in the polyubiquitination of proteins related to glycogen metabolism. Thus, it has been reported that laforin and malin form a functional complex that acts as a key regulator of glycogen metabolism and that also plays a crucial role in protein homeostasis (proteostasis). Regarding this last function, it has been shown that cells are more sensitive to ER stress and show defects in proteasome and autophagy activities in the absence of a functional laforin-malin complex. More recently, we have demonstrated that oxidative stress accompanies these proteostasis defects and that various LD models show an increase in reactive oxygen species and oxidative stress products together with a dysregulated antioxidant enzyme expression and activity. In this review we discuss possible connections between the multiple defects in protein homeostasis present in LD and oxidative stress.
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Affiliation(s)
- Carlos Romá-Mateo
- Fundación Investigación Clinico de Valencia, Instituto de Investigación Sanitaria, Valencia, Spain; Department of Physiology, School of Medicine and Dentistry, University of Valencia, E46010 Valencia, Spain
| | - Carmen Aguado
- Centro de Investigación Biomédica en Red de Enfermedades Raras, Valencia, Spain; Centro de Investigación Príncipe Felipe, Valencia, Spain
| | - José Luis García-Giménez
- Fundación Investigación Clinico de Valencia, Instituto de Investigación Sanitaria, Valencia, Spain; Department of Physiology, School of Medicine and Dentistry, University of Valencia, E46010 Valencia, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras, Valencia, Spain
| | - Erwin Knecht
- Centro de Investigación Biomédica en Red de Enfermedades Raras, Valencia, Spain; Centro de Investigación Príncipe Felipe, Valencia, Spain
| | - Pascual Sanz
- Centro de Investigación Biomédica en Red de Enfermedades Raras, Valencia, Spain; Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Científicas, Valencia, Spain
| | - Federico V Pallardó
- Fundación Investigación Clinico de Valencia, Instituto de Investigación Sanitaria, Valencia, Spain; Department of Physiology, School of Medicine and Dentistry, University of Valencia, E46010 Valencia, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras, Valencia, Spain.
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17
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Abstract
The ubiquitin-proteasome system is the major degradation pathway for short-lived proteins in eukaryotic cells. Targets of the ubiquitin-proteasome-system are proteins regulating a broad range of cellular processes including cell cycle progression, gene expression, the quality control of proteostasis and the response to geno- and proteotoxic stress. Prior to degradation, the proteasomal substrate is marked with a poly-ubiquitin chain. The key protease of the ubiquitin system is the proteasome. In dividing cells, proteasomes exist as holo-enzymes composed of regulatory and core particles. The regulatory complex confers ubiquitin-recognition and ATP dependence on proteasomal protein degradation. The catalytic sites are located in the proteasome core particle. Proteasome holo-enzymes are predominantly nuclear suggesting a major requirement for proteasomal proteolysis in the nucleus. In cell cycle arrested mammalian or quiescent yeast cells, proteasomes deplete from the nucleus and accumulate in granules at the nuclear envelope (NE) / endoplasmic reticulum ( ER) membranes. In prolonged quiescence, proteasome granules drop off the nuclear envelopeNE / ER membranes and migrate as droplet-like entitiesstable organelles throughout the cytoplasm, as thoroughly investigated in yeast. When quiescence yeast cells are allowed to resume growth, proteasome granules clear and proteasomes are rapidly imported into the nucleus. Here, we summarize our knowledge about the enigmatic structure of proteasome storage granules and the trafficking of proteasomes and their substrates between the cyto- and nucleoplasm. Most of our current knowledge is based on studies in yeast. Their translation to mammalian cells promises to provide keen insight into protein degradation in non-dividing cells, which comprise the majority of our body’s cells.
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Affiliation(s)
- Maisha Chowdhury
- Department of Biochemistry, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Cordula Enenkel
- Department of Biochemistry, University of Toronto, Toronto, ON, M5S 1A8, Canada
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18
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Abstract
The ubiquitin-proteasome system is the major degradation pathway for short-lived proteins in eukaryotic cells. Targets of the ubiquitin-proteasome-system are proteins regulating a broad range of cellular processes including cell cycle progression, gene expression, the quality control of proteostasis and the response to geno- and proteotoxic stress. Prior to degradation, the proteasomal substrate is marked with a poly-ubiquitin chain. The key protease of the ubiquitin system is the proteasome. In dividing cells, proteasomes exist as holo-enzymes composed of regulatory and core particles. The regulatory complex confers ubiquitin-recognition and ATP dependence on proteasomal protein degradation. The catalytic sites are located in the proteasome core particle. Proteasome holo-enzymes are predominantly nuclear suggesting a major requirement for proteasomal proteolysis in the nucleus. In cell cycle arrested mammalian or quiescent yeast cells, proteasomes deplete from the nucleus and accumulate in granules at the nuclear envelope (NE) / endoplasmic reticulum ( ER) membranes. In prolonged quiescence, proteasome granules drop off the nuclear envelopeNE / ER membranes and migrate as droplet-like entitiesstable organelles throughout the cytoplasm, as thoroughly investigated in yeast. When quiescence yeast cells are allowed to resume growth, proteasome granules clear and proteasomes are rapidly imported into the nucleus. Here, we summarize our knowledge about the enigmatic structure of proteasome storage granules and the trafficking of proteasomes and their substrates between the cyto- and nucleoplasm. Most of our current knowledge is based on studies in yeast. Their translation to mammalian cells promises to provide keen insight into protein degradation in non-dividing cells, which comprise the majority of our body's cells.
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Affiliation(s)
- Maisha Chowdhury
- Department of Biochemistry, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Cordula Enenkel
- Department of Biochemistry, University of Toronto, Toronto, ON, M5S 1A8, Canada
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19
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Mechanism and Regulation of Autophagy and Its Role in Neuronal Diseases. Mol Neurobiol 2014; 52:1190-1209. [DOI: 10.1007/s12035-014-8921-4] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Accepted: 09/29/2014] [Indexed: 12/31/2022]
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20
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Patananan AN, Capri J, Whitelegge JP, Clarke SG. Non-repair pathways for minimizing protein isoaspartyl damage in the yeast Saccharomyces cerevisiae. J Biol Chem 2014; 289:16936-53. [PMID: 24764295 DOI: 10.1074/jbc.m114.564385] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The spontaneous degradation of asparaginyl and aspartyl residues to isoaspartyl residues is a common type of protein damage in aging organisms. Although the protein-l-isoaspartyl (d-aspartyl) O-methyltransferase (EC 2.1.1.77) can initiate the repair of l-isoaspartyl residues to l-aspartyl residues in most organisms, no gene homolog or enzymatic activity is present in the budding yeast Saccharomyces cerevisiae. Therefore, we used biochemical approaches to elucidate how proteins containing isoaspartyl residues are metabolized in this organism. Surprisingly, the level of isoaspartyl residues in yeast proteins (50-300 pmol of isoaspartyl residues/mg of protein extract) is comparable with organisms with protein-l-isoaspartyl (d-aspartyl) O-methyltransferase, suggesting a novel regulatory pathway. Interfering with common protein quality control mechanisms by mutating and inhibiting the proteasomal and autophagic pathways in vivo did not increase isoaspartyl residue levels compared with wild type or uninhibited cells. However, the inhibition of metalloproteases in in vitro aging experiments by EDTA resulted in an ∼3-fold increase in the level of isoaspartyl-containing peptides. Characterization by mass spectrometry of these peptides identified several proteins involved in metabolism as targets of isoaspartyl damage. Further analysis of these peptides revealed that many have an N-terminal isoaspartyl site and originate from proteins with short half-lives. These results suggest that one or more metalloproteases participate in limiting isoaspartyl formation by robust proteolysis.
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Affiliation(s)
- Alexander N Patananan
- From the Department of Chemistry and Biochemistry and the Molecular Biology Institute and
| | - Joseph Capri
- the Pasarow Mass Spectrometry Laboratory, Neuropsychiatric Institute-Semel Institute for Neuroscience and Human Behavior, UCLA, Los Angeles, California 90095
| | - Julian P Whitelegge
- the Pasarow Mass Spectrometry Laboratory, Neuropsychiatric Institute-Semel Institute for Neuroscience and Human Behavior, UCLA, Los Angeles, California 90095
| | - Steven G Clarke
- From the Department of Chemistry and Biochemistry and the Molecular Biology Institute and
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21
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Proteomic remodeling of proteasome in right heart failure. J Mol Cell Cardiol 2014; 66:41-52. [DOI: 10.1016/j.yjmcc.2013.10.015] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/22/2013] [Revised: 09/13/2013] [Accepted: 10/22/2013] [Indexed: 12/30/2022]
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22
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García-Giménez JL, Seco-Cervera M, Aguado C, Romá-Mateo C, Dasí F, Priego S, Markovic J, Knecht E, Sanz P, Pallardó FV. Lafora disease fibroblasts exemplify the molecular interdependence between thioredoxin 1 and the proteasome in mammalian cells. Free Radic Biol Med 2013; 65:347-359. [PMID: 23850970 DOI: 10.1016/j.freeradbiomed.2013.07.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Revised: 06/27/2013] [Accepted: 07/01/2013] [Indexed: 11/30/2022]
Abstract
Thioredoxin 1 (Trx1) is a key regulator of cellular redox balance and participates in cellular signaling events. Recent evidence from yeast indicates that members of the Trx family interact with the 20S proteasome, indicating redox regulation of proteasome activity. However, there is little information about the interrelationship of Trx proteins with the proteasome system in mammalian cells, especially in the nucleus. Here, we have investigated this relationship under various cellular conditions in mammalian cells. We show that Trx1 levels and its subcellular localization (cytosol, endoplasmic reticulum, and nucleus) depend on proteasome activity during the cell cycle in NIH3T3 fibroblasts and under stress conditions, when proteasomes are inhibited. In addition, we also studied in these cells how the main cellular antioxidant systems are stimulated when proteasome activity is inhibited. Finally, we describe a reduction in Trx1 levels in Lafora disease fibroblasts and demonstrate that the nuclear colocalization of Trx1 with 20S proteasomes in laforin-deficient cells is altered compared with control cells. Our results indicate a close relationship between Trx1 and the 20S nuclear proteasome and give a new perspective to the study of diseases or physiopathological conditions in which defects in the proteasome system are associated with oxidative stress.
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Affiliation(s)
- José Luis García-Giménez
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Valencia, Spain; Fundación del Hospital Clínico Universitat de Valencia-INCLIVA, Valencia, Spain; Department of Physiology, University of Valencia, 46010 Valencia, Spain
| | - Marta Seco-Cervera
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Valencia, Spain
| | - Carmen Aguado
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Valencia, Spain; Centro de Investigación Príncipe Felipe, Valencia, Spain
| | - Carlos Romá-Mateo
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Valencia, Spain; Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Científicas, Valencia, Spain
| | - Francisco Dasí
- Fundación del Hospital Clínico Universitat de Valencia-INCLIVA, Valencia, Spain; Department of Physiology, University of Valencia, 46010 Valencia, Spain
| | - Sonia Priego
- Research Core Facility, Medical School, University of Valencia, 46010 Valencia, Spain
| | - Jelena Markovic
- Research Core Facility, Medical School, University of Valencia, 46010 Valencia, Spain
| | - Erwin Knecht
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Valencia, Spain; Centro de Investigación Príncipe Felipe, Valencia, Spain
| | - Pascual Sanz
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Valencia, Spain; Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Científicas, Valencia, Spain
| | - Federico V Pallardó
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Valencia, Spain; Fundación del Hospital Clínico Universitat de Valencia-INCLIVA, Valencia, Spain; Department of Physiology, University of Valencia, 46010 Valencia, Spain.
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23
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Shabaneh TB, Downey SL, Goddard AL, Screen M, Lucas MM, Eastman A, Kisselev AF. Molecular basis of differential sensitivity of myeloma cells to clinically relevant bolus treatment with bortezomib. PLoS One 2013; 8:e56132. [PMID: 23460792 PMCID: PMC3584083 DOI: 10.1371/journal.pone.0056132] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2012] [Accepted: 01/05/2013] [Indexed: 01/07/2023] Open
Abstract
The proteasome inhibitor bortezomib (Velcade) is prescribed for the treatment of multiple myeloma. Clinically achievable concentrations of bortezomib cause less than 85% inhibition of the chymotrypsin-like activity of the proteasome, but little attention has been paid as to whether in vitro studies are representative of this level of inhibition. Patients receive bortezomib as an intravenous or subcutaneous bolus injection, resulting in maximum proteasome inhibition within one hour followed by a gradual recovery of activity. In contrast, most in vitro studies use continuous treatment so that activity never recovers. Replacing continuous treatment with 1 h-pulse treatment increases differences in sensitivity in a panel of 7 multiple myeloma cell lines from 5.3-fold to 18-fold, and reveals that the more sensitive cell lines undergo apoptosis at faster rates. Clinically achievable inhibition of active sites was sufficient to induce cytotoxicity only in one cell line. At concentrations of bortezomib that produced similar inhibition of peptidase activities a different extent of inhibition of protein degradation was observed, providing an explanation for the differential sensitivity. The amount of protein degraded per number of active proteasomes correlated with sensitivity to bortezomib. Thus, (i) in vitro studies of proteasome inhibitors should be conducted at pharmacologically achievable concentrations and duration of treatment; (ii) a similar level of inhibition of active sites results in a different extent of inhibition of protein breakdown in different cell lines, and hence a difference in sensitivity.
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Affiliation(s)
- Tamer B. Shabaneh
- Norris Cotton Cancer Center, The Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire, United States of America
- Department of Pharmacology and Toxicology, The Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire, United States of America
| | - Sondra L. Downey
- Norris Cotton Cancer Center, The Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire, United States of America
- Department of Pharmacology and Toxicology, The Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire, United States of America
| | - Ayrton L. Goddard
- Norris Cotton Cancer Center, The Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire, United States of America
- Department of Pharmacology and Toxicology, The Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire, United States of America
- Department of Biology & Biochemistry, University of Bath, Bath, United Kingdom
| | - Michael Screen
- Norris Cotton Cancer Center, The Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire, United States of America
- Department of Pharmacology and Toxicology, The Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire, United States of America
- Department of Biology & Biochemistry, University of Bath, Bath, United Kingdom
| | - Marcella M. Lucas
- Norris Cotton Cancer Center, The Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire, United States of America
- Department of Pharmacology and Toxicology, The Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire, United States of America
- Department of Biology & Biochemistry, University of Bath, Bath, United Kingdom
| | - Alan Eastman
- Norris Cotton Cancer Center, The Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire, United States of America
- Department of Pharmacology and Toxicology, The Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire, United States of America
| | - Alexei F. Kisselev
- Norris Cotton Cancer Center, The Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire, United States of America
- Department of Pharmacology and Toxicology, The Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire, United States of America
- * E-mail:
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24
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Vidal-Donet JM, Cárcel-Trullols J, Casanova B, Aguado C, Knecht E. Alterations in ROS activity and lysosomal pH account for distinct patterns of macroautophagy in LINCL and JNCL fibroblasts. PLoS One 2013; 8:e55526. [PMID: 23408996 PMCID: PMC3567113 DOI: 10.1371/journal.pone.0055526] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2012] [Accepted: 12/27/2012] [Indexed: 12/21/2022] Open
Abstract
Neuronal ceroid lipofuscinoses (NCL) are lysosomal storage disorders characterized by the accumulation of lipofuscin within lysosomes. Late infantile (LINCL) and juvenile (JNCL) are their most common forms and are caused by loss-of-function mutations in tripeptidyl peptidase 1 (TPP1), a lysosomal endopeptidase, and CLN3 protein (CLN3p), whose location and function is still controversial. LINCL patients suffer more severely from NCL consequences than JNCL patients, in spite of having in common an abnormal accumulation of material with a similar composition in the lysosomes. To identify distinctive characteristics that could explain the differences in the severity of LINCL and JNCL pathologies, we compared the protein degradation mechanisms in patientś fibroblasts. Pulse-chase experiments show a significant decrease in protein degradation by macroautophagy in fibroblasts bearing TPP1 (CLN2) and CLN3p (CLN3) mutations. In CLN2 fibroblasts, LC3-II levels and other procedures indicate an impaired formation of autophagosomes, which confirms the pulse-chase experiments. This defect is linked to an accumulation of reactive oxygen species (ROS), an upregulation of the Akt-mTOR signalling pathway and increased activities of the p38α and ERK1/2 MAPKs. In CLN3 fibroblasts, LC3-II analysis indicates impairment in autophagosome maturation and there is also a defect in fluid phase endocytosis, two alterations that can be related to an observed increase of 0.5 units in lysosomal pH. CLN3 fibroblasts also accumulate ROS but to a lower extent than CLN2. TPP1 activity is completely abrogated in CLN2 and partially diminished in CLN3 fibroblasts. TPP1 cleaves small hydrophobic proteins like subunit c of mitochondrial ATP synthase and the lack or a lower activity of this enzyme can contribute to lipofuscin accumulation. These alterations in TPP1 activity lead to an increased ROS production, especially in CLN2 in which it is aggravated by a decrease in catalase activity. This could explain the earlier appearance of the symptoms in the LINCL form.
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Affiliation(s)
| | - Jaime Cárcel-Trullols
- Laboratory of Cellular Biology, Centro de Investigación Príncipe Felipe, Valencia, Spain
| | | | - Carmen Aguado
- Laboratory of Cellular Biology, Centro de Investigación Príncipe Felipe, Valencia, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Valencia, Spain
| | - Erwin Knecht
- Laboratory of Cellular Biology, Centro de Investigación Príncipe Felipe, Valencia, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Valencia, Spain
- * E-mail:
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Höhn A, König J, Grune T. Protein oxidation in aging and the removal of oxidized proteins. J Proteomics 2013; 92:132-59. [PMID: 23333925 DOI: 10.1016/j.jprot.2013.01.004] [Citation(s) in RCA: 159] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2012] [Accepted: 01/08/2013] [Indexed: 12/12/2022]
Abstract
Reactive oxygen species (ROS) are generated constantly within cells at low concentrations even under physiological conditions. During aging the levels of ROS can increase due to a limited capacity of antioxidant systems and repair mechanisms. Proteins are among the main targets for oxidants due to their high rate constants for several reactions with ROS and their abundance in biological systems. Protein damage has an important influence on cellular viability since most protein damage is non-repairable, and has deleterious consequences on protein structure and function. In addition, damaged and modified proteins can form cross-links and provide a basis for many senescence-associated alterations and may contribute to a range of human pathologies. Two proteolytic systems are responsible to ensure the maintenance of cellular functions: the proteasomal (UPS) and the lysosomal system. Those degrading systems provide a last line of antioxidative protection, removing irreversible damaged proteins and recycling amino acids for the continuous protein synthesis. But during aging, both systems are affected and their proteolytic activity declines significantly. Here we highlight the recent advantages in the understanding of protein oxidation and the fate of these damaged proteins during aging. This article is part of a Special Issue entitled: Posttranslational Protein modifications in biology and Medicine.
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Affiliation(s)
- Annika Höhn
- Department of Nutritional Toxicology, Institute of Nutrition, Friedrich Schiller University Jena, 07743 Jena, Germany
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26
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Montioli R, Oppici E, Cellini B, Roncador A, Dindo M, Voltattorni CB. S250F variant associated with aromatic amino acid decarboxylase deficiency: molecular defects and intracellular rescue by pyridoxine. Hum Mol Genet 2013; 22:1615-24. [PMID: 23321058 DOI: 10.1093/hmg/ddt011] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Dopa or aromatic amino acid decarboxylase (DDC, AADC) is a pyridoxal 5'-phosphate-dependent enzyme that catalyses the production of the neurotransmitters dopamine and serotonin. Among the so far identified mutations associated with AADC deficiency, an inherited rare neurometabolic disease, the S250F mutation is the most frequent one. Here, for the first time, the molecular basis of the deficit of the S250F variant was investigated both in vitro and in cellular systems. Ser250 is not essential for the catalytic activity of the enzyme. However, its mutation to Phe causes a ~7-fold reduction of catalytic efficiency and a conformational change in the proximity of the mutated residue that is transmitted to the active site. In cellular extracts of E. coli and mammalian cells, both the specific activity and the protein level of the variant decrease with respect to the wild-type. The results with mammalian cells indicate that the mutation does not affect intracellular mRNA levels, and are consistent with a model where S250F undergoes a degradation process via the proteasome, possibly through an ubiquitination process occurring faster than in the wild-type. Overall, biochemical and cell biology experiments show that loss of function of S250F occurs by two distinct but not exclusive mechanisms affecting activity and folding. Importantly, 4-phenylbutirric acid (4-PBA) or, to a major extent, pyridoxine increase the expression level and, in a dose-dependent manner, the decarboxylase specific activity of mutant-expressing cells. This strongly suggests that 4-PBA and/or pyridoxine administration may be of important value in therapy of patients bearing the S250F mutation.
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Affiliation(s)
- Riccardo Montioli
- Department of Life Sciences and Reproduction, University of Verona, Verona, Italy
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28
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Xu Y, Tian C, Wang SB, Xie WL, Guo Y, Zhang J, Shi Q, Chen C, Dong XP. Activation of the macroautophagic system in scrapie-infected experimental animals and human genetic prion diseases. Autophagy 2012; 8:1604-20. [PMID: 22874564 DOI: 10.4161/auto.21482] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Macroautophagy is an important process for removing misfolded and aggregated protein in cells, the dysfunction of which has been directly linked to an increasing number of neurodegenerative disorders. However, the details of macroautophagy in prion diseases remain obscure. Here we demonstrated that in the terminal stages of scrapie strain 263K-infected hamsters and human genetic prion diseases, the microtubule-associated protein 1 light chain 3 (LC3) was converted from the cytosolic form to the autophagosome-bound membrane form. Macroautophagy substrate sequestosome 1 (SQSTM1) and polyubiquitinated proteins were downregulated in the brains of sick individuals, indicating enhanced macroautophagic protein degradation. The levels of mechanistic target of rapamycin (MTOR) and phosphorylated MTOR (p-MTOR) were significantly decreased, which implies that this enhancement of the macroautophagic response is likely through the MTOR pathway which is a negative regulator for the initiation of macroautophagy. Dynamic assays of the autophagic system in the brains of scrapie experimental hamsters after inoculation showed that alterations of the autophagic system appeared along with the deposits of PrP(Sc) in the infected brains. Immunofluorescent assays revealed specific staining of autophagosomes in neurons that were not colocalized with deposits of PrP(Sc) in the brains of scrapie infected hamsters, however, autophagosome did colocalize with PrP(Sc) in a prion-infected cell line after treatment with bafilomycin A(1). These results suggest that activation of macroautophagy in brains is a disease-correlative phenomenon in prion diseases.
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Affiliation(s)
- Yin Xu
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
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29
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Sishi BJN, Bester DJ, Wergeland A, Loos B, Jonassen AK, van Rooyen J, Engelbrecht AM. Daunorubicin therapy is associated with upregulation of E3 ubiquitin ligases in the heart. Exp Biol Med (Maywood) 2012; 237:219-26. [PMID: 22328594 DOI: 10.1258/ebm.2011.011106] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Daunorubicin (DNR) and doxorubicin (DOX) are two of the most effective anthracycline drugs known for the treatment of systemic neoplasms and solid tumors. However, their clinical use is hampered due to profound cardiotoxicity. The mechanism by which DNR injures the heart remains to be fully elucidated. Recent reports have indicated that DOX activates ubiquitin proteasome-mediated degradation of specific transcription factors; however, no reports exist on the effect of DNR on the E3 ubiquitin ligases, MURF-1 (muscle ring finger 1) and MAFbx (muscle atrophy F-box). The aim of this study was to investigate the effect of DNR treatment on the protein and organelle degradation systems in the heart and to elucidate some of the signalling mechanisms involved. Adult rats were divided into two groups where one group received six intraperitoneal injections of 2 mg/kg DNR on alternate days and the other group received saline injections as control. Hearts were excised and perfused on a working heart system the day after the last injection and freeze-clamped for biochemical analysis. DNR treatment significantly attenuated cardiac function and increased apoptosis in the heart. DNR-induced cardiac cytotoxicity was associated with upregulation of the E3 ligases, MURF-1 and MAFbx and also caused significant increases in two markers of autophagy, beclin-1 and LC3. These changes observed in the heart were also associated with attenuation of the phosphoinositide 3-kinase/Akt signalling pathway.
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Affiliation(s)
- Balindiwe J N Sishi
- Department of Physiological Sciences, Stellenbosch University, Stellenbosch, South Africa
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30
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Ghislat G, Aguado C, Knecht E. Annexin A5 stimulates autophagy and inhibits endocytosis. J Cell Sci 2012; 125:92-107. [PMID: 22266906 DOI: 10.1242/jcs.086728] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Macroautophagy is a major lysosomal catabolic process activated particularly under starvation in eukaryotic cells. A new organelle, the autophagosome, engulfs cytoplasmic substrates, which are degraded after fusion with endosomes and/or lysosomes. During a shotgun proteome analysis of purified lysosomal membranes from mouse fibroblasts, a Ca(2+)-dependent phospholipid-binding protein, annexin A5, was found to increase on lysosomal membranes under starvation. This suggests a role for this protein, an abundant annexin with a still unknown intracellular function, in starvation-induced lysosomal degradation. Transient overexpression and silencing experiments showed that annexin A5 increased lysosomal protein degradation, and colocalisation experiments, based on GFP sensitivity to lysosomal acidic pH, indicated that this was mainly the result of inducing autophagosome-lysosome fusion. Annexin A5 also inhibited the endocytosis of a fluid-phase marker and cholera toxin, but not receptor-mediated endocytosis. Therefore, we propose a double and opposite role of annexin A5 in regulating the endocytic and autophagic pathways and the fusion of autophagosomes with lysosomes and endosomes.
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Affiliation(s)
- Ghita Ghislat
- Laboratorio de Biología Celular, Centro de Investigación Príncipe Felipe, Valencia, Spain
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31
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Criado O, Aguado C, Gayarre J, Duran-Trio L, Garcia-Cabrero AM, Vernia S, San Millán B, Heredia M, Romá-Mateo C, Mouron S, Juana-López L, Domínguez M, Navarro C, Serratosa JM, Sanchez M, Sanz P, Bovolenta P, Knecht E, Rodriguez de Cordoba S. Lafora bodies and neurological defects in malin-deficient mice correlate with impaired autophagy. Hum Mol Genet 2011; 21:1521-33. [PMID: 22186026 DOI: 10.1093/hmg/ddr590] [Citation(s) in RCA: 111] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Lafora disease (LD), a fatal neurodegenerative disorder characterized by the presence of intracellular inclusions called Lafora bodies (LBs), is caused by loss-of-function mutations in laforin or malin. Previous studies suggested a role of these proteins in the regulation of glycogen biosynthesis, in glycogen dephosphorylation and in the modulation of the intracellular proteolytic systems. However, the contribution of each of these processes to LD pathogenesis is unclear. We have generated a malin-deficient (Epm2b-/-) mouse with a phenotype similar to that of LD patients. By 3-6 months of age, Epm2b-/- mice present neurological and behavioral abnormalities that correlate with a massive presence of LBs in the cortex, hippocampus and cerebellum. Sixteen-day-old Epm2b-/- mice, without detectable LBs, show an impairment of macroautophagy (hereafter called autophagy), which remains compromised in adult animals. These data demonstrate similarities between the Epm2a-/- and Epm2b-/- mice that provide further insights into LD pathogenesis. They illustrate that the dysfunction of autophagy is a consequence of the lack of laforin-malin complexes and a common feature of both mouse models of LD. Because this dysfunction precedes other pathological manifestations, we propose that decreased autophagy plays a primary role in the formation of LBs and it is critical in LD pathogenesis.
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Affiliation(s)
- Olga Criado
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, 28040 Madrid, Spain
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32
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Cambridge SB, Gnad F, Nguyen C, Bermejo JL, Krüger M, Mann M. Systems-wide proteomic analysis in mammalian cells reveals conserved, functional protein turnover. J Proteome Res 2011; 10:5275-84. [PMID: 22050367 DOI: 10.1021/pr101183k] [Citation(s) in RCA: 194] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The turnover of each protein in the mammalian proteome is a functionally important characteristic. Here, we employed high-resolution mass spectrometry to quantify protein dynamics in nondividing mammalian cells. The ratio of externally supplied versus endogenous amino acids to de novo protein synthesis was about 17:1. Using subsaturating SILAC labeling, we obtained accurate turnover rates of 4106 proteins in HeLa and 3528 proteins in C2C12 cells. Comparison of these human and mouse cell lines revealed a highly significant turnover correlation of protein orthologs and thus high species conservation. Functionally, we observed statistically significant trends for the turnover of phosphoproteins and gene ontology categories that showed extensive covariation between mouse and human. Likewise, the members of some protein complexes, such as the proteasome, have highly similar turnover rates. The high species conservation and the low complex variances thus imply great regulatory fine-tuning of protein turnover.
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Affiliation(s)
- Sidney B Cambridge
- Max-Planck-Institute for Biochemistry, Am Klopferspitz 18, 82152 Munich-Martinsried, Germany
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33
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Kurz T, Eaton JW, Brunk UT. The role of lysosomes in iron metabolism and recycling. Int J Biochem Cell Biol 2011; 43:1686-97. [PMID: 21907822 DOI: 10.1016/j.biocel.2011.08.016] [Citation(s) in RCA: 140] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2011] [Revised: 08/25/2011] [Accepted: 08/26/2011] [Indexed: 02/07/2023]
Abstract
Iron is the most abundant transition metal in the earth's crust. It cycles easily between ferric (oxidized; Fe(III)) and ferrous (reduced; Fe(II)) and readily forms complexes with oxygen, making this metal a central player in respiration and related redox processes. However, 'loose' iron, not within heme or iron-sulfur cluster proteins, can be destructively redox-active, causing damage to almost all cellular components, killing both cells and organisms. This may explain why iron is so carefully handled by aerobic organisms. Iron uptake from the environment is carefully limited and carried out by specialized iron transport mechanisms. One reason that iron uptake is tightly controlled is that most organisms and cells cannot efficiently excrete excess iron. When even small amounts of intracellular free iron occur, most of it is safely stored in a non-redox-active form in ferritins. Within nucleated cells, iron is constantly being recycled from aged iron-rich organelles such as mitochondria and used for construction of new organelles. Much of this recycling occurs within the lysosome, an acidic digestive organelle. Because of this, most lysosomes contain relatively large amounts of redox-active iron and are therefore unusually susceptible to oxidant-mediated destabilization or rupture. In many cell types, iron transit through the lysosomal compartment can be remarkably brisk. However, conditions adversely affecting lysosomal iron handling (or oxidant stress) can contribute to a variety of acute and chronic diseases. These considerations make normal and abnormal lysosomal handling of iron central to the understanding and, perhaps, therapy of a wide range of diseases.
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Affiliation(s)
- Tino Kurz
- Division of Pharmacology, Faculty of Health Sciences, Linköping University, 581 85 Linköping, Sweden.
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34
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Out with the old, in with the new? Comparing methods for measuring protein degradation. Cell Biol Int 2011; 35:457-62. [PMID: 21476986 DOI: 10.1042/cbi20110055] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Protein degradation is a critical factor in controlling cellular protein abundance. Here, we compare classical methods for determining protein degradation rates to a novel GFP (green fluorescent protein) fusion protein based method that assesses the intrinsic stability of cloned cDNA library products by flow cytometry [Yen et al. (2008) Science 322, 918]. While no method is perfect, we conclude that chimeric gene reporter approaches, though powerful, should be applied cautiously, due principally to GFP (or other reporter tag) interference with protein organelle targeting or incorporation into macromolecular assemblies, both of which cause spuriously high degradation rates.
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35
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CSN1 inhibits c-Jun phosphorylation and down-regulates ectopic expression of JNK1. Protein Cell 2011; 2:423-32. [PMID: 21604193 DOI: 10.1007/s13238-011-1043-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2011] [Accepted: 04/08/2011] [Indexed: 10/18/2022] Open
Abstract
CSN1 is a component of the COP9 signalosome (CSN), a conserved protein complex with pleiotropic functions in many organs and cell types. CSN regulates ubiquitinproteasome dependent protein degradation via the deneddylation and the associated deubiquitination activities. In addition, CSN associates with protein kinases and modulates cell signaling, particularly the activator protein 1 (AP-1) pathway. We have shown previously that CSN1 suppresses AP-1 transcription activity and inhibits ultraviolet (UV) and serum activation of c-fos expression. Here we show that CSN1 can inhibit phosphorylation of proto-oncogene c-Jun product and repress c-Jun dependent transcription. Further, CSN1 dramatically downregulates ectopic expression of c-Jun N-terminal kinase 1 (JNK1) in cultured cells. The decline in JNK1 is not caused by excessive proteolysis or by 3' UTR-dependent mRNA instability, but by CSN1-dependent repression of one or multiple steps in transcriptional and posttranscriptional mechanisms. Thus, in contrast to CSN5/Jab1, which promotes AP-1 activity, CSN1 displays a negative effect on the AP-1 pathway. Finally, we discuss about the dynamic equilibrium of the CSN complexes in regulation of the AP-1 pathway.
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36
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Sanchez CG, Penfornis P, Oskowitz AZ, Boonjindasup AG, Cai DZ, Dhule SS, Rowan BG, Kelekar A, Krause DS, Pochampally RR. Activation of autophagy in mesenchymal stem cells provides tumor stromal support. Carcinogenesis 2011; 32:964-72. [PMID: 21317300 DOI: 10.1093/carcin/bgr029] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Recent studies have implicated multipotential mesenchymal stem cells (MSCs) as an aid to breast cancer cell proliferation and metastasis, partly as a result of the MSCs secretome. As the tumor gets beyond 2 mm in diameter, the stromal cells could undergo starvation due to the lack of sufficient nutrients in solid tumor microenvironment. In this study, we investigated the survival mechanisms used by stressed stromal cells in breast cancers. We used serum-deprived mesenchymal stem cells (SD-MSCs) and MCF-7 breast cancer cells as model system with a hypothesis that stromal cells in the nutrient-deprived core utilize survival mechanisms for supporting surrounding cells. We tested this hypothesis using in vivo tumor xenografts in immunodeficient mice, which indicated that SD-MSCs supported MCF-7 tumor growth by protection from apoptosis. Histochemical assays showed that SD-MSCs-injected tumors exhibited higher cellularity, decreased apoptosis and decreased differentiation. Beclin-1 staining indicated autophagic areas surrounded by actively proliferating cells. Furthermore, in vitro studies demonstrate that SD-MSCs survive using autophagy and secrete paracrine factors that support tumor cells following nutrient/serum deprivation. Western blot and immunocytochemistry analysis of SD-MSCs demonstrated upregulation and perinuclear relocation of autophagy key regulators such as beclin-1, ATG10, ATG12, MAP-LC3 and lysosomes. Electron microscopic analysis detected a time-dependent increase in autophagosome formation and HDAC6 activity assays indicated the upregulation of autophagy. Taken together, these data suggest that under nutrient-deprived conditions that can occur in solid tumors, stromal cells utilize autophagy for survival and also secrete anti-apoptotic factors that can facilitate solid tumor survival and growth.
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Affiliation(s)
- Cecilia G Sanchez
- Gene Therapy Center, Tulane University Health Science Center, 1430 Tulane avenue, New Orleans, LA 70112, USA
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37
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Ravikumar B, Sarkar S, Davies JE, Futter M, Garcia-Arencibia M, Green-Thompson ZW, Jimenez-Sanchez M, Korolchuk VI, Lichtenberg M, Luo S, Massey DCO, Menzies FM, Moreau K, Narayanan U, Renna M, Siddiqi FH, Underwood BR, Winslow AR, Rubinsztein DC. Regulation of mammalian autophagy in physiology and pathophysiology. Physiol Rev 2010; 90:1383-435. [PMID: 20959619 DOI: 10.1152/physrev.00030.2009] [Citation(s) in RCA: 1340] [Impact Index Per Article: 95.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
(Macro)autophagy is a bulk degradation process that mediates the clearance of long-lived proteins and organelles. Autophagy is initiated by double-membraned structures, which engulf portions of cytoplasm. The resulting autophagosomes ultimately fuse with lysosomes, where their contents are degraded. Although the term autophagy was first used in 1963, the field has witnessed dramatic growth in the last 5 years, partly as a consequence of the discovery of key components of its cellular machinery. In this review we focus on mammalian autophagy, and we give an overview of the understanding of its machinery and the signaling cascades that regulate it. As recent studies have also shown that autophagy is critical in a range of normal human physiological processes, and defective autophagy is associated with diverse diseases, including neurodegeneration, lysosomal storage diseases, cancers, and Crohn's disease, we discuss the roles of autophagy in health and disease, while trying to critically evaluate if the coincidence between autophagy and these conditions is causal or an epiphenomenon. Finally, we consider the possibility of autophagy upregulation as a therapeutic approach for various conditions.
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Affiliation(s)
- Brinda Ravikumar
- Department of Medical Genetics, University of Cambridge, Cambridge Institute for Medical Research, Addenbrooke’s Hospital, Cambridge, United Kingdom
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38
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Dasuri K, Ebenezer PJ, Zhang L, Fernandez-Kim SO, Uranga RM, Gavilán E, Di Blasio A, Keller JN. Selective vulnerability of neurons to acute toxicity after proteasome inhibitor treatment: implications for oxidative stress and insolubility of newly synthesized proteins. Free Radic Biol Med 2010; 49:1290-7. [PMID: 20678570 PMCID: PMC3175605 DOI: 10.1016/j.freeradbiomed.2010.07.014] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/24/2010] [Revised: 07/13/2010] [Accepted: 07/19/2010] [Indexed: 12/19/2022]
Abstract
Maintaining protein homeostasis is vital to cell viability, with numerous studies demonstrating a role for proteasome inhibition occurring during the aging of a variety of tissues and, presumably, contributing to the disruption of cellular homeostasis during aging. In this study we sought to elucidate the differences between neurons and astrocytes in regard to basal levels of protein synthesis, proteasome-mediated protein degradation, and sensitivity to cytotoxicity after proteasome inhibitor treatment. In these studies we demonstrate that neurons have an increased vulnerability, compared to astrocyte cultures, to proteasome-inhibitor-induced cytotoxicity. No significant difference was observed between these two cell types in regard to the basal rates of protein synthesis, or basal rates of protein degradation, in the pool of short-lived proteins. After proteasome inhibitor treatment neuronal crude lysates were observed to undergo greater increases in the levels of ubiquitinated and oxidized proteins and selectively exhibited increased levels of newly synthesized proteins accumulating within the insoluble protein pool, compared to astrocytes. Together, these data suggest a role for increased oxidized proteins and sequestration of newly synthesized proteins in the insoluble protein pool, as potential mediators of the selective neurotoxicity after proteasome inhibitor treatment. The implications for neurons exhibiting increased sensitivity to acute proteasome inhibitor exposure, and the corresponding changes in protein homeostasis observed after proteasome inhibition, are discussed in the context of both aging and age-related disorders of the nervous system.
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Affiliation(s)
- Kalavathi Dasuri
- Pennington Biomedical Research Center, Louisiana State University System, Baton Rouge, Louisiana, USA
| | - Philip J. Ebenezer
- Pennington Biomedical Research Center, Louisiana State University System, Baton Rouge, Louisiana, USA
| | - Le Zhang
- Pennington Biomedical Research Center, Louisiana State University System, Baton Rouge, Louisiana, USA
| | - Sun Ok Fernandez-Kim
- Pennington Biomedical Research Center, Louisiana State University System, Baton Rouge, Louisiana, USA
| | - Romina M. Uranga
- Instituto de Investigaciones Bioquímicas de Bahía Blanca, Universidad Nacional del sur and Consejo Nacional de Investigaciones Científicas y Técnicas, Bahía Blanca,Argentina
| | - Elena Gavilán
- Pennington Biomedical Research Center, Louisiana State University System, Baton Rouge, Louisiana, USA
| | - Alessia Di Blasio
- Pennington Biomedical Research Center, Louisiana State University System, Baton Rouge, Louisiana, USA
| | - Jeffrey N Keller
- Pennington Biomedical Research Center, Louisiana State University System, Baton Rouge, Louisiana, USA
- Corresponding author: Dr Jeffrey N. Keller, Pennington Biomedical Research Center/LSU System, 6400 Perkins Road, Baton Rouge, LA 70808-4124, (P): 225-763-3190; (E):
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39
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Korolchuk VI, Menzies FM, Rubinsztein DC. Mechanisms of cross-talk between the ubiquitin-proteasome and autophagy-lysosome systems. FEBS Lett 2009; 584:1393-8. [PMID: 20040365 DOI: 10.1016/j.febslet.2009.12.047] [Citation(s) in RCA: 426] [Impact Index Per Article: 28.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2009] [Revised: 12/22/2009] [Accepted: 12/23/2009] [Indexed: 11/15/2022]
Abstract
The ubiquitin proteasome system (UPS) and macroautophagy (hereafter called autophagy) were, for a long time, regarded as independent degradative pathways with few or no points of interaction. This view started to change recently, in the light of findings that have suggested that ubiquitylation can target substrates for degradation via both pathways. Moreover, perturbations in the flux through either pathway have been reported to affect the activity of the other system, and a number of mechanisms have been proposed to rationalise the link between the UPS and autophagy. Here we critically review these findings and outline some outstanding issues that still await clarification.
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Affiliation(s)
- Viktor I Korolchuk
- Department of Medical Genetics, University of Cambridge, Cambridge Institute for Medical Research, Addenbrooke's Hospital, Cambridge, UK
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40
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Pérez-Sala D, Boya P, Ramos I, Herrera M, Stamatakis K. The C-terminal sequence of RhoB directs protein degradation through an endo-lysosomal pathway. PLoS One 2009; 4:e8117. [PMID: 19956591 PMCID: PMC2780327 DOI: 10.1371/journal.pone.0008117] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2009] [Accepted: 11/05/2009] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Protein degradation is essential for cell homeostasis. Targeting of proteins for degradation is often achieved by specific protein sequences or posttranslational modifications such as ubiquitination. METHODOLOGY/PRINCIPAL FINDINGS By using biochemical and genetic tools we have monitored the localization and degradation of endogenous and chimeric proteins in live primary cells by confocal microscopy and ultra-structural analysis. Here we identify an eight amino acid sequence from the C-terminus of the short-lived GTPase RhoB that directs the rapid degradation of both RhoB and chimeric proteins bearing this sequence through a lysosomal pathway. Elucidation of the RhoB degradation pathway unveils a mechanism dependent on protein isoprenylation and palmitoylation that involves sorting of the protein into multivesicular bodies, mediated by the ESCRT machinery. Moreover, RhoB sorting is regulated by late endosome specific lipid dynamics and is altered in human genetic lipid traffic disease. CONCLUSIONS/SIGNIFICANCE Our findings characterize a short-lived cytosolic protein that is degraded through a lysosomal pathway. In addition, we define a novel motif for protein sorting and rapid degradation, which allows controlling protein levels by means of clinically used drugs.
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Affiliation(s)
- Dolores Pérez-Sala
- Department of Chemical and Physical Biology, Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Madrid, Spain.
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41
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Sun Q, Kelly GM. Post-translational modification of CASK leads to its proteasome-dependent degradation. Int J Biochem Cell Biol 2009; 42:90-7. [PMID: 19781660 DOI: 10.1016/j.biocel.2009.09.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2009] [Revised: 09/03/2009] [Accepted: 09/17/2009] [Indexed: 01/08/2023]
Abstract
CASK is a member of the membrane-associated guanylate kinase family. In mammals it is an essential protein, as CASK knockout mice die after birth and its deletion in humans has developmental consequences. CASK plays a role in the transcription of genes required for forebrain development, and in the nervous systems of Drosophila and C. elegans, it participates in receptor localization at the plasma membrane. This role in organizing supramolecular protein complexes to appropriate subcellular regions is shared in mammals and is regulated by phosphorylation. CASK is a kinase and regulator of cell proliferation and adhesion, which adds to an expanding list of roles. In this study we report for the first time that CASK is degraded in a characteristic fashion in mammalian cells. We found that CASK is a long-lived protein despite the fact that it contains three putative PEST sequences. Finally, we provide detailed evidence that CASK degradation is mediated through a ubiquitin-proteasome pathway and this is phosphorylation-dependent. Together, these results provide evidence that post-translational modifications to CASK are major regulatory steps leading to its proteasomal degradation. This regulation not only has important implications on how CASK participates in its many disparate roles, but highlights how altering this regulation may contribute to the pathogenesis of human disease.
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Affiliation(s)
- Qizhi Sun
- Department of Biology, University of Western Ontario, London, ON, Canada N6A 5B7
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42
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Knecht E, Aguado C, Cárcel J, Esteban I, Esteve JM, Ghislat G, Moruno JF, Vidal JM, Sáez R. Intracellular protein degradation in mammalian cells: recent developments. Cell Mol Life Sci 2009; 66:2427-43. [PMID: 19399586 PMCID: PMC11115841 DOI: 10.1007/s00018-009-0030-6] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2009] [Accepted: 04/02/2009] [Indexed: 12/16/2022]
Abstract
In higher organisms, dietary proteins are broken down into amino acids within the digestive tract but outside the cells, which incorporate the resulting amino acids into their metabolism. However, under certain conditions, an organism loses more nitrogen than is assimilated in the diet. This additional loss was found in the past century to come from intracellular proteins and started an intensive research that produced an enormous expansion of the field and a dispersed literature. Therefore, our purpose is to provide an updated summary of the current knowledge on the proteolytic machinery involved in intracellular protein degradation and its physiological and pathological relevance, especially addressed to newcomers in the field who may find further details in more specialized reviews. However, even providing a general overview, this is an extremely wide field and, therefore, we mainly focus on mammalian cells, while other cells will be mentioned only for comparison purposes.
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Affiliation(s)
- Erwin Knecht
- Centro de Investigación Príncipe Felipe, Valencia, Spain.
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43
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Nedelsky NB, Todd PK, Taylor JP. Autophagy and the ubiquitin-proteasome system: collaborators in neuroprotection. Biochim Biophys Acta Mol Basis Dis 2008; 1782:691-9. [PMID: 18930136 DOI: 10.1016/j.bbadis.2008.10.002] [Citation(s) in RCA: 258] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2008] [Revised: 10/07/2008] [Accepted: 10/08/2008] [Indexed: 11/26/2022]
Abstract
Protein degradation is an essential cellular function that, when dysregulated or impaired, can lead to a wide variety of disease states. The two major intracellular protein degradation systems are the ubiquitin-proteasome system (UPS) and autophagy, a catabolic process that involves delivery of cellular components to the lysosome for degradation. While the UPS has garnered much attention as it relates to neurodegenerative disease, important links between autophagy and neurodegeneration have also become evident. Furthermore, recent studies have revealed interaction between the UPS and autophagy, suggesting a coordinated and complementary relationship between these degradation systems that becomes critical in times of cellular stress. Here we describe autophagy and review evidence implicating this system as an important player in the pathogenesis of neurodegenerative disease. We discuss the role of autophagy in neurodegeneration and review its neuroprotective functions as revealed by experimental manipulation in disease models. Finally, we explore potential parallels and connections between autophagy and the UPS, highlighting their collaborative roles in protecting against neurodegenerative disease.
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Affiliation(s)
- Natalia B Nedelsky
- Department of Neurology, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
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44
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Cooper S, Shedden K. Microarrays and the relationship of mRNA variation to protein variation during the cell cycle. J Theor Biol 2007; 249:574-81. [PMID: 17915257 DOI: 10.1016/j.jtbi.2007.08.019] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2007] [Revised: 08/13/2007] [Accepted: 08/16/2007] [Indexed: 01/26/2023]
Abstract
Microarray analyses have led to the postulated existence and identification of numerous genes that are believed to be expressed and presumably to act in a cell-cycle-specific manner because their expression varies during the cell cycle. It is important to see how protein variation can be produced from mRNA variation. We have calculated the protein content throughout the cell cycle resulting from cell-cycle-specific mRNA expression, and compared the result to protein content resulting from constant, cell-cycle independent, mRNA expression. For stable proteins, cell-cycle-specific mRNA expression leads to a maximum 2-fold change in protein content compared to proteins synthesized from constantly expressed mRNA. More realistic sinusoidal patterns of mRNA expression exhibit much smaller ratios of 1.25 or lower, even for extremely large amplitudes in mRNA expression. For unstable proteins that have a cycle-independent half-life, only at extremely short protein half-lives does mRNA variation have a significant impact on variation of protein content during the division cycle. We also apply these findings to proteins with a cycle-specific decay pattern. mRNA variations during the eukaryotic division cycle variation of mRNA during the cell cycle can have only a minimal affect on the variation of protein content during the cell cycle. We conclude that mRNA variations during the division cycle, as measured by microarrays, cannot by themselves, identify cycle-specific functions related to protein variations.
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Affiliation(s)
- Stephen Cooper
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109-0620, USA.
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45
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Esteban I, Aguado C, Sánchez M, Knecht E. Regulation of various proteolytic pathways by insulin and amino acids in human fibroblasts. FEBS Lett 2007; 581:3415-21. [PMID: 17610878 DOI: 10.1016/j.febslet.2007.06.043] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2007] [Revised: 06/15/2007] [Accepted: 06/18/2007] [Indexed: 02/08/2023]
Abstract
Intracellular protein degradation is a regulated process with several proteolytic pathways. Although regulation of macroautophagy has been investigated in some detail in hepatocytes and in few other cells, less is known on this regulation in other cells and proteolytic pathways. We show that in human fibroblasts insulin and amino acids reduce protein degradation by different signalling pathways and that this inhibition proceeds in part via the mammalian target of rapamycin, especially with amino acids, which probably increase lysosomal pH. Moreover, the regulatory amino acids (Phe, Arg, Met, Tyr, Trp and Cys) are partially different from other cells. Finally, and in addition to macroautophagy, insulin and amino acids modify, to different extents and sometimes in opposite directions, the activities of other proteolytic pathways.
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Affiliation(s)
- Inmaculada Esteban
- Laboratorio de Biología Celular, Centro de Investigación Príncipe Felipe, Avda. Autopista del Saler 16, 46013-Valencia, Spain
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46
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Mariño G, Salvador-Montoliu N, Fueyo A, Knecht E, Mizushima N, López-Otín C. Tissue-specific Autophagy Alterations and Increased Tumorigenesis in Mice Deficient in Atg4C/Autophagin-3. J Biol Chem 2007; 282:18573-18583. [PMID: 17442669 DOI: 10.1074/jbc.m701194200] [Citation(s) in RCA: 313] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Atg4C/autophagin-3 is a member of a family of cysteine proteinases proposed to be involved in the processing and delipidation of the mammalian orthologues of yeast Atg8, an essential component of an ubiquitin-like modification system required for execution of autophagy. To date, the in vivo role of the different members of this family of proteinases remains unclear. To gain further insights into the functional relevance of Atg4 orthologues, we have generated mutant mice deficient in Atg4C/autophagin-3. These mice are viable and fertile and do not display any obvious abnormalities, indicating that they are able to develop the autophagic response required during the early neonatal period. However, Atg4C-/--starved mice show a decreased autophagic activity in the diaphragm as assessed by immunoblotting studies and by fluorescence microscopic analysis of samples from Atg4C-/- GFP-LC3 transgenic mice. In addition, animals deficient in Atg4C show an increased susceptibility to develop fibrosarcomas induced by chemical carcinogens. Based on these results, we propose that Atg4C is not essential for autophagy development under normal conditions but is required for a proper autophagic response under stressful conditions such as prolonged starvation. We also propose that this enzyme could play an in vivo role in events associated with tumor progression.
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Affiliation(s)
- Guillermo Mariño
- Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología, Universidad de Oviedo, 33006 Oviedo, Spain
| | - Natalia Salvador-Montoliu
- Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología, Universidad de Oviedo, 33006 Oviedo, Spain
| | - Antonio Fueyo
- Biología Funcional, Facultad de Medicina, Instituto Universitario de Oncología, Universidad de Oviedo, 33006 Oviedo, Spain
| | - Erwin Knecht
- Laboratorio de Biologia Celular, Centro de Investigacion Principe Felipe, 46013 Valencia, Spain
| | - Noboru Mizushima
- Department of Bioregulation and Metabolism, Tokyo Metropolitan Institute of Medical Science, Tokyo 113-8613, Japan; Department of Physiology and Cell Biology, Tokyo Medical and Dental University, Tokyo 113-8519, Japan; SORST, Japan Science and Technology Agency, Kawaguchi 332-0012, Japan
| | - Carlos López-Otín
- Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología, Universidad de Oviedo, 33006 Oviedo, Spain
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Abstract
PURPOSE OF REVIEW Protein synthesis and degradation govern protein turnover, which underlies the adaptation of organisms to changing developmental, physiological and environmental needs. The cellular mechanisms of these processes have been increasingly uncovered. Recent findings establishing additional links between protein synthesis and degradation are the topic of this review. RECENT FINDINGS Several major developments in the field have taken place recently. First, the role of lysosomal-autophagosomal degradation, the established amino acid supplier for protein synthesis, has been demonstrated for additional diverse aspects of cellular physiology. Second, cytosolic protein degradation initiated by the proteasome has been assigned a critical role in sustaining ongoing protein synthesis upon acute nutrient restriction. A number of regulatory possibilities to modulate the intracellular amino acid flux by means of proteasomal degradation are discussed. Finally, the field of translation factor regulation by their degradation has emerged recently and is described here. SUMMARY The elucidation of mechanisms determining protein turnover and, thus, cellular adaptation will help us to understand the (patho)physiological conditions caused or accompanying acute and chronic nutrient deficiencies and should lead to new therapeutic strategies to handle them.
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Affiliation(s)
- Ramunas M Vabulas
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Martinsried, Germany.
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48
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Ding Q, Cecarini V, Keller JN. Interplay between protein synthesis and degradation in the CNS: physiological and pathological implications. Trends Neurosci 2007; 30:31-6. [PMID: 17126920 DOI: 10.1016/j.tins.2006.11.003] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2006] [Revised: 09/28/2006] [Accepted: 11/16/2006] [Indexed: 01/23/2023]
Abstract
Compromise of the ubiquitin-proteasome system (UPS) is a potential basis for multiple physiological abnormalities and pathologies in the CNS. This could be because reduced protein turnover leads to bulk intracellular protein accumulation. However, conditions associated with compromised UPS function are also associated with impairments in protein synthesis, and impairment of UPS function is sufficient to inhibit protein synthesis. These data suggest that the toxicity of UPS inhibition need not depend on gross intracellular protein accumulation, and indicate the potential for crosstalk between the UPS and protein-synthesis pathways. In this review, we discuss evidence for interplay between the UPS and protein-synthesis machinery, and outline the implications of this crosstalk for physiological and pathological processes in the CNS.
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Affiliation(s)
- Qunxing Ding
- Department of Anatomy and Neurobiology, and Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY 40536-0230, USA
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49
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Yewdell JW, Nicchitta CV. The DRiP hypothesis decennial: support, controversy, refinement and extension. Trends Immunol 2006; 27:368-73. [PMID: 16815756 DOI: 10.1016/j.it.2006.06.008] [Citation(s) in RCA: 165] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2006] [Revised: 05/19/2006] [Accepted: 06/14/2006] [Indexed: 10/24/2022]
Abstract
In 1996, to explain the rapid presentation of viral proteins to CD8+ T cells, it was proposed that peptides presented by MHC class I molecules derive from defective ribosomal products (DRiPs), presumed to be polypeptides arising from in-frame translation that fail to achieve native structure owing to inevitable imperfections in transcription, translation, post-translational modifications or protein folding. Here, we consider findings that address the DRiP hypothesis, and extend the hypothesis by proposing that cells possess specialized machinery, possibly in the form of "immunoribosomes", to couple protein synthesis to antigen presentation.
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Affiliation(s)
- Jonathan W Yewdell
- Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, MD 20892-0440, USA.
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50
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Martín de Llano JJ, Fuertes G, Andreu EJ, Puig O, Chaves FJ, Soutar AK, Armengod ME, Knecht E. A single point mutation in the low-density lipoprotein receptor switches the degradation of its mature protein from the proteasome to the lysosome. Int J Biochem Cell Biol 2006; 38:1340-51. [PMID: 16530458 DOI: 10.1016/j.biocel.2006.01.014] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2005] [Revised: 01/02/2006] [Accepted: 01/17/2006] [Indexed: 11/28/2022]
Abstract
Pathogenic mutations in the low-density lipoprotein receptor prevent cholesterol uptake and cause familial hypercholesterolemia. In comparison to the biogenesis and endocytic trafficking of this receptor and some of its mutants, their degradation mechanisms are not well understood. Therefore, to gain some insights into this aspect, we analyzed the effects of proteasomal and lysosomal inhibitors on the levels of the wild type low-density lipoprotein receptor and a mutant form, C358Y, which was prevalent in a sample of Spanish familial hypercholesterolemia patients. In transfected cells, the mutant C358Y exhibited lower activity than the wild type receptor, as well as retarded post-translational processing of its precursor to the mature form. Interestingly, about 30% of the mutant precursor was degraded by a lysosomal pathway. Moreover, its mature form was more rapidly degraded than the wild type receptor (half lives of 5.3 and 10.9 h, respectively) and its degradation was exclusively dependent on a lysosomal pathway. In contrast, the mature form of the wild type receptor was mainly degraded by proteasomes and, to a minor extent (30%), by lysosomes. We conclude that a single mutation in the low-density lipoprotein receptor switches the degradation of the mature receptor from a proteasomal to a lysosomal pathway which degrades the protein at a faster rate. This suggests cooperation of proteasomes and lysosomes in the degradation of the low-density lipoprotein receptor and adds an intriguing new aspect to our understanding of receptor-mediated endocytosis.
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Affiliation(s)
- José Javier Martín de Llano
- Laboratorio de Biología Celular, Centro de Investigación Príncipe Felipe, Avda. Autopista del Saler 16, 46013 Valencia, Spain
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