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Franco JC, Nogueira MLC, Gandelini GM, Pinheiro GMS, Gonçalves CC, Barbosa LRS, Young JC, Ramos CHI. Sorghum bicolor SbHSP110 has an elongated shape and is able of protecting against aggregation and replacing human HSPH1/HSP110 in refolding and disaggregation assays. Biopolymers 2023; 114:e23532. [PMID: 36825649 DOI: 10.1002/bip.23532] [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: 09/01/2022] [Revised: 02/06/2023] [Accepted: 02/08/2023] [Indexed: 02/25/2023]
Abstract
Perturbations in the native structure, often caused by stressing cellular conditions, not only impair protein function but also lead to the formation of aggregates, which can accumulate in the cell leading to harmful effects. Some organisms, such as plants, express the molecular chaperone HSP100 (homologous to HSP104 from yeast), which has the remarkable capacity to disaggregate and reactivate proteins. Recently, studies with animal cells, which lack a canonical HSP100, have identified the involvement of a distinct system composed of HSP70/HSP40 that needs the assistance of HSP110 to efficiently perform protein breakdown. As sessile plants experience stressful conditions more severe than those experienced by animals, we asked whether a plant HSP110 could also play a role in collaborating with HSP70/HSP40 in a system that increases the efficiency of disaggregation. Thus, the gene for a putative HSP110 from the cereal Sorghum bicolor was cloned and the protein, named SbHSP110, purified. For comparison purposes, human HsHSP110 (HSPH1/HSP105) was also purified and investigated in parallel. First, a combination of spectroscopic and hydrodynamic techniques was used for the characterization of the conformation and stability of recombinant SbHSP110, which was produced folded. Second, small-angle X-ray scattering and combined predictors of protein structure indicated that SbHSP110 and HsHSP110 have similar conformations. Then, the chaperone activities, which included protection against aggregation, refolding, and reactivation, were investigated, showing that SbHSP110 and HsHSP110 have similar functional activities. Altogether, the results add to the structure/function relationship study of HSP110s and support the hypothesis that plants have multiple strategies to act upon the reactivation of protein aggregates.
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Affiliation(s)
- Juliana C Franco
- Institute of Chemistry, University of Campinas UNICAMP, Campinas, SP, Brazil
| | - Maria L C Nogueira
- Institute of Chemistry, University of Campinas UNICAMP, Campinas, SP, Brazil
| | | | | | - Conrado C Gonçalves
- Institute of Chemistry, University of Campinas UNICAMP, Campinas, SP, Brazil
| | - Leandro R S Barbosa
- Institute of Physics, University of São Paulo, São Paulo, SP, Brazil.,Brazilian Synchrotron Light Laboratory (LNLS), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, SP, Brazil
| | - Jason C Young
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada
| | - Carlos H I Ramos
- Institute of Chemistry, University of Campinas UNICAMP, Campinas, SP, Brazil.,National Institute of Science & Technology of Structural Biology and Bioimage (INCTBEB), Rio de Janeiro, Brazil
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2
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Kukharsky MS, Everett MW, Lytkina OA, Raspopova MA, Kovrazhkina EA, Ovchinnikov RK, Antohin AI, Moskovtsev AA. Protein Homeostasis Dysregulation in Pathogenesis of Neurodegenerative Diseases. Mol Biol 2022. [DOI: 10.1134/s0026893322060115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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3
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Hajibarat Z, Saidi A. Senescence-associated proteins and nitrogen remobilization in grain filling under drought stress condition. J Genet Eng Biotechnol 2022; 20:101. [PMID: 35819732 PMCID: PMC9276853 DOI: 10.1186/s43141-022-00378-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 06/14/2022] [Indexed: 11/25/2022]
Abstract
Background Plants use escape strategies including premature senescence and leaf reduction to cope in response to drought stress, which in turn reduces plant leaves and photosynthesis. This strategy allows the new generation (seeds) to survive under drought but, plants experience more yield loss during stress condition. The amount of damage caused by drought stress is compensated by the expression of genes involved in regulating leaf aging. Leaf senescence alters the expression of thousands of genes and ultimately affecting grain protein content, grain yield, and nitrogen utilization efficiency. Also, under drought stress, nitrogen in the soil will not become as much available and causes the beginning and acceleration of the senescence process of leaves. The main body of the abstract This review identified proteins signaling and functional proteins involved in senescence. Further, transcription factors and cell wall degradation enzymes (proteases) related to senescence during drought stress were surveyed. We discuss the regulatory pathways of genes as a result of the degradation of proteins during senescence process. Senescence is strongly influenced by plant hormones and environmental factors including the availability of nitrogen. During maturity or drought stress, reduced nitrogen uptake can cause nitrogen to be remobilized from leaves and stems to seeds, eventually leading to leaf senescence. Under these conditions, genes involved in chloroplast degradation and proteases show increased expression. The functional (proteases) and regulatory proteins such as protein kinases and phosphatases as well as transcription factors (AP2/ERF, NAC, WRKY, MYB, and bZIP) are involved in leaf senescence and drought stress. Short conclusion In this review, senescence-associated proteins involved in leaf senescence and regulatory and functional proteins in response to drought stress during grain filling were surveyed. The present study predicts on the role of nitrogen transporters, transcription factors and regulatory genes involved in the late stages of plant growth with the aim of understanding their mechanisms of action during grain filling stage. For a better understanding, the relevant evidence for the balance between grain filling and protein breakdown during grain filling in cereals is presented.
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Affiliation(s)
- Zohreh Hajibarat
- Department of Plant Sciences and Biotechnology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran
| | - Abbas Saidi
- Department of Plant Sciences and Biotechnology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran.
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4
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Hackett PT, Jia X, Li L, Ward DM. Posttranslational regulation of mitochondrial frataxin and identification of compounds that increase frataxin levels in Friedreich's ataxia. J Biol Chem 2022; 298:101982. [PMID: 35472330 PMCID: PMC9127368 DOI: 10.1016/j.jbc.2022.101982] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Revised: 04/18/2022] [Accepted: 04/19/2022] [Indexed: 11/18/2022] Open
Abstract
Friedreich's ataxia (FRDA) is a degenerative disease caused by a decrease in the mitochondrial protein frataxin (Fxn), which is involved in iron-sulfur cluster (ISC) synthesis. Diminutions in Fxn result in decreased ISC synthesis, increased mitochondrial iron accumulation, and impaired mitochondrial function. Here, we show that conditions that result in increased mitochondrial reactive oxygen species in yeast or mammalian cell culture give rise to increased turnover of Fxn but not of other ISC synthesis proteins. We demonstrate that the mitochondrial Lon protease is involved in Fxn degradation and that iron export through the mitochondrial metal transporter Mmt1 protects yeast Fxn from degradation. We also determined that when FRDA fibroblasts were grown in media containing elevated iron, mitochondrial reactive oxygen species increased and Fxn decreased compared to WT fibroblasts. Furthermore, we screened a library of FDA-approved compounds and identified 38 compounds that increased yeast Fxn levels, including the azole bifonazole, antiparasitic fipronil, antitumor compound dibenzoylmethane, antihypertensive 4-hydroxychalcone, and a nonspecific anion channel inhibitor 4,4-diisothiocyanostilbene-2,2-sulfonic acid. We show that top hits 4-hydroxychalcone and dibenzoylmethane increased mRNA levels of transcription factor nuclear factor erythroid 2-related factor 2 in FRDA patient-derived fibroblasts, as well as downstream antioxidant targets thioredoxin, glutathione reductase, and superoxide dismutase 2. Taken together, these findings reveal that FRDA progression may be in part due to oxidant-mediated decreases in Fxn and that some approved compounds may be effective in increasing mitochondrial Fxn in FRDA, delaying disease progression.
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Affiliation(s)
- Peter T Hackett
- Department of Pathology, Division of Microbiology and Immunology, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Xuan Jia
- Department of Pathology, Division of Microbiology and Immunology, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Liangtao Li
- Department of Pathology, Division of Microbiology and Immunology, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Diane M Ward
- Department of Pathology, Division of Microbiology and Immunology, University of Utah School of Medicine, Salt Lake City, Utah, USA.
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5
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Computational prediction and redesign of aberrant protein oligomerization. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2020; 169:43-83. [DOI: 10.1016/bs.pmbts.2019.11.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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6
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Chaari A. Molecular chaperones biochemistry and role in neurodegenerative diseases. Int J Biol Macromol 2019; 131:396-411. [DOI: 10.1016/j.ijbiomac.2019.02.148] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 02/25/2019] [Accepted: 02/25/2019] [Indexed: 02/07/2023]
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7
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Lorenzo-Pouso AI, Pérez-Sayáns M, Bravo SB, López-Jornet P, García-Vence M, Alonso-Sampedro M, Carballo J, García-García A. Protein-Based Salivary Profiles as Novel Biomarkers for Oral Diseases. DISEASE MARKERS 2018; 2018:6141845. [PMID: 30524521 PMCID: PMC6247606 DOI: 10.1155/2018/6141845] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 09/26/2018] [Accepted: 10/04/2018] [Indexed: 12/11/2022]
Abstract
The Global Burden of Oral Diseases affects 3.5 billion people worldwide, representing the number of people affected by the burden of untreated dental caries, severe periodontal disease, and edentulism. Thus, much more efforts in terms of diagnostics and treatments must be provided in the fight of these outcomes. In this sense, recently, the study of saliva as biological matrix has been identified as a new landmark initiative in the search of novel and useful biomarkers to prevent and diagnose these conditions. Specifically, saliva is a rich reservoir of different proteins and peptides and accessible due to recent advances in molecular biology and specially in targeted and unbiased proteomics technologies. Nonetheless, emerging barriers are an obstacle to the study of the salivary proteome in an effective way. This review aims at giving an overall perspective of salivary biomarkers identified in several oral diseases by means of molecular biology approaches.
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Affiliation(s)
- Alejandro I. Lorenzo-Pouso
- Oral Medicine, Oral Surgery and Implantology Unit, Faculty of Medicine and Dentistry, Universidade de Santiago de Compostela, Health Research Institute of Santiago de Compostela (IDIS), Santiago de Compostela, A Coruña, Spain
| | - Mario Pérez-Sayáns
- Oral Medicine, Oral Surgery and Implantology Unit, Faculty of Medicine and Dentistry, Universidade de Santiago de Compostela, Health Research Institute of Santiago de Compostela (IDIS), Santiago de Compostela, A Coruña, Spain
| | - Susana B. Bravo
- Proteomic Unit, Health Research Institute of Santiago de Compostela (IDIS), Santiago de Compostela, A Coruña, Spain
| | - Pía López-Jornet
- Department of Oral Medicine, Faculty of Medicine, Regional Campus of International Excellence “Campus Mare Nostrum”, University of Murcia, Espinardo, Murcia, Spain
| | - María García-Vence
- Proteomic Unit, Health Research Institute of Santiago de Compostela (IDIS), Santiago de Compostela, A Coruña, Spain
| | - Manuela Alonso-Sampedro
- Department of Internal Medicine and Clinical Epidemiology, Santiago de Compostela University Hospital Complex (CHUS), Health Research Institute of Santiago de Compostela (IDIS), Santiago de Compostela, Galicia, Spain
| | - Javier Carballo
- Department of Food Technology, Faculty of Sciences, University of Vigo-Ourense Campus, Ourense, Spain
| | - Abel García-García
- Oral Medicine, Oral Surgery and Implantology Unit, Faculty of Medicine and Dentistry, Universidade de Santiago de Compostela, Health Research Institute of Santiago de Compostela (IDIS), Santiago de Compostela, A Coruña, Spain
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8
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Abstract
Diverse proteolytic pathways regulate chloroplasts. Recent work has revealed significant new roles for chloroplast ubiquitination in stress adaptation, involving targeted protein removal through the ubiquitin-proteasome system, or selective, whole-chloroplast degradation.
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Affiliation(s)
- Qihua Ling
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK
| | - Paul Jarvis
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK.
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9
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Kitazaki K, Arakawa T, Matsunaga M, Yui-Kurino R, Matsuhira H, Mikami T, Kubo T. Post-translational mechanisms are associated with fertility restoration of cytoplasmic male sterility in sugar beet (Beta vulgaris). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 83:290-9. [PMID: 26031622 DOI: 10.1111/tpj.12888] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Revised: 05/08/2015] [Accepted: 05/15/2015] [Indexed: 05/20/2023]
Abstract
Genetic conflict between cytoplasmically inherited elements and nuclear genes arising from their different transmission patterns can be seen in cytoplasmic male sterility (CMS), the mitochondrion-encoded inability to shed functional pollen. CMS is associated with a mitochondrial open reading frame (ORF) that is absent from non-sterility inducing mitochondria (S-orf). Nuclear genes that suppress CMS are called restorer-of-fertility (Rf) genes. Post-transcriptional and translational repression of S-orf mediates the molecular action of Rf that encodes a class of RNA-binding proteins with pentatricopeptide repeat (PPR) motifs. Besides the PPR-type of Rfs, there are also non-PPR Rfs, but the molecular interactions between non-PPR Rf and S-orf have not been described. In this study, we investigated the interaction of bvORF20, a non-PPR Rf from sugar beet (Beta vulgaris), with preSatp6, the S-orf from sugar beet. Anthers expressing bvORF20 contained a protein that interacted with preSATP6 protein. Analysis of anthers and transgenic calli expressing a FLAG-tagged bvORF20 suggested the binding of preSATP6 to bvORF20. To see the effect of bvORF20 on preSATP6, which exists as a 250-kDa protein complex in CMS plants, signal bands of preSATP6 in bvORF20-expressing and non-expressing anthers were compared by immunoblotting combined with Blue Native polyacrylamide gel electrophoresis. The signal intensity of the 250-kDa band decreased significantly, and 200- and 150-kDa bands appeared in bvORF20-expressing anthers. Transgenic callus expressing bvORF20 also generated the 200- and 150-kDa bands. The 200-kDa complex is likely to include both preSATP6 and bvORF20. Post-translational interaction between preSATP6 and bvORF20 appears to alter the higher order structure of preSATP6 that may lead to fertility restoration in sugar beet.
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Affiliation(s)
- Kazuyoshi Kitazaki
- Research Faculty of Agriculture, Hokkaido University, N-9, W-9, Kita-ku, Sapporo, Hokkaido, 060-8589, Japan
| | - Takumi Arakawa
- Research Faculty of Agriculture, Hokkaido University, N-9, W-9, Kita-ku, Sapporo, Hokkaido, 060-8589, Japan
| | - Muneyuki Matsunaga
- Research Faculty of Agriculture, Hokkaido University, N-9, W-9, Kita-ku, Sapporo, Hokkaido, 060-8589, Japan
| | - Rika Yui-Kurino
- Research Faculty of Agriculture, Hokkaido University, N-9, W-9, Kita-ku, Sapporo, Hokkaido, 060-8589, Japan
| | - Hiroaki Matsuhira
- Research Faculty of Agriculture, Hokkaido University, N-9, W-9, Kita-ku, Sapporo, Hokkaido, 060-8589, Japan
| | - Tetsuo Mikami
- Research Faculty of Agriculture, Hokkaido University, N-9, W-9, Kita-ku, Sapporo, Hokkaido, 060-8589, Japan
| | - Tomohiko Kubo
- Research Faculty of Agriculture, Hokkaido University, N-9, W-9, Kita-ku, Sapporo, Hokkaido, 060-8589, Japan
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10
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Uversky VN. Intrinsically disordered proteins and their (disordered) proteomes in neurodegenerative disorders. Front Aging Neurosci 2015; 7:18. [PMID: 25784874 PMCID: PMC4345837 DOI: 10.3389/fnagi.2015.00018] [Citation(s) in RCA: 118] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Accepted: 02/13/2015] [Indexed: 12/14/2022] Open
Affiliation(s)
- Vladimir N Uversky
- Department of Molecular Medicine, USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida Tampa, FL, USA ; Biology Department, Faculty of Science, King Abdulaziz University Jeddah, Saudi Arabia ; Institute for Biological Instrumentation, Russian Academy of Sciences Pushchino, Russia ; Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences St. Petersburg, Russia
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11
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Goto-Yamada S, Mano S, Nakamori C, Kondo M, Yamawaki R, Kato A, Nishimura M. Chaperone and Protease Functions of LON Protease 2 Modulate the Peroxisomal Transition and Degradation with Autophagy. ACTA ACUST UNITED AC 2014; 55:482-96. [DOI: 10.1093/pcp/pcu017] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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12
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Ryan BJ, Henehan GT. Overview of approaches to preventing and avoiding proteolysis during expression and purification of proteins. ACTA ACUST UNITED AC 2013; Chapter 5:Unit5.25. [PMID: 23377852 DOI: 10.1002/0471140864.ps0525s71] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Proteases are enzymes that cleave proteins. They occur widely in nature and play a fundamental role in cellular homeostasis; however, their presence can result in unwanted protein degradation during recombinant protein expression and purification. This unit introduces proteases, specifically focusing on the types commonly encountered during production of recombinant proteins. The strategies used to avoid and to prevent proteolysis are also described, with extensive consideration of the molecular, technical, and logistic methodologies involved.
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Affiliation(s)
- Barry J Ryan
- Food Science and Environmental Health, Dublin Institute of Technology, Dublin, Ireland
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13
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Chaari A, Hoarau-Véchot J, Ladjimi M. Applying chaperones to protein-misfolding disorders: molecular chaperones against α-synuclein in Parkinson's disease. Int J Biol Macromol 2013; 60:196-205. [PMID: 23748003 DOI: 10.1016/j.ijbiomac.2013.05.032] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2013] [Revised: 05/28/2013] [Accepted: 05/29/2013] [Indexed: 02/04/2023]
Abstract
Parkinson's disease (PD) is a neurodegenerative disorder characterized by the accumulation of a protein called α-synuclein (α-syn) into inclusions known as lewy bodies (LB) within neurons. This accumulation is also due to insufficient formation and activity of dopamine produced in certain neurons within the substantia nigra. Lewy bodies are the pathological hallmark of the idiopathic disorder and the cascade that allows α-synuclein to misfold, aggregate and form these inclusions has been the subject of intensive research. Targeting these early steps of oligomerization is one of the main therapeutic approaches in order to develop neurodegenerative-modifying agents. Because the folding and refolding of alpha synuclein is the key point of this cascade, we are interested in this review to summarize the role of some molecular chaperones proteins such as Hsp70, Hsp90 and small heat shock proteins (sHsp) and Hsp 104. Hsp70 and its co-chaperone, Hsp70 and small heat shock proteins can prevent neurodegeneration by preventing α-syn misfolding, oligomerization and aggregation in vitro and in Parkinson disease animal models. Hsp104 is able to resolve disordered protein aggregates and cross beta amyloid conformers. Together, these chaperones have a complementary effect and can be a target for therapeutic intervention in PD.
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Affiliation(s)
- Ali Chaari
- Department of Biochemistry, Weill Cornell Medical College in Qatar, Qatar Foundation, Education City, Doha, Qatar.
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14
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Trougakos IP, Sesti F, Tsakiri E, Gorgoulis VG. Non-enzymatic post-translational protein modifications and proteostasis network deregulation in carcinogenesis. J Proteomics 2013; 92:274-98. [PMID: 23500136 DOI: 10.1016/j.jprot.2013.02.024] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2013] [Revised: 02/19/2013] [Accepted: 02/27/2013] [Indexed: 12/25/2022]
Abstract
Organisms are constantly challenged by stressors and thus the maintenance of biomolecules functionality is essential for the assurance of cellular homeostasis. Proteins carry out the vast majority of cellular functions by mostly participating in multimeric protein assemblies that operate as protein machines. Cells have evolved a complex proteome quality control network for the rescue, when possible, or the degradation of damaged polypeptides. Nevertheless, despite these proteostasis ensuring mechanisms, new protein synthesis, and the replication-mediated dilution of proteome damage in mitotic cells, the gradual accumulation of stressors during aging (or due to lifestyle) results in increasingly damaged proteome. Non-enzymatic post-translational protein modifications mostly arise by unbalanced redox homeostasis and/or high glucose levels and may cause disruption of proteostasis as they can alter protein function. This outcome may then increase genomic instability due to reduced fidelity in processes like DNA replication or repair. Herein, we present a synopsis of the major non-enzymatic post-translation protein modifications and of the proteostasis network deregulation in carcinogenesis. We propose that activation of the proteostasis ensuring mechanisms in premalignant cells has tumor-preventive effects, whereas considering that over-activation of these mechanisms represents a hallmark of advanced tumors, their inhibition provides a strategy for the development of anti-tumor therapies. This article is part of a Special Issue entitled: Posttranslational Protein modifications in biology and Medicine.
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Affiliation(s)
- Ioannis P Trougakos
- Department of Cell Biology and Biophysics, Faculty of Biology, University of Athens, Panepistimiopolis, Athens 15784, Greece.
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15
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Genetic dissection of peroxisome-associated matrix protein degradation in Arabidopsis thaliana. Genetics 2012; 193:125-41. [PMID: 23150599 DOI: 10.1534/genetics.112.146100] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Peroxisomes are organelles that sequester certain metabolic pathways; many of these pathways generate H(2)O(2), which can damage proteins. However, little is known about how damaged or obsolete peroxisomal proteins are degraded. We exploit developmentally timed peroxisomal content remodeling in Arabidopsis thaliana to elucidate peroxisome-associated protein degradation. Isocitrate lyase (ICL) is a peroxisomal glyoxylate cycle enzyme necessary for early seedling development. A few days after germination, photosynthesis begins and ICL is degraded. We previously found that ICL is stabilized when a peroxisome-associated ubiquitin-conjugating enzyme and its membrane anchor are both mutated, suggesting that matrix proteins might exit the peroxisome for ubiquitin-dependent cytosolic degradation. To identify additional components needed for peroxisome-associated matrix protein degradation, we mutagenized a line expressing GFP-ICL, which is degraded similarly to endogenous ICL, and identified persistent GFP-ICL fluorescence (pfl) mutants. We found three pfl mutants that were defective in PEROXIN14 (PEX14/At5g62810), which encodes a peroxisomal membrane protein that assists in importing proteins into the peroxisome matrix, indicating that proteins must enter the peroxisome for efficient degradation. One pfl mutant was missing the peroxisomal 3-ketoacyl-CoA thiolase encoded by the PEROXISOME DEFECTIVE1 (PED1/At2g33150) gene, suggesting that peroxisomal metabolism influences the rate of matrix protein degradation. Finally, one pfl mutant that displayed normal matrix protein import carried a novel lesion in PEROXIN6 (PEX6/At1g03000), which encodes a peroxisome-tethered ATPase that is involved in recycling matrix protein receptors back to the cytosol. The isolation of pex6-2 as a pfl mutant supports the hypothesis that matrix proteins can exit the peroxisome for cytosolic degradation.
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Costa IM, Nasser THT, Demasi M, Nascimento RMP, Netto LES, Miyamoto S, Prado FM, Monteiro G. The promoter of filamentation (POF1) protein from Saccharomyces cerevisiae is an ATPase involved in the protein quality control process. BMC Microbiol 2011; 11:268. [PMID: 22204397 PMCID: PMC3282682 DOI: 10.1186/1471-2180-11-268] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2011] [Accepted: 12/28/2011] [Indexed: 12/05/2022] Open
Abstract
Background The gene YCL047C, which has been renamed promoter of filamentation gene (POF1), has recently been described as a cell component involved in yeast filamentous growth. The objective of this work is to understand the molecular and biological function of this gene. Results Here, we report that the protein encoded by the POF1 gene, Pof1p, is an ATPase that may be part of the Saccharomyces cerevisiae protein quality control pathway. According to the results, Δpof1 cells showed increased sensitivity to hydrogen peroxide, tert-butyl hydroperoxide, heat shock and protein unfolding agents, such as dithiothreitol and tunicamycin. Besides, the overexpression of POF1 suppressed the sensitivity of Δpct1, a strain that lacks a gene that encodes a phosphocholine cytidylyltransferase, to heat shock. In vitro analysis showed, however, that the purified Pof1p enzyme had no cytidylyltransferase activity but does have ATPase activity, with catalytic efficiency comparable to other ATPases involved in endoplasmic reticulum-associated degradation of proteins (ERAD). Supporting these findings, co-immunoprecipitation experiments showed a physical interaction between Pof1p and Ubc7p (an ubiquitin conjugating enzyme) in vivo. Conclusions Taken together, the results strongly suggest that the biological function of Pof1p is related to the regulation of protein degradation.
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Affiliation(s)
- Iris M Costa
- Departamento de Tecnologia Bioquímico-Farmacêutica, Faculdade de Ciências Farmacêuticas, Universidade de São Paulo - USP, São Paulo-SP, Brazil
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17
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Yamanaka K, Sasagawa Y, Ogura T. Recent advances in p97/VCP/Cdc48 cellular functions. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2011; 1823:130-7. [PMID: 21781992 DOI: 10.1016/j.bbamcr.2011.07.001] [Citation(s) in RCA: 136] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2011] [Revised: 07/06/2011] [Accepted: 07/06/2011] [Indexed: 10/18/2022]
Abstract
p97/VCP/Cdc48 is one of the best-characterized type II AAA (ATPases associated with diverse cellular activities) ATPases. p97 is suggested to be a ubiquitin-selective chaperone and its key function is to disassemble protein complexes. p97 is involved in a wide variety of cellular activities. Recently, novel functions, namely autophagy and mitochondrial quality control, for p97 have been uncovered. p97 was identified as a causative factor for inclusion body myopathy associated with Paget disease of bone and frontotemporal dementia (IBMPFD) and more recently as a causative factor for amyotrophic lateral sclerosis (ALS). In this review, we will summarize and discuss recent progress and topics in p97 functions and the relationship to its associated diseases.
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Affiliation(s)
- Kunitoshi Yamanaka
- Department of Molecular Cell Biology, Institute of Molecular Embryology and Genetics, Kumamoto University, 2-2-1 Honjo, Kumamoto 860-0811, Japan
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De Marchis F, Pompa A, Mannucci R, Morosinotto T, Bellucci M. A plant secretory signal peptide targets plastome-encoded recombinant proteins to the thylakoid membrane. PLANT MOLECULAR BIOLOGY 2011; 76:427-41. [PMID: 20714919 DOI: 10.1007/s11103-010-9676-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2010] [Accepted: 07/21/2010] [Indexed: 05/29/2023]
Abstract
Plastids are considered promising bioreactors for the production of recombinant proteins, but the knowledge of the mechanisms regulating foreign protein folding, targeting, and accumulation in these organelles is still incomplete. Here we demonstrate that a plant secretory signal peptide is able to target a plastome-encoded recombinant protein to the thylakoid membrane. The fusion protein zeolin with its native signal peptide expressed by tobacco (Nicotiana tabacum) transplastomic plants was directed into the chloroplast thylakoid membranes, whereas the zeolin mutant devoid of the signal peptide, Δzeolin, is instead accumulated in the stroma. We also show that zeolin folds in the thylakoid membrane where it accumulates as trimers able to form disulphide bonds. Disulphide bonds contribute to protein accumulation since zeolin shows a higher accumulation level with respect to stromal Δzeolin, whose folding is hampered as the protein accumulates at low amounts in a monomeric form and it is not oxidized. Thus, post-transcriptional processes seem to regulate the stability and accumulation of plastid-synthesized zeolin. The most plausible zeolin targeting mechanism to thylakoid is discussed herein.
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Affiliation(s)
- Francesca De Marchis
- Istituto di Genetica Vegetale, Consiglio Nazionale delle Ricerche (CNR), via della Madonna Alta 130, 06128 Perugia, Italy
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19
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Francis BR, Thorsness PE. Hsp90 and mitochondrial proteases Yme1 and Yta10/12 participate in ATP synthase assembly in Saccharomyces cerevisiae. Mitochondrion 2011; 11:587-600. [PMID: 21439406 DOI: 10.1016/j.mito.2011.03.008] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2010] [Revised: 02/22/2011] [Accepted: 03/15/2011] [Indexed: 10/18/2022]
Abstract
Hsc82 and Hsp82, the Hsp90 family proteins of yeast, are both required for fermentative growth at 37°C. Inactivation of either of the mitochondrial AAA proteases, Yme1 or Yta10/12, allows fermentative growth of hsc82∆ or hsp82∆ strains at 37°C. Genetic evidence indicates interaction of Hsc82/Hsp82 with the Yme1 and Yta10/Yta12 complexes in promoting F(1)F(o)-ATPase activity, with Hsc82 specifically required for F(1)-ATPase assembly. A previously reported mutation in Rpt3, one of the six ATPases of the proteasome, suppresses yme1∆ phenotypes and increases transcription of HSC82 but not HSP82. These genetic interactions describe a functional role for Hsp90 proteins in mitochondrial biogenesis.
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Affiliation(s)
- Brian R Francis
- Department of Molecular Biology, University of Wyoming, Laramie, WY 82071, USA
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20
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Bulteau AL, Bayot A. Mitochondrial proteases and cancer. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2010; 1807:595-601. [PMID: 21194520 DOI: 10.1016/j.bbabio.2010.12.011] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2010] [Revised: 12/13/2010] [Accepted: 12/18/2010] [Indexed: 01/12/2023]
Abstract
Mitochondria are a major source of intracellular reactive oxygen species, the production of which increases with cancer. The deleterious effects of reactive oxygen species may be responsible for the impairment of mitochondrial function observed during various pathophysiological states associated with oxidative stress and cancer. These organelles are also targets of oxidative damage (oxidation of mitochondrial DNA, lipids, protein). An important factor for protein maintenance in the presence of oxidative stress is enzymatic reversal of oxidative modifications and/or protein degradation. Failure of these processes is likely a critical component of the cancer process. Mitochondrial proteases degrade misfolded and non-assemble polypeptides, thus performing quality control surveillance in the organelle. Mitochondrial proteases may be directly involved in cancer development as recently shown for HtrA2/Omi or may regulate crucial mitochondrial molecule such as cytochrome c oxidase 4 a subunit of the cytochrome c oxidase complex degraded by the Lon protease. Thus, the role of mitochondrial proteases is further addressed in the context of oxidative stress and cancer.
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Affiliation(s)
- Anne-Laure Bulteau
- CRICM-INSERM-UMRS975, CNRS UMR 7225-UPMC, Hôpital de la Salpétrière, Bâtiment Pharmacie, 47 Bd de l'Hôpital, 75651 Paris Cedex 13, France.
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21
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Uversky VN. Flexible Nets of Malleable Guardians: Intrinsically Disordered Chaperones in Neurodegenerative Diseases. Chem Rev 2010; 111:1134-66. [DOI: 10.1021/cr100186d] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Vladimir N. Uversky
- Department of Molecular Medicine, University of South Florida, Tampa, Florida 33612, United States, Institute for Intrinsically Disordered Protein Research, Center for Computational Biology and Bioinformatics, University of Indiana School of Medicine, Indianapolis, Indiana 46202, United States, and Institute for Biological Instrumentation, Russian Academy of Sciences, 142292 Pushchino, Moscow Region, Russia
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Bayot A, Gareil M, Rogowska-Wrzesinska A, Roepstorff P, Friguet B, Bulteau AL. Identification of novel oxidized protein substrates and physiological partners of the mitochondrial ATP-dependent Lon-like protease Pim1. J Biol Chem 2010; 285:11445-57. [PMID: 20150421 DOI: 10.1074/jbc.m109.065425] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
ATP-dependent proteases are currently emerging as key regulators of mitochondrial functions. Among these proteolytic systems, Pim1, a Lon-like serine protease in Saccharomyces cerevisiae, is involved in the control of selective protein turnover in the mitochondrial matrix. In the absence of Pim1, yeast cells have been shown to accumulate electron-dense inclusion bodies in the matrix space, to lose integrity of mitochondrial genome, and to be respiration-deficient. Because of the severity of phenotypes associated with the depletion of Pim1, this protease appears to be an essential component of the protein quality control machinery in mitochondria and to exert crucial functions during the biogenesis of this organelle. Nevertheless, its physiological substrates and partners are not fully characterized. Therefore, we used the combination of different proteomic techniques to assess the nature of oxidized protein substrates and physiological partners of Pim1 protease under non-repressing growth conditions. The results presented here supply evidence that Pim1-mediated proteolysis is required for elimination of oxidatively damaged proteins in mitochondria.
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Affiliation(s)
- Aurélien Bayot
- Laboratoire de Biologie Cellulaire du Vieillissement, UR4, Vieillissement, Stress et Inflammation, Université Pierre et Marie Curie-Paris 6, Case Courrier 256, Batiment A, 5ème Etage, 7 Quai Saint Bernard, 75252 Paris Cedex 05, France
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24
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25
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Kress W, Weber-Ban E. The alternating power stroke of a 6-cylinder AAA protease chaperone engine. Mol Cell 2009; 35:545-7. [PMID: 19748349 DOI: 10.1016/j.molcel.2009.08.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
In this issue of Molecular Cell, Augustin et al. (2009) describe the regulatory coupling of adjacent ATP subunits in the mitochondrial AAA protease ring along with the responsible molecular determinants and uncover its importance for membrane dislocation of substrates.
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Affiliation(s)
- Wolfgang Kress
- ETH Zurich, Institute of Molecular Biology and Biophysics, Switzerland
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26
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Kaur N, Reumann S, Hu J. Peroxisome biogenesis and function. THE ARABIDOPSIS BOOK 2009; 7:e0123. [PMID: 22303249 PMCID: PMC3243405 DOI: 10.1199/tab.0123] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Peroxisomes are small and single membrane-delimited organelles that execute numerous metabolic reactions and have pivotal roles in plant growth and development. In recent years, forward and reverse genetic studies along with biochemical and cell biological analyses in Arabidopsis have enabled researchers to identify many peroxisome proteins and elucidate their functions. This review focuses on the advances in our understanding of peroxisome biogenesis and metabolism, and further explores the contribution of large-scale analysis, such as in sillco predictions and proteomics, in augmenting our knowledge of peroxisome function In Arabidopsis.
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Affiliation(s)
| | - Sigrun Reumann
- Centre for Organelle Research, Faculty of Science and Technology, University of Stavanger, N-4036 Stavanger, Norway
| | - Jianping Hu
- MSU-DOE Plant Research Laboratory and
- Plant Biology Department, Michigan State University, East Lansing, MI 48824
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Wang P, Bouwman FG, Mariman ECM. Generally detected proteins in comparative proteomics--a matter of cellular stress response? Proteomics 2009; 9:2955-66. [PMID: 19415655 DOI: 10.1002/pmic.200800826] [Citation(s) in RCA: 127] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The specificity of proteins identified by proteomics as biomarkers for defined conditions or as components of biological processes and pathways is crucial. We critically reviewed differentially expressed proteins from comparative proteomic studies identified by 2-DE followed by MS, especially with MALDI technique. Based on 66 of those studies, a list of 44 proteins is presented as generally detected proteins regardless of species, in vivo or in vitro conditions, tissues and organs, and experimental objective. Similarly, a list of 28 generally detected protein families is presented. The enriched functions linked to these generally detected proteins reveal that there are some common biological features beyond the technical limitations. Cellular stress response can be the universal reason as to why these proteins are generally expressed differentially. Using those proteins as biomarkers for cellular processes other than stress response should be done with caution. In future proteomic studies more profound approaches should be applied to look beyond these proteins to find specific biomarkers. Our results are discussed in relation to a recent viewpoint publication by Petrak et al. [Proteomics 2008, 8, 1744-1749].
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Affiliation(s)
- Ping Wang
- Department of Human Biology, Nutrition and Toxicology Research Institute Maastricht, Maastricht University, Maastricht, The Netherlands
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Iyer S, Thomas RR, Portell FR, Dunham LD, Quigley CK, Bennett JP. Recombinant mitochondrial transcription factor A with N-terminal mitochondrial transduction domain increases respiration and mitochondrial gene expression. Mitochondrion 2009; 9:196-203. [PMID: 19460293 DOI: 10.1016/j.mito.2009.01.012] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2008] [Revised: 01/26/2009] [Accepted: 01/27/2009] [Indexed: 10/21/2022]
Abstract
We developed a scalable procedure to produce human mitochondrial transcription factor A (TFAM) modified with an N-terminal protein transduction domain (PTD) and mitochondrial localization signal (MLS) that allow it to cross membranes and enter mitochondria through its "mitochondrial transduction domain" (MTD=PTD+MLS). Alexa488-labeled MTD-TFAM rapidly entered the mitochondrial compartment of cybrid cells carrying the G11778A LHON mutation. MTD-TFAM reversibly increased respiration and levels of respiratory proteins. In vivo treatment of mice with MTD-TFAM increased motor endurance and complex I-driven respiration in mitochondria from brain and skeletal muscle. MTD-TFAM increases mitochondrial bioenergetics and holds promise for treatment of mitochondrial diseases involving deficiencies of energy production.
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Affiliation(s)
- Shilpa Iyer
- Center for the Study of Neurodegenerative Diseases and The Morris K. Udall Parkinson's Disease Research Center of Excellence, University of Virginia, PO Box 800394, Charlottesville, VA 22908, United States
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29
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Hipkiss AR. Carnosine and its possible roles in nutrition and health. ADVANCES IN FOOD AND NUTRITION RESEARCH 2009; 57:87-154. [PMID: 19595386 DOI: 10.1016/s1043-4526(09)57003-9] [Citation(s) in RCA: 150] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
The dipeptide carnosine has been observed to exert antiaging activity at cellular and whole animal levels. This review discusses the possible mechanisms by which carnosine may exert antiaging action and considers whether the dipeptide could be beneficial to humans. Carnosine's possible biological activities include scavenger of reactive oxygen species (ROS) and reactive nitrogen species (RNS), chelator of zinc and copper ions, and antiglycating and anticross-linking activities. Carnosine's ability to react with deleterious aldehydes such as malondialdehyde, methylglyoxal, hydroxynonenal, and acetaldehyde may also contribute to its protective functions. Physiologically carnosine may help to suppress some secondary complications of diabetes, and the deleterious consequences of ischemic-reperfusion injury, most likely due to antioxidation and carbonyl-scavenging functions. Other, and much more speculative, possible functions of carnosine considered include transglutaminase inhibition, stimulation of proteolysis mediated via effects on proteasome activity or induction of protease and stress-protein gene expression, upregulation of corticosteroid synthesis, stimulation of protein repair, and effects on ADP-ribose metabolism associated with sirtuin and poly-ADP-ribose polymerase (PARP) activities. Evidence for carnosine's possible protective action against secondary diabetic complications, neurodegeneration, cancer, and other age-related pathologies is briefly discussed.
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Affiliation(s)
- Alan R Hipkiss
- School of Clinicial and Experimental Medicine, College of Medical and Dental Sciences, The Univeristy of Birmingham, Edgbaston, Birmingham, UK
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30
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Hipkiss AR. Error-protein metabolism and ageing. Biogerontology 2008; 10:523-9. [PMID: 18923917 DOI: 10.1007/s10522-008-9188-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2008] [Accepted: 04/25/2008] [Indexed: 01/19/2023]
Abstract
Ageing and many associated pathologies are accompanied by accumulation of altered proteins. It is suggested that erroneous polypeptide biosynthesis, cytosolic and mitochondrial, is not an insignificant source of aberrant protein in growing and non-mitotic cells. It is proposed that (i) synthesis of sufficient proteases and chaperone proteins necessary for rapid elimination of altered proteins, from cytoplasmic and mitochondrial compartments, is related to cellular protein biosynthetic potential, and (ii) cells growing slowly, or not at all, automatically generate lower levels of protease/chaperone molecules than cells growing rapidly, due to decreased general rate of protein synthesis and lowered amount of error-protein produced per cell. Hence the increased vulnerability of mature organisms may be explained, at least in part, by the decline in constitutive protease/chaperone protein biosynthesis. Upregulation of mitochondria biogenesis, induced by dietary restriction or aerobic exercise, may also increase protease/chaperone protein synthesis, which would improve cellular ability to degrade both error-proteins and proteins damaged post-synthetically by reactive oxygen species etc. These proposals may help explain, in part, the latency of those age-related pathologies where altered proteins accumulate only late in life, and the beneficial effects of aerobic exercise and dietary restriction.
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Affiliation(s)
- Alan R Hipkiss
- Centre for Translational Medicine and Therapeutics, William Harvey Research Institute, Bart's and the London Queen Mary's School of Medicine and Dentistry, London, UK.
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31
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Friguet B, Bulteau AL, Petropoulos I. Mitochondrial protein quality control: Implications in ageing. Biotechnol J 2008; 3:757-64. [DOI: 10.1002/biot.200800041] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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32
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Towards the control of intracellular protein turnover: mitochondrial Lon protease inhibitors versus proteasome inhibitors. Biochimie 2007; 90:260-9. [PMID: 18021745 DOI: 10.1016/j.biochi.2007.10.010] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2007] [Accepted: 10/19/2007] [Indexed: 01/21/2023]
Abstract
Cellular protein homeostasis results from the combination of protein biogenesis processes and protein quality control mechanisms, which contribute to the functional state of cells under normal and stress conditions. Proteolysis constitutes the final step by which short-lived, misfolded and damaged intracellular proteins are eliminated. Protein turnover and oxidatively modified protein degradation are mainly achieved by the proteasome in the cytosol and nucleus of eukaryotic cells while several ATP-dependent proteases including the matrix protease Lon take part in the mitochondrial protein degradation. Moreover, Lon protease seems to play a major role in the elimination of oxidatively modified proteins in the mitochondrial matrix. Specific inhibitors are commonly used to assess cellular functions of proteolytic systems as well as to identify their protein substrates. Here, we present and discuss known proteasome and Lon protease inhibitors. To date, very few inhibitors of Lon have been described and no specific inhibitors of this protease are available. The current knowledge on both catalytic mechanisms and inhibitors of these two proteases is first described and attempts to define specific non-peptidic inhibitors of the human Lon protease are presented.
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