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Gastelum S, Michael AF, Bolger TA. Saccharomyces cerevisiae as a research tool for RNA-mediated human disease. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 15:e1814. [PMID: 37671427 DOI: 10.1002/wrna.1814] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 07/25/2023] [Accepted: 07/26/2023] [Indexed: 09/07/2023]
Abstract
The budding yeast, Saccharomyces cerevisiae, has been used for decades as a powerful genetic tool to study a broad spectrum of biological topics. With its ease of use, economic utility, well-studied genome, and a highly conserved proteome across eukaryotes, it has become one of the most used model organisms. Due to these advantages, it has been used to study an array of complex human diseases. From broad, complex pathological conditions such as aging and neurodegenerative disease to newer uses such as SARS-CoV-2, yeast continues to offer new insights into how cellular processes are affected by disease and how affected pathways might be targeted in therapeutic settings. At the same time, the roles of RNA and RNA-based processes have become increasingly prominent in the pathology of many of these same human diseases, and yeast has been utilized to investigate these mechanisms, from aberrant RNA-binding proteins in amyotrophic lateral sclerosis to translation regulation in cancer. Here we review some of the important insights that yeast models have yielded into the molecular pathology of complex, RNA-based human diseases. This article is categorized under: RNA in Disease and Development > RNA in Disease.
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Affiliation(s)
- Stephanie Gastelum
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona, USA
| | - Allison F Michael
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA
| | - Timothy A Bolger
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA
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2
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Chen X, Muñoz-Arellano AJ, Petranovic D. UBB +1 reduces amyloid-β cytotoxicity by activation of autophagy in yeast. Aging (Albany NY) 2021; 13:23953-23980. [PMID: 34751669 PMCID: PMC8610117 DOI: 10.18632/aging.203681] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 07/02/2021] [Indexed: 04/20/2023]
Abstract
UBB+1 is a mutated version of ubiquitin B peptide caused by a transcriptional frameshift due to the RNA polymerase II "slippage". The accumulation of UBB+1 has been linked to ubiquitin-proteasome system (UPS) dysfunction and neurodegeneration. Alzheimer's disease (AD) is defined as a progressive neurodegeneration and aggregation of amyloid-β peptides (Aβ) is a prominent neuropathological feature of AD. In our previous study, we found that yeast cells expressing UBB+1 at lower level display an increased resistance to cellular stresses under conditions of chronological aging. In order to examine the molecular mechanisms behind, here we performed genome-wide transcriptional analyses and molecular/cellular biology assays. We found that low UBB+1 expression activated the autophagy pathway, increased vacuolar activity, and promoted transport of autophagic marker ATG8p into vacuole. Furthermore, we introduced low UBB+1 expression to our humanized yeast AD models, that constitutively express Aβ42 and Aβ40 peptide, respectively. The co-expression of UBB+1 with Aβ42 or Aβ40 peptide led to reduced intracellular Aβ levels, ameliorated viability, and increased chronological life span. In an autophagy deficient background strain (atg1Δ), intracellular Aβ levels were not affected by UBB+1 expression. Our findings offer insights for reducing intracellular Aβ toxicity via autophagy-dependent cellular pathways under low level of UBB+1 expression.
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Affiliation(s)
- Xin Chen
- Division of Systems and Synthetic Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, Gothenburg, Sweden
| | - Ana Joyce Muñoz-Arellano
- Division of Systems and Synthetic Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Dina Petranovic
- Division of Systems and Synthetic Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, Gothenburg, Sweden
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3
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Banasiak K, Szulc NA, Pokrzywa W. The Dose-Dependent Pleiotropic Effects of the UBB +1 Ubiquitin Mutant. Front Mol Biosci 2021; 8:650730. [PMID: 33842548 PMCID: PMC8032880 DOI: 10.3389/fmolb.2021.650730] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 02/02/2021] [Indexed: 11/23/2022] Open
Abstract
The proteolytic machinery activity diminishes with age, leading to abnormal accumulation of aberrant proteins; furthermore, a decline in protein degradation capacity is associated with multiple age-related proteinopathies. Cellular proteostasis can be maintained via the removal of ubiquitin (Ub)-tagged damaged and redundant proteins by the ubiquitin-proteasome system (UPS). However, during aging, central nervous system (CNS) cells begin to express a frameshift-mutated Ub, UBB+1. Its accumulation is a neuropathological hallmark of tauopathy, including Alzheimer’s disease and polyglutamine diseases. Mechanistically, in cell-free and cell-based systems, an increase in the UBB+1 concentration disrupts proteasome processivity, leading to increased aggregation of toxic proteins. On the other hand, a low level of UBB+1 improves stress resistance and extends lifespan. Here we summarize recent findings regarding the impact of UBB+1 on Ub signaling and neurodegeneration. We also review the molecular basis of how UBB+1 affects UPS components as well as its dose-dependent switch between cytoprotective and cytotoxic roles.
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Affiliation(s)
- Katarzyna Banasiak
- Laboratory of Protein Metabolism, International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland
| | - Natalia A Szulc
- Laboratory of Protein Metabolism, International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland
| | - Wojciech Pokrzywa
- Laboratory of Protein Metabolism, International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland
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4
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Sénécaut N, Alves G, Weisser H, Lignières L, Terrier S, Yang-Crosson L, Poulain P, Lelandais G, Yu YK, Camadro JM. Novel Insights into Quantitative Proteomics from an Innovative Bottom-Up Simple Light Isotope Metabolic (bSLIM) Labeling Data Processing Strategy. J Proteome Res 2021; 20:1476-1487. [PMID: 33573382 PMCID: PMC8459934 DOI: 10.1021/acs.jproteome.0c00478] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Simple light isotope metabolic labeling (SLIM labeling) is an innovative method to quantify variations in the proteome based on an original in vivo labeling strategy. Heterotrophic cells grown in U-[12C] as the sole source of carbon synthesize U-[12C]-amino acids, which are incorporated into proteins, giving rise to U-[12C]-proteins. This results in a large increase in the intensity of the monoisotope ion of peptides and proteins, thus allowing higher identification scores and protein sequence coverage in mass spectrometry experiments. This method, initially developed for signal processing and quantification of the incorporation rate of 12C into peptides, was based on a multistep process that was difficult to implement for many laboratories. To overcome these limitations, we developed a new theoretical background to analyze bottom-up proteomics data using SLIM-labeling (bSLIM) and established simple procedures based on open-source software, using dedicated OpenMS modules, and embedded R scripts to process the bSLIM experimental data. These new tools allow computation of both the 12C abundance in peptides to follow the kinetics of protein labeling and the molar fraction of unlabeled and 12C-labeled peptides in multiplexing experiments to determine the relative abundance of proteins extracted under different biological conditions. They also make it possible to consider incomplete 12C labeling, such as that observed in cells with nutritional requirements for nonlabeled amino acids. These tools were validated on an experimental dataset produced using various yeast strains of Saccharomyces cerevisiae and growth conditions. The workflows are built on the implementation of appropriate calculation modules in a KNIME working environment. These new integrated tools provide a convenient framework for the wider use of the SLIM-labeling strategy.
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Affiliation(s)
- Nicolas Sénécaut
- ≪ Mitochondria, Metals, and Oxidative Stress ≫ Group, Université de Paris-CNRS, Institut Jacques Monod, 75013 Paris, France
| | - Gelio Alves
- National Center for Biotechnology Information, NLM, NIH, Bethesda, Maryland 20894, United States
| | | | - Laurent Lignières
- ProteoSeine@IJM, Université de Paris-CNRS, Institut Jacques Monod, 75013 Paris, France
| | - Samuel Terrier
- ProteoSeine@IJM, Université de Paris-CNRS, Institut Jacques Monod, 75013 Paris, France
| | - Lilian Yang-Crosson
- ≪ Mitochondria, Metals, and Oxidative Stress ≫ Group, Université de Paris-CNRS, Institut Jacques Monod, 75013 Paris, France
| | - Pierre Poulain
- ≪ Mitochondria, Metals, and Oxidative Stress ≫ Group, Université de Paris-CNRS, Institut Jacques Monod, 75013 Paris, France
| | - Gaëlle Lelandais
- Institut de Biologie Intégrative de la Cellule, 91190 Orsay, France
| | - Yi-Kuo Yu
- National Center for Biotechnology Information, NLM, NIH, Bethesda, Maryland 20894, United States
| | - Jean-Michel Camadro
- ≪ Mitochondria, Metals, and Oxidative Stress ≫ Group, Université de Paris-CNRS, Institut Jacques Monod, 75013 Paris, France
- ProteoSeine@IJM, Université de Paris-CNRS, Institut Jacques Monod, 75013 Paris, France
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5
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Verheijen BM, Morimoto S, Sasaki R, Oyanagi K, Kokubo Y, Kuzuhara S, van Leeuwen FW. Expression of Mutant Ubiquitin and Proteostasis Impairment in Kii Amyotrophic Lateral Sclerosis/Parkinsonism-Dementia Complex Brains. J Neuropathol Exp Neurol 2021; 79:902-907. [PMID: 32647880 DOI: 10.1093/jnen/nlaa056] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 05/28/2020] [Indexed: 12/16/2022] Open
Abstract
Kii amyotrophic lateral sclerosis/parkinsonism-dementia complex (ALS/PDC) is a progressive neurodegenerative disorder that is endemic to the Kii peninsula of Japan. The disorder is clinically characterized by a variable combination of parkinsonism, dementia, and motor neuron symptoms. Despite extensive investigations, the etiology and pathogenesis of ALS/PDC remain unclear. At the neuropathological level, Kii ALS/PDC is characterized by neuronal loss and tau-dominant polyproteinopathy. Here, we report the accumulation of several proteins involved in protein homeostasis pathways, that is, the ubiquitin-proteasome system and the autophagy-lysosome pathway, in postmortem brain tissue from a number of Kii ALS/PDC cases (n = 4). Of particular interest is the presence of a mutant ubiquitin protein (UBB+1), which is indicative of disrupted ubiquitin homeostasis. The findings suggest that abnormal protein aggregation is linked to impaired protein homeostasis pathways in Kii ALS/PDC.
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Affiliation(s)
- Bert M Verheijen
- From the Departments of Translational Neuroscience and Neurology, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Satoru Morimoto
- Department of Oncologic Pathology, Mie University, Graduate School of Medicine
| | - Ryogen Sasaki
- Department of Neurology, Kuwana City Medical Center, Mie
| | - Kiyomitsu Oyanagi
- Division of Neuropathology, Department of Brain Disease Research, Shinshu University School of Medicine, Matsumoto, Nagano
| | - Yasumasa Kokubo
- Kii ALS/PDC Research Center, Mie University Graduate School of Regional Innovation Studies
| | - Shigeki Kuzuhara
- Neurology and Medicine, School of Nursing, Suzuka University of Medical Science, Mie, Japan
| | - Fred W van Leeuwen
- Department of Neuroscience, Maastricht University, Maastricht, The Netherlands
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6
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Braun RJ, Büttner S. Editorial: Modeling Neurodegeneration in Yeast. Front Mol Neurosci 2021; 14:645190. [PMID: 33732109 PMCID: PMC7957005 DOI: 10.3389/fnmol.2021.645190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 02/05/2021] [Indexed: 11/13/2022] Open
Affiliation(s)
- Ralf J Braun
- Research Division for Neurodegenerative Diseases, Center of Biosciences, Danube Private University, Krems an der Donau, Austria
| | - Sabrina Büttner
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden.,Institute of Molecular Biosciences, University of Graz, Graz, Austria
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7
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Escobar-Henriques M, Anton V. Mitochondrial Surveillance by Cdc48/p97: MAD vs. Membrane Fusion. Int J Mol Sci 2020; 21:E6841. [PMID: 32961852 PMCID: PMC7555132 DOI: 10.3390/ijms21186841] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Revised: 09/07/2020] [Accepted: 09/08/2020] [Indexed: 11/16/2022] Open
Abstract
Cdc48/p97 is a ring-shaped, ATP-driven hexameric motor, essential for cellular viability. It specifically unfolds and extracts ubiquitylated proteins from membranes or protein complexes, mostly targeting them for proteolytic degradation by the proteasome. Cdc48/p97 is involved in a multitude of cellular processes, reaching from cell cycle regulation to signal transduction, also participating in growth or death decisions. The role of Cdc48/p97 in endoplasmic reticulum-associated degradation (ERAD), where it extracts proteins targeted for degradation from the ER membrane, has been extensively described. Here, we present the roles of Cdc48/p97 in mitochondrial regulation. We discuss mitochondrial quality control surveillance by Cdc48/p97 in mitochondrial-associated degradation (MAD), highlighting the potential pathologic significance thereof. Furthermore, we present the current knowledge of how Cdc48/p97 regulates mitofusin activity in outer membrane fusion and how this may impact on neurodegeneration.
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Affiliation(s)
- Mafalda Escobar-Henriques
- Institute for Genetics, Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Center for Molecular Medicine Cologne (CMMC), University of Cologne, Joseph-Stelzmann-Straße 26, 50931 Cologne, Germany;
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8
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Verheijen BM, Lussier C, Müller-Hübers C, Garruto RM, Oyanagi K, Braun RJ, van Leeuwen FW. Activation of the Unfolded Protein Response and Proteostasis Disturbance in Parkinsonism-Dementia of Guam. J Neuropathol Exp Neurol 2020; 79:34-45. [PMID: 31750913 DOI: 10.1093/jnen/nlz110] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 09/15/2019] [Accepted: 10/14/2019] [Indexed: 12/14/2022] Open
Abstract
Guam parkinsonism-dementia (G-PD) is a progressive and fatal neurodegenerative disorder among the native inhabitants of the Mariana Islands that manifests clinically with parkinsonism as well as dementia. Neuropathologically, G-PD is characterized by abundant neurofibrillary tangles composed of hyperphosphorylated tau, marked deposition of transactive response DNA-binding protein 43 kDa (TDP-43), and neuronal loss. The mechanisms that underlie neurodegeneration in G-PD are poorly understood. Here, we report that the unfolded protein response (UPR) is activated in G-PD brains. Specifically, we show that the endoplasmic reticulum (ER) chaperone binding immunoglobulin protein/glucose-regulated protein 78 kDa and phosphorylated (activated) ER stress sensor protein kinase RNA-like ER kinase accumulate in G-PD brains. Furthermore, proteinaceous aggregates in G-PD brains are found to contain several proteins related to the ubiquitin-proteasome system (UPS) and the autophagy pathway, two major mechanisms for intracellular protein degradation. In particular, a mutant ubiquitin (UBB+1), whose presence is a marker for UPS dysfunction, is shown to accumulate in G-PD brains. We demonstrate that UBB+1 is a potent modifier of TDP-43 aggregation and cytotoxicity in vitro. Overall, these data suggest that UPR activation and intracellular proteolytic pathways are intimately connected with the accumulation of aggregated proteins in G-PD.
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Affiliation(s)
- Bert M Verheijen
- Department of Translational Neuroscience (BMV); Department of Neurology and Neurosurgery, University Medical Center Utrecht Brain Center, Utrecht University (BMV), Utrecht, The Netherlands; Institute of Cell Biology, University of Bayreuth, Bayreuth, Germany (CL, CM-H, RJB); Department of Anthropology (RMG); Department of Biological Sciences, Binghamton University, State University of New York (RMG), Binghamton, New York; Division of Neuropathology, Department of Brain Disease Research, Shinshu University School of Medicine, Matsumoto, Nagano, Japan (KO); Brain Research Laboratory, Hatsuishi Hospital, Kashiwa, Chiba, Japan (KO); Faculty of Medicine/Dental Medicine, Danube Private University, Krems an der Donau, Austria (RJB); and Department of Neuroscience, Faculty of Health, Medicine and Life Sciences, Maastricht University, Maastricht, The Netherlands (FWvL)
| | - Celina Lussier
- Department of Translational Neuroscience (BMV); Department of Neurology and Neurosurgery, University Medical Center Utrecht Brain Center, Utrecht University (BMV), Utrecht, The Netherlands; Institute of Cell Biology, University of Bayreuth, Bayreuth, Germany (CL, CM-H, RJB); Department of Anthropology (RMG); Department of Biological Sciences, Binghamton University, State University of New York (RMG), Binghamton, New York; Division of Neuropathology, Department of Brain Disease Research, Shinshu University School of Medicine, Matsumoto, Nagano, Japan (KO); Brain Research Laboratory, Hatsuishi Hospital, Kashiwa, Chiba, Japan (KO); Faculty of Medicine/Dental Medicine, Danube Private University, Krems an der Donau, Austria (RJB); and Department of Neuroscience, Faculty of Health, Medicine and Life Sciences, Maastricht University, Maastricht, The Netherlands (FWvL)
| | - Cora Müller-Hübers
- Department of Translational Neuroscience (BMV); Department of Neurology and Neurosurgery, University Medical Center Utrecht Brain Center, Utrecht University (BMV), Utrecht, The Netherlands; Institute of Cell Biology, University of Bayreuth, Bayreuth, Germany (CL, CM-H, RJB); Department of Anthropology (RMG); Department of Biological Sciences, Binghamton University, State University of New York (RMG), Binghamton, New York; Division of Neuropathology, Department of Brain Disease Research, Shinshu University School of Medicine, Matsumoto, Nagano, Japan (KO); Brain Research Laboratory, Hatsuishi Hospital, Kashiwa, Chiba, Japan (KO); Faculty of Medicine/Dental Medicine, Danube Private University, Krems an der Donau, Austria (RJB); and Department of Neuroscience, Faculty of Health, Medicine and Life Sciences, Maastricht University, Maastricht, The Netherlands (FWvL)
| | - Ralph M Garruto
- Department of Translational Neuroscience (BMV); Department of Neurology and Neurosurgery, University Medical Center Utrecht Brain Center, Utrecht University (BMV), Utrecht, The Netherlands; Institute of Cell Biology, University of Bayreuth, Bayreuth, Germany (CL, CM-H, RJB); Department of Anthropology (RMG); Department of Biological Sciences, Binghamton University, State University of New York (RMG), Binghamton, New York; Division of Neuropathology, Department of Brain Disease Research, Shinshu University School of Medicine, Matsumoto, Nagano, Japan (KO); Brain Research Laboratory, Hatsuishi Hospital, Kashiwa, Chiba, Japan (KO); Faculty of Medicine/Dental Medicine, Danube Private University, Krems an der Donau, Austria (RJB); and Department of Neuroscience, Faculty of Health, Medicine and Life Sciences, Maastricht University, Maastricht, The Netherlands (FWvL)
| | - Kiyomitsu Oyanagi
- Department of Translational Neuroscience (BMV); Department of Neurology and Neurosurgery, University Medical Center Utrecht Brain Center, Utrecht University (BMV), Utrecht, The Netherlands; Institute of Cell Biology, University of Bayreuth, Bayreuth, Germany (CL, CM-H, RJB); Department of Anthropology (RMG); Department of Biological Sciences, Binghamton University, State University of New York (RMG), Binghamton, New York; Division of Neuropathology, Department of Brain Disease Research, Shinshu University School of Medicine, Matsumoto, Nagano, Japan (KO); Brain Research Laboratory, Hatsuishi Hospital, Kashiwa, Chiba, Japan (KO); Faculty of Medicine/Dental Medicine, Danube Private University, Krems an der Donau, Austria (RJB); and Department of Neuroscience, Faculty of Health, Medicine and Life Sciences, Maastricht University, Maastricht, The Netherlands (FWvL)
| | - Ralf J Braun
- Department of Translational Neuroscience (BMV); Department of Neurology and Neurosurgery, University Medical Center Utrecht Brain Center, Utrecht University (BMV), Utrecht, The Netherlands; Institute of Cell Biology, University of Bayreuth, Bayreuth, Germany (CL, CM-H, RJB); Department of Anthropology (RMG); Department of Biological Sciences, Binghamton University, State University of New York (RMG), Binghamton, New York; Division of Neuropathology, Department of Brain Disease Research, Shinshu University School of Medicine, Matsumoto, Nagano, Japan (KO); Brain Research Laboratory, Hatsuishi Hospital, Kashiwa, Chiba, Japan (KO); Faculty of Medicine/Dental Medicine, Danube Private University, Krems an der Donau, Austria (RJB); and Department of Neuroscience, Faculty of Health, Medicine and Life Sciences, Maastricht University, Maastricht, The Netherlands (FWvL)
| | - Fred W van Leeuwen
- Department of Translational Neuroscience (BMV); Department of Neurology and Neurosurgery, University Medical Center Utrecht Brain Center, Utrecht University (BMV), Utrecht, The Netherlands; Institute of Cell Biology, University of Bayreuth, Bayreuth, Germany (CL, CM-H, RJB); Department of Anthropology (RMG); Department of Biological Sciences, Binghamton University, State University of New York (RMG), Binghamton, New York; Division of Neuropathology, Department of Brain Disease Research, Shinshu University School of Medicine, Matsumoto, Nagano, Japan (KO); Brain Research Laboratory, Hatsuishi Hospital, Kashiwa, Chiba, Japan (KO); Faculty of Medicine/Dental Medicine, Danube Private University, Krems an der Donau, Austria (RJB); and Department of Neuroscience, Faculty of Health, Medicine and Life Sciences, Maastricht University, Maastricht, The Netherlands (FWvL)
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9
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Yuen SC, Zhu H, Leung SW. A Systematic Bioinformatics Workflow With Meta-Analytics Identified Potential Pathogenic Factors of Alzheimer's Disease. Front Neurosci 2020; 14:209. [PMID: 32231518 PMCID: PMC7083177 DOI: 10.3389/fnins.2020.00209] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 02/25/2020] [Indexed: 12/17/2022] Open
Abstract
Potential pathogenic factors, other than well-known APP, APOE4, and PSEN, can be further identified from transcriptomics studies of differentially expressed genes (DEGs) that are specific for Alzheimer’s disease (AD), but findings are often inconsistent or even contradictory. Evidence corroboration by combining meta-analysis and bioinformatics methods may help to resolve existing inconsistencies and contradictions. This study aimed to demonstrate a systematic workflow for evidence synthesis of transcriptomic studies using both meta-analysis and bioinformatics methods to identify potential pathogenic factors. Transcriptomic data were assessed from GEO and ArrayExpress after systematic searches. The DEGs and their dysregulation states from both DNA microarray and RNA sequencing datasets were analyzed and corroborated by meta-analysis. Statistically significant DEGs were used for enrichment analysis based on KEGG and protein–protein interaction network (PPIN) analysis based on STRING. AD-specific modules were further determined by the DIAMOnD algorithm, which identifies significant connectivity patterns between specific disease-associated proteins and non-specific proteins. Within AD-specific modules, the nodes of highest degrees (>95th percentile) were considered as potential pathogenic factors. After systematic searches of 225 datasets, extensive meta-analyses among 25 datasets (21 DNA microarray datasets and 4 RNA sequencing datasets) identified 9,298 DEGs. The dysregulated genes and pathways in AD were associated with impaired amyloid-β (Aβ) clearance. From the AD-specific module, Fyn, and EGFR were the most statistically significant and biologically relevant. This meta-analytical study suggested that the reduced Aβ clearance in AD pathogenesis was associated with the genes encoding Fyn and EGFR, which were key receptors in Aβ downstream signaling.
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Affiliation(s)
- Sze Chung Yuen
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, China
| | - Hongmei Zhu
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, China
| | - Siu-Wai Leung
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, China.,School of Informatics, College of Science and Engineering, University of Edinburgh, Edinburgh, United Kingdom
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10
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Abstract
Alzheimer's disease (AD) is the most common form of dementia, most prevalent in the elderly population and has a significant impact on individuals and their family as well as the health care system and the economy. While the number of patients affected by various forms of dementia including AD is on the increase, there is currently no cure. Although genome-wide association studies have identified genetic markers for familial AD, the molecular mechanisms underlying the initiation and development of both familial and sporadic AD remain poorly understood. Most neurodegenerative diseases and in particular those associated with dementia have been defined as proteinopathies due to the presence of intra- and/or extracellular protein aggregates in the brain of affected individuals. Although loss of proteostasis in AD has been known for decades, it is only in recent years that we have come to appreciate the role of ubiquitin-dependent mechanisms in brain homeostasis and in brain diseases. Ubiquitin is a highly versatile post-translational modification which regulates many aspects of protein fate and function, including protein degradation by the Ubiquitin-Proteasome System (UPS), autophagy-mediated removal of damaged organelles and proteins, lysosomal turnover of membrane proteins and of extracellular molecules brought inside the cell through endocytosis. Amyloid-β (Aβ) fragments as well as hyperphosphorylation of Tau are hallmarks of AD, and these are found in extracellular plaques and intracellular fibrils in the brain of individuals with AD, respectively. Yet, whether it is the oligomeric or the soluble species of Aβ and Tau that mediate toxicity is still unclear. These proteins impact on mitochondrial energy metabolism, inflammation, as well as a number of housekeeping processes including protein degradation through the UPS and autophagy. In this chapter, we will discuss the role of ubiquitin in neuronal homeostasis as well as in AD; summarise crosstalks between the enzymes that regulate protein ubiquitination and the toxic proteins Tau and Aβ; highlight emerging molecular mechanisms in AD as well as future strategies which aim to exploit the ubiquitin system as a source for next-generation therapeutics.
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11
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Sampaio-Marques B, Ludovico P. Linking cellular proteostasis to yeast longevity. FEMS Yeast Res 2019; 18:4970764. [PMID: 29800380 DOI: 10.1093/femsyr/foy043] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 04/12/2018] [Indexed: 12/19/2022] Open
Abstract
Proteostasis is a cellular housekeeping process that refers to the healthy maintenance of the cellular proteome that governs the fate of proteins from synthesis to degradation. Perturbations of proteostasis might result in protein dysfunction with consequent deleterious effects that can culminate in cell death. To deal with the loss of proteostasis, cells are supplied with a highly sophisticated and interconnected network that integrates as major players the molecular chaperones and the protein degradation pathways. It is well recognized that the ability of cells to maintain proteostasis declines during ageing, although the precise mechanisms are still elusive. Indeed, genetic or pharmacological enhancement of the proteostasis network has been shown to extend lifespan in a variety of ageing models. Therefore, an improved understanding of the interventions/mechanisms that contribute to cellular protein quality control will have a huge impact on the ageing field. This mini-review centers on the current knowledge about the major pathways that contribute for the maintenance of Saccharomyces cerevisiae proteostasis, with particular emphasis on the developments that highlight the multidimensional nature of the proteostasis network in the maintenance of proteostasis, as well as the age-dependent changes on this network.
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Affiliation(s)
- Belém Sampaio-Marques
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus Gualtar, 4710-057 Braga, Portugal.,ICVS/3B's-PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Paula Ludovico
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus Gualtar, 4710-057 Braga, Portugal.,ICVS/3B's-PT Government Associate Laboratory, Braga/Guimarães, Portugal
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12
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Shin TH, Seo C, Lee DY, Ji M, Manavalan B, Basith S, Chakkarapani SK, Kang SH, Lee G, Paik MJ, Park CB. Silica-coated magnetic nanoparticles induce glucose metabolic dysfunction in vitro via the generation of reactive oxygen species. Arch Toxicol 2019; 93:1201-1212. [DOI: 10.1007/s00204-019-02402-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 01/31/2019] [Indexed: 12/31/2022]
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13
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Verheijen BM, Stevens JAA, Gentier RJG, van 't Hekke CD, van den Hove DLA, Hermes DJHP, Steinbusch HWM, Ruijter JM, Grimm MOW, Haupenthal VJ, Annaert W, Hartmann T, van Leeuwen FW. Paradoxical effects of mutant ubiquitin on Aβ plaque formation in an Alzheimer mouse model. Neurobiol Aging 2018; 72:62-71. [PMID: 30216939 DOI: 10.1016/j.neurobiolaging.2018.08.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 07/03/2018] [Accepted: 08/10/2018] [Indexed: 01/08/2023]
Abstract
Amyloid-β (Aβ) plaques are a prominent pathological hallmark of Alzheimer's disease (AD). They consist of aggregated Aβ peptides, which are generated through sequential proteolytic processing of the transmembrane protein amyloid precursor protein (APP) and several Aβ-associated factors. Efficient clearance of Aβ from the brain is thought to be important to prevent the development and progression of AD. The ubiquitin-proteasome system (UPS) is one of the major pathways for protein breakdown in cells and it has been suggested that impaired UPS-mediated removal of protein aggregates could play an important role in the pathogenesis of AD. To study the effects of an impaired UPS on Aβ pathology in vivo, transgenic APPSwe/PS1ΔE9 mice (APPPS1) were crossed with transgenic mice expressing mutant ubiquitin (UBB+1), a protein-based inhibitor of the UPS. Surprisingly, the APPPS1/UBB+1 crossbreed showed a remarkable decrease in Aβ plaque load during aging. Further analysis showed that UBB+1 expression transiently restored PS1-NTF expression and γ-secretase activity in APPPS1 mice. Concurrently, UBB+1 decreased levels of β-APP-CTF, which is a γ-secretase substrate. Although UBB+1 reduced Aβ pathology in APPPS1 mice, it did not improve the behavioral deficits in these animals.
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Affiliation(s)
- Bert M Verheijen
- Department of Psychiatry and Neuropsychology, Faculty of Health Medicine and Life Sciences, Maastricht University, Maastricht, The Netherlands
| | - Jo A A Stevens
- Department of Psychiatry and Neuropsychology, Faculty of Health Medicine and Life Sciences, Maastricht University, Maastricht, The Netherlands
| | - Romina J G Gentier
- Department of Psychiatry and Neuropsychology, Faculty of Health Medicine and Life Sciences, Maastricht University, Maastricht, The Netherlands
| | - Christian D van 't Hekke
- Department of Psychiatry and Neuropsychology, Faculty of Health Medicine and Life Sciences, Maastricht University, Maastricht, The Netherlands
| | - Daniel L A van den Hove
- Department of Psychiatry and Neuropsychology, Faculty of Health Medicine and Life Sciences, Maastricht University, Maastricht, The Netherlands; Department of Psychiatry, Psychosomatics and Psychotherapy, University of Würzburg, Würzburg, Germany
| | - Denise J H P Hermes
- Department of Psychiatry and Neuropsychology, Faculty of Health Medicine and Life Sciences, Maastricht University, Maastricht, The Netherlands
| | - Harry W M Steinbusch
- Department of Psychiatry and Neuropsychology, Faculty of Health Medicine and Life Sciences, Maastricht University, Maastricht, The Netherlands
| | - Jan M Ruijter
- Department of Medical Biology, Academic Medical Center, Amsterdam, The Netherlands
| | - Marcus O W Grimm
- Deutsches Institut für Demenzprävention, University of Saarland, Experimental Neurology, Homburg, Germany
| | - Viola J Haupenthal
- Deutsches Institut für Demenzprävention, University of Saarland, Experimental Neurology, Homburg, Germany
| | - Wim Annaert
- VIB Center for Brain and Disease Research and KU Leuven, Gasthuisberg, Belgium
| | - Tobias Hartmann
- Deutsches Institut für Demenzprävention, University of Saarland, Experimental Neurology, Homburg, Germany
| | - Fred W van Leeuwen
- Department of Psychiatry and Neuropsychology, Faculty of Health Medicine and Life Sciences, Maastricht University, Maastricht, The Netherlands.
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14
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Seynnaeve D, Vecchio MD, Fruhmann G, Verelst J, Cools M, Beckers J, Mulvihill DP, Winderickx J, Franssens V. Recent Insights on Alzheimer's Disease Originating from Yeast Models. Int J Mol Sci 2018; 19:E1947. [PMID: 29970827 PMCID: PMC6073265 DOI: 10.3390/ijms19071947] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 06/29/2018] [Accepted: 06/30/2018] [Indexed: 01/28/2023] Open
Abstract
In this review article, yeast model-based research advances regarding the role of Amyloid-β (Aβ), Tau and frameshift Ubiquitin UBB+1 in Alzheimer’s disease (AD) are discussed. Despite having limitations with regard to intercellular and cognitive AD aspects, these models have clearly shown their added value as complementary models for the study of the molecular aspects of these proteins, including their interplay with AD-related cellular processes such as mitochondrial dysfunction and altered proteostasis. Moreover, these yeast models have also shown their importance in translational research, e.g., in compound screenings and for AD diagnostics development. In addition to well-established Saccharomyces cerevisiae models, new upcoming Schizosaccharomyces pombe, Candida glabrata and Kluyveromyces lactis yeast models for Aβ and Tau are briefly described. Finally, traditional and more innovative research methodologies, e.g., for studying protein oligomerization/aggregation, are highlighted.
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Affiliation(s)
- David Seynnaeve
- Functional Biology, KU Leuven, Kasteelpark Arenberg 31, 3000 Leuven, Belgium.
| | - Mara Del Vecchio
- Functional Biology, KU Leuven, Kasteelpark Arenberg 31, 3000 Leuven, Belgium.
| | - Gernot Fruhmann
- Functional Biology, KU Leuven, Kasteelpark Arenberg 31, 3000 Leuven, Belgium.
| | - Joke Verelst
- Functional Biology, KU Leuven, Kasteelpark Arenberg 31, 3000 Leuven, Belgium.
| | - Melody Cools
- Functional Biology, KU Leuven, Kasteelpark Arenberg 31, 3000 Leuven, Belgium.
| | - Jimmy Beckers
- Functional Biology, KU Leuven, Kasteelpark Arenberg 31, 3000 Leuven, Belgium.
| | - Daniel P Mulvihill
- School of Biosciences, University of Kent, Canterbury CT2 7NJ, Kent, UK.
| | - Joris Winderickx
- Functional Biology, KU Leuven, Kasteelpark Arenberg 31, 3000 Leuven, Belgium.
| | - Vanessa Franssens
- Functional Biology, KU Leuven, Kasteelpark Arenberg 31, 3000 Leuven, Belgium.
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15
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Muñoz-Arellano AJ, Chen X, Molt A, Meza E, Petranovic D. Different Expression Levels of Human Mutant Ubiquitin B +1 (UBB +1) Can Modify Chronological Lifespan or Stress Resistance of Saccharomyces cerevisiae. Front Mol Neurosci 2018; 11:200. [PMID: 29950972 PMCID: PMC6008557 DOI: 10.3389/fnmol.2018.00200] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 05/18/2018] [Indexed: 11/13/2022] Open
Abstract
The ubiquitin-proteasome system (UPS) is the main pathway responsible for the degradation of misfolded proteins, and its dysregulation has been implicated in several neurodegenerative diseases, including Alzheimer's disease (AD). UBB+1, a mutant variant of ubiquitin B, was found to accumulate in neurons of AD patients and it has been linked to UPS dysfunction and neuronal death. Using the yeast Saccharomyces cerevisiae as a model system, we constitutively expressed UBB+1 to evaluate its effects on proteasome function and cell death, particularly under conditions of chronological aging. We showed that the expression of UBB+1 caused inhibition of the three proteasomal proteolytic activities (caspase-like (β1), trypsin-like (β2) and chymotrypsin-like (β5) activities) in yeast. Interestingly, this inhibition did not alter cell viability of growing cells. Moreover, we showed that cells expressing UBB+1 at lower level displayed an increased capacity to degrade induced misfolded proteins. When we evaluated cells during chronological aging, UBB+1 expression at lower level, prevented cells to accumulate reactive oxygen species (ROS) and avert apoptosis, dramatically increasing yeast life span. Since proteasome inhibition by UBB+1 has previously been shown to induce chaperone expression and thus protect against stress, we evaluated our UBB+1 model under heat shock and oxidative stress. Higher expression of UBB+1 caused thermotolerance in yeast due to induction of chaperones, which occurred to a lesser extent at lower expression level of UBB+1 (where we observed the phenotype of extended life span). Altering UPS capacity by differential expression of UBB+1 protects cells against several stresses during chronological aging. This system can be valuable to study the effects of UBB+1 on misfolded proteins involved in neurodegeneration and aging.
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Affiliation(s)
- Ana Joyce Muñoz-Arellano
- Division of Systems and Synthetic Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Xin Chen
- Division of Systems and Synthetic Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden.,Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, Gothenburg, Sweden
| | - Andrea Molt
- Division of Systems and Synthetic Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Eugenio Meza
- Division of Systems and Synthetic Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Dina Petranovic
- Division of Systems and Synthetic Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden.,Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, Gothenburg, Sweden
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16
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Verheijen BM, Oyanagi K, van Leeuwen FW. Dysfunction of Protein Quality Control in Parkinsonism-Dementia Complex of Guam. Front Neurol 2018; 9:173. [PMID: 29615966 PMCID: PMC5869191 DOI: 10.3389/fneur.2018.00173] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2017] [Accepted: 03/06/2018] [Indexed: 12/12/2022] Open
Abstract
Guam parkinsonism–dementia complex (G-PDC) is an enigmatic neurodegenerative disease that is endemic to the Pacific island of Guam. G-PDC patients are clinically characterized by progressive cognitive impairment and parkinsonism. Neuropathologically, G-PDC is characterized by abundant neurofibrillary tangles, which are composed of hyperphosphorylated tau, marked deposition of 43-kDa TAR DNA-binding protein, and neuronal loss. Although both genetic and environmental factors have been implicated, the etiology and pathogenesis of G-PDC remain unknown. Recent neuropathological studies have provided new clues about the pathomechanisms involved in G-PDC. For example, deposition of abnormal components of the protein quality control system in brains of G-PDC patients indicates a role for proteostasis imbalance in the disease. This opens up promising avenues for new research on G-PDC and could have important implications for the study of other neurodegenerative disorders.
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Affiliation(s)
- Bert M Verheijen
- Department of Translational Neuroscience, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands.,Department of Neurology and Neurosurgery, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Kiyomitsu Oyanagi
- Division of Neuropathology, Department of Brain Disease Research, Shinshu University School of Medicine, Nagano, Japan.,Brain Research Laboratory, Hatsuishi Hospital, Chiba, Japan
| | - Fred W van Leeuwen
- Department of Neuroscience, Faculty of Health, Medicine and Life Sciences, Maastricht University, Maastricht, Netherlands
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17
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Dumit VI, Zerbes RM, Kaeser-Pebernard S, Rackiewicz M, Wall MT, Gretzmeier C, Küttner V, van der Laan M, Braun RJ, Dengjel J. Respiratory status determines the effect of emodin on cell viability. Oncotarget 2018; 8:37478-37490. [PMID: 28415582 PMCID: PMC5514923 DOI: 10.18632/oncotarget.16396] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Accepted: 03/01/2017] [Indexed: 12/20/2022] Open
Abstract
The anthraquinone emodin has been shown to have antineoplastic properties and a wealth of unconnected effects have been linked to its use, most of which are likely secondary outcomes of the drug treatment. The primary activity of emodin on cells has remained unknown. In the present study we demonstrate dramatic and extensive effects of emodin on the redox state of cells and on mitochondrial homeostasis, irrespectively of the cell type and organism, ranging from the yeast Saccharomyces cerevisiae to human cell lines and primary cells. Emodin binds to redox-active enzymes and its effectiveness depends on the oxidative and respiratory status of cells. We show that cells with efficient respiratory metabolism are less susceptible to emodin, whereas cells under glycolytic metabolism are more vulnerable to the compound. Our findings indicate that emodin acts in a similar way as known uncouplers of the mitochondrial electron transport chain and causes oxidative stress that particularly disturbs cancer cells.
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Affiliation(s)
- Verónica I Dumit
- Freiburg Institute for Advanced Studies (FRIAS), University of Freiburg, Freiburg, Germany.,Center for Biological Systems Analysis (ZBSA), Freiburg, Germany.,Department of Dermatology, Medical Center, University of Freiburg, Freiburg, Germany.,Core Facility Proteomics, ZBSA, University of Freiburg, Freiburg, Germany
| | - Ralf M Zerbes
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, Freiburg, Germany.,Faculty of Biology, University of Freiburg, Freiburg, Germany
| | | | - Michal Rackiewicz
- Center for Biological Systems Analysis (ZBSA), Freiburg, Germany.,Department of Dermatology, Medical Center, University of Freiburg, Freiburg, Germany.,Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Mona T Wall
- Freiburg Institute for Advanced Studies (FRIAS), University of Freiburg, Freiburg, Germany.,Center for Biological Systems Analysis (ZBSA), Freiburg, Germany
| | - Christine Gretzmeier
- Center for Biological Systems Analysis (ZBSA), Freiburg, Germany.,Department of Dermatology, Medical Center, University of Freiburg, Freiburg, Germany
| | - Victoria Küttner
- Center for Biological Systems Analysis (ZBSA), Freiburg, Germany.,Department of Dermatology, Medical Center, University of Freiburg, Freiburg, Germany
| | - Martin van der Laan
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, Freiburg, Germany.,BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg, Germany.,Medical Biochemistry and Molecular Biology, Center for Molecular Signaling, PZMS, Saarland University, Homburg, Germany
| | - Ralf J Braun
- Institute of Cell Biology, University of Bayreuth, Bayreuth, Germany
| | - Jörn Dengjel
- Freiburg Institute for Advanced Studies (FRIAS), University of Freiburg, Freiburg, Germany.,Center for Biological Systems Analysis (ZBSA), Freiburg, Germany.,Department of Dermatology, Medical Center, University of Freiburg, Freiburg, Germany.,BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg, Germany.,Department of Biology, University of Fribourg, Fribourg, Switzerland
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18
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Biczo G, Vegh ET, Shalbueva N, Mareninova OA, Elperin J, Lotshaw E, Gretler S, Lugea A, Malla SR, Dawson D, Ruchala P, Whitelegge J, French SW, Wen L, Husain SZ, Gorelick FS, Hegyi P, Rakonczay Z, Gukovsky I, Gukovskaya AS. Mitochondrial Dysfunction, Through Impaired Autophagy, Leads to Endoplasmic Reticulum Stress, Deregulated Lipid Metabolism, and Pancreatitis in Animal Models. Gastroenterology 2018; 154:689-703. [PMID: 29074451 PMCID: PMC6369139 DOI: 10.1053/j.gastro.2017.10.012] [Citation(s) in RCA: 226] [Impact Index Per Article: 37.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Revised: 10/04/2017] [Accepted: 10/16/2017] [Indexed: 12/14/2022]
Abstract
BACKGROUND & AIMS Little is known about the signaling pathways that initiate and promote acute pancreatitis (AP). The pathogenesis of AP has been associated with abnormal increases in cytosolic Ca2+, mitochondrial dysfunction, impaired autophagy, and endoplasmic reticulum (ER) stress. We analyzed the mechanisms of these dysfunctions and their relationships, and how these contribute to development of AP in mice and rats. METHODS Pancreatitis was induced in C57BL/6J mice (control) and mice deficient in peptidylprolyl isomerase D (cyclophilin D, encoded by Ppid) by administration of L-arginine (also in rats), caerulein, bile acid, or an AP-inducing diet. Parameters of pancreatitis, mitochondrial function, autophagy, ER stress, and lipid metabolism were measured in pancreatic tissue, acinar cells, and isolated mitochondria. Some mice with AP were given trehalose to enhance autophagic efficiency. Human pancreatitis tissues were analyzed by immunofluorescence. RESULTS Mitochondrial dysfunction in pancreas of mice with AP was induced by either mitochondrial Ca2+ overload or through a Ca2+ overload-independent pathway that involved reduced activity of ATP synthase (80% inhibition in pancreatic mitochondria isolated from rats or mice given L-arginine). Both pathways were mediated by cyclophilin D and led to mitochondrial depolarization and fragmentation. Mitochondrial dysfunction caused pancreatic ER stress, impaired autophagy, and deregulation of lipid metabolism. These pathologic responses were abrogated in cyclophilin D-knockout mice. Administration of trehalose largely prevented trypsinogen activation, necrosis, and other parameters of pancreatic injury in mice with L-arginine AP. Tissues from patients with pancreatitis had markers of mitochondrial damage and impaired autophagy, compared with normal pancreas. CONCLUSIONS In different animal models, we find a central role for mitochondrial dysfunction, and for impaired autophagy as its principal downstream effector, in development of AP. In particular, the pathway involving enhanced interaction of cyclophilin D with ATP synthase mediates L-arginine-induced pancreatitis, a model of severe AP the pathogenesis of which has remained unknown. Strategies to restore mitochondrial and/or autophagic function might be developed for treatment of AP.
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Affiliation(s)
- Gyorgy Biczo
- David Geffen School of Medicine, University of California at Los Angeles, California
- VA Greater Los Angeles Healthcare System, Los Angeles, California
- First Department of Medicine, University of Szeged, Szeged, Hungary
- Department of Pathophysiology, University of Szeged, Szeged, Hungary
| | - Eszter T. Vegh
- David Geffen School of Medicine, University of California at Los Angeles, California
- VA Greater Los Angeles Healthcare System, Los Angeles, California
- First Department of Medicine, University of Szeged, Szeged, Hungary
- Department of Pathophysiology, University of Szeged, Szeged, Hungary
| | - Natalia Shalbueva
- David Geffen School of Medicine, University of California at Los Angeles, California
- VA Greater Los Angeles Healthcare System, Los Angeles, California
| | - Olga A. Mareninova
- David Geffen School of Medicine, University of California at Los Angeles, California
- VA Greater Los Angeles Healthcare System, Los Angeles, California
| | - Jason Elperin
- David Geffen School of Medicine, University of California at Los Angeles, California
- VA Greater Los Angeles Healthcare System, Los Angeles, California
| | - Ethan Lotshaw
- David Geffen School of Medicine, University of California at Los Angeles, California
- VA Greater Los Angeles Healthcare System, Los Angeles, California
| | - Sophie Gretler
- David Geffen School of Medicine, University of California at Los Angeles, California
- VA Greater Los Angeles Healthcare System, Los Angeles, California
| | - Aurelia Lugea
- Cedars-Sinai Medical Center, Los Angeles, California
| | - Sudarshan R. Malla
- David Geffen School of Medicine, University of California at Los Angeles, California
- VA Greater Los Angeles Healthcare System, Los Angeles, California
| | - David Dawson
- David Geffen School of Medicine, University of California at Los Angeles, California
| | - Piotr Ruchala
- David Geffen School of Medicine, University of California at Los Angeles, California
| | - Julian Whitelegge
- David Geffen School of Medicine, University of California at Los Angeles, California
| | | | - Li Wen
- Department of Pediatric GI, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Sohail Z. Husain
- Department of Pediatric GI, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | | | - Peter Hegyi
- Institute for Translational Medicine and First Department of Medicine, University of Pecs, Pecs, Hungary
- Translational Gastroenterology Research Group, University of Szeged, Szeged, Hungary
| | - Zoltan Rakonczay
- First Department of Medicine, University of Szeged, Szeged, Hungary
- Department of Pathophysiology, University of Szeged, Szeged, Hungary
| | - Ilya Gukovsky
- David Geffen School of Medicine, University of California at Los Angeles, California
- VA Greater Los Angeles Healthcare System, Los Angeles, California
| | - Anna S. Gukovskaya
- David Geffen School of Medicine, University of California at Los Angeles, California
- VA Greater Los Angeles Healthcare System, Los Angeles, California
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19
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Higuchi-Sanabria R, Frankino PA, Paul JW, Tronnes SU, Dillin A. A Futile Battle? Protein Quality Control and the Stress of Aging. Dev Cell 2018; 44:139-163. [PMID: 29401418 PMCID: PMC5896312 DOI: 10.1016/j.devcel.2017.12.020] [Citation(s) in RCA: 92] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Revised: 11/30/2017] [Accepted: 12/20/2017] [Indexed: 12/15/2022]
Abstract
There exists a phenomenon in aging research whereby early life stress can have positive impacts on longevity. The mechanisms underlying these observations suggest a robust, long-lasting induction of cellular defense mechanisms. These include the various unfolded protein responses of the endoplasmic reticulum (ER), cytosol, and mitochondria. Indeed, ectopic induction of these pathways, in the absence of stress, is sufficient to increase lifespan in organisms as diverse as yeast, worms, and flies. Here, we provide an overview of the protein quality control mechanisms that operate in the cytosol, mitochondria, and ER and discuss how they affect cellular health and viability during stress and aging.
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Affiliation(s)
- Ryo Higuchi-Sanabria
- Department of Molecular and Cell Biology, Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Phillip Andrew Frankino
- Department of Molecular and Cell Biology, Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Joseph West Paul
- Department of Molecular and Cell Biology, Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Sarah Uhlein Tronnes
- Department of Molecular and Cell Biology, Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Andrew Dillin
- Department of Molecular and Cell Biology, Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA; The Glenn Center for Aging Research, University of California, Berkeley, Berkeley, CA 94720, USA.
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20
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Verheijen BM, van Leeuwen FW. Commentary: The landscape of transcription errors in eukaryotic cells. Front Genet 2017; 8:219. [PMID: 29313848 PMCID: PMC5735076 DOI: 10.3389/fgene.2017.00219] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Accepted: 12/05/2017] [Indexed: 12/18/2022] Open
Affiliation(s)
- Bert M Verheijen
- Laboratory of Experimental Neurology, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Fred W van Leeuwen
- Department of Neuroscience, Maastricht University, Maastricht, Netherlands
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21
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Gout JF, Li W, Fritsch C, Li A, Haroon S, Singh L, Hua D, Fazelinia H, Smith Z, Seeholzer S, Thomas K, Lynch M, Vermulst M. The landscape of transcription errors in eukaryotic cells. SCIENCE ADVANCES 2017; 3:e1701484. [PMID: 29062891 PMCID: PMC5650487 DOI: 10.1126/sciadv.1701484] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 09/21/2017] [Indexed: 05/09/2023]
Abstract
Accurate transcription is required for the faithful expression of genetic information. To understand the molecular mechanisms that control the fidelity of transcription, we used novel sequencing technology to provide the first comprehensive analysis of the fidelity of transcription in eukaryotic cells. Our results demonstrate that transcription errors can occur in any gene, at any location, and affect every aspect of protein structure and function. In addition, we show that multiple proteins safeguard the fidelity of transcription and provide evidence suggesting that errors that evade these layers of RNA quality control profoundly affect the physiology of living cells. Together, these observations demonstrate that there is an inherent limit to the faithful expression of the genome and suggest that the impact of mutagenesis on cellular health and fitness is substantially greater than currently appreciated.
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Affiliation(s)
| | - Weiyi Li
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Clark Fritsch
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19102, USA
- Department of Cellular and Molecular Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Annie Li
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19102, USA
| | - Suraiya Haroon
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19102, USA
| | - Larry Singh
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19102, USA
| | - Ding Hua
- Protein and Proteomics Core, Children’s Hospital of Philadelphia, Philadelphia, PA 19102, USA
| | - Hossein Fazelinia
- Protein and Proteomics Core, Children’s Hospital of Philadelphia, Philadelphia, PA 19102, USA
| | - Zach Smith
- Center for Genomics and Bioinformatics, Indiana University, Bloomington, IN 47405, USA
| | - Steven Seeholzer
- Protein and Proteomics Core, Children’s Hospital of Philadelphia, Philadelphia, PA 19102, USA
| | - Kelley Thomas
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, NH 03824, USA
| | - Michael Lynch
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
- Corresponding author. (M.V.); (M.L.)
| | - Marc Vermulst
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19102, USA
- Corresponding author. (M.V.); (M.L.)
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22
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Verheijen BM, Gentier RJG, Hermes DJHP, van Leeuwen FW, Hopkins DA. Selective Transgenic Expression of Mutant Ubiquitin in Purkinje Cell Stripes in the Cerebellum. CEREBELLUM (LONDON, ENGLAND) 2017; 16:746-750. [PMID: 27966098 PMCID: PMC5427096 DOI: 10.1007/s12311-016-0838-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The ubiquitin-proteasome system (UPS) is one of the major mechanisms for protein breakdown in cells, targeting proteins for degradation by enzymatically conjugating them to ubiquitin molecules. Intracellular accumulation of ubiquitin-B+1 (UBB+1), a frameshift mutant of ubiquitin-B, is indicative of a dysfunctional UPS and has been implicated in several disorders, including neurodegenerative disease. UBB+1-expressing transgenic mice display widespread labeling for UBB+1 in brain and exhibit behavioral deficits. Here, we show that UBB+1 is specifically expressed in a subset of parasagittal stripes of Purkinje cells in the cerebellar cortex of a UBB+1-expressing mouse model. This expression pattern is reminiscent of that of the constitutively expressed Purkinje cell antigen HSP25, a small heat shock protein with neuroprotective properties.
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Affiliation(s)
- Bert M Verheijen
- Department of Neuroscience, Faculty of Health, Medicine and Life Sciences, Maastricht University, Maastricht, The Netherlands.
- Lab of Experimental Neurology, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, The Netherlands.
| | - Romina J G Gentier
- Department of Neuroscience, Faculty of Health, Medicine and Life Sciences, Maastricht University, Maastricht, The Netherlands
| | - Denise J H P Hermes
- Department of Neuroscience, Faculty of Health, Medicine and Life Sciences, Maastricht University, Maastricht, The Netherlands
| | - Fred W van Leeuwen
- Department of Neuroscience, Faculty of Health, Medicine and Life Sciences, Maastricht University, Maastricht, The Netherlands
| | - David A Hopkins
- Department of Neuroscience, Faculty of Health, Medicine and Life Sciences, Maastricht University, Maastricht, The Netherlands
- Department of Medical Neuroscience, Dalhousie University, Halifax, Nova Scotia, Canada
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23
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Stekovic S, Ruckenstuhl C, Royer P, Winkler-Hermaden C, Carmona-Gutierrez D, Fröhlich KU, Kroemer G, Madeo F. The neuroprotective steroid progesterone promotes mitochondrial uncoupling, reduces cytosolic calcium and augments stress resistance in yeast cells. MICROBIAL CELL (GRAZ, AUSTRIA) 2017; 4:191-199. [PMID: 28660203 PMCID: PMC5473691 DOI: 10.15698/mic2017.06.577] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Accepted: 05/22/2017] [Indexed: 11/13/2022]
Abstract
The steroid hormone progesterone is not only a crucial sex hormone, but also serves as a neurosteroid, thus playing an important role in brain function. Epidemiological data suggest that progesterone improves the recovery of patients after traumatic brain injury. Brain injuries are often connected to elevated calcium spikes, reactive oxygen species (ROS) and programmed cell death affecting neurons. Here, we establish a yeast model to study progesterone-mediated cytoprotection. External supply of progesterone protected yeast cells from apoptosis-inducing stress stimuli and resulted in elevated mitochondrial oxygen uptake accompanied by a drop in ROS generation and ATP levels during chronological aging. In addition, cellular Ca2+ concentrations were reduced upon progesterone treatment, and this effect occurred independently of known Ca2+ transporters and mitochondrial respiration. All effects were also independent of Dap1, the yeast orthologue of the progesterone receptor. Altogether, our observations provide new insights into the cytoprotective effects of progesterone.
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Affiliation(s)
- Slaven Stekovic
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, 8010 Graz, Austria
| | - Christoph Ruckenstuhl
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, 8010 Graz, Austria
| | - Philipp Royer
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, 8010 Graz, Austria
| | | | | | - Kai-Uwe Fröhlich
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, 8010 Graz, Austria
| | - Guido Kroemer
- Equipe 11 labellisée par la Ligue contre le Cancer, Centre de Recherche des Cordeliers, Paris, France
- Karolinska Institute, Department of Women's and Children's Health, Karolinska University Hospital, 17176 Stockholm, Sweden
| | - Frank Madeo
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, 8010 Graz, Austria
- BioTechMed Graz, Austria
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24
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Shin TH, Lee S, Choi KR, Lee DY, Kim Y, Paik MJ, Seo C, Kang S, Jin MS, Yoo TH, Kang SH, Lee G. Quality and freshness of human bone marrow-derived mesenchymal stem cells decrease over time after trypsinization and storage in phosphate-buffered saline. Sci Rep 2017; 7:1106. [PMID: 28439086 PMCID: PMC5430841 DOI: 10.1038/s41598-017-01315-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Accepted: 03/29/2017] [Indexed: 12/31/2022] Open
Abstract
Human bone marrow-derived mesenchymal stem cells (hBM-MSCs) have been studied for their therapeutic potential. However, evaluating the quality of hBM-MSCs before transplantation remains a challenge. We addressed this issue in the present study by investigating deformation, the expression of genes related to reactive oxygen species (ROS) generation, changes in amino acid profiles, and membrane fluidity in hBM-MSCs. Deformability and cell size were decreased after storage for 6 and 12 h, respectively, in phosphate-buffered saline. Intracellular ROS levels also increased over time, which was associated with altered expression of genes related to ROS generation and amino acid metabolism. Membrane fluidity measurements revealed higher Laurdan generalized polarization values at 6 and 12 h; however, this effect was reversed by N-acetyl-l-cysteine-treatment. These findings indicate that the quality and freshness of hBM-MSCs is lost over time after dissociation from the culture dish for transplantation, highlighting the importance of using freshly trypsinized cells in clinical applications.
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Affiliation(s)
- Tae Hwan Shin
- Department of Molecular Science and Technology, Ajou University, Suwon, Republic of Korea.,Department of Physiology and Department of Biomedical Sciences, Ajou University School of Medicine, Suwon, Republic of Korea
| | - Seungah Lee
- Department of Applied Chemistry and Institute of Natural Sciences, Kyung Hee University, Yongin-si, Republic of Korea
| | - Ki Ryung Choi
- Department of Physiology and Department of Biomedical Sciences, Ajou University School of Medicine, Suwon, Republic of Korea.,Pharmicell Co., Ltd., Sungnam, Republic of Korea
| | - Da Yeon Lee
- Department of Physiology and Department of Biomedical Sciences, Ajou University School of Medicine, Suwon, Republic of Korea
| | - Yongman Kim
- Pharmicell Co., Ltd., Sungnam, Republic of Korea
| | - Man Jeong Paik
- College of Pharmacy, Sunchon National University, Suncheon, Republic of Korea
| | - Chan Seo
- College of Pharmacy, Sunchon National University, Suncheon, Republic of Korea
| | - Seok Kang
- Hanyang University School of Medicine, Seoul, Republic of Korea
| | - Moon Suk Jin
- Biological Sciences, Ajou University, Suwon, Republic of Korea
| | - Tae Hyeon Yoo
- Department of Molecular Science and Technology, Ajou University, Suwon, Republic of Korea
| | - Seong Ho Kang
- Department of Applied Chemistry and Institute of Natural Sciences, Kyung Hee University, Yongin-si, Republic of Korea.
| | - Gwang Lee
- Department of Physiology and Department of Biomedical Sciences, Ajou University School of Medicine, Suwon, Republic of Korea.
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25
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Braun RJ, Westermann B. With the Help of MOM: Mitochondrial Contributions to Cellular Quality Control. Trends Cell Biol 2017; 27:441-452. [PMID: 28291566 DOI: 10.1016/j.tcb.2017.02.007] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Revised: 02/15/2017] [Accepted: 02/16/2017] [Indexed: 11/16/2022]
Abstract
Mitochondria are essential organelles because they have key roles in cellular energy metabolism and many other metabolic pathways. Several quality control systems have evolved to ensure that dysfunctional mitochondria are either repaired or eliminated. The activities of these pathways are crucial for cellular health because they maintain functional mitochondria. In addition, the cytosolic ubiquitin-proteasome system (UPS) and the mitochondria-associated degradation pathway (MAD) share some of their core components, are functionally tightly interconnected, and mutually modulate their activities. Thus, the mitochondrial outer membrane (MOM) actively supports quality control systems in extramitochondrial compartments. Furthermore, mitochondrial quality surveillance systems also act on cytosolic or endoplasmic reticulum (ER) substrates and modulate immune responses. Therefore, mitochondria contribute to cellular quality control and homeostasis on several levels.
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Affiliation(s)
- Ralf J Braun
- Institut für Zellbiologie, Universität Bayreuth, Universitätsstraße 30, 95440 Bayreuth, Germany.
| | - Benedikt Westermann
- Institut für Zellbiologie, Universität Bayreuth, Universitätsstraße 30, 95440 Bayreuth, Germany.
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26
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Fruhmann G, Seynnaeve D, Zheng J, Ven K, Molenberghs S, Wilms T, Liu B, Winderickx J, Franssens V. Yeast buddies helping to unravel the complexity of neurodegenerative disorders. Mech Ageing Dev 2017; 161:288-305. [DOI: 10.1016/j.mad.2016.05.002] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Revised: 04/22/2016] [Accepted: 05/02/2016] [Indexed: 12/31/2022]
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27
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Carmona-Gutierrez D, Hughes AL, Madeo F, Ruckenstuhl C. The crucial impact of lysosomes in aging and longevity. Ageing Res Rev 2016; 32:2-12. [PMID: 27125853 DOI: 10.1016/j.arr.2016.04.009] [Citation(s) in RCA: 159] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Revised: 03/26/2016] [Accepted: 04/23/2016] [Indexed: 02/07/2023]
Abstract
Lysosomes are the main catabolic organelles of a cell and play a pivotal role in a plethora of cellular processes, including responses to nutrient availability and composition, stress resistance, programmed cell death, plasma membrane repair, development, and cell differentiation. In line with this pleiotropic importance for cellular and organismal life and death, lysosomal dysfunction is associated with many age-related pathologies like Parkinson's and Alzheimer's disease, as well as with a decline in lifespan. Conversely, targeting lysosomal functional capacity is emerging as a means to promote longevity. Here, we analyze the current knowledge on the prominent influence of lysosomes on aging-related processes, such as their executory and regulatory roles during general and selective macroautophagy, or their storage capacity for amino acids and ions. In addition, we review and discuss the roles of lysosomes as active players in the mechanisms underlying known lifespan-extending interventions like, for example, spermidine or rapamycin administration. In conclusion, this review aims at critically examining the nature and pliability of the different layers, in which lysosomes are involved as a control hub for aging and longevity.
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28
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Kainz K, Tadic J, Zimmermann A, Pendl T, Carmona-Gutierrez D, Ruckenstuhl C, Eisenberg T, Madeo F. Methods to Assess Autophagy and Chronological Aging in Yeast. Methods Enzymol 2016; 588:367-394. [PMID: 28237110 DOI: 10.1016/bs.mie.2016.09.086] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Autophagy is a catabolic process that is crucial for cellular homeostasis and adaptive response to changing environments. Importantly, autophagy has been shown to be induced in many longevity-associated scenarios and to be required to maintain lifespan extension. Notably, autophagy is a highly conserved cellular process among eukaryotes, and the yeast Saccharomyces cerevisiae has become a universal model system for unraveling the molecular machinery underlying autophagic mechanisms. Here, we discuss different protocols to monitor survival and autophagy of yeast cells upon chronological aging. These include the use of propidium iodide to assess the loss of cell membrane integrity, as well as clonogenic assays to directly determine survival rates. Additionally, we describe methods to quantify autophagic flux, including the alkaline phosphatase activity or the GFP liberation assays, which measure the delivery of autophagosomal cargo to the vacuole. In sum, we have recapped established protocols used to evaluate a link between lifespan extension and autophagy in yeast.
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Affiliation(s)
- K Kainz
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Graz, Austria
| | - J Tadic
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Graz, Austria
| | - A Zimmermann
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Graz, Austria
| | - T Pendl
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Graz, Austria
| | - D Carmona-Gutierrez
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Graz, Austria
| | - C Ruckenstuhl
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Graz, Austria
| | - T Eisenberg
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Graz, Austria; BioTechMed-Graz, Graz, Austria
| | - F Madeo
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Graz, Austria; BioTechMed-Graz, Graz, Austria.
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29
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Cardioprotection and lifespan extension by the natural polyamine spermidine. Nat Med 2016; 22:1428-1438. [PMID: 27841876 DOI: 10.1038/nm.4222] [Citation(s) in RCA: 738] [Impact Index Per Article: 92.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Accepted: 09/24/2016] [Indexed: 12/13/2022]
Abstract
Aging is associated with an increased risk of cardiovascular disease and death. Here we show that oral supplementation of the natural polyamine spermidine extends the lifespan of mice and exerts cardioprotective effects, reducing cardiac hypertrophy and preserving diastolic function in old mice. Spermidine feeding enhanced cardiac autophagy, mitophagy and mitochondrial respiration, and it also improved the mechano-elastical properties of cardiomyocytes in vivo, coinciding with increased titin phosphorylation and suppressed subclinical inflammation. Spermidine feeding failed to provide cardioprotection in mice that lack the autophagy-related protein Atg5 in cardiomyocytes. In Dahl salt-sensitive rats that were fed a high-salt diet, a model for hypertension-induced congestive heart failure, spermidine feeding reduced systemic blood pressure, increased titin phosphorylation and prevented cardiac hypertrophy and a decline in diastolic function, thus delaying the progression to heart failure. In humans, high levels of dietary spermidine, as assessed from food questionnaires, correlated with reduced blood pressure and a lower incidence of cardiovascular disease. Our results suggest a new and feasible strategy for protection against cardiovascular disease.
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30
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Braun RJ, Zerbes RM, Steinberg F, Gris D, Dumit VI. Threading Granules in Freiburg. 2 nd International Symposium on "One Mitochondrion, Many Diseases - Biological and Molecular Perspectives", a FRIAS Junior Researcher Conference, Freiburg im Breisgau, Germany, March 9 th/10 th, 2016. MICROBIAL CELL 2016; 3:565-568. [PMID: 28357325 PMCID: PMC5349212 DOI: 10.15698/mic2016.11.540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Altered mitochondrial activities play an important role in many different human
disorders, including cancer and neurodegeneration. At the Freiburg Institute of
Advanced Studies (FRIAS) Junior Researcher Conference “One Mitochondrion, Many
Diseases - Biological and Molecular Perspectives” (University of Freiburg,
Freiburg, Germany), junior and experienced researches discussed common and
distinct mechanisms of mitochondrial contributions to various human
disorders.
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Affiliation(s)
- Ralf J Braun
- Institute of Cell Biology, University of Bayreuth, 95440 Bayreuth, Germany
| | - Ralf M Zerbes
- Institute for Biochemistry and Molecular Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Florian Steinberg
- ZBSA Center for Biological Systems Analysis, AG Steinberg, University of Freiburg, 79104 Freiburg, Germany
| | - Denis Gris
- Program of Immunology, Department of Pediatrics, CR-CHUS, Faculty of Medicine and Health Sciences, University of Sherbrooke, Sherbrooke, QC, Canada
| | - Verónica I Dumit
- ZBSA Center for Biological Systems Analysis, Core Facility Proteomics, University of Freiburg, 79104 Freiburg, Germany
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31
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Atkins JF, Loughran G, Bhatt PR, Firth AE, Baranov PV. Ribosomal frameshifting and transcriptional slippage: From genetic steganography and cryptography to adventitious use. Nucleic Acids Res 2016; 44:7007-78. [PMID: 27436286 PMCID: PMC5009743 DOI: 10.1093/nar/gkw530] [Citation(s) in RCA: 165] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 05/26/2016] [Indexed: 12/15/2022] Open
Abstract
Genetic decoding is not ‘frozen’ as was earlier thought, but dynamic. One facet of this is frameshifting that often results in synthesis of a C-terminal region encoded by a new frame. Ribosomal frameshifting is utilized for the synthesis of additional products, for regulatory purposes and for translational ‘correction’ of problem or ‘savior’ indels. Utilization for synthesis of additional products occurs prominently in the decoding of mobile chromosomal element and viral genomes. One class of regulatory frameshifting of stable chromosomal genes governs cellular polyamine levels from yeasts to humans. In many cases of productively utilized frameshifting, the proportion of ribosomes that frameshift at a shift-prone site is enhanced by specific nascent peptide or mRNA context features. Such mRNA signals, which can be 5′ or 3′ of the shift site or both, can act by pairing with ribosomal RNA or as stem loops or pseudoknots even with one component being 4 kb 3′ from the shift site. Transcriptional realignment at slippage-prone sequences also generates productively utilized products encoded trans-frame with respect to the genomic sequence. This too can be enhanced by nucleic acid structure. Together with dynamic codon redefinition, frameshifting is one of the forms of recoding that enriches gene expression.
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Affiliation(s)
- John F Atkins
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland School of Microbiology, University College Cork, Cork, Ireland Department of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA
| | - Gary Loughran
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - Pramod R Bhatt
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - Andrew E Firth
- Division of Virology, Department of Pathology, University of Cambridge, Hills Road, Cambridge CB2 0QQ, UK
| | - Pavel V Baranov
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
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32
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Chen X, Petranovic D. Role of frameshift ubiquitin B protein in Alzheimer's disease. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2016; 8:300-13. [DOI: 10.1002/wsbm.1340] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Revised: 03/10/2016] [Accepted: 03/19/2016] [Indexed: 12/20/2022]
Affiliation(s)
- Xin Chen
- Systems and Synthetic Biology, Department of Biology and Biological Engineering; Chalmers University of Technology; Göteborg Sweden
| | - Dina Petranovic
- Systems and Synthetic Biology, Department of Biology and Biological Engineering; Chalmers University of Technology; Göteborg Sweden
- Novo Nordisk Foundation Center for Biosustainability; Chalmers University of Technology; Göteborg Sweden
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33
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Kaushik S, Cuervo AM. Proteostasis and aging. Nat Med 2016; 21:1406-15. [PMID: 26646497 DOI: 10.1038/nm.4001] [Citation(s) in RCA: 549] [Impact Index Per Article: 68.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2015] [Accepted: 11/02/2015] [Indexed: 12/12/2022]
Abstract
Accumulation of intracellular damage is an almost universal hallmark of aging. An improved understanding of the systems that contribute to cellular protein quality control has shed light on the reasons for the increased vulnerability of the proteome to stress in aging cells. Maintenance of protein homeostasis, or proteostasis, is attained through precisely coordinated systems that rapidly correct unwanted proteomic changes. Here we focus on recent developments that highlight the multidimensional nature of the proteostasis networks, which allow for coordinated protein homeostasis intracellularly, in between cells and even across organs, as well as on how they affect common age-associated diseases when they malfunction in aging.
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Affiliation(s)
- Susmita Kaushik
- Department of Developmental and Molecular Biology, Institute for Aging Studies, Albert Einstein College of Medicine, New York, New York, USA
| | - Ana Maria Cuervo
- Department of Developmental and Molecular Biology, Institute for Aging Studies, Albert Einstein College of Medicine, New York, New York, USA
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34
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Franz A, Kevei É, Hoppe T. Double-edged alliance: mitochondrial surveillance by the UPS and autophagy. Curr Opin Cell Biol 2015; 37:18-27. [DOI: 10.1016/j.ceb.2015.08.004] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Revised: 08/17/2015] [Accepted: 08/18/2015] [Indexed: 11/24/2022]
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35
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Shrestha A, Megeney LA. Yeast proteinopathy models: a robust tool for deciphering the basis of neurodegeneration. MICROBIAL CELL 2015; 2:458-465. [PMID: 28357271 PMCID: PMC5354604 DOI: 10.15698/mic2015.12.243] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Protein quality control or proteostasis is an essential determinant of basic cell health and aging. Eukaryotic cells have evolved a number of proteostatic mechanisms to ensure that proteins retain functional conformation, or are rapidly degraded when proteins misfold or self-aggregate. Disruption of proteostasis is now widely recognized as a key feature of aging related illness, specifically neurodegenerative disease. For example, Alzheimer’s disease, Huntington’s disease, Parkinson’s disease and Amyotrophic Lateral Sclerosis (ALS) each target and afflict distinct neuronal cell subtypes, yet this diverse array of human pathologies share the defining feature of aberrant protein aggregation within the affected cell population. Here, we review the use of budding yeast as a robust proxy to study the intersection between proteostasis and neurodegenerative disease. The humanized yeast model has proven to be an amenable platform to identify both, conserved proteostatic mechanisms across eukaryotic phyla and novel disease specific molecular dysfunction. Moreover, we discuss the intriguing concept that yeast specific proteins may be utilized as bona fide therapeutic agents, to correct proteostasis errors across various forms of neurodegeneration.
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Affiliation(s)
- Amit Shrestha
- Ottawa Hospital Research Institute, Regenerative Medicine Program, Sprott Centre for Stem Cell Research, The Ottawa Hospital, Ottawa, Ontario, Canada. ; Department of Cellular and Molecular Medicine University of Ottawa, Ottawa, Ontario, Canada
| | - Lynn A Megeney
- Ottawa Hospital Research Institute, Regenerative Medicine Program, Sprott Centre for Stem Cell Research, The Ottawa Hospital, Ottawa, Ontario, Canada. ; Department of Cellular and Molecular Medicine University of Ottawa, Ottawa, Ontario, Canada ; Department of Medicine, University of Ottawa, Ottawa, Ontario, Canada
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36
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Gentier RJ, van Leeuwen FW. Misframed ubiquitin and impaired protein quality control: an early event in Alzheimer's disease. Front Mol Neurosci 2015; 8:47. [PMID: 26388726 PMCID: PMC4557111 DOI: 10.3389/fnmol.2015.00047] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Accepted: 08/18/2015] [Indexed: 12/21/2022] Open
Abstract
Amyloid β (Aβ) plaque formation is a prominent cellular hallmark of Alzheimer's disease (AD). To date, immunization trials in AD patients have not been effective in terms of curing or ameliorating dementia. In addition, γ-secretase inhibitor strategies await clinical improvements in AD. These approaches were based upon the idea that autosomal dominant mutations in amyloid precursor protein (APP) and Presenilin 1 (PS1) genes are predictive for treatment of all AD patients. However most AD patients are of the sporadic form which partly explains the failures to treat this multifactorial disease. The major risk factor for developing sporadic AD (SAD) is aging whereas the Apolipoprotein E polymorphism (ε4 variant) is the most prominent genetic risk factor. Other medium-risk factors such as triggering receptor expressed on myeloid cells 2 (TREM2) and nine low risk factors from Genome Wide Association Studies (GWAS) were associated with AD. Recently, pooled GWAS studies identified protein ubiquitination as one of the key modulators of AD. In addition, a brain site specific strategy was used to compare the proteomes of AD patients by an Ingenuity Pathway Analysis. This strategy revealed numerous proteins that strongly interact with ubiquitin (UBB) signaling, and pointing to a dysfunctional ubiquitin proteasome system (UPS) as a causal factor in AD. We reported that DNA-RNA sequence differences in several genes including ubiquitin do occur in AD, the resulting misframed protein of which accumulates in the neurofibrillary tangles (NFTs). This suggests again a functional link between neurodegeneration of the AD type and loss of protein quality control by the UPS. Progress in this field is discussed and modulating the activity of the UPS opens an attractive avenue of research towards slowing down the development of AD and ameliorating its effects by discovering prime targets for AD therapeutics.
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Affiliation(s)
- Romina J. Gentier
- Department of Neuroscience, Faculty of Health, Medicine and Life Sciences, Maastricht UniversityMaastricht, Netherlands
| | - Fred W. van Leeuwen
- Department of Neuroscience, Faculty of Health, Medicine and Life Sciences, Maastricht UniversityMaastricht, Netherlands
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37
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Ross JM, Olson L, Coppotelli G. Mitochondrial and Ubiquitin Proteasome System Dysfunction in Ageing and Disease: Two Sides of the Same Coin? Int J Mol Sci 2015; 16:19458-76. [PMID: 26287188 PMCID: PMC4581307 DOI: 10.3390/ijms160819458] [Citation(s) in RCA: 78] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2015] [Revised: 07/23/2015] [Accepted: 08/07/2015] [Indexed: 12/13/2022] Open
Abstract
Mitochondrial dysfunction and impairment of the ubiquitin proteasome system have been described as two hallmarks of the ageing process. Additionally, both systems have been implicated in the etiopathogenesis of many age-related diseases, particularly neurodegenerative disorders, such as Alzheimer's and Parkinson's disease. Interestingly, these two systems are closely interconnected, with the ubiquitin proteasome system maintaining mitochondrial homeostasis by regulating organelle dynamics, the proteome, and mitophagy, and mitochondrial dysfunction impairing cellular protein homeostasis by oxidative damage. Here, we review the current literature and argue that the interplay of the two systems should be considered in order to better understand the cellular dysfunction observed in ageing and age-related diseases. Such an approach may provide valuable insights into molecular mechanisms underlying the ageing process, and further discovery of treatments to counteract ageing and its associated diseases. Furthermore, we provide a hypothetical model for the heterogeneity described among individuals during ageing.
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Affiliation(s)
- Jaime M Ross
- Department of Neuroscience, Karolinska Institutet, Retzius väg 8, Stockholm 171 77, Sweden.
| | - Lars Olson
- Department of Neuroscience, Karolinska Institutet, Retzius väg 8, Stockholm 171 77, Sweden.
| | - Giuseppe Coppotelli
- Department of Neuroscience, Karolinska Institutet, Retzius väg 8, Stockholm 171 77, Sweden.
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38
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Chen X, Petranovic D. Amyloid-β peptide-induced cytotoxicity and mitochondrial dysfunction in yeast. FEMS Yeast Res 2015; 15:fov061. [PMID: 26152713 DOI: 10.1093/femsyr/fov061] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/01/2015] [Indexed: 12/22/2022] Open
Abstract
Alzheimer's disease (AD) is the most common neurodegenerative disease, characterized by deposits of amyloid-β (Aβ) peptides. However, the underlying molecular mechanisms of neuron cell dysfunction and cell death in AD still remain poorly understood. Yeast Saccharomyces cerevisiae shares many conserved biological processes with all eukaryotic cells, including human neurons. Thanks to relatively simple and quick genetic and environmental manipulations, the large knowledge base and data collections, this organism has become a valuable tool to unravel fundamental intracellular mechanisms underlying neurodegeneration. In this study, we have used yeast as a model system to study the effects of intracellular Aβ peptides and we found that cells constitutively producing native Aβ directed to the secretory pathway exhibited a lower growth rate, lower biomass yield, lower respiratory rate, increased oxidative stress, hallmarks of mitochondrial dysfunction and ubiquitin-proteasome system dysfunction. These findings are relevant for better understanding the role of Aβ in cell stress and cell damage.
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Affiliation(s)
- Xin Chen
- Systems and Synthetic Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, SE-412 96 Göteborg, Sweden
| | - Dina Petranovic
- Systems and Synthetic Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, SE-412 96 Göteborg, Sweden Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, SE-412 96 Göteborg, Sweden
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39
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Braun RJ, Dumit VI, Monpays C, Roucou X, Serrano D, St-Pierre J, Waters PJ, Bates I, Gris D. Struggling for breath in Sherbrooke - 1st Symposium on "One mitochondrion, many diseases" in Sherbrooke, Québec, Canada, March 11th, 2015. MICROBIAL CELL 2015; 2:208-213. [PMID: 28357294 PMCID: PMC5349142 DOI: 10.15698/mic2015.06.207] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Ralf J Braun
- Institute of Cell Biology, University of Bayreuth, 95440 Bayreuth, Germany
| | - Verónica I Dumit
- ZBSA Center for Biological Systems Analysis, Core Facility Proteomics, University of Freiburg, Freiburg, Germany. ; Department of Dermatology, Medical Center - University of Freiburg, Freiburg, Germany
| | - Cécile Monpays
- Department of Pharmacology and Physiology, University of Sherbrooke Hospital Centre (CHUS), Sherbrooke, QC, Canada
| | - Xavier Roucou
- Department of Biochemistry, Faculty of Medicine and Health Sciences, University of Sherbrooke, Sherbrooke, QC, Canada
| | - Daniel Serrano
- Immunology Division, Department of Pediatrics, Faculty of Medicine and Health Sciences, University of Sherbrooke, Sherbrooke, QC, Canada
| | - Julie St-Pierre
- Goodmann Cancer Research Centre & Department of Biochemistry, McGill University, Montréal, QC, Canada
| | - Paula J Waters
- Medical Genetics Service, Department of Pediatrics, University of Sherbrooke Hospital Centre (CHUS), Sherbrooke, QC, Canada
| | - Ian Bates
- Carl Zeiss Canada MicroImaging, Toronto, ON, Canada
| | - Denis Gris
- Program of Immunology, Department of Pediatrics, CR-CHUS, Faculty of Medicine and Health Sciences, University of Sherbrooke, Sherbrooke, QC, Canada
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Braun RJ. Ubiquitin-dependent proteolysis in yeast cells expressing neurotoxic proteins. Front Mol Neurosci 2015; 8:8. [PMID: 25814926 PMCID: PMC4357299 DOI: 10.3389/fnmol.2015.00008] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Accepted: 02/24/2015] [Indexed: 01/16/2023] Open
Abstract
Critically impaired protein degradation is discussed to contribute to neurodegenerative disorders, including Parkinson's, Huntington's, Alzheimer's, and motor neuron diseases. Misfolded, aggregated, or surplus proteins are efficiently degraded via distinct protein degradation pathways, including the ubiquitin-proteasome system, autophagy, and vesicular trafficking. These pathways are regulated by covalent modification of target proteins with the small protein ubiquitin and are evolutionary highly conserved from humans to yeast. The yeast Saccharomyces cerevisiae is an established model for deciphering mechanisms of protein degradation, and for the elucidation of pathways underlying programmed cell death. The expression of human neurotoxic proteins triggers cell death in yeast, with neurotoxic protein-specific differences. Therefore, yeast cell death models are suitable for analyzing the role of protein degradation pathways in modulating cell death upon expression of disease-causing proteins. This review summarizes which protein degradation pathways are affected in these yeast models, and how they are involved in the execution of cell death. I will discuss to which extent this mimics the situation in other neurotoxic models, and how this may contribute to a better understanding of human disorders.
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Affiliation(s)
- Ralf J Braun
- Institut für Zellbiologie, Universität Bayreuth Bayreuth, Germany
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