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Hipp MS, Hartl FU. Interplay of Proteostasis Capacity and Protein Aggregation: Implications for Cellular Function and Disease. J Mol Biol 2024; 436:168615. [PMID: 38759929 DOI: 10.1016/j.jmb.2024.168615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 05/13/2024] [Accepted: 05/13/2024] [Indexed: 05/19/2024]
Abstract
Eukaryotic cells are equipped with an intricate proteostasis network (PN), comprising nearly 3,000 components dedicated to preserving proteome integrity and sustaining protein homeostasis. This protective system is particularly important under conditions of external and intrinsic cell stress, where inherently dynamic proteins may unfold and lose functionality. A decline in proteostasis capacity is associated with the aging process, resulting in a reduced folding efficiency of newly synthesized proteins and a deficit in the cellular capacity to degrade misfolded proteins. A critical consequence of PN insufficiency is the accumulation of cytotoxic protein aggregates that underlie various age-related neurodegenerative conditions and other pathologies. By interfering with specific proteostasis components, toxic aggregates place an excessive burden on the PN's ability to maintain proteome integrity. This initiates a feed-forward loop, wherein the generation of misfolded and aggregated proteins ultimately leads to proteostasis collapse and cellular demise.
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Affiliation(s)
- Mark S Hipp
- Department of Biomedical Sciences, University Medical Center Groningen, University of Groningen, Antonius Deusinglaan, 1, 9713 AV Groningen, the Netherlands; Research School of Behavioural and Cognitive Neurosciences, University of Groningen, Groningen, the Netherlands; School of Medicine and Health Sciences, Carl von Ossietzky University Oldenburg, Oldenburg, Germany.
| | - F Ulrich Hartl
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany; Munich Cluster for Systems Neurology (SyNergy), Munich, Germany; Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA.
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2
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Giovannetti M, Rodríguez-Palero MJ, Fabrizio P, Nicolle O, Bedet C, Michaux G, Witting M, Artal-Sanz M, Palladino F. SIN-3 transcriptional coregulator maintains mitochondrial homeostasis and polyamine flux. iScience 2024; 27:109789. [PMID: 38746662 PMCID: PMC11091686 DOI: 10.1016/j.isci.2024.109789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 01/30/2024] [Accepted: 04/16/2024] [Indexed: 06/05/2024] Open
Abstract
Mitochondrial function relies on the coordinated transcription of mitochondrial and nuclear genomes to assemble respiratory chain complexes. Across species, the SIN3 coregulator influences mitochondrial functions, but how its loss impacts mitochondrial homeostasis and metabolism in the context of a whole organism is unknown. Exploring this link is important because SIN3 haploinsufficiency causes intellectual disability/autism syndromes and SIN3 plays a role in tumor biology. Here we show that loss of C. elegans SIN-3 results in transcriptional deregulation of mitochondrial- and nuclear-encoded mitochondrial genes, potentially leading to mito-nuclear imbalance. Consistent with impaired mitochondrial function, sin-3 mutants show extensive mitochondrial fragmentation by transmission electron microscopy (TEM) and in vivo imaging, and altered oxygen consumption. Metabolomic analysis of sin-3 mutant animals revealed a mitochondria stress signature and deregulation of methionine flux, resulting in decreased S-adenosyl methionine (SAM) and increased polyamine levels. Our results identify SIN3 as a key regulator of mitochondrial dynamics and metabolic flux, with important implications for human pathologies.
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Affiliation(s)
- Marina Giovannetti
- Laboratory of Biology and Modeling of the Cell, UMR5239 CNRS/Ecole Normale Supérieure de Lyon, INSERM U1210, UMS 3444 Biosciences Lyon Gerland, Université de Lyon, Lyon, France
| | - María-Jesús Rodríguez-Palero
- Andalusian Centre for Developmental Biology (CABD), Consejo Superior de Investigaciones Científicas/Junta de Andalucía/Universidad Pablo de Olavide and Department of Molecular Biology and Biochemical Engineering, Universidad Pablo de Olavide, 41013 Sevilla, Spain
| | - Paola Fabrizio
- Laboratory of Biology and Modeling of the Cell, UMR5239 CNRS/Ecole Normale Supérieure de Lyon, INSERM U1210, UMS 3444 Biosciences Lyon Gerland, Université de Lyon, Lyon, France
| | - Ophélie Nicolle
- University Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes), UMR 6290, 35000 Rennes, France
| | - Cécile Bedet
- Laboratory of Biology and Modeling of the Cell, UMR5239 CNRS/Ecole Normale Supérieure de Lyon, INSERM U1210, UMS 3444 Biosciences Lyon Gerland, Université de Lyon, Lyon, France
| | - Grégoire Michaux
- University Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes), UMR 6290, 35000 Rennes, France
| | - Michael Witting
- Metabolomics and Proteomics Core, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
- Chair of Analytical Food Chemistry, TUM School of Life Sciences, Technical University of Munich, Maximus-von-Imhof Forum 2, 85354 Freising, Weihenstephan, Germany
| | - Marta Artal-Sanz
- Andalusian Centre for Developmental Biology (CABD), Consejo Superior de Investigaciones Científicas/Junta de Andalucía/Universidad Pablo de Olavide and Department of Molecular Biology and Biochemical Engineering, Universidad Pablo de Olavide, 41013 Sevilla, Spain
| | - Francesca Palladino
- Laboratory of Biology and Modeling of the Cell, UMR5239 CNRS/Ecole Normale Supérieure de Lyon, INSERM U1210, UMS 3444 Biosciences Lyon Gerland, Université de Lyon, Lyon, France
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3
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Tang Q, Chen X. Nascent Proteomics: Chemical Tools for Monitoring Newly Synthesized Proteins. Angew Chem Int Ed Engl 2023; 62:e202305866. [PMID: 37309018 DOI: 10.1002/anie.202305866] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 06/10/2023] [Accepted: 06/12/2023] [Indexed: 06/14/2023]
Abstract
Cellular proteins are dynamically regulated in response to environmental stimuli. Conventional proteomics compares the entire proteome in different cellular states to identify differentially expressed proteins, which suffers from limited sensitivity for analyzing acute and subtle changes. To address this challenge, nascent proteomics has been developed, which selectively analyzes the newly synthesized proteins, thus offering a more sensitive and timely insight into the dynamic changes of the proteome. In this Minireview, we discuss recent advancements in nascent proteomics, with an emphasis on methodological developments. Also, we delve into the current challenges and provide an outlook on the future prospects of this exciting field.
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Affiliation(s)
- Qi Tang
- College of Chemistry and Molecular Engineering, Beijing National Laboratory for Molecular Sciences, Peking University, Beijing, 100871, China
| | - Xing Chen
- College of Chemistry and Molecular Engineering, Peking-Tsinghua Center for Life Science, Beijing National Laboratory for Molecular Sciences, Synthetic and Functional Biomolecules Center, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing, 100871, China
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4
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Glastad KM, Roessler J, Gospocic J, Bonasio R, Berger SL. Long ant life span is maintained by a unique heat shock factor. Genes Dev 2023; 37:398-417. [PMID: 37257919 PMCID: PMC10270196 DOI: 10.1101/gad.350250.122] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 05/09/2023] [Indexed: 06/02/2023]
Abstract
Eusocial insect reproductive females show strikingly longer life spans than nonreproductive female workers despite high genetic similarity. In the ant Harpegnathos saltator (Hsal), workers can transition to reproductive "gamergates," acquiring a fivefold prolonged life span by mechanisms that are poorly understood. We found that gamergates have elevated expression of heat shock response (HSR) genes in the absence of heat stress and enhanced survival with heat stress. This HSR gene elevation is driven in part by gamergate-specific up-regulation of the gene encoding a truncated form of a heat shock factor most similar to mammalian HSF2 (hsalHSF2). In workers, hsalHSF2 was bound to DNA only upon heat stress. In gamergates, hsalHSF2 bound to DNA even in the absence of heat stress and was localized to gamergate-biased HSR genes. Expression of hsalHSF2 in Drosophila melanogaster led to enhanced heat shock survival and extended life span in the absence of heat stress. Molecular characterization illuminated multiple parallels between long-lived flies and gamergates, underscoring the centrality of hsalHSF2 to extended ant life span. Hence, ant caste-specific heat stress resilience and extended longevity can be transferred to flies via hsalHSF2. These findings reinforce the critical role of proteostasis in health and aging and reveal novel mechanisms underlying facultative life span extension in ants.
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Affiliation(s)
- Karl M Glastad
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
- Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Julian Roessler
- Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Janko Gospocic
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
- Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Roberto Bonasio
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
- Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Shelley L Berger
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA;
- Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
- Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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5
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Fatma T, Ahmed Khan H, Ahmed A, Adnan F, Zeshan, Virk N, Faraz Bhatti M. Functional annotation and comparative analysis of four Botrytis cinerea mitogenomes reported from Punjab, Pakistan. Saudi J Biol Sci 2023; 30:103605. [PMID: 36950365 PMCID: PMC10025148 DOI: 10.1016/j.sjbs.2023.103605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 02/02/2023] [Accepted: 02/19/2023] [Indexed: 02/25/2023] Open
Abstract
Botrytis cinerea is one of the top phytopathogenic fungus which ubiquitously cause grey mold on a variety of horticultural plants. The mechanism of respiration in the fungus occurs within the mitochondria. Mitogenomes serve as a key molecular marker for the investigation of fungal evolutionary patterns. This study aimed at the complete assembly, characterization, and comparative relationship of four mitogenomes of Botrytis cinerea strains including Kst5C, Kst14A, Kst32B, Kst33A, respectively. High throughput sequencing of four mitogenomes allowed the full assembly and annotation of these sequences. The total genome length of these 4 isolates Kst5C Kst14A, Kst32B, Kst33A was 69,986 bp, 77,303 bp, 76,204 bp and 55, 226 bp respectively. The distribution of features represented 2 ribosomal RNA genes,14 respiration encoding proteins, 1 mitochondrial ribosomal protein-encoding gene, along with varying numbers of transfer RNA genes, protein-coding genes, mobile intronic regions and homing endonuclease genes including LAGLIDADG and GIY-YIG domains were found in all four mitogenomes. The comparative analyses performed also decipher significant results for four mitogenomes among fungal isolates included in the study. This is the first report on the detailed annotation of mitogenomes as a proof for investigation of variation patterns present with in the B. cinerea causing grey mold on strawberries in Pakistan. This study will also contribute to the rapid evolutionary analysis and population patterns present among Botrytis cinerea.
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Affiliation(s)
- Tehsin Fatma
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), 44000 Islamabad, Pakistan
| | - Haris Ahmed Khan
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), 44000 Islamabad, Pakistan
| | - Aqeel Ahmed
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), 44000 Islamabad, Pakistan
| | - Fazal Adnan
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), 44000 Islamabad, Pakistan
| | - Zeshan
- Institute of Environmental Sciences and Engineering (IESE), National University of Sciences and Technology (NUST), 44000 Islamabad, Pakistan
| | - Nasar Virk
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), 44000 Islamabad, Pakistan
| | - Muhammad Faraz Bhatti
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), 44000 Islamabad, Pakistan
- Corresponding author.
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6
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Aging Hallmarks and the Role of Oxidative Stress. Antioxidants (Basel) 2023; 12:antiox12030651. [PMID: 36978899 PMCID: PMC10044767 DOI: 10.3390/antiox12030651] [Citation(s) in RCA: 72] [Impact Index Per Article: 72.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 02/26/2023] [Accepted: 03/01/2023] [Indexed: 03/08/2023] Open
Abstract
Aging is a complex biological process accompanied by a progressive decline in the physical function of the organism and an increased risk of age-related chronic diseases such as cardiovascular diseases, cancer, and neurodegenerative diseases. Studies have established that there exist nine hallmarks of the aging process, including (i) telomere shortening, (ii) genomic instability, (iii) epigenetic modifications, (iv) mitochondrial dysfunction, (v) loss of proteostasis, (vi) dysregulated nutrient sensing, (vii) stem cell exhaustion, (viii) cellular senescence, and (ix) altered cellular communication. All these alterations have been linked to sustained systemic inflammation, and these mechanisms contribute to the aging process in timing not clearly determined yet. Nevertheless, mitochondrial dysfunction is one of the most important mechanisms contributing to the aging process. Mitochondria is the primary endogenous source of reactive oxygen species (ROS). During the aging process, there is a decline in ATP production and elevated ROS production together with a decline in the antioxidant defense. Elevated ROS levels can cause oxidative stress and severe damage to the cell, organelle membranes, DNA, lipids, and proteins. This damage contributes to the aging phenotype. In this review, we summarize recent advances in the mechanisms of aging with an emphasis on mitochondrial dysfunction and ROS production.
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Tang J, Ma YC, Chen YL, Yang RQ, Liu HC, Wang X, Ni B, Zou CG, Zhang KQ. Vitellogenin accumulation leads to reproductive senescence by impairing lysosomal function. SCIENCE CHINA. LIFE SCIENCES 2023; 66:439-452. [PMID: 36680676 DOI: 10.1007/s11427-022-2242-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Accepted: 11/19/2022] [Indexed: 01/22/2023]
Abstract
The maintenance of proteostasis is essential for cellular and organism healthspan. How proteostasis collapse influences reproductive span remains largely unclear. In Caenorhabditis elegans, excess accumulation of vitellogenins, the major components in yolk proteins, is crucial for the development of the embryo and occurs throughout the whole body during the aging process. Here, we show that vitellogenin accumulation leads to reproduction cessation. Excess vitellogenin is accumulated in the intestine and transported into the germline, impairing lysosomal activity in these tissues. The lysosomal function in the germline is required for reproductive span by maintaining oocyte quality. In contrast, autophagy and sperm depletion are not involved in vitellogenin accumulation-induced reproductive aging. Our findings provide insights into how proteome imbalance has an impact on reproductive aging and imply that improvement of lysosomal function is an effective approach for mid-life intervention for maintaining reproductive health in mammals.
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Affiliation(s)
- Jie Tang
- Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming, 650091, China
- Yunnan Key Laboratory of Vaccine Research Development on Severe Infectious Disease, Institute of Medical Biology, Chinese Academy of Medical Sciences, and Peking Union Medical College (CAMS & PUMC), Kunming, 650118, China
| | - Yi-Cheng Ma
- Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming, 650091, China
| | - Yuan-Li Chen
- Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming, 650091, China
- Faculty of Basic Medicine, Kunming Medical University, Kunming, 650500, China
| | - Rui-Qiu Yang
- Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming, 650091, China
| | - Heng-Chen Liu
- Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming, 650091, China
| | - Xin Wang
- Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming, 650091, China
| | - Baosen Ni
- Institute of Biology and Environmental Engineering, School of Chemistry, Biology & Environment, Yuxi Normal University, Yuxi, 653100, China
| | - Cheng-Gang Zou
- Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming, 650091, China.
| | - Ke-Qin Zhang
- Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming, 650091, China.
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Sarkar A, Kumar L, Hameed R, Nazir A. Multiple checkpoints of protein clearance machinery are modulated by a common microRNA, miR-4813-3p, through its putative target genes: Studies employing transgenic C. elegans model. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2022; 1869:119342. [PMID: 35998789 DOI: 10.1016/j.bbamcr.2022.119342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 08/14/2022] [Accepted: 08/17/2022] [Indexed: 06/15/2023]
Abstract
In order to maintain cellular homeostasis and a healthy state, aberrant and aggregated proteins are to be recognized and rapidly cleared from cells. Parkinson's disease, known to be associated with multiple factors; presents with impaired clearance of aggregated alpha synuclein as a key factor. We endeavored to study microRNA molecules with potential role on regulating multiple checkpoints of protein quality control within cells. Carrying out global miRNA profiling in a transgenic C. elegans model that expresses human alpha synuclein, we identified novel miRNA, miR-4813-3p, as a significantly downregulated molecule. Further studying its putative downstream target genes, we were able to mechanistically characterize six genes gbf-1, vha-5, cup-5, cpd-2, acs-1 and C27A12.7, which relate to endpoints associated with alpha synuclein expression, oxidative stress, locomotory behavior, autophagy and apoptotic pathways. Our study reveals the novel role of miR-4813-3p and provides potential functional characterization of its putative target genes, in regulating the various pathways associated with PQC network. miR-4813-3p modulates ERUPR, MTUPR, autophagosome-lysosomal-pathway and the ubiquitin-proteasomal-system, making this molecule an interesting target for further studies towards therapeutically addressing multifactorial aspect of Parkinson's disease.
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Affiliation(s)
- Arunabh Sarkar
- Division of Neuroscience and Ageing Biology, CSIR-Central Drug Research Institute, Lucknow, UP, India
| | - Lalit Kumar
- Division of Neuroscience and Ageing Biology, CSIR-Central Drug Research Institute, Lucknow, UP, India
| | - Rohil Hameed
- Division of Neuroscience and Ageing Biology, CSIR-Central Drug Research Institute, Lucknow, UP, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Aamir Nazir
- Division of Neuroscience and Ageing Biology, CSIR-Central Drug Research Institute, Lucknow, UP, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
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9
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Shrivastava A, Sandhof CA, Reinle K, Jawed A, Ruger-Herreros C, Schwarz D, Creamer D, Nussbaum-Krammer C, Mogk A, Bukau B. The cytoprotective sequestration activity of small heat shock proteins is evolutionarily conserved. J Cell Biol 2022; 221:213447. [PMID: 36069810 PMCID: PMC9458469 DOI: 10.1083/jcb.202202149] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 07/21/2022] [Accepted: 08/16/2022] [Indexed: 11/22/2022] Open
Abstract
The chaperone-mediated sequestration of misfolded proteins into inclusions is a pivotal cellular strategy to maintain proteostasis in Saccharomyces cerevisiae, executed by small heat shock proteins (sHsps) Hsp42 and Btn2. Direct homologs of Hsp42 and Btn2 are absent in other organisms, questioning whether sequestration represents a conserved proteostasis strategy and, if so, which factors are involved. We examined sHsps from Escherchia coli, Caenorhabditis elegans, and humans for their ability to complement the defects of yeast sequestrase mutants. We show that sequestration of misfolded proteins is an original and widespread activity among sHsps executed by specific family members. Sequestrase positive C. elegans' sHsps harbor specific sequence features, including a high content of aromatic and methionine residues in disordered N-terminal extensions. Those sHsps buffer limitations in Hsp70 capacity in C. elegans WT animals and are upregulated in long-lived daf-2 mutants, contributing to lifespan extension. Cellular protection by sequestration of misfolded proteins is, therefore, an evolutionarily conserved activity of the sHsp family.
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Affiliation(s)
- Aseem Shrivastava
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Carl Alexander Sandhof
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Kevin Reinle
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Areeb Jawed
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Carmen Ruger-Herreros
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Dominic Schwarz
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Declan Creamer
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Carmen Nussbaum-Krammer
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Axel Mogk
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Bernd Bukau
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
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10
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English AM, Moon SL. Measuring Bulk Translation Activity in Single Mammalian Cells During the Integrated Stress Response. Methods Mol Biol 2022; 2428:63-73. [PMID: 35171473 DOI: 10.1007/978-1-0716-1975-9_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The attenuation of global translation is a critical outcome of the integrated stress response (ISR). Consequently, it is important to effectively detect and measure protein synthesis in studies seeking to evaluate the ISR. This chapter details two methods, surface sensing of translation (SUnSET) and fluorescent noncanonical amino acid tagging (FUNCAT), to measure global translation activity in individual cells using fluorescence microscopy as a read-out. Detecting bulk translation activity in single cells is advantageous for the concurrent observation of newly synthesized proteins and other cellular structures and to identify differences in translation activity among individuals within a population of cells.
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Affiliation(s)
- Alyssa M English
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
- Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI, USA
| | - Stephanie L Moon
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA.
- Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI, USA.
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11
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Sarkar A, Nazir A. Carrying Excess Baggage Can Slowdown Life: Protein Clearance Machineries That Go Awry During Aging and the Relevance of Maintaining Them. Mol Neurobiol 2021; 59:821-840. [PMID: 34792731 DOI: 10.1007/s12035-021-02640-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 11/05/2021] [Indexed: 01/07/2023]
Abstract
Cellular homeostasis is maintained by rapid and systematic cleansing of aberrant and aggregated proteins within cells. Neurodegenerative diseases (NDs) especially Parkinson's and Alzheimer's disease are known to be associated with multiple factors, most important being impaired clearance of aggregates, resulting in the accumulation of specific aggregated protein in the brain. Protein quality control (PQC) of proteostasis network comprises proteolytic machineries and chaperones along with their regulators to ensure precise operation and maintenance of proteostasis. Such regulatory factors coordinate among each other multiple functional aspects related to proteins, including their synthesis, folding, transport, and degradation. During aging due to inevitable endogenous and external stresses, sustaining a proteome balance is a challenging task. Such stresses decline the capacity of the proteostasis network compromising the proteome integrity, affecting the fundamental physiological processes including reproductive fitness of the organism. This review focuses on highlighting proteome-wide changes during aging and the strategies for proteostasis improvements. The possibility of augmenting the proteostasis network either via genetic or pharmacological interventions may be a promising strategy towards delaying age-associated pathological consequences due to proteome disbalance, thus promoting healthy aging and prolonged longevity.
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Affiliation(s)
- Arunabh Sarkar
- Division of Neuroscience and Ageing Biology, CSIR-Central Drug Research Institute, Lucknow, UP, 226031, India
| | - Aamir Nazir
- Division of Neuroscience and Ageing Biology, CSIR-Central Drug Research Institute, Lucknow, UP, 226031, India.
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12
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Verma K, Verma M, Chaphalkar A, Chakraborty K. Recent advances in understanding the role of proteostasis. Fac Rev 2021; 10:72. [PMID: 34632458 PMCID: PMC8483240 DOI: 10.12703/r/10-72] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Maintenance of a functional proteome is achieved through the mechanism of proteostasis that involves precise coordination between molecular machineries assisting a protein from its conception to demise. Although each organelle within a cell has its own set of proteostasis machinery, inter-organellar communication and cell non-autonomous signaling bring forth the multidimensional nature of the proteostasis network. Exposure to extrinsic and intrinsic stressors can challenge the proteostasis network, leading to the accumulation of aberrant proteins or a decline in the proteostasis components, as seen during aging and in several diseases. Here, we summarize recent advances in understanding the role of proteostasis and its regulation in aging and disease, including monogenetic and infectious diseases. We highlight some of the emerging as well as unresolved questions in proteostasis that need to be addressed to overcome pathologies associated with damaged proteins and to promote healthy aging.
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Affiliation(s)
- Kanika Verma
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, Delhi, India
- Academy of Scientific and Innovative Research, CSIR-HRDC, Ghaziabad, Uttar Pradesh, India
| | - Monika Verma
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, Delhi, India
- Academy of Scientific and Innovative Research, CSIR-HRDC, Ghaziabad, Uttar Pradesh, India
| | - Aseem Chaphalkar
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, Delhi, India
- Academy of Scientific and Innovative Research, CSIR-HRDC, Ghaziabad, Uttar Pradesh, India
| | - Kausik Chakraborty
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, Delhi, India
- Academy of Scientific and Innovative Research, CSIR-HRDC, Ghaziabad, Uttar Pradesh, India
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13
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Evans HT, Blackmore D, Götz J, Bodea LG. De novo proteomic methods for examining the molecular mechanisms underpinning long-term memory. Brain Res Bull 2021; 169:94-103. [PMID: 33465403 DOI: 10.1016/j.brainresbull.2020.12.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 12/07/2020] [Accepted: 12/21/2020] [Indexed: 01/19/2023]
Abstract
Memory formation is a fundamental function of the nervous system that enables the experience-based adaptation of behaviour. The formation, recall and updating of long-term memory (LTM) requires new protein synthesis through its direct involvement in neuronal processes, such as long-term potentiation (LTP), long-term depression (LTD) and synaptic scaling. We discuss the advantages and limitations of several emerging techniques which enable the tagging of newly synthesised proteins, including stable isotope labelling with amino acids in cell culture (SILAC), puromycin labelling, and non-canonical amino acid (NCAA) labelling. We further present how these methods allow for the identification and visualisation of proteins which are newly synthesised during different stages of memory formation. These emerging techniques will continue to expand our understanding of how memories are formed, consolidated and retrieved.
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Affiliation(s)
- Harrison Tudor Evans
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane QLD 4072, Australia
| | - Daniel Blackmore
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane QLD 4072, Australia
| | - Jürgen Götz
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane QLD 4072, Australia.
| | - Liviu-Gabriel Bodea
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane QLD 4072, Australia.
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14
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McAlary L, Chew YL, Lum JS, Geraghty NJ, Yerbury JJ, Cashman NR. Amyotrophic Lateral Sclerosis: Proteins, Proteostasis, Prions, and Promises. Front Cell Neurosci 2020; 14:581907. [PMID: 33328890 PMCID: PMC7671971 DOI: 10.3389/fncel.2020.581907] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 09/22/2020] [Indexed: 12/13/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is characterized by the progressive degeneration of the motor neurons that innervate muscle, resulting in gradual paralysis and culminating in the inability to breathe or swallow. This neuronal degeneration occurs in a spatiotemporal manner from a point of onset in the central nervous system (CNS), suggesting that there is a molecule that spreads from cell-to-cell. There is strong evidence that the onset and progression of ALS pathology is a consequence of protein misfolding and aggregation. In line with this, a hallmark pathology of ALS is protein deposition and inclusion formation within motor neurons and surrounding glia of the proteins TAR DNA-binding protein 43, superoxide dismutase-1, or fused in sarcoma. Collectively, the observed protein aggregation, in conjunction with the spatiotemporal spread of symptoms, strongly suggests a prion-like propagation of protein aggregation occurs in ALS. In this review, we discuss the role of protein aggregation in ALS concerning protein homeostasis (proteostasis) mechanisms and prion-like propagation. Furthermore, we examine the experimental models used to investigate these processes, including in vitro assays, cultured cells, invertebrate models, and murine models. Finally, we evaluate the therapeutics that may best prevent the onset or spread of pathology in ALS and discuss what lies on the horizon for treating this currently incurable disease.
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Affiliation(s)
- Luke McAlary
- Illawarra Health and Medical Research Institute, University of Wollongong, Wollongong, NSW, Australia
- Molecular Horizons and School of Chemistry and Molecular Bioscience, Faculty of Science, Medicine and Health, University of Wollongong, Wollongong, NSW, Australia
| | - Yee Lian Chew
- Illawarra Health and Medical Research Institute, University of Wollongong, Wollongong, NSW, Australia
- Molecular Horizons and School of Chemistry and Molecular Bioscience, Faculty of Science, Medicine and Health, University of Wollongong, Wollongong, NSW, Australia
| | - Jeremy Stephen Lum
- Illawarra Health and Medical Research Institute, University of Wollongong, Wollongong, NSW, Australia
- Molecular Horizons and School of Chemistry and Molecular Bioscience, Faculty of Science, Medicine and Health, University of Wollongong, Wollongong, NSW, Australia
| | - Nicholas John Geraghty
- Illawarra Health and Medical Research Institute, University of Wollongong, Wollongong, NSW, Australia
- Molecular Horizons and School of Chemistry and Molecular Bioscience, Faculty of Science, Medicine and Health, University of Wollongong, Wollongong, NSW, Australia
| | - Justin John Yerbury
- Illawarra Health and Medical Research Institute, University of Wollongong, Wollongong, NSW, Australia
- Molecular Horizons and School of Chemistry and Molecular Bioscience, Faculty of Science, Medicine and Health, University of Wollongong, Wollongong, NSW, Australia
| | - Neil R. Cashman
- Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, BC, Canada
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15
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Hoffman TE, Hanneman WH, Moreno JA. Network Simulations Reveal Molecular Signatures of Vulnerability to Age-Dependent Stress and Tau Accumulation. Front Mol Biosci 2020; 7:590045. [PMID: 33195439 PMCID: PMC7606936 DOI: 10.3389/fmolb.2020.590045] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 09/30/2020] [Indexed: 01/02/2023] Open
Abstract
Alzheimer’s disease (AD) is the leading cause of dementia and one of the most common causes of death worldwide. As an age-dependent multifactorial disease, the causative triggers of AD are rooted in spontaneous declines in cellular function and metabolic capacity with increases in protein stressors such as the tau protein. This multitude of age-related processes that cause neurons to change from healthy states to ones vulnerable to the damage seen in AD are difficult to simultaneously investigate and even more difficult to quantify. Here we aimed to diminish these gaps in our understanding of neuronal vulnerability in AD development by using simulation methods to theoretically quantify an array of cellular stress responses and signaling molecules. This temporally-descriptive molecular signature was produced using a novel multimethod simulation approach pioneered by our laboratory for biological research; this methodology combines hierarchical agent-based processes and continuous equation-based modeling in the same interface, all while maintaining intrinsic distributions that emulate natural biological stochasticity. The molecular signature was validated for a normal organismal aging trajectory using experimental longitudinal data from Caenorhabditis elegans and rodent studies. In addition, we have further predicted this aging molecular signature for cells impacted by the pathogenic tau protein, giving rise to distinct stress response conditions needed for cytoprotective aging. Interestingly, our simulation experiments showed that oxidative stress signaling (via daf-16 and skn-1 activities) does not substantially protect cells from all the early stressors of aging, but that it is essential in preventing a late-life degenerative cellular phenotype. Together, our simulation experiments aid in elucidating neurodegenerative triggers in the onset of AD for different genetic conditions. The long-term goal of this work is to provide more detailed diagnostic and prognostic tools for AD development and progression, and to provide more comprehensive preventative measures for this disease.
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Affiliation(s)
- Timothy E Hoffman
- Department of Environmental and Radiological Health Sciences, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, United States
| | - William H Hanneman
- Department of Environmental and Radiological Health Sciences, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, United States
| | - Julie A Moreno
- Department of Environmental and Radiological Health Sciences, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, United States
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16
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Abstract
Ageing is a major risk factor for the development of many diseases, prominently including neurodegenerative disorders such as Alzheimer disease and Parkinson disease. A hallmark of many age-related diseases is the dysfunction in protein homeostasis (proteostasis), leading to the accumulation of protein aggregates. In healthy cells, a complex proteostasis network, comprising molecular chaperones and proteolytic machineries and their regulators, operates to ensure the maintenance of proteostasis. These factors coordinate protein synthesis with polypeptide folding, the conservation of protein conformation and protein degradation. However, sustaining proteome balance is a challenging task in the face of various external and endogenous stresses that accumulate during ageing. These stresses lead to the decline of proteostasis network capacity and proteome integrity. The resulting accumulation of misfolded and aggregated proteins affects, in particular, postmitotic cell types such as neurons, manifesting in disease. Recent analyses of proteome-wide changes that occur during ageing inform strategies to improve proteostasis. The possibilities of pharmacological augmentation of the capacity of proteostasis networks hold great promise for delaying the onset of age-related pathologies associated with proteome deterioration and for extending healthspan.
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17
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Basisty N, Holtz A, Schilling B. Accumulation of "Old Proteins" and the Critical Need for MS-based Protein Turnover Measurements in Aging and Longevity. Proteomics 2020; 20:e1800403. [PMID: 31408259 PMCID: PMC7015777 DOI: 10.1002/pmic.201800403] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 07/31/2019] [Indexed: 12/31/2022]
Abstract
Aging and age-related diseases are accompanied by proteome remodeling and progressive declines in cellular machinery required to maintain protein homeostasis (proteostasis), such as autophagy, ubiquitin-mediated degradation, and protein synthesis. While many studies have focused on capturing changes in proteostasis, the identification of proteins that evade these cellular processes has recently emerged as an approach to studying the aging proteome. With advances in proteomic technology, it is possible to monitor protein half-lives and protein turnover at the level of individual proteins in vivo. For large-scale studies, these technologies typically include the use of stable isotope labeling coupled with MS and comprehensive assessment of protein turnover rates. Protein turnover studies have revealed groups of highly relevant long-lived proteins (LLPs), such as the nuclear pore complexes, extracellular matrix proteins, and protein aggregates. Here, the role of LLPs during aging and age-related diseases and the methods used to identify and quantify their changes are reviewed. The methods available to conduct studies of protein turnover, used in combination with traditional proteomic methods, will enable the field to perform studies in a systems biology context, as changes in proteostasis may not be revealed in studies that solely measure differential protein abundances.
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Affiliation(s)
| | - Anja Holtz
- The Buck Institute for Research on AgingNovatoCAUSA
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18
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Evans HT, Bodea LG, Götz J. Cell-specific non-canonical amino acid labelling identifies changes in the de novo proteome during memory formation. eLife 2020; 9:e52990. [PMID: 31904341 PMCID: PMC6944461 DOI: 10.7554/elife.52990] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 12/13/2019] [Indexed: 12/15/2022] Open
Abstract
The formation of spatial long-term memory (LTM) requires the de novo synthesis of distinct sets of proteins; however, a non-biased examination of the de novo proteome in this process is lacking. Here, we generated a novel mouse strain, which enables cell-type-specific labelling of newly synthesised proteins with non-canonical amino acids (NCAAs) by genetically restricting the expression of the mutant tRNA synthetase, NLL-MetRS, to hippocampal neurons. By combining this labelling technique with an accelerated version of the active place avoidance task and bio-orthogonal non-canonical amino acid tagging (BONCAT) followed by SWATH quantitative mass spectrometry, we identified 156 proteins that were altered in synthesis in hippocampal neurons during spatial memory formation. In addition to observing increased synthesis of known proteins important in memory-related processes, such as glutamate receptor recycling, we also identified altered synthesis of proteins associated with mRNA splicing as a potential mechanism involved in spatial LTM formation.
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Affiliation(s)
- Harrison Tudor Evans
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain InstituteThe University of QueenslandBrisbaneAustralia
| | - Liviu-Gabriel Bodea
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain InstituteThe University of QueenslandBrisbaneAustralia
| | - Jürgen Götz
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain InstituteThe University of QueenslandBrisbaneAustralia
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19
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Perez MF, Lehner B. Vitellogenins - Yolk Gene Function and Regulation in Caenorhabditis elegans. Front Physiol 2019; 10:1067. [PMID: 31551797 PMCID: PMC6736625 DOI: 10.3389/fphys.2019.01067] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 08/05/2019] [Indexed: 12/14/2022] Open
Abstract
Vitellogenins are a family of yolk proteins that are by far the most abundant among oviparous animals. In the model nematode Caenorhabditis elegans, the 6 vitellogenins are among the most highly expressed genes in the adult hermaphrodite intestine, which produces copious yolk to provision eggs. In this article we review what is known about the vitellogenin genes and proteins in C. elegans, in comparison with vitellogenins in other taxa. We argue that the primary purpose of abundant vitellogenesis in C. elegans is to support post-embryonic development and fertility, rather than embryogenesis, especially in harsh environments. Increasing vitellogenin provisioning underlies several post-embryonic phenotypic alterations associated with advancing maternal age, demonstrating that vitellogenins can act as an intergenerational signal mediating the influence of parental physiology on progeny. We also review what is known about vitellogenin regulation - how tissue-, sex- and stage-specificity of expression is achieved, how vitellogenins are regulated by major signaling pathways, how vitellogenin expression is affected by extra-intestinal tissues and how environmental experience affects vitellogenesis. Lastly, we speculate whether C. elegans vitellogenins may play other roles in worm physiology.
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Affiliation(s)
- Marcos Francisco Perez
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Ben Lehner
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
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20
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Dall KB, Færgeman NJ. Metabolic regulation of lifespan from a C. elegans perspective. GENES & NUTRITION 2019; 14:25. [PMID: 31428207 PMCID: PMC6694653 DOI: 10.1186/s12263-019-0650-x] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 08/01/2019] [Indexed: 02/07/2023]
Abstract
Decline of cellular functions especially cognitive is a major deficit that arises with age in humans. Harnessing the strengths of small and genetic tractable model systems has revealed key conserved regulatory biochemical and signaling pathways that control aging. Here, we review some of the key signaling and biochemical pathways that coordinate aging processes with special emphasis on Caenorhabditis elegans as a model system and discuss how nutrients and metabolites can regulate lifespan by coordinating signaling and epigenetic programs. We focus on central nutrient-sensing pathways such as mTOR and insulin/insulin-like growth factor signaling and key transcription factors including the conserved basic helix-loop-helix transcription factor HLH-30/TFEB.
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Affiliation(s)
- Kathrine B. Dall
- Department of Biochemistry and Molecular Biology, Villum Center for Bioanalytical Sciences, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
| | - Nils J. Færgeman
- Department of Biochemistry and Molecular Biology, Villum Center for Bioanalytical Sciences, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
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21
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Evans HT, Benetatos J, van Roijen M, Bodea L, Götz J. Decreased synthesis of ribosomal proteins in tauopathy revealed by non-canonical amino acid labelling. EMBO J 2019; 38:e101174. [PMID: 31268600 PMCID: PMC6600635 DOI: 10.15252/embj.2018101174] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 04/12/2019] [Accepted: 04/17/2019] [Indexed: 01/06/2023] Open
Abstract
Tau is a scaffolding protein that serves multiple cellular functions that are perturbed in neurodegenerative diseases, including Alzheimer's disease (AD) and frontotemporal dementia (FTD). We have recently shown that amyloid-β, the second hallmark of AD, induces de novo protein synthesis of tau. Importantly, this activation was found to be tau-dependent, raising the question of whether FTD-tau by itself affects protein synthesis. We therefore applied non-canonical amino acid labelling to visualise and identify newly synthesised proteins in the K369I tau transgenic K3 mouse model of FTD. This revealed massively decreased protein synthesis in neurons containing pathologically phosphorylated tau, a finding confirmed in P301L mutant tau transgenic rTg4510 mice. Using quantitative SWATH-MS proteomics, we identified changes in 247 proteins of the de novo proteome of K3 mice. These included decreased synthesis of the ribosomal proteins RPL23, RPLP0, RPL19 and RPS16, a finding that was validated in both K3 and rTg4510 mice. Together, our findings present a potential pathomechanism by which pathological tau interferes with cellular functions through the dysregulation of ribosomal protein synthesis.
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Affiliation(s)
- Harrison Tudor Evans
- Clem Jones Centre for Ageing Dementia ResearchQueensland Brain InstituteThe University of QueenslandBrisbaneQldAustralia
| | - Joseph Benetatos
- Clem Jones Centre for Ageing Dementia ResearchQueensland Brain InstituteThe University of QueenslandBrisbaneQldAustralia
| | | | - Liviu‐Gabriel Bodea
- Clem Jones Centre for Ageing Dementia ResearchQueensland Brain InstituteThe University of QueenslandBrisbaneQldAustralia
| | - Jürgen Götz
- Clem Jones Centre for Ageing Dementia ResearchQueensland Brain InstituteThe University of QueenslandBrisbaneQldAustralia
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22
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Hong J, Dauros-Singorenko P, Whitcombe A, Payne L, Blenkiron C, Phillips A, Swift S. Analysis of the Escherichia coli extracellular vesicle proteome identifies markers of purity and culture conditions. J Extracell Vesicles 2019; 8:1632099. [PMID: 31275533 PMCID: PMC6598517 DOI: 10.1080/20013078.2019.1632099] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2018] [Revised: 04/15/2019] [Accepted: 06/10/2019] [Indexed: 02/06/2023] Open
Abstract
Bacteria release nano-sized extracellular vesicles (EVs) into the extracellular milieu. Bacterial EVs contain molecular cargo originating from the parent bacterium and have important roles in bacterial survival and pathogenesis. Using 8-plex iTRAQ approaches, we profiled the EV proteome of two Escherichia coli strains, uropathogenic (UPEC) 536 and probiotic Nissle 1917. For these strains, we compared the proteome of crude input EVs prepared by ultracentrifugation alone with EVs purified by either density gradient centrifugation (DGC) or size exclusion chromatography (SEC). We further compared the proteome of EVs from bacterial cultures that were grown in iron-restricted (R) and iron-supplemented (RF) conditions. Overall, outer membrane components were highly enriched, and bacterial inner membrane components were significantly depleted in both UPEC and Nissle EVs, in keeping with an outer membrane origin. In addition, we found enrichment of ribosome-related Gene Ontology terms in UPEC EVs and proteins involved in glycolytic processes and ligase activity in Nissle EVs. We have identified that three proteins (RbsB of UPEC in R; YoeA of UPEC in RF; BamA of Nissle in R) were consistently enriched in the DGC- and SEC-purified EV samples in comparison to their crude input EV, whereas conversely the 60 kDa chaperonin GroEL was enriched in the crude input EVs for both UPEC and Nissle in R condition. Such proteins may have utility as technical markers for assessing the purity of E. coli EV preparations. Several proteins were changed in their abundance depending on the iron availability in the media. Data are available via ProteomeXchange with identifier PXD011345. In summary, we have undertaken a comprehensive characterization of the protein content of E. coli EVs and found evidence of specific EV cargos for physiological activity and conserved protein cargo that may find utility as markers in the future. Abbreviation: DGC: density gradient centrifugation; DTT: 1,4-dithiothreitol; EV: extracellular vesicles; FDR: false discovery rate; GO: Gene Ontology; R: iron-restricted; RF: iron-supplemented; iTRAQ: isobaric tags for relative and absolute quantitation; OMV: outer membrane vesicle; SWATH-MS: sequential window acquisition of all theoretical mass spectra; SEC: size exclusion chromatography.
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Affiliation(s)
- Jiwon Hong
- School of Biological Sciences, University of Auckland, Auckland, New Zealand.,Surgical and Translational Research Centre, University of Auckland, Auckland, New Zealand
| | - Priscila Dauros-Singorenko
- School of Biological Sciences, University of Auckland, Auckland, New Zealand.,Department of Molecular Medicine and Pathology, University of Auckland, Auckland, New Zealand
| | - Alana Whitcombe
- Department of Molecular Medicine and Pathology, University of Auckland, Auckland, New Zealand
| | - Leo Payne
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Cherie Blenkiron
- School of Biological Sciences, University of Auckland, Auckland, New Zealand.,Department of Molecular Medicine and Pathology, University of Auckland, Auckland, New Zealand.,Department of Obstetrics and Gynecology, University of Auckland, Auckland, New Zealand
| | - Anthony Phillips
- School of Biological Sciences, University of Auckland, Auckland, New Zealand.,Surgical and Translational Research Centre, University of Auckland, Auckland, New Zealand
| | - Simon Swift
- Department of Molecular Medicine and Pathology, University of Auckland, Auckland, New Zealand
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23
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Soares TR, Reis SD, Pinho BR, Duchen MR, Oliveira JMA. Targeting the proteostasis network in Huntington's disease. Ageing Res Rev 2019; 49:92-103. [PMID: 30502498 PMCID: PMC6320389 DOI: 10.1016/j.arr.2018.11.006] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 11/19/2018] [Accepted: 11/26/2018] [Indexed: 12/31/2022]
Abstract
Huntington's disease (HD) is an autosomal dominant neurodegenerative disorder caused by a polyglutamine expansion mutation in the huntingtin protein. Expansions above 40 polyglutamine repeats are invariably fatal, following a symptomatic period characterised by choreiform movements, behavioural abnormalities, and cognitive decline. While mutant huntingtin (mHtt) is widely expressed from early life, most patients with HD present in mid-adulthood, highlighting the role of ageing in disease pathogenesis. mHtt undergoes proteolytic cleavage, misfolding, accumulation, and aggregation into inclusion bodies. The emerging model of HD pathogenesis proposes that the chronic production of misfolded mHtt overwhelms the chaperone machinery, diverting other misfolded clients to the proteasome and the autophagy pathways, ultimately leading to a global collapse of the proteostasis network. Multiple converging hypotheses also implicate ageing and its impact in the dysfunction of organelles as additional contributing factors to the collapse of proteostasis in HD. In particular, mitochondrial function is required to sustain the activity of ATP-dependent chaperones and proteolytic machinery. Recent studies elucidating mitochondria-endoplasmic reticulum interactions and uncovering a dedicated proteostasis machinery in mitochondria, suggest that mitochondria play a more active role in the maintenance of cellular proteostasis than previously thought. The enhancement of cytosolic proteostasis pathways shows promise for HD treatment, protecting cells from the detrimental effects of mHtt accumulation. In this review, we consider how mHtt and its post translational modifications interfere with protein quality control pathways, and how the pharmacological and genetic modulation of components of the proteostasis network impact disease phenotypes in cellular and in vivo HD models.
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Affiliation(s)
- Tânia R Soares
- REQUIMTE/LAQV, Department of Drug Sciences, Pharmacology Lab, Faculty of Pharmacy, University of Porto, 4050-313, Porto, Portugal; Department of Cell and Developmental Biology, University College London, London, WC1E 6BT, UK
| | - Sara D Reis
- REQUIMTE/LAQV, Department of Drug Sciences, Pharmacology Lab, Faculty of Pharmacy, University of Porto, 4050-313, Porto, Portugal
| | - Brígida R Pinho
- REQUIMTE/LAQV, Department of Drug Sciences, Pharmacology Lab, Faculty of Pharmacy, University of Porto, 4050-313, Porto, Portugal
| | - Michael R Duchen
- Department of Cell and Developmental Biology, University College London, London, WC1E 6BT, UK; Consortium for Mitochondrial Research (CfMR), University College London, Gower Street, WC1E 6BT, London, UK
| | - Jorge M A Oliveira
- REQUIMTE/LAQV, Department of Drug Sciences, Pharmacology Lab, Faculty of Pharmacy, University of Porto, 4050-313, Porto, Portugal; Consortium for Mitochondrial Research (CfMR), University College London, Gower Street, WC1E 6BT, London, UK.
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24
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Abstract
Protein homeostasis, or proteostasis, is required for proper cell function and thus must be
under tight maintenance in all circumstances. In crowded cell conditions, protein folding is sometimes
unfavorable, and this condition is worsened during stress situations. Cells cope with such stress
through the use of a Protein Quality Control system, which uses molecular chaperones and heat shock
proteins as its major players. This system aids with folding, avoiding misfolding and/or reversing aggregation.
A pivotal regulator of the response to heat stress is Heat Shock Factor, which is recruited to
the promoters of the chaperone genes, inducting their expression. This mini review aims to cover our
general knowledge on the structure and function of this factor.
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Affiliation(s)
- Natália Galdi Quel
- Institute of Chemistry and Institute of Biology, University of Campinas - UNICAMP, Campinas, Brazil
| | - Carlos H.I. Ramos
- Institute of Chemistry and Institute of Biology, University of Campinas - UNICAMP, Campinas, Brazil
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25
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Multilayered Reprogramming in Response to Persistent DNA Damage in C. elegans. Cell Rep 2018; 20:2026-2043. [PMID: 28854356 PMCID: PMC5583510 DOI: 10.1016/j.celrep.2017.08.028] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Revised: 06/30/2017] [Accepted: 08/04/2017] [Indexed: 11/23/2022] Open
Abstract
DNA damage causally contributes to aging and age-related diseases. Mutations in nucleotide excision repair (NER) genes cause highly complex congenital syndromes characterized by growth retardation, cancer susceptibility, and accelerated aging in humans. Orthologous mutations in Caenorhabditis elegans lead to growth delay, genome instability, and accelerated functional decline, thus allowing investigation of the consequences of persistent DNA damage during development and aging in a simple metazoan model. Here, we conducted proteome, lipidome, and phosphoproteome analysis of NER-deficient animals in response to UV treatment to gain comprehensive insights into the full range of physiological adaptations to unrepaired DNA damage. We derive metabolic changes indicative of a tissue maintenance program and implicate an autophagy-mediated proteostatic response. We assign central roles for the insulin-, EGF-, and AMPK-like signaling pathways in orchestrating the adaptive response to DNA damage. Our results provide insights into the DNA damage responses in the organismal context.
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26
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Mergoud dit Lamarche A, Molin L, Pierson L, Mariol M, Bessereau J, Gieseler K, Solari F. UNC-120/SRF independently controls muscle aging and lifespan in Caenorhabditis elegans. Aging Cell 2018; 17:e12713. [PMID: 29314608 PMCID: PMC5847867 DOI: 10.1111/acel.12713] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/20/2017] [Indexed: 12/21/2022] Open
Abstract
Aging is commonly defined as the loss of global homeostasis, which results from progressive alteration of all organs function. This model is currently challenged by recent data showing that interventions that extend lifespan do not always increase the overall fitness of the organism. These data suggest the existence of tissue-specific factors that regulate the pace of aging in a cell-autonomous manner. Here, we investigated aging of Caenorhabditis elegans striated muscles at the subcellular and the physiological level. Our data show that muscle aging is characterized by a dramatic decrease in the expression of genes encoding proteins required for muscle contraction, followed by a change in mitochondria morphology, and an increase in autophagosome number. Myofilaments, however, remain unaffected during aging. We demonstrated that the conserved transcription factor UNC-120/SRF regulates muscle aging biomarkers. Interestingly, the role of UNC-120/SRF in the control of muscle aging can be dissociated from its broader effect on lifespan. In daf-2/insulin/IGF1 receptor mutants, which exhibit a delayed appearance of muscle aging biomarkers and are long-lived, disruption of unc-120 accelerates muscle aging but does not suppress the lifespan phenotype of daf-2 mutant. Conversely, unc-120 overexpression delays muscle aging but does not increase lifespan. Overall, we demonstrate that UNC-120/SRF controls the pace of muscle aging in a cell-autonomous manner downstream of the insulin/IGF1 receptor.
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Affiliation(s)
- Adeline Mergoud dit Lamarche
- University of LyonUniversity of Lyon1 Claude Bernard Lyon1NeuroMyoGene InstituteCNRS UMR5310INSERM U1217LyonFrance
| | - Laurent Molin
- University of LyonUniversity of Lyon1 Claude Bernard Lyon1NeuroMyoGene InstituteCNRS UMR5310INSERM U1217LyonFrance
| | - Laura Pierson
- University of LyonUniversity of Lyon1 Claude Bernard Lyon1NeuroMyoGene InstituteCNRS UMR5310INSERM U1217LyonFrance
| | - Marie‐Christine Mariol
- University of LyonUniversity of Lyon1 Claude Bernard Lyon1NeuroMyoGene InstituteCNRS UMR5310INSERM U1217LyonFrance
| | - Jean‐Louis Bessereau
- University of LyonUniversity of Lyon1 Claude Bernard Lyon1NeuroMyoGene InstituteCNRS UMR5310INSERM U1217LyonFrance
- Hospices Civils de LyonFaculté de Médecine Lyon EstLyonFrance
| | - Kathrin Gieseler
- University of LyonUniversity of Lyon1 Claude Bernard Lyon1NeuroMyoGene InstituteCNRS UMR5310INSERM U1217LyonFrance
| | - Florence Solari
- University of LyonUniversity of Lyon1 Claude Bernard Lyon1NeuroMyoGene InstituteCNRS UMR5310INSERM U1217LyonFrance
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27
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Abstract
Progressive loss of proteostasis is a hallmark of aging that is marked by declines in various components of proteostasis machinery, including: autophagy, ubiquitin-mediated degradation, protein synthesis, and others. While declines in proteostasis have historically been observed as changes in these processes, or as bulk changes in the proteome, recent advances in proteomic methodologies have enabled the comprehensive measurement of turnover directly at the level of individual proteins in vivo. These methods, which utilize a combination of stable-isotope labeling, mass spectrometry, and specialized software analysis, have now been applied to various studies of aging and longevity. Here we review the role of proteostasis in aging and longevity, with a focus on the proteomic methods available to conduct protein turnover in aging models and the insights these studies have provided thus far.
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28
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Abstract
Ageing leads to dramatic changes in the physiology of many different tissues resulting in a spectrum of pathology. Nonetheless, many lines of evidence suggest that ageing is driven by highly conserved cell intrinsic processes, and a set of unifying hallmarks of ageing has been defined. Here, we survey reports of age-linked changes in basal gene expression across eukaryotes from yeast to human and identify six gene expression hallmarks of cellular ageing: downregulation of genes encoding mitochondrial proteins; downregulation of the protein synthesis machinery; dysregulation of immune system genes; reduced growth factor signalling; constitutive responses to stress and DNA damage; dysregulation of gene expression and mRNA processing. These encompass widely reported features of ageing such as increased senescence and inflammation, reduced electron transport chain activity and reduced ribosome synthesis, but also reveal a surprising lack of gene expression responses to known age-linked cellular stresses. We discuss how the existence of conserved transcriptomic hallmarks relates to genome-wide epigenetic differences underlying ageing clocks, and how the changing transcriptome results in proteomic alterations where data is available and to variations in cell physiology characteristic of ageing. Identification of gene expression events that occur during ageing across distant organisms should be informative as to conserved underlying mechanisms of ageing, and provide additional biomarkers to assess the effects of diet and other environmental factors on the rate of ageing.
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Affiliation(s)
- Stephen Frenk
- Department of Genetics, University of North Carolina, Chapel Hill, NC, 27599-3280, USA
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29
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Xia T, Horton ER, Salcini AE, Pocock R, Cox TR, Erler JT. Proteomic Characterization of Caenorhabditis elegans Larval Development. Proteomics 2017; 18. [PMID: 29178193 DOI: 10.1002/pmic.201700238] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Revised: 11/03/2017] [Indexed: 11/06/2022]
Abstract
The nematode Caenorhabditis elegans is widely used as a model organism to study cell and developmental biology. Quantitative proteomics of C. elegans is still in its infancy and, so far, most studies have been performed on adult worm samples. Here, we used quantitative mass spectrometry to characterize protein level changes across the four larval developmental stages (L1-L4) of C. elegans. In total, we identified 4130 proteins, and quantified 1541 proteins that were present across all four stages in three biological replicates from independent experiments. Using hierarchical clustering and functional ontological analyses, we identified 21 clusters containing proteins with similar protein profiles across the four stages, and highlighted the most overrepresented biological functions in each of these protein clusters. In addition, we used the dataset to identify putative larval stage-specific proteins in each individual developmental stage, as well as in the early and late developmental stages. In summary, this dataset provides system-wide analysis of protein level changes across the four C. elegans larval developmental stages, which serves as a useful resource for the C. elegans research community. MS data were deposited in ProteomeXchange (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository with the primary accession identifier PXD006676.
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Affiliation(s)
- Tian Xia
- Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark
| | - Edward R Horton
- Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark
| | | | - Roger Pocock
- Department of Anatomy and Developmental Biology, Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Monash University, Melbourne, Australia
| | - Thomas R Cox
- Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark.,Cancer Division, Garvan Institute of Medical Research and The Kinghorn Cancer Centre, St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, Australia
| | - Janine T Erler
- Biotech Research and Innovation Centre, University of Copenhagen, Copenhagen, Denmark
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30
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Scior A, Buntru A, Arnsburg K, Ast A, Iburg M, Juenemann K, Pigazzini ML, Mlody B, Puchkov D, Priller J, Wanker EE, Prigione A, Kirstein J. Complete suppression of Htt fibrilization and disaggregation of Htt fibrils by a trimeric chaperone complex. EMBO J 2017; 37:282-299. [PMID: 29212816 DOI: 10.15252/embj.201797212] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Revised: 10/19/2017] [Accepted: 10/26/2017] [Indexed: 02/06/2023] Open
Abstract
Huntington's disease (HD) is a neurodegenerative disorder caused by an expanded CAG trinucleotide repeat in the huntingtin gene (HTT). Molecular chaperones have been implicated in suppressing or delaying the aggregation of mutant Htt. Using in vitro and in vivo assays, we have identified a trimeric chaperone complex (Hsc70, Hsp110, and J-protein) that completely suppresses fibrilization of HttExon1Q48 The composition of this chaperone complex is variable as recruitment of different chaperone family members forms distinct functional complexes. The trimeric chaperone complex is also able to resolubilize Htt fibrils. We confirmed the biological significance of these findings in HD patient-derived neural cells and on an organismal level in Caenorhabditis elegans Among the proteins in this chaperone complex, the J-protein is the concentration-limiting factor. The single overexpression of DNAJB1 in HEK293T cells is sufficient to profoundly reduce HttExon1Q97 aggregation and represents a target of future therapeutic avenues for HD.
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Affiliation(s)
- Annika Scior
- Leibniz-Institute for Molecular Pharmacology (FMP) im Forschungsverbund Berlin, Berlin, Germany
| | | | - Kristin Arnsburg
- Leibniz-Institute for Molecular Pharmacology (FMP) im Forschungsverbund Berlin, Berlin, Germany
| | - Anne Ast
- Max Delbrueck Center for Molecular Medicine, Berlin, Germany
| | - Manuel Iburg
- Leibniz-Institute for Molecular Pharmacology (FMP) im Forschungsverbund Berlin, Berlin, Germany
| | - Katrin Juenemann
- Leibniz-Institute for Molecular Pharmacology (FMP) im Forschungsverbund Berlin, Berlin, Germany
| | - Maria Lucia Pigazzini
- Leibniz-Institute for Molecular Pharmacology (FMP) im Forschungsverbund Berlin, Berlin, Germany.,Charité - Universitätsmedizin and NeuroCure Cluster of Excellence, Berlin, Germany
| | - Barbara Mlody
- Max Delbrueck Center for Molecular Medicine, Berlin, Germany
| | - Dmytro Puchkov
- Leibniz-Institute for Molecular Pharmacology (FMP) im Forschungsverbund Berlin, Berlin, Germany
| | - Josef Priller
- Department of Neuropsychiatry and Laboratory of Molecular Psychiatry, Charite Universitätsmedizin Berlin, Berlin, Germany
| | - Erich E Wanker
- Max Delbrueck Center for Molecular Medicine, Berlin, Germany
| | | | - Janine Kirstein
- Leibniz-Institute for Molecular Pharmacology (FMP) im Forschungsverbund Berlin, Berlin, Germany
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31
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Omics Approaches for Identifying Physiological Adaptations to Genome Instability in Aging. Int J Mol Sci 2017; 18:ijms18112329. [PMID: 29113067 PMCID: PMC5713298 DOI: 10.3390/ijms18112329] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Revised: 10/25/2017] [Accepted: 10/29/2017] [Indexed: 12/25/2022] Open
Abstract
DNA damage causally contributes to aging and age-related diseases. The declining functioning of tissues and organs during aging can lead to the increased risk of succumbing to aging-associated diseases. Congenital syndromes that are caused by heritable mutations in DNA repair pathways lead to cancer susceptibility and accelerated aging, thus underlining the importance of genome maintenance for withstanding aging. High-throughput mass-spectrometry-based approaches have recently contributed to identifying signalling response networks and gaining a more comprehensive understanding of the physiological adaptations occurring upon unrepaired DNA damage. The insulin-like signalling pathway has been implicated in a DNA damage response (DDR) network that includes epidermal growth factor (EGF)-, AMP-activated protein kinases (AMPK)- and the target of rapamycin (TOR)-like signalling pathways, which are known regulators of growth, metabolism, and stress responses. The same pathways, together with the autophagy-mediated proteostatic response and the decline in energy metabolism have also been found to be similarly regulated during natural aging, suggesting striking parallels in the physiological adaptation upon persistent DNA damage due to DNA repair defects and long-term low-level DNA damage accumulation occurring during natural aging. These insights will be an important starting point to study the interplay between signalling networks involved in progeroid syndromes that are caused by DNA repair deficiencies and to gain new understanding of the consequences of DNA damage in the aging process.
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32
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Baxi K, Ghavidel A, Waddell B, Harkness TA, de Carvalho CE. Regulation of Lysosomal Function by the DAF-16 Forkhead Transcription Factor Couples Reproduction to Aging in Caenorhabditis elegans. Genetics 2017; 207:83-101. [PMID: 28696216 PMCID: PMC5586388 DOI: 10.1534/genetics.117.204222] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Accepted: 07/03/2017] [Indexed: 02/06/2023] Open
Abstract
Aging in eukaryotes is accompanied by widespread deterioration of the somatic tissue. Yet, abolishing germ cells delays the age-dependent somatic decline in Caenorhabditis elegans In adult worms lacking germ cells, the activation of the DAF-9/DAF-12 steroid signaling pathway in the gonad recruits DAF-16 activity in the intestine to promote longevity-associated phenotypes. However, the impact of this pathway on the fitness of normally reproducing animals is less clear. Here, we explore the link between progeny production and somatic aging and identify the loss of lysosomal acidity-a critical regulator of the proteolytic output of these organelles-as a novel biomarker of aging in C. elegans The increase in lysosomal pH in older worms is not a passive consequence of aging, but instead is timed with the cessation of reproduction, and correlates with the reduction in proteostasis in early adult life. Our results further implicate the steroid signaling pathway and DAF-16 in dynamically regulating lysosomal pH in the intestine of wild-type worms in response to the reproductive cycle. In the intestine of reproducing worms, DAF-16 promotes acidic lysosomes by upregulating the expression of v-ATPase genes. These findings support a model in which protein clearance in the soma is linked to reproduction in the gonad via the active regulation of lysosomal acidification.
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Affiliation(s)
- Kunal Baxi
- Department of Biology, University of Saskatchewan, Saskatoon, Saskatchewan S7N5E2, Canada
| | - Ata Ghavidel
- Department of Anatomy and Cell Biology, University of Saskatchewan, Saskatoon, Saskatchewan S7N5E2, Canada
| | - Brandon Waddell
- Department of Biology, University of Saskatchewan, Saskatoon, Saskatchewan S7N5E2, Canada
| | - Troy A Harkness
- Department of Anatomy and Cell Biology, University of Saskatchewan, Saskatoon, Saskatchewan S7N5E2, Canada
| | - Carlos E de Carvalho
- Department of Biology, University of Saskatchewan, Saskatoon, Saskatchewan S7N5E2, Canada
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33
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Harvald EB, Sprenger RR, Dall KB, Ejsing CS, Nielsen R, Mandrup S, Murillo AB, Larance M, Gartner A, Lamond AI, Færgeman NJ. Multi-omics Analyses of Starvation Responses Reveal a Central Role for Lipoprotein Metabolism in Acute Starvation Survival in C. elegans. Cell Syst 2017; 5:38-52.e4. [PMID: 28734827 DOI: 10.1016/j.cels.2017.06.004] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Revised: 03/03/2017] [Accepted: 06/08/2017] [Indexed: 12/21/2022]
Abstract
Starvation causes comprehensive metabolic changes, which are still not fully understood. Here, we used quantitative proteomics and RNA sequencing to examine the temporal starvation responses in wild-type Caenorhabditis elegans and animals lacking the transcription factor HLH-30. Our findings show that starvation alters the abundance of hundreds of proteins and mRNAs in a temporal manner, many of which are involved in central metabolic pathways, including lipoprotein metabolism. We demonstrate that premature death of hlh-30 animals under starvation can be prevented by knockdown of either vit-1 or vit-5, encoding two different lipoproteins. We further show that the size and number of intestinal lipid droplets under starvation are altered in hlh-30 animals, which can be rescued by knockdown of vit-1. Taken together, this indicates that survival of hlh-30 animals under starvation is closely linked to regulation of intestinal lipid stores. We provide the most detailed poly-omic analysis of starvation responses to date, which serves as a resource for further mechanistic studies of starvation.
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Affiliation(s)
- Eva Bang Harvald
- Department of Biochemistry and Molecular Biology, Villum Center for Bioanalytical Sciences, University of Southern Denmark, Odense M, Denmark
| | - Richard R Sprenger
- Department of Biochemistry and Molecular Biology, Villum Center for Bioanalytical Sciences, University of Southern Denmark, Odense M, Denmark
| | - Kathrine Brændgaard Dall
- Department of Biochemistry and Molecular Biology, Villum Center for Bioanalytical Sciences, University of Southern Denmark, Odense M, Denmark
| | - Christer S Ejsing
- Department of Biochemistry and Molecular Biology, Villum Center for Bioanalytical Sciences, University of Southern Denmark, Odense M, Denmark
| | - Ronni Nielsen
- Department of Biochemistry and Molecular Biology, Villum Center for Bioanalytical Sciences, University of Southern Denmark, Odense M, Denmark
| | - Susanne Mandrup
- Department of Biochemistry and Molecular Biology, Villum Center for Bioanalytical Sciences, University of Southern Denmark, Odense M, Denmark
| | - Alejandro Brenes Murillo
- Department of Biochemistry and Molecular Biology, Villum Center for Bioanalytical Sciences, University of Southern Denmark, Odense M, Denmark
| | - Mark Larance
- Centre for Gene Regulation and Expression, College of Life Science, University of Dundee, Dow Street, Dundee, UK
| | - Anton Gartner
- Centre for Gene Regulation and Expression, College of Life Science, University of Dundee, Dow Street, Dundee, UK
| | - Angus I Lamond
- Centre for Gene Regulation and Expression, College of Life Science, University of Dundee, Dow Street, Dundee, UK
| | - Nils J Færgeman
- Department of Biochemistry and Molecular Biology, Villum Center for Bioanalytical Sciences, University of Southern Denmark, Odense M, Denmark.
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34
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Dhondt I, Petyuk VA, Bauer S, Brewer HM, Smith RD, Depuydt G, Braeckman BP. Changes of Protein Turnover in Aging Caenorhabditis elegans. Mol Cell Proteomics 2017; 16:1621-1633. [PMID: 28679685 DOI: 10.1074/mcp.ra117.000049] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Indexed: 11/06/2022] Open
Abstract
Protein turnover rates severely decline in aging organisms, including C. elegans However, limited information is available on turnover dynamics at the individual protein level during aging. We followed changes in protein turnover at one-day resolution using a multiple-pulse 15N-labeling and accurate mass spectrometry approach. Forty percent of the proteome shows gradual slowdown in turnover with age, whereas only few proteins show increased turnover. Decrease in protein turnover was consistent for only a minority of functionally related protein subsets, including tubulins and vitellogenins, whereas randomly diverging turnover patterns with age were the norm. Our data suggests increased heterogeneity of protein turnover of the translation machinery, whereas protein turnover of ubiquitin-proteasome and antioxidant systems are well-preserved over time. Hence, we presume that maintenance of quality control mechanisms is a protective strategy in aging worms, although the ultimate proteome collapse is inescapable.
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Affiliation(s)
- Ineke Dhondt
- From the ‡Laboratory for Aging Physiology and Molecular Evolution, Biology Department, Ghent University, K.L. Ledeganckstraat 35, 9000 Ghent Belgium
| | - Vladislav A Petyuk
- §Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Sophie Bauer
- From the ‡Laboratory for Aging Physiology and Molecular Evolution, Biology Department, Ghent University, K.L. Ledeganckstraat 35, 9000 Ghent Belgium
| | - Heather M Brewer
- §Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Richard D Smith
- §Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Geert Depuydt
- From the ‡Laboratory for Aging Physiology and Molecular Evolution, Biology Department, Ghent University, K.L. Ledeganckstraat 35, 9000 Ghent Belgium.,¶Laboratory for Functional Genomics and Proteomics, Department of Biology, KU Leuven, Naamsestraat 59, 3000 Leuven, Belgium
| | - Bart P Braeckman
- From the ‡Laboratory for Aging Physiology and Molecular Evolution, Biology Department, Ghent University, K.L. Ledeganckstraat 35, 9000 Ghent Belgium;
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35
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Abstract
The incidence and prevalence of cardiac diseases, which are the main cause of death worldwide, are likely to increase because of population ageing. Prevailing theories about the mechanisms of ageing feature the gradual derailment of cellular protein homeostasis (proteostasis) and loss of protein quality control as central factors. In the heart, loss of protein patency, owing to flaws in genetically-determined design or because of environmentally-induced 'wear and tear', can overwhelm protein quality control, thereby triggering derailment of proteostasis and contributing to cardiac ageing. Failure of protein quality control involves impairment of chaperones, ubiquitin-proteosomal systems, autophagy, and loss of sarcomeric and cytoskeletal proteins, all of which relate to induction of cardiomyocyte senescence. Targeting protein quality control to maintain cardiac proteostasis offers a novel therapeutic strategy to promote cardiac health and combat cardiac disease. Currently marketed drugs are available to explore this concept in the clinical setting.
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Affiliation(s)
- Robert H Henning
- Department of Clinical Pharmacy and Pharmacology, University Medical Centre Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands
| | - Bianca J J M Brundel
- Department of Physiology, Amsterdam Cardiovascular Sciences, VU University Medical Center, De Boelelaan 1117, 1081 HZ Amsterdam, The Netherlands
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36
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Abstract
A healthy proteome is essential for cell survival. Protein misfolding is linked to a rapidly expanding list of human diseases, ranging from neurodegenerative diseases to aging and cancer. Many of these diseases are characterized by the accumulation of misfolded proteins in intra- and extracellular inclusions, such as amyloid plaques. The clear link between protein misfolding and disease highlights the need to better understand the elaborate machinery that manages proteome homeostasis, or proteostasis, in the cell. Proteostasis depends on a network of molecular chaperones and clearance pathways involved in the recognition, refolding, and/or clearance of aberrant proteins. Recent studies reveal that an integral part of the cellular management of misfolded proteins is their spatial sequestration into several defined compartments. Here, we review the properties, function, and formation of these compartments. Spatial sequestration plays a central role in protein quality control and cellular fitness and represents a critical link to the pathogenesis of protein aggregation-linked diseases.
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Affiliation(s)
| | - Rahul S Samant
- Department of Biology, Stanford University, Stanford, California 94305; , ,
| | - Judith Frydman
- Department of Biology, Stanford University, Stanford, California 94305; , ,
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37
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Endoplasmic Reticulum Stress Caused by Lipoprotein Accumulation Suppresses Immunity against Bacterial Pathogens and Contributes to Immunosenescence. mBio 2017; 8:mBio.00778-17. [PMID: 28559483 PMCID: PMC5449662 DOI: 10.1128/mbio.00778-17] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
The unfolded protein response (UPR) is a stress response pathway that is activated upon increased unfolded and/or misfolded proteins in the endoplasmic reticulum (ER), and enhanced ER stress response prolongs life span and improves immunity. However, the mechanism by which ER stress affects immunity remains poorly understood. Using the nematode Caenorhabditis elegans, we show that mutations in the lipoproteins vitellogenins, which are homologs of human apolipoprotein B-100, resulted in upregulation of the UPR. Lipoprotein accumulation in the intestine adversely affects the immune response and the life span of the organism, suggesting that it could be a contributing factor to immunosenescence. We show that lipoprotein accumulation inhibited the expression of several immune genes encoding proteins secreted by the intestinal cells in an IRE-1-independent manner. Our studies provide a mechanistic explanation for adverse effects caused by protein aggregation and ER stress on immunity and highlight the role of an IRE-1-independent pathway in the suppression of the expression of genes encoding secreted proteins. Increased accumulation of unfolded and/or misfolded proteins in the endoplasmic reticulum (ER) leads to enhanced ER stress. However, the mechanism(s) by which ER stress affects immunity remain understudied. Using the nematode C. elegans, we showed that mutations in lipoproteins lead to their accumulation in the intestine, causing ER stress and adversely affecting the life span of the organisms and their resistance to pathogen infection. Our results indicate that the ER stress caused by lipoprotein accumulation significantly reduced the levels of expression of genes encoding secreted immune effectors, contributing to immunosenescence. It is known that ER stress may suppress gene expression via IRE-1, which is a sensor of ER stress. The novel mechanism uncovered in our study is IRE-1 independent, which highlights the role of a novel process by which ER stress suppresses innate immunity.
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38
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Radwan M, Wood RJ, Sui X, Hatters DM. When proteostasis goes bad: Protein aggregation in the cell. IUBMB Life 2017; 69:49-54. [PMID: 28066979 DOI: 10.1002/iub.1597] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 12/09/2016] [Indexed: 12/12/2022]
Abstract
Protein aggregation is a hallmark of the major neurodegenerative diseases including Alzheimer's, Parkinson's, Huntington's and motor neuron and is a symptom of a breakdown in the management of proteome foldedness. Indeed, it is remarkable that under normal conditions cells can keep their proteome in a highly crowded and confined space without uncontrollable aggregation. Proteins pose a particular challenge relative to other classes of biomolecules because upon synthesis they must typically follow a complex folding pathway to reach their functional conformation (native state). Non-native conformations, including the unfolded nascent chain, are highly prone to aberrant interactions, leading to aggregation. Here we review recent advances in knowledge of proteostasis, approaches to monitor proteostasis and the impact that protein aggregation has on biology. We also include discussion of the outstanding challenges. © 2017 IUBMB Life, 69(2):49-54, 2017.
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Affiliation(s)
- Mona Radwan
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, 30 Flemington Road, Melbourne, Victoria, Australia
| | - Rebecca J Wood
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, 30 Flemington Road, Melbourne, Victoria, Australia
| | - Xiaojing Sui
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, 30 Flemington Road, Melbourne, Victoria, Australia
| | - Danny M Hatters
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, 30 Flemington Road, Melbourne, Victoria, Australia
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39
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Kikis EA. The struggle by Caenorhabditis elegans to maintain proteostasis during aging and disease. Biol Direct 2016; 11:58. [PMID: 27809888 PMCID: PMC5093949 DOI: 10.1186/s13062-016-0161-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Accepted: 10/24/2016] [Indexed: 01/07/2023] Open
Abstract
The presence of only small amounts of misfolded protein is an indication of a healthy proteome. Maintaining proteome health, or more specifically, “proteostasis,” is the purview of the “proteostasis network.” This network must respond to constant fluctuations in the amount of destabilized proteins caused by errors in protein synthesis and exposure to acute proteotoxic conditions. Aging is associated with a gradual increase in damaged and misfolded protein, which places additional stress on the machinery of the proteostasis network. In fact, despite the ability of the proteostasis machinery to readjust its stoichiometry in an attempt to maintain homeostasis, the capacity of cells to buffer against misfolding is strikingly limited. Therefore, subtle changes in the folding environment that occur during aging can significantly impact the health of the proteome. This decline and eventual collapse in proteostasis is most pronounced in individuals with neurodegenerative disorders such as Alzheimer’s Disease, Parkinson’s Disease, and Huntington’s Disease that are caused by the misfolding, aggregation, and toxicity of certain proteins. This review discusses how C. elegans models of protein misfolding have contributed to our current understanding of the proteostasis network, its buffering capacity, and its regulation. Reviewers: This article was reviewed by Luigi Bubacco, Patrick Lewis and Xavier Roucou.
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Affiliation(s)
- Elise A Kikis
- Biology Department, The University of the South, 735 University Avenue, Sewanee, TN, 37383, USA.
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40
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Zimmerman SM, Kim SK. New insights into old worm proteomes. WORM 2016; 5:e1184391. [PMID: 27695651 DOI: 10.1080/21624054.2016.1184391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Accepted: 04/20/2016] [Indexed: 10/21/2022]
Abstract
Aging is accompanied by large-scale changes in the proteome, which could have important consequences for cellular and organismal physiology. In this commentary, we review recent studies characterizing the aging proteome in C. elegans. We assess the evidence that the rates of protein synthesis, folding, and degradation change with age in C. elegans, and evaluate whether changes in these pathways limit normal lifespan. We also discuss large-scale studies measuring changes in the proteome with age that suggest that a failure to excrete reproductive proteins in post-reproductive animals plays a role in changing protein levels with age.
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Affiliation(s)
| | - Stuart K Kim
- Department of Genetics, Stanford University, Stanford, CA, USA; Department of Developmental Biology, Stanford University, Stanford, CA, USA
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41
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Abstract
Aging is a universal phenomenon in metazoans, characterized by a general decline of the organism physiology associated with an increased risk of mortality and morbidity. Aging of an organism correlates with a decline in function of its cells, as shown for muscle, immune, and neuronal cells. As the DNA content of most cells within an organism remains largely identical throughout the life span, age-associated transcriptional changes must be achieved by epigenetic mechanisms. However, how aging may impact on the epigenetic state of cells is only beginning to be understood. In light of a growing number of studies demonstrating that noncoding RNAs can provide molecular signals that regulate expression of protein-coding genes and define epigenetic states of cells, we hypothesize that noncoding RNAs could play a direct role in inducing age-associated profiles of gene expression. In this context, the role of long noncoding RNAs (lncRNAs) as regulators of gene expression might be important for the overall transcriptional landscape observed in aged human cells. The possible functions of lncRNAs and other noncoding RNAs, and their roles in the regulation of aging-related cellular pathways will be analyzed.
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42
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Deep Proteome Analysis Identifies Age-Related Processes in C. elegans. Cell Syst 2016; 3:144-159. [PMID: 27453442 PMCID: PMC5003814 DOI: 10.1016/j.cels.2016.06.011] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Revised: 05/11/2016] [Accepted: 06/21/2016] [Indexed: 11/22/2022]
Abstract
Effective network analysis of protein data requires high-quality proteomic datasets. Here, we report a near doubling in coverage of the C. elegans adult proteome, identifying >11,000 proteins in total with ∼9,400 proteins reproducibly detected in three biological replicates. Using quantitative mass spectrometry, we identify proteins whose abundances vary with age, revealing a concerted downregulation of proteins involved in specific metabolic pathways and upregulation of cellular stress responses with advancing age. Among these are ∼30 peroxisomal proteins, including the PRX-5/PEX5 import protein. Functional experiments confirm that protein import into the peroxisome is compromised in vivo in old animals. We also studied the behavior of the set of age-variant proteins in chronologically age-matched, long-lived daf-2 insulin/IGF-1-pathway mutants. Unexpectedly, the levels of many of these age-variant proteins did not scale with extended lifespan. This indicates that, despite their youthful appearance and extended lifespans, not all aspects of aging are reset in these long-lived mutants. Near doubling in C. elegans proteome coverage with age-dependent protein measurements Putative sub-cellular localization assignments for >6,000 nematode proteins Peroxisome protein import impaired during aging Most age-variant proteins do not scale with biological age in insulin/IGF-1 mutants
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Ferreira E, Shaw DM, Oddo S. Identification of learning-induced changes in protein networks in the hippocampi of a mouse model of Alzheimer's disease. Transl Psychiatry 2016; 6:e849. [PMID: 27378549 PMCID: PMC4969764 DOI: 10.1038/tp.2016.114] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Revised: 04/27/2016] [Accepted: 05/05/2016] [Indexed: 12/22/2022] Open
Abstract
Memory loss is the most profound clinical manifestation in Alzheimer's disease (AD); however, the molecular mechanisms underlying these deficits are poorly understood. Identification of the molecular pathways involved in the onset of cognitive deficits may lead to the identification of key events in the pathogenesis of AD. Using isobaric tags for relative and absolute quantitation (iTRAQ) and proteomic methods, here we identified learning-induced changes in the hippocampal proteome of non-transgenic (NonTg) and 3 × Tg-AD mice, a widely used animal model of AD. We found that expression of 192 proteins was differentially regulated by learning in NonTg mice. Notably, of these 192 proteins, only 28 were also differentially regulated by learning in 3 × Tg-AD mice, whereas the levels of 164 proteins were uniquely changed in NonTg mice but not in 3 × Tg-AD mice. These data suggest that during learning, 3 × Tg-AD mice fail to differentially regulate 164 proteins. Gene ontology and protein interaction analyses indicated that these proteins were overrepresented in RNA processing, specifically RNA transport, splicing and mRNA translation initiation pathways. These findings suggest that mRNA-processing events that take place during learning and memory are significantly altered in 3 × Tg-AD mice.
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Affiliation(s)
- E Ferreira
- Neurodegenerative Disease Research Center, Biodesign Institute School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - D M Shaw
- Neurodegenerative Disease Research Center, Biodesign Institute School of Life Sciences, Arizona State University, Tempe, AZ, USA
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - S Oddo
- Neurodegenerative Disease Research Center, Biodesign Institute School of Life Sciences, Arizona State University, Tempe, AZ, USA
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
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Zeng Y, Guo W, Xu G, Wang Q, Feng L, Long S, Liang F, Huang Y, Lu X, Li S, Zhou J, Burgunder JM, Pang J, Pei Z. Xyloketal-derived small molecules show protective effect by decreasing mutant Huntingtin protein aggregates in Caenorhabditis elegans model of Huntington's disease. DRUG DESIGN DEVELOPMENT AND THERAPY 2016; 10:1443-51. [PMID: 27110099 PMCID: PMC4835117 DOI: 10.2147/dddt.s94666] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Huntington's disease is an autosomal-dominant neurodegenerative disorder, with chorea as the most prominent manifestation. The disease is caused by abnormal expansion of CAG codon repeats in the IT15 gene, which leads to the expression of a glutamine-rich protein named mutant Huntingtin (Htt). Because of its devastating disease burden and lack of valid treatment, development of more effective therapeutics for Huntington's disease is urgently required. Xyloketal B, a natural product from mangrove fungus, has shown protective effects against toxicity in other neurodegenerative disease models such as Parkinson's and Alzheimer's diseases. To identify potential neuroprotective molecules for Huntington's disease, six derivatives of xyloketal B were screened in a Caenorhabditis elegans Huntington's disease model; all six compounds showed a protective effect. Molecular docking studies indicated that compound 1 could bind to residues GLN369 and GLN393 of the mutant Htt protein, forming a stable trimeric complex that can prevent the formation of mutant Htt aggregates. Taken together, we conclude that xyloketal derivatives could be novel drug candidates for treating Huntington's disease. Molecular target analysis is a good method to simulate the interaction between proteins and drug compounds. Further, protective candidate drugs could be designed in future using the guidance of molecular docking results.
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Affiliation(s)
- Yixuan Zeng
- Department of Neurology, National Key Clinical Department and Key Discipline of Neurology, Guangdong Key Laboratory for Diagnosis and Treatment of Major Neurological Disease, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, People's Republic of China; Guangzhou Center, Chinese Huntington's Disease Network, Guangzhou, Guangdong, People's Republic of China
| | - Wenyuan Guo
- Department of Neurology, National Key Clinical Department and Key Discipline of Neurology, Guangdong Key Laboratory for Diagnosis and Treatment of Major Neurological Disease, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, People's Republic of China
| | - Guangqing Xu
- Department of Rehabilitation, The First Affiliated Hospital, Guangzhou, Guangdong, People's Republic of China
| | - Qinmei Wang
- Key laboratory on Assisted Circulation, Ministry of Health, Department of Cardiovascular Medicine of the First Affiliated Hospital, Guangzhou, Guangdong, People's Republic of China
| | - Luyang Feng
- Department of Neurology, National Key Clinical Department and Key Discipline of Neurology, Guangdong Key Laboratory for Diagnosis and Treatment of Major Neurological Disease, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, People's Republic of China; Guangzhou Center, Chinese Huntington's Disease Network, Guangzhou, Guangdong, People's Republic of China
| | - Simei Long
- Department of Neurology, National Key Clinical Department and Key Discipline of Neurology, Guangdong Key Laboratory for Diagnosis and Treatment of Major Neurological Disease, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, People's Republic of China
| | - Fengyin Liang
- Department of Neurology, National Key Clinical Department and Key Discipline of Neurology, Guangdong Key Laboratory for Diagnosis and Treatment of Major Neurological Disease, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, People's Republic of China
| | - Yi Huang
- Department of Neurology, National Key Clinical Department and Key Discipline of Neurology, Guangdong Key Laboratory for Diagnosis and Treatment of Major Neurological Disease, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, People's Republic of China
| | - Xilin Lu
- Department of Neurology, National Key Clinical Department and Key Discipline of Neurology, Guangdong Key Laboratory for Diagnosis and Treatment of Major Neurological Disease, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, People's Republic of China
| | - Shichang Li
- School of Chemistry and Chemical Engineering, Sun Yat-sen University, Guangzhou, Guangdong, People's Republic of China
| | - Jiebin Zhou
- School of Chemistry and Chemical Engineering, Sun Yat-sen University, Guangzhou, Guangdong, People's Republic of China
| | - Jean-Marc Burgunder
- Swiss Huntington's Disease Center, Department of Neurology, University of Bern, Bern, Switzerland
| | - Jiyan Pang
- School of Chemistry and Chemical Engineering, Sun Yat-sen University, Guangzhou, Guangdong, People's Republic of China
| | - Zhong Pei
- Department of Neurology, National Key Clinical Department and Key Discipline of Neurology, Guangdong Key Laboratory for Diagnosis and Treatment of Major Neurological Disease, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, People's Republic of China; Guangzhou Center, Chinese Huntington's Disease Network, Guangzhou, Guangdong, People's Republic of China
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Wiersma M, Henning RH, Brundel BJJM. Derailed Proteostasis as a Determinant of Cardiac Aging. Can J Cardiol 2016; 32:1166.e11-20. [PMID: 27345610 DOI: 10.1016/j.cjca.2016.03.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Revised: 02/21/2016] [Accepted: 03/07/2016] [Indexed: 01/12/2023] Open
Abstract
Age comprises the single most important risk factor for cardiac disease development. The incidence and prevalence of cardiac diseases, which represents the main cause of death worldwide, will increase even more because of the aging population. A hallmark of aging is that it is accompanied by a gradual derailment of proteostasis (eg, the homeostasis of protein synthesis, folding, assembly, trafficking, function, and degradation). Loss of proteostasis is highly relevant to cardiomyocytes, because they are postmitotic cells and therefore not constantly replenished by proliferation. The derailment of proteostasis during aging is thus an important factor that preconditions for the development of age-related cardiac diseases, such as atrial fibrillation. In turn, frailty of proteostasis in aging cardiomyocytes is exemplified by its accelerated derailment in multiple cardiac diseases. Here, we review 2 major components of the proteostasis network, the stress-responsive and protein degradation pathways, in healthy and aged cardiomyocytes. Furthermore, we discuss the relation between derailment of proteostasis and age-related cardiac diseases, including atrial fibrillation. Finally, we introduce novel therapeutic targets that might possibly attenuate cardiac aging and thus limit cardiac disease progression.
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Affiliation(s)
- Marit Wiersma
- Department of Clinical Pharmacy and Pharmacology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands; Department of Physiology, Institute for Cardiovascular Research, VU University Medical Center, Amsterdam, The Netherlands
| | - Robert H Henning
- Department of Clinical Pharmacy and Pharmacology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Bianca J J M Brundel
- Department of Clinical Pharmacy and Pharmacology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands; Department of Physiology, Institute for Cardiovascular Research, VU University Medical Center, Amsterdam, The Netherlands.
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Yen CA, Curran SP. Gene-diet interactions and aging in C. elegans. Exp Gerontol 2016; 86:106-112. [PMID: 26924670 DOI: 10.1016/j.exger.2016.02.012] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Revised: 02/16/2016] [Accepted: 02/24/2016] [Indexed: 02/06/2023]
Abstract
Diet is the most variable aspect of life history, as most individuals have a large diversity of food choices, varying in the type and amount that they ingest. In the short-term, diet can affect metabolism and energy levels. However, in the long run, the net deficiency or excess of calories from diet can influence the progression and severity of age-related diseases. An old and yet still debated question is: how do specific dietary choices impact health- and lifespan? It is clear that genetics can play a critical role - perhaps just as important as diet choices. For example, poor diet in combination with genetic susceptibility can lead to metabolic disorders, such as obesity and type 2 diabetes. Recent work in Caenorhabditis elegans has identified the existence of diet-gene pairs, where the consequence of mutating a specific gene is only realized on specific diets. Many core metabolic pathways are conserved from worm to human. Although only a handful of these diet-gene pairs has been characterized, there are potentially hundreds, if not thousands, of such interactions, which may explain the variability in the rates of aging in humans and the incidence and severity of age-related diseases.
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Affiliation(s)
- Chia An Yen
- University of Southern California, Dornsife College of Letters, Arts, and Science, Department of Molecular and Computational Biology, United States
| | - Sean P Curran
- University of Southern California, Dornsife College of Letters, Arts, and Science, Department of Molecular and Computational Biology, United States; University of Southern California, Davis School of Gerontology, United States.
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Berber S, Wood M, Llamosas E, Thaivalappil P, Lee K, Liao BM, Chew YL, Rhodes A, Yucel D, Crossley M, Nicholas HR. Homeodomain-Interacting Protein Kinase (HPK-1) regulates stress responses and ageing in C. elegans. Sci Rep 2016; 6:19582. [PMID: 26791749 PMCID: PMC4726358 DOI: 10.1038/srep19582] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Accepted: 12/15/2015] [Indexed: 11/22/2022] Open
Abstract
Proteins of the Homeodomain-Interacting Protein Kinase (HIPK) family regulate an array of processes in mammalian systems, such as the DNA damage response, cellular proliferation and apoptosis. The nematode Caenorhabditis elegans has a single HIPK homologue called HPK-1. Previous studies have implicated HPK-1 in longevity control and suggested that this protein may be regulated in a stress-dependent manner. Here we set out to expand these observations by investigating the role of HPK-1 in longevity and in the response to heat and oxidative stress. We find that levels of HPK-1 are regulated by heat stress, and that HPK-1 contributes to survival following heat or oxidative stress. Additionally, we show that HPK-1 is required for normal longevity, with loss of HPK-1 function leading to a faster decline of physiological processes that reflect premature ageing. Through microarray analysis, we have found that HPK-1-regulated genes include those encoding proteins that serve important functions in stress responses such as Phase I and Phase II detoxification enzymes. Consistent with a role in longevity assurance, HPK-1 also regulates the expression of age-regulated genes. Lastly, we show that HPK-1 functions in the same pathway as DAF-16 to regulate longevity and reveal a new role for HPK-1 in development.
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Affiliation(s)
- Slavica Berber
- School of Molecular Bioscience, University of Sydney, Sydney, Australia
| | - Mallory Wood
- School of Molecular Bioscience, University of Sydney, Sydney, Australia
| | - Estelle Llamosas
- School of Molecular Bioscience, University of Sydney, Sydney, Australia
| | | | - Karen Lee
- School of Molecular Bioscience, University of Sydney, Sydney, Australia
| | - Bing Mana Liao
- School of Molecular Bioscience, University of Sydney, Sydney, Australia
| | - Yee Lian Chew
- School of Molecular Bioscience, University of Sydney, Sydney, Australia
| | - Aaron Rhodes
- School of Molecular Bioscience, University of Sydney, Sydney, Australia
| | - Duygu Yucel
- School of Molecular Bioscience, University of Sydney, Sydney, Australia
| | - Merlin Crossley
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Kensington, Australia
| | - Hannah R Nicholas
- School of Molecular Bioscience, University of Sydney, Sydney, Australia
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Bensaddek D, Narayan V, Nicolas A, Murillo AB, Gartner A, Kenyon CJ, Lamond AI. Micro-proteomics with iterative data analysis: Proteome analysis in C. elegans at the single worm level. Proteomics 2016; 16:381-92. [PMID: 26552604 PMCID: PMC4819713 DOI: 10.1002/pmic.201500264] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Revised: 09/21/2015] [Accepted: 11/02/2015] [Indexed: 01/01/2023]
Abstract
Proteomics studies typically analyze proteins at a population level, using extracts prepared from tens of thousands to millions of cells. The resulting measurements correspond to average values across the cell population and can mask considerable variation in protein expression and function between individual cells or organisms. Here, we report the development of micro‐proteomics for the analysis of Caenorhabditis elegans, a eukaryote composed of 959 somatic cells and ∼1500 germ cells, measuring the worm proteome at a single organism level to a depth of ∼3000 proteins. This includes detection of proteins across a wide dynamic range of expression levels (>6 orders of magnitude), including many chromatin‐associated factors involved in chromosome structure and gene regulation. We apply the micro‐proteomics workflow to measure the global proteome response to heat‐shock in individual nematodes. This shows variation between individual animals in the magnitude of proteome response following heat‐shock, including variable induction of heat‐shock proteins. The micro‐proteomics pipeline thus facilitates the investigation of stochastic variation in protein expression between individuals within an isogenic population of C. elegans. All data described in this study are available online via the Encyclopedia of Proteome Dynamics (http://www.peptracker.com/epd), an open access, searchable database resource.
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Affiliation(s)
- Dalila Bensaddek
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dow Street, Dundee, United Kingdom
| | - Vikram Narayan
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dow Street, Dundee, United Kingdom.,Department of Biochemistry and Biophysics, Genentech Hall, University of California, San Francisco, CA, USA
| | - Armel Nicolas
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dow Street, Dundee, United Kingdom
| | - Alejandro Brenes Murillo
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dow Street, Dundee, United Kingdom
| | - Anton Gartner
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dow Street, Dundee, United Kingdom
| | - Cynthia J Kenyon
- Department of Biochemistry and Biophysics, Genentech Hall, University of California, San Francisco, CA, USA
| | - Angus I Lamond
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dow Street, Dundee, United Kingdom
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Zimmerman SM, Hinkson IV, Elias JE, Kim SK. Reproductive Aging Drives Protein Accumulation in the Uterus and Limits Lifespan in C. elegans. PLoS Genet 2015; 11:e1005725. [PMID: 26656270 PMCID: PMC4676719 DOI: 10.1371/journal.pgen.1005725] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2015] [Accepted: 11/13/2015] [Indexed: 11/26/2022] Open
Abstract
Aging in Caenorhabditis elegans is characterized by widespread physiological and molecular changes, but the mechanisms that determine the rate at which these changes occur are not well understood. In this study, we identify a novel link between reproductive aging and somatic aging in C. elegans. By measuring global age-related changes in the proteome, we identify a previously uncharacterized group of secreted proteins in the adult uterus that dramatically increase in abundance with age. This accumulation is blunted in animals with an extended reproductive period and accelerated in sterile animals lacking a germline. Uterine proteins are not removed in old post-reproductive animals or in young vulvaless worms, indicating that egg-laying is necessary for their rapid removal in wild-type young animals. Together, these results suggest that age-induced infertility contributes to extracellular protein accumulation in the uterus with age. Finally, we show that knocking down multiple age-increased proteins simultaneously extends lifespan. These results provide a mechanistic example of how the cessation of reproduction contributes to detrimental changes in the soma, and demonstrate how the timing of reproductive decline can influence the rate of aging. To understand the process of aging at the molecular level in C. elegans, we measured changes in protein abundance with age, determined whether these age-related protein changes lead to dysfunction in old animals, and have elucidated one of the upstream pathways responsible for these aging changes. We found that egg-laying in young worms permits removal of a novel class of proteins present in the uterus. When the reproductive period ends, the removal of uterine proteins stops, causing them to accumulate to toxic levels. This shows that the timing of reproductive decline influences the rate of somatic aging. The concept that the reproductive period has a direct role in specifying the rate of aging of the soma likely applies to other species as well.
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Affiliation(s)
- Stephanie M. Zimmerman
- Department of Genetics, Stanford University, Stanford, California, United States of America
| | - Izumi V. Hinkson
- Department of Chemical and Systems Biology, Stanford University, Stanford, California, United States of America
| | - Joshua E. Elias
- Department of Chemical and Systems Biology, Stanford University, Stanford, California, United States of America
| | - Stuart K. Kim
- Department of Genetics, Stanford University, Stanford, California, United States of America
- Department of Developmental Biology, Stanford University, Stanford, California, United States of America
- * E-mail:
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Metabolome and proteome changes with aging in Caenorhabditis elegans. Exp Gerontol 2015; 72:67-84. [PMID: 26390854 DOI: 10.1016/j.exger.2015.09.013] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Revised: 09/15/2015] [Accepted: 09/16/2015] [Indexed: 01/13/2023]
Abstract
To expand the understanding of aging in the model organism Caenorhabditis elegans, global quantification of metabolite and protein levels in young and aged nematodes was performed using mass spectrometry. With age, there was a decreased abundance of proteins functioning in transcription termination, mRNA degradation, mRNA stability, protein synthesis, and proteasomal function. Furthermore, there was altered S-adenosyl methionine metabolism as well as a decreased abundance of the S-adenosyl methionine synthetase (SAMS-1) protein. Other aging-related changes included alterations in free fatty acid levels and composition, decreased levels of ribosomal proteins, decreased levels of NADP-dependent isocitrate dehydrogenase (IDH1), a shift in the cellular redox state, an increase in sorbitol content, alterations in free amino acid levels, and indications of altered muscle function and sarcoplasmic reticulum Ca(2+) homeostasis. There were also decreases in pyrimidine and purine metabolite levels, most markedly nitrogenous bases. Supplementing the culture medium with cytidine (a pyrimidine nucleoside) or hypoxanthine (a purine base) increased lifespan slightly, suggesting that aging-induced alterations in ribonucleotide metabolism affect lifespan. An age-related increase in body size, lipotoxicity from ectopic yolk lipoprotein accumulation, a decline in NAD(+) levels, and mitochondrial electron transport chain dysfunction may explain many of these changes. In addition, dietary restriction in aged worms resulting from sarcopenia of the pharyngeal pump likely decreases the abundance of SAMS-1, possibly leading to decreased phosphatidylcholine levels, larger lipid droplets, and ER and mitochondrial stress. The complementary use of proteomics and metabolomics yielded unique insights into the molecular processes altered with age in C. elegans.
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