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Park SG, Keller A, Kaiser NK, Bruce JE. Interactome dynamics during heat stress signal transmission and reception. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.29.591712. [PMID: 38746244 PMCID: PMC11092488 DOI: 10.1101/2024.04.29.591712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Among evolved molecular mechanisms, cellular stress response to altered environmental conditions to promote survival is among the most fundamental. The presence of stress-induced unfolded or misfolded proteins and molecular registration of these events constitute early steps in cellular stress response. However, what stress-induced changes in protein conformations and protein-protein interactions within cells initiate stress response and how these features are recognized by cellular systems are questions that have remained difficult to answer, requiring new approaches. Quantitative in vivo chemical cross-linking coupled with mass spectrometry (qXL-MS) is an emerging technology that provides new insight on protein conformations, protein-protein interactions and how the interactome changes during perturbation within cells, organelles, and even tissues. In this work, qXL-MS and quantitative proteome analyses were applied to identify significant time-dependent interactome changes that occur prior to large-scale proteome abundance remodeling within cells subjected to heat stress. Interactome changes were identified within minutes of applied heat stress, including stress-induced changes in chaperone systems as expected due to altered functional demand. However, global analysis of all interactome changes revealed the largest significant enrichment in the gene ontology molecular function term of RNA binding. This group included more than 100 proteins among multiple components of protein synthesis machinery, including mRNA binding, spliceosomes, and ribosomes. These interactome data provide new conformational insight on the complex relationship that exists between transcription, translation and cellular stress response mechanisms. Moreover, stress-dependent interactome changes suggest that in addition to conformational stabilization of RNA-binding proteins, adaptation of RNA as interacting ligands offers an additional fitness benefit resultant from generally lower RNA thermal stability. As such, RNA ligands also serve as fundamental temperature sensors that signal stress through decreased conformational regulation of their protein partners as was observed in these interactome dynamics.
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Thomas C, Erni R, Wu JY, Fischer F, Lamers G, Grigolon G, Mitchell SJ, Zarse K, Carreira EM, Ristow M. A naturally occurring polyacetylene isolated from carrots promotes health and delays signatures of aging. Nat Commun 2023; 14:8142. [PMID: 38065964 PMCID: PMC10709416 DOI: 10.1038/s41467-023-43672-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 11/16/2023] [Indexed: 12/18/2023] Open
Abstract
To ameliorate or even prevent signatures of aging in ultimately humans, we here report the identification of a previously undescribed polyacetylene contained in the root of carrots (Daucus carota), hereafter named isofalcarintriol, which we reveal as potent promoter of longevity in the nematode C. elegans. We assign the absolute configuration of the compound as (3 S,8 R,9 R,E)-heptadeca-10-en-4,6-diyne-3,8,9-triol, and develop a modular asymmetric synthesis route for all E-isofalcarintriol stereoisomers. At the molecular level, isofalcarintriol affects cellular respiration in mammalian cells, C. elegans, and mice, and interacts with the α-subunit of the mitochondrial ATP synthase to promote mitochondrial biogenesis. Phenotypically, this also results in decreased mammalian cancer cell growth, as well as improved motility and stress resistance in C. elegans, paralleled by reduced protein accumulation in nematodal models of neurodegeneration. In addition, isofalcarintriol supplementation to both wild-type C57BL/6NRj mice on high-fat diet, and aged mice on chow diet results in improved glucose metabolism, increased exercise endurance, and attenuated parameters of frailty at an advanced age. Given these diverse effects on health parameters in both nematodes and mice, isofalcarintriol might become a promising mitohormesis-inducing compound to delay, ameliorate, or prevent aging-associated diseases in humans.
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Affiliation(s)
- Carolin Thomas
- Laboratory of Energy Metabolism, Institute of Translational Medicine, Department of Health Sciences and Technology, Swiss Federal Institute (ETH) Zurich, Schorenstrasse 16, 8603, Schwerzenbach, Switzerland
| | - Reto Erni
- Laboratory of Chemistry and Applied Biosciences, Department of Organic Chemistry, Swiss Federal Institute (ETH) Zurich, Vladimir-Prelog-Weg 1-5/10, Zurich, 8093, Switzerland
- Biozentrum, University of Basel, Basel, 4056, Switzerland
| | - Jia Yee Wu
- Laboratory of Energy Metabolism, Institute of Translational Medicine, Department of Health Sciences and Technology, Swiss Federal Institute (ETH) Zurich, Schorenstrasse 16, 8603, Schwerzenbach, Switzerland
| | - Fabian Fischer
- Laboratory of Energy Metabolism, Institute of Translational Medicine, Department of Health Sciences and Technology, Swiss Federal Institute (ETH) Zurich, Schorenstrasse 16, 8603, Schwerzenbach, Switzerland
- CureVac SE, Tübingen, 72076, Germany
| | - Greta Lamers
- Laboratory of Energy Metabolism, Institute of Translational Medicine, Department of Health Sciences and Technology, Swiss Federal Institute (ETH) Zurich, Schorenstrasse 16, 8603, Schwerzenbach, Switzerland
| | - Giovanna Grigolon
- Laboratory of Energy Metabolism, Institute of Translational Medicine, Department of Health Sciences and Technology, Swiss Federal Institute (ETH) Zurich, Schorenstrasse 16, 8603, Schwerzenbach, Switzerland
| | - Sarah J Mitchell
- Ludwig Princeton Branch, Princeton University, Princeton, NJ, 08540, USA
| | - Kim Zarse
- Laboratory of Energy Metabolism, Institute of Translational Medicine, Department of Health Sciences and Technology, Swiss Federal Institute (ETH) Zurich, Schorenstrasse 16, 8603, Schwerzenbach, Switzerland
- Institute of Experimental Endocrinology, Charité Universitätsmedizin Berlin, Berlin, 10117, Germany
| | - Erick M Carreira
- Laboratory of Chemistry and Applied Biosciences, Department of Organic Chemistry, Swiss Federal Institute (ETH) Zurich, Vladimir-Prelog-Weg 1-5/10, Zurich, 8093, Switzerland.
| | - Michael Ristow
- Laboratory of Energy Metabolism, Institute of Translational Medicine, Department of Health Sciences and Technology, Swiss Federal Institute (ETH) Zurich, Schorenstrasse 16, 8603, Schwerzenbach, Switzerland.
- Institute of Experimental Endocrinology, Charité Universitätsmedizin Berlin, Berlin, 10117, Germany.
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Lee H, Lee SJV. Recent Progress in Regulation of Aging by Insulin/IGF-1 Signaling in Caenorhabditis elegans. Mol Cells 2022; 45:763-770. [PMID: 36380728 PMCID: PMC9676989 DOI: 10.14348/molcells.2022.0097] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 08/18/2022] [Accepted: 08/20/2022] [Indexed: 11/18/2022] Open
Abstract
Caenorhabditis elegans has been used as a major model organism to identify genetic factors that regulate organismal aging and longevity. Insulin/insulin-like growth factor 1 (IGF- 1) signaling (IIS) regulates aging in many species, ranging from nematodes to humans. C. elegans is a nonpathogenic genetic nematode model, which has been extensively utilized to identify molecular and cellular components that function in organismal aging and longevity. Here, we review the recent progress in the role of IIS in aging and longevity, which involves direct regulation of protein and RNA homeostasis, stress resistance, metabolism and the activities of the endocrine system. We also discuss recently identified genetic factors that interact with canonical IIS components to regulate aging and health span in C. elegans. We expect this review to provide valuable insights into understanding animal aging, which could eventually help develop anti-aging drugs for humans.
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Affiliation(s)
- Hanseul Lee
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea
| | - Seung-Jae V. Lee
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea
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Fischer F, Benner C, Goyala A, Grigolon G, Vitiello D, Wu J, Zarse K, Ewald CY, Ristow M. Ingestion of single guide RNAs induces gene overexpression and extends lifespan in Caenorhabditis elegans via CRISPR activation. J Biol Chem 2022; 298:102085. [PMID: 35636511 PMCID: PMC9243178 DOI: 10.1016/j.jbc.2022.102085] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 05/17/2022] [Accepted: 05/18/2022] [Indexed: 11/21/2022] Open
Abstract
Inhibition of gene expression in Caenorhabditis elegans, a versatile model organism for studying the genetics of development and aging, is achievable by feeding nematodes with bacteria expressing specific dsRNAs. Overexpression of hypoxia-inducible factor 1 (hif-1) or heat-shock factor 1 (hsf-1) by conventional transgenesis has previously been shown to promote nematodal longevity. However, it is unclear whether other methods of gene overexpression are feasible, particularly with the advent of CRISPR-based techniques. Here, we show that feeding C. elegans engineered to stably express a Cas9-derived synthetic transcription factor with bacteria expressing promoter-specific single guide RNAs (sgRNAs) also allows activation of gene expression. We demonstrate that CRISPR activation via ingested sgRNAs specific for the respective promoter regions of hif-1 or hsf-1 increases gene expression and extends lifespan of C. elegans. Furthermore, and as an in silico resource for future studies aiming to use CRISPR activation in C. elegans, we provide predicted promoter-specific sgRNA target sequences for >13,000 C. elegans genes with experimentally defined transcription start sites. We anticipate that the approach and components described herein will help to facilitate genome-wide gene overexpression studies, for example, to identify modulators of aging or other phenotypes of interest, by enabling induction of transcription by feeding of sgRNA-expressing bacteria to nematodes.
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Affiliation(s)
- Fabian Fischer
- Energy Metabolism Laboratory, Department of Health Sciences and Technology, Institute of Translational Medicine, Swiss Federal Institute of Technology (ETH) Zurich, Schwerzenbach, Switzerland.
| | - Christoph Benner
- Energy Metabolism Laboratory, Department of Health Sciences and Technology, Institute of Translational Medicine, Swiss Federal Institute of Technology (ETH) Zurich, Schwerzenbach, Switzerland; Science and Policy Program, Life Science Zurich Graduate School, Zurich, Switzerland
| | - Anita Goyala
- Extracellular Matrix Regeneration Laboratory, Department of Health Sciences and Technology, Institute of Translational Medicine, Swiss Federal Institute of Technology (ETH) Zurich, Schwerzenbach, Switzerland
| | - Giovanna Grigolon
- Energy Metabolism Laboratory, Department of Health Sciences and Technology, Institute of Translational Medicine, Swiss Federal Institute of Technology (ETH) Zurich, Schwerzenbach, Switzerland
| | - Davide Vitiello
- Energy Metabolism Laboratory, Department of Health Sciences and Technology, Institute of Translational Medicine, Swiss Federal Institute of Technology (ETH) Zurich, Schwerzenbach, Switzerland
| | - JiaYee Wu
- Energy Metabolism Laboratory, Department of Health Sciences and Technology, Institute of Translational Medicine, Swiss Federal Institute of Technology (ETH) Zurich, Schwerzenbach, Switzerland
| | - Kim Zarse
- Energy Metabolism Laboratory, Department of Health Sciences and Technology, Institute of Translational Medicine, Swiss Federal Institute of Technology (ETH) Zurich, Schwerzenbach, Switzerland; Charité - Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Experimental Endocrinology and Diabetology, Berlin, Germany
| | - Collin Y Ewald
- Extracellular Matrix Regeneration Laboratory, Department of Health Sciences and Technology, Institute of Translational Medicine, Swiss Federal Institute of Technology (ETH) Zurich, Schwerzenbach, Switzerland
| | - Michael Ristow
- Energy Metabolism Laboratory, Department of Health Sciences and Technology, Institute of Translational Medicine, Swiss Federal Institute of Technology (ETH) Zurich, Schwerzenbach, Switzerland; Charité - Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Experimental Endocrinology and Diabetology, Berlin, Germany.
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Fischer F, Grigolon G, Benner C, Ristow M. Evolutionarily conserved transcription factors as regulators of longevity and targets for geroprotection. Physiol Rev 2022; 102:1449-1494. [PMID: 35343830 DOI: 10.1152/physrev.00017.2021] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Aging is the single largest risk factor for many debilitating conditions, including heart diseases, stroke, cancer, diabetes, and neurodegenerative disorders. While far from understood in its full complexity, it is scientifically well-established that aging is influenced by genetic and environmental factors, and can be modulated by various interventions. One of aging's early hallmarks are aberrations in transcriptional networks, controlling for example metabolic homeostasis or the response to stress. Evidence in different model organisms abounds that a number of evolutionarily conserved transcription factors, which control such networks, can affect lifespan and healthspan across species. These transcription factors thus potentially represent conserved regulators of longevity and are emerging as important targets in the challenging quest to develop treatments to mitigate age-related diseases, and possibly even to slow aging itself. This review provides an overview of evolutionarily conserved transcription factors that impact longevity or age-related diseases in at least one multicellular model organism (nematodes, flies, or mice), and/or are tentatively linked to human aging. Discussed is the general evidence for transcriptional regulation of aging and disease, followed by a more detailed look at selected transcription factor families, the common metabolic pathways involved, and the targeting of transcription factors as a strategy for geroprotective interventions.
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Affiliation(s)
- Fabian Fischer
- Energy Metabolism Laboratory, Institute of Translational Medicine, Department of Health Sciences and Technology, Swiss Federal Institute of Technology (ETH) Zurich, Schwerzenbach, Switzerland
| | - Giovanna Grigolon
- Energy Metabolism Laboratory, Institute of Translational Medicine, Department of Health Sciences and Technology, Swiss Federal Institute of Technology (ETH) Zurich, Schwerzenbach, Switzerland
| | - Christoph Benner
- Energy Metabolism Laboratory, Institute of Translational Medicine, Department of Health Sciences and Technology, Swiss Federal Institute of Technology (ETH) Zurich, Schwerzenbach, Switzerland
| | - Michael Ristow
- Energy Metabolism Laboratory, Institute of Translational Medicine, Department of Health Sciences and Technology, Swiss Federal Institute of Technology (ETH) Zurich, Schwerzenbach, Switzerland
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