1
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Kim D, Trang K, Pees B, Karimzadegan S, Bodkhe R, Hammond S, Shapira M. Identification of intestinal mediators of Caenorhabditis elegans DBL-1/BMP immune signaling shaping gut microbiome composition. mBio 2025; 16:e0370324. [PMID: 39878514 PMCID: PMC11898619 DOI: 10.1128/mbio.03703-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2024] [Accepted: 01/07/2025] [Indexed: 01/31/2025] Open
Abstract
The composition of the gut microbiome is determined by a complex interplay of diet, host genetics, microbe-microbe interactions, abiotic factors, and stochasticity. Previous studies have demonstrated the importance of host genetics in community assembly of the Caenorhabditis elegans gut microbiome and identified a central role for DBL-1/BMP immune signaling in determining the abundance of gut Enterobacteriaceae. However, the effects of DBL-1 signaling on gut bacteria were found to depend on its activation in extra-intestinal tissues, highlighting a gap in our understanding of the proximal factors that determine microbiome composition. In the present study, we used RNA-seq gene expression analysis of wildtype, dbl-1 and sma-3 mutants, and dbl-1 over-expressors to identify candidate DBL-1/BMP targets that may mediate the pathway's effects on gut commensals. Bacterial colonization experiments in mutants, or following RNAi-mediated knock-down of candidate genes specifically in the intestine, demonstrated their local contribution to intestinal control of Enterobacteriaceae abundance. Furthermore, epistasis analysis suggested that these contributions were downstream of the DBL-1 pathway, together suggesting that examined candidates were intestinal effectors and mediators of DBL-1 signaling, contributing to the shaping of gut microbiome composition.IMPORTANCECompared to the roles of diet, environmental availability, or lifestyle in determining gut microbiome composition, that of genetic factors is the least understood and often underestimated. The identification of intestinal effectors of distinct molecular functions that control enteric bacteria offers a glimpse into the genetic logic of microbiome control as well as a list of targets for future exploration of this logic.
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Affiliation(s)
- Dan Kim
- Department of Integrative Biology, University of California, Berkeley, Berkeley, California, USA
| | - Kenneth Trang
- Department of Integrative Biology, University of California, Berkeley, Berkeley, California, USA
| | - Barbara Pees
- Department of Integrative Biology, University of California, Berkeley, Berkeley, California, USA
| | - Siavash Karimzadegan
- Department of Integrative Biology, University of California, Berkeley, Berkeley, California, USA
| | - Rahul Bodkhe
- Department of Integrative Biology, University of California, Berkeley, Berkeley, California, USA
| | - Sabrina Hammond
- Department of Integrative Biology, University of California, Berkeley, Berkeley, California, USA
| | - Michael Shapira
- Department of Integrative Biology, University of California, Berkeley, Berkeley, California, USA
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2
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Cheng E, Lu R, Gerhold AR. Non-autonomous insulin signaling delays mitotic progression in C. elegans germline stem and progenitor cells. PLoS Genet 2024; 20:e1011351. [PMID: 39715269 PMCID: PMC11706408 DOI: 10.1371/journal.pgen.1011351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2024] [Revised: 01/07/2025] [Accepted: 11/25/2024] [Indexed: 12/25/2024] Open
Abstract
Stem and progenitor cell mitosis is essential for tissue development and homeostasis. How these cells ensure proper chromosome segregation, and thereby maintain mitotic fidelity, in the complex physiological environment of a living animal is poorly understood. Here we use in situ live-cell imaging of C. elegans germline stem and progenitor cells (GSPCs) to ask how the signaling environment influences stem and progenitor cell mitosis in vivo. Through a candidate screen we identify a new role for the insulin/IGF receptor (IGFR), daf-2, during GSPC mitosis. Mitosis is delayed in daf-2/IGFR mutants, and these delays require canonical, DAF-2/IGFR to DAF-16/FoxO insulin signaling, here acting cell non-autonomously from the soma. Interestingly, mitotic delays in daf-2/IGFR mutants depend on the spindle assembly checkpoint but are not accompanied by a loss of mitotic fidelity. Correspondingly, we show that caloric restriction, which delays GSPC mitosis and compromises mitotic fidelity, does not act via the canonical insulin signaling pathway, and instead requires AMP-activated kinase (AMPK). Together this work demonstrates that GSPC mitosis is influenced by at least two genetically separable signaling pathways and highlights the importance of signaling networks for proper stem and progenitor cell mitosis in vivo.
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Affiliation(s)
- Eric Cheng
- Department of Biology, McGill University, Montréal, Canada
| | - Ran Lu
- Department of Biology, McGill University, Montréal, Canada
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3
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Mahapatra A, Dhakal A, Noguchi A, Vadlamani P, Hundley HA. ADAR-mediated regulation of PQM-1 expression in neurons impacts gene expression throughout C. elegans and regulates survival from hypoxia. PLoS Biol 2023; 21:e3002150. [PMID: 37747897 PMCID: PMC10553819 DOI: 10.1371/journal.pbio.3002150] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 10/05/2023] [Accepted: 08/23/2023] [Indexed: 09/27/2023] Open
Abstract
The ability to alter gene expression programs in response to changes in environmental conditions is central to the ability of an organism to thrive. For most organisms, the nervous system serves as the master regulator in communicating information about the animal's surroundings to other tissues. The information relay centers on signaling pathways that cue transcription factors in a given cell type to execute a specific gene expression program, but also provide a means to signal between tissues. The transcription factor PQM-1 is an important mediator of the insulin signaling pathway contributing to longevity and the stress response as well as impacting survival from hypoxia. Herein, we reveal a novel mechanism for regulating PQM-1 expression specifically in neural cells of larval animals. Our studies reveal that the RNA-binding protein (RBP), ADR-1, binds to pqm-1 mRNA in neural cells. This binding is regulated by the presence of a second RBP, ADR-2, which when absent leads to reduced expression of both pqm-1 and downstream PQM-1 activated genes. Interestingly, we find that neural pqm-1 expression is sufficient to impact gene expression throughout the animal and affect survival from hypoxia, phenotypes that we also observe in adr mutant animals. Together, these studies reveal an important posttranscriptional gene regulatory mechanism in Caenorhabditis elegans that allows the nervous system to sense and respond to environmental conditions to promote organismal survival from hypoxia.
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Affiliation(s)
- Ananya Mahapatra
- Genome, Cell and Developmental Biology Graduate Program, Indiana University, Bloomington, Indiana, United States of America
| | - Alfa Dhakal
- Cell, Molecular and Cancer Biology Graduate Program, Indiana University School of Medicine–Bloomington, Bloomington, Indiana, United States of America
| | - Aika Noguchi
- Department of Biology, Indiana University, Bloomington, Indiana, United States of America
| | - Pranathi Vadlamani
- Medical Sciences Program, Indiana University School of Medicine–Bloomington, Bloomington, Indiana, United States of America
| | - Heather A. Hundley
- Department of Biology, Indiana University, Bloomington, Indiana, United States of America
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4
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Mahapatra A, Dhakal A, Noguchi A, Vadlamani P, Hundley HA. ADARs employ a neural-specific mechanism to regulate PQM-1 expression and survival from hypoxia. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.05.539519. [PMID: 37205482 PMCID: PMC10187282 DOI: 10.1101/2023.05.05.539519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
The ability to alter gene expression programs in response to changes in environmental conditions is central to the ability of an organism to thrive. For most organisms, the nervous system serves as the master regulator in communicating information about the animal's surroundings to other tissues. The information relay centers on signaling pathways that cue transcription factors in a given cell type to execute a specific gene expression program, but also provide a means to signal between tissues. The transcription factor PQM-1 is an important mediator of the insulin signaling pathway contributing to longevity and the stress response as well as impacting survival from hypoxia. Herein, we reveal a novel mechanism for regulating PQM-1 expression specifically in neural cells of larval animals. Our studies reveal that the RNA binding protein, ADR-1, binds to pqm-1 mRNA in neural cells. This binding is regulated by the presence of a second RNA binding protein, ADR-2, which when absent leads to reduced expression of both pqm-1 and downstream PQM-1 activated genes. Interestingly, we find that neural pqm-1 expression is sufficient to impact gene expression throughout the animal and affect survival from hypoxia; phenotypes that we also observe in adr mutant animals. Together, these studies reveal an important post-transcriptional gene regulatory mechanism that allows the nervous system to sense and respond to environmental conditions to promote organismal survival from hypoxia.
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Affiliation(s)
- Ananya Mahapatra
- Genome, Cell and Developmental Biology Graduate Program, Indiana University, Bloomington IN, 47405 USA
| | - Alfa Dhakal
- Cell, Molecular and Cancer Biology Graduate Program, Indiana University School of Medicine – Bloomington, Bloomington IN, 47405 USA
| | - Aika Noguchi
- Department of Biology, Indiana University, Bloomington IN 47405 USA
| | - Pranathi Vadlamani
- Medical Sciences Program, Indiana University School of Medicine – Bloomington, Bloomington IN, 47405 USA
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5
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Papsdorf K, Miklas JW, Hosseini A, Cabruja M, Morrow CS, Savini M, Yu Y, Silva-García CG, Haseley NR, Murphy LM, Yao P, de Launoit E, Dixon SJ, Snyder MP, Wang MC, Mair WB, Brunet A. Lipid droplets and peroxisomes are co-regulated to drive lifespan extension in response to mono-unsaturated fatty acids. Nat Cell Biol 2023; 25:672-684. [PMID: 37127715 PMCID: PMC10185472 DOI: 10.1038/s41556-023-01136-6] [Citation(s) in RCA: 53] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 03/23/2023] [Indexed: 05/03/2023]
Abstract
Dietary mono-unsaturated fatty acids (MUFAs) are linked to longevity in several species. But the mechanisms by which MUFAs extend lifespan remain unclear. Here we show that an organelle network involving lipid droplets and peroxisomes is critical for MUFA-induced longevity in Caenorhabditis elegans. MUFAs upregulate the number of lipid droplets in fat storage tissues. Increased lipid droplet number is necessary for MUFA-induced longevity and predicts remaining lifespan. Lipidomics datasets reveal that MUFAs also modify the ratio of membrane lipids and ether lipids-a signature associated with decreased lipid oxidation. In agreement with this, MUFAs decrease lipid oxidation in middle-aged individuals. Intriguingly, MUFAs upregulate not only lipid droplet number but also peroxisome number. A targeted screen identifies genes involved in the co-regulation of lipid droplets and peroxisomes, and reveals that induction of both organelles is optimal for longevity. Our study uncovers an organelle network involved in lipid homeostasis and lifespan regulation, opening new avenues for interventions to delay aging.
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Affiliation(s)
| | - Jason W Miklas
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Amir Hosseini
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Matias Cabruja
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Christopher S Morrow
- Department of Molecular Metabolism, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Marzia Savini
- Department of Molecular and Human Genetics, Huffington Center on Aging, Baylor College of Medicine, Houston, TX, USA
| | - Yong Yu
- Department of Molecular and Human Genetics, Huffington Center on Aging, Baylor College of Medicine, Houston, TX, USA
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, China
| | - Carlos G Silva-García
- Department of Molecular Metabolism, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | | | | | - Pallas Yao
- Department of Molecular Metabolism, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | | | - Scott J Dixon
- Department of Biology, Stanford University, Stanford, CA, USA
| | | | - Meng C Wang
- Department of Molecular and Human Genetics, Huffington Center on Aging, Baylor College of Medicine, Houston, TX, USA
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - William B Mair
- Department of Molecular Metabolism, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Anne Brunet
- Department of Genetics, Stanford University, Stanford, CA, USA.
- Glenn Laboratories for the Biology of Aging, Stanford University, Stanford, CA, USA.
- Wu Tsai Institute of Neurosciences, Stanford University, Stanford, CA, USA.
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6
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Thies JL, Willicott K, Craig ML, Greene MR, DuGay CN, Caldwell GA, Caldwell KA. Xanthine Dehydrogenase Is a Modulator of Dopaminergic Neurodegeneration in Response to Bacterial Metabolite Exposure in C. elegans. Cells 2023; 12:1170. [PMID: 37190079 PMCID: PMC10136629 DOI: 10.3390/cells12081170] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 04/03/2023] [Accepted: 04/11/2023] [Indexed: 05/17/2023] Open
Abstract
Oxidative stress is a contributing factor to Parkinson's disease (PD). Considering the prevalence of sporadic PD, environmental exposures are postulated to increase reactive oxygen species and either incite or exacerbate neurodegeneration. We previously determined that exposure to the common soil bacterium, Streptomyces venezuelae (S. ven), enhanced oxidative stress and mitochondrial dysfunction in Caenorhabditis elegans, leading to dopaminergic (DA) neurodegeneration. Here, S. ven metabolite exposure in C. elegans was followed by RNA-Seq analysis. Half of the differentially identified genes (DEGs) were associated with the transcription factor DAF-16 (FOXO), which is a key node in regulating stress response. Our DEGs were enriched for Phase I (CYP) and Phase II (UGT) detoxification genes and non-CYP Phase I enzymes associated with oxidative metabolism, including the downregulated xanthine dehydrogenase gene, xdh-1. The XDH-1 enzyme exhibits reversible interconversion to xanthine oxidase (XO) in response to calcium. S. ven metabolite exposure enhanced XO activity in C. elegans. The chelation of calcium diminishes the conversion of XDH-1 to XO and results in neuroprotection from S. ven exposure, whereas CaCl2 supplementation enhanced neurodegeneration. These results suggest a defense mechanism that delimits the pool of XDH-1 available for interconversion to XO, and associated ROS production, in response to metabolite exposure.
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Affiliation(s)
- Jennifer L. Thies
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL 35487, USA
| | - Karolina Willicott
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL 35487, USA
| | - Maici L. Craig
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL 35487, USA
| | - Madeline R. Greene
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL 35487, USA
| | - Cassandra N. DuGay
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL 35487, USA
| | - Guy A. Caldwell
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL 35487, USA
- Center for Neurodegeneration and Experimental Therapeutics, Department of Neurology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Kim A. Caldwell
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL 35487, USA
- Center for Neurodegeneration and Experimental Therapeutics, Department of Neurology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
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7
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Endogenous DAF-16 spatiotemporal activity quantitatively predicts lifespan extension induced by dietary restriction. Commun Biol 2023; 6:203. [PMID: 36807646 PMCID: PMC9941123 DOI: 10.1038/s42003-023-04562-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 02/07/2023] [Indexed: 02/22/2023] Open
Abstract
In many organisms, dietary restriction (DR) leads to lifespan extension through the activation of cell protection and pro-longevity gene expression programs. In the nematode C. elegans, the DAF-16 transcription factor is a key aging regulator that governs the Insulin/IGF-1 signaling pathway and undergoes translocation from the cytoplasm to the nucleus of cells when animals are exposed to food limitation. However, how large is the influence of DR on DAF-16 activity, and its subsequent impact on lifespan has not been quantitatively determined. In this work, we assess the endogenous activity of DAF-16 under various DR regimes by coupling CRISPR/Cas9-enabled fluorescent tagging of DAF-16 with quantitative image analysis and machine learning. Our results indicate that DR regimes induce strong endogenous DAF-16 activity, although DAF-16 is less responsive in aged individuals. DAF-16 activity is in turn a robust predictor of mean lifespan in C. elegans, accounting for 78% of its variability under DR. Analysis of tissue-specific expression aided by a machine learning tissue classifier reveals that, under DR, the largest contribution to DAF-16 nuclear intensity originates from the intestine and neurons. DR also drives DAF-16 activity in unexpected locations such as the germline and intestinal nucleoli.
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8
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Tabarraei H, Waddell BM, Raymond K, Murray SM, Wang Y, Choe KP, Wu CW. CCR4-NOT subunit CCF-1/CNOT7 promotes transcriptional activation to multiple stress responses in Caenorhabditis elegans. Aging Cell 2023; 22:e13795. [PMID: 36797658 PMCID: PMC10086529 DOI: 10.1111/acel.13795] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 01/13/2023] [Accepted: 02/01/2023] [Indexed: 02/18/2023] Open
Abstract
CCR4-NOT is a versatile eukaryotic protein complex that controls multiple steps in gene expression regulation from synthesis to decay. In yeast, CCR4-NOT has been implicated in stress response regulation, though this function in other organisms remains unclear. In a genome-wide RNAi screen, we identified a subunit of the CCR4-NOT complex, ccf-1, as a requirement for the C. elegans transcriptional response to cadmium and acrylamide stress. Using whole-transcriptome RNA sequencing, we show that the knockdown of ccf-1 attenuates the activation of a broad range of stress-protective genes in response to cadmium and acrylamide, including those encoding heat shock proteins and xenobiotic detoxification. Consistently, survival assays show that the knockdown of ccf-1 decreases C. elegans stress resistance and normal lifespan. A yeast 2-hybrid screen using a CCF-1 bait identified the homeobox transcription factor PAL-1 as a physical interactor. Knockdown of pal-1 inhibits the activation of ccf-1 dependent stress genes and reduces C. elegans stress resistance. Gene expression analysis reveals that knockdown of ccf-1 and pal-1 attenuates the activation of elt-2 and elt-3 under stress that encode master transcriptional co-regulators of stress response in the C. elegans, and that overexpression of ELT-2 can suppress ccf-1's requirement for gene transcription in a stress-dependent manner. Our findings reveal a new role for CCR4-NOT in the environmental stress response and define its role in stress resistance and longevity in C. elegans.
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Affiliation(s)
- Hadi Tabarraei
- Department of Veterinary Biomedical Sciences, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Brandon M Waddell
- Department of Veterinary Biomedical Sciences, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Kelly Raymond
- Department of Veterinary Biomedical Sciences, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Sydney M Murray
- Department of Veterinary Biomedical Sciences, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Ying Wang
- Department of Biology and Genetics Institute, University of Florida, Gainesville, Florida, USA
| | - Keith P Choe
- Department of Biology and Genetics Institute, University of Florida, Gainesville, Florida, USA
| | - Cheng-Wei Wu
- Department of Veterinary Biomedical Sciences, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada.,Toxicology Centre, University of Saskatchewan, Saskatoon, Saskatchewan, Canada.,Department of Biochemistry, Microbiology and Immunology, College of Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
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9
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Shaul NC, Jordan JM, Falsztyn IB, Ryan Baugh L. Insulin/IGF-dependent Wnt signaling promotes formation of germline tumors and other developmental abnormalities following early-life starvation in Caenorhabditis elegans. Genetics 2023; 223:iyac173. [PMID: 36449574 PMCID: PMC9910406 DOI: 10.1093/genetics/iyac173] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 03/25/2022] [Accepted: 10/31/2022] [Indexed: 12/02/2022] Open
Abstract
The Developmental Origins of Health and Disease hypothesis postulates that early-life stressors can predispose people to disease later in life. In the roundworm Caenorhabditis elegans, prolonged early-life starvation causes germline tumors, uterine masses, and other gonad abnormalities to develop in well-fed adults. Reduction of insulin/insulin-like growth factor (IGF) signaling (IIS) during larval development suppresses these starvation-induced abnormalities. However, molecular mechanisms at play in formation and suppression of starvation-induced abnormalities are unclear. Here we describe mechanisms through which early-life starvation and reduced IIS affect starvation-induced abnormalities. Transcriptome sequencing revealed that expression of genes in the Wnt signaling pathway is upregulated in adults starved as young larvae, and that knockdown of the insulin/IGF receptor daf-2/InsR decreases their expression. Reduction of Wnt signaling through RNAi or mutation reduced starvation-induced abnormalities, and hyperactivation of Wnt signaling produced gonad abnormalities in worms that had not been starved. Genetic and reporter-gene analyses suggest that Wnt signaling acts downstream of IIS in the soma to cell-nonautonomously promote germline hyperproliferation. In summary, this work reveals that IIS-dependent transcriptional regulation of Wnt signaling promotes starvation-induced gonad abnormalities, illuminating signaling mechanisms that contribute to adult pathology following early-life starvation.
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Affiliation(s)
- Nathan C Shaul
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - James M Jordan
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - Ivan B Falsztyn
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - L Ryan Baugh
- Department of Biology, Duke University, Durham, NC 27708, USA
- Center for Genomic and Computational Biology, Duke University, Durham, NC 27708, USA
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10
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Miles J, Townend S, Milonaitytė D, Smith W, Hodge F, Westhead DR, van Oosten-Hawle P. Transcellular chaperone signaling is an intercellular stress-response distinct from the HSF-1-mediated heat shock response. PLoS Biol 2023; 21:e3001605. [PMID: 36780563 PMCID: PMC9956597 DOI: 10.1371/journal.pbio.3001605] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 02/24/2023] [Accepted: 01/20/2023] [Indexed: 02/15/2023] Open
Abstract
Organismal proteostasis is maintained by intercellular signaling processes including cell nonautonomous stress responses such as transcellular chaperone signaling (TCS). When TCS is activated upon tissue-specific knockdown of hsp-90 in the Caenorhabditis elegans intestine, heat-inducible hsp-70 is induced in muscle cells at the permissive temperature resulting in increased heat stress resistance and lifespan extension. However, our understanding of the molecular mechanism and signaling factors mediating transcellular activation of hsp-70 expression from one tissue to another is still in its infancy. Here, we conducted a combinatorial approach using transcriptome RNA-Seq profiling and a forward genetic mutagenesis screen to elucidate how stress signaling from the intestine to the muscle is regulated. We find that the TCS-mediated "gut-to-muscle" induction of hsp-70 expression is suppressed by HSF-1 and instead relies on transcellular-X-cross-tissue (txt) genes. We identify a key role for the PDZ-domain guanylate cyclase txt-1 and the homeobox transcription factor ceh-58 as signaling hubs in the stress receiving muscle cells to initiate hsp-70 expression and facilitate TCS-mediated heat stress resistance and lifespan extension. Our results provide a new view on cell-nonautonomous regulation of "inter-tissue" stress responses in an organism that highlight a key role for the gut. Our data suggest that the HSF-1-mediated heat shock response is switched off upon TCS activation, in favor of an intercellular stress-signaling route to safeguard survival.
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Affiliation(s)
- Jay Miles
- School of Molecular and Cell Biology & Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Sarah Townend
- School of Molecular and Cell Biology & Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Dovilė Milonaitytė
- School of Molecular and Cell Biology & Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - William Smith
- School of Molecular and Cell Biology & Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Francesca Hodge
- School of Molecular and Cell Biology & Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - David R. Westhead
- School of Molecular and Cell Biology & Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Patricija van Oosten-Hawle
- School of Molecular and Cell Biology & Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
- * E-mail:
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11
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Li Q, Xiao M, Li N, Cai W, Zhao C, Liu B, Zeng F. Application of
Caenorhabditis elegans
in the evaluation of food nutrition: A review. EFOOD 2023. [DOI: 10.1002/efd2.68] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023] Open
Affiliation(s)
- Quancen Li
- College of Food Science Fujian Agriculture and Forestry University Fuzhou China
| | - Meifang Xiao
- College of Food Science Fujian Agriculture and Forestry University Fuzhou China
| | - Na Li
- College of Food Science Fujian Agriculture and Forestry University Fuzhou China
| | - Wenwen Cai
- College of Food Science Fujian Agriculture and Forestry University Fuzhou China
| | - Chao Zhao
- College of Food Science Fujian Agriculture and Forestry University Fuzhou China
- College of Marine Sciences Fujian Agriculture and Forestry University Fuzhou China
- Engineering Research Center of Fujian Subtropical Fruit and Vegetable Processing Fujian Agriculture and Forestry University Fuzhou China
| | - Bin Liu
- College of Food Science Fujian Agriculture and Forestry University Fuzhou China
- Engineering Research Center of Fujian Subtropical Fruit and Vegetable Processing Fujian Agriculture and Forestry University Fuzhou China
- National Engineering Research Center of JUNCAO Technology Fujian Agriculture and Forestry University Fuzhou China
| | - Feng Zeng
- College of Food Science Fujian Agriculture and Forestry University Fuzhou China
- Engineering Research Center of Fujian Subtropical Fruit and Vegetable Processing Fujian Agriculture and Forestry University Fuzhou China
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12
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Ham S, Kim SS, Park S, Kim EJE, Kwon S, Park HEH, Jung Y, Lee SJV. Systematic transcriptome analysis associated with physiological and chronological aging in Caenorhabditis elegans. Genome Res 2022; 32:2003-2014. [PMID: 36351769 PMCID: PMC9808617 DOI: 10.1101/gr.276515.121] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 10/19/2022] [Indexed: 11/11/2022]
Abstract
Aging is associated with changes in a variety of biological processes at the transcriptomic level, including gene expression. Two types of aging occur during a lifetime: chronological and physiological aging. However, dissecting the difference between chronological and physiological ages at the transcriptomic level has been a challenge because of its complexity. We analyzed the transcriptomic features associated with physiological and chronological aging using Caenorhabditis elegans as a model. Many structural and functional transcript elements, such as noncoding RNAs and intron-derived transcripts, were up-regulated with chronological aging. In contrast, mRNAs with many biological functions, including RNA processing, were down-regulated with physiological aging. We also identified an age-dependent increase in the usage of distal 3' splice sites in mRNA transcripts as a biomarker of physiological aging. Our study provides crucial information for dissecting chronological and physiological aging at the transcriptomic level.
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Affiliation(s)
- Seokjin Ham
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Yuseong-gu, Daejeon 34141, South Korea
| | - Sieun S Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Yuseong-gu, Daejeon 34141, South Korea
| | - Sangsoon Park
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Yuseong-gu, Daejeon 34141, South Korea
| | - Eun Ji E Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Yuseong-gu, Daejeon 34141, South Korea
| | - Sujeong Kwon
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Yuseong-gu, Daejeon 34141, South Korea
| | - Hae-Eun H Park
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Yuseong-gu, Daejeon 34141, South Korea
| | - Yoonji Jung
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Yuseong-gu, Daejeon 34141, South Korea
| | - Seung-Jae V Lee
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Yuseong-gu, Daejeon 34141, South Korea
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13
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Intestine-specific removal of DAF-2 nearly doubles lifespan in Caenorhabditis elegans with little fitness cost. Nat Commun 2022; 13:6339. [PMID: 36284093 PMCID: PMC9596710 DOI: 10.1038/s41467-022-33850-4] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 10/05/2022] [Indexed: 12/25/2022] Open
Abstract
Twenty-nine years following the breakthrough discovery that a single-gene mutation of daf-2 doubles Caenorhabditis elegans lifespan, it remains unclear where this insulin/IGF-1 receptor gene is expressed and where it acts to regulate ageing. Using knock-in fluorescent reporters, we determined that daf-2 and its downstream transcription factor daf-16 are expressed ubiquitously. Using tissue-specific targeted protein degradation, we determined that intracellular DAF-2-to-DAF-16 signaling in the intestine plays a major role in lifespan regulation, while that in the hypodermis, neurons, and germline plays a minor role. Notably, intestine-specific loss of DAF-2 activates DAF-16 in and outside the intestine, causes almost no adverse effects on development and reproduction, and extends lifespan by 94% in a way that partly requires non-intestinal DAF-16. Consistent with intestine supplying nutrients to the entire body, evidence from this and other studies suggests that altered metabolism, particularly down-regulation of protein and RNA synthesis, mediates longevity by reduction of insulin/IGF-1 signaling.
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14
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Zhang Y, Zhou Q, Lu L, Zhao C, Zhang H, Liu R, Pu Y, Yin L. Integrating Transcriptomics and Free Fatty Acid Profiling Analysis Reveal Cu Induces Shortened Lifespan and Increased Fat Accumulation and Oxidative Damage in C. elegans. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2022; 2022:5297342. [PMID: 36017239 PMCID: PMC9398846 DOI: 10.1155/2022/5297342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 07/03/2022] [Accepted: 08/01/2022] [Indexed: 11/28/2022]
Abstract
Nowadays, human beings are exposed to Cu in varieties of environmental mediums, resulting in health risks needing urgent attention. Our research found that Cu shortened lifespan and induced aging-related phenotypes of Caenorhabditis elegans (C. elegans). Transcriptomics data showed differential expression genes induced by Cu were mainly involved in regulation of metabolism and longevity, especially in fatty acid metabolism. Quantitative detection of free fatty acid by GC/MS further found that Cu upregulated free fatty acids of C. elegans. A mechanism study confirmed that Cu promoted the fat accumulation in nematodes, which was owing to disorder of fatty acid desaturase and CoA synthetase, endoplasmic reticulum unfolded protein response (UPRER), mitochondrial membrane potential, and unfolded protein response (UPRmt). In addition, Cu activated oxidative stress and prevented DAF-16 translocating into nuclear with a concomitant reduction in the expression of environmental stress-related genes. Taken together, the research suggested that Cu promoted aging and induced fat deposition and oxidative damage.
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Affiliation(s)
- Ying Zhang
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education of China; School of Public Health, Southeast University, Nanjing 210009, Jiangsu, China
| | - Qian Zhou
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education of China; School of Public Health, Southeast University, Nanjing 210009, Jiangsu, China
| | - Lu Lu
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education of China; School of Public Health, Southeast University, Nanjing 210009, Jiangsu, China
| | - Chao Zhao
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education of China; School of Public Health, Southeast University, Nanjing 210009, Jiangsu, China
| | - Hu Zhang
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education of China; School of Public Health, Southeast University, Nanjing 210009, Jiangsu, China
| | - Ran Liu
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education of China; School of Public Health, Southeast University, Nanjing 210009, Jiangsu, China
| | - Yuepu Pu
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education of China; School of Public Health, Southeast University, Nanjing 210009, Jiangsu, China
| | - Lihong Yin
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education of China; School of Public Health, Southeast University, Nanjing 210009, Jiangsu, China
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15
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Hodge F, Bajuszova V, van Oosten-Hawle P. The Intestine as a Lifespan- and Proteostasis-Promoting Signaling Tissue. FRONTIERS IN AGING 2022; 3:897741. [PMID: 35821863 PMCID: PMC9261303 DOI: 10.3389/fragi.2022.897741] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 05/09/2022] [Indexed: 11/13/2022]
Abstract
In multicellular organisms such as Caenorhabditis elegans, cellular stress stimuli and responses are communicated between tissues to promote organismal health- and lifespan. The nervous system is the predominant regulator of cell nonautonomous proteostasis that orchestrates systemic stress responses to integrate both internal and external stimuli. This review highlights the role of the intestine in mediating cell nonautonomous stress responses and explores recent findings that suggest a central role for the intestine to regulate organismal proteostasis. As a tissue that receives and further transduces signals from the nervous system in response to dietary restriction, heat- and oxidative stress, and hypoxia, we explore evidence suggesting the intestine is a key regulatory organ itself. From the perspective of naturally occurring stressors such as dietary restriction and pathogen infection we highlight how the intestine can function as a key regulator of organismal proteostasis by integrating insulin/IGF-like signaling, miRNA-, neuropeptide- and metabolic signaling to alter distal tissue functions in promoting survival, health- and lifespan.
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Affiliation(s)
| | | | - Patricija van Oosten-Hawle
- Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom
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16
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Yang L, Ye Q, Zhang X, Li K, Liang X, Wang M, Shi L, Luo S, Zhang Q, Zhang X. Pyrroloquinoline quinone extends Caenorhabditis elegans' longevity through the insulin/IGF1 signaling pathway-mediated activation of autophagy. Food Funct 2021; 12:11319-11330. [PMID: 34647561 DOI: 10.1039/d1fo02128a] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Aging is the leading cause of human morbidity and death worldwide. Pyrroloquinoline quinone (PQQ) is a water-soluble vitamin-like compound that has strong anti-oxidant capacity. Beneficial effects of PQQ on lifespan have been discovered in the model organism Caenorhabditis elegans (C. elegans), yet the underlying mechanisms remain unclear. In the current study, we hypothesized that the longevity-extending effect of PQQ may be linked to autophagy and insulin/IGF1 signaling (IIS) in C. elegans. Our data demonstrate that PQQ at a concentration of 1 mM maximally extended the mean life of C. elegans by 33.1%. PQQ increased locomotion and anti-stress ability, and reduced fat accumulation and reactive oxygen species (ROS) levels. There was no significant lifespan extension in PQQ-treated daf-16, daf-2, and bec-1 mutants, suggesting that these IIS- and autophagy-related genes may mediate the anti-aging effects of the PQQ. Furthermore, PQQ raised mRNA expression and the nuclear localization of the pivotal transcription factor daf-16, and then activated its downstream targets sod-3, clt-1, and hsp16.2. Enhanced activity of the autophagy pathway was also observed in PQQ-fed C. elegans, as evidenced by increased expression of the key autophagy genes including lgg-1, and bec-1, and also by an increase in the GFP::LGG-1 puncta. Inactivation of the IIS pathway-related genes daf-2 or daf-16 by RNAi partially blocked the increase in autophagy activity caused by PQQ treatment, suggesting that autophagy may be regulated by IIS. This study demonstrates that anti-aging properties of PQQ, in the C. elegans model, may be mediated via the IIS pathway and autophagy.
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Affiliation(s)
- Liu Yang
- Department of Nutrition and Food Science, School of Public Health, Tianjin Medical University, Tianjin 300070, China. .,Tianjin Key Laboratory of Environment, Nutrition and Public Health, Center for International Collaborative Research on Environment, Nutrition and Public Health, Tianjin Medical University, Tianjin 300070, China
| | - Qi Ye
- Department of Nutrition and Food Science, School of Public Health, Tianjin Medical University, Tianjin 300070, China. .,Tianjin Key Laboratory of Environment, Nutrition and Public Health, Center for International Collaborative Research on Environment, Nutrition and Public Health, Tianjin Medical University, Tianjin 300070, China
| | - Xuguang Zhang
- Science and Technology Centre, By-Health Co. Ltd, Guangzhou, China
| | - Ke Li
- Department of Nutrition and Food Science, School of Public Health, Tianjin Medical University, Tianjin 300070, China. .,Tianjin Key Laboratory of Environment, Nutrition and Public Health, Center for International Collaborative Research on Environment, Nutrition and Public Health, Tianjin Medical University, Tianjin 300070, China
| | - Xiaoshan Liang
- Department of Nutrition and Food Science, School of Public Health, Tianjin Medical University, Tianjin 300070, China. .,Tianjin Key Laboratory of Environment, Nutrition and Public Health, Center for International Collaborative Research on Environment, Nutrition and Public Health, Tianjin Medical University, Tianjin 300070, China
| | - Meng Wang
- Department of Nutrition and Food Science, School of Public Health, Tianjin Medical University, Tianjin 300070, China. .,Tianjin Key Laboratory of Environment, Nutrition and Public Health, Center for International Collaborative Research on Environment, Nutrition and Public Health, Tianjin Medical University, Tianjin 300070, China
| | - Linran Shi
- Department of Nutrition and Food Science, School of Public Health, Tianjin Medical University, Tianjin 300070, China. .,Tianjin Key Laboratory of Environment, Nutrition and Public Health, Center for International Collaborative Research on Environment, Nutrition and Public Health, Tianjin Medical University, Tianjin 300070, China
| | - Suhui Luo
- Department of Nutrition and Food Science, School of Public Health, Tianjin Medical University, Tianjin 300070, China. .,Tianjin Key Laboratory of Environment, Nutrition and Public Health, Center for International Collaborative Research on Environment, Nutrition and Public Health, Tianjin Medical University, Tianjin 300070, China
| | - Qiang Zhang
- Tianjin Key Laboratory of Environment, Nutrition and Public Health, Center for International Collaborative Research on Environment, Nutrition and Public Health, Tianjin Medical University, Tianjin 300070, China.,Department of Occupational and Environmental Health, School of Public Health, Tianjin Medical University, Tianjin 300070, China
| | - Xumei Zhang
- Department of Nutrition and Food Science, School of Public Health, Tianjin Medical University, Tianjin 300070, China. .,Tianjin Key Laboratory of Environment, Nutrition and Public Health, Center for International Collaborative Research on Environment, Nutrition and Public Health, Tianjin Medical University, Tianjin 300070, China
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17
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Context-specific regulation of lysosomal lipolysis through network-level diverting of transcription factor interactions. Proc Natl Acad Sci U S A 2021; 118:2104832118. [PMID: 34607947 DOI: 10.1073/pnas.2104832118] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/02/2021] [Indexed: 11/18/2022] Open
Abstract
Plasticity in multicellular organisms involves signaling pathways converting contexts-either natural environmental challenges or laboratory perturbations-into context-specific changes in gene expression. Congruently, the interactions between the signaling molecules and transcription factors (TF) regulating these responses are also context specific. However, when a target gene responds across contexts, the upstream TF identified in one context is often inferred to regulate it across contexts. Reconciling these stable TF-target gene pair inferences with the context-specific nature of homeostatic responses is therefore needed. The induction of the Caenorhabditis elegans genes lipl-3 and lipl-4 is observed in many genetic contexts and is essential to survival during fasting. We find DAF-16/FOXO mediating lipl-4 induction in all contexts tested; hence, lipl-4 regulation seems context independent and compatible with across-context inferences. In contrast, DAF-16-mediated regulation of lipl-3 is context specific. DAF-16 reduces the induction of lipl-3 during fasting, yet it promotes it during oxidative stress. Through discrete dynamic modeling and genetic epistasis, we define that DAF-16 represses HLH-30/TFEB-the main TF activating lipl-3 during fasting. Contrastingly, DAF-16 activates the stress-responsive TF HSF-1 during oxidative stress, which promotes C. elegans survival through induction of lipl-3 Furthermore, the TF MXL-3 contributes to the dominance of HSF-1 at the expense of HLH-30 during oxidative stress but not during fasting. This study shows how context-specific diverting of functional interactions within a molecular network allows cells to specifically respond to a large number of contexts with a limited number of molecular players, a mode of transcriptional regulation we name "contextualized transcription."
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18
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Cooper JF, Guasp RJ, Arnold ML, Grant BD, Driscoll M. Stress increases in exopher-mediated neuronal extrusion require lipid biosynthesis, FGF, and EGF RAS/MAPK signaling. Proc Natl Acad Sci U S A 2021; 118:e2101410118. [PMID: 34475208 PMCID: PMC8433523 DOI: 10.1073/pnas.2101410118] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 06/23/2021] [Indexed: 01/08/2023] Open
Abstract
In human neurodegenerative diseases, neurons can transfer toxic protein aggregates to surrounding cells, promoting pathology via poorly understood mechanisms. In Caenorhabditis elegans, proteostressed neurons can expel neurotoxic proteins in large, membrane-bound vesicles called exophers. We investigated how specific stresses impact neuronal trash expulsion to show that neuronal exopher production can be markedly elevated by oxidative and osmotic stress. Unexpectedly, we also found that fasting dramatically increases exophergenesis. Mechanistic dissection focused on identifying nonautonomous factors that sense and activate the fasting-induced exopher response revealed that DAF16/FOXO-dependent and -independent processes are engaged. Fasting-induced exopher elevation requires the intestinal peptide transporter PEPT-1, lipid synthesis transcription factors Mediator complex MDT-15 and SBP-1/SREPB1, and fatty acid synthase FASN-1, implicating remotely initiated lipid signaling in neuronal trash elimination. A conserved fibroblast growth factor (FGF)/RAS/MAPK signaling pathway that acts downstream of, or in parallel to, lipid signaling also promotes fasting-induced neuronal exopher elevation. A germline-based epidermal growth factor (EGF) signal that acts through neurons is also required for exopher production. Our data define a nonautonomous network that links food availability changes to remote, and extreme, neuronal homeostasis responses relevant to aggregate transfer biology.
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Affiliation(s)
- Jason F Cooper
- Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, NJ 08854
| | - Ryan J Guasp
- Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, NJ 08854
| | - Meghan Lee Arnold
- Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, NJ 08854
| | - Barth D Grant
- Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, NJ 08854
- Rutgers Center for Lipid Research, Rutgers University, New Brunswick, NJ 08901
| | - Monica Driscoll
- Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, NJ 08854;
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19
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Meiler A, Marchiano F, Haering M, Weitkunat M, Schnorrer F, Habermann BH. AnnoMiner is a new web-tool to integrate epigenetics, transcription factor occupancy and transcriptomics data to predict transcriptional regulators. Sci Rep 2021; 11:15463. [PMID: 34326396 PMCID: PMC8322331 DOI: 10.1038/s41598-021-94805-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 07/14/2021] [Indexed: 11/23/2022] Open
Abstract
Gene expression regulation requires precise transcriptional programs, led by transcription factors in combination with epigenetic events. Recent advances in epigenomic and transcriptomic techniques provided insight into different gene regulation mechanisms. However, to date it remains challenging to understand how combinations of transcription factors together with epigenetic events control cell-type specific gene expression. We have developed the AnnoMiner web-server, an innovative and flexible tool to annotate and integrate epigenetic, and transcription factor occupancy data. First, AnnoMiner annotates user-provided peaks with gene features. Second, AnnoMiner can integrate genome binding data from two different transcriptional regulators together with gene features. Third, AnnoMiner offers to explore the transcriptional deregulation of genes nearby, or within a specified genomic region surrounding a user-provided peak. AnnoMiner’s fourth function performs transcription factor or histone modification enrichment analysis for user-provided gene lists by utilizing hundreds of public, high-quality datasets from ENCODE for the model organisms human, mouse, Drosophila and C. elegans. Thus, AnnoMiner can predict transcriptional regulators for a studied process without the strict need for chromatin data from the same process. We compared AnnoMiner to existing tools and experimentally validated several transcriptional regulators predicted by AnnoMiner to indeed contribute to muscle morphogenesis in Drosophila. AnnoMiner is freely available at http://chimborazo.ibdm.univ-mrs.fr/AnnoMiner/.
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Affiliation(s)
- Arno Meiler
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Fabio Marchiano
- Aix-Marseille University, CNRS, IBDM UMR 7288, The Turing Centre for Living systems (CENTURI), Aix-Marseille University, Parc Scientifique de Luminy Case 907, 163, Avenue de Luminy, 13009, Marseille, France
| | - Margaux Haering
- Aix-Marseille University, CNRS, IBDM UMR 7288, The Turing Centre for Living systems (CENTURI), Aix-Marseille University, Parc Scientifique de Luminy Case 907, 163, Avenue de Luminy, 13009, Marseille, France
| | - Manuela Weitkunat
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Frank Schnorrer
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany.,Aix-Marseille University, CNRS, IBDM UMR 7288, The Turing Centre for Living systems (CENTURI), Aix-Marseille University, Parc Scientifique de Luminy Case 907, 163, Avenue de Luminy, 13009, Marseille, France
| | - Bianca H Habermann
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany. .,Aix-Marseille University, CNRS, IBDM UMR 7288, The Turing Centre for Living systems (CENTURI), Aix-Marseille University, Parc Scientifique de Luminy Case 907, 163, Avenue de Luminy, 13009, Marseille, France.
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20
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Li WJ, Wang CW, Tao L, Yan YH, Zhang MJ, Liu ZX, Li YX, Zhao HQ, Li XM, He XD, Xue Y, Dong MQ. Insulin signaling regulates longevity through protein phosphorylation in Caenorhabditis elegans. Nat Commun 2021; 12:4568. [PMID: 34315882 PMCID: PMC8316574 DOI: 10.1038/s41467-021-24816-z] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 07/01/2021] [Indexed: 12/22/2022] Open
Abstract
Insulin/IGF-1 Signaling (IIS) is known to constrain longevity by inhibiting the transcription factor FOXO. How phosphorylation mediated by IIS kinases regulates lifespan beyond FOXO remains unclear. Here, we profile IIS-dependent phosphorylation changes in a large-scale quantitative phosphoproteomic analysis of wild-type and three IIS mutant Caenorhabditis elegans strains. We quantify more than 15,000 phosphosites and find that 476 of these are differentially phosphorylated in the long-lived daf-2/insulin receptor mutant. We develop a machine learning-based method to prioritize 25 potential lifespan-related phosphosites. We perform validations to show that AKT-1 pT492 inhibits DAF-16/FOXO and compensates the loss of daf-2 function, that EIF-2α pS49 potently inhibits protein synthesis and daf-2 longevity, and that reduced phosphorylation of multiple germline proteins apparently transmits reduced DAF-2 signaling to the soma. In addition, an analysis of kinases with enriched substrates detects that casein kinase 2 (CK2) subunits negatively regulate lifespan. Our study reveals detailed functional insights into longevity.
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Affiliation(s)
- Wen-Jun Li
- School of Life Sciences, Peking University, Beijing, China
- National Institute of Biological Sciences, Beijing, China
| | - Chen-Wei Wang
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Nanjing University Institute of Artificial Intelligence Biomedicine, Nanjing, Jiangsu, China
| | - Li Tao
- National Institute of Biological Sciences, Beijing, China
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Yong-Hong Yan
- National Institute of Biological Sciences, Beijing, China
| | - Mei-Jun Zhang
- National Institute of Biological Sciences, Beijing, China
- Annoroad Gene Tech. Co., Ltd., Beijing, China
| | - Ze-Xian Liu
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Yu-Xin Li
- National Institute of Biological Sciences, Beijing, China
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Han-Qing Zhao
- National Institute of Biological Sciences, Beijing, China
| | - Xue-Mei Li
- School of Life Sciences, Peking University, Beijing, China
- National Institute of Biological Sciences, Beijing, China
| | - Xian-Dong He
- National Institute of Biological Sciences, Beijing, China
| | - Yu Xue
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China.
- Nanjing University Institute of Artificial Intelligence Biomedicine, Nanjing, Jiangsu, China.
| | - Meng-Qiu Dong
- National Institute of Biological Sciences, Beijing, China.
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, China.
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21
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Grushko D, Boocholez H, Levine A, Cohen E. Temporal requirements of SKN-1/NRF as a regulator of lifespan and proteostasis in Caenorhabditis elegans. PLoS One 2021; 16:e0243522. [PMID: 34197476 PMCID: PMC8248617 DOI: 10.1371/journal.pone.0243522] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Accepted: 06/11/2021] [Indexed: 11/18/2022] Open
Abstract
Lowering the activity of the Insulin/IGF-1 Signaling (IIS) cascade results in elevated stress resistance, enhanced protein homeostasis (proteostasis) and extended lifespan of worms, flies and mice. In the nematode Caenorhabditis elegans (C. elegans), the longevity phenotype that stems from IIS reduction is entirely dependent upon the activities of a subset of transcription factors including the Forkhead factor DAF-16/FOXO (DAF-16), Heat Shock Factor-1 (HSF-1), SKiNhead/Nrf (SKN-1) and ParaQuat Methylviologen responsive (PQM-1). While DAF-16 determines lifespan exclusively during early adulthood and governs proteostasis in early adulthood and midlife, HSF-1 executes these functions foremost during development. Despite the central roles of SKN-1 as a regulator of lifespan and proteostasis, the temporal requirements of this transcription factor were unknown. Here we employed conditional knockdown techniques and discovered that in C. elegans, SKN-1 is primarily important for longevity and proteostasis during late larval development through early adulthood. Our findings indicate that events that occur during late larval developmental through early adulthood affect lifespan and proteostasis and suggest that subsequent to HSF-1, SKN-1 sets the conditions, partially overlapping temporally with DAF-16, that enable IIS reduction to promote longevity and proteostasis. Our findings raise the intriguing possibility that HSF-1, SKN-1 and DAF-16 function in a coordinated and sequential manner to promote healthy aging.
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Affiliation(s)
- Danielle Grushko
- Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel–Canada (IMRIC), The Hebrew University School of Medicine, Jerusalem, Israel
| | - Hana Boocholez
- Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel–Canada (IMRIC), The Hebrew University School of Medicine, Jerusalem, Israel
| | - Amir Levine
- Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel–Canada (IMRIC), The Hebrew University School of Medicine, Jerusalem, Israel
| | - Ehud Cohen
- Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel–Canada (IMRIC), The Hebrew University School of Medicine, Jerusalem, Israel
- * E-mail:
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22
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Zhang F, Weckhorst JL, Assié A, Hosea C, Ayoub CA, Khodakova AS, Cabrera ML, Vidal Vilchis D, Félix MA, Samuel BS. Natural genetic variation drives microbiome selection in the Caenorhabditis elegans gut. Curr Biol 2021; 31:2603-2618.e9. [PMID: 34048707 PMCID: PMC8222194 DOI: 10.1016/j.cub.2021.04.046] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Revised: 04/12/2021] [Accepted: 04/19/2021] [Indexed: 02/07/2023]
Abstract
Host genetic landscapes can shape microbiome assembly in the animal gut by contributing to the establishment of distinct physiological environments. However, the genetic determinants contributing to the stability and variation of these microbiome types remain largely undefined. Here, we use the free-living nematode Caenorhabditis elegans to identify natural genetic variation among wild strains of C. elegans that drives assembly of distinct microbiomes. To achieve this, we first established a diverse model microbiome that represents the strain-level phylogenetic diversity naturally encountered by C. elegans in the wild. Using this community, we show that C. elegans utilizes immune, xenobiotic, and metabolic signaling pathways to favor the assembly of different microbiome types. Variations in these pathways were associated with enrichment for specific commensals, including the Alphaproteobacteria Ochrobactrum. Using RNAi and mutant strains, we showed that host selection for Ochrobactrum is mediated specifically by host insulin signaling pathways. Ochrobactrum recruitment is blunted in the absence of DAF-2/IGFR and modulated by the competitive action of insulin signaling transcription factors DAF-16/FOXO and PQM-1/SALL2. Further, the ability of C. elegans to enrich for Ochrobactrum as adults is correlated with faster animal growth rates and larger body size at the end of development. These results highlight a new role for the highly conserved insulin signaling pathways in the regulation of gut microbiome composition in C. elegans.
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Affiliation(s)
- Fan Zhang
- Alkek Center for Metagenomics and Microbiome Research and Department of Molecular Virology and Microbiology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA
| | - Jessica L Weckhorst
- Alkek Center for Metagenomics and Microbiome Research and Department of Molecular Virology and Microbiology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA; Program in Quantitative and Computational Biosciences, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA
| | - Adrien Assié
- Alkek Center for Metagenomics and Microbiome Research and Department of Molecular Virology and Microbiology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA
| | - Ciara Hosea
- Alkek Center for Metagenomics and Microbiome Research and Department of Molecular Virology and Microbiology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA; Program in Development, Disease Models and Therapeutics, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA
| | - Christopher A Ayoub
- Alkek Center for Metagenomics and Microbiome Research and Department of Molecular Virology and Microbiology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA
| | - Anastasia S Khodakova
- Alkek Center for Metagenomics and Microbiome Research and Department of Molecular Virology and Microbiology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA
| | - Mario Loeza Cabrera
- Alkek Center for Metagenomics and Microbiome Research and Department of Molecular Virology and Microbiology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA; Program in Development, Disease Models and Therapeutics, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA
| | - Daniela Vidal Vilchis
- Alkek Center for Metagenomics and Microbiome Research and Department of Molecular Virology and Microbiology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA
| | - Marie-Anne Félix
- Ecole Normale Supérieure, IBENS, CNRS UMR8197, INSERM U1024, Paris, France
| | - Buck S Samuel
- Alkek Center for Metagenomics and Microbiome Research and Department of Molecular Virology and Microbiology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA; Program in Quantitative and Computational Biosciences, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA; Program in Development, Disease Models and Therapeutics, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA.
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23
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Uno M, Tani Y, Nono M, Okabe E, Kishimoto S, Takahashi C, Abe R, Kurihara T, Nishida E. Neuronal DAF-16-to-intestinal DAF-16 communication underlies organismal lifespan extension in C. elegans. iScience 2021; 24:102706. [PMID: 34235410 PMCID: PMC8246587 DOI: 10.1016/j.isci.2021.102706] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 08/20/2020] [Accepted: 06/08/2021] [Indexed: 12/20/2022] Open
Abstract
Previous studies have revealed the importance of inter-tissue communications for lifespan regulation. However, the inter-tissue network responsible for lifespan regulation is not well understood, even in a simple organism Caenorhabditis elegans. To understand the mechanisms underlying systemic lifespan regulation, we focused on lifespan regulation by the insulin/insulin-like growth factor-1 signaling (IIS) pathway; IIS reduction activates the DAF-16/FOXO transcription factor, which results in lifespan extension. Our tissue-specific knockdown and knockout analyses demonstrated that IIS reduction in neurons and the intestine markedly extended lifespan. DAF-16 activation in neurons resulted in DAF-16 activation in the intestine and vice versa. Our dual gene manipulation method revealed that intestinal and neuronal DAF-16 mediate longevity induced by daf-2 knockout in neurons and the intestine, respectively. In addition, the systemic regulation of intestinal DAF-16 required the IIS pathway in intestinal and neurons. Collectively, these results highlight the importance of the neuronal DAF-16-to-intestinal DAF-16 communication for organismal lifespan regulation. Neurons and the intestine are important in the regulation of lifespan Neuronal daf-2 KO activates not only neuronal DAF-16 but also intestinal DAF-16 Intestinal daf-2 KO activates not only intestinal DAF-16 but also neuronal DAF-16 DAF-16-to-DAF-16 communication between neurons and the intestine regulates lifespan
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Affiliation(s)
- Masaharu Uno
- RIKEN Center for Biosystems Dynamics Research (BDR), Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan.,Department of Cell and Developmental Biology, Graduate School of Biostudies, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Yuri Tani
- Department of Cell and Developmental Biology, Graduate School of Biostudies, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Masanori Nono
- RIKEN Center for Biosystems Dynamics Research (BDR), Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan.,Department of Cell and Developmental Biology, Graduate School of Biostudies, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Emiko Okabe
- RIKEN Center for Biosystems Dynamics Research (BDR), Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan.,Department of Cell and Developmental Biology, Graduate School of Biostudies, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Saya Kishimoto
- RIKEN Center for Biosystems Dynamics Research (BDR), Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan.,Department of Cell and Developmental Biology, Graduate School of Biostudies, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Chika Takahashi
- RIKEN Center for Biosystems Dynamics Research (BDR), Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan.,Department of Cell and Developmental Biology, Graduate School of Biostudies, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Ryoji Abe
- Department of Cell and Developmental Biology, Graduate School of Biostudies, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Takuya Kurihara
- Department of Cell and Developmental Biology, Graduate School of Biostudies, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Eisuke Nishida
- RIKEN Center for Biosystems Dynamics Research (BDR), Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan.,Department of Cell and Developmental Biology, Graduate School of Biostudies, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
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24
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Radeke LJ, Herman MA. Take a Walk to the Wild Side of Caenorhabditis elegans-Pathogen Interactions. Microbiol Mol Biol Rev 2021; 85:e00146-20. [PMID: 33731489 PMCID: PMC8139523 DOI: 10.1128/mmbr.00146-20] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Microbiomes form intimate functional associations with their hosts. Much has been learned from correlating changes in microbiome composition to host organismal functions. However, in-depth functional studies require the manipulation of microbiome composition coupled with the precise interrogation of organismal physiology-features available in few host study systems. Caenorhabditis elegans has proven to be an excellent genetic model organism to study innate immunity and, more recently, microbiome interactions. The study of C. elegans-pathogen interactions has provided in depth understanding of innate immune pathways, many of which are conserved in other animals. However, many bacteria were chosen for these studies because of their convenience in the lab setting or their implication in human health rather than their native interactions with C. elegans In their natural environment, C. elegans feed on a variety of bacteria found in rotting organic matter, such as rotting fruits, flowers, and stems. Recent work has begun to characterize the native microbiome and has identified a common set of bacteria found in the microbiome of C. elegans While some of these bacteria are beneficial to C. elegans health, others are detrimental, leading to a complex, multifaceted understanding of bacterium-nematode interactions. Current research on nematode-bacterium interactions is focused on these native microbiome components, both their interactions with each other and with C. elegans We will summarize our knowledge of bacterial pathogen-host interactions in C. elegans, as well as recent work on the native microbiome, and explore the incorporation of these bacterium-nematode interactions into studies of innate immunity and pathogenesis.
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Affiliation(s)
- Leah J Radeke
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Michael A Herman
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
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25
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Aghayeva U, Bhattacharya A, Sural S, Jaeger E, Churgin M, Fang-Yen C, Hobert O. DAF-16/FoxO and DAF-12/VDR control cellular plasticity both cell-autonomously and via interorgan signaling. PLoS Biol 2021; 19:e3001204. [PMID: 33891586 PMCID: PMC8099054 DOI: 10.1371/journal.pbio.3001204] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 05/05/2021] [Accepted: 03/23/2021] [Indexed: 01/08/2023] Open
Abstract
Many cell types display the remarkable ability to alter their cellular phenotype in response to specific external or internal signals. Such phenotypic plasticity is apparent in the nematode Caenorhabditis elegans when adverse environmental conditions trigger entry into the dauer diapause stage. This entry is accompanied by structural, molecular, and functional remodeling of a number of distinct tissue types of the animal, including its nervous system. The transcription factor (TF) effectors of 3 different hormonal signaling systems, the insulin-responsive DAF-16/FoxO TF, the TGFβ-responsive DAF-3/SMAD TF, and the steroid nuclear hormone receptor, DAF-12/VDR, a homolog of the vitamin D receptor (VDR), were previously shown to be required for entering the dauer arrest stage, but their cellular and temporal focus of action for the underlying cellular remodeling processes remained incompletely understood. Through the generation of conditional alleles that allowed us to spatially and temporally control gene activity, we show here that all 3 TFs are not only required to initiate tissue remodeling upon entry into the dauer stage, as shown before, but are also continuously required to maintain the remodeled state. We show that DAF-3/SMAD is required in sensory neurons to promote and then maintain animal-wide tissue remodeling events. In contrast, DAF-16/FoxO or DAF-12/VDR act cell-autonomously to control anatomical, molecular, and behavioral remodeling events in specific cell types. Intriguingly, we also uncover non-cell autonomous function of DAF-16/FoxO and DAF-12/VDR in nervous system remodeling, indicating the presence of several insulin-dependent interorgan signaling axes. Our findings provide novel perspectives into how hormonal systems control tissue remodeling.
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Affiliation(s)
- Ulkar Aghayeva
- Department of Biological Sciences, Howard Hughes Medical Institute, Columbia University, New York, New York, United States of America
| | - Abhishek Bhattacharya
- Department of Biological Sciences, Howard Hughes Medical Institute, Columbia University, New York, New York, United States of America
| | - Surojit Sural
- Department of Biological Sciences, Howard Hughes Medical Institute, Columbia University, New York, New York, United States of America
| | - Eliza Jaeger
- Department of Biological Sciences, Howard Hughes Medical Institute, Columbia University, New York, New York, United States of America
| | - Matthew Churgin
- Department of Bioengineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Christopher Fang-Yen
- Department of Bioengineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Oliver Hobert
- Department of Biological Sciences, Howard Hughes Medical Institute, Columbia University, New York, New York, United States of America
- * E-mail:
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26
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Mutlu AS, Duffy J, Wang MC. Lipid metabolism and lipid signals in aging and longevity. Dev Cell 2021; 56:1394-1407. [PMID: 33891896 DOI: 10.1016/j.devcel.2021.03.034] [Citation(s) in RCA: 150] [Impact Index Per Article: 37.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 03/05/2021] [Accepted: 03/29/2021] [Indexed: 02/06/2023]
Abstract
Lipids play crucial roles in regulating aging and longevity. In the past few decades, a series of genetic pathways have been discovered to regulate lifespan in model organisms. Interestingly, many of these regulatory pathways are linked to lipid metabolism and lipid signaling. Lipid metabolic enzymes undergo significant changes during aging and are regulated by different longevity pathways. Lipids also actively modulate lifespan and health span as signaling molecules. In this review, we summarize recent insights into the roles of lipid metabolism and lipid signaling in aging and discuss lipid-related interventions in promoting longevity.
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Affiliation(s)
- Ayse Sena Mutlu
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jonathon Duffy
- Developmental Biology Graduate Program, Baylor College of Medicine, Houston, TX 77030, USA
| | - Meng C Wang
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX 77030, USA; Developmental Biology Graduate Program, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Howard Hughes Medical Institute, Baylor College of Medicine, Houston, TX 77030, USA.
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27
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Senchuk MM, Van Raamsdonk JM, Moore DJ. Multiple genetic pathways regulating lifespan extension are neuroprotective in a G2019S LRRK2 nematode model of Parkinson's disease. Neurobiol Dis 2021; 151:105267. [PMID: 33450392 PMCID: PMC7925424 DOI: 10.1016/j.nbd.2021.105267] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 12/17/2020] [Accepted: 01/10/2021] [Indexed: 01/02/2023] Open
Abstract
Mutations in the leucine-rich repeat kinase 2 (LRRK2) gene are the most frequent cause of late-onset, familial Parkinson's disease (PD), and LRRK2 variants are associated with increased risk for sporadic PD. While advanced age represents the strongest risk factor for disease development, it remains unclear how different age-related pathways interact to regulate LRRK2-driven late-onset PD. In this study, we employ a C. elegans model expressing PD-linked G2019S LRRK2 to examine the interplay between age-related pathways and LRRK2-induced dopaminergic neurodegeneration. We find that multiple genetic pathways that regulate lifespan extension can provide robust neuroprotection against mutant LRRK2. However, the level of neuroprotection does not strictly correlate with the magnitude of lifespan extension, suggesting that lifespan can be experimentally dissociated from neuroprotection. Using tissue-specific RNAi, we demonstrate that lifespan-regulating pathways, including insulin/insulin-like growth factor-1 (IGF-1) signaling, target of rapamycin (TOR), and mitochondrial respiration, can be directly manipulated in neurons to mediate neuroprotection. We extend this finding for AGE-1/PI3K, where pan-neuronal versus dopaminergic neuronal restoration of AGE-1 reveals both cell-autonomous and non-cell-autonomous neuroprotective mechanisms downstream of insulin signaling. Our data demonstrate the importance of distinct lifespan-regulating pathways in the pathogenesis of LRRK2-linked PD, and suggest that extended longevity is broadly neuroprotective via the actions of these pathways at least in part within neurons. This study further highlights the complex interplay that occurs between cells and tissues during organismal aging and disease manifestation.
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Affiliation(s)
- Megan M Senchuk
- Department of Neurodegenerative Science, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Jeremy M Van Raamsdonk
- Department of Neurology and Neurosurgery, McGill University, Montreal, Quebec H4A 3J1, Canada; Metabolic Disorders and Complications Program, Brain Repair and Integrative Neuroscience Program, Research Institute of the McGill University Health Centre, Montreal, Quebec H4A 3J1, Canada; Department of Genetics, Harvard Medical School, Cambridge, MA 02115, USA.
| | - Darren J Moore
- Department of Neurodegenerative Science, Van Andel Institute, Grand Rapids, MI 49503, USA.
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28
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Qi Z, Ji H, Le M, Li H, Wieland A, Bauer S, Liu L, Wink M, Herr I. Sulforaphane promotes C. elegans longevity and healthspan via DAF-16/DAF-2 insulin/IGF-1 signaling. Aging (Albany NY) 2021; 13:1649-1670. [PMID: 33471780 PMCID: PMC7880325 DOI: 10.18632/aging.202512] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 12/18/2020] [Indexed: 12/12/2022]
Abstract
The broccoli-derived isothiocyanate sulforaphane inhibits inflammation, oxidative stress and cancer, but its effect on healthspan and longevity are unclear. We used the C. elegans nematode model and fed the wildtype and 9 mutant strains ±sulforaphane. The lifespan, phenotype, pharyngeal pumping, mobility, lipofuscin accumulation, and RNA and protein expression of the nematodes were assessed by using Kaplan-Meier survival analysis, in vivo live imaging, fluorescence microscopy, and qRT-PCR. Sulforaphane increased the lifespan and promoted a health-related phenotype by increasing mobility, appetite and food intake and reducing lipofuscin accumulation. Mechanistically, sulforaphane inhibited DAF-2-mediated insulin/insulin-like growth factor signaling and its downstream targets AGE-1, AKT-1/AKT-2. This was associated with increased nuclear translocation of the FOXO transcription factor homolog DAF-16. In turn, the target genes sod-3, mtl-1 and gst-4, known to enhance stress resistance and lifespan, were upregulated. These results indicate that sulforaphane prolongs the lifespan and healthspan of C. elegans through insulin/IGF-1 signaling. Our results provide the basis for a nutritional sulforaphane-enriched strategy for the promotion of healthy aging and disease prevention.
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Affiliation(s)
- Zhimin Qi
- Molecular OncoSurgery, Section Surgical Research, Department of General, Visceral and Transplant Surgery, University of Heidelberg, Heidelberg, Germany
| | - Huihui Ji
- Molecular OncoSurgery, Section Surgical Research, Department of General, Visceral and Transplant Surgery, University of Heidelberg, Heidelberg, Germany
| | - Monika Le
- Molecular OncoSurgery, Section Surgical Research, Department of General, Visceral and Transplant Surgery, University of Heidelberg, Heidelberg, Germany
| | - Hanmei Li
- Institute of Pharmacy and Molecular Biotechnology, University of Heidelberg, Heidelberg, Germany
| | - Angela Wieland
- Molecular OncoSurgery, Section Surgical Research, Department of General, Visceral and Transplant Surgery, University of Heidelberg, Heidelberg, Germany
| | - Sonja Bauer
- Molecular OncoSurgery, Section Surgical Research, Department of General, Visceral and Transplant Surgery, University of Heidelberg, Heidelberg, Germany
| | - Li Liu
- Molecular OncoSurgery, Section Surgical Research, Department of General, Visceral and Transplant Surgery, University of Heidelberg, Heidelberg, Germany
| | - Michael Wink
- Institute of Pharmacy and Molecular Biotechnology, University of Heidelberg, Heidelberg, Germany
| | - Ingrid Herr
- Molecular OncoSurgery, Section Surgical Research, Department of General, Visceral and Transplant Surgery, University of Heidelberg, Heidelberg, Germany
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29
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Ewe CK, Alok G, Rothman JH. Stressful development: integrating endoderm development, stress, and longevity. Dev Biol 2020; 471:34-48. [PMID: 33307045 DOI: 10.1016/j.ydbio.2020.12.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Revised: 12/02/2020] [Accepted: 12/03/2020] [Indexed: 10/22/2022]
Abstract
In addition to performing digestion and nutrient absorption, the intestine serves as one of the first barriers to the external environment, crucial for protecting the host from environmental toxins, pathogenic invaders, and other stress inducers. The gene regulatory network (GRN) governing embryonic development of the endoderm and subsequent differentiation and maintenance of the intestine has been well-documented in C. elegans. A key regulatory input that initiates activation of the embryonic GRN for endoderm and mesoderm in this animal is the maternally provided SKN-1 transcription factor, an ortholog of the vertebrate Nrf1 and 2, which, like C. elegans SKN-1, perform conserved regulatory roles in mediating a variety of stress responses across metazoan phylogeny. Other key regulatory factors in early gut development also participate in stress response as well as in innate immunity and aging and longevity. In this review, we discuss the intersection between genetic nodes that mediate endoderm/intestine differentiation and regulation of stress and homeostasis. We also consider how direct signaling from the intestine to the germline, in some cases involving SKN-1, facilitates heritable epigenetic changes, allowing transmission of adaptive stress responses across multiple generations. These connections between regulation of endoderm/intestine development and stress response mechanisms suggest that varying selective pressure exerted on the stress response pathways may influence the architecture of the endoderm GRN, thereby leading to genetic and epigenetic variation in early embryonic GRN regulatory events.
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Affiliation(s)
- Chee Kiang Ewe
- Department of MCD Biology and Neuroscience Research Institute, University of California Santa Barbara, Santa Barbara, CA, USA.
| | - Geneva Alok
- Department of MCD Biology and Neuroscience Research Institute, University of California Santa Barbara, Santa Barbara, CA, USA.
| | - Joel H Rothman
- Department of MCD Biology and Neuroscience Research Institute, University of California Santa Barbara, Santa Barbara, CA, USA.
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30
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Baugh LR, Hu PJ. Starvation Responses Throughout the Caenorhabditiselegans Life Cycle. Genetics 2020; 216:837-878. [PMID: 33268389 PMCID: PMC7768255 DOI: 10.1534/genetics.120.303565] [Citation(s) in RCA: 80] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 08/17/2020] [Indexed: 02/07/2023] Open
Abstract
Caenorhabditis elegans survives on ephemeral food sources in the wild, and the species has a variety of adaptive responses to starvation. These features of its life history make the worm a powerful model for studying developmental, behavioral, and metabolic starvation responses. Starvation resistance is fundamental to life in the wild, and it is relevant to aging and common diseases such as cancer and diabetes. Worms respond to acute starvation at different times in the life cycle by arresting development and altering gene expression and metabolism. They also anticipate starvation during early larval development, engaging an alternative developmental program resulting in dauer diapause. By arresting development, these responses postpone growth and reproduction until feeding resumes. A common set of signaling pathways mediates systemic regulation of development in each context but with important distinctions. Several aspects of behavior, including feeding, foraging, taxis, egg laying, sleep, and associative learning, are also affected by starvation. A variety of conserved signaling, gene regulatory, and metabolic mechanisms support adaptation to starvation. Early life starvation can have persistent effects on adults and their descendants. With its short generation time, C. elegans is an ideal model for studying maternal provisioning, transgenerational epigenetic inheritance, and developmental origins of adult health and disease in humans. This review provides a comprehensive overview of starvation responses throughout the C. elegans life cycle.
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Affiliation(s)
- L Ryan Baugh
- Department of Biology, Center for Genomic and Computational Biology, Duke University, Durham, North Carolina 27708 and
| | - Patrick J Hu
- Departments of Medicine and Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232
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31
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Su L, Zhao T, Li H, Li H, Su X, Ba X, Zhang Y, Huang B, Lu J, Li X. ELT-2 promotes O-GlcNAc transferase OGT-1 expression to modulate Caenorhabditis elegans lifespan. J Cell Biochem 2020; 121:4898-4907. [PMID: 32628333 DOI: 10.1002/jcb.29817] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 06/08/2020] [Accepted: 06/17/2020] [Indexed: 11/12/2022]
Abstract
O-GlcNAc transferase (OGT) is the enzyme catalyzing protein O-GlcNAcylation by addition of a single O-linked-β-N-acetylglucosamine molecule (O-GlcNAc) to nuclear and cytoplasmic targets, and it uses uridine diphosphate-N-acetylglucosamine (UDP-GlcNAc) as a donor. As UDP-GlcNAc is the final product of the nutrient-sensing hexosamine signaling pathway, overexpression or knockout of ogt in mammals or invertebrate models influences cellular nutrient-response signals and increases susceptibility to chronic diseases of aging. Evidence shows that OGT expression levels decrease in tissues of older mice and rats. However, how OGT expression is modulated in the aging process remains poorly understood. In Caenorhabditis elegans, the exclusive mammalian OGT ortholog OGT-1 is crucial for lifespan control. Here, we observe that worm OGT-1 expression gradually reduces during aging. By combining prediction via the "MATCH" algorithm and luciferase reporter assays, GATA factor ELT-2, the homolog of human GATA4, is identified as a transcriptional factor driving OGT-1 expression. Chromatin immunoprecipitation-quantitative polymerase chain reaction and electrophoretic mobility shift assays show ELT-2 directly binds to and activates the ogt-1 promoter. Knockdown of elt-2 decreases the global O-GlcNAc modification level and reduces the lifespan of wild-type worms. The reduction in lifespan caused by elt-2 RNA interference is abrogated by the loss of ogt-1. These results imply that GATA factors are able to activate OGT expression, which could be beneficial for longevity and the development of therapeutic treatment for aging-related diseases.
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Affiliation(s)
- Liangping Su
- The Key Laboratory of Molecular Epigenetics of the Ministry of Education, Northeast Normal University, Changchun, China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Tingting Zhao
- The Institute of Genetics and Cytology, Northeast Normal University, Changchun, China
| | - Hongyuan Li
- The Key Laboratory of Molecular Epigenetics of the Ministry of Education, Northeast Normal University, Changchun, China
- Laboratory of Chemical Biology, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, China
| | - Hongmei Li
- The Key Laboratory of Molecular Epigenetics of the Ministry of Education, Northeast Normal University, Changchun, China
| | - Xin Su
- The Key Laboratory of Molecular Epigenetics of the Ministry of Education, Northeast Normal University, Changchun, China
| | - Xueqing Ba
- The Key Laboratory of Molecular Epigenetics of the Ministry of Education, Northeast Normal University, Changchun, China
| | - Yu Zhang
- The Institute of Genetics and Cytology, Northeast Normal University, Changchun, China
| | - Baiqu Huang
- The Institute of Genetics and Cytology, Northeast Normal University, Changchun, China
| | - Jun Lu
- The Institute of Genetics and Cytology, Northeast Normal University, Changchun, China
| | - Xiaoxue Li
- The Key Laboratory of Molecular Epigenetics of the Ministry of Education, Northeast Normal University, Changchun, China
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32
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Mallick A, Ranawade A, van den Berg W, Gupta BP. Axin-Mediated Regulation of Lifespan and Muscle Health in C. elegans Requires AMPK-FOXO Signaling. iScience 2020; 23:101843. [PMID: 33319173 PMCID: PMC7724191 DOI: 10.1016/j.isci.2020.101843] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 10/14/2020] [Accepted: 11/17/2020] [Indexed: 12/17/2022] Open
Abstract
Aging is a significant risk factor for several diseases. Studies have uncovered multiple signaling pathways that modulate aging, including insulin/insulin-like growth factor-1 signaling (IIS). In Caenorhabditis elegans, the key regulator of IIS is DAF-16/FOXO. One of the kinases that affects DAF-16 function is the AMPK catalytic subunit homolog AAK-2. In this study, we report that PRY-1/Axin plays an essential role in AAK-2 and DAF-16-mediated regulation of life span. The pry-1 mutant transcriptome contains many genes associated with aging and muscle function. Consistent with this, pry-1 is strongly expressed in muscles, and muscle-specific overexpression of pry-1 extends life span, delays muscle aging, and improves mitochondrial morphology in AAK-2-DAF-16-dependent manner. Furthermore, PRY-1 is necessary for AAK-2 phosphorylation. Taken together, our data demonstrate that PRY-1 functions in muscles to promote the life span of animals. This study establishes Axin as a major regulator of muscle health and aging. pry-1 transcriptome contains genes linked to aging and muscle function pry-1 functions in muscles to maintain life span and mitochondrial network Muscle-specific overexpression of pry-1 extends life span and promotes muscle health PRY-1-mediated life span extension depends on AAK-2-DAF-16 signaling
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Affiliation(s)
- Avijit Mallick
- Department of Biology, McMaster University, Hamilton, ON L8S-4K1, Canada
| | - Ayush Ranawade
- Department of Biology, McMaster University, Hamilton, ON L8S-4K1, Canada
| | | | - Bhagwati P Gupta
- Department of Biology, McMaster University, Hamilton, ON L8S-4K1, Canada
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33
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Application of Transcriptional Gene Modules to Analysis of Caenorhabditis elegans' Gene Expression Data. G3-GENES GENOMES GENETICS 2020; 10:3623-3638. [PMID: 32759329 PMCID: PMC7534440 DOI: 10.1534/g3.120.401270] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Identification of co-expressed sets of genes (gene modules) is used widely for grouping functionally related genes during transcriptomic data analysis. An organism-wide atlas of high-quality gene modules would provide a powerful tool for unbiased detection of biological signals from gene expression data. Here, using a method based on independent component analysis we call DEXICA, we have defined and optimized 209 modules that broadly represent transcriptional wiring of the key experimental organism C. elegans. These modules represent responses to changes in the environment (e.g., starvation, exposure to xenobiotics), genes regulated by transcriptions factors (e.g., ATFS-1, DAF-16), genes specific to tissues (e.g., neurons, muscle), genes that change during development, and other complex transcriptional responses to genetic, environmental and temporal perturbations. Interrogation of these modules reveals processes that are activated in long-lived mutants in cases where traditional analyses of differentially expressed genes fail to do so. Additionally, we show that modules can inform the strength of the association between a gene and an annotation (e.g., GO term). Analysis of “module-weighted annotations” improves on several aspects of traditional annotation-enrichment tests and can aid in functional interpretation of poorly annotated genes. We provide an online interactive resource with tutorials at http://genemodules.org/, in which users can find detailed information on each module, check genes for module-weighted annotations, and use both of these to analyze their own gene expression data (generated using any platform) or gene sets of interest.
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Heimbucher T, Hog J, Gupta P, Murphy CT. PQM-1 controls hypoxic survival via regulation of lipid metabolism. Nat Commun 2020; 11:4627. [PMID: 33009389 PMCID: PMC7532158 DOI: 10.1038/s41467-020-18369-w] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 07/31/2020] [Indexed: 12/25/2022] Open
Abstract
Animals have evolved responses to low oxygen conditions to ensure their survival. Here, we have identified the C. elegans zinc finger transcription factor PQM-1 as a regulator of the hypoxic stress response. PQM-1 is required for the longevity of insulin signaling mutants, but surprisingly, loss of PQM-1 increases survival under hypoxic conditions. PQM-1 functions as a metabolic regulator by controlling oxygen consumption rates, suppressing hypoxic glycogen levels, and inhibiting the expression of the sorbitol dehydrogenase-1 SODH-1, a crucial sugar metabolism enzyme. PQM-1 promotes hypoxic fat metabolism by maintaining the expression of the stearoyl-CoA desaturase FAT-7, an oxygen consuming, rate-limiting enzyme in fatty acid biosynthesis. PQM-1 activity positively regulates fat transport to developing oocytes through vitellogenins under hypoxic conditions, thereby increasing survival rates of arrested progeny during hypoxia. Thus, while pqm-1 mutants increase survival of mothers, ultimately this loss is detrimental to progeny survival. Our data support a model in which PQM-1 controls a trade-off between lipid metabolic activity in the mother and her progeny to promote the survival of the species under hypoxic conditions. Animals respond to hypoxic stress by adjusting metabolic processes to balance survival and reproduction. Here the authors identify the transcription factor PQM-1 as a metabolic regulator that balances hypoxic lipid and carbohydrate metabolism in C. elegans to limit somatic integrity and promote progeny survival.
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Affiliation(s)
- Thomas Heimbucher
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, 08544, USA. .,Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA. .,Bioinformatics and Molecular Genetics, Faculty of Biology, University of Freiburg, Freiburg, 79104, Baden-Wuerttemberg, Germany.
| | - Julian Hog
- Bioinformatics and Molecular Genetics, Faculty of Biology, University of Freiburg, Freiburg, 79104, Baden-Wuerttemberg, Germany
| | - Piyush Gupta
- Bioinformatics and Molecular Genetics, Faculty of Biology, University of Freiburg, Freiburg, 79104, Baden-Wuerttemberg, Germany
| | - Coleen T Murphy
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, 08544, USA. .,Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA.
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Jones LM, Chen Y, van Oosten-Hawle P. Redefining proteostasis transcription factors in organismal stress responses, development, metabolism, and health. Biol Chem 2020; 401:1005-1018. [DOI: 10.1515/hsz-2019-0385] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 02/26/2020] [Indexed: 12/19/2022]
Abstract
AbstractEukaryotic organisms have evolved complex and robust cellular stress response pathways to ensure maintenance of proteostasis and survival during fluctuating environmental conditions. Highly conserved stress response pathways can be triggered and coordinated at the cell-autonomous and cell-nonautonomous level by proteostasis transcription factors, including HSF1, SKN-1/NRF2, HIF1, and DAF-16/FOXO that combat proteotoxic stress caused by environmental challenges. While these transcription factors are often associated with a specific stress condition, they also direct “noncanonical” transcriptional programs that serve to integrate a multitude of physiological responses required for development, metabolism, and defense responses to pathogen infections. In this review, we outline the established function of these key proteostasis transcription factors at the cell-autonomous and cell-nonautonomous level and discuss a newly emerging stress responsive transcription factor, PQM-1, within the proteostasis network. We look beyond the canonical stress response roles of proteostasis transcription factors and highlight their function in integrating different physiological stimuli to maintain cytosolic organismal proteostasis.
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Affiliation(s)
- Laura M. Jones
- School of Molecular and Cell Biology and Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Yannic Chen
- School of Molecular and Cell Biology and Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Patricija van Oosten-Hawle
- School of Molecular and Cell Biology and Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
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36
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Han M, Zhao Y, Song W, Wang C, Mu C, Li R. Changes in microRNAs Expression Profile of Mimetic Aging Mice Treated with Melanin from Sepiella japonica Ink. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:5616-5622. [PMID: 32345009 DOI: 10.1021/acs.jafc.0c00291] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
A natural melanin extracted from Sepiella japonica ink (MSJI) is a polymer with antioxidant properties. In this study, the effects of MSJI treatment on microRNAs differentially expressed during aging in mimetic mice were investigated. The results revealed that 8 miRNAs: mmu-miR-1971, mmu-miR-3070b-3p, mmu-miR-320-3p, mmu-miR-342-3p, mmu-miR-350-3p, mmu-miR-5132-5p, mmu-miR-697, and mmu-miR-712-5p showed significantly different expression between mice treated with MSJI gavage and aging mice. GO analysis and signaling pathway analysis revealed that the predicted target genes were involved in diverse biological processes such as steroid and cholesterol metabolism, xenobiotic, demethylation, and circadian regulation of gene expression, suggesting a potential role in antiaging. The dual-luciferase reporter gene assay confirmed the downregulation of mmu-miR-697 in HS samples and targeting of the Gpt2 which plays an important role in aging. This study supports the hypothesis that MSJI prolongs the cell cycle by acting as an antioxidant to delay decrepitude.
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Affiliation(s)
- Meng Han
- Key Laboratory of Applied Marine Biotechnology, Ministry of Education, Ningbo University, Ningbo 315211, P. R. China
| | - Yun Zhao
- Key Laboratory of Applied Marine Biotechnology, Ministry of Education, Ningbo University, Ningbo 315211, P. R. China
| | - Weiwei Song
- Key Laboratory of Applied Marine Biotechnology, Ministry of Education, Ningbo University, Ningbo 315211, P. R. China
- Collaborative Innovation Center for Zhejiang Marine High-Efficiency and Healthy Aquaculture, Ningbo University, Ningbo 315211, P. R. China
| | - Chunlin Wang
- Key Laboratory of Applied Marine Biotechnology, Ministry of Education, Ningbo University, Ningbo 315211, P. R. China
- Collaborative Innovation Center for Zhejiang Marine High-Efficiency and Healthy Aquaculture, Ningbo University, Ningbo 315211, P. R. China
| | - Changkao Mu
- Key Laboratory of Applied Marine Biotechnology, Ministry of Education, Ningbo University, Ningbo 315211, P. R. China
- Collaborative Innovation Center for Zhejiang Marine High-Efficiency and Healthy Aquaculture, Ningbo University, Ningbo 315211, P. R. China
| | - Ronghua Li
- Key Laboratory of Applied Marine Biotechnology, Ministry of Education, Ningbo University, Ningbo 315211, P. R. China
- Collaborative Innovation Center for Zhejiang Marine High-Efficiency and Healthy Aquaculture, Ningbo University, Ningbo 315211, P. R. China
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Machiela E, Liontis T, Dues DJ, Rudich PD, Traa A, Wyman L, Kaufman C, Cooper JF, Lew L, Nadarajan S, Senchuk MM, Van Raamsdonk JM. Disruption of mitochondrial dynamics increases stress resistance through activation of multiple stress response pathways. FASEB J 2020; 34:8475-8492. [PMID: 32385951 PMCID: PMC7313680 DOI: 10.1096/fj.201903235r] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 04/05/2020] [Accepted: 04/15/2020] [Indexed: 12/17/2022]
Abstract
Mitochondria are dynamic organelles that can change shape and size depending on the needs of the cell through the processes of mitochondrial fission and fusion. In this work, we investigated the role of mitochondrial dynamics in organismal stress response. By using C. elegans as a genetic model, we could visualize mitochondrial morphology in a live organism with well‐established stress assays and well‐characterized stress response pathways. We found that disrupting mitochondrial fission (DRP1/drp‐1) or fusion (OPA1/eat‐3, MFN/fzo‐1) genes caused alterations in mitochondrial morphology that impacted both mitochondrial function and physiologic rates. While both mitochondrial fission and mitochondrial fusion mutants showed increased sensitivity to osmotic stress and anoxia, surprisingly we found that the mitochondrial fusion mutants eat‐3 and fzo‐1 are more resistant to both heat stress and oxidative stress. In exploring the mechanism of increased stress resistance, we found that disruption of mitochondrial fusion genes resulted in the upregulation of multiple stress response pathways. Overall, this work demonstrates that disrupting mitochondrial dynamics can have opposite effects on resistance to different types of stress. Our results suggest that disruption of mitochondrial fusion activates multiple stress response pathways that enhance resistance to specific stresses.
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Affiliation(s)
- Emily Machiela
- Laboratory of Aging and Neurodegenerative Disease, Center for Neurodegenerative Science, Van Andel Research Institute, Grand Rapids, MI, USA
| | - Thomas Liontis
- Department of Neurology and Neurosurgery, McGill University, Montreal, QC, Canada.,Metabolic Disorders and Complications Program, and Brain Repair and Integrative Neuroscience Program, Research Institute of the McGill University Health Centre, Montreal, QC, Canada
| | - Dylan J Dues
- Laboratory of Aging and Neurodegenerative Disease, Center for Neurodegenerative Science, Van Andel Research Institute, Grand Rapids, MI, USA
| | - Paige D Rudich
- Department of Neurology and Neurosurgery, McGill University, Montreal, QC, Canada.,Metabolic Disorders and Complications Program, and Brain Repair and Integrative Neuroscience Program, Research Institute of the McGill University Health Centre, Montreal, QC, Canada
| | - Annika Traa
- Department of Neurology and Neurosurgery, McGill University, Montreal, QC, Canada.,Metabolic Disorders and Complications Program, and Brain Repair and Integrative Neuroscience Program, Research Institute of the McGill University Health Centre, Montreal, QC, Canada
| | - Leslie Wyman
- Laboratory of Aging and Neurodegenerative Disease, Center for Neurodegenerative Science, Van Andel Research Institute, Grand Rapids, MI, USA
| | - Corah Kaufman
- Laboratory of Aging and Neurodegenerative Disease, Center for Neurodegenerative Science, Van Andel Research Institute, Grand Rapids, MI, USA
| | - Jason F Cooper
- Laboratory of Aging and Neurodegenerative Disease, Center for Neurodegenerative Science, Van Andel Research Institute, Grand Rapids, MI, USA
| | - Leira Lew
- Laboratory of Aging and Neurodegenerative Disease, Center for Neurodegenerative Science, Van Andel Research Institute, Grand Rapids, MI, USA
| | | | - Megan M Senchuk
- Laboratory of Aging and Neurodegenerative Disease, Center for Neurodegenerative Science, Van Andel Research Institute, Grand Rapids, MI, USA
| | - Jeremy M Van Raamsdonk
- Laboratory of Aging and Neurodegenerative Disease, Center for Neurodegenerative Science, Van Andel Research Institute, Grand Rapids, MI, USA.,Department of Neurology and Neurosurgery, McGill University, Montreal, QC, Canada.,Metabolic Disorders and Complications Program, and Brain Repair and Integrative Neuroscience Program, Research Institute of the McGill University Health Centre, Montreal, QC, Canada.,Department of Genetics, Harvard Medical School, Boston, MA, USA.,Division of Experimental Medicine, Department of Medicine, McGill University, Montreal, QC, Canada
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38
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Martínez Corrales G, Alic N. Evolutionary Conservation of Transcription Factors Affecting Longevity. Trends Genet 2020; 36:373-382. [PMID: 32294417 DOI: 10.1016/j.tig.2020.02.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 02/12/2020] [Accepted: 02/18/2020] [Indexed: 12/29/2022]
Abstract
The increasing number of older people is resulting in an increased prevalence of age-related diseases. Research has shown that the ageing process itself is a potential point of intervention. Indeed, gene expression can be optimised for health in older ages through manipulation of transcription factor (TF) activity. This review is focused on the ever-growing number of TFs whose effects on ageing are evolutionarily conserved. These regulate a plethora of functions, including stress resistance, metabolism, and growth. They are engaged in complex interactions within and between different cell types, impacting the physiology of the entire organism. Since ageing is not programmed, the conservation of their effects on lifespan is most likely a reflection of the conservation of their functions in youth.
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Abstract
The functional health of the proteome is determined by properties of the proteostasis network (PN) that regulates protein synthesis, folding, macromolecular assembly, translocation, and degradation. In eukaryotes, the PN also integrates protein biogenesis across compartments within the cell and between tissues of metazoans for organismal health and longevity. Additionally, in metazoans, proteome stability and the functional health of proteins is optimized for development and yet declines throughout aging, accelerating the risk for misfolding, aggregation, and cellular dysfunction. Here, I describe the cell-nonautonomous regulation of organismal PN by tissue communication and cell stress-response pathways. These systems are robust from development through reproductive maturity and are genetically programmed to decline abruptly in early adulthood by repression of the heat shock response and other cell-protective stress responses, thus compromising the ability of cells and tissues to properly buffer against the cumulative stress of protein damage during aging. While the failure of multiple protein quality control processes during aging challenges cellular function and tissue health, genetic studies, and the identification of small-molecule proteostasis regulators suggests strategies that can be employed to reset the PN with potential benefit on cellular health and organismal longevity.
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Affiliation(s)
- Richard I Morimoto
- Department of Molecular Biosciences, Rice Institute for Biomedical Research, Northwestern University, Evanston, Illinois 60208
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40
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Sala AJ, Bott LC, Brielmann RM, Morimoto RI. Embryo integrity regulates maternal proteostasis and stress resilience. Genes Dev 2020; 34:678-687. [PMID: 32217667 PMCID: PMC7197353 DOI: 10.1101/gad.335422.119] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 03/10/2020] [Indexed: 12/22/2022]
Abstract
The proteostasis network is regulated by transcellular communication to promote health and fitness in metazoans. In Caenorhabditis elegans, signals from the germline initiate the decline of proteostasis and repression of cell stress responses at reproductive maturity, indicating that commitment to reproduction is detrimental to somatic health. Here we show that proteostasis and stress resilience are also regulated by embryo-to-mother communication in reproductive adults. To identify genes that act directly in the reproductive system to regulate somatic proteostasis, we performed a tissue targeted genetic screen for germline modifiers of polyglutamine aggregation in muscle cells. We found that inhibiting the formation of the extracellular vitelline layer of the fertilized embryo inside the uterus suppresses aggregation, improves stress resilience in an HSF-1-dependent manner, and restores the heat-shock response in the somatic tissues of the parent. This pathway relies on DAF-16/FOXO activation in vulval tissues to maintain stress resilience in the mother, suggesting that the integrity of the embryo is monitored by the vulva to detect damage and initiate an organismal protective response. Our findings reveal a previously undescribed transcellular pathway that links the integrity of the developing progeny to proteostasis regulation in the parent.
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Affiliation(s)
- Ambre J Sala
- Department of Molecular Biosciences, Rice Institute for Biomedical Research, Northwestern University, Evanston, Illinois 60208, USA
| | - Laura C Bott
- Department of Molecular Biosciences, Rice Institute for Biomedical Research, Northwestern University, Evanston, Illinois 60208, USA
| | - Renee M Brielmann
- Department of Molecular Biosciences, Rice Institute for Biomedical Research, Northwestern University, Evanston, Illinois 60208, USA
| | - Richard I Morimoto
- Department of Molecular Biosciences, Rice Institute for Biomedical Research, Northwestern University, Evanston, Illinois 60208, USA
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41
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Zhao Y, Dong S, Kong Y, Rui Q, Wang D. Molecular basis of intestinal canonical Wnt/β-catenin BAR-1 in response to simulated microgravity in Caenorhabditis elegans. Biochem Biophys Res Commun 2020; 522:198-204. [DOI: 10.1016/j.bbrc.2019.11.082] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 11/14/2019] [Indexed: 12/29/2022]
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42
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McCorrison J, Girke T, Goetz LH, Miller RA, Schork NJ. Genetic Support for Longevity-Enhancing Drug Targets: Issues, Preliminary Data, and Future Directions. J Gerontol A Biol Sci Med Sci 2019; 74:S61-S71. [PMID: 31724058 PMCID: PMC7330475 DOI: 10.1093/gerona/glz206] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Indexed: 12/16/2022] Open
Abstract
Interventions meant to promote longevity and healthy aging have often been designed or observed to modulate very specific gene or protein targets. If there are naturally occurring genetic variants in such a target that affect longevity as well as the molecular function of that target (eg, the variants influence the expression of the target, acting as "expression quantitative trait loci" or "eQTLs"), this could support a causal relationship between the pharmacologic modulation of the target and longevity and thereby validate the target at some level. We considered the gene targets of many pharmacologic interventions hypothesized to enhance human longevity and explored how many variants there are in those targets that affect gene function (eg, as expression quantitative trait loci). We also determined whether variants in genes associated with longevity-related phenotypes affect gene function or are in linkage disequilibrium with variants that do, and whether pharmacologic studies point to compounds exhibiting activity against those genes. Our results are somewhat ambiguous, suggesting that integrating genetic association study results with functional genomic and pharmacologic studies is necessary to shed light on genetically mediated targets for longevity-enhancing drugs. Such integration will require more sophisticated data sets, phenotypic definitions, and bioinformatics approaches to be useful.
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Affiliation(s)
- Jamison McCorrison
- Graduate Program in Bioinformatics and Systems Biology, University of California–San Diego, Phoenix, Arizona
| | - Thomas Girke
- Institute for Integrative Genome Biology, University of California, Riverside, Phoenix, Arizona
| | - Laura H Goetz
- Department of Quantitative Medicine and Systems Biology, The Translational Genomics Research Institute (TGen), Phoenix, Arizona
- Department of Medical Oncology, City of Hope National Medical Center, Duarte, California
| | - Richard A Miller
- Department of Pathology, Ann Arbor
- Glenn Center for the Biology of Aging, University of Michigan, Ann Arbor
| | - Nicholas J Schork
- Department of Quantitative Medicine and Systems Biology, The Translational Genomics Research Institute (TGen), Phoenix, Arizona
- Department of Population Sciences, City of Hope National Medical Center, Duarte, California
- Department of Psychiatry, University of California–San Diego
- Department of Family Medicine and Public Health, University of California–San Diego
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43
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Roitenberg N, Cohen E. Lipid Assemblies at the Crossroads of Aging, Proteostasis, and Neurodegeneration. Trends Cell Biol 2019; 29:954-963. [PMID: 31669295 DOI: 10.1016/j.tcb.2019.09.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 09/12/2019] [Accepted: 09/24/2019] [Indexed: 12/22/2022]
Abstract
The proteostasis network (PN) is a nexus of mechanisms that act in concert to maintain the integrity of the proteome. Efficiency of the PN declines with age, resulting in the accumulation of misfolded proteins, and in some cases in the development of neurodegenerative disorders. Thus, maintaining an active and efficient PN through the late stages of life could delay or prevent neurodegeneration. Indeed, altering the activity of aging-regulating pathways protects model organisms from neurodegeneration-linked toxic protein aggregation. Here, we delineate evidence that the formation and integrity of lipid assemblies are affected by aging-regulating pathways, and describe the roles of these structures in proteostasis maintenance. We also highlight future research directions and discuss the possibility that compounds which modulate lipid assemblies could be used for the treatment of neurodegenerative disorders.
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Affiliation(s)
- Noa Roitenberg
- Department of Biochemistry and Molecular Biology, the Institute for Medical Research Israel - Canada (IMRIC), the Hebrew University School of Medicine, Jerusalem 91120, Israel
| | - Ehud Cohen
- Department of Biochemistry and Molecular Biology, the Institute for Medical Research Israel - Canada (IMRIC), the Hebrew University School of Medicine, Jerusalem 91120, Israel.
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Dobson AJ, Boulton-McDonald R, Houchou L, Svermova T, Ren Z, Subrini J, Vazquez-Prada M, Hoti M, Rodriguez-Lopez M, Ibrahim R, Gregoriou A, Gkantiragas A, Bähler J, Ezcurra M, Alic N. Longevity is determined by ETS transcription factors in multiple tissues and diverse species. PLoS Genet 2019; 15:e1008212. [PMID: 31356597 PMCID: PMC6662994 DOI: 10.1371/journal.pgen.1008212] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 05/27/2019] [Indexed: 01/17/2023] Open
Abstract
Ageing populations pose one of the main public health crises of our time. Reprogramming gene expression by altering the activities of sequence-specific transcription factors (TFs) can ameliorate deleterious effects of age. Here we explore how a circuit of TFs coordinates pro-longevity transcriptional outcomes, which reveals a multi-tissue and multi-species role for an entire protein family: the E-twenty-six (ETS) TFs. In Drosophila, reduced insulin/IGF signalling (IIS) extends lifespan by coordinating activation of Aop, an ETS transcriptional repressor, and Foxo, a Forkhead transcriptional activator. Aop and Foxo bind the same genomic loci, and we show that, individually, they effect similar transcriptional programmes in vivo. In combination, Aop can both moderate or synergise with Foxo, dependent on promoter context. Moreover, Foxo and Aop oppose the gene-regulatory activity of Pnt, an ETS transcriptional activator. Directly knocking down Pnt recapitulates aspects of the Aop/Foxo transcriptional programme and is sufficient to extend lifespan. The lifespan-limiting role of Pnt appears to be balanced by a requirement for metabolic regulation in young flies, in which the Aop-Pnt-Foxo circuit determines expression of metabolic genes, and Pnt regulates lipolysis and responses to nutrient stress. Molecular functions are often conserved amongst ETS TFs, prompting us to examine whether other Drosophila ETS-coding genes may also affect ageing. We show that five out of eight Drosophila ETS TFs play a role in fly ageing, acting from a range of organs and cells including the intestine, adipose and neurons. We expand the repertoire of lifespan-limiting ETS TFs in C. elegans, confirming their conserved function in ageing and revealing that the roles of ETS TFs in physiology and lifespan are conserved throughout the family, both within and between species. Understanding the basic biology of ageing may help us to reduce the burden of ill-health that old age brings. Ageing is modulated by changes to gene expression, which are orchestrated by the coordinate activity of proteins called transcription factors (TFs). E-twenty six (ETS) TFs are a large family with cellular functions that are conserved across animal taxa. In this study, we examine a longevity-promoting transcriptional circuit composed of two ETS TFs, Pnt and Aop, and Foxo, a forkhead TF with evolutionarily-conserved pro-longevity functions. This leads us to demonstrate that the activity of the majority of ETS TFs in multiple tissues and even different animal taxa regulates lifespan, indicating that roles in ageing are a general feature of this family of transcriptional regulators.
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Affiliation(s)
- Adam J. Dobson
- Institute of Healthy Ageing, Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
| | - Richard Boulton-McDonald
- Institute of Healthy Ageing, Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
| | - Lara Houchou
- Institute of Healthy Ageing, Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
| | - Tatiana Svermova
- Institute of Healthy Ageing, Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
| | - Ziyu Ren
- Institute of Healthy Ageing, Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
| | - Jeremie Subrini
- Institute of Healthy Ageing, Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
| | | | - Mimoza Hoti
- Institute of Healthy Ageing, Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
| | - Maria Rodriguez-Lopez
- Institute of Healthy Ageing, Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
| | - Rita Ibrahim
- Institute of Healthy Ageing, Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
| | - Afroditi Gregoriou
- Institute of Healthy Ageing, Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
| | - Alexis Gkantiragas
- Institute of Healthy Ageing, Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
| | - Jürg Bähler
- Institute of Healthy Ageing, Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
| | - Marina Ezcurra
- School of Biosciences, University of Kent, Canterbury, United Kingdom
| | - Nazif Alic
- Institute of Healthy Ageing, Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
- * E-mail:
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45
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Jordan JM, Hibshman JD, Webster AK, Kaplan REW, Leinroth A, Guzman R, Maxwell CS, Chitrakar R, Bowman EA, Fry AL, Hubbard EJA, Baugh LR. Insulin/IGF Signaling and Vitellogenin Provisioning Mediate Intergenerational Adaptation to Nutrient Stress. Curr Biol 2019; 29:2380-2388.e5. [PMID: 31280992 PMCID: PMC6650306 DOI: 10.1016/j.cub.2019.05.062] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 04/19/2019] [Accepted: 05/24/2019] [Indexed: 12/22/2022]
Abstract
The roundworm C. elegans reversibly arrests larval development during starvation [1], but extended early-life starvation reduces reproductive success [2, 3]. Maternal dietary restriction (DR) buffers progeny from starvation as young larvae, preserving reproductive success [4]. However, the developmental basis of reduced fertility following early-life starvation is unknown, and it is unclear how maternal diet modifies developmental physiology in progeny. We show here that extended starvation in first-stage (L1) larvae followed by unrestricted feeding results in a variety of developmental abnormalities in the reproductive system, including proliferative germ-cell tumors and uterine masses that express neuronal and epidermal cell fate markers. We found that maternal DR and reduced maternal insulin/insulin-like growth factor (IGF) signaling (IIS) increase oocyte provisioning of vitellogenin lipoprotein, reducing penetrance of starvation-induced abnormalities in progeny, including tumors. Furthermore, we show that maternal DR and reduced maternal IIS reduce IIS in progeny. daf-16/FoxO and skn-1/Nrf, transcriptional effectors of IIS, are required in progeny for maternal DR and increased vitellogenin provisioning to suppress starvation-induced abnormalities. daf-16/FoxO activity in somatic tissues is sufficient to suppress starvation-induced abnormalities, suggesting cell-nonautonomous regulation of reproductive system development. This work reveals that early-life starvation compromises reproductive development and that vitellogenin-mediated intergenerational insulin/IGF-to-insulin/IGF signaling mediates adaptation to nutrient availability.
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Affiliation(s)
- James M Jordan
- Department of Biology, Duke University, Durham, NC 27708, USA
| | | | - Amy K Webster
- Department of Biology, Duke University, Durham, NC 27708, USA
| | | | | | - Ryan Guzman
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - Colin S Maxwell
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - Rojin Chitrakar
- Department of Biology, Duke University, Durham, NC 27708, USA
| | | | - Amanda L Fry
- Skirball Institute of Biomolecular Medicine, Department of Cell Biology, New York University School of Medicine, New York, NY 10016, USA
| | - E Jane Albert Hubbard
- Skirball Institute of Biomolecular Medicine, Department of Cell Biology, New York University School of Medicine, New York, NY 10016, USA
| | - L Ryan Baugh
- Department of Biology, Duke University, Durham, NC 27708, USA.
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46
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Su L, Li H, Huang C, Zhao T, Zhang Y, Ba X, Li Z, Zhang Y, Huang B, Lu J, Zhao Y, Li X. Muscle-Specific Histone H3K36 Dimethyltransferase SET-18 Shortens Lifespan of Caenorhabditis elegans by Repressing daf-16a Expression. Cell Rep 2019. [PMID: 29514099 DOI: 10.1016/j.celrep.2018.02.029] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Mounting evidence shows that histone methylation, a typical epigenetic mark, is crucial for gene expression regulation during aging. Decreased trimethylation of Lys 36 on histone H3 (H3K36me3) in worms and yeast is reported to shorten lifespan. The function of H3K36me2 in aging remains unclear. In this study, we identified Caenorhabditis elegans SET-18 as a histone H3K36 dimethyltransferase. SET-18 deletion extended lifespan and increased oxidative stress resistance, dependent on daf-16 activity in the insulin/IGF pathway. In set-18 mutants, transcription of daf-16 isoform a (daf-16a) was specifically upregulated. Accordingly, a decrease in H3K36me2 on daf-16a promoter was observed. Muscle-specific expression of SET-18 increased in aged worms (day 7 and day 11), attributable to elevation of global H3K36me2 and inhibition of daf-16a expression. Consequently, longevity was shortened. These findings suggested that chromatic repression mediated by tissue-specific H3K36 dimethyltransferase might be detrimental to lifespan and may have implications in human age-related diseases.
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Affiliation(s)
- Liangping Su
- Key Laboratory of Molecular Epigenetics of the Ministry of Education, Northeast Normal University, Changchun 130024, China
| | - Hongyuan Li
- Key Laboratory of Molecular Epigenetics of the Ministry of Education, Northeast Normal University, Changchun 130024, China
| | - Cheng Huang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education, Northeast Normal University, Changchun 130024, China
| | - Tingting Zhao
- Institute of Genetics and Cytology, Northeast Normal University, Changchun 130024, China
| | - Yongjun Zhang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education, Northeast Normal University, Changchun 130024, China
| | - Xueqing Ba
- Institute of Genetics and Cytology, Northeast Normal University, Changchun 130024, China
| | - Zhongwei Li
- Institute of Genetics and Cytology, Northeast Normal University, Changchun 130024, China
| | - Yu Zhang
- Institute of Genetics and Cytology, Northeast Normal University, Changchun 130024, China
| | - Baiqu Huang
- Institute of Genetics and Cytology, Northeast Normal University, Changchun 130024, China
| | - Jun Lu
- Institute of Genetics and Cytology, Northeast Normal University, Changchun 130024, China.
| | - Yanmei Zhao
- Key Laboratory of RNA Biology, Beijing Key Laboratory of Noncoding RNA, Institute of Biophysics, CAS Center for Excellence in Biomacromolecules, Chinese Academy of Sciences, Beijing 100101, China.
| | - Xiaoxue Li
- Key Laboratory of Molecular Epigenetics of the Ministry of Education, Northeast Normal University, Changchun 130024, China.
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47
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Li S, Zhao H, Zhang P, Liang C, Zhang Y, Hsu A, Dong M. DAF-16 stabilizes the aging transcriptome and is activated in mid-aged Caenorhabditis elegans to cope with internal stress. Aging Cell 2019; 18:e12896. [PMID: 30773782 PMCID: PMC6516157 DOI: 10.1111/acel.12896] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2018] [Accepted: 11/03/2018] [Indexed: 12/31/2022] Open
Abstract
The roles and regulatory mechanisms of transcriptome changes during aging are unclear. It has been proposed that the transcriptome suffers decay during aging owing to age‐associated down‐regulation of transcription factors. In this study, we characterized the role of a transcription factor DAF‐16, which is a highly conserved lifespan regulator, in the normal aging process of Caenorhabditis elegans. We found that DAF‐16 translocates into the nucleus in aged wild‐type worms and activates the expression of hundreds of genes in response to age‐associated cellular stress. Most of the age‐dependent DAF‐16 targets are different from the canonical DAF‐16 targets downstream of insulin signaling. This and other evidence suggest that activation of DAF‐16 during aging is distinct from activation of DAF‐16 due to reduced signaling from DAF‐2. Further analysis showed that it is due in part to a loss of proteostasis during aging. We also found that without daf‐16, dramatic gene expression changes occur as early as on adult day 2, indicating that DAF‐16 acts to stabilize the transcriptome during normal aging. Our results thus reveal that normal aging is not simply a process in which the gene expression program descends into chaos due to loss of regulatory activities; rather, there is active transcriptional regulation during aging.
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Affiliation(s)
- Shang‐Tong Li
- School of Life Sciences Tsinghua University Beijing China
- Peking University‐Tsinghua University‐National Institute of Biological Sciences (PTN) Joint Graduate Program Beijing China
- National Institute of Biological Sciences Beijing China
| | - Han‐Qing Zhao
- National Institute of Biological Sciences Beijing China
| | - Pan Zhang
- National Institute of Biological Sciences Beijing China
| | - Chung‐Yi Liang
- Research Center for Healthy Aging China Medical University Taichung Taiwan
| | | | - Ao‐Lin Hsu
- Research Center for Healthy Aging China Medical University Taichung Taiwan
- Institute of Biochemistry and Molecular Biology National Yang‐Ming University Taipei Taiwan
- Department of Internal Medicine, Division of Geriatric and Palliative Medicine University of Michigan Ann Arbor Michigan
| | - Meng‐Qiu Dong
- National Institute of Biological Sciences Beijing China
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University Beijing China
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48
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Dietary Restriction Extends Lifespan through Metabolic Regulation of Innate Immunity. Cell Metab 2019; 29:1192-1205.e8. [PMID: 30905669 PMCID: PMC6506407 DOI: 10.1016/j.cmet.2019.02.013] [Citation(s) in RCA: 108] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Revised: 12/13/2018] [Accepted: 02/22/2019] [Indexed: 12/19/2022]
Abstract
Chronic inflammation predisposes to aging-associated disease, but it is unknown whether immunity regulation might be important for extending healthy lifespan. Here we show that in C. elegans, dietary restriction (DR) extends lifespan by modulating a conserved innate immunity pathway that is regulated by p38 signaling and the transcription factor ATF-7. Longevity from DR depends upon p38-ATF-7 immunity being intact but downregulated to a basal level. p38-ATF-7 immunity accelerates aging when hyperactive, influences lifespan independently of pathogen exposure, and is activated by nutrients independently of mTORC1, a major DR mediator. Longevity from reduced insulin/IGF-1 signaling (rIIS) also involves p38-ATF-7 downregulation, with signals from DAF-16/FOXO reducing food intake. We conclude that p38-ATF-7 is an immunometabolic pathway that senses bacterial and nutrient signals, that immunity modulation is critical for DR, and that DAF-16/FOXO couples appetite to growth regulation. These conserved mechanisms may influence aging in more complex organisms.
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49
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Prasanth MI, Venkatesh D, Murali D, Bhaskar JP, Krishnan V, Balamurugan K. Understanding the role of DAF-16 mediated pathway in Caenorhabditis elegans during UV-A mediated photoaging process. Arch Gerontol Geriatr 2019; 82:279-285. [DOI: 10.1016/j.archger.2019.03.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 03/04/2019] [Accepted: 03/11/2019] [Indexed: 01/08/2023]
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50
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Cytoplasmic and Mitochondrial NADPH-Coupled Redox Systems in the Regulation of Aging. Nutrients 2019; 11:nu11030504. [PMID: 30818813 PMCID: PMC6471790 DOI: 10.3390/nu11030504] [Citation(s) in RCA: 113] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 02/20/2019] [Accepted: 02/21/2019] [Indexed: 12/20/2022] Open
Abstract
The reduced form of nicotinamide adenine dinucleotide phosphate (NADPH) protects against redox stress by providing reducing equivalents to antioxidants such as glutathione and thioredoxin. NADPH levels decline with aging in several tissues, but whether this is a major driving force for the aging process has not been well established. Global or neural overexpression of several cytoplasmic enzymes that synthesize NADPH have been shown to extend lifespan in model organisms such as Drosophila suggesting a positive relationship between cytoplasmic NADPH levels and longevity. Mitochondrial NADPH plays an important role in the protection against redox stress and cell death and mitochondrial NADPH-utilizing thioredoxin reductase 2 levels correlate with species longevity in cells from rodents and primates. Mitochondrial NADPH shuttles allow for some NADPH flux between the cytoplasm and mitochondria. Since a decline of nicotinamide adenine dinucleotide (NAD+) is linked with aging and because NADP+ is exclusively synthesized from NAD+ by cytoplasmic and mitochondrial NAD+ kinases, a decline in the cytoplasmic or mitochondrial NADPH pool may also contribute to the aging process. Therefore pro-longevity therapies should aim to maintain the levels of both NAD+ and NADPH in aging tissues.
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