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Xue Y, Xue B, Zhang L. Multi-Omics Integrative Analysis to Reveal the Impacts of Shewanella algae on the Development and Lifespan of Marine Nematode Litoditis marina. Int J Mol Sci 2024; 25:9111. [PMID: 39201797 PMCID: PMC11354469 DOI: 10.3390/ijms25169111] [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: 07/23/2024] [Revised: 08/19/2024] [Accepted: 08/20/2024] [Indexed: 09/03/2024] Open
Abstract
Understanding how habitat bacteria affect animal development, reproduction, and aging is essential for deciphering animal biology. Our recent study showed that Shewanella algae impaired Litoditis marina development and lifespan, compared with Escherichia coli OP50 feeding; however, the underlying mechanisms remain unclear. Here, multi-omics approaches, including the transcriptome of both L. marina and bacteria, as well as the comparative bacterial metabolome, were utilized to investigate how bacterial food affects animal fitness and physiology. We found that genes related to iron ion binding and oxidoreductase activity pathways, such as agmo-1, cdo-1, haao-1, and tdo-2, were significantly upregulated in L. marina grown on S. algae, while extracellular structural components-related genes were significantly downregulated. Next, we observed that bacterial genes belonging to amino acid metabolism and ubiquinol-8 biosynthesis were repressed, while virulence genes were significantly elevated in S. algae. Furthermore, metabolomic analysis revealed that several toxic metabolites, such as puromycin, were enriched in S. algae, while many nucleotides were significantly enriched in OP50. Moreover, we found that the "two-component system" was enriched in S. algae, whereas "purine metabolism" and "one-carbon pool by folate" were significantly enriched in E. coli OP50. Collectively, our data provide new insights to decipher how diet modulates animal fitness and biology.
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Affiliation(s)
- Yiming Xue
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (Y.X.); (B.X.)
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao 266237, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao 266071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Beining Xue
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (Y.X.); (B.X.)
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao 266237, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao 266071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Liusuo Zhang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (Y.X.); (B.X.)
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao 266237, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao 266071, China
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2
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Pitkänen M, Matilainen O. Milk Fat Globule Membrane-Containing Protein Powder Promotes Fitness in Caenorhabditis elegans. Nutrients 2024; 16:2290. [PMID: 39064733 PMCID: PMC11280102 DOI: 10.3390/nu16142290] [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: 06/24/2024] [Revised: 07/10/2024] [Accepted: 07/15/2024] [Indexed: 07/28/2024] Open
Abstract
Milk-derived peptides and milk fat globule membrane (MFGM) have gained interest as health-promoting food ingredients. However, the mechanisms by which these nutraceuticals modulate the function of biological systems often remain unclear. We utilized Caenorhabditis elegans to elucidate how MFGM-containing protein powder (MProPow), previously used in a clinical trial, affect the physiology of this model organism. Our results demonstrate that MProPow does not affect lifespan but promotes the fitness of the animals. Surprisingly, gene expression analysis revealed that MProPow decreases the expression of genes functioning on innate immunity, which also translates into reduced survival on pathogenic bacteria. One of the innate immunity-associated genes showing reduced expression upon MProPow supplementation is cpr-3, the homolog of human cathepsin B. Interestingly, knockdown of cpr-3 enhances fitness, but not in MProPow-treated animals, suggesting that MProPow contributes to fitness by downregulating the expression of this gene. In summary, this research highlights the value of C. elegans in testing the biological activity of food supplements and nutraceuticals. Furthermore, this study should encourage investigations into whether milk-derived peptides and MFGM mediate their beneficial effects through the modulation of cathepsin B expression in humans.
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Affiliation(s)
| | - Olli Matilainen
- The Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, 00790 Helsinki, Finland;
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Valera-Alberni M, Yao P, Romero-Sanz S, Lanjuin A, Mair WB. Novel Imaging Tools to Study Mitochondrial Dynamics in Caenorhabditis elegans. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.16.603730. [PMID: 39071403 PMCID: PMC11275731 DOI: 10.1101/2024.07.16.603730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
Mitochondria exhibit a close interplay between their structure and function. Understanding this intricate relationship requires advanced imaging techniques that can capture the dynamic nature of mitochondria and their impact on cellular processes. However, much of the work on mitochondrial dynamics has been done in single celled organisms or in vitro cell culture. Here, we introduce novel genetic tools for live imaging of mitochondrial networks in the nematode Caenorhabditis elegans , addressing a pressing need for advanced techniques in studying organelle dynamics within live intact multicellular organisms. Through a comprehensive analysis, we directly compare our tools with existing methods, demonstrating their advantages for visualizing mitochondrial morphology and contrasting their impact on organismal physiology. We reveal limitations of conventional techniques, while showcasing the utility and versatility of our approaches, including endogenous CRISPR tags and ectopic labeling. By providing a guide for selecting the most suitable tools based on experimental goals, our work advances mitochondrial research in C. elegans and enhances the strategic integration of diverse imaging modalities for a holistic understanding of organelle dynamics in living organisms.
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Austad SN, Smith JR, Hoffman JM. Amino acid restriction, aging, and longevity: an update. FRONTIERS IN AGING 2024; 5:1393216. [PMID: 38757144 PMCID: PMC11096585 DOI: 10.3389/fragi.2024.1393216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Accepted: 04/18/2024] [Indexed: 05/18/2024]
Abstract
Various so-called dietary restriction paradigms have shown promise for extending health and life. All such paradigms rely on ad libitum (hereafter ad lib) feeding, something virtually never employed in animals whose long-term health we value, either as a control or, except for food restriction itself, for both control and treatment arms of the experiment. Even though the mechanism(s) remain only vaguely understood, compared to ad lib-fed animals a host of dietary manipulations, including calorie restriction, low protein, methionine, branched-chain amino acids, and even low isoleucine have demonstrable health benefits in laboratory species in a standard laboratory environment. The remaining challenge is to determine whether these health benefits remain in more realistic environments and how they interact with other health enhancing treatments such as exercise or emerging geroprotective drugs. Here we review the current state of the field of amino acid restriction on longevity of animal models and evaluate its translational potential.
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Affiliation(s)
- S. N. Austad
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL, United States
| | - J. R. Smith
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL, United States
| | - J. M. Hoffman
- Department of Biological Sciences, Augusta University, Augusta, GA, United States
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5
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Thiruppathi G, Mohankumar A, Kalaiselvi D, Velumani M, Saravana Bhavan P, Premasudha P, Tawata S, Sundararaj P. Geroprotective Effect of Levilactobacillus brevis and Weizmannia coagulans in Caenorhabditis elegans. Probiotics Antimicrob Proteins 2024; 16:589-605. [PMID: 37036656 DOI: 10.1007/s12602-023-10060-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/06/2023] [Indexed: 04/11/2023]
Abstract
The prophylactic use of lactic acid bacteria (LAB) to maintain human health is one of the most important research areas in recent times. LAB supplementation confers a wide range of health benefits to the host, but few studies have focused on their possible role in delaying the aging process. This study explored the health and life-promoting properties of two LAB, Levilactobacillus brevis and Weizmannia coagulans, using the Caenorhabditis elegans model. We found that L. brevis and W. coagulans enhanced the intestinal integrity and intestinal barrier functions without affecting the overall physiological functions of C. elegans. Wild-type worms preconditioned with LAB strains increased their survival under oxidative and thermal stress conditions by reducing intracellular reactive oxygen levels. Live L. brevis and W. coagulans significantly extended the lifespan of C. elegans under standard laboratory conditions independently of dietary restrictions. Genetic and reporter gene expression analysis revealed that L. brevis and W. coagulans extend lifespan via insulin/insulin-like growth factor-1 signaling and the p38 MAPK signaling axis. Furthermore, sirtuin, JNK MAPK, and mitochondrial respiratory complexes were found to be partially involved in W. coagulans-mediated lifespan extension and stress resilience. Preconditioning with LAB ameliorated age-related functional decline in C. elegans and reduced ectopic fat deposition in an NHR-49-dependent manner. Together, our findings indicated that L. brevis and W. coagulans are worth exploring further as "gerobiotic" candidates to delay aging and improve the healthspan of the host.
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Affiliation(s)
| | - Amirthalingam Mohankumar
- PAK Research Center, University of the Ryukyus, Senbaru 1, Nishihara-Cho, Okinawa, 903-0213, Japan.
| | - Duraisamy Kalaiselvi
- Department of Agricultural Chemistry, Institute of Environmentally Friendly Agriculture, College of Agriculture and Life Science, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Muthusamy Velumani
- Department of Nanoscience and Technology, Bharathiar University, Coimbatore, Tamil Nadu, 641046, India
| | | | - Paramasivam Premasudha
- Department of Nanoscience and Technology, Bharathiar University, Coimbatore, Tamil Nadu, 641046, India
| | - Shinkichi Tawata
- PAK Research Center, University of the Ryukyus, Senbaru 1, Nishihara-Cho, Okinawa, 903-0213, Japan
| | - Palanisamy Sundararaj
- Department of Zoology, Bharathiar University, Coimbatore, Tamil Nadu, 641046, India.
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Turner CD, Ramos CM, Curran SP. Disrupting the SKN-1 homeostat: mechanistic insights and phenotypic outcomes. FRONTIERS IN AGING 2024; 5:1369740. [PMID: 38501033 PMCID: PMC10944932 DOI: 10.3389/fragi.2024.1369740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 02/15/2024] [Indexed: 03/20/2024]
Abstract
The mechanisms that govern maintenance of cellular homeostasis are crucial to the lifespan and healthspan of all living systems. As an organism ages, there is a gradual decline in cellular homeostasis that leads to senescence and death. As an organism lives into advanced age, the cells within will attempt to abate age-related decline by enhancing the activity of cellular stress pathways. The regulation of cellular stress responses by transcription factors SKN-1/Nrf2 is a well characterized pathway in which cellular stress, particularly xenobiotic stress, is abated by SKN-1/Nrf2-mediated transcriptional activation of the Phase II detoxification pathway. However, SKN-1/Nrf2 also regulates a multitude of other processes including development, pathogenic stress responses, proteostasis, and lipid metabolism. While this process is typically tightly regulated, constitutive activation of SKN-1/Nrf2 is detrimental to organismal health, this raises interesting questions surrounding the tradeoff between SKN-1/Nrf2 cryoprotection and cellular health and the ability of cells to deactivate stress response pathways post stress. Recent work has determined that transcriptional programs of SKN-1 can be redirected or suppressed to abate negative health outcomes of constitutive activation. Here we will detail the mechanisms by which SKN-1 is controlled, which are important for our understanding of SKN-1/Nrf2 cytoprotection across the lifespan.
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Affiliation(s)
- Chris D. Turner
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, United States
| | - Carmen M. Ramos
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, United States
- Dornsife College of Letters, Arts, and Sciences, Department of Molecular and Computational Biology, University of Southern California, Los Angeles, CA, United States
| | - Sean P. Curran
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, United States
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Sengupta T, St. Ange J, Kaletsky R, Moore RS, Seto RJ, Marogi J, Myhrvold C, Gitai Z, Murphy CT. A natural bacterial pathogen of C. elegans uses a small RNA to induce transgenerational inheritance of learned avoidance. PLoS Genet 2024; 20:e1011178. [PMID: 38547071 PMCID: PMC10977744 DOI: 10.1371/journal.pgen.1011178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 02/09/2024] [Indexed: 04/02/2024] Open
Abstract
C. elegans can learn to avoid pathogenic bacteria through several mechanisms, including bacterial small RNA-induced learned avoidance behavior, which can be inherited transgenerationally. Previously, we discovered that a small RNA from a clinical isolate of Pseudomonas aeruginosa, PA14, induces learned avoidance and transgenerational inheritance of that avoidance in C. elegans. Pseudomonas aeruginosa is an important human pathogen, and there are other Pseudomonads in C. elegans' natural habitat, but it is unclear whether C. elegans ever encounters PA14-like bacteria in the wild. Thus, it is not known if small RNAs from bacteria found in C. elegans' natural habitat can also regulate host behavior and produce heritable behavioral effects. Here we screened a set of wild habitat bacteria, and found that a pathogenic Pseudomonas vranovensis strain isolated from the C. elegans microbiota, GRb0427, regulates worm behavior: worms learn to avoid this pathogenic bacterium following exposure, and this learned avoidance is inherited for four generations. The learned response is entirely mediated by bacterially-produced small RNAs, which induce avoidance and transgenerational inheritance, providing further support that such mechanisms of learning and inheritance exist in the wild. We identified Pv1, a small RNA expressed in P. vranovensis, that has a 16-nucleotide match to an exon of the C. elegans gene maco-1. Pv1 is both necessary and sufficient to induce learned avoidance of Grb0427. However, Pv1 also results in avoidance of a beneficial microbiome strain, P. mendocina. Our findings suggest that bacterial small RNA-mediated regulation of host behavior and its transgenerational inheritance may be functional in C. elegans' natural environment, and that this potentially maladaptive response may favor reversal of the transgenerational memory after a few generations. Our data also suggest that different bacterial small RNA-mediated regulation systems evolved independently, but define shared molecular features of bacterial small RNAs that produce transgenerationally-inherited effects.
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Affiliation(s)
- Titas Sengupta
- Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Jonathan St. Ange
- Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Rachel Kaletsky
- Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Rebecca S. Moore
- Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Renee J. Seto
- Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Jacob Marogi
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Cameron Myhrvold
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Zemer Gitai
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Coleen T. Murphy
- Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
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DuMez-Kornegay RN, Baker LS, Morris AJ, DeLoach WLM, Dowen RH. Kombucha Tea-associated microbes remodel host metabolic pathways to suppress lipid accumulation. PLoS Genet 2024; 20:e1011003. [PMID: 38547054 PMCID: PMC10977768 DOI: 10.1371/journal.pgen.1011003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 02/22/2024] [Indexed: 04/02/2024] Open
Abstract
The popularity of the ancient, probiotic-rich beverage Kombucha Tea (KT) has surged in part due to its purported health benefits, which include protection against metabolic diseases; however, these claims have not been rigorously tested and the mechanisms underlying host response to the probiotics in KT are unknown. Here, we establish a reproducible method to maintain C. elegans on a diet exclusively consisting of Kombucha Tea-associated microbes (KTM), which mirrors the microbial community found in the fermenting culture. KT microbes robustly colonize the gut of KTM-fed animals and confer normal development and fecundity. Intriguingly, animals consuming KTMs display a marked reduction in total lipid stores and lipid droplet size. We find that the reduced fat accumulation phenotype is not due to impaired nutrient absorption, but rather it is sustained by a programed metabolic response in the intestine of the host. KTM consumption triggers widespread transcriptional changes within core lipid metabolism pathways, including upregulation of a suite of lysosomal lipase genes that are induced during lipophagy. The elevated lysosomal lipase activity, coupled with a decrease in lipid droplet biogenesis, is partially required for the reduction in host lipid content. We propose that KTM consumption stimulates a fasting-like response in the C. elegans intestine by rewiring transcriptional programs to promote lipid utilization. Our results provide mechanistic insight into how the probiotics in Kombucha Tea reshape host metabolism and how this popular beverage may impact human metabolism.
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Affiliation(s)
- Rachel N. DuMez-Kornegay
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Lillian S. Baker
- Department of Biology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Alexis J. Morris
- Department of Biology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Whitney L. M. DeLoach
- Department of Biology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Robert H. Dowen
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Department of Biology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Department of Cell Biology and Physiology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Integrative Program for Biological and Genome Sciences, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
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Nair T, Weathers BA, Stuhr NL, Nhan JD, Curran SP. Serotonin deficiency from constitutive SKN-1 activation drives pathogen apathy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.10.579755. [PMID: 38405962 PMCID: PMC10888766 DOI: 10.1101/2024.02.10.579755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
When an organism encounters a pathogen, the host innate immune system activates to defend against pathogen colonization and toxic xenobiotics produced. C. elegans employ multiple defense systems to ensure survival when exposed to Pseudomonas aeruginosa including activation of the cytoprotective transcription factor SKN-1/NRF2. Although wildtype C. elegans quickly learn to avoid pathogens, here we describe a peculiar apathy-like behavior towards PA14 in animals with constitutive activation of SKN-1, whereby animals choose not to leave and continue to feed on the pathogen even when a non-pathogenic and healthspan-promoting food option is available. Although lacking the urgency to escape the infectious environment, animals with constitutive SKN-1 activity are not oblivious to the presence of the pathogen and display the typical pathogen-induced intestinal distension and eventual demise. SKN-1 activation, specifically in neurons and intestinal tissues, orchestrates a unique transcriptional program which leads to defects in serotonin signaling that is required from both neurons and non-neuronal tissues. Serotonin depletion from SKN-1 activation limits pathogen defense capacity, drives the pathogen-associated apathy behaviors and induces a synthetic sensitivity to selective serotonin reuptake inhibitors. Taken together, our work reveals new insights into how animals perceive environmental pathogens and subsequently alter behavior and cellular programs to promote survival. KEY POINTS Identify an apathy-like behavioral response for pathogens resulting from the constitutive activation of the cytoprotective transcription factor SKN-1.Uncover the obligate role for serotonin synthesis in both neuronal and non-neuronal cells for the apathy-like state and ability of serotonin treatment to restore normal behaviors.Characterize the timing and tissue specificity of SKN-1 nuclear localization in neurons and intestinal cells in response to pathogen exposure.Define the unique and context-specific transcriptional signatures of animals with constitutive SKN-1 activation when exposed to pathogenic environments.Reveal necessity for both neuronal and non-neuronal serotonin signaling in host survival from pathogen infection.
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10
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Shrestha B, Tallila M, Matilainen O. Folate receptor overexpression induces toxicity in a diet-dependent manner in C. elegans. Sci Rep 2024; 14:1066. [PMID: 38212621 PMCID: PMC10784478 DOI: 10.1038/s41598-024-51700-9] [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: 09/06/2023] [Accepted: 01/08/2024] [Indexed: 01/13/2024] Open
Abstract
Folate receptor (FR) alpha (FOLR1) and beta (FOLR2) are membrane-anchored folate transporters that are expressed at low levels in normal tissues, while their expression is strongly increased in several cancers. Intriguingly, although the function of these receptors in, for example, development and cancer has been studied intensively, their role in aging is still unknown. To address this, we utilized Caenorhabditis elegans, in which FOLR-1 is the sole ortholog of folate receptors. We found that the loss of FOLR-1 does not affect reproduction, physical condition, proteostasis or lifespan, indicating that it is not required for folate transport to maintain health. Interestingly, we found that FOLR-1 is detectably expressed only in uterine-vulval cells, and that the histone-binding protein LIN-53 inhibits its expression in other tissues. Furthermore, whereas knockdown of lin-53 is known to shorten lifespan, we found that the loss of FOLR-1 partially rescues this phenotype, suggesting that elevated folr-1 expression is detrimental for health. Indeed, our data demonstrate that overexpression of folr-1 is toxic, and that this phenotype is dependent on diet. Altogether, this work could serve as a basis for further studies to elucidate the organismal effects of abnormal FR expression in diseases such as cancer.
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Affiliation(s)
- Bideep Shrestha
- The Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Milla Tallila
- The Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Olli Matilainen
- The Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland.
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Hull B, Irby IM, Miller KM, Anderson A, Gardea EA, Sutphin GL. Experimental variables that impact outcomes in Caenorhabditis elegans aging stress response. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.09.574889. [PMID: 38260451 PMCID: PMC10802420 DOI: 10.1101/2024.01.09.574889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Cellular stress is a fundamental component of age-associated disease. Cells encounter various forms of stress - oxidative stress, protein misfolding, DNA damage, etc. - and respond by activating specific, well-defined stress response pathways. As we age, the burden of stress and resulting damage increases while our cells' ability to deal with the consequences becomes diminished due to dysregulation of cellular stress response pathways. Many interventions that extend lifespan activate one or more stress response pathways or allow cells to maintain normal stress response later in life. The nematode Caenorhabditis elegans is a commonly used model for both aging and stress response research. As such, stress response experiments are regularly conducted as part of studies focused on mechanisms of aging in C. elegans. However, experimental design across experiments in the field are highly variable, including stressor dose, age at exposure, culture type (liquid vs. solid), bacterial strain used as a food source, and environmental temperature. These differences can result in different experimental outcomes, making comparison of results between studies challenging. Here we evaluate several experimental variables that are variable in the published literature and find that each can meaningfully alter experimental outcomes for multiple stressors. Our goal is to raise awareness of the issue of experimental variability within the field and suggest a standardized experimental design to serve as a set of guidelines for future experiments. By adopting these guidelines as a starting point, and explicitly noting differences in specific experiments, we aim to promote rigor and reproducibility, ultimately fostering more interpretable and translatable outcomes in geroscience research.
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12
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Foster SG, Mathew S, Labarre A, Parker JA, Tompkins TA, Binda S. Lacticaseibacillus rhamnosus HA-114 and Bacillus subtilis R0179 Prolong Lifespan and Mitigate Amyloid-β Toxicity in C. elegans via Distinct Mechanisms. J Alzheimers Dis 2024; 101:49-60. [PMID: 39093068 PMCID: PMC11380293 DOI: 10.3233/jad-230948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
Abstract
Background Recent advances linking gut dysbiosis with neurocognitive disorders such as Alzheimer's disease (AD) suggest that the microbiota-gut-brain axis could be targeted for AD prevention, management, or treatment. Objective We sought to identify probiotics that can delay Aβ-induced paralysis. Methods Using C. elegans expressing human amyloid-β (Aβ)1-42 in body wall muscles (GMC101), we assessed the effects of several probiotic strains on paralysis. Results We found that Lacticaseibacillus rhamnosus HA-114 and Bacillus subtilis R0179, but not their supernatants or heat-treated forms, delayed paralysis and prolonged lifespan without affecting the levels of amyloid-β aggregates. To uncover the mechanism involved, we explored the role of two known pathways involved in neurogenerative diseases, namely mitophagy, via deletion of the mitophagy factor PINK-1, and fatty acid desaturation, via deletion of the Δ9 desaturase FAT-5. Pink-1 deletion in GMC101 worms did not modify the life-prolonging and anti-paralysis effects of HA-114 but reduced the protective effect of R0179 against paralysis without affecting its life-prolonging effect. Upon fat5 deletion in GMC101 worms, the monounsaturated C14:1 and C16:1 FAs conserved their beneficial effect while the saturated C14:0 and C16:0 FAs did not. The beneficial effects of R0179 on both lifespan and paralysis remained unaffected by fat-5 deletion, while the beneficial effect of HA-114 on paralysis and lifespan was significantly reduced. Conclusions Collectively with clinical and preclinical evidence in other models, our results suggest that HA-114 or R0179 could be studied as potential therapeutical adjuncts in neurodegenerative diseases such as AD.
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Affiliation(s)
- Stuart G Foster
- Rosell Institute for Microbiome and Probiotics, Montreal, QC, Canada
| | - Shibi Mathew
- Rosell Institute for Microbiome and Probiotics, Montreal, QC, Canada
| | - Audrey Labarre
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal and Department of Neuroscience, University of Montreal, Montreal, QC, Canada
| | - J Alex Parker
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal and Department of Neuroscience, University of Montreal, Montreal, QC, Canada
| | - Thomas A Tompkins
- Rosell Institute for Microbiome and Probiotics, Montreal, QC, Canada
| | - Sylvie Binda
- Rosell Institute for Microbiome and Probiotics, Montreal, QC, Canada
- Lallemand Health Solutions Inc., Blagnac Cedex, France
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13
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Turner CD, Stuhr NL, Ramos CM, Van Camp BT, Curran SP. A dicer-related helicase opposes the age-related pathology from SKN-1 activation in ASI neurons. Proc Natl Acad Sci U S A 2023; 120:e2308565120. [PMID: 38113255 PMCID: PMC10756303 DOI: 10.1073/pnas.2308565120] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 11/02/2023] [Indexed: 12/21/2023] Open
Abstract
Coordination of cellular responses to stress is essential for health across the lifespan. The transcription factor SKN-1 is an essential homeostat that mediates survival in stress-inducing environments and cellular dysfunction, but constitutive activation of SKN-1 drives premature aging thus revealing the importance of turning off cytoprotective pathways. Here, we identify how SKN-1 activation in two ciliated ASI neurons in Caenorhabditis elegans results in an increase in organismal transcriptional capacity that drives pleiotropic outcomes in peripheral tissues. An increase in the expression of established SKN-1 stress response and lipid metabolism gene classes of RNA in the ASI neurons, in addition to the increased expression of several classes of noncoding RNA, define a molecular signature of animals with constitutive SKN-1 activation and diminished healthspan. We reveal neddylation as a unique regulator of the SKN-1 homeostat that mediates SKN-1 abundance within intestinal cells. Moreover, RNAi-independent activity of the dicer-related DExD/H-box helicase, drh-1, in the intestine, can oppose the effects of aberrant SKN-1 transcriptional activation and delays age-dependent decline in health. Taken together, our results uncover a cell nonautonomous circuit to maintain organism-level homeostasis in response to excessive SKN-1 transcriptional activity in the sensory nervous system.
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Affiliation(s)
- Chris D. Turner
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA90089
- Molecular and Computational Biology, University of Southern California, Los Angeles, CA90089
| | - Nicole L. Stuhr
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA90089
- Molecular and Computational Biology, University of Southern California, Los Angeles, CA90089
| | - Carmen M. Ramos
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA90089
- Molecular and Computational Biology, University of Southern California, Los Angeles, CA90089
| | - Bennett T. Van Camp
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA90089
| | - Sean P. Curran
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA90089
- Molecular and Computational Biology, University of Southern California, Los Angeles, CA90089
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14
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Frézal L, Saglio M, Zhang G, Noble L, Richaud A, Félix MA. Genome-wide association and environmental suppression of the mortal germline phenotype of wild C. elegans. EMBO Rep 2023; 24:e58116. [PMID: 37983674 DOI: 10.15252/embr.202358116] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 10/19/2023] [Accepted: 10/27/2023] [Indexed: 11/22/2023] Open
Abstract
The animal germline lineage needs to be maintained along generations. However, some Caenorhabditis elegans wild isolates display a mortal germline phenotype, leading to sterility after several generations at 25°C. Using a genome-wide association approach, we detect a significant peak on chromosome III around 5 Mb, confirmed by introgressions. Thus, a seemingly deleterious genotype is maintained at intermediate frequency in the species. Environmental rescue is a likely explanation, and indeed associated bacteria and microsporidia suppress the phenotype of wild isolates as well as mutants in small RNA inheritance (nrde-2) and histone modifications (set-2). Escherichia coli strains of the K-12 lineage suppress the phenotype compared to B strains. By shifting a wild strain from E. coli K-12 to E. coli B, we find that memory of the suppressing condition is maintained over several generations. Thus, the mortal germline phenotype of wild C. elegans is in part revealed by laboratory conditions and may represent variation in epigenetic inheritance and environmental interactions. This study also points to the importance of non-genetic memory in the face of environmental variation.
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Affiliation(s)
- Lise Frézal
- Institut de Biologie de l'Ecole Normale Supérieure, CNRS, Inserm, Paris, France
| | - Marie Saglio
- Institut de Biologie de l'Ecole Normale Supérieure, CNRS, Inserm, Paris, France
| | - Gaotian Zhang
- Institut de Biologie de l'Ecole Normale Supérieure, CNRS, Inserm, Paris, France
| | - Luke Noble
- Institut de Biologie de l'Ecole Normale Supérieure, CNRS, Inserm, Paris, France
| | - Aurélien Richaud
- Institut de Biologie de l'Ecole Normale Supérieure, CNRS, Inserm, Paris, France
| | - Marie-Anne Félix
- Institut de Biologie de l'Ecole Normale Supérieure, CNRS, Inserm, Paris, France
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15
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Ramos CM, Curran SP. Comparative analysis of the molecular and physiological consequences of constitutive SKN-1 activation. GeroScience 2023; 45:3359-3370. [PMID: 37751046 PMCID: PMC10643742 DOI: 10.1007/s11357-023-00937-9] [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: 06/28/2023] [Accepted: 09/04/2023] [Indexed: 09/27/2023] Open
Abstract
Molecular homeostats play essential roles across all levels of biological organization to ensure a return to normal function after responding to abnormal internal and environmental events. SKN-1 is an evolutionarily conserved cytoprotective transcription factor that is integral for the maintenance of cellular homeostasis upon exposure to a variety of stress conditions. Despite the essentiality of turning on SKN-1/NRF2 in response to exogenous and endogenous stress, animals with chronic activation of SKN-1 display premature loss of health with age, and ultimately, diminished lifespan. Previous genetic models of constitutive SKN-1 activation include gain-of-function alleles of skn-1 and loss-of-function alleles of wdr-23 that impede the turnover of SKN-1 by the ubiquitin proteasome. Here, we define a novel gain-of-function mutation in the xrep-4 locus that results in constitutive activation of SKN-1 in the absence of stress. Although each of these genetic mutations results in continuously unregulated transcriptional output from SKN-1, the physiological consequences of each model on development, stress resistance, reproduction, lipid homeostasis, and lifespan are distinct. Here, we provide a comprehensive assessment of the differential healthspan impacts across multiple models of constitutive SKN-1 activation. Although our results reveal the universal need to reign in the uncontrolled activity of cytoprotective transcription factors, we also define the unique signatures of each model of constitutive SKN-1 activation, which provides innovative solutions for the design of molecular "off-switches" of unregulated transcriptional homeostats.
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Affiliation(s)
- Carmen M Ramos
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, 90089, USA
- Dornsife College of Letters, Arts, and Sciences, Department of Molecular and Computational Biology, University of Southern California, Los Angeles, CA, 90089, USA
| | - Sean P Curran
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, 90089, USA.
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16
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Yasuda K, Miyazawa M, Ishii T, Ishii N. The role of nutrition and oxidative stress as aging factors in Caenorhabditis elegans. J Clin Biochem Nutr 2023; 73:173-177. [PMID: 37970544 PMCID: PMC10636583 DOI: 10.3164/jcbn.23-44] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 06/26/2023] [Indexed: 11/17/2023] Open
Abstract
The molecular mechanism of aging, which has been a "black box" for many years, has been elucidated in recent years, and the nematode C. elegans, which is a model animal for aging research, has played a major role in its elucidation. From the analysis of C. elegans longevity-related mutant genes, many signal transduction systems, with the insulin/insulin-like growth factor signal transduction system at the core, have emerged. It has become clear that this signal transduction system is greatly affected by external nutrients and is involved in the downstream regulation of oxidative stress, which is considered to be one of the main causes of aging.
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Affiliation(s)
- Kayo Yasuda
- Department of Health Management, Undergraduate School of Health Studies, Tokai University, 4-1-1 Kitakaname, Hiratsuka, Kanagawa 259-1292, Japan
| | - Masaki Miyazawa
- Department of Health Management, Undergraduate School of Health Studies, Tokai University, 4-1-1 Kitakaname, Hiratsuka, Kanagawa 259-1292, Japan
| | - Takamasa Ishii
- Department of Molecular Life Science, Tokai University School of Medicine, 143 Shimokasuya, Isehara, Kanagawa 259-1193, Japan
| | - Naoaki Ishii
- Office of Professor Emeritus, Tokai University, 4-1-1 Kitakaname, Hiratsuka, Kanagawa 259-1292, Japan
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17
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Emerson FJ, Lee SS. Chromatin: the old and young of it. Front Mol Biosci 2023; 10:1270285. [PMID: 37877123 PMCID: PMC10591336 DOI: 10.3389/fmolb.2023.1270285] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 09/20/2023] [Indexed: 10/26/2023] Open
Abstract
Aging affects nearly all aspects of our cells, from our DNA to our proteins to how our cells handle stress and communicate with each other. Age-related chromatin changes are of particular interest because chromatin can dynamically respond to the cellular and organismal environment, and many modifications at chromatin are reversible. Changes at chromatin occur during aging, and evidence from model organisms suggests that chromatin factors could play a role in modulating the aging process itself, as altering proteins that work at chromatin often affect the lifespan of yeast, worms, flies, and mice. The field of chromatin and aging is rapidly expanding, and high-resolution genomics tools make it possible to survey the chromatin environment or track chromatin factors implicated in longevity with precision that was not previously possible. In this review, we discuss the state of chromatin and aging research. We include examples from yeast, Drosophila, mice, and humans, but we particularly focus on the commonly used aging model, the worm Caenorhabditis elegans, in which there are many examples of chromatin factors that modulate longevity. We include evidence of both age-related changes to chromatin and evidence of specific chromatin factors linked to longevity in core histones, nuclear architecture, chromatin remodeling, and histone modifications.
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Affiliation(s)
| | - Siu Sylvia Lee
- Lee Lab, Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, United States
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18
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Turner CD, Stuhr NL, Ramos CM, Van Camp BT, Curran SP. A dicer-related helicase opposes the age-related pathology from SKN-1 activation in ASI neurons. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.01.560409. [PMID: 37873147 PMCID: PMC10592859 DOI: 10.1101/2023.10.01.560409] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Coordination of cellular responses to stress are essential for health across the lifespan. The transcription factor SKN-1 is an essential homeostat that mediates survival in stress-inducing environments and cellular dysfunction, but constitutive activation of SKN-1 drives premature aging thus revealing the importance of turning off cytoprotective pathways. Here we identify how SKN-1 activation in two ciliated ASI neurons in C. elegans results in an increase in organismal transcriptional capacity that drives pleiotropic outcomes in peripheral tissues. An increase in the expression of established SKN-1 stress response and lipid metabolism gene classes of RNA in the ASI neurons, in addition to the increased expression of several classes of non-coding RNA, define a molecular signature of animals with constitutive SKN-1 activation and diminished healthspan. We reveal neddylation as a novel regulator of the SKN-1 homeostat that mediates SKN-1 abundance within intestinal cells. Moreover, RNAi-independent activity of the dicer-related DExD/H-box helicase, drh-1 , in the intestine, can oppose the e2ffects of aberrant SKN-1 transcriptional activation and delays age-dependent decline in health. Taken together, our results uncover a cell non-autonomous circuit to maintain organism-level homeostasis in response to excessive SKN-1 transcriptional activity in the sensory nervous system. SIGNIFICANCE STATEMENT Unlike activation, an understudied fundamental question across biological systems is how to deactivate a pathway, process, or enzyme after it has been turned on. The irony that the activation of a transcription factor that is meant to be protective can diminish health was first documented by us at the organismal level over a decade ago, but it has long been appreciated that chronic activation of the human ortholog of SKN-1, NRF2, could lead to chemo- and radiation resistance in cancer cells. A colloquial analogy to this biological idea is a sink faucet that has an on valve without a mechanism to shut the water off, which will cause the sink to overflow. Here, we define this off valve.
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19
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Madhu B, Lakdawala MF, Gumienny TL. The DBL-1/TGF-β signaling pathway tailors behavioral and molecular host responses to a variety of bacteria in Caenorhabditis elegans. eLife 2023; 12:e75831. [PMID: 37750680 PMCID: PMC10567113 DOI: 10.7554/elife.75831] [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: 12/07/2021] [Accepted: 09/25/2023] [Indexed: 09/27/2023] Open
Abstract
Generating specific, robust protective responses to different bacteria is vital for animal survival. Here, we address the role of transforming growth factor β (TGF-β) member DBL-1 in regulating signature host defense responses in Caenorhabditis elegans to human opportunistic Gram-negative and Gram-positive pathogens. Canonical DBL-1 signaling is required to suppress avoidance behavior in response to Gram-negative, but not Gram-positive bacteria. We propose that in the absence of DBL-1, animals perceive some bacteria as more harmful. Animals activate DBL-1 pathway activity in response to Gram-negative bacteria and strongly repress it in response to select Gram-positive bacteria, demonstrating bacteria-responsive regulation of DBL-1 signaling. DBL-1 signaling differentially regulates expression of target innate immunity genes depending on the bacterial exposure. These findings highlight a central role for TGF-β in tailoring a suite of bacteria-specific host defenses.
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Affiliation(s)
- Bhoomi Madhu
- Department of Biology, Texas Woman’s UniversityDentonUnited States
- Perelman School of Medicine, University of PennsylvaniaPhiladelphiaUnited States
| | - Mohammed Farhan Lakdawala
- Department of Biology, Texas Woman’s UniversityDentonUnited States
- AbbVie (United States)WorcesterUnited States
| | - Tina L Gumienny
- Department of Biology, Texas Woman’s UniversityDentonUnited States
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20
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Stuhr NL, Curran SP. Different methods of killing bacteria diets differentially influence Caenorhabditis elegans physiology. MICROPUBLICATION BIOLOGY 2023; 2023:10.17912/micropub.biology.000902. [PMID: 37746065 PMCID: PMC10514698 DOI: 10.17912/micropub.biology.000902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Figures] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 08/03/2023] [Accepted: 08/21/2023] [Indexed: 09/26/2023]
Abstract
Across species, diet plays a critical role in most, if not all life history traits. Caenorhabditis elegans is an important and facile organism for research across modalities, but the use of live bacteria as sources of nutrition can exert pleiotropic outcomes that stem from the action of host-pathogen defenses. Recently, a powerful new approach to readily generate dead and metabolically inactive Escherichia coli was developed that enabled reproducible measures of health across the lifespan. Here we further characterize additional comparisons of developmental and physiological parameters of animals fed either bacteria killed by treatment with ultraviolet (UV) light and bactericidal antibiotics or low-dose paraformaldehyde (PFA). Unlike bacteria killed by UV/Antibiotic treatment, PFA-killed diets resulted in a 25% reduction in body size just prior to adulthood and an overall reduction in stored intracellular lipids. Moreover, a small but reproducible number of animals fed PFA-killed bacteria display age-dependent depletion of somatic lipids, which does not normally occur on live bacteria or bacteria killed by UV/antibiotics. Lastly, animals fed PFA-treated, but not UV-antibiotic treated bacteria display a 10% increase in crawling speed. Taken together, these new data more thoroughly define the physiological impact two methodologies to prepare C. elegans diets that should be considered during experimental design.
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Affiliation(s)
- Nicole L. Stuhr
- Molecular and Computational Biology, University of Southern California, Los Angeles, California, United States
| | - Sean P. Curran
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, California, United States
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21
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Santos J, Matos M, Flatt T, Chelo IM. Microbes are potential key players in the evolution of life histories and aging in Caenorhabditis elegans. Ecol Evol 2023; 13:e10537. [PMID: 37753311 PMCID: PMC10518755 DOI: 10.1002/ece3.10537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 08/07/2023] [Accepted: 09/01/2023] [Indexed: 09/28/2023] Open
Abstract
Microbes can have profound effects on host fitness and health and the appearance of late-onset diseases. Host-microbe interactions thus represent a major environmental context for healthy aging of the host and might also mediate trade-offs between life-history traits in the evolution of host senescence. Here, we have used the nematode Caenorhabditis elegans to study how host-microbe interactions may modulate the evolution of life histories and aging. We first characterized the effects of two non-pathogenic and one pathogenic Escherichia coli strains, together with the pathogenic Serratia marcescens DB11 strain, on population growth rates and survival of C. elegans from five different genetic backgrounds. We then focused on an outbred C. elegans population, to understand if microbe-specific effects on the reproductive schedule and in traits such as developmental rate and survival were also expressed in the presence of males and standing genetic variation, which could be relevant for the evolution of C. elegans and other nematode species in nature. Our results show that host-microbe interactions have a substantial host-genotype-dependent impact on the reproductive aging and survival of the nematode host. Although both pathogenic bacteria reduced host survival in comparison with benign strains, they differed in how they affected other host traits. Host fertility and population growth rate were affected by S. marcescens DB11 only during early adulthood, whereas this occurred at later ages with the pathogenic E. coli IAI1. In both cases, these effects were largely dependent on the host genotypes. Given such microbe-specific genotypic differences in host life history, we predict that the evolution of reproductive schedules and senescence might be critically contingent on host-microbe interactions in nature.
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Affiliation(s)
- Josiane Santos
- cE3c – Centre for Ecology, Evolution and Environmental Changes & CHANGE – Global Change and Sustainability InstituteLisboaPortugal
- Departamento de Biologia Animal, Faculdade de CiênciasUniversidade de LisboaLisboaPortugal
| | - Margarida Matos
- cE3c – Centre for Ecology, Evolution and Environmental Changes & CHANGE – Global Change and Sustainability InstituteLisboaPortugal
- Departamento de Biologia Animal, Faculdade de CiênciasUniversidade de LisboaLisboaPortugal
| | - Thomas Flatt
- Department of BiologyUniversity of FribourgFribourgSwitzerland
| | - Ivo M. Chelo
- cE3c – Centre for Ecology, Evolution and Environmental Changes & CHANGE – Global Change and Sustainability InstituteLisboaPortugal
- Departamento de Biologia Animal, Faculdade de CiênciasUniversidade de LisboaLisboaPortugal
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22
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Beydoun S, Kitto ES, Wang E, Huang S, Leiser SF. Methodology to Metabolically Inactivate Bacteria for Caenorhabditis elegans Research. J Vis Exp 2023:10.3791/65775. [PMID: 37578251 PMCID: PMC11064985 DOI: 10.3791/65775] [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] [Indexed: 08/15/2023] Open
Abstract
Caenorhabditis elegans is a common model organism for research in genetics, development, aging, metabolism, and behavior. Because C. elegans consume a diet of live bacteria, the metabolic activity of their food source can confound experiments looking for the direct effects of various interventions on the worm. To avoid the confounding effects of bacterial metabolism, C. elegans researchers have used multiple methods to metabolically inactivate bacteria, including ultraviolet (UV)-irradiation, heat-killing, and antibiotics. UV treatment is relatively low-throughput and cannot be used in liquid culture because each plate must be examined for successful bacterial killing. A second treatment method, heat-killing, negatively affects the texture and nutritional quality of the bacteria, leading to the developmental arrest of C. elegans. Finally, antibiotic treatment can directly alter C. elegans physiology in addition to preventing bacterial growth. This manuscript describes an alternative method to metabolically inactivate bacteria using paraformaldehyde (PFA). PFA treatment cross-links proteins within bacterial cells to prevent metabolic activity while preserving cellular structure and nutritional content. This method is high-throughput and can be used in liquid culture or solid plates, as testing one plate of PFA-treated bacteria for growth validates the whole batch. Metabolic inactivation through PFA treatment can be used to eliminate the confounding effects of bacterial metabolism on studies of drug or metabolite supplementation, stress resistance, metabolomics, and behavior in C. elegans.
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Affiliation(s)
- Safa Beydoun
- Molecular and Integrative Physiology Department, University of Michigan, Ann Arbor
| | - Elizabeth S Kitto
- Molecular and Integrative Physiology Department, University of Michigan, Ann Arbor
| | - Emily Wang
- Molecular and Integrative Physiology Department, University of Michigan, Ann Arbor
| | - Shijiao Huang
- Molecular and Integrative Physiology Department, University of Michigan, Ann Arbor
| | - Scott F Leiser
- Molecular and Integrative Physiology Department, University of Michigan, Ann Arbor; Department of Internal Medicine, University of Michigan, Ann Arbor;
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23
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Gaeta AL, Willicott K, Willicott CW, McKay LE, Keogh CM, Altman TJ, Kimble LC, Yarbrough AL, Caldwell KA, Caldwell GA. Mechanistic impacts of bacterial diet on dopaminergic neurodegeneration in a Caenorhabditis elegans α-synuclein model of Parkinson's disease. iScience 2023; 26:106859. [PMID: 37260751 PMCID: PMC10227375 DOI: 10.1016/j.isci.2023.106859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 04/03/2023] [Accepted: 05/08/2023] [Indexed: 06/02/2023] Open
Abstract
Failure of inherently protective cellular processes and misfolded protein-associated stress contribute to the progressive loss of dopamine (DA) neurons characteristic of Parkinson's disease (PD). A disease-modifying role for the microbiome has recently emerged in PD, representing an impetus to employ the soil-dwelling nematode, Caenorhabditis elegans, as a preclinical model to correlate changes in gene expression with neurodegeneration in transgenic animals grown on distinct bacterial food sources. Even under tightly controlled conditions, hundreds of differentially expressed genes and a robust neuroprotective response were discerned between clonal C. elegans strains overexpressing human alpha-synuclein in the DA neurons fed either one of only two subspecies of Escherichia coli. Moreover, this neuroprotection persisted in a transgenerational manner. Genetic analysis revealed a requirement for the double-stranded RNA (dsRNA)-mediated gene silencing machinery in conferring neuroprotection. In delineating the contribution of individual genes, evidence emerged for endopeptidase activity and heme-associated pathway(s) as mechanistic components for modulating dopaminergic neuroprotection.
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Affiliation(s)
- Anthony L. Gaeta
- 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
| | - Corey W. Willicott
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL 35487, USA
| | - Luke E. McKay
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL 35487, USA
| | - Candice M. Keogh
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL 35487, USA
| | - Tyler J. Altman
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL 35487, USA
| | - Logan C. Kimble
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL 35487, USA
| | - Abigail L. Yarbrough
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL 35487, USA
| | - Kim A. Caldwell
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL 35487, USA
- Center for Convergent Bioscience and Medicine, The University of Alabama, Tuscaloosa, AL 35487, USA
- Alabama Research Institute on Aging, The University of Alabama, Tuscaloosa, AL 35487, USA
- Department of Neurology, Center for Neurodegeneration and Experimental Therapeutics, Nathan Shock Center of Excellence for Basic Research in the Biology of Aging, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Guy A. Caldwell
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL 35487, USA
- Center for Convergent Bioscience and Medicine, The University of Alabama, Tuscaloosa, AL 35487, USA
- Department of Neurology, Center for Neurodegeneration and Experimental Therapeutics, Nathan Shock Center of Excellence for Basic Research in the Biology of Aging, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
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24
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Wong SQ, Ryan CJ, Bonal DM, Mills J, Lapierre LR. Neuronal HLH-30/TFEB modulates peripheral mitochondrial fragmentation to improve thermoresistance in Caenorhabditis elegans. Aging Cell 2023; 22:e13741. [PMID: 36419219 PMCID: PMC10014052 DOI: 10.1111/acel.13741] [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: 04/09/2022] [Revised: 09/29/2022] [Accepted: 10/31/2022] [Indexed: 11/25/2022] Open
Abstract
Transcription factor EB (TFEB) is a conserved master transcriptional activator of autophagy and lysosomal genes that modulates organismal lifespan regulation and stress resistance. As neurons can coordinate organism-wide processes, we investigated the role of neuronal TFEB in stress resistance and longevity. To this end, the Caenorhabditis elegans TFEB ortholog, hlh-30, was rescued panneuronally in hlh-30 loss of function mutants. While important in the long lifespan of daf-2 animals, neuronal HLH-30/TFEB was not sufficient to restore normal lifespan in short-lived hlh-30 mutants. However, neuronal HLH-30/TFEB rescue mediated robust improvements in the heat stress resistance of wildtype but not daf-2 animals. Notably, these mechanisms can be uncoupled, as neuronal HLH-30/TFEB requires DAF-16/FOXO to regulate longevity but not thermoresistance. Through further transcriptomics profiling and functional analysis, we discovered that neuronal HLH-30/TFEB modulates neurotransmission through the hitherto uncharacterized protein W06A11.1 by inducing peripheral mitochondrial fragmentation and organismal heat stress resistance in a non-cell autonomous manner. Taken together, this study uncovers a novel mechanism of heat stress protection mediated by neuronal HLH-30/TFEB.
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Affiliation(s)
- Shi Quan Wong
- Department of Molecular Biology, Cell Biology and BiochemistryBrown UniversityProvidenceRhode IslandUSA
| | - Catherine J. Ryan
- Department of Molecular Biology, Cell Biology and BiochemistryBrown UniversityProvidenceRhode IslandUSA
| | - Dennis M. Bonal
- Pathobiology Graduate Program, Division of Biology & MedicineBrown UniversityProvidenceRhode IslandUSA
| | - Joslyn Mills
- Department of Molecular Biology, Cell Biology and BiochemistryBrown UniversityProvidenceRhode IslandUSA
- Department of BiologyWheaton CollegeNortonMassachusettsUSA
| | - Louis R. Lapierre
- Department of Molecular Biology, Cell Biology and BiochemistryBrown UniversityProvidenceRhode IslandUSA
- Département de Chimie et BiochimieUniversité de MonctonMonctonNew BrunswickCanada
- New Brunswick Center for Precision MedicineMonctonNew BrunswickCanada
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25
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Duran-Izquierdo M, Taboada-Alquerque M, Sierra-Marquez L, Alvarez-Ortega N, Stashenko E, Olivero-Verbel J. Hydroalcoholic extract of Haematoxylum brasiletto protects Caenorhabditis elegans from cadmium-induced toxicity. BMC Complement Med Ther 2022; 22:184. [PMID: 35818043 PMCID: PMC9272861 DOI: 10.1186/s12906-022-03654-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 06/09/2022] [Indexed: 11/20/2022] Open
Abstract
Background H. brasiletto is used in popular culture due to its therapeutic properties, including antioxidant, anti-inflammatory and antiproliferative properties, although little is known about its role as a protector against metal toxicity. This study aimed to investigate the chemical composition and efficacy of the hydroalcoholic extract from H. brasiletto (HAE-Hbrasiletto) collected in northern Colombia to defend against cadmium (Cd)-induced toxicity. Methods Phytochemical characterization was performed using HPLC-ESI-QTOF. Caenorhabditis elegans was employed to assess the shielding effect of HAE-Hbrasiletto against Cd toxicity in vivo, and the 2,2-diphenyl-1-picrylhydrazyl (DPPH) assay was utilized to measure radical scavenging activity. Results The main secondary metabolites identified by HPLC-ESI-QTOF in the extracts were hematoxylins (brazilein and hematein) and protosappanins (protosappanin A, B and C, 10-O-methylprotosappanin B, and protosappanin A dimethyl acetal). The HAE-Hbrasiletto elicited low lethality in N2 worms and significantly reduced the Cd-induced death of the nematodes. It also improved Cd-induced motility inhibition, as well as body length and reproduction reduction provoked by the heavy metal. The extract displayed a good capacity to halt Cd-induced DAF-16 translocation. As this last process was associated with lethality (r = 0.962, p < 0.01), the antioxidant properties of the extract may contribute to ameliorating tissue damage induced by oxidative stress from Cd exposure. Conclusion HAE-Hbrasiletto has remarkable properties to protect against Cd-induced toxicity. Supplementary Information The online version contains supplementary material available at 10.1186/s12906-022-03654-6. Most secondary metabolites tentatively identified in H. brasiletto are homoisoflavones. Hidroalcoholic extract of H. brasiletto protects C. elegans from Cd toxicity The extract diminished Cd-induced damage to reproduction, growth, and locomotion. Cd-induced oxidative stress and translocation of DAF-16 are blocked by the extract.
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Yerevanian A, Murphy LM, Emans S, Zhou Y, Ahsan FM, Baker D, Li S, Adedoja A, Cedillo L, Stuhr NL, Gnanatheepam E, Dao K, Jain M, Curran SP, Georgakoudi I, Soukas AA. Riboflavin depletion promotes longevity and metabolic hormesis in Caenorhabditis elegans. Aging Cell 2022; 21:e13718. [PMID: 36181246 PMCID: PMC9649603 DOI: 10.1111/acel.13718] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 08/16/2022] [Accepted: 08/31/2022] [Indexed: 01/25/2023] Open
Abstract
Riboflavin is an essential cofactor in many enzymatic processes and in the production of flavin adenine dinucleotide (FAD). Here, we report that the partial depletion of riboflavin through knockdown of the C. elegans riboflavin transporter 1 (rft-1) promotes metabolic health by reducing intracellular flavin concentrations. Knockdown of rft-1 significantly increases lifespan in a manner dependent upon AMP-activated protein kinase (AMPK)/aak-2, the mitochondrial unfolded protein response, and FOXO/daf-16. Riboflavin depletion promotes altered energetic and redox states and increases adiposity, independent of lifespan genetic dependencies. Riboflavin-depleted animals also exhibit the activation of caloric restriction reporters without any reduction in caloric intake. Our findings indicate that riboflavin depletion activates an integrated hormetic response that promotes lifespan and healthspan in C. elegans.
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Affiliation(s)
- Armen Yerevanian
- Department of Medicine, Diabetes Unit and Center for Genomic MedicineMassachusetts General HospitalBostonMassachusettsUSA
- Department of MedicineHarvard Medical SchoolBostonMassachusettsUSA
| | - Luke M. Murphy
- Department of Medicine, Diabetes Unit and Center for Genomic MedicineMassachusetts General HospitalBostonMassachusettsUSA
- Department of MedicineHarvard Medical SchoolBostonMassachusettsUSA
| | - Sinclair Emans
- Department of Medicine, Diabetes Unit and Center for Genomic MedicineMassachusetts General HospitalBostonMassachusettsUSA
- Department of MedicineHarvard Medical SchoolBostonMassachusettsUSA
| | - Yifei Zhou
- Department of Medicine, Diabetes Unit and Center for Genomic MedicineMassachusetts General HospitalBostonMassachusettsUSA
- Department of MedicineHarvard Medical SchoolBostonMassachusettsUSA
| | - Fasih M. Ahsan
- Department of Medicine, Diabetes Unit and Center for Genomic MedicineMassachusetts General HospitalBostonMassachusettsUSA
- Department of MedicineHarvard Medical SchoolBostonMassachusettsUSA
| | - Daniel Baker
- Department of Medicine, Diabetes Unit and Center for Genomic MedicineMassachusetts General HospitalBostonMassachusettsUSA
- Department of MedicineHarvard Medical SchoolBostonMassachusettsUSA
| | - Sainan Li
- Department of Medicine, Diabetes Unit and Center for Genomic MedicineMassachusetts General HospitalBostonMassachusettsUSA
- Department of MedicineHarvard Medical SchoolBostonMassachusettsUSA
| | - Adebanjo Adedoja
- Department of Medicine, Diabetes Unit and Center for Genomic MedicineMassachusetts General HospitalBostonMassachusettsUSA
- Department of MedicineHarvard Medical SchoolBostonMassachusettsUSA
| | - Lucydalila Cedillo
- Department of Medicine, Diabetes Unit and Center for Genomic MedicineMassachusetts General HospitalBostonMassachusettsUSA
- Department of MedicineHarvard Medical SchoolBostonMassachusettsUSA
| | - Nicole L. Stuhr
- Leonard Davis School of GerontologyUniversity of Southern CaliforniaLos AngelesCaliforniaUSA
| | - Einstein Gnanatheepam
- Department of Biomedical EngineeringTufts University School of EngineeringMedfordMassachusettsUSA
| | - Khoi Dao
- Department of Medicine and PharmacologyUniversity of California San DiegoSan DiegoCaliforniaUSA
| | - Mohit Jain
- Department of Medicine and PharmacologyUniversity of California San DiegoSan DiegoCaliforniaUSA
| | - Sean P. Curran
- Leonard Davis School of GerontologyUniversity of Southern CaliforniaLos AngelesCaliforniaUSA
| | - Irene Georgakoudi
- Department of Biomedical EngineeringTufts University School of EngineeringMedfordMassachusettsUSA
| | - Alexander A. Soukas
- Department of Medicine, Diabetes Unit and Center for Genomic MedicineMassachusetts General HospitalBostonMassachusettsUSA
- Department of MedicineHarvard Medical SchoolBostonMassachusettsUSA
- Broad Institute of Harvard and MITCambridgeMassachusettsUSA
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Legüe M, Caneo M, Aguila B, Pollak B, Calixto A. Interspecies effectors of a transgenerational memory of bacterial infection in Caenorhabditis elegans. iScience 2022; 25:104627. [PMID: 35800768 PMCID: PMC9254006 DOI: 10.1016/j.isci.2022.104627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 04/16/2022] [Accepted: 06/13/2022] [Indexed: 11/24/2022] Open
Abstract
The inheritance of memory is an adaptive trait. Microbes challenge the immunity of organisms and trigger behavioral adaptations that can be inherited, but how bacteria produce inheritance of a trait is unknown. We use Caenorhabditis elegans and its bacteria to study the transgenerational RNA dynamics of interspecies crosstalk leading to a heritable behavior. A heritable response of C. elegans to microbes is the pathogen-induced diapause (PIDF), a state of suspended animation to evade infection. We identify RsmY, a small RNA involved in quorum sensing in Pseudomonas aeruginosa as a trigger of PIDF. The histone methyltransferase (HMT) SET-18/SMYD3 and the argonaute HRDE-1, which promotes multi-generational silencing in the germline, are also needed for PIDF initiation. The HMT SET-25/EHMT2 is necessary for memory maintenance in the transgenerational lineage. Our work is a starting point to understanding microbiome-induced inheritance of acquired traits, and the transgenerational influence of microbes in health and disease.
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Affiliation(s)
- Marcela Legüe
- Centro Interdisciplinario de Neurociencia de Valparaíso, Facultad de Ciencias, Universidad de Valparaíso, Valparaíso 2366103, Chile
| | - Mauricio Caneo
- Centro Interdisciplinario de Neurociencia de Valparaíso, Facultad de Ciencias, Universidad de Valparaíso, Valparaíso 2366103, Chile
| | - Blanca Aguila
- Centro Interdisciplinario de Neurociencia de Valparaíso, Facultad de Ciencias, Universidad de Valparaíso, Valparaíso 2366103, Chile
- Programa de Doctorado en Microbiología, Universidad de Chile, Santiago de Chile, Chile
| | | | - Andrea Calixto
- Centro Interdisciplinario de Neurociencia de Valparaíso, Facultad de Ciencias, Universidad de Valparaíso, Valparaíso 2366103, Chile
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Dietary differences can confound animal studies. Nature 2022; 605:778-779. [DOI: 10.1038/d41586-022-01393-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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29
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Reproductive Span of Caenorhabditis elegans Is Extended by Microbacterium sp. J Nematol 2022; 54:20220010. [PMID: 35860519 PMCID: PMC9260829 DOI: 10.2478/jofnem-2022-0010] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Indexed: 11/20/2022] Open
Abstract
Abstract
The reproductive span (RS) of organisms could be affected by different factors during their lifetime. In the model nematode, Caenorhabditis elegans, RS is affected by both genetic and environmental factors. However, none of the factors identified so far were related to environmental bacteria, which may incidentally appear anywhere in the habitats of C. elegans. We aimed to find environmental bacteria that could affect the RS of C. elegans and related species. We tested 109 bacterial isolates and found that Microbacterium sp. CFBb37 increased the RS and lifespan of C. elegans but reduced its brood size. We studied the effect of M. sp. CFBb37 on the RS of Caenorhabditis briggsae, Caenorhabditis tropicalis, and another Rhabditidae family species, Protorhabditis sp., and found similar trends of RS extension in all three cases, suggesting that this bacterial species may induce the extension of RS broadly among Caenorhabditis species and possibly for many other Rhabditidae. This work will facilitate future research on the mechanism underlying the bacterial extension of RS of nematodes and possibly other animals.
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30
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The evolving role of the Caenorhabditis elegans model as a tool to advance studies in nutrition and health. Nutr Res 2022; 106:47-59. [DOI: 10.1016/j.nutres.2022.05.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 05/20/2022] [Accepted: 05/22/2022] [Indexed: 12/29/2022]
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Cornwell A, Llop JR, Salzman P, Rasmussen N, Thakar J, Samuelson AV. The Replica Set Method is a Robust, Accurate, and High-Throughput Approach for Assessing and Comparing Lifespan in C. elegans Experiments. FRONTIERS IN AGING 2022; 3:861701. [PMID: 35821830 PMCID: PMC9261357 DOI: 10.3389/fragi.2022.861701] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 04/05/2022] [Indexed: 11/17/2022]
Abstract
The advent of feeding based RNAi in Caenorhabditis elegans led to an era of gene discovery in aging research. Hundreds of gerogenes were discovered, and many are evolutionarily conserved, raising the exciting possibility that the underlying genetic basis for healthy aging in higher vertebrates could be quickly deciphered. Yet, the majority of putative gerogenes have still only been cursorily characterized, highlighting the need for high-throughput, quantitative assessments of changes in aging. A widely used surrogate measure of aging is lifespan. The traditional way to measure mortality in C. elegans tracks the deaths of individual animals over time within a relatively small population. This traditional method provides straightforward, direct measurements of median and maximum lifespan for the sampled population. However, this method is time consuming, often underpowered, and involves repeated handling of a set of animals over time, which in turn can introduce contamination or possibly damage increasingly fragile, aged animals. We have previously developed an alternative "Replica Set" methodology, which minimizes handling and increases throughput by at least an order of magnitude. The Replica Set method allows changes in lifespan to be measured for over one hundred feeding-based RNAi clones by one investigator in a single experiment- facilitating the generation of large quantitative phenotypic datasets, a prerequisite for development of biological models at a systems level. Here, we demonstrate through analysis of lifespan experiments simulated in silico that the Replica Set method is at least as precise and accurate as the traditional method in evaluating and estimating lifespan, and requires many fewer total animal observations across the course of an experiment. Furthermore, we show that the traditional approach to lifespan experiments is more vulnerable than the Replica Set method to experimental and measurement error. We find no compromise in statistical power for Replica Set experiments, even for moderate effect sizes, or when simulated experimental errors are introduced. We compare and contrast the statistical analysis of data generated by the two approaches, and highlight pitfalls common with the traditional methodology. Collectively, our analysis provides a standard of measure for each method across comparable parameters, which will be invaluable in both experimental design and evaluation of published data for lifespan studies.
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Affiliation(s)
- Adam Cornwell
- Department of Biomedical Genetics, University of Rochester Medical Center, Rochester, NY, United States
| | - Jesse R. Llop
- Department of Biomedical Genetics, University of Rochester Medical Center, Rochester, NY, United States
| | - Peter Salzman
- Department of Biostatistics and Computational Biology, University of Rochester Medical Center, Rochester, NY, United States
| | - Niels Rasmussen
- Department of Biomedical Genetics, University of Rochester Medical Center, Rochester, NY, United States
| | - Juilee Thakar
- Department of Biomedical Genetics, University of Rochester Medical Center, Rochester, NY, United States
- Department of Biostatistics and Computational Biology, University of Rochester Medical Center, Rochester, NY, United States
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY, United States
| | - Andrew V. Samuelson
- Department of Biomedical Genetics, University of Rochester Medical Center, Rochester, NY, United States
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Villa O, Stuhr NL, Yen CA, Crimmins EM, Arpawong TE, Curran SP. Genetic variation in ALDH4A1 is associated with muscle health over the lifespan and across species. eLife 2022; 11:74308. [PMID: 35470798 PMCID: PMC9106327 DOI: 10.7554/elife.74308] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 04/13/2022] [Indexed: 11/13/2022] Open
Abstract
The influence of genetic variation on the aging process, including the incidence and severity of age-related diseases, is complex. Here, we define the evolutionarily conserved mitochondrial enzyme ALH-6/ALDH4A1 as a predictive biomarker for age-related changes in muscle health by combining Caenorhabditis elegans genetics and a gene-wide association scanning (GeneWAS) from older human participants of the US Health and Retirement Study (HRS). In a screen for mutations that activate oxidative stress responses, specifically in the muscle of C. elegans, we identified 96 independent genetic mutants harboring loss-of-function alleles of alh-6, exclusively. Each of these genetic mutations mapped to the ALH-6 polypeptide and led to the age-dependent loss of muscle health. Intriguingly, genetic variants in ALDH4A1 show associations with age-related muscle-related function in humans. Taken together, our work uncovers mitochondrial alh-6/ALDH4A1 as a critical component to impact normal muscle aging across species and a predictive biomarker for muscle health over the lifespan. Ageing is inevitable, but what makes one person ‘age well’ and another decline more quickly remains largely unknown. While many aspects of ageing are clearly linked to genetics, the specific genes involved often remain unidentified. Sarcopenia is an age-related condition affecting the muscles. It involves a gradual loss of muscle mass that becomes faster with age, and is associated with loss of mobility, decreased quality of life, and increased risk of death. Around half of all people aged 80 and over suffer from sarcopenia. Several lifestyle factors, especially poor diet and lack of exercise, are associated with the condition, but genetics is also involved: the condition accelerates more quickly in some people than others, and even fit, physically active individuals can be affected. To study the genetics of conditions like sarcopenia, researchers often use animals like flies or worms, which have short generation times but share genetic similarities with humans. For example, the worm Caenorhabditis elegans has equivalents of several human muscle genes, including the gene alh-6. In worms, alh-6 is important for maintaining energy supply to the muscles, and mutating it not only leads to muscle damage but also to premature ageing. Given this insight, Villa, Stuhr, Yen et al. wanted to determine if variation in the human version of alh-6, ALDH4A1, also contributes to individual differences in muscle ageing and decline in humans. Evaluating variation in this gene required a large amount of genetic data from older adults. These were taken from a continuous study that follows >35,000 older adults. Importantly, the study collects not only information on gene sequences but also measures of muscle health and performance over time for each individual. Analysis of these genetic data revealed specific small variations in the DNA of ALDH4A1, all of which associated with reduced muscle health. Follow-up experiments in worms used genetic engineering techniques to test how variation in the worm alh-6 gene could influence age-related health. The resulting mutant worms developed muscle problems much earlier than their normal counterparts, supporting the role of alh-6/ALDH4A1 in determining muscle health across the lifespan of both worms and humans. These results have identified a key influencer of muscle health during ageing in worms, and emphasize the importance of validating effects of genetic variation among humans during this process. Villa, Stuhr, Yen et al. hope that this study will help researchers find more genetic ‘markers’ of muscle health, and ultimately allow us to predict an individual’s risk of sarcopenia based on their genetic make-up.
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Affiliation(s)
- Osvaldo Villa
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, United States
| | - Nicole L Stuhr
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, United States.,Dornsife College of Letters, Arts, and Science, Department of Molecular and Computational Biology, University of Southern California, Los Angeles, United States
| | - Chia-An Yen
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, United States.,Dornsife College of Letters, Arts, and Science, Department of Molecular and Computational Biology, University of Southern California, Los Angeles, United States
| | - Eileen M Crimmins
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, United States
| | - Thalida Em Arpawong
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, United States
| | - Sean P Curran
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, United States.,Dornsife College of Letters, Arts, and Science, Department of Molecular and Computational Biology, University of Southern California, Los Angeles, United States.,Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, United States
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33
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Kalichamy SS, Alcantara AV, Yoon KH, Lee JI. A Simple Protocol to Analyze the Effects of Simulated Microgravity on Nematodes. BIOL BULL+ 2022. [DOI: 10.1134/s1062359021150097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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34
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Stuhr NL, Nhan JD, Hammerquist AM, Van Camp B, Reoyo D, Curran SP. Rapid Lipid Quantification in Caenorhabditis elegans by Oil Red O and Nile Red Staining. Bio Protoc 2022; 12:e4340. [PMID: 35592599 PMCID: PMC8918222 DOI: 10.21769/bioprotoc.4340] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 09/29/2021] [Accepted: 01/12/2022] [Indexed: 01/21/2023] Open
Abstract
The ability to stain lipid stores in vivo allows for the facile assessment of metabolic status in individuals of a population following genetic and environmental manipulation or pharmacological treatment. In the animal model Caenorhabditis elegans, lipids are stored in and mobilized from intracellular lipid droplets in the intestinal and hypodermal tissues. The abundance, size, and distribution of these lipids can be readily assessed by two staining methods for neutral lipids: Oil Red O (ORO) and Nile Red (NR). ORO and NR can be used to quantitatively measure lipid droplet abundance, while ORO can also define tissue distribution and lipid droplet size. C. elegans are a useful animal model in studying pathways relating to aging, fat storage, and metabolism, as their transparent nature allows for easy microscopic assessment of lipid droplets. This is done by fixation and permeabilization, staining with NR or ORO, image capture on a microscope, and computational identification and quantification of lipid droplets in individuals within a cohort. To ensure reproducibility in lipid measurements, we provide a detailed protocol to measure intracellular lipid dynamics in C. elegans. Graphic abstract: Flow chart depicting the preparation of C. elegans for fat staining protocols.
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Affiliation(s)
- Nicole L Stuhr
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, United States.,Department of Molecular and Computational Biology, Dornsife College of Letters, Arts and Science, University of Southern California, Los Angeles, United States
| | - James D Nhan
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, United States.,Department of Molecular and Computational Biology, Dornsife College of Letters, Arts and Science, University of Southern California, Los Angeles, United States
| | - Amy M Hammerquist
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, United States.,Department of Molecular and Computational Biology, Dornsife College of Letters, Arts and Science, University of Southern California, Los Angeles, United States
| | - Bennett Van Camp
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, United States
| | - David Reoyo
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, United States
| | - Sean P Curran
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, United States.,Department of Molecular and Computational Biology, Dornsife College of Letters, Arts and Science, University of Southern California, Los Angeles, United States.,Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, United States
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35
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Duangjan C, Curran SP. Oolonghomobisflavans from Camellia sinensis increase Caenorhabditis elegans lifespan and healthspan. GeroScience 2022; 44:533-545. [PMID: 34637108 PMCID: PMC8811050 DOI: 10.1007/s11357-021-00462-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 09/14/2021] [Indexed: 12/22/2022] Open
Abstract
Tea polyphenols are widely considered as excellent antioxidant agents which can contribute to human health and longevity. However, the identification of the active biomolecules in complex tea extracts that promote health and longevity are not fully known. Here we used the nematode Caenorhabditis elegans to analyze the health benefits and longevity effects of Camellia sinensis oolong tea extracts (QFT, NFT, and CFT) and oolonghomobisflavan A and oolonghomobisflavan B, which are present in oolong tea extracts. Our results showed that oolong tea extracts and oolonghomobisflavans prolong lifespan and improved healthspan by curtailing the age-related decline in muscle activity and the accumulation of age pigment (lipofuscin). We found that the lifespan and healthspan promoting effects of oolong tea extracts and oolonghomobisflavans were positively correlated with the stress resistance via DAF-16/FOXO transcription factor. Furthermore, oolong tea extracts and oolonghomobisflavans displayed protective effects against Aβ- and polyQ-induced neuro/proteotoxicity. Overall, our study provides new evidence to support the health benefits of oolong tea and importantly identify oolonghomobisflavans as potent bioactive molecules that promote health when supplemented with a normal diet. As such, oolonghomobisflavans represent a valuable new class of compounds that promote healthy aging.
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Affiliation(s)
- Chatrawee Duangjan
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, USA
| | - Sean P Curran
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, USA.
- Molecular and Computational Biology, Dornsife College of Letters, Arts, and Science, University of Southern California, Los Angeles, USA.
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36
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Fueser H, Pilger C, Kong C, Huser T, Traunspurger W. Polystyrene microbeads influence lipid storage distribution in C. elegans as revealed by coherent anti-Stokes Raman scattering (CARS) microscopy. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 294:118662. [PMID: 34896225 DOI: 10.1016/j.envpol.2021.118662] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Revised: 12/04/2021] [Accepted: 12/07/2021] [Indexed: 06/14/2023]
Abstract
The exposure of Caenorhabditis elegans to polystyrene (PS) beads of a wide range of sizes impedes feeding, by reducing food consumption, and has been linked to inhibitory effects on the reproductive capacity of this nematode, as determined in standardized toxicity tests. Lipid storage provides energy for longevity, growth, and reproduction and may influence the organismal response to stress, including the food deprivation resulting from microplastics exposure. However, the effects of microplastics on energy storage have not been investigated in detail. In this study, C. elegans was exposed to ingestible sizes of PS beads in a standardized toxicity test (96 h) and in a multigeneration test (∼21 days), after which lipid storage was quantitatively analyzed in individual adults using coherent anti-Stokes Raman scattering (CARS) microscopy. The results showed that lipid storage distribution in C. elegans was altered when worms were exposed to microplastics in form of PS beads. For example, when exposed to 0.1-μm PS beads, the lipid droplet count was 93% higher, the droplets were up to 56% larger, and the area of the nematode body covered by lipids was up to 79% higher than in unexposed nematodes. The measured values tended to increase as PS bead sizes decreased. Cultivating the nematodes for 96 h under restricted food conditions in the absence of beads reproduced the altered lipid storage and suggested that it was triggered by food deprivation, including that induced by the dilutional effects of PS bead exposure. Our study demonstrates the utility of CARS microscopy to comprehensively image the smaller microplastics (<10 μm) ingested by nematodes and possibly other biota in investigations of the effects at the level of the individual organism.
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Affiliation(s)
- Hendrik Fueser
- Bielefeld University, Animal Ecology, Konsequenz 45, 33615, Bielefeld, Germany.
| | - Christian Pilger
- Bielefeld University, Biomolecular Photonics, Universitätsstraße 25, 33615, Bielefeld, Germany
| | - Cihang Kong
- Bielefeld University, Biomolecular Photonics, Universitätsstraße 25, 33615, Bielefeld, Germany
| | - Thomas Huser
- Bielefeld University, Biomolecular Photonics, Universitätsstraße 25, 33615, Bielefeld, Germany
| | - Walter Traunspurger
- Bielefeld University, Animal Ecology, Konsequenz 45, 33615, Bielefeld, Germany
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Jiang S, Jiang CP, Cao P, Liu YH, Gao CH, Yi XX. Sonneradon A Extends Lifespan of Caenorhabditis elegans by Modulating Mitochondrial and IIS Signaling Pathways. Mar Drugs 2022; 20:md20010059. [PMID: 35049915 PMCID: PMC8778700 DOI: 10.3390/md20010059] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 01/03/2022] [Accepted: 01/04/2022] [Indexed: 12/15/2022] Open
Abstract
Aging is related to the lowered overall functioning and increased risk for various age-related diseases in humans. Sonneradon A (SDA), a new compound first extracted from the edible fruits of mangrove Sonneratia apetala, showed remarkable antiaging activity. However, the role of SDA in antiaging remains unclear. In this article, we studied the function of SDA in antiaging by using the animal model Caenorhabditis elegans. Results showed that SDA inhibited production of reactive oxygen species (ROS) by 53%, and reduced the accumulation of aging markers such as lipids and lipofuscins. Moreover, SDA also enhanced the innate immune response to Pseudomonas aeruginosa infection. Genetic analysis of a series of mutants showed that SDA extended the lifespan of the mutants of eat-2 and glp-1. Together, this effect may be related to the enhanced resistance to oxidative stress via mitochondrial and insulin/insulin-like growth factor-1 signaling (IIS) pathways. The results of this study provided new evidence for an antiaging effect of SDA in C. elegans, as well as insights into the implication of antiaging activity of SDA in higher organisms.
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Katju V, Konrad A, Deiss TC, Bergthorsson U. Mutation rate and spectrum in obligately outcrossing Caenorhabditis elegans mutation accumulation lines subjected to RNAi-induced knockdown of the mismatch repair gene msh-2. G3 GENES|GENOMES|GENETICS 2022; 12:6407146. [PMID: 34849777 PMCID: PMC8727991 DOI: 10.1093/g3journal/jkab364] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 10/13/2021] [Indexed: 01/09/2023]
Abstract
DNA mismatch repair (MMR), an evolutionarily conserved repair pathway shared by prokaryotic and eukaryotic species alike, influences molecular evolution by detecting and correcting mismatches, thereby protecting genetic fidelity, reducing the mutational load, and preventing lethality. Herein we conduct the first genome-wide evaluation of the alterations to the mutation rate and spectrum under impaired activity of the MutSα homolog, msh-2, in Caenorhabditis elegans male–female fog-2(lf) lines. We performed mutation accumulation (MA) under RNAi-induced knockdown of msh-2 for up to 50 generations, followed by next-generation sequencing of 19 MA lines and the ancestral control. msh-2 impairment in the male–female background substantially increased the frequency of nuclear base substitutions (∼23×) and small indels (∼328×) relative to wildtype hermaphrodites. However, we observed no increase in the mutation rates of mtDNA, and copy-number changes of single-copy genes. There was a marked increase in copy-number variation of rDNA genes under MMR impairment. In C. elegans, msh-2 repairs transitions more efficiently than transversions and increases the AT mutational bias relative to wildtype. The local sequence context, including sequence complexity, G + C-content, and flanking bases influenced the mutation rate. The X chromosome exhibited lower substitution and higher indel rates than autosomes, which can either result from sex-specific mutation rates or a nonrandom distribution of mutable sites between chromosomes. Provided the observed difference in mutational pattern is mostly due to MMR impairment, our results indicate that the specificity of MMR varies between taxa, and is more efficient in detecting and repairing small indels in eukaryotes relative to prokaryotes.
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Affiliation(s)
- Vaishali Katju
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX 77845, USA
| | - Anke Konrad
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX 77845, USA
- Faculdade de Ciência da Universidade de Lisboa (FCUL), CE3C—Centre for Ecology, Evolution and Environmental Changes, 1749-016 Lisboa, Portugal
| | - Thaddeus C Deiss
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX 77845, USA
| | - Ulfar Bergthorsson
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX 77845, USA
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Urban ND, Cavataio JP, Berry Y, Vang B, Maddali A, Sukpraphrute RJ, Schnell S, Truttmann MC. Explaining inter-lab variance in C. elegans N2 lifespan: Making a case for standardized reporting to enhance reproducibility. Exp Gerontol 2021; 156:111622. [PMID: 34793939 PMCID: PMC8938996 DOI: 10.1016/j.exger.2021.111622] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 11/02/2021] [Accepted: 11/04/2021] [Indexed: 02/02/2023]
Abstract
The nematode Caenorhabditis elegans is a powerful model organism for studying cell development, apoptosis, neuronal circuits, and aging. The isolate N2 is recognized by the C. elegans community as the reference wild-type strain. Interestingly, the lifespan of presumably isogenic C. elegans N2 worms-even when grown under comparable conditions-varies significantly amongst distinct laboratories. This hinders the inter-laboratory comparability of C. elegans lifespan data and raises questions regarding data interpretation and reproducibility. Here, we hypothesized slight alterations in experimental design and worm handling could explain the observed discrepancies. To test this hypothesis, we collected and assessed data from over 1000 published C. elegans N2 lifespan assays as well as corresponding methodological meta-data. We find that mean N2 lifespans range from approximately 7 days to upwards of 35 days, despite laboratories disclosing seemingly comparable experimental conditions. We further demonstrate that, in addition to temperature, the use of the chemical sterilizer 5-fluoro-2'-deoxyuridine (FUDR) may change N2 lifespan. Additionally, we observed differences in average N2 lifespan from experiments originating from distinct geographic locations, indicating a potential effect of location-specific factors on experimental outcomes. Taken as a whole, our work indicates the sum of many small, rather than a few critical, differences in experimental conditions may account for the observed variance in N2 lifespan. We also find that the absence of standardized experimental methods and the insufficient disclosure of experiment details in the peer-reviewed literature limits the inter-lab comparability of published results. We thus propose the establishment of a succinct reporting standard for C. elegans lifespan experiments to increase the reliability and reproducibility, and thus scientific value, of these studies.
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Affiliation(s)
- Nicholas D. Urban
- Department of Molecular & Integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Joseph P. Cavataio
- Department of Molecular & Integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Yasmeen Berry
- Undergraduate Research Opportunity Program, University of Michigan, Ann Arbor, MI 48109, USA
| | - Brandon Vang
- Undergraduate Research Opportunity Program, University of Michigan, Ann Arbor, MI 48109, USA
| | - Anirudh Maddali
- Undergraduate Research Opportunity Program, University of Michigan, Ann Arbor, MI 48109, USA
| | - Richard J. Sukpraphrute
- Undergraduate Research Opportunity Program, University of Michigan, Ann Arbor, MI 48109, USA
| | - Santiago Schnell
- Department of Molecular & Integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA,Department of Biological Sciences and Department of Applied and Computational Mathematics and Statistics, University of Notre Dame, Notre Dame, IN 46556
| | - Matthias C. Truttmann
- Department of Molecular & Integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA,Geriatrics Center, University of Michigan, Ann Arbor, MI 48109, USA,Corresponding author at: BSRB, 109 Zina Pitcher Place, Ann Arbor 48109, MI, USA., (M.C. Truttmann)
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Vega NM, Ludington WB. From a parts list to assembly instructions and an operating manual: how small host models can re-write microbiome theory. Curr Opin Microbiol 2021; 64:146-151. [PMID: 34739919 DOI: 10.1016/j.mib.2021.10.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Revised: 08/10/2021] [Accepted: 10/08/2021] [Indexed: 10/20/2022]
Affiliation(s)
- Nic M Vega
- Biology Department, Emory University, Atlanta, GA, United States.
| | - William B Ludington
- Department of Embryology, Carnegie Institution of Washington, Baltimore, MD, United States
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Methylmercury-Induced Metabolic Alterations in Caenorhabditis elegans Are Diet-Dependent. TOXICS 2021; 9:toxics9110287. [PMID: 34822679 PMCID: PMC8619518 DOI: 10.3390/toxics9110287] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 09/22/2021] [Accepted: 10/29/2021] [Indexed: 01/12/2023]
Abstract
Methylmercury (MeHg) is a well-known neurotoxicant; however, its role in metabolic diseases has been gaining wider attention. Chronic exposure to MeHg in human populations shows an association with diabetes mellitus and metabolic syndrome (MS). As the incidences of both obesity and MS are on the rise globally, it is important to understand the potential role of MeHg in the development of the disease. There is a dearth of information on dietary interactions between MeHg and lipids, which play an important role in developing MS. We have previously shown that MeHg increases food seeking behaviors, lipid levels, fat storage, and pro-adipogenic gene expression in C. elegans fed the standard OP50 Escherichia coli diet. However, we hypothesized that these metabolic changes could be prevented if the worms were fed a bacterial diet lower in lipid content. We tested whether C. elegans developed metabolic alterations in response to MeHg if they were fed two alternative E. coli strains (HT115 and HB101) that are known absorb significantly less lipids from their media. Additionally, to explore the effect of a high-lipid and high-cholesterol diet on MeHg-induced metabolic dysfunction, we supplemented the OP50 strain with twice the standard concentration of cholesterol in the nematode growth media. Wild-type worms fed either the HB101 or HT115 diet were more resistant to MeHg than the worms fed the OP50 diet, showing a significant right-hand shift in the dose–response survival curve. Worms fed the OP50 diet supplemented with cholesterol were more sensitive to MeHg, showing a significant left-hand shift in the dose–response survival curve. Changes in sensitivity to MeHg by differential diet were not due to altered MeHg intake in the worms as measured by inductively coupled mass spectrometry. Worms fed the low-fat diets showed protection from MeHg-induced metabolic changes, including decreased food consumption, lower triglyceride content, and lower fat storage than the worms fed either of the higher-fat diets. Oxidative stress is a common characteristic of both MeHg exposure and high-fat diets. Worms fed either OP50 or OP50 supplemented with cholesterol and treated with MeHg had significantly higher levels of reactive oxygen species, carbonylated proteins, and loss of glutathione than the worms fed the HT115 or HB101 low-lipid diets. Taken together, our data suggest a synergistic effect of MeHg and dietary lipid levels on MeHg toxicity and fat metabolism in C. elegans, which may affect the ability of MeHg to cause metabolic dysfunction.
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Dinić M, Jakovljević S, Đokić J, Popović N, Radojević D, Strahinić I, Golić N. Probiotic-mediated p38 MAPK immune signaling prolongs the survival of Caenorhabditis elegans exposed to pathogenic bacteria. Sci Rep 2021; 11:21258. [PMID: 34711881 PMCID: PMC8553853 DOI: 10.1038/s41598-021-00698-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 10/15/2021] [Indexed: 11/18/2022] Open
Abstract
The host-microbiota cross-talk represents an important factor contributing to innate immune response and host resistance during infection. It has been shown that probiotic lactobacilli exhibit the ability to modulate innate immunity and enhance pathogen elimination. Here we showed that heat-inactivated probiotic strain Lactobacillus curvatus BGMK2-41 stimulates immune response and resistance of the Caenorhabditis elegans against Staphylococcus aureus and Pseudomonas aeruginosa. By employing qRT-PCR and western blot analysis we showed that heat-inactivated BGMK2-41 activated PMK-1/p38 MAPK immunity pathway which prolongs the survival of C. elegans exposed to pathogenic bacteria in nematode killing assays. The C. elegans pmk-1 mutant was used to demonstrate a mechanistic basis for the antimicrobial potential of BGMK2-41, showing that BGMK2-41 upregulated PMK-1/p38 MAPK dependent transcription of C-type lectins, lysozymes and tight junction protein CLC-1. Overall, this study suggests that PMK-1/p38 MAPK-dependent immune regulation by BGMK2-41 is essential for probiotic-mediated C. elegans protection against gram-positive and gram-negative bacteria and could be further explored for development of probiotics with the potential to increase resistance of the host towards pathogens.
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Affiliation(s)
- Miroslav Dinić
- Laboratory for Molecular Microbiology (LMM), Institute of Molecular Genetics and Genetic Engineering (IMGGE), University of Belgrade, Belgrade, Serbia.
| | - Stefan Jakovljević
- Laboratory for Molecular Microbiology (LMM), Institute of Molecular Genetics and Genetic Engineering (IMGGE), University of Belgrade, Belgrade, Serbia
| | - Jelena Đokić
- Laboratory for Molecular Microbiology (LMM), Institute of Molecular Genetics and Genetic Engineering (IMGGE), University of Belgrade, Belgrade, Serbia
| | - Nikola Popović
- Laboratory for Molecular Microbiology (LMM), Institute of Molecular Genetics and Genetic Engineering (IMGGE), University of Belgrade, Belgrade, Serbia
| | - Dušan Radojević
- Laboratory for Molecular Microbiology (LMM), Institute of Molecular Genetics and Genetic Engineering (IMGGE), University of Belgrade, Belgrade, Serbia
| | - Ivana Strahinić
- Laboratory for Molecular Microbiology (LMM), Institute of Molecular Genetics and Genetic Engineering (IMGGE), University of Belgrade, Belgrade, Serbia
| | - Nataša Golić
- Laboratory for Molecular Microbiology (LMM), Institute of Molecular Genetics and Genetic Engineering (IMGGE), University of Belgrade, Belgrade, Serbia
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43
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Scharf A, Pohl F, Egan BM, Kocsisova Z, Kornfeld K. Reproductive Aging in Caenorhabditis elegans: From Molecules to Ecology. Front Cell Dev Biol 2021; 9:718522. [PMID: 34604218 PMCID: PMC8481778 DOI: 10.3389/fcell.2021.718522] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 08/04/2021] [Indexed: 11/13/2022] Open
Abstract
Aging animals display a broad range of progressive degenerative changes, and one of the most fascinating is the decline of female reproductive function. In the model organism Caenorhabditis elegans, hermaphrodites reach a peak of progeny production on day 2 of adulthood and then display a rapid decline; progeny production typically ends by day 8 of adulthood. Since animals typically survive until day 15 of adulthood, there is a substantial post reproductive lifespan. Here we review the molecular and cellular changes that occur during reproductive aging, including reductions in stem cell number and activity, slowing meiotic progression, diminished Notch signaling, and deterioration of germ line and oocyte morphology. Several interventions have been identified that delay reproductive aging, including mutations, drugs and environmental factors such as temperature. The detailed description of reproductive aging coupled with interventions that delay this process have made C. elegans a leading model system to understand the mechanisms that drive reproductive aging. While reproductive aging has dramatic consequences for individual fertility, it also has consequences for the ecology of the population. Population dynamics are driven by birth and death, and reproductive aging is one important factor that influences birth rate. A variety of theories have been advanced to explain why reproductive aging occurs and how it has been sculpted during evolution. Here we summarize these theories and discuss the utility of C. elegans for testing mechanistic and evolutionary models of reproductive aging.
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Affiliation(s)
- Andrea Scharf
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, United States
| | - Franziska Pohl
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, United States.,Department of Medicine, Washington University School of Medicine, St. Louis, MO, United States
| | - Brian M Egan
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, United States
| | - Zuzana Kocsisova
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, United States
| | - Kerry Kornfeld
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, United States
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Mining nematode protein secretomes to explain lifestyle and host specificity. PLoS Negl Trop Dis 2021; 15:e0009828. [PMID: 34587193 PMCID: PMC8504978 DOI: 10.1371/journal.pntd.0009828] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 10/11/2021] [Accepted: 09/21/2021] [Indexed: 12/15/2022] Open
Abstract
Parasitic nematodes are highly successful pathogens, inflicting disease on humans, animals and plants. Despite great differences in their life cycles, host preference and transmission modes, these parasites share a common capacity to manipulate their host's immune system. This is at least partly achieved through the release of excretory/secretory proteins, the most well-characterized component of nematode secretomes, that are comprised of functionally diverse molecules. In this work, we analyzed published protein secretomes of parasitic nematodes to identify common patterns as well as species-specific traits. The 20 selected organisms span 4 nematode clades, including plant pathogens, animal parasites, and the free-living species Caenorhabditis elegans. Transthyretin-like proteins were the only component common to all adult secretomes; many other protein classes overlapped across multiple datasets. The glycolytic enzymes aldolase and enolase were present in all parasitic species, but missing from C. elegans. Secretomes from larval stages showed less overlap between species. Although comparison of secretome composition across species and life-cycle stages is challenged by the use of different methods and depths of sequencing among studies, our workflow enabled the identification of conserved protein families and pinpointed elements that may have evolved as to enable parasitism. This strategy, extended to more secretomes, may be exploited to prioritize therapeutic targets in the future.
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45
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Ke W, Reed JN, Yang C, Higgason N, Rayyan L, Wählby C, Carpenter AE, Civelek M, O’Rourke EJ. Genes in human obesity loci are causal obesity genes in C. elegans. PLoS Genet 2021; 17:e1009736. [PMID: 34492009 PMCID: PMC8462697 DOI: 10.1371/journal.pgen.1009736] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 09/24/2021] [Accepted: 07/23/2021] [Indexed: 12/13/2022] Open
Abstract
Obesity and its associated metabolic syndrome are a leading cause of morbidity and mortality. Given the disease's heavy burden on patients and the healthcare system, there has been increased interest in identifying pharmacological targets for the treatment and prevention of obesity. Towards this end, genome-wide association studies (GWAS) have identified hundreds of human genetic variants associated with obesity. The next challenge is to experimentally define which of these variants are causally linked to obesity, and could therefore become targets for the treatment or prevention of obesity. Here we employ high-throughput in vivo RNAi screening to test for causality 293 C. elegans orthologs of human obesity-candidate genes reported in GWAS. We RNAi screened these 293 genes in C. elegans subject to two different feeding regimens: (1) regular diet, and (2) high-fructose diet, which we developed and present here as an invertebrate model of diet-induced obesity (DIO). We report 14 genes that promote obesity and 3 genes that prevent DIO when silenced in C. elegans. Further, we show that knock-down of the 3 DIO genes not only prevents excessive fat accumulation in primary and ectopic fat depots but also improves the health and extends the lifespan of C. elegans overconsuming fructose. Importantly, the direction of the association between expression variants in these loci and obesity in mice and humans matches the phenotypic outcome of the loss-of-function of the C. elegans ortholog genes, supporting the notion that some of these genes would be causally linked to obesity across phylogeny. Therefore, in addition to defining causality for several genes so far merely correlated with obesity, this study demonstrates the value of model systems compatible with in vivo high-throughput genetic screening to causally link GWAS gene candidates to human diseases.
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Affiliation(s)
- Wenfan Ke
- Department of Biology, College of Arts and Sciences, University of Virginia, Charlottesville, Virginia, United States of America
| | - Jordan N. Reed
- Department of Biomedical Engineering, School of Engineering and Applied Science, University of Virginia, Charlottesville, Virginia, United States of America
| | - Chenyu Yang
- Department of Biology, College of Arts and Sciences, University of Virginia, Charlottesville, Virginia, United States of America
| | - Noel Higgason
- Department of Biology, College of Arts and Sciences, University of Virginia, Charlottesville, Virginia, United States of America
| | - Leila Rayyan
- Department of Biology, College of Arts and Sciences, University of Virginia, Charlottesville, Virginia, United States of America
| | - Carolina Wählby
- Department of Information Technology and SciLifeLab, Uppsala University, Uppsala, Sweden
| | - Anne E. Carpenter
- Imaging Platform, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Mete Civelek
- Department of Biomedical Engineering, School of Engineering and Applied Science, University of Virginia, Charlottesville, Virginia, United States of America
- Center for Public Health Genomics, School of Medicine, University of Virginia, Charlottesville, Virginia, United States of America
| | - Eyleen J. O’Rourke
- Department of Biology, College of Arts and Sciences, University of Virginia, Charlottesville, Virginia, United States of America
- Department of Cell Biology, School of Medicine, University of Virginia, Charlottesville, Virginia, United States of America
- * E-mail:
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Viri V, Arveiler M, Lehnert T, Gijs MAM. An In Vivo Microfluidic Study of Bacterial Load Dynamics and Absorption in the C. elegans Intestine. MICROMACHINES 2021; 12:832. [PMID: 34357242 PMCID: PMC8304684 DOI: 10.3390/mi12070832] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 07/13/2021] [Accepted: 07/15/2021] [Indexed: 01/19/2023]
Abstract
Caenorhabditiselegans (C. elegans) has gained importance as a model for studying host-microbiota interactions and bacterial infections related to human pathogens. Assessing the fate of ingested bacteria in the worm's intestine is therefore of great interest, in particular with respect to normal bacterial digestion or intestinal colonization by pathogens. Here, we report an in vivo study of bacteria in the gut of C. elegans. We take advantage of a polydimethylsiloxane (PDMS) microfluidic device enabling passive immobilization of adult worms under physiological conditions. Non-pathogenic Escherichia coli (E. coli) bacteria expressing either pH-sensitive or pH-insensitive fluorescence reporters as well as fluorescently marked indigestible microbeads were used for the different assays. Dynamic fluorescence patterns of the bacterial load in the worm gut were conveniently monitored by time-lapse imaging. Cyclic motion of the bacterial load due to peristaltic activity of the gut was observed and biochemical digestion of E. coli was characterized by high-resolution fluorescence imaging of the worm's intestine. We could discriminate between individual intact bacteria and diffuse signals related to disrupted bacteria that can be digested. From the decay of the diffuse fluorescent signal, we determined a digestion time constant of 14 ± 4 s. In order to evaluate the possibility to perform infection assays with our platform, immobilized C. elegans worms were fed pathogenic Mycobacterium marinum (M. marinum) bacteria. We analyzed bacterial fate and accumulation in the gut of N2 worms and mitochondrial stress response in a hsp-6::gfp mutant.
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Affiliation(s)
| | | | | | - Martin A. M. Gijs
- Laboratory of Microsystems, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland; (V.V.); (M.A.); (T.L.)
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47
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McIntyre G, Wright J, Wong HT, Lamendella R, Chan J. Effects of FUdR on gene expression in the C. elegans bacterial diet OP50. BMC Res Notes 2021; 14:207. [PMID: 34103088 PMCID: PMC8186096 DOI: 10.1186/s13104-021-05624-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2020] [Accepted: 05/19/2021] [Indexed: 11/23/2022] Open
Abstract
Objective Many C. elegans aging studies use the compound 5-fluro-2ʹ-deoxyuridine (FUdR) to produce a synchronous population of worms. However, the effects of FUdR on the bacterial gene expression of OP50 E. coli, the primary laboratory C. elegans food source, is not fully understood. This is particularly relevant as studies suggest that intestinal microbes can affect C. elegans physiology. Therefore, it is imperative that we understand how exposure to FUdR can affect gene expression changes in OP50 E. coli. Results An RNAseq dataset comprised of expression patterns of 2900 E. coli genes in the strain OP50, which were seeded on either nematode growth media (NGM) plates or on FUdR (50 µM) supplemented NGM plates, was analyzed. Analysis showed differential gene expression in genes involved in general transport, amino acid biosynthesis, transcription, iron transport, and antibiotic resistance. We specifically highlight metabolic enzymes in the l-histidine biosynthesis pathway as differentially expressed between NGM and FUdR exposed OP50. We conclude that OP50 exposed to FUdR results in differential expression of many genes, including those in amino acid biosynthetic pathways. Supplementary Information The online version contains supplementary material available at 10.1186/s13104-021-05624-6.
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Affiliation(s)
- Grace McIntyre
- Department of Biology, Marian University, 3200 Cold Spring Rd, Indianapolis, IN, 46222, USA
| | - Justin Wright
- Department of Biology, Juniata College, 1700 Moore St, Huntingdon, PA, 16652, USA
| | - Hoi Tong Wong
- Department of Biology, Juniata College, 1700 Moore St, Huntingdon, PA, 16652, USA
| | - Regina Lamendella
- Department of Biology, Juniata College, 1700 Moore St, Huntingdon, PA, 16652, USA
| | - Jason Chan
- Department of Biology, Marian University, 3200 Cold Spring Rd, Indianapolis, IN, 46222, USA.
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48
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Nakano Y, Moriuchi M, Fukushima Y, Hayashi K, Suico MA, Kai H, Koutaki G, Shuto T. Intrapopulation analysis of longitudinal lifespan in Caenorhabditis elegans identifies W09D10.4 as a novel AMPK-associated healthspan shortening factor. J Pharmacol Sci 2020; 145:241-252. [PMID: 33602504 DOI: 10.1016/j.jphs.2020.12.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 12/11/2020] [Accepted: 12/17/2020] [Indexed: 11/27/2022] Open
Abstract
Caenorhabditis elegans is a model organism widely used for longevity studies. Current advances have been made in the methods that allow automated monitoring of C. elegans behavior. However, ordinary manual assays as well as automated methods have yet to achieve qualitative whole-life analysis of C. elegans longevity based on intrapopulation variation. Here, we utilized live-cell analysis system to determine the parameters of nematode lifespans. Image-based superposition method enabled to determine not only frailty in worms, but also to measure individual and longitudinal lifespan, healthspan, and frailspan. Notably, k-means clustering via principal component analysis revealed four clusters with distinct longevity patterns in wild-type C. elegans. Physiological relevance of clustering was confirmed by assays with pharmacological and/or genetic manipulation of AMP-activated protein kinase (AMPK), a crucial regulator of healthspan. Finally, we focused on W09D10.4 among the possible regulators extracted by integrative expression analysis with existing data sets. Importantly, W09D10.4 knockdown increased the high-healthspan populations only in the presence of AMPK, suggesting that W09D10.4 is a novel AMPK-associated healthspan shortening factor in C. elegans. Overall, the study establishes a novel platform of longitudinal lifespan in C. elegans, which is user-friendly, and may be a useful pharmacological tool to identify healthspan modulatory factors.
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Affiliation(s)
- Yoshio Nakano
- Department of Molecular Medicine, Graduate School of Pharmaceutical Science, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto, 862-0973, Japan; Program for Leading Graduate Schools "HIGO (Health Life Science: Interdisciplinary and Global Oriented) Program", 5-1 Oe-honmachi, Chuo-ku, Kumamoto, 862-0973, Japan
| | - Masataka Moriuchi
- Department of Molecular Medicine, Graduate School of Pharmaceutical Science, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto, 862-0973, Japan; Program for Leading Graduate Schools "HIGO (Health Life Science: Interdisciplinary and Global Oriented) Program", 5-1 Oe-honmachi, Chuo-ku, Kumamoto, 862-0973, Japan
| | - Yutaro Fukushima
- Department of Molecular Medicine, Graduate School of Pharmaceutical Science, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto, 862-0973, Japan; Program for Leading Graduate Schools "HIGO (Health Life Science: Interdisciplinary and Global Oriented) Program", 5-1 Oe-honmachi, Chuo-ku, Kumamoto, 862-0973, Japan
| | - Kyotaro Hayashi
- Department of Electrical and Computer Engineering, Kumamoto University, 2-39-1 Kurokami, Chuo-ku, Kumamoto, 860-8555, Japan
| | - Mary Ann Suico
- Department of Molecular Medicine, Graduate School of Pharmaceutical Science, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto, 862-0973, Japan
| | - Hirofumi Kai
- Department of Molecular Medicine, Graduate School of Pharmaceutical Science, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto, 862-0973, Japan
| | - Go Koutaki
- Department of Electrical and Computer Engineering, Kumamoto University, 2-39-1 Kurokami, Chuo-ku, Kumamoto, 860-8555, Japan
| | - Tsuyoshi Shuto
- Department of Molecular Medicine, Graduate School of Pharmaceutical Science, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto, 862-0973, Japan.
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