1
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Wang G, Laranjeiro R, LeValley S, Van Raamsdonk JM, Driscoll M. The glyoxylate shunt protein ICL-1 protects from mitochondrial superoxide stress through activation of the mitochondrial unfolded protein response. Free Radic Biol Med 2023; 208:771-779. [PMID: 37758122 DOI: 10.1016/j.freeradbiomed.2023.09.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 09/05/2023] [Accepted: 09/24/2023] [Indexed: 10/03/2023]
Abstract
Disrupting mitochondrial superoxide dismutase (SOD) causes neonatal lethality in mice and death of flies within 24 h after eclosion. Deletion of mitochondrial sod genes in C. elegans impairs fertility as well, but surprisingly is not detrimental to survival of progeny generated. The comparison of metabolic pathways among mouse, flies and nematodes reveals that mice and flies lack the glyoxylate shunt, a shortcut that bypasses part of the tricarboxylic acid (TCA) cycle. Here we show that ICL-1, the sole protein that catalyzes the glyoxylate shunt, is critical for protection against embryonic lethality resulting from elevated levels of mitochondrial superoxide. In exploring the mechanism by which ICL-1 protects against ROS-mediated embryonic lethality, we find that ICL-1 is required for the efficient activation of mitochondrial unfolded protein response (UPRmt) and that ATFS-1, a key UPRmt transcription factor and an activator of icl-1 gene expression, is essential to limit embryonic/neonatal lethality in animals lacking mitochondrial SOD. In sum, we identify a biochemical pathway that highlights a molecular strategy for combating toxic mitochondrial superoxide consequences in cells.
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Affiliation(s)
- Guoqiang Wang
- Department of Molecular Biology and Biochemistry, School of Arts and Sciences, Rutgers, the State University of New Jersey, Piscataway, NJ, USA
| | - Ricardo Laranjeiro
- Department of Molecular Biology and Biochemistry, School of Arts and Sciences, Rutgers, the State University of New Jersey, Piscataway, NJ, USA
| | - Stephanie LeValley
- Laboratory of Aging and Neurodegenerative Disease, Center for Neurodegenerative Science, Van Andel Research Institute, Grand Rapids, MI, USA
| | - Jeremy M Van Raamsdonk
- Laboratory of Aging and Neurodegenerative Disease, Center for Neurodegenerative Science, Van Andel Research Institute, Grand Rapids, MI, USA; Department of Neurology and Neurosurgery, McGill University, Montreal, QC, Canada; Metabolic Disorders and Complications Program, and Brain Repair and Integrative Neuroscience Program, Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada; Division of Experimental Medicine, McGill University, Montreal, QC, Canada
| | - Monica Driscoll
- Department of Molecular Biology and Biochemistry, School of Arts and Sciences, Rutgers, the State University of New Jersey, Piscataway, NJ, USA.
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2
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Maushe D, Ogi V, Divakaran K, Verdecia Mogena AM, Himmighofen PA, Machado RAR, Towbin BD, Ehlers RU, Molina C, Parisod C, Maud Robert CA. Stress tolerance in entomopathogenic nematodes: Engineering superior nematodes for precision agriculture. J Invertebr Pathol 2023:107953. [PMID: 37336478 DOI: 10.1016/j.jip.2023.107953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 06/13/2023] [Accepted: 06/16/2023] [Indexed: 06/21/2023]
Abstract
Entomopathogenic nematodes (EPNs) are soil-dwelling parasitic roundworms commonly used as biocontrol agents of insect pests in agriculture. EPN dauer juveniles locate and infect a host in which they will grow and multiply until resource depletion. During their free-living stage, EPNs face a series of internal and environmental stresses. Their ability to overcome these challenges is crucial to determine their infection success and survival. In this review, we provide a comprehensive overview of EPN response to stresses associated with starvation, low/elevated temperatures, desiccation, osmotic stress, hypoxia, and ultra-violet light. We further report EPN defense strategies to cope with biotic stressors such as viruses, bacteria, fungi, and predatory insects. By comparing the genetic and biochemical basis of these strategies to the nematode model Caenorhabditis elegans, we provide new avenues and targets to select and engineer precision nematodes adapted to specific field conditions.
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Affiliation(s)
- Dorothy Maushe
- Institute of Plant Sciences, University of Bern, Altenbergrain 21, CH-3013 Bern, Switzerland
| | - Vera Ogi
- Institute of Plant Sciences, University of Bern, Altenbergrain 21, CH-3013 Bern, Switzerland
| | - Keerthi Divakaran
- Institute of Plant Sciences, University of Bern, Altenbergrain 21, CH-3013 Bern, Switzerland
| | | | - Paul Anton Himmighofen
- Institute of Plant Sciences, University of Bern, Altenbergrain 21, CH-3013 Bern, Switzerland
| | - Ricardo A R Machado
- Institute of Biology, University of Neuchâtel, Rue Emile Argand 11, CH-2000 Neuchâtel, Switzerland
| | - Benjamin Daniel Towbin
- Institute of Cell Biology, University of Bern, Baltzerstrasse 4, CH-3012 Bern, Switzerland
| | - Ralf-Udo Ehlers
- e- nema GmbH, Klausdorfer Str. 28-36, DE-24223 Schwentinental, Germany
| | - Carlos Molina
- e- nema GmbH, Klausdorfer Str. 28-36, DE-24223 Schwentinental, Germany
| | - Christian Parisod
- Department of Biology, University of Fribourg, Chemin du Musée 10, CH-1700 Fribourg, Switzerland
| | - Christelle Aurélie Maud Robert
- Institute of Plant Sciences, University of Bern, Altenbergrain 21, CH-3013 Bern, Switzerland; Oeschger Centre for Climate Change Research, University of Bern, Hochschulstrasse 4, CH-3012 Bern, Switzerland.
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3
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Staab TA, McIntyre G, Wang L, Radeny J, Bettcher L, Guillen M, Peck MP, Kalil AP, Bromley SP, Raftery D, Chan JP. The lipidomes of C. elegans with mutations in asm-3/acid sphingomyelinase and hyl-2/ceramide synthase show distinct lipid profiles during aging. Aging (Albany NY) 2023; 15:650-674. [PMID: 36787434 PMCID: PMC9970312 DOI: 10.18632/aging.204515] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 02/01/2023] [Indexed: 02/16/2023]
Abstract
Lipid metabolism affects cell and physiological functions that mediate animal healthspan and lifespan. Lipidomics approaches in model organisms have allowed us to better understand changes in lipid composition related to age and lifespan. Here, using the model C. elegans, we examine the lipidomes of mutants lacking enzymes critical for sphingolipid metabolism; specifically, we examine acid sphingomyelinase (asm-3), which breaks down sphingomyelin to ceramide, and ceramide synthase (hyl-2), which synthesizes ceramide from sphingosine. Worm asm-3 and hyl-2 mutants have been previously found to be long- and short-lived, respectively. We analyzed longitudinal lipid changes in wild type animals compared to mutants at 1-, 5-, and 10-days of age. We detected over 700 different lipids in several lipid classes. Results indicate that wildtype animals exhibit increased triacylglycerols (TAG) at 10-days compared to 1-day, and decreased lysophoshatidylcholines (LPC). We find that 10-day hyl-2 mutants have elevated total polyunsaturated fatty acids (PUFA) and increased LPCs compared to 10-day wildtype animals. These changes mirror another short-lived model, the daf-16/FOXO transcription factor that is downstream of the insulin-like signaling pathway. In addition, we find that hyl-2 mutants have poor oxidative stress response, supporting a model where mutants with elevated PUFAs may accumulate more oxidative damage. On the other hand, 10-day asm-3 mutants have fewer TAGs. Intriguingly, asm-3 mutants have a similar lipid composition as the long-lived, caloric restriction model eat-2/mAChR mutant. Together, these analyses highlight the utility of lipidomic analyses to characterize metabolic changes during aging in C. elegans.
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Affiliation(s)
- Trisha A. Staab
- Department of Biology, Marian University, Indianapolis, IN 46222, USA
| | - Grace McIntyre
- Department of Biology, Marian University, Indianapolis, IN 46222, USA
| | - Lu Wang
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA 98195, USA
| | - Joycelyn Radeny
- Department of Biology, Juniata College, Huntingdon, PA 16652, USA
| | - Lisa Bettcher
- Northwest Metabolomics Research Center, University of Washington, Seattle, WA 98195, USA
| | - Melissa Guillen
- Department of Biology, Marian University, Indianapolis, IN 46222, USA
| | - Margaret P. Peck
- Department of Biology, Juniata College, Huntingdon, PA 16652, USA
| | - Azia P. Kalil
- Department of Biology, Juniata College, Huntingdon, PA 16652, USA
| | | | - Daniel Raftery
- Northwest Metabolomics Research Center, University of Washington, Seattle, WA 98195, USA
| | - Jason P. Chan
- Department of Biology, Marian University, Indianapolis, IN 46222, USA
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4
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Choi HS, Bhat A, Howington MB, Schaller ML, Cox RL, Huang S, Beydoun S, Miller HA, Tuckowski AM, Mecano J, Dean ES, Jensen L, Beard DA, Evans CR, Leiser SF. FMO rewires metabolism to promote longevity through tryptophan and one carbon metabolism in C. elegans. Nat Commun 2023; 14:562. [PMID: 36732543 PMCID: PMC9894935 DOI: 10.1038/s41467-023-36181-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 01/19/2023] [Indexed: 02/04/2023] Open
Abstract
Flavin containing monooxygenases (FMOs) are promiscuous enzymes known for metabolizing a wide range of exogenous compounds. In C. elegans, fmo-2 expression increases lifespan and healthspan downstream of multiple longevity-promoting pathways through an unknown mechanism. Here, we report that, beyond its classification as a xenobiotic enzyme, fmo-2 expression leads to rewiring of endogenous metabolism principally through changes in one carbon metabolism (OCM). These changes are likely relevant, as we find that genetically modifying OCM enzyme expression leads to alterations in longevity that interact with fmo-2 expression. Using computer modeling, we identify decreased methylation as the major OCM flux modified by FMO-2 that is sufficient to recapitulate its longevity benefits. We further find that tryptophan is decreased in multiple mammalian FMO overexpression models and is a validated substrate for FMO-2. Our resulting model connects a single enzyme to two previously unconnected key metabolic pathways and provides a framework for the metabolic interconnectivity of longevity-promoting pathways such as dietary restriction. FMOs are well-conserved enzymes that are also induced by lifespan-extending interventions in mice, supporting a conserved and important role in promoting health and longevity through metabolic remodeling.
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Affiliation(s)
- Hyo Sub Choi
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Ajay Bhat
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Marshall B Howington
- Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Megan L Schaller
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Rebecca L Cox
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Shijiao Huang
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Safa Beydoun
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Hillary A Miller
- Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Angela M Tuckowski
- Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Joy Mecano
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Elizabeth S Dean
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Lindy Jensen
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Daniel A Beard
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Charles R Evans
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Scott F Leiser
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, 48109, USA.
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, 48109, USA.
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5
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Yang WH, Chen PH, Chang HH, Kwok HL, Stern A, Soo PC, Chen JH, Yang HC. Impaired immune response and barrier function in GSPD-1-deficient C. elegans infected with Klebsiella pneumoniae. CURRENT RESEARCH IN MICROBIAL SCIENCES 2023; 4:100181. [PMID: 36798906 PMCID: PMC9926097 DOI: 10.1016/j.crmicr.2023.100181] [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] [Indexed: 01/28/2023] Open
Abstract
gspd-1-RNAi knockdown Caenorhabditis elegans was used as an immune-compromised model to investigate the role of G6PD in host-pathogen interactions. A shorted lifespan, increased bacterial burden and bacterial translocation were observed in gspd-1-knockdown C. elegans infected with Klebsiella pneumoniae (KP). RNAseq revealed that the innate immune pathway, including clc-1 and tsp-1, was affected by gspd-1 knockdown. qPCR confirmed that tight junction (zoo-1, clc-1) and immune-associated genes (tsp-1) were down-regulated in gspd-1-knockdown C. elegans and following infection with KP. The down-regulation of antimicrobial effector lysozymes, including lys-1, lys-2, lys-7, lys-8, ilys-2 and ilys-3, was found in gspd-1-knockdown C. elegans infected with KP. Deletion of clc-1, tsp-1, lys-7, and daf-2 in gspd-1-knockdown C. elegans infected with KP abolished the shorten lifespan seen in the Mock control. GSPD-1 deficiency in C. elegans resulted in bacterial accumulation and lethality, possibly due to a defective immune response. These findings indicate that GSPD-1 has a protective role in microbial defense in C. elegans by preventing bacterial colonization through bacterial clearance.
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Affiliation(s)
- Wan-Hua Yang
- Department of Pathology and Laboratory Medicine, Taipei Veterans General Hospital, Hsinchu Branch, Hsinchu, Taiwan
| | - Po-Hsiang Chen
- Research Center for Chinese Herbal Medicine, Graduate Institute of Health Industry Technology, College of Human Ecology, Chang Gung University of Science and Technology, Taoyuan, Taiwan
| | - Hung-Hsin Chang
- Department of Medical Laboratory Science and Biotechnology, Yuanpei University of Medical Technology, Hsinchu 30041, Taiwan
| | - Hong Luen Kwok
- Department of Medical Laboratory Science and Biotechnology, Yuanpei University of Medical Technology, Hsinchu 30041, Taiwan
| | - Arnold Stern
- Grossman School of Medicine, New York University, New York, NY, USA
| | - Po-Chi Soo
- Department of Laboratory Medicine and Biotechnology, College of Medicine, Tzu Chi University, Hualien, Taiwan
| | - Jiun-Han Chen
- Department of Medical Laboratory Science and Biotechnology, Yuanpei University of Medical Technology, Hsinchu 30041, Taiwan
| | - Hung-Chi Yang
- Department of Medical Laboratory Science and Biotechnology, Yuanpei University of Medical Technology, Hsinchu 30041, Taiwan,Corresponding author.
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6
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Beaudoin-Chabot C, Wang L, Celik C, Abdul Khalid ATF, Thalappilly S, Xu S, Koh JH, Lim VWX, Low AD, Thibault G. The unfolded protein response reverses the effects of glucose on lifespan in chemically-sterilized C. elegans. Nat Commun 2022; 13:5889. [PMID: 36261415 PMCID: PMC9582010 DOI: 10.1038/s41467-022-33630-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 09/27/2022] [Indexed: 12/02/2022] Open
Abstract
Metabolic diseases often share common traits, including accumulation of unfolded proteins in the endoplasmic reticulum (ER). Upon ER stress, the unfolded protein response (UPR) is activated to limit cellular damage which weakens with age. Here, we show that Caenorhabditis elegans fed a bacterial diet supplemented high glucose at day 5 of adulthood (HGD-5) extends their lifespan, whereas exposed at day 1 (HGD-1) experience shortened longevity. We observed a metabolic shift only in HGD-1, while glucose and infertility synergistically prolonged the lifespan of HGD-5, independently of DAF-16. Notably, we identified that UPR stress sensors ATF-6 and PEK-1 contributed to the longevity of HGD-5 worms, while ire-1 ablation drastically increased HGD-1 lifespan. Together, we postulate that HGD activates the otherwise quiescent UPR in aged worms to overcome ageing-related stress and restore ER homeostasis. In contrast, young animals subjected to HGD provokes unresolved ER stress, conversely leading to a detrimental stress response.
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Affiliation(s)
| | - Lei Wang
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
- Department Physiology and Biophysics, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - Cenk Celik
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
| | | | - Subhash Thalappilly
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
| | - Shiyi Xu
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
| | - Jhee Hong Koh
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
| | - Venus Wen Xuan Lim
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
| | - Ann Don Low
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
| | - Guillaume Thibault
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore.
- Mechanobiology Institute, National University of Singapore, Singapore, 117411, Singapore.
- Institute of Molecular and Cell Biology, A*STAR, Singapore, 138673, Singapore.
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7
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Wang Y, Guo K, Wang Q, Zhong G, Zhang W, Jiang Y, Mao X, Li X, Huang Z. Caenorhabditis elegans as an emerging model in food and nutrition research: importance of standardizing base diet. Crit Rev Food Sci Nutr 2022; 64:3167-3185. [PMID: 36200941 DOI: 10.1080/10408398.2022.2130875] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
As a model organism that has helped revolutionize life sciences, Caenorhabditis elegans has been increasingly used in nutrition research. Here we explore the tradeoffs between pros and cons of its use as a dietary model based primarily on literature review from the past decade. We first provide an overview of its experimental strengths as an animal model, focusing on lifespan and healthspan, behavioral and physiological phenotypes, and conservation of key nutritional pathways. We then summarize recent advances of its use in nutritional studies, e.g. food preference and feeding behavior, sugar status and metabolic reprogramming, lifetime and transgenerational nutrition tracking, and diet-microbiota-host interactions, highlighting cutting-edge technologies originated from or developed in C. elegans. We further review current challenges of using C. elegans as a nutritional model, followed by in-depth discussions on potential solutions. In particular, growth scales and throughputs, food uptake mode, and axenic culture of C. elegans are appraised in the context of food research. We also provide perspectives for future development of chemically defined nematode food ("NemaFood") for C. elegans, which is now widely accepted as a versatile and affordable in vivo model and has begun to show transformative potential to pioneer nutrition science.
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Affiliation(s)
- Yuqing Wang
- Institute for Food Nutrition and Human Health, School of Food Science and Engineering, South China University of Technology, Guangzhou, China
- Guangdong Province Key Laboratory for Biocosmetics, Guangzhou, China
| | - Kaixin Guo
- Institute for Food Nutrition and Human Health, School of Food Science and Engineering, South China University of Technology, Guangzhou, China
- The First Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Qiangqiang Wang
- Institute for Food Nutrition and Human Health, School of Food Science and Engineering, South China University of Technology, Guangzhou, China
- Guangdong Province Key Laboratory for Biocosmetics, Guangzhou, China
| | - Guohuan Zhong
- Institute for Food Nutrition and Human Health, School of Food Science and Engineering, South China University of Technology, Guangzhou, China
- Center for Bioresources and Drug Discovery, School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, China
| | - Wenjun Zhang
- Center for Bioresources and Drug Discovery, School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, China
| | - Yiyi Jiang
- Guangdong Province Key Laboratory for Biocosmetics, Guangzhou, China
- Perfect Life & Health Institute, Zhongshan, Guangdong, China
| | - Xinliang Mao
- Guangdong Province Key Laboratory for Biocosmetics, Guangzhou, China
- Perfect Life & Health Institute, Zhongshan, Guangdong, China
| | - Xiaomin Li
- Guangdong Province Key Laboratory for Biocosmetics, Guangzhou, China
- Perfect Life & Health Institute, Zhongshan, Guangdong, China
| | - Zebo Huang
- Institute for Food Nutrition and Human Health, School of Food Science and Engineering, South China University of Technology, Guangzhou, China
- Guangdong Province Key Laboratory for Biocosmetics, Guangzhou, China
- Center for Bioresources and Drug Discovery, School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, China
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8
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Cai H, Wu P, Vandemeulebroucke L, Dhondt I, Rasulova M, Vierstraete A, Braeckman BP. Axenic Culture of Caenorhabditis elegans Alters Lysosomal/Proteasomal Balance and Increases Neuropeptide Expression. Int J Mol Sci 2022; 23:11517. [PMID: 36232823 PMCID: PMC9570027 DOI: 10.3390/ijms231911517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 09/23/2022] [Accepted: 09/26/2022] [Indexed: 11/21/2022] Open
Abstract
Axenically cultured C. elegans show many characteristic traits of worms subjected to dietary restriction, such as slowed development, reduced fertility, and increased stress resistance. Hence, the term axenic dietary restriction (ADR) is often applied. ADR dramatically extends the worm lifespan compared to other DR regimens such as bacterial dilution. However, the underlying molecular mechanisms still remain unclear. The primary goal of this study is to comprehensively investigate transcriptional alterations that occur when worms are subjected to ADR and to estimate the molecular and physiological changes that may underlie ADR-induced longevity. One of the most enriched clusters of up-regulated genes under ADR conditions is linked to lysosomal activity, while proteasomal genes are significantly down-regulated. The up-regulation of genes specifically involved in amino acid metabolism is likely a response to the high peptide levels found in axenic culture medium. Genes related to the integrity and function of muscles and the extracellular matrix are also up-regulated. Consistent down-regulation of genes involved in DNA replication and repair may reflect the reduced fertility phenotype of ADR worms. Neuropeptide genes are found to be largely up-regulated, suggesting a possible involvement of neuroendocrinal signaling in ADR-induced longevity. In conclusion, axenically cultured worms seem to rely on increased amino acid catabolism, relocate protein breakdown from the cytosol to the lysosomes, and do not invest in DNA maintenance but rather retain muscle integrity and the extracellular matrix. All these changes may be coordinated by peptidergic signaling.
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Affiliation(s)
- Huaihan Cai
- Laboratory of Aging Physiology and Molecular Evolution, Department of Biology, Ghent University, 9000 Ghent, Belgium
- Overseas Pharmaceuticals, Ltd., Room 201, Building C1, No. 11 Kaiyuan Avenue, Huangpu District, Guangzhou 510530, China
| | - Ping Wu
- Laboratory of Aging Physiology and Molecular Evolution, Department of Biology, Ghent University, 9000 Ghent, Belgium
| | - Lieselot Vandemeulebroucke
- Laboratory of Aging Physiology and Molecular Evolution, Department of Biology, Ghent University, 9000 Ghent, Belgium
| | - Ineke Dhondt
- Laboratory of Aging Physiology and Molecular Evolution, Department of Biology, Ghent University, 9000 Ghent, Belgium
| | - Madina Rasulova
- Laboratory of Aging Physiology and Molecular Evolution, Department of Biology, Ghent University, 9000 Ghent, Belgium
| | - Andy Vierstraete
- Laboratory of Aging Physiology and Molecular Evolution, Department of Biology, Ghent University, 9000 Ghent, Belgium
| | - Bart P. Braeckman
- Laboratory of Aging Physiology and Molecular Evolution, Department of Biology, Ghent University, 9000 Ghent, Belgium
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9
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Lefoulon E, McMullen JG, Stock SP. Transcriptomic Analysis of Steinernema Nematodes Highlights Metabolic Costs Associated to Xenorhabdus Endosymbiont Association and Rearing Conditions. Front Physiol 2022; 13:821845. [PMID: 35283769 PMCID: PMC8914265 DOI: 10.3389/fphys.2022.821845] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 02/01/2022] [Indexed: 12/13/2022] Open
Abstract
Entomopathogenic nematodes of the genus Steinernema have a mutualistic relationship with bacteria of the genus Xenorhabdus and together they form an antagonist partnership against their insect hosts. The nematodes (third-stage infective juveniles, or IJs) protect the bacteria from the external environmental stressors and vector them from one insect host to another. Xenorhabdus produce secondary metabolites and antimicrobial compounds inside the insect that protect the cadaver from soil saprobes and scavengers. The bacteria also become the nematodes’ food, allowing them to grow and reproduce. Despite these benefits, it is yet unclear what the potential metabolic costs for Steinernema IJs are relative to the maintenance and vectoring of Xenorhabdus. In this study, we performed a comparative dual RNA-seq analysis of IJs of two nematode-bacteria partnerships: Steinernema carpocapsae-Xenorhabdus nematophila and Steinernema. puntauvense-Xenorhbdus bovienii. For each association, three conditions were studied: (1) IJs reared in the insect (in vivo colonized), (2) colonized IJs reared on liver-kidney agar (in vitro colonized), and (3) IJs depleted by the bacteria reared on liver-kidney agar (in vitro aposymbiotic). Our study revealed the downregulation of numerous genes involved in metabolism pathways, such as carbohydrate, amino acid, and lipid metabolism when IJs were reared in vitro, both colonized and without the symbiont. This downregulation appears to impact the longevity pathway, with the involvement of glycogen and trehalose metabolism, as well as arginine metabolism. Additionally, a differential expression of the venom protein known to be secreted by the nematodes was observed when both Steinernema species were depleted of their symbiotic partners. These results suggest Steinernema IJs may have a mechanism to adapt their virulence in absence of their symbionts.
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Affiliation(s)
- Emilie Lefoulon
- School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, AZ, United States
| | - John G. McMullen
- Department of Biology, Indiana University, Bloomington, IN, United States
| | - S. Patricia Stock
- School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, AZ, United States
- College of Agriculture, California State University Chico, Chico, CA, United States
- *Correspondence: S. Patricia Stock,
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10
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Zečić A, Dhondt I, Braeckman BP. Accumulation of Glycogen and Upregulation of LEA-1 in C. elegans daf-2(e1370) Support Stress Resistance, Not Longevity. Cells 2022; 11:245. [PMID: 35053361 PMCID: PMC8773926 DOI: 10.3390/cells11020245] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 12/26/2021] [Accepted: 01/07/2022] [Indexed: 02/04/2023] Open
Abstract
DAF-16-dependent activation of a dauer-associated genetic program in the C. elegans insulin/IGF-1 daf-2(e1370) mutant leads to accumulation of large amounts of glycogen with concomitant upregulation of glycogen synthase, GSY-1. Glycogen is a major storage sugar in C. elegans that can be used as a short-term energy source for survival, and possibly as a reservoir for synthesis of a chemical chaperone trehalose. Its role in mitigating anoxia, osmotic and oxidative stress has been demonstrated previously. Furthermore, daf-2 mutants show increased abundance of the group 3 late embryogenesis abundant protein LEA-1, which has been found to act in synergy with trehalose to exert its protective role against desiccation and heat stress in vitro, and to be essential for desiccation tolerance in C. elegans dauer larvae. Here we demonstrate that accumulated glycogen is not required for daf-2 longevity, but specifically protects against hyperosmotic stress, and serves as an important energy source during starvation. Similarly, lea-1 does not act to support daf-2 longevity. Instead, it contributes to increased resistance of daf-2 mutants to heat, osmotic, and UV stress. In summary, our experimental results suggest that longevity and stress resistance can be uncoupled in IIS longevity mutants.
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Affiliation(s)
| | | | - Bart P. Braeckman
- Laboratory of Aging Physiology and Molecular Evolution, Department of Biology, Ghent University, K. L. Ledeganckstraat 35, B-9000 Ghent, Belgium; (A.Z.); (I.D.)
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11
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Shi J, Wang Y, Lei Y, Chen X, Liu Y, Xu YJ. Lipidome reveals the alleviation of krill oil on the impairment of acrylamide. Food Funct 2022; 13:8012-8021. [DOI: 10.1039/d2fo00781a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Krill oil has rich content of polyunsaturated fatty acids and various biological functions. Previous researches have demonstrated that krill oil is helpful to improve the locomotion via antioxidation and regulation...
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12
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Thomas MJ, Cassidy ER, Robinson DS, Walstrom KM. Kinetic characterization and thermostability of C. elegans cytoplasmic and mitochondrial malate dehydrogenases. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2021; 1870:140722. [PMID: 34619358 DOI: 10.1016/j.bbapap.2021.140722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 09/30/2021] [Accepted: 10/01/2021] [Indexed: 10/20/2022]
Abstract
Malate dehydrogenase (MDH) catalyzes the conversion of NAD+ and malate to NADH and oxaloacetate in the citric acid cycle. Eukaryotes have one MDH isozyme that is imported into the mitochondria and one in the cytoplasm. We overexpressed and purified Caenorhabditis elegans cytoplasmic MDH-1 and mitochondrial MDH-2 in E. coli. Our goal was to compare the kinetic and structural properties of these enzymes because C. elegans can survive adverse environmental conditions, such as lack of food and elevated temperatures. In steady-state enzyme kinetics assays, we measured KM values for oxaloacetate of 54 and 52 μM and KM values for NADH of 61 and 107 μM for MDH-1 and MDH-2, respectively. We partially purified endogenous MDH-1 and MDH-2 from a mixed population of worms and separated them using anion exchange chromatography. Both endogenous enzymes had a KM for oxaloacetate similar to that of the corresponding recombinant enzyme. Recombinant MDH-1 and MDH-2 had maximum activity at 40 °C and 35 °C, respectively. In a thermotolerance assay, MDH-1 was much more thermostable than MDH-2. Protein homology modeling predicted that MDH-1 had more intersubunit salt-bridges than mammalian MDH1 enzymes, and these ionic interactions may contribute to its thermostability. In contrast, the MDH-2 homology model predicted fewer intersubunit ionic interactions compared to mammalian MDH2 enzymes. These results suggest that the increased stability of MDH-1 may facilitate its ability to remain active in adverse environmental conditions. In contrast, MDH-2 may use other strategies, such as protein binding partners, to function under similar conditions.
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Affiliation(s)
- Matthew J Thomas
- Department of Natural Sciences, State College of Florida, Bradenton, FL 34207, USA
| | - Emma R Cassidy
- Division of Natural Sciences, New College of Florida, Sarasota, FL 34243, USA
| | - Devin S Robinson
- Division of Natural Sciences, New College of Florida, Sarasota, FL 34243, USA
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13
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Li WJ, Wang CW, Tao L, Yan YH, Zhang MJ, Liu ZX, Li YX, Zhao HQ, Li XM, He XD, Xue Y, Dong MQ. Insulin signaling regulates longevity through protein phosphorylation in Caenorhabditis elegans. Nat Commun 2021; 12:4568. [PMID: 34315882 PMCID: PMC8316574 DOI: 10.1038/s41467-021-24816-z] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 07/01/2021] [Indexed: 12/22/2022] Open
Abstract
Insulin/IGF-1 Signaling (IIS) is known to constrain longevity by inhibiting the transcription factor FOXO. How phosphorylation mediated by IIS kinases regulates lifespan beyond FOXO remains unclear. Here, we profile IIS-dependent phosphorylation changes in a large-scale quantitative phosphoproteomic analysis of wild-type and three IIS mutant Caenorhabditis elegans strains. We quantify more than 15,000 phosphosites and find that 476 of these are differentially phosphorylated in the long-lived daf-2/insulin receptor mutant. We develop a machine learning-based method to prioritize 25 potential lifespan-related phosphosites. We perform validations to show that AKT-1 pT492 inhibits DAF-16/FOXO and compensates the loss of daf-2 function, that EIF-2α pS49 potently inhibits protein synthesis and daf-2 longevity, and that reduced phosphorylation of multiple germline proteins apparently transmits reduced DAF-2 signaling to the soma. In addition, an analysis of kinases with enriched substrates detects that casein kinase 2 (CK2) subunits negatively regulate lifespan. Our study reveals detailed functional insights into longevity.
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Affiliation(s)
- Wen-Jun Li
- School of Life Sciences, Peking University, Beijing, China
- National Institute of Biological Sciences, Beijing, China
| | - Chen-Wei Wang
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Nanjing University Institute of Artificial Intelligence Biomedicine, Nanjing, Jiangsu, China
| | - Li Tao
- National Institute of Biological Sciences, Beijing, China
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Yong-Hong Yan
- National Institute of Biological Sciences, Beijing, China
| | - Mei-Jun Zhang
- National Institute of Biological Sciences, Beijing, China
- Annoroad Gene Tech. Co., Ltd., Beijing, China
| | - Ze-Xian Liu
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Yu-Xin Li
- National Institute of Biological Sciences, Beijing, China
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Han-Qing Zhao
- National Institute of Biological Sciences, Beijing, China
| | - Xue-Mei Li
- School of Life Sciences, Peking University, Beijing, China
- National Institute of Biological Sciences, Beijing, China
| | - Xian-Dong He
- National Institute of Biological Sciences, Beijing, China
| | - Yu Xue
- Key Laboratory of Molecular Biophysics of Ministry of Education, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Center for Artificial Intelligence Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China.
- Nanjing University Institute of Artificial Intelligence Biomedicine, Nanjing, Jiangsu, China.
| | - Meng-Qiu Dong
- National Institute of Biological Sciences, Beijing, China.
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, China.
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14
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Lourenço AB, Rodríguez-Palero MJ, Doherty MK, Cabrerizo Granados D, Hernando-Rodríguez B, Salas JJ, Venegas-Calerón M, Whitfield PD, Artal-Sanz M. The Mitochondrial PHB Complex Determines Lipid Composition and Interacts With the Endoplasmic Reticulum to Regulate Ageing. Front Physiol 2021; 12:696275. [PMID: 34276415 PMCID: PMC8281979 DOI: 10.3389/fphys.2021.696275] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 06/03/2021] [Indexed: 11/13/2022] Open
Abstract
Metabolic disorders are frequently associated with physiological changes that occur during ageing. The mitochondrial prohibitin complex (PHB) is an evolutionary conserved context-dependent modulator of longevity, which has been linked to alterations in lipid metabolism but which biochemical function remains elusive. In this work we aimed at elucidating the molecular mechanism by which depletion of mitochondrial PHB shortens the lifespan of wild type animals while it extends that of insulin signaling receptor (daf-2) mutants. A liquid chromatography coupled with mass spectrometry approach was used to characterize the worm lipidome of wild type and insulin deficient animals upon PHB depletion. Toward a mechanistic interpretation of the insights coming from this analysis, we used a combination of biochemical, microscopic, and lifespan analyses. We show that PHB depletion perturbed glycerophospholipids and glycerolipids pools differently in short- versus long-lived animals. Interestingly, PHB depletion in otherwise wild type animals induced the endoplasmic reticulum (ER) unfolded protein response (UPR), which was mitigated in daf-2 mutants. Moreover, depletion of DNJ-21, which functionally interacts with PHB in mitochondria, mimicked the effect of PHB deficiency on the UPRER and on the lifespan of wild type and insulin signaling deficient mutants. Our work shows that PHB differentially modulates lipid metabolism depending on the worm’s metabolic status and provides evidences for a new link between PHB and ER homeostasis in ageing regulation.
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Affiliation(s)
- Artur B Lourenço
- Andalusian Centre for Developmental Biology (CABD), CSIC-Universidad Pablo de Olavide-Junta de Andalucía, Seville, Spain.,Department of Molecular Biology and Biochemical Engineering, Universidad Pablo de Olavide, Seville, Spain
| | - María Jesús Rodríguez-Palero
- Andalusian Centre for Developmental Biology (CABD), CSIC-Universidad Pablo de Olavide-Junta de Andalucía, Seville, Spain.,Department of Molecular Biology and Biochemical Engineering, Universidad Pablo de Olavide, Seville, Spain
| | - Mary K Doherty
- Division of Biomedical Science, University of the Highlands and Islands, Inverness, United Kingdom
| | - David Cabrerizo Granados
- Andalusian Centre for Developmental Biology (CABD), CSIC-Universidad Pablo de Olavide-Junta de Andalucía, Seville, Spain.,Department of Molecular Biology and Biochemical Engineering, Universidad Pablo de Olavide, Seville, Spain
| | - Blanca Hernando-Rodríguez
- Andalusian Centre for Developmental Biology (CABD), CSIC-Universidad Pablo de Olavide-Junta de Andalucía, Seville, Spain.,Department of Molecular Biology and Biochemical Engineering, Universidad Pablo de Olavide, Seville, Spain
| | - Joaquín J Salas
- Instituto de la Grasa (CSIC), Universidad Pablo de Olavide, Seville, Spain
| | | | - Phillip D Whitfield
- Division of Biomedical Science, University of the Highlands and Islands, Inverness, United Kingdom
| | - Marta Artal-Sanz
- Andalusian Centre for Developmental Biology (CABD), CSIC-Universidad Pablo de Olavide-Junta de Andalucía, Seville, Spain.,Department of Molecular Biology and Biochemical Engineering, Universidad Pablo de Olavide, Seville, Spain
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15
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Pereira CV, Gitschlag BL, Patel MR. Cellular mechanisms of mtDNA heteroplasmy dynamics. Crit Rev Biochem Mol Biol 2021; 56:510-525. [PMID: 34120542 DOI: 10.1080/10409238.2021.1934812] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Heteroplasmy refers to the coexistence of more than one variant of the mitochondrial genome (mtDNA). Mutated or partially deleted mtDNAs can induce chronic metabolic impairment and cause mitochondrial diseases when their heteroplasmy levels exceed a critical threshold. These mutant mtDNAs can be maternally inherited or can arise de novo. Compelling evidence has emerged showing that mutant mtDNA levels can vary and change in a nonrandom fashion across generations and amongst tissues of an individual. However, our lack of understanding of the basic cellular and molecular mechanisms of mtDNA heteroplasmy dynamics has made it difficult to predict who will inherit or develop mtDNA-associated diseases. More recently, with the advances in technology and the establishment of tractable model systems, insights into the mechanisms underlying the selection forces that modulate heteroplasmy dynamics are beginning to emerge. In this review, we summarize evidence from different organisms, showing that mutant mtDNA can experience both positive and negative selection. We also review the recently identified mechanisms that modulate heteroplasmy dynamics. Taken together, this is an opportune time to survey the literature and to identify key cellular pathways that can be targeted to develop therapies for diseases caused by heteroplasmic mtDNA mutations.
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Affiliation(s)
- Claudia V Pereira
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - Bryan L Gitschlag
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - Maulik R Patel
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA.,Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA.,Diabetes Research and Training Center, Vanderbilt University School of Medicine, Nashville, TN, USA
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16
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Haçariz O, Viau C, Karimian F, Xia J. The symbiotic relationship between Caenorhabditis elegans and members of its microbiome contributes to worm fitness and lifespan extension. BMC Genomics 2021; 22:364. [PMID: 34011272 PMCID: PMC8136213 DOI: 10.1186/s12864-021-07695-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 05/10/2021] [Indexed: 12/15/2022] Open
Abstract
Background A healthy microbiome influences host physiology through a mutualistic relationship, which can be important for the host to cope with cellular stress by promoting fitness and survival. The mammalian microbiome is highly complex and attributing host phenotypes to a specific member of the microbiome can be difficult. The model organism Caenorhabditis elegans and its native microbiome, discovered recently, can serve as a more tractable, experimental model system to study host-microbiome interactions. In this study, we investigated whether certain members of C. elegans native microbiome would offer a benefit to their host and putative molecular mechanisms using a combination of phenotype screening, omics profiling and functional validation. Results A total of 16 members of C. elegans microbiome were screened under chemically-induced toxicity. Worms grown with Chryseobacterium sp. CHNTR56 MYb120 or Comamonas sp. 12022 MYb131, were most resistant to oxidative chemical stress (SiO2 nanoparticles and juglone), as measured by progeny output. Further investigation showed that Chryseobacterium sp. CHNTR56 positively influenced the worm’s lifespan, whereas the combination of both isolates had a synergistic effect. RNAseq analysis of young adult worms, grown with either isolate, revealed the enrichment of cellular detoxification mechanisms (glutathione metabolism, drug metabolism and metabolism of xenobiotics) and signaling pathways (TGF-beta and Wnt signaling pathways). Upregulation of cysteine synthases (cysl genes) in the worms, associated with glutathione metabolism, was also observed. Nanopore sequencing uncovered that the genomes of the two isolates have evolved to favor the specific route of the de novo synthesis pathway of vitamin B6 (cofactor of cysl enzymes) through serC or pdxA2 homologs. Finally, co-culture with vitamin B6 extended worm lifespan. Conclusions In summary, our study indicates that certain colonizing members of C. elegans have genomic diversity in vitamin B6 synthesis and promote host fitness and lifespan extension. The regulation of host cellular detoxification genes (i.e. gst) along with cysl genes at the transcriptome level and the bacterium-specific vitamin B6 synthesis mechanism at the genome level are in an agreement with enhanced host glutathione-based cellular detoxification due to this interspecies relationship. C. elegans is therefore a promising alternative model to study host-microbiome interactions in host fitness and lifespan. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07695-y.
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Affiliation(s)
- Orçun Haçariz
- Institute of Parasitology, McGill University, Montreal, Quebec, Canada
| | - Charles Viau
- Institute of Parasitology, McGill University, Montreal, Quebec, Canada
| | - Farial Karimian
- Institute of Parasitology, McGill University, Montreal, Quebec, Canada
| | - Jianguo Xia
- Institute of Parasitology, McGill University, Montreal, Quebec, Canada. .,Department of Animal Science, McGill University, Montreal, Quebec, Canada.
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17
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Salzer L, Witting M. Quo Vadis Caenorhabditis elegans Metabolomics-A Review of Current Methods and Applications to Explore Metabolism in the Nematode. Metabolites 2021; 11:metabo11050284. [PMID: 33947148 PMCID: PMC8146106 DOI: 10.3390/metabo11050284] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 04/27/2021] [Accepted: 04/28/2021] [Indexed: 12/11/2022] Open
Abstract
Metabolomics and lipidomics recently gained interest in the model organism Caenorhabditis elegans (C. elegans). The fast development, easy cultivation and existing forward and reverse genetic tools make the small nematode an ideal organism for metabolic investigations in development, aging, different disease models, infection, or toxicology research. The conducted type of analysis is strongly depending on the biological question and requires different analytical approaches. Metabolomic analyses in C. elegans have been performed using nuclear magnetic resonance (NMR) spectroscopy, direct infusion mass spectrometry (DI-MS), gas-chromatography mass spectrometry (GC-MS) and liquid chromatography mass spectrometry (LC-MS) or combinations of them. In this review we provide general information on the employed techniques and their advantages and disadvantages in regard to C. elegans metabolomics. Additionally, we reviewed different fields of application, e.g., longevity, starvation, aging, development or metabolism of secondary metabolites such as ascarosides or maradolipids. We also summarised applied bioinformatic tools that recently have been used for the evaluation of metabolomics or lipidomics data from C. elegans. Lastly, we curated metabolites and lipids from the reviewed literature, enabling a prototypic collection which serves as basis for a future C. elegans specific metabolome database.
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Affiliation(s)
- Liesa Salzer
- Research Unit Analytical BioGeoChemistry, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany;
| | - Michael Witting
- Research Unit Analytical BioGeoChemistry, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany;
- Metabolomics and Proteomics Core, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
- Chair of Analytical Food Chemistry, TUM School of Life Sciences, Technical University of Munich, Maximus-von-Imhof-Forum 2, 85354 Freising, Germany
- Correspondence:
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18
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Acetyl-CoA Metabolism and Histone Acetylation in the Regulation of Aging and Lifespan. Antioxidants (Basel) 2021; 10:antiox10040572. [PMID: 33917812 PMCID: PMC8068152 DOI: 10.3390/antiox10040572] [Citation(s) in RCA: 65] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 03/31/2021] [Accepted: 04/02/2021] [Indexed: 12/16/2022] Open
Abstract
Acetyl-CoA is a metabolite at the crossroads of central metabolism and the substrate of histone acetyltransferases regulating gene expression. In many tissues fasting or lifespan extending calorie restriction (CR) decreases glucose-derived metabolic flux through ATP-citrate lyase (ACLY) to reduce cytoplasmic acetyl-CoA levels to decrease activity of the p300 histone acetyltransferase (HAT) stimulating pro-longevity autophagy. Because of this, compounds that decrease cytoplasmic acetyl-CoA have been described as CR mimetics. But few authors have highlighted the potential longevity promoting roles of nuclear acetyl-CoA. For example, increasing nuclear acetyl-CoA levels increases histone acetylation and administration of class I histone deacetylase (HDAC) inhibitors increases longevity through increased histone acetylation. Therefore, increased nuclear acetyl-CoA likely plays an important role in promoting longevity. Although cytoplasmic acetyl-CoA synthetase 2 (ACSS2) promotes aging by decreasing autophagy in some peripheral tissues, increased glial AMPK activity or neuronal differentiation can stimulate ACSS2 nuclear translocation and chromatin association. ACSS2 nuclear translocation can result in increased activity of CREB binding protein (CBP), p300/CBP-associated factor (PCAF), and other HATs to increase histone acetylation on the promoter of neuroprotective genes including transcription factor EB (TFEB) target genes resulting in increased lysosomal biogenesis and autophagy. Much of what is known regarding acetyl-CoA metabolism and aging has come from pioneering studies with yeast, fruit flies, and nematodes. These studies have identified evolutionary conserved roles for histone acetylation in promoting longevity. Future studies should focus on the role of nuclear acetyl-CoA and histone acetylation in the control of hypothalamic inflammation, an important driver of organismal aging.
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19
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Rasulova M, Zečić A, Monje Moreno JM, Vandemeulebroucke L, Dhondt I, Braeckman BP. Elevated Trehalose Levels in C. elegans daf-2 Mutants Increase Stress Resistance, Not Lifespan. Metabolites 2021; 11:metabo11020105. [PMID: 33673074 PMCID: PMC7917784 DOI: 10.3390/metabo11020105] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 02/04/2021] [Accepted: 02/10/2021] [Indexed: 12/20/2022] Open
Abstract
The C. elegans insulin/IGF-1 (insulin-like growth factor 1) signaling mutant daf-2 recapitulates the dauer metabolic signature—a shift towards lipid and carbohydrate accumulation—which may be linked to its longevity and stress resistance phenotypes. Trehalose, a disaccharide of glucose, is highly upregulated in daf‑2 mutants and it has been linked to proteome stabilization and protection against heat, cold, desiccation, and hypoxia. Earlier studies suggested that elevated trehalose levels can explain up to 43% of the lifespan extension observed in daf-2 mutants. Here we demonstrate that trehalose accumulation is responsible for increased osmotolerance, and to some degree thermotolerance, rather than longevity in daf-2 mutants. This indicates that particular stress resistance phenotypes can be uncoupled from longevity.
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20
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Gitschlag BL, Tate AT, Patel MR. Nutrient status shapes selfish mitochondrial genome dynamics across different levels of selection. eLife 2020; 9:56686. [PMID: 32959778 PMCID: PMC7508553 DOI: 10.7554/elife.56686] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 08/17/2020] [Indexed: 12/23/2022] Open
Abstract
Cooperation and cheating are widespread evolutionary strategies. While cheating confers an advantage to individual entities within a group, competition between groups favors cooperation. Selfish or cheater mitochondrial DNA (mtDNA) proliferates within hosts while being selected against at the level of host fitness. How does environment shape cheater dynamics across different selection levels? Focusing on food availability, we address this question using heteroplasmic Caenorhabditis elegans. We find that the proliferation of selfish mtDNA within hosts depends on nutrient status stimulating mtDNA biogenesis in the developing germline. Interestingly, mtDNA biogenesis is not sufficient for this proliferation, which also requires the stress-response transcription factor FoxO/DAF-16. At the level of host fitness, FoxO/DAF-16 also prevents food scarcity from accelerating the selection against selfish mtDNA. This suggests that the ability to cope with nutrient stress can promote host tolerance of cheaters. Our study delineates environmental effects on selfish mtDNA dynamics at different levels of selection.
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Affiliation(s)
- Bryan L Gitschlag
- Department of Biological Sciences, Vanderbilt University, Nashville, United States
| | - Ann T Tate
- Department of Biological Sciences, Vanderbilt University, Nashville, United States
| | - Maulik R Patel
- Department of Biological Sciences, Vanderbilt University, Nashville, United States.,Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, United States.,Diabetes Research and Training Center, Vanderbilt University School of Medicine, Nashville, United States
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21
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Kim J, Lee SH, Cho M, Lee JY, Choi DH, Lee HY, Cho S, Min KJ, Suh Y. Small Molecule from Natural Phytochemical Mimics Dietary Restriction by Modulating FoxO3a and Metabolic Reprogramming. ACTA ACUST UNITED AC 2020; 4:e1900248. [PMID: 32558394 DOI: 10.1002/adbi.201900248] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2019] [Revised: 03/08/2020] [Indexed: 01/10/2023]
Abstract
Many studies utilizing animal models have revealed the genetic and pharmacogenetic modulators of the rate of organismal aging. However, finding routes for healthy aging during extended life remains one of the largest questions. With regards to an antiaging reagent, it has been shown that natural phytochemical syringaresinol (SYR) delays cellular senescence by activating sirtuin1 (SIRT1). Here, it is found that SYR treatment results in metabolic changes similar to those observed during dietary restriction (DR). The DR mimetic effects are mediated by FoxO3a-dependent SIRT1 activation and insulin/insuline growth factor-1 signaling modulation. The direct binding of SYR-FoxO3a is identified and this could partially explain the DR-like phenotype. The report gives a clue as to how the longevity gene involves the DR pathway and suggests that natural phytochemicals applied as a geroprotector mimics DR effects.
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Affiliation(s)
- Juewon Kim
- Bioscience Research Lab, R&D Unit, Amorepacific Corporation, Yongin, 17074, South Korea
| | - Shin-Hae Lee
- Department of Biological Sciences, Inha University, Incheon, 22201, South Korea
| | - Miook Cho
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Jee-Young Lee
- Molecular Design Team, New Drug Development Center, Daegu-Gyeongbuk Medical Innovation Foundation (DGMIF), Daegu, 41061, South Korea
| | - Dong-Hwa Choi
- Biocenter, Gyeonggido Business and Science Accelerator, Suwon, 16229, South Korea
| | - Hye-Yeon Lee
- Department of Biological Sciences, Inha University, Incheon, 22201, South Korea
| | - Siyoung Cho
- Bioscience Research Lab, R&D Unit, Amorepacific Corporation, Yongin, 17074, South Korea
| | - Kyung-Jin Min
- Department of Biological Sciences, Inha University, Incheon, 22201, South Korea
| | - Yousin Suh
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
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22
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Penkov S, Raghuraman BK, Erkut C, Oertel J, Galli R, Ackerman EJM, Vorkel D, Verbavatz JM, Koch E, Fahmy K, Shevchenko A, Kurzchalia TV. A metabolic switch regulates the transition between growth and diapause in C. elegans. BMC Biol 2020; 18:31. [PMID: 32188449 PMCID: PMC7081555 DOI: 10.1186/s12915-020-0760-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Accepted: 02/27/2020] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Metabolic activity alternates between high and low states during different stages of an organism's life cycle. During the transition from growth to quiescence, a major metabolic shift often occurs from oxidative phosphorylation to glycolysis and gluconeogenesis. We use the entry of Caenorhabditis elegans into the dauer larval stage, a developmentally arrested stage formed in response to harsh environmental conditions, as a model to study the global metabolic changes and underlying molecular mechanisms associated with growth to quiescence transition. RESULTS Here, we show that the metabolic switch involves the concerted activity of several regulatory pathways. Whereas the steroid hormone receptor DAF-12 controls dauer morphogenesis, the insulin pathway maintains low energy expenditure through DAF-16/FoxO, which also requires AAK-2/AMPKα. DAF-12 and AAK-2 separately promote a shift in the molar ratios between competing enzymes at two key branch points within the central carbon metabolic pathway diverting carbon atoms from the TCA cycle and directing them to gluconeogenesis. When both AAK-2 and DAF-12 are suppressed, the TCA cycle is active and the developmental arrest is bypassed. CONCLUSIONS The metabolic status of each developmental stage is defined by stoichiometric ratios within the constellation of metabolic enzymes driving metabolic flux and controls the transition between growth and quiescence.
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Affiliation(s)
- Sider Penkov
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany. .,Paul Langerhans Institute Dresden of the Helmholtz Zentrum München at the University Hospital and Faculty of Medicine Carl Gustav Carus of TU Dresden, Dresden, Germany. .,Institute for Clinical Chemistry and Laboratory Medicine, University Clinic and Medical Faculty, TU Dresden, Dresden, Germany.
| | | | - Cihan Erkut
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.,Present address: German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jana Oertel
- Institute of Resource Ecology at the Helmholtz-Zentrum Dresden-Rossendorf, Dresden, Germany
| | - Roberta Galli
- Faculty of Medicine Carl Gustav Carus, Department of Anesthesiology and Intensive Care Medicine, Clinical Sensoring and Monitoring, TU Dresden, Dresden, Germany
| | | | - Daniela Vorkel
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Jean-Marc Verbavatz
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.,Institut Jacques Monod, Université de Paris/CNRS, Paris, France
| | - Edmund Koch
- Faculty of Medicine Carl Gustav Carus, Department of Anesthesiology and Intensive Care Medicine, Clinical Sensoring and Monitoring, TU Dresden, Dresden, Germany
| | - Karim Fahmy
- Institute of Resource Ecology at the Helmholtz-Zentrum Dresden-Rossendorf, Dresden, Germany
| | - Andrej Shevchenko
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
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23
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DAF-16/FoxO in Caenorhabditis elegans and Its Role in Metabolic Remodeling. Cells 2020; 9:cells9010109. [PMID: 31906434 PMCID: PMC7017163 DOI: 10.3390/cells9010109] [Citation(s) in RCA: 88] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 12/30/2019] [Accepted: 12/31/2019] [Indexed: 12/31/2022] Open
Abstract
DAF-16, the only forkhead box transcription factors class O (FoxO) homolog in Caenorhabditis elegans, integrates signals from upstream pathways to elicit transcriptional changes in many genes involved in aging, development, stress, metabolism, and immunity. The major regulator of DAF-16 activity is the insulin/insulin-like growth factor 1 (IGF-1) signaling (IIS) pathway, reduction of which leads to lifespan extension in worms, flies, mice, and humans. In C. elegans daf-2 mutants, reduced IIS leads to a heterochronic activation of a dauer survival program during adulthood. This program includes elevated antioxidant defense and a metabolic shift toward accumulation of carbohydrates (i.e., trehalose and glycogen) and triglycerides, and activation of the glyoxylate shunt, which could allow fat-to-carbohydrate conversion. The longevity of daf-2 mutants seems to be partially supported by endogenous trehalose, a nonreducing disaccharide that mammals cannot synthesize, which points toward considerable differences in downstream mechanisms by which IIS regulates aging in distinct groups.
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24
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Cytoplasmic and Mitochondrial NADPH-Coupled Redox Systems in the Regulation of Aging. Nutrients 2019; 11:nu11030504. [PMID: 30818813 PMCID: PMC6471790 DOI: 10.3390/nu11030504] [Citation(s) in RCA: 91] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 02/20/2019] [Accepted: 02/21/2019] [Indexed: 12/20/2022] Open
Abstract
The reduced form of nicotinamide adenine dinucleotide phosphate (NADPH) protects against redox stress by providing reducing equivalents to antioxidants such as glutathione and thioredoxin. NADPH levels decline with aging in several tissues, but whether this is a major driving force for the aging process has not been well established. Global or neural overexpression of several cytoplasmic enzymes that synthesize NADPH have been shown to extend lifespan in model organisms such as Drosophila suggesting a positive relationship between cytoplasmic NADPH levels and longevity. Mitochondrial NADPH plays an important role in the protection against redox stress and cell death and mitochondrial NADPH-utilizing thioredoxin reductase 2 levels correlate with species longevity in cells from rodents and primates. Mitochondrial NADPH shuttles allow for some NADPH flux between the cytoplasm and mitochondria. Since a decline of nicotinamide adenine dinucleotide (NAD+) is linked with aging and because NADP+ is exclusively synthesized from NAD+ by cytoplasmic and mitochondrial NAD+ kinases, a decline in the cytoplasmic or mitochondrial NADPH pool may also contribute to the aging process. Therefore pro-longevity therapies should aim to maintain the levels of both NAD+ and NADPH in aging tissues.
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25
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Gao AW, Smith RL, van Weeghel M, Kamble R, Janssens GE, Houtkooper RH. Identification of key pathways and metabolic fingerprints of longevity in C. elegans. Exp Gerontol 2018; 113:128-140. [PMID: 30300667 PMCID: PMC6224709 DOI: 10.1016/j.exger.2018.10.003] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2018] [Revised: 08/16/2018] [Accepted: 10/04/2018] [Indexed: 12/22/2022]
Abstract
Impaired insulin/IGF-1 signaling (IIS) and caloric restriction (CR) prolong lifespan in the nematode C. elegans. However, a cross comparison of these longevity pathways using a multi-omics integration approach is lacking. In this study, we aimed to identify key pathways and metabolite fingerprints of longevity that are shared between IIS and CR worm models using multi-omics integration. We generated transcriptomics and metabolomics data from long-lived worm strains, i.e. daf-2 (impaired IIS) and eat-2 (CR model) and compared them with the wild-type strain N2. Transcriptional profiling identified shared longevity signatures, such as an upregulation of lipid storage and defense responses, and downregulation of macromolecule synthesis and developmental processes. Metabolomics profiling identified an increase in the levels of glycerol‑3P, adenine, xanthine, and AMP, and a decrease in the levels of the amino acid pool, as well as the C18:0, C17:1, C19:1, C20:0 and C22:0 fatty acids. After we integrated transcriptomics and metabolomics data based on the annotations in KEGG, our results highlighted increased amino acid metabolism and an upregulation of purine metabolism as a commonality between the two long-lived mutants. Overall, our findings point towards the existence of shared metabolic pathways that are likely important for lifespan extension and provide novel insights into potential regulators and metabolic fingerprints for longevity. Multi-omics integration identified common longevity signatures. Amino acid metabolism was increased in both daf-2 and eat-2 mutants. Purine biosynthesis pathway was enhanced in the long-lived mutants.
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Affiliation(s)
- Arwen W Gao
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC, University of Amsterdam, Amsterdam Gastroenterology & Metabolism, 1105 AZ Amsterdam, the Netherlands
| | - Reuben L Smith
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC, University of Amsterdam, Amsterdam Gastroenterology & Metabolism, 1105 AZ Amsterdam, the Netherlands
| | - Michel van Weeghel
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC, University of Amsterdam, Amsterdam Gastroenterology & Metabolism, 1105 AZ Amsterdam, the Netherlands
| | - Rashmi Kamble
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC, University of Amsterdam, Amsterdam Gastroenterology & Metabolism, 1105 AZ Amsterdam, the Netherlands
| | - Georges E Janssens
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC, University of Amsterdam, Amsterdam Gastroenterology & Metabolism, 1105 AZ Amsterdam, the Netherlands
| | - Riekelt H Houtkooper
- Laboratory Genetic Metabolic Diseases, Amsterdam UMC, University of Amsterdam, Amsterdam Gastroenterology & Metabolism, 1105 AZ Amsterdam, the Netherlands.
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26
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Alcántar-Fernández J, Navarro RE, Salazar-Martínez AM, Pérez-Andrade ME, Miranda-Ríos J. Caenorhabditis elegans respond to high-glucose diets through a network of stress-responsive transcription factors. PLoS One 2018; 13:e0199888. [PMID: 29990370 PMCID: PMC6039004 DOI: 10.1371/journal.pone.0199888] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 06/15/2018] [Indexed: 02/07/2023] Open
Abstract
High-glycemic-index diets, as well as a sedentary lifestyle are considered as determinant factors for the development of obesity, type 2 diabetes, and cardiovascular diseases in humans. These diets have been shown to shorten the life span of C. elegans in a manner that is dependent on insulin signaling, but the participation of other signaling pathways have not been addressed. In this study, we have determined that worms fed with high-glucose diets show alterations in glucose content and uptake, triglyceride content, body size, number of eggs laid, egg-laying defects, and signs of oxidative stress and accelerated aging. Additionally, we analyzed the participation of different key regulators of carbohydrate and lipid metabolism, oxidative stress and longevity such as SKN-1/NRF2, HIF-1/HIF1α, SBP-1/SREBP, CRH-1/CREB, CEP-1/p53, and DAF-16/FOXO, in the reduction of lifespan in glucose-fed worms.
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Affiliation(s)
- Jonathan Alcántar-Fernández
- Programa de Doctorado en Ciencias Biomédicas, Universidad Nacional Autónoma de México (UNAM), México, Ciudad de México, México
- Unidad de Genética de la Nutrición, Depto. de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, UNAM e Instituto Nacional de Pediatría, México, Ciudad de México, México
| | - Rosa E. Navarro
- Departamento de Biología Celular y Desarrollo, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Ana María Salazar-Martínez
- Departamento de Medicina Genómica y Toxicología Ambiental, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Martha Elva Pérez-Andrade
- Unidad de Genética de la Nutrición, Depto. de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, UNAM e Instituto Nacional de Pediatría, México, Ciudad de México, México
| | - Juan Miranda-Ríos
- Unidad de Genética de la Nutrición, Depto. de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, UNAM e Instituto Nacional de Pediatría, México, Ciudad de México, México
- * E-mail:
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27
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Gusarov I, Nudler E. Glycogen at the Crossroad of Stress Resistance, Energy Maintenance, and Pathophysiology of Aging. Bioessays 2018; 40:e1800033. [DOI: 10.1002/bies.201800033] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 05/31/2018] [Indexed: 01/06/2023]
Affiliation(s)
- Ivan Gusarov
- Department of Biochemistry and Molecular Pharmacology; New York University School of Medicine; New York NY 10016 USA
| | - Evgeny Nudler
- Department of Biochemistry and Molecular Pharmacology; New York University School of Medicine; New York NY 10016 USA
- Howard Hughes Medical Institute; New York University School of Medicine; New York NY 10016 USA
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28
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Multilayered Reprogramming in Response to Persistent DNA Damage in C. elegans. Cell Rep 2018; 20:2026-2043. [PMID: 28854356 PMCID: PMC5583510 DOI: 10.1016/j.celrep.2017.08.028] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Revised: 06/30/2017] [Accepted: 08/04/2017] [Indexed: 11/23/2022] Open
Abstract
DNA damage causally contributes to aging and age-related diseases. Mutations in nucleotide excision repair (NER) genes cause highly complex congenital syndromes characterized by growth retardation, cancer susceptibility, and accelerated aging in humans. Orthologous mutations in Caenorhabditis elegans lead to growth delay, genome instability, and accelerated functional decline, thus allowing investigation of the consequences of persistent DNA damage during development and aging in a simple metazoan model. Here, we conducted proteome, lipidome, and phosphoproteome analysis of NER-deficient animals in response to UV treatment to gain comprehensive insights into the full range of physiological adaptations to unrepaired DNA damage. We derive metabolic changes indicative of a tissue maintenance program and implicate an autophagy-mediated proteostatic response. We assign central roles for the insulin-, EGF-, and AMPK-like signaling pathways in orchestrating the adaptive response to DNA damage. Our results provide insights into the DNA damage responses in the organismal context.
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29
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Han N, Chae JW, Jeon J, Lee J, Back HM, Song B, Kwon KI, Kim SK, Yun HY. Prediction of Methionine and Homocysteine levels in Zucker diabetic fatty (ZDF) rats as a T2DM animal model after consumption of a Methionine-rich diet. Nutr Metab (Lond) 2018; 15:14. [PMID: 29449868 PMCID: PMC5807833 DOI: 10.1186/s12986-018-0247-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Accepted: 01/22/2018] [Indexed: 12/23/2022] Open
Abstract
Background Although alterations in the methionine metabolism cycle (MMC) have been associated with vascular complications of diabetes, there have not been consistent results about the levels of methionine and homocysteine in type 2 diabetes mellitus (T2DM). The aim of the current study was to predict changes in plasma methionine and homocysteine concentrations after simulated consumption of methionine-rich foods, following the development of a mathematical model for MMC in Zucker Diabetic Fatty (ZDF) rats, as a representative T2DM animal model. Method The model building and simulation were performed using NONMEM® (ver. 7.3.0) assisted by Perl-Speaks-NONMEM (PsN, ver. 4.3.0). Model parameters were derived using first-order conditional estimation method with interactions permitted among the parameters (FOCE-INTER). NCA was conducted using Phoenix (ver. 6.4.0). For all tests, we considered a P-value < 0.05 to reflect statistical significance. Results Our model featured seven compartments that considered all parts of the cycle by applying non-linear mixed effects model. Conversion of S-adenosyl-L-homocysteine (SAH) to homocysteine increased and the metabolism of homocysteine was reduced under diabetic conditions, and consequently homocysteine accumulated in the elimination phase. Using our model, we performed simulations to compare the changes in plasma methionine and homocysteine concentrations between ZDF and normal rats, by multiple administrations of the methionine-rich diet of 1 mmol/kg, daily for 60 days. The levels of methionine and homocysteine were elevated approximately two- and three-fold, respectively, in ZDF rats, while there were no changes observed in the normal control rats. Conclusion These results can be interpreted to mean that both methionine and homocysteine will accumulate in patients with T2DM, who regularly consume high-methionine foods.
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Affiliation(s)
- Nayoung Han
- 1College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826 Republic of Korea
| | - Jung-Woo Chae
- 2College of Pharmacy, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134 Republic of Korea
| | - Jihyun Jeon
- 2College of Pharmacy, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134 Republic of Korea
| | - Jaeyeon Lee
- 2College of Pharmacy, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134 Republic of Korea.,New Drug Development Center, Osong Medical Innovation Foundation, 123 Osongsaengmyeong-ro, Osong-eup, Heungdeok-gu, Cheongju-si, Chungbuk 28160 Republic of Korea
| | - Hyun-Moon Back
- 2College of Pharmacy, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134 Republic of Korea
| | - Byungjeong Song
- 2College of Pharmacy, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134 Republic of Korea.,Drug Discovery Center, JW Pharmaceutical, 2477 Nambusunhwan-ro, Seocho-gu, Seoul 06725 Republic of Korea
| | - Kwang-Il Kwon
- 2College of Pharmacy, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134 Republic of Korea
| | - Sang Kyum Kim
- 2College of Pharmacy, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134 Republic of Korea
| | - Hwi-Yeol Yun
- 2College of Pharmacy, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134 Republic of Korea
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30
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Feng Z, Hanson RW, Berger NA, Trubitsyn A. Reprogramming of energy metabolism as a driver of aging. Oncotarget 2017; 7:15410-20. [PMID: 26919253 PMCID: PMC4941250 DOI: 10.18632/oncotarget.7645] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Accepted: 02/11/2016] [Indexed: 12/15/2022] Open
Abstract
Aging is characterized by progressive loss of cellular function and integrity. It has been thought to be driven by stochastic molecular damage. However, genetic and environmental maneuvers enhancing mitochondrial function or inhibiting glycolysis extend lifespan and promote healthy aging in many species. In post-fertile Caenorhabditis elegans, a progressive decline in phosphoenolpyruvate carboxykinase with age, and a reciprocal increase in pyruvate kinase shunt energy metabolism from oxidative metabolism to anaerobic glycolysis. This reduces the efficiency and total of energy generation. As a result, energy-dependent physical activity and other cellular functions decrease due to unmatched energy demand and supply. In return, decrease in physical activity accelerates this metabolic shift, forming a vicious cycle. This metabolic event is a determinant of aging, and is retarded by caloric restriction to counteract aging. In this review, we summarize these and other evidence supporting the idea that metabolic reprogramming is a driver of aging. We also suggest strategies to test this hypothesis
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Affiliation(s)
- Zhaoyang Feng
- Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Richard W Hanson
- Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, OH, USA.,Case Comprehensive Cancer Center, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Nathan A Berger
- Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, OH, USA.,Case Comprehensive Cancer Center, School of Medicine, Case Western Reserve University, Cleveland, OH, USA.,Department of Medicine, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Alexander Trubitsyn
- Institute of Biology and Soil Sciences of Far Eastern Brach of Russian Academy of Science, Vladivostok, Russia
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31
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McDonald MK, Fritz JA, Jia D, Scheuchner D, Snyder FF, Stanislaus A, Curle J, Li L, Stabler SP, Allen RH, Mains PE, Gravel RA. Identification of ABC transporters acting in vitamin B 12 metabolism in Caenorhabditis elegans. Mol Genet Metab 2017; 122:160-171. [PMID: 29153845 DOI: 10.1016/j.ymgme.2017.11.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/10/2017] [Revised: 11/10/2017] [Accepted: 11/10/2017] [Indexed: 01/19/2023]
Abstract
Vitamin B12 (cobalamin, Cbl) is a micronutrient essential to human health. Cbl is not utilized as is but must go through complex subcellular and metabolic processing to generate two cofactor forms: methyl-Cbl for methionine synthase, a cytosolic enzyme; and adenosyl-Cbl for methylmalonyl-CoA mutase, a mitochondrial enzyme. Some 10-12 human genes have been identified responsible for the intracellular conversion of Cbl to cofactor forms, including genes that code for ATP-binding cassette (ABC) transporters acting at the lysosomal and plasma membranes. However, the gene for mitochondrial uptake is not known. We hypothesized that ABC transporters should be candidates for other uptake and efflux functions, including mitochondrial transport, and set out to screen ABC transporter mutants for blocks in Cbl utilization using the nematode roundworm Caenorhabditis elegans. Thirty-seven mutant ABC transporters were screened for the excretion of methylmalonic acid (MMA), which should result from loss of Cbl transport into the mitochondria. One mutant, wht-6, showed elevated MMA excretion and reduced [14C]-propionate incorporation, pointing to a functional block in methylmalonyl-CoA mutase. In contrast, the wht-6 mutant appeared to have a normal cytosolic pathway based on analysis of cystathionine excretion, suggesting that cytosolic methionine synthase was functioning properly. Further, the MMA excretion in wht-6 could be partially reversed by including vitamin B12 in the assay medium. The human ortholog of wht-6 is a member of the G family of ABC transporters. We propose wht-6 as a candidate for the transport of Cbl into mitochondria and suggest that a member of the corresponding ABCG family of ABC transporters has this role in humans. Our ABC transporter screen also revealed that mrp-1 and mrp-2 mutants excreted lower MMA than wild type, suggesting they were concentrating intracellular Cbl, consistent with the cellular efflux defect proposed for the mammalian MRP1 ABC transporter.
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Affiliation(s)
- Megan K McDonald
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, T2N 4N1, Canada; Alberta Children's Hospital Research Institute, University of Calgary, Calgary, T2N 4N1, Canada
| | - Julie-Anne Fritz
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, T2N 4N1, Canada; Alberta Children's Hospital Research Institute, University of Calgary, Calgary, T2N 4N1, Canada
| | - Dongxin Jia
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, T2N 4N1, Canada; Alberta Children's Hospital Research Institute, University of Calgary, Calgary, T2N 4N1, Canada
| | - Deborah Scheuchner
- Department of Medical Genetics, University of Calgary, Calgary, T2N 4N1, Canada
| | - Floyd F Snyder
- Department of Medical Genetics, University of Calgary, Calgary, T2N 4N1, Canada
| | - Avalyn Stanislaus
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada
| | - Jared Curle
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada
| | - Liang Li
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2G2, Canada
| | - Sally P Stabler
- Division of Hematology, University of Colorado Denver, Aurora, CO, USA
| | - Robert H Allen
- Division of Hematology, University of Colorado Denver, Aurora, CO, USA
| | - Paul E Mains
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, T2N 4N1, Canada; Alberta Children's Hospital Research Institute, University of Calgary, Calgary, T2N 4N1, Canada
| | - Roy A Gravel
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, T2N 4N1, Canada; Alberta Children's Hospital Research Institute, University of Calgary, Calgary, T2N 4N1, Canada.
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32
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Visscher M, De Henau S, Wildschut MHE, van Es RM, Dhondt I, Michels H, Kemmeren P, Nollen EA, Braeckman BP, Burgering BMT, Vos HR, Dansen TB. Proteome-wide Changes in Protein Turnover Rates in C. elegans Models of Longevity and Age-Related Disease. Cell Rep 2017; 16:3041-3051. [PMID: 27626671 DOI: 10.1016/j.celrep.2016.08.025] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Revised: 05/10/2016] [Accepted: 08/05/2016] [Indexed: 11/16/2022] Open
Abstract
The balance between protein synthesis and protein breakdown is a major determinant of protein homeostasis, and loss of protein homeostasis is one of the hallmarks of aging. Here we describe pulsed SILAC-based experiments to estimate proteome-wide turnover rates of individual proteins. We applied this method to determine protein turnover rates in Caenorhabditis elegans models of longevity and Parkinson's disease, using both developing and adult animals. Whereas protein turnover in developing, long-lived daf-2(e1370) worms is about 30% slower than in controls, the opposite was observed in day 5 adult worms, in which protein turnover in the daf-2(e1370) mutant is twice as fast as in controls. In the Parkinson's model, protein turnover is reduced proportionally over the entire proteome, suggesting that the protein homeostasis network has a strong ability to adapt. The findings shed light on the relationship between protein turnover and healthy aging.
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Affiliation(s)
- Marieke Visscher
- Center for Molecular Medicine, Molecular Cancer Research Section, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG Utrecht, the Netherlands
| | - Sasha De Henau
- Center for Molecular Medicine, Molecular Cancer Research Section, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG Utrecht, the Netherlands
| | - Mattheus H E Wildschut
- Center for Molecular Medicine, Molecular Cancer Research Section, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG Utrecht, the Netherlands
| | - Robert M van Es
- Center for Molecular Medicine, Molecular Cancer Research Section, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG Utrecht, the Netherlands
| | - Ineke Dhondt
- Laboratory for Aging Physiology and Molecular Evolution, Biology Department, Ghent University, Proeftuinstraat 86 N1, 9000 Ghent, Belgium
| | - Helen Michels
- European Research Institute for the Biology of Aging, University Medical Centre Groningen, University of Groningen, 9700 AD Groningen, the Netherlands
| | - Patrick Kemmeren
- Center for Molecular Medicine, Molecular Cancer Research Section, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG Utrecht, the Netherlands
| | - Ellen A Nollen
- European Research Institute for the Biology of Aging, University Medical Centre Groningen, University of Groningen, 9700 AD Groningen, the Netherlands
| | - Bart P Braeckman
- Laboratory for Aging Physiology and Molecular Evolution, Biology Department, Ghent University, Proeftuinstraat 86 N1, 9000 Ghent, Belgium
| | - Boudewijn M T Burgering
- Center for Molecular Medicine, Molecular Cancer Research Section, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG Utrecht, the Netherlands
| | - Harmjan R Vos
- Center for Molecular Medicine, Molecular Cancer Research Section, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG Utrecht, the Netherlands.
| | - Tobias B Dansen
- Center for Molecular Medicine, Molecular Cancer Research Section, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG Utrecht, the Netherlands.
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33
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Hibshman JD, Doan AE, Moore BT, Kaplan RE, Hung A, Webster AK, Bhatt DP, Chitrakar R, Hirschey MD, Baugh LR. daf-16/FoxO promotes gluconeogenesis and trehalose synthesis during starvation to support survival. eLife 2017; 6. [PMID: 29063832 PMCID: PMC5655125 DOI: 10.7554/elife.30057] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2017] [Accepted: 09/25/2017] [Indexed: 12/21/2022] Open
Abstract
daf-16/FoxO is required to survive starvation in Caenorhabditis elegans, but how daf-16IFoxO promotes starvation resistance is unclear. We show that daf-16/FoxO restructures carbohydrate metabolism by driving carbon flux through the glyoxylate shunt and gluconeogenesis and into synthesis of trehalose, a disaccharide of glucose. Trehalose is a well-known stress protectant, capable of preserving membrane organization and protein structure during abiotic stress. Metabolomic, genetic, and pharmacological analyses confirm increased trehalose synthesis and further show that trehalose not only supports survival as a stress protectant but also serves as a glycolytic input. Furthermore, we provide evidence that metabolic cycling between trehalose and glucose is necessary for this dual function of trehalose. This work demonstrates that daf-16/FoxO promotes starvation resistance by shifting carbon metabolism to drive trehalose synthesis, which in turn supports survival by providing an energy source and acting as a stress protectant. Most animals rarely have access to a constant supply of food, and so have evolved ways to cope with times of plenty and times of shortage. Insulin is a hormone that travels throughout the body to signal when an animal is well fed. Insulin signaling inhibits the activity of a protein called FoxO, which otherwise switches on and off hundreds of genes to control the starvation response. The roundworm, Caenorhabditis elegans, has been well studied in the laboratory, and often has to cope with starvation in the wild. These worms can pause their development if no food is available, or divert to a different developmental path if they anticipate that food will be short in future. As with more complex animals, the worm responds to starvation by reducing insulin-like signaling, which in turn activates a FoxO protein called daf-16. When the worms stop feeding, daf-16 is switched on, which is crucial for survival. It was known how daf-16 stops the roundworm’s development, but it was not known how it helps the worms to survive starvation. Now, Hibshman et al. have compared normal roundworm larvae to larvae that are missing the gene for daf-16 to determine how this protein influences the roundworm’s ability to survive starvation. The worms were examined with and without food, to look for which genes were switched on and off by daf-16 during starvation. This revealed that daf-16 controls metabolism, activating a metabolic shortcut that makes the worms produce glucose and begin turning it into another type of sugar, called trehalose. This sugar usually promotes survival in conditions where water is limiting, like dehydration and high salt, but it can also be broken down to release energy. The levels of trehalose in the worms rose within hours of the onset of starvation. To confirm the importance of trehalose in surviving starvation, roundworms with mutations in genes involved in glucose or trehalose production were examined, as was the effect of giving starving worms glucose or trehalose. Disrupting the production of sugars caused the worms to die sooner of starvation, while supplementing with sugar had the opposite effect meaning the worms survived for longer. Taken together, these findings reveal that daf-16 protects against starvation by shifting metabolism towards the production of trehalose. This helps worms to survive by both protecting them from stress and providing them with a source of energy. These findings not only extend the current understanding of how animals respond to starvation, but could also lead to improved understanding of diseases where this response goes wrong, including diabetes and obesity.
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Affiliation(s)
- Jonathan D Hibshman
- Department of Biology, Duke University, Durham, United States.,University Program in Genetics and Genomics, Duke University, Durham, United States
| | | | - Brad T Moore
- Department of Biology, Duke University, Durham, United States
| | - Rebecca Ew Kaplan
- Department of Biology, Duke University, Durham, United States.,University Program in Genetics and Genomics, Duke University, Durham, United States
| | - Anthony Hung
- Department of Biology, Duke University, Durham, United States
| | - Amy K Webster
- Department of Biology, Duke University, Durham, United States.,University Program in Genetics and Genomics, Duke University, Durham, United States
| | - Dhaval P Bhatt
- Duke Molecular Physiology Institute, Duke University, Durham, United States
| | - Rojin Chitrakar
- Department of Biology, Duke University, Durham, United States
| | - Matthew D Hirschey
- Duke Molecular Physiology Institute, Duke University, Durham, United States.,Department of Medicine, Duke University, Durham, United States.,Department of Pharmacology & Cancer Biology, Duke University, Durham, United States
| | - L Ryan Baugh
- Department of Biology, Duke University, Durham, United States.,University Program in Genetics and Genomics, Duke University, Durham, United States
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34
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Watts JL, Ristow M. Lipid and Carbohydrate Metabolism in Caenorhabditis elegans. Genetics 2017; 207:413-446. [PMID: 28978773 PMCID: PMC5629314 DOI: 10.1534/genetics.117.300106] [Citation(s) in RCA: 102] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Accepted: 08/02/2017] [Indexed: 12/14/2022] Open
Abstract
Lipid and carbohydrate metabolism are highly conserved processes that affect nearly all aspects of organismal biology. Caenorhabditis elegans eat bacteria, which consist of lipids, carbohydrates, and proteins that are broken down during digestion into fatty acids, simple sugars, and amino acid precursors. With these nutrients, C. elegans synthesizes a wide range of metabolites that are required for development and behavior. In this review, we outline lipid and carbohydrate structures as well as biosynthesis and breakdown pathways that have been characterized in C. elegans We bring attention to functional studies using mutant strains that reveal physiological roles for specific lipids and carbohydrates during development, aging, and adaptation to changing environmental conditions.
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Affiliation(s)
- Jennifer L Watts
- School of Molecular Biosciences and Center for Reproductive Biology, Washington State University, Pullman, Washington 99164
| | - Michael Ristow
- Energy Metabolism Laboratory, Institute of Translational Medicine, Department of Health Sciences and Technology, Swiss Federal Institute of Technology Zurich, 8603 Schwerzenbach-Zurich, Switzerland
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35
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Dhondt I, Petyuk VA, Bauer S, Brewer HM, Smith RD, Depuydt G, Braeckman BP. Changes of Protein Turnover in Aging Caenorhabditis elegans. Mol Cell Proteomics 2017; 16:1621-1633. [PMID: 28679685 DOI: 10.1074/mcp.ra117.000049] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Indexed: 11/06/2022] Open
Abstract
Protein turnover rates severely decline in aging organisms, including C. elegans However, limited information is available on turnover dynamics at the individual protein level during aging. We followed changes in protein turnover at one-day resolution using a multiple-pulse 15N-labeling and accurate mass spectrometry approach. Forty percent of the proteome shows gradual slowdown in turnover with age, whereas only few proteins show increased turnover. Decrease in protein turnover was consistent for only a minority of functionally related protein subsets, including tubulins and vitellogenins, whereas randomly diverging turnover patterns with age were the norm. Our data suggests increased heterogeneity of protein turnover of the translation machinery, whereas protein turnover of ubiquitin-proteasome and antioxidant systems are well-preserved over time. Hence, we presume that maintenance of quality control mechanisms is a protective strategy in aging worms, although the ultimate proteome collapse is inescapable.
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Affiliation(s)
- Ineke Dhondt
- From the ‡Laboratory for Aging Physiology and Molecular Evolution, Biology Department, Ghent University, K.L. Ledeganckstraat 35, 9000 Ghent Belgium
| | - Vladislav A Petyuk
- §Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Sophie Bauer
- From the ‡Laboratory for Aging Physiology and Molecular Evolution, Biology Department, Ghent University, K.L. Ledeganckstraat 35, 9000 Ghent Belgium
| | - Heather M Brewer
- §Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Richard D Smith
- §Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Geert Depuydt
- From the ‡Laboratory for Aging Physiology and Molecular Evolution, Biology Department, Ghent University, K.L. Ledeganckstraat 35, 9000 Ghent Belgium.,¶Laboratory for Functional Genomics and Proteomics, Department of Biology, KU Leuven, Naamsestraat 59, 3000 Leuven, Belgium
| | - Bart P Braeckman
- From the ‡Laboratory for Aging Physiology and Molecular Evolution, Biology Department, Ghent University, K.L. Ledeganckstraat 35, 9000 Ghent Belgium;
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36
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Mitochondrial form, function and signalling in aging. Biochem J 2017; 473:3421-3449. [PMID: 27729586 DOI: 10.1042/bcj20160451] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Accepted: 06/17/2016] [Indexed: 02/07/2023]
Abstract
Aging is often accompanied by a decline in mitochondrial mass and function in different tissues. Additionally, cell resistance to stress is frequently found to be prevented by higher mitochondrial respiratory capacity. These correlations strongly suggest mitochondria are key players in aging and senescence, acting by regulating energy homeostasis, redox balance and signalling pathways central in these processes. However, mitochondria display a wide array of functions and signalling properties, and the roles of these different characteristics are still widely unexplored. Furthermore, differences in mitochondrial properties and responses between tissues and cell types, and how these affect whole body metabolism are also still poorly understood. This review uncovers aspects of mitochondrial biology that have an impact upon aging in model organisms and selected mammalian cells and tissues.
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37
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Lobanov AV, Heaphy SM, Turanov AA, Gerashchenko MV, Pucciarelli S, Devaraj RR, Xie F, Petyuk VA, Smith RD, Klobutcher LA, Atkins JF, Miceli C, Hatfield DL, Baranov PV, Gladyshev VN. Position-dependent termination and widespread obligatory frameshifting in Euplotes translation. Nat Struct Mol Biol 2017; 24:61-68. [PMID: 27870834 PMCID: PMC5295771 DOI: 10.1038/nsmb.3330] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Accepted: 10/31/2016] [Indexed: 11/09/2022]
Abstract
The ribosome can change its reading frame during translation in a process known as programmed ribosomal frameshifting. These rare events are supported by complex mRNA signals. However, we found that the ciliates Euplotes crassus and Euplotes focardii exhibit widespread frameshifting at stop codons. 47 different codons preceding stop signals resulted in either +1 or +2 frameshifts, and +1 frameshifting at AAA was the most frequent. The frameshifts showed unusual plasticity and rapid evolution, and had little influence on translation rates. The proximity of a stop codon to the 3' mRNA end, rather than its occurrence or sequence context, appeared to designate termination. Thus, a 'stop codon' is not a sufficient signal for translation termination, and the default function of stop codons in Euplotes is frameshifting, whereas termination is specific to certain mRNA positions and probably requires additional factors.
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Affiliation(s)
- Alexei V. Lobanov
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusets, USA
| | - Stephen M. Heaphy
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - Anton A. Turanov
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusets, USA
| | - Maxim V. Gerashchenko
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusets, USA
| | - Sandra Pucciarelli
- School of Biosciences and Biotechnology, University of Camerino, Camerino, Italy
| | - Raghul R. Devaraj
- School of Biosciences and Biotechnology, University of Camerino, Camerino, Italy
| | - Fang Xie
- Pacific Northwest National Laboratory, Richland, Washington, USA
| | | | - Richard D. Smith
- Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Lawrence A. Klobutcher
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, Connecticut, USA
| | - John F. Atkins
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - Cristina Miceli
- School of Biosciences and Biotechnology, University of Camerino, Camerino, Italy
| | - Dolph L. Hatfield
- Molecular Biology of Selenium Section, Mouse Cancer Genetics Program, Center for Cancer Research, National Institutes of Health, Bethesda, Maryland, USA
| | - Pavel V. Baranov
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - Vadim N. Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusets, USA
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38
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Braeckman BP, Dhondt I. Lifespan extension in Caenorhabditis elegans insulin/IGF-1 signalling mutants is supported by non-vertebrate physiological traits. NEMATOLOGY 2017. [DOI: 10.1163/15685411-00003060] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The insulin/IGF-1 signalling (IIS) pathway connects nutrient levels to metabolism, growth and lifespan in eukaryotes ranging from yeasts to humans, including nematodes such as the genetic model organismCaenorhabditis elegans. The link between ageing and the IIS pathway has been thoroughly studied inC. elegans; upon reduced IIS signalling, a genetic survival program is activated resulting in a drastic lifespan extension. One of the components of this program is the upregulation of antioxidant activity but experiments failed to show a clear causal relation to longevity. However, oxidative damage, such as protein carbonyls, accumulates at a slower pace in long-livedC. elegansmutants with reduced IIS. This is probably not achieved by increased macroautophagy, a process that sequesters cellular components to be eliminated as protein turnover rates are slowed down in IIS mutants. The IIS mutantdaf-2, bearing a mutation in the insulin/IGF-1 receptor, recapitulates the dauer survival program, including accumulation of fat and glycogen. Fat can be converted into glucose and glycogenviathe glyoxylate shunt, a pathway absent in vertebrates. These carbohydrates can be used as substrates for trehalose synthesis, also absent in mammals. Trehalose, a non-reducing homodimer of glucose, stabilises intracellular components and is responsible for almost half of the lifespan extension in IIS mutants. Hence, the molecular mechanisms by which lifespan is extended under reduced IIS may differ substantially between phyla that have an active glyoxylate cycle and trehalose synthesis, such as ecdysozoans and fungi, and vertebrate species such as mammals.
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Affiliation(s)
- Bart P. Braeckman
- Biology Department, Ghent University, Proeftuinstraat 86 N1, Ghent, Belgium
| | - Ineke Dhondt
- Biology Department, Ghent University, Proeftuinstraat 86 N1, Ghent, Belgium
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39
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Dhondt I, Petyuk VA, Cai H, Vandemeulebroucke L, Vierstraete A, Smith RD, Depuydt G, Braeckman BP. FOXO/DAF-16 Activation Slows Down Turnover of the Majority of Proteins in C. elegans. Cell Rep 2016; 16:3028-3040. [PMID: 27626670 PMCID: PMC5434875 DOI: 10.1016/j.celrep.2016.07.088] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Revised: 04/08/2016] [Accepted: 07/01/2016] [Indexed: 02/03/2023] Open
Abstract
Most aging hypotheses assume the accumulation of damage, resulting in gradual physiological decline and, ultimately, death. Avoiding protein damage accumulation by enhanced turnover should slow down the aging process and extend the lifespan. However, lowering translational efficiency extends rather than shortens the lifespan in C. elegans. We studied turnover of individual proteins in the long-lived daf-2 mutant by combining SILeNCe (stable isotope labeling by nitrogen in Caenorhabditiselegans) and mass spectrometry. Intriguingly, the majority of proteins displayed prolonged half-lives in daf-2, whereas others remained unchanged, signifying that longevity is not supported by high protein turnover. This slowdown was most prominent for translation-related and mitochondrial proteins. In contrast, the high turnover of lysosomal hydrolases and very low turnover of cytoskeletal proteins remained largely unchanged. The slowdown of protein dynamics and decreased abundance of the translational machinery may point to the importance of anabolic attenuation in lifespan extension, as suggested by the hyperfunction theory.
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Affiliation(s)
- Ineke Dhondt
- Laboratory for Aging Physiology and Molecular Evolution, Biology Department, Ghent University, Proeftuinstraat 86 N1, 9000 Ghent, Belgium
| | - Vladislav A Petyuk
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Huaihan Cai
- Laboratory for Aging Physiology and Molecular Evolution, Biology Department, Ghent University, Proeftuinstraat 86 N1, 9000 Ghent, Belgium
| | - Lieselot Vandemeulebroucke
- Laboratory for Aging Physiology and Molecular Evolution, Biology Department, Ghent University, Proeftuinstraat 86 N1, 9000 Ghent, Belgium
| | - Andy Vierstraete
- Laboratory for Aging Physiology and Molecular Evolution, Biology Department, Ghent University, Proeftuinstraat 86 N1, 9000 Ghent, Belgium
| | - Richard D Smith
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Geert Depuydt
- Laboratory for Aging Physiology and Molecular Evolution, Biology Department, Ghent University, Proeftuinstraat 86 N1, 9000 Ghent, Belgium; Laboratory for Functional Genomics and Proteomics, Department of Biology, KU Leuven, Naamsestraat 59, 3000 Leuven, Belgium
| | - Bart P Braeckman
- Laboratory for Aging Physiology and Molecular Evolution, Biology Department, Ghent University, Proeftuinstraat 86 N1, 9000 Ghent, Belgium.
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40
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Martell J, Seo Y, Bak DW, Kingsley SF, Tissenbaum HA, Weerapana E. Global Cysteine-Reactivity Profiling during Impaired Insulin/IGF-1 Signaling in C. elegans Identifies Uncharacterized Mediators of Longevity. Cell Chem Biol 2016; 23:955-66. [PMID: 27499530 DOI: 10.1016/j.chembiol.2016.06.015] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2016] [Revised: 06/23/2016] [Accepted: 06/27/2016] [Indexed: 12/11/2022]
Abstract
In the nematode Caenorhabditis elegans, inactivating mutations in the insulin/IGF-1 receptor, DAF-2, result in a 2-fold increase in lifespan mediated by DAF-16, a FOXO-family transcription factor. Downstream protein activities that directly regulate longevity during impaired insulin/IGF-1 signaling (IIS) are poorly characterized. Here, we use global cysteine-reactivity profiling to identify protein activity changes during impaired IIS. Upon confirming that cysteine reactivity is a good predictor of functionality in C. elegans, we profiled cysteine-reactivity changes between daf-2 and daf-16;daf-2 mutants, and identified 40 proteins that display a >2-fold change. Subsequent RNAi-mediated knockdown studies revealed that lbp-3 and K02D7.1 knockdown caused significant increases in lifespan and dauer formation. The proteins encoded by these two genes, LBP-3 and K02D7.1, are implicated in intracellular fatty acid transport and purine metabolism, respectively. These studies demonstrate that cysteine-reactivity profiling can be complementary to abundance-based transcriptomic and proteomic studies, serving to identify uncharacterized mediators of C. elegans longevity.
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Affiliation(s)
- Julianne Martell
- Department of Chemistry, Boston College, Chestnut Hill, MA 02467, USA
| | - Yonghak Seo
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Daniel W Bak
- Department of Chemistry, Boston College, Chestnut Hill, MA 02467, USA
| | - Samuel F Kingsley
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Heidi A Tissenbaum
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA; Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
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41
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Depuydt G, Shanmugam N, Rasulova M, Dhondt I, Braeckman BP. Increased Protein Stability and Decreased Protein Turnover in the Caenorhabditis elegans Ins/IGF-1 daf-2 Mutant. J Gerontol A Biol Sci Med Sci 2016; 71:1553-1559. [PMID: 26865495 PMCID: PMC5106850 DOI: 10.1093/gerona/glv221] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 11/11/2015] [Indexed: 01/07/2023] Open
Abstract
In Caenorhabditis elegans, cellular proteostasis is likely essential for longevity. Autophagy has been shown to be essential for lifespan extension of daf-2 insulin/IGF mutants. Therefore, it can be hypothesized that daf-2 mutants achieve this phenotype by increasing protein turnover. However, such a mechanism would exert a substantial energy cost. By using classical 35S pulse-chase labeling, we observed that protein synthesis and degradation rates are decreased in young adults of the daf-2 insulin/IGF mutants. Although reduction of protein turnover may be energetically favorable, it may lead to accumulation and aggregation of damaged proteins. As this has been shown not to be the case in daf-2 mutants, another mechanism must exist to maintain proteostasis in this strain. We observed that proteins isolated from daf-2 mutants are more soluble in acidic conditions due to increased levels of trehalose. This suggests that trehalose may decrease the potential for protein aggregation and increases proteostasis in the daf-2 mutants. We postulate that daf-2 mutants save energy by decreasing protein turnover rates and instead stabilize their proteome by trehalose.
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Affiliation(s)
- Geert Depuydt
- Laboratory for Aging Physiology and Molecular Evolution, Department of Biology, Ghent University, Belgium.,Laboratory for Functional Genomics and Proteomics, Department of Biology, KU Leuven, Belgium
| | - Nilesh Shanmugam
- Laboratory for Aging Physiology and Molecular Evolution, Department of Biology, Ghent University, Belgium
| | - Madina Rasulova
- Laboratory for Aging Physiology and Molecular Evolution, Department of Biology, Ghent University, Belgium
| | - Ineke Dhondt
- Laboratory for Aging Physiology and Molecular Evolution, Department of Biology, Ghent University, Belgium
| | - Bart P Braeckman
- Laboratory for Aging Physiology and Molecular Evolution, Department of Biology, Ghent University, Belgium.
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42
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Yuan Y, Hakimi P, Kao C, Kao A, Liu R, Janocha A, Boyd-Tressler A, Hang X, Alhoraibi H, Slater E, Xia K, Cao P, Shue Q, Ching TT, Hsu AL, Erzurum SC, Dubyak GR, Berger NA, Hanson RW, Feng Z. Reciprocal Changes in Phosphoenolpyruvate Carboxykinase and Pyruvate Kinase with Age Are a Determinant of Aging in Caenorhabditis elegans. J Biol Chem 2016; 291:1307-19. [PMID: 26631730 PMCID: PMC4714217 DOI: 10.1074/jbc.m115.691766] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Revised: 11/30/2015] [Indexed: 01/01/2023] Open
Abstract
Aging involves progressive loss of cellular function and integrity, presumably caused by accumulated stochastic damage to cells. Alterations in energy metabolism contribute to aging, but how energy metabolism changes with age, how these changes affect aging, and whether they can be modified to modulate aging remain unclear. In locomotory muscle of post-fertile Caenorhabditis elegans, we identified a progressive decrease in cytosolic phosphoenolpyruvate carboxykinase (PEPCK-C), a longevity-associated metabolic enzyme, and a reciprocal increase in glycolytic pyruvate kinase (PK) that were necessary and sufficient to limit lifespan. Decline in PEPCK-C with age also led to loss of cellular function and integrity including muscle activity, and cellular senescence. Genetic and pharmacologic interventions of PEPCK-C, muscle activity, and AMPK signaling demonstrate that declines in PEPCK-C and muscle function with age interacted to limit reproductive life and lifespan via disrupted energy homeostasis. Quantifications of metabolic flux show that reciprocal changes in PEPCK-C and PK with age shunted energy metabolism toward glycolysis, reducing mitochondrial bioenergetics. Last, calorie restriction countered changes in PEPCK-C and PK with age to elicit anti-aging effects via TOR inhibition. Thus, a programmed metabolic event involving PEPCK-C and PK is a determinant of aging that can be modified to modulate aging.
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Affiliation(s)
| | | | - Clara Kao
- From the Departments of Pharmacology
| | | | - Ruifu Liu
- From the Departments of Pharmacology
| | - Allison Janocha
- the Department of Pathobiology, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, Ohio 44195
| | | | - Xi Hang
- From the Departments of Pharmacology, the School of Pharmacy, Suzhou Health College, Suzhou, Jiangsu 215009, China, and
| | | | | | - Kevin Xia
- From the Departments of Pharmacology
| | | | | | - Tsui-Ting Ching
- the Departments of Internal Medicine, Division of Geriatric Medicine, and
| | - Ao-Lin Hsu
- the Departments of Internal Medicine, Division of Geriatric Medicine, and Molecular and Integrative Physiology, University of Michigan, Ann Arbor, Michigan 48109
| | - Serpil C Erzurum
- the Department of Pathobiology, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, Ohio 44195
| | - George R Dubyak
- From the Departments of Pharmacology, Physiology and Biophysics, and
| | - Nathan A Berger
- Departments of Biochemistry and Medicine, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106
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Gomes LC, Odedra D, Dikic I, Pohl C. Autophagy and modular restructuring of metabolism control germline tumor differentiation and proliferation in C. elegans. Autophagy 2016; 12:529-46. [PMID: 26759963 PMCID: PMC4835962 DOI: 10.1080/15548627.2015.1136771] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Autophagy can act either as a tumor suppressor or as a survival mechanism for established tumors. To understand how autophagy plays this dual role in cancer, in vivo models are required. By using a highly heterogeneous C. elegans germline tumor, we show that autophagy-related proteins are expressed in a specific subset of tumor cells, neurons. Inhibition of autophagy impairs neuronal differentiation and increases tumor cell number, resulting in a shorter life span of animals with tumors, while induction of autophagy extends their life span by impairing tumor proliferation. Fasting of animals with fully developed tumors leads to a doubling of their life span, which depends on modular changes in transcription including switches in transcription factor networks and mitochondrial metabolism. Hence, our results suggest that metabolic restructuring, cell-type specific regulation of autophagy and neuronal differentiation constitute central pathways preventing growth of heterogeneous tumors.
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Affiliation(s)
- Ligia C Gomes
- a Buchmann Institute for Molecular Life Sciences, Goethe University , Frankfurt (Main) , Germany.,b Institute of Biochemistry II, School of Medicine, Goethe University , Frankfurt (Main) , Germany
| | - Devang Odedra
- a Buchmann Institute for Molecular Life Sciences, Goethe University , Frankfurt (Main) , Germany.,b Institute of Biochemistry II, School of Medicine, Goethe University , Frankfurt (Main) , Germany
| | - Ivan Dikic
- a Buchmann Institute for Molecular Life Sciences, Goethe University , Frankfurt (Main) , Germany.,b Institute of Biochemistry II, School of Medicine, Goethe University , Frankfurt (Main) , Germany.,c Department of Immunology and Medical Genetics , University of Split, School of Medicine , Split , Croatia
| | - Christian Pohl
- a Buchmann Institute for Molecular Life Sciences, Goethe University , Frankfurt (Main) , Germany.,b Institute of Biochemistry II, School of Medicine, Goethe University , Frankfurt (Main) , Germany
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44
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MacInnes AW. The role of the ribosome in the regulation of longevity and lifespan extension. WILEY INTERDISCIPLINARY REVIEWS-RNA 2016; 7:198-212. [PMID: 26732699 DOI: 10.1002/wrna.1325] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Revised: 11/14/2015] [Accepted: 11/17/2015] [Indexed: 12/11/2022]
Abstract
The most energy-consuming process that a cell must undertake to stay viable is the continuous biogenesis of ribosomes for the translation of RNA into protein. Given the inextricable links between energy consumption and cellular lifespan, it is not surprising that mutations and environmental cues that reduce ribosome biogenesis result in an extension of eukaryotic lifespan. This review goes into detail describing recent discoveries of different and often unexpected elements that play a role in the regulation of longevity by virtue of their ribosome biogenesis functions. These roles include controlling the transcription and processing of ribosomal RNA (rRNA), the translation of ribosomal protein (RP) genes, and the number of ribosomes overall. Together these findings suggest that a fundamental mechanism across eukaryotic species for extending lifespan is to slow down or halt the expenditure of cellular energy that is normally absorbed by the manufacturing and assembly of new ribosomes.
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Lourenço AB, Muñoz-Jiménez C, Venegas-Calerón M, Artal-Sanz M. Analysis of the effect of the mitochondrial prohibitin complex, a context-dependent modulator of longevity, on the C. elegans metabolome. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2015; 1847:1457-68. [PMID: 26092086 PMCID: PMC4580209 DOI: 10.1016/j.bbabio.2015.06.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Revised: 05/11/2015] [Accepted: 06/03/2015] [Indexed: 11/25/2022]
Abstract
The mitochondrial prohibitin complex, composed of two proteins, PHB-1 and PHB-2, is a context-dependent modulator of longevity. Specifically, prohibitin deficiency shortens the lifespan of otherwise wild type worms, while it dramatically extends the lifespan under compromised metabolic conditions. This extremely intriguingly phenotype has been linked to alterations in mitochondrial function and in fat metabolism. However, the true function of the mitochondrial prohibitin complex remains elusive. Here, we used gas chromatography coupled to a flame ionization detector (GC/FID) and 1H NMR spectroscopy to gain molecular insights into the effect of prohibitin depletion on the Caenorhabditis elegans metabolome. We analysed the effect of prohibitin deficiency in two different developmental stages and under two different conditions, which result in opposing longevity phenotypes, namely wild type worms and daf-2(e1370) insulin signalling deficient mutants. Prohibitin depletion was shown to alter the fatty acid (GC/FID) and 1H NMR metabolic profiles of wild type animals both at the fourth larval stage of development (L4) and at the young adult (YA) stage, while being more pronounced at the later stage. Furthermore, wild type and the diapause mutant daf-2(e1370), either expressing or not prohibitin, were clearly distinguishable based on their metabolic profiles, revealing changes in fatty acid composition, as well as in carbohydrate and amino acid metabolism. Moreover, the metabolic data indicate that daf-2(e1370) mutants are more robust than the wild type animals to changes induced by prohibitin depletion. The impact of prohibitin depletion on the C. elegans metabolome will be discussed herein in the scope of its effect on longevity. This article is part of a Special Issue entitled: Mitochondrial Dysfunction in Aging. Guest Editor: Aleksandra Trifunovic Impact of the mitochondrial prohibitin (PHB) complex on the C. elegans metabolome Depletion of individual PHB subunits results in similar metabolic profiles. PHB affects fatty acid composition, amino acid and carbohydrate metabolism. daf-2 mutants are more robust than wild type worms to the effect of PHB depletion. Modulation of fermentation may contribute to the longevity of PHB-depleted worms.
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Affiliation(s)
- Artur B Lourenço
- Andalusian Centre for Developmental Biology (CABD), CSIC, Universidad Pablo de Olavide-Junta de Andalucía, Carretera de Utrera, km 1, 41013 Sevilla, Spain
| | - Celia Muñoz-Jiménez
- Andalusian Centre for Developmental Biology (CABD), CSIC, Universidad Pablo de Olavide-Junta de Andalucía, Carretera de Utrera, km 1, 41013 Sevilla, Spain
| | - Mónica Venegas-Calerón
- Department of Biochemistry and Molecular Biology of Plant Products, Instituto de la Grasa (IG-CSIC), Ctra. Utrera Km 1, Campus Universitario Pablo de Olavide, 41013, Sevilla, Spain
| | - Marta Artal-Sanz
- Andalusian Centre for Developmental Biology (CABD), CSIC, Universidad Pablo de Olavide-Junta de Andalucía, Carretera de Utrera, km 1, 41013 Sevilla, Spain.
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Essers PB, Nonnekens J, Goos YJ, Betist MC, Viester MD, Mossink B, Lansu N, Korswagen HC, Jelier R, Brenkman AB, MacInnes AW. A Long Noncoding RNA on the Ribosome Is Required for Lifespan Extension. Cell Rep 2015; 10:339-345. [PMID: 25600869 DOI: 10.1016/j.celrep.2014.12.029] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2014] [Revised: 08/29/2014] [Accepted: 12/13/2014] [Indexed: 11/18/2022] Open
Abstract
The biogenesis of ribosomes and their coordination of protein translation consume an enormous amount of cellular energy. As such, it has been established that the inhibition of either process can extend eukaryotic lifespan. Here, we used next-generation sequencing to compare ribosome-associated RNAs from normal strains of Caenorhabditis elegans to those carrying the life-extending daf-2 mutation. We found a long noncoding RNA (lncRNA), transcribed telomeric sequence 1 (tts-1), on ribosomes of the daf-2 mutant. Depleting tts-1 in daf-2 mutants increases ribosome levels and significantly shortens their extended lifespan. We find tts-1 is also required for the longer lifespan of the mitochondrial clk-1 mutants but not the feeding-defective eat-2 mutants. In line with this, the clk-1 mutants express more tts-1 and fewer ribosomes than the eat-2 mutants. Our results suggest that the expression of tts-1 functions in different longevity pathways to reduce ribosome levels in a way that promotes life extension.
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Affiliation(s)
- Paul B Essers
- Hubrecht Institute, KNAW and University Medical Center Utrecht, 3584 CT Utrecht, the Netherlands
| | - Julie Nonnekens
- Hubrecht Institute, KNAW and University Medical Center Utrecht, 3584 CT Utrecht, the Netherlands
| | - Yvonne J Goos
- Hubrecht Institute, KNAW and University Medical Center Utrecht, 3584 CT Utrecht, the Netherlands
| | - Marco C Betist
- Hubrecht Institute, KNAW and University Medical Center Utrecht, 3584 CT Utrecht, the Netherlands
| | - Marjon D Viester
- Hubrecht Institute, KNAW and University Medical Center Utrecht, 3584 CT Utrecht, the Netherlands
| | - Britt Mossink
- Hubrecht Institute, KNAW and University Medical Center Utrecht, 3584 CT Utrecht, the Netherlands
| | - Nico Lansu
- Hubrecht Institute, KNAW and University Medical Center Utrecht, 3584 CT Utrecht, the Netherlands
| | - Hendrik C Korswagen
- Hubrecht Institute, KNAW and University Medical Center Utrecht, 3584 CT Utrecht, the Netherlands
| | - Rob Jelier
- Centre of Microbial and Plant Genetics, KU Leuven, Kasteelpark Arenberg 20, 3001 Leuven, Belgium
| | - Arjan B Brenkman
- Section Metabolic Diseases, Department of Molecular Cancer Research, Wilhelmina Children's Hospital, University Medical Center Utrecht, 3508 AB Utrecht, the Netherlands
| | - Alyson W MacInnes
- Hubrecht Institute, KNAW and University Medical Center Utrecht, 3584 CT Utrecht, the Netherlands.
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Abstract
Over a century ago, the zoologist Emile Maupas first identified the nematode, Rhabditis elegans, in the soil in Algiers. Subsequent work and phylogenic studies renamed the species Caenorhabditis elegans or more commonly referred to as C. elegans; (Caeno meaning recent; rhabditis meaning rod; elegans meaning nice). However, it was not until 1963, when Sydney Brenner, already successful from his work on DNA, RNA, and the genetic code, suggested the future of biological research lay in model organisms. Brenner believed that biological research required a model system that could grow in vast quantities in the lab, were cheap to maintain and had a simple body plan, and he chose the nematode C. elegans to fulfill such a role. Since that time, C. elegans has emerged as one of the premiere model systems for aging research. This paper reviews some initial identification of mutants with altered lifespan with a focus on genetics and then discusses advantages and disadvantages for using C. elegans as a model system to understand human aging. This review focuses on molecular genetics aspects of this model organism.
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Affiliation(s)
- Heidi A Tissenbaum
- Program in Gene Function and Expression, Program in Molecular Medicine, University of Massachusetts Medical School , Worcester , MA 01605 , USA
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Van Assche R, Temmerman L, Dias DA, Boughton B, Boonen K, Braeckman BP, Schoofs L, Roessner U. Metabolic profiling of a transgenic Caenorhabditis elegans Alzheimer model. Metabolomics 2014; 11:477-486. [PMID: 25750603 PMCID: PMC4342517 DOI: 10.1007/s11306-014-0711-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/24/2014] [Accepted: 07/11/2014] [Indexed: 12/30/2022]
Abstract
Despite decades of research, no early-onset biomarkers are currently available for Alzheimer's disease, a cureless neurodegenerative disease afflicting millions worldwide. In this study, transgenic Caenorhabditis elegans were used to investigate changes in the metabolome after induced expression of amyloid-β. GC- and LC-MS-based platforms determined a total of 157 differential features. Some of these were identified using in-house (GC-MS) or public libraries (LC-MS), revealing changes in allantoin, cystathionine and tyrosine levels. Since C. elegans is far better suited to metabolomics studies than most other model systems, the accordance of these findings with vertebrate literature is promising and argues for further use of C. elegans as a model of human pathology in the study of AD.
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Affiliation(s)
- Roel Van Assche
- Functional Genomics and Proteomics, Department of Biology, KU Leuven, Leuven, Belgium
| | - Liesbet Temmerman
- Functional Genomics and Proteomics, Department of Biology, KU Leuven, Leuven, Belgium
| | - Daniel A Dias
- Metabolomics Australia, School of Botany, University of Melbourne, Melbourne, Australia
| | - Berin Boughton
- Metabolomics Australia, School of Botany, University of Melbourne, Melbourne, Australia
| | - Kurt Boonen
- Functional Genomics and Proteomics, Department of Biology, KU Leuven, Leuven, Belgium
| | - Bart P Braeckman
- Laboratory for Aging Physiology and Molecular Evolution, Department of Biology, Ghent University, Ghent, Belgium
| | - Liliane Schoofs
- Functional Genomics and Proteomics, Department of Biology, KU Leuven, Leuven, Belgium
| | - Ute Roessner
- Metabolomics Australia, School of Botany, University of Melbourne, Melbourne, Australia
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