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Transcriptome Analysis of the Marine Nematode Litoditis marina in a Chemically Defined Food Environment with Stearic Acid Supplementation. JOURNAL OF MARINE SCIENCE AND ENGINEERING 2022. [DOI: 10.3390/jmse10030428] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Stearic acid represents one of the most abundant fatty acids in the Western diet and profoundly regulates health and diseases of animals and human beings. We previously showed that stearic acid supplementation promoted development of the terrestrial model nematode Caenorhabditis elegans in chemically defined CeMM food environment. However, whether stearic acid regulates development of other nematodes remains unknown. Here, we found that dietary supplementation with stearic acid could promote the development of the marine nematode Litoditis marina, belonging to the same family as C. elegans, indicating the conserved roles of stearic acid in developmental regulation. We further employed transcriptome analysis to analyze genome-wide transcriptional signatures of L. marina with dietary stearic acid supplementation. We found that stearic acid might promote development of L. marina via upregulation of the expression of genes involved in aminoacyl-tRNA biosynthesis, translation initiation and elongation, ribosome biogenesis, and transmembrane transport. In addition, we observed that the expression of neuronal signaling-related genes was decreased. This study provided important insights into how a single fatty acid stearic acid regulates development of marine nematode, and further studies with CRISPR genome editing will facilitate demonstrating the molecular mechanisms underlying how a single metabolite regulates animal development and health.
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Hastings J, Mains A, Virk B, Rodriguez N, Murdoch S, Pearce J, Bergmann S, Le Novère N, Casanueva O. Multi-Omics and Genome-Scale Modeling Reveal a Metabolic Shift During C. elegans Aging. Front Mol Biosci 2019; 6:2. [PMID: 30788345 PMCID: PMC6372924 DOI: 10.3389/fmolb.2019.00002] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 01/17/2019] [Indexed: 12/24/2022] Open
Abstract
In this contribution, we describe a multi-omics systems biology study of the metabolic changes that occur during aging in Caenorhabditis elegans. Sampling several time points from young adulthood until early old age, our study covers the full duration of aging and include transcriptomics, and targeted MS-based metabolomics. In order to focus on the metabolic changes due to age we used two strains that are metabolically close to wild-type, yet are conditionally non-reproductive. Using these data in combination with a whole-genome model of the metabolism of C. elegans and mathematical modeling, we predicted metabolic fluxes during early aging. We find that standard Flux Balance Analysis does not accurately predict in vivo measured fluxes nor age-related changes associated with the Citric Acid cycle. We present a novel Flux Balance Analysis method where we combined biomass production and targeted metabolomics information to generate an objective function that is more suitable for aging studies. We validated this approach with a detailed case study of the age-associated changes in the Citric Acid cycle. Our approach provides a comprehensive time-resolved multi-omics and modeling resource for studying the metabolic changes during normal aging in C. elegans.
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Affiliation(s)
- Janna Hastings
- Department of Epigenetics, Babraham Institute, Cambridge, United Kingdom
| | - Abraham Mains
- Department of Epigenetics, Babraham Institute, Cambridge, United Kingdom
| | - Bhupinder Virk
- Department of Epigenetics, Babraham Institute, Cambridge, United Kingdom
| | - Nicolas Rodriguez
- Department of Epigenetics, Babraham Institute, Cambridge, United Kingdom
| | - Sharlene Murdoch
- Department of Epigenetics, Babraham Institute, Cambridge, United Kingdom
| | - Juliette Pearce
- Department of Epigenetics, Babraham Institute, Cambridge, United Kingdom
| | - Sven Bergmann
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
| | - Nicolas Le Novère
- Department of Epigenetics, Babraham Institute, Cambridge, United Kingdom
| | - Olivia Casanueva
- Department of Epigenetics, Babraham Institute, Cambridge, United Kingdom
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Lambie EJ, Bruce RD, Zielich J, Yuen SN. Novel Alleles of gon-2, a C. elegans Ortholog of Mammalian TRPM6 and TRPM7, Obtained by Genetic Reversion Screens. PLoS One 2015; 10:e0143445. [PMID: 26606136 PMCID: PMC4659536 DOI: 10.1371/journal.pone.0143445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Accepted: 11/04/2015] [Indexed: 11/19/2022] Open
Abstract
TRP (Transient Receptor Potential) cation channels of the TRPM subfamily have been found to be critically important for the regulation of Mg2+ homeostasis in both protostomes (e.g., the nematode, C. elegans, and the insect, D. melanogaster) and deuterostomes (e.g., humans). Although significant progress has been made toward understanding how the activities of these channels are regulated, there are still major gaps in our understanding of the potential regulatory roles of extensive, evolutionarily conserved, regions of these proteins. The C. elegans genes, gon-2, gtl-1 and gtl-2, encode paralogous TRP cation channel proteins that are similar in sequence and function to human TRPM6 and TRPM7. We isolated fourteen revertants of the missense mutant, gon-2(q338), and these mutations affect nine different residues within GON-2. Since eight of the nine affected residues are situated within regions that have high similarity to human TRPM1,3,6 and 7, these mutations identify sections of these channels that are potentially critical for channel regulation. We also isolated a single mutant allele of gon-2 during a screen for revertants of the Mg2+-hypersensitive phenotype of gtl-2(-) mutants. This allele of gon-2 converts a serine to phenylalanine within the highly conserved TRP domain, and is antimorphic against both gon-2(+) and gtl-1(+). Interestingly, others have reported that mutation of the corresponding residue in TRPM7 to glutamate results in deregulated channel activity.
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Affiliation(s)
- Eric J. Lambie
- Department of Cell and Developmental Biology, Ludwig Maximilian University, Munich, Germany
- * E-mail:
| | - Robert D. Bruce
- Dept. of Internal Medicine, Madigan Army Medical Center, Fort Lewis-McChord, Washington, United States of America
| | - Jeffrey Zielich
- Department of Cell and Developmental Biology, Ludwig Maximilian University, Munich, Germany
| | - Sonia N. Yuen
- Department of Otolaryngology, Boston Children’s Hospital, Boston, Massachusetts, United States of America
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Lambie EJ, Tieu PJ, Lebedeva N, Church DL, Conradt B. CATP-6, a C. elegans ortholog of ATP13A2 PARK9, positively regulates GEM-1, an SLC16A transporter. PLoS One 2013; 8:e77202. [PMID: 24130856 PMCID: PMC3793975 DOI: 10.1371/journal.pone.0077202] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2013] [Accepted: 09/06/2013] [Indexed: 11/27/2022] Open
Abstract
In previous work, we found that gain-of-function mutations that hyperactivate GEM-1 (an SLC16A transporter protein) can bypass the requirement for GON-2 (a TRPM channel protein) during the initiation of gonadogenesis in C. elegans. Consequently, we proposed that GEM-1 might function as part of a Mg2+ uptake pathway that functions in parallel to GON-2. In this study, we report that CATP-6, a C. elegans ortholog of the P5B ATPase, ATP13A2 (PARK9), is necessary for gem-1 gain-of-function mutations to suppress the effects of gon-2 inactivation. One possible explanation for this observation is that GEM-1 serves to activate CATP-6, which then functions as a Mg2+ transporter. However, we found that overexpression of GEM-1 can alleviate the requirement for CATP-6 activity, suggesting that CATP-6 probably acts as a non-essential upstream positive regulator of GEM-1. Our results are consistent with the notion that P5B ATPases govern intracellular levels of Mg2+ and/or Mn2+ by regulating the trafficking of transporters and other proteins associated with the plasma membrane.
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Affiliation(s)
- Eric J. Lambie
- Department of Cell and Developmental Biology, Ludwig-Maximillians-University, Munich, Planegg-Martinsried, Germany
- * E-mail:
| | - Pamela J. Tieu
- Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire, United States of America
| | - Nadja Lebedeva
- Department of Cell and Developmental Biology, Ludwig-Maximillians-University, Munich, Planegg-Martinsried, Germany
| | - Diane L. Church
- Parkinson's Center, Dartmouth Hitchcock Medical Center, Lebanon, New Hampshire, United States of America
| | - Barbara Conradt
- Department of Cell and Developmental Biology, Ludwig-Maximillians-University, Munich, Planegg-Martinsried, Germany
- CIPS Center for Integrated Protein Science, Ludwig-Maximilians-University, Munich, Germany
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Mapping mutations in C. elegans. Methods Cell Biol 2011. [PMID: 22118272 DOI: 10.1016/b978-0-12-544172-8.00001-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
At present, the principal goal of mapping is to establish correspondence between a mutation identified via a change in phenotype and an alteration in the DNA sequence of the genome. Recent advances in molecular biology and bioinformatics have greatly facilitated this procedure, but certain standard methods, such as the three-factor cross, continue to be extremely useful for high-resolution mapping and separation of tightly linked mutations. This chapter provides both general guidelines and specific procedures for the characterization and mapping of newly isolated mutations in C. elegans. Procedures are included for dealing with mutations that cannot be propagated as homozygotes, as well as mutations that can only be scored in specialized genetic backgrounds, for example, suppressor, enhancer, and modifier mutations.
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Mouchiroud L, Molin L, Kasturi P, Triba MN, Dumas ME, Wilson MC, Halestrap AP, Roussel D, Masse I, Dallière N, Ségalat L, Billaud M, Solari F. Pyruvate imbalance mediates metabolic reprogramming and mimics lifespan extension by dietary restriction in Caenorhabditis elegans. Aging Cell 2011; 10:39-54. [PMID: 21040400 DOI: 10.1111/j.1474-9726.2010.00640.x] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Dietary restriction (DR) is the most universal intervention known to extend animal lifespan. DR also prevents tumor development in mammals, and this effect requires the tumor suppressor PTEN. However, the metabolic and cellular processes that underly the beneficial effects of DR are poorly understood. We identified slcf-1 in an RNAi screen for genes that extend Caenorhabditis elegans lifespan in a PTEN/daf-18-dependent manner. We showed that slcf-1 mutation, which increases average lifespan by 40%, mimics DR in worms fed ad libitum. An NMR-based metabolomic characterization of slcf-1 mutants revealed lower lipid levels compared to wild-type animals, as expected for dietary-restricted animals, but also higher pyruvate content. Epistasis experiments and metabolic measurements support a model in which the long lifespan of slcf-1 mutants relies on increased mitochondrial pyruvate metabolism coupled to an adaptive response to oxidative stress. This response requires DAF-18/PTEN and the previously identified DR effectors PHA-4/FOXA, HSF-1/HSF1, SIR-2.1/SIRT-1, and AMPK/AAK-2. Overall, our data show that pyruvate homeostasis plays a central role in lifespan control in C. elegans and that the beneficial effects of DR results from a hormetic mechanism involving the mitochondria. Analysis of the SLCF-1 protein sequence predicts that slcf-1 encodes a plasma membrane transporter belonging to the conserved monocarboxylate transporter family. These findings suggest that inhibition of this transporter homolog in mammals might also promote a DR response.
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Affiliation(s)
- Laurent Mouchiroud
- UMR5201, CNRS, Université de Lyon, Centre Léon Bérard, 28 Rue Laennec, Lyon 69373, France
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Abstract
Transient receptor potential (TRP) channels represent a superfamily of cation channels found in all eukaryotes. The C. elegans genome encodes seventeen TRP channels covering all of the seven TRP subfamilies. Genetic analyses in C. elegans have implicated TRP channels in a wide spectrum of behavioral and physiological processes, ranging from sensory transduction (e.g. chemosensation, touch sensation, proprioception and osmosensation) to fertilization, drug dependence, organelle biogenesis, apoptosis, gene expression, and neurotransmitter/hormone release. Many C. elegans TRP channels share similar activation and regulatory mechanisms with their vertebrate counterparts. Studies in C. elegans have also revealed some previously unrecognized functions and regulatory mechanisms of TRP channels. C. elegans represents an excellent genetic model organism for the study of function and regulation of TRP channels in vivo.
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Affiliation(s)
- Rui Xiao
- Department of Molecular and Integrative Physiology, Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA.
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Iwasa H, Yu S, Xue J, Driscoll M. Novel EGF pathway regulators modulate C. elegans healthspan and lifespan via EGF receptor, PLC-gamma, and IP3R activation. Aging Cell 2010; 9:490-505. [PMID: 20497132 DOI: 10.1111/j.1474-9726.2010.00575.x] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Improving health of the rapidly growing aging population is a critical medical, social, and economic goal. Identification of genes that modulate healthspan, the period of mid-life vigor that precedes significant functional decline, will be an essential part of the effort to design anti-aging therapies. Because locomotory decline in humans is a major contributor to frailty and loss of independence and because slowing of movement is a conserved feature of aging across phyla, we screened for genetic interventions that extend locomotory healthspan of Caenorhabditis elegans. From a group of 54 genes previously noted to encode secreted proteins similar in sequence to extracellular domains of insulin receptor, we identified two genes for which RNAi knockdown delayed age-associated locomotory decline, conferring a high performance in advanced age phenotype (Hpa). Unexpectedly, we found that hpa-1 and hpa-2 act through the EGF pathway, rather than the insulin signaling pathway, to control systemic healthspan benefits without detectable developmental consequences. Further analysis revealed a potent role of EGF signaling, acting via downstream phospholipase C-gammaplc-3 and inositol-3-phosphate receptor itr-1, to promote healthy aging associated with low lipofuscin levels, enhanced physical performance, and extended lifespan. This study identifies HPA-1 and HPA-2 as novel negative regulators of EGF signaling and constitutes the first report of EGF signaling as a major pathway for healthy aging. Our data raise the possibility that EGF family members should be investigated for similar activities in higher organisms.
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Affiliation(s)
- Hiroaki Iwasa
- Department of Medical Biochemistry, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo 113-8510, Japan
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Korta DZ, Hubbard EJA. Soma-germline interactions that influence germline proliferation in Caenorhabditis elegans. Dev Dyn 2010; 239:1449-59. [PMID: 20225254 PMCID: PMC3323287 DOI: 10.1002/dvdy.22268] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Caenorhabditis elegans boasts a short lifecycle and high fecundity, two features that make it an attractive and powerful genetic model organism. Several recent studies indicate that germline proliferation, a prerequisite to optimal fecundity, is tightly controlled over the course of development. Cell proliferation control includes regulation of competence to proliferate, a poorly understood aspect of cell fate specification, as well as cell-cycle control. Furthermore, dynamic regulation of cell proliferation occurs in response to multiple external signals. The C. elegans germ line is proving a valuable model for linking genetic, developmental, systemic, and environmental control of cell proliferation. Here, we consider recent studies that contribute to our understanding of germ cell proliferation in C. elegans. We focus primarily on somatic control of germline proliferation, how it differs at different life stages, and how it can be altered in the context of the life cycle and changes in environmental status.
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Affiliation(s)
- Dorota Z. Korta
- Developmental Genetics Program, Department of Pathology, Helen and Martin Kimmel Center for Stem Cell Biology, Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, New York
| | - E. Jane Albert Hubbard
- Developmental Genetics Program, Department of Pathology, Helen and Martin Kimmel Center for Stem Cell Biology, Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, New York
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Teramoto T, Sternick LA, Kage-Nakadai E, Sajjadi S, Siembida J, Mitani S, Iwasaki K, Lambie EJ. Magnesium excretion in C. elegans requires the activity of the GTL-2 TRPM channel. PLoS One 2010; 5:e9589. [PMID: 20221407 PMCID: PMC2833210 DOI: 10.1371/journal.pone.0009589] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2009] [Accepted: 02/11/2010] [Indexed: 11/25/2022] Open
Abstract
Systemic magnesium homeostasis in mammals is primarily governed by the activities of the TRPM6 and TRPM7 cation channels, which mediate both uptake by the intestinal epithelial cells and reabsorption by the distal convoluted tubule cells in the kidney. In the nematode, C. elegans, intestinal magnesium uptake is dependent on the activities of the TRPM channel proteins, GON-2 and GTL-1. In this paper we provide evidence that another member of the TRPM protein family, GTL-2, acts within the C. elegans excretory cell to mediate the excretion of excess magnesium. Thus, the activity of GTL-2 balances the activities of the paralogous TRPM channel proteins, GON-2 and GTL-1.
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Affiliation(s)
- Takayuki Teramoto
- Department of Biology, Kyushu University, Higashi-ku, Fukuoka, Japan
| | - Laura A. Sternick
- Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire, United States of America
| | - Eriko Kage-Nakadai
- Department of Physiology, Tokyo Women's Medical University School of Medicine, Tokyo, Japan
| | - Shirine Sajjadi
- Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire, United States of America
| | - Jakub Siembida
- Department of Molecular Pharmacology & Biological Chemistry, Northwestern University Feinberg School of Medicine, Chicago, Illinois, United States of America
| | - Shohei Mitani
- Department of Physiology, Tokyo Women's Medical University School of Medicine, Tokyo, Japan
| | - Kouichi Iwasaki
- Department of Molecular Pharmacology & Biological Chemistry, Northwestern University Feinberg School of Medicine, Chicago, Illinois, United States of America
| | - Eric J. Lambie
- Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire, United States of America
- * E-mail:
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Davis DE, Roh HC, Deshmukh K, Bruinsma JJ, Schneider DL, Guthrie J, Robertson JD, Kornfeld K. The cation diffusion facilitator gene cdf-2 mediates zinc metabolism in Caenorhabditis elegans. Genetics 2009; 182:1015-33. [PMID: 19448268 PMCID: PMC2728845 DOI: 10.1534/genetics.109.103614] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2009] [Accepted: 05/12/2009] [Indexed: 12/11/2022] Open
Abstract
Zinc is essential for many cellular processes. To use Caenorhabditis elegans to study zinc metabolism, we developed culture conditions allowing full control of dietary zinc and methods to measure zinc content of animals. Dietary zinc dramatically affected growth and zinc content; wild-type worms survived from 7 microm to 1.3 mm dietary zinc, and zinc content varied 27-fold. We investigated cdf-2, which encodes a predicted zinc transporter in the cation diffusion facilitator family. cdf-2 mRNA levels were increased by high dietary zinc, suggesting cdf-2 promotes zinc homeostasis. CDF-2 protein was expressed in intestinal cells and localized to cytosolic vesicles. A cdf-2 loss-of-function mutant displayed impaired growth and reduced zinc content, indicating that CDF-2 stores zinc by transport into the lumen of vesicles. The relationships between three cdf genes, cdf-1, cdf-2, and sur-7, were analyzed in double and triple mutant animals. A cdf-1 mutant displayed increased zinc content, whereas a cdf-1 cdf-2 double mutant had intermediate zinc content, suggesting cdf-1 and cdf-2 have antagonistic functions. These studies advance C. elegans as a model of zinc metabolism and identify cdf-2 as a new gene that has a critical role in zinc storage.
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Affiliation(s)
- Diana E Davis
- Department of Developmental Biology, Washington University School of Medicine, Saint Louis, Missouri 63110, USA
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