1
|
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.
Collapse
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
| | | |
Collapse
|
2
|
Developmental plasticity and the response to nutrient stress in Caenorhabditis elegans. Dev Biol 2021; 475:265-276. [PMID: 33549550 DOI: 10.1016/j.ydbio.2021.01.015] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 12/24/2020] [Accepted: 01/29/2021] [Indexed: 11/23/2022]
Abstract
Developmental plasticity refers the ability of an organism to adapt to various environmental stressors, one of which is nutritional stress. Caenorhabditis elegans require various nutrients to successfully progress through all the larval stages to become a reproductive adult. If nutritional criteria are not satisfied, development can slow or completely arrest. In poor growth conditions, the animal can enter various diapause stages, depending on its developmental progress. In C. elegans, there are three well-characterized diapauses: the L1 arrest, the dauer diapause, and adult reproductive diapause, each associated with drastic changes in metabolism and germline development. At the centre of these changes is AMP-activated protein kinase (AMPK). AMPK is a metabolic regulator that maintains energy homeostasis, particularly during times of nutrient stress. Without AMPK, metabolism is disrupted during dauer, leading to the rapid consumption of lipid stores as well as misregulation of metabolic enzymes, leading to reduced survival. During the L1 arrest and dauer diapause, AMPK is responsible for ensuring germline quiescence by modifying the germline chromatin landscape to maintain germ cell integrity until conditions improve. Similar to classic hormonal signalling, small RNAs also play a critical role in regulating development and behaviour in a cell non-autonomous fashion. Thus, during the challenges associated with developmental plasticity, AMPK summons an army of signalling pathways to work collectively to preserve reproductive fitness during these periods of unprecedented uncertainty.
Collapse
|
3
|
Goncalves J, Wan Y, Guo X, Rha K, LeBoeuf B, Zhang L, Estler K, Garcia LR. Succinate Dehydrogenase-Regulated Phosphoenolpyruvate Carboxykinase Sustains Copulation Fitness in Aging C. elegans Males. iScience 2020; 23:100990. [PMID: 32240955 PMCID: PMC7115159 DOI: 10.1016/j.isci.2020.100990] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 02/18/2020] [Accepted: 03/11/2020] [Indexed: 01/02/2023] Open
Abstract
Dysregulated metabolism accelerates reduced decision-making and locomotor ability during aging. To identify mechanisms for delaying behavioral decline, we investigated how C. elegans males sustain their copulatory behavior during early to mid-adulthood. We found that in mid-aged males, gluco-/glyceroneogenesis, promoted by phosphoenolpyruvate carboxykinase (PEPCK), sustains competitive reproductive behavior. C. elegans' PEPCK paralogs, pck-1 and pck-2, increase in expression during the first 2 days of adulthood. Insufficient PEPCK expression correlates with reduced egl-2-encoded ether-a-go-go K+ channel expression and premature hyper-excitability of copulatory circuits. For copulation, pck-1 is required in neurons, whereas pck-2 is required in the epidermis. However, PCK-2 is more essential, because we found that epidermal PCK-2 likely supplements the copulation circuitry with fuel. We identified the subunit A of succinate dehydrogenase SDHA-1 as a potent modulator of PEPCK expression. We postulate that during mid-adulthood, reduction in mitochondrial physiology signals the upregulation of cytosolic PEPCK to sustain the male's energy demands. C. elegans upregulates pck-1- and pck-2-encoded PEPCK during early adulthood Loss of PEPCK causes premature male copulatory behavior decline Epidermal PEPCK is required to sustain the copulatory fitness Subunit A of succinate dehydrogenase antagonizes PEPCK expression
Collapse
Affiliation(s)
- Jimmy Goncalves
- Department of Biology, Texas A&M University, College Station, TX 77843, USA
| | - Yufeng Wan
- Department of Biology, Texas A&M University, College Station, TX 77843, USA
| | - Xiaoyan Guo
- Institute for Neurodegenerative Diseases, University of California, San Francisco, CA 94158, USA
| | - Kyoungsun Rha
- Department of Biology, Texas A&M University, College Station, TX 77843, USA
| | - Brigitte LeBoeuf
- Department of Biology, Texas A&M University, College Station, TX 77843, USA
| | - Liusuo Zhang
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, Shandong 266071, China
| | - Kerolayne Estler
- Department of Biology, Texas A&M University, College Station, TX 77843, USA
| | - L René Garcia
- Department of Biology, Texas A&M University, College Station, TX 77843, USA.
| |
Collapse
|
4
|
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.
Collapse
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
| | | |
Collapse
|
5
|
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: 73] [Impact Index Per Article: 18.3] [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.
Collapse
|
6
|
Christy SF, Wernick RI, Lue MJ, Velasco G, Howe DK, Denver DR, Estes S. Adaptive Evolution under Extreme Genetic Drift in Oxidatively Stressed Caenorhabditis elegans. Genome Biol Evol 2018; 9:3008-3022. [PMID: 29069345 PMCID: PMC5714194 DOI: 10.1093/gbe/evx222] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/21/2017] [Indexed: 12/30/2022] Open
Abstract
A mutation-accumulation (MA) experiment with Caenorhabditis elegans nematodes was conducted in which replicate, independently evolving lines were initiated from a low-fitness mitochondrial electron transport chain mutant, gas-1. The original intent of the study was to assess the effect of electron transport chain dysfunction involving elevated reactive oxygen species production on patterns of spontaneous germline mutation. In contrast to results of standard MA experiments, gas-1 MA lines evolved slightly higher mean fitness alongside reduced among-line genetic variance compared with their ancestor. Likewise, the gas-1 MA lines experienced partial recovery to wildtype reactive oxygen species levels. Whole-genome sequencing and analysis revealed that the molecular spectrum but not the overall rate of nuclear DNA mutation differed from wildtype patterns. Further analysis revealed an enrichment of mutations in loci that occur in a gas-1-centric region of the C. elegans interactome, and could be classified into a small number of functional-genomic categories. Characterization of a backcrossed four-mutation set isolated from one gas-1 MA line revealed this combination to be beneficial on both gas-1 mutant and wildtype genetic backgrounds. Our combined results suggest that selection favoring beneficial mutations can be powerful even under unfavorable population genetic conditions, and agree with fitness landscape theory predicting an inverse relationship between population fitness and the likelihood of adaptation.
Collapse
Affiliation(s)
| | | | | | | | - Dana K Howe
- Department of Integrative Biology, Oregon State University
| | - Dee R Denver
- Department of Integrative Biology, Oregon State University
| | | |
Collapse
|
7
|
Llorens C, Arcos SC, Robertson L, Ramos R, Futami R, Soriano B, Ciordia S, Careche M, González-Muñoz M, Jiménez-Ruiz Y, Carballeda-Sangiao N, Moneo I, Albar JP, Blaxter M, Navas A. Functional insights into the infective larval stage of Anisakis simplex s.s., Anisakis pegreffii and their hybrids based on gene expression patterns. BMC Genomics 2018; 19:592. [PMID: 30086708 PMCID: PMC6080401 DOI: 10.1186/s12864-018-4970-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 07/30/2018] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Anisakis simplex sensu stricto and Anisakis pegreffii are sibling species of nematodes parasitic on marine mammals. Zoonotic human infection with third stage infective larvae causes anisakiasis, a debilitating and potentially fatal disease. These 2 species show evidence of hybridisation in geographical areas where they are sympatric. How the species and their hybrids differ is still poorly understood. RESULTS Third stage larvae of Anisakis simplex s.s., Anisakis pegreffii and hybrids were sampled from Merluccius merluccius (Teleosti) hosts captured in waters of the FAO 27 geographical area. Specimens of each species and hybrids were distinguished with a diagnostic genetic marker (ITS). RNA was extracted from pools of 10 individuals of each taxon. Transcriptomes were generated using Illumina RNA-Seq, and assembled de novo. A joint assembly (here called merged transcriptome) of all 3 samples was also generated. The inferred transcript sets were functionally annotated and compared globally and also on subsets of secreted proteins and putative allergen families. While intermediary metabolism appeared to be typical for nematodes in the 3 evaluated taxa, their transcriptomes present strong levels of differential expression and enrichment, mainly of transcripts related to metabolic pathways and gene ontologies associated to energy metabolism and other pathways, with significant presence of excreted/secreted proteins, most of them allergens. The allergome of the 2 species and their hybrids has also been thoroughly studied; at least 74 different allergen families were identified in the transcriptomes. CONCLUSIONS A. simplex s.s., A. pegreffi and their hybrids differ in gene expression patterns in the L3 stage. Strong parent-of-origin effects were observed: A. pegreffi alleles dominate in the expression patterns of hybrids albeit the latter, and A. pegreffii also display significant differences indicating that hybrids are intermediate biological entities among their parental species, and thus of outstanding interest in the study of speciation in nematodes. Analyses of differential expression based on genes coding for secreted proteins suggests that co-infections presents different repertoires of released protein to the host environment. Both species and their hybrids, share more allergen genes than previously thought and are likely to induce overlapping disease responses.
Collapse
Affiliation(s)
- C. Llorens
- Biotechvana, Scientific Park, University of Valencia, Calle Catedrático José Beltrán 2, 46980 Paterna, Valencia Spain
| | - S. C. Arcos
- Departamento Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales, CSIC, Calle José Gutiérrez Abascal, 2, 28006 Madrid, Spain
| | - L. Robertson
- Departamento Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales, CSIC, Calle José Gutiérrez Abascal, 2, 28006 Madrid, Spain
| | - R. Ramos
- Unidad de Genómica, Campus de Cantoblanco, Scientific Park of Madrid, Calle Faraday, 7, Campus de Cantoblanco, 28049 Madrid, Spain
| | - R. Futami
- Biotechvana, Scientific Park, University of Valencia, Calle Catedrático José Beltrán 2, 46980 Paterna, Valencia Spain
| | - B. Soriano
- Biotechvana, Scientific Park, University of Valencia, Calle Catedrático José Beltrán 2, 46980 Paterna, Valencia Spain
| | - S. Ciordia
- Unidad de Proteomica Centro Nacional de Biotecnología, CSIC, Calle Darwin, 3, 28049 Madrid, Spain
| | - M. Careche
- Instituto de Ciencia y Tecnología de Alimentos y Nutrición (ICTAN), Calle José Antonio Novais, 10, 28040 Madrid, Spain
| | - M. González-Muñoz
- Servicio de Immunología, Hospital Universitario La Paz, Paseo de la Castellana, 261, 28046 Madrid, Spain
| | - Y. Jiménez-Ruiz
- Departamento Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales, CSIC, Calle José Gutiérrez Abascal, 2, 28006 Madrid, Spain
| | - N. Carballeda-Sangiao
- Servicio de Immunología, Hospital Universitario La Paz, Paseo de la Castellana, 261, 28046 Madrid, Spain
| | - I. Moneo
- Servicio de Immunología, Hospital Universitario La Paz, Paseo de la Castellana, 261, 28046 Madrid, Spain
| | - J. P. Albar
- Unidad de Proteomica Centro Nacional de Biotecnología, CSIC, Calle Darwin, 3, 28049 Madrid, Spain
| | - M. Blaxter
- Edinburgh Genomics, and Institute of Evolutionary Biology, School of Biological Sciences, The King’s Buildings, The University of Edinburgh, Edinburgh, EH9 3JT UK
| | - A. Navas
- Departamento Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales, CSIC, Calle José Gutiérrez Abascal, 2, 28006 Madrid, Spain
| |
Collapse
|
8
|
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: 96] [Impact Index Per Article: 13.7] [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.
Collapse
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
| |
Collapse
|
9
|
Ziv T, Chalifa-Caspi V, Denekamp N, Plaschkes I, Kierszniowska S, Blais I, Admon A, Lubzens E. Dormancy in Embryos: Insight from Hydrated Encysted Embryos of an Aquatic Invertebrate. Mol Cell Proteomics 2017; 16:1746-1769. [PMID: 28729386 DOI: 10.1074/mcp.ra117.000109] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Indexed: 11/06/2022] Open
Abstract
Numerous aquatic invertebrates remain dormant for decades in a hydrated state as encysted embryos. In search for functional pathways associated with this form of dormancy, we used label-free quantitative proteomics to compare the proteomes of hydrated encysted dormant embryos (resting eggs; RE) with nondormant embryos (amictic eggs; AM) of the rotifer Brachionus plicatilisA total of 2631 proteins were identified in rotifer eggs. About 62% proteins showed higher abundance in AM relative to RE (Fold Change>3; p = 0.05). Proteins belonging to numerous putative functional pathways showed dramatic changes during dormancy. Most striking were changes in the mitochondria indicating an impeded metabolism. A comparison between the abundance of proteins and their corresponding transcript levels, revealed higher concordance for RE than for AM. Surprisingly, numerous highly abundant dormancy related proteins show corresponding high mRNA levels in metabolically inactive RE. As these mRNAs and proteins degrade at the time of exit from dormancy they may serve as a source of nucleotides and amino acids during the exit from dormancy. Because proteome analyses point to a similarity in functional pathways of hydrated RE and desiccated life forms, REs were dried. Similar hatching and reproductive rates were found for wet and dried REs, suggesting analogous pathways for long-term survival in wet or dry forms. Analysis by KEGG pathways revealed a few general strategies for dormancy, proposing an explanation for the low transcriptional similarity among dormancies across species, despite the resemblance in physiological phenotypes.
Collapse
Affiliation(s)
- Tamar Ziv
- From the ‡Faculty of Biology, Technion-Israel Institute of Technology, Haifa, Israel
| | - Vered Chalifa-Caspi
- §National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Nadav Denekamp
- ¶Israel Oceanographic and Limnological Research, Haifa, Israel
| | - Inbar Plaschkes
- §National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | | | - Idit Blais
- **Division of Reproductive Endocrinology and IVF, Department of Obstetrics and Gynecology, Carmel Medical Center, Haifa, Israel
| | - Arie Admon
- From the ‡Faculty of Biology, Technion-Israel Institute of Technology, Haifa, Israel
| | - Esther Lubzens
- From the ‡Faculty of Biology, Technion-Israel Institute of Technology, Haifa, Israel;
| |
Collapse
|
10
|
Cui S, Wang L, Qiu J, Liu Z, Geng X. Comparative metabolomics analysis of Callosobruchus chinensis larvae under hypoxia, hypoxia/hypercapnia and normoxia. PEST MANAGEMENT SCIENCE 2017; 73:1267-1276. [PMID: 27718517 DOI: 10.1002/ps.4455] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Revised: 10/02/2016] [Accepted: 10/02/2016] [Indexed: 06/06/2023]
Abstract
BACKGROUND Insect tolerance to low oxygen (hypoxia) and high carbon dioxide (hypercapnia) is critical for insect control. On the basis of bioassay, metabolism profiles were built to investigate adaptive mechanisms in bean weevil under hypoxia (2% O2 ), hypoxia/hypercapnia (2% O2 + 18% CO2 ) and normoxia (control, 20% O2 + 80% N2 ) using gas chromatography/time-of-flight mass spectrometry (GC/TOF-MS). RESULTS The growth and development of bean weevils were significantly suppressed by the two hypoxia conditions; hypercapnia enhanced the mortality, but after 24 days of exposure, the surviving insects emerged as adults earlier than those under hypoxia only. Metabolism profiles also showed striking differences in metabolites among the treatment and control groups, both quantitatively and qualitatively. Pairwise comparisons of the three groups showed that 61 metabolites changed significantly, 40 in the hypoxia group and 37 in the hypoxia/hypercapnia group relative to the control group, while only 16 were shared equally by the hypoxia and hypoxia/hypercapnia groups. Increased metabolites were mainly carbohydrates, amino acids and organic acids, while free fatty acids were decreased. Furthermore, the changes were strengthened by the addition of hypercapnia, but excluding free fatty acids. CONCLUSION The findings show that bean weevil has high tolerance to hypoxia or even hypoxia/hypercapnia at biologically achievable levels and provide more direct evidence for stored product insect mechanism regulation under hypoxia stress, especially free fatty acid regulation by hypercapnia but not by hypoxia. © 2016 Society of Chemical Industry.
Collapse
Affiliation(s)
- Sufen Cui
- Key Laboratory of Urban Agriculture (South), Ministry of Agriculture, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Lei Wang
- Key Laboratory of Urban Agriculture (South), Ministry of Agriculture, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Jiangping Qiu
- Key Laboratory of Urban Agriculture (South), Ministry of Agriculture, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Zhicheng Liu
- Key Laboratory of Urban Agriculture (South), Ministry of Agriculture, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Xueqing Geng
- Key Laboratory of Urban Agriculture (South), Ministry of Agriculture, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| |
Collapse
|
11
|
Hussey R, Stieglitz J, Mesgarzadeh J, Locke TT, Zhang YK, Schroeder FC, Srinivasan S. Pheromone-sensing neurons regulate peripheral lipid metabolism in Caenorhabditis elegans. PLoS Genet 2017; 13:e1006806. [PMID: 28545126 PMCID: PMC5456406 DOI: 10.1371/journal.pgen.1006806] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Revised: 06/02/2017] [Accepted: 05/05/2017] [Indexed: 12/03/2022] Open
Abstract
It is now established that the central nervous system plays an important role in regulating whole body metabolism and energy balance. However, the extent to which sensory systems relay environmental information to modulate metabolic events in peripheral tissues has remained poorly understood. In addition, it has been challenging to map the molecular mechanisms underlying discrete sensory modalities with respect to their role in lipid metabolism. In previous work our lab has identified instructive roles for serotonin signaling as a surrogate for food availability, as well as oxygen sensing, in the control of whole body metabolism. In this study, we now identify a role for a pair of pheromone-sensing neurons in regulating fat metabolism in C. elegans, which has emerged as a tractable and highly informative model to study the neurobiology of metabolism. A genetic screen revealed that GPA-3, a member of the Gα family of G proteins, regulates body fat content in the intestine, the major metabolic organ for C. elegans. Genetic and reconstitution studies revealed that the potent body fat phenotype of gpa-3 null mutants is controlled from a pair of neurons called ADL(L/R). We show that cAMP functions as the second messenger in the ADL neurons, and regulates body fat stores via the neurotransmitter acetylcholine, from downstream neurons. We find that the pheromone ascr#3, which is detected by the ADL neurons, regulates body fat stores in a GPA-3-dependent manner. We define here a third sensory modality, pheromone sensing, as a major regulator of body fat metabolism. The pheromone ascr#3 is an indicator of population density, thus we hypothesize that pheromone sensing provides a salient 'denominator' to evaluate the amount of food available within a population and to accordingly adjust metabolic rate and body fat levels. The central nervous system plays a vital role in regulating whole body metabolism and energy balance. However, the precise cellular, genetic and molecular mechanisms underlying these effects remain a major unsolved mystery. C. elegans has emerged as a tractable and highly informative model to study the neurobiology of metabolism. Previously, we have identified instructive roles for serotonin signaling as a surrogate for food availability, as well as oxygen sensing, in the control of whole body metabolism. In our current study we have identified a role for a pair of pheromone-sensing neurons in regulating fat metabolism in C. elegans. cAMP acts as a second messenger in these neurons, and regulates body fat stores via acetylcholine signaling in the nervous system. We find that the population-density-sensing pheromone detected by these neurons regulates body fat stores. Together, we define a third sensory modality, population density sensing, as a major regulator of body fat metabolism.
Collapse
Affiliation(s)
- Rosalind Hussey
- Department of Molecular Medicine and Department of Neuroscience, The Scripps Research Institute, La Jolla, California, United States of America
- Dorris Neuroscience Center, The Scripps Research Institute, La Jolla, California, United States of America
| | - Jon Stieglitz
- Kellogg School of Science and Technology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Jaleh Mesgarzadeh
- Department of Molecular Medicine and Department of Neuroscience, The Scripps Research Institute, La Jolla, California, United States of America
- Department of Biology, University of California, San Diego, La Jolla, California, United States of America
| | - Tiffany T. Locke
- Department of Biology, University of California, San Diego, La Jolla, California, United States of America
| | - Ying K. Zhang
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York, United States of America
| | - Frank C. Schroeder
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York, United States of America
| | - Supriya Srinivasan
- Department of Molecular Medicine and Department of Neuroscience, The Scripps Research Institute, La Jolla, California, United States of America
- Dorris Neuroscience Center, The Scripps Research Institute, La Jolla, California, United States of America
- * E-mail:
| |
Collapse
|
12
|
Zhao JY, Zhao XT, Sun JT, Zou LF, Yang SX, Han X, Zhu WC, Yin Q, Hong XY. Transcriptome and proteome analyses reveal complex mechanisms of reproductive diapause in the two-spotted spider mite, Tetranychus urticae. INSECT MOLECULAR BIOLOGY 2017; 26:215-232. [PMID: 28001328 DOI: 10.1111/imb.12286] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Although a variety of factors underlying diapause have been identified in arthropods and other organisms, the molecular mechanisms regulating diapause are still largely unknown. Here, to better understand this process, we examined diapause-associated genes in the two-spotted spider mite, Tetranychus urticae, by comparing the transcriptomes and proteomes of early diapausing and reproductive adult females. Amongst genes underlying diapause revealed by the transcriptomic and proteomic data sets, we described the noticeable change in Ca2+ -associated genes, including 65 Ca2+ -binding protein genes and 23 Ca2+ transporter genes, indicating that Ca2+ signalling has a substantial role in diapause regulation. Other interesting changes in diapause included up-regulation of (1) glutamate receptors that may be involved in synaptic plasticity changes, (2) genes involved in cytoskeletal reorganization including genes encoding each of the components of thick and thin filaments, tubulin and members of integrin signalling and (3) genes involved in anaerobic energy metabolism, which reflects a shift to anaerobic energy metabolism in early diapausing mites.
Collapse
Affiliation(s)
- J-Y Zhao
- Department of Entomology, Nanjing Agricultural University, Nanjing, China
| | - X-T Zhao
- Department of Entomology, Nanjing Agricultural University, Nanjing, China
| | - J-T Sun
- Department of Entomology, Nanjing Agricultural University, Nanjing, China
| | - L-F Zou
- Beijing Genomics Institute-Shenzhen, Shenzhen, China
| | - S-X Yang
- Department of Entomology, Nanjing Agricultural University, Nanjing, China
| | - X Han
- Department of Entomology, Nanjing Agricultural University, Nanjing, China
| | - W-C Zhu
- Department of Entomology, Nanjing Agricultural University, Nanjing, China
| | - Q Yin
- Beijing Genomics Institute-Shenzhen, Shenzhen, China
| | - X-Y Hong
- Department of Entomology, Nanjing Agricultural University, Nanjing, China
| |
Collapse
|
13
|
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.
Collapse
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
| |
Collapse
|
14
|
Yilmaz LS, Walhout AJM. A Caenorhabditis elegans Genome-Scale Metabolic Network Model. Cell Syst 2016; 2:297-311. [PMID: 27211857 DOI: 10.1016/j.cels.2016.04.012] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Revised: 03/08/2016] [Accepted: 04/15/2016] [Indexed: 11/30/2022]
Abstract
Caenorhabditis elegans is a powerful model to study metabolism and how it relates to nutrition, gene expression, and life history traits. However, while numerous experimental techniques that enable perturbation of its diet and gene function are available, a high-quality metabolic network model has been lacking. Here, we reconstruct an initial version of the C. elegans metabolic network. This network model contains 1,273 genes, 623 enzymes, and 1,985 metabolic reactions and is referred to as iCEL1273. Using flux balance analysis, we show that iCEL1273 is capable of representing the conversion of bacterial biomass into C. elegans biomass during growth and enables the predictions of gene essentiality and other phenotypes. In addition, we demonstrate that gene expression data can be integrated with the model by comparing metabolic rewiring in dauer animals versus growing larvae. iCEL1273 is available at a dedicated website (wormflux.umassmed.edu) and will enable the unraveling of the mechanisms by which different macro- and micronutrients contribute to the animal's physiology.
Collapse
Affiliation(s)
- L Safak Yilmaz
- Programs in Systems Biology and Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA.
| | - Albertha J M Walhout
- Programs in Systems Biology and Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA.
| |
Collapse
|
15
|
Ellen Kreipke R, Wang Y, Miklas JW, Mathieu J, Ruohola-Baker H. Metabolic remodeling in early development and cardiomyocyte maturation. Semin Cell Dev Biol 2016; 52:84-92. [PMID: 26912118 DOI: 10.1016/j.semcdb.2016.02.004] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Revised: 01/22/2016] [Accepted: 02/01/2016] [Indexed: 12/17/2022]
Abstract
Aberrations in metabolism contribute to a large number of diseases, such as diabetes, obesity, cancer, and cardiovascular diseases, that have a substantial impact on the mortality rates and quality of life worldwide. However, the mechanisms leading to these changes in metabolic state--and whether they are conserved between diseases--is not well understood. Changes in metabolism similar to those seen in pathological conditions are observed during normal development in a number of different cell types. This provides hope that understanding the mechanism of these metabolic switches in normal development may provide useful insight in correcting them in pathological cases. Here, we focus on the metabolic remodeling observed both in early stage embryonic stem cells and during the maturation of cardiomyocytes.
Collapse
Affiliation(s)
- Rebecca Ellen Kreipke
- Department of Biochemistry, University of Washington, School of Medicine, Seattle, WA 98195, USA; Institute for Stem Cell and Regenerative Medicine, University of Washington, School of Medicine, Seattle, WA 98109, USA
| | - Yuliang Wang
- Institute for Stem Cell and Regenerative Medicine, University of Washington, School of Medicine, Seattle, WA 98109, USA; Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR 97239, USA; Computational Biology Program, Oregon Health & Science University, Portland, OR 97239, USA
| | - Jason Wayne Miklas
- Institute for Stem Cell and Regenerative Medicine, University of Washington, School of Medicine, Seattle, WA 98109, USA; Department of Bioengineering, University of Washington, Seattle, WA 98195, USA
| | - Julie Mathieu
- Department of Biochemistry, University of Washington, School of Medicine, Seattle, WA 98195, USA; Institute for Stem Cell and Regenerative Medicine, University of Washington, School of Medicine, Seattle, WA 98109, USA
| | - Hannele Ruohola-Baker
- Department of Biochemistry, University of Washington, School of Medicine, Seattle, WA 98195, USA; Institute for Stem Cell and Regenerative Medicine, University of Washington, School of Medicine, Seattle, WA 98109, USA; Department of Bioengineering, University of Washington, Seattle, WA 98195, USA.
| |
Collapse
|
16
|
Expression of Genes Encoding the Enzymes for Glycogen and Trehalose Metabolism in L3 and L4 Larvae of Anisakis simplex. J Parasitol Res 2015; 2015:438145. [PMID: 26783451 PMCID: PMC4689960 DOI: 10.1155/2015/438145] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Accepted: 10/22/2015] [Indexed: 11/17/2022] Open
Abstract
Trehalose and glycogen metabolism plays an important role in supporting life processes in many nematodes, including Anisakis simplex. Nematodes, cosmopolitan helminths parasitizing sea mammals and humans, cause a disease known as anisakiasis. The aim of this study was to investigate the expression of genes encoding the enzymes involved in the metabolism of trehalose and glycogen—trehalose-6-phosphate synthase (TPS), trehalose-6-phosphate phosphatase (TPP), glycogen synthase (GS), and glycogen phosphorylase (GP)—in stage L3 and stage L4 larvae of A. simplex. The expression of mRNA all four genes, tps, tpp, gs, and gp, was examined by real-time polymerase chain reaction. The A. simplex ribosomal gene (18S) was used as a reference gene. Enzymatic activity was determined. The expression of trehalose enzyme genes was higher in L3 than in L4 larvae, but an inverse relationship was noted for the expression of gs and gp genes.
Collapse
|
17
|
Abstract
Food availability determines developmental rate, behavior, and survival of animals. Animals that enter diapause or hibernate in response to lack of food have a double advantage: they are able to adapt to environmental and cellular challenges and survive to these challenges for a prolonged time. The metabolic and physiological adaptations that make possible diapause and hibernation also provide a favorable cellular environment for tissue protection. This review highlights the benefits of dormancy on neuronal protection in the model organism Caenorhabditis elegans and small mammals such as squirrels. Additionally, I discuss the link between metabolic restructuring occurring in diapause and changes in gene expression with the increased capacity of diapausing animals to protect neurons from degeneration and potentially foster their regeneration.
Collapse
Affiliation(s)
- Andrea Calixto
- Center for Genomics and Bioinformatics, Faculty of Sciences, Universidad Mayor, Santiago, Chile.
| |
Collapse
|
18
|
Erkut C, Kurzchalia TV. The C. elegans dauer larva as a paradigm to study metabolic suppression and desiccation tolerance. PLANTA 2015; 242:389-396. [PMID: 25868548 DOI: 10.1007/s00425-015-2300-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2014] [Accepted: 04/07/2015] [Indexed: 06/04/2023]
Abstract
The hypometabolic, stress-resistant dauer larva of Caenorhabditis elegans serves as an excellent model to study the molecular mechanisms of desiccation tolerance, such as maintenance of membrane organization, protein folding, xenobiotic and ROS detoxification in the dry state. Many organisms from diverse taxa of life have the remarkable ability to survive extreme desiccation in the nature by entering an ametabolic state known as anhydrobiosis (life without water). The hallmark of the anhydrobiotic state is the achievement and maintenance of an exceedingly low metabolic rate, as well as preservation of the structural integrity of the cell. Although described more than three centuries ago, the biochemical and biophysical mechanisms underlying this phenomenon are still not fully comprehended. This is mainly due to the fact that anhydrobiosis in animals was studied using non-model organisms, which are very difficult, if not impossible, to manipulate at the molecular level. Recently, we introduced the roundworm (nematode) Caenorhabditis elegans as a model for anhydrobiosis. Taking advantage of powerful genetic, biochemical and biophysical tools, we investigated several aspects of anhydrobiosis in a particular developmental stage (the dauer larva) of this organism. First, our studies allowed confirming the previously suggested role of the disaccharide trehalose in the preservation of lipid membranes. Moreover, in addition to known pathways such as reactive oxygen species defense, heat-shock and intrinsically disordered protein expression, evidence for some novel strategies of anhydrobiosis has been obtained. These are increased glyoxalase activity, polyamine and polyunsaturated fatty acid biosynthesis. All these pathways may constitute a generic toolbox of anhydrobiosis, which is possibly conserved between animals and plants.
Collapse
Affiliation(s)
- Cihan Erkut
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstraße 108, 01307, Dresden, Germany
| | | |
Collapse
|
19
|
Effects of the mitochondrial respiratory chain on longevity in C. elegans. Exp Gerontol 2014; 56:245-55. [DOI: 10.1016/j.exger.2014.03.028] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Revised: 03/27/2014] [Accepted: 03/28/2014] [Indexed: 12/21/2022]
|
20
|
Depuydt G, Xie F, Petyuk VA, Smolders A, Brewer HM, Camp DG, Smith RD, Braeckman BP. LC-MS proteomics analysis of the insulin/IGF-1-deficient Caenorhabditis elegans daf-2(e1370) mutant reveals extensive restructuring of intermediary metabolism. J Proteome Res 2014; 13:1938-56. [PMID: 24555535 PMCID: PMC3993954 DOI: 10.1021/pr401081b] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2013] [Indexed: 12/11/2022]
Abstract
The insulin/IGF-1 receptor is a major known determinant of dauer formation, stress resistance, longevity, and metabolism in Caenorhabditis elegans. In the past, whole-genome transcript profiling was used extensively to study differential gene expression in response to reduced insulin/IGF-1 signaling, including the expression levels of metabolism-associated genes. Taking advantage of the recent developments in quantitative liquid chromatography mass spectrometry (LC-MS)-based proteomics, we profiled the proteomic changes that occur in response to activation of the DAF-16 transcription factor in the germline-less glp-4(bn2);daf-2(e1370) receptor mutant. Strikingly, the daf-2 profile suggests extensive reorganization of intermediary metabolism, characterized by the upregulation of many core intermediary metabolic pathways. These include glycolysis/gluconeogenesis, glycogenesis, pentose phosphate cycle, citric acid cycle, glyoxylate shunt, fatty acid β-oxidation, one-carbon metabolism, propionate and tyrosine catabolism, and complexes I, II, III, and V of the electron transport chain. Interestingly, we found simultaneous activation of reciprocally regulated metabolic pathways, which is indicative of spatiotemporal coordination of energy metabolism and/or extensive post-translational regulation of these enzymes. This restructuring of daf-2 metabolism is reminiscent to that of hypometabolic dauers, allowing the efficient and economical utilization of internal nutrient reserves and possibly also shunting metabolites through alternative energy-generating pathways to sustain longevity.
Collapse
Affiliation(s)
- Geert Depuydt
- Biology
Department, Ghent University, Proeftuinstraat 86 N1, B-9000 Ghent, Belgium
| | - Fang Xie
- Biological
Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Vladislav A. Petyuk
- Biological
Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Arne Smolders
- Biology
Department, Ghent University, Proeftuinstraat 86 N1, B-9000 Ghent, Belgium
| | - Heather M. Brewer
- Biological
Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - David G. Camp
- Biological
Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Richard D. Smith
- Biological
Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Bart P. Braeckman
- Biology
Department, Ghent University, Proeftuinstraat 86 N1, B-9000 Ghent, Belgium
| |
Collapse
|
21
|
Flatt T, Amdam GV, Kirkwood TBL, Omholt SW. Life-history evolution and the polyphenic regulation of somatic maintenance and survival. QUARTERLY REVIEW OF BIOLOGY 2013; 88:185-218. [PMID: 24053071 DOI: 10.1086/671484] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Here we discuss life-history evolution from the perspective of adaptive phenotypic plasticity, with a focus on polyphenisms for somatic maintenance and survival. Polyphenisms are adaptive discrete alternative phenotypes that develop in response to changes in the environment. We suggest that dauer larval diapause and its associated adult phenotypes in the nematode (Caenorhabditis elegans), reproductive dormancy in the fruit fly (Drosophila melanogaster) and other insects, and the worker castes of the honey bee (Apis mellifera) are examples of what may be viewed as the polyphenic regulation of somatic maintenance and survival. In these and other cases, the same genotype can--depending upon its environment--express either of two alternative sets of life-history phenotypes that differ markedly with respect to somatic maintenance, survival ability, and thus life span. This plastic modulation of somatic maintenance and survival has traditionally been underappreciated by researchers working on aging and life history. We review the current evidence for such adaptive life-history switches and their molecular regulation and suggest that they are caused by temporally and/or spatially varying, stressful environments that impose diversifying selection, thereby favoring the evolution of plasticity of somatic maintenance and survival under strong regulatory control. By considering somatic maintenance and survivorship from the perspective of adaptive life-history switches, we may gain novel insights into the mechanisms and evolution of aging.
Collapse
Affiliation(s)
- Thomas Flatt
- Institut für Populationsgenetik, Vetmeduni Vienna, A-1210 Vienna, Austria.
| | | | | | | |
Collapse
|
22
|
The ubiquitin ligase CHIP prevents SirT6 degradation through noncanonical ubiquitination. Mol Cell Biol 2013; 33:4461-72. [PMID: 24043303 DOI: 10.1128/mcb.00480-13] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The ubiquitin ligase CHIP (carboxyl terminus of Hsp70-interacting protein) regulates protein quality control, and CHIP deletion accelerates aging and reduces the life span in mice. Here, we reveal a mechanism for CHIP's influence on longevity by demonstrating that CHIP stabilizes the sirtuin family member SirT6, a lysine deacetylase/ADP ribosylase involved in DNA repair, metabolism, and longevity. In CHIP-deficient cells, SirT6 protein half-life is substantially reduced due to increased proteasome-mediated degradation, but CHIP overexpression in these cells increases SirT6 protein expression without affecting SirT6 transcription. CHIP noncanonically ubiquitinates SirT6 at K170, which stabilizes SirT6 and prevents SirT6 canonical ubiquitination by other ubiquitin ligases. In CHIP-depleted cells, SirT6 K170 mutation increases SirT6 half-life and prevents proteasome-mediated degradation. The global decrease in SirT6 expression in the absence of CHIP is associated with decreased SirT6 promoter occupancy, which increases histone acetylation and promotes downstream gene transcription in CHIP-depleted cells. Cells lacking CHIP are hypersensitive to DNA-damaging agents, but DNA repair and cell viability are rescued by enforced expression of SirT6. The discovery of this CHIP-SirT6 interaction represents a novel protein-stabilizing mechanism and defines an intersection between protein quality control and epigenetic regulation to influence pathways that regulate the biology of aging.
Collapse
|
23
|
Finley JW, Sandlin C, Holliday DL, Keenan MJ, Prinyawiwatkul W, Zheng J. Legumes reduced intestinal fat deposition in the Caenorhabditis elegans model system. J Funct Foods 2013. [DOI: 10.1016/j.jff.2013.03.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
|
24
|
Miltsch SM, Krücken J, Demeler J, Ramünke S, Harder A, von Samson-Himmelstjerna G. Interactions of anthelmintic drugs in Caenorhabditis elegans neuro-muscular ion channel mutants. Parasitol Int 2013; 62:591-8. [PMID: 23707730 DOI: 10.1016/j.parint.2013.05.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2012] [Revised: 05/13/2013] [Accepted: 05/14/2013] [Indexed: 11/29/2022]
Abstract
Due to the increasing development of anthelmintic resistance in nematodes worldwide, it is important to search for anthelmintic compounds with new modes of action and also to investigate the possibility to combine compounds with possible synergistic effects. There might also be the chance to take advantage of the fact that nematode populations which have developed resistance against one anthelmintic class might respond hypersusceptibly to another drug class. The aim of this study was to investigate responses of Caenorhabditis elegans populations with mutations in neuro-muscular ion channels to different anthelmintic classes. Furthermore, potential synergistic effects between two anthelmintic compounds from different classes, i.e. emodepside and tribendimidine, were studied. Although there was neither a synergistic nor an antagonistic effect between emodepside and tribendimidine, other types of interactions could be identified. The C. elegans GABAA-receptor (GABAA-R) unc-49 mutants, showing decreased emodepside susceptibility, were more susceptible to tribendimidine than wild-type C. elegans. In contrast, the reverse phenomenon - hypersusceptibility to emodepside in tribendimidine resistant acetylcholine-receptor (AChR) loss of function mutants - was not observed. Moreover, the slo-1 mutant strain (completely emodepside resistant) also showed hypersusceptibility to piperazine. Interestingly, neither the GABAA-R unc-49 mutants nor the AChR mutants showed decreased susceptibility against piperazine, although there were some studies that indicated an involvement of GABAA-R or AChR in the piperazine mode of action. In conclusion, the present study provides evidence suggesting that interactions between commercially available anthelmintic drugs with different modes of action might be a relatively common phenomenon but this has to be carefully worked out for each anthelmintic and each anthelmintic drug combination. Moreover, results obtained in C. elegans will have to be confirmed using parasitic nematodes in the future.
Collapse
Affiliation(s)
- Sandra M Miltsch
- Institute for Parasitology and Tropical Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
| | | | | | | | | | | |
Collapse
|
25
|
Edwards CB, Copes N, Brito AG, Canfield J, Bradshaw PC. Malate and fumarate extend lifespan in Caenorhabditis elegans. PLoS One 2013; 8:e58345. [PMID: 23472183 PMCID: PMC3589421 DOI: 10.1371/journal.pone.0058345] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2012] [Accepted: 02/03/2013] [Indexed: 11/18/2022] Open
Abstract
Malate, the tricarboxylic acid (TCA) cycle metabolite, increased lifespan and thermotolerance in the nematode C. elegans. Malate can be synthesized from fumarate by the enzyme fumarase and further oxidized to oxaloacetate by malate dehydrogenase with the accompanying reduction of NAD. Addition of fumarate also extended lifespan, but succinate addition did not, although all three intermediates activated nuclear translocation of the cytoprotective DAF-16/FOXO transcription factor and protected from paraquat-induced oxidative stress. The glyoxylate shunt, an anabolic pathway linked to lifespan extension in C. elegans, reversibly converts isocitrate and acetyl-CoA to succinate, malate, and CoA. The increased longevity provided by malate addition did not occur in fumarase (fum-1), glyoxylate shunt (gei-7), succinate dehydrogenase flavoprotein (sdha-2), or soluble fumarate reductase F48E8.3 RNAi knockdown worms. Therefore, to increase lifespan, malate must be first converted to fumarate, then fumarate must be reduced to succinate by soluble fumarate reductase and the mitochondrial electron transport chain complex II. Reduction of fumarate to succinate is coupled with the oxidation of FADH2 to FAD. Lifespan extension induced by malate depended upon the longevity regulators DAF-16 and SIR-2.1. Malate supplementation did not extend the lifespan of long-lived eat-2 mutant worms, a model of dietary restriction. Malate and fumarate addition increased oxygen consumption, but decreased ATP levels and mitochondrial membrane potential suggesting a mild uncoupling of oxidative phosphorylation. Malate also increased NADPH, NAD, and the NAD/NADH ratio. Fumarate reduction, glyoxylate shunt activity, and mild mitochondrial uncoupling likely contribute to the lifespan extension induced by malate and fumarate by increasing the amount of oxidized NAD and FAD cofactors.
Collapse
Affiliation(s)
- Clare B. Edwards
- Department of Cell Biology, Microbiology, and Molecular Biology, University of South Florida Tampa, Florida, United States of America
| | - Neil Copes
- Department of Cell Biology, Microbiology, and Molecular Biology, University of South Florida Tampa, Florida, United States of America
| | - Andres G. Brito
- Department of Cell Biology, Microbiology, and Molecular Biology, University of South Florida Tampa, Florida, United States of America
| | - John Canfield
- Department of Cell Biology, Microbiology, and Molecular Biology, University of South Florida Tampa, Florida, United States of America
| | - Patrick C. Bradshaw
- Department of Cell Biology, Microbiology, and Molecular Biology, University of South Florida Tampa, Florida, United States of America
- * E-mail:
| |
Collapse
|
26
|
Geier FM, Fuchs S, Valbuena G, Leroi AM, Bundy JG. Profiling the metabolic signature of senescence. Methods Mol Biol 2013; 965:355-371. [PMID: 23296671 DOI: 10.1007/978-1-62703-239-1_24] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Aging is a complex process, which involves changes in different cellular functions that all can be integrated on the metabolite level. This means that different gene regulation pathways that affect aging might lead to similar changes in metabolism and result in a metabolic signature of senescence. In this chapter, we describe how to establish a metabolic signature of senescence by analyzing the metabolome of various longevity mutants of the model organism Caenorhabditis elegans using gas chromatography-mass spectrometry (GC-MS). Since longevity-associated genes exist for other model organisms and humans, this analysis could be universally applied to body fluids or whole tissue samples for studing the relationship between senescence and metabolism.
Collapse
Affiliation(s)
- Florian M Geier
- Biomolecular Medicine, Department of Surgery and Cancer, Imperial College, London, UK
| | | | | | | | | |
Collapse
|
27
|
Physiological control of germline development. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2013; 757:101-31. [PMID: 22872476 DOI: 10.1007/978-1-4614-4015-4_5] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The intersection between developmental programs and environmental conditions that alter physiology is a growing area of research interest. The C. elegans germ line is emerging as a particularly sensitive and powerful model for these studies. The germ line is subject to environmentally regulated diapause points that allow worms to withstand harsh conditions both prior to and after reproduction commences. It also responds to more subtle changes in physiological conditions. Recent studies demonstrate that different aspects of germ line development are sensitive to environmental and physiological changes and that conserved signaling pathways such as the AMPK, Insulin/IGF, TGFβ, and TOR-S6K, and nuclear hormone receptor pathways mediate this sensitivity. Some of these pathways genetically interact with but appear distinct from previously characterized mechanisms of germline cell fate control such as Notch signaling. Here, we review several aspects of hermaphrodite germline development in the context of "feasting," "food-limited," and "fasting" conditions. We also consider connections between lifespan, metabolism and the germ line, and we comment on special considerations for examining germline development under altered environmental and physiological conditions. Finally, we summarize the major outstanding questions in the field.
Collapse
|
28
|
PDHK-2 deficiency is associated with attenuation of lipase-mediated fat consumption for the increased survival of Caenorhabditis elegans dauers. PLoS One 2012; 7:e41755. [PMID: 22848591 PMCID: PMC3407204 DOI: 10.1371/journal.pone.0041755] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2012] [Accepted: 06/25/2012] [Indexed: 11/19/2022] Open
Abstract
In Caenorhabditis elegans, slow fat consumption has been suggested to contribute to the extension of the survival rate during nutritionally adverse conditions. Here, we investigated the potential role of pyruvate dehydrogenase kinase (PDHK)-2, the C. elegans homolog of mammalian PDK, effects on fat metabolism under nutritional conditions. PDHK-2 was expressed at low levels under well-fed conditions but was highly induced during long-term starvation and in the dauer state. This increase in pdhk-2 expression was regulated by both DAF-16 and NHR-49. Dauer-specific induction of PDHK-2 was abolished upon entry into the post-dauer stage. Interestingly, in the long-term dauer state, stored fat levels were higher in daf-2(e1370);pdhk-2 double mutants than in daf-2(e1370), suggesting a positive relationship between PDHK-2 activity and fat consumption. PDHK-2 deficiency has been shown to lead to greater preservation of residual fats, which would be predicted to contribute to survival during the dauer state. A test of this prediction showed that the survival rates of daf-2(e1370);pdhk-2(tm3075) and daf-2(e1370);pdhk-2(tm3086) double mutants were higher than that of daf-2(e1370), suggesting that loss of either the ATP-binding domain (tm3075) or branched chain keto-acid dehydrogenase kinase domain (tm3086) of PDHK-2 leads to reduced fat consumption and thus favors increased dauer survival. This attenuated fat consumption in the long-term dauer state of C. elegans daf-2 (e1370);pdhk-2 mutants was associated with concomitant down-regulation of the lipases ATGL (adipose triglyceride lipase), HSL (hormone-sensitive lipase), and C07E3.9 (phospholipase). In contrast, PDHK-2 overexpression in wild-type starved worms induced lipase expression and promoted abnormal dauer formation. Thus, we propose that PDHK-2 serves as a molecular bridge, connecting fat metabolism and survival under nutritionally adverse conditions in C. elegans.
Collapse
|
29
|
Sinha A, Sommer RJ, Dieterich C. Divergent gene expression in the conserved dauer stage of the nematodes Pristionchus pacificus and Caenorhabditis elegans. BMC Genomics 2012; 13:254. [PMID: 22712530 PMCID: PMC3443458 DOI: 10.1186/1471-2164-13-254] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2011] [Accepted: 04/12/2012] [Indexed: 11/20/2022] Open
Abstract
Background An organism can respond to changing environmental conditions by adjusting gene regulation and by forming alternative phenotypes. In nematodes, these mechanisms are coupled because many species will form dauer larvae, a stress-resistant and non-aging developmental stage, when exposed to unfavorable environmental conditions, and execute gene expression programs that have been selected for the survival of the animal in the wild. These dauer larvae represent an environmentally induced, homologous developmental stage across many nematode species, sharing conserved morphological and physiological properties. Hence it can be expected that some core components of the associated transcriptional program would be conserved across species, while others might diverge over the course of evolution. However, transcriptional and metabolic analysis of dauer development has been largely restricted to Caenorhabditis elegans. Here, we use a transcriptomic approach to compare the dauer stage in the evolutionary model system Pristionchus pacificus with the dauer stage in C. elegans. Results We have employed Agilent microarrays, which represent 20,446 P. pacificus and 20,143 C. elegans genes to show an unexpected divergence in the expression profiles of these two nematodes in dauer and dauer exit samples. P. pacificus and C. elegans differ in the dynamics and function of genes that are differentially expressed. We find that only a small number of orthologous gene pairs show similar expression pattern in the dauers of the two species, while the non-orthologous fraction of genes is a major contributor to the active transcriptome in dauers. Interestingly, many of the genes acquired by horizontal gene transfer and orphan genes in P. pacificus, are differentially expressed suggesting that these genes are of evolutionary and functional importance. Conclusion Our data set provides a catalog for future functional investigations and indicates novel insight into evolutionary mechanisms. We discuss the limited conservation of core developmental and transcriptional programs as a common aspect of animal evolution.
Collapse
Affiliation(s)
- Amit Sinha
- Max-Planck Institute for Developmental Biology, Department for Evolutionary Biology, Tübingen, Germany
| | | | | |
Collapse
|
30
|
Differential Expression ESTs Associated with Fluorosis in Rats Liver. Comp Funct Genomics 2012; 2012:208390. [PMID: 22400010 PMCID: PMC3286904 DOI: 10.1155/2012/208390] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2011] [Accepted: 11/26/2011] [Indexed: 12/22/2022] Open
Abstract
The fluoride has volcanic activity and abundantly exists in environment combining with other elements as fluoride compounds. Recent researches indicated that the molecular mechanisms of intracellular fluoride toxicity were very complex. However, the molecular mechanisms underlying the effects on gene expression of chronic fluoride-induced damage is unknown, especially the detailed regulatory process of mitochondria. In the present study, we screened the differential expression ESTs associated with fluorosis by DDRT-PCR in rat liver. We gained 8 genes, 3 new ESTs, and 1 unknown function sequence and firstly demonstrated that microsomal glutathione S-transferase 1 (MGST1), ATP synthase H+ transporting mitochondrial F0 complex subunit C1, selenoprotein S, mitochondrial IF1 protein, and mitochondrial succinyl-CoA synthetase alpha subunit were participated in mitochondria metabolism, functional and structural damage process caused by chronic fluorosis. This information will be very helpful for understanding the molecular mechanisms of fluorosis.
Collapse
|
31
|
Abstract
Phenotypic plasticity refers to the ability of an organism to adopt different phenotypes depending on environmental conditions. In animals and plants, the progression of juvenile development and the formation of dormant stages are often associated with phenotypic plasticity, indicating the importance of phenotypic plasticity for life-history theory. Phenotypic plasticity has long been emphasized as a crucial principle in ecology and as facilitator of phenotypic evolution. In nematodes, several examples of phenotypic plasticity have been studied at the genetic and developmental level. In addition, the influence of different environmental factors has been investigated under laboratory conditions. These studies have provided detailed insight into the molecular basis of phenotypic plasticity and its ecological and evolutionary implications. Here, we review recent studies on the formation of dauer larvae in Caenorhabditis elegans, the evolution of nematode parasitism and the generation of a novel feeding trait in Pristionchus pacificus. These examples reveal a conserved and co-opted role of an endocrine signaling module involving the steroid hormone dafachronic acid. We will discuss how hormone signaling might facilitate life-history and morphological evolution.
Collapse
|
32
|
Brown FD, D'Anna I, Sommer RJ. Host-finding behaviour in the nematode Pristionchus pacificus. Proc Biol Sci 2011; 278:3260-9. [PMID: 21411455 PMCID: PMC3169022 DOI: 10.1098/rspb.2011.0129] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2011] [Accepted: 02/22/2011] [Indexed: 02/01/2023] Open
Abstract
Costs and benefits of foraging have been studied in predatory animals. In nematodes, ambushing or cruising behaviours represent adaptations that optimize foraging strategies for survival and host finding. A behaviour associated with host finding of ambushing nematode dauer juveniles is a sit-and-wait behaviour, otherwise known as nictation. Here, we test the function of nictation by relating occurrence of nictation in Pristionchus pacificus dauer juveniles to the ability to attach to laboratory host Galleria mellonella. We used populations of recently isolated and mutagenized laboratory strains. We found that nictation can be disrupted using a classical forward genetic approach and characterized two novel nictation-defective mutant strains. We identified two recently isolated strains from la Réunion island, one with a higher proportion of nictating individuals than the laboratory strain P. pacificus PS312. We found a positive correlation between nictation frequencies and host attachment in these strains. Taken together, our combination of genetic analyses with natural variation studies presents a new approach to the investigation of behavioural and ecological functionality. We show that nictation behaviour in P. pacificus nematodes serves as a host-finding behaviour. Our results suggest that nictation plays a role in the evolution of new life-history strategies, such as the evolution of parasitism.
Collapse
Affiliation(s)
- Federico D Brown
- Department of Evolutionary Biology, Max Planck Institute for Developmental Biology, Spemannstrasse 37, Tübingen 72076, Germany.
| | | | | |
Collapse
|
33
|
Chinopoulos C. The "B space" of mitochondrial phosphorylation. J Neurosci Res 2011; 89:1897-904. [PMID: 21541983 DOI: 10.1002/jnr.22659] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2010] [Revised: 02/09/2011] [Accepted: 03/10/2011] [Indexed: 11/07/2022]
Abstract
It was recently shown that, in progressively depolarizing mitochondria, the F(0) -F(1) ATP synthase and the adenine nucleotide translocase (ANT) may change directionality independently from each other (Chinopoulos et al. [2010] FASEB J. 24:2405). When the membrane potentials at which these two molecular entities reverse directionality, termed reversal potential (Erev), are plotted as a function of matrix ATP/ADP ratio, an area of the plot is bracketed by the Erev_ATPase and the Erev_ANT, which we call "B space". Both reversal potentials are dynamic, in that they depend on the fluctuating values of the participating reactants; however, Erev_ATPase is almost always more negative than Erev_ANT. Here we review the conditions that define the boundaries of the "B space". Emphasis is placed on the role of matrix substrate-level phosphorylation, because during metabolic compromise this mechanism could maintain mitochondrial membrane potential and prevent the influx of cytosolic ATP destined for hydrolysis by the reversed F(0) -F(1) ATP synthase.
Collapse
|
34
|
Hand SC, Menze MA, Borcar A, Patil Y, Covi JA, Reynolds JA, Toner M. Metabolic restructuring during energy-limited states: insights from Artemia franciscana embryos and other animals. JOURNAL OF INSECT PHYSIOLOGY 2011; 57:584-94. [PMID: 21335009 PMCID: PMC3104064 DOI: 10.1016/j.jinsphys.2011.02.010] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2010] [Revised: 02/07/2011] [Accepted: 02/09/2011] [Indexed: 05/21/2023]
Abstract
Many life history stages of animals that experience environmental insults enter developmental arrested states that are characterized by reduced cellular proliferation, with or without a concurrent reduction in overall metabolism. In the case of the most profound metabolic arrest reported in invertebrates, i.e., anaerobic quiescence in Artemia franciscana embryos, acidification of the intracellular milieu is a major factor governing catabolic and anabolic downregulation. Release of ions from intracellular compartments is the source for approximately 50% of the proton equivalents needed for the 1.5 unit acidification that is observed. Recovery from the metabolic arrest requires re-sequestration of the protons with a vacuolar-type ATPase (V-ATPase). The remarkable facet of this mechanism is the ability of embryonic cells to survive the dissipation of intracellular ion gradients. Across many diapause-like states, the metabolic reduction and subsequent matching of energy demand is accomplished by shifting energy metabolism from oxidative phosphorylation to aerobic glycolysis. Molecular pathways that are activated to induce these resilient hypometabolic states include stimulation of the AMP-activated protein kinase (AMPK) and insulin signaling via suite of daf (dauer formation) genes for diapause-like states in nematodes and insects. Contributing factors for other metabolically depressed states involve hypoxia-inducible factor-1 and downregulation of the pyruvate dehydrogenase complex. Metabolic similarities between natural states of stasis and some cancer phenotypes are noteworthy. Reduction of flux through oxidative phosphorylation helps prevent cell death in certain cancer types, similar to the way it increases viability of dauer stages in Caenorhabditis elegans. Mechanisms that underlie natural stasis are being used to pre-condition mammalian cells prior to cell biostabilization and storage.
Collapse
Affiliation(s)
- Steven C Hand
- Division of Cellular, Developmental and Integrative Biology, Department of Biological, Sciences, Louisiana State University, Baton Rouge, LA 70803, USA.
| | | | | | | | | | | | | |
Collapse
|
35
|
Narasimhan SD, Yen K, Bansal A, Kwon ES, Padmanabhan S, Tissenbaum HA. PDP-1 links the TGF-β and IIS pathways to regulate longevity, development, and metabolism. PLoS Genet 2011; 7:e1001377. [PMID: 21533078 PMCID: PMC3080858 DOI: 10.1371/journal.pgen.1001377] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2010] [Accepted: 03/18/2011] [Indexed: 12/11/2022] Open
Abstract
The insulin/IGF-1 signaling (IIS) pathway is a conserved regulator of longevity, development, and metabolism. In Caenorhabditis elegans IIS involves activation of DAF-2 (insulin/IGF-1 receptor tyrosine kinase), AGE-1 (PI 3-kinase), and additional downstream serine/threonine kinases that ultimately phosphorylate and negatively regulate the single FOXO transcription factor homolog DAF-16. Phosphatases help to maintain cellular signaling homeostasis by counterbalancing kinase activity. However, few phosphatases have been identified that negatively regulate the IIS pathway. Here we identify and characterize pdp-1 as a novel negative modulator of the IIS pathway. We show that PDP-1 regulates multiple outputs of IIS such as longevity, fat storage, and dauer diapause. In addition, PDP-1 promotes DAF-16 nuclear localization and transcriptional activity. Interestingly, genetic epistasis analyses place PDP-1 in the DAF-7/TGF-β signaling pathway, at the level of the R-SMAD proteins DAF-14 and DAF-8. Further investigation into how a component of TGF-β signaling affects multiple outputs of IIS/DAF-16, revealed extensive crosstalk between these two well-conserved signaling pathways. We find that PDP-1 modulates the expression of several insulin genes that are likely to feed into the IIS pathway to regulate DAF-16 activity. Importantly, dysregulation of IIS and TGF-β signaling has been implicated in diseases such as Type 2 Diabetes, obesity, and cancer. Our results may provide a new perspective in understanding of the regulation of these pathways under normal conditions and in the context of disease.
Collapse
Affiliation(s)
- Sri Devi Narasimhan
- Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Kelvin Yen
- Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Ankita Bansal
- Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Eun-Soo Kwon
- Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Srivatsan Padmanabhan
- Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Heidi A. Tissenbaum
- Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
- * E-mail:
| |
Collapse
|
36
|
Hulme SE, Whitesides GM. Die Chemie und der Wurm: Caenorhabditis elegans als Plattform für das Zusammenführen von chemischer und biologischer Forschung. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201005461] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
|
37
|
Hulme SE, Whitesides GM. Chemistry and the Worm: Caenorhabditis elegans as a Platform for Integrating Chemical and Biological Research. Angew Chem Int Ed Engl 2011; 50:4774-807. [DOI: 10.1002/anie.201005461] [Citation(s) in RCA: 104] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2010] [Indexed: 12/15/2022]
|
38
|
Karp X, Hammell M, Ow MC, Ambros V. Effect of life history on microRNA expression during C. elegans development. RNA (NEW YORK, N.Y.) 2011; 17:639-651. [PMID: 21343388 PMCID: PMC3062175 DOI: 10.1261/rna.2310111] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2010] [Accepted: 01/11/2011] [Indexed: 05/30/2023]
Abstract
Animals have evolved mechanisms to ensure the robustness of developmental outcomes to changing environments. MicroRNA expression may contribute to developmental robustness because microRNAs are key post-transcriptional regulators of developmental gene expression and can affect the expression of multiple target genes. Caenorhabditis elegans provides an excellent model to study developmental responses to environmental conditions. In favorable environments, C. elegans larvae develop rapidly and continuously through four larval stages. In contrast, in unfavorable conditions, larval development may be interrupted at either of two diapause stages: The L1 diapause occurs when embryos hatch in the absence of food, and the dauer diapause occurs after the second larval stage in response to environmental stimuli encountered during the first two larval stages. Dauer larvae are stress resistant and long lived, permitting survival in harsh conditions. When environmental conditions improve, dauer larvae re-enter development, and progress through two post-dauer larval stages to adulthood. Strikingly, all of these life history options (whether continuous or interrupted) involve an identical pattern and sequence of cell division and cell fates. To identify microRNAs with potential functions in buffering development in the context of C. elegans life history options, we used multiplex real-time PCR to assess the expression of 107 microRNAs throughout development in both continuous and interrupted life histories. We identified 17 microRNAs whose developmental profile of expression is affected by dauer life history and/or L1 diapause, compared to continuous development. Hence these microRNAs could function to regulate gene expression programs appropriate for different life history options in the developing worm.
Collapse
Affiliation(s)
- Xantha Karp
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
| | | | | | | |
Collapse
|
39
|
Aitlhadj L, Ávila DS, Benedetto A, Aschner M, Stürzenbaum SR. Environmental exposure, obesity, and Parkinson's disease: lessons from fat and old worms. ENVIRONMENTAL HEALTH PERSPECTIVES 2011; 119:20-8. [PMID: 20797931 PMCID: PMC3018495 DOI: 10.1289/ehp.1002522] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2010] [Accepted: 08/25/2010] [Indexed: 05/02/2023]
Abstract
BACKGROUND A common link has been exposed, namely, that metal exposure plays a role in obesity and in Parkinson's disease (PD). This link may help to elucidate mechanisms of neurotoxicity. OBJECTIVE We reviewed the utility of the nematode, Caenorhabditis elegans, as a model organism to study neurodegeneration in obesity and Parkinson's disease (PD), with an emphasis on the neurotransmitter, dopamine (DA). DATA SOURCES A PubMed literature search was performed using the terms "obesity" and any of the following: "C. elegans," "central nervous system," "neurodegeneration," "heavy metals," "dopamine" or "Parkinson's disease." We reviewed the identified studies, including others cited therein, to summarize the current evidence of neurodegeneration in obesity and PD, with an emphasis on studies carried out in C. elegans and environmental toxins in the etiology of both diseases. DATA EXTRACTION AND DATA SYNTHESIS Heavy metals and DA have both been linked to diet-induced obesity, which has led to the notion that the mechanism of environmentally induced neurodegeneration in PD may also apply to obesity. C. elegans has been instrumental in expanding our mechanism-based knowledge of PD, and this species is emerging as a good model of obesity. With well-established toxicity and neurogenetic assays, it is now feasible to explore the putative link between metal- and chemical-induced neurodegeneration. CONCLUSIONS One side effect of an aging population is an increase in the prevalence of obesity, metabolic disorders, and neurodegenerative orders, diseases that are likely to co-occur. Environmental toxins, especially heavy metals, may prove to be a previously neglected part of the puzzle.
Collapse
Affiliation(s)
- Layla Aitlhadj
- King’s College London, Pharmaceutical Science Division, London, United Kingdom
| | - Daiana Silva Ávila
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Alexandre Benedetto
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Michael Aschner
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | | |
Collapse
|
40
|
Jones LM, Staffa K, Perally S, LaCourse EJ, Brophy PM, Hamilton JV. Proteomic analyses of Caenorhabditis elegans dauer larvae and long-lived daf-2 mutants implicates a shared detoxification system in longevity assurance. J Proteome Res 2010; 9:2871-81. [PMID: 20392130 DOI: 10.1021/pr9009639] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The insulin/insulin-like growth factor-1 (IGF-1) signaling system is a public regulator of aging in the model animals Caenorhabditis elegans, Drosophila melanogaster, and Mus musculus. For the first time, proteomic analyses of the environmentally resistant and 'nonaging' C. elegans dauer stage and long-lived daf-2 mutants has provided a unique insight into the protein changes which mediate survival against endogenously produced toxins. These changes support a diversion of energy consumption away from anabolic processes toward enhanced cellular maintenance and detoxification processes as previously described by the 'Green Theory of Aging'. Important components of this enhanced longevity system identified in this proteomics study include the alpha-crystallin family of small heat shock proteins, anti-ROS defense systems and cellular phase II detoxification (in daf-2 only). Among those proteins involved in phase II cellular detoxification that were significantly upregulated was a Pi-class glutathione transferase (GST) CE00302. Targeting this GST with RNAi revealed compensatory regulation within the Pi-class GSTs. Furthermore, a recombinant form of the GST protein was found to detoxify and/or bind short-chain aldehydic natural toxic products of lipid peroxidation and long-chained fatty-acids at physiologically relevant concentrations, which may indicate a role in longevity.
Collapse
Affiliation(s)
- Laura M Jones
- Aberystwyth University, Institute of Biological, Environmental and Rural Sciences, United Kingdom.
| | | | | | | | | | | |
Collapse
|
41
|
Abstract
Lifespan can be lengthened by genetic and environmental modifications. Study of these might provide valuable insights into the mechanism of aging. Low doses of radiation and short-term exposure to heat and high concentrations of oxygen prolong the lifespan of the nematode Caenorhabditis elegans. These might be caused by adaptive responses to harmful environmental conditions. Single-gene mutations have been found to extend lifespan in C. elegans, Drosophila and mice. So far, the best-characterized system is the C. elegans mutant in the daf-2, insulin/IGF-I receptor gene that is the component of the insulin/IGF-I signaling pathway. The mutant animals live twice as long as the wild type. The insulin/IGF-I signaling pathway regulates the activity of DAF-16, a FOXO transcription factor. However, the unified explanation for the function of DAF-16 transcription targets in the lifespan extension is not yet fully established. As both of the Mn superoxide dismutase (MnSOD) isoforms (sod-2 and sod-3) are found to be targets of DAF-16, we attempted to assess their functions in regulating lifespan and oxidative stress responsivity. We show that the double deletions of sod-2 and sod-3 genes induced oxidative-stress sensitivity but do not shorten lifespan in the daf-2 mutant background, indicating that oxidative stress is not necessarily a limiting factor for longevity. Furthermore, the deletion in the sod-3 gene lengthens lifespan in the daf-2 mutant. We conclude that the MnSOD systems in C. elegans fine-tune the insulin/IGF-I-signaling based regulation of longevity by acting not as anti-oxidants but as physiological-redox-signaling modulators.
Collapse
Affiliation(s)
- Yoko Honda
- Department of Genomics for Longevity and Health, Tokyo Metropolitan Institute of Gerontology, Tokyo, Japan.
| | | | | |
Collapse
|
42
|
Abstract
Caenorhabditis elegans, a free-living soil nematode, is an ideal model system for studying various physiological problems relevant to human diseases. Despite its short history, C. elegans proteomics is receiving great attention in multiple research areas, including the genome annotation, major signaling pathways (e.g. TGF-beta and insulin/IGF-1 signaling), verification of RNA interference-mediated gene targeting, aging, disease models, as well as peptidomic analysis of neuropeptides involved in behavior and locomotion. For example, a proteome-wide profiling of developmental and aging processes not only provides basic information necessary for constructing a molecular network, but also identifies important target proteins for chemical modulation. Although C. elegans has a simple body system and neural circuitry, it exhibits very complicated functions ranging from feeding to locomotion. Investigation of these functions through proteomic analysis of various C. elegans neuropeptides, some of which are not found in the predicted genome sequence, would open a new field of peptidomics. Given the importance of nematode infection in plants and mammalian pathogenesis pathways, proteomics could be applied to investigate the molecular mechanisms underlying plant- or animal-nematode pathogenesis and to identify novel antinematodal drugs. Thus, C. elegans proteomics, in combination of other molecular, biological and genetic techniques, would provide a versatile new tool box for the systematic analysis of gene functions throughout the entire life cycle of this nematode.
Collapse
Affiliation(s)
- Yhong-Hee Shim
- Department of Bioscience and Biotechnology, BMIC, Konkuk University, Gwangjin-Ku, Seoul, Korea
| | | |
Collapse
|
43
|
Salminen A, Kaarniranta K. Glycolysis links p53 function with NF-kappaB signaling: impact on cancer and aging process. J Cell Physiol 2010; 224:1-6. [PMID: 20301205 DOI: 10.1002/jcp.22119] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
In 1930, Otto Warburg observed that cancer cells produce an increased amount of their energy through aerobic glycolysis and subsequently, this was called the Warburg effect. During aging, the capacity for mitochondrial respiration clearly declines and aerobic glycolysis appears to compensate for the deficiency in oxidative metabolism. This shift in energy production, both in aging and cancer, could protect from the toxic effects of oxygen free radicals whereas increased glycolysis can have adverse effects. It was recently demonstrated that the glycolysis-linked protein O-glycosylation can potentiate the catalytic activity of IKK beta and subsequently trigger NF-kappaB signaling. It seems that tumor suppressor oncogene p53 has an important role in the regulation of protein O-glycosylation since p53 is a potent inhibitor of glycolysis, for example, via TIGAR protein expression. Aging is known to repress the function of p53 and this could enhance glycolysis and NF-kappaB signaling. We will discuss the role of p53 in the regulation of glycolysis-dependent activation of NF-kappaB signaling in both cancer and aging process.
Collapse
Affiliation(s)
- Antero Salminen
- Department of Neurology, Institute of Clinical Medicine, University of Kuopio, Kuopio, Finland.
| | | |
Collapse
|
44
|
Zheng J, Enright F, Keenan M, Finley J, Zhou J, Ye J, Greenway F, Senevirathne RN, Gissendanner CR, Manaois R, Prudente A, King JM, Martin R. Resistant starch, fermented resistant starch, and short-chain fatty acids reduce intestinal fat deposition in Caenorhabditis elegans. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2010; 58:4744-4748. [PMID: 20353151 DOI: 10.1021/jf904583b] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Obesity is a growing global public health dilemma. The objective of this project is to develop and validate a screening mechanism for bioactive compounds that may reduce body fat and promote health. Resistant starch (RS) reduces body fat in rodents. Amylose starch that has a high content of RS, endogenous compounds obtained from the ceca of amylose starch fed mice (fermented RS), and individual short-chain fatty acids (SCFA) were tested. The Caenorhabditis elegans model and Nile red staining were selected to determine the intestinal fat deposition response to bioactive components. The fluorescence intensity of Nile red was reduced to 76.5% (amylose starch), 78.8% (fermented RS), 63.6% (butyrate), or 28-80% (SCFAs) of controls, respectively (P < 0.001). The reduced intestinal fat deposition suggests reduced food intake or increased energy expenditure. C. elegans is a practical animal model to screen for bioactive compounds that may prevent or treat obesity.
Collapse
Affiliation(s)
- Jolene Zheng
- Veterinary Science Department, LSU AgCenter, Louisiana StateUniversity, Baton Rouge, Louisiana 70803, USA.
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
45
|
Sikora J, Urinovská J, Majer F, Poupetová H, Hlavatá J, Kostrouchová M, Ledvinová J, Hrebícek M. Bioinformatic and biochemical studies point to AAGR-1 as the ortholog of human acid alpha-glucosidase in Caenorhabditis elegans. Mol Cell Biochem 2010; 341:51-63. [PMID: 20349118 DOI: 10.1007/s11010-010-0436-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2009] [Accepted: 03/11/2010] [Indexed: 10/19/2022]
Abstract
Human acid alpha-glucosidase (GAA, EC 3.2.1.20) is a lysosomal enzyme that belongs to the glycoside hydrolase family 31 (GH31) and catalyses the hydrolysis of alpha-1,4- and alpha-1,6-glucosidic linkages at acid pH. Hereditary deficiency of GAA results in lysosomal glycogen storage disease type II (GSDII, Pompe disease). The aim of this study was to assess GH31 proteins in Caenorhabditis elegans (C. elegans) to identify the ortholog of human GAA. Bioinformatic searches for GAA ortholog in C. elegans genome revealed four acid alpha-glucosidase-related (aagr-1-4) genes. Multiple sequence alignment of AAGRs with other GH31 proteins demonstrated their evolutionary conservation. Phylogenetic analyses suggested clustering of AAGR-1 and -2 with acid-active and AAGR-3 and -4 with neutral-active GH31 enzymes. In order to prove the AAGRs' predicted alpha-glucosidase activity, we performed RNA interference of all four aagr genes. The impact on the alpha-glucosidase activity was evaluated at pH 4.0 (acid) and pH 6.5 (neutral), with or without the inhibitor acarbose. AAGR-1 and -2 expressed acidic alpha-glucosidase activity; on the contrary, AAGR-3 not -4 represented the predominant neutral alpha-glucosidase activity in C. elegans. Similar results were obtained in each of aagr-1 and -4 deletion mutants. Moreover, based on our structural models of AAGRs and these biochemical experiments, we hypothesize that the enzymatic sensitivity of AAGR-2 and human maltase-glucoamylase to the inhibitor acarbose is associated with a tyrosine residue in the GH31 active site, whereas acarbose resistance of AAGR-1 and human GAA is associated with the corresponding tryptophane in the active site. Acid-active AAGR-1 may thus represent the ortholog of human GAA in C. elegans.
Collapse
Affiliation(s)
- Jakub Sikora
- 1st Faculty of Medicine, Institute of Inherited Metabolic Disorders, Charles University in Prague, Ke Karlovu 2, Prague 2, Czech Republic.
| | | | | | | | | | | | | | | |
Collapse
|
46
|
Ruzanov P, Riddle DL. Deep SAGE analysis of the Caenorhabditis elegans transcriptome. Nucleic Acids Res 2010; 38:3252-62. [PMID: 20129939 PMCID: PMC2879516 DOI: 10.1093/nar/gkq035] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
We employed the Tag-seq technique to generate global transcription profiles for different strains and life stages of the nematode C. elegans. Tag-seq generates cDNA tags as does Serial Analysis of Gene Expression (SAGE), but the method yields a much larger number of tags, generating much larger data sets than SAGE. We examined differences in the performance of SAGE and Tag-seq by comparing gene expression data for 13 pairs of libraries. We identified genes for which expression was consistently changed in long-lived worms. Additional genes emerged in the deeper Tag-seq profiles, including several ‘signature’ genes found among those zup-regulated in long-lived dauer larvae (cki-1, aak-2 and daf-16). Fifty to sixty percent of the genes differentially expressed in daf-2(−) versus daf-2(+) adults had fragmentary or no functional annotation, suggesting the involvement of as yet unstudied pathways in aging. We were able to distinguish between changes in gene expression associated with altered genotype or altered growth conditions. We found 62 cases of possible mRNA isoform switching in the 13 Tag-seq libraries, whereas the 13 SAGE libraries allowed detection of only 15 such occurrences. We observed strong expression of anti-sense transcripts for several mitochondrial genes, but nuclear anti-sense transcripts were neither abundant nor consistently expressed among the libraries.
Collapse
Affiliation(s)
- Peter Ruzanov
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | | |
Collapse
|
47
|
Abstract
A major goal of aging research is to identify interventions that prolong
lifespan in distantly related organisms. In recent years, genetic studies
in both nematodes and rodents have reported that moderate inactivation of
genes important for mitochondrial electron transport chain (ETC) function
can promote longevity. We performed an RNAi screen to probe the role of
ETC components in modulating lifespan in the fruit flyDrosophila
melanogaster. In this Research Perspective, we discuss our findings
and how they may relate to similar studies in worms and mice.
Collapse
|
48
|
Hutter H, Ng MP, Chen N. GExplore: a web server for integrated queries of protein domains, gene expression and mutant phenotypes. BMC Genomics 2009; 10:529. [PMID: 19917126 PMCID: PMC2779824 DOI: 10.1186/1471-2164-10-529] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2009] [Accepted: 11/16/2009] [Indexed: 01/17/2023] Open
Abstract
Background The majority of the genes even in well-studied multi-cellular model organisms have not been functionally characterized yet. Mining the numerous genome wide data sets related to protein function to retrieve potential candidate genes for a particular biological process remains a challenge. Description GExplore has been developed to provide a user-friendly database interface for data mining at the gene expression/protein function level to help in hypothesis development and experiment design. It supports combinatorial searches for proteins with certain domains, tissue- or developmental stage-specific expression patterns, and mutant phenotypes. GExplore operates on a stand-alone database and has fast response times, which is essential for exploratory searches. The interface is not only user-friendly, but also modular so that it accommodates additional data sets in the future. Conclusion GExplore is an online database for quick mining of data related to gene and protein function, providing a multi-gene display of data sets related to the domain composition of proteins as well as expression and phenotype data. GExplore is publicly available at: http://genome.sfu.ca/gexplore/
Collapse
Affiliation(s)
- Harald Hutter
- Department of Biological Sciences, Simon Fraser University, Burnaby, Canada.
| | | | | |
Collapse
|
49
|
Phillips D, Aponte AM, French SA, Chess DJ, Balaban RS. Succinyl-CoA synthetase is a phosphate target for the activation of mitochondrial metabolism. Biochemistry 2009; 48:7140-9. [PMID: 19527071 DOI: 10.1021/bi900725c] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Succinyl-CoA synthetase (SCS) is the only mitochondrial enzyme capable of ATP production via substrate level phosphorylation in the absence of oxygen, but it also plays a key role in the citric acid cycle, ketone metabolism, and heme synthesis. Inorganic phosphate (P(i)) is a signaling molecule capable of activating oxidative phosphorylation at several sites, including NADH generation and as a substrate for ATP formation. In this study, it was shown that P(i) binds the porcine heart SCS alpha-subunit (SCSalpha) in a noncovalent manner and enhances its enzymatic activity, thereby providing a new target for P(i) activation in mitochondria. Coupling 32P labeling of intact mitochondria with SDS gel electrophoresis revealed that 32P labeling of SCSalpha was enhanced in substrate-depleted mitochondria. Using mitochondrial extracts and purified bacterial SCS (BSCS), we showed that this enhanced 32P labeling resulted from a simple binding of 32P, not covalent protein phosphorylation. The ability of SCSalpha to retain its 32P throughout the SDS denaturing gel process was unique over the entire mitochondrial proteome. In vitro studies also revealed a P(i)-induced activation of SCS activity by more than 2-fold when mitochondrial extracts and purified BSCS were incubated with millimolar concentrations of P(i). Since the level of 32P binding to SCSalpha was increased in substrate-depleted mitochondria, where the matrix P(i) concentration is increased, we conclude that SCS activation by P(i) binding represents another mitochondrial target for the P(i)-induced activation of oxidative phosphorylation and anaerobic ATP production in energy-limited mitochondria.
Collapse
Affiliation(s)
- Darci Phillips
- Laboratory of Cardiac Energetics, National Heart, Lung, and Blood Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland 20892-1061, USA
| | | | | | | | | |
Collapse
|
50
|
Bushell WC. Longevity: potential life span and health span enhancement through practice of the basic yoga meditation regimen. Ann N Y Acad Sci 2009; 1172:20-7. [PMID: 19735236 DOI: 10.1111/j.1749-6632.2009.04538.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
This chapter briefly reviews recent psychological, physiological, molecular biological, and anthropological research which has important implications, both direct and indirect, for the recognition and understanding of the potential life span and health span enhancing effects of the basic yoga meditational regimen. This regimen consists of meditation, yogic breath control practices, physical exercises (of both a postural- and movement-based, including aerobic nature), and dietary practices. While each of these component categories exhibit variations in different schools, lineages, traditions, and cultures, the focus of this chapter is primarily on basic forms of relaxation meditation and breath control, as well as postural and aerobic physical exercises (e.g., yogic prostration regimens, see below), and a standard form of yogic or ascetic diet, all of which constitute a basic form of regimen found in many if not most cultures, though with variations.
Collapse
Affiliation(s)
- William C Bushell
- Anthropology Program, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.
| |
Collapse
|