151
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Dirksen P, Marsh SA, Braker I, Heitland N, Wagner S, Nakad R, Mader S, Petersen C, Kowallik V, Rosenstiel P, Félix MA, Schulenburg H. The native microbiome of the nematode Caenorhabditis elegans: gateway to a new host-microbiome model. BMC Biol 2016; 14:38. [PMID: 27160191 PMCID: PMC4860760 DOI: 10.1186/s12915-016-0258-1] [Citation(s) in RCA: 245] [Impact Index Per Article: 30.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Accepted: 04/19/2016] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Host-microbe associations underlie many key processes of host development, immunity, and life history. Yet, none of the current research on the central model species Caenorhabditis elegans considers the worm's natural microbiome. Instead, almost all laboratories exclusively use the canonical strain N2 and derived mutants, maintained through routine bleach sterilization in monoxenic cultures with an E. coli strain as food. Here, we characterize for the first time the native microbiome of C. elegans and assess its influence on nematode life history characteristics. RESULTS Nematodes sampled directly from their native habitats carry a species-rich bacterial community, dominated by Proteobacteria such as Enterobacteriaceae and members of the genera Pseudomonas, Stenotrophomonas, Ochrobactrum, and Sphingomonas. The C. elegans microbiome is distinct from that of the worm's natural environment and the congeneric species C. remanei. Exposure to a derived experimental microbiome revealed that bacterial composition is influenced by host developmental stage and genotype. These experiments also showed that the microbes enhance host fitness under standard and also stressful conditions (e.g., high temperature and either low or high osmolarity). Taking advantage of the nematode's transparency, we further demonstrate that several Proteobacteria are able to enter the C. elegans gut and that an Ochrobactrum isolate even seems to be able to persist in the intestines under stressful conditions. Moreover, three Pseudomonas isolates produce an anti-fungal effect in vitro which we show can contribute to the worm's defense against fungal pathogens in vivo. CONCLUSION This first systematic analysis of the nematode's native microbiome reveals a species-rich bacterial community to be associated with C. elegans, which is likely of central importance for our understanding of the worm's biology. The information acquired and the microbial isolates now available for experimental work establishes C. elegans as a tractable model for the in-depth dissection of host-microbiome interactions.
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Affiliation(s)
- Philipp Dirksen
- Department of Evolutionary Ecology and Genetics, Zoological Institute, Christian-Albrechts University, Am Botanischen Garten 3-9, 24118, Kiel, Germany
| | - Sarah Arnaud Marsh
- Institute of Biology of the Ecole Normale Supérieure (IBENS), CNRS, Inserm, 46 rue d'Ulm, 75230, Paris Cedex 05, France
- Institut Pasteur, 25-28 rue du Docteur Roux, 75724, Paris Cedex 15, France
| | - Ines Braker
- Department of Evolutionary Ecology and Genetics, Zoological Institute, Christian-Albrechts University, Am Botanischen Garten 3-9, 24118, Kiel, Germany
| | - Nele Heitland
- Department of Evolutionary Ecology and Genetics, Zoological Institute, Christian-Albrechts University, Am Botanischen Garten 3-9, 24118, Kiel, Germany
| | - Sophia Wagner
- Department of Evolutionary Ecology and Genetics, Zoological Institute, Christian-Albrechts University, Am Botanischen Garten 3-9, 24118, Kiel, Germany
| | - Rania Nakad
- Department of Evolutionary Ecology and Genetics, Zoological Institute, Christian-Albrechts University, Am Botanischen Garten 3-9, 24118, Kiel, Germany
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases, University of Cologne, Joseph-Stelzmann-Str. 26, 50931, Cologne, Germany
| | - Sebastian Mader
- Department of Evolutionary Ecology and Genetics, Zoological Institute, Christian-Albrechts University, Am Botanischen Garten 3-9, 24118, Kiel, Germany
| | - Carola Petersen
- Department of Evolutionary Ecology and Genetics, Zoological Institute, Christian-Albrechts University, Am Botanischen Garten 3-9, 24118, Kiel, Germany
| | - Vienna Kowallik
- Department of Evolutionary Ecology and Genetics, Zoological Institute, Christian-Albrechts University, Am Botanischen Garten 3-9, 24118, Kiel, Germany
- Max Planck Institute for Evolutionary Biology, August-Thienemann-Strasse 2, 24306, Plön, Germany
| | - Philip Rosenstiel
- Institute of Clinical Molecular Biology, Christian-Albrechts University, Am Botanischen Garten 1-3, 24118, Kiel, Germany
| | - Marie-Anne Félix
- Institute of Biology of the Ecole Normale Supérieure (IBENS), CNRS, Inserm, 46 rue d'Ulm, 75230, Paris Cedex 05, France
| | - Hinrich Schulenburg
- Department of Evolutionary Ecology and Genetics, Zoological Institute, Christian-Albrechts University, Am Botanischen Garten 3-9, 24118, Kiel, Germany.
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152
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Dopamine regulates body size in Caenorhabditis elegans. Dev Biol 2016; 412:128-138. [DOI: 10.1016/j.ydbio.2016.02.021] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Revised: 01/08/2016] [Accepted: 02/23/2016] [Indexed: 12/31/2022]
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153
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Yen CA, Curran SP. Gene-diet interactions and aging in C. elegans. Exp Gerontol 2016; 86:106-112. [PMID: 26924670 DOI: 10.1016/j.exger.2016.02.012] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Revised: 02/16/2016] [Accepted: 02/24/2016] [Indexed: 02/06/2023]
Abstract
Diet is the most variable aspect of life history, as most individuals have a large diversity of food choices, varying in the type and amount that they ingest. In the short-term, diet can affect metabolism and energy levels. However, in the long run, the net deficiency or excess of calories from diet can influence the progression and severity of age-related diseases. An old and yet still debated question is: how do specific dietary choices impact health- and lifespan? It is clear that genetics can play a critical role - perhaps just as important as diet choices. For example, poor diet in combination with genetic susceptibility can lead to metabolic disorders, such as obesity and type 2 diabetes. Recent work in Caenorhabditis elegans has identified the existence of diet-gene pairs, where the consequence of mutating a specific gene is only realized on specific diets. Many core metabolic pathways are conserved from worm to human. Although only a handful of these diet-gene pairs has been characterized, there are potentially hundreds, if not thousands, of such interactions, which may explain the variability in the rates of aging in humans and the incidence and severity of age-related diseases.
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Affiliation(s)
- Chia An Yen
- University of Southern California, Dornsife College of Letters, Arts, and Science, Department of Molecular and Computational Biology, United States
| | - Sean P Curran
- University of Southern California, Dornsife College of Letters, Arts, and Science, Department of Molecular and Computational Biology, United States; University of Southern California, Davis School of Gerontology, United States.
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154
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RETRACTED: Gut-Colonizing Bacteria Promote C. elegans Innate Immunity by Producing Nitric Oxide. Cell Rep 2016; 14:1301-1307. [DOI: 10.1016/j.celrep.2016.01.032] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Revised: 12/09/2015] [Accepted: 12/28/2015] [Indexed: 11/19/2022] Open
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155
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Assembly of the Caenorhabditis elegans gut microbiota from diverse soil microbial environments. ISME JOURNAL 2016; 10:1998-2009. [PMID: 26800234 PMCID: PMC5029150 DOI: 10.1038/ismej.2015.253] [Citation(s) in RCA: 225] [Impact Index Per Article: 28.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Revised: 11/22/2015] [Accepted: 12/01/2015] [Indexed: 01/15/2023]
Abstract
It is now well accepted that the gut microbiota contributes to our health. However, what determines the microbiota composition is still unclear. Whereas it might be expected that the intestinal niche would be dominant in shaping the microbiota, studies in vertebrates have repeatedly demonstrated dominant effects of external factors such as host diet and environmental microbial diversity. Hypothesizing that genetic variation may interfere with discerning contributions of host factors, we turned to Caenorhabditis elegans as a new model, offering the ability to work with genetically homogenous populations. Deep sequencing of 16S rDNA was used to characterize the (previously unknown) worm gut microbiota as assembled from diverse produce-enriched soil environments under laboratory conditions. Comparisons of worm microbiotas with those in their soil environment revealed that worm microbiotas resembled each other even when assembled from different microbial environments, and enabled defining a shared core gut microbiota. Community analyses indicated that species assortment in the worm gut was non-random and that assembly rules differed from those in their soil habitat, pointing at the importance of competitive interactions between gut-residing taxa. The data presented fills a gap in C. elegans biology. Furthermore, our results demonstrate a dominant contribution of the host niche in shaping the gut microbiota.
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156
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Gracida X, Norris AD, Calarco JA. Regulation of Tissue-Specific Alternative Splicing: C. elegans as a Model System. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 907:229-61. [DOI: 10.1007/978-3-319-29073-7_10] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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157
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Tejeda-Benitez L, Olivero-Verbel J. Caenorhabditis elegans, a Biological Model for Research in Toxicology. REVIEWS OF ENVIRONMENTAL CONTAMINATION AND TOXICOLOGY 2016; 237:1-35. [PMID: 26613986 DOI: 10.1007/978-3-319-23573-8_1] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Caenorhabditis elegans is a nematode of microscopic size which, due to its biological characteristics, has been used since the 1970s as a model for research in molecular biology, medicine, pharmacology, and toxicology. It was the first animal whose genome was completely sequenced and has played a key role in the understanding of apoptosis and RNA interference. The transparency of its body, short lifespan, ability to self-fertilize and ease of culture are advantages that make it ideal as a model in toxicology. Due to the fact that some of its biochemical pathways are similar to those of humans, it has been employed in research in several fields. C. elegans' use as a biological model in environmental toxicological assessments allows the determination of multiple endpoints. Some of these utilize the effects on the biological functions of the nematode and others use molecular markers. Endpoints such as lethality, growth, reproduction, and locomotion are the most studied, and usually employ the wild type Bristol N2 strain. Other endpoints use reporter genes, such as green fluorescence protein, driven by regulatory sequences from other genes related to different mechanisms of toxicity, such as heat shock, oxidative stress, CYP system, and metallothioneins among others, allowing the study of gene expression in a manner both rapid and easy. These transgenic strains of C. elegans represent a powerful tool to assess toxicity pathways for mixtures and environmental samples, and their numbers are growing in diversity and selectivity. However, other molecular biology techniques, including DNA microarrays and MicroRNAs have been explored to assess the effects of different toxicants and samples. C. elegans has allowed the assessment of neurotoxic effects for heavy metals and pesticides, among those more frequently studied, as the nematode has a very well defined nervous system. More recently, nanoparticles are emergent pollutants whose toxicity can be explored using this nematode. Overall, almost every type of known toxicant has been tested with this animal model. In the near future, the available knowledge on the life cycle of C. elegans should allow more studies on reproduction and transgenerational toxicity for newly developed chemicals and materials, facilitating their introduction in the market. The great diversity of endpoints and possibilities of this animal makes it an easy first-choice for rapid toxicity screening or to detail signaling pathways involved in mechanisms of toxicity.
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Affiliation(s)
- Lesly Tejeda-Benitez
- Environmental and Computational Chemistry Group, School of Pharmaceutical Sciences, Zaragocilla Campus, University of Cartagena, Cartagena, 130014, Colombia.
| | - Jesus Olivero-Verbel
- Environmental and Computational Chemistry Group, School of Pharmaceutical Sciences, Zaragocilla Campus, University of Cartagena, Cartagena, 130014, Colombia.
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158
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Medkour Y, Svistkova V, Titorenko VI. Cell-Nonautonomous Mechanisms Underlying Cellular and Organismal Aging. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2015; 321:259-97. [PMID: 26811290 DOI: 10.1016/bs.ircmb.2015.09.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Cell-autonomous mechanisms underlying cellular and organismal aging in evolutionarily distant eukaryotes have been established; these mechanisms regulate longevity-defining processes within a single eukaryotic cell. Recent findings have provided valuable insight into cell-nonautonomous mechanisms modulating cellular and organismal aging in eukaryotes across phyla; these mechanisms involve a transmission of various longevity factors between different cells, tissues, and organisms. Herein, we review such cell-nonautonomous mechanisms of aging in eukaryotes. We discuss the following: (1) how low molecular weight transmissible longevity factors modulate aging and define longevity of cells in yeast populations cultured in liquid media or on solid surfaces, (2) how communications between proteostasis stress networks operating in neurons and nonneuronal somatic tissues define longevity of the nematode Caenorhabditis elegans by modulating the rates of aging in different tissues, and (3) how different bacterial species colonizing the gut lumen of C. elegans define nematode longevity by modulating the rate of organismal aging.
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Affiliation(s)
- Younes Medkour
- Department of Biology, Concordia University, Montreal, Quebec, Canada
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159
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Ding W, Smulan LJ, Hou NS, Taubert S, Watts JL, Walker AK. s-Adenosylmethionine Levels Govern Innate Immunity through Distinct Methylation-Dependent Pathways. Cell Metab 2015; 22:633-45. [PMID: 26321661 PMCID: PMC4598287 DOI: 10.1016/j.cmet.2015.07.013] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Revised: 05/29/2015] [Accepted: 07/17/2015] [Indexed: 12/13/2022]
Abstract
s-adenosylmethionine (SAM) is the sole methyl donor modifying histones, nucleic acids, and phospholipids. Its fluctuation affects hepatic phosphatidylcholine (PC) synthesis or may be linked to variations in DNA or histone methylation. Physiologically, low SAM is associated with lipid accumulation, tissue injury, and immune responses in fatty liver disease. However, molecular connections among SAM limitation, methyltransferases, and disease-associated phenotypes are unclear. We find that low SAM can activate or attenuate Caenorhabditis elegans immune responses. Immune pathways are stimulated downstream of PC production on a non-pathogenic diet. In contrast, distinct SAM-dependent mechanisms limit survival on pathogenic Pseudomonas aeruginosa. C. elegans undertakes a broad transcriptional response to pathogens and we find that low SAM restricts H3K4me3 at Pseudomonas-responsive promoters, limiting their expression. Furthermore, this response depends on the H3K4 methyltransferase set-16/MLL. Thus, our studies provide molecular links between SAM and innate immune functions and suggest that SAM depletion may limit stress-induced gene expression.
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Affiliation(s)
- Wei Ding
- Program in Molecular Medicine, UMass Worcester, 373 Plantation Street, Worcester, MA 01605, USA
| | - Lorissa J Smulan
- Program in Molecular Medicine, UMass Worcester, 373 Plantation Street, Worcester, MA 01605, USA
| | - Nicole S Hou
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics (CMMT) and Child & Family Research Institute (CFRI), University of British Columbia (UBC), Vancouver, BC V5Z 4H4, Canada
| | - Stefan Taubert
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics (CMMT) and Child & Family Research Institute (CFRI), University of British Columbia (UBC), Vancouver, BC V5Z 4H4, Canada
| | - Jennifer L Watts
- School of Molecular Biosciences, Washington State University, Pullman, WA 99164-6340, USA
| | - Amy K Walker
- Program in Molecular Medicine, UMass Worcester, 373 Plantation Street, Worcester, MA 01605, USA.
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160
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Dialogue between E. coli free radical pathways and the mitochondria of C. elegans. Proc Natl Acad Sci U S A 2015; 112:12456-61. [PMID: 26392561 DOI: 10.1073/pnas.1517448112] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The microbial world presents a complex palette of opportunities and dangers to animals, which have developed surveillance and response strategies to hints of microbial intent. We show here that the mitochondrial homeostatic response pathway of the nematode Caenorhabditis elegans responds to Escherichia coli mutations that activate free radical detoxification pathways. Activation of C. elegans mitochondrial responses could be suppressed by additional mutations in E. coli, suggesting that C. elegans responds to products of E. coli to anticipate challenges to its mitochondrion. Out of 50 C. elegans gene inactivations known to mediate mitochondrial defense, we found that 7 genes were required for C. elegans response to a free radical producing E. coli mutant, including the bZip transcription factor atfs-1 (activating transcription factor associated with stress). An atfs-1 loss-of-function mutant was partially resistant to the effects of free radical-producing E. coli mutant, but a constitutively active atfs-1 mutant growing on wild-type E. coli inappropriately activated the pattern of mitochondrial responses normally induced by an E. coli free radical pathway mutant. Carbonylated proteins from free radical-producing E. coli mutant may directly activate the ATFS-1/bZIP transcription factor to induce mitochondrial stress response: feeding C. elegans with H2O2-treated E. coli induces the mitochondrial unfolded protein response, and inhibition of a gut peptide transporter partially suppressed C. elegans response to free radical damaged E. coli.
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161
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Sowa JN, Mutlu AS, Xia F, Wang MC. Olfaction Modulates Reproductive Plasticity through Neuroendocrine Signaling in Caenorhabditis elegans. Curr Biol 2015; 25:2284-9. [PMID: 26279229 DOI: 10.1016/j.cub.2015.07.023] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Revised: 07/07/2015] [Accepted: 07/09/2015] [Indexed: 11/26/2022]
Abstract
Reproductive plasticity describes the ability of organisms to adjust parameters such as volume, rate, or timing of progeny production in order to maximize successful reproduction under different environmental conditions. Reproductive plasticity in response to environmental variation has been observed in a wide range of animals; however, the mechanisms involved in translating environmental cues into reproductive outcomes remain unknown. Here, we show that olfaction modulates reproductive timing and senescence through neuroendocrine signaling in Caenorhabditis elegans. On their preferred diet, worms demonstrate an increased rate of reproduction and an early onset of reproductive aging. Perception of the preferred diet's odor by AWB olfactory neurons elicits these adjustments by increasing germline proliferation, and optogenetic stimulation of AWB neurons is sufficient to accelerate reproductive timing in the absence of dietary inputs. Furthermore, AWB neurons act through neuropeptide signaling to regulate reproductive rate and senescence. These findings reveal a neuroendocrine nexus linking olfactory sensation and reproduction in response to environmental variation and indicate the significance of olfaction in the regulation of reproductive decline during aging.
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Affiliation(s)
- Jessica N Sowa
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ayse Sena Mutlu
- Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Fan Xia
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Meng C Wang
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, USA.
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162
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MacNeil LT, Pons C, Arda HE, Giese GE, Myers CL, Walhout AJM. Transcription Factor Activity Mapping of a Tissue-Specific in vivo Gene Regulatory Network. Cell Syst 2015; 1:152-162. [PMID: 26430702 DOI: 10.1016/j.cels.2015.08.003] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
A wealth of physical interaction data between transcription factors (TFs) and DNA has been generated, but these interactions often do not have apparent regulatory consequences. Thus, equating physical interaction data with gene regulatory networks (GRNs) is problematic. Here, we comprehensively assay TF activity, rather than binding, to construct a network of gene regulatory interactions in the C. elegans intestine. By manually observing the in vivo tissue-specific knockdown of 921 TFs on a panel of 19 fluorescent transcriptional reporters, we identified a GRN of 411 interactions between 19 promoters and 177 TFs. This GRN shows only modest overlap with physical interactions, indicating that many regulatory interactions are indirect. We applied nested effects modeling to uncover information flow between TFs in the intestine that converges on a small set of physical TF-promoter interactions. We found numerous cell nonautonomous regulatory interactions, illustrating tissue-to-tissue communication. Altogether, our study illuminates the complexity of gene regulation in the context of a living animal.
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Affiliation(s)
- Lesley T MacNeil
- Program in Systems Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA ; Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Carles Pons
- Department of Computer Science and Engineering, University of Minnesota-Twin Cities, Minneapolis, MN 55455, USA
| | - H Efsun Arda
- Program in Systems Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA ; Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Gabrielle E Giese
- Program in Systems Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Chad L Myers
- Department of Computer Science and Engineering, University of Minnesota-Twin Cities, Minneapolis, MN 55455, USA
| | - Albertha J M Walhout
- Program in Systems Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA ; Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
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163
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Yu L, Yan X, Ye C, Zhao H, Chen X, Hu F, Li H. Bacterial Respiration and Growth Rates Affect the Feeding Preferences, Brood Size and Lifespan of Caenorhabditis elegans. PLoS One 2015. [PMID: 26222828 PMCID: PMC4519269 DOI: 10.1371/journal.pone.0134401] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Bacteria serve as live food and nutrients for bacterial-feeding nematodes (BFNs) in soils, and influence nematodes behavior and physiology through their metabolism. Five bacterial taxa (Bacillus amyloliquefaciens JX1, Variovorax sp. JX14, Bacillus megaterium JX15, Pseudomonas fluorescens Y1 and Escherichia coli OP50) and the typical BFN Caenorhabditis elegans were selected to study the effects of bacterial respiration and growth rates on the feeding preferences, brood size and lifespan of nematodes. P. fluorescens Y1 and E. coli OP50 were found to be more active, with high respiration and rapid growth, whereas B. amyloliquefaciens JX1 and B. megaterium JX15 were inactive. The nematode C. elegans preferred active P. fluorescens Y1 and E. coli OP50 obviously. Furthermore, worms that fed on these two active bacteria produced more offspring but had shorter lifespan, while inactive and less preferred bacteria had increased nematodes lifespan and decreased the brood size. Based on these results, we propose that the bacterial activity may influence the behavior and life traits of C. elegans in the following ways: (1) active bacteria reproduce rapidly and emit high levels of CO2 attracting C. elegans; (2) these active bacteria use more resources in the nematodes’ gut to sustain their survival and reproduction, thereby reducing the worm's lifespan; (3) inactive bacteria may provide less food for worms than active bacteria, thus increasing nematodes lifespan but decreasing their fertility. Nematodes generally require a balance between their preferred foods and beneficial foods, only preferred food may not be beneficial for nematodes.
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Affiliation(s)
- Li Yu
- Soil Ecology Lab, College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing, 210095, People’s Republic of China
| | - Xiaomei Yan
- Soil Ecology Lab, College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing, 210095, People’s Republic of China
| | - Chenglong Ye
- Soil Ecology Lab, College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing, 210095, People’s Republic of China
| | - Haiyan Zhao
- College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing, 210095, People’s Republic of China
| | - Xiaoyun Chen
- Soil Ecology Lab, College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing, 210095, People’s Republic of China
| | - Feng Hu
- Soil Ecology Lab, College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing, 210095, People’s Republic of China
| | - Huixin Li
- Soil Ecology Lab, College of Resources and Environmental Science, Nanjing Agricultural University, Nanjing, 210095, People’s Republic of China
- * E-mail:
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164
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RNAi Interrogation of Dietary Modulation of Development, Metabolism, Behavior, and Aging in C. elegans. Cell Rep 2015; 11:1123-33. [PMID: 25959815 DOI: 10.1016/j.celrep.2015.04.024] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Revised: 01/29/2015] [Accepted: 04/11/2015] [Indexed: 02/06/2023] Open
Abstract
Diet affects nearly every aspect of animal life such as development, metabolism, behavior, and aging, both directly by supplying nutrients and indirectly through gut microbiota. C. elegans feeds on bacteria, and like other animals, different bacterial diets induce distinct dietary responses in the worm. However, the lack of certain critical tools hampers the use of worms as a model for dietary signaling. Here, we genetically engineered the bacterial strain OP50, the standard laboratory diet for C. elegans, making it compatible for dsRNA production and delivery. Using this RNAi-compatible OP50 strain and the other bacterial strain HT115, we feed worms different diets while delivering RNAi to interrogate the genetic basis underlying diet-dependent differential modulation of development, metabolism, behavior, and aging. We show by RNAi that neuroendocrine and mTOR pathways are involved in mediating differential dietary responses. This genetic tool greatly facilitates the use of C. elegans as a model for dietary signaling.
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165
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Lezzerini M, van de Ven K, Veerman M, Brul S, Budovskaya YV. Specific RNA Interference in Caenorhabditis elegans by Ingested dsRNA Expressed in Bacillus subtilis. PLoS One 2015; 10:e0124508. [PMID: 25928543 PMCID: PMC4416053 DOI: 10.1371/journal.pone.0124508] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Accepted: 03/15/2015] [Indexed: 01/10/2023] Open
Abstract
In nematodes, genome-wide RNAi-screening has been widely used as a rapid and efficient method to identify genes involved in the aging processes. By far the easiest way of inducing RNA interference (RNAi) in Caenorhabditis elegans is by feeding Escherichia coli that expresses specific double stranded RNA (dsRNA) to knockdown translation of targeted mRNAs. However, it has been shown that E. coli is mildly pathogenic to C. elegans and this pathogenicity might influence aging and the accuracy of the RNAi-screening during aging may as well be affected. Here, we describe a novel system that utilizes the non-pathogenic bacterium Bacillus subtilis, to express dsRNA and therefore eliminates the effects of bacterial pathogenicity from the genetic analysis of aging.
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Affiliation(s)
- Marco Lezzerini
- Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Koen van de Ven
- Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Martijn Veerman
- Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Stanley Brul
- Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Yelena V Budovskaya
- Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
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166
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Caenorhabditis elegans microRNAs of the let-7 family act in innate immune response circuits and confer robust developmental timing against pathogen stress. Proc Natl Acad Sci U S A 2015; 112:E2366-75. [PMID: 25897023 DOI: 10.1073/pnas.1422858112] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Animals maintain their developmental robustness against natural stresses through numerous regulatory mechanisms, including the posttranscriptional regulation of gene expression by microRNAs (miRNAs). Caenorhabditis elegans miRNAs of the let-7 family (let-7-Fam) function semiredundantly to confer robust stage specificity of cell fates in the hypodermal seam cell lineages. Here, we show reciprocal regulatory interactions between let-7-Fam miRNAs and the innate immune response pathway in C. elegans. Upon infection of C. elegans larvae with the opportunistic human pathogen Pseudomonas aeruginosa, the developmental timing defects of certain let-7-Fam miRNA mutants are enhanced. This enhancement is mediated by the p38 MAPK innate immune pathway acting in opposition to let-7-Fam miRNA activity, possibly via the downstream Activating Transcription Factor-7 (ATF-7). Furthermore, let-7-Fam miRNAs appear to exert negative regulation on the worm's resistance to P. aeruginosa infection. Our results show that the inhibition of pathogen resistance by let-7 involves downstream heterochronic genes and the p38 MAPK pathway. These findings suggest that let-7-Fam miRNAs are integrated into innate immunity gene regulatory networks, such that this family of miRNAs modulates immune responses while also ensuring robust timing of developmental events under pathogen stress.
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167
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Diaz SA, Mooring EQ, Rens EG, Restif O. Association with pathogenic bacteria affects life-history traits and population growth in Caenorhabditis elegans. Ecol Evol 2015; 5:1653-63. [PMID: 25937908 PMCID: PMC4409413 DOI: 10.1002/ece3.1461] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Revised: 02/09/2015] [Accepted: 02/16/2015] [Indexed: 12/02/2022] Open
Abstract
Determining the relationship between individual life-history traits and population dynamics is an essential step to understand and predict natural selection. Model organisms that can be conveniently studied experimentally at both levels are invaluable to test the rich body of theoretical literature in this area. The nematode Caenorhabditis elegans, despite being a well-established workhorse in genetics, has only recently received attention from ecologists and evolutionary biologists, especially with respect to its association with pathogenic bacteria. In order to start filling the gap between the two areas, we conducted a series of experiments aiming at measuring life-history traits as well as population growth of C. elegans in response to three different bacterial strains: Escherichia coli OP50, Salmonella enterica Typhimurium, and Pseudomonas aeruginosa PAO1. Whereas previous studies had established that the latter two reduced the survival of nematodes feeding on them compared to E. coli OP50, we report for the first time an enhancement in reproductive success and population growth for worms feeding on S. enterica Typhimurium. Furthermore, we used an age-specific population dynamic model, parameterized using individual life-history assays, to successfully predict the growth of populations over three generations. This study paves the way for more detailed and quantitative experimental investigation of the ecology and evolution of C. elegans and the bacteria it interacts with, which could improve our understanding of the fate of opportunistic pathogens in the environment.
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Affiliation(s)
- S Anaid Diaz
- Disease Dynamics Unit, Department of Veterinary Medicine, University of CambridgeMadingley Road, Cambridge, CB3 0ES, UK
| | - Eric Q Mooring
- Disease Dynamics Unit, Department of Veterinary Medicine, University of CambridgeMadingley Road, Cambridge, CB3 0ES, UK
| | - Elisabeth G Rens
- Disease Dynamics Unit, Department of Veterinary Medicine, University of CambridgeMadingley Road, Cambridge, CB3 0ES, UK
- Delft Institute of Applied Mathematics, EEMCS Faculty, Delft University of TechnologyDelft, The Netherlands
| | - Olivier Restif
- Disease Dynamics Unit, Department of Veterinary Medicine, University of CambridgeMadingley Road, Cambridge, CB3 0ES, UK
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168
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Meisel JD, Panda O, Mahanti P, Schroeder FC, Kim DH. Chemosensation of bacterial secondary metabolites modulates neuroendocrine signaling and behavior of C. elegans. Cell 2015; 159:267-80. [PMID: 25303524 DOI: 10.1016/j.cell.2014.09.011] [Citation(s) in RCA: 187] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Revised: 07/03/2014] [Accepted: 09/03/2014] [Indexed: 11/30/2022]
Abstract
Discrimination between pathogenic and beneficial microbes is essential for host organism immunity and homeostasis. Here, we show that chemosensory detection of two secondary metabolites produced by Pseudomonas aeruginosa modulates a neuroendocrine signaling pathway that promotes avoidance behavior in the simple animal host Caenorhabditis elegans. Secondary metabolites phenazine-1-carboxamide and pyochelin activate a G-protein-signaling pathway in the ASJ chemosensory neuron pair that induces expression of the neuromodulator DAF-7/TGF-β. DAF-7, in turn, activates a canonical TGF-β signaling pathway in adjacent interneurons to modulate aerotaxis behavior and promote avoidance of pathogenic P. aeruginosa. Our data provide a chemical, genetic, and neuronal basis for how the behavior and physiology of a simple animal host can be modified by the microbial environment and suggest that secondary metabolites produced by microbes may provide environmental cues that contribute to pathogen recognition and host survival.
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Affiliation(s)
- Joshua D Meisel
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Oishika Panda
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Parag Mahanti
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Frank C Schroeder
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Dennis H Kim
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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169
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Zhang L, Gualberto DG, Guo X, Correa P, Jee C, Garcia LR. TMC-1 attenuates C. elegans development and sexual behaviour in a chemically defined food environment. Nat Commun 2015; 6:6345. [PMID: 25695879 DOI: 10.1038/ncomms7345] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Accepted: 01/21/2015] [Indexed: 01/22/2023] Open
Abstract
Although diet affects growth and behaviour, the adaptive mechanisms that coordinate these processes in non-optimal food sources are unclear. Here we show that the C. elegans tmc-1 channel, which is homologous to the mammalian tmc deafness genes, attenuates development and inhibits sexual behaviour in non-optimal food, the synthetic CeMM medium. In CeMM medium, signalling from the pharyngeal MC neurons and body wall muscles slows larval development. However, in the non-standard diet, mutation in tmc-1 accelerates development, by impairing the excitability of these cells. The tmc-1 larva can immediately generate ATP when fed CeMM, and their fast development requires insulin signalling. Our findings suggest that the tmc-1 channel indirectly affects metabolism in wild-type animals. In addition to regulating the development, we show that mutating tmc-1 can relax diet-induced inhibition of male sexual behaviour, thus indicating that a single regulator can be genetically modified to promote growth rate and reproductive success in new environments.
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Affiliation(s)
- Liusuo Zhang
- Department of Biology, Howard Hughes Medical Institute, Texas A&M University, 3258 TAMU College Station, Texas 77843-3258, USA
| | - Daisy G Gualberto
- Department of Biology, Howard Hughes Medical Institute, Texas A&M University, 3258 TAMU College Station, Texas 77843-3258, USA
| | - Xiaoyan Guo
- Department of Biology, Howard Hughes Medical Institute, Texas A&M University, 3258 TAMU College Station, Texas 77843-3258, USA
| | - Paola Correa
- Department of Biology, Howard Hughes Medical Institute, Texas A&M University, 3258 TAMU College Station, Texas 77843-3258, USA
| | - Changhoon Jee
- Department of Biology, Howard Hughes Medical Institute, Texas A&M University, 3258 TAMU College Station, Texas 77843-3258, USA
| | - L Rene Garcia
- Department of Biology, Howard Hughes Medical Institute, Texas A&M University, 3258 TAMU College Station, Texas 77843-3258, USA
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170
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Abstract
The microbial mechanisms and key metabolites that shape the composition of the human gut microbiota are largely unknown, impeding efforts to manipulate dysbiotic microbial communities toward stability and health. Vitamins, which by definition are not synthesized in sufficient quantities by the host and can mediate fundamental biological processes in microbes, represent an attractive target for reshaping microbial communities. Here, we discuss how vitamin B12 (cobalamin) impacts diverse host-microbe symbioses. Although cobalamin is synthesized by some human gut microbes, it is a precious resource in the gut and is likely not provisioned to the host in significant quantities. However, this vitamin may make an unrecognized contribution in shaping the structure and function of human gut microbial communities.
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Affiliation(s)
- Patrick H Degnan
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Michiko E Taga
- Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Andrew L Goodman
- Department of Microbial Pathogenesis and Microbial Sciences Institute, Yale University, New Haven, CT 06516, USA.
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171
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Yilmaz LS, Walhout AJM. Worms, bacteria, and micronutrients: an elegant model of our diet. Trends Genet 2014; 30:496-503. [PMID: 25172020 PMCID: PMC4399232 DOI: 10.1016/j.tig.2014.07.010] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Revised: 07/22/2014] [Accepted: 07/22/2014] [Indexed: 01/21/2023]
Abstract
Micronutrients are required in small proportions in a diet to carry out key metabolic roles for biomass and energy production. Humans receive micronutrients either directly from their diet or from gut microbiota that metabolize other nutrients. The nematode Caenorhabditis elegans and its bacterial diet provide a relatively simple and genetically tractable model to study both direct and microbe-mediated effects of micronutrients. Recently, this model has been used to gain insight into the relationship between micronutrients, physiology, and metabolism. In particular, two B-type vitamins, vitamin B12 and folate, have been studied in detail. Here we review how C. elegans and its bacterial diet provide a powerful interspecies systems biology model that facilitates the precise delineation of micronutrient effects and the mechanisms involved.
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Affiliation(s)
- Lutfu Safak Yilmaz
- Program in Systems Biology, Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Albertha J M Walhout
- Program in Systems Biology, Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA.
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172
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Abstract
Over the past decade, studies conducted in Caenorhabditis elegans have helped to uncover the ancient and complex origins of body fat regulation. This review highlights the powerful combination of genetics, pharmacology, and biochemistry used to study energy balance and the regulation of cellular fat metabolism in C. elegans. The complete wiring diagram of the C. elegans nervous system has been exploited to understand how the sensory nervous system regulates body fat and how food perception is coupled with the production of energy via fat metabolism. As a model organism, C. elegans also offers a unique opportunity to discover neuroendocrine factors that mediate direct communication between the nervous system and the metabolic tissues. The coming years are expected to reveal a wealth of information on the neuroendocrine control of body fat in C. elegans.
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Affiliation(s)
- Supriya Srinivasan
- Department of Chemical Physiology and Dorris Neuroscience Center, The Scripps Research Institute (TSRI), La Jolla, California 92037;
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173
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Watson E, Walhout AJM. Caenorhabditis elegans metabolic gene regulatory networks govern the cellular economy. Trends Endocrinol Metab 2014; 25:502-8. [PMID: 24731597 PMCID: PMC4178166 DOI: 10.1016/j.tem.2014.03.004] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/11/2014] [Revised: 03/13/2014] [Accepted: 03/14/2014] [Indexed: 11/24/2022]
Abstract
Diet greatly impacts metabolism in health and disease. In response to the presence or absence of specific nutrients, metabolic gene regulatory networks sense the metabolic state of the cell and regulate metabolic flux accordingly, for instance by the transcriptional control of metabolic enzymes. Here, we discuss recent insights regarding metazoan metabolic regulatory networks using the nematode Caenorhabditis elegans as a model, including the modular organization of metabolic gene regulatory networks, the prominent impact of diet on the transcriptome and metabolome, specialized roles of nuclear hormone receptors (NHRs) in responding to dietary conditions, regulation of metabolic genes and metabolic regulators by miRNAs, and feedback between metabolic genes and their regulators.
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Affiliation(s)
- Emma Watson
- Program in Systems Biology, Program in Molecular Medicine, University of Massachusetts Medical School, 55 North Lake Ave, Worcester, MA, 01655, USA
| | - Albertha J M Walhout
- Program in Systems Biology, Program in Molecular Medicine, University of Massachusetts Medical School, 55 North Lake Ave, Worcester, MA, 01655, USA.
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174
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Mizunuma M, Neumann‐Haefelin E, Moroz N, Li Y, Blackwell TK. mTORC2-SGK-1 acts in two environmentally responsive pathways with opposing effects on longevity. Aging Cell 2014; 13:869-78. [PMID: 25040785 PMCID: PMC4172656 DOI: 10.1111/acel.12248] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/11/2014] [Indexed: 01/22/2023] Open
Abstract
The nematode worm Caenorhabditis elegans provides a powerful system for elucidating how genetic, metabolic, nutritional, and environmental factors influence aging. The mechanistic target of rapamycin (mTOR) kinase is important in growth, disease, and aging and is present in the mTORC1 and mTORC2 complexes. In diverse eukaryotes, lifespan can be increased by inhibition of mTORC1, which transduces anabolic signals to stimulate protein synthesis and inhibit autophagy. Less is understood about mTORC2, which affects C. elegans lifespan in a complex manner that is influenced by the bacterial food source. mTORC2 regulates C. elegans growth, reproduction, and lipid metabolism by activating the SGK-1 kinase, but current data on SGK-1 and lifespan seem to be conflicting. Here, by analyzing the mTORC2 component Rictor (RICT-1), we show that mTORC2 modulates longevity by activating SGK-1 in two pathways that affect lifespan oppositely. RICT-1/mTORC2 limits longevity by directing SGK-1 to inhibit the stress-response transcription factor SKN-1/Nrf in the intestine. Signals produced by the bacterial food source determine how this pathway affects SKN-1 and lifespan. In addition, RICT-1/mTORC2 functions in neurons in an SGK-1-mediated pathway that increases lifespan at lower temperatures. RICT-1/mTORC2 and SGK-1 therefore oppose or accelerate aging depending upon the context in which they are active. Our findings reconcile data on SGK-1 and aging, show that the bacterial microenvironment influences SKN-1/Nrf, mTORC2 functions, and aging, and identify two longevity-related mTORC2 functions that involve SGK-regulated responses to environmental cues.
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Affiliation(s)
- Masaki Mizunuma
- Joslin Diabetes Center Harvard Stem Cell Institute Harvard Medical School Department of Genetics Boston MA 02215USA
- Department of Molecular Biotechnology Graduate School of Advanced Sciences of Matter Hiroshima University Higashi‐Hiroshima 739‐8530 Japan
| | - Elke Neumann‐Haefelin
- Joslin Diabetes Center Harvard Stem Cell Institute Harvard Medical School Department of Genetics Boston MA 02215USA
- Renal Division University Hospital Freiburg Freiburg 79106Germany
| | - Natalie Moroz
- Joslin Diabetes Center Harvard Stem Cell Institute Harvard Medical School Department of Genetics Boston MA 02215USA
- Division of Biological Sciences Department of Genetics and Complex Diseases Harvard School of Public Health Boston MA 02115USA
| | - Yujie Li
- Renal Division University Hospital Freiburg Freiburg 79106Germany
| | - T. Keith Blackwell
- Joslin Diabetes Center Harvard Stem Cell Institute Harvard Medical School Department of Genetics Boston MA 02215USA
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175
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Ostojic I, Boll W, Waterson MJ, Chan T, Chandra R, Pletcher SD, Alcedo J. Positive and negative gustatory inputs affect Drosophila lifespan partly in parallel to dFOXO signaling. Proc Natl Acad Sci U S A 2014; 111:8143-8. [PMID: 24847072 PMCID: PMC4050613 DOI: 10.1073/pnas.1315466111] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
In Caenorhabditis elegans, a subset of gustatory neurons, as well as olfactory neurons, shortens lifespan, whereas a different subset of gustatory neurons lengthens it. Recently, the lifespan-shortening effect of olfactory neurons has been reported to be conserved in Drosophila. Here we show that the Drosophila gustatory system also affects lifespan in a bidirectional manner. We find that taste inputs shorten lifespan through inhibition of the insulin pathway effector dFOXO, whereas other taste inputs lengthen lifespan in parallel to this pathway. We also note that the gustatory influence on lifespan does not necessarily depend on food intake levels. Finally, we identify the nature of some of the taste inputs that could shorten versus lengthen lifespan. Together our data suggest that different gustatory cues can modulate the activities of distinct signaling pathways, including different insulin-like peptides, to promote physiological changes that ultimately affect lifespan.
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Affiliation(s)
- Ivan Ostojic
- Growth Control Unit, Friedrich Miescher Institute for Biomedical Research, CH-4058 Basel, Switzerland
| | - Werner Boll
- Institute of Molecular Life Sciences, University of Zurich, CH-8057 Zurich, Switzerland
| | | | - Tammy Chan
- Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030; and
| | - Rashmi Chandra
- Department of Biological Sciences, Wayne State University, Detroit, MI 48202
| | - Scott D Pletcher
- Program in Cellular and Molecular Biology,Department of Molecular and Integrative Physiology, andGeriatrics Center, University of Michigan, Ann Arbor, MI 48109
| | - Joy Alcedo
- Growth Control Unit, Friedrich Miescher Institute for Biomedical Research, CH-4058 Basel, Switzerland;Department of Biological Sciences, Wayne State University, Detroit, MI 48202
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176
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Lim MA, Bence KK, Sandesara I, Andreux P, Auwerx J, Ishibashi J, Seale P, Kalb RG. Genetically altering organismal metabolism by leptin-deficiency benefits a mouse model of amyotrophic lateral sclerosis. Hum Mol Genet 2014; 23:4995-5008. [PMID: 24833719 DOI: 10.1093/hmg/ddu214] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a fatal, neurodegenerative disease that causes death of motor neurons. ALS patients and mouse models of familial ALS display organismal level metabolic dysfunction, which includes increased energy expenditure despite decreased lean mass. The pathophysiological relevance of abnormal energy homeostasis to motor neuron disease remains unclear. Leptin is an adipocyte-derived hormone that regulates whole-animal energy expenditure. Here, we report that placing mutant superoxide dismutase 1 (SOD1) mice in a leptin-deficient background improves energy homeostasis and slows disease progression. Leptin-deficient mutant SOD1 mice possess increased bodyweight and fat mass, as well as decreased energy expenditure. These observations coincide with enhanced survival, improved strength and decreased motor neuron loss. These results suggest that altering whole-body energy metabolism in mutant SOD1 mice can mitigate disease progression. We propose that manipulations that increase fat mass and reduce energy expenditure will be beneficial in the setting of motor neuron disease.
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Affiliation(s)
- Maria A Lim
- Division of Neurology, Department of Pediatrics, Research Institute, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA, Neuroscience Graduate Group
| | - Kendra K Bence
- Neuroscience Graduate Group, Department of Animal Biology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ishani Sandesara
- Division of Neurology, Department of Pediatrics, Research Institute, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Pénélope Andreux
- Laboratory for Integrative and Systems Physiology, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Johan Auwerx
- Laboratory for Integrative and Systems Physiology, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Jeff Ishibashi
- Institute for Diabetes, Obesity and Metabolism, Department of Cell and Developmental Biology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Patrick Seale
- Institute for Diabetes, Obesity and Metabolism, Department of Cell and Developmental Biology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Robert G Kalb
- Division of Neurology, Department of Pediatrics, Research Institute, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA, Neuroscience Graduate Group, Department of Neurology and
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177
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Fassbinder-Orth CA. Methods for quantifying gene expression in ecoimmunology: from qPCR to RNA-Seq. Integr Comp Biol 2014; 54:396-406. [PMID: 24812328 DOI: 10.1093/icb/icu023] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Historically, the use of cutting-edge molecular techniques to study immunological gene expression and related cellular pathways has been largely limited to model organisms. Few studies have been performed that quantify the molecular immunological responses of non-model species, especially in response to environmental factors, life-history events, or exposure to parasites. This dearth of information has largely occurred due to the lack of available non-model species-specific gene sequences and immunological reagents and also due to prohibitively expensive technology. However, with the rapid development of various sequencing and transcriptomic technologies, profiling the gene expression of non-model organisms has become possible. Technologies and concepts explored here include an overview of current technologies for quantifying gene expression, including: qPCR, multiplex branched DNA assays, microarrays, and profiling gene expression (RNA sequencing [RNA-Seq]) based on next-generation sequencing. Examples of the advancement of these technologies in non-model systems are discussed. Additionally, applications, limitations, and feasibility of the use of these methodologies in non-model systems to address questions in ecological immunology and disease-ecology are specifically addressed.
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178
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Heintz C, Mair W. You are what you host: microbiome modulation of the aging process. Cell 2014; 156:408-11. [PMID: 24485451 DOI: 10.1016/j.cell.2014.01.025] [Citation(s) in RCA: 148] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Revised: 01/06/2014] [Accepted: 01/13/2014] [Indexed: 01/23/2023]
Abstract
The critical impact that microbiota have on health and disease makes the interaction between host and microbiome increasingly important as we evaluate therapeutics. Here, we highlight growing evidence that, beyond disease, microbes also affect the most fundamental of host physiological phenotypes, the rate of aging itself.
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Affiliation(s)
| | - William Mair
- Harvard School of Public Health, Boston, MA 02115, USA.
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179
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Amrit FRG, Ratnappan R, Keith SA, Ghazi A. The C. elegans lifespan assay toolkit. Methods 2014; 68:465-75. [PMID: 24727064 DOI: 10.1016/j.ymeth.2014.04.002] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Revised: 04/01/2014] [Accepted: 04/03/2014] [Indexed: 12/24/2022] Open
Abstract
Since the discovery of single gene mutations that double its lifespan, the nematode Caenorhabditis elegans has provided remarkable insights into the biology of aging. The precisely measurable lifespan of worms has proven to be an efficient tool to assess the impact of various genetic, physiological and environmental factors on organismal aging. In this article, we describe methods to set up and monitor experiments to determine worm lifespan. We include procedures used for classical, small-scale lifespan assays that are generally performed on solid media, and review recent advances in high-throughput, automated longevity experiments conducted in liquid culture and microfluidic devices. In addition, tools that help analyze this data to obtain survival statistics are summarized, and C. elegans strains that offer particular advantages for lifespan studies are listed.
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Affiliation(s)
- Francis Raj Gandhi Amrit
- Department of Pediatrics, University of Pittsburgh School of Medicine, 7129 Rangos Research Centre, Children's Hospital of Pittsburgh, 4401 Penn Avenue, Pittsburgh, PA 15224, United States
| | - Ramesh Ratnappan
- Department of Pediatrics, University of Pittsburgh School of Medicine, 7129 Rangos Research Centre, Children's Hospital of Pittsburgh, 4401 Penn Avenue, Pittsburgh, PA 15224, United States
| | - Scott Alexander Keith
- Department of Pediatrics, University of Pittsburgh School of Medicine, 7129 Rangos Research Centre, Children's Hospital of Pittsburgh, 4401 Penn Avenue, Pittsburgh, PA 15224, United States
| | - Arjumand Ghazi
- Department of Pediatrics, University of Pittsburgh School of Medicine, 7129 Rangos Research Centre, Children's Hospital of Pittsburgh, 4401 Penn Avenue, Pittsburgh, PA 15224, United States.
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180
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Nikoletopoulou V, Kyriakakis E, Tavernarakis N. Cellular and molecular longevity pathways: the old and the new. Trends Endocrinol Metab 2014; 25:212-23. [PMID: 24388148 DOI: 10.1016/j.tem.2013.12.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/03/2013] [Revised: 11/26/2013] [Accepted: 12/02/2013] [Indexed: 01/08/2023]
Abstract
Human lifespan has been increasing steadily during modern times, mainly due to medical advancements that combat infant mortality and various life-threatening diseases. However, this gratifying longevity rise is accompanied by growing incidences of devastating age-related pathologies. Understanding the cellular and molecular mechanisms that underlie aging and regulate longevity is of utmost relevance towards offsetting the impact of age-associated disorders and increasing the quality of life for the elderly. Several evolutionarily conserved pathways that modulate lifespan have been identified in organisms ranging from yeast to primates. Here we survey recent findings highlighting the interplay of various genetic, epigenetic, and cell-specific factors, and also symbiotic relationships, as longevity determinants. We further discuss outstanding matters within the framework of emerging, integrative views of aging.
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Affiliation(s)
- Vassiliki Nikoletopoulou
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology - Hellas, Heraklion 71110, Crete, Greece
| | - Emmanouil Kyriakakis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology - Hellas, Heraklion 71110, Crete, Greece
| | - Nektarios Tavernarakis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology - Hellas, Heraklion 71110, Crete, Greece.
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181
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Ehmke M, Luthe K, Schnabel R, Döring F. S-Adenosyl methionine synthetase 1 limits fat storage in Caenorhabditis elegans. GENES & NUTRITION 2014; 9:386. [PMID: 24510589 PMCID: PMC3968293 DOI: 10.1007/s12263-014-0386-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2013] [Accepted: 01/27/2014] [Indexed: 11/30/2022]
Abstract
Cytosolic lipid droplets are versatile, evolutionarily conserved organelles that are important for the storage and utilization of lipids in almost all cell types. To obtain insight into the physiological importance of lipid droplet size, we isolated and characterized a new S-adenosyl methionine synthetase 1 (SAMS-1)-deficient Caenorhabditis elegans mutant, which have enlarged lipid droplets throughout its life cycle. We found that the sams-1 mutant showed a markedly reduced body size and progeny number; impaired synthesis of phosphatidylcholine, a major membrane phospholipid; and elevated expression of key lipogenic genes, such as dgat-2, resulting in the accumulation of triacylglyceride in fewer, but larger, lipid droplets. The sams-1 mutant store more than 50 % (wild type: 10 %) of its intestinal fat in large lipid droplets, ≥10 μm(3) in size. In response to starvation, SAMS-1 deficiency causes reduced depletion of a subset of lipid droplets located in the anterior intestine. Given the importance of liberation of fatty acids from lipid droplets, we propose that the physiological function of SAMS-1, a highly conserved enzyme involved in one-carbon metabolism, is the limitation of fat storage to ensure proper growth and reproduction.
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Affiliation(s)
- Madeleine Ehmke
- />Department of Molecular Prevention, Institute of Human Nutrition and Food Sciences, University of Kiel, Heinrich-Hecht-Platz 10, 24118 Kiel, Germany
| | - Katharina Luthe
- />Department of Developmental Genetics, Institute of Genetics, TU Braunschweig, Spielmannstr. 7, 38106 Brunswick, Germany
| | - Ralf Schnabel
- />Department of Developmental Genetics, Institute of Genetics, TU Braunschweig, Spielmannstr. 7, 38106 Brunswick, Germany
| | - Frank Döring
- />Department of Molecular Prevention, Institute of Human Nutrition and Food Sciences, University of Kiel, Heinrich-Hecht-Platz 10, 24118 Kiel, Germany
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182
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Watson E, MacNeil LT, Ritter AD, Yilmaz LS, Rosebrock AP, Caudy AA, Walhout AJM. Interspecies systems biology uncovers metabolites affecting C. elegans gene expression and life history traits. Cell 2014; 156:759-70. [PMID: 24529378 PMCID: PMC4169190 DOI: 10.1016/j.cell.2014.01.047] [Citation(s) in RCA: 143] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2013] [Revised: 10/09/2013] [Accepted: 01/09/2014] [Indexed: 01/07/2023]
Abstract
Diet greatly influences gene expression and physiology. In mammals, elucidating the effects and mechanisms of individual nutrients is challenging due to the complexity of both the animal and its diet. Here, we used an interspecies systems biology approach with Caenorhabditis elegans and two of its bacterial diets, Escherichia coli and Comamonas aquatica, to identify metabolites that affect the animal's gene expression and physiology. We identify vitamin B12 as the major dilutable metabolite provided by Comamonas aq. that regulates gene expression, accelerates development, and reduces fertility but does not affect lifespan. We find that vitamin B12 has a dual role in the animal: it affects development and fertility via the methionine/S-Adenosylmethionine (SAM) cycle and breaks down the short-chain fatty acid propionic acid, preventing its toxic buildup. Our interspecies systems biology approach provides a paradigm for understanding complex interactions between diet and physiology.
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Affiliation(s)
- Emma Watson
- Program in Systems Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA; Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Lesley T MacNeil
- Program in Systems Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA; Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Ashlyn D Ritter
- Program in Systems Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA; Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - L Safak Yilmaz
- Program in Systems Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA; Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Adam P Rosebrock
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto M5S 3E1, Canada
| | - Amy A Caudy
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto M5S 3E1, Canada
| | - Albertha J M Walhout
- Program in Systems Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA; Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA.
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183
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Abstract
Diet affects cellular metabolism and organismal life history traits. Pang and Curran (2014) use Caenorhabditis elegans and its bacterial diets to unveil genetic perturbations in proline catabolism that shorten lifespan, but, only on specific Escherichia coli diets, thereby unveiling a genome-encoded adaptive response to different nutritional states.
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Affiliation(s)
- Albertha J M Walhout
- Program in Systems Biology, Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA.
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184
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Pang S, Curran SP. Adaptive capacity to bacterial diet modulates aging in C. elegans. Cell Metab 2014; 19:221-31. [PMID: 24440036 PMCID: PMC3979424 DOI: 10.1016/j.cmet.2013.12.005] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/10/2013] [Revised: 10/20/2013] [Accepted: 12/11/2013] [Indexed: 12/01/2022]
Abstract
Diet has a substantial impact on cellular metabolism and physiology. Animals must sense different food sources and utilize distinct strategies to adapt to diverse diets. Here we show that Caenorhabditis elegans lifespan is regulated by their adaptive capacity to different diets, which is controlled by alh-6, a conserved proline metabolism gene. alh-6 mutants age prematurely when fed an Escherichia coli OP50 but not HT115 diet. Remarkably, this diet-dependent aging phenotype is determined by exposure to food during development. Mechanistically, the alh-6 mutation triggers diet-induced mitochondrial defects and increased generation of ROS, likely due to accumulation of its substrate 1-pyrroline-5-carboxylate. We also identify that neuromedin U receptor signaling is essential for diet-induced mitochondrial changes and premature aging. Moreover, dietary restriction requires alh-6 to induce longevity. Collectively, our data reveal a homeostatic mechanism that animals employ to cope with potential dietary insults and uncover an example of lifespan regulation by dietary adaptation.
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Affiliation(s)
- Shanshan Pang
- Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
| | - Sean P Curran
- Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA; Department of Molecular and Computational Biology, Dornsife College of Letters, Arts, and Sciences, University of Southern California, Los Angeles, CA 90089, USA; Department of Biochemistry and Molecular Biology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA.
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185
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Affiliation(s)
- Dennis H. Kim
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139;
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186
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Clark LC, Hodgkin J. Commensals, probiotics and pathogens in the Caenorhabditis elegans model. Cell Microbiol 2013; 16:27-38. [PMID: 24168639 DOI: 10.1111/cmi.12234] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2013] [Revised: 10/08/2013] [Accepted: 10/09/2013] [Indexed: 02/06/2023]
Abstract
Caenorhabditis elegans is a useful model host for a wide variety of microorganisms that have implications for human health. Recent surveys of mammalian and metazoan microbiota demonstrate the often profound effects of gut commensal bacteria on host lifespan, health and development. Work using C. elegans has revealed the surprising extent to which bacterial metabolism can interact with host pathways with examples from Escherichia coli folate metabolism and Bacillus subtilis nitric oxide synthesis. The C. elegans model has also shed light on the mechanisms by which probiotic bacteria influence lifespan.
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Affiliation(s)
- Laura C Clark
- Department of Biochemistry, University of Oxford, Oxford, UK
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187
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Kassahun H, Nilsen H. Active transcriptomic and proteomic reprogramming in the C. elegans nucleotide excision repair mutant xpa-1. WORM 2013; 2:e27337. [PMID: 24744987 DOI: 10.4161/worm.27337] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2013] [Accepted: 11/25/2013] [Indexed: 01/04/2023]
Abstract
Oxidative stress promotes human aging and contributes to common neurodegenerative diseases. Endogenous DNA damage induced by oxidative stress is believed to be an important promoter of neurodegenerative diseases. Although a large amount of evidence correlates a reduced DNA repair capacity with aging and neurodegenerative disease, there is little direct evidence of causality. Moreover, the contribution of oxidative DNA damage to the aging process is poorly understood. We have used the nematode Caenorhabditis elegans to study the contribution of oxidative DNA damage and repair to aging. C. elegans is particularly well suited to tackle this problem because it has a minimum complexity DNA repair system, which enables us to circumvent the important limitation presented by the extensive redundancy of DNA repair enzymes in mammals.
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Affiliation(s)
- Henok Kassahun
- The Biotechnology Centre; University of Oslo; Oslo, Norway
| | - Hilde Nilsen
- The Biotechnology Centre; University of Oslo; Oslo, Norway
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188
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Macneil LT, Walhout AJ. Food, pathogen, signal: The multifaceted nature of a bacterial diet. WORM 2013; 2:e26454. [PMID: 24744980 PMCID: PMC3917966 DOI: 10.4161/worm.26454] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2013] [Accepted: 09/10/2013] [Indexed: 02/08/2023]
Abstract
C. elegans, both in the wild and in the lab, live on a diet of live bacteria. The bacterial diet provides nutrients for C. elegans, but can also play a number of other roles in C. elegans physiology. Recently, we compared the effects of different bacterial diets on life history traits and gene expression. Here, we discuss our recent findings in the context of other dietary studies and highlight challenges in understanding dietary effects. For instance, since bacteria can be pathogenic it can be difficult to disentangle pathogenic from dietary effects. Here we summarize different bacterial diets used for C. elegans and how they affect the animal.
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Affiliation(s)
- Lesley T Macneil
- Program in Systems Biology; Program in Molecular Medicine; University of Massachusetts Medical School; Worcester, MA USA
| | - Albertha Jm Walhout
- Program in Systems Biology; Program in Molecular Medicine; University of Massachusetts Medical School; Worcester, MA USA
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189
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Fuxman Bass JI, Tamburino AM, Mori A, Beittel N, Weirauch MT, Reece-Hoyes JS, Walhout AJM. Transcription factor binding to Caenorhabditis elegans first introns reveals lack of redundancy with gene promoters. Nucleic Acids Res 2013; 42:153-62. [PMID: 24068555 PMCID: PMC3874175 DOI: 10.1093/nar/gkt858] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Gene expression is controlled through the binding of transcription factors (TFs) to regulatory genomic regions. First introns are longer than other introns in multiple eukaryotic species and are under selective constraint. Here we explore the importance of first introns in TF binding in the nematode Caenorhabditis elegans by combining computational predictions and experimentally derived TF–DNA interaction data. We found that first introns of C. elegans genes, particularly those for families enriched in long first introns, are more conserved in length, have more conserved predicted TF interactions and are bound by more TFs than other introns. We detected a significant positive correlation between first intron size and the number of TF interactions obtained from chromatin immunoprecipitation assays or determined by yeast one-hybrid assays. TFs that bind first introns are largely different from those binding promoters, suggesting that the different interactions are complementary rather than redundant. By combining first intron and promoter interactions, we found that genes that share a large fraction of TF interactions are more likely to be co-expressed than when only TF interactions with promoters are considered. Altogether, our data suggest that C. elegans gene regulation may be additive through the combined effects of multiple regulatory regions.
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Affiliation(s)
- Juan I Fuxman Bass
- Program in Systems Biology, Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA, Center for Autoimmune Genomics and Etiology (CAGE), Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA and Divisions of Rheumatology and Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
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190
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Cabreiro F, Gems D. Worms need microbes too: microbiota, health and aging in Caenorhabditis elegans. EMBO Mol Med 2013; 5:1300-10. [PMID: 23913848 PMCID: PMC3799487 DOI: 10.1002/emmm.201100972] [Citation(s) in RCA: 133] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2013] [Revised: 06/07/2013] [Accepted: 06/12/2013] [Indexed: 12/24/2022] Open
Abstract
Many animal species live in close association with commensal and symbiotic microbes (microbiota). Recent studies have revealed that the status of gastrointestinal tract microbiota can influence nutrition-related syndromes such as obesity and type-2 diabetes, and perhaps aging. These morbidities have a profound impact in terms of individual suffering, and are an increasing economic burden to modern societies. Several theories have been proposed for the influence of microbiota on host metabolism, but these largely remain to be proven. In this article we discuss how microbiota may be manipulated (via pharmacology, diet, or gene manipulation) in order to alter metabolism, immunity, health and aging in the host. The nematode Caenorhabditis elegans in combination with one microbial species is an excellent, defined model system to investigate the mechanisms of host–microbiota interactions, particularly given the combined power of worm and microbial genetics. We also discuss the multifaceted nature of the worm–microbe relationship, which likely encompasses predation, commensalism, pathogenicity and necromeny.
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Affiliation(s)
- Filipe Cabreiro
- Institute of Healthy Ageing, and Research Department of Genetics, Evolution and Environment, University College London, London, UK.
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191
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Watson E, MacNeil LT, Arda HE, Zhu LJ, Walhout AJ. Integration of metabolic and gene regulatory networks modulates the C. elegans dietary response. Cell 2013; 153:253-66. [PMID: 23540702 PMCID: PMC3817025 DOI: 10.1016/j.cell.2013.02.050] [Citation(s) in RCA: 93] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2012] [Revised: 12/15/2012] [Accepted: 02/05/2013] [Indexed: 12/16/2022]
Abstract
Expression profiles are tailored according to dietary input. However, the networks that control dietary responses remain largely uncharacterized. Here, we combine forward and reverse genetic screens to delineate a network of 184 genes that affect the C. elegans dietary response to Comamonas DA1877 bacteria. We find that perturbation of a mitochondrial network composed of enzymes involved in amino acid metabolism and the TCA cycle affects the dietary response. In humans, mutations in the corresponding genes cause inborn diseases of amino acid metabolism, most of which are treated by dietary intervention. We identify several transcription factors (TFs) that mediate the changes in gene expression upon metabolic network perturbations. Altogether, our findings unveil a transcriptional response system that is poised to sense dietary cues and metabolic imbalances, illustrating extensive communication between metabolic networks in the mitochondria and gene regulatory networks in the nucleus.
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Affiliation(s)
- Emma Watson
- Program in Systems Biology, University of Massachusetts Medical School, Worcester, MA
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA
| | - Lesley T. MacNeil
- Program in Systems Biology, University of Massachusetts Medical School, Worcester, MA
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA
| | - H. Efsun Arda
- Program in Systems Biology, University of Massachusetts Medical School, Worcester, MA
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA
| | - Lihua Julie Zhu
- Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, MA
| | - Albertha J.M. Walhout
- Program in Systems Biology, University of Massachusetts Medical School, Worcester, MA
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA
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192
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Ritter AD, Shen Y, Fuxman Bass J, Jeyaraj S, Deplancke B, Mukhopadhyay A, Xu J, Driscoll M, Tissenbaum HA, Walhout AJM. Complex expression dynamics and robustness in C. elegans insulin networks. Genome Res 2013; 23:954-65. [PMID: 23539137 PMCID: PMC3668363 DOI: 10.1101/gr.150466.112] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Gene families expand by gene duplication, and resulting paralogs diverge through mutation. Functional diversification can include neofunctionalization as well as subfunctionalization of ancestral functions. In addition, redundancy in which multiple genes fulfill overlapping functions is often maintained. Here, we use the family of 40 Caenorhabditis elegans insulins to gain insight into the balance between specificity and redundancy. The insulin/insulin-like growth factor (IIS) pathway comprises a single receptor, DAF-2. To date, no single insulin-like peptide recapitulates all DAF-2-associated phenotypes, likely due to redundancy between insulin-like genes. To provide a first-level annotation of potential patterns of redundancy, we comprehensively delineate the spatiotemporal and conditional expression of all 40 insulins in living animals. We observe extensive dynamics in expression that can explain the lack of simple patterns of pairwise redundancy. We propose a model in which gene families evolve to attain differential alliances in different tissues and in response to a range of environmental stresses.
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Affiliation(s)
- Ashlyn D Ritter
- Program in Systems Biology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
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