101
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Mazzarella N, Giangrieco I, Visone S, Santonicola P, Achenbach J, Zampi G, Tamburrini M, Di Schiavi E, Ciardiello MA. Green kiwifruit extracts protect motor neurons from death in a spinal muscular atrophy model in Caenorhabditis elegans. Food Sci Nutr 2019; 7:2327-2335. [PMID: 31367361 PMCID: PMC6657744 DOI: 10.1002/fsn3.1078] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 04/30/2019] [Accepted: 05/04/2019] [Indexed: 12/17/2022] Open
Abstract
Kiwifruit is considered a functional food and a good source of nutraceuticals. Among the possible beneficial effects of kiwifruit species, a neuroprotective activity exerted in rats with learning and memory impairment induced by exposure to different chemicals was reported. We sought to investigate the neuroprotective activities of kiwifruit toward spinal muscular atrophy (SMA). To this purpose, we have used a recently developed Caenorhabditis elegans SMA model, displaying an age-dependent degeneration of motor neurons detected as locomotory defects, disappearance of fluorescent markers, and apoptotic death of targeted neurons. Although an anti-nematode activity is reported for kiwifruit, it has been verified that neither green (Actinidia deliciosa, cultivar Hayward) nor gold (Actinidia chinensis, cultivar Hort 16A) kiwifruit extracts cause detectable effects on wild-type C. elegans growth and life cycle. Conversely, green kiwifruit extracts have a clear effect on the C. elegans SMA model by partially rescuing the degeneration and death of motor neurons and the locomotion impairment. The gold species does not show the same effect. The components responsible for the neuroprotection are macromolecules with a molecular weight higher than 3 kDa, present in the green and not in the yellow kiwifruit. In conclusion, this is the first study reporting a protective activity of green kiwifruit toward motor neurons. In addition, we demonstrate that C. elegans is an animal model suitable to study the biological activities contained in kiwifruit. Therefore, this model can be exploited for future investigations aimed at identifying kiwifruit molecules with potential applications in the field of human health.
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Affiliation(s)
| | | | - Serena Visone
- Institute of Biosciences and BioResourcesCNRNaplesItaly
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102
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Burga A, Ben-David E, Lemus Vergara T, Boocock J, Kruglyak L. Fast genetic mapping of complex traits in C. elegans using millions of individuals in bulk. Nat Commun 2019; 10:2680. [PMID: 31213597 PMCID: PMC6582151 DOI: 10.1038/s41467-019-10636-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Accepted: 05/16/2019] [Indexed: 02/03/2023] Open
Abstract
Genetic studies of complex traits in animals have been hindered by the need to generate, maintain, and phenotype large panels of recombinant lines. We developed a new method, C. elegans eXtreme Quantitative Trait Locus (ceX-QTL) mapping, that overcomes this obstacle via bulk selection on millions of unique recombinant individuals. We use ceX-QTL to map a drug resistance locus with high resolution. We also map differences in gene expression in live worms and discovered that mutations in the co-chaperone sti-1 upregulate the transcription of HSP-90. Lastly, we use ceX-QTL to map loci that influence fitness genome-wide confirming previously reported causal variants and uncovering new fitness loci. ceX-QTL is fast, powerful and cost-effective, and will accelerate the study of complex traits in animals.
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Affiliation(s)
- Alejandro Burga
- Department of Human Genetics, Department of Biological Chemistry, and Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, CA, 90095, USA.
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna, Austria.
| | - Eyal Ben-David
- Department of Human Genetics, Department of Biological Chemistry, and Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, CA, 90095, USA.
| | - Tzitziki Lemus Vergara
- Department of Human Genetics, Department of Biological Chemistry, and Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - James Boocock
- Department of Human Genetics, Department of Biological Chemistry, and Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Leonid Kruglyak
- Department of Human Genetics, Department of Biological Chemistry, and Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, CA, 90095, USA.
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103
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Large-scale cultivation of Caenorhabditis elegans in a bioreactor using a labor-friendly fed-batch approach. Biotechniques 2019; 67:33-39. [PMID: 31184491 DOI: 10.2144/btn-2019-0008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Caenorhabditis elegans is an invertebrate model organism used in many areas of biology including developmental biology and the identification of molecular mechanisms and pathways. However, several experimental approaches require large quantities of worms, which is limiting and time-consuming. We present a protocol that uses modern fermentation methodology to effectively produce large numbers of C. elegans using a 7-l bioreactor in a fed-batch cultivation procedure. The production is modular and flexible as well as being a self-controlled system, thus not much labor is required until harvesting C. elegans. The high-yield worm cultivation is flexible and simple to amend, and now allows for the extended application of C. elegans as a model organism and expression system, including large-scale protein production.
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104
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RNA sequencing dataset characterizing transcriptomic responses to dietary changes in Caenorhabditis elegans. Data Brief 2019; 25:104006. [PMID: 31223636 PMCID: PMC6565610 DOI: 10.1016/j.dib.2019.104006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Accepted: 05/09/2019] [Indexed: 12/20/2022] Open
Abstract
Transcriptome analysis using next generation sequencing (NGS) technology provides the capability to understand global changes in gene expression throughout a range of tissue samples. The nematode Caenorhabditis elegans (C. elegans) is a well-established genetic system used for analyzing a number of biological processes. C. elegans are a bacteria-eating soil nematode, and changes in bacterial diet have been shown to cause a number of physiological and molecular changes. Here we used Illumina RNA sequencing (RNA-seq) analysis to characterize the mRNA transcriptome of mixed C. elegans populations fed differing strains of bacteria to further understand dietary changes at the molecular level. Raw FASTQ files for the RNA-seq libraries are deposited in the NCBI Sequence Read Archive (SRA) and have been assigned BioProject accession PRJNA412551.
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105
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Biology is the root of variability: cautionary tales in Caenorhabditis elegans biology. Biochem Soc Trans 2019; 47:887-896. [PMID: 31127069 DOI: 10.1042/bst20190001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 04/29/2019] [Accepted: 04/30/2019] [Indexed: 12/31/2022]
Abstract
Abstract
Reproducibility is critical for the standardization, interpretation, and progression of research. However, many factors increase variability and reduce reproducibility. In Caenorhabditis elegans research, there are many possible causes of variability that may explain why experimental outcomes sometimes differ between laboratories and between experiments. Factors contributing to experimental variability include the genetic background of both C. elegans and its bacterial diet, differences in media composition, intergenerational and transgenerational effects that may be carried over for generations, and the use of chemicals or reagents that may have unexpected consequences. This review summarizes sources of variability in C. elegans research and serves to identify laboratory practices that could influence reproducibility.
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106
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Pheromones and Nutritional Signals Regulate the Developmental Reliance on let-7 Family MicroRNAs in C. elegans. Curr Biol 2019; 29:1735-1745.e4. [PMID: 31104929 DOI: 10.1016/j.cub.2019.04.034] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 04/03/2019] [Accepted: 04/11/2019] [Indexed: 12/31/2022]
Abstract
Adverse environmental conditions can affect rates of animal developmental progression and lead to temporary developmental quiescence (diapause), exemplified by the dauer larva stage of the nematode Caenorhabditis elegans (C. elegans). Remarkably, patterns of cell division and temporal cell-fate progression in C. elegans larvae are not affected by changes in developmental trajectory. However, the underlying physiological and gene regulatory mechanisms that ensure robust developmental patterning despite substantial plasticity in developmental progression are largely unknown. Here, we report that diapause-inducing pheromones correct heterochronic developmental cell lineage defects caused by insufficient expression of let-7 family microRNAs in C. elegans. Moreover, two conserved endocrine signaling pathways, DAF-7/TGF-β and DAF-2/Insulin, that confer on the larva diapause and non-diapause alternative developmental trajectories interact with the nuclear hormone receptor, DAF-12, to initiate and regulate a rewiring of the genetic circuitry controlling temporal cell fates. This rewiring includes engagement of certain heterochronic genes, lin-46, lin-4, and nhl-2, that are previously associated with an altered genetic program in post-diapause animals, in combination with a novel ligand-independent DAF-12 activity, to downregulate the critical let-7 family target Hunchback-like-1 (HBL-1). Our results show how pheromone or endocrine signaling pathways can coordinately regulate both developmental progression and cell-fate transitions in C. elegans larvae under stress so that the developmental schedule of cell fates remains unaffected by changes in developmental trajectory.
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107
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The C. elegans intestine: organogenesis, digestion, and physiology. Cell Tissue Res 2019; 377:383-396. [DOI: 10.1007/s00441-019-03036-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Accepted: 04/12/2019] [Indexed: 12/16/2022]
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108
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Zečić A, Dhondt I, Braeckman BP. The nutritional requirements of Caenorhabditis elegans. GENES AND NUTRITION 2019; 14:15. [PMID: 31080524 PMCID: PMC6501307 DOI: 10.1186/s12263-019-0637-7] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 04/10/2019] [Indexed: 12/14/2022]
Abstract
Animals require sufficient intake of a variety of nutrients to support their development, somatic maintenance and reproduction. An adequate diet provides cell building blocks, chemical energy to drive cellular processes and essential nutrients that cannot be synthesised by the animal, or at least not in the required amounts. Dietary requirements of nematodes, including Caenorhabditis elegans have been extensively studied with the major aim to develop a chemically defined axenic medium that would support their growth and reproduction. At the same time, these studies helped elucidating important aspects of nutrition-related biochemistry and metabolism as well as the establishment of C. elegans as a powerful model in studying evolutionarily conserved pathways, and the influence of the diet on health.
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Affiliation(s)
- Aleksandra Zečić
- Department of Biology, Laboratory of Aging Physiology and Molecular Evolution, Ghent University, 9000 Ghent, Belgium
| | - Ineke Dhondt
- Department of Biology, Laboratory of Aging Physiology and Molecular Evolution, Ghent University, 9000 Ghent, Belgium
| | - Bart P Braeckman
- Department of Biology, Laboratory of Aging Physiology and Molecular Evolution, Ghent University, 9000 Ghent, Belgium
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109
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Anderson A, McMullan R. Neuronal and non-neuronal signals regulate Caernorhabditis elegans avoidance of contaminated food. Philos Trans R Soc Lond B Biol Sci 2019; 373:rstb.2017.0255. [PMID: 29866922 PMCID: PMC6000145 DOI: 10.1098/rstb.2017.0255] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/06/2017] [Indexed: 01/24/2023] Open
Abstract
One way in which animals minimize the risk of infection is to reduce their contact with contaminated food. Here, we establish a model of pathogen-contaminated food avoidance using the nematode worm Caernorhabditis elegans. We find that avoidance of pathogen-contaminated food protects C. elegans from the deleterious effects of infection and, using genetic approaches, demonstrate that multiple sensory neurons are required for this avoidance behaviour. In addition, our results reveal that the avoidance of contaminated food requires bacterial adherence to non-neuronal cells in the tail of C. elegans that are also required for the cellular immune response. Previous studies in C. elegans have contributed significantly to our understanding of molecular and cellular basis of host–pathogen interactions and our model provides a unique opportunity to gain basic insights into how animals avoid contaminated food. This article is part of the Theo Murphy meeting issue ‘Evolution of pathogen and parasite avoidance behaviours’.
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Affiliation(s)
- Alexandra Anderson
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - Rachel McMullan
- School of Life, Health and Chemical Sciences, The Open University, Milton Keynes, Buckinghamshire MK7 2AA, UK
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110
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Marsac R, Pinson B, Saint-Marc C, Olmedo M, Artal-Sanz M, Daignan-Fornier B, Gomes JE. Purine Homeostasis Is Necessary for Developmental Timing, Germline Maintenance and Muscle Integrity in Caenorhabditis elegans. Genetics 2019; 211:1297-1313. [PMID: 30700528 PMCID: PMC6456310 DOI: 10.1534/genetics.118.301062] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Accepted: 01/24/2019] [Indexed: 12/12/2022] Open
Abstract
Purine homeostasis is ensured through a metabolic network widely conserved from prokaryotes to humans. Purines can either be synthesized de novo, reused, or produced by interconversion of extant metabolites using the so-called recycling pathway. Although thoroughly characterized in microorganisms, such as yeast or bacteria, little is known about regulation of the purine biosynthesis network in metazoans. In humans, several diseases are linked to purine metabolism through as yet poorly understood etiologies. Particularly, the deficiency in adenylosuccinate lyase (ADSL)-an enzyme involved both in the purine de novo and recycling pathways-causes severe muscular and neuronal symptoms. In order to address the mechanisms underlying this deficiency, we established Caenorhabditis elegans as a metazoan model organism to study purine metabolism, while focusing on ADSL. We show that the purine biosynthesis network is functionally conserved in C. elegans Moreover, adsl-1 (the gene encoding ADSL in C. elegans) is required for developmental timing, germline stem cell maintenance and muscle integrity. Importantly, these traits are not affected when solely the de novo pathway is abolished, and we present evidence that germline maintenance is linked specifically to ADSL activity in the recycling pathway. Hence, our results allow developmental and tissue specific phenotypes to be ascribed to separable steps of the purine metabolic network in an animal model.
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Affiliation(s)
- Roxane Marsac
- Institut de Biochimie et Génétique Cellulaires, Université de Bordeaux and CNRS UMR5095, 33077 Bordeaux cedex, France
| | - Benoît Pinson
- Institut de Biochimie et Génétique Cellulaires, Université de Bordeaux and CNRS UMR5095, 33077 Bordeaux cedex, France
| | - Christelle Saint-Marc
- Institut de Biochimie et Génétique Cellulaires, Université de Bordeaux and CNRS UMR5095, 33077 Bordeaux cedex, France
| | - María Olmedo
- Andalusian Center for Developmental Biology, Consejo Superior de Investigaciones Científicas/Junta de Andalucía/Universidad Pablo de Olavide, Department of Molecular Biology and Biochemical Engineering, 41013 Seville, Spain
| | - Marta Artal-Sanz
- Andalusian Center for Developmental Biology, Consejo Superior de Investigaciones Científicas/Junta de Andalucía/Universidad Pablo de Olavide, Department of Molecular Biology and Biochemical Engineering, 41013 Seville, Spain
| | - Bertrand Daignan-Fornier
- Institut de Biochimie et Génétique Cellulaires, Université de Bordeaux and CNRS UMR5095, 33077 Bordeaux cedex, France
| | - José-Eduardo Gomes
- Institut de Biochimie et Génétique Cellulaires, Université de Bordeaux and CNRS UMR5095, 33077 Bordeaux cedex, France
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111
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Xu A, Zhang Z, Ko SH, Fisher AL, Liu Z, Chen L. Microtubule regulators act in the nervous system to modulate fat metabolism and longevity through DAF-16 in C. elegans. Aging Cell 2019; 18:e12884. [PMID: 30638295 PMCID: PMC6413656 DOI: 10.1111/acel.12884] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2018] [Revised: 10/26/2018] [Accepted: 11/03/2018] [Indexed: 12/16/2022] Open
Abstract
Microtubule (MT) regulation is involved in both neuronal function and the maintenance of neuronal structure, and MT dysregulation appears to be a general downstream indicator and effector of age‐related neurodegeneration. But the role of MTs in natural aging is largely unknown. Here, we demonstrate a role of MT regulators in regulating longevity. We find that loss of EFA‐6, a modulator of MT dynamics, can delay both neuronal aging and extend the lifespan of C. elegans. Through the use of genetic mutants affecting other MT‐regulating genes in C. elegans, we find that loss of MT stabilizing genes (including ptrn‐1 and ptl‐1) shortens lifespan, while loss of MT destabilizing gene hdac‐6 extends lifespan. Via the use of tissue‐specific transgenes, we further show that these MT regulators can act in the nervous system to modulate lifespan. Through RNA‐seq analyses, we found that genes involved in lipid metabolism were differentially expressed in MT regulator mutants, and via the use of Nile Red and Oil Red O staining, we show that the MT regulator mutants have altered fat storage. We further find that the increased fat storage and extended lifespan of the long‐lived MT regulator mutants are dependent on the DAF‐16/FOXO transcription factor. Our results suggest that neuronal MT status might affect organismal aging through DAF‐16‐regulated changes in fat metabolism, and therefore, MT‐based therapies might represent a novel intervention to promote healthy aging.
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Affiliation(s)
- Aiping Xu
- Barshop Institute for Longevity and Aging Studies; San Antonio Texas
- Department of Cell Systems and Anatomy; UTHSCSA; San Antonio Texas
| | - Zhao Zhang
- Department of Molecular Medicine; UTHSCSA; San Antonio Texas
| | - Su-Hyuk Ko
- Barshop Institute for Longevity and Aging Studies; San Antonio Texas
- Department of Cell Systems and Anatomy; UTHSCSA; San Antonio Texas
- Department of Molecular Medicine; UTHSCSA; San Antonio Texas
| | - Alfred L. Fisher
- Center for Healthy Aging; UTHSCSA; San Antonio Texas
- Division of Geriatrics, Gerontology, and Palliative Medicine, Department of Medicine; UTHSCSA; San Antonio Texas
- GRECC, South Texas VA Healthcare System; San Antonio Texas
| | - Zhijie Liu
- Department of Molecular Medicine; UTHSCSA; San Antonio Texas
| | - Lizhen Chen
- Barshop Institute for Longevity and Aging Studies; San Antonio Texas
- Department of Cell Systems and Anatomy; UTHSCSA; San Antonio Texas
- Department of Molecular Medicine; UTHSCSA; San Antonio Texas
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112
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Wang B, Huang B, Chen J, Li W, Yang L, Yao L, Niu Q. Whole-genome analysis of the colonization-resistant bacterium Phytobacter sp. SCO41 T isolated from Bacillus nematocida B16-fed adult Caenorhabditis elegans. Mol Biol Rep 2019; 46:1563-1575. [PMID: 30879274 DOI: 10.1007/s11033-018-04574-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 12/13/2018] [Indexed: 12/31/2022]
Abstract
Colonization resistance is an important attribute for bacterial interactions with hosts, but the mechanism is still not completely clear. In this study, we found that Phytobacter sp. SCO41T can effectively inhibit the in vivo colonization of Bacillus nematocida B16 in Caenorhabditis elegans, and we revealed the colonization resistance mechanism. Three strains of colonization-resistant bacteria, SCO41T, BX15, and BC7, were isolated from the intestines of the free-living nematode C. elegans derived from rotten fruit and soil. The primary characteristics and genome map of one of the three isolates was investigated to explore the underlying mechanism of colonization resistance in C. elegans. In addition, we performed exogenous iron supplementation and gene cluster knockout experiments to validate the sequencing results. The results showed that relationship was close among the three strains, which was identified as belonging to the genus Phytobacter. The type strain is SCO41T (= CICC 24103T = KCTC 52362T). Whole genome analysis showed that csgA, csgB, csgC, csgE, csgF, and csgG were involved in the curli adhesive process and that fepA, fepB, fepC, fepD, and fepG played important roles in SCO41T against the colonization of B. nematocida B16 in C. elegans by competing for iron. Exogenous iron supplementation showed that exogenous iron can increase the colonization of B. nematocida B16, which was additionally confirmed by a deletion mutant strain. The csg gene family contributes to the colonization of SCO41T in C. elegans. Curli potentially contribute to the colonization of SCO41T in C. elegans, and enterobactin has a key role in SCO41T to resist the colonization of B. nematocida B16 by competing for iron.
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Affiliation(s)
- Bowen Wang
- Department of Life Science and Biotechnology, Nanyang Normal University, Nanyang, 473000, People's Republic of China
| | - Bingfen Huang
- Department of Life Science and Biotechnology, Nanyang Normal University, Nanyang, 473000, People's Republic of China
| | - Junmei Chen
- Department of Life Science and Biotechnology, Nanyang Normal University, Nanyang, 473000, People's Republic of China
| | - Wenpeng Li
- Department of Life Science and Biotechnology, Nanyang Normal University, Nanyang, 473000, People's Republic of China
| | - Ling Yang
- Nanyang Academy of Agricultural Sciences, Nanyang, 473083, Henan, People's Republic of China
| | - Lunguang Yao
- Henan Key Laboratory of Ecological Security for Water Source Region of Mid-line of South-to-North Diversion Project of Henan Province, Nanyang, People's Republic of China.
| | - Qiuhong Niu
- Department of Life Science and Biotechnology, Nanyang Normal University, Nanyang, 473000, People's Republic of China. .,China-UK-NYNU-RRes Joint Laboratory of Insect Biology, Nanyang Normal University, Nanyang, 473000, People's Republic of China.
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113
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Revtovich AV, Lee R, Kirienko NV. Interplay between mitochondria and diet mediates pathogen and stress resistance in Caenorhabditis elegans. PLoS Genet 2019; 15:e1008011. [PMID: 30865620 PMCID: PMC6415812 DOI: 10.1371/journal.pgen.1008011] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Accepted: 02/09/2019] [Indexed: 12/22/2022] Open
Abstract
Diet is a crucial determinant of organismal biology; interactions between the host, its diet, and its microbiota are critical to determining the health of an organism. A variety of genetic and biochemical means were used to assay stress sensitivity in C. elegans reared on two standard laboratory diets: E. coli OP50, the most commonly used food for C. elegans, or E. coli HT115, which is typically used for RNAi-mediated gene knockdown. We demonstrated that the relatively subtle shift to a diet of E. coli HT115 had a dramatic impact on C. elegans's survival after exposure to pathogenic or abiotic stresses. Interestingly, this was independent of canonical host defense pathways. Instead the change arises from improvements in mitochondrial health, likely due to alleviation of a vitamin B12 deficiency exhibited by worms reared on an E. coli OP50 diet. Increasing B12 availability, by feeding on E. coli HT115, supplementing E. coli OP50 with exogenous vitamin B12, or overexpression of the B12 transporter, improved mitochondrial homeostasis and increased resistance. Loss of the methylmalonyl-CoA mutase gene mmcm-1/MUT, which requires vitamin B12 as a cofactor, abolished these improvements, establishing a genetic basis for the E. coli OP50-incurred sensitivity. Our study forges a mechanistic link between a dietary deficiency (nutrition/microbiota) and a physiological consequence (host sensitivity), using the host-microbiota-diet framework.
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Affiliation(s)
- Alexey V. Revtovich
- Department of BioSciences, Rice University, Houston TX, United States of America
| | - Ryan Lee
- Department of BioSciences, Rice University, Houston TX, United States of America
| | - Natalia V. Kirienko
- Department of BioSciences, Rice University, Houston TX, United States of America
- * E-mail:
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114
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Rhizobium induces DNA damage in Caenorhabditis elegans intestinal cells. Proc Natl Acad Sci U S A 2019; 116:3784-3792. [PMID: 30808764 DOI: 10.1073/pnas.1815656116] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
In their natural habitat of rotting fruit, the nematode Caenorhabditis elegans feeds on the complex bacterial communities that thrive in this rich growth medium. Hundreds of diverse bacterial strains cultured from such rotting fruit allow C. elegans growth and reproduction when tested individually. In screens for C. elegans responses to single bacterial strains associated with nematodes in fruit, we found that Rhizobium causes a genome instability phenotype; we observed abnormally long or fragmented intestinal nuclei due to aberrant nuclear division, or defective karyokinesis. The karyokinesis defects were restricted to intestinal cells and required close proximity between bacteria and the worm. A genetic screen for C. elegans mutations that cause the same intestinal karyokinesis defect followed by genome sequencing of the isolated mutant strains identified mutations that disrupt DNA damage repair pathways, suggesting that Rhizobium may cause DNA damage in C. elegans intestinal cells. We hypothesized that such DNA damage is caused by reactive oxygen species produced by Rhizobium and found that hydrogen peroxide added to benign Escherichia coli can cause the same intestinal karyokinesis defects in WT C. elegans Supporting this model, free radical scavengers suppressed the Rhizobium-induced C. elegans DNA damage. Thus, Rhizobium may signal to eukaryotic hosts via reactive oxygen species, and the host may respond with DNA damage repair pathways.
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115
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Berg M, Monnin D, Cho J, Nelson L, Crits-Christoph A, Shapira M. TGFβ/BMP immune signaling affects abundance and function of C. elegans gut commensals. Nat Commun 2019; 10:604. [PMID: 30723205 PMCID: PMC6363772 DOI: 10.1038/s41467-019-08379-8] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Accepted: 12/20/2018] [Indexed: 01/12/2023] Open
Abstract
The gut microbiota contributes to host health and fitness, and imbalances in its composition are associated with pathology. However, what shapes microbiota composition is not clear, in particular the role of genetic factors. Previous work in Caenorhabditis elegans defined a characteristic worm gut microbiota significantly influenced by host genetics. The current work explores the role of central regulators of host immunity and stress resistance, employing qPCR and CFU counts to measure abundance of core microbiota taxa in mutants raised on synthetic communities of previously-isolated worm gut commensals. This revealed a bloom, specifically of Enterobacter species, in immune-compromised TGFβ/BMP mutants. Imaging of fluorescently labeled Enterobacter showed that TGFβ/BMP-exerted control operated primarily in the anterior gut and depended on multi-tissue contributions. Enterobacter commensals are common in the worm gut, contributing to infection resistance. However, disruption of TGFβ/BMP signaling turned a normally beneficial Enterobacter commensal to pathogenic. These results demonstrate specificity in gene-microbe interactions underlying gut microbial homeostasis and highlight the pathogenic potential of their disruption.
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Affiliation(s)
- Maureen Berg
- Department of Integrative Biology, University of California, Berkeley, CA, 94720, USA
| | - David Monnin
- Department of Integrative Biology, University of California, Berkeley, CA, 94720, USA
| | - Juhyun Cho
- Department of Integrative Biology, University of California, Berkeley, CA, 94720, USA
| | - Lydia Nelson
- Department of Integrative Biology, University of California, Berkeley, CA, 94720, USA
| | - Alex Crits-Christoph
- Graduate Group in Microbiology, University of California, Berkeley, CA, 94720, USA
| | - Michael Shapira
- Department of Integrative Biology, University of California, Berkeley, CA, 94720, USA.
- Graduate Group in Microbiology, University of California, Berkeley, CA, 94720, USA.
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Jenkins T, Brindley P, Gasser R, Cantacessi C. Helminth Microbiomes – A Hidden Treasure Trove? Trends Parasitol 2019; 35:13-22. [DOI: 10.1016/j.pt.2018.10.007] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Revised: 10/27/2018] [Accepted: 10/31/2018] [Indexed: 12/14/2022]
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117
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A novel gene-diet pair modulates C. elegans aging. PLoS Genet 2018; 14:e1007608. [PMID: 30125273 PMCID: PMC6117094 DOI: 10.1371/journal.pgen.1007608] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Revised: 08/30/2018] [Accepted: 08/02/2018] [Indexed: 12/26/2022] Open
Abstract
Diet profoundly affects metabolism and incidences of age-related diseases. Animals adapt their physiology to different food-types, modulating complex life-history traits like aging. The molecular mechanisms linking adaptive capacity to diet with aging are less known. We identify FLR-4 kinase as a novel modulator of aging in C. elegans, depending on bacterial diet. FLR-4 functions to prevent differential activation of the p38MAPK pathway in response to diverse food-types, thereby maintaining normal life span. In a kinase-dead flr-4 mutant, E. coli HT115 (K12 strain), but not the standard diet OP50 (B strain), is able to activate p38MAPK, elevate expression of cytoprotective genes through the nuclear hormone receptor NHR-8 and enhance life span. Interestingly, flr-4 and dietary restriction utilize similar pathways for longevity assurance, suggesting cross-talks between cellular modules that respond to diet quality and quantity. Together, our study discovers a new C. elegans gene-diet pair that controls the plasticity of aging. For animals living in the wild, being able to utilize a wide range of diet is evolutionarily advantageous as they can survive even when their optimal diet is depleted. Since diet is known to influence the rate of aging, animals seem to have evolved intricate mechanisms to maintain homeostasis and normal life span, but the molecular mechanisms are less understood. Using a small nematode, C. elegans as a model, we show that the adaptive capacity to different diet is maintained by a kinase gene. When this gene is mutated, worms start living longer on one strain of bacterial diet but not on the other. We identify the molecular cascade required for this food-type-dependent longevity. We show that this cascade of events significantly overlaps with the pathway that determine food quantity-dependent life span enhancement. Our study thus elucidates a part of the molecular monitoring system that regulates longevity dependent on the available quality and quantity of diet.
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118
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Akduman N, Rödelsperger C, Sommer RJ. Culture-based analysis of Pristionchus-associated microbiota from beetles and figs for studying nematode-bacterial interactions. PLoS One 2018; 13:e0198018. [PMID: 29864131 PMCID: PMC5986141 DOI: 10.1371/journal.pone.0198018] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Accepted: 05/12/2018] [Indexed: 12/20/2022] Open
Abstract
The interplay with bacteria is of crucial importance for the interaction of multicellular organisms with their environments. Studying the associations between the nematode model organisms Caenorhabditis elegans and Pristionchus pacificus with bacteria constitutes a powerful system to investigate these interactions at a mechanistic level. P. pacificus is found in association with scarab beetles in nature and recent studies revealed the succession and dynamics of this nematode and its microbiome during the decomposition of one particular host species, the rhinoceros beetle Oryctes borbonicus on La Réunion Island. However, these studies were performed using culture-free methods, with no attempt made to establish bacterial cultures from the beetle-nematode ecosystem and to investigate the effects of these microbes on life history traits in P. pacificus. Here, we establish and characterize a collection of 136 bacterial strains that have been isolated from scarab beetles and figs, another Pristionchus-associated environment, as a resource for studying their effect on various nematode traits. Classification based on 16S sequencing identified members of four bacterial phyla with the class of Gammaproteobacteria representing the majority with 81 strains. Assessing the survival of P. pacificus on individual bacteria allowed us to propose candidate groups of pathogens such as Bacillaceae, Actinobacteria, and Serratia. In combination with chemoattraction data, it was revealed that P. pacificus is able to recognize and avoid certain groups of pathogens, but not others. Our collection of bacterial strains forms a natural resource to study the effects of bacterial diet on development and other traits. Furthermore, these results will form the basis of future studies to elucidate the molecular mechanisms of recognition and pathogenicity.
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Affiliation(s)
- Nermin Akduman
- Max Planck Institute for Developmental Biology, Department of Evolutionary Biology, Max-Planck-Ring 5, Tübingen, Germany
| | - Christian Rödelsperger
- Max Planck Institute for Developmental Biology, Department of Evolutionary Biology, Max-Planck-Ring 5, Tübingen, Germany
| | - Ralf J. Sommer
- Max Planck Institute for Developmental Biology, Department of Evolutionary Biology, Max-Planck-Ring 5, Tübingen, Germany
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119
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Neuron-specific regulation of superoxide dismutase amid pathogen-induced gut dysbiosis. Redox Biol 2018; 17:377-385. [PMID: 29857312 PMCID: PMC6007053 DOI: 10.1016/j.redox.2018.05.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Revised: 05/12/2018] [Accepted: 05/14/2018] [Indexed: 12/26/2022] Open
Abstract
Superoxide dismutase, an enzyme that converts superoxide into less-toxic hydrogen peroxide and oxygen, has been shown to mediate behavioral response to pathogens. However, it remains largely unknown how superoxide dismutase is regulated in the nervous system amid pathogen-induced gut dysbiosis. Although there are five superoxide dismutases in C. elegans, our genetic analyses suggest that SOD-1 is the primary superoxide dismutase to mediate the pathogen avoidance response. When C. elegans are fed a P. aeruginosa diet, the lack of SOD-1 contributes to enhanced lethality. We found that guanylyl cyclases GCY-5 and GCY-22 and neuropeptide receptor NPR-1 act antagonistically to regulate SOD-1 expression in the gustatory neuron ASER. After C. elegans ingests a diet that contributes to high levels of oxidative stress, the temporal regulation of SOD-1 and the SOD-1–dependent response in the gustatory system demonstrates a sophisticated mechanism to fine-tune behavioral plasticity. Our results may provide the initial glimpse of a strategy by which a multicellular organism copes with oxidative stress amid gut dysbiosis.
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120
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Schwarzer M, Strigini M, Leulier F. Gut Microbiota and Host Juvenile Growth. Calcif Tissue Int 2018; 102:387-405. [PMID: 29214457 DOI: 10.1007/s00223-017-0368-y] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 11/18/2017] [Indexed: 02/07/2023]
Abstract
Good genes, good food, good friends. That is what parents hope will sustain and nurture the harmonious growth of their children. The impact of the genetic background and nutrition on postnatal growth has been in the spot light for long, but the good friends have come to the scene only recently. Among the good friends perhaps the most crucial ones are those that we are carrying within ourselves. They comprise the trillions of microbes that collectively constitute each individual's intestinal microbiota. Indeed, recent epidemiological and field studies in humans, supported by extensive experimental data on animal models, demonstrate a clear role of the intestinal microbiota on their host's juvenile growth, especially under suboptimal nutrient conditions. Genuinely integrative approaches applicable to invertebrate and vertebrate systems combine tools from genetics, developmental biology, microbiology, nutrition, and physiology to reveal how gut microbiota affects growth both positively and negatively, in healthy and pathological conditions. It appears that certain natural or engineered gut microbiota communities can positively impact insulin/IGF-1 and steroid hormone signaling, thus contributing to the host juvenile development and maturation.
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Affiliation(s)
- Martin Schwarzer
- Institut de Génomique Fonctionnelle de Lyon (IGFL), Université de Lyon, Ecole Normale Supérieure de Lyon, CNRS UMR 5242, Université Claude Bernard Lyon 1, 69364, Lyon Cedex 07, France.
- Laboratory of Gnotobiology, Institute of Microbiology of the Czech Academy of Sciences, Nový Hrádek, Czech Republic.
| | - Maura Strigini
- INSERM, U1059, Sainbiose, Université de Lyon, Université Jean Monnet, Faculté de Médecine, Campus Santé Innovation, 42023, Saint-Étienne, France.
| | - François Leulier
- Institut de Génomique Fonctionnelle de Lyon (IGFL), Université de Lyon, Ecole Normale Supérieure de Lyon, CNRS UMR 5242, Université Claude Bernard Lyon 1, 69364, Lyon Cedex 07, France
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121
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Na H, Ponomarova O, Giese GE, Walhout AJM. C. elegans MRP-5 Exports Vitamin B12 from Mother to Offspring to Support Embryonic Development. Cell Rep 2018; 22:3126-3133. [PMID: 29562169 PMCID: PMC5896776 DOI: 10.1016/j.celrep.2018.02.100] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Revised: 01/05/2018] [Accepted: 02/26/2018] [Indexed: 01/16/2023] Open
Abstract
Vitamin B12 functions as a cofactor for methionine synthase to produce the anabolic methyl donor S-adenosylmethionine (SAM) and for methylmalonyl-CoA mutase to catabolize the short-chain fatty acid propionate. In the nematode Caenorhabditis elegans, maternally supplied vitamin B12 is required for the development of offspring. However, the mechanism for exporting vitamin B12 from the mother to the offspring is not yet known. Here, we use RNAi of more than 200 transporters with a vitamin B12-sensor transgene to identify the ABC transporter MRP-5 as a candidate vitamin B12 exporter. We show that the injection of vitamin B12 into the gonad of mrp-5 deficient mothers rescues embryonic lethality in the offspring. Altogether, our findings identify a maternal mechanism for the transit of an essential vitamin to support the development of the next generation.
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Affiliation(s)
- Huimin Na
- Program in Systems Biology and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Olga Ponomarova
- Program in Systems Biology and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Gabrielle E Giese
- Program in Systems Biology and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Albertha J M Walhout
- Program in Systems Biology and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA.
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122
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GERBABA TEKLUK, GREEN-HARRISON LUKE, BURET ANDREG. Modeling Host-Microbiome Interactions in Caenorhabditis elegans. J Nematol 2018. [DOI: 10.21307/jofnem-2017-082] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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123
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Abstract
Understanding how the human gut microbiota might influence ageing is challenging. The gut microbiota is a hugely complex ecology of organisms that varies greatly with individuals and time, making age-related changes difficult to measure. However, elderly and younger populations do show differences in gut microbe composition. The key question is whether these differences only reflect age-related changes in host physiology and diet, or if microbes can drive host ageing? Model organisms allow this question to be addressed. Longitudinal analyses in the fruit fly Drosophila melanogaster show that changes in microbial composition precedes intestinal and host ageing, and antibiotic treatment increases lifespan, implicating microbes in accelerating ageing. Antibiotics also extend the lifespan of middle-aged killifish but additional transplantation of gut microbes from young killifish extends lifespan further, suggesting a positive effect of microbes associated with young animals. Microbes from old, but not young, mice induce inflammation when added to germ-free mice suggesting that microbes become more harmful to the host with age. These studies implicate broad classes of bacteria, particularly members of the phylum Proteobacteria, as drivers of ageing in a feed-forward loop with intestinal degradation and inflammation. The nematode Caenorhabditis elegans can be associated with single strains of genetically-tractable bacteria, and this simplified system has revealed specific interventions in bacterial metabolism, such as inhibition of bacterial folate synthesis, that extend animal lifespan. Transferring this understanding to the human microbiota is challenging but promises to reveal how manipulation of the gut microbiota might be a route to maintain health in old age.
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124
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Kundu P, Blacher E, Elinav E, Pettersson S. Our Gut Microbiome: The Evolving Inner Self. Cell 2017; 171:1481-1493. [PMID: 29245010 DOI: 10.1016/j.cell.2017.11.024] [Citation(s) in RCA: 369] [Impact Index Per Article: 52.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Revised: 10/30/2017] [Accepted: 11/09/2017] [Indexed: 02/06/2023]
Abstract
The "holobiont" concept, defined as the collective contribution of the eukaryotic and prokaryotic counterparts to the multicellular organism, introduces a complex definition of individuality enabling a new comprehensive view of human evolution and personalized characteristics. Here, we provide snapshots of the evolving microbial-host associations and relations during distinct milestones across the lifespan of a human being. We discuss the current knowledge of biological symbiosis between the microbiome and its host and portray the challenges in understanding these interactions and their potential effects on human physiology, including microbiome-nervous system inter-relationship and its relevance to human variation and individuality.
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Affiliation(s)
- Parag Kundu
- Singapore Centre for Environmental Life Sciences Engineering, 60 Nanyang Drive, Singapore 637551, Singapore; Lee Kong Chian School of Medicine, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore.
| | - Eran Blacher
- Department of Immunology, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Eran Elinav
- Department of Immunology, Weizmann Institute of Science, 7610001 Rehovot, Israel.
| | - Sven Pettersson
- Singapore Centre for Environmental Life Sciences Engineering, 60 Nanyang Drive, Singapore 637551, Singapore; Lee Kong Chian School of Medicine, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore; Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, SE-171 77 Stockholm, Sweden.
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125
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Gerbaba TK, Green-Harrison L, Buret AG. Modeling Host-Microbiome Interactions in Caenorhabditis elegans. J Nematol 2017; 49:348-356. [PMID: 29353922 PMCID: PMC5770281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Indexed: 06/07/2023] Open
Abstract
The microbiome influences host processes including nutritional availability, development, immunity, and behavioral responses. Caenorhabditis elegans is a powerful model to study molecular mechanisms of host-microbial interactions. Recent efforts have been made to profile the natural microbiome of C. elegans, laying a foundation for mechanistic studies of host-microbiome interactions in this genetically tractable model system. Studies using single-species microbes, multi-microbial systems, and humanized worm-microbiome interaction studies reveal metabolic and microbial-microbial interactions relevant in higher organisms. This article discusses recent developments in modeling the effects of host-microbiome interactions in C. elegans.
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Affiliation(s)
- Teklu K Gerbaba
- Department of Medicine, Queen's University, Kingston, ON, Canada
| | - Luke Green-Harrison
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Andre G Buret
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
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126
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Krejci A, Tennessen JM. Metabolism in time and space – exploring the frontier of developmental biology. Development 2017; 144:3193-3198. [DOI: 10.1242/dev.150573] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Despite the fact that metabolic studies played a prominent role in the early history of developmental biology research, the field of developmental metabolism was largely ignored following the advent of modern molecular biology. Metabolism, however, has recently re-emerged as a focal point of biomedical studies and, as a result, developmental biologists are once again exploring the chemical and energetic forces that shape growth, development and maturation. In May 2017, a diverse group of scientists assembled at the EMBO/EMBL Symposium ‘Metabolism in Time and Space’ to discuss how metabolism influences cellular and developmental processes. The speakers not only described how metabolic flux adapts to the energetic needs of a developing organism, but also emphasized that metabolism can directly regulate developmental progression. Overall, and as we review here, this interdisciplinary meeting provided a valuable forum to explore the interface between developmental biology and metabolism.
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Affiliation(s)
- Alena Krejci
- University of South Bohemia, Faculty of Science, Branisovska 31, 37005 Ceske Budejovice, Czech Republic
- Biology Centre, Institute of Entomology, Czech Academy of Sciences, Branisovska 31, 37005 Ceske Budejovice, Czech Republic
| | - Jason M. Tennessen
- Department of Biology, Indiana University, 1001 East Third Street, Bloomington, IN 47405, USA
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127
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Mori A, Holdorf AD, Walhout AJM. Many transcription factors contribute to C. elegans growth and fat storage. Genes Cells 2017; 22:770-784. [PMID: 28791781 DOI: 10.1111/gtc.12516] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Accepted: 06/10/2017] [Indexed: 12/17/2022]
Abstract
Reverse genetic screens by RNA interference (RNAi) in model organisms such as the nematode Caenorhabditis elegans have provided numerous insights into gene function, thereby connecting genotype to phenotype. However, genes that contribute only subtly are often missed because relatively large numbers of measurements and reliable quantification are required to overcome experimental and biological noise that may mask subtle phenotypic effects. Here, we address this challenge by focusing on two phenotypes in C. elegans: growth and fat storage. We carried out comprehensive RNAi knockdown of transcription factors (TFs), as these are known important regulators of biological processes during development and the maintenance of homeostasis. Microscopy images of TF knockdown animals stained with Oil Red O (ORO) were captured, and body size (proxy for growth) and ORO staining intensity (proxy for fat storage) were precisely quantified using a newly developed imaging tool we named IPPOME (Image Processing for Precise and Objective MEasurement). We found that a surprisingly large proportion of TFs contribute to growth and fat storage, but that most TFs have only subtle, yet significant effects. This study provides a blueprint for studies of other genes and phenotypes in C. elegans.
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Affiliation(s)
- Akihiro Mori
- Program in Systems Biology, Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - Amy D Holdorf
- Program in Systems Biology, Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - 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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128
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Smolentseva O, Gusarov I, Gautier L, Shamovsky I, DeFrancesco AS, Losick R, Nudler E. Mechanism of biofilm-mediated stress resistance and lifespan extension in C. elegans. Sci Rep 2017; 7:7137. [PMID: 28769037 PMCID: PMC5540977 DOI: 10.1038/s41598-017-07222-8] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 06/26/2017] [Indexed: 01/16/2023] Open
Abstract
Bacteria naturally form communities of cells known as biofilms. However the physiological roles of biofilms produced by non-pathogenic microbiota remain largely unknown. To assess the impact of a biofilm on host physiology we explored the effect of several non-pathogenic biofilm-forming bacteria on Caenorhabditis elegans. We show that biofilm formation by Bacillus subtilis, Lactobacillus rhamnosus and Pseudomonas fluorescens induces C. elegans stress resistance. Biofilm also protects against pathogenic infection and prolongs lifespan. Total mRNA analysis identified a set of host genes that are upregulated in response to biofilm formation by B. subtilis. We further demonstrate that mtl-1 is responsible for the biofilm-mediated increase in oxidative stress resistance and lifespan extension. Induction of mtl-1 and hsp-70 promotes biofilm-mediated thermotolerance. ilys-2 activity accounts for biofilm-mediated resistance to Pseudomonas aeruginosa killing. These results reveal the importance of non-pathogenic biofilms for host physiology and provide a framework to study commensal biofilms in higher organisms.
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Affiliation(s)
- Olga Smolentseva
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, 10016, USA
| | - Ivan Gusarov
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, 10016, USA
| | - Laurent Gautier
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, 10016, USA
| | - Ilya Shamovsky
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, 10016, USA
| | - Alicia S DeFrancesco
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, 02138, USA
| | - Richard Losick
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, 02138, USA
| | - Evgeny Nudler
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, 10016, USA.
- Howard Hughes Medical Institute, New York University School of Medicine, New York, NY, 10016, USA.
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129
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Shapira M. Host–microbiota interactions in Caenorhabditis elegans and their significance. Curr Opin Microbiol 2017. [DOI: 10.1016/j.mib.2017.05.012] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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130
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Sleeping Beauty? Developmental Timing, Sleep, and the Circadian Clock in Caenorhabditis elegans. ADVANCES IN GENETICS 2017; 97:43-80. [PMID: 28838356 DOI: 10.1016/bs.adgen.2017.05.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The genetics toolkit is pretty successful in drilling down into minutiae. The big challenge is to integrate the information from this specialty as well as those of biochemistry, physiology, behavior, and anatomy to explain how fundamental biological processes really work. Sleep, the circadian clock and development all qualify as overarching processes that encompass levels from molecule to behavior as part of their known mechanisms. They overlap each other, such that understanding the mechanisms of one can lead to insights into one of the others. In this essay, we consider how the experimental approaches and findings relating to Caenorhabditis elegans development and lethargus on one hand, and to the circadian clock and sleep in higher organisms on the other, could complement and enhance one another.
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131
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Chaudhari SN, Mukherjee M, Vagasi AS, Bi G, Rahman MM, Nguyen CQ, Paul L, Selhub J, Kipreos ET. Bacterial Folates Provide an Exogenous Signal for C. elegans Germline Stem Cell Proliferation. Dev Cell 2017; 38:33-46. [PMID: 27404357 DOI: 10.1016/j.devcel.2016.06.013] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Revised: 05/04/2016] [Accepted: 06/09/2016] [Indexed: 11/29/2022]
Abstract
Here we describe an in vitro primary culture system for Caenorhabditis elegans germline stem cells. This culture system was used to identify a bacterial folate as a positive regulator of germ cell proliferation. Folates are a family of B-complex vitamins that function in one-carbon metabolism to allow the de novo synthesis of amino acids and nucleosides. We show that germ cell proliferation is stimulated by the folate 10-formyl-tetrahydrofolate-Glun both in vitro and in animals. Other folates that can act as vitamins to rescue folate deficiency lack this germ cell stimulatory activity. The bacterial folate precursor dihydropteroate also promotes germ cell proliferation in vitro and in vivo, despite its inability to promote one-carbon metabolism. The folate receptor homolog FOLR-1 is required for the stimulation of germ cells by 10-formyl-tetrahydrofolate-Glun and dihydropteroate. This work defines a folate and folate-related compound as exogenous signals to modulate germ cell proliferation.
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Affiliation(s)
- Snehal N Chaudhari
- Department of Cellular Biology, University of Georgia, Athens, GA 30602, USA
| | | | - Alexandra S Vagasi
- Department of Cellular Biology, University of Georgia, Athens, GA 30602, USA
| | - Gaofeng Bi
- Jean Mayer USDA Human Nutrition Research Center on Aging, Tufts University, Boston, MA 02111, USA
| | - Mohammad M Rahman
- Department of Genetics, University of Georgia, Athens, GA 30602, USA
| | - Christine Q Nguyen
- Department of Cellular Biology, University of Georgia, Athens, GA 30602, USA
| | - Ligi Paul
- Jean Mayer USDA Human Nutrition Research Center on Aging, Tufts University, Boston, MA 02111, USA
| | - Jacob Selhub
- Jean Mayer USDA Human Nutrition Research Center on Aging, Tufts University, Boston, MA 02111, USA
| | - Edward T Kipreos
- Department of Cellular Biology, University of Georgia, Athens, GA 30602, USA.
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132
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Guo Y, Xun Z, Coffman SR, Chen F. The Shift of the Intestinal Microbiome in the Innate Immunity-Deficient Mutant rde-1 Strain of C. elegans upon Orsay Virus Infection. Front Microbiol 2017; 8:933. [PMID: 28611740 PMCID: PMC5446984 DOI: 10.3389/fmicb.2017.00933] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2017] [Accepted: 05/08/2017] [Indexed: 01/19/2023] Open
Abstract
The status of intestinal microbiota is a determinant of host health. However, the alteration of the gut microbiota caused by the innate immune response to virus infection is unclear. Caenorhabditis elegans and its natural virus Orsay provide an excellent model of host–virus interactions. We evaluated the intestinal microbial community complexity of the wild-type N2 and the innate immunity-deficient mutant rde-1 (ne219) strains of C. elegans upon Orsay virus infection. The gut microbiota diversity was decreased in rde-1 (ne219) mutant animals, and a large number of genes were associated with the difference between infected and uninfected rde-1 (ne219) mutant animals. Therefore, this study provides the first evaluation of the alterations caused by Orsay virus on intestinal microbiota in wildtype and innate immunity-deficient animals using C. elegans as the model species. Our findings indicate that virus infection may alters the microbiome in animals with defective immune response.
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Affiliation(s)
- Yuanyuan Guo
- School of Life Science, Peking UniversityBeijing, China
| | - Zhe Xun
- Central Laboratory, Peking University School of StomatologyBeijing, China
| | | | - Feng Chen
- Central Laboratory, Peking University School of StomatologyBeijing, China
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133
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Gao AW, Chatzispyrou IA, Kamble R, Liu YJ, Herzog K, Smith RL, van Lenthe H, Vervaart MAT, van Cruchten A, Luyf AC, van Kampen A, Pras-Raves ML, Vaz FM, Houtkooper RH. A sensitive mass spectrometry platform identifies metabolic changes of life history traits in C. elegans. Sci Rep 2017; 7:2408. [PMID: 28546536 PMCID: PMC5445081 DOI: 10.1038/s41598-017-02539-w] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Accepted: 04/12/2017] [Indexed: 12/21/2022] Open
Abstract
Abnormal nutrient metabolism is a hallmark of aging, and the underlying genetic and nutritional framework is rapidly being uncovered, particularly using C. elegans as a model. However, the direct metabolic consequences of perturbations in life history of C. elegans remain to be clarified. Based on recent advances in the metabolomics field, we optimized and validated a sensitive mass spectrometry (MS) platform for identification of major metabolite classes in worms and applied it to study age and diet related changes. Using this platform that allowed detection of over 600 metabolites in a sample of 2500 worms, we observed marked changes in fatty acids, amino acids and phospholipids during worm life history, which were independent from the germ-line. Worms underwent a striking shift in lipid metabolism after early adulthood that was at least partly controlled by the metabolic regulator AAK-2/AMPK. Most amino acids peaked during development, except aspartic acid and glycine, which accumulated in aged worms. Dietary intervention also influenced worm metabolite profiles and the regulation was highly specific depending on the metabolite class. Altogether, these MS-based methods are powerful tools to perform worm metabolomics for aging and metabolism-oriented studies.
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Affiliation(s)
- Arwen W Gao
- Laboratory Genetic Metabolic Diseases, Academic Medical Center, 1105 AZ, Amsterdam, The Netherlands
| | - Iliana A Chatzispyrou
- Laboratory Genetic Metabolic Diseases, Academic Medical Center, 1105 AZ, Amsterdam, The Netherlands
| | - Rashmi Kamble
- Laboratory Genetic Metabolic Diseases, Academic Medical Center, 1105 AZ, Amsterdam, The Netherlands
| | - Yasmine J Liu
- Laboratory Genetic Metabolic Diseases, Academic Medical Center, 1105 AZ, Amsterdam, The Netherlands
| | - Katharina Herzog
- Laboratory Genetic Metabolic Diseases, Academic Medical Center, 1105 AZ, Amsterdam, The Netherlands
| | - Reuben L Smith
- Laboratory Genetic Metabolic Diseases, Academic Medical Center, 1105 AZ, Amsterdam, The Netherlands
| | - Henk van Lenthe
- Laboratory Genetic Metabolic Diseases, Academic Medical Center, 1105 AZ, Amsterdam, The Netherlands
| | - Martin A T Vervaart
- Laboratory Genetic Metabolic Diseases, Academic Medical Center, 1105 AZ, Amsterdam, The Netherlands
| | - Arno van Cruchten
- Laboratory Genetic Metabolic Diseases, Academic Medical Center, 1105 AZ, Amsterdam, The Netherlands
| | - Angela C Luyf
- Department of Clinical Epidemiology, Biostatistics and Bioinformatics, Academic Medical Center, 1105 AZ, Amsterdam, The Netherlands
| | - Antoine van Kampen
- Department of Clinical Epidemiology, Biostatistics and Bioinformatics, Academic Medical Center, 1105 AZ, Amsterdam, The Netherlands
| | - Mia L Pras-Raves
- Laboratory Genetic Metabolic Diseases, Academic Medical Center, 1105 AZ, Amsterdam, The Netherlands.,Department of Clinical Epidemiology, Biostatistics and Bioinformatics, Academic Medical Center, 1105 AZ, Amsterdam, The Netherlands
| | - Frédéric M Vaz
- Laboratory Genetic Metabolic Diseases, Academic Medical Center, 1105 AZ, Amsterdam, The Netherlands
| | - Riekelt H Houtkooper
- Laboratory Genetic Metabolic Diseases, Academic Medical Center, 1105 AZ, Amsterdam, The Netherlands.
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134
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Schulenburg H, Félix MA. The Natural Biotic Environment of Caenorhabditis elegans. Genetics 2017; 206:55-86. [PMID: 28476862 PMCID: PMC5419493 DOI: 10.1534/genetics.116.195511] [Citation(s) in RCA: 249] [Impact Index Per Article: 35.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 02/28/2017] [Indexed: 01/05/2023] Open
Abstract
Organisms evolve in response to their natural environment. Consideration of natural ecological parameters are thus of key importance for our understanding of an organism's biology. Curiously, the natural ecology of the model species Caenorhabditis elegans has long been neglected, even though this nematode has become one of the most intensively studied models in biological research. This lack of interest changed ∼10 yr ago. Since then, an increasing number of studies have focused on the nematode's natural ecology. Yet many unknowns still remain. Here, we provide an overview of the currently available information on the natural environment of C. elegans We focus on the biotic environment, which is usually less predictable and thus can create high selective constraints that are likely to have had a strong impact on C. elegans evolution. This nematode is particularly abundant in microbe-rich environments, especially rotting plant matter such as decomposing fruits and stems. In this environment, it is part of a complex interaction network, which is particularly shaped by a species-rich microbial community. These microbes can be food, part of a beneficial gut microbiome, parasites and pathogens, and possibly competitors. C. elegans is additionally confronted with predators; it interacts with vector organisms that facilitate dispersal to new habitats, and also with competitors for similar food environments, including competitors from congeneric and also the same species. Full appreciation of this nematode's biology warrants further exploration of its natural environment and subsequent integration of this information into the well-established laboratory-based research approaches.
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Affiliation(s)
- Hinrich Schulenburg
- Zoological Institute, Christian-Albrechts Universitaet zu Kiel, 24098 Kiel, Germany
| | - Marie-Anne Félix
- Institut de Biologie de l'Ecole Normale Supérieure, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, École Normale Supérieure, L'université de Recherche Paris Sciences et Lettres, 75005, France
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135
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García-González AP, Ritter AD, Shrestha S, Andersen EC, Yilmaz LS, Walhout AJM. Bacterial Metabolism Affects the C. elegans Response to Cancer Chemotherapeutics. Cell 2017; 169:431-441.e8. [PMID: 28431244 PMCID: PMC5484065 DOI: 10.1016/j.cell.2017.03.046] [Citation(s) in RCA: 158] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Revised: 02/09/2017] [Accepted: 03/28/2017] [Indexed: 12/18/2022]
Abstract
The human microbiota greatly affects physiology and disease; however, the contribution of bacteria to the response to chemotherapeutic drugs remains poorly understood. Caenorhabditis elegans and its bacterial diet provide a powerful system to study host-bacteria interactions. Here, we use this system to study how bacteria affect the C. elegans response to chemotherapeutics. We find that different bacterial species can increase the response to one drug yet decrease the effect of another. We perform genetic screens in two bacterial species using three chemotherapeutic drugs: 5-fluorouracil (5-FU), 5-fluoro-2'-deoxyuridine (FUDR), and camptothecin (CPT). We find numerous bacterial nucleotide metabolism genes that affect drug efficacy in C. elegans. Surprisingly, we find that 5-FU and FUDR act through bacterial ribonucleotide metabolism to elicit their cytotoxic effects in C. elegans rather than by thymineless death or DNA damage. Our study provides a blueprint for characterizing the role of bacteria in the host response to chemotherapeutics.
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Affiliation(s)
- Aurian P García-González
- Program in Systems Biology and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Ashlyn D Ritter
- Program in Systems Biology and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Shaleen Shrestha
- Program in Systems Biology and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Erik C Andersen
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - L Safak Yilmaz
- Program in Systems Biology and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Albertha J M Walhout
- Program in Systems Biology and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA.
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136
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Zhang F, Berg M, Dierking K, Félix MA, Shapira M, Samuel BS, Schulenburg H. Caenorhabditis elegans as a Model for Microbiome Research. Front Microbiol 2017; 8:485. [PMID: 28386252 PMCID: PMC5362939 DOI: 10.3389/fmicb.2017.00485] [Citation(s) in RCA: 101] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Accepted: 03/08/2017] [Indexed: 11/25/2022] Open
Abstract
The nematode Caenorhabditis elegans is used as a central model system across biological disciplines. Surprisingly, almost all research with this worm is performed in the absence of its native microbiome, possibly affecting generality of the obtained results. In fact, the C. elegans microbiome had been unknown until recently. This review brings together results from the first three studies on C. elegans microbiomes, all published in 2016. Meta-analysis of the data demonstrates a considerable conservation in the composition of the microbial communities, despite the distinct geographical sample origins, study approaches, labs involved and perturbations during worm processing. The C. elegans microbiome is enriched and in some cases selective for distinct phylotypes compared to corresponding substrate samples (e.g., rotting fruits, decomposing plant matter, and compost soil). The dominant bacterial groups include several Gammaproteobacteria (Enterobacteriaceae, Pseudomonaceae, and Xanthomonodaceae) and Bacteroidetes (Sphingobacteriaceae, Weeksellaceae, Flavobacteriaceae). They are consistently joined by several rare putative keystone taxa like Acetobacteriaceae. The bacteria are able to enhance growth of nematode populations, as well as resistance to biotic and abiotic stressors, including high/low temperatures, osmotic stress, and pathogenic bacteria and fungi. The associated microbes thus appear to display a variety of effects beneficial for the worm. The characteristics of these effects, their relevance for C. elegans fitness, the presence of specific co-adaptations between microbiome members and the worm, and the molecular underpinnings of microbiome-host interactions represent promising areas of future research, for which the advantages of C. elegans as an experimental system should prove of particular value.
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Affiliation(s)
- Fan Zhang
- Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine Houston, TX, USA
| | - Maureen Berg
- Department of Integrative Biology, University of California, Berkeley Berkeley, CA, USA
| | - Katja Dierking
- Zoological Institute, Christian-Albrechts University Kiel Kiel, Germany
| | - Marie-Anne Félix
- Centre National de la Recherche Scientifique, Institut de Biologie de l'Ecole Normale Supérieure, Institut National de la Santé et de la Recherche Médicale, ENS, PSL Research University Paris, France
| | - Michael Shapira
- Department of Integrative Biology, University of California, Berkeley Berkeley, CA, USA
| | - Buck S Samuel
- Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine Houston, TX, USA
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137
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Leulier F, MacNeil LT, Lee WJ, Rawls JF, Cani PD, Schwarzer M, Zhao L, Simpson SJ. Integrative Physiology: At the Crossroads of Nutrition, Microbiota, Animal Physiology, and Human Health. Cell Metab 2017; 25:522-534. [PMID: 28273475 PMCID: PMC6200423 DOI: 10.1016/j.cmet.2017.02.001] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Revised: 01/30/2017] [Accepted: 01/31/2017] [Indexed: 02/07/2023]
Abstract
Nutrition is paramount in shaping all aspects of animal biology. In addition, the influence of the intestinal microbiota on physiology is now widely recognized. Given that diet also shapes the intestinal microbiota, this raises the question of how the nutritional environment and microbial assemblages together influence animal physiology. This research field constitutes a new frontier in the field of organismal biology that needs to be addressed. Here we review recent studies using animal models and humans and propose an integrative framework within which to define the study of the diet-physiology-microbiota systems and ultimately link it to human health. Nutritional Geometry sits centrally in the proposed framework and offers means to define diet compositions that are optimal for individuals and populations.
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Affiliation(s)
- François Leulier
- Institut de Génomique Fonctionnelle de Lyon (IGFL), Université de Lyon, Ecole Normale Supérieure de Lyon, CNRS UMR 5242, Université Claude Bernard Lyon 1, F-69364 Lyon Cedex 07, France.
| | - Lesley T MacNeil
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S4K1, Canada; Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, ON L8S4K1, Canada; Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON L8S4K1, Canada
| | - Won-Jae Lee
- School of Biological Science, Institute of Molecular Biology and Genetics, National Creative Research Initiative Center for Hologenomics, Seoul National University, Seoul 151-742, South Korea
| | - John F Rawls
- Department of Molecular Genetics and Microbiology, Center for the Genomics of Microbial Systems, Duke University School of Medicine, Durham, NC 27710, USA
| | - Patrice D Cani
- Université Catholique de Louvain, Louvain Drug Research Institute, WELBIO (Walloon Excellence in Life Sciences and Biotechnology), Metabolism and Nutrition Research Group, B-1200 Brussels, Belgium
| | - Martin Schwarzer
- Institut de Génomique Fonctionnelle de Lyon (IGFL), Université de Lyon, Ecole Normale Supérieure de Lyon, CNRS UMR 5242, Université Claude Bernard Lyon 1, F-69364 Lyon Cedex 07, France
| | - Liping Zhao
- State Key Laboratory of Microbial Metabolism and Ministry of Education Key Laboratory of Systems Biomedicine, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Stephen J Simpson
- Charles Perkins Centre, University of Sydney, Sydney 2006, Australia; School of Life and Environmental Sciences, University of Sydney, Sydney 2006, Australia
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138
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Zhang J, Holdorf AD, Walhout AJ. C. elegans and its bacterial diet as a model for systems-level understanding of host-microbiota interactions. Curr Opin Biotechnol 2017; 46:74-80. [PMID: 28189107 PMCID: PMC5544573 DOI: 10.1016/j.copbio.2017.01.008] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 01/19/2017] [Accepted: 01/20/2017] [Indexed: 02/06/2023]
Abstract
Resident microbes of the human body, particularly the gut microbiota, provide essential functions for the host, and, therefore, have important roles in human health as well as mitigating disease. It is difficult to study the mechanisms by which the microbiota affect human health, especially at a systems-level, due to heterogeneity of human genomes, the complexity and heterogeneity of the gut microbiota, the challenge of growing these bacteria in the laboratory, and the lack of bacterial genetics in most microbiotal species. In the last few years, the interspecies model of the nematode Caenorhabditis elegans and its bacterial diet has proven powerful for studying host-microbiota interactions, as both the animal and its bacterial diet can be subjected to large-scale and high-throughput genetic screening. The high level of homology between many C. elegans and human genes, as well as extensive similarities between human and C. elegans metabolism, indicates that the findings obtained from this interspecies model may be broadly relevant to understanding how the human microbiota affects physiology and disease. In this review, we summarize recent systems studies on how bacteria interact with C. elegans and affect life history traits.
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Affiliation(s)
- Jingyan Zhang
- Program in Systems Biology and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Amy D Holdorf
- Program in Systems Biology and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Albertha Jm Walhout
- Program in Systems Biology and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA.
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139
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Yilmaz LS, Walhout AJ. Metabolic network modeling with model organisms. Curr Opin Chem Biol 2017; 36:32-39. [PMID: 28088694 PMCID: PMC5458607 DOI: 10.1016/j.cbpa.2016.12.025] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 12/21/2016] [Indexed: 12/25/2022]
Abstract
Flux balance analysis (FBA) with genome-scale metabolic network models (GSMNM) allows systems level predictions of metabolism in a variety of organisms. Different types of predictions with different accuracy levels can be made depending on the applied experimental constraints ranging from measurement of exchange fluxes to the integration of gene expression data. Metabolic network modeling with model organisms has pioneered method development in this field. In addition, model organism GSMNMs are useful for basic understanding of metabolism, and in the case of animal models, for the study of metabolic human diseases. Here, we discuss GSMNMs of most highly used model organisms with the emphasis on recent reconstructions.
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Affiliation(s)
- L Safak Yilmaz
- Program in Systems Biology, Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, United States.
| | - Albertha Jm Walhout
- Program in Systems Biology, Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, United States.
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140
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Mendoza AD, Woodruff TK, Wignall SM, O'Halloran TV. Zinc availability during germline development impacts embryo viability in Caenorhabditis elegans. Comp Biochem Physiol C Toxicol Pharmacol 2017; 191:194-202. [PMID: 27664515 PMCID: PMC5210184 DOI: 10.1016/j.cbpc.2016.09.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Revised: 09/02/2016] [Accepted: 09/06/2016] [Indexed: 11/29/2022]
Abstract
Zinc is an essential metal that serves as a cofactor in a variety of cellular processes, including meiotic maturation. Cellular control of zinc uptake, availability and efflux is closely linked to meiotic progression in rodent and primate reproduction where large fluctuations in zinc levels are critical at several steps in the oocyte-to-embryo transition. Despite these well-documented roles of zinc fluxes during meiosis, only a few of the genes encoding key zinc receptors, membrane-spanning transporters, and downstream signaling pathway factors have been identified to date. Furthermore, little is known about analogous roles for zinc fluxes in the context of a whole organism. Here, we evaluate whether zinc availability regulates germline development and oocyte viability in the nematode Caenorhabditis elegans, an experimentally flexible model organism. We find that similar to mammals, mild zinc limitation in C. elegans profoundly impacts the reproductive axis: the brood size is significantly reduced under conditions of zinc limitation where other physiological functions are not perturbed. Zinc limitation in this organism has a more pronounced impact on oocytes than sperm and this leads to the decrease in viable embryo production. Moreover, acute zinc limitation of isolated zygotes prevents extrusion of the second polar body during meiosis and leads to aneuploid embryos. Thus, the zinc-dependent steps in C. elegans gametogenesis roughly parallel those described in meiotic-to-mitotic transitions in mammals.
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Affiliation(s)
- Adelita D Mendoza
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA; The Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA
| | - Teresa K Woodruff
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA; The Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA; Department of Obstetrics and Gynecology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Sarah M Wignall
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA.
| | - Thomas V O'Halloran
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA; The Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA; Department of Chemistry, Northwestern University, Evanston, IL 60208, USA.
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141
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Fuxman Bass JI, Pons C, Kozlowski L, Reece-Hoyes JS, Shrestha S, Holdorf AD, Mori A, Myers CL, Walhout AJ. A gene-centered C. elegans protein-DNA interaction network provides a framework for functional predictions. Mol Syst Biol 2016; 12:884. [PMID: 27777270 PMCID: PMC5081483 DOI: 10.15252/msb.20167131] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Transcription factors (TFs) play a central role in controlling spatiotemporal gene expression and the response to environmental cues. A comprehensive understanding of gene regulation requires integrating physical protein–DNA interactions (PDIs) with TF regulatory activity, expression patterns, and phenotypic data. Although great progress has been made in mapping PDIs using chromatin immunoprecipitation, these studies have only characterized ~10% of TFs in any metazoan species. The nematode C. elegans has been widely used to study gene regulation due to its compact genome with short regulatory sequences. Here, we delineated the largest gene‐centered metazoan PDI network to date by examining interactions between 90% of C. elegans TFs and 15% of gene promoters. We used this network as a backbone to predict TF binding sites for 77 TFs, two‐thirds of which are novel, as well as integrate gene expression, protein–protein interaction, and phenotypic data to predict regulatory and biological functions for multiple genes and TFs.
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Affiliation(s)
- Juan I Fuxman Bass
- Program in Systems Biology and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Carles Pons
- Department of Computer Science and Engineering, University of Minnesota-Twin Cities, Minneapolis, MN, USA
| | - Lucie Kozlowski
- Program in Systems Biology and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - John S Reece-Hoyes
- Program in Systems Biology and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Shaleen Shrestha
- Program in Systems Biology and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Amy D Holdorf
- Program in Systems Biology and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Akihiro Mori
- Program in Systems Biology and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Chad L Myers
- Department of Computer Science and Engineering, University of Minnesota-Twin Cities, Minneapolis, MN, USA
| | - Albertha Jm Walhout
- Program in Systems Biology and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA
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142
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Watson E, Yilmaz LS, Walhout AJM. Understanding Metabolic Regulation at a Systems Level: Metabolite Sensing, Mathematical Predictions, and Model Organisms. Annu Rev Genet 2016; 49:553-75. [PMID: 26631516 DOI: 10.1146/annurev-genet-112414-055257] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Metabolic networks are extensively regulated to facilitate tissue-specific metabolic programs and robustly maintain homeostasis in response to dietary changes. Homeostatic metabolic regulation is achieved through metabolite sensing coupled to feedback regulation of metabolic enzyme activity or expression. With a wealth of transcriptomic, proteomic, and metabolomic data available for different cell types across various conditions, we are challenged with understanding global metabolic network regulation and the resulting metabolic outputs. Stoichiometric metabolic network modeling integrated with "omics" data has addressed this challenge by generating nonintuitive, testable hypotheses about metabolic flux rewiring. Model organism studies have also yielded novel insight into metabolic networks. This review covers three topics: the feedback loops inherent in metabolic regulatory networks, metabolic network modeling, and interspecies studies utilizing Caenorhabditis elegans and various bacterial diets that have revealed novel metabolic paradigms.
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Affiliation(s)
- Emma Watson
- Program in Systems Biology, Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605; , ,
| | - L Safak Yilmaz
- Program in Systems Biology, Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605; , ,
| | - Albertha J M Walhout
- Program in Systems Biology, Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605; , ,
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143
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Chen L, Zhang J, Xu J, Wan L, Teng K, Xiang J, Zhang R, Huang Z, Liu Y, Li W, Liu X. rBmαTX14 Increases the Life Span and Promotes the Locomotion of Caenorhabditis Elegans. PLoS One 2016; 11:e0161847. [PMID: 27611314 PMCID: PMC5017660 DOI: 10.1371/journal.pone.0161847] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Accepted: 08/12/2016] [Indexed: 12/02/2022] Open
Abstract
The scorpion has been extensively used in various pharmacological profiles or as food supplies. The exploration of scorpion venom has been reported due to the presence of recombinant peptides. rBmαTX14 is an α-neurotoxin extracted from the venom gland of the East Asian scorpion Buthus martensii Karsch and can affect ion channel conductance. Here, we investigated the functions of rBmαTX14 using the Caenorhabditis elegans model. Using western blot analysis, rBmαTX14 was shown to be expressed both in the cytoplasm and inclusion bodies in the E.coli Rosetta (DE3) strain. Circular dichroism spectroscopy analysis demonstrated that purified rBmαTX14 retained its biological structures. Next, feeding nematodes with E.coli Rosetta (DE3) expressing rBmαTX14 caused extension of the life span and promoted the locomotion of the nematodes. In addition, we identified several genes that play various roles in the life span and locomotion of C. elegans through microarray analysis and quantitative real-time PCR. Furthermore, if the amino acid site H15 of rBmαTX14 was mutated, rBmαTX14 no longer promoted the C. elegans life span. In conclusion, the results not only demonstrated the functions and mechanism of rBmαTX14 in C. elegans, but also provided the new sight in the utility of recombinant peptides from scorpion venom.
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Affiliation(s)
- Lan Chen
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China
| | - Ju Zhang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China
| | - Jie Xu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China
| | - Lu Wan
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China
| | - Kaixuan Teng
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China
| | - Jin Xiang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China
| | - Rui Zhang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China
| | - Zebo Huang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China
- Guangdong Province Key Laboratory for Biotechnology Drug Candidates, School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, 510006, China
| | - Yongmei Liu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China
| | - Wenhua Li
- School of Life Science, Wuhan University, Wuhan, 430071, China
| | - Xin Liu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China
- * E-mail:
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144
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Gritti N, Kienle S, Filina O, van Zon JS. Long-term time-lapse microscopy of C. elegans post-embryonic development. Nat Commun 2016; 7:12500. [PMID: 27558523 PMCID: PMC5512614 DOI: 10.1038/ncomms12500] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Accepted: 07/08/2016] [Indexed: 11/09/2022] Open
Abstract
We present a microscopy technique that enables long-term time-lapse microscopy at single-cell resolution in moving and feeding Caenorhabditis elegans larvae. Time-lapse microscopy of C. elegans post-embryonic development is challenging, as larvae are highly motile. Moreover, immobilization generally leads to rapid developmental arrest. Instead, we confine larval movement to microchambers that contain bacteria as food, and use fast image acquisition and image analysis to follow the dynamics of cells inside individual larvae, as they move within each microchamber. This allows us to perform fluorescence microscopy of 10-20 animals in parallel with 20 min time resolution. We demonstrate the power of our approach by analysing the dynamics of cell division, cell migration and gene expression over the full ∼48 h of development from larva to adult. Our approach now makes it possible to study the behaviour of individual cells inside the body of a feeding and growing animal.
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Affiliation(s)
- Nicola Gritti
- FOM Institute AMOLF, Science Park 104, Amsterdam 1098 XG, The Netherlands
| | - Simone Kienle
- FOM Institute AMOLF, Science Park 104, Amsterdam 1098 XG, The Netherlands
| | - Olga Filina
- FOM Institute AMOLF, Science Park 104, Amsterdam 1098 XG, The Netherlands
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145
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Fluorescent Beads Are a Versatile Tool for Staging Caenorhabditis elegans in Different Life Histories. G3-GENES GENOMES GENETICS 2016; 6:1923-33. [PMID: 27172224 PMCID: PMC4938646 DOI: 10.1534/g3.116.030163] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Precise staging of Caenorhabditis elegans is essential for developmental studies in different environmental conditions. In favorable conditions, larvae develop continuously through four larval stages separated by molting periods. Distinguishing molting from intermolt larvae has been achieved using transgenes with molting reporters, therefore requiring strain constructions, or careful observation of individuals for pharyngeal pumping or behavioral quiescence. In unfavorable conditions, larvae can enter the stress-resistant and developmentally arrested dauer larva stage. Identifying dauer larvae has been based on their ability to withstand detergent selection, precluding identification of recovering animals or of mutants with defects in dauer morphogenesis. Here, we describe a simple method to distinguish molting larvae or dauer larvae from intermolt larvae that bypasses the limitations of current methods. Fluorescent latex beads are mixed with the bacterial food source and ingested by intermolt larvae and adults. Molting and dauer larvae do not feed, and therefore lack beads in their digestive tract. The presence of beads can be determined using a dissecting microscope at magnifications as low as 100 ×, or by using a wormsorter for high-throughput experiments. We find that continuously developing bead-lacking larvae display hallmarks of molting, including expression of the mlt-10::gfp molting marker and a lack of pharyngeal pumping. Furthermore, wild-type and mutant dauer larvae produced by any of three common methods are accurately identified by a lack of beads. Importantly, this method is effective in SDS-sensitive mutant backgrounds and can identify recovering dauer larvae, a stage for which there is no other method of positive selection.
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146
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Watson E, Olin-Sandoval V, Hoy MJ, Li CH, Louisse T, Yao V, Mori A, Holdorf AD, Troyanskaya OG, Ralser M, Walhout AJ. Metabolic network rewiring of propionate flux compensates vitamin B12 deficiency in C. elegans. eLife 2016; 5. [PMID: 27383050 PMCID: PMC4951191 DOI: 10.7554/elife.17670] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Accepted: 06/20/2016] [Indexed: 12/20/2022] Open
Abstract
Metabolic network rewiring is the rerouting of metabolism through the use of alternate enzymes to adjust pathway flux and accomplish specific anabolic or catabolic objectives. Here, we report the first characterization of two parallel pathways for the breakdown of the short chain fatty acid propionate in Caenorhabditis elegans. Using genetic interaction mapping, gene co-expression analysis, pathway intermediate quantification and carbon tracing, we uncover a vitamin B12-independent propionate breakdown shunt that is transcriptionally activated on vitamin B12 deficient diets, or under genetic conditions mimicking the human diseases propionic- and methylmalonic acidemia, in which the canonical B12-dependent propionate breakdown pathway is blocked. Our study presents the first example of transcriptional vitamin-directed metabolic network rewiring to promote survival under vitamin deficiency. The ability to reroute propionate breakdown according to B12 availability may provide C. elegans with metabolic plasticity and thus a selective advantage on different diets in the wild.
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Affiliation(s)
- Emma Watson
- Program in Systems Biology, University of Massachusetts Medical School, Worcester, United States.,Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, United States
| | | | - Michael J Hoy
- Program in Systems Biology, University of Massachusetts Medical School, Worcester, United States.,Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, United States
| | - Chi-Hua Li
- Program in Systems Biology, University of Massachusetts Medical School, Worcester, United States.,Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, United States
| | - Timo Louisse
- Program in Systems Biology, University of Massachusetts Medical School, Worcester, United States.,Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, United States
| | - Victoria Yao
- Department of Computer Science, Princeton University, Princeton, United States.,Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, United States
| | - Akihiro Mori
- Program in Systems Biology, University of Massachusetts Medical School, Worcester, United States.,Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, United States
| | - Amy D Holdorf
- Program in Systems Biology, University of Massachusetts Medical School, Worcester, United States.,Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, United States
| | - Olga G Troyanskaya
- Department of Computer Science, Princeton University, Princeton, United States.,Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, United States.,Simons Center for Data Analysis, Simons Foundation, New York, United States
| | - Markus Ralser
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom.,The Francis Crick Institute, Mill Hill Laboratory, London, United Kingdom
| | - Albertha Jm Walhout
- Program in Systems Biology, University of Massachusetts Medical School, Worcester, United States.,Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, United States
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147
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Samuel BS, Rowedder H, Braendle C, Félix MA, Ruvkun G. Caenorhabditis elegans responses to bacteria from its natural habitats. Proc Natl Acad Sci U S A 2016; 113:E3941-9. [PMID: 27317746 PMCID: PMC4941482 DOI: 10.1073/pnas.1607183113] [Citation(s) in RCA: 228] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Most Caenorhabditis elegans studies have used laboratory Escherichia coli as diet and microbial environment. Here we characterize bacteria of C. elegans' natural habitats of rotting fruits and vegetation to provide greater context for its physiological responses. By the use of 16S ribosomal DNA (rDNA)-based sequencing, we identified a large variety of bacteria in C. elegans habitats, with phyla Proteobacteria, Bacteroidetes, Firmicutes, and Actinobacteria being most abundant. From laboratory assays using isolated natural bacteria, C. elegans is able to forage on most bacteria (robust growth on ∼80% of >550 isolates), although ∼20% also impaired growth and arrested and/or stressed animals. Bacterial community composition can predict wild C. elegans population states in both rotting apples and reconstructed microbiomes: alpha-Proteobacteria-rich communities promote proliferation, whereas Bacteroidetes or pathogens correlate with nonproliferating dauers. Combinatorial mixtures of detrimental and beneficial bacteria indicate that bacterial influence is not simply nutritional. Together, these studies provide a foundation for interrogating how bacteria naturally influence C. elegans physiology.
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Affiliation(s)
- Buck S Samuel
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114
| | - Holli Rowedder
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114
| | - Christian Braendle
- CNRS, INSERM, Institute of Biology Valrose, University of Nice Sophia Antipolis, Parc Valrose, 06108 Nice, France
| | - Marie-Anne Félix
- Institute of Biology of the Ecole Normale Supérieure, CNRS UMR8197, Ecole Normale Supérieure, INSERM U1024, 75005 Paris, France
| | - Gary Ruvkun
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114;
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148
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Sánchez-Blanco A, Rodríguez-Matellán A, González-Paramás A, González-Manzano S, Kim SK, Mollinedo F. Dietary and microbiome factors determine longevity in Caenorhabditis elegans. Aging (Albany NY) 2016; 8:1513-39. [PMID: 27510225 PMCID: PMC4993345 DOI: 10.18632/aging.101008] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Accepted: 07/31/2016] [Indexed: 12/20/2022]
Abstract
Diet composition affects organismal health. Nutrient uptake depends on the microbiome. Caenorhabditis elegans fed a Bacillus subtilis diet live longer than those fed the standard Escherichia coli diet. Here we report that this longevity difference is primarily caused by dietary coQ, an antioxidant synthesized by E. coli but not by B. subtilis. CoQ-supplemented E. coli fed worms have a lower oxidation state yet live shorter than coQ-less B. subtilis fed worms. We showed that mutations affecting longevity for E. coli fed worms do not always lead to similar effects when worms are fed B. subtilis. We propose that coQ supplementation by the E. coli diet alters the worm cellular REDOX homeostasis, thus decreasing longevity. Our results highlight the importance of microbiome factors in longevity, argue that antioxidant supplementation can be detrimental, and suggest that the C. elegans standard E. coli diet can alter the effect of signaling pathways on longevity.
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Affiliation(s)
- Adolfo Sánchez-Blanco
- Instituto de Biología Molecular y Celular del Cáncer, Centro de Investigación del Cáncer, CSIC-Universidad de Salamanca, Campus Miguel de Unamuno, E-37007 Salamanca, Spain
- Current address: Department of Biology, University of Hartford, West Hartford, CT 06117, USA
| | - Alberto Rodríguez-Matellán
- Instituto de Biología Molecular y Celular del Cáncer, Centro de Investigación del Cáncer, CSIC-Universidad de Salamanca, Campus Miguel de Unamuno, E-37007 Salamanca, Spain
- Current address: Centro de Biología Molecular Severo Ochoa (CSIC-UAM), E‐28049 Madrid, Spain
| | - Ana González-Paramás
- Grupo de Investigación en Polifenoles, Facultad de Farmacia, Unidad de Nutrición y Bromatología, Universidad de Salamanca, E-37007 Salamanca, Spain
| | - Susana González-Manzano
- Grupo de Investigación en Polifenoles, Facultad de Farmacia, Unidad de Nutrición y Bromatología, Universidad de Salamanca, E-37007 Salamanca, Spain
| | - Stuart K. Kim
- Departments of Developmental Biology and Genetics, Stanford University, Stanford, CA 94305, USA
| | - Faustino Mollinedo
- Instituto de Biología Molecular y Celular del Cáncer, Centro de Investigación del Cáncer, CSIC-Universidad de Salamanca, Campus Miguel de Unamuno, E-37007 Salamanca, Spain
- Current address: Laboratory of Cell Death and Cancer Therapy, Department of Cellular and Molecular Medicine, Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas (CSIC), E-28040 Madrid, Spain
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149
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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.
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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.
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150
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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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