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Nanda S, Jacques MA, Wang W, Myers CL, Yilmaz LS, Walhout AJ. Systems-level transcriptional regulation of Caenorhabditis elegans metabolism. Mol Syst Biol 2023; 19:e11443. [PMID: 36942755 PMCID: PMC10167481 DOI: 10.15252/msb.202211443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 03/03/2023] [Accepted: 03/07/2023] [Indexed: 03/23/2023] Open
Abstract
Metabolism is controlled to ensure organismal development and homeostasis. Several mechanisms regulate metabolism, including allosteric control and transcriptional regulation of metabolic enzymes and transporters. So far, metabolism regulation has mostly been described for individual genes and pathways, and the extent of transcriptional regulation of the entire metabolic network remains largely unknown. Here, we find that three-quarters of all metabolic genes are transcriptionally regulated in the nematode Caenorhabditis elegans. We find that many annotated metabolic pathways are coexpressed, and we use gene expression data and the iCEL1314 metabolic network model to define coregulated subpathways in an unbiased manner. Using a large gene expression compendium, we determine the conditions where subpathways exhibit strong coexpression. Finally, we develop "WormClust," a web application that enables a gene-by-gene query of genes to view their association with metabolic (sub)-pathways. Overall, this study sheds light on the ubiquity of transcriptional regulation of metabolism and provides a blueprint for similar studies in other organisms, including humans.
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Affiliation(s)
- Shivani Nanda
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Marc-Antoine Jacques
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Wen Wang
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Chad L Myers
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, USA
| | - L Safak Yilmaz
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Albertha Jm Walhout
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
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Application of Caenorhabditis elegans in Lipid Metabolism Research. Int J Mol Sci 2023; 24:ijms24021173. [PMID: 36674689 PMCID: PMC9860639 DOI: 10.3390/ijms24021173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 01/01/2023] [Accepted: 01/05/2023] [Indexed: 01/11/2023] Open
Abstract
Over the last decade, the development and prevalence of obesity have posed a serious public health risk, which has prompted studies on the regulation of adiposity. With the ease of genetic manipulation, the diversity of the methods for characterizing body fat levels, and the observability of feeding behavior, Caenorhabditis elegans (C. elegans) is considered an excellent model for exploring energy homeostasis and the regulation of the cellular fat storage. In addition, the homology with mammals in the genes related to the lipid metabolism allows many aspects of lipid modulation by the regulators of the central nervous system to be conserved in this ideal model organism. In recent years, as the complex network of genes that maintain an energy balance has been gradually expanded and refined, the regulatory mechanisms of lipid storage have become clearer. Furthermore, the development of methods and devices to assess the lipid levels has become a powerful tool for studies in lipid droplet biology and the regulation of the nematode lipid metabolism. Herein, based on the rapid progress of C. elegans lipid metabolism-related studies, this review outlined the lipid metabolic processes, the major signaling pathways of fat storage regulation, and the primary experimental methods to assess the lipid content in nematodes. Therefore, this model system holds great promise for facilitating the understanding, management, and therapies of human obesity and other metabolism-related diseases.
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Bhattacharya S, Horowitz BB, Zhang J, Li X, Zhang H, Giese GE, Holdorf AD, Walhout AJ. A metabolic regulatory network for the Caenorhabditis elegans intestine. iScience 2022; 25:104688. [PMID: 35847555 PMCID: PMC9283940 DOI: 10.1016/j.isci.2022.104688] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 06/12/2022] [Accepted: 06/24/2022] [Indexed: 11/12/2022] Open
Abstract
Metabolic perturbations can affect gene expression, for instance to rewire metabolism. While numerous efforts have measured gene expression in response to individual metabolic perturbations, methods that determine all metabolic perturbations that affect the expression for a given gene or set of genes have not been available. Here, we use a gene-centered approach to derive a first-pass metabolic regulatory network for Caenorhabditis elegans by performing RNAi of more than 1,400 metabolic genes with a set of 19 promoter reporter strains that express a fluorescent protein in the animal's intestine. We find that metabolic perturbations generally increase promoter activity, which contrasts with transcription factor (TF) RNAi, which tends to repress promoter activity. We identify several TFs that modulate promoter activity in response to perturbations of the electron transport chain and explore complex genetic interactions among metabolic pathways. This work provides a blueprint for a systems-level understanding of how metabolism affects gene expression.
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Affiliation(s)
- Sushila Bhattacharya
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Brent B. Horowitz
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Jingyan Zhang
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Xuhang Li
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Hefei Zhang
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Gabrielle E. Giese
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Amy D. Holdorf
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Albertha J.M. Walhout
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
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Workflow for Segmentation of Caenorhabditis elegans from Fluorescence Images for the Quantitation of Lipids. APPLIED SCIENCES-BASEL 2021. [DOI: 10.3390/app112311420] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The small and transparent nematode Caenorhabditis elegans is increasingly employed for phenotypic in vivo chemical screens. The influence of compounds on worm body fat stores can be assayed with Nile red staining and imaging. Segmentation of C. elegans from fluorescence images is hereby a primary task. In this paper, we present an image-processing workflow that includes machine-learning-based segmentation of C. elegans directly from fluorescence images and quantifies their Nile red lipid-derived fluorescence. The segmentation is based on a J48 classifier using pixel entropies and is refined by size-thresholding. The accuracy of segmentation was >90% in our external validation. Binarization with a global threshold set to the brightness of the vehicle control group worms of each experiment allows a robust and reproducible quantification of worm fluorescence. The workflow is available as a script written in the macro language of imageJ, allowing the user additional manual control of classification results and custom specification settings for binarization. Our approach can be easily adapted to the requirements of other fluorescence image-based experiments with C. elegans.
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5
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Zeng L, Li X, Preusch CB, He GJ, Xu N, Cheung TH, Qu J, Mak HY. Nuclear receptors NHR-49 and NHR-79 promote peroxisome proliferation to compensate for aldehyde dehydrogenase deficiency in C. elegans. PLoS Genet 2021; 17:e1009635. [PMID: 34237064 PMCID: PMC8291716 DOI: 10.1371/journal.pgen.1009635] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 07/20/2021] [Accepted: 06/02/2021] [Indexed: 12/26/2022] Open
Abstract
The intracellular level of fatty aldehydes is tightly regulated by aldehyde dehydrogenases to minimize the formation of toxic lipid and protein adducts. Importantly, the dysregulation of aldehyde dehydrogenases has been implicated in neurologic disorder and cancer in humans. However, cellular responses to unresolved, elevated fatty aldehyde levels are poorly understood. Here, we report that ALH-4 is a C. elegans aldehyde dehydrogenase that specifically associates with the endoplasmic reticulum, mitochondria and peroxisomes. Based on lipidomic and imaging analysis, we show that the loss of ALH-4 increases fatty aldehyde levels and reduces fat storage. ALH-4 deficiency in the intestine, cell-nonautonomously induces NHR-49/NHR-79-dependent hypodermal peroxisome proliferation. This is accompanied by the upregulation of catalases and fatty acid catabolic enzymes, as indicated by RNA sequencing. Such a response is required to counteract ALH-4 deficiency since alh-4; nhr-49 double mutant animals are sterile. Our work reveals unexpected inter-tissue communication of fatty aldehyde levels and suggests pharmacological modulation of peroxisome proliferation as a therapeutic strategy to tackle pathology related to excess fatty aldehydes. Fatty aldehydes are generated during the turnover of membrane lipids and when cells are under oxidative stress. Because excess fatty aldehydes form toxic adducts with proteins and lipids, their levels are tightly controlled by a family of aldehyde dehydrogenases whose dysfunction has been implicated in genetic disease and cancer in humans. Here, we characterize mutant C. elegans that lack a conserved, membrane-associated aldehyde dehydrogenase ALH-4. Despite elevated levels of fatty aldehydes, these mutant worms survive by increasing the abundance of peroxisomes, which are important organelles for lipid metabolism. Such peroxisome proliferative response depends on the activation of transcription factors NHR-49 and NHR-79, via putative endocrine signals. Accordingly, the fertility of alh-4 mutant worms relies on NHR-49. Our work suggests a latent mechanism that may be activated during aldehyde dehydrogenase deficiency.
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Affiliation(s)
- Lidan Zeng
- Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Xuesong Li
- Biophotonics Research Laboratory, Department of Electronic and Computer Engineering, The Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Christopher B. Preusch
- Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Gary J. He
- Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Ningyi Xu
- The MOE Key Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang, China
| | - Tom H. Cheung
- Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong SAR, China
- Center for Stem Cell Research, The Hong Kong University of Science and Technology, Hong Kong SAR, China
- State Key Laboratory in Molecular Neuroscience, The Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Jianan Qu
- Biophotonics Research Laboratory, Department of Electronic and Computer Engineering, The Hong Kong University of Science and Technology, Hong Kong SAR, China
| | - Ho Yi Mak
- Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong SAR, China
- * E-mail:
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Andrews DGH. A new method for measuring the size of nematodes using image processing. Biol Methods Protoc 2020; 5:bpz020. [PMID: 32161812 PMCID: PMC6994075 DOI: 10.1093/biomethods/bpz020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 12/03/2019] [Accepted: 12/18/2019] [Indexed: 11/14/2022] Open
Abstract
Many studies have been made on nematodes, especially Caenorhabditis Elegans, which are used as a model organism. In many studies, the size of the nematode is important. This article describes a method of measuring the length, volume and surface area of nematodes from photographs. The method uses the imaging software ImageJ, which is in the public domain. Two macros are described. The first converts the images into binary form, and the second uses several built-in functions to measure the length of the worm and its diameter along its length. If it is assumed that the worm has a circular cross-section, then the volume and surface area of the nematode can be calculated. This is a cheap and easy technique.
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Affiliation(s)
- David G H Andrews
- School of Engineering, Technology and Design, Canterbury Christ Church University, North Holmes Road, Canterbury CT1 1QU, UK
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Jia X, Xu M, Yang A, Zhao Y, Liu D, Huang J, Proksch P, Lin W. Reducing Effect of Farnesylquinone on Lipid Mass in C. elegans by Modulating Lipid Metabolism. Mar Drugs 2019; 17:md17060336. [PMID: 31195687 PMCID: PMC6627328 DOI: 10.3390/md17060336] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 05/23/2019] [Accepted: 05/29/2019] [Indexed: 11/17/2022] Open
Abstract
Bioassay-guided fractionation of marine-derived fungi revealed that the EtOAc fraction from the fermentation broth of a mutated fungal strain Streptomyces nitrosporeus YBH10-5 had lipid-lowering effects in HepG2 cells. Chromatographic separation of the EtOAc fraction resulted in the isolation of 11 PKS-based derivatives, including a structurally unique meroterpenoid namely nitrosporeunol H (1). The structure of compound 1 was determined by the analysis of spectroscopic data. Further bioassay resulted in farnesylquinone (2) and its analogues to exert in vivo fat-reducing effects in C.elegans worm model. The underlying mode of action of compound 2 in the context of live worms was investigated, uncovering that compound 2 enhanced the mitochondrial β-oxidation rate and changed the transcriptional level of energy metabolism genes. Additional experiments revealed that compound 2 exerted its effects in C. elegans partially through repressing FAT-5, an isoform of stearoyl-CoA desaturase (SCD) which catalyzes the conversion of saturated fatty acids to monounsaturated fatty acids, thereafter leading to the modification of the fatty acid profile. Thus, compound 2 was suggested to be a promising lead for further optimization to treat obesity.
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Affiliation(s)
- Xihua Jia
- State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing 100191, China.
| | - Manglin Xu
- State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing 100191, China.
| | - Aigang Yang
- State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing 100191, China.
| | - Yan Zhao
- State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing 100191, China.
| | - Dong Liu
- State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing 100191, China.
| | - Jian Huang
- State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing 100191, China.
| | - Peter Proksch
- Institute für Pharmazeutische Biologie und Biotechnologie, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany.
| | - Wenhan Lin
- State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing 100191, China.
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