Systems biology analysis using a genome-scale metabolic model shows that phosphine triggers global metabolic suppression in a resistant strain of<i>C. elegans</i>

Chan, Angelo H. C.; Hattwell, Jake P. N.; Ebert, Paul R.; Schirra, Horst Joachim

doi:10.1101/144386

Cited by 9 publications

(11 citation statements)

References 78 publications

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“…ElegCyc used PathwayTools (Karp et al, 2016 ), while iCEL1273 is based on a new workflow developed by the authors. Finally, in 2017 CeCon, also based on PathwayTools, was published by Ma et al ( 2017 ). Table 1 summarizes key metrics of each model.…”

Section: Resultsmentioning

confidence: 99%

“…To begin merging, ElegCyc was obtained in SBML format from the Supplementary Information of Gebauer et al ( 2016 ), and an SBML format of CeCon (Ma et al, 2017 ) was exported from Pathway Tools. The two models were then translated into the MetaNetX format (Moretti et al, 2016 ), and imported into MATLAB for merging.…”

Section: Methodsmentioning

confidence: 99%

“…One can then observe how these landscapes evolve upon mutations and in different environments, or to predict drug targets and biomarkers. For C. elegans , several such metabolic reconstructions exist (Büchel et al, 2013 ; Gebauer et al, 2016 ; Yilmaz and Walhout, 2016 ; Ma et al, 2017 ) (see Figure 1 ). We have been working with the whole community to reconcile and develop a single model, representing the best consensus of known metabolism in C. elegans .…”

Section: Introductionmentioning

confidence: 99%

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Modeling Meets Metabolomics—The WormJam Consensus Model as Basis for Metabolic Studies in the Model Organism Caenorhabditis elegans

Witting

Hastings

Rodríguez

et al. 2018

Front. Mol. Biosci.

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Metabolism is one of the attributes of life and supplies energy and building blocks to organisms. Therefore, understanding metabolism is crucial for the understanding of complex biological phenomena. Despite having been in the focus of research for centuries, our picture of metabolism is still incomplete. Metabolomics, the systematic analysis of all small molecules in a biological system, aims to close this gap. In order to facilitate such investigations a blueprint of the metabolic network is required. Recently, several metabolic network reconstructions for the model organism Caenorhabditis elegans have been published, each having unique features. We have established the WormJam Community to merge and reconcile these (and other unpublished models) into a single consensus metabolic reconstruction. In a series of workshops and annotation seminars this model was refined with manual correction of incorrect assignments, metabolite structure and identifier curation as well as addition of new pathways. The WormJam consensus metabolic reconstruction represents a rich data source not only for in silico network-based approaches like flux balance analysis, but also for metabolomics, as it includes a database of metabolites present in C. elegans, which can be used for annotation. Here we present the process of model merging, correction and curation and give a detailed overview of the model. In the future it is intended to expand the model toward different tissues and put special emphasizes on lipid metabolism and secondary metabolism including ascaroside metabolism in accordance to their central role in C. elegans physiology.

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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Modeling Meets Metabolomics—The WormJam Consensus Model as Basis for Metabolic Studies in the Model Organism Caenorhabditis elegans

Witting

Hastings

Rodríguez

et al. 2018

Front. Mol. Biosci.

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“…Several GSMs for the biomedical model organisms Caenorhabditis elegans have been described and recently merged into the WormJam consensus model [7][8][9][10]. This model aims to represent accurately the current knowledge on C. elegans metabolism to facilitate both modeling and metabolomics data analysis.…”

Section: Introductionmentioning

confidence: 99%

Suggestions for Standardized Identifiers for Fatty Acyl Compounds in Genome Scale Metabolic Models and Their Application to the WormJam Caenorhabditis elegans Model

Witting

2020

Metabolites

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Genome scale metabolic models (GSMs) are a representation of the current knowledge on the metabolism of a given organism or superorganism. They group metabolites, genes, enzymes and reactions together to form a mathematical model and representation that can be used to analyze metabolic networks in silico or used for analysis of omics data. Beside correct mass and charge balance, correct structural annotation of metabolites represents an important factor for analysis of these metabolic networks. However, several metabolites in different GSMs have no or only partial structural information associated with them. Here, a new systematic nomenclature for acyl-based metabolites such as fatty acids, acyl-carnitines, acyl-coenzymes A or acyl-carrier proteins is presented. This nomenclature enables one to encode structural details in the metabolite identifiers and improves human readability of reactions. As proof of principle, it was applied to the fatty acid biosynthesis and degradation in the Caenorhabditis elegans consensus model WormJam.

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“…During the workshop, ongoing efforts were identified that are merging and reconciling the two published models mentioned above, as well as other unpublished models developed in different labs (http://cai-gsmodel.cai.uq.edu.au), 8 into consensus reconstructions. The models are partially overlapping and far from complete; many metabolites that can be identified and quantified in C. elegans are not represented.…”

Section: Introductionmentioning

confidence: 99%

WormJam: A consensusC. elegansMetabolic Reconstruction and Metabolomics Community and Workshop Series

Hastings

Mains

Artal‐Sanz

et al. 2017

Worm

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Systems biology analysis using a genome-scale metabolic model shows that phosphine triggers global metabolic suppression in a resistant strain ofC. elegans

Cited by 9 publications

References 78 publications

Modeling Meets Metabolomics—The WormJam Consensus Model as Basis for Metabolic Studies in the Model Organism Caenorhabditis elegans

Modeling Meets Metabolomics—The WormJam Consensus Model as Basis for Metabolic Studies in the Model Organism Caenorhabditis elegans

Suggestions for Standardized Identifiers for Fatty Acyl Compounds in Genome Scale Metabolic Models and Their Application to the WormJam Caenorhabditis elegans Model

WormJam: A consensusC. elegansMetabolic Reconstruction and Metabolomics Community and Workshop Series

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