A Caenorhabditis elegans Genome-Scale Metabolic Network Model
Program in Systems Biology; Program in Molecular Medicine; UMass Metabolic Network
Cellular and Molecular Physiology | Computational Biology | Genomics | Systems and Integrative Physiology | Systems Biology
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.
DOI of Published Version
Cell Syst. 2016 May 25;2(5):297-311. doi: 10.1016/j.cels.2016.04.012. Epub 2016 May 19. Link to article on publisher's site
Yilmaz LS, Walhout AJ. (2016). A Caenorhabditis elegans Genome-Scale Metabolic Network Model. Systems Biology Publications. https://doi.org/10.1016/j.cels.2016.04.012. Retrieved from https://escholarship.umassmed.edu/sysbio_pubs/89