Horizontal gene transfer and metabolism in Caenorhabditis elegans
Biochemistry
Animal Physiology and Biochemistry
Biological and Biomimetic Chemistry
Final Report Abstract
The metabolome is the entirety of small molecules found in an organism, a highly complex and largely uncharacterized mixture mostly resulting from the activity of diverse biosynthetic pathways. Modern mass spectrometry enables the relative quantification of thousands of metabolites at a time. The initial focus of this project was on using metabolomics to identify the role of genes that originated from horizontal gene transfer (HGT), a process in which genes from a different species are integrated into the genome of an organism. The goal was to assess the role of HGT in the metabolism of the nematode, Caenorhabditis elegans. Metabolites are detected by liquid chromatography coupled to mass spectrometry (LC/MS), with their mass-to-charge ratio and retention time defining molecular features that are used as minimal information for comparative analysis. In untargeted metabolomics, key workflow steps include LC-MS feature detection, comparative statistical analysis and structure elucidation using MS fragmentation in combination with other methods. Different software solutions were best suited for each of these steps, and it became clear that there was a need for a new computational tool that would streamline steps for identification and further investigation of metabolites. As a consequence, the focus of my work shifted towards learning to write code and building a new software tool. The result of this effort is Metaboseek, a comprehensive, interactive metabolomics platform that integrates a range of existing tools along with newly implemented data analysis functionality in a purpose-built graphical user interface. Metaboseek includes statistical analysis modules, mass spectrometry data viewers, molecular formula prediction tools and a molecular networking module that allows exploration of chemically related metabolites even when their structures are unknown. To showcase its utility, Metaboseek was successfully used to investigate the peroxisomal alpha oxidation pathway in C. elegans. This pathway is responsible for the breakdown of beta-branched fatty acids. Such compounds are found in the nematode’s diet, but some substrates of the pathway are produced through utilization of a gene that likely stems from a bacterium and has integrated into an ancestor of C. elegans via HGT. Metaboseek is an open-source software that is extensively documented and freely available.
Publications
- (2020). Deep interrogation of metabolism using a pathway-targeted click-chemistry approach. Journal of the American Chemical Society, 142(43), 18449–18459
Hoki, J. S., Le, H. H., Mellott, K. E., Zhang, Y. K., Fox, B. W., Rodrigues, P. R., Yu, Y., Helf, M. J. … Schroeder, F. C.
(See online at https://doi.org/10.1021/jacs.0c06877) - (2020). Modular metabolite assembly in caenorhabditis elegans depends on carboxylesterases and formation of lysosome-related organelles. ELife, 9(1), 1–42
Le, H. H., Wrobel, C. J. J., Cohen, S. M., Yu, J., Park, H., Helf, M. J., … Schroeder, F. C.
(See online at https://doi.org/10.7554/eLife.61886) - (2021). A Practical Guide to Metabolomics Software Development. Analytical Chemistry, 93(4), 1912–1923
Chang, H. Y., Colby, S. M., Du, X., Gomez, J. D., Helf, M. J., Kechris, K., … Young, J. D.
(See online at https://doi.org/10.1021/acs.analchem.0c03581)
