2015 Beckman Symposium   

Francesca Ponce

Presentation Date:
August-8-2014

Presenter:
Francesca Ponce

Title:
03 - Metabolic mapping in C. elegans

Institution:
University of Florida

Department:
Biochemistry and Molecular Biology

Description:
The €metabolome€ represents the complete set of metabolites in a cell, tissue, organ or whole organism. The nematode Caenorhabditis elegans is a powerful model system to study molecular, developmental biology and metabolic regulation. Metabolomics is a powerful means to provide a snapshot of the physiology of a system by measuring levels of its metabolome. The metabolic profiling of known C. elegans knockout mutants and the characterization of the effect of the knockout allele in a metabolic pathway can provide valuable functional genomic and metabolic data. To select the most convenient mutants and to assess the coverage of the knockout genes, we selected single allele deletion mutants from the National BioResource Project (NBRP) (1967 genes) and also gene knockouts from the C. elegans RNAi database (16257 genes) provided by Source BioScience to extend the coverage. We assigned ortholog identifiers to the genes and then mapped the knockout genes to metabolic maps in the KEGG Database (1,2) using KEGG Mapper and MBRole(3) to find the metabolic pathways that have best coverage. After selecting the most convenient mutants, we propose to utilize a new mass-spectrometry-based technique technique called isotopic ratio outlier analysis (IROA)(4) to identify the metabolites. This method will allow us to identify the accurate molecular formulas of the detected compounds and the relative concentrations of all the metabolites. Using this method, we will explore the role that each gene plays in the regulation of metabolic pathways and explain the changes in the metabolome by gene knockout perturbations. 1. Kanehisa M, Goto S. KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res. [Internet]. 2000 Jan 1 [cited 2014 Mar 24];28(1):27_30. Available from: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=102409&tool=pmcentrez&rendertype=abstract 2. Kanehisa M, Goto S, Sato Y, Kawashima M, Furumichi M, Tanabe M. Data, information, knowledge and principle: back to metabolism in KEGG. Nucleic Acids Res. [Internet]. 2014 Jan [cited 2014 Mar 22];42(Database issue):D199_205. Available from: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3965122&tool=pmcentrez&rendertype=abstract 3. Chagoyen M, Pazos F. MBRole: enrichment analysis of metabolomic data. Bioinformatics [Internet]. 2011 Mar 1 [cited 2014 Apr 1];27(5):730_1. Available from: http://www.ncbi.nlm.nih.gov/pubmed/21208985 4. Stupp GS, Clendinen CS, Ajredini R, Szewc MA, Garrett T, Menger RF, et al. Isotopic ratio outlier analysis global metabolomics of Caenorhabditis elegans. Anal. Chem. [Internet]. 2013 Dec 17 [cited 2014 Apr 1];85(24):11858_65. Available from: http://www.ncbi.nlm.nih.gov/pubmed/24274725


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