METABOLISM PROJECT The Metabolism Project will provide the experimental infrastructure (enzymology, microbiology, transcriptomics, and metabolomics) for testing the EFI's sequence/structure-based tools for predicting in vitro enzymatic activities and in vivo metabolic functions. In using those tools, the Metabolism Project will take the lead in developing integrated strategies for discovering novel metabolic pathways and providing direction for enhancing the tools.
The Specific Aims of the Metabolism Project are: 1) coordinate selection of targets for protein production by the Protein Core, protein purification and ligand screening by the Ligand Discovery Project, and integrative pathway mapping by the Modeling Project; 2) measure in vitro enzymatic activities of targets produced by the Protein Core to validate predictions from integrative pathway mapping by the Modeling Project; 3) construct null (knockout) strains of genes encoding enzymes for which in vitro activities are predicted by the Modeling Project; 4) perform targeted transcript analyses by qRT-PCR and, when appropriate, genome-wide transcriptomics by RNA-Seq to confirm predicted metabolic functions predicting by the Modeling Project; 5) analyze metabolites (metabolomics) predicted by the Modeling Project in wild type and knockout/overexpression strains under conditions in which phenotypes are observed, with the in vitro assigned activity facilitating both chromatographic fractionation of total metabolites and subsequent mass spectroscopic analysis; and 6) transfer in vitro enzymatic activities and in vivo metabolic functions to UniProt to update/correct the annotations for the individual binding proteins and enzymes in the metabolic pathways that are predicted and verified.
|Gerlt, John A (2017) Genomic Enzymology: Web Tools for Leveraging Protein Family Sequence-Function Space and Genome Context to Discover Novel Functions. Biochemistry 56:4293-4308|