Team:UGA-Georgia/Modeling

Our Model

Idea:

To increase geraniol yield by mapping the entire lipid biosynthesis pathway in M. maripaludis, performing a genome-scale flux balance analysis and developing strategies for the over production of isoprenoid compounds.

Results:

We designed a metabolic model (fig. 1) for isoprenoid biosynthesis based upon the complete pathway, including stoichiometric values of acetyl-CoA, ATP, and other compounds required for cell growth. The Biocyc, KEGG, IMG, and SEED databases were used to identify candidate genes/enzymesresponsible for each reaction.

In Progress:

Complete a genome-scale flux balance analysis using the COBRA toolbox in MATLAB® and develop strategies for the overproduction of isoprenoid compounds. COBRA is a systems biology approach for use in MATLAB® software capable of running simulations given any mutation, environmental condition, up/down-regulation, gene insertion/deletion, etc. After constructing the model, we may then insert new reactions of interest (e.g. geraniol synthase) and optimize specific biomass towards overproduction of isoprenoid compounds. The software will effectively calculate the most efficient ‘strain’ for our biomass query including knock-outs of unnecessary interfering genes, optimal growth conditions, and up/down regulation of particular genes.

Outlook:

Build a regulatory model for isoprenoid biosynthesis in M. maripaludis, allowing further model optimization. Using primary literature, we will identify enzyme kinetics and effectors, missing genes/enzymes and regulation upon each individual reaction.

Discussion:

Optimization of biomass production in M. maripaludis will lead us to results that demand the effective up-regulation and down-regulation of certain genes in the pathway that act upon the flux of biomass. For this to become a practical solution, one must establish a library of regulators that can provide variable levels of expression. This led us to our next project – Establishing and characterizing the first Ribosome Binding Site (RBS) library in methanogens.

Fig. 1

Image of MATLAB interface.