A BRG Biofuels Metabolic Engineering Project

1. A BRG Biofuels Metabolic Engineering Project Ron Caspi Mario Latendresse Peter Karp October 2010 Pathway Tools Workshop Bioinformatics Research Group SRI International Caspi@ai.sri.com Latendre@ai.sri.com Pkarp@ai.sri.com

2. Two Main Parts • This project will be conducted in the BRG group. Funded by the Department of Energy (DOE) under the direction of Peter Karp, PI • Soon to be started • The project has two main parts: • Curating MetaCyc for biofuel pathways under the supervision of Ron Caspi, co-PI; • A computational tool to infer new pathways, co-PI, Mario Latendresse. (Not biofuels specific)

3. Computational Tool • Basic statement of the problem: Given a source and target metabolites, what are the possible metabolic pathways from the source to the target in a given organism? • And rank these pathways based on their quality • And constrained these pathways: number of carbon atoms from the source to the target, length of pathway, number of genes to delete or add, and so on

4. Computational Tool Approach • Use a searching algorithm (A*) that can use expert knowledge as well as precise evaluation algorithms of the quality of pathways found • Based on • Tracing of carbon atoms in pathways. From the source to target, the number of carbon atoms can be evaluated. • Gibbs free energy of reactions will help the evaluation of the feasibility of existing and new pathways. • A prototype A*, based on compound similarity, has been written to find the shortest pathway between two compounds

5. The A* algorithm • A general searching algorithm in a tree-like search space • Uses two evaluating functions g(path) and h(rest-path) • Function g evaluates the path (length, Gibbs energy, cost of enzymes, and so on) seen so far • Function h evaluates the potential of current path (based on heuristics) to the target metabolite • Next node to search is based on the value of h: go in the best direction • Function h can use expert knowledge as well as precise calculations

6. A* Searching

7. A* Prototype Results • Found all the pathways described in the paper by McShan, Rao, Shah on Pathminer, Bioinformatics, Vol. 19, no 13, 2003. • For example, from citrate to L-histidine (E. coli) • In less than a second or a few seconds for a seven step pathways • Proof of concept since the feasibility of such pathways is not proven: not enough constrained applied so far

8. Gibbs Free Energy Computation by the Group Contribution Method • Prototype implementation of Jankowski’s method • Still needs a full evaluation

9. Curation of Biofuel Pathways in MetaCyc • Identify lignocellulose degrading enzymes and curate them into MetaCyc • Expand the coverage of hydrogenases in MetaCyc to include representatives of all known classes and subtypes • Expand MetaCyc coverage of fatty acids and lipids biosynthetic enzymes to reflect currently known metabolic and genetic information about oil production in algae and cyanobacteria • We will identify biochemically verified pathways involved in processes relevant to biofuel production

10. Graphical Extension of Pathway Tools Show complex polymers degradation processes that involve multiple enzymes attacking simultaneously a complex molecule at different sites

11. Validating the Computational Tool • The new biofuel pathways will be used to evaluate the capability of the computational tool.

12. A BRG Biofuels Metabolic Engineering Project Questions?