Thrust 2: Microbial Metabolic Engineering

CBiRC has assembled a world-class team of scientists that are well known for their work on microbial metabolic engineering. The team is focused on developing microbial platform technologies with the aim of redirecting the process of fatty acid assembly. The team focuses on strain characterization and optimization combined with analysis of flux, bioinformatics, proteomics and metabolomics.

Participating faculty:

  1. Nancy A. Da Silva (Thrust Leader), Chemical Engineering & Materials Science, University of California – Irvine
  2. Laura R. Jarboe (Thrust Co-Leader), Chemical & Biological Engineering, Iowa State University
  3. Julie A. Dickerson, Electrical & Computer Engineering, Iowa State University
  4. Ramon Gonzalez, Chemical & Biomolecular Engineering, W. M. Rice University
  5. Costas D. Maranas, Chemical Engineering, Pennsylvania State University
  6. Ka-Yiu San, Bioengineering, W. M. Rice University
  7. Suzanne B. Sandmeyer, Biological Chemistry, University of California –Irvine
  8. Jacqueline V. Shanks, Chemical & Biological Engineering, Iowa State University
  9. Zengyi Shao, Chemical & Biological Engineering, Iowa State University

Overview of technologies:

While the discovery of new pathways for the synthesis of small molecules with novel structures is a critical first step, significant effort is still required to develop efficient microbial strains in order to produce these molecules in an economically viable manner. The focus of the microbial metabolic engineering thrust is thus to develop microbial platforms using a systems approach to produce small polyketide-based molecules by incorporating new synthesis pathways discovered from Thrust 1 at high yields, high rates, and high product titers. Specifically, the microbial production platforms will have the following properties:

Integration of new pathways into the production platforms Efficient pathway design to allow proper balance between cell growth and product formation Balanced carbon and co-factor flow Maintenance of robust performance even at high product titers Robust cell growth and address scale-up issues with industrial input.

Thrust 2 projects:

Project Lead Project Title Project Goals
Ka-Yiu San, Rice University Strain Construction and Optimization in E. coli The goal of the project is to develop metabolic engineering tools to design and construct efficient Escherichia coli strains for high level production of fatty acid-like molecules from glucose.
Nancy Da Silva, University of California–Irvine Strain Construction and Optimization in S. cerevisiae The goal of the work is to develop the required integrated techniques and tools, and to design and construct efficient Saccharomyces cerevisiae strains for high level production of fatty acidlike molecules from glucose.
Ka-Yiu San, Rice University Strain Characterization and Optimization in
E. coli
The goal of the project is to characterize the production strains under various operating conditions and to further optimize their performance. The results/data from this project will be used to design omics experiments and to guide further genetic manipulations for strain improvement.
Nancy Da Silva, University of California–Irvine Strain Characterization and Optimization in
S. cerevisiae
The goal of this work is to characterize the production strains under various operating conditions and to further optimize their performance.
Ramon Gonzalez, Rice University Omics Experiments
in E. coli
The overall goal of this project is to conduct functional genomics studies of E. coli strains engineered for the production of fatty acids and methylketones and their wild types. Functional genomics tools to be used will allow the system-wide characterization of gene and protein expression along with metabolites. These include DNA microarrays for gene expression profiling, 2-D Fluorescence Difference Gel Electrophoresis (2-D DIGE) combined with Mass Spectroscopy for protein identification and quantification of their expression levels, and Nuclear Magnetic Resonance and Mass Spectroscopy for metabolite identification and quantification. Strains engineered to produce and/or tolerate high levels of fatty acids and methylketones will be profiled using the aforementioned approaches.
Laura Jarboe, Iowa State University Omics Experiments in S. cerevisiae The goal of this project is to characterize the genome-wide properties associated with the production of and adaptation to short chain fatty acids at a high titer. Previous studies have shown that yeast is sensitive to growth inhibition by concentrations as low as 20 mg/L octanoic acid. Because a successful biocatalyst must tolerate concentrations higher than 20 mg/L, identifying and relieving these inhibitory effects is critical. Starting with the transcriptome and eventually expanding to proteomic and metabolomic analysis, these studies will aid in the identification of stress points and metabolic bottlenecks in fatty acid production. Additionally, these studies will enable further understanding of the fatty acid production pathways and their regulation.
Jackie Shanks, Iowa State University Flux Analysis in E. coli The goal of the project is to construct metabolic flux maps for E. coli and S. cerevisiae, for both the wild-type and engineered strains and under various operating conditions. The flux maps from this project will be used to guide further genetic manipulations for strain improvement.
Jackie Shanks, Iowa State University Flux Analysis in S. cerevisiae The goal of the project is to construct metabolic flux maps for E. coli and S. cerevisiae, for both the wild-type and engineered strains and under various operating conditions. The flux maps from this project will be used to guide further genetic manipulations for strain improvement.
Julie Dickerson, Iowa State University Bioinformatics in E. coli Develop models to integrated in-house omics data with existing databases to provide a system-wide view of the production strains. Develop tools based on a systems-wide approach to provide insights and suggestions for further strain improvement.
Ramon Gonzalez, Rice University Beta-Oxidation Pathway Reversal in E.coli This project aims to reconstruct a functional reversal of the beta-oxidation cycle as a platform for the synthesis of functionalized carboxylic acids.