Collaborative Research: Metabolic Engineering of E. coli Sugar-Utilization Regulatory Systems for the Consumption of Plant Biomass Sugars

EPA Grant Number: R831441
Title: Collaborative Research: Metabolic Engineering of E. coli Sugar-Utilization Regulatory Systems for the Consumption of Plant Biomass Sugars
Investigators: San, Ka-Yiu , Gonzalez, Ramon , Shanks, Jacqueline V.
Current Investigators: San, Ka-Yiu
Institution: Rice University , Iowa State University
Current Institution: Rice University
EPA Project Officer: Richards, April
Project Period: December 22, 2003 through December 21, 2007
Project Amount: $200,000
RFA: Interagency Announcement of Opportunities in Metabolic Engineering (2001) RFA Text |  Recipients Lists
Research Category: Technology for a Sustainable Environment , Health Effects , Sustainability


The overall objective of this project is to metabolically engineer the E. coli SURS to utilize sugar mixtures obtained from plant biomass. We will introduce specific genetic modifications to the SURS and analyze the consequences of these changes at the cellular level. The specific goals are to: (1) construct E. coli strains with modified SURS and evaluate their capability to efficiently utilize sugar mixtures (glucose, xylose and arabinose); (2) evaluate changes in the regulation of gene expression at the genomic scale resulting from engineering E. coli SURS; (3) identify functional metabolic pathways and quantify their fluxes in SURS mutants and wild type strains by using a novel flux analysis technique based on bondomer analysis of 2D NMR bond-labeling experiments; (4) integrate these results using a novel genetic network-based MFA model that combines gene expression and metabolic flux data; and (5) propose further genetic/environmental modification for improving the capacity of SURS mutants for fermenting sugar mixtures.


Metabolic engineering (ME) is a proven powerful approach to studying and optimizing fermentation processes. It consists of the following steps, all of which will be used in the proposed project: (1) construction of recombinant strains with improved properties (defined as synthesis), (2) analysis of the recombinant strains, especially their performance compared with the original strain background, and (3) design of the next target for genetic engineering. Since the SURS involve several global regulators, it is likely that its modification will result in pleiotropic effects. Therefore, tools that allow large-scale study of cellular responses to these modifications (i.e. NMR-based metabolic flux analysis, MFA, and genome-wide transcriptional analysis) will be used. A novel genetic network-based MFA model will be used to integrate the results.

Expected Results:

The benefits from this project will be two-fold. First, from an applied standpoint, the project will provide a powerful tool for designing of rational modifications of the SURS to obtain recombinant strains capable of efficiently metabolizing sugar mixtures. Second, from a fundamental standpoint, this project will contribute to a better understanding of the role of SURS in regulating both sugar utilization and several other cellular functions.

Publications and Presentations:

Publications have been submitted on this project: View all 9 publications for this project

Supplemental Keywords:

Engineering, metabolic engineering, genetic engineering, genetic regulatory circuit, bacteria, sugar, glucose, xylose, sugar mixture, sugar utilization, NMR, metabolic flux analysis, modeling, gene array, genetic regulation, pathway engineering, renewable resources., RFA, Scientific Discipline, Sustainable Industry/Business, Sustainable Environment, Technology for Sustainable Environment, Ecology and Ecosystems, gene expression patterns, plant biomass sugars, E coli Sugar-Utilization Regulatory Systems, genetic engineering

Progress and Final Reports:

  • 2004 Progress Report
  • 2005 Progress Report
  • 2006 Progress Report
  • Final Report