Grantee Research Project Results
2004 Progress Report: Collaborative Research: Metabolic Engineering of E. coli Sugar-Utilization Regulatory Systems for the Consumption of Plant Biomass Sugars
EPA Grant Number: R831441Title: Collaborative Research: Metabolic Engineering of E. coli Sugar-Utilization Regulatory Systems for the Consumption of Plant Biomass Sugars
Investigators: San, Ka-Yiu
Institution: Rice University
EPA Project Officer: Richards, April
Project Period: December 22, 2003 through December 21, 2007
Project Period Covered by this Report: December 22, 2003 through December 21, 2004
Project Amount: $200,000
RFA: Interagency Announcement of Opportunities in Metabolic Engineering (2001) RFA Text | Recipients Lists
Research Category: Technology for a Sustainable Environment , Human Health , Sustainable and Healthy Communities
Objective:
The overall objective of this collaborative project is to engineer metabolically the Escherichia coli sugar-utilization regulatory systems (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 utilize sugar mixtures (glucose, xylose, and arabinose) efficiently; (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 nuclear magnetic resonance bond-labeling experiments; (4) integrate these results using a novel genetic network-based metabolic flux analysis 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.
The specific aims of this project are: (1) develop an integrated, quantitative model that captures existing mechanistic knowledge about SURS from literature and existing data and (2) refine the model with in-house experiments from Iowa State University.
Progress Summary:
Lignocellulosic biomass, such as agricultural and wood residues, crops, and byproduct streams, provides a low-cost and uniquely sustainable resource for producing many fuels and chemicals. The microbial transformation of its constituent sugars (5- and 6-carbon sugars) into commodity chemicals is one of the most important steps in this process. This has been identified as a high-priority research area in the “Technology Vision 2020” for the U.S. chemical industry, published by the U.S. Department of Energy. The process requires an organism, such as E. coli, that is capable of fermenting sugar mixtures containing 5- and 6-carbon sugars. When E. coli is grown on sugar mixtures, the delayed and frequently incomplete consumption of other sugars, caused by the presence of glucose, results in low yields and productivities of the desired product. E. coli possesses sophisticated regulatory systems (referred to as sugar-utilization regulatory systems, SURS) that control the utilization of different sugars. SURS regulate the preferential utilization of specific sugars from a sugar mixture, the induction of several genes caused by the presence of glucose, and the direction of carbon flow.
We are designing a framework for the development of an algorithm that is capable of capturing the inner working of sugar-utilization regulatory systems in response to the availability of various carbon sources. Our current mechanistic model is based on a set of algebraic-differential equations, which describe the dynamics of various components within the systems. The approach of this algorithm is described below. We have r regulators whose activity evolves according to the mapping dgr/dt = F(gr, glu, xyl). Here glu and xyl denote glucose and xylose concentrations, respectively. These regulators, such as Mlc, CRP, cAMP, and Cra, determine the state of s structural genes via the mapping dgs/dt = G(gr). These regulators influence the expression levels of the genes code for enzymes that catalyze s reactions; flux balance on these reactions leads to the stoichiometric system S(gs(n))v = b for the s reaction rates, v, given the feed rates, b and n denote the nth instant of time. The current model is built on the knowledge reported in the literature.
Future Activities:
The next phase of the project will involve: (1) extending the current mechanistic model based on algebraic-differential equations to include more state variables to represent the actual system better; and (2) incorporating the experimental results from our Iowa State University collaborators into our model.
Journal Articles:
No journal articles submitted with this report: View all 9 publications for this projectSupplemental Keywords:
metabolic engineering, E. coli, sugar-utilization regulatory systems, SURs, genetic modification, 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 engineeringProgress and Final Reports:
Original AbstractThe perspectives, information and conclusions conveyed in research project abstracts, progress reports, final reports, journal abstracts and journal publications convey the viewpoints of the principal investigator and may not represent the views and policies of ORD and EPA. Conclusions drawn by the principal investigators have not been reviewed by the Agency.