Open AccessCollaborative Research: Metabolic Engineering of E. coli Sugar-Utilization Regulatory Systems for the Consumption of Plant Biomass Sugars.
Author(s) -
Ramón González,
Jacqueline V. Shanks,
K-Y. San .
Publication year - 2006
Language(s) - English
Resource type - Reports
DOI - 10.2172/878340
Subject(s) - catabolite repression , metabolic engineering , metabolic network , biochemical engineering , sugar , biomass (ecology) , metabolic pathway , adaptability , xylose , flux (metallurgy) , fermentation , computational biology , lignocellulosic biomass , systems biology , microbiology and biotechnology , computer science , biology , biochemistry , chemistry , metabolism , gene , engineering , mutant , ecology , agronomy , organic chemistry
The overall objective of this project is to metabolically engineer the E. coli sugar-utilization regulatory systems (SURS) to utilize sugar mixtures obtained from plant biomass. Of particular relevance is the implementation of a metabolic engineering cycle aided by functional genomics and systems biology tools. Our findings will help in the establishment of a platform for the efficient production of fuels and chemicals from lignocellulosic sugars. Our research has improved the understanding of the role of SURS in regulating sugar utilization and several other cellular functions. For example, we discovered that Mlc, a global regulatory protein, regulates the utilization of xylose and demonstrated the existence of an important link between catabolite repression and respiratory/fermentative metabolism. The study of SURS mutants also revealed a connection between flagellar biosynthesis and catabolite repression. Several tools were also developed as part of this project. A novel tool (Elementary Network Decomposition, END) to help elucidate the network topology of regulatory systems was developed and its utility as a discovery tool was demonstrated by applying it to the SURS in E. coli. A novel method (and software) to estimate metabolic fluxes that uses labeling experiments and eliminates reliance on extracellular fluxes was also developed. Although not initially considered in the scope of this project, we have developed a novel and superior method for optimization of HPLC separation and applied it to the simultaneous quantification of different functionalities (sugars, organic acids, ethanol, etc.) present in our fermentation samples. Currently under development is a genetic network driven metabolic flux analysis framework to integrate transcriptional and flux data