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Manipulation of the carbon storage regulator system for metabolite remodeling and biofuel production in Escherichia coli

Adrienne E McKee12, Becky J Rutherford124, Dylan C Chivian12, Edward K Baidoo12, Darmawi Juminaga12, Dwight Kuo12, Peter I Benke12, Jeffrey A Dietrich123, Suzanne M Ma12, Adam P Arkin123, Christopher J Petzold12, Paul D Adams12, Jay D Keasling1234 and Swapnil R Chhabra12*

Author Affiliations

1 Joint BioEnergy Institute, Emeryville, CA, USA

2 Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA

3 Department of Bioengineering, University of California, Berkeley, CA, USA

4 Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, USA

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Microbial Cell Factories 2012, 11:79  doi:10.1186/1475-2859-11-79

Published: 13 June 2012

Abstract

Background

Microbial engineering strategies that elicit global metabolic perturbations have the capacity to increase organism robustness for targeted metabolite production. In particular, perturbations to regulators of cellular systems that impact glycolysis and amino acid production while simultaneously decreasing fermentation by-products such as acetate and CO2 make ideal targets. Intriguingly, perturbation of the Carbon Storage Regulator (Csr) system has been previously implicated in large changes in central carbon metabolism in E. coli. Therefore, we hypothesized that perturbation of the Csr system through the CsrA-CsrB ribonucleoprotein complex might increase production of biofuels and their intermediates from heterologous pathways.

Results

We engaged the CsrA-CsrB ribonucleoprotein complex of E. coli via overexpression of CsrB. CsrB is a 350-nucleotide non-coding RNA that antagonizes CsrA, an RNA-binding protein that regulates translation of specific mRNA targets. By using shotgun proteomics and targeted metabolomics we established that elevation of CsrB levels leads to alterations in metabolite and protein levels in glycolysis, the TCA cycle and amino acid levels. Consequently, we show that such changes can be suitably applied to improve the production of desired compounds through the native fatty acid and heterologous n-butanol and isoprenoid pathways by up to two-fold. We also observed concomitant decreases in undesirable fermentation by-products such as acetate and CO2.

Conclusions

We have demonstrated that simple engineering of the RNA-based Csr global regulatory system constitutes a novel approach to obtaining pathway-independent improvements within engineered hosts. Additionally, since Csr is conserved across most prokaryotic species, this approach may also be amenable to a wide variety of production hosts.

Keywords:
Metabolic engineering; Global regulators; Heterologous pathway; Carbon storage; Biofuels; Metabolomics; Proteomics