Journal
CELL SYSTEMS
Volume 2, Issue 5, Pages 335-346Publisher
CELL PRESS
DOI: 10.1016/j.cels.2016.04.004
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Funding
- Joint BioEnergy Institute
- US Department of Energy, Office of Science, Office of Biological and Environmental Research [DE-AC02-05CH11231]
- Swiss National Science Foundation [p2elp2_148961]
- National Institutes of Health [GM057089]
- Office of Science of the U.S. Department of Energy [DE-AC02-05CH11231]
- NNF Center for Biosustainability [Network Reconstruction] Funding Source: researchfish
- Novo Nordisk Fonden [NNF10CC1016517] Funding Source: researchfish
- Swiss National Science Foundation (SNF) [P2ELP2_148961] Funding Source: Swiss National Science Foundation (SNF)
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Understanding the complex interactions that occur between heterologous and native biochemical pathways represents a major challenge in metabolic engineering and synthetic biology. We present a workflow that integrates metabolomics, proteomics, and genome-scale models of Escherichia coli metabolism to study the effects of introducing a heterologous pathway into a microbial host. This workflow incorporates complementary approaches from computational systems biology, metabolic engineering, and synthetic biology; provides molecular insight into how the host organism microenvironment changes due to pathway engineering; and demonstrates how biological mechanisms underlying strain variation can be exploited as an engineering strategy to increase product yield. As a proof of concept, we present the analysis of eight engineered strains producing three biofuels: isopentenol, limonene, and bisabolene. Application of this workflow identified the roles of candidate genes, pathways, and biochemical reactions in observed experimental phenomena and facilitated the construction of a mutant strain with improved productivity. The contributed workflow is available as an open-source tool in the form of iPython notebooks.
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