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Title: Characterizing Strain Variation in Engineered E. coli Using a Multi-Omics-Based Workflow

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.
Authors:
 [1] ;  [2] ;  [3] ;  [4] ;  [3] ;  [3] ;  [3] ;  [5] ;  [5] ;  [5] ;  [5] ;  [5] ;  [3] ;  [6] ;  [3] ;  [7] ;  [8] ;  [3]
  1. Joint Bioenergy Institute (JBEI), Emeryville, CA (United States); Univ. of San Diego, San Diego, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
  2. Joint Bioenergy Institute (JBEI), Emeryville, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Amyris, Emeryville, CA (United States)
  3. Joint Bioenergy Institute (JBEI), Emeryville, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
  4. Joint Bioenergy Institute (JBEI), Emeryville, CA (United States); Univ. of California, Berkeley, CA (United States)
  5. Univ. of California, San Diego, CA (United States)
  6. Univ. of California, San Diego, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
  7. Joint Bioenergy Institute (JBEI), Emeryville, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Technical Univ. of Denmark, Horsholm (Denmark); Univ. of California, Berkeley, CA (United States)
  8. Univ. of California, San Diego, CA (United States); Technical Univ. of Denmark, Horsholm (Denmark)
Publication Date:
Grant/Contract Number:
AC02-05CH11231
Type:
Published Article
Journal Name:
Cell Systems
Additional Journal Information:
Journal Volume: 2; Journal Issue: 5; Journal ID: ISSN 2405-4712
Publisher:
Elsevier
Research Org:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES
OSTI Identifier:
1358462
Alternate Identifier(s):
OSTI ID: 1326435; OSTI ID: 1393044