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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

Brunk, Elizabeth, George, Kevin W., Alonso-Gutierrez, Jorge, Thompson, Mitchell, Baidoo, Edward, Wang, George, Petzold, Christopher J., McCloskey, Douglas, Monk, Jonathan, Yang, Laurence, O’Brien, Edward J., Batth, Tanveer S., Martin, Hector  Garcia, Feist, Adam, Adams, Paul D., Keasling, Jay D., Palsson, Bernhard O., and Lee, Taek Soon. Characterizing Strain Variation in Engineered E. coli Using a Multi-Omics-Based Workflow. United States: N. p., Web. doi:10.1016/j.cels.2016.04.004.
Brunk, Elizabeth, George, Kevin W., Alonso-Gutierrez, Jorge, Thompson, Mitchell, Baidoo, Edward, Wang, George, Petzold, Christopher J., McCloskey, Douglas, Monk, Jonathan, Yang, Laurence, O’Brien, Edward J., Batth, Tanveer S., Martin, Hector  Garcia, Feist, Adam, Adams, Paul D., Keasling, Jay D., Palsson, Bernhard O., & Lee, Taek Soon. Characterizing Strain Variation in Engineered E. coli Using a Multi-Omics-Based Workflow. United States. doi:10.1016/j.cels.2016.04.004.
Brunk, Elizabeth, George, Kevin W., Alonso-Gutierrez, Jorge, Thompson, Mitchell, Baidoo, Edward, Wang, George, Petzold, Christopher J., McCloskey, Douglas, Monk, Jonathan, Yang, Laurence, O’Brien, Edward J., Batth, Tanveer S., Martin, Hector  Garcia, Feist, Adam, Adams, Paul D., Keasling, Jay D., Palsson, Bernhard O., and Lee, Taek Soon. 2016. "Characterizing Strain Variation in Engineered E. coli Using a Multi-Omics-Based Workflow". United States. doi:10.1016/j.cels.2016.04.004.
@article{osti_1358462,
title = {Characterizing Strain Variation in Engineered E. coli Using a Multi-Omics-Based Workflow},
author = {Brunk, Elizabeth and George, Kevin W. and Alonso-Gutierrez, Jorge and Thompson, Mitchell and Baidoo, Edward and Wang, George and Petzold, Christopher J. and McCloskey, Douglas and Monk, Jonathan and Yang, Laurence and O’Brien, Edward J. and Batth, Tanveer S. and Martin, Hector  Garcia and Feist, Adam and Adams, Paul D. and Keasling, Jay D. and Palsson, Bernhard O. and Lee, Taek Soon},
abstractNote = {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.},
doi = {10.1016/j.cels.2016.04.004},
journal = {Cell Systems},
number = 5,
volume = 2,
place = {United States},
year = {2016},
month = {5}
}