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

Research output: Contribution to journalJournal articleResearchpeer-review

  • Elizabeth Brunk
  • Kevin W George
  • Jorge Alonso-Gutierrez
  • Mitchell Thompson
  • Edward Baidoo
  • George Wang
  • Christopher J Petzold
  • Douglas McCloskey
  • Jonathan Monk
  • Laurence Yang
  • Edward J O'Brien
  • Batth, Tanveer Singh
  • Hector Garcia Martin
  • Adam Feist
  • Paul D Adams
  • Jay D Keasling
  • Bernhard O Palsson
  • Taek Soon Lee

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.

Original languageEnglish
JournalCell Systems
Volume2
Issue number5
Pages (from-to)335-46
Number of pages12
ISSN2405-4712
DOIs
Publication statusPublished - 25 May 2016

ID: 204046309