title: Characterizing Strain Variation in Engineered E. coli Using a Multi-Omics-Based Workflow.
abstract: 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.affiliation: Joint Bioenergy Institute (JBEI), 5885 Hollis Street, Emeryville, CA 94608, USA; Department of Bioengineering, University of California, San Diego, San Diego, CA 92093, USA; Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
authors.forename: Elizabeth
authors.initials: E
authors.lastname: Brunk
authors.affiliation: Joint Bioenergy Institute (JBEI), 5885 Hollis Street, Emeryville, CA 94608, USA; Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
authors.forename: Kevin W
authors.initials: KW
authors.lastname: George
authors.affiliation: Joint Bioenergy Institute (JBEI), 5885 Hollis Street, Emeryville, CA 94608, USA; Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
authors.forename: Jorge
authors.initials: J
authors.lastname: Alonso-Gutierrez
authors.affiliation: Joint Bioenergy Institute (JBEI), 5885 Hollis Street, Emeryville, CA 94608, USA; Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA.
authors.forename: Mitchell
authors.initials: M
authors.lastname: Thompson
authors.affiliation: Joint Bioenergy Institute (JBEI), 5885 Hollis Street, Emeryville, CA 94608, USA; Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
authors.forename: Edward
authors.initials: E
authors.lastname: Baidoo
authors.affiliation: Joint Bioenergy Institute (JBEI), 5885 Hollis Street, Emeryville, CA 94608, USA; Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
authors.forename: George
authors.initials: G
authors.lastname: Wang
authors.affiliation: Joint Bioenergy Institute (JBEI), 5885 Hollis Street, Emeryville, CA 94608, USA; Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
authors.forename: Christopher J
authors.initials: CJ
authors.lastname: Petzold
authors.affiliation: Department of Bioengineering, University of California, San Diego, San Diego, CA 92093, USA.
authors.forename: Douglas
authors.initials: D
authors.lastname: McCloskey
authors.affiliation: Department of Bioengineering, University of California, San Diego, San Diego, CA 92093, USA.
authors.forename: Jonathan
authors.initials: J
authors.lastname: Monk
authors.affiliation: Department of Bioengineering, University of California, San Diego, San Diego, CA 92093, USA.
authors.forename: Laurence
authors.initials: L
authors.lastname: Yang
authors.affiliation: Department of Bioengineering, University of California, San Diego, San Diego, CA 92093, USA.
authors.forename: Edward J
authors.initials: EJ
authors.lastname: O'Brien
authors.affiliation: Joint Bioenergy Institute (JBEI), 5885 Hollis Street, Emeryville, CA 94608, USA.
authors.forename: Tanveer S
authors.initials: TS
authors.lastname: Batth
authors.affiliation: Joint Bioenergy Institute (JBEI), 5885 Hollis Street, Emeryville, CA 94608, USA; Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
authors.forename: Hector Garcia
authors.initials: HG
authors.lastname: Martin
authors.affiliation: Department of Bioengineering, University of California, San Diego, San Diego, CA 92093, USA; Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
authors.forename: Adam
authors.initials: A
authors.lastname: Feist
authors.affiliation: Joint Bioenergy Institute (JBEI), 5885 Hollis Street, Emeryville, CA 94608, USA; Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
authors.forename: Paul D
authors.initials: PD
authors.lastname: Adams
authors.affiliation: Joint Bioenergy Institute (JBEI), 5885 Hollis Street, Emeryville, CA 94608, USA; Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2970 Horsholm, Denmark; Department of Chemical & Biomolecular Engineering, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA.
authors.forename: Jay D
authors.initials: JD
authors.lastname: Keasling
authors.affiliation: Department of Bioengineering, University of California, San Diego, San Diego, CA 92093, USA; The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2970 Horsholm, Denmark. Electronic address: palsson@eng.ucsd.edu.
authors.forename: Bernhard O
authors.initials: BO
authors.lastname: Palsson
authors.affiliation: Joint Bioenergy Institute (JBEI), 5885 Hollis Street, Emeryville, CA 94608, USA; Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA. Electronic address: tslee@lbl.gov.
authors.forename: Taek Soon
authors.initials: TS
authors.lastname: Lee
mesh_terms: D056804:Biofuels; D019295:Computational Biology; D004926:Escherichia coli; D029968:Escherichia coli Proteins; D060847:Metabolic Engineering; D008954:Models, Biological; D058615:Synthetic Biology; D057188:Workflow
chemical_list: D056804:Biofuels; D029968:Escherichia coli Proteins