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

Research output: Contribution to journal › Journal article › Research › peer-review

Standard

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

In: Cell Systems, Vol. 2, No. 5, 2016, p. 335-346.

Research output: Contribution to journal › Journal article › Research › peer-review

Harvard

Brunk, E, George, KW, Alonso-Gutierrez, J, Thompson, M, Baidoo, E, Wang, G, Petzold, CJ, McCloskey, D, Monk, J, Yang, L, O'Brien, EJ, Batth, TS, Martin, HG, Feist, A, Adams, PD, Keasling, JD, Palsson, BO & Lee, TS 2016, 'Characterizing Strain Variation in Engineered E. coli Using a Multi-Omics-Based Workflow', Cell Systems, vol. 2, no. 5, pp. 335-346. https://doi.org/10.1016/j.cels.2016.04.004

APA

Brunk, E., George, K. W., Alonso-Gutierrez, J., Thompson, M., Baidoo, E., Wang, G., Petzold, C. J., McCloskey, D., Monk, J., Yang, L., O'Brien, E. J., Batth, T. S., Martin, H. G., Feist, A., Adams, P. D., Keasling, J. D., Palsson, B. O., & Lee, T. S. (2016). Characterizing Strain Variation in Engineered E. coli Using a Multi-Omics-Based Workflow. Cell Systems, 2(5), 335-346. https://doi.org/10.1016/j.cels.2016.04.004

Vancouver

Brunk E, George KW, Alonso-Gutierrez J, Thompson M, Baidoo E, Wang G et al. Characterizing Strain Variation in Engineered E. coli Using a Multi-Omics-Based Workflow. Cell Systems. 2016;2(5):335-346. https://doi.org/10.1016/j.cels.2016.04.004

Author

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. In: Cell Systems. 2016 ; Vol. 2, No. 5. pp. 335-346.

Bibtex

@article{453bf531f741458e897b804d51174ef1,
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.",
author = "Elizabeth Brunk and George, {Kevin W} and Jorge Alonso-Gutierrez and Mitchell Thompson and Edward Baidoo and George Wang and Petzold, {Christopher J} and Douglas McCloskey and Jonathan Monk and Laurence Yang and O'Brien, {Edward J} and Batth, {Tanveer S.} and Martin, {Hector Garcia} and Adam Feist and Adams, {Paul D} and Keasling, {Jay D} and Palsson, {Bernhard O} and Lee, {Taek Soon}",
note = "Copyright {\textcopyright} 2016 Elsevier Inc. All rights reserved.",
year = "2016",
doi = "10.1016/j.cels.2016.04.004",
language = "English",
volume = "2",
pages = "335--346",
journal = "Cell Systems",
issn = "2405-4712",
publisher = "Cell Press",
number = "5",

}

RIS

TY - JOUR

T1 - Characterizing Strain Variation in Engineered E. coli Using a Multi-Omics-Based Workflow

AU - Brunk, Elizabeth

AU - George, Kevin W

AU - Alonso-Gutierrez, Jorge

AU - Thompson, Mitchell

AU - Baidoo, Edward

AU - Wang, George

AU - Petzold, Christopher J

AU - McCloskey, Douglas

AU - Monk, Jonathan

AU - Yang, Laurence

AU - O'Brien, Edward J

AU - Batth, Tanveer S.

AU - Martin, Hector Garcia

AU - Feist, Adam

AU - Adams, Paul D

AU - Keasling, Jay D

AU - Palsson, Bernhard O

AU - Lee, Taek Soon

N1 - Copyright © 2016 Elsevier Inc. All rights reserved.

PY - 2016

Y1 - 2016

N2 - 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.

AB - 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.

U2 - 10.1016/j.cels.2016.04.004

DO - 10.1016/j.cels.2016.04.004

M3 - Journal article

C2 - 27211860

VL - 2

SP - 335

EP - 346

JO - Cell Systems

JF - Cell Systems

SN - 2405-4712

IS - 5

ER -

ID: 204046309