Thermodynamically constrained Flux and Control Analysis of Escherichia coli

Liliana Angeles-Martineza; Michael Binns; Constantinos Theodoropoulos; Pedro de Atauri; Marta Cascante

doi:10.1016/B978-0-444-59520-1.50134-2

Thermodynamically constrained Flux and Control Analysis of Escherichia coli

Liliana Angeles-Martineza, Michael Binns, Constantinos Theodoropoulos, Pedro de Atauri, Marta Cascante

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

Abstract

Flux Balance Analysis allows calculation of the theoretical maximum yield of desired products given a metabolic network and some experimentally determined fluxes. However these " optimal" values are often based on thermodynamically infeasible flux distributions. A methodology for the optimisation of fluxes and concentrations subject to thermodynamic constraints is implemented and applied to Escherichia coli to calculate the ranges of possible fluxes and concentrations. The resulting flux bounds together with a random sampling approach to calculate ranges of possible control coefficients, summarised using the control bias concept, are used in this work to indicate potential targets for improving the production of succinic acid with the aid of this organism. The steps with the highest control bias were found to be the glycerol uptake and the steps that bypass the pentose-phosphate pathway. The steps showing strongest negative control were the CO 2 extraction from the system and reactions redirecting pyruvate towards byproducts such as ethanol and formate and away from succinic acid. © 2012 Elsevier B.V.

Original language	English
Title of host publication	Computer Aided Chemical Engineering\|Comput. Aided Chem. Eng.
Publisher	Elsevier BV
Pages	1377-1381
Number of pages	4
Volume	30
DOIs	https://doi.org/10.1016/B978-0-444-59520-1.50134-2
Publication status	Published - 2012
Event	22nd European Symposium on Computer Aided Process Engineering - University College London, Gower Street, London, UK, WC1E 6BT Duration: 17 Jun 2012 → 20 Jun 2012

Conference

Conference	22nd European Symposium on Computer Aided Process Engineering
City	University College London, Gower Street, London, UK, WC1E 6BT
Period	17/06/12 → 20/06/12

Keywords

Escherichia coli
Flux and Control Analysis
Thermodynamics

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10.1016/B978-0-444-59520-1.50134-2

Cite this

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title = "Thermodynamically constrained Flux and Control Analysis of Escherichia coli",

abstract = "Flux Balance Analysis allows calculation of the theoretical maximum yield of desired products given a metabolic network and some experimentally determined fluxes. However these {"} optimal{"} values are often based on thermodynamically infeasible flux distributions. A methodology for the optimisation of fluxes and concentrations subject to thermodynamic constraints is implemented and applied to Escherichia coli to calculate the ranges of possible fluxes and concentrations. The resulting flux bounds together with a random sampling approach to calculate ranges of possible control coefficients, summarised using the control bias concept, are used in this work to indicate potential targets for improving the production of succinic acid with the aid of this organism. The steps with the highest control bias were found to be the glycerol uptake and the steps that bypass the pentose-phosphate pathway. The steps showing strongest negative control were the CO 2 extraction from the system and reactions redirecting pyruvate towards byproducts such as ethanol and formate and away from succinic acid. {\textcopyright} 2012 Elsevier B.V.",

keywords = "Escherichia coli, Flux and Control Analysis, Thermodynamics",

author = "Liliana Angeles-Martineza and Michael Binns and Constantinos Theodoropoulos and {de Atauri}, Pedro and Marta Cascante",

year = "2012",

doi = "10.1016/B978-0-444-59520-1.50134-2",

language = "English",

volume = "30",

pages = "1377--1381",

booktitle = "Computer Aided Chemical Engineering|Comput. Aided Chem. Eng.",

publisher = "Elsevier BV",

address = "Netherlands",

note = "22nd European Symposium on Computer Aided Process Engineering ; Conference date: 17-06-2012 Through 20-06-2012",

}

Angeles-Martineza, L, Binns, M, Theodoropoulos, C, de Atauri, P & Cascante, M 2012, Thermodynamically constrained Flux and Control Analysis of Escherichia coli. in Computer Aided Chemical Engineering|Comput. Aided Chem. Eng.. vol. 30, Elsevier BV, pp. 1377-1381, 22nd European Symposium on Computer Aided Process Engineering, University College London, Gower Street, London, UK, WC1E 6BT, 17/06/12. https://doi.org/10.1016/B978-0-444-59520-1.50134-2

TY - GEN

T1 - Thermodynamically constrained Flux and Control Analysis of Escherichia coli

AU - Angeles-Martineza, Liliana

AU - Binns, Michael

AU - Theodoropoulos, Constantinos

AU - de Atauri, Pedro

AU - Cascante, Marta

PY - 2012

Y1 - 2012

N2 - Flux Balance Analysis allows calculation of the theoretical maximum yield of desired products given a metabolic network and some experimentally determined fluxes. However these " optimal" values are often based on thermodynamically infeasible flux distributions. A methodology for the optimisation of fluxes and concentrations subject to thermodynamic constraints is implemented and applied to Escherichia coli to calculate the ranges of possible fluxes and concentrations. The resulting flux bounds together with a random sampling approach to calculate ranges of possible control coefficients, summarised using the control bias concept, are used in this work to indicate potential targets for improving the production of succinic acid with the aid of this organism. The steps with the highest control bias were found to be the glycerol uptake and the steps that bypass the pentose-phosphate pathway. The steps showing strongest negative control were the CO 2 extraction from the system and reactions redirecting pyruvate towards byproducts such as ethanol and formate and away from succinic acid. © 2012 Elsevier B.V.

AB - Flux Balance Analysis allows calculation of the theoretical maximum yield of desired products given a metabolic network and some experimentally determined fluxes. However these " optimal" values are often based on thermodynamically infeasible flux distributions. A methodology for the optimisation of fluxes and concentrations subject to thermodynamic constraints is implemented and applied to Escherichia coli to calculate the ranges of possible fluxes and concentrations. The resulting flux bounds together with a random sampling approach to calculate ranges of possible control coefficients, summarised using the control bias concept, are used in this work to indicate potential targets for improving the production of succinic acid with the aid of this organism. The steps with the highest control bias were found to be the glycerol uptake and the steps that bypass the pentose-phosphate pathway. The steps showing strongest negative control were the CO 2 extraction from the system and reactions redirecting pyruvate towards byproducts such as ethanol and formate and away from succinic acid. © 2012 Elsevier B.V.

KW - Escherichia coli

KW - Flux and Control Analysis

KW - Thermodynamics

U2 - 10.1016/B978-0-444-59520-1.50134-2

DO - 10.1016/B978-0-444-59520-1.50134-2

M3 - Conference contribution

VL - 30

SP - 1377

EP - 1381

BT - Computer Aided Chemical Engineering|Comput. Aided Chem. Eng.

PB - Elsevier BV

T2 - 22nd European Symposium on Computer Aided Process Engineering

Y2 - 17 June 2012 through 20 June 2012

ER -

Thermodynamically constrained Flux and Control Analysis of Escherichia coli

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Keywords

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