Literature DB >> 18623053

Parametric sensitivity of stoichiometric flux balance models applied to wild-type Escherichia coli metabolism.

A Varma1, B O Palsson.   

Abstract

Stoichiometrically based flux balance models provide a method to quantify the metabolic pathway fluxes within a living cell. Predictions of flux balance models are expected to have applications in pathway engineering as well as in bioprocess design and control. These models utilize optimality principles applied to metabolic pathway stoichiometry along with the metabolic requirements for growth to determine the flux distribution in a metabolic network. A flux balance model has been developed for Escherichia coli W3110 using five experimentally determined strain-specific parameters. In this report, we determine the sensitivity of the predictions of the flux balance model to these five strain-specific parameters. Model predictions are shown to be sensitive to the two parameters describing metabolic capacity, while they are relatively insensitive to the three parameters that describe the metabolic requirements for growth. Thus, when stoichiometrically based models are formulated for additional strains one needs to measure the metabolic capacity (maximum rates of nutrient and oxygen utilization) accurately. Determination of metabolic capacity from batch experiments is relatively easy to perform. On the other hand, the harder to determine maintenance parameters need not be as accurately determined. (c) 1995 John Wiley & Sons, Inc.

Entities:  

Year:  1995        PMID: 18623053     DOI: 10.1002/bit.260450110

Source DB:  PubMed          Journal:  Biotechnol Bioeng        ISSN: 0006-3592            Impact factor:   4.530


  17 in total

1.  Expanded metabolic reconstruction of Helicobacter pylori (iIT341 GSM/GPR): an in silico genome-scale characterization of single- and double-deletion mutants.

Authors:  Ines Thiele; Thuy D Vo; Nathan D Price; Bernhard Ø Palsson
Journal:  J Bacteriol       Date:  2005-08       Impact factor: 3.490

Review 2.  Reconstruction of biochemical networks in microorganisms.

Authors:  Adam M Feist; Markus J Herrgård; Ines Thiele; Jennie L Reed; Bernhard Ø Palsson
Journal:  Nat Rev Microbiol       Date:  2008-12-31       Impact factor: 60.633

3.  A genome-scale metabolic reconstruction of Mycoplasma genitalium, iPS189.

Authors:  Patrick F Suthers; Madhukar S Dasika; Vinay Satish Kumar; Gennady Denisov; John I Glass; Costas D Maranas
Journal:  PLoS Comput Biol       Date:  2009-02-13       Impact factor: 4.475

4.  Integrating Kinetic Model of E. coli with Genome Scale Metabolic Fluxes Overcomes Its Open System Problem and Reveals Bistability in Central Metabolism.

Authors:  Ahmad A Mannan; Yoshihiro Toya; Kazuyuki Shimizu; Johnjoe McFadden; Andrzej M Kierzek; Andrea Rocco
Journal:  PLoS One       Date:  2015-10-15       Impact factor: 3.240

Review 5.  Metabolic Network Modeling of Microbial Interactions in Natural and Engineered Environmental Systems.

Authors:  Octavio Perez-Garcia; Gavin Lear; Naresh Singhal
Journal:  Front Microbiol       Date:  2016-05-18       Impact factor: 5.640

6.  Systems analysis of metabolism in the pathogenic trypanosomatid Leishmania major.

Authors:  Arvind K Chavali; Jeffrey D Whittemore; James A Eddy; Kyle T Williams; Jason A Papin
Journal:  Mol Syst Biol       Date:  2008-03-25       Impact factor: 11.429

7.  A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information.

Authors:  Adam M Feist; Christopher S Henry; Jennifer L Reed; Markus Krummenacker; Andrew R Joyce; Peter D Karp; Linda J Broadbelt; Vassily Hatzimanikatis; Bernhard Ø Palsson
Journal:  Mol Syst Biol       Date:  2007-06-26       Impact factor: 11.429

8.  Genome-scale reconstruction of the metabolic network in Staphylococcus aureus N315: an initial draft to the two-dimensional annotation.

Authors:  Scott A Becker; Bernhard Ø Palsson
Journal:  BMC Microbiol       Date:  2005-03-07       Impact factor: 3.605

9.  Flux Balance Analysis of Plant Metabolism: The Effect of Biomass Composition and Model Structure on Model Predictions.

Authors:  Huili Yuan; C Y Maurice Cheung; Peter A J Hilbers; Natal A W van Riel
Journal:  Front Plant Sci       Date:  2016-04-26       Impact factor: 5.753

10.  Parameter estimation in tree graph metabolic networks.

Authors:  Laura Astola; Hans Stigter; Maria Victoria Gomez Roldan; Fred van Eeuwijk; Robert D Hall; Marian Groenenboom; Jaap J Molenaar
Journal:  PeerJ       Date:  2016-09-20       Impact factor: 2.984

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