scholarly journals Simulation of Escherichia coli Dynamics in Biofilms and Submerged Colonies with an Individual-Based Model Including Metabolic Network Information

2017 ◽  
Vol 8 ◽  
Author(s):  
Ignace L. M. M. Tack ◽  
Philippe Nimmegeers ◽  
Simen Akkermans ◽  
Ihab Hashem ◽  
Jan F. M. Van Impe
Keyword(s):  
Escherichia Coli ◽  
Metabolic Network ◽  
Individual Based Model ◽  
Network Information

scholarly journals A low-complexity metabolic network model for the respiratory and fermentative metabolism of Escherichia coli

PLoS ONE ◽  
2018 ◽  
Vol 13 (8) ◽  
pp. e0202565 ◽  
Author(s):  
Ignace L. M. M. Tack ◽  
Philippe Nimmegeers ◽  
Simen Akkermans ◽  
Filip Logist ◽  
Jan F. M. Van Impe
Keyword(s):  
Escherichia Coli ◽  
Metabolic Network ◽  
Network Model ◽  
Low Complexity ◽  
Fermentative Metabolism ◽  
Metabolic Network Model

scholarly journals Global metabolic network reorganization by adaptive mutations allows fast growth of Escherichia coli on glycerol

2014 ◽  
Vol 5 (1) ◽  
Author(s):  
Kian-Kai Cheng ◽  
Baek-Seok Lee ◽  
Takeshi Masuda ◽  
Takuro Ito ◽  
Kazutaka Ikeda ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Metabolic Network ◽  
Fast Growth ◽  
Adaptive Mutations

Prospecting hydrogen production of Escherichia coli by metabolic network modeling

2013 ◽  
Vol 38 (27) ◽  
pp. 11780-11789 ◽  
Author(s):  
Jenni J. Seppälä ◽  
Antti Larjo ◽  
Tommi Aho ◽  
Olli Yli-Harja ◽  
Matti T. Karp ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Hydrogen Production ◽  
Metabolic Network ◽  
Network Modeling ◽  
Metabolic Network Modeling

scholarly journals An Unexpected Route to an Essential Cofactor:Escherichia coliRelies on Threonine for Thiamine Biosynthesis

mBio ◽  
2016 ◽  
Vol 7 (1) ◽  
Author(s):  
Jannell V. Bazurto ◽  
Kristen R. Farley ◽  
Diana M. Downs
Keyword(s):  
Escherichia Coli ◽  
Metabolic Network ◽  
Metabolic Networks ◽  
Thiamine Pyrophosphate ◽  
Metabolic Potential ◽  
E Coli ◽  
Regulatory Strategies ◽  
Phosphoribosylpyrophosphate Amidotransferase ◽  
Pyrimidine Moiety ◽  
Thiamine Biosynthesis

ABSTRACTMetabolism consists of biochemical reactions that are combined to generate a robust metabolic network that can respond to perturbations and also adapt to changing environmental conditions.Escherichia coliandSalmonella entericaare closely related enterobacteria that share metabolic components, pathway structures, and regulatory strategies. The synthesis of thiamine inS. entericahas been used to define a node of the metabolic network by analyzing alternative inputs to thiamine synthesis from diverse metabolic pathways. To assess the conservation of metabolic networks in organisms with highly conserved components, metabolic contributions to thiamine synthesis inE. coliwere investigated. Unexpectedly, we found that, unlikeS. enterica,E. colidoes not use the phosphoribosylpyrophosphate (PRPP) amidotransferase (PurF) as the primary enzyme for synthesis of phosphoribosylamine (PRA).In fact, our data showed that up to 50% of the PRA used byE. colito make thiamine requires the activities of threonine dehydratase (IlvA) and anthranilate synthase component II (TrpD). Significantly, the IlvA- and TrpD-dependent pathway to PRA functions inS. entericaonly in the absence of a functionalreactiveintermediatedeaminase (RidA) enzyme, bringing into focus how these closely related bacteria have distinct metabolic networks.IMPORTANCEIn most bacteria, includingSalmonellastrains andEscherichia coli, synthesis of the pyrimidine moiety of the essential coenzyme, thiamine pyrophosphate (TPP), shares enzymes with the purine biosynthetic pathway. Phosphoribosylpyrophosphate amidotransferase, encoded by thepurFgene, generates phosphoribosylamine (PRA) and is considered the first enzyme in the biosynthesis of purines and the pyrimidine moiety of TPP. We show here that, unlikeSalmonella,E. colisynthesizes significant thiamine from PRA derived from threonine using enzymes from the isoleucine and tryptophan biosynthetic pathways. These data show that two closely related organisms can have distinct metabolic network structures despite having similar enzyme components, thus emphasizing caveats associated with predicting metabolic potential from genome content.

scholarly journals Hybrid dynamic modeling of Escherichia coli central metabolic network combining Michaelis–Menten and approximate kinetic equations

Biosystems ◽  
2010 ◽  
Vol 100 (2) ◽  
pp. 150-157 ◽  
Author(s):  
Rafael S. Costa ◽  
Daniel Machado ◽  
Isabel Rocha ◽  
Eugénio C. Ferreira
Keyword(s):  
Escherichia Coli ◽  
Metabolic Network ◽  
Dynamic Modeling ◽  
Kinetic Equations

scholarly journals Analysis of Metabolic Network of Synthetic Escherichia coli Producing Linalool Using Constraint-based Modeling

2012 ◽  
Vol 11 ◽  
pp. 24-35 ◽  
Author(s):  
Iyarest Tawornsamretkit ◽  
Rattana Thanasomboon ◽  
Jittrawan Thaiprasit ◽  
Dujduan Waraho ◽  
Supapon Cheevadhanarak ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Metabolic Network ◽  
Constraint Based Modeling

scholarly journals Inactivation of Metabolic Genes Causes Short- and Long-Range dys-Regulation in Escherichia coli Metabolic Network

PLoS ONE ◽  
2013 ◽  
Vol 8 (12) ◽  
pp. e78360 ◽  
Author(s):  
Dinesh Kumar Barupal ◽  
Sang Jun Lee ◽  
Edward D. Karoly ◽  
Sankar Adhya
Keyword(s):  
Escherichia Coli ◽  
Metabolic Network ◽  
Long Range ◽  
Metabolic Genes

scholarly journals Systematic Analysis of Conservation Relations in Escherichia coli Genome-Scale Metabolic Network Reveals Novel Growth Media

2006 ◽  
Vol 90 (8) ◽  
pp. 2659-2672 ◽  
Author(s):  
Marcin Imieliński ◽  
Calin Belta ◽  
Harvey Rubin ◽  
Ádam Halász
Keyword(s):  
Escherichia Coli ◽  
Metabolic Network ◽  
Growth Media ◽  
Systematic Analysis ◽  
Genome Scale
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