Access the full text.
Sign up today, get DeepDyve free for 14 days.
Loading next page...
/lp/springer-journals/metabolic-engineering-in-silico-m6adhETOYC
References (97)
-
C. Ginther, J. Ingraham (1974)
Nucleoside diphosphokinase of Salmonella typhimurium.The Journal of biological chemistry, 249 11
-
J. Pramanik, J. Keasling (1997)
Stoichiometric model of Escherichia coli metabolism: incorporation of growth-rate dependent biomass composition and mechanistic energy requirements.Biotechnology and bioengineering, 56 4
-
J. Krömer, C. Wittmann, H. Schröder, E. Heinzle (2006)
Metabolic pathway analysis for rational design of L-methionine production by Escherichia coli and Corynebacterium glutamicum.Metabolic engineering, 8 4
-
J. Nielsen (2003)
It Is All about MetabolicFluxesJournal of Bacteriology, 185
-
(2001)
Metody modelirovaniya dinamiki molekul yarno geneticheskikh sistem . Sistemnaya komp ’ yuternaya biologiya ( Dynamics Simulation Methods for Molecular – Genetic Systems -
F. Shiraishi, M. Savageau (1992)
The tricarboxylic acid cycle in Dictyostelium discoideum. I. Formulation of alternative kinetic representations.The Journal of biological chemistry, 267 32
-
W. Leuchtenberger, K. Huthmacher, K. Drauz (2005)
Biotechnological production of amino acids and derivatives: current status and prospectsApplied Microbiology and Biotechnology, 69
-
J. Bailey (1991)
Toward a science of metabolic engineeringScience, 252
-
V. Hatzimanikatis, C. Floudas, J. Bailey (1996)
Analysis and design of metabolic reaction networks via mixed‐integer linear optimizationAiche Journal, 42
-
V. Likhoshvai, A. Ratushny (2007)
Generalized Hill Function Method for Modeling Molecular ProcessesJournal of bioinformatics and computational biology, 5 2B
-
W. Wiechert (2002)
Modeling and simulation: tools for metabolic engineering.Journal of biotechnology, 94 1
-
R. Barkovich, J. Liao (2001)
REVIEW Metabolic Engineering of IsoprenoidsMetabolic Engineering, 3
-
B. Hernández-Bermejo, V. Fairén, A. Sorribas (2000)
Power-law modeling based on least-squares criteria: consequences for system analysis and simulation.Mathematical biosciences, 167 2
-
M. Ikeda (2006)
Towards bacterial strains overproducing l-tryptophan and other aromatics by metabolic engineeringApplied Microbiology and Biotechnology, 69
-
B. Hernández-Bermejo, V. Fairén, A. Sorribas (1999)
Power-law modeling based on least-squares minimization criteria.Mathematical biosciences, 161 1-2
-
Jamey Young, K. Henne, J. Morgan, A. Konopka, D. Ramkrishna (2008)
Integrating cybernetic modeling with pathway analysis provides a dynamic, systems‐level description of metabolic controlBiotechnology and Bioengineering, 100
-
C. Staercke, F. Vliet, X. Xi, C. Rani, M. Ladjimi, A. Jacobs, F. Triniolles, G. Hervé, R. Cunin (1995)
Intramolecular transmission of the ATP regulatory signal in Escherichia coli aspartate transcarbamylase: specific involvement of a clustered set of amino acid interactions at an interface between regulatory and catalytic subunits.Journal of molecular biology, 246 1
-
A. Varma, B. Palsson (1995)
Parametric sensitivity of stoichiometric flux balance models applied to wild‐type Escherichia coli metabolismBiotechnology and Bioengineering, 45
-
J. Bailey (1998)
Mathematical Modeling and Analysis in Biochemical Engineering: Past Accomplishments and Future OpportunitiesBiotechnology Progress, 14
-
C. Chassagnole, N. Noisommit-Rizzi, J. Schmid, K. Mauch, M. Reuss (2002)
Dynamic modeling of the central carbon metabolism of Escherichia coli.Biotechnology and bioengineering, 79 1
-
V. Hatzimanikatis, Marcel Emmerling, Uwe Sauer, J. Bailey (1998)
Application of mathematical tools for metabolic design of microbial ethanol production.Biotechnology and bioengineering, 58 2-3
-
Bmc Bioinformatics, I. Nikerel, W. Winden, W. Gulik, J. Heijnen (2006)
A method for estimation of elasticities in metabolic networks using steady state and dynamic metabolomics data and linlog kineticsBMC Bioinformatics, 7
-
Q. Hua, A. Joyce, S. Fong, B. Palsson (2006)
Metabolic analysis of adaptive evolution for in silico‐designed lactate‐producing strainsBiotechnology and Bioengineering, 95
-
A. Burgard, Prit Pharkya, C. Maranas (2003)
Optknock: A bilevel programming framework for identifying gene knockout strategies for microbial strain optimizationBiotechnology and Bioengineering, 84
-
W. Donovan, S. Kushner (1983)
Purification and characterization of orotidine-5'-phosphate decarboxylase from Escherichia coli K-12Journal of Bacteriology, 156
-
Gene Jiang, Sonia Nikolova, David Clark (2001)
Regulation of the ldhA gene, encoding the fermentative lactate dehydrogenase of Escherichia coli.Microbiology, 147 Pt 9
-
T. Kim, Seung Sohn, H. Kim, Sang Lee (2008)
Strategies for systems‐level metabolic engineeringBiotechnology Journal, 3
-
F. Bruggeman, F. Boogerd, H. Westerhoff (2005)
The multifarious short‐term regulation of ammonium assimilation of Escherichia coli: dissection using an in silico replicaThe FEBS Journal, 272
-
A. Varma, B. Palsson (1994)
Predictions for oxygen supply control to enhance population stability of engineered production strainsBiotechnology and Bioengineering, 43
-
B. Teusink, C. Larsson, Jasper Diderich, P. Richard, K. Dam, L. Gustafsson, H. Westerhoff (1996)
Synchronized Heat Flux Oscillations in Yeast Cell Populations*The Journal of Biological Chemistry, 271
-
J. Heijnen (2005)
Approximative kinetic formats used in metabolic network modelingBiotechnology and Bioengineering, 91
-
Evgeniya Oshchepkova-Nedosekina, V. Likhoshvai (2007)
A mathematical model for the adenylosuccinate synthetase reaction involved in purine biosynthesisTheoretical Biology & Medical Modelling, 4
-
V. Hatzimanikatis, J. Liao (2002)
A memorial review of Jay Bailey's contribution in prokaryotic metabolic engineering.Biotechnology and bioengineering, 79 5
-
J. Shu, M. Shuler (1989)
A mathematical model for the growth of a single cell of E. coli on a glucose/glutamine/ammonium mediumBiotechnology and Bioengineering, 33
-
A. Joyce, B. Palsson (2008)
Predicting gene essentiality using genome-scale in silico models.Methods in molecular biology, 416
-
J. Vallino, G. Stephanopoulos (2000)
Metabolic flux distributions in Corynebacterium glutamicum during growth and lysine overproductionBiotechnology and Bioengineering, 41
-
J. Wild, S. Loughrey-Chen, T. Corder (1989)
In the presence of CTP, UTP becomes an allosteric inhibitor of aspartate transcarbamoylase.Proceedings of the National Academy of Sciences of the United States of America, 86 1
-
R. Desai, Latonia Harris, Neil Welker, E. Papoutsakis (1999)
Metabolic flux analysis elucidates the importance of the acid-formation pathways in regulating solvent production by Clostridium acetobutylicum.Metabolic engineering, 1 3
-
J. Macdonnell, Faylene Lunn, S. Bearne (2004)
Inhibition of E. coli CTP synthase by the "positive" allosteric effector GTP.Biochimica et biophysica acta, 1699 1-2
-
J. Robin, B. Penverne, G. Hervé (1989)
Carbamoyl phosphate biosynthesis and partition in pyrimidine and arginine pathways of Escherichia coli. In situ properties of carbamoyl-phosphate synthase, ornithine transcarbamylase and aspartate transcarbamylase in permeabilized cells.European journal of biochemistry, 183 3
-
D. Visser, J. Schmid, K. Mauch, M. Reuss, J. Heijnen (2004)
Optimal re-design of primary metabolism in Escherichia coli using linlog kinetics.Metabolic engineering, 6 4
-
F. Vital-Lopez, A. Armaou, E. Nikolaev, C. Maranas (2006)
A Computational Procedure for Optimal Engineering Interventions Using Kinetic Models of MetabolismBiotechnology Progress, 22
-
K. Gadkar, F. III, J. Edwards, R. Mahadevan (2005)
Estimating optimal profiles of genetic alterations using constraint-based models.Biotechnology and bioengineering, 89 2
-
Latonia Harris, R. Desai, N. Welker, E. Papoutsakis (2000)
Characterization of recombinant strains of the Clostridium acetobutylicum butyrate kinase inactivation mutant: need for new phenomenological models for solventogenesis and butanol inhibition?Biotechnology and bioengineering, 67 1
-
D. Visser, J. Heijnen (2003)
Dynamic simulation and metabolic re-design of a branched pathway using linlog kinetics.Metabolic engineering, 5 3
-
J. Reed, Thuy Vo, C. Schilling, B. Palsson (2003)
An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR)Genome Biology, 4
-
S. Dien, Shintaro Iwatani, Y. Usuda, K. Matsui (2006)
Theoretical analysis of amino acid-producing Escherichia coli using a stoichiometric model and multivariate linear regression.Journal of bioscience and bioengineering, 102 1
-
R. Daniel, B. Kokel, E. Caminade, A. Martel, F. Goffic (1996)
Assay of Escherichia coli dihydroorotase with enantiomeric substrate: practical preparation of carbamyl L-aspartate and high-performance liquid chromatography analysis of catalysis product.Analytical biochemistry, 239 2
-
R. Ramakrishna, J. Edwards, A. McCulloch, B. Palsson (2001)
Flux-balance analysis of mitochondrial energy metabolism: consequences of systemic stoichiometric constraints.American journal of physiology. Regulatory, integrative and comparative physiology, 280 3
-
Reinhart Heinrich, S. Rapoport, T. Rapoport (1977)
Metabolic regulation and mathematical models.Progress in biophysics and molecular biology, 32 1
-
A. Cornish-Bowden (1977)
An automatic method for deriving steady-state rate equations.The Biochemical journal, 165 1
-
O. Reséndis-Antonio, J. Reed, S. Encarnación-Guevara, J. Collado-Vides, B. Palsson (2007)
Metabolic Reconstruction and Modeling of Nitrogen Fixation in Rhizobium etliPLoS Computational Biology, 3
-
L. Drozdov-Tikhomirov, G. Scurida, A. Davidov, A. Alexandrov, R. Zvyagilskaya (2006)
Mathematical Modeling of Living Cell Metabolism Using the Method of Steady-state Stoichiometric Flux BalanceJournal of bioinformatics and computational biology, 4 4
-
J. Higgins (1964)
A CHEMICAL MECHANISM FOR OSCILLATION OF GLYCOLYTIC INTERMEDIATES IN YEAST CELLS.Proceedings of the National Academy of Sciences of the United States of America, 51
-
Ailen Sánchez, G. Bennett, K. San (2006)
Batch culture characterization and metabolic flux analysis of succinate-producing Escherichia coli strains.Metabolic engineering, 8 3
-
C. Schilling, M. Covert, Iman Famili, G. Church, J. Edwards, B. Palsson (2002)
Genome-Scale Metabolic Model of Helicobacter pylori 26695Journal of Bacteriology, 184
-
Alexander Kern, Emma Tilley, I. Hunter, M. Legiša, A. Glieder (2007)
Engineering primary metabolic pathways of industrial micro-organisms.Journal of biotechnology, 129 1
-
G. Stephanopoulos (1999)
Metabolic fluxes and metabolic engineering.Metabolic engineering, 1 1
-
J. Akowski, R. Bauerle (1997)
Steady-state kinetics and inhibitor binding of 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase (tryptophan sensitive) from Escherichia coli.Biochemistry, 36 50
-
G. Stephanopoulos, H. Alper, J. Moxley (2004)
Exploiting biological complexity for strain improvement through systems biologyNature Biotechnology, 22
-
Francisco Llaneras, J. Picó (2008)
Stoichiometric modelling of cell metabolism.Journal of bioscience and bioengineering, 105 1
-
Prit Pharkya, A. Burgard, C. Maranas (2003)
Exploring the overproduction of amino acids using the bilevel optimization framework OptKnockBiotechnology and Bioengineering, 84
-
I. Villadsen, O. Michelsen (1977)
Regulation of PRPP and nucleoside tri and tetraphosphate pools in Escherichia coli under conditions of nitrogen starvationJournal of Bacteriology, 130
-
S. Fong, A. Burgard, C. Herring, E. Knight, F. Blattner, C. Maranas, B. Palsson (2005)
In silico design and adaptive evolution of Escherichia coli for production of lactic acid.Biotechnology and bioengineering, 91 5
-
I. Nikerel, W. Winden, P. Verheijen, J. Heijnen (2009)
Model reduction and a priori kinetic parameter identifiability analysis using metabolome time series for metabolic reaction networks with linlog kinetics.Metabolic engineering, 11 1
-
A. Lynch, E. Lin (1996)
Transcriptional control mediated by the ArcA two-component response regulator protein of Escherichia coli: characterization of DNA binding at target promotersJournal of Bacteriology, 178
-
I. Carré, L. Edmunds (1993)
Oscillator control of cell division in Euglena: cyclic AMP oscillations mediate the phasing of the cell division cycle by the circadian clock.Journal of cell science, 104 ( Pt 4)
-
G. Sprenger (2007)
From scratch to value: engineering Escherichia coli wild type cells to the production of l-phenylalanine and other fine chemicals derived from chorismateApplied Microbiology and Biotechnology, 75
-
A. Varma, B. Palsson (1994)
Stoichiometric flux balance models quantitatively predict growth and metabolic by-product secretion in wild-type Escherichia coli W3110Applied and Environmental Microbiology, 60
-
D. Cameron, I. Tong (1993)
Cellular and metabolic engineeringApplied Biochemistry and Biotechnology, 38
-
Prit Pharkya, A. Burgard, C. Maranas (2004)
OptStrain: a computational framework for redesign of microbial production systems.Genome research, 14 11
-
Н.Н. Назипова, N. Nazipova (2007)
Rate Calculation for Metabolic Reactions in a Living and Growing Cell by the Method of Steady-State Stoichiometric Flux BalanceMathematical Biology and Bioinformatics, 2
-
N. Bucurenci, L. Serina, Cristina Zaharia, Stéphanie Landais, A. Danchin, O. Bārzu (1998)
Mutational Analysis of UMP Kinase fromEscherichia coliJournal of Bacteriology, 180
-
J. Edwards, R. Ibarra, B. Palsson (2001)
In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental dataNature Biotechnology, 19
-
Stephen Spiro, J. Guest (1991)
Adaptive responses to oxygen limitation in Escherichia coli.Trends in biochemical sciences, 16 8
-
C. Tseng, Jeffery Albrecht, R. Gunsalus (1996)
Effect of microaerophilic cell growth conditions on expression of the aerobic (cyoABCDE and cydAB) and anaerobic (narGHJI, frdABCD, and dmsABC) respiratory pathway genes in Escherichia coliJournal of Bacteriology, 178
-
E. Tarmy, N. Kaplan (1968)
Kinetics of Escherichia coli B D-lactate dehydrogenase and evidence for pyruvate-controlled change in conformation.The Journal of biological chemistry, 243 10
-
V. Wendisch, M. Bott, B. Eikmanns (2006)
Metabolic engineering of Escherichia coli and Corynebacterium glutamicum for biotechnological production of organic acids and amino acids.Current opinion in microbiology, 9 3
-
R. Desai, L. Nielsen, E. Papoutsakis (1999)
Stoichiometric modeling of Clostridium acetobutylicum fermentations with non-linear constraints.Journal of biotechnology, 71 1-3
-
E. Voit, M. Savageau (1987)
Accuracy of alternative representations for integrated biochemical systems.Biochemistry, 26 21
-
T. Khlebodarova, O. Podkolodnaya, D. Oshchepkov, Denis Miginsky, E. Ananko, E. Ignatieva (2006)
Artsite Database: Comparison of In Vitro Selected and Natural Binding Sites of Eukaryotic Transcription Factors -
Liang Wu, Weiming Wang, W. Winden, W. Gulik, J. Heijnen (2004)
A new framework for the estimation of control parameters in metabolic pathways using lin-log kinetics.European journal of biochemistry, 271 16
-
I. Compan, Danlèle Touati (1994)
Anaerobic activation of arcA transcription in Escherichia coli: roles of Fnr and ArcAMolecular Microbiology, 11
-
E. Papoutsakis (1984)
Equations and calculations for fermentations of butyric acid bacteriaBiotechnology and Bioengineering, 26
-
Jette Thykaer, J. Nielsen (2003)
Metabolic engineering of -lactam productionMetabolic Engineering
-
J. Nielsen (1997)
Metabolic control analysis of biochemical pathways based on a thermokinetic description of reaction rates.The Biochemical journal, 321 ( Pt 1)
-
F. Hommais, E. Krin, J. Coppee, C. Lacroix, E. Yeramian, A. Danchin, P. Bertin (2004)
GadE (YhiE): a novel activator involved in the response to acid environment in Escherichia coli.Microbiology, 150 Pt 1
-
O. Björnberg, A. Grüner, P. Roepstorff, K. Jensen (1999)
The activity of Escherichia coli dihydroorotate dehydrogenase is dependent on a conserved loop identified by sequence homology, mutagenesis, and limited proteolysis.Biochemistry, 38 10
-
J. Lee, H. Yun, Adam Feist, B. Palsson, S. Lee (2008)
Genome-scale reconstruction and in silico analysis of the Clostridium acetobutylicum ATCC 824 metabolic networkApplied Microbiology and Biotechnology, 80
-
M. Domach, S. Leung, R. Cahn, G. Cocks, M. Shuler (1984)
Computer model for glucose‐limited growth of a single cell of Escherichia coli B/r‐ABiotechnology and Bioengineering, 26
-
M. Shimosaka, Y. Fukuda, K. Murata, A. Kimura (1984)
Purine-mediated growth inhibition caused by a pyrE mutation in Escherichia coli K-12Journal of Bacteriology, 160
-
S. Peretti, J. Bailey (1986)
Mechanistically detailed model of cellular metabolism for glucose‐limited growth of Escherichia coli B/r‐ABiotechnology and Bioengineering, 28
-
J. Hochstadt-Ozer, E. Stadtman (1971)
The regulation of purine utilization in bacteria. I. Purification of adenine phosphoribosyltransferase from Escherichia coli K12 and control of activity by nucleotides.The Journal of biological chemistry, 246 17
-
Jin Kim, J. Varner, D. Ramkrishna (2008)
A hybrid model of anaerobic E. coli GJT001: Combination of elementary flux modes and cybernetic variablesBiotechnology Progress, 24
-
M. Ataai, M. Shuler (1985)
Simulation of the growth pattern of a single cell of Escherichia coli under anaerobic conditionsBiotechnology and Bioengineering, 27
-
Helen Wilson, Cynthia Archer, Junke Liu, C. Turnbough (1992)
Translational control of pyrC expression mediated by nucleotide-sensitive selection of transcriptional start sites in Escherichia coliJournal of Bacteriology, 174
-
R. Ibarra, J. Edwards, B. Palsson (2002)
Escherichia coli K-12 undergoes adaptive evolution to achieve in silico predicted optimal growthNature, 420
- Publisher
- Springer Journals
- Copyright
- Copyright © 2010 by Pleiades Publishing, Ltd.
- Subject
- Life Sciences; Medical Microbiology ; Microbiology ; Biochemistry, general
- ISSN
- 0003-6838
- eISSN
- 1608-3024
- DOI
- 10.1134/S0003683810070021
- Publisher site
- See Article on Publisher Site
Abstract
This review briefs on the main directions in the field of mathematical modeling of metabolic processes aimed at a rational design of genetically modified organisms. The class of generalized Hill functions is described, and their application to modeling of nonlinear processes in Escherichia coli metabolic systems is illustrated by several examples. A model for the pyrimidine biosynthesis in E. coli, taking into account the nonlinear effects of a negative allosteric regulation of enzyme activities involved in the control of the subsequent stages by the end products of synthesis, is considered. It has been shown that the model displays its own continuous oscillation mode of functioning with a period of approximately 50 min, which is close to the duration of E. coli cell cycle. The need in considering the nonlinear effects in the models as essential elements in the function of metabolic systems far from equilibrium is discussed.
Journal
Applied Biochemistry and Microbiology – Springer Journals
Published: Nov 3, 2010