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Modeling metabolic networks in C. glutamicum: a comparison of rate laws in combination with various parameter optimization strategies

Andreas Dräger, Marcel Kronfeld, Michael J Ziller, Jochen Supper, Hannes Planatscher, Jørgen B Magnus, Marco Oldiges, Oliver Kohlbacher, Andreas Zell
2009 BMC Systems Biology  
in C. glutamicum.  ...  We investigate the modeling process using multiple kinetic equations together with various parameter optimization methods for a well-characterized example network, the biosynthesis of valine and leucine  ...  This work addresses both questions and tries to identify an optimal model for a well-studied example network: the metabolism of L-valine (Val) and L-leucine (Leu) in Corynebacterium glutamicum, an aerobic  ... 
doi:10.1186/1752-0509-3-5 pmid:19144170 pmcid:PMC2661887 fatcat:mzoe7eoppvduxojkkwu5rffqse

Emerging Corynebacterium glutamicum systems biology

Volker F. Wendisch, Michael Bott, Jörn Kalinowski, Marco Oldiges, Wolfgang Wiechert
2006 Journal of Biotechnology  
Metabolic flux analysis may be viewed as the first systems approach to C. glutamicum physiology since it combines isotope labeling data with metabolic network models of the biosynthetic and central metabolic  ...  for C. glutamicum.  ...  Acknowledgements The support of the Bundesministerium für Bildung und Forschung (BMBF) through grant 031U113D/031U213D is gratefully acknowledged.  ... 
doi:10.1016/j.jbiotec.2005.12.002 pmid:16406159 fatcat:w6f2mvgatjgjdjlvnegm2suqyy

Comparing various evolutionary algorithms on the parameter optimization of the valine and leucine biosynthesis in corynebacterium glutamicum

Andreas Drager, Jochen Supper, Hannes Planatscher, Jorgen B. Magnus, Marco Oldiges, Andreas Zell
2007 2007 IEEE Congress on Evolutionary Computation  
Here we focus on the metabolic subnetwork of the valine and leucine biosynthesis in C. glutamicum.  ...  mass-action rate law.  ...  ACKNOWLEGEMENTS A. D. and J. S. are funded by the NGFN-II EP project no. 0313323. We are grateful to Ralf Takors, Klaus Beyreuther and Oliver Kohlbacher.  ... 
doi:10.1109/cec.2007.4424528 dblp:conf/cec/DragerSPMOZ07 fatcat:p2u6hozn7nf3za2xh6xrzafxme

High-Quality Genome-Scale Reconstruction of Corynebacterium glutamicum ATCC 13032

Martina Feierabend, Alina Renz, Elisabeth Zelle, Katharina Nöh, Wolfgang Wiechert, Andreas Dräger
2021 Frontiers in Microbiology  
The in silico model proved fruitful in adding knowledge to the metabolism of C. glutamicum: iCGB21FR still produces L-glutamate with the knock-out of the enzyme pyruvate carboxylase, despite the common  ...  A deep understanding of the biochemical processes in C. glutamicum is essential for a sustainable enhancement of the microbe's productivity.  ...  Modeling metabolic networks in C. glutamicum : a comparison of rate laws in combination with various parameter optimization strategies. BMC Syst.  ... 
doi:10.3389/fmicb.2021.750206 pmid:34867870 pmcid:PMC8634658 fatcat:xjlx4p22irfkbeoch6bxdaoeem

Systematic Applications of Metabolomics in Metabolic Engineering

Robert Dromms, Mark Styczynski
2012 Metabolites  
best ways to inform strategies to engineer a cell to produce a target compound.  ...  We then review some of the most common approaches for computational modeling of cell-wide metabolism, including constraint-based models, and discuss current computational approaches that explicitly use  ...  This work was supported by a DARPA Young Faculty Award and NSF award #1125684. RAD was also supported by the NSF Stem Cell Biomanufacturing IGERT program.  ... 
doi:10.3390/metabo2041090 pmid:24957776 pmcid:PMC3901235 fatcat:disnfzhryncchi52bayhsid6w4

Genome-Scale Metabolic Models of Saccharomyces cerevisiae [chapter]

Intawat Nookaew, Roberto Olivares-Hernández, Sakarindr Bhumiratana, Jens Nielsen
2011 Msphere  
With the reconstruction of the yeast genome-scale metabolic (GSM) network and in silico simulation of the GSM model, the nature of the underlying cellular processes can be tested and validated with the  ...  In this chapter, the principle concepts for construction, simulation and validation of GSM models, progressive applications of the yeast GSM models, and future perspectives are described.  ...  In another study of the yeast metabolic network, Blank and co-workers (96) used iLL672 combined with 13 C tracer experiments for genome-scale 13 C flux analysis.  ... 
doi:10.1007/978-1-61779-173-4_25 pmid:21863502 fatcat:smfjzejtmrdbtel5dc5afuwcym

Kinetic models in industrial biotechnology – Improving cell factory performance

Joachim Almquist, Marija Cvijovic, Vassily Hatzimanikatis, Jens Nielsen, Mats Jirstrand
2014 Metabolic Engineering  
Emphasis is on modeling methodology concepts, including model network structure, kinetic rate expressions, parameter estimation, optimization methods, identifiability analysis, model reduction, and model  ...  Kinetic models are particularly suitable towards this end because they are capable of representing the complex biochemistry of cells in a more complete way compared to most other types of models.  ...  Acknowledgments This work has been supported by the EU Framework VII project SYSINBIO -Systems Biology as a Driver for Industrial Biotechnology (call FP7-KBBE-2007-1).  ... 
doi:10.1016/j.ymben.2014.03.007 pmid:24747045 fatcat:7nankknr4batfkyvrgzx5mpl2m

Modelling Cell Metabolism: A Review on Constraint-Based Steady-State and Kinetic Approaches

Mohammadreza Yasemi, Mario Jolicoeur
2021 Processes  
We have also assessed the significance of metabolic model parameterization in kinetic models, summarizing a standard parameter estimation procedure frequently employed in kinetic metabolic modelling literature  ...  Remarkable successes in these fields emerged from heuristics approaches, for instance, with the introduction of effective strategies for genetic modifications, drug developments and optimization of bioprocess  ...  Conflicts of Interest: The authors declare no conflict of interest.  ... 
doi:10.3390/pr9020322 fatcat:vg2yj4qpxnbidoqihl7gkrtzie

A review of metabolic and enzymatic engineering strategies for designing and optimizing performance of microbial cell factories

Amanda K. Fisher, Benjamin G. Freedman, David R. Bevan, Ryan S. Senger
2014 Computational and Structural Biotechnology Journal  
In addition, recent advances in genome-scale modeling have enabled the derivation of metabolic engineering strategies, which can be implemented using the genomic tools reviewed here as well.  ...  This review highlights the progress of computational models for the rational design of an MCF to produce a target bio-commodity.  ...  the tuf gene promoter in C. glutamicum.  ... 
doi:10.1016/j.csbj.2014.08.010 pmid:25379147 pmcid:PMC4212277 fatcat:zexamia3cbh5digdpmllirvn6q

Analysis of l-glutamic acid fermentation by using a dynamic metabolic simulation model of Escherichia coli

Yousuke Nishio, Soichi Ogishima, Masao Ichikawa, Yohei Yamada, Yoshihiro Usuda, Tadashi Masuda, Hiroshi Tanaka
2013 BMC Systems Biology  
The observed increase in L-glutamic acid production verified the biologically meaningful predictive power of our dynamic metabolic simulation model.  ...  Further exhaustive sensitivity analysis will facilitate identification of novel factors involved in the metabolic regulation of amino acid fermentation.  ...  Elementary mode analysis is also used to analyze metabolic network analysis to obtain all possible combinations of reaction networks [14, 15] .  ... 
doi:10.1186/1752-0509-7-92 pmid:24053676 pmcid:PMC3851129 fatcat:agz2qdprubfe3l5ymetfr5lgmq

k-OptForce: Integrating Kinetics with Flux Balance Analysis for Strain Design

Anupam Chowdhury, Ali R. Zomorrodi, Costas D. Maranas, Daniel A. Beard
2014 PLoS Computational Biology  
In this paper, we introduce k-OptForce, which integrates the available kinetic descriptions of metabolic steps with stoichiometric models to sharpen the prediction of intervention strategies for improving  ...  It enables identification of a minimal set of interventions comprised of both enzymatic parameter changes (for reactions with available kinetics) and reaction flux changes (for reactions with only stoichiometric  ...  The procedure builds upon the OptForce procedure [9] by augmenting the metabolic network description with kinetic rate laws whenever available.  ... 
doi:10.1371/journal.pcbi.1003487 pmid:24586136 pmcid:PMC3930495 fatcat:mbwmuzbuinb73fev3vbqr5y5by

Modeling and simulation: tools for metabolic engineering

Wolfgang Wiechert
2002 Journal of Biotechnology  
Optimization: Once models are available that are predictive, at least in some parameter region, the ultimate goal of modeling in metabolic engineering can be tackled which is the computation of an optimal  ...  analysis, optimization of regulatory architectures and the evaluation of rapid sampling experiments. analysis of metabolic networks.  ...  By applying this strategy all forward and backward fluxes in the anaplerosis of C. glutamicum have recently been quantitated (Petersen et al., 2000) .  ... 
doi:10.1016/s0168-1656(01)00418-7 pmid:11792451 fatcat:cpd3o56h7resnavi6lu5pz2w24

In SilicoConstraint-Based Strain Optimization Methods: the Quest for Optimal Cell Factories

Paulo Maia, Miguel Rocha, Isabel Rocha
2015 Microbiology and Molecular Biology Reviews  
Constraint-based models of metabolism, together within silicostrain design algorithms, promise to reveal insights into the best genetic design strategies, a step further toward achieving that goal.  ...  In this work, a thorough analysis of the mainin silicoconstraint-based strain design strategies and algorithms is presented, their application in real-world case studies is analyzed, and a path for the  ...  FluxDesign was validated first for the production of L-lysine in C. glutamicum, where a 2-fold increase in yield was achieved in comparison with an existing strain (179) , and later for the production  ... 
doi:10.1128/mmbr.00014-15 pmid:26609052 pmcid:PMC4711187 fatcat:f6w6ny2dgvdifobydgenzowkmu

In silico analyses for the discovery of tuberculosis drug targets

B. K.-S. Chung, T. Dick, D.-Y. Lee
2013 Journal of Antimicrobial Chemotherapy  
Here, we review key concepts in network analysis for target discovery in tuberculosis and provide a summary of potential TB drug targets identified by the individual methods.  ...  To exploit the increasing amount of bacterial biology information, a variety of in silico methods have been developed and applied to large-scale biological models to identify candidate antibacterial targets  ...  Acknowledgements We are grateful to Bee-Hoang Gan and Gail Mei-Ern Lee for helping in the literature survey. Transparency declarations None to declare.  ... 
doi:10.1093/jac/dkt273 pmid:23838951 fatcat:pf7cvtmdvrgglaujblbssgnwbm

Computational Methods to Interpret and Integrate Metabolomic Data [chapter]

Feng Li, Jiangxin Wang, Lei Nie, Weiwen Zhang
2012 Metabolomics  
Finding biochemically plausible pathways between metabolites in a metabolic network is a central problem in computational metabolic modeling.  ...  Traditionally, kinetic models are constructed using rate equations derived to describe conditions in vitro and thus rely on the use of in vitro measured kinetic parameters.  ...  Analytical chemistry is combined with sophisticated informatics and statistics tools to determine and understand metabolic changes upon genetic or environmental perturbations.  ... 
doi:10.5772/32517 fatcat:ety5vgnvfnaw5evchxhgbab3wy
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