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Metabolic flux analysis and metabolic engineering of microorganisms

Hyun Uk Kim, Tae Yong Kim, Sang Yup Lee
2008 Molecular Biosystems  
Various computational aspects of constraints-based flux analysis including genome-scale stoichiometric models, additional constraints used for the improved accuracy, and several algorithms for identifying  ...  Recent advances in metabolic flux analysis including genome-scale constraintsbased flux analysis and its applications in metabolic engineering are reviewed.  ...  Acknowledgements This work was supported by the Korean Systems Biology Program from the Ministry of Science and Technology through the Korea Science and Engineering Foundation (No.  ... 
doi:10.1039/b712395g pmid:18213404 fatcat:gsdpia4ohngntdc6d34qnyedmq

Stoichiometric capacitance reveals the theoretical capabilities of metabolic networks

Abdelhalim Larhlimi, Georg Basler, Sergio Grimbs, Joachim Selbig, Zoran Nikoloski
2012 Computer applications in the biosciences : CABIOS  
Motivation: Metabolic engineering aims at modulating the capabilities of metabolic networks by changing the activity of biochemical reactions.  ...  The existing constraint-based approaches for metabolic engineering have proven useful, but are limited only to reactions catalogued in various pathway databases.  ...  METHODS Optimization-based approaches Metabolic networks are composed of metabolites inter-converted by a set of biochemical reactions.  ... 
doi:10.1093/bioinformatics/bts381 pmid:22962473 pmcid:PMC3436808 fatcat:ovv7v5poazhclg7j2f6d7wunhq

Thermodynamic constraints for biochemical networks

Daniel A. Beard, Eric Babson, Edward Curtis, Hong Qian
2004 Journal of Theoretical Biology  
The constraint-based approach to analysis of biochemical systems has emerged as a useful tool for rational metabolic engineering.  ...  Here, we show that the network structure (i.e., the stoichiometric matrix) alone provides a system of constraints on the fluxes in a biochemical network which are feasible according to both mass balance  ...  However, none of the classic works on metabolic pathway analysis and constraint-based analysis has explicitly treated nonequilibrium network thermodynamics.  ... 
doi:10.1016/j.jtbi.2004.01.008 pmid:15135031 fatcat:xu7yehsmbjgyrljz3h76ys2isu

Constraint-based modeling of metabolomic systems [chapter]

Daniel A. Beard, Hong Qian
2005 Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics  
Further Reading Schilling CH, Letscher D and Palsson BO (2000)  ...  The S ij entries of the stoichiometric matrix are determined by the stoichiometric numbers appearing in the reactions in the network.  ...  Constraint-based analysis of metabolic systems requires definition of the constraints acting on biochemical variables (fluxes, concentrations, enzyme activities) and determining appropriate objective functions  ... 
doi:10.1002/047001153x.g308203 fatcat:neqxgiomhjhg5ajxfulvtbeeou

Thirteen Years of Building Constraint-Based In Silico Models of Escherichia coli

J. L. Reed, B. O. Palsson
2003 Journal of Bacteriology  
The few parameters used in a constraint-based framework enable models to be built quickly and to encompass a larger portion of biochemical reaction networks than the portion currently encompassed by other  ...  Stoichiometric constraints can be represented by the matrix equation Sv ϭ 0, where S is the stoichiometric matrix describing all the reactions in the network and v is a vector describing the fluxes through  ...  ACKNOWLEDGMENTS We acknowledge the support of grants from NSF (grant BES 01-20363) and NIH (grant GM 57089).  ... 
doi:10.1128/jb.185.9.2692-2699.2003 pmid:12700248 pmcid:PMC154396 fatcat:qnud74jc4rdzjfmbaa3vglf4km

MC3: a steady-state model and constraint consistency checker for biochemical networks

Mona Yousofshahi, Ehsan Ullah, Russell Stern, Soha Hassoun
2013 BMC Systems Biology  
Results: We present a review of common issues in stoichiometric models typically uncovered during pathway analysis and constraint-based optimization, and we detail succinct and efficient ways to find them  ...  matrix, S, and (b) flagging issues that arise during constraint-based optimization.  ...  Methods Modeling of biochemical networks A biochemical network is represented using a stoichiometric matrix S [21, 22] .  ... 
doi:10.1186/1752-0509-7-129 pmid:24261865 pmcid:PMC4222687 fatcat:b6p5bwdjzbbxxeubof7336noom

Stoichiometric Foundation of Large-Scale Biochemical System Analysis [chapter]

Daniel A. Beard, Hong Qian, James B. Bassingthwaighte
2004 Natural Computing Series  
Study of the feasible behavior of a system, given a set of stoichiometric constraints, forms the basis of flux balance analysis, and more generally, stoichiometric network theory.  ...  Duffin's work is a treasure which proves highly relevant to current constraint-based modeling of biochemical networks.  ... 
doi:10.1007/978-3-642-18734-6_1 fatcat:bgpecdxnxjgbxppx2tbbn6whfi

The Escherichia coli MG1655 in silico metabolic genotype: Its definition, characteristics, and capabilities

J. S. Edwards, B. O. Palsson
2000 Proceedings of the National Academy of Sciences of the United States of America  
It was shown that based on stoichiometric and capacity constraints the in silico analysis was able to qualitatively predict the growth potential of mutant strains in 86% of the cases examined.  ...  Herein, it is demonstrated that the synthesis of in silico metabolic genotypes based on genomic, biochemical, and strain-specific information is possible, and that systems analysis methods are available  ...  National Institutes of Health Grant GM 57089 and National Science Foundation Grant MCB 9873384 supported this research.  ... 
doi:10.1073/pnas.97.10.5528 pmid:10805808 pmcid:PMC25862 fatcat:qq52ayqktbe55jqg3osydje7na

Ab initio prediction of thermodynamically feasible reaction directions from biochemical network stoichiometry

Feng Yang, Hong Qian, Daniel A. Beard
2005 Metabolic Engineering  
Based on knowledge of only reaction stoichiometry, certain aspects of network functionality and robustness can be predicted.  ...  Analysis of the stoichiometric structure of metabolic networks provides insights into the relationships between structure, function, and regulation of metabolic systems.  ...  in biochemical reaction systems and thus are useful in constraint-based analysis.  ... 
doi:10.1016/j.ymben.2005.03.002 pmid:16140239 fatcat:ub2g42wuarfvnpg42m5wr7k73a

Biochemical and statistical network models for systems biology

Nathan D Price, Ilya Shmulevich
2007 Current Opinion in Biotechnology  
Biochemical Reaction Networks Biochemical reaction networks represent the underlying chemistry of the system, and thus at a minimum represent stoichiometric relationships between inter-converted biomolecules  ...  Such constraints are based upon properties such as enzyme capacity, reaction stoichiometry and thermodynamics associated with reaction directionality and biochemical loops.  ...  Biochemical Reaction Networks Biochemical reaction networks represent the underlying chemistry of the system, and thus at a minimum represent stoichiometric relationships between inter-converted biomolecules  ... 
doi:10.1016/j.copbio.2007.07.009 pmid:17681779 pmcid:PMC2034526 fatcat:bpdls7rhbvdwjkoedgnkdzd5ci

Flux balance analysis of biological systems: applications and challenges

K. Raman, N. Chandra
2009 Briefings in Bioinformatics  
In particular, constraint-based analyses of metabolic networks have gained considerable popularity for simulating cellular metabolism, of which flux balance analysis (FBA), is most widely used.  ...  Unlike mechanistic simulations that depend on accurate kinetic data, which are scarcely available, FBA is based on the principle of conservation of mass in a network, which utilizes the stoichiometric  ...  However, several challenges remain in the construction and analysis of constraint-based models, particularly in terms of the accurate definition of the metabolic network, the various constraints, as well  ... 
doi:10.1093/bib/bbp011 pmid:19287049 fatcat:542cezsctjdmznnpwyfwpkdj3a

PathwayAnalyser: A Systems Biology Tool for Flux Analysis of Metabolic Pathways

Karthik Raman, Nagasuma Chandra
2008 Nature Precedings  
Flux Balance Analysis (FBA) and Minimisation of Metabolic Adjustment (MoMA) are two of the popular techniques for the constraint-based analysis of metabolic pathways.  ...  Stoichiometric and constraint-based analyses of metabolic pathways has been gaining ground in the recent past with the increase in the quality and number of pathway databases available and the curation  ...  Flux Balance Analysis (FBA) is one such constraint-based method, for the analysis of biochemical systems [3, 4] .  ... 
doi:10.1038/npre.2008.1868.1 fatcat:5mjvgvbjwjhrxggbkozxbrhq2q

Identification of metabolic pathways using pathfinding approaches: a systematic review

Zeyad Abd Algfoor, Mohd Shahrizal Sunar, Afnizanfaizal Abdullah, Hoshang Kolivand
2016 Briefings in Functional Genomics  
Three major types of studies are elaborated: stoichiometric identifi-cation models, pathway-based graph analysis and pathfinding approaches in cellular metabolism.  ...  Moreover, stoichiometric and pathfinding approaches in metabolic pathway analysis are discussed.  ...  Figure 1 . 1 (A) A metabolic network reconstruction consists of a list of stoichiometrically balanced biochemical reactions.  ... 
doi:10.1093/bfgp/elw002 pmid:26969656 fatcat:mq5kxsnqg5abbgjva5q6bomsia

Metabolic Network Discovery by Top-Down and Bottom-Up Approaches and Paths for Reconciliation

Tunahan Çakır, Mohammad Jafar Khatibipour
2014 Frontiers in Bioengineering and Biotechnology  
This study reviews the strengths of constraint-based analysis and network inference methods reported in the metabolic systems biology field; then elaborates on the potential paths to reconcile the two  ...  Keywords: constraint-based models, metabolic network inference, active metabolic state, metabolome, network biology, reverse engineering, flux-balance analysis  ...  (ii) At a higher level, the information on the stoichiometry of reactions can be incorporated, leading to a directed stoichiometric biochemical network.  ... 
doi:10.3389/fbioe.2014.00062 pmid:25520953 pmcid:PMC4253960 fatcat:l2tsj6oflretrh2a436hoza32u

The underlying pathway structure of biochemical reaction networks

C. H. Schilling, B. O. Palsson
1998 Proceedings of the National Academy of Sciences of the United States of America  
The functional capabilities of biochemical reaction networks, and thus the choices that cells can make, are reflected in the null space of their stoichiometric matrix.  ...  In this study, we show how the mass balance constraints that govern the function of biochemical reaction networks lead to the translation of this problem into the realm of linear algebra.  ...  We thank the Whitaker Foundation and their support through graduate fellowships in biomedical engineering.  ... 
doi:10.1073/pnas.95.8.4193 pmid:9539712 pmcid:PMC22464 fatcat:rj2tmvm6wncgbaemzfxcbhgogq
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