Flux modules in metabolic networks

被引：14

作者：

Mueller, Arne C. ^{[1
,2
,3
]}

Bockmayr, Alexander ^{[1
,4
]}

机构：

[1] Free Univ Berlin, Dept Math & Comp Sci, D-14195 Berlin, Germany

[2] Max Planck Inst Mol Genet, IMPRS CBSC, D-14195 Berlin, Germany

[3] Berlin Math Sch, Berlin, Germany

[4] DFG Res Ctr Matheon, Berlin, Germany

来源：

JOURNAL OF MATHEMATICAL BIOLOGY | 2014年 / 69卷 / 05期

关键词：

Metabolic network; Flux balance analysis; Elementary flux modes; Modules; GENOME-SCALE MODELS; COMPUTATION; CONSTRAINTS; DEFINITION; PATHWAYS;

D O I：

10.1007/s00285-013-0731-1

中图分类号：

Q [生物科学];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

The huge number of elementary flux modes in genome-scale metabolic networks makes analysis based on elementary flux modes intrinsically difficult. However, it has been shown that the elementary flux modes with optimal yield often contain highly redundant information. The set of optimal-yield elementary flux modes can be compressed using modules. Up to now, this compression was only possible by first enumerating the whole set of all optimal-yield elementary flux modes. We present a direct method for computing modules of the thermodynamically constrained optimal flux space of a metabolic network. This method can be used to decompose the set of optimal-yield elementary flux modes in a modular way and to speed up their computation. In addition, it provides a new form of coupling information that is not obtained by classical flux coupling analysis. We illustrate our approach on a set of model organisms.

引用

页码：1151 / 1179

页数：29

共 31 条

[1]

[Anonymous], 2003, GRADUATE TEXTS MATH

[2]

[Anonymous], 1994, J BIOL SYSTEMS, DOI DOI 10.1142/S0218339094000131

[3] Thermodynamic constraints for biochemical networks [J].

Beard, DA ;

Babson, E ;

Curtis, E ;

Qian, H .

JOURNAL OF THEORETICAL BIOLOGY, 2004, 228 (03) :327-333

[4] Flux coupling analysis of genome-scale metabolic network reconstructions [J].

Burgard, AP ;

Nikolaev, EV ;

Schilling, CH ;

Maranas, CD .

GENOME RESEARCH, 2004, 14 (02) :301-312

[5] Computing the shortest elementary flux modes in genome-scale metabolic networks [J].

de Figueiredo, Luis F. ;

Podhorski, Adam ;

Rubio, Angel ;

Kaleta, Christoph ;

Beasley, John E. ;

Schuster, Stefan ;

Planes, Francisco J. .

BIOINFORMATICS, 2009, 25 (23) :3158-3165

[6] Genome-scale models of bacterial metabolism: reconstruction and applications [J].

Durot, Maxime ;

Bourguignon, Pierre-Yves ;

Schachter, Vincent .

FEMS MICROBIOLOGY REVIEWS, 2009, 33 (01) :164-190

[7] The biomass objective function [J].

Feist, Adam M. ;

Palsson, Bernhard O. .

CURRENT OPINION IN MICROBIOLOGY, 2010, 13 (03) :344-349

[8] A variational principle for computing nonequilibrium fluxes and potentials in genome-scale biochemical networks [J].

Fleming, R. M. T. ;

Maes, C. M. ;

Saunders, M. A. ;

Ye, Y. ;

Palsson, B. O. .

JOURNAL OF THEORETICAL BIOLOGY, 2012, 292 :71-77

[9] Optimal flux spaces of genome-scale stoichiometric models are determined by a few subnetworks [J].

Kelk, Steven M. ;

Olivier, Brett G. ;

Stougie, Leen ;

Bruggeman, Frank J. .

SCIENTIFIC REPORTS, 2012, 2

[10] Selection of objective function in genome scale flux balance analysis for process feed development in antibiotic production [J].

Khannapho, Chiraphan ;

Zhao, Hongjuan ;

Bonde, Bhushan K. ;

Kierzek, Andrzej M. ;

Avignone-Rossa, Claudio A. ;

Bushell, Michael E. .

METABOLIC ENGINEERING, 2008, 10 (05) :227-233

← 1 2 3 4 →