Elementary mode analysis: A useful metabolic pathway analysis tool for characterizing cellular metabolism

Applied Microbiology and Biotechnology

Volumn 81, Issue 5, 2009, Pages 813-826

  Trinh, Cong T ^a,b   Wlaschin, Aaron ^a,b,c   Srienc, Friedrich ^a,b  

^a University of Minnesota   (United States)

^b UNIVERSITY OF MINNESOTA   (United States)

^c GENERAL MILLS INC   (United States)

Author keywords

Control effective flux; Elementary mode; Extreme pathway; Genetic knockout analysis; Metabolic engineering; Metabolic flux ratio; Metabolic pathway analysis; Minimal cell; Minimal cut set; Rational strain design; Robustness; Weighting factors

Indexed keywords

ELEMENTARY MODE; EXTREME PATHWAY; GENETIC KNOCKOUT ANALYSIS; METABOLIC ENGINEERING; METABOLIC FLUX RATIO; METABOLIC PATHWAY ANALYSIS; MINIMAL CELL; MINIMAL CUT SET; RATIONAL STRAIN DESIGN; ROBUSTNESS; WEIGHTING FACTORS;

BIOCHEMISTRY; CONTROL THEORY; CYTOLOGY; GENETIC ENGINEERING; METABOLISM; ROBUSTNESS (CONTROL SYSTEMS);

PHYSIOLOGY;

CYTOLOGY; GENETIC ENGINEERING; METABOLISM; PHYSIOLOGY;

BIOCHEMICAL PROCESSES; BIOTECHNOLOGY; CELL PHYSIOLOGICAL PHENOMENA; COMPUTATIONAL BIOLOGY; METABOLIC NETWORKS AND PATHWAYS;

EID: 58149154663     PISSN: 01757598     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00253-008-1770-1     Document Type: Short Survey

References (98)

1. S Alexeeva B de Kort G Sawers KJ Hellingwerf MJ de Mattos 2000 Effects of limited aeration and of the ArcAB system on intermediary pyruvate catabolism in Escherichia coli J Bacteriol 182 4934 4940
2. N Barkai S Leibler 1997 Robustness in simple biochemical networks Nature 387 913 917
3. J Behre T Wilhelm A von Kamp E Ruppin S Schuster 2008 Structural robustness of metabolic networks with respect to multiple knockouts J Theor Biol 252 433 441
4. SL Bell BO Palsson 2005 Expa: a program for calculating extreme pathways in biochemical reaction networks Bioinformatics 21 1739 1740
5. DA Benson I Karsch-Mizrachi DJ Lipman J Ostell DL Wheeler 2008 GenBank Nucleic Acids Res 36 D25 30
6. T Cakir B Kirdar KO Ulgen 2004 Metabolic pathway analysis of yeast strengthens the bridge between transcriptomics and metabolic networks Biotechnol Bioeng 86 251 260
7. T Cakir B Kirdar ZI Onsan KO Ulgen J Nielsen 2007 Effect of carbon source perturbations on transcriptional regulation of metabolic fluxes in Saccharomyces cerevisiae BMC Syst Biol 1 18
8. RP Carlson 2007 Metabolic systems cost-benefit analysis for interpreting network structure and regulation Bioinformatics 23 1258 1264
9. R Carlson F Srienc 2004 Fundamental Escherichia coli biochemical pathways for biomass and energy production: identification of reactions Biotech Bioeng 85 1 18
10. R Carlson F Srienc 2004 Fundamental Escherichia coli biochemical pathways for biomass and energy production: creation of overall flux states Biotechnol Bioeng 86 149 162
11. R Carlson D Fell F Srienc 2002 Metabolic pathway analysis of a recombinant yeast for rational strain development Biotechnol Bioeng 79 121 134
12. R Carlson A Wlaschin F Srienc 2005 Kinetic studies and biochemical pathway analysis of anaerobic poly-(R)-3-hydroxybutyric acid synthesis in Escherichia coli Appl Environ Microbiol 71 713 720
13. R Caspi H Foerster CA Fulcher R Hopkinson J Ingraham P Kaipa M Krummenacker S Paley J Pick SY Rhee C Tissier P Zhang PD Karp 2006 MetaCyc: a multiorganism database of metabolic pathways and enzymes Nucl Acids Res 34 D511 516
14. BL Clarke 1981 Complete set of steady states for the general stoichiometric dynamical system J Chem Phys 75 4970 4979
15. BL Clarke 1988 Stoichiometric network analysis Cell Biophys 12 237
16. MW Covert BO Palsson 2003 Constraints-based models: regulation of gene expression reduces the steady-state solution space J Theor Biol 221 309 325
17. SC Diniz IV Voss A Steinbuchel 2006 Optimization of cyanophycin production in recombinant strains of Pseudomonas putida and Ralstonia eutropha employing elementary mode analysis and statistical experimental design Biotechnol Bioeng 93 698 717
18. NC Duarte SA Becker N Jamshidi I Thiele ML Mo TD Vo R Srivas BO Palsson 2007 Global reconstruction of the human metabolic network based on genomic and bibliomic data Proc Natl Acad Sci U S A 104 1777 1782
19. JS Edwards BO Palsson 2000 Robustness analysis of the Escherichia coli metabolic network Biotechnol Prog 16 927
20. JS Edwards BO Palsson 2000 The Escherichia coli MG1655 in silico metabolic genotype: its definition, characteristics, and capabilities Proc Natl Acad Sci U S A 97 5528 5533
21. Edwards JS, Ramakrishna R, Schilling CH, Palsson BO (1999) Metabolic flux balance analysis. In: Lee SY, Papoutsakis ET (eds) Metabolic engineering. Marcel Dekker, New York, pp 13-57
22. JS Edwards RU Ibarra BO Palsson 2001 In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental data Nat Biotech 19 125 130
23. M Feinberg FJM Horn 1974 Dynamics of open chemical systems and the algebraic structure of the underlying reaction network Chem Eng Sci 29 775 787
24. J Gagneur S Klamt 2004 Computation of elementary modes: a unifying framework and the new binary approach BMC Bioinformatics 5 175
25. S Hoops S Sahle R Gauges C Lee J Pahle N Simus M Singhal L Xu P Mendes U Kummer 2006 COPASI-a COmplex PAthway SImulator Bioinformatics 22 3067 3074
26. M Kanehisa M Araki S Goto M Hattori M Hirakawa M Itoh T Katayama S Kawashima S Okuda T Tokimatsu Y Yamanishi 2008 KEGG for linking genomes to life and the environment Nucleic Acids Res 36 D480 4
27. PD Karp IM Keseler A Shearer M Latendresse M Krummenacker SM Paley I Paulsen J Collado-Vides S Gama-Castro M Peralta-Gil A Santos-Zavaleta MI Penaloza-Spinola C Bonavides-Martinez J Ingraham 2007 Multidimensional annotation of the Escherichia coli K-12 genome Nucleic Acids Res 35 7577 7590
28. KJ Kauffman P Prakash JS Edwards 2003 Advances in flux balance analysis Curr Opin Biotechnol 14 491 496
29. S Klamt 2006 Generalized concept of minimal cut sets in biochemical networks BioSystems 83 233 247
30. S Klamt J Stelling 2002 Combinatorial complexity of pathway analysis in metabolic networks Mol Biol Rep 29 233 236
31. S Klamt J Stelling 2003 Two approaches for metabolic pathway analysis Trends Biotechnol 21 64 69
32. S Klamt ED Gilles 2004 Minimal cut sets in biochemical reaction networks Bioinformatics 20 226 234
33. S Klamt S Schuster ED Gilles 2002 Calculability analysis in underdetermined metabolic networks illustrated by a model of the central metabolism in purple nonsulfur bacteria Biotechnol Bioeng 77 734 751
34. S Klamt J Stelling M Ginkel ED Gilles 2003 FluxAnalyzer: exploring structure, pathways, and flux distributions in metabolic networks on interactive flux maps Bioinformatics 19 261 269
35. S Klamt J Gagneur A von Kamp 2005 Algorithmic approaches for computing elementary modes in large biochemical reaction networks Syst Biol (Stevenage) 152 249 255
36. S Klamt J Saez-Rodriguez ED Gilles 2007 Structural and functional analysis of cellular networks with CellNetAnalyzer BMC Syst Biol 1 2
37. I Koch BH Junker M Heiner 2005 Application of Petri net theory for modelling and validation of the sucrose breakdown pathway in the potato tuber Bioinformatics 21 1219 1226
38. JO Kromer C Wittmann H Schroder E Heinzle 2006 Metabolic pathway analysis for rational design of L-methionine production by Escherichia coli and Corynebacterium glutamicum Metab Eng 8 353 369
39. H Kurata Q Zhao R Okuda K Shimizu 2007 Integration of enzyme activities into metabolic flux distributions by elementary mode analysis BMC Systems Biology 1 31
40. JC Liao SY Hou YP Chao 1996 Pathway analysis, engineering, and physiological considerations for redirecting central metabolism Biotechnol Bioeng 52 129 140
41. ML Mavrovouniotis G Stephanopoulos G Stephanopoulos 1990 Computer-aided synthesis of biochemical pathways Biotechnol Bioeng 36 1119 1132
42. ML Mavrovouniotis G Stephanopoulos G Stephanopoulos 1996 Qualitative analysis of biochemical reaction systems Comp Biol Med 26 9 24
43. PC Milner 1964 The possible mechanisms of complex reactions involving consecutive steps J Electrochem Soc 111 228
44. I Nookaew A Meechai C Thammarongtham K Laoteng V Ruanglek S Cheevadhanarak J Nielsen S Bhumiratana 2007 Identification of flux regulation coefficients from elementary flux modes: a systems biology tool for analysis of metabolic networks Biotechnol Bioeng 97 1535 1549
45. JA Papin ND Price JS Edwards BBO Palsson 2002 The genome-scale metabolic extreme pathway structure in Haemophilus influenzae shows significant network redundancy J Theor Biol 215 67 82
46. JA Papin ND Price BO Palsson 2002 Extreme pathway lengths and reaction participation in genome-scale metabolic networks Genome Res 12 1889 1900
47. JA Papin ND Price SJ Wiback DA Fell BO Palsson 2003 Metabolic pathways in the post-genome era Trends Biochem Sci 28 250 258
48. JA Papin J Stelling ND Price S Klamt S Schuster BO Palsson 2004 Comparison of network-based pathway analysis methods Trends Biotechnol 22 400 405
49. T Pfeiffer I Sanchez-Valdenebro J Nuno F Montero S Schuster 1999 METATOOL: for studying metabolic networks Bioinformatics 15 251 257
50. MG Poolman DA Fell CA Raines 2003 Elementary modes analysis of photosynthate metabolism in the chloroplast stroma Eur J Biochem 270 430 439
51. MG Poolman KV Venkatesh MK Pidcock DA Fell 2004 A method for the determination of flux in elementary modes, and its application to Lactobacillus rhamnosus Biotechnol Bioeng 88 601 612
52. MG Poolman C Sebu MK Pidcock DA Fell 2007 Modular decomposition of metabolic systems via null-space analysis J Theor Biol 249 691 705
53. ND Price JA Papin BO Palsson 2002 Determination of redundancy and systems properties of the metabolic network of Helicobacter pylori using genome-scale extreme pathway analysis Genome Res 12 760 769
54. ND Price JL Reed JA Papin I Famili BO Palsson 2003 Analysis of metabolic capabilities using singular value decomposition of extreme pathway matrices Biophys J 84 794 804
55. ND Price JL Reed BO Palsson 2004 Genome-scale models of microbial cells: evaluating the consequences of constraints Nat Rev Microbiol 2 886 897
56. I Prigogine 1945 Modération et transformations irréversibles des systèmes ouverts Bull Acad Roy Belg Cl Sci 31 600 606
57. H Qian DA Beard 2005 Thermodynamics of stoichiometric biochemical networks in living systems far from equilibrium Biophys Chem 114 213 220
58. H Qian DA Beard S Liang 2003 Stoichiometric network theory for nonequilibrium biochemical systems Eur J Biochem 270 415 421
59. C Reder 1988 Metabolic control theory: a structural approach J Theor Biol 135 175 201
60. Rockafellar RT (1970) Convex analysis. Princeton University Press, Princeton
61. Roels JA (1983) Energetics and kinetics in biotechnology. Elsevier, Amsterdam
62. Samatova NF (2002) Parallel out-of-core algorithm for genome-scale enumeration of metabolic systemic pathways. Parallel and Distributed Processing Symposium, Proceedings International, IPDPS 2002, Abstracts and CD-ROM 185-192
63. CH Schilling BO Palsson 2000 Assessment of the metabolic capabilities of Haemophilus influenzae Rd through a genome-scale pathway analysis J Theor Biol 203 249 283
64. CH Schilling D Letscher BO Palsson 2000 Theory for the systemic definition of metabolic pathways and their use in interpreting metabolic function from a pathway-oriented perspective J Theor Biol 203 229 248
65. R Schuetz L Kuepfer U Sauer 2007 Systematic evaluation of objective functions for predicting intracellular fluxes in Escherichia coli Mol Syst Biol 3 1 15
66. S Schuster R Schuster 1991 Detecting strictly detailed balanced subnetworks in open chemical reaction networks J Math Chem 6 17 40
67. R Schuster S Schuster 1993 Refined algorithm and computer program calculating all non-negative fluxes admissible in steady states of biochemical reaction systems with and without some fluxes rates fixed CABIOS 9 79 85
68. S Schuster S Hilgetag 1994 On elementary flux modes in biochemical reaction systems at steady state J Biol Syst 2 165 182
69. S Schuster T Dandekar DA Fell 1999 Detection of elementary flux modes in biochemical networks: a promising tool for pathway analysis and metabolic engineering Trends Biotechnol 17 53 60
70. S Schuster DA Fell T Dandekar 2000 A general definition of metabolic pathways useful for systematic organization and analysis of complex metabolic networks Nat Biotechnol 18 326 332
71. S Schuster T Pfeiffer F Moldenhauer I Koch T Dandekar 2002 Exploring the pathway structure of metabolism: decomposition into subnetworks and application to Mycoplasma pneumoniae Bioinformatics 18 351 361
72. S Schuster C Hilgetag JH Woods DA Fell 2002 Reaction routes in biochemical reaction systems: algebraic properties, validated calculation procedure and example from nucleotide metabolism J Math Biol 45 153 181
73. J Schwartz M Kanehisa 2005 A quadratic programming approach for decomposing steady-state metabolic flux distributions onto elementary modes Bioinformatics ii21 204 205
74. J Schwartz M Kanehisa 2006 Quantitative elementary mode analysis of metabolic pathways: the example of yeast glycolysis BMC Bioinformatics 7 186
75. R Schwarz P Musch A von Kamp B Engels H Schirmer S Schuster T Dandekar 2005 YANA-a software tool for analyzing flux modes, gene-expression and enzyme activities BMC Bioinformatics 6 135
76. R Schwarz C Liang C Kaleta M Kuhnel E Hoffmann S Kuznetsov M Hecker G Griffiths S Schuster T Dandekar 2007 Integrated network reconstruction, visualization and analysis using YANAsquare BMC Bioinformatics 8 313
77. JM Schwartz C Gaugain JC Nacher A de Daruvar M Kanehisa 2007 Observing metabolic functions at the genome scale Genome Biol 8 R123
78. D Segre D Vitkup GM Church 2002 Analysis of optimality in natural and perturbed metabolic networks PNAS 99 15112 15117
79. A Seressiotis JE Bailey 1988 MPS: an artificially intelligent software system for the analysis and synthesis of metabolic pathways Biotechnol Bioeng 31 587 602
80. J Stelling S Klamt K Bettenbrock S Schuster ED Gilles 2002 Metabolic network structure determines key aspects of functionality and regulation Nature 420 190 193
81. J Stelling U Sauer Z Szallasi FJ Doyle 3rd J Doyle 2004 Robustness of cellular functions Cell 118 675 685
82. Stephanopoulos G, Aristidou AA, Nielsen JH (1998) Metabolic engineering: principles and methodologies. Academic, San Diego
83. CT Trinh R Carlson A Wlaschin F Srienc 2006 Design, construction and performance of the most efficient biomass producing E. coli bacterium Metab Eng 8 628 638
84. CT Trinh P Unrean F Srienc 2008 Minimal Escherichia coli cell for the most efficient production of ethanol from hexoses and pentoses Appl Environ Microbiol 74 3634 3643
85. R Urbanczik 2006 SNA-a toolbox for the stoichiometric analysis of metabolic networks BMC Bioinformatics 7 129
86. R Urbanczik C Wagner 2005 Functional stoichiometric analysis of metabolic networks Bioinformatics 21 4176 4180
87. R Urbanczik C Wagner 2005 An improved algorithm for stoichiometric network analysis: theory and applications Bioinformatics 21 1203 1210
88. SJ Van Dien ME Lidstrom 2002 Stoichiometric model for evaluating the metabolic capabilities of the facultative methylotroph Methylobacterium extorquens AM1, with application to reconstruction of C3 and C4 metabolism Biotechnol Bioeng 78 296 312
89. N Vijayasankaran R Carlson F Srienc 2005 Metabolic pathway structures for recombinant protein synthesis in Escherichia coli Appl Microbiol Biotechnol 68 737 746
90. A von Kamp S Schuster 2006 Metatool 5.0: fast and flexible elementary modes analysis Bioinformatics 22 1930 1931
91. C Wagner 2004 Nullspace approach to determine the elementary modes of chemical reaction systems J Phys Chem B 108 2425 2431
92. Q Wang Y Yang H Ma X Zhao 2007 Metabolic network properties help assign weights to elementary modes to understand physiological flux distributions Bioinformatics 23 1049 1052
93. SJ Wiback BO Palsson 2002 Extreme pathway analysis of human red blood cell metabolism Biophys J 83 808 818
94. SJ Wiback R Mahadevan BO Palsson 2003 Reconstructing metabolic flux vectors from extreme pathways: defining the alpha-spectrum J Theor Biol 224 313 324
95. SJ Wiback R Mahadevan BO Palsson 2004 Using metabolic flux data to further constrain the metabolic solution space and predict internal flux patterns: the Escherichia coli spectrum Biotechnol Bioeng 86 317 331
96. 13C metabolic flux analysis Metabolic Engineering 3 195 206
97. T Wilhelm J Behre S Schuster 2004 Analysis of structural robustness of metabolic networks Syst Biol (Stevenage) 1 114 120
98. AP Wlaschin CT Trinh R Carlson F Srienc 2006 The fractional contributions of elementary modes to the metabolism of Escherichia coli and their estimation from reaction entropies Metab Eng 8 338 352