Predicting outcomes of steady-state 13C isotope tracing experiments using Monte Carlo sampling

BMC Systems Biology

Volumn 6, Issue , 2012, Pages

  Schellenberger, Jan ^a   Zielinski, Daniel C ^a   Choi, Wing ^a   Madireddi, Sunthosh ^a   Portnoy, Vasiliy ^a   Scott, David A ^b   Reed, Jennifer L ^c   Osterman, Andrei L ^b   Palsson, Bernhard T ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b BURNHAM INSTITUTE   (United States)

^c University of Wisconsin Madison   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ESCHERICHIA COLI;

CARBON; DIAGNOSTIC AGENT;

ALGORITHM; ARTICLE; BIOLOGICAL MODEL; ESCHERICHIA COLI; KINETICS; METABOLISM; METHODOLOGY; MONTE CARLO METHOD; PHYSIOLOGY; SYSTEMS BIOLOGY;

ALGORITHMS; CARBON ISOTOPES; ESCHERICHIA COLI; KINETICS; METABOLIC NETWORKS AND PATHWAYS; MODELS, BIOLOGICAL; MONTE CARLO METHOD; SYSTEMS BIOLOGY;

EID: 84856291750     PISSN: None     EISSN: 17520509     Source Type: Journal    
DOI: 10.1186/1752-0509-6-9     Document Type: Article

References (38)

1. Heiden MGV, Cantley LC, Thompson CB. Understanding the Warburg Effect: The Metabolic Requirements of Cell Proliferation. Science 2009, 324(5930):1029-1033. 10.1126/science.1160809, 2849637, 19460998.
2. Herrgard MJ, Fong SS, Palsson BO. Identification of genome-scale metabolic network models using experimentally measured flux profiles. PLoS Comput Biol 2006, 2(7):e72. 10.1371/journal.pcbi.0020072, 1487183, 16839195.
3. Wiback S, Mahadevan R, Palsson B. Using Metabolic Flux Data to Further Constrain the Metabolic Solution Space and Predict Internal Flux Patterns: The Escherichia coli alpha-Spectrum. Biotechnology and Bioengineering 2004, 86(3):317-31. 10.1002/bit.20011, 15083512.
4. Mollney M, Wiechert W, Kownatzki D, de Graaf AA. Bidirectional Reaction Steps in Metabolic Networks: IV. Optimal Design of Isotopomer Labeling Experiments. Biotechnology and Bioengineering 1999, 66(2):86-103. 10.1002/(SICI)1097-0290(1999)66:2<86::AID-BIT2>3.0.CO;2-A, 10567067.
5. Sauer U. Metabolic networks in motion: 13C-based flux analysis. Molecular Systems Biology 2006,
6. Wiechert W. 13C metabolic flux analysis. Metab Eng 2001, 3(3):195-206. 10.1006/mben.2001.0187, 11461141.
7. Suthers PF, Burgard AP, Dasika MS, Nowroozi F, Van Dien S, Keasling JD, Maranas CD. Metabolic flux elucidation for large-scale models using 13C labeled isotopes. Metab Eng 2007, 9(5-6):387-405. 10.1016/j.ymben.2007.05.005, 2121621, 17632026.
8. Zamboni N, Fendt SM, Ruhl M, Sauer U. (13)C-based metabolic flux analysis. Nat Protoc 2009, 4(6):878-92. 10.1038/nprot.2009.58, 19478804.
9. Schmidt K, Carlsen M, Nielsen J, Villadsen J. Modeling Isotopomer Distributions in Biochemical Reaction Networks Using Isotopomer Mapping Matrices. Biotechnology and Bioengineering 1997, 55(6):831-40. 10.1002/(SICI)1097-0290(19970920)55:6<831::AID-BIT2>3.0.CO;2-H, 18636594.
10. Metallo CM, Walther JL, Stephanopoulos G. Evaluation of 13C isotopic tracers for metabolic flux analysis in mammalian cells. J Biotechnol 2009, 144(3):167-74. 10.1016/j.jbiotec.2009.07.010, 3026314, 19622376.
11. Chang Y, Suthers PF, Maranas CD. Identification of Optimal Measurement Sets for Complete Flux Elucidation in Metabolic Flux Analysis Experiments. Biotechnology and Bioengineering 2008, 100(6):1039-1049. 10.1002/bit.21926, 18553391.
12. Price ND, Reed JL, Palsson B. Genome-scale models of microbial cells: evaluating the consequences of constraints. Nat Rev Microbiol 2004, 2(11):886-897. 10.1038/nrmicro1023, 15494745.
13. Reed JL, Famili I, Thiele I, Palsson BO. Towards multidimensional genome annotation. Nat Rev Genet 2006, 7(2):130-41. 10.1038/nrg1769, 16418748.
14. Schellenberger J, Park JO, Conrad TM, Palsson BO. BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions. BMC Bioinformatics 2010, 11:213. 10.1186/1471-2105-11-213, 2874806, 20426874.
15. Thiele I, Palsson BO. A protocol for generating a high-quality genome-scale metabolic reconstruction. Nat Protoc 2010, 5:93-121. 3125167, 20057383.
16. Reed J, Vo T, Schilling CH, Palsson B. An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR). Genome Biology 2003, 4(9):R54.1-R54.12.
17. Feist AM, Palsson BO. The biomass objective function. Curr Opin Microbiol 2010,
18. Edwards J, Palsson B. The Escherichia coli MG1655 in silico metabolic genotype: Its definition, characteristics, and capabilities. Proc Natl Acad Sci USA 2000, 97(10):5528-5533. 10.1073/pnas.97.10.5528, 25862, 10805808.
19. Covert MW, Knight EM, Reed JL, Herrgard MJ, Palsson BO. Integrating high-throughput and computational data elucidates bacterial networks. Nature 2004, 429(6987):92-6. 10.1038/nature02456, 15129285.
20. Hua Q, Joyce AR, Fong SS, Palsson BO. Metabolic analysis of adaptive evolution for in silico designed lactate-producing strains. Biotechnol Bioeng 2006, 95(5):992-1002. 10.1002/bit.21073, 16807925.
21. Burgard AP, Pharkya P, Maranas CD. Optknock: a bilevel programming framework for identifying gene knockout strategies for microbial strain optimization. Biotechnol Bioeng 2003, 84(6):647-57. 10.1002/bit.10803, 14595777.
22. Feist AM, Zielinski DC, Orth JD, Schellenberger J, Herrgard MJ, Palsson BO. Model-driven evaluation of the production potential for growth-coupled products of Escherichia coli. Metab Eng 2009,
23. Feist AM, Palsson B. The growing scope of applications of genome-scale metabolic reconstructions using Escherichia coli. Nat Biotech 2008, 26(6):659-667.
24. Schellenberger J, Palsson BO. Use of randomized sampling for analysis of metabolic networks. J Biol Chem 2009, 284(9):5457-61.
25. Fischer E, Zamboni N, Sauer U. High-throughput metabolic flux analysis based on gas chromatography-mass spectrometry derived 13C constraints. Anal Biochem 2004, 325(2):308-16. 10.1016/j.ab.2003.10.036, 14751266.
26. Zhao J, Shimizu K. Metabolic flux analysis of Escherichia coli K12 grown on 13C-labeled acetate and glucose using GC-MS and powerful flux calculation method. J Biotechnol 2003, 101(2):101-17. 10.1016/S0168-1656(02)00316-4, 12568740.
27. Schilling CH, Schuster S, Palsson BO, Heinrich R. Metabolic pathway analysis: basic concepts and scientific applications in the post-genomic era. Biotechnology Progress 1999, 15(3):296-303. 10.1021/bp990048k, 10356246.
28. Antoniewicz MR, Kraynie DF, Laffend LA, Gonzalez-Lergier J, Kelleher JK, Stephanopoulos G. Metabolic flux analysis in a nonstationary system: Fed-batch fermentation of a high yielding strain of E. coli producing 1,3-propanediol. Metab Eng 2007,
29. Yuan J, Bennett BD, Raobinowitz JD. Kinetic flux profiling for quantitation of cellular metabolic fluxes. Nature Protocols 2008, 3:1328-1340. 10.1038/nprot.2008.131, 2710581, 18714301.
30. Schellenberger J, Que R, Fleming RMT, Thiele I, Orth JD, Feist AM, Zielinski DC, Bordbar A, Lewis NE, Rahmanian S, Kang J, Hyduke DR, Palsson B. Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0. Nature Protocols 2011, 6:1290-1307. 10.1038/nprot.2011.308, 21886097.
31. Edwards JS, Palsson BO. Multiple steady states in kinetic models of red cell metabolism. Journal of Theoretical Biology 2000, 207:125-7. 10.1006/jtbi.2000.2165, 11027485.
32. Kaufmann DE SR. Direction choice for accelerated convergence in hit-and-run sampling. Operations Research 1998, 46:84-95.
33. Lewis NE, Schramm G, Bordbar A, Schellenberger J, Andersen MP, Cheng JK, Patel N, Yee A, Lewis RA, Eils R, Konig R, Palsson BO. Large-scale in silico modeling of metabolic interactions between cell types in the human brain. Nature Biotechnology 2010, 28:1279-1285. 10.1038/nbt.1711, 3140076, 21102456.
34. Bordbar A, Lewis NE, Schellenberger J, Palsson BO, Jamshidi N. Insight into human alveolar macrophage and M. tuberculosis interactions via metabolic reconstructions. Molecular Systems Biology 2010, 6(422).
35. Wiechert W, Mollney M, Isermann N, Wurzel M, de Graaf AA. Bidirectional reaction steps in metabolic networks: III. Explicit solution and analysis of isotopomer labeling systems. Biotechnol Bioeng 1999, 66(2):69-85. 10.1002/(SICI)1097-0290(1999)66:2<69::AID-BIT1>3.0.CO;2-6, 10567066.
36. Antoniewicz MR, Kelleher JK, Stephanopoulos G. Elementary metabolite units (EMU): a novel framework for modeling isotopic distributions. Metab Eng 2007, 9:68-86. 10.1016/j.ymben.2006.09.001, 1994654, 17088092.
37. Nanchen A, Fuhrer T, Sauer U. Determination of metabolic flux ratios from 13C-experiments and gas chromatography-mass spectrometry data: protocol and principles. Methods Mol Biol 2007, 358:177-97. 10.1007/978-1-59745-244-1_11, 17035687.
38. van Winden WA, Wittmann C, Heinzle E, Heijnen JJ. Correcting mass isotopomer distributions for naturally occurring isotopes. Biotechnol Bioeng 2002, 80(4):477-9. 10.1002/bit.10393, 12325156.