Shrinking the Metabolic Solution Space Using Experimental Datasets

PLoS Computational Biology

Volumn 8, Issue 8, 2012, Pages

  Reed, Jennifer L ^a  

^a University of Wisconsin Madison   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

GENE EXPRESSION; METABOLISM;

CONSTRAINT-BASED MODELING; CONSTRAINTS-BASED MODELING; DRUG DISCOVERY; FLUX DISTRIBUTIONS; GENOME-SCALE MODEL; MAIN PARAMETERS; MULTI SPECIES INTERACTIONS; REACTION STOICHIOMETRY; RECENT RESEARCHES; SOLUTION SPACE;

METABOLIC ENGINEERING;

ACCURACY; GENE EXPRESSION; GENOME; INTRACELLULAR TRANSPORT; MATHEMATICAL COMPUTING; METABOLISM; METABOLITE; MOLECULAR DYNAMICS; PREDICTION; PROTEIN EXPRESSION; REVIEW; THERMODYNAMICS; TRANSCRIPTION REGULATION;

EID: 84866128045     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1002662     Document Type: Review

References (53)

1. Kim HU, Kim SY, Jeong H, Kim TY, Kim JJ, et al. (2011) Integrative genome-scale metabolic analysis of Vibrio vulnificus for drug targeting and discovery. Mol Syst Biol 7: 460.
2. Park JM, Kim TY, Lee SY, (2009) Constraints-based genome-scale metabolic simulation for systems metabolic engineering. Biotechnol Adv 27: 979-988.
3. Pal C, Papp B, Lercher MJ, Csermely P, Oliver SG, et al. (2006) Chance and necessity in the evolution of minimal metabolic networks. Nature 440: 667-670.
4. Kumar VS, Maranas CD, (2009) GrowMatch: an automated method for reconciling in silico/in vivo growth predictions. PLoS Comput Biol 5: e1000308 doi:10.1371/journal.pcbi.1000308.
5. Reed JL, Patel TR, Chen KH, Joyce AR, Applebee MK, et al. (2006) Systems approach to refining genome annotation. Proc Natl Acad Sci U S A 103: 17480-17484.
6. Satish Kumar V, Dasika MS, Maranas CD, (2007) Optimization based automated curation of metabolic reconstructions. BMC Bioinformatics 8: 212.
7. Bordbar A, Lewis NE, Schellenberger J, Palsson BO, Jamshidi N, (2010) Insight into human alveolar macrophage and M. tuberculosis interactions via metabolic reconstructions. Mol Syst Biol 6: 422.
8. Stolyar S, Van Dien S, Hillesland KL, Pinel N, Lie TJ, et al. (2007) Metabolic modeling of a mutualistic microbial community. Mol Syst Biol 3: 92.
9. Zomorrodi AR, Maranas CD, (2012) OptCom: a multi-level optimization framework for the metabolic modeling and analysis of microbial communities. PLoS Comp Biol 8: e1002363 doi:10.1371/journal.pcbi.1002363.
10. Zhuang K, Izallalen M, Mouser P, Richter H, Risso C, et al. (2011) Genome-scale dynamic modeling of the competition between Rhodoferax and Geobacter in anoxic subsurface environments. ISME J 5: 305-316.
11. Thiele I, Palsson BO, (2010) A protocol for generating a high-quality genome-scale metabolic reconstruction. Nat Protoc 5: 93-121.
12. Henry CS, DeJongh M, Best AA, Frybarger PM, Linsay B, et al. (2010) High-throughput generation, optimization and analysis of genome-scale metabolic models. Nat Biotechnol 28: 977-982.
13. Kanehisa M, Goto S, (2000) KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res 28: 27-30.
14. Karp PD, Paley SM, Krummenacker M, Latendresse M, Dale JM, et al. (2010) Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology. Brief Bioinform 11: 40-79.
15. Lewis NE, Nagarajan H, Palsson BO, (2012) Constraining the metabolic genotype-phenotype relationship using a phylogeny of in silico methods. Nat Rev Microbiol 10: 291-305.
16. Orth JD, Thiele I, Palsson BO, (2010) What is flux balance analysis? Nat Biotechnol 28: 245-248.
17. Schellenberger J, Que R, Fleming RM, Thiele I, Orth JD, et al. (2011) Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0. Nat Protoc 6: 1290-1307.
18. Jensen PA, Papin JA, (2011) Functional integration of a metabolic network model and expression data without arbitrary thresholding. Bioinformatics 27: 541-547.
19. Fleming RM, Thiele I, (2011) von Bertalanffy 1.0: a COBRA toolbox extension to thermodynamically constrain metabolic models. Bioinformatics 27: 142-143.
20. Zur H, Ruppin E, Shlomi T, (2010) iMAT: an integrative metabolic analysis tool. Bioinformatics 26: 3140-3142.
21. Kummel A, Panke S, Heinemann M, (2006) Putative regulatory sites unraveled by network-embedded thermodynamic analysis of metabolome data. Mol Syst Biol 2: 2006.0034.
22. Fleming RM, Thiele I, Nasheuer HP, (2009) Quantitative assignment of reaction directionality in constraint-based models of metabolism: application to Escherichia coli. Biophys Chem 145: 47-56.
23. Henry CS, Broadbelt LJ, Hatzimanikatis V, (2007) Thermodynamics-based metabolic flux analysis. Biophys J 92: 1792-1805.
24. Beg QK, Vazquez A, Ernst J, de Menezes MA, Bar-Joseph Z, et al. (2007) Intracellular crowding defines the mode and sequence of substrate uptake by Escherichia coli and constrains its metabolic activity. Proc Natl Acad Sci U S A 104: 12663-12668.
25. Vazquez A, Beg QK, Demenezes MA, Ernst J, Bar-Joseph Z, et al. (2008) Impact of the solvent capacity constraint on E. coli metabolism. BMC Syst Biol 2: 7.
26. Vazquez A, de Menezes MA, Barabasi AL, Oltvai ZN, (2008) Impact of limited solvent capacity on metabolic rate, enzyme activities, and metabolite concentrations of S. cerevisiae glycolysis. PLoS Comp Biol 4: e1000195 doi:10.1371/journal.pcbi.1000195.
27. Shlomi T, Benyamini T, Gottlieb E, Sharan R, Ruppin E, (2011) Genome-scale metabolic modeling elucidates the role of proliferative adaptation in causing the Warburg effect. PLoS Comput Biol 7: e1002018 doi:10.1371/journal.pcbi.1002018.
28. Zhuang K, Vemuri GN, Mahadevan R, (2011) Economics of membrane occupancy and respiro-fermentation. Mol Syst Biol 7: 500.
29. Pinchuk GE, Hill EA, Geydebrekht OV, De Ingeniis J, Zhang X, et al. (2010) Constraint-based model of Shewanella oneidensis MR-1 metabolism: a tool for data analysis and hypothesis generation. PLoS Comput Biol 6: e1000822 doi:10.1371/journal.pcbi.1000822.
30. Raghunathan A, Reed J, Shin S, Palsson B, Daefler S, (2009) Constraint-based analysis of metabolic capacity of Salmonella typhimurium during host-pathogen interaction. BMC Syst Biol 3: 38.
31. Lewis NE, Hixson KK, Conrad TM, Lerman JA, Charusanti P, et al. (2010) Omic data from evolved E. coli are consistent with computed optimal growth from genome-scale models. Mol Syst Biol 6: 390.
32. Colijn C, Brandes A, Zucker J, Lun DS, Weiner B, et al. (2009) Interpreting expression data with metabolic flux models: predicting mycobacterium tuberculosis mycolic acid production. PLoS Comput Biol 5: e1000489 doi:10.1371/journal.pcbi.1000489.
33. Becker SA, Palsson BO, (2008) Context-specific metabolic networks are consistent with experiments. PLoS Comput Biol 4: e1000082 doi:10.1371/journal.pcbi.1000082.
34. Shlomi T, Cabili MN, Herrgard MJ, Palsson BO, Ruppin E, (2008) Network-based prediction of human tissue-specific metabolism. Nat Biotechnol 26: 1003-1010.
35. Moxley JF, Jewett MC, Antoniewicz MR, Villas-Boas SG, Alper H, et al. (2009) Linking high-resolution metabolic flux phenotypes and transcriptional regulation in yeast modulated by the global regulator Gcn4p. Proc Natl Acad Sci U S A 106: 6477-6482.
36. De Smet R, Marchal K, (2010) Advantages and limitations of current network inference methods. Nat Rev Microbiol 8: 717-729.
37. Rodionov DA, (2007) Comparative genomic reconstruction of transcriptional regulatory networks in bacteria. Chem Rev 107: 3467-3497.
38. Herrgard MJ, Covert MW, Palsson BO, (2004) Reconstruction of microbial transcriptional regulatory networks. Curr Opin Biotechnol 15: 70-77.
39. Covert MW, Schilling CH, Palsson B, (2001) Regulation of gene expression in flux balance models of metabolism. J Theor Biol 213: 73-88.
40. Covert MW, Knight EM, Reed JL, Herrgard MJ, Palsson BO, (2004) Integrating high-throughput and computational data elucidates bacterial networks. Nature 429: 92-96.
41. Covert MW, Palsson BO, (2002) Transcriptional regulation in constraints-based metabolic models of Escherichia coli. J Biol Chem 277: 28058-28064.
42. Shlomi T, Eisenberg Y, Sharan R, Ruppin E, (2007) A genome-scale computational study of the interplay between transcriptional regulation and metabolism. Mol Syst Biol 3: 101.
43. Chandrasekaran S, Price ND, (2010) Probabilistic integrative modeling of genome-scale metabolic and regulatory networks in Escherichia coli and Mycobacterium tuberculosis. Proc Natl Acad Sci U S A 107: 17845-17850.
44. Feng X, Xu Y, Chen Y, Tang YJ, (2012) Integrating flux balance analysis into kinetic models to decipher the dynamic metabolism of Shewanella oneidensis MR-1. PLoS Comput Biol 8: e1002376 doi:10.1371/journal.pcbi.1002376.
45. Hanly TJ, Henson MA, (2011) Dynamic flux balance modeling of microbial co-cultures for efficient batch fermentation of glucose and xylose mixtures. Biotechnol Bioeng 108: 376-385.
46. Schomburg I, Chang A, Ebeling C, Gremse M, Heldt C, et al. (2004) BRENDA, the enzyme database: updates and major new developments. Nucleic Acids Res 32: D431-D433.
47. Wittig U, Kania R, Golebiewski M, Rey M, Shi L, et al. (2012) SABIO-RK-database for biochemical reaction kinetics. Nucleic acids res 40: D790-D796.
48. Jamshidi N, Palsson BO, (2008) Formulating genome-scale kinetic models in the post-genome era. Mol Syst Biol 4: 171.
49. Fleming RM, Thiele I, Provan G, Nasheuer HP, (2010) Integrated stoichiometric, thermodynamic and kinetic modelling of steady state metabolism. J Theor Biol 264: 683-692.
50. Smallbone K, Simeonidis E, Swainston N, Mendes P, (2010) Towards a genome-scale kinetic model of cellular metabolism. BMC Syst Biol 4: 6.
51. Soh KC, Miskovic L, Hatzimanikatis V, (2012) From network models to network responses: integration of thermodynamic and kinetic properties of yeast genome-scale metabolic networks. FEMS Yeast Res 12: 129-143.
52. Yizhak K, Benyamini T, Liebermeister W, Ruppin E, Shlomi T, (2010) Integrating quantitative proteomics and metabolomics with a genome-scale metabolic network model. Bioinformatics 26: i255-i260.
53. Taffs R, Aston JE, Brileya K, Jay Z, Klatt CG, et al. (2009) In silico approaches to study mass and energy flows in microbial consortia: a syntrophic case study. BMC Syst Biol 3: 114.