Maximal sum of metabolic exchange fluxes outperforms biomass yield as a predictor of growth rate of microorganisms

PLoS ONE

Volumn 9, Issue 5, 2014, Pages

  Zarecki, Raphy ^a   Oberhardt, Matthew A ^a   Yizhak, Keren ^a   Wagner, Allon ^a   Segal, Ella Shtifman ^a   Freilich, Shiri ^b   Henry, Christopher S ^c   Gophna, Uri ^a   Ruppin, Eytan ^a  

^a TEL AVIV UNIVERSITY   (Israel)

^b VOLCANI CENTER   (Israel)

^c ARGONNE NATIONAL LABORATORY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANALYTIC METHOD; ARTICLE; BIOENGINEERING; BIOMASS; CANCER INHIBITION; CATABOLISM; CELL GROWTH; CODON USAGE; COMPUTER MODEL; GROWTH RATE; MATHEMATICAL COMPUTING; MICROORGANISM; NONHUMAN; PREDICTION; SUM OF METABOLIC EXCHANGE FLUX; BACTERIUM; BIOCHEMISTRY; BIOLOGICAL MODEL; COMPUTER PROGRAM; COMPUTER SIMULATION; CULTURE MEDIUM; FUNGUS; GROWTH, DEVELOPMENT AND AGING; METABOLISM;

CULTURE MEDIUM;

BACTERIA; BIOCHEMICAL PROCESSES; BIOMASS; COMPUTER SIMULATION; CULTURE MEDIA; FUNGI; METABOLIC NETWORKS AND PATHWAYS; MODELS, BIOLOGICAL; SOFTWARE;

EID: 84901425704     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0098372     Document Type: Article

References (29)

1. Oberhardt MA, Palsson BO, Papin JA (2009) Applications of genome-scale metabolic reconstructions. Mol Syst Biol 5: 320.
2. Fong SS, Palsson BO (2004) Metabolic gene-deletion strains of Escherichia coli evolve to computationally predicted growth phenotypes. Nat Genet 36: 1056-1058. (Pubitemid 41184464)
3. Oh YK, Palsson BO, Park SM, Schilling CH, Mahadevan R (2007) Genome-scale reconstruction of metabolic network in bacillus subtilis based on high-throughput phenotyping and gene essentiality data. J Biol Chem.
4. Maynard Smith J (1978) Optimization Theory in Evolution. Annual Review of Ecology and Systematics 9: 31-56.
5. Schuster S, Pfeiffer T, Fell DA (2008) Is maximization of molar yield in metabolic networks favoured by evolution? J Theor Biol 252: 497-504.
6. Knorr AL, Jain R, Srivastava R (2006) Bayesian-based selection of metabolic objective functions. Bioinformatics.
7. Segre D, Vitkup D, Church GM (2002) Analysis of optimality in natural and perturbed metabolic networks. Proc Natl Acad Sci U S A 99: 15112-15117. (Pubitemid 35334618)
8. Shlomi T, Berkman O, Ruppin E (2005) Regulatory on/off minimization of metabolic flux changes after genetic perturbations. Proc Natl Acad Sci U S A 102: 7695-7700. (Pubitemid 40741033)
9. Schuetz R, Kuepfer L, Sauer U (2007) Systematic evaluation of objective functions for predicting intracellular fluxes in Escherichia coli. Mol Syst Biol 3: 119.
10. Karr JR, Sanghvi JC, Macklin DN, Gutschow MV, Jacobs JM, et al. (2012) A whole-cell computational model predicts phenotype from genotype. Cell 150: 389-401.
11. Thiele I, Jamshidi N, Fleming RM, Palsson BO (2009) Genome-scale reconstruction of Escherichia coli's transcriptional and translational machinery: a knowledge base, its mathematical formulation, and its functional characterization. PLoS Comput Biol 5: e1000312.
12. Lerman JA, Hyduke DR, Latif H, Portnoy VA, Lewis NE, et al. (2012) In silico method for modelling metabolism and gene product expression at genome scale. Nat Commun 3: 929.
13. O'Brien EJ, Lerman JA, Chang RL, Hyduke DR, Palsson BO (2013) Genome-scale models of metabolism and gene expression extend and refine growth phenotype prediction. Mol Syst Biol 9: 693.
14. Adadi R, Volkmer B, Milo R, Heinemann M, Shlomi T (2012) Prediction of Microbial Growth Rate versus Biomass Yield by a Metabolic Network with Kinetic Parameters. PLoS Comput Biol 8: e1002575.
15. Monod J (1949) The growth of bacterial cultures. Annu Rev Microbiol 3: 371-394.
16. Chao L, Levin BR, Stewart FM (1977) Complex Community in a Simple Habitat - Experimental-Study with Bacteria and Phage. Ecology 58: 369-378.
17. Whiteley M, Ott JR, Weaver EA, McLean RJ (2001) Effects of community composition and growth rate on aquifer biofilm bacteria and their susceptibility to betadine disinfection. Environ Microbiol 3: 43-52. (Pubitemid 33124633)
18. Yim H, Haselbeck R, Niu W, Pujol-Baxley C, Burgard A, et al. (2011) Metabolic engineering of Escherichia coli for direct production of 1,4-butanediol. Nat Chem Biol 7: 445-452.
19. Vieira-Silva S, Rocha EP (2010) The systemic imprint of growth and its uses in ecological (meta)genomics. PLoS Genet 6: e1000808.
20. Groeneveld P, Stouthamer AH, Westerhoff HV (2009) Super life-how and why 'cell selection' leads to the fastest-growing eukaryote. FEBS J 276: 254-270.
21. 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.
22. Schuetz R, Zamboni N, Zampieri M, Heinemann M, Sauer U (2012) Multidimensional optimality of microbial metabolism. Science 336: 601-604.
23. 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.
24. Feist AM, Henry CS, Reed JL, Krummenacker M, Joyce AR, et al. (2007) A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information. Mol Syst Biol 3: 121.
25. Mahadevan R, Schilling CH (2003) The effects of alternate optimal solutions in constraint-based genome-scale metabolic models. Metab Eng 5: 264-276. (Pubitemid 38122488)
26. Soga N, Kinosita K, Jr., Yoshida M, Suzuki T (2012) Kinetic equivalence of transmembrane pH and electrical potential differences in ATP synthesis. J Biol Chem 287: 9633-9639.
27. Fischer S, Graber P (1999) Comparison of DeltapH- and Delta***φ***-driven ATP synthesis catalyzed by the H(+)-ATPases from Escherichia coli or chloroplasts reconstituted into liposomes. FEBS Lett 457: 327-332. (Pubitemid 29414716)
28. Brooijmans R, Smit B, Santos F, van Riel J, de Vos WM, et al. (2009) Heme and menaquinone induced electron transport in lactic acid bacteria. Microb Cell Fact 8: 28.
29. Reed JL, Vo TD, Schilling CH, Palsson BO (2003) An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR). Genome Biol 4: R54.