Microbial metabolism: Optimal control of uptake versus synthesis

PeerJ

Volumn 2014, Issue 1, 2014, Pages 1-12

  Frank, Steven A ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Bacteria; Demography; Kin selection; Life history; Metabolic tradeoff; Vitamins

Indexed keywords

ORGANIC COMPOUND;

ARTICLE; BIOCHEMISTRY; DEMOGRAPHY; DYNAMICS; EVOLUTION; GENETIC VARIABILITY; MATHEMATICAL MODEL; MICROBIAL COMMUNITY; MICROBIAL METABOLISM; NONHUMAN; PREDICTION; SYNTHESIS;

EID: 84895749885     PISSN: None     EISSN: 21678359     Source Type: Journal    
DOI: 10.7717/peerj.267     Document Type: Article

References (26)

1. Banga JR. 2008. Optimization in computational systems biology. BMC Systems Biology 2:47
2. Bertrand EM, Allen AE, Dupont CL, NordenKrichmar TM, Bai J, Valas RE, Saito MA. 2012. Influence of cobalamin scarcity on diatom molecular physiology and identification of a cobalamin acquisition protein. Proceedings of the National Academy of Sciences of the United States of America 109:E1762-E1771
3. Crespi BJ. 2001. The evolution of social behavior in microorganisms. Trends in Ecology & Evolution 16:178-183
4. Diard M, Garcia V,Maier L, Remus-Emsermann MNP, Regoes RR, Ackermann M, Hardt W-D. 2013. Stabilization of cooperative virulence by the expression of an avirulent phenotype. Nature 494:353-356
5. Ebenhoh O, Heinrich R. 2001. Evolutionary optimization of metabolic pathways. Theoretical reconstruction of the stoichiometry of ATP and NADH producing systems. Bulletin of Mathematical Biology 63:21-55
6. Fisher RA. 1930. The Genetical Theory of Natural Selection. Clarendon: Oxford
7. Frank SA. 1996.Models of parasite virulence. Quarterly Review of Biology 71:37-78
8. Frank SA. 1998. Foundations of Social Evolution. Princeton, New Jersey: Princeton University Press.
9. Frank SA. 2010a. Demography and the tragedy of the commons. Journal of Evolutionary Biology 23:32-39
10. Frank SA. 2010b. A general model of the public goods dilemma. Journal of Evolutionary Biology 23:1245-1250
11. Frank SA. 2010c.Microbial secretor cheater dynamics. Philosophical Transactions of the Royal Society B 365:2515-2522
12. Frank SA. 2010d. The trade-off between rate and yield in the design of microbial metabolism. Journal of Evolutionary Biology 23:609-613
13. Frank SA. 2013.Microbial evolution: regulatory design prevents cancer-like overgrowths. Current Biology 23:R343-R346
14. Gardner A,West SA, Griffin AS. 2007. Is bacterial persistence a social trait? PLoS ONE 2:e752
15. Hamilton WD. 1970. Selfish and spiteful behaviour in an evolutionary model. Nature 228:1218-1220
16. Handl J, Kell DB, Knowles J. 2007.Multiobjective optimization in bioinformatics and computational biology. IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB) 4:279-292
17. Higuera C, Villaverde AF, Banga JR, Ross J,Moran F. 2012.Multi-criteria optimization of regulation in metabolic networks. PloS ONE 7:e41122
18. Maynard Smith J. 1982. Evolution and the Theory of Games. Cambridge: Cambridge University Press.
19. Pfeiffer T, Schuster S, Bonhoeffer S. 2001. Cooperation and competition in the evolution of ATP-producing pathways. Science 292:504-507
20. Roth JR, Lawrence JG, Bobik TA. 1996. Cobalamin (coenzyme B12): synthesis and biological significance. Annual Reviews inMicrobiology 50:137-181
21. Schuetz R, Kuepfer L, Sauer U. 2007. Systematic evaluation of objective functions for predicting intracellular fluxes in Escherichia coli. Molecular Systems Biology 3:119
22. Schuetz R, Zamboni N, Zampieri M, Heinemann M, Sauer U. 2012.Multidimensional optimality of microbial metabolism. Science 336:601-604
23. Sendin JO, Exler O, Banga JR. 2010.Multi-objective mixed integer strategy for the optimisation of biological networks. IET Systems Biology 4:236-248
24. Stearns SC. 1992. The Evolution of Life Histories. New York: Oxford University Press.
25. Storn R, Price K. 1997. Differential evolution: a simple and efficient heuristic for global optimization over continuous spaces. Journal of Global Optimization 11:341-359
26. West SA, Diggle SP, Buckling A, Gardner A, Griffin AS. 2007. The social lives of microbes. Annual Review of Ecology and Systematics 38:53-77