Open Access Research

Model-based analysis of an adaptive evolution experiment with Escherichia coli in a pyruvate limited continuous culture with glycerol

Ronny Feuer1*, Katrin Gottlieb2, Gero Viertel3, Johannes Klotz3, Steffen Schober3, Martin Bossert3, Oliver Sawodny1, Georg Sprenger2 and Michael Ederer1

Author Affiliations

1 Institute for System Dynamics, University of Stuttgart, Pfaffenwaldring 9, 70569 Stuttgart, Germany

2 Institute of Microbiology, University of Stuttgart, Stuttgart, Germany

3 Institute of Communications Engineering, University of Ulm, Ulm, Germany

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EURASIP Journal on Bioinformatics and Systems Biology 2012, 2012:14  doi:10.1186/1687-4153-2012-14

Published: 3 October 2012

Abstract

Bacterial strains that were genetically blocked in important metabolic pathways and grown under selective conditions underwent a process of adaptive evolution: certain pathways may have been deregulated and therefore allowed for the circumvention of the given block. A block of endogenous pyruvate synthesis from glycerol was realized by a knockout of pyruvate kinase and phosphoenolpyruvate carboxylase in E. coli. The resulting mutant strain was able to grow on a medium containing glycerol and lactate, which served as an exogenous pyruvate source. Heterologous expression of a pyruvate carboxylase gene from Corynebacterium glutamicum was used for anaplerosis of the TCA cycle. Selective conditions were controlled in a continuous culture with limited lactate feed and an excess of glycerol feed. After 200–300 generations pyruvate-prototrophic mutants were isolated. The genomic analysis of an evolved strain revealed that the genotypic basis for the regained pyruvate-prototrophy was not obvious. A constraint-based model of the metabolism was employed to compute all possible detours around the given metabolic block by solving a hierarchy of linear programming problems. The regulatory network was expected to be responsible for the adaptation process. Hence, a Boolean model of the transcription factor network was connected to the metabolic model. Our model analysis only showed a marginal impact of transcriptional control on the biomass yield on substrate which is a key variable in the selection process. In our experiment, microarray analysis confirmed that transcriptional control probably played a minor role in the deregulation of the alternative pathways for the circumvention of the block.