Global metabolic network reorganization by adaptive mutations allows fast growth of Escherichia coli on glycerol

Kian-Kai Cheng, Baek-Seok Lee, Takeshi Masuda, Takuro Ito, Kazutaka Ikeda, Akiyoshi Hirayama, Lingli Deng, Jiyang Dong, Kazuyuki Shimizu, Tomoyoshi Soga, Masaru Tomita, Bernhard O. Palsson and Martin Robert ()
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Kian-Kai Cheng: Institute for Advanced Biosciences, Keio University
Baek-Seok Lee: Institute for Advanced Biosciences, Keio University
Takeshi Masuda: Institute for Advanced Biosciences, Keio University
Takuro Ito: Institute for Advanced Biosciences, Keio University
Kazutaka Ikeda: Institute for Advanced Biosciences, Keio University
Akiyoshi Hirayama: Institute for Advanced Biosciences, Keio University
Lingli Deng: Xiamen University
Jiyang Dong: Xiamen University
Kazuyuki Shimizu: Institute for Advanced Biosciences, Keio University
Tomoyoshi Soga: Institute for Advanced Biosciences, Keio University
Masaru Tomita: Institute for Advanced Biosciences, Keio University
Bernhard O. Palsson: University of California, San Diego
Martin Robert: Institute for Advanced Biosciences, Keio University

Nature Communications, 2014, vol. 5, issue 1, 1-9

Abstract: Abstract Comparative whole-genome sequencing enables the identification of specific mutations during adaptation of bacteria to new environments and allelic replacement can establish their causality. However, the mechanisms of action are hard to decipher and little has been achieved for epistatic mutations, especially at the metabolic level. Here we show that a strain of Escherichia coli carrying mutations in the rpoC and glpK genes, derived from adaptation in glycerol, uses two distinct metabolic strategies to gain growth advantage. A 27-bp deletion in the rpoC gene first increases metabolic efficiency. Then, a point mutation in the glpK gene promotes growth by improving glycerol utilization but results in increased carbon wasting as overflow metabolism. In a strain carrying both mutations, these contrasting carbon/energy saving and wasting mechanisms work together to give an 89% increase in growth rate. This study provides insight into metabolic reprogramming during adaptive laboratory evolution for fast cellular growth.

Date: 2014
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DOI: 10.1038/ncomms4233

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