Effect of slow growth on metabolism of Escherichia coli, as revealed by global metabolite pool ("metabolome") analysis

Abstract

Escherichia coli growing on glucose in minimal medium controls its metabolite pools in response to environmental conditions. The extent of pool changes was followed through two-dimensional thin-layer chromatography of all 14C-glucose labelled compounds extracted from bacteria. The patterns of metabolites and spot intensities detected by phosphorimaging were found to reproducibly differ depending on culture conditions. Clear trends were apparent in the pool sizes of several of the 70 most abundant metabolites extracted from bacteria growing in glucose-limited chemostats at different growth rates. The pools of glutamate, aspartate, trehalose, and adenosine as well as UDP-sugars and putrescine changed markedly. The data on pools observed by two-dimensional thin-layer chromatography were confirmed for amino acids by independent analysis. Other unidentified metabolites also displayed different spot intensities under various conditions, with four trend patterns depending on growth rate. As RpoS controls a number of metabolic genes in response to nutrient limitation, an rpoS mutant was also analyzed for metabolite pools. The mutant had altered metabolite profiles, but only some of the changes at slow growth rates were ascribable to the known control of metabolic genes by RpoS. These results indicate that total metabolite pool ("metabolome") analysis offers a means of revealing novel aspects of cellular metabolism and global regulation.

FIG. 1

The metabolome of E. coli growing on glucose. Extracts were obtained from chemostat-grown bacteria at low (a) or high (b) dilution rate with limiting 0.02% glucose or from an exponentially growing culture with 0.2% glucose (c). The extracts were subjected to TLC in solvent system A, and the phosphorimages were labelled with the positions of spots corresponding to the following: 1, glutamate; 2, trehalose; 3, glucose; 4, UDP-glucose plus UDP-galactose; 5, adenosine; 6, aspartate; 7, lysine; 8, UDP-N-acetylglucosamine; 9, glutathione; 10, putrescine. The lettered spots were unidentified compounds mentioned in the text. The origin of the chromatographs was the bottom left.

FIG. 2

The metabolome of E. coli growing on glucose and the effect of an rpoS mutation. The details are as for Fig. 1 except that the extracts were subject to TLC in solvent system B. Panels d and e represent the metabolomes of the rpoS mutant BW2996 growing at low (0.1 h⁻¹) and high (0.6 h⁻¹) dilution rates, respectively.

FIG. 3

Changes in pool sizes as determined by metabolome analysis. The spots corresponding to the compounds identified (a) and unidentified (b) in Fig. 1 and 2 were quantitated with ImageQuant software in four to six independent determinations.

FIG. 3

Changes in pool sizes as determined by metabolome analysis. The spots corresponding to the compounds identified (a) and unidentified (b) in Fig. 1 and 2 were quantitated with ImageQuant software in four to six independent determinations.

FIG. 4

Glutamate pools measured by HPLC analysis. Duplicate samples of the five types of cell extract obtained as for Fig. 2 were analyzed for amino acids by using an AminoMate system. The mean of the glutamate quantities obtained for each type of sample is shown.