Growth of Escherichia coli MG1655 on LB medium: monitoring utilization of sugars, alcohols, and organic acids with transcriptional microarrays

Abstract

Microorganisms respond to environmental changes by reprogramming their metabolism primarily through altered patterns of gene expression. DNA microarrays provide a tool for exploiting microorganisms as living sensors of their environment. The potential of DNA microarrays to reflect availability of nutrient components during fermentations on complex media was examined by monitoring global gene expression throughout batch cultivation of Escherichia coli MG1655 on Luria-Bertani (LB) medium. Gene expression profiles group into pathways that clearly demonstrate the metabolic changes occurring in the course of fermentation. Functional analysis of the gene expression related to metabolism of sugars, alcohols, and organic acids revealed that E. coli growing on LB medium switches from a sequential mode of substrate utilization to the simultaneous one in the course of the growth. Maltose and maltodextrins are the first of these substrates to support growth. Utilization of these nutrients associated with the highest growth rate of the culture was followed by simultaneous induction of enzymes involved in assimilation of a large group of other carbon sources including D-mannose, melibiose, D-galactose, L-fucose, L-rhamnose, D-mannitol, amino sugars, trehalose, L-arabinose, glycerol, and lactate. Availability of these nutrients to the cells was monitored by induction of corresponding transport and/or catabolic systems specific for each of the compounds.

Adaptation and Heterogeneity of Escherichia coli MC1000 Growing in Complex Environments

“…However, it offers several sugars (next to alcohols and organic acids), i.e., trehalose, arabinose, lactose, and maltose, in significant levels (22). In fact, the level of the major sugar component of LB medium (trehalose) has been reported to be as high as 17% (1,22,40). Trehalose (with an ␣,␣-1,1-glucoside bond between two ␣-glucose units) may thus offer the major entrance to the glycolytic pathway for organisms growing in LB medium.…”

“…All results were positive; in other words, all populations inoculated at 10 3 CFU/ml reached concentrations of 10 7 CFU/ml in late exponential phase (after 9 h), whereas the ancestor was not able to grow (except in D-trehalose, where it reached 10 6 CFU/ml after 9 h). LB medium is known to contain little glucose, which disappears after 2 h of growth of E. coli (1). However, it offers several sugars (next to alcohols and organic acids), i.e., trehalose, arabinose, lactose, and maltose, in significant levels (22).…”

“…Such growth media usually contain inexpensive complex carbon and nitrogen sources that allow good performance (1,2,3,4,5). Besides the complexity of growth media, other parameters, such as mixing efficiency and perturbation, are also understood to allow variability of local substrate concentrations, pH, temperature, and oxygen levels (6).…”

Effects of Fis on Escherichia coli gene expression during different growth stages

“…Hence, there was a growth phase-dependent switch in regulatory emphasis from stimulating certain transport functions during the early exponential growth phase to repressing alternative transport and binding functions during the late-exponential growth phase. Sequential changes in the mode of E. coli substrate utilization during growth in the complex LB medium may also trigger a sequential induction of corresponding transport or catabolic systems during different growth stages (Baev et al, 2006). Therefore, some of these changes in transport gene expression might not be observed in a defined growth medium.…”

Nitrogen Assimilation in Escherichia coli: Putting Molecular Data into a Systems Perspective

“…In the first short phase, the sugars are used for growth, while thereafter, the various catabolizable amino acids present in LB broth are consumed (549). The growth pattern in LB medium is complex, as a switch occurs from a sequential mode to a simultaneous mode of substrate utilization (550). Also, during growth on a mixture of amino acids (serine, aspartate, tryptophan, glutamate, glycine, threonine, and alanine) as C and N sources, a characteristic pattern of sequential and simultaneous consumption was observed (551).…”