Metabolic Changes Associated With Adaptive Diversification in Escherichia coli

Abstract

During a 1000-generation evolution experiment, two types of morphologically and kinetically distinct bacteria repeatedly diverged from a common ancestor in a fully sympatric seasonal environment containing glucose and acetate. To investigate the metabolic modifications associated with this adaptive diversification, we compared transcription profiles of the two derived types and the common ancestor. Both derived types share a suite of common metabolic changes that may represent adaptation to the environment preceding the diversification event. These include improved translation efficiency, glucose uptake capacity via the mal/ lamB genes, upregulation of various transporters during stationary phase, and likely the disruption of the rbs operon. The diversification event is associated with the overexpression of genes involved in the TCA cycle, glyoxylate shunt, acetate consumption, and anaerobic respiration in one type and in acetate excretion in the other. These results reveal that competition for both carbon and oxygen have likely played an important role in the adaptation of Escherichia coli during this adaptive diversification event, where one derived type mainly consumes glucose at a fast rate when oxygen is not limiting, and the other derived type consumes glucose and acetate at a slower rate, even when oxygen is limiting.

Parallel Evolutionary Dynamics of Adaptive Diversification in Escherichia coli

“…Assuming a single origin for each mutation, we infer that these shared mutations occurred before the two sequenced clones last shared a common ancestor. Phenotypically, the FS type represents a novel metabolic strategy, while the SS type is more similar to the ancestral strain [11],[27],[28],[30], and this difference is reflected in the underlying genetics. In all three populations, the FS clones are more genetically distant from the ancestor than the SS clones (paired t test, n  = 4 independent comparisons, two-tailed p  = 0.0008).…”

“…From each population, we chose two large colonies with unambiguous SS growth profiles and two small colonies with unambiguous FS growth profiles for sequencing. For population 20, we used previously isolated clones [30], also from day 156 of the experiment. In this experiment, replicate populations were founded from isogenic lines of E. coli B and cultured in well-mixed condition for 183 d (∼1,230 generations) with daily (∼6.7 generations) transfers to fresh medium (Text S1).…”

Epistasis and frequency dependence influence the fitness of an adaptive mutation in a diversifying lineage

“…In the present work, we use an experimental system in which initially isogenic populations of Escherichia coli B diversified into populations containing two different ecotypes, i.e. bacterial strains occupying different ecological niches, during 1200 generations of experimental evolution (Le Gac et al. 2008; Spencer et al.…”

“…They are named FS (Fast Switcher) and SS (Slow Switcher) in reference to the way they switch from the consumption of one carbon source to the other. SS is a fast glucose consumer and FS an efficient glucose and acetate consumer (Le Gac et al. 2008).…”

“…2008). An analysis of global gene expression (Le Gac et al. 2008) revealed that numerous genes controlled by ArcA, a global regulator of gene expression in response to the redox conditions of growth, are differentially expressed in the two ecotypes.…”