Adaptive laboratory evolution of Escherichia coli is clever, but its reach is also relatively short

Adaptive laboratory evolution (ALE) is used extensively in industrial microbiology and metabolic engineering for organism improvement. The extensive amount of data available for evolved Escherichia coli – its alleleome - provides an opportunity to assess the effectiveness of this technique in sampling this organism’s available amino acid space. Consistent with the underlying nature of the biological code, among approximately 25,000 amino acid substitutions less than half of the possible amino acid shifts are observed. The directionality of amino acid shifts associated with high growth temperature is not observed in E. coli strains evolved for thermotolerance, other than a possibly significant enrichment of aspartate to glutamate shifts. These results reinforce the relatively constrained nature of short-term E. coli evolutionary experiments, highlighting the need for consideration of complementary approaches for organism improvement.