Although we have a good understanding of adaptation at the organismal level, there is a paucity of data addressing how organisms adapt at the molecular level. Our study builds on a laboratory experiment carried out by Richard Lenski and colleagues in which 12 replicate bacterial populations were evolved from a common ancestor in an identical glucose-limited environment for >60,000 generations. The fitness of each population increased relative to the ancestor. Whole genome and candidate gene sequencing has found that the fixed mutations are concentrated in relatively few genes. One of these target genes is pykF, which encodes for the glycolytic enzyme pyruvate kinase, which is central to the regulation of energy metabolism. There are eight different mutations found scattered across pyruvate kinase. How are the mutations in pykF causing the increased fitness found in the bacterial phenotype?

Interestingly, the fitness, functional and stability data for the adaptively evolved pyruvate kinase enzymes demonstrate different fitness effects and dynamics. However, the crystal structures and solution structural profiles (SAXS) are surprisingly similar. In conclusion, although the long-term evolution experiment demonstrates a high degree of parallelism with respect to fitness and mutational patterns, our data suggest much less parallelism with respect to protein function. Moreover, our results point to protein dynamics as an important mode for adaptive evolution in proteins.