Characterization of beneficial mutations in unsaturated fatty acid biosynthesis that are recurrent dead-ends in a long-term evolution experiment with Escherichia coli

Microbes provide an invaluable tool for watching evolution in action. Throughout more than 55,000 generations, lineages of Escherichia coli cells in a long-term evolution experiment (LTEE) grew in a minimal glucose environment and explored different mutational paths to higher fitness. Genome sequencing identifies genes that accrue mutations early in evolution across the twelve evolving populations. These parallel mutations typically provide a significant fitness benefit and often fix in the population. However, some mutations seem to lead to evolutionary dead-ends. In 7 of the 12 LTEE populations, lineages with mutations in the gene coding for the lipid synthesis repressor, fabR, gain traction within the population, but always eventually go extinct. To parse out the fitness benefits and downstream effects, strains with these mutations were constructed. These mutations increase the growth rate and may affect the length of lag phase after each daily transfer. Another mutation that often fixes within eventually successful clades is within the stress response global regulator spoT. A connection between spoT and fabR mutations could be the key to understanding the eventual outcomes within these lineages. Decreased fatty acid synthesis (repressed by FabR) during glucose starvation activates the global repressor SpoT to produce the cellular "alarmone" (p)ppGpp, inhibiting cell growth during the stringent response. Thus, it is possible that fabR mutations that prolong fatty acid synthesis and spoT mutations that alter the production of (p)ppGpp may both benefit cells by affecting the stringent response. In addition, when these two mutations are combined in a single strain they confer nearly an identical increase in fitness as the single mutations alone, strengthening the argument that they may target the same cellular pathway. Preliminary gene expression analyses of fabR mutants confirmed an expected increase in unsaturated fatty acid synthesis and also found signs that membrane damage responses were activated. It is possible that fabR mutants are near a stability cliff that makes them unable to access otherwise beneficial further mutations. Ultimately, this work will elucidate how interactions between the physiological effects of mutations on evolutionary paths to higher fitness may lead to differences in evolvability that ultimately determine success or extinction.