Experimental evolution reveals the genetic basis and systems biology of superoxide stress tolerance

E. coli frequently encounters oxidative stress both in its natural environment or in industrial biotechnology. Elucidating the mechanisms behind tolerance to oxidative stress would be beneficial for understanding pathogenesis as well as improving production strain fitness. We make use of adaptive laboratory evolution to develop two strains of E. coli which exhibit 500% increased tolerance to paraquat stress compared to wild type. Evolved strains tolerate oxidative stress by reduction of flux through TCA, dyregulation of iron-uptake genes, and up-regulation of cell motility or iron-sulfur cluster repair genes. Tolerization adaptive laboratory evolution to increase tolerance to paraquat. Transcriptomics was performed on 2 end point strains and WT with and without addition of paraquat. Ribosome profiling was performed on WT, 1 end point strain and a mid-point strain to investigate read-through of a non-sense mutation in aceE PQ1 and PQ2 are end-point strains from an adaptive laboratory evolution (ALE) which took place over 33 days and a total of 8x10^11 cumulative cell divisions (CCD). GLU4 is the wild type strain which comes from LaCroix et. al. 2015 (doi: 10.1128/AEM.02246-14 ). The MP strain was isolated from the midpoint of the evolution of PQ2 at 6x10^11 CCD. Genome mutations for these strains will be available at ALEdb (Phaneuf et. al. 2019 - https://doi.org/10.1093/nar/gky983)