Genetic Mutations That Drive Evolutionary Rescue to Lethal Temperature in Escherichia coli

Abstract

Evolutionary rescue occurs when adaptation restores population growth against a lethal stressor. Here, we studied evolutionary rescue by conducting experiments with Escherichia coli at the lethal temperature of 43.0 °C, to determine the adaptive mutations that drive rescue and to investigate their effects on fitness and gene expression. From hundreds of populations, we observed that ∼9% were rescued by genetic adaptations. We sequenced 26 populations and identified 29 distinct mutations. Of these populations, 21 had a mutation in the hslVU or rpoBC operon, suggesting that mutations in either operon could drive rescue. We isolated seven strains of E. coli carrying a putative rescue mutation in either the hslVU or rpoBC operon to investigate the mutations’ effects. The single rescue mutations increased E. coli’s relative fitness by an average of 24% at 42.2 °C, but they decreased fitness by 3% at 37.0 °C, illustrating that antagonistic pleiotropy likely affected the establishment of rescue in our system. Gene expression analysis revealed only 40 genes were upregulated across all seven mutations, and these were enriched for functions in translational and flagellar production. As with previous experiments with high temperature adaptation, the rescue mutations tended to restore gene expression toward the unstressed state, but they also caused a higher proportion of novel gene expression patterns. Overall, we find that rescue is infrequent, that it is facilitated by a limited number of mutational targets, and that rescue mutations may have qualitatively different effects than mutations that arise from evolution to nonlethal stressors.

Whole-genome sequencing analysis of two heat-evolved Escherichia coli strains

“…There is considerable evidence that the HslVU protein complex plays an important role in adaptation to high temperature growth. Mutations in hslVU have been shown to increase the T max in minimal media [ 76 ], impair growth on rich media plates at high temperatures [ 77 ], not impair high temperature rich media plate growth [ 78 , 79 ] and arise mostly when adapting to 37 °C and not higher temperatures [ 80 ]. Mutations in this operon have also been shown to change the expression of hundreds of genes [ 76 ], lead to small cells in minimal media but not rich media [ 77 ], not significantly change cell size in minimal media [ 81 ], and lead to changes in the timing of chromosome separation and/or cell constriction [ 81 ].…”

Structure and Phylogeny of Chloroplast and Mitochondrial Genomes of a Chlorophycean Algae Pectinodesmus pectinatus (Scenedesmaceae, Sphaeropleales)

“…As is known, rpoB, rpoC1 and rpoC2 genes encoded β, β and β" subunits of the PEP core, respectively. Notably, there were two rpoB (rpoBa and rpoBb), two rpoC (rpoC1 and rpoC2) in chloroplast genome of P. pectinatus, different from some green algae and land plants in which rpoB and rpoC genes formed a separate operon designated as RPOBC [57]. In contrast, there is only one rpoB in several plant species, such as Arabidopsis, indicating the evolution factors affecting the evolution of rpoB protein.…”

Genome and transcriptomic analysis of the adaptation of Escherichia coli to environmental stresses

“…24 of these 40 genes were involved in transport, ribosome assembly and amino acid and nucleotide pathways. This suggests that changes in gene expression support the translation process, perhaps to increase the efficiency of microbes at high temperatures [48] . In the future, proteomic analyses may provide deeper insights regarding the changes and evolutionary mechanisms induced by rescuing mutations.…”