Altered expression of a quality control protease in E. coli reshapes the in vivo mutational landscape of a model enzyme

• Main Authors: Samuel Thompson, Yang Zhang, Christine Ingle, Kimberly A Reynolds, Tanja Kortemme
• Format: Article
• Language: English
• Published: eLife Sciences Publications Ltd 2020-07-01
• Series: eLife
• Subjects: proteostasis; mutational landscapes; activity-stability trade-offs; protein engineering; antibiotic resistance
• Online Access: https://elifesciences.org/articles/53476

Protein mutational landscapes are shaped by the cellular environment, but key factors and their quantitative effects are often unknown. Here we show that Lon, a quality control protease naturally absent in common E. coli expression strains, drastically reshapes the mutational landscape of the metabolic enzyme dihydrofolate reductase (DHFR). Selection under conditions that resolve highly active mutants reveals that 23.3% of all single point mutations in DHFR are advantageous in the absence of Lon, but advantageous mutations are largely suppressed when Lon is reintroduced. Protein stability measurements demonstrate extensive activity-stability tradeoffs for the advantageous mutants and provide a mechanistic explanation for Lon’s widespread impact. Our findings suggest possibilities for tuning mutational landscapes by modulating the cellular environment, with implications for protein design and combatting antibiotic resistance.