Comprehensive fitness maps of Hsp90 show widespread environmental dependence

Abstract

Gene-environment interactions have long been theorized to influence molecular evolution. However, the environmental dependence of most mutations remains unknown. Using deep mutational scanning, we engineered budding yeast with all 44,604 single codon changes encoding 14,160 amino acid variants in Hsp90 and quantified growth effects under standard laboratory conditions and under five stress conditions (elevated temperature, nitrogen starvation, elevated salinity, high ethanol concentration, and oxidative stress caused by diamide). To our knowledge these are the largest comprehensive fitness maps of point mutant growth effects that have been determined. The growth effects of many variants differed between each of the conditions, indicating that environmental conditions can have a large impact on the evolution of Hsp90. Multiple variants provided growth advantages relative to wildtype Hsp90 under individual conditions, however these variants tended to exhibit growth defects in other environments. The diversity of Hsp90 sequences observed in extant eukaryotes preferentially contain amino acid variants that supported robust growth under all tested conditions. Thus, rather than favoring substitutions in individual conditions, the long-term selective pressure on Hsp90 may have been that of fluctuating environments, leading to robustness under a variety of conditions.

Comprehensive exploration of the translocation, stability and substrate recognition requirements in VIM-2 lactamase

“…Finally, we demonstrated that VIM-type variants have been continuously evolving by enhancing their resistance as well as altering their substrate specificity in nature. The study of natural variation also reinforces the observation that mutations found to be neutral or beneficial in an experimental setting tend to be enriched in nature as well 34,66 . It is likely that many new VIM variants will emerge in the future, and our results will provide a valuable basis to predict likely mutations and estimate the resistance of newly found variants.…”

“…Essential and temperature dependent residues display an enrichment of sidechain-backbone h-bonding relative to the proportion of h-bonding residues in each class ( Supplementary Fig. 8b, Supplementary Data 7), suggesting-when combined with the formation of a hydrophobic core-these residues are largely involved in protein folding and stability 39,46,66…”

Co-Chaperones in Targeting and Delivery of Misfolded Proteins to the 26S Proteasome

“…Moreover, like other molecular chaperones, HSP90 acts as a buffer upon environmental stress conditions by supporting folding and activation of client proteins. Accordingly, a recent study found that HSP90 has evolved to support growth in multiple stress conditions, and thus to provide cellular robustness [ 119 ].…”

Ancestral sequence reconstruction - An underused approach to understand the evolution of gene function in plants?

“…More recently, this work was expanded to encompass a large and complete multiallelic intragenic fitness landscape of 640 systematically engineered mutations in the protein. Intriguingly, they report local ruggedness in the fitness-landscape topography as well as the existence of epistatic hotspot mutations which combine to render predictability inherently difficult in the absence of mutation-specific information [223] . The study in Arabidopsis is even more epic.…”