Hsp90 shapes adaptation by controlling the fitness consequences of regulatory variation

The essential, stress-responsive protein chaperone Hsp90 impacts adaptation from microbes to humans. Yet the molecular mechanisms involved remain unclear and are often presumed to be driven by variation in opening reading frames. Here, we identify over 1,000 natural genotype-to-phenotype associations governed by Hsp90 at single-nucleotide resolution in Saccharomyces cerevisiae. Strikingly, cis-regulatory variants contributed to the chaperones effect on heredity more strongly than coding variation. Most of these mutations nonetheless impacted clients of Hsp90 or targets of its direct binding partners. The chaperones influence was especially potent on evolutionarily young genes, highlighting its influence on variation central to novelty. Synthetic reconstructions and genome editing revealed that Hsp90 may regulate the relationship between activity and phenotype for many dosage-sensitive genes. The unexpected role of the chaperone in buffering the effects of regulatory variants and releasing their consequences under stress suggests a mechanism for its widespread effects on evolution and development.