Lessons from Experimental Protein Fitness Landscapes

Abstract

Protein fitness landscapes provide new lenses into the biophysical underpinnings of protein structure and function and how these relate to health, disease, and fitness. We developed the first systematic approach to measure how all individual amino acid variants impact protein function. We recently completed fitness analyses of all 14,160 individual amino acid variants of yeast Hsp90 under six different environmental conditions. To our knowledge, these are the largest comprehensive fitness landscapes that have been determined. The growth effects of many variants differed in each of the conditions, indicating that environment can have a large impact on Hsp90 folding and function. For example, we observed more than 600 temperature sensitive amino acid variants that supported wildtype-like growth at standard temperature (30°C) and null-like growth at elevated temperature (37°C). Analyses of individual mutations indicates two main mechanisms underlying temperature sensitive Hsp90 variants: increased demand for Hsp90 function at elevated temperature, and additional challenges for Hsp90 to fold into native and active conformations at elevated temperature. In addition to increased sensitivity to mutations in stress conditions, multiple Hsp90 variants outcompeted wildtype under certain conditions, but these variants tended to exhibit fitness costs in other environments. The diversity of Hsp90 sequences observed in extant eukaryotes preferentially contain substitutions that support robust growth under all tested conditions. Natural selection on Hsp90 appears to have hindered the accumulation of variants that are adaptive under individual conditions in favor of Hsp90 sequences that are robust to a variety of stressful conditions. Our findings are consistent with most natural populations experiencing a variety of stress conditions consistently over their evolutionary history.