Comparative analysis of the impact of Heat shock protein 90 kDa or Cdc37 mutation on the yeast proteome

Hsp90 is an abundant and essential molecular chaperone that is required for the folding and/or activity of up to 15%-20% of all yeast proteins. Hsp90 and its cochaperone Cdc37 are of interest due to their cooperative role in chaperoning oncogenic protein kinases. We previously grouped mutants in Saccharomyces cerevisiae Hsp90 into different categories based on the step of the adenosine triphosphate-dependent Hsp90 folding cycle that is disrupted. Here we used a quantitative proteomic approach to compare the impact of two different mutations that target the initial step of loading clients onto Hsp90, one in Hsp90 and one in Cdc37. We also included two Hsp90 mutants that target other steps in the folding pathway. We tested the effects at either 25°C or after a 1-h heat shock at 37°C. As expected, the Cdc37 mutant and the Hsp90 mutant that affects the loading step had similar effects, particularly on protein kinases, demonstrating the potential for using proteomics for testing the impact of alteration of the folding pathway. We also identified non-kinase proteins that may use a similar Cdc37-mediated pathway. Surprisingly, protein kinases were a small subset of the proteins impacted by Cdc37 alteration, challenging the notion that Cdc37 is a kinase-specific cochaperone. We also identified proteins that were most strongly affected by Hsc82 mutants that impact steps other than the loading step. Further analysis of how Hsp90 and cochaperones interact with these additional proteins may provide novel insights into alternative methods of client loading or other poorly understood steps in the folding cycle.