The Hsp90-dependent proteome is conserved and enriched for hub proteins with high levels of protein-protein connectivity

Hsp90 is one of the most abundant and conserved proteins in the cell. Reduced levels or activity of Hsp90 causes defects in many cellular processes and also reveals genetic and non genetic variation within a population. Despite information about Hsp90 protein- protein interactions, a global view of theHsp90-regulated proteome in yeast is unavailable. To investigate the degree of dependency of individual yeast proteins onHsp90,we used the "stable isotope labeling by amino acids in cell culture" method coupled with mass spectrometry to quantify around 4,000 proteins in low-Hsp90 cells. We observed that 904 proteins changed in their abundance by more than 1.5-fold.When compared with the transcriptome of the same population of cells, two-thirds of the mis regulated proteins were observed to be affected posttranscriptionally, of which the majority were down regulated. Further analyses indicated that the down regulated proteins are highly conserved and assume central roles in cellular net works with a high number of protein interacting partners, suggesting that Hsp90 buffers genetic and non genetic variation through regulating protein network hubs. The down regulated proteins were enriched for essential proteins previously not known to be Hsp90-dependent. Finally, we observed that down regulation of transcription factors and mating pathway components by attenuating Hsp90 function led to decreased target gene expression and pheromone response, respectively, providing a direct link between observed proteome regulation and cellular phenotypes.