Qualitative and Quantitative Multiplexed Proteomic Analysis of Complex Yeast Protein Fractions That Modulate the Assembly of the Yeast Prion Sup35p

BACKGROUND The aggregation of the baker's yeast prion Sup35p is at the origin of the transmissible [PSI(+)] trait. We and others have shown that molecular chaperones modulate Sup35p aggregation. However, other protein classes might be involved in [PSI(+)] formation. RESULTS We designed a functional proteomic study that combines two techniques to identify modulators of Sup35p aggregation and describe the changes associated to [PSI(+)] formation. The first allows measuring the effect of fractionated Saccharomyces cerevisiae cytosolic extracts from [PSI(+)] and [psi(-)] yeast cells on Sup35p assembly. The second is a multiplex qualitative and quantitative comparison of protein composition of active and inactive fractions using a gel-free and label-free LC-MS approach. We identify changes in proteins involved in translation, folding, degradation, oxido-reduction and metabolic processes. CONCLUSION Our functional proteomic study provides the first inventory list of over 300 proteins that directly or indirectly affect Sup35p aggregation and [PSI(+)] formation. Our results highlight the complexity of the cellular changes accompanying [PSI(+)] formation and pave the way for in vitro studies aimed to document the effect of individual and/or combinations of proteins identified here, susceptible of affecting Sup35p assembly.