title: Qualitative and quantitative multiplexed proteomic analysis of complex yeast protein fractions that modulate the assembly of the yeast prion Sup35p.
abstract: 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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Laboratoire d'Enzymologie et Biochimie Structurales, Centre National de la Recherche Scientifique, Gif-sur-Yvette, France. redeker@lebs.cnrs-gif.fr
authors.forename: Virginie
authors.initials: V
authors.lastname: Redeker
authors.forename: Chris
authors.initials: C
authors.lastname: Hughes
authors.forename: Jimmy
authors.initials: J
authors.lastname: Savistchenko
authors.forename: Johannes P C
authors.initials: JP
authors.lastname: Vissers
authors.forename: Ronald
authors.initials: R
authors.lastname: Melki
mesh_terms: D002853:Chromatography, Liquid; D003600:Cytosol / Q000378:metabolism; D013058:Mass Spectrometry; D010454:Peptide Termination Factors / Q000737:chemistry* / Q000378:metabolism*; D011328:Prions / Q000737:chemistry* / Q000378:metabolism*; D017510:Protein Folding; D055503:Protein Multimerization; D020836:Protein Structure, Quaternary; D059748:Proteolysis; D040901:Proteomics / Q000379:methods*; D012441:Saccharomyces cerevisiae / Q000166:cytology / Q000378:metabolism*; D029701:Saccharomyces cerevisiae Proteins / Q000737:chemistry* / Q000378:metabolism*
chemical_list: D010454:Peptide Termination Factors; D011328:Prions; C068068:SUP35 protein, S cerevisiae; D029701:Saccharomyces cerevisiae Proteins