This is supplementary website for the following paper:
Jeremy O’Connell, Mark Tsechansky, Ariel Royal, Dan Boutz, Andrew D. Ellington, Edward M. Marcotte, A proteomic survey of widespread protein aggregation in yeast, Molecular BioSystems, in press (2014).
Nearly 200 subcellular protein bodies have been found in yeast by screening libraries of fluorescently tagged proteins, but cellular roles for these bodies—typically proteins accumulated into large intracellular foci—remain mysterious. We systematically tested foci for roles as metabolic pathway organizing centers, as aggregates, or as protein storage bodies. Tests of induction conditions and co-localization suggested most foci probably do not represent multi-enzyme organizing centers; more likely, they represent aggregates or storage bodies. Heat shock or arsenic stress tended to shift the same proteins into insoluble form, as quantified by mass spectrometry of native proteins. Moreover, affinity purification of several foci-forming proteins showed enrichment for co-purifying chaperones. Finally, the occurrence of glutamine synthetase foci correlated with markers of cell age, while treatment with rapamycin antagonized their formation. Thus, in yeast, we observed broad rejection of the hypothesis that subcellular protein foci generally serve as functional organizing centers for metabolic pathways; rather, widespread aggregation appears common across diverse, normally diffuse cytoplasmic proteins and is increased with age and induced by multiple types of cell stress.
Shotgun proteomics experimental design
To be added
Shotgun proteomics datasets
- RAW files - http://data.marcottelab.org/MSdata/Widespreadaggregation.2013/RAW/
- mzXML files - http://data.marcottelab.org/MSdata/Widespreadaggregation.2013/mzXML/
- FASTA file - http://data.marcottelab.org/MSdata/Widespreadaggregation.2013/fasta
Database search results
- We used 3 search engines (Tide, InsPecT, MS-GFDB) before MSblender integration.
- We used the relative abundance version of the APEX quantification method for quantification.
To be added