LoQAtE--Localization and Quantitation ATlas of the yeast proteomE. A new tool for multiparametric dissection of single-protein behavior in response to biological perturbations in yeast

Abstract

Living organisms change their proteome dramatically to sustain a stable internal milieu in fluctuating environments. To study the dynamics of proteins during stress, we measured the localization and abundance of the Saccharomyces cerevisiae proteome under various growth conditions and genetic backgrounds using the GFP collection. We created a database (DB) called 'LoQAtE' (Localizaiton and Quantitation Atlas of the yeast proteomE), available online at http://www.weizmann.ac.il/molgen/loqate/, to provide easy access to these data. Using LoQAtE DB, users can get a profile of changes for proteins of interest as well as querying advanced intersections by either abundance changes, primary localization or localization shifts over the tested conditions. Currently, the DB hosts information on 5330 yeast proteins under three external perturbations (DTT, H₂O₂ and nitrogen starvation) and two genetic mutations [in the chaperonin containing TCP1 (CCT) complex and in the proteasome]. Additional conditions will be uploaded regularly. The data demonstrate hundreds of localization and abundance changes, many of which were not detected at the level of mRNA. LoQAtE is designed to allow easy navigation for non-experts in high-content microscopy and data are available for download. These data should open up new perspectives on the significant role of proteins while combating external and internal fluctuations.

Figure 1.

Screen shots of two result windows in a LoQAtE search. The LoQAtE allows various search functions to be performed. Both quick search and advanced search (Search by abundance or localization) (A) enables querying for large groups of proteins and results in the entire localization and abundance data for each protein being presented. In addition, the results of each search can be downloaded in an excel table or as raw images. ‘Search by movement’ (B) allows the user to choose a movement of interest represented as an arrow on a schematic representation of the cell and receive information on all proteins that are assigned to this category.

Figure 2.

Application of LoQAtE to study regulatory networks. Two advanced search options were used to put-together a list of all yeast TFs that changed abundance (search by abundance) or localization (search by movement). (A) Example of change in localization during nitrogen starvation. Scale bar represents 5 µ. (B) The list of 33 TFs was compared with microarray data on expression changes under the same stress condition (14) to uncover that 16 of them were not documented to have any change in their transcripts under the exact same experimental conditions. (C) Using the DB for regulatory motifs (YEASTRACT), we extracted the targets for these 16 TFs and found that an enormous fraction of all changes in protein levels found in LoQAtE during nitrogen starvation (using the Search by Abundance option) (22–24) can be explained by 10 of the TFs.