The Yeast Reference Interactome
Environmental Yeast Reference Interactome
Literature Benchmark
5209
Background
YeRI
The Center for Cancer Systems Biology (CCSB) at Dana-Farber Cancer Institute is expanding on previous mapping efforts by constructing a proteome-wide map of binary yeast protein-protein interactions, testing ~99% of the SGD-annotated yeast protein-coding genes. All pairwise combinations of yeast protein-coding genes, for which we have a clone available, have been interrogated systematically to identify binary protein-protein interactions, leading to the generation of a fourth map of the yeast protein-protein interactome, referred as YI-II that has been integrated with previously published systematic maps.
EYRI
The Roth lab at the University of Toronto and the University of Pittsburgh has generated the proteome-scale map of binary protein-protein interactions across multiple environments for the yeast S. cerevisiae, the first such map for any eukaryotic cell. Binary protein-protein interactions were interrogated proteome-scale across baseline, DNA damage, oxidative stress, and carbon starvation environments to yield an Environmental Yeast Reference Interactome (EYRI). This portal also includes pilot screens interrogating ~1 million yeast protein pairs across 31 environments.
Method
YeRI
Pairwise combinations of yeast protein-coding genes were tested systematically using high throughput yeast two-hybrid (Y2H) screens to detect protein-protein interactions. All four systematic maps were generated using different assay versions of the canonical yeast two-hybrid system, described in table 1. For maps generated at CCSB (Yu et al and YI-II), the precision of the dataset was tested by validating some of the interactions in multiple orthogonal assays (Venkatesan et al). In total, 4,556 high-quality protein-protein interactions (PPIs) involving 2,552 proteins have been identified by the four maps.
Table 1: Summary of Y2H assay versions
| Version | Strains | Vector details | ||
| Plasmid | Yeast origin of replication | Reporters | ||
|
Uetz screen |
YULH, N106r |
pOBD2, pOAD |
CEN |
GAL1::URA3, GAL1::lacZ |
|
Ito core |
PJ69-2A, MaV204K |
pGBK-RC, pGAD-RD |
CEN |
GAL1::HIS3, GAL2::ADE2, SPAL10::URA3 |
|
YI-I |
Y8800, Y8930 |
pDEST-DB, pDEST-AD |
CEN |
GAL1::HIS3, GAL2::ADE2 |
|
YI-II |
Y8800, Y8930 |
pQZ212, pQZ213 |
2ยต |
GAL1::HIS3, GAL2::ADE2 |
In addition to systematically identifying PPIs experimentally, the yeast interactome map also contains PPIs of comparable high quality from literature curation databases. This subset of literature-curated PPIs currently comprises 5,589 PPIs.
EYRI
To generate the Environmental Yeast Reference Interactome (EYRI) we improved the previous barcode fusion genetics yeast two-hybrid (BFG-Y2H) system (Yachie et al. 2016) by use of a fluorescent reporter (GFP), calling the new method fBFG-Y2H. Furthermore, by constructing a proteome-wide barcoded collection, we applied fBFG-Y2H to generate the Environmental Yeast Reference Interactome (EYRI): an environment-dependent atlas of protein interactions, which includes proteome-scale maps across four environments. To propose local mechanisms and identify global patterns of cellular response to changing environments, we further supplemented this resource with transcriptome and phosphoproteome measurements in matching environments.