About

This project is described in the preprint:

https://www.biorxiv.org/content/10.1101/2021.03.16.435663v1

 

As of today, four high-quality systematic yeast PPI datasets are available via this web portal. 

 

Systematic efforts

Uetz-screen: The first mapping effort of the yeast protein interactome (Uetz et al. Nature 2000). Only the subset of PPIs detected in the high-throughput screen of an activation library (692 PPIs), are reported on this web-portal. 

 

Ito-core: The second mapping effort of the yeast interactome (Ito et al. PNAS 2001). Only PPIs from the core data (more than 3 IST hits, 841 PPIs) are reported on this web-portal. 

 

CCSB-YI1: The third systematic map (Yu et al. Science 2008), constructed at CCSB, identified 1,809 binary PPIs after three Y2H screens.

 

YeRI: Our latest mapping effort led to the identification of 1,910 PPIs after testing ~99% of the yeast proteome. This new map was constructed using a novel Y2H assay version, which uses high-copy number 2µ vectors instead of centromeric vectors used by the previously published maps (Uetz library, Ito core and YI-I).

 

The union of these four systematically generated PPI datasets is refered to as ABBI-21, for atlas of binary biophysical interactions, generated in 2021.

 

Y2H screen description of YeRI

Y2H bait and prey libraries: Yeast ORFs from the Harvard Institute of Proteomics collection were transferred by Gateway recombinational cloning (Invitrogen) into Y2H destination vectors pDEST-DB-QZ212 to generate Gal4 DNA binding domain hybrid proteins (DB-ORF) and pDEST-AD-QZ213 to generate Gal4 activation domain hybrid proteins (AD-ORF) as described previously (Dreze et al, Methods in Enzymology 2010).

 

Yeast strains: Yeast strains Y8930 (Genotype: MATa leu2-3,112 trp1-901 his3Δ200 ura3-52 gal4Δ gal80Δ GAL2::ADE2 GAL1::HIS3@LYS2 GAL7::lacZ@met2 cyh2R) and Y8800 (Genotype: MATa leu2-3,112 trp1-901 his3Δ200 ura3-52 gal4Δ gal80Δ GAL2::ADE2 GAL1::HIS3@LYS2 GAL7::lacZ@met2 cyh2R) were transformed with individual DB-ORF and AD-ORF constructs respectively.

 

Vector details:

 

Y2H screens and assay versions: Fresh overnight cultures of individual Y8930:DB-ORF yeast strains were mated against Y8800:AD-ORF mini-libraries containing ~700 different Y8800:AD-ORF yeast strains. After overnight growth at 30ºC in liquid rich medium (YEPD), mated yeast cells were transferred into SC-Leu-Trp liquid media to select for diploids. After overnight incubation at 30ºC diploid yeast cells were spotted onto SC-Leu-Trp-His+1mM 3AT solid media to select for activation of the GAL1::HIS3 reporter gene.

 

Requirements to run the portal

The web browser must be configured to accept cookies. Both Java and JavaScript must be enabled. Java JRE/JDK must be newer than version 1.4.2.

 

Acknowledgments

CCSB interactome mapping and ORFeome cloning efforts are supported by federal grants from the National Human Genome Research Institute.