High-Throughput Characterization of Protein-Protein Interactions by Reprogramming Yeast Mating

High-throughput methods for screening protein-protein interactions (PPIs) enable the rapid characterization of engineered binding proteins and interaction networks. While existing methods are powerful, none allow quantitative library-on-library characterization of PPIs in a modifiable extracellular environment. Here, we show that sexual agglutination of S. cerevisiae can be reprogrammed to link PPI strength with mating efficiency using yeast synthetic agglutination (YSA). Validation of YSA with 96 previously characterized interactions shows a strong log-linear relationship between mating efficiency and PPI strength for interactions with KDs ranging from 500 pM to 25 M. Using induced chromosomal translocation to pair barcodes representing interacting proteins, thousands of distinct interactions can be screened in a single pot. YSA binding interactions occur in a controllable extracellular environment, and thus studying the effects of environmental factors on PPI networks is possible. YSA enables the high-throughput, quantitative characterization of PPI networks in a fully defined extracellular environment at a library-on-library scale.