SoPPIs: a highly parallelized protein–protein-interaction screening method in prokaryotic and eukaryotic hosts

Protein–protein interactions (PPIs) are at the heart of most cellular processes but despite recent progress, their genome-wide analysis remains challenging. With this in mind, we have developed SoPPIs (sequencing of PPIs), a powerful method that facilitates parallelized PPI analyses using an innovative combination of the split-Cre/loxP system and high-throughput DNA sequencing. Sequential recombination of plasmids encodes information about pairs of interacting proteins in recombined DNA, facilitating their easy and cost-efficient identification by next-generation sequencing. Importantly, SoPPIs works with most soluble proteins, can be implemented in any cell type that can be transformed with episomal plasmids, and is in principle capable of interrogating all possible PPIs in an organism in a single experiment. To demonstrate the power of SoPPIs, we analyzed the composition of the Arabidopsis thaliana LSm/Sm ring, an evolutionarily highly conserved core component of the spliceosome and performed parallelized library screens to identify LSm/Sm-interacting proteins. Given its versatility and usability, we expect SoPPIs to quickly gain popularity and help provide insights into the PPI networks underlying complex biological systems.