Isolation and mapping of self-assembling protein domains encoded by the Saccharomyces cerevisiae genome using lambda repressor fusions.

Understanding how proteins are able to form stable complexes is of fundamental interest from the perspective of protein structure and function. Here we show that lambda repressor fusions can be used to identify and characterize homotypic interaction domains encoded by the genome of Saccharomyces cerevisiae, using a selection for polypeptides that can drive the assembly of the DNA binding domain of bacteriophage lambda repressor. Three high complexity libraries were constructed by cloning random fragments of S. cerevisiae DNA as lambda repressor fusions. Repressor fusions encoding homotypic interactions were recovered, identifying oligomerization units in 35 yeast proteins. Seventeen of these interaction domains have not been previously reported, while the other 18 represent homotypic interactions that have been characterized at varying levels of detail. The novel interactions include several predicted coiled-coils as well as domains of unknown structure. With the availability of genomic sequences it should be possible to apply this approach, which provides information about protein-protein interactions that is complementary to that obtained from yeast two-hybrid screens, on a genome-wide scale in yeast or other organisms where large-scale protein-protein interaction data is not available.