Frequent assembly of chimeric complexes in the protein interaction network of an interspecies hybrid

Hybrids between species often show extreme phenotypes. The molecular determinants underlying such phenotypes are yet to be comprehensively explored. In this study, we investigated the phenotypes of an interspecies diploid hybrid in terms of protein-protein interactions detected by protein correlation profiling. We used two yeast species, Saccharomyces cerevisiae and Saccharomyces uvarum, which are interfertile, but yet have proteins diverged enough to be differentiated using mass spectrometry. Most of the protein-protein interactions are similar between hybrid and parents, and are consistent with the assembly of chimeric complexes, which we validated using an orthogonal approach for prefoldin complex. We also identify instances of altered protein-protein interactions in the hybrid, for instance in complexes related to proteostasis and in mitochondrial protein complexes. Overall, this study uncovers likely frequent occurrence of chimeric protein complexes with few exceptions, which may result from incompatibilities or imbalances between the parental proteomes.