Recurrent innovation of protein-protein interactions in theDrosophilapiRNA pathway

Abstract

Despite being essential for fertility, genome defence pathway genes often evolve rapidly. However, little is known about the molecular basis of this adaptation. Here, we characterize the evolution of a protein interaction network within the PIWI-interacting small RNA (piRNA) genome defence pathway inDrosophilaat unprecedented scale and evolutionary resolution. We uncover pervasive rapid evolution of a protein interaction network anchored at the Heterochromatin Protein 1 (HP1) paralog Rhino. Using complementary phylogenetic analysis, high-throughput yeast-two-hybrid matrix screening, andin vivointeraction analyses in cross-species transgenic flies, we characterized at least three distinct evolutionary protein interaction trajectories across ~40 million years ofDrosophilaevolution. The comprehensive cross-species interaction data set covering 11 piRNA pathway proteins of fiveDrosophilaspecies revealed several protein interactions that are fully conserved, indicating functional conservation despite overall rapid amino acid sequence change. Other interactions are preserved through co-evolution and were detected only between proteins in closely related and within species. We also identified sets of species-restricted protein interactions which, through rewiring of a Rhino-anchored transcription factor network, may preserve critical roles in enabling and adapting piRNA production from heterochromatic loci. In sum, our analyses dissected principles of interaction evolution in an adaptively evolving protein-protein interaction network uncovering evolutionary and functional insight into germline piRNA production acrossDrosophilaspecies. Our work provides key experimental evidence in support of a fundamental model proposing that intermolecular interaction innovation is a major molecular mechanism of evolutionary adaptation in protein-coding genes.