Entering new circles: Expansion of the LC8/DYNLL1 interactome in the ciliary-centrosomal network through system-driven motif evolution

Abstract

LC8 is a eukaryotic hub protein that presents a highly conserved interface recognized by short linear motifs (SLiMs) in partner proteins. LC8 was originally associated with the dynein motor complex and was also suggested to promote dimerization of partner proteins. However, the growing list of validated partners with diverse functions suggests that LC8 plays a more general cellular role which is still not fully understood. In this work, we combined computational and experimental approaches in order to gain insights into the LC8 interaction network at the system level. Our machine-learning based pipeline together with functional enrichment analysis revealed that LC8 plays a central role in the ciliary-centrosomal system with several partners involved in various types of ciliopathies. By integrating proteomic data and functional annotations, we identified a high confidence, ciliary-centrosomal specific LC8 partner list of 57 proteins, 15 of which are central to centriole life-cycle organization. Validated binding motifs and the detailed characterization of the interaction with protein OFD1 emphasized the important role of LC8, which was confirmed by confocal microscopy. OFD1, which is a central player in this system, also stood out as an early and highly conserved LC8 partner. However, additional partners showed a more recent evolutionary origin featuring novel proteins as well as novel motifs. Altogether, our results highlight that LC8 plays a major role in the ciliary-centrosomal system and its interaction network underwent a major expansion. This system driven motif evolution contributed to the increased complexity of the organization and regulation of the ciliary-centrosomal system.