Analysis of cell-cycle regulatory linear motifs bound by the pRb retinoblastoma tumor suppressor

PALOPOLI, NICOLÁS; LANG BENJAMIN; SHARAN MALVIKA; BABU MM; GIBSON TJ; CHEMES L.B.

Cambridge

Simposio; Symposium Protein Folding Evolution and Interactions; 2017

St Catherine's College

Linear motifs are key elements of regulatory protein interaction networks. Viruses take advantage of this by evolving linear motifs that hijack and disrupt the host network. Therefore, identifying relevant linear motifs and their binding strength is central to understanding host regulation and viral pathogenesis. However, the degenerate nature of linear motifs makes their identification challenging. The pRb retinoblastoma tumor suppressor protein is a central cell-cycle regulator inactivated in human cancer and targeted by carcinogenic viruses including human papillomavirus and Merkel cell polyomavirus. Many pRb interactions are mediated by the LxCxE motif, present in host and viral proteins. In this study, we undertook a comprehensive analysis of the pRb-binding LxCxE motif in order to improve our ability to identify binders and our understanding of the pRb interaction network. We found that the LxCxE motif was associated with a diversity of protein functions and architectures (Fig. 1). Analysis of sequence alignments representing 1,150 motifs from 13 host proteins and 577 motifs from 6 viral families allowed us to expand the [LI].C.[DE] definition with novel features that account for all relevant contact sites. The positioning of these features differed between viral and cellular motifs, and appeared more constrained in viruses. Host L/C/E core residues were strongly conserved compared to the disordered regions within which they were embedded (p=7.3*10-7, Wilcoxon-ranked test) and were under similar constraint than structural residues (p=0.72). We have identified novel features that expand the definition of the LxCxE motif and will improve its proteome-wide identification. Host LxCxE motifs are highly conserved within vertebrates, suggesting that they play a key role in the pRb network. The central role of the LxCxE motif in viral pathogenesis is underscored by its striking conservation across plant and animal viruses.