A Structure-Guided Mutation in the Major Capsid Protein Retargets BK Polyomavirus

Abstract

Viruses within a family often vary in their cellular tropism and pathogenicity. In many cases, these variations are due to viruses switching their specificity from one cell surface receptor to another. The structural requirements that underlie such receptor switching are not well understood especially for carbohydrate-binding viruses, as methods capable of structure-specificity studies are only relatively recently being developed for carbohydrates. We have characterized the receptor specificity, structure and infectivity of the human polyomavirus BKPyV, the causative agent of polyomavirus-associated nephropathy, and uncover a molecular switch for binding different carbohydrate receptors. We show that the b-series gangliosides GD3, GD2, GD1b and GT1b all can serve as receptors for BKPyV. The crystal structure of the BKPyV capsid protein VP1 in complex with GD3 reveals contacts with two sialic acid moieties in the receptor, providing a basis for the observed specificity. Comparison with the structure of simian virus 40 (SV40) VP1 bound to ganglioside GM1 identifies the amino acid at position 68 as a determinant of specificity. Mutation of this residue from lysine in BKPyV to serine in SV40 switches the receptor specificity of BKPyV from GD3 to GM1 both in vitro and in cell culture. Our findings highlight the plasticity of viral receptor binding sites and form a template to retarget viruses to different receptors and cell types.

Crystallographic and Glycan Microarray Analysis of Human Polyomavirus 9 VP1 Identifies N -Glycolyl Neuraminic Acid as a Receptor Candidate

“…The BKPyV and SV40 VP1 proteins share a high degree of sequence identity and bind terminal sialic acid in a mostly conserved binding site that differs from the one observed in HPyV9 and LPyV (26,30). However, SV40 displays a preference for receptors containing Neu5Gc over receptors containing Neu5Ac (38), whereas the sialic acid binding site of BKPyV exclusively binds to the smaller Neu5Ac and cannot accommodate the larger glycolyl chain of Neu5Gc (30). Thus, for these two viruses, the receptor specificities correlate well with the biosynthetically available variants of sialic acids in the respective hosts.…”

“…VP1 is the major polyomavirus capsid protein, and a collection of available VP1 structures from different polyomaviruses shows that the protein adopts a jelly roll fold and assembles into a homopentamer around a central cavity (24)(25)(26)(27)(28)(29)(30)(31). While the pentameric core structure is conserved in all VP1 proteins, these structures from different polyomaviruses exhibit substantial differences in the sequence, length, and conformation of their surface-exposed loops.…”

“…These highly variable regions contain the sites for receptor engagement (25)(26)(27)29) as well as antibody binding (21)(22)(23)32). All human polyomavirus VP1 structures known to date engage glycans terminating in 5-N-acetyl neuraminic acid (Neu5Ac) as receptors (27,(29)(30)(31), with, in some cases, drastically different interactions taking place.…”

“…For example, the polyomavirus simian virus 40 (SV40) preferentially binds to the Neu5Gc version of its GM1 ganglioside receptor (38), and this specificity is thought to limit SV40 infections in humans. On the other hand, the closely related human BKPyV exclusively recognizes receptors containing Neu5Ac but not those containing Neu5Gc (30). Similarly, animal rotavirus strains have variable preferences for Neu5Gc or Neu5Ac.…”

Genetic variability of the VP1 gene of BK and JC polyomaviruses in HIV-infected patients

“…External domains of BC and HI loops are the most important domain of the VP1 and play a crucial role in binding to cell surface receptors. Mutations in the VP1 gene, especially in outer loops, may alter biological characteristics of the virus and lead to the selection of more aggressive variants of the virus with different spread and infectivity [33].…”