New Structural Insights into the Genome and Minor Capsid Proteins of BK Polyomavirus using Cryo-Electron Microscopy

Abstract

SummaryBK polyomavirus is the causative agent of several diseases in transplant patients and the immunosuppressed. In order to better understand the structure and life cycle of BK, we produced infectious virions and VP1-only virus-like particles in cell culture, and determined their three-dimensional structures using cryo-electron microscopy (EM) and single-particle image processing. The resulting 7.6-Å resolution structure of BK and 9.1-Å resolution of the virus-like particles are the highest-resolution cryo-EM structures of any polyomavirus. These structures confirm that the architecture of the major structural protein components of these human polyomaviruses are similar to previous structures from other hosts, but give new insight into the location and role of the enigmatic minor structural proteins, VP2 and VP3. We also observe two shells of electron density, which we attribute to a structurally ordered part of the viral genome, and discrete contacts between this density and both VP1 and the minor capsid proteins.

Genome packaging within icosahedral capsids and large-scale segmentation in viral genomic sequences

“…The packaging with the such numbers of nucleosomes cannot be in a complete correspondence with the icosahedral symmetry and a part of randomization in nucleosome positioning within capsid observed experimentally (Keller et al, 2009;Saper et al, 2013;Hurdiss et al, 2016) can be attributed to such incomplete correspondence. By analogy with the cryo-EM asymmetric reconstruction for MS2, the results by Saper et al (2013) and Hurdiss et al (2016) indicate the presence of internal fraction in DNA packaging. Such packaging mode can in part be related to the repulsion of positively charged histones from capsid.…”

Icosahedral viruses defined by their positively charged domains: a signature for viral identity and capsid assembly strategy

“…Some viral capsids rely more heavily on CP-CP interactions for assembly, as suggested by the formation of empty capsids in the absence of positively charged domains (e.g., Hepadnaviridae (4)), while others are entirely dependent on R-arms to form the capsid (e.g., Nodaviridae (16) and Alphatetraviridae (John E. Johnson, personal communication). Polyomaviridae and Papillomaviridae are known to pack their genome with histones, suggesting that the R-arms are not sufficient to stabilize or condense the stiffer dsDNA (34). The 8 outliers viruses families in the linear fit represent alternative assembly strategies with little contribution of electrostatic interactions between the capsid and the genome.…”

A VP2/3-derived peptide exhibits potent antiviral activity against BK and JC polyomaviruses by targeting a novel VP1 binding site

“…(VLPs) containing only VP1 is the presence of minor structural proteins at the base of the VP1 297 pentamer pore (Hurdiss et al, 2016). Based on the structural studies presented in Figure 2,3, the 298 proposed mechanism of antiviral action by D1min is through binding of the peptide to the VP1 pore.…”

“…522Multiple structures have been reported previously for infectious polyomavirus virions using both 523 X-ray crystallography and cryo-electron microscopy (cryo-EM), with most reporting the minor 524 structural proteins VP2/3 as a globular density at the base of the VP1 pentamer(Griffith et al, 525 1992;Hurdiss et al, 2016;Liddington et al, 1991). More recently, a cryo-EM structure of an 526 infectious BKV virion mapped the resolved C-terminus of VP2/3, including the region containing 527 the D1min sequence, at the base of the VP1 pentamer(Hurdiss et al, 2018).…”