A novel capsid protein network allows the characteristic inner membrane structure of Marseilleviridae giant viruses

Abstract

Marseilleviridae is a family of the new order of giant viruses, which exhibit a characteristic inner membrane. Here, we investigated the entire structure of tokyovirus, a species of Marseillevirus at 7.7 Å resolution using 1 MV high-voltage cryo-EM and single particle analysis. The minor capsid lattice formed by five proteins, shows a novel structure compared to other icosahedral giant viruses. Under the minor capsid proteins, scaffold proteins connect two five-fold vertices and interact with the inner membrane. Previously reported giant viruses utilise ″tape measure″ proteins, proposed to control its capsid size, which could not be identified in tokyovirus, but scaffold proteins appear to perform a similar role. A density on top of the major capsid protein was identified, which suggested to be a 14kDa glycoprotein. Our observations suggest that the icosahedral particle of Marseilleviridae is constructed with a novel capsid protein network, which allows the characteristic inner membrane structure.

The 4.4 Å structure of the giant Melbournevirus virion belonging to the Marseilleviridae family

“…As reported in other giant virus capsids (Chihara et al 2021, Fang et al 2019, Born et al, 2018, the five-fold axis of the Melbournevirus capsid is filled with a penton base protein pentamer. We performed a rigid body fit of the penton base protein from PBCV-1 (Fang et al, 2019) to this density, but the quality of the fit was marginal.…”

“…3B, C). Previously, Okamoto et al reported that an uncharacterised protein, MEL_236, appeared to have the same abundance as the MCP protein (Okamoto et al, 2018 the correct size (given a margin of error for SDS-PAGE size determination) to correspond with the PAS stain-sensitive kDa protein of tokyovirus previously reported (Chihara et al, 2021).…”

“…Figure 2 shows the capsid viewed from the inside, filtered by local resolution, and focussed on the asymmetric unit encompassing a two, three and fivefold symmetry axes, describing the details of the protein network formed with mCPs. Each component is labelled according to the nomenclature proposed in the segmentation of tokyovirus by Chihara et al (Chihara et al, 2021) and closely follows the motifs previously described. These are individually detailed as follows.…”

“…2). With the improved resolution of the Melbournevirus block-based reconstruction, we can clearly see one of the pentasymmetron component proteins (named as PC-α (Chihara et al, 2021)) revealing two quadruple bundles (each reminiscent of a ferritin monomer (Kayama et al, 2021)) of α-helices, stacked one on top of the other (Fig. 2, Fig.…”

“…The tokyovirus cryo-EM map elucidated the novel capsid protein network of the giant virus including the scaffold proteins which could assist in the formation of the characteristic internal membrane extrusion at the fivefold vertices of the capsid and function in a similar manner to a tape measure protein (Xian et al, 2020). Furthermore, it suggested a glycosylated cap protein was sitting on the MCP trimer (Chihara et al, 2021).…”