Cryo-EM study of slow bee paralysis virus at low pH reveals iflavirus genome release mechanism

Abstract

Viruses from the family Iflaviridae are insect pathogens. Many of them, including slow bee paralysis virus (SBPV), cause lethal diseases in honeybees and bumblebees, resulting in agricultural losses. Iflaviruses have nonenveloped icosahedral virions containing single-stranded RNA genomes. However, their genome release mechanism is unknown. Here, we show that low pH promotes SBPV genome release, indicating that the virus may use endosomes to enter host cells. We used cryo-EM to study a heterogeneous population of SBPV virions at pH 5.5. We determined the structures of SBPV particles before and after genome release to resolutions of 3.3 and 3.4 Å, respectively. The capsids of SBPV virions in low pH are not expanded. Thus, SBPV does not appear to form "altered" particles with pores in their capsids before genome release, as is the case in many related picornaviruses. The egress of the genome from SBPV virions is associated with a loss of interpentamer contacts mediated by N-terminal arms of VP2 capsid proteins, which result in the expansion of the capsid. Pores that are 7 Å in diameter form around icosahedral threefold symmetry axes. We speculate that they serve as channels for the genome release. Our findings provide an atomic-level characterization of the genome release mechanism of iflaviruses.electron microscopy | uncoating | honeybee | structure | virus

Virion structure and genome delivery mechanism of sacbrood honeybee virus

“…Furthermore, the presence of two expansion intermediates suggests that the empty SBV capsids are dynamic. The possible role of pores at threefold axes of SBV capsids as channels for genome release is consistent with our previous study of the genome release of SBPV ( 15 ). In contrast, Organtini et al ( 13 ) speculated that the genome of DWV may escape from particles through a channel in a fivefold vertex of its capsid.…”

“…An alternative approach is to label the capsid proteins according to their homology with picornavirus proteins ( 14 ). The homology-based convention was used in the previous structural studies of SBPV and DWV ( 7 , 8 , 15 ). Application of the molecular weight convention results in different gene orders of SBV, DWV, and SBPV.…”

The atomic structures of shrimp nodaviruses reveal new dimeric spike structures and particle polymorphism

“…Our T = 3 PvNV-LP and previous MrNV-LP exhibit different rotation and translation of the dimeric P-domains. Such movements of the P-domains have been observed also in slow bee paralysis virus and deformed wing virus under conditions of high salt or low pH 36,37 . To explain the arrangement of surface dimeric P-domains, our crystal structures of the PvNVPd and MrNVPd impose two possibilities of spatial organizations: a parallel conformation or an X-shaped conformation through rolling and tilting over the T = 3 virion surface.…”

Cryo-Electron Microscopy Structure of Seneca Valley Virus Procapsid

“…The B particle is antigenically different from the native virion and has a different protein composition. Altered empty capsids have been structurally characterized in detail for several enterovirus members, such as PV (44), rhinoviruses (45), enterovirus 71 (EV71) (46), coxsackieviruses (47), and equine rhinitis A virus (48), as well as for other picornaviruses, such as kobuviruses (49), or for picorna-like viruses, such as bee viruses (50,51). In all these cases the structures show a capsid expanded by 4 to 6%, lacking VP4, and showing more disorder on the interior of the capsid.…”