Near atomic structure of flexible filamentous pepino mosaic virus by high resolution cryo-EM

Flexible filamentous viruses belonging to the Alphaflexiviridae family cause from severe to mild diseases in agricultural crops, often reducing yield and crop quality. Viral particles from the Alphaflexiviridae group are formed by a (+)ssRNA molecule encapsidated by single capsid protein (CP) monomers arranged in helical fashion. Pepino mosaic virus (PepMV) is a flexible filamentous plant virus belonging to the genus Potexvirus included in the family Alphaflexiviridae which genome consists of a ~6.4 kb (+)ssRNA and encodes five proteins. We report here the structure of intact PepMV virions by cryoEM at 3.9 Å resolution (Agirrezabala et al., 2015). The results and the resolution achieved (Figure 1) allowed the modeling of the CP, the (+)ssRNA and their relative interactions. The CP was modeled starting with the CP from PapMV (Yang et al., 2012), clearly showing a similar folding of the α‐helical domain for the Alphaflexiviridae family. The ssRNA is allocated and protected in a continuous groove of high electropositive potential built up by the CP in helical arrangement. The CP polymerize through a flexible N‐terminal arm providing the structural basis for the flexibility of the virus, in similar organization as the observed for BaMV (DiMaio et al., 2015). Interestingly, the overall structure and organization of CP from PepMV is similar to the organization of nucleoproteins from the Bunyaviridae family, a group of enveloped (‐)ssRNA viruses. Common features include: the folding and arrangement of the α‐helical main domain; the groove for the ssRNA; the N‐terminal arm for polymerization; and the relative position between all these elements. Although structural homology between viruses revealed by their atomic structures is common, in the current case, the different nature of capsid protein and nucleoprotein might have profound evolutionary implications.