An in silico study of tymovirus virocells

We used computational tools to study the tymoviral proteome. Past gene sequence comparisons had shown that tymovirus genomes encode five proteins already identified in other viruses; however, our AlphaFold3 modelling found, in addition to their five α-helical and β-sheet structures, five regions of 'intrinsically disordered protein' (IDP). Notably, one of these IDPs is the movement protein (MP), distinguishing it from the structured MPs of other plant viruses. The MP is the largest IDP having some features of structured proteins including genus-specific conserved motifs. All tymovirid methyltransferases (Mtases) have a novel structure that includes a membrane-targeting domain (MTD) at their C-termini. Modelling showed that polymers of 3 or 11 copies of the Mtase:MTD are favoured; the former form complexes with the viral RNA-dependent RNA polymerases, whereas the latter form short rounded cylinders with an equatorial groove. The cylinders are similar in size to the necks of vesicles previously found in the outer chloroplast membranes of all tymovirus-infected plants. The DisLipPred program found that the outer groove of the polymeric cylinders was probably lipophilic and so able to associate stably with plasma membranes. The vesicles are probably the 'replication organelles' of tymoviruses and the cylinders possibly the 'replication organelle organizers'. Modelling also indicated that the tymovirus helicase may function as a tetramer and that the coat protein may form trimer intermediates for assembling the virions. Our study has revealed some of the complexity and three-dimensionality of the viral components of tymovirus virocells.