On the protein-nucleic acid interplay in dsRNA viruses

Viruses harbouring double-stranded RNA (dsRNA) genomes are highly diverse and their host range spans from bacteria to fungi, plants and mammals. dsRNA viruses share a number of characteristics including the possession of icosahedrally symmetric capsids which shelter their genomes. As many other icosahedral capsids, those of dsRNA viruses have been extensively characterised by cryogenic electron microscopy (cryo-EM). In contrast, in situ structures of genomes and genome-associated proteins such as RNA-dependent RNA polymerases (RdRPs) are scarce due to their characteristic asymmetry and high degree of heterogeneity. This thesis sets to expand the arsenal of image processing algorithms aimed at overcoming such hurdles and to resolve the architectures of capsid interiors in quiescent and mRNA-producing i.e. transcribing φ6 nucleocapsids (QNCs and TNCs), as well as rotavirus QNCs. The φ6 genome is organised in spooled fashion, bearing strong resemblance to the canonical arrangement of viral dsDNA genomes. In φ6 QNCs 12,000 base pairs accounting for over 90% of the entire genome are modelled. φ6 TNCs depict the concerted rearrangements required to activate transcription, namely the outer capsid disassembly, inner capsid expansion and RdRP reorganisation. Rotavirus QNCs paint an entirely different picture as the RdRP-dsRNA interplay displays such extraordinary flexibility that thousands of unique capsid interior arrangements are made possible. Taken together, these results further the understanding of virus capsid interiors and highlight important disparities among dsRNA viruses.