Structural diversity and conservation among CRESS-DNA bacilladnaviruses revealed through cryo-EM and computational modelling

Abstract

Viruses that infect single-celled algae strongly regulate microalgae growth and community composition through cell lysis, enable nutrient recycling in marine ecosystems, and offer valuable insights into early stages of viral evolution. One major group, the Bacilladnaviridae family of single-stranded DNA viruses, infects diatoms in marine environments. Here, we present the capsid structure of Chaetoceros lorenzianus DNA virus (ClorDNAV, Protobacilladnavirus chaelor) determined at 2.2 [A] resolution, thereby expanding the known structural diversity within the Cressdnaviricota phylum. The ClorDNAV capsid protein (CP) contains a conserved jelly-roll fold and a surface-exposed projection domain, with both N- and C-termini oriented toward the capsid interior. A low-resolution reconstruction of the genome revealed a spooled arrangement of the outer DNA layer, similar to that observed in Chaetoceros tenuissimus DNA virus type II (CtenDNAV-II). Structural comparison with CtenDNAV-II revealed five key CP differences: the absence of surface-exposed C-terminal tails in ClorDNAV, the presence of a helical domain, differences in the projection domain conformation, variation in the number of {beta}-strands in the jelly-roll fold, and the lack of ion-attributed densities at subunit interfaces. Together with the genome reconstruction, these findings underscore the importance of experimentally determined structures for understanding viral architecture and evolution. To complement these results, we analyzed AlphaFold3-predicted CPs from all classified Bacilladnaviridae genera. These models confirmed the conservation of the jelly-roll fold across the family while revealing variability in the surface-exposed and terminal regions, likely reflecting host-specific adaptations and genome packaging strategies. Together, the experimental and predicted structures provide a comprehensive view of structural conservation and divergence in Bacilladnaviridae. Furthermore, the results provide additional structural evidence for the evolution of ssDNA Bacilladnaviridae from a noda-like ssRNA virus ancestor and suggest a shared genome organization within Bacilladnaviridae that resembles those observed in viruses with double-stranded genomes.