CryoTEM and image reconstruction of STIV. Turrets extend 13 nm above the virus surface. Image courtesy of Mark Young, (Montana State University-Bozeman, USA).

The structure of a virus that infects a hyperthermophilic archaeon has just been published in the Proceedings of the National Academy of Sciences (USA). The major coat protein in the capsid has striking similarities to both animal and bacterial viruses — raising the exciting prospect that some viruses might have a common ancestor from more than 3 billion years ago.

Of more than 5,000 viruses that have been characterized, only a tiny fraction are parasites of archaeal species. Hyperthermophilic archaea inhabit hostile niches such as boiling hot springs, and evolutionary analyses indicate that this group is one of the most ancient lineages in the tree of life. Virus evolution has not been as easy to address, owing to the lack of homology between viral genes. Now, attention has focused on structural similarities between viral proteins.

Viruses that replicate in archaeal species have been isolated in the past, including four viruses that replicate in Sulfolobus species, but each virus is unrelated to other viruses using genome sequence comparisons. Four new families have been created for these archaeal viruses: Fuselloviridae (spindle-shaped), Rudiviridae (rod-shaped), Lipothrixviridae (filamentous) and Guttaviridae (teardrop).

The virus isolated in this study replicates in a close relative of Sulfolobus solfataricus, but turned out to be different to the other viruses previously isolated from Sulfolobus species. The double-stranded DNA genome contained only 3 open reading frames (ORFs) that had any similarity to previously sequenced genes. Using cryoTEM (transmission electron microscopy) to solve the structure of the virus particle to 27-Å resolution, Rice and co-workers found surprising structural features. The capsid is icosahedral with unusual turret-like protruberances, so the authors have named this virus STIV — Sulfolobus turreted icosahedral virus.

Importantly, the STIV capsid has a similar organization to the capsids of the human adenovirus, bacteriophage PRD1 and an algal virus PBCV-1. Moreover, docking the crystal structures of the major capsid proteins of human adenovirus and PRD1 onto the STIV major capsid protein revealed that all three proteins have a similar arrangement of structural features including β-sheets. Plus, in common with the animal and bacterial viruses, there might be a lipid envelope present, which must be confirmed biochemically.

The lack of ORFs that are conserved between viruses isolated from archaeal species has been puzzling because it might be expected that important genes encoding proteins that govern genome replication, for example, would be conserved. Perhaps parallel evolution in these ecologically isolated species generated their incredible diversity. Going back to basics and using shape as a defining characteristic, like traditional naturalists, has borne fruit for these researchers. By coupling genomics with structural biology, the lineages of the tree of life — even for viruses — might yet be defined.