Abstract
The extraordinary morphologies of viruses infecting hyperthermophilic archaea clearly distinguish them from bacterial and eukaryotic viruses. Moreover, their genomes code for proteins that to a large extend have no related sequences in the extent databases. However, a small pool of genes is shared by overlapping subsets of these viruses, and the most conserved gene, exemplified by the ORF109 of the Acidianus Filamentous Virus 3, AFV3, is present on genomes of members of three viral familes, the Lipothrixviridae, Rudiviridae, and "Bicaudaviridae", as well as of the unclassified Sulfolobus Turreted Icosahedral Virus, STIV. We present here the crystal structure of the protein (Mr = 13.1 kD, 109 residues) encoded by the AFV3 ORF 109 in two different crystal forms at 1.5 and 1.3 Å resolution. The structure of AFV3-109 is a five stranded β-sheet with loops on one side and three helices on the other. It forms a dimer adopting the shape of a cradle that encompasses the best conserved regions of the sequence. No protein with a related fold could be identified except for the ortholog from STIV1, whose structure was deposited at the Protein Data Bank. We could clearly identify a well bound glycerol inside the cradle, contacting exclusively totally conserved residues. This interaction was confirmed in solution by fluorescence titration. Although the function of AFV3-109 cannot be deduced directly from its structure, structural homology with the STIV1 protein, and the size and charge distribution of the cavity suggested it could interact with nucleic acids. Fluorescence quenching titrations also showed that AFV3-109 interacts with dsDNA. Genomic sequence analysis revealed bacterial homologs of AFV3-109 as a part of a putative previously unidentified prophage sequences in some Firmicutes.
Highlights
Studies on viral diversity in geothermally heated aquatic environments, at temperatures above 80°C, resulted in isolation of about two dozens of double-stranded DNA viruses infecting members of the third domain of life, the Archaea [1]
The detailed analysis of their genomes led to the conclusion that hyperthermophilic archaeal viruses are evolutionarily unrelated to other known viruses, and form a singular group in the viral world with a unique origin, or more likely, multiple origins [2]
A most prominent feature of the genomes of hyperthermophilic archaeal viruses is an extremely low number of genes coding for proteins homologous to any sequences in the existing sequence databases, be it proteins of other viruses or those of cellular life forms [2]
Summary
Studies on viral diversity in geothermally heated aquatic environments, at temperatures above 80°C, resulted in isolation of about two dozens of double-stranded DNA viruses infecting members of the third domain of life, the Archaea [1]. Based on morphological and genomic characteristics, these viruses have been assigned to seven novel viral families: stiff, rod-shaped Rudiviridae [3], filamentous Lipothrixviridae [4,5,6,7], spindle-shaped Fuselloviridae [810], droplet-shaped SNDV [11], spherical "Globuloviridae" [12,13], bottle-shaped "Ampullaviridae" [14], and two-tailed "Bicaudaviridae" [15]. A most prominent feature of the genomes of hyperthermophilic archaeal viruses is an extremely low number of genes coding for proteins homologous to any sequences in the existing sequence databases, be it proteins of other viruses or those of cellular life forms [2]. The later protein family has three bacterial representatives in Bacillus subtilis, Clostridium beijerincki, and Alkaliphilus metalliredigenes, with all other members found in archaeal viruses: members of the families Rudiviridae, Lipothrixviridae, Bicaudaviridae and the unclassified STIV [2]. The strong conservation of this protein in otherwise very different virus families suggests it may play an important function
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