The structure of a thermophilic archaeal virus shows a double-stranded DNA viral capsid type that spans all domains of life

Abstract

Of the three domains of life (Eukarya, Bacteria, and Archaea), the least understood is Archaea and its associated viruses. Many Archaea are extremophiles, with species that are capable of growth at some of the highest temperatures and extremes of pH of all known organisms. Phylogenetic rRNA-encoding DNA analysis places many of the hyperthermophilic Archaea (species with an optimum growth >80°C) at the base of the universal tree of life, suggesting that thermophiles were among the first forms of life on earth. Very few viruses have been identified from Archaea as compared to Bacteria and Eukarya. We report here the structure of a hyperthermophilic virus isolated from an archaeal host found in hot springs in Yellowstone National Park. The sequence of the circular double-stranded DNA viral genome shows that it shares little similarity to other known genes in viruses or other organisms. By comparing the tertiary and quaternary structures of the coat protein of this virus with those of a bacterial and an animal virus, we find conformational relationships among all three, suggesting that some viruses may have a common ancestor that precedes the division into three domains of life >3 billion years ago.

Assessment of a metaviromic dataset generated from nearshore Lake Michigan

“…The study of viruses in the environment, particularly those infectious to bacteria (bacteriophages) and other prokaryotes, has been driven in recent years by several exciting discoveries (Rice et al 2004;Zhao et al 2013). With the advent of improved genomic techniques for molecular-level analyses, microbiologists are slowly uncovering the depth of viral diversity indigenous to areas other than human physiology.…”

Viral assemblage composition in Yellowstone acidic hot springs assessed by network analysis

“…Of the four characterized Rudiviridae, SIRV-1 and SIRV-2 (Prangishvili et al, 1999) were found associated together within their own distinct groups (ARV-1 and SRV are described below). Spherical viruses STIV-1 and STIV-2 (from the proposed 'Turriviridae'; Rice et al, 2004;Happonen et al, 2010) were also found tightly centered within a single group as well. The largest viral group in the seeded network was the SIRV-1 and 2 group, comprising 3.2% of the network contigs (0.15% of reads) and 1.9% of all contigs.…”

Hot new virus, deep connections

“…By simply discovering and describing STIV, Rice et al (1) have rendered a service to science. The properties of biological organisms cannot be predicted from first principles, because they are the products of evolution.…”

“…The function of the turrets is not known, but a plausible guess is that they have a role in attaching the virus to the cell and initiating infection. The morphological features are the basis for the authors' name for the virus: STIV, for Sulfolobus turreted icosahedral virus (1).…”

“…Many examples of such discoveries can be cited (cycads, duck-billed platypuses, giant tortoises, Komodo dragons, and animalcules among them) and, in the most successful cases (think of Mr. Darwin), the new creature(s) dramatically enhanced our understanding of the structure and history of the biological world as a whole. Fortunately for the excitement quotient of modern-day natural historians, Mother Nature's reservoir of undiscovered bizarre and wonderful organisms is not yet empty, and a new one makes the transition from unknown to known with the report by Rice et al (1) in this issue of PNAS.…”