Structural and functional studies of archaeal viruses

Abstract

Viruses populate virtually every ecosystem on the planet, including the extreme acidic, thermal, and saline environments where archaeal organisms can dominate. For example, recent studies have identified crenarchaeal viruses in the hot springs of Yellowstone National Park and other high temperature environments worldwide. These viruses are often morphologically and genetically unique, with genomes that show little similarity to genes of known function, complicating efforts to understand their viral life cycles. Here, we review progress in understanding these fascinating viruses at the molecular level and the evolutionary insights coming from these studies.

FIGURE 1.

Morphological diversity in crenarchaeal viruses. A, clockwise, beginning at upper left: STIV (8), a PSV-like virus, Sulfolobus neozealandicus droplet-shaped virus (SNDV) (47), SSV1 (48), STSV1 (9), an ATV-like virus, an SIRV virus, and S. icelandicus filamentous virus (SIFV) (10). Micrographs of SIRV, PSV-like, and ATV-like viruses from Yellowstone National Park are the courtesy of M. J. Y. Other panels are reproduced, with permission, from Refs. –, , and . B, cryoelectron microscopy reconstruction of the STIV particle (8) showing a cutaway view (20) of the T = 31 icosahedral capsid with turret-like projections that extend from each of the 5-fold vertices. Portions of the protein shell (blue) and inner lipid layer (yellow) have been removed to reveal the interior.

FIGURE 2.

SSV1 genome. A, ORFs are shown as open arrows, whereas transcript identities are shown in the interior (black lines). Predicted membrane proteins are indicated (+), as are proteins containing cysteine (*). RHH, ribbon-helix-helix. B, shown is the distribution of cysteine in the hyperthermophilic viral metagenome. Eighteen crenarchaeal viral genomes were combined to create a viral metagenome (19). Similar to the analyses of P. aerophilum (45) and STIV (32), a genome enriched in intracellular proteins was produced by removing predicted extracellular proteins, membrane proteins, proteins exhibiting metal-binding motifs, and proteins found in purified viral particles. A preference for even numbers of cysteines in the predicted intracellular proteins of the metagenome is clearly seen, suggesting an abundance of intracellular disulfide bonds.