Structural and Functional Studies of Archaeal Viruses

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.The last decade has seen resurgent interest in the study of viruses that lie outside traditional agricultural and medical interests. One reason is the growing appreciation of the enormous abundance and impact of viruses on the greater biosphere. For example, the oceans are thought to contain ∼10³¹ viruses, a truly astronomical number (1), making viruses the most abundant biological entities in this ecosystem, where they catalyze turnover of 20% of the oceanic biomass per day (1). Remarkably, the virosphere has now been shown to extend to almost every known environment on earth, including the extreme acidic, thermal, and saline environments where archaeal organisms can be dominant. Thus, because of their abundance and variety, viruses are now thought to represent the greatest reservoir of genetic diversity on the planet (2).A second reason to study archaeal viruses is a growing appreciation for the roles viruses play in evolution. Remarkably with >500 cellular genomes sequenced to date, most show a significant amount of viral or virus-like sequence within their genome, further evidence that viruses play a central role in horizontal gene transfer and help drive the evolution of their hosts. Roles for viruses in cellular evolution are also being considered. Current hypotheses contend that viruses have catalyzed several major evolutionary transitions, including the invention of DNA and DNA replication mechanisms (3), the origin of the eukaryotic nucleus (4), and thus a role in the formation of the three domains of life. In addition, there is also considerable interest in viral genesis and evolution in and of itself. To evaluate these hypotheses and to analyze evolutionary relationships among viruses, knowledge of viruses infecting the archaea is essential, yet these viruses are vastly understudied. Finally, interest in archaeal viruses stems also from the exceptional molecular insight viruses have traditionally provided into host processes; archaeal viruses are certain to provide new insights into the molecular biology of this poorly understood domain of life.Pioneering studies by Wolfram Zillig et al. (5) identified the first archaeal viruses. Although initial studies suggested that viruses infecting the euryarchaea (principally halophiles and methanogens) were similar to head-tail bacteriophage, studies of viruses infecting the hyperthermophilic crenarchaea revealed morphologies suggesting new viral families. Indeed, work by several laboratories has led to the identification of seven new viral families infecting the crenarchaea, the Globuloviridae, Guttaviridae, Fuselloviridae, Bicaudaviridae, Ampullaviridae, Rudiviridae, and Lipothrixviridae (Fig. 1) (6, 7), with STIV³ (8) and STSV1 (9) awaiting assignment. All of these viruses contain double-stranded DNA genomes ranging in size from 13.7 to 75.3 kilobase pairs, encoding 31–74 ORFs. Although many package a circular genome, the filamentous Lipothrixviridae and rod-shaped Rudiviridae are notable exceptions and are the only viruses in any domain known to encapsidate linear double-stranded DNA. Although most crenarchaeal viruses are enveloped, the Rudiviridae are devoid of lipid, and with the exception of the Fuselloviridae, they employ a lytic life cycle, although only STIV and ATV (Bicaudaviridae) are known to cause cell lysis (11).⁴Open in a separate windowFIGURE 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. 8–10, 47, and 48. 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.The exceptional morphology of these viruses has been reviewed (6, 7) and thus is only summarized here (Fig. 1). For the rod-shaped Rudiviridae, plugs are seen at both ends, from which three short tail fibers emanate, whereas the Lipothrixviridae show mop- or claw-like structures at both ends (6). Similarly, the non-tailed icosahedral viruses, STIV and euryarchaeal SH1, have large turrets or spikes that project from the surface (8, 12). In each case, these structures are thought to facilitate virus-host interactions. In contrast, other crenarchaeal viruses utilize a fusiform or lemon-shaped virion, a morphology unique to archaeal viruses. These fusiform viruses generally contain tail fibers or an extended tail on one end that is also involved in host recognition. For ATV, however, nascent particles are devoid of tails when released from the host (13). Remarkably, extended tails develop at both ends of the virion in an extracellular maturation process. Finally, Acidianus bottle-shaped virus (Ampullaviridae) shows an exceptional morphology that differs in its basic architecture from any known virus.