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

Sulfolobus turreted icosahedral virus (STIV), an archaeal virus that infects the hyperthermoacidophile Sulfolobus solfataricus, is one of the most well-studied viruses of the domain Archaea. STIV shares structural, morphological, and sequence similarities with viruses from other domains of life, all of which are thought to belong to the same viral lineage. Several of these common features include a conserved coat protein fold, an internal lipid membrane, and a DNA-packaging ATPase. B204 is the ATPase encoded by STIV and is thought to drive packaging of viral DNA during the replication process. Here, we report the crystal structure of B204 along with the biochemical analysis of B204 mutants chosen based on structural information and sequence conservation patterns observed among members of the same viral lineage and the larger FtsK/HerA superfamily to which B204 belongs. Both in vitro ATPase activity assays and transfection assays with mutant forms of B204 confirmed the essentiality of conserved and nonconserved positions. We also have identified two distinct particle morphologies during an STIV infection that differ in the presence or absence of the B204 protein. The biochemical and structural data presented here are not only informative for the STIV replication process but also can be useful in deciphering DNA-packaging mechanisms for other viruses belonging to this lineage. IMPORTANCE STIV is a virus that infects a host from the domainArchaea that replicates in high-temperature, acidic environments. While STIV has many unique features, there exist several striking similarities between this virus and others that replicate in different environments and infect a broad range of hosts from Bacteria and Eukarya. Aside from structural features shared by viruses from this lineage, there exists a significant level of sequence similarity between the ATPase genes carried by these different viruses; this gene encodes an enzyme thought to provide energy that drives DNA packaging into the virion during infection. The experiments described here highlight the elements of this enzyme that are essential for proper function and also provide supporting evidence that B204 is present in the mature STIV virion. In Sulfolobus turreted icosahedral virus (STIV), the open reading frame B204 (previously described as B164) (1, 2) encodes a putative ATPase that is predicted to function as the molecular motor driving viral DNA packaging during infection (3). Interestingly, it has been demonstrated that viruses harboring ATPases homologous to B204 share other common features, such as a spherical morphology, an internal lipid membrane, and a structurally homologous coat protein fold (termed the double ␤-barrel or double jelly roll fold) (4). The structural and functional assessment of viruses belonging to this putative viral lineage can provide insights on viral infection strategies across the three domains of life. In the case of B204, understanding its function has implications for mechanisms by which an ancient molecular motor may h...

Section: Methodsmentioning

confidence: 99%

Structure-Based Mutagenesis of Sulfolobus Turreted Icosahedral Virus B204 Reveals Essential Residues in the Virion-Associated DNA-Packaging ATPase

Dellas

Snyder

Dills

et al. 2016

“…Approximately 11 liters of CHAS hot spring water was collected (2 September 2013), and cells were removed by in-line filtration through a 0.4-m polycarbonate filter (Millipore, Billerica, MA). An iron precipitation method was used to concentrate viral particles (18,32). Briefly, the pH of the hot spring sample was raised to pH 4.0 to induce the formation of virus-trapping iron clusters, and the resulting precipitate was collected by filtration onto a 0.8-m polycarbonate filter (Millipore).…”

Section: Viral Metagenomicsmentioning

confidence: 99%

“…A hot spring water sample was collected in January 2008. Sample collection, virus purification, DNA extraction, amplification by multiple-displacement amplification, GS FLX 454 sequencing by the University of Illinois Sequencing Center, and assembly were described previously (18).…”

Section: Viral Metagenomicsmentioning

confidence: 99%

“…These findings demonstrate the value of viral metagenomics at the gene, community, and population levels to inform viral ecology. Viral metagenomic studies of acidic hot springs (17)(18)(19) and hypersaline environments (20,21) have led to the discovery of partial and full genomes of new archaeal viruses as well as viral groups formed by the clustering of related metagenomic contigs and estimates of total virus community diversity (18,22).…”

mentioning

confidence: 99%

See 1 more Smart Citation

Acidianus Tailed Spindle Virus: a New Archaeal Large Tailed Spindle Virus Discovered by Culture-Independent Methods

Hochstein

Amenábar

Munson-McGee

et al. 2016

The field of viral metagenomics has expanded our understanding of viral diversity from all three domains of life (Archaea, Bacteria, and Eukarya). Traditionally, viral metagenomic studies provide information about viral gene content but rarely provide knowledge about virion morphology and/or cellular host identity. Here we describe a new virus, Acidianus tailed spindle virus (ATSV), initially identified by bioinformatic analysis of viral metagenomic data sets from a high-temperature (80°C) acidic (pH 2) hot spring located in Yellowstone National Park, followed by more detailed characterization using only environmental samples without dependency on culturing. Characterization included the identification of the large tailed spindle virion morphology, determination of the complete 70.8-kb circular double-stranded DNA (dsDNA) viral genome content, and identification of its cellular host. Annotation of the ATSV genome revealed a potential three-domain gene product containing an N-terminal leucine-rich repeat domain, followed by a likely posttranslation regulatory region consisting of high serine and threonine content, and a C-terminal ESCRT-III domain, suggesting interplay with the host ESCRT system. The host of ATSV, which is most closely related to Acidianus hospitalis, was determined by a combination of analysis of cellular clustered regularly interspaced short palindromic repeat (CRISPR)/Cas loci and dual viral and cellular fluorescence in situ hybridization (viral FISH) analysis of environmental samples and confirmed by culture-based infection studies. This work provides an expanded pathway for the discovery, isolation, and characterization of new viruses using culture-independent approaches and provides a platform for predicting and confirming virus hosts. IMPORTANCEVirus discovery and characterization have been traditionally accomplished by using culture-based methods. While a valuable approach, it is limited by the availability of culturable hosts. In this research, we report a virus-centered approach to virus discovery and characterization, linking viral metagenomic sequences to a virus particle, its sequenced genome, and its host directly in environmental samples, without using culture-dependent methods. This approach provides a pathway for the discovery, isolation, and characterization of new viruses. While this study used an acidic hot spring environment to characterize a new archaeal virus, Acidianus tailed spindle virus (ATSV), the approach can be generally applied to any environment to expand knowledge of virus diversity in all three domains of life. O ur knowledge and understanding of archaeal viruses (viruses that infect Archaea) are limited. Only 117 archaeal viruses are described at some level, with only a few being characterized in any significant depth (1-4). Remarkably, these relatively few archaeal viruses have formed 16 new virus families (5) and have expanded our appreciation of virion morphology, diversity, and gene content (5-7). Known archaeal viruses infect just 16 of 98 known gen...

“…Six viral and 20 cellular metagenomic data sets from Yellowstone hot springs (18)(19)(20) were queried by BLAST for the presence of large spindle virus-like virus MCP sequences. Relatives of ATSV (94 to 100% identity), ATV (65%), and SMV1 (70 to 82%) MCPs were found in DNA metagenomes from 5 hot springs (Fig.…”

mentioning

confidence: 99%

Large Tailed Spindle Viruses of Archaea: a New Way of Doing Viral Business

Hochstein

Bollschweiler

Engelhardt

et al. 2015

bViruses of Archaea continue to surprise us. Archaeal viruses have revealed new morphologies, protein folds, and gene content. This is especially true for large spindle viruses, which infect only Archaea. We present a comparison of particle morphologies, major coat protein structures, and gene content among the five characterized large spindle viruses to elucidate defining characteristics. Structural similarities and a core set of genes support the grouping of the large spindle viruses into a new superfamily. Viruses infecting hosts in the third domain of life (Archaea) have long fascinated virologists due to their unusual morphologies and unique genetic content (1, 2). This is particularly true for the large tailed spindle viruses, which infect only Archaea. These viruses package circular double-stranded DNA (dsDNA) genomes within spindle (or lemon)-shaped virions and have tails protruding from one or both ends. To date, five of these large spindle viruses have been isolated from crenarchaeal hosts replicating in high-temperature hot springs around the world. These include the Acidianus two-tailed virus (ATV), Sulfolobus tengchongensis spindle-shaped virus 1 (STSV1) and STSV2, and Sulfolobus monocaudavirus 1 (SMV1) (3-7). The fifth member is a new virus, Acidianus tailed spindle virus (ATSV; proposed name), which we recently isolated from Crater Hills Alice Spring, a high-temperature (80°C) acidic (pH 2) hot spring in Yellowstone National Park (USA) (Fig. 1A). The 71-kb circular dsDNA genome of ATSV shares ϳ25% of its genes with STSV1 and -2 and a smaller subset with the other large spindle viruses. We and others (8) propose that large spindle viruses are distinguished from the smaller spindle-shaped Fuselloviridae archaeal viruses based on fundamental differences in their major structural proteins, genome content, and overall virion structures.The virion structures of large spindle viruses are often pleomorphic, and for each specific virus, the dimensions of the central lemon-shaped capsid can vary in width and length. For example, ATSV dimensions range from 69 by 133 nm to 138 by 221 nm. The ATSV tails also vary greatly in length, ranging from 35 to 720 nm. Tail lengths are also variable in STSV1 and -2 and SMV1. In contrast to these single-tailed viruses, ATV is initially released from the infected cell as a tailless virion (3). Remarkably, extracellular ATV then develops two elongated tails extending from opposite ends of the spindle-shaped head. In rare cases, two-tailed particles have also been observed for some of the single-tailed viruses (4, 6). However, there is no evidence yet that these tails extend once progeny virions are released from the infected cell. Importantly, cryoelectron tomography suggests that unlike the classical headtailed structures of some bacteriophage, the tails of these large spindle viruses are a continuous structure with the spindle head (Fig. 1A). Finally, both ATV and ATSV have 5-nm-width tail fibers extending 15 to 25 nm from the tips of their tails that are likely involve...