The Crystal Structure of D212 from
            <i>Sulfolobus</i>
            Spindle-Shaped Virus Ragged Hills Reveals a New Member of the PD-(D/E)XK Nuclease Superfamily

Menon, Smita; Eilers, Brian J.; Young, Mark; Lawrence, C. Martin

doi:10.1128/jvi.01663-09

Cited by 21 publications

(24 citation statements)

References 59 publications

(77 reference statements)

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“…The X-ray structure of the D244 orthologue from the Sulfolobus spindle-shaped virus Ragged Hills revealed that the protein is a member of the PD-(D/E)XK nuclease superfamily (84), arguing against the possibility that D244 plays a structural role in virion formation. We could not detect D244 in our virus preparation, although its presence in amounts that were below our detection limit cannot be ruled out.…”

Section: Discussionmentioning

confidence: 99%

Sulfolobus Spindle-Shaped Virus 1 Contains Glycosylated Capsid Proteins, a Cellular Chromatin Protein, and Host-Derived Lipids

Quemin

Pietilä

Oksanen

et al. 2015

J Virol

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Geothermal and hypersaline environments are rich in virus-like particles, among which spindle-shaped morphotypes dominate. Currently, viruses with spindle-or lemon-shaped virions are exclusive to Archaea and belong to two distinct viral families. The larger of the two families, the Fuselloviridae, comprises tail-less, spindle-shaped viruses, which infect hosts from phylogenetically distant archaeal lineages. Sulfolobus spindle-shaped virus 1 (SSV1) is the best known member of the family and was one of the first hyperthermophilic archaeal viruses to be isolated. SSV1 is an attractive model for understanding virus-host interactions in Archaea; however, the constituents and architecture of SSV1 particles remain only partially characterized. Here, we have conducted an extensive biochemical characterization of highly purified SSV1 virions and identified four virus-encoded structural proteins, VP1 to VP4, as well as one DNA-binding protein of cellular origin. The virion proteins VP1, VP3, and VP4 undergo posttranslational modification by glycosylation, seemingly at multiple sites. VP1 is also proteolytically processed. In addition to the viral DNA-binding protein VP2, we show that viral particles contain the Sulfolobus solfataricus chromatin protein Sso7d. Finally, we provide evidence indicating that SSV1 virions contain glycerol dibiphytanyl glycerol tetraether (GDGT) lipids, resolving a long-standing debate on the presence of lipids within SSV1 virions. A comparison of the contents of lipids isolated from the virus and its host cell suggests that GDGTs are acquired by the virus in a selective manner from the host cytoplasmic membrane, likely during progeny egress. Viruses infecting extremophilic archaea have evolved to withstand very high temperatures, low or high pH, or near-saturating salt concentrations (1-5). Remarkably, most of these viruses do not seem to be evolutionarily related to viruses of bacteria or eukaryotes and display a considerable diversity of unique virion morphotypes (3, 4). Indeed, 11 novel viral families have been established by the International Committee for the Taxonomy of Viruses (ICTV) for the classification of archaeal viruses, emphasizing the uniqueness of rod-shaped, spindle-shaped, dropletshaped, or even bottle-shaped particles that have never been observed among viruses infecting bacteria or eukaryotes (3). Functional studies proved to be highly challenging due to the lack of similarity between the protein sequences and structures of archaeal viruses and those from other viruses and cellular organisms (6-10). Among the morphotypes that are exclusively associated with archaea, spindle-shaped viruses are particularly widespread (11) and have been isolated from highly different environments, including deep-sea hydrothermal vents (12-14), hypersaline environments (15-18), anoxic freshwaters (19), cold Antarctic lakes (20), terrestrial hot springs (21-23), and acidic mines (24).Recently, we refined the evolutionary relationships among spindle-shaped viruses by assessing the morph...

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Section: Discussionmentioning

confidence: 99%

Sulfolobus Spindle-Shaped Virus 1 Contains Glycosylated Capsid Proteins, a Cellular Chromatin Protein, and Host-Derived Lipids

Quemin

Pietilä

Oksanen

et al. 2015

J Virol

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“…A second reason to suspect insertion into telomeres is that the predicted MoTeR1 RT protein shares amino acid residues found in the RELendo domains of RTs encoded by site-specific retroelements that recognize and cleave their genomic targets. The MoTeRs encode proteins with a slight variant of the PD-(D/E) motif, namely AD-D, which happens to be present in the HincII restriction enzyme (Menon et al 2010) and several newly identified type II endonucleases (Kosinski et al 2005). The presence of a REL-endo domain suggests that MoTeR insertion also initiates through the recognition and cleavage of a specific sequence-in this case, telomere repeats.…”

Section: Discussionmentioning

confidence: 99%

Telomere-Targeted Retrotransposons in the Rice Blast Fungus Magnaporthe oryzae: Agents of Telomere Instability

Starnes¹,

Thornbury

Новикова

et al. 2012

Genetics

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The fungus Magnaporthe oryzae is a serious pathogen of rice and other grasses. Telomeric restriction fragments in Magnaporthe isolates that infect perennial ryegrass (prg) are hotspots for genomic rearrangement and undergo frequent, spontaneous alterations during fungal culture. The telomeres of rice-infecting isolates are very stable by comparison. Sequencing of chromosome ends from a number of prg-infecting isolates revealed two related non-LTR retrotransposons (M. oryzae Telomeric Retrotransposons or MoTeRs) inserted in the telomere repeats. This contrasts with rice pathogen telomeres that are uninterrupted by other sequences. Genetic evidence indicates that the MoTeR elements are responsible for the observed instability. MoTeRs represent a new family of telomere-targeted transposons whose members are found exclusively in fungi.T ELOMERES are the sequences that form the ends of linear chromosomes and are essential for maintaining the integrity of terminal DNA. In most organisms, the telomeres are composed of tandem arrays of short sequence motifs that are added on to the 39 ends of chromosomes by telomerase-a specialized reverse transcriptase (Greider and Blackburn 1989;Yu et al. 1990). This prevents the loss of DNA that would normally occur as a result of conservative DNA replication. The telomeres are bound by numerous proteins that shelter the terminal sequences from degradation (Garvik et al. 1995;Vodenicharov and Wellinger 2006) and illegitimate recombination (Dubois et al. 2002). Certain Diptera lack telomerase and, instead, their chromosome termini are maintained by different types of repeats (Saiga and Edstrom 1985;Biessmann et al. 1998;. The most striking example is in Drosophila whose telomeres are composed of arrays of non-LTR retrotransposons George et al. 2006), which are capable of transposing to free DNA ends (Traverse and Pardue 1988;Biessmann et al. 1990). The extension of chromosome ends through the addition of transposon sequences not only solves the end-replication problem but also serves to establish a nucleoprotein complex that is essential for protecting the chromosome ends and maintaining telomere homoeostasis (Fanti et al. 1998;Perrini et al. 2004).In many organisms, the telomeres are attached to a specific sequence that is duplicated (although often not perfectly) at many, and sometimes all, chromosome ends. Such sequences, which usually are TG-rich and often contain short tandem repeats, define a distinct distal subtelomere domain (Pryde et al. 1997). In addition to possessing distally located subtelomere domains, several organisms have proximal domains that contain genes and gene families that are also variously dispersed among different chromosome ends (Pryde et al. 1997). High levels of subtelomere polymorphism are found in many organisms, including vertebrates (Wilkie et al. 1991;Bassham et al. 1998;Baird et al. 2000;Mefford et al. 2001), insects (Biessmann et al. 1998Anderson et al. 2008;Kern and Begun 2008), plants (Yang et al. 2005), and fungi (Naumov et al. 1995Na...

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“…The only nonessential core gene was vp3, which is surprising considering its high degree of conservation and presence as a minor structural protein within the virion (17,18,20). Because the VP3 and proteolytically processed VP1 proteins are highly similar (Fig.…”

Section: Discussionmentioning

confidence: 98%

“…SSV1-B251 possesses NTP binding motifs and is predicted to be homologous to the bacterial dnaA gene (28). The structure of SSV8-D212, a homologue of SSV1-D244, has a predicted nuclease fold, although activity was not demonstrated biochemically (20). SSV1-D244 was identified in one study by mass spectrometry of purified SSV1 virions, but it was not detected in a later analysis (18,20).…”

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confidence: 99%

“…The structure of SSV8-D212, a homologue of SSV1-D244, has a predicted nuclease fold, although activity was not demonstrated biochemically (20). SSV1-D244 was identified in one study by mass spectrometry of purified SSV1 virions, but it was not detected in a later analysis (18,20). The structure of SSV1-D63 displays a four-helix bundle that is characteristic of a large number of proteins, making a functional prediction difficult (29).…”

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confidence: 99%

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Extreme Mutation Tolerance: Nearly Half of the Archaeal Fusellovirus Sulfolobus Spindle-Shaped Virus 1 Genes Are Not Required for Virus Function, Including the Minor Capsid Protein Gene vp3

Iverson

Goodman

Gorchels

et al. 2017

J Virol

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Viruses infecting the Archaea harbor a tremendous amount of genetic diversity. This is especially true for the spindle-shaped viruses of the family Fuselloviridae, where Ͼ90% of the viral genes do not have detectable homologs in public databases. This significantly limits our ability to elucidate the role of viral proteins in the infection cycle. To address this, we have developed genetic techniques to study the well-characterized fusellovirus Sulfolobus spindle-shaped virus 1 (SSV1), which infects Sulfolobus solfataricus in volcanic hot springs at 80°C and pH 3. Here, we present a new comparative genome analysis and a thorough genetic analysis of SSV1 using both specific and random mutagenesis and thereby generate mutations in all open reading frames. We demonstrate that almost half of the SSV1 genes are not essential for infectivity, and the requirement for a particular gene correlates well with its degree of conservation within the Fuselloviridae. The major capsid gene vp1 is essential for SSV1 infectivity. However, the universally conserved minor capsid gene vp3 could be deleted without a loss in infectivity and results in virions with abnormal morphology. IMPORTANCE Most of the putative genes in the spindle-shaped archaeal hyperthermophile fuselloviruses have no sequences that are clearly similar to characterized genes. In order to determine which of these SSV genes are important for function, we disrupted all of the putative genes in the prototypical fusellovirus, SSV1. Surprisingly, about half of the genes could be disrupted without destroying virus function. Even deletions of one of the known structural protein genes that is present in all known fuselloviruses, vp3, allows the production of infectious viruses. However, viruses lacking vp3 have abnormal shapes, indicating that the vp3 gene is important for virus structure. Identification of essential genes will allow focused research on minimal SSV genomes and further understanding of the structure of these unique, ubiquitous, and extremely stable archaeal viruses.

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The Crystal Structure of D212 from Sulfolobus Spindle-Shaped Virus Ragged Hills Reveals a New Member of the PD-(D/E)XK Nuclease Superfamily

Cited by 21 publications

References 59 publications

Sulfolobus Spindle-Shaped Virus 1 Contains Glycosylated Capsid Proteins, a Cellular Chromatin Protein, and Host-Derived Lipids

Sulfolobus Spindle-Shaped Virus 1 Contains Glycosylated Capsid Proteins, a Cellular Chromatin Protein, and Host-Derived Lipids

Telomere-Targeted Retrotransposons in the Rice Blast Fungus Magnaporthe oryzae: Agents of Telomere Instability

Extreme Mutation Tolerance: Nearly Half of the Archaeal Fusellovirus Sulfolobus Spindle-Shaped Virus 1 Genes Are Not Required for Virus Function, Including the Minor Capsid Protein Gene vp3

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