Archaeal viruses and bacteriophages: comparisons and contrasts

Pietilä, Maija K.; Demina, Tatiana A.; Atanasova, Nina S.; Oksanen, Hanna M.; Bamford, Dennis H.

doi:10.1016/j.tim.2014.02.007

Cited by 91 publications

(92 citation statements)

References 115 publications

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“…Archaea and their viruses thrive in extreme environments, and most of archaeal viruses characterized so far infect extremophiles, either hyperhalophiles or hyperthermophiles [4][5][6]29]. Viruses infecting archaea display diverse virion morphotypes, some of which are unique.…”

Section: Introductionmentioning

confidence: 99%

“…Viruses infecting archaea display diverse virion morphotypes, some of which are unique. Consequently, archaeal viruses have been classified into over ten viral families and one floating genus, Salterprovirus, by the International Committee on Taxonomy of Viruses (ICTV) [19,29]. To date, about 140 archaeal viruses have been isolated, and most of these belong to the order Caudovirales, which is composed of three families of icosahedral tailed viruses [4-6, 19, 29].…”

Section: Introductionmentioning

confidence: 99%

“…To date, about 140 archaeal viruses have been isolated, and most of these belong to the order Caudovirales, which is composed of three families of icosahedral tailed viruses [4-6, 19, 29]. In addition to these, spherical and linear, spindle-, bottle-and dropletshaped, and pleomorphic viruses are known to infect archaea [4,6,29].…”

Section: Introductionmentioning

confidence: 99%

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Pleolipoviridae, a newly proposed family comprising archaeal pleomorphic viruses with single-stranded or double-stranded DNA genomes

et al. 2015

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Viruses infecting archaea show a variety of virion morphotypes, and they are currently classified into more than ten viral families or corresponding groups. A pleomorphic virus morphotype is very common among haloarchaeal viruses, and to date, several such viruses have been isolated. Here, we propose the classification of eight such viruses and formation of a new family, Pleolipoviridae (from the Greek pleo for more or many and lipos for lipid), containing three genera, Alpha-, Beta-, and Gammapleolipovirus. The proposal is currently under review by the International Committee on Taxonomy of Viruses (ICTV). The members of the proposed family Pleolipoviridae infect halophilic archaea and are nonlytic. They share structural and genomic features and differ from any other classified virus. The virion of pleolipoviruses is composed of a pleomorphic membrane vesicle enclosing the genome. All pleolipoviruses have two major structural protein species, internal membrane and spike proteins. Although the genomes of the pleolipoviruses are single-or double-stranded, linear or circular DNA molecules, they share the same genome organization and gene synteny and show significant similarity at the amino acid level. The canonical features common to all members of the proposed family Pleolipoviridae show that they are closely related and thus form a new viral family.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Pleolipoviridae, a newly proposed family comprising archaeal pleomorphic viruses with single-stranded or double-stranded DNA genomes

et al. 2015

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“…iruses infecting extremophilic archaea have evolved to withstand very high temperatures, low or high pH, or near-saturating salt concentrations (1)(2)(3)(4)(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).…”

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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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“…Most viruses exhibit both morphological and genomic novelties, which have been extensively reviewed in several recent general reviews (3,9,(43)(44)(45)) and compared to those of bacterial viruses (46,47). Many excellent reviews on different archaeal viruses have been published, and the most recent ones include those on structural genomics of archaeal viruses (48,49); lytic viruses and their exceptional release mechanism (50,51); the molecular biology of rudiviruses (52), fuselloviruses (53), and Sulfolobus turreted icosahedral virus (STIV) (51,54,55); as well as lipids of archaeal viruses (56).…”

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Archaeal Extrachromosomal Genetic Elements

Wang

Peng

Shah

et al. 2015

Microbiol Mol Biol Rev

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SUMMARY Research on archaeal extrachromosomal genetic elements (ECEs) has progressed rapidly in the past decade. To date, over 60 archaeal viruses and 60 plasmids have been isolated. These archaeal viruses exhibit an exceptional diversity in morphology, with a wide array of shapes, such as spindles, rods, filaments, spheres, head-tails, bottles, and droplets, and some of these new viruses have been classified into one order, 10 families, and 16 genera. Investigation of model archaeal viruses has yielded important insights into mechanisms underlining various steps in the viral life cycle, including infection, DNA replication and transcription, and virion egression. Many of these mechanisms are unprecedented for any known bacterial or eukaryal viruses. Studies of plasmids isolated from different archaeal hosts have also revealed a striking diversity in gene content and innovation in replication strategies. Highly divergent replication proteins are identified in both viral and plasmid genomes. Genomic studies of archaeal ECEs have revealed a modular sequence structure in which modules of DNA sequence are exchangeable within, as well as among, plasmid families and probably also between viruses and plasmids. In particular, it has been suggested that ECE-host interactions have shaped the coevolution of ECEs and their archaeal hosts. Furthermore, archaeal hosts have developed defense systems, including the innate restriction-modification (R-M) system and the adaptive CRISPR (clustered regularly interspaced short palindromic repeats) system, to restrict invasive plasmids and viruses. Together, these interactions permit a delicate balance between ECEs and their hosts, which is vitally important for maintaining an innovative gene reservoir carried by ECEs. In conclusion, while research on archaeal ECEs has just started to unravel the molecular biology of these genetic entities and their interactions with archaeal hosts, it is expected to accelerate in the next decade.

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Archaeal viruses and bacteriophages: comparisons and contrasts

Cited by 91 publications

References 115 publications

Pleolipoviridae, a newly proposed family comprising archaeal pleomorphic viruses with single-stranded or double-stranded DNA genomes

Pleolipoviridae, a newly proposed family comprising archaeal pleomorphic viruses with single-stranded or double-stranded DNA genomes

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

Archaeal Extrachromosomal Genetic Elements

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