Archaeal Viruses from High-Temperature Environments

Munson-McGee, Jacob; Snyder, Jamie C.; Young, Mark

doi:10.3390/genes9030128

Cited by 58 publications

(47 citation statements)

References 103 publications

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“…Viruses infecting archaea are notoriously diverse in terms of their virion morphologies and gene contents (Pietilä et al, 2014;Wang et al, 2015;Prangishvili et al, 2017;Krupovic et al, 2018;Munson-McGee et al, 2018). Comparative structural and genomic studies show that the archaeal virosphere can be generally divided into two large fractions, the archaea-specific viruses and the cosmopolitan viruses (Iranzo et al, 2016b).…”

Section: Introductionmentioning

confidence: 99%

Integrated mobile genetic elements in Thaumarchaeota

Krupovìč

Makarova

Wolf

et al. 2019

Environmental Microbiology

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Summary To explore the diversity of mobile genetic elements (MGE) associated with archaea of the phylum Thaumarchaeota, we exploited the property of most MGE to integrate into the genomes of their hosts. Integrated MGE (iMGE) were identified in 20 thaumarchaeal genomes amounting to 2 Mbp of mobile thaumarchaeal DNA. These iMGE group into five major classes: (i) proviruses, (ii) casposons, (iii) insertion sequence‐like transposons, (iv) integrative‐conjugative elements and (v) cryptic integrated elements. The majority of the iMGE belong to the latter category and might represent novel families of viruses or plasmids. The identified proviruses are related to tailed viruses of the order Caudovirales and to tailless icosahedral viruses with the double jelly‐roll capsid proteins. The thaumarchaeal iMGE are all connected within a gene sharing network, highlighting pervasive gene exchange between MGE occupying the same ecological niche. The thaumarchaeal mobilome carries multiple auxiliary metabolic genes, including multicopper oxidases and ammonia monooxygenase subunit C (AmoC), and stress response genes, such as those for universal stress response proteins (UspA). Thus, iMGE might make important contributions to the fitness and adaptation of their hosts. We identified several iMGE carrying type I‐B CRISPR‐Cas systems and spacers matching other thaumarchaeal iMGE, suggesting antagonistic interactions between coexisting MGE and symbiotic relationships with the ir archaeal hosts.

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Section: Introductionmentioning

confidence: 99%

Integrated mobile genetic elements in Thaumarchaeota

Krupovìč

Makarova

Wolf

et al. 2019

Environmental Microbiology

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“…However, we know far less about viruses that infect archaea, the third domain of life. New forms of such viruses continue to emerge at a surprising rate 2 , 3 , suggesting that our sampling of such viruses remains quite sparse. In this paper we describe a novel filamentous double-stranded (ds) DNA virus that infects a host living in nearly boiling acid, and show how components of the virion (proteins and lipids) can diverge considerably while preserving the overall virion organization and mode of the dsDNA packaging.…”

Section: Introductionmentioning

confidence: 99%

Structural conservation in a membrane-enveloped filamentous virus infecting a hyperthermophilic acidophile

et al. 2018

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Different forms of viruses that infect archaea inhabiting extreme environments continue to be discovered at a surprising rate, suggesting that the current sampling of these viruses is sparse. We describe here Sulfolobus filamentous virus 1 (SFV1), a membrane-enveloped virus infecting Sulfolobus shibatae. The virus encodes two major coat proteins which display no apparent sequence similarity with each other or with any other proteins in databases. We have used cryo-electron microscopy at 3.7 Å resolution to show that these two proteins form a nearly symmetrical heterodimer, which wraps around A-form DNA, similar to what has been shown for SIRV2 and AFV1, two other archaeal filamentous viruses. The thin (∼ 20 Å) membrane of SFV1 is mainly archaeol, a lipid species that accounts for only 1% of the host lipids. Our results show how relatively conserved structural features can be maintained across evolution by both proteins and lipids that have diverged considerably.

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“…However, the success of the metagenomic surveys depends on the feasibility of obtaining a sufficient concentration of virus genomes in the sample. In the case of extreme thermal environments, the natural habitats of crenarchaea, the concentration of extracellular virions is notoriously low (Inskeep et al ., ; Bolduc et al ., ; Munson‐McGee et al ., ). Accordingly, direct metagenomic sequencing of environmental samples often yields incomplete viral genomes.…”

Section: Introductionmentioning

confidence: 97%

New archaeal viruses discovered by metagenomic analysis of viral communities in enrichment cultures

Liu

Brandt

Ishino

et al. 2019

Environmental Microbiology

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Summary Viruses infecting hyperthermophilic archaea of the phylum Crenarchaeota display enormous morphological and genetic diversity, and are classified into 12 families. Eight of these families include only one or two species, indicating sparse sampling of the crenarchaeal virus diversity. In an attempt to expand the crenarchaeal virome, we explored virus diversity in the acidic, hot spring Umi Jigoku in Beppu, Japan. Environmental samples were used to establish enrichment cultures under conditions favouring virus replication. The host diversity in the enrichment cultures was restricted to members of the order Sulfolobales. Metagenomic sequencing of the viral communities yielded seven complete or near‐complete double‐stranded DNA virus genomes. Six of these genomes could be attributed to polyhedral and filamentous viruses that were observed by electron microscopy in the enrichment cultures. Two icosahedral viruses represented species in the family Portogloboviridae. Among the filamentous viruses, two were identified as new species in the families Rudiviridae and Lipothrixviridae, whereas two other formed a group seemingly distinct from the known virus genera. No particle morphotype could be unequivocally assigned to the seventh viral genome, which apparently represents a new virus type. Our results suggest that filamentous viruses are globally distributed and are prevalent virus types in extreme geothermal environments.

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Archaeal Viruses from High-Temperature Environments

Cited by 58 publications

References 103 publications

Integrated mobile genetic elements in Thaumarchaeota

Integrated mobile genetic elements in Thaumarchaeota

Structural conservation in a membrane-enveloped filamentous virus infecting a hyperthermophilic acidophile

New archaeal viruses discovered by metagenomic analysis of viral communities in enrichment cultures

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