Archaeal Viruses: Diversity, Replication, and Structure

Dellas, Nikki; Snyder, Jamie C.; Bolduc, Benjamin; Young, Mark

doi:10.1146/annurev-virology-031413-085357

Cited by 54 publications

(61 citation statements)

References 150 publications

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“…Until relatively recent times, the only methodology available to study these viruses was through the cultivation of their hosts (López-López et al 2013). By systematically applying this approach, our knowledge on viruses populating (hyper)thermal environments over the last 30 years has considerably expanded thanks to the pioneer work of Wolfram Zillig and, subsequently, of several groups in Europe and USA (Bize et al 2008;Dellas et al 2013Dellas et al , 2014Diemer and Stedman 2012;Haring et al 2005;Peng et al 2012;Prangishvili et al 2001Prangishvili et al , 2006Prangishvili and Rice et al 2001Rice et al , 2004Snyder et al 2011;Snyder and Young 2013;Zillig et al 1996). While enrichment cultures have been invaluable in the study of thermophilic viruses, contextual information, such as relative abundance, diversity, and distribution, was mainly unknown.…”

Section: Viral Metagenomicsmentioning

confidence: 99%

Metagenomics of microbial and viral life in terrestrial geothermal environments

Strazzulli

Fusco

Cobucci‐Ponzano

et al. 2017

Rev Environ Sci Biotechnol

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Geothermally heated regions of Earth, such as terrestrial volcanic areas (fumaroles, hot springs, and geysers) and deep-sea hydrothermal vents, represent a variety of different environments populated by extremophilic archaeal and bacterial microorganisms. Since most of these microbes thriving in such harsh biotopes, they are often recalcitrant to cultivation; therefore, ecological, physiological and phylogenetic studies of these microbial populations have been hampered for a long time. More recently, culture-independent methodologies coupled with the fast development of next generation sequencing technologies as well as with the continuous advances in computational biology, have allowed the production of large amounts of metagenomic data. Specifically, these approaches have assessed the phylogenetic composition and functional potential of microbial consortia thriving within these habitats, shedding light on how extreme physico-chemical conditions and biological interactions have shaped such microbial communities. Metagenomics allowed to better understand that the exposure to an extreme range of selective pressures in such severe environments, accounts for genomic flexibility and metabolic versatility of microbial and viral communities, and makes extreme-and hyper-thermophiles suitable for bioprospecting purposes, representing an interesting source for novel thermostable proteins that can be potentially used in several industrial processes.Keywords Hyperthermophiles Á Geothermal environments Á Microbial and viral metagenomics Á CRISPR Á Enzyme discovery BackgroundHot springs populated by extreme thermophiles (T opt : 65-79°C) and hyperthermophiles (T opt [ 80°C) (DeCastro et al. 2016) are very diverse and some of them show combinations of extreme chemo-physical conditions, such as temperature, acidic or alkaline pHs, high pressure, and high concentrations of salts and heavy metals (López-López et al. 2013). As with all studies of environmental microbiology, our understanding of the composition, functional and physiological dynamics, and evolution of extreme-and hyper-thermophilic microbial consortia has lagged A. Strazzulli Á M. Moracci Á P. Contursi

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Section: Viral Metagenomicsmentioning

confidence: 99%

Metagenomics of microbial and viral life in terrestrial geothermal environments

Strazzulli

Fusco

Cobucci‐Ponzano

et al. 2017

Rev Environ Sci Biotechnol

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“…A hallmark of archaeal viruses is the high morphological diversity of the capsids that enclose their genetic material Pina et al 2011;Prangishvili 2013;Dellas et al 2014). Even though viruses have only been isolated from a limited set of archaeal species, the high structural diversity of those isolated has led to the description of several new viral families (Pina et al 2011;Krupovic et al 2016;Adriaenssens et al 2017).…”

Section: Introductionmentioning

confidence: 99%

Structure and assembly mechanism of virus-associated pyramids

Quax

Daum

2017

Biophys Rev

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Viruses have developed intricate molecular machines to infect, replicate within and escape from their host cells. Perhaps one of the most intriguing of these mechanisms is the pyramidal egress structure that has evolved in archaeal viruses, such as SIRV2 or STIV1. The structure and mechanism of these virus-associated pyramids (VAPs) has been studied by cryo-electron tomography and complementary biochemical techniques, revealing that VAPs are formed by multiple copies of a virus-encoded 10-kDa protein (PVAP) that integrate into the cell membrane and assemble into hollow, sevenfold symmetric pyramids. In this process, growing VAPs puncture the protective surface layer and ultimately open to release newly replicated viral particles into the surrounding medium. PVAP has the striking capability to spontaneously integrate and self-assemble into VAPs in biological membranes of the archaea, bacteria and eukaryotes. This renders the VAP a universal membrane remodelling system. In this review, we provide an overview of the VAP structure and assembly mechanism and discuss the possible use of VAPs in nanobiotechnology.

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“…These archaeal viruses comprise members originally isolated from high temperature environments (37 of the 67 viruses) and viruses not expected to be present in hot spring environments (30 mostly halophile viruses from mesophilic environments), such as those infecting members of the Euryarchaeota (for a review of archaeal viruses, see Prangishvili, 2013;Dellas et al, 2014). The vast majority of known viral genomes did not map to any of the network clusters (1786/1812).…”

Section: Network Viral Groups: What They Representmentioning

confidence: 99%

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

et al. 2015

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Understanding of viral assemblage structure in natural environments remains a daunting task. Total viral assemblage sequencing (for example, viral metagenomics) provides a tractable approach. However, even with the availability of next-generation sequencing technology it is usually only possible to obtain a fragmented view of viral assemblages in natural ecosystems. In this study, we applied a network-based approach in combination with viral metagenomics to investigate viral assemblage structure in the high temperature, acidic hot springs of Yellowstone National Park, USA. Our results show that this approach can identify distinct viral groups and provide insights into the viral assemblage structure. We identified 110 viral groups in the hot springs environment, with each viral group likely representing a viral family at the sub-family taxonomic level. Most of these viral groups are previously unknown DNA viruses likely infecting archaeal hosts. Overall, this study demonstrates the utility of combining viral assemblage sequencing approaches with network analysis to gain insights into viral assemblage structure in natural ecosystems.

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Archaeal Viruses: Diversity, Replication, and Structure

Cited by 54 publications

References 150 publications

Metagenomics of microbial and viral life in terrestrial geothermal environments

Metagenomics of microbial and viral life in terrestrial geothermal environments

Structure and assembly mechanism of virus-associated pyramids

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

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