Living Side by Side with a Virus: Characterization of Two Novel Plasmids from Thermococcus prieurii, a Host for the Spindle-Shaped Virus TPV1

Gorlas, Aurore; Krupovìč, Mart; Forterre, Patrick; Geslin, Claire

doi:10.1128/aem.00525-13

Cited by 24 publications

(28 citation statements)

References 52 publications

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“…For this reason, it has been proposed that the two plasmids be classified into a new plasmid group (190). Consistent with this notion, plasmid tree analysis revealed that pGT5, pTN1, and pTP1, another thermococcal RCR plasmid (191), form one clade, which we propose to denote the pGT5 plasmid family, whereas pTA1 and pAMT11 form another clade (Fig. 11).…”

Section: Genomic Featuressupporting

confidence: 55%

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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Section: Genomic Featuressupporting

confidence: 55%

Archaeal Extrachromosomal Genetic Elements

Wang

Peng

Shah

et al. 2015

Microbiol Mol Biol Rev

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“…and and Table ). These proteins are also encoded by MGEs from other families in Thermococcales, such as the plasmid pTN3 (Gaudin et al ., ), the virus TPV1 (Gorlas et al ., ) and the integrated plasmid TKV1 (Fukui et al ., ) and by MGEs from other archaeal lineages (Krupovič et al ., ; Krupovic et al ., ). Moreover, one or several genes encoding MCM proteins are present in all archaeal genomes and correspond to chromosomal replicative helicases (Raymann et al ., ).…”

Section: Resultsmentioning

confidence: 99%

The global distribution and evolutionary history of the pT26‐2 archaeal plasmid family

Badel

Erauso

Gomez

et al. 2019

Environmental Microbiology

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Summary Although plasmids play an important role in biological evolution, the number of plasmid families well‐characterized in terms of geographical distribution and evolution remains limited, especially in archaea. Here, we describe the first systematic study of an archaeal plasmid family, the pT26‐2 plasmid family. The in‐depth analysis of the distribution, biogeography and host–plasmid co‐evolution patterns of 26 integrated and 3 extrachromosomal plasmids of this plasmid family shows that they are widespread in Thermococcales and Methanococcales isolated from around the globe but are restricted to these two orders. All members of the family share seven core genes but employ different integration and replication strategies. Phylogenetic analysis of the core genes and CRISPR spacer distribution suggests that plasmids of the pT26‐2 family evolved with their hosts independently in Thermococcales and Methanococcales, despite these hosts exhibiting similar geographic distribution. Remarkably, core genes are conserved even in integrated plasmids that have lost replication genes and/or replication origins suggesting that they may be beneficial for their hosts. We hypothesize that the core proteins encode for a novel type of DNA/protein transfer mechanism, explaining the widespread oceanic distribution of the pT26‐2 plasmid family.

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“…Finally, module 10 includes two small rolling-circle plasmids, Archaeoglobus profundus plasmid pGS5 (71) and Thermococcus prieurii plasmid pTP2 (72), which connect to members of the genus Alphapleolipovirus (Halorubrum pleomorphic viruses 1, 2, and 6) through an RCRE. The latter protein is also shared with the putative provirus MVV, which is related to Turriviridae from module 6, as well as with the Sulfolobus monocaudavirus 2 (SMV2) from module 9.…”

Section: Figmentioning

confidence: 99%

Bipartite Network Analysis of the Archaeal Virosphere: Evolutionary Connections between Viruses and Capsidless Mobile Elements

Iranzo

Koonin

Prangishvili

et al. 2016

J Virol

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Archaea and particularly hyperthermophilic crenarchaea are hosts to many unusual viruses with diverse virion shapes and distinct gene compositions. As is typical of viruses in general, there are no universal genes in the archaeal virosphere. Therefore, to obtain a comprehensive picture of the evolutionary relationships between viruses, network analysis methods are more productive than traditional phylogenetic approaches. Here we present a comprehensive comparative analysis of genomes and proteomes from all currently known taxonomically classified and unclassified, cultivated and uncultivated archaeal viruses. We constructed a bipartite network of archaeal viruses that includes two classes of nodes, the genomes and gene families that connect them. Dissection of this network using formal community detection methods reveals strong modularity, with 10 distinct modules and 3 putative supermodules. However, compared to similar previously analyzed networks of eukaryotic and bacterial viruses, the archaeal virus network is sparsely connected. With the exception of the tailed viruses related to bacteriophages of the order Caudovirales and the families Turriviridae and Sphaerolipoviridae that are linked to a distinct supermodule of eukaryotic and bacterial viruses, there are few connector genes shared by different archaeal virus modules. In contrast, most of these modules include, in addition to viruses, capsidless mobile elements, emphasizing tight evolutionary connections between the two types of entities in archaea. The relative contributions of distinct evolutionary origins, in particular from nonviral elements, and insufficient sampling to the sparsity of the archaeal virus network remain to be determined by further exploration of the archaeal virosphere. V iruses infecting archaea are among the most mysterious denizens of the virosphere. Archaeal viruses display a rich diversity of virion morphotypes and can be broadly divided into two categories: those that are structurally and genetically related to bacterial or eukaryotic viruses and those that are archaeon specific (1-4). The cosmopolitan fraction of archaeal viruses includes (i) head-tailed viruses of the order Caudovirales, with the 3 included families, Siphoviridae, Myoviridae, and Podoviridae; (ii) tailless icosahedral viruses of the families Sphaerolipoviridae and Turriviridae; and (iii) enveloped pleomorphic viruses of the family Pleolipoviridae. All of these viruses, except for those of the family Turriviridae, propagate in members of the archaeal phylum Euryarchaeota, whereas most of the archaeon-specific virus groups infect hyperthermophilic organisms of the phylum Crenarchaeota.The order Caudovirales contains three families, the Siphoviridae, Myoviridae, and Podoviridae, and includes both bacterial and archaeal viruses. Members of the Caudovirales feature icosahedral capsids and helical tails attached to one of the vertices of the capsid. These viruses have been largely isolated from hyperhalophilic archaea (order Halobacteriales), although one...

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Living Side by Side with a Virus: Characterization of Two Novel Plasmids from Thermococcus prieurii, a Host for the Spindle-Shaped Virus TPV1

Cited by 24 publications

References 52 publications

Archaeal Extrachromosomal Genetic Elements

Archaeal Extrachromosomal Genetic Elements

The global distribution and evolutionary history of the pT26‐2 archaeal plasmid family

Bipartite Network Analysis of the Archaeal Virosphere: Evolutionary Connections between Viruses and Capsidless Mobile Elements

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