Temperate membrane-containing halophilic archaeal virus SNJ1 has a circular dsDNA genome identical to that of plasmid pHH205

Zhang, Ziqian; Liu, Ying; Wang, Shuai; Yang, Dawei; Cheng, Yichen; Hu, Jiani; Chen, Jin; Mei, Yadong; Shen, Ping; Bamford, Dennis H.; Chen, Xiangdong

doi:10.1016/j.virol.2012.05.036

Cited by 53 publications

(78 citation statements)

References 58 publications

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“…However, for several phages, such as P4 or N15, nonintegrating, stably inherited plasmid forms of prophages have been described (175,176), which is suggestive of the evolutionary transition between viruses and nonviral selfish elements. Similar observations have been reported for viruses of Haloarchaea (177) and for eukaryotic viruses such as herpesviruses (178).…”

Section: Rolling Circle Replicons: Multiple Transitions From Viruses supporting

confidence: 88%

Virus World as an Evolutionary Network of Viruses and Capsidless Selfish Elements

Koonin

Dolja

2014

Microbiol Mol Biol Rev

219

211

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SUMMARY Viruses were defined as one of the two principal types of organisms in the biosphere, namely, as capsid-encoding organisms in contrast to ribosome-encoding organisms, i.e., all cellular life forms. Structurally similar, apparently homologous capsids are present in a huge variety of icosahedral viruses that infect bacteria, archaea, and eukaryotes. These findings prompted the concept of the capsid as the virus “self” that defines the identity of deep, ancient viral lineages. However, several other widespread viral “hallmark genes” encode key components of the viral replication apparatus (such as polymerases and helicases) and combine with different capsid proteins, given the inherently modular character of viral evolution. Furthermore, diverse, widespread, capsidless selfish genetic elements, such as plasmids and various types of transposons, share hallmark genes with viruses. Viruses appear to have evolved from capsidless selfish elements, and vice versa, on multiple occasions during evolution. At the earliest, precellular stage of life's evolution, capsidless genetic parasites most likely emerged first and subsequently gave rise to different classes of viruses. In this review, we develop the concept of a greater virus world which forms an evolutionary network that is held together by shared conserved genes and includes both bona fide capsid-encoding viruses and different classes of capsidless replicons. Theoretical studies indicate that selfish replicons (genetic parasites) inevitably emerge in any sufficiently complex evolving ensemble of replicators. Therefore, the key signature of the greater virus world is not the presence of a capsid but rather genetic, informational parasitism itself, i.e., various degrees of reliance on the information processing systems of the host.

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Section: Rolling Circle Replicons: Multiple Transitions From Viruses supporting

confidence: 88%

Virus World as an Evolutionary Network of Viruses and Capsidless Selfish Elements

Koonin

Dolja

2014

Microbiol Mol Biol Rev

219

211

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“…The circular dsDNA genome is significantly smaller than the linear genomes of alphasphaerolipoviruses; however, it is in the size range of the circular genomes of the newly proposed gammasphaerolipoviruses (Table 1, also see 2B). Ten structural proteins have been identified in the virion of SNJ1 [59], which is in the same range as for alphasphaerolipoviruses.…”

Section: Genus Betasphaerolipovirusmentioning

confidence: 86%

“…The sequence of the circular dsDNA is identical to the previously described Natrinema sp. J7-1 plasmid pHH205 [57,59]. Virion size and morphology are shared with other members of the family ( Table 1).…”

Section: Genus Betasphaerolipovirusmentioning

confidence: 99%

“…IN93 is a temperate phage, which integrates into a tRNA gene in the host chromosome. The only other temperate sphaerolipovirus, SNJ1, persists within the cell in an extrachromosomal, episomal form [59]. P23-77, P23-72 and P23-65H are strictly lytic, with cell lysis occurring *90 min postinfection [20].…”

Section: Life Cyclementioning

confidence: 99%

“…Recently, the fourth SH1-like membrane-containing halovirus, Natrinema sp. J7-1 virus SNJ1, has been isolated [59]. Unlike other SH1-like viruses, SNJ1 has a temperate life cycle, and its genome is a circular, rather than linear, dsDNA molecule.…”

Section: Introductionmentioning

confidence: 99%

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Gammasphaerolipovirus, a newly proposed bacteriophage genus, unifies viruses of halophilic archaea and thermophilic bacteria within the novel family Sphaerolipoviridae

et al. 2014

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A new family of viruses named Sphaerolipoviridae has been proposed recently. It comprises icosahedral, tailless haloarchaeal viruses with an internal lipid membrane located between the protein capsid and the dsDNA genome. The proposed family Sphaerolipoviridae was divided into two genera: Alphasphaerolipovirus, including Haloarcula hispanica viruses SH1, PH1 and HHIV-2, and Betasphaerolipovirus, including Natrinema virus SNJ1. Here, we propose to expand the family Sphaerolipoviridae to include a group of bacteriophages infecting extreme thermophilic Thermus thermophilus and sharing a number of structural and genomic properties with archaeal sphaerolipoviruses. This new group comprises two members, lytic phage P23-77 and temperate phage IN93, as well as putative members P23-72 and P23-65H. In addition, several related proviruses have been discovered as integrated elements in bacterial genomes of the families Thermus and Meiothermus. Morphology of the virus particles and the overall capsid architecture of these bacteriophages resembles that of archaeal members of the Sphaerolipoviridae, including an unusual capsid arrangement in a T = 28 dextro lattice. Alpha-and betasphaerolipoviruses share with P23-77-like bacteriophages a conserved block of core genes that encode a putative genome-packaging ATPase and the two major capsid proteins (MCPs). The recently determined X-ray structure of the small and large MCPs of P23-77 revealed a single beta-barrel (jelly-roll) fold that is superimposable with the cryo-EM density maps of the SH1 capsomers. Given the common features of these viruses, we propose to include the so far unclassified P23-77-like bacteriophages into a new genus, ''Gammasphaerolipovirus'', within the family Sphaerolipoviridae.

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Membrane-Containing Icosahedral Bacteriophage PRD1: The Dawn of Viral Lineages

Oksanen

Abrescia

2019

Advances in Experimental Medicine and Biology

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Membrane-containing enterobacterial phage PRD1 was isolated from sewage more than forty years ago. At the time none would have expected the impact that unravelling its biology would have on modern virology and on the way we understand virus assembly, evolution, and classification today. PRD1 structural analyses have provided a framework for understanding some aspects of virus evolutionintroducing the concept of 'viral lineages' -where the three dimensional structures of virus capsids represent the fingerprint for evolutionary relationship which cannot be traced from the sequence data. In this review we summarise those findings that have led to the concept of viral lineages and the multidisciplinary efforts made in elucidating its life cycle and that have rendered PRD1 a model system not only for the family Tectiviridae to which it belongs, but more generally to complex doublestranded DNA viruses enclosing a membrane vesicle beneath the capsid shell.

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Temperate membrane-containing halophilic archaeal virus SNJ1 has a circular dsDNA genome identical to that of plasmid pHH205

Cited by 53 publications

References 58 publications

Virus World as an Evolutionary Network of Viruses and Capsidless Selfish Elements

Virus World as an Evolutionary Network of Viruses and Capsidless Selfish Elements

Gammasphaerolipovirus, a newly proposed bacteriophage genus, unifies viruses of halophilic archaea and thermophilic bacteria within the novel family Sphaerolipoviridae

Membrane-Containing Icosahedral Bacteriophage PRD1: The Dawn of Viral Lineages

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