Lipothrixviridae

Lipothrixviridae
	Acidianus filamentous virus 3 (AFV3), genus Betalipothrixvirus
Virus classification
(unranked):	Virus
Realm:	Adnaviria
Kingdom:	Zilligvirae
Phylum:	Taleaviricota
Class:	Tokiviricetes
Order:	Ligamenvirales
Family:	Lipothrixviridae
Genera
	Alphalipothrixvirus; Betalipothrixvirus; Deltalipothrixvirus;
Synonyms
	TTV1 group ICTV 1987;

Lipothrixviridae is a family of viruses in the order Ligamenvirales. Thermophilic archaea in the phylum Thermoproteota serve as natural hosts. There are 11 species in this family, assigned to 4 genera.^[1]^[2]^[3]^[4]^[5]

Taxonomy

The following genera and species are assigned to the family:^[2]

The family consists of three genera: Alphalipothrixvirus, Betalipothrixvirus, and Deltalipothrixvirus. Captovirus used to be in this family as the genus Gammalipothrixvirus, but now it is the only genus in the family Ungulaviridae.^[6]^[7] They are classified into genera based on their genomic properties and on the diversity of their terminal appendages, which are involved in host cell recognition. The originally proposed genus Alphalipothrixvirus was renamed Alphatristromavirus and moved to family Tristromaviridae.^[8]^[9] In 2020, the genus Alphalipothrixvirus was recreated for classification of Sulfolobus filamentous virus 1^[10] and Sulfolobales Beppu filamentous virus 2.^[11]

In the genus Gammalipothrixvirus claw-like structures are found at either end of the virion.

Members of the Lipothrixviridae share structural and genomic characteristics with viruses from the Rudiviridae family, which contains non-enveloped rod-shaped viruses. Viruses from the two families have linear dsDNA genomes and share up to nine genes. In addition, the filamentous particles of rudiviruses and lipothrixviruses are built from structurally similar, homologous major capsid proteins. Due to these shared properties viruses from the two families are classified into an order Ligamenvirales.^[12]

Members of the Ligamenvirales are structurally related to viruses of the family Tristromaviridae which, similar to lipothrixviruses, are enveloped and encode two paralogous major capsid proteins with the same fold as those of ligamenviruses.^[13] Due to these structural similarities, order Ligamenvirales and family Tristromaviridae were proposed to be unified within a class 'Tokiviricetes' (toki means ‘thread’ in Georgian and viricetes is an official suffix for a virus class).^[13]

Virology

The viruses are enveloped and filamentous. The capsid varies considerably in length – 410–1950 nanometers (nm) – and is 24–38 nm in diameter. The envelope has a monolayer structure and includes di-phytanyl tetraethers lipids.^{[citation needed]}

From either end of the viron are protrusions extending from the core through the envelope. The capsid itself is elongated and exhibits helical symmetry. The core itself is helical.^{[citation needed]}

There are two major capsid proteins (MCP1 and MCP2). MCP1 and MCP2 form a heterodimer, which wraps around the linear dsDNA genome transforming it into A-form. Interaction between the genome and the MCPs leads to condensation of the genome into the virion superhelix.^[10]^[14]^[15] Genomes are linear, up to 40 kb in length.^[1]

Genus	Structure	Symmetry	Capsid	Genomic arrangement	Genomic segmentation
Alphalipothrixvirus	Filamentous	Helical	Enveloped	Linear	Monopartite
Betalipothrixvirus	Filamentous	Helical	Enveloped	Linear	Monopartite
Deltalipothrixvirus	Filamentous	Helical	Enveloped	Linear	Monopartite

Life cycle

Viral replication is cytoplasmic. Entry into the host cell is achieved by adsorption to the host cell. Acidianus filamentous virus 1 was found to bind to cellular pili-like appendages. DNA templated transcription is the method of transcription. Archaea serve as the natural host. Transmission routes are passive diffusion.^[1]

Virion assembly and egress have been studied in the case of Sulfolobus islandicus filamentous virus (SIFV). The virions assemble inside the cell. Binding of the major capsid protein dimers to the linear dsDNA genome lead to the assembly of nucleocapsids, which are subsequently enveloped intracellularly through an unknown mechanism.^[16] All lipothrixviruses are likely to be lytic viruses. In the case of betalipothrixviruses and deltalipothrixviruses, virions are released through pyramidal portals, referred to as virus-associated pyramids (VAPs). The VAPs of SIFV have a hexagonal base (i.e., constructed from six triangular facets).^[16]

Genus	Host details	Tissue tropism	Entry details	Release details	Replication site	Assembly site	Transmission
Alphalipothrixvirus	Archaea: Saccharolobus	None	Injection	Unknown	Cytoplasm	Cytoplasm	Passive diffusion
Betalipothrixvirus	Archaea: Acidianus, Saccharolobus	None	Injection	Lytic	Cytoplasm	Cytoplasm	Passive diffusion
Deltalipothrixvirus	Archaea: Acidianus	None	Injection	Lytic	Cytoplasm	Cytoplasm	Passive diffusion

References

^ ^a ^b ^c "Viral Zone". ExPASy. Retrieved 15 June 2015.
^ ^a ^b "Virus Taxonomy: 2020 Release". International Committee on Taxonomy of Viruses (ICTV). March 2021. Retrieved 14 May 2021.
^ Arnold, H.P., Zillig, W., Ziese, U., Holz, I., Crosby, M., Utterback, T., Weidmann, J.F., Kristjanson, J.K., Klenk, H.P., Nelson, K.E. and Fraser, C.M. (2000). A novel lipothrixvirus, SIFV, of the extremely thermophilic crenarchaeon Sulfolobus. Virology, 267, 252–266.
^ Janekovic, D., Wunderl S, Holz I, Zillig W, Gierl A, Neumann H (1983) TTV1, TTV2 and TTV3, a family of viruses of the extremely thermophilic anaerobic, sulphur reducing, archaeabacterium Thermoproteus tenax. Mol. Gen. Genet. 19239–19245
^ Bettstetter, M., Peng, X., Garrett, R.A. and Prangishvili, D. (2003). AFV-1, a novel virus infecting hyperthermophilic archaea of the genus Acidianus. Virology, 315, 68–79.
^ "Current ICTV Taxonomy Release | ICTV".
^ Häring M, Vestergaard G, Brügger K, Rachel R, Garrett RA, Prangishvili D (2005) Structure and genome organization of AFV2, a novel archaeal lipothrixvirus with unusual terminal and core structures. J Bacteriol 187(11): 3855–3858 doi:10.1128/JB.187.11.3855-3858.2005
^ Prangishvili, D; Rensen, E; Mochizuki, T; Krupovic, M; ICTV Report, Consortium (February 2019). "ICTV Virus Taxonomy Profile: Tristromaviridae". The Journal of General Virology. 100 (2): 135–136. doi:10.1099/jgv.0.001190. PMID 30540248.
^ "ICTV Report Tristromaviridae".
^ ^a ^b Liu, Y; Osinski, T; Wang, F; Krupovic, M; Schouten, S; Kasson, P; Prangishvili, D; Egelman, EH (2018). "Structural conservation in a membrane-enveloped filamentous virus infecting a hyperthermophilic acidophile". Nature Communications. 9 (1): 3360. Bibcode:2018NatCo...9.3360L. doi:10.1038/s41467-018-05684-6. PMC 6105669. PMID 30135568.
^ Liu, Y; Brandt, D; Ishino, S; Ishino, Y; Koonin, EV; Kalinowski, J; Krupovic, M; Prangishvili, D (2019). "New archaeal viruses discovered by metagenomic analysis of viral communities in enrichment cultures". Environmental Microbiology. 21 (6): 2002–2014. Bibcode:2019EnvMi..21.2002L. doi:10.1111/1462-2920.14479. PMC 11128462. PMID 30451355. S2CID 53950297.
^ Prangishvili D, Krupovic M (2012). "A new proposed taxon for double-stranded DNA viruses, the order "Ligamenvirales"". Arch Virol. 157 (4): 791–795. doi:10.1007/s00705-012-1229-7. PMID 22270758.
^ ^a ^b Wang, Fengbin; Baquero, Diana P; Su, Zhangli; Osinski, Tomasz; Prangishvili, David; Egelman, Edward H; Krupovic, Mart (2020). "Structure of a filamentous virus uncovers familial ties within the archaeal virosphere". Virus Evolution. 6 (1): veaa023. doi:10.1093/ve/veaa023. PMC 7189273. PMID 32368353.
^ Kasson, P; DiMaio, F; Yu, X; Lucas-Staat, S; Krupovic, M; Schouten, S; Prangishvili, D; Egelman, EH (2017). "Model for a novel membrane envelope in a filamentous hyperthermophilic virus". eLife. 6: e26268. doi:10.7554/eLife.26268. PMC 5517147. PMID 28639939.
^ Wang, F; Baquero, DP; Beltran, LC; Su, Z; Osinski, T; Zheng, W; Prangishvili, D; Krupovic, M; Egelman, EH (2020). "Structures of filamentous viruses infecting hyperthermophilic archaea explain DNA stabilization in extreme environments". Proceedings of the National Academy of Sciences of the United States of America. 117 (33): 19643–19652. Bibcode:2020PNAS..11719643W. doi:10.1073/pnas.2011125117. PMC 7443925. PMID 32759221.
^ ^a ^b Baquero, DP; Gazi, AD; Sachse, M; Liu, J; Schmitt, C; Moya-Nilges, M; Schouten, S; Prangishvili, D; Krupovic, M (2021). "A filamentous archaeal virus is enveloped inside the cell and released through pyramidal portals". Proceedings of the National Academy of Sciences of the United States of America. 118 (32): e2105540118. Bibcode:2021PNAS..11805540B. doi:10.1073/pnas.2105540118. PMC 8364153. PMID 34341107.