Siphoviridae

Siphoviridae
	Typical structure of a siphovirus
Virus classification
(unranked):	Virus
Realm:	Duplodnaviria
Kingdom:	Heunggongvirae
Phylum:	Uroviricota
Class:	Caudoviricetes
Order:	Caudovirales
Family:	Siphoviridae
Genera
	see text
Synonyms[1]
	Styloviridae;

Siphoviridae is a family of double-stranded DNA viruses in the order Caudovirales. Bacteria and archaea serve as natural hosts. There are currently 783 species in this family, divided among 265 genera and 13 subfamilies.[2][3] The characteristic structural features of this family are a nonenveloped head and noncontractile tail.

Structure

Viruses in Siphoviridae are non-enveloped, with icosahedral and head-tail geometries[2] (morphotype B1) or a prolate capsid (morphotype B2), and T=7 symmetry. The diameter is around 60 nm.[2] Members of this family are also characterized by their filamentous, cross-banded, noncontractile tails, usually with short terminal and subterminal fibers. Genomes are double stranded and linear, around 50kb in length,[2] containing about 70 genes. The guanine/cytosine content is usually around 52%.

Life cycle

Viral replication is cytoplasmic. Entry into the host cell is achieved by adsorption into the host cell. Replication follows the replicative transposition model. DNA-templated transcription is the method of transcription. Translation takes place by -1 ribosomal frameshifting, and +1 ribosomal frameshifting. The virus exits the host cell by lysis, and holin/endolysin/spanin proteins.[2] Bacteria and archaea serve as the natural host. Transmission routes are passive diffusion.[2]

Taxonomy

The following subfamilies are recognized:[3]

Arquatrovirinae
Bclasvirinae
Chebruvirinae
Dclasvirinae
Dolichocephalovirinae
Guernseyvirinae
Langleyhallvirinae
Mccleskeyvirinae
Mclasvirinae
Nclasvirinae
Nymbaxtervirinae
Pclasvirinae
Tybeckvirinae

The following genera are unassigned to a subfamily:[3]

Abbeymikolonvirus
Abidjanvirus
Ahduovirus
Amigovirus
Anatolevirus
Andrewvirus
Andromedavirus
Appavirus
Apricotvirus
Armstrongvirus
Attisvirus
Attoomivirus
Austintatiousvirus
Bantamvirus
Barnyardvirus
Beetrevirus
Bernalvirus
Betterkatzvirus
Bingvirus
Biseptimavirus
Bowservirus
Bridgettevirus
Britbratvirus
Bronvirus
Brussowvirus
Casadabanvirus
Cbastvirus
Cecivirus
Ceduovirus
Ceetrepovirus
Cequinquevirus
Chenonavirus
Cheoctovirus
Chivirus
Chunghsingvirus
Cimpunavirus
Cinunavirus
Coetzeevirus
Coralvirus
Corndogvirus
Cronusvirus
Daredevilvirus
Decurrovirus
Delepquintavirus
Demosthenesvirus
Detrevirus
Dhillonvirus
Dismasvirus
Doucettevirus
Edenvirus
Efquatrovirus
Eiauvirus
Eisenstarkvirus
Elerivirus
Emalynvirus
Eyrevirus
Fairfaxidumvirus
Farahnazvirus
Feofaniavirus
Fibralongavirus
Franklinbayvirus
Fromanvirus
Gaiavirus
Galaxyvirus
Galunavirus
Gamtrevirus
Gesputvirus
Getseptimavirus
Ghobesvirus
Gilesvirus
Gillianvirus
Godonkavirus
Goodmanvirus
Gordonvirus
Gordtnkvirus
Gorganvirus
Gorjumvirus
Gustavvirus
Harrisonvirus
Hedwigvirus
Helsingorvirus
Hendrixvirus
Hiyaavirus
Holosalinivirus
Homburgvirus
Ikedavirus
Ilzatvirus
Incheonvrus
Inhavirus
Jacevirus
Jenstvirus
Juiceboxvirus
Kairosalinivirus
Kelleziovirus
Kilunavirus
Klementvirus
Kojivirus
Korravirus
Kostyavirus
Krampusvirus
Kryptosalinivirus
Lacusarxvirus
Lambdavirus
Lanavirus
Laroyevirus
Lentavirus
Liebevirus
Liefievirus
Lokivirus
Lomovskayavirus
Luckybarnesvirus
Luckytenvirus
Lughvirus
Lwoffvirus
Magadivirus
Majavirus
Manhattanvirus
Mapvirus
Mardecavirus
Marvinvirus
Maxrubnervirus
Mementomorivirus
Metamorphoovirus
Minunavirus
Moineauvirus
Montyvirus
Mudcatvirus
Murrayvirus
Nanhaivirus
Nazgulvirus
Neferthenavirus
Nickievirus
Nipunavirus
Nonagvirus
Nonanavirus
Nyceiraevirus
Oengusvirus
Omegavirus
Oneupvirus
Orchidvirus
Oshimavirus
Pahexavirus
Pamexvirus
Papyrusvirus
Patiencevirus
Pbi1virus
Pepyhexavirus
Phietavirus
Phifelvirus
Picardvirus
Pikminvirus
Poushouvirus
Priunavirus
Psavirus
Psimunavirus
Pulverervirus
Quhwahvirus
Raleighvirus
Ravinvirus
Rerduovirus
Rigallicvirus
Rimavirus
Rogerhendrixvirus
Ronaldovirus
Roufvirus
Rowavirus
Ruthyvirus
Samistivirus
Samunavirus
Samwavirus
Sanovirus
Sansavirus
Saphexavirus
Sashavirus
Sasvirus
Saundersvirus
Scapunavirus
Schnabeltiervirus
Schubertvirus
Septimatrevirus
Seuratvirus
Seussvirus
Sextaecvirus
Sitaravirus
Skunavirus
Slashvirus
Smoothievirus
Sonalivirus
Soupsvirus
Sourvirus
Spbetavirus
Squashvirus
Stanholtvirus
Steinhofvirus
Tankvirus
Terapinvirus
Tigunavirus
Timquatrovirus
Tinduovirus
Titanvirus
Tortellinivirus
Triavirus
Trigintaduovirus
Trinavirus
Trinevirus
Trippvirus
Unahavirus
Vashvirus
Vegasvirus
Vendettavirus
Vhulanivirus
Vidquintavirus
Vieuvirus
Vividuovirus
Vojvodinavirus
Wbetavirus
Weaselvirus
Wildcatvirus
Wilnyevirus
Wizardvirus
Woesvirus
Woodruffvirus
Xiamenvirus
Xipdecavirus
Yangvirus
Yuavirus
Yvonnevirus
Zetavirus

Additionally, there is one species that is unassigned to a subfamily and genus:[3] Rhodococcus virus RGL3.

Proposed genera

Electron micrographs of siphovirus from P. acnes. Phages were negatively stained and subjected to transmission electron microscopy. The phages have a head of approximately 55 nm in diameter, loaded with genetic material. Their tails have a size of 150 × 10 nm and are flexible and non-contractile. In the lower micrograph, PAD25 is adhering to bacterial cell debris, and two phages have lost their heads. All phages were classified as Siphoviruses based on their morphology.[4]

The following genera have been proposed but are not currently ratified by the International Committee on Taxonomy of Viruses:[5][6][7][8][9][10]

Genus Cba39unalikevirus; type species: Cellulophaga phage phi39:1
- Species:
  - Cellulophaga phage phi39:1
Genus Cba46unalikevirus; type species: Cellulophaga phage phi46:1
- Species:
  - Cellulophaga phage phi46:1
Genus Cba18unalikevirus; type species: Cellulophaga phage phi18:1
- Species:
  - Cellulophaga phage phi18:1
  - Cellulophaga phage phi12:1
  - Cellulophaga phage phi12:3
  - Cellulophaga phage phi17:1
  - Cellulophaga phage phi18:2
Genus Cba10unalikevirus; type species: Cellulophaga phage phi10:1
- Species:
  - Cellulophaga phage phi10:1
  - Cellulophaga phage phi19:1
Genus Cba13unalikevirus; type species: Cellulophaga phage phi13:1
- Species:
  - Cellulophaga phage phi13:1
  - Cellulophaga phage phi19:2
  - Cellulophaga phage phiST
Genus Jk06likevirus; type species: Escherichia phage Jk06
- Species
  - Escherichia phage Eb49
  - Escherichia phage Jk06
  - Escherichia phage Rogue1
  - Escherichia phage AHP24
  - Escherichia phage AHS24
  - Escherichia phage AHP42
  - Escherichia phage AKS96
  - Enterobacteria phage phiJLA23
  - Enterobacteria phage phiKP26
Genus Kp36likevirus; type species: Klebsiella phage KP36
- Species
  - Enterobacter phage F20
  - Klebsiella phage KP36
Genus R1tlikevirus; type species: Lactococcus phage r1t
- Species
  - Lactococcus phage r1t
Genus Rtplikevirus; type species: Escherichia phage Rtp
- Species
  - Escherichia phage Rtp
  - Enterobacteria phage vB_EcoS_ACG-M12
Genus Tlslikevirus; type species: Escherichia phage Tls
- Species
  - Escherichia phage Tls
  - Salmonella phage FSL SP-126

Unclassified

In addition to the above viruses, many members of Siphoviridae have been grouped into an unclassified group with no genus assignment.[11] This group includes numerous phages known to infect Lactobacillus, Mycobacterium, Streptococcus, and other bacteria.

References

Safferman, R.S.; Cannon, R.E.; Desjardins, P.R.; Gromov, B.V.; Haselkorn, R.; Sherman, L.A.; Shilo, M. (1983). "Classification and Nomenclature of Viruses of Cyanobacteria". Intervirology. 19 (2): 61–66. doi:10.1159/000149339. PMID 6408019.
"Viral Zone". ExPASy. Retrieved 1 July 2015.
"Virus Taxonomy: 2019 Release". talk.ictvonline.org. International Committee on Taxonomy of Viruses. Retrieved 5 May 2020.
Lood R, Mörgelin M, Holmberg A, Rasmussen M, Collin M (2008). "Inducible Siphoviruses in superficial and deep tissue isolates of Propionibacterium acnes". BMC Microbiol. 8: 139. doi:10.1186/1471-2180-8-139. PMC 2533672. PMID 18702830.
Proux C, van Sinderen D, Suarez J, Garcia P, Ladero V, Fitzgerald GF, Desiere F, Brüssow H (2002). "The dilemma of phage taxonomy illustrated by comparative genomics of Sfi21-like Siphoviridae in lactic acid bacteria". J. Bacteriol. 184 (21): 6026–36. doi:10.1128/JB.184.21.6026-6036.2002. PMC 135392. PMID 12374837.
Gutiérrez, D; Adriaenssens, EM; Martínez, B; Rodríguez, A; Lavigne, R; Kropinski, AM; García, P (11 September 2013). "Three proposed new bacteriophage genera of staphylococcal phages: "3alikevirus", "77likevirus" and "Phietalikevirus"". Archives of Virology. 159 (2): 389–98. doi:10.1007/s00705-013-1833-1. PMID 24022640.
Taxonomy Proposals Awaiting Ratification at ICTV
Taxonomy Proposals Pending at ICTV
Holmfeldt, K.; Solonenko, N.; Shah, M.; Corrier, K.; Riemann, L.; Verberkmoes, N. C.; Sullivan, M. B. (2013). "Twelve previously unknown phage genera are ubiquitous in global oceans". Proceedings of the National Academy of Sciences. 110 (31): 12798–803. doi:10.1073/pnas.1305956110. PMC 3732932. PMID 23858439.
Niu, Y. D.; McAllister, T. A.; Nash, J. H. E.; Kropinski, A. M.; Stanford, K. (2014). "Four Escherichia coli O157:H7 Phages: A New Bacteriophage Genus and Taxonomic Classification of T1-Like Phages". PLoS ONE. 9 (6): e100426. doi:10.1371/journal.pone.0100426. PMC 4070988. PMID 24963920.
"unclassified Siphoviridae". NCBI Taxonomy.

External links

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[1] Safferman, R.S.; Cannon, R.E.; Desjardins, P.R.; Gromov, B.V.; Haselkorn, R.; Sherman, L.A.; Shilo, M. (1983). "Classification and Nomenclature of Viruses of Cyanobacteria". Intervirology. 19 (2): 61–66. doi:10.1159/000149339. PMID 6408019.

[ViralZone-2] "Viral Zone". ExPASy. Retrieved 1 July 2015.

[ICTV-3] "Virus Taxonomy: 2019 Release". talk.ictvonline.org. International Committee on Taxonomy of Viruses. Retrieved 5 May 2020.

[pmid18702830-4] Lood R, Mörgelin M, Holmberg A, Rasmussen M, Collin M (2008). "Inducible Siphoviruses in superficial and deep tissue isolates of Propionibacterium acnes". BMC Microbiol. 8: 139. doi:10.1186/1471-2180-8-139. PMC 2533672. PMID 18702830.

[5] Proux C, van Sinderen D, Suarez J, Garcia P, Ladero V, Fitzgerald GF, Desiere F, Brüssow H (2002). "The dilemma of phage taxonomy illustrated by comparative genomics of Sfi21-like Siphoviridae in lactic acid bacteria". J. Bacteriol. 184 (21): 6026–36. doi:10.1128/JB.184.21.6026-6036.2002. PMC 135392. PMID 12374837.

[6] Gutiérrez, D; Adriaenssens, EM; Martínez, B; Rodríguez, A; Lavigne, R; Kropinski, AM; García, P (11 September 2013). "Three proposed new bacteriophage genera of staphylococcal phages: "3alikevirus", "77likevirus" and "Phietalikevirus"". Archives of Virology. 159 (2): 389–98. doi:10.1007/s00705-013-1833-1. PMID 24022640.

[7] Taxonomy Proposals Awaiting Ratification at ICTV

[8] Taxonomy Proposals Pending at ICTV

[9] Holmfeldt, K.; Solonenko, N.; Shah, M.; Corrier, K.; Riemann, L.; Verberkmoes, N. C.; Sullivan, M. B. (2013). "Twelve previously unknown phage genera are ubiquitous in global oceans". Proceedings of the National Academy of Sciences. 110 (31): 12798–803. doi:10.1073/pnas.1305956110. PMC 3732932. PMID 23858439.

[10] Niu, Y. D.; McAllister, T. A.; Nash, J. H. E.; Kropinski, A. M.; Stanford, K. (2014). "Four Escherichia coli O157:H7 Phages: A New Bacteriophage Genus and Taxonomic Classification of T1-Like Phages". PLoS ONE. 9 (6): e100426. doi:10.1371/journal.pone.0100426. PMC 4070988. PMID 24963920.

[11] "unclassified Siphoviridae". NCBI Taxonomy.