Siphoviridae

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.

Siphoviridae
TME picture of an Escherichia virus HK97 virion, Siphoviridae
Virus classification
(unranked): Virus
Realm: Duplodnaviria
Kingdom: Heunggongvirae
Phylum: Uroviricota
Class: Caudoviricetes
Order: Caudovirales
Family: Siphoviridae
Genera

see text

Synonyms[1]
  • Styloviridae

Structure

Typical structure of a siphovirus

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 50 kb in langht,[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 Cutibacterium acnes (formerly Propionibacterium 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

  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.
  2. "Viral Zone". ExPASy. Retrieved 1 July 2015.
  3. "Virus Taxonomy: 2019 Release". talk.ictvonline.org. International Committee on Taxonomy of Viruses. Retrieved 5 May 2020.
  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.

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