Siphoviridae

From Wikipedia, the free encyclopedia
Jump to navigation Jump to search
Siphoviridae
BacteriophageHK97.jpg
TME picture of an Escherichia virus HK97 virion, Siphoviridae
Virus classification e
(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[edit]

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[edit]

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[edit]

The following subfamilies are recognized:[3]

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

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

Proposed genera[edit]

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[edit]

In addition to the above viruses, many members of Siphoviridae have been grouped into an unclassified group with no genus assignment. This group includes numerous phages known to infect Lactobacillus, Mycobacterium, Streptococcus, and other bacteria.[11] Bacteriophage PBC1 is an unclassified member of the family that infects the spore-forming bacterium Bacillus cereus.[12]

References[edit]

  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. ^ a b c d e f "Viral Zone". ExPASy. Retrieved 1 July 2015.
  3. ^ a b c d "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.
  12. ^ Kong, M; Kim, M; Ryu, S (June 2012). "Complete Genome Sequence of Bacillus cereus Bacteriophage PBC1". Journal of Virology. 86 (11): 6379–80. doi:10.1128/JVI.00706-12. PMC 3372192. PMID 22570248.

External links[edit]