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Siphoviridae

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Siphoviridae
Virus classification
Group:
Group I (dsDNA)
Order:
Caudovirales
Family:
Siphoviridae
Genera
Synonyms
  • Styloviridae[1]

Siphoviridae is a family of double-stranded DNA viruses in the order Caudovirales. Bacteria and archaea serve as natural hosts. There are currently 313 species in this family, divided among 47 genera.[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%.

Virion Structure Table
Genus Structure Symmetry Capsid Genomic arrangement Genomic segmentation
Pbiunalikevirus Head-Tail T=7 Non-enveloped Linear Monopartite
Yualikevirus Head-Tail T=7 Non-enveloped Linear Monopartite
Sfi1unalikevirus Head-Tail T=7 Non-enveloped Linear Monopartite
Phijlunalikevirus Head-Tail T=7 Non-enveloped Linear Monopartite
Che8likevirus Head-Tail T=7 Non-enveloped Linear Monopartite
Bronlikevirus Head-Tail T=7 Non-enveloped Linear Monopartite
Sap6likevirus Head-Tail T=7 Non-enveloped Linear Monopartite
Andromedalikevirus Head-Tail T=7 Non-enveloped Linear Monopartite
Sfi21dtunalikevirus Head-Tail T=7 Non-enveloped Linear Monopartite
Pgonelikevirus Head-Tail T=7 Non-enveloped Linear Monopartite
Lambdalikevirus Head-Tail T=7, levo Non-enveloped Linear Monopartite
Skunalikevirus Head-Tail T=7 Non-enveloped Linear Monopartite
Cjwunalikevirus Head-Tail T=7 Non-enveloped Linear Monopartite
Corndoglikevirus Head-Tail T=7 Non-enveloped Linear Monopartite
Phifllikevirus Head-Tail T=7 Non-enveloped Linear Monopartite
Xp10likevirus Head-Tail T=7 Non-enveloped Linear Monopartite
Tunalikevirus Head-Tail T=7 Non-enveloped Linear Monopartite
Wbetalikevirus Head-Tail T=7 Non-enveloped Linear Monopartite
D3112likevirus Head-Tail T=7 Non-enveloped Linear Monopartite
77likevirus Head-Tail T=7 Non-enveloped Linear Monopartite
Charlielikevirus Head-Tail T=7 Non-enveloped Linear Monopartite
D3likevirus Head-Tail T=7 Non-enveloped Linear Monopartite
T5likevirus Head-Tail T=13 Non-enveloped Linear Monopartite
Tp2unalikevirus Head-Tail T=7 Non-enveloped Linear Monopartite
T5likevirus Head-Tail T=7 Non-enveloped Linear Monopartite
Reylikevirus Head-Tail T=7 Non-enveloped Linear Monopartite
Hk578likevirus Head-Tail T=7 Non-enveloped Linear Monopartite
3alikevirus Head-Tail T=7 Non-enveloped Linear Monopartite
Che9clikevirus Head-Tail T=7 Non-enveloped Linear Monopartite
Phietalikevirus Head-Tail T=7 Non-enveloped Linear Monopartite
Tm4likevirus Head-Tail T=7 Non-enveloped Linear Monopartite
Halolikevirus Head-Tail T=7 Non-enveloped Linear Monopartite
Phic3unalikevirus Head-Tail T=7 Non-enveloped Linear Monopartite
Iebhlikevirus Head-Tail T=7 Non-enveloped Linear Monopartite
Chilikevirus Head-Tail T=7 Non-enveloped Linear Monopartite
N15likevirus Head-Tail T=7 Non-enveloped Linear Monopartite
C5likevirus Head-Tail T=7 Non-enveloped Linear Monopartite
Phie125likevirus Head-Tail T=7 Non-enveloped Linear Monopartite
P23likevirus Head-Tail T=7 Non-enveloped Linear Monopartite
Psimunalikevirus Head-Tail T=7 Non-enveloped Linear Monopartite
Jerseylikevirus Head-Tail T=7 Non-enveloped Linear Monopartite
Spbetalikevirus Head-Tail T=7 Non-enveloped Linear Monopartite
Bignuzlikevirus Head-Tail T=7 Non-enveloped Linear Monopartite
C2likevirus Head-Tail T=7 Non-enveloped Linear Monopartite
Barnyardlikevirus Head-Tail T=7 Non-enveloped Linear Monopartite
Omegalikevirus Head-Tail T=7 Non-enveloped Linear Monopartite
Phicbklikevirus Head-Tail T=7 Non-enveloped Linear Monopartite
L5likevirus Head-Tail T=7 Non-enveloped Linear Monopartite

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]

Life Cycle Table
Genus Host details Tissue tropism Entry details Release details Replication site Assembly site Transmission
Pbiunalikevirus Bacteria None Injection Lysis Cytoplasm Cytoplasm Passive diffusion
Yualikevirus Bacteria None Injection Lysis Cytoplasm Cytoplasm Passive diffusion
Sfi1unalikevirus Bacteria None Injection Lysis Cytoplasm Cytoplasm Passive diffusion
Phijlunalikevirus Bacteria None Injection Lysis Cytoplasm Cytoplasm Passive diffusion
Che8likevirus Bacteria None Injection Lysis Cytoplasm Cytoplasm Passive diffusion
Bronlikevirus Bacteria None Injection Lysis Cytoplasm Cytoplasm Passive diffusion
Sap6likevirus Bacteria None Injection Lysis Cytoplasm Cytoplasm Passive diffusion
Andromedalikevirus Bacteria None Injection Lysis Cytoplasm Cytoplasm Passive diffusion
Sfi21dtunalikevirus Bacteria None Injection Lysis Cytoplasm Cytoplasm Passive diffusion
Pgonelikevirus Bacteria None Injection Lysis Cytoplasm Cytoplasm Passive diffusion
Lambdalikevirus Bacteria None Injection Lysis Cytoplasm Cytoplasm Passive diffusion
Skunalikevirus Bacteria None Injection Lysis Cytoplasm Cytoplasm Passive diffusion
Cjwunalikevirus Bacteria None Injection Lysis Cytoplasm Cytoplasm Passive diffusion
Corndoglikevirus Bacteria None Injection Lysis Cytoplasm Cytoplasm Passive diffusion
Phifllikevirus Bacteria None Injection Lysis Cytoplasm Cytoplasm Passive diffusion
Xp10likevirus Bacteria None Injection Lysis Cytoplasm Cytoplasm Passive diffusion
Tunalikevirus Bacteria None Injection Lysis Cytoplasm Cytoplasm Passive diffusion
Wbetalikevirus Bacteria None Injection Lysis Cytoplasm Cytoplasm Passive diffusion
D3112likevirus Bacteria None Injection Lysis Cytoplasm Cytoplasm Passive diffusion
77likevirus Bacteria None Injection Lysis Cytoplasm Cytoplasm Passive diffusion
Charlielikevirus Bacteria None Injection Lysis Cytoplasm Cytoplasm Passive diffusion
D3likevirus Bacteria None Injection Lysis Cytoplasm Cytoplasm Passive diffusion
T5likevirus Bacteria None Injection Lysis Cytoplasm Cytoplasm Passive diffusion
Tp2unalikevirus Bacteria None Injection Lysis Cytoplasm Cytoplasm Passive diffusion
T5likevirus Bacteria None Injection Lysis Cytoplasm Cytoplasm Passive diffusion
Reylikevirus Bacteria None Injection Lysis Cytoplasm Cytoplasm Passive diffusion
Hk578likevirus Bacteria None Injection Lysis Cytoplasm Cytoplasm Passive diffusion
3alikevirus Bacteria None Injection Lysis Cytoplasm Cytoplasm Passive diffusion
Che9clikevirus Bacteria None Injection Lysis Cytoplasm Cytoplasm Passive diffusion
Phietalikevirus Bacteria None Injection Lysis Cytoplasm Cytoplasm Passive diffusion
Tm4likevirus Bacteria None Injection Lysis Cytoplasm Cytoplasm Passive diffusion
Halolikevirus Bacteria None Injection Lysis Cytoplasm Cytoplasm Passive diffusion
Phic3unalikevirus Bacteria None Injection Lysis Cytoplasm Cytoplasm Passive diffusion
Iebhlikevirus Bacteria None Injection Lysis Cytoplasm Cytoplasm Passive diffusion
Chilikevirus Bacteria None Injection Lysis Cytoplasm Cytoplasm Passive diffusion
N15likevirus Bacteria None Injection Lysis Cytoplasm Cytoplasm Passive diffusion
C5likevirus Bacteria None Injection Lysis Cytoplasm Cytoplasm Passive diffusion
Phie125likevirus Bacteria None Injection Lysis Cytoplasm Cytoplasm Passive diffusion
P23likevirus Bacteria None Injection Lysis Cytoplasm Cytoplasm Passive diffusion
Psimunalikevirus Bacteria; archea None Injection Lysis Cytoplasm Cytoplasm Passive diffusion
Jerseylikevirus Bacteria None Injection Lysis Cytoplasm Cytoplasm Passive diffusion
Spbetalikevirus Bacteria None Injection Lysis Cytoplasm Cytoplasm Passive diffusion
Bignuzlikevirus Bacteria None Injection Lysis Cytoplasm Cytoplasm Passive diffusion
C2likevirus Bacteria None Injection Lysis Cytoplasm Cytoplasm Passive diffusion
Barnyardlikevirus Bacteria None Injection Lysis Cytoplasm Cytoplasm Passive diffusion
Omegalikevirus Bacteria None Injection Lysis Cytoplasm Cytoplasm Passive diffusion
Phicbklikevirus Bacteria None Injection Lysis Cytoplasm Cytoplasm Passive diffusion
L5likevirus Bacteria None Injection Lysis Cytoplasm Cytoplasm Passive diffusion

Taxonomy

Group: dsDNA

[3]

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 organisation of genes in the genera L5likevirus, Lambdalikevirus, Phic3unalikevirus, and Psimunalikevirus and the proposed genera Sfi2likevirus, Sfi1likevirus, Sk1likevirus, and Tm4likevirus suggests that these may form a lambda supergroup (or subfamily).[5]

The following genera have been proposed but are not currently ratified by the International Committee on Taxonomy of Viruses:[6][7][8][9][10][11]

  • 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.[12] 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. ^ a b c d e f "Viral Zone". ExPASy. Retrieved 1 July 2015.
  3. ^ a b ICTV. "Virus Taxonomy: 2014 Release". Retrieved 1 July 2015.
  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.{{cite journal}}: CS1 maint: unflagged free DOI (link)
  5. ^ Brüssow H, Desiere F (2001). "Comparative phage genomics and the evolution of Siphoviridae: insights from dairy phages". Mol Microbiol. 39 (2): 213–22. doi:10.1046/j.1365-2958.2001.02228.x. PMID 11136444.
  6. ^ 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.
  7. ^ 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: 389–98. doi:10.1007/s00705-013-1833-1. PMID 24022640.
  8. ^ Taxonomy Proposals Awaiting Ratification at ICTV
  9. ^ Taxonomy Proposals Pending at ICTV
  10. ^ 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. doi:10.1073/pnas.1305956110. PMC 3732932. PMID 23858439.
  11. ^ 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.{{cite journal}}: CS1 maint: unflagged free DOI (link)
  12. ^ "unclassified Siphoviridae". NCBI Taxonomy.

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