Siphoviridae

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.

Siphoviridae
Typical structure of a siphovirus
Virus classification
(unranked): Virus
Phylum: incertae sedis
Class: incertae sedis
Order: Caudovirales
Family: Siphoviridae
Genera
Synonyms
  • Styloviridae[1]

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
GenusStructureSymmetryCapsidGenomic arrangementGenomic segmentation
PbiunalikevirusHead-TailT=7Non-envelopedLinearMonopartite
YualikevirusHead-TailT=7Non-envelopedLinearMonopartite
Sfi1unalikevirusHead-TailT=7Non-envelopedLinearMonopartite
PhijlunalikevirusHead-TailT=7Non-envelopedLinearMonopartite
Che8likevirusHead-TailT=7Non-envelopedLinearMonopartite
BronlikevirusHead-TailT=7Non-envelopedLinearMonopartite
Sap6likevirusHead-TailT=7Non-envelopedLinearMonopartite
AndromedalikevirusHead-TailT=7Non-envelopedLinearMonopartite
Sfi21dtunalikevirusHead-TailT=7Non-envelopedLinearMonopartite
PgonelikevirusHead-TailT=7Non-envelopedLinearMonopartite
LambdalikevirusHead-TailT=7, levoNon-envelopedLinearMonopartite
SkunalikevirusHead-TailT=7Non-envelopedLinearMonopartite
CjwunalikevirusHead-TailT=7Non-envelopedLinearMonopartite
CorndoglikevirusHead-TailT=7Non-envelopedLinearMonopartite
PhifllikevirusHead-TailT=7Non-envelopedLinearMonopartite
Xp10likevirusHead-TailT=7Non-envelopedLinearMonopartite
TunalikevirusHead-TailT=7Non-envelopedLinearMonopartite
WbetalikevirusHead-TailT=7Non-envelopedLinearMonopartite
D3112likevirusHead-TailT=7Non-envelopedLinearMonopartite
77likevirusHead-TailT=7Non-envelopedLinearMonopartite
CharlielikevirusHead-TailT=7Non-envelopedLinearMonopartite
D3likevirusHead-TailT=7Non-envelopedLinearMonopartite
T5likevirusHead-TailT=13Non-envelopedLinearMonopartite
Tp2unalikevirusHead-TailT=7Non-envelopedLinearMonopartite
T5likevirusHead-TailT=7Non-envelopedLinearMonopartite
ReylikevirusHead-TailT=7Non-envelopedLinearMonopartite
Hk578likevirusHead-TailT=7Non-envelopedLinearMonopartite
3alikevirusHead-TailT=7Non-envelopedLinearMonopartite
Che9clikevirusHead-TailT=7Non-envelopedLinearMonopartite
PhietalikevirusHead-TailT=7Non-envelopedLinearMonopartite
Tm4likevirusHead-TailT=7Non-envelopedLinearMonopartite
HalolikevirusHead-TailT=7Non-envelopedLinearMonopartite
Phic3unalikevirusHead-TailT=7Non-envelopedLinearMonopartite
IebhlikevirusHead-TailT=7Non-envelopedLinearMonopartite
ChilikevirusHead-TailT=7Non-envelopedLinearMonopartite
N15likevirusHead-TailT=7Non-envelopedLinearMonopartite
C5likevirusHead-TailT=7Non-envelopedLinearMonopartite
Phie125likevirusHead-TailT=7Non-envelopedLinearMonopartite
P23likevirusHead-TailT=7Non-envelopedLinearMonopartite
PsimunalikevirusHead-TailT=7Non-envelopedLinearMonopartite
JerseylikevirusHead-TailT=7Non-envelopedLinearMonopartite
SpbetalikevirusHead-TailT=7Non-envelopedLinearMonopartite
BignuzlikevirusHead-TailT=7Non-envelopedLinearMonopartite
C2likevirusHead-TailT=7Non-envelopedLinearMonopartite
BarnyardlikevirusHead-TailT=7Non-envelopedLinearMonopartite
OmegalikevirusHead-TailT=7Non-envelopedLinearMonopartite
PhicbklikevirusHead-TailT=7Non-envelopedLinearMonopartite
L5likevirusHead-TailT=7Non-envelopedLinearMonopartite

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
GenusHost detailsTissue tropismEntry detailsRelease detailsReplication siteAssembly siteTransmission
PbiunalikevirusBacteriaNoneInjectionLysisCytoplasmCytoplasmPassive diffusion
YualikevirusBacteriaNoneInjectionLysisCytoplasmCytoplasmPassive diffusion
Sfi1unalikevirusBacteriaNoneInjectionLysisCytoplasmCytoplasmPassive diffusion
PhijlunalikevirusBacteriaNoneInjectionLysisCytoplasmCytoplasmPassive diffusion
Che8likevirusBacteriaNoneInjectionLysisCytoplasmCytoplasmPassive diffusion
BronlikevirusBacteriaNoneInjectionLysisCytoplasmCytoplasmPassive diffusion
Sap6likevirusBacteriaNoneInjectionLysisCytoplasmCytoplasmPassive diffusion
AndromedalikevirusBacteriaNoneInjectionLysisCytoplasmCytoplasmPassive diffusion
Sfi21dtunalikevirusBacteriaNoneInjectionLysisCytoplasmCytoplasmPassive diffusion
PgonelikevirusBacteriaNoneInjectionLysisCytoplasmCytoplasmPassive diffusion
LambdalikevirusBacteriaNoneInjectionLysisCytoplasmCytoplasmPassive diffusion
SkunalikevirusBacteriaNoneInjectionLysisCytoplasmCytoplasmPassive diffusion
CjwunalikevirusBacteriaNoneInjectionLysisCytoplasmCytoplasmPassive diffusion
CorndoglikevirusBacteriaNoneInjectionLysisCytoplasmCytoplasmPassive diffusion
PhifllikevirusBacteriaNoneInjectionLysisCytoplasmCytoplasmPassive diffusion
Xp10likevirusBacteriaNoneInjectionLysisCytoplasmCytoplasmPassive diffusion
TunalikevirusBacteriaNoneInjectionLysisCytoplasmCytoplasmPassive diffusion
WbetalikevirusBacteriaNoneInjectionLysisCytoplasmCytoplasmPassive diffusion
D3112likevirusBacteriaNoneInjectionLysisCytoplasmCytoplasmPassive diffusion
77likevirusBacteriaNoneInjectionLysisCytoplasmCytoplasmPassive diffusion
CharlielikevirusBacteriaNoneInjectionLysisCytoplasmCytoplasmPassive diffusion
D3likevirusBacteriaNoneInjectionLysisCytoplasmCytoplasmPassive diffusion
T5likevirusBacteriaNoneInjectionLysisCytoplasmCytoplasmPassive diffusion
Tp2unalikevirusBacteriaNoneInjectionLysisCytoplasmCytoplasmPassive diffusion
T5likevirusBacteriaNoneInjectionLysisCytoplasmCytoplasmPassive diffusion
ReylikevirusBacteriaNoneInjectionLysisCytoplasmCytoplasmPassive diffusion
Hk578likevirusBacteriaNoneInjectionLysisCytoplasmCytoplasmPassive diffusion
3alikevirusBacteriaNoneInjectionLysisCytoplasmCytoplasmPassive diffusion
Che9clikevirusBacteriaNoneInjectionLysisCytoplasmCytoplasmPassive diffusion
PhietalikevirusBacteriaNoneInjectionLysisCytoplasmCytoplasmPassive diffusion
Tm4likevirusBacteriaNoneInjectionLysisCytoplasmCytoplasmPassive diffusion
HalolikevirusBacteriaNoneInjectionLysisCytoplasmCytoplasmPassive diffusion
Phic3unalikevirusBacteriaNoneInjectionLysisCytoplasmCytoplasmPassive diffusion
IebhlikevirusBacteriaNoneInjectionLysisCytoplasmCytoplasmPassive diffusion
ChilikevirusBacteriaNoneInjectionLysisCytoplasmCytoplasmPassive diffusion
N15likevirusBacteriaNoneInjectionLysisCytoplasmCytoplasmPassive diffusion
C5likevirusBacteriaNoneInjectionLysisCytoplasmCytoplasmPassive diffusion
Phie125likevirusBacteriaNoneInjectionLysisCytoplasmCytoplasmPassive diffusion
P23likevirusBacteriaNoneInjectionLysisCytoplasmCytoplasmPassive diffusion
PsimunalikevirusBacteria; archeaNoneInjectionLysisCytoplasmCytoplasmPassive diffusion
JerseylikevirusBacteriaNoneInjectionLysisCytoplasmCytoplasmPassive diffusion
SpbetalikevirusBacteriaNoneInjectionLysisCytoplasmCytoplasmPassive diffusion
BignuzlikevirusBacteriaNoneInjectionLysisCytoplasmCytoplasmPassive diffusion
C2likevirusBacteriaNoneInjectionLysisCytoplasmCytoplasmPassive diffusion
BarnyardlikevirusBacteriaNoneInjectionLysisCytoplasmCytoplasmPassive diffusion
OmegalikevirusBacteriaNoneInjectionLysisCytoplasmCytoplasmPassive diffusion
PhicbklikevirusBacteriaNoneInjectionLysisCytoplasmCytoplasmPassive diffusion
L5likevirusBacteriaNoneInjectionLysisCytoplasmCytoplasmPassive 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. "Viral Zone". ExPASy. Retrieved 1 July 2015.
  3. 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.
  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 (2): 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): 12798–803. 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.
  12. "unclassified Siphoviridae". NCBI Taxonomy.

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