Siphoviridae

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Siphoviridae
Siphoviridae.svg
Typical structure of a siphovirus
Virus classification Red Pencil Icon.png
(unranked): Virus
Phylum: incertae sedis
Class: incertae sedis
Order: Caudovirales
Family:Siphoviridae
Genera
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 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.

Contents

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 x 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. Siphovirus.tiff
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.

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]

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.

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C2likevirus is a genus of viruses in the family Siphoviridae, unassigned to a sub-family. Bacteria serve as the natural host, with transmission achieved through passive diffusion. There are currently two species in this genus, including the type species Lactococcus phage c2.

L5likevirus is a genus of viruses in the order Caudovirales, in the family Siphoviridae. Bacteria serve as natural hosts, with transmission achieved through passive diffusion.. There are currently 62 species in this genus, including the type species Mycobacterium phage L5.

N15likevirus is a genus of viruses in the order Caudovirales, in the family Siphoviridae. Bacteria serve as natural hosts, with transmission achieved through passive diffusion. There is currently only one species in this genus: the type species Enterobacteria phage N15.

T5likevirus is a genus of viruses in the order Caudovirales, in the family Siphoviridae. Bacteria serve as the natural host, with transmission achieved through passive diffusion. There are currently eight species in this genus, including the type species Enterobacteria phage T5.

Tunalikevirus is a genus of viruses in the order Caudovirales, in the family Siphoviridae. Bacteria serve as natural hosts. There are currently nine species in this genus, including the type species Enterobacteria phage T1.

References

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  2. 1 2 3 4 5 6 "Viral Zone". ExPASy. Retrieved 1 July 2015.
  3. 1 2 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.