Siphoviridae

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Siphoviridae
Siphoviridae.svg
Typical structure of a siphovirus
Virus classification
Group: Group I (dsDNA)
Order: Caudovirales
Family: Siphoviridae
Genera
Synonyms
  • Styloviridae

Siphoviridae are a family of double-stranded DNA viruses infecting only bacteria. These viruses may also be referred to as bacteriophages. The characteristic structural features of this family are a nonenveloped head and noncontractile tail.

Virology[edit]

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.[1]

Virions of viruses in this family have an icosahedral capsid (morphotype B1) or a prolate capsid (morphotype B2). These capsids have no envelope and are generally about 60 nanometers in diameter. Members of this family are also characterized by their filamentous, cross-banded, noncontractile tails, usually with short terminal and subterminal fibers.

The genome of Siphoviridae phages is double stranded and linear. It is typically about 50 kilobases in length and contains about 70 genes. The guanine/cytosine content is usually around 52%.

Taxonomy[edit]

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 lamba supergroup (or subfamily).[2]

The c2-like viruses have oblate heads.

The following viruses have been classified into genera:[3][4][2]

Other genera awaiting classification into subfamilies:

  • Genus L5likevirus; type species: Mycobacterium phage L5
    • Species:
      • Mycobacteria phage D29
      • Mycobacterium phage L5
      • Mycobacterium phage Swu1 (proposed)
      • Mycobacterium phage Che12 (proposed)
      • Mycobacterium phage Trixie (proposed)
      • Mycobacterium phage Turbido (proposed)
      • Mycobacterium phage Ta17a (proposed)
      • Mycobacterium phage Redrock (proposed)
      • Mycobacterium phage Pukovnik (proposed)
      • Mycobacterium phage Ericb (proposed)
      • Mycobacterium phage Hammer (proposed)
      • Mycobacterium phage Gladiator (proposed)
      • Mycobacterium phage Jeffabunny (proposed)
      • Mycobacterium phage Bxb1 (proposed)
      • Mycobacterium phage Billknuckles (proposed)
      • Mycobacterium phage Switzer (proposed)
      • Mycobacterium phage Kssjeb (proposed)
      • Mycobacterium phage U2 (proposed)
      • Mycobacterium phage Mrgordo (proposed)
      • Mycobacterium phage Museum (proposed)
      • Mycobacterium phage Lesedi (proposed)
      • Mycobacterium phage Solon (proposed)
      • Mycobacterium phage Bethlehem (proposed)
      • Mycobacterium phage Kbg (proposed)
      • Mycobacterium phage Kugel (proposed)
      • Mycobacterium phage Bruns (proposed)
      • Mycobacterium phage Violet (proposed)
      • Mycobacterium phage Euphoria (proposed)
      • Mycobacterium phage Bpbiebs31 (proposed)
      • Mycobacterium phage Nepal (proposed)
      • Mycobacterium phage Doom (proposed)
      • Mycobacterium phage Marcell (proposed)
      • Mycobacterium phage Lockley (proposed)
      • Mycobacterium phage Skipole (proposed)
      • Mycobacterium phage Jc27 (proposed)
      • Mycobacterium phage Jasper (proposed)
      • Mycobacterium phage Ridgecb (proposed)
      • Mycobacterium phage Perseus (proposed)
      • Mycobacterium phage Bxz2 (proposed)
      • Mycobacterium phage Jhc117 (proposed)
      • Mycobacterium phage Microwolf (proposed)
      • Mycobacterium phage Wonder (proposed)
      • Mycobacterium phage Heldan (proposed)
      • Mycobacterium phage Rockstar (proposed)
      • Mycobacterium phage Peaches (proposed)
      • Mycobacterium phage Arturo (proposed)
      • Mycobacterium phage Lhtscc (proposed)
      • Mycobacterium phage Backyardigan (proposed)
      • Mycobacterium phage Benedict (proposed)
      • Mycobacterium phage George (proposed)
      • Mycobacterium phage Cuco (proposed)
      • Mycobacterium phage Tiger (proposed)
      • Mycobacterium phage Timshel (proposed)
      • Mycobacterium phage Saintus (proposed)
      • Mycobacterium phage Astro (proposed)
      • Mycobacterium phage Packman (proposed)
      • Mycobacterium phage Alma (proposed)
      • Mycobacterium phage Rebeuca (proposed)
      • Mycobacterium phage Goose (proposed)
      • Mycobacterium phage Twister (proposed)
      • Rhodococcus phage Rgl3 (proposed)
      • Rhodococcus phage Rer2 (proposed)

Proposed Genera[edit]

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 3alikevirus; type species: Staphylococcus phage 3A
    • Species
      • Staphylococcus phage 3A
      • Staphylococcus phage phiSauS-IPLA35
      • Staphylococcus phage phiSLT
      • Staphylococcus phage 47
      • Staphylococcus phage phi 12
      • Staphylococcus phage 42E
  • Genus 77likevirus; type species: Staphylococcus phage 77
    • Species
      • Staphylococcus phage 77
      • Staphylococcus phage phiPVL108
      • Staphylococcus phage phi13
  • Genus Andromedalikevirus; type species: Bacillus phage Andromeda
    • Species
      • Bacillus phage Andromeda
      • Bacillus phage Eoghan
      • Bacillus phage Taylor
      • Bacillus phage Curly
      • Bacillus phage Finn
      • Bacillus phage Glittering
      • Bacillus phage Blastoid
      • Bacillus phage Riggi
  • Genus Barnyardlikevirus; type species: Mycobacterium phage Barnyard
    • Species
      • Mycobacterium phage Barnyard
      • Mycobacterium phage Predator
      • Mycobacterium phage Konstantine
      • Mycobacterium phage Patience
  • Genus Bignuzlikevirus; type species: Mycobacterium phage BigNuz
    • Species
      • Mycobacterium phage BigNuz
      • Mycobacterium phage Jebeks
  • Genus Bronlikevirus; type species: '
    • Species
      • Mycobacterium phage LeBron
      • Mycobacterium phage JoeDirt
      • Mycobacterium phage Rumpelstiltskin
      • Mycobacterium phage Faith1
  • Genus C5likevirus; type species: Lactobacillus phage C5
    • Species
      • Lactobacillus phage C5
      • Lactobacillus phage LL-Ku
  • 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 Charlielikevirus; type species: Mycobacterium phage Charlie
    • Species
      • Mycobacterium phage Charlie
      • Mycobacterium phage Redi
  • Genus Che8likevirus; type species: Mycobacterium phage Che8
    • Species
      • Mycobacterium phage Che8
      • Mycobacterium phage PMC
      • Mycobacterium phage Mutaforma13
      • Mycobacterium phage DotProduct
      • Mycobacterium phage GUmbie
      • Mycobacterium phage Llij
      • Mycobacterium phage Spartacus
      • Mycobacterium phage Pacc40
      • Mycobacterium phage Ibhubesi
      • Mycobacterium phage Tweety
      • Mycobacterium phage Taj
      • Mycobacterium phage Wee
      • Mycobacterium phage Dorothy
      • Mycobacterium phage DeadP
      • Mycobacterium phage SG4
      • Mycobacterium phage Boomer
      • Mycobacterium phage DLane
      • Mycobacterium phage Ardmore
      • Mycobacterium phage Fruitloop
      • Mycobacterium phage ShiLan
      • Mycobacterium phage Drago
      • Mycobacterium phage Ramsey
      • Mycobacterium phage RockyHorror
      • Mycobacterium phage Mozy
      • Mycobacterium phage Shauna1
      • Mycobacterium phage Che9d
      • Mycobacterium phage Avani
      • Mycobacterium phage Yoshi
  • Genus Che9clikevirus; type species: Mycobacterium phage Che9c
    • Species
      • Mycobacterium phage Che9c
      • Mycobacterium phage Brujita
      • Mycobacterium phage Babsiella
  • Genus Chilikevirus; type species: Salmonella phage Chi
    • Species
      • Salmonella phage Chi
      • Salmonella phage SPN19
      • Salmonella phage iEPS5
      • Salmonella phage Fslsp088
      • Salmonella phage Fslsp030
  • Genus Cjwunalikevirus; type species: Mycobacterium phage CJW1
    • Species
      • Mycobacterium phage CJW1
      • Mycobacterium phage Pumpkin
      • Mycobacterium phage 244
      • Mycobacterium phage Porky
      • Mycobacterium phage Bask21
      • Mycobacterium phage SirDuracell
      • Mycobacterium phage Eureka
      • Mycobacterium phage Kostya
      • Mycobacterium phage Toto
  • Genus Corndoglikevirus; type species: Mycobacterium phage Corndog
    • Species
      • Mycobacterium phage Corndog
      • Mycobacterium phage Firecracker
  • Genus D3likevirus; type species: Pseudomonas phage D3
    • Species
      • Pseudomonas phage D3
      • Pseudomonas phage PMG1
  • Genus D3112likevirus; type species: Pseudomonas phage D3112
    • Species
      • Pseudomonas phage D3112
      • Pseudomonas phage Dms3
      • Pseudomonas phage Fha0480
      • Pseudomonas phage Lpb1
      • Pseudomonas phage Mp22
      • Pseudomonas phage Mp29
      • Pseudomonas phage Mp38
      • Pseudomonas phage Pa1phi
  • Genus Halolikevirus; type species: '
    • Species
      • Mycobacterium phage Halo
      • Mycobacterium phage Liefie
  • Genus Hk578likevirus; type species: '
    • Species
      • Escherichia phage HK578
      • Sodalis phage SO-1
      • Shigella phage EP23
      • Enterobacteria phage JL1
      • Enterobacteria phage SSL-2009a
  • Genus Iebhlikevirus; type species: Bacillus phage IEBH
    • Species
      • Bacillus phage IEBH
      • Bacillus phage 250
  • Genus Jerseylikevirus; type species: Salmonella phage Jersey
    • Species
      • Salmonella phage Jersey
      • Salmonella phage Setp3
      • Salmonella phage Ent1
      • Salmonella phage Se2
      • Salmonella phage wksl3
      • Salmonella phage Ss3e
  • 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 Omegalikevirus; type species: Mycobacterium phage Omega
    • Species
      • Mycobacterium phage Omega
      • Mycobacterium phage LittleE
      • Mycobacterium phage Courthouse
      • Mycobacterium phage Optimus
      • Mycobacterium phage Baka
      • Mycobacterium phage Thibault
  • Genus P23likevirus; type species: Thermus phage P2345
    • Species
      • Thermus phage P2345
      • Thermus phage P7426
  • Genus Pbiunalikevirus; type species: Mycobacterium phage PBI1
    • Species
      • Mycobacterium phage PBI1
  • Genus Phicbklikevirus; type species: Caulobacter phage PhiCbK
    • Species
      • Caulobacter phage PhiCbK
      • Caulobacter phage CcrMagneto
      • Caulobacter phage CcrSwift
      • Caulobacter phage CcrKarma
      • Caulobacter phage CcrRogue
  • Genus Phie125likevirus; type species: Burkholderia phage PhiE125
    • Species
      • Burkholderia phage PhiE125
      • Burkholderia phage Phi1026b
      • Burkholderia phage Phi6442
  • Genus Phietalikevirus; type species: Staphylococcus phage phiETA
    • Group phiETA type:
      • Species
        • Staphylococcus phage 29
        • Staphylococcus phage 52A
        • Staphylococcus phage 55
        • Staphylococcus phage 71
        • Staphylococcus phage 80
        • Staphylococcus phage 88
        • Staphylococcus phage 92
        • Staphylococcus phage 96
        • Staphylococcus phage phiETA
        • Staphylococcus phage phiETA3
        • Staphylococcus phage phiMR11
        • Staphylococcus aureus phage phiNM4
        • Staphylococcus phage X2
  • Group phiETA2 type:
    • Species
      • Staphylococcus phage phiETA2
      • Staphylococcus phage 11
      • Staphylococcus phage 53
      • Staphylococcus phage 69
      • Staphylococcus phage 80alpha
      • Staphylococcus phage 85
      • Staphylococcus phage 187
      • Staphylococcus phage phiMR25
      • Staphylococcus aureus phage phiNM1
      • Staphylococcus aureus phage phiNM2
      • Staphylococcus phage phiSauS-IPLA88
      • Staphylococcus phage SAP-26
  • Group 37 type:
    • Species
      • Staphylococcus phage 37
      • Staphylococcus phage CNPH82
      • Staphylococcus phage EW
      • Staphylococcus phage PH15
      • Staphylococcus phage vB_SepiS-phiIPLA5
      • Staphylococcus phage vB_SepiS-phiIPLA7
  • Genus Phiflunalikevirus; type species: Enterococcus phage PhiFL1
    • Species
      • Enterococcus phage PhiFL1
      • Enterococcus phage PhiFL2
      • Enterococcus phage PhiFL3
  • Genus Phijlunalikevirus; type species: Lactobacillus phage phiJL-1
    • Species
      • Lactobacillus phage phiJL-1
      • Pediococcus phage clP1
      • Lactobacillus phage ATCC 8014-B1
  • Genus Reylikevirus; type species: Mycobacterium phage Rey
    • Species
      • Mycobacterium phage Rey
  • 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 Sap6likevirus; type species: Enterococcus phage SAP6
    • Species
      • Enterococcus phage SAP6
      • Enterococcus phage BC-611
      • Enterococcus phage IME-Ef1
      • Streptococcus phage SP-QS1
      • Enterococcus phage VD-13
  • Genus Sfi11likevirus; type species: Streptococcus phage Sfi11
    • Species
      • Streptococcus phage Sfi11
      • Lactococcus phage Tuc2009
      • Lactococcus phage TP901-1
  • Genus Sfi21dtunalikevirus (synonyms 939likevirus and Sfi2likevirus); type species: Streptococcus phage DT1
    • Species
      • Streptococcus phage DT1
      • Streptococcus phage Sfi19
      • Streptococcus phage Sfi21
      • Streptococcus phage Abc2
      • Streptococcus phage 7201
      • Lactobacillus phage A2
      • Lactococcus phage bIL285
      • Lactococcus phage bIL286
      • Lactococcus phage bIL309
      • Lactococcus phage BK5-T
      • Staphylococcus phage PVL
  • Genus Skunalikevirus (synonym 936likevirus); type species: Lactococcus phage sk1
    • Species
      • Lactococcus phage Sk1
      • Lactococcus phage bIL170
      • Lactococcus phage jj50
      • Lactococcus phage 712
      • Lactococcus phage P008
      • Lactococcus phage Sl4
      • Lactococcus phage CB13
      • Lactococcus phage CB14
      • Lactococcus phage CB19
      • Lactococcus phage CB20
      • Lactococcus phage Bibb29
      • Lactococcus phage P2
      • Lactococcus phage ASCC273
      • Lactococcus phage ASCC191
      • Lactococcus phage ASCC281
      • Lactococcus phage ASCC532
      • Lactococcus phage ASCC465
  • Genus Tlslikevirus; type species: Escherichia phage Tls
    • Species
      • Escherichia phage Tls
      • Salmonella phage FSL SP-126
  • Genus Tm4likevirus; type species: Mycobacterium phage TM4
    • Species
      • Mycobacterium phage TM4
      • Mycobacterium phage Angelica
      • Mycobacterium phage JAWS
      • Mycobacterium phage CrimD
      • Mycobacterium phage Anaya
      • Mycobacterium phage Pixie
      • Mycobacterium phage MacnCheese
      • Mycobacterium phage Larva
      • Mycobacterium phage Fionn
  • Genus Tp2unalikevirus; type species: Bacillus phage Tp21
    • Species
      • Bacillus phage Tp21
      • Bacillus phage Bmbtp2
  • Genus Wbetalikevirus; type species: Bacillus phage Wbeta
    • Species
      • Bacillus phage Wbeta
  • Genus Xp10likevirus; type species: Xanthomonas phage Xp10
    • Species
      • Xanthomonas phage Xp10
      • Xanthomonas phage OP1
      • Xanthomonas phage Xop411
      • Xanthomonas phage PhiL7
      • Xanthomonas phage CP1

Unclassified[edit]

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[edit]

  1. ^ 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. 
  2. ^ a b 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. 
  3. ^ NCBI Taxonomy (Siphoviridae)
  4. ^ International Committee on Taxonomy of Viruses
  5. ^ "The Dilemma of Phage Taxonomy Illustrated by Comparative Genomics of Sfi21-Like Siphoviridae in Lactic Acid Bacteria". Journal of Bacteriology. September 2014. doi:10.1128/JB.184.21.6026-6036.2002. 
  6. ^ "Three proposed new bacteriophage genera of staphylococcal phages: “3alikevirus”, “77likevirus” and “Phietalikevirus”". Archives of Virology. 11 Sep 2013. doi:10.1007/s00705-013-1833-1. 
  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. doi:10.1073/pnas.1305956110.  edit
  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.  edit
  11. ^ "unclassified Siphoviridae". NCBI Taxonomy. 

External Links[edit]