Podoviridae

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Podoviridae
Podoviridae.svg
Typical structure of a podovirus
Virus classification e
(unranked): Virus
Realm: Duplodnaviria
Kingdom: Heunggongvirae
Phylum: Uroviricota
Class: Caudoviricetes
Order: Caudovirales
Family: Podoviridae
Subfamilies and genera

see text

Podoviridae is a family of viruses in the order Caudovirales. Bacteria serve as natural hosts. There are currently 132 species in this family, divided among 3 subfamilies and 45 genera.[1][2] This family is characterized by having very short, noncontractile tails.

Structure[edit]

Electron micrograph of podovirus ΦCP7R of Clostridium perfringens.
Genomes of some podoviruses of Clostridium perfringens

Viruses in Podoviridae are non-enveloped, with icosahedral and head-tail geometries. The diameter is around 60 nm,[1] and consists of 72 capsomers. The head protein has a molecular mass of ~38 kiloDaltons and is present in 460 copies per virion. There are 9 structural proteins. The tail is non-contractile and has 6 short subterminal fibers. It is thick and rod-shaped and built of stacked disks. The maximum length is ~17 nm.

The double stranded DNA genome is linear, around 40-42kb in length,[1] and encodes ~55 genes. The guanine + cytosine content is ~50%. It has terminally redundant sequences and is nonpermuted. By weight, the genome constitutes ~50% of the viron. The genome encodes 9 structural proteins, an adenylated transferase B type DNA polymerase and an RNA polymerase. Three internal proteins constitute the polymerase complex. Two classes of genes are recognized (early and late). This classification is based on the timing of transcription that is temporally regulated. Genes with related functions are clustered together. Genome replication is bidirectional.

Life cycle[edit]

Viral replication is cytoplasmic. Entry into the host cell is achieved by adsorption into the host cell. Replication follows the DNA strand displacement model. DNA-templated transcription is the method of transcription. The virus exits the host cell by lysis, and holin/endolysin/spanin proteins. Bacteria serve as the natural host. Transmission routes are passive diffusion.[1]

Taxonomy[edit]

Genera within this family have ~40% homology between corresponding proteins. Subfamilies have ~20% homology between corresponding proteins.

The following subfamilies and their genera are recognized (-virinae denotes subfamily and -virus denotes genus):[2]

The following genera are not assigned to a subfamily:[2]

The following species are unassigned to a genus:[2]

Proposed genera[edit]

The following genera have been proposed but are not currently ratified by the International Committee on Taxonomy of Viruses:[3][4][5][6][7][8]

  • Genus 119xlikevirus; type species: Pseudomonas phage 119X
    • Species:
      • Pseudomonas phage 119X
  • Genus Cba40unalikevirus; type species: Cellulophaga phage phi40:1
    • Species:
      • Cellulophaga phage phi40:1
      • Cellulophaga phage phi38:1
  • Genus Cba183likevirus; type species: Cellulophaga phage phi18:3
    • Species:
      • Cellulophaga phage phi18:3
      • Cellulophaga phage phi13:2
      • Cellulophaga phage phi19:3
      • Cellulophaga phage phi46:3
  • Genus Cba142likevirus; type species: Cellulophaga phage phi14:2
    • Species:
      • Cellulophaga phage phi14:2
  • Genus Cba4unalikevirus; type species: Cellulophaga phage phi4:1
    • Species:
      • Cellulophaga phage phi4:1
      • Cellulophaga phage phi17:2
  • Genus Cpvunalikevirus; type species: Clostridium phage CpV1
    • Species:
      • Clostridium phage CpV1
  • Genus Gap227likevirus; type species: Cronobacter phage vB CsaP GAP227
    • Species:
      • Cronobacter phage vB CsaP GAP227
      • Yersinia phage phiR8-01
      • Yersinia phage phi80-18
      • Aeromonas phage phiAS7
  • Genus P60likevirus (synonyms = Marine Picocyanobacteria Podovirus subgroup or MPP subgroup); type species: Synechococcus phage P60
    • Species:
      • Synechococcus phage P60
  • Genus pelagiphages (informal); type species: Pelagibacter phage HTVC010P
    • Species:
      • Pelagibacter phage HTVC010P MAR122
      • Pelagibacter phage HTVC010P MAR123
      • Pelagibacter phage HTVC010P MAR124
  • Genus Vp2likevirus; type species: Vibrio phage VP2
    • Species:
      • Vibrio phage VP2
  • Genus Ys6unalikevirus; type species: Weissella phage phiYS61
    • Species:
      • Weissella phage phiYS61

In 2017, it was proposed to add crAssphage to this family.[9]

References[edit]

  1. ^ a b c d "Viral Zone". ExPASy. Retrieved 1 July 2015.
  2. ^ a b c d "Virus Taxonomy: 2019 Release". talk.ictvonline.org. International Committee on Taxonomy of Viruses. Retrieved 4 May 2020.
  3. ^ Lavigne, R.; Seto, D.; Mahadevan, P.; Ackermann, H. W.; Kropinski, A. M. (2008). "Unifying classical and molecular taxonomic classification: analysis of the Podoviridae using BLASTP-based tools". Research in Microbiology. 159 (5): 406–14. doi:10.1016/j.resmic.2008.03.005. PMID 18555669.
  4. ^ Abbasifar R, Kropinski AM, Sabour PM, Ackermann HW, Alanis Villa A, Abbasifar A, Griffiths MW (2013). "The Genome of Cronobacter sakazakii Bacteriophage vB_CsaP_GAP227 Suggests a New Genus within the Autographivirinae". Genome Announc. 1 (1). doi:10.1128/genomeA.00122-12. PMC 3569369. PMID 23409275.
  5. ^ Labrie SJ, Frois-Moniz K, Osburne MS, Kelly L, Roggensack SE, Sullivan MB, Gearin G, Zeng Q, Fitzgerald M, Henn MR, Chisholm SW (2013). "Genomes of marine cyanopodoviruses reveal multiple origins of diversity" (PDF). Environ. Microbiol. 15 (5): 1356–76. doi:10.1111/1462-2920.12053. hdl:1721.1/78852. PMID 23320838.
  6. ^ Kleppen HP, Holo H, Jeon SR, Nes IF, Yoon SS (2012) A novel bacteriophage of the Podoviridae family infecting Weissella cibaria isolated from kimchi. Appl Environ Microbiol doi:10.1128/AEM.00031-12
  7. ^ Mizuno, C. M.; Rodriguez-Valera, F.; Kimes, N. E.; Ghai, R. (2013). "Expanding the Marine Virosphere Using Metagenomics". PLOS Genetics. 9 (12): e1003987. doi:10.1371/journal.pgen.1003987. PMC 3861242. PMID 24348267.
  8. ^ 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): 12798–12803. doi:10.1073/pnas.1305956110. PMC 3732932. PMID 23858439.
  9. ^ Natalya Yutin, Kira S. Makarova, Ayal B. Gussow, Mart Krupovic, Anca Segall, Robert A. Edwards & Eugene V. Koonin: Discovery of an expansive bacteriophage family that includes the most abundant viruses from the human gut, in: Nature Microbiology3, pages38–46 (2018), published online November 13th, 2017, doi:10.1038/s41564-017-0053-y; and Eugene V. Koonin: Behind the paper: The most abundant human-associated virus no longer an orphan, November 13th, 2017

External links[edit]