Podoviridae

Podoviridae
	Typical structure of a podovirus
Virus classification
(unranked):	Virus
Phylum:	incertae sedis
Class:	incertae sedis
Order:	Caudovirales
Family:	Podoviridae
Subfamilies and genera
	Autographivirinae Phikmvlikevirus; Sp6likevirus; T7likevirus; ; Picovirinae Ahjdlikevirus; Phi29likevirus; ; Unassigned to a sub-family Bcep22likevirus; Bppunalikevirus; Epsilon15likevirus; F116likevirus; Luz24likevirus; N4likevirus; P22likevirus; Phieco32likevirus; crAssphage?[1]; ;

Podoviridae is a family of viruses in the order Caudovirales. Bacteria serve as natural hosts. There are currently 50 species in this family, divided among 20 genera.[2][3] This family is characterized by having very short, noncontractile tails.

Structure

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,[2] 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,[2] 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.

Genus	Structure	Symmetry	Capsid	Genomic arrangement	Genomic segmentation
Phikmvlikevirus	Head-Tail	T=7	Non-enveloped	Linear	Monopartite
Sp6likevirus	Head-Tail	T=7	Non-enveloped	Linear	Monopartite
T7likevirus	Head-Tail	T=7	Non-enveloped	Linear	Monopartite
Ahjdlikevirus	Head-Tail	T=4	Non-enveloped	Linear	Monopartite
Phi29likevirus	Head-Tail	T=3, Q=5	Non-enveloped	Linear	Monopartite
Bcep22likevirus	Head-Tail	T=7	Non-enveloped	Linear	Monopartite
Bppunalikevirus	Head-Tail	T=7	Non-enveloped	Linear	Monopartite
Epsilon15likevirus	Head-Tail	T=7	Non-enveloped	Linear	Monopartite
F116likevirus	Head-Tail	T=7	Non-enveloped	Linear	Monopartite
Luz24likevirus	Head-Tail		Non-enveloped	Linear	Monopartite
N4likevirus	Head-Tail	T=9	Non-enveloped	Linear	Monopartite
P22likevirus	Head-Tail	T=7	Non-enveloped	Linear	Monopartite
Phieco32likevirus	Head-Tail		Non-enveloped	Linear	Monopartite

In 2017 it has been proposed to add crassphage to this family.[1]

Life cycle

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. [2]

Genus	Host details	Tissue tropism	Entry details	Release details	Replication site	Assembly site	Transmission
Phikmvlikevirus	Bacteria	None	Injection	Lysis	Cytoplasm	Cytoplasm	Passive diffusion
Sp6likevirus	Bacteria	None	Injection	Lysis	Cytoplasm	Cytoplasm	Passive diffusion
T7likevirus	Bacteria	None	Injection	Lysis	Cytoplasm	Cytoplasm	Passive diffusion
Ahjdlikevirus	Bacteria: gram positive	None	Injection	Lysis	Cytoplasm	Cytoplasm	Passive diffusion
Phi29likevirus	Bacteria	None	Injection	Lysis	Cytoplasm	Cytoplasm	Passive diffusion
Bcep22likevirus	Bacteria	None	Injection	Lysis	Cytoplasm	Cytoplasm	Passive diffusion
Bppunalikevirus	Bacteria	None	Injection	Lysis	Cytoplasm	Cytoplasm	Passive diffusion
Epsilon15likevirus	Bacteria	None	Injection	Lysis	Cytoplasm	Cytoplasm	Passive diffusion
F116likevirus	Bacteria	None	Injection	Lysis	Cytoplasm	Cytoplasm	Passive diffusion
Luz24likevirus	Bacteria	None	Injection	Lysis	Cytoplasm	Cytoplasm	Passive diffusion
N4likevirus	Bacteria	None	Injection	Lysis	Cytoplasm	Cytoplasm	Passive diffusion
P22likevirus	Bacteria	None	Injection	Lysis	Cytoplasm	Cytoplasm	Passive diffusion
Phieco32likevirus	Bacteria	None	Injection	Lysis	Cytoplasm	Cytoplasm	Passive diffusion

Taxonomy

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

This family is divided into two subfamilies (Autographivirinae and Picovirinae) and a number of genera awaiting classification into subfamilies.[4][5]

Group: dsDNA

Order: Caudovirales

Family: Podoviridae
- Sub-Family: Autographivirinae
  - Genus: Phikmvlikevirus
    
    Pantoea phage Limelight
    
    Pantoea phage Limezero
    
    Pseudomonas phage LKA1
    
    Pseudomonas phage phiKMV
  - Genus: Sp6likevirus
    
    Enterobacteria phage K5
    
    Enterobacteria phage K1-5
    
    Enterobacteria phage K1E
    
    Enterobacteria phage SP6
    
    Erwinia amylovora phage Era103
  - Genus: T7likevirus
    
    Enterobacteria phage T7
    
    Kluyvera phage Kvp1
    
    Pseudomonad phage gh-1
  - Genus: Unassigned
    
    Prochlorococcus phage P-SSP7
    
    Synechococcus phage P60
    
    Synechococcus phage syn5
- Sub-Family: Picovirinae
  - Genus: Ahjdlikevirus
    
    Staphylococcus phage 44AHJD
    
    Streptococcus phage C1
  - Genus: Phi29likevirus
    
    Bacillus phage B103
    
    Bacillus phage GA-1
    
    Bacillus phage phi29
    
    Kurthia phage 6
  - Genus: Unassigned
    
    Actinomyces phage Av-1
    
    Mycoplasma phage P1
    
    Streptococcus phage Cp-1
- Sub-Family: Unassigned
  - Genus: Bcep22likevirus
    
    Burkholderia phage Bcep22
    
    Burkholderia phage Bcepil02
    
    Burkholderia phage Bcepmigl
    
    Burkholderia phage Dc1
  - Genus: Bppunalikevirus
    
    Bordetella phage BPP-1
    
    Burkholderia phage BcepC6B
  - Genus: Epsilon15likevirus
    
    Escherichia phage PhiV10
    
    Salmonella phage epsilon15
  - Genus: F116likevirus
    
    Pseudomonas phage F116
    
    Pseudomonas phage H66
  - Genus: Luz24likevirus
    
    Pseudomonas phage LUZ24
    
    Pseudomonas phage PaP3
  - Genus: N4likevirus
    
    Escherichia phage N4
  - Genus: P22likevirus
    
    Enterobacteria phage P22
    
    Salmonella phage HK620
    
    Salmonella phage ST64T
    
    Shigella phage Sf6
  - Genus: Phieco32likevirus
    
    Enterobacteria phage Phieco32
  - Genus: Unassigned
    
    Endosymbiont phage APSE-1
    
    Lactococcus phage KSY1
    
    Phormidium phage Pf-WMP3
    
    Phormidium phage Pf-WMP4
    
    Pseudomonas phage 119X
    
    Pseudomonas phage F116
    
    Roseobacter phage SIO1
    
    Vibrio phage VpV262

[3]

Proposed genera

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 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

References

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
"Viral Zone". ExPASy. Retrieved 1 July 2015.
ICTV. "Virus Taxonomy: 2014 Release". Retrieved 1 July 2015.
"International Committee on Taxonomy of Viruses". ictvonline.org. Virology Division of IUMS. 2014. Retrieved August 14, 2014.
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.
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.
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.
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
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.
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.

External links

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[Koonin2017-1] 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

[ViralZone-2] "Viral Zone". ExPASy. Retrieved 1 July 2015.

[ICTV-3] ICTV. "Virus Taxonomy: 2014 Release". Retrieved 1 July 2015.

[4] "International Committee on Taxonomy of Viruses". ictvonline.org. Virology Division of IUMS. 2014. Retrieved August 14, 2014.

[Lavigne-5] 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.

[6] 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.

[Labrie2012-7] 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.

[Kleppen2012-8] 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

[9] 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.

[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): 12798–12803. doi:10.1073/pnas.1305956110. PMC 3732932. PMID 23858439.

Podoviridae

Typical structure of a podovirus
Virus classification
(unranked):	Virus
Phylum:	incertae sedis
Class:	incertae sedis
Order:	Caudovirales
Family:	*Podoviridae*
Subfamilies and genera
Autographivirinae Phikmvlikevirus Sp6likevirus T7likevirus Picovirinae Ahjdlikevirus Phi29likevirus Unassigned to a sub-family Bcep22likevirus Bppunalikevirus Epsilon15likevirus F116likevirus Luz24likevirus N4likevirus P22likevirus Phieco32likevirus crAssphage?[1]