Phikzvirus

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Phikzvirus
Systematics
Classification : Viruses
Area : Duplodnaviria
Empire : Heunggongvirae
Phylum : Uroviricota
Class : Caudoviricetes
Order : Caudovirales
Family : Myoviridae
Genre : Phikzvirus
Taxonomic characteristics
Genome : dsDNA linear
Baltimore : Group 1
Symmetry : icosahedral, tailed
Cover : no
Scientific name
Phikzvirus
Left

Phikzvirus (outdated: Phikzlikevirus , PhiKZ-like viruses , PhiKZ-like viruses ) is a genus of viruses of the family Myoviridae in the order Caudovirales , whose natural hosts are bacteria of the genus Pseudomonas (Pseudomonads). They are therefore (non taxonomically ) as bacteriophages classified . Currently (as of April 8, 2020) the International Committee on Taxonomy of Viruses (ICTV)recognizesthree species (species) in this genus, including the type species Pseudomonas virus PhiKZ (alias Pseudomonas phage PhiKZ , φKZ).

Phages in this genus are considered large or ' jumbo phages '. It is known that three species of this genus - in addition to φKZ, the species φPA3 and 201φ2-1 that have not yet been confirmed by ICTV - develop a structure called a 'phage nucleus' in the host cell (see also viroplasma ). This is similar in function to a eukaryotic cell nucleus in that it contains DNA as well as replication and transcription machinery . The phage core made of a tubulin -like protein PhuZ and a shell protein ( English shell protein ) gp105 . They provide the virus with immunity against the host's defenses ( restriction enzymes and the CRISPR-Cas system ).

Systematics

As of April 8, 2020, the following species are officially confirmed by the ICTV:

Group: dsDNA (Baltimore Group 1 )

  • Genus: Phikzvirus (obsolete Phikzlikevirus )
  • Pseudomonas phage KTN4 (scientific Pseudomonas phage KTN4 )
 Candidates not yet confirmed by the ICTV are currently according to NCBI:
  • Species " Pseudomonas phage 201phi2-1 " (alias " Pseudomonas chlororaphis phage 201phi2-1 ", 201φ2-1)
  • Species " Pseudomonas phage PA02 " (PA02)
  • Species " Pseudomonas phage PA1C " (PA1C)
  • Species " Pseudomonas phage PaSz-1_45_270k "
  • Species " Pseudomonas phage PaZh_1 " (PaZh_1)
  • Species " Pseudomonas phage Phabio "
  • Species " Pseudomonas phage PhiPA3 " (φPA3)
  • Species " Pseudomonas phage Psa21 " (Psa21)
  • Species " Pseudomonas phage vB_PaeM_PS119XW "

The previously listed species Pseudomonas virus EL ( Pseudomonas virus EL , outdated Pseudomonas phage EL ) has been moved within the Myoviridae to the new genus Elvirus , because the genetic match with the type species φKZ is too low.

The species Pseudomonas phage Lin68 , which was previously also listed here, was deleted due to a lack of available genome data, as it is not possible to determine the genetic relationship.

construction

The virus particles ( virions ) in the genus Phikzvirus are not enveloped and have a head and tail . The head has an icosahedral symmetry with a triangulation number T = 27, it has a relatively large diameter of about 140  nm . The tail is about 160 nm long and 35 nm wide.

Genome

The genome consists of a single circular double-stranded DNA segment ( dsDNA , monopartite). Some of the species have been fully sequenced and are available on ICTV. The genome lengths are between 211 and 280  kbp (kilobase pairs). There are 201 to 306 encoded proteins.

Propagation cycle

The virus replication is cytoplasmic, d. H. it takes place in the cell plasma . The virus binds to the host cell using its terminal fibers (at the end of its tail) and expels the viral DNA into the interior of the host cell by contraction of its tail envelope. The transcription method is DNA-based transcription.

Once the viral genes have replicated, the procapsid (the precursor to the capsid ) is assembled and the DNA packaged. The tail is then assembled and the mature virions are finally released by lysis .

The natural hosts are bacteria; transmission occurs through passive diffusion.

Giant phages

Double-stranded DNA phages with a genome size of more than 540  kbp are called megaphages, smaller ones with more than 200 kbp are called jumbo phages. Other authors put the limit for megaphages at 500 kbp. All phages with more than 200 kbp (ie jumbo phage and mega phages) are called " english huge phages " ( Giant phage summarized). These names are non- taxonomic classifications that do not express any relationships per se .

Research history

With the ICTV report of 2009, the genus as PhiKZ-like viruses was accepted as a new genus for the first time together with three species contained in it. In 2012 the name was changed to Phikzlikevirus , later to the current Phikzvirus .

Individual evidence

  1. a b c d ICTV: ICTV Taxonomy history: Enterobacteria phage T4 , EC 51, Berlin, Germany, July 2019; Email ratification March 2020 (MSL # 35)
  2. a b c d Viral Zone . ExPASy. Retrieved April 6, 2020.
  3. a b ICTV: ICTV Master Species List 2018b.v2 , MSL # 34v
  4. NCBI: Phikzvirus (genus)
  5. V Chaikeeratisak, K Nguyen, ME Egan, ML Erb, A Vavilina, J Pogliano: The phage Nucleus and tubulin Spindle Are Conserved among Large Pseudomonas Phages. . In: Cell reports . 20, No. 7, August 15, 2017, pp. 1563–1571. doi : 10.1016 / j.celrep.2017.07.064 . PMID 28813669 . PMC 6028189 (free full text).
  6. NCBI: (no rank)
  7. NCBI: unclassified Phikzvirus
  8. NCBI: Pseudomonas phage 201phi2-1 (species)
  9. Pseudomonas phage 201phi2-1 , on: Virus-Host DB, TAX: 198110
  10. Proteomes - Pseudomonas phage 201phi2-1 , on: UniProt
  11. NCBI: Pseudomonas phage PA02 (species)
  12. NCBI: Pseudomonas phage PA1C (species)
  13. NCBI: Pseudomonas phage PA1C (species)
  14. NCBI: Pseudomonas phage PaSz-1_45_270k (species)
  15. NCBI: Pseudomonas phage Phabio (species)
  16. NCBI: Pseudomonas phage PhiPA3 (species)
  17. NCBI: Pseudomonas phage Psa21 (species)
  18. NCBI: Pseudomonas phage vB_PaeM_PS119XW (species)
  19. a b ICTV: Elvirus
  20. NCBI: Phikzvirus Complete Genomes . Retrieved April 8, 2020.
  21. Audra E. Devoto, Joanne M. Santini et al. : Megaphages infect Prevotella and variants are widespread in gut microbiomes , in: Nature Microbiology, Volume 4, pp. 693-700, January 28, 2019, doi: 10.1038 / s41564-018-0338-9 , especially Table 1 and Supplementary Figure 11
  22. a b Basem Al-Shayeb, Rohan Sachdeva, L. Chen, Jillian F. Banfield et al .: Clades of huge phages from across Earth's ecosystems , in: Nature from February 12, 2020, doi: 10.1038 / s41586-020-2007 -4 , previously bioRxiv : 10.1101 / 572362v1 ( preprint full text). The authors apparently abbreviate kilobase pairs in double-stranded nucleic acids with kb instead of kbp.
  23. ICTV: ICTV Taxonomy history: Pseudomonas virus phiKZ

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