Bacillus Virus Phi29

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Bacillus Virus Phi29
Bacillus phage phi29.jpg

Bacillus Virus Phi29

Systematics
Classification : Viruses
Area : Duplodnaviria
Empire : Heunggongvirae
Phylum : Uroviricota
Class : Caudoviricetes
Order : Caudovirales
Family : Podoviridae
Subfamily : Picovirinae
Genre : Salas virus
Type : Bacillus Virus Phi29
Taxonomic characteristics
Genome : dsDNA linear
Baltimore : Group 1
Symmetry : icosahedral
Cover : no
Scientific name
Bacillus virus phi29
Short name
Φ29
Left
NCBI  Taxonomy: 10756
ViralZone ( ExPASy , SIB): 520 (genus)
ICTV Taxon History: 201850600

Bacillus virus Phi29 ( scientifically Bacillus virus phi29 , obsolete Bacillus phage phi29 , Φ29 ) is a species of virus in the order Caudovirales . Your genome consists of double-stranded DNA (dsDNA). The DNA molecule is in a linear form, i.e. it is not closed in a circle. The natural hosts are bacteria of the genus Bacillus (bacilli), therefore these viruses are classified as bacteriophages (or phages for short). ThePZA and Φ15 strains also belong to this species. The closest relatives are the species Bacillus virus B103 (with the strain Nf), Bacillus virus GA1 , as well as the candidates " Bacillus phage BS32 ", " Bacillus phage M2 " and " Bacillus phage M2Y ". All of these phages belong to the genus Salasvirus in the subfamily Picovirinae of the virus family Podoviridae . The Φ29 phages are the smallest Bacillus phages isolated todate and are among the smallest known dsDNA phages.

construction

The virions (virus particles) of Φ29 have a head-to-tail structure with an icosahedral “head” and a short “tail” through which the viral genetic material (the linear dsDNA) enters the cell interior of the host bacterium after infection. The head ( capsid ) has a slightly elongated shape of 45 × 54  nm , it has a symmetry with triangulation number T = 3, Q = 5. The tail is non- contractile with a "collar" of 25 appendages in the neck region. There are 25 fibrils on the head , but these have been lost in some laboratory strains. These structures are used to recognize the host cell and attach to it.

Genome

The genome is as generally described in the genus Salsa virus from a single linear piece (segment) of double-stranded DNA having a length of 16 to 20  kbp and encodes about 20 to 30 genes .

Propagation cycle

The following process essentially follows the description on ViralZone:

  • The phage first attaches itself to the host bacterium with the help of the tail fibrils.
  • The virus' own DNA is then injected through the tail into the cell plasma of the host cell.
  • This is followed by transcription (reading the DNA and generating a messenger RNA - mRNA ) and translation (generating a protein from the mRNA) of some of the virus's “early” genes.
  • It follows the replication of the DNA genome by strand displacement ( english beach displacement ) by the viral DNA polymerase ( φ29 DNA polymerase ).
  • The transcription and translation of “late” genes is in the final phase of gene expression.
  • In the assembly phase that follows , the “procapsides” are first put together. These are the still empty capsids of the which are not filled with nucleic acid - DNA or RNA - or nucleoprotein
  • The genome is packaged ( English viral genome packaging ), for details see below .
  • Attaching the tail to the capsids completes the assembly.
  • The mature virions are finally released by lysis (bursting and death of the host cell).

Systematics

External system

Order : caudovirales

Candidates according to NCBI not yet confirmed by ICTV:

Synonyms

Unofficial synonyms for the species are according to NCBI:

  • Bacillus phage phi-29
  • Bacillus phage phi29
  • Bacillus subtilis phage phi29
  • Bacteriophage phi-29
  • Phage phi-29

Tribes

According to NCBI, strains of the species Φ29 are:

  • Bacillus phage phi29
  • Bacillus phage PZA (PZA)
  • Phage phi-15 (Φ15)

Bacteriophage pRNA

During replication , as with other linear dsDNA viruses, the viral genome is packaged into the previously formed viral procapsid. The exact processes were investigated using phage Φ29 as an example:

The packaging of DNA in the procapsid requires a molecular motor that uses adenosine triphosphate (ATP) as energy to bring about the actually energetically unfavorable movement. As with some other bacteriophage also is an essential part of this motor, a RNA molecule, which (as pRNA English RNA packaging ) is referred to. This is a special form of non-coding RNA ( English non-coding RNA , ncRNA), which is not the same these proteins coded . Structural analyzes of this packaging engine have shown that the pRNA molecule exhibits five-fold symmetry when it is bound to the procapsid. It is believed that the pRNA through the connector capsid protein ( English capsid protein connector is attached).

Only the first 120 bases of the pRNA are essential for packaging the viral DNA. The pRNA presumably consists of two sections (domains), one of which corresponds to the first 120 bases and the second to the remaining 50 bases.

use

The φ29 DNA polymerase is used for various methods of isothermal DNA amplification such as the Gibson assembly and multidisplacement amplification .

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. ↑ S. Mc Grath S, D. van Sinderen D (Ed.): Bacteriophage: Genetics and Molecular Biology , 1st edition, Caister Academic Press, 2007, ISBN 978-1-904455-14-1 .
  3. ↑ Ana Camacho, Fernando Jimenez, Javier Torre, Jose L. Carrascosa, Rafael P. Mellado, Eladio Vinuela, Margarita Salas, Cesar Vasquez: Assembly of Bacillus subtilis Phage Phi29. 1. Mutants in the Cistrons Coding for the Structural Proteins . In: European Journal of Biochemistry . 73, No. 1, February 1977, pp. 39-55. doi : 10.1111 / j.1432-1033.1977.tb11290.x .
  4. ↑ WJJ Meijer, JA Horcajadas, M. Salas: phi29 Family of Phages . In: Microbiology and Molecular Biology Reviews . 65, No. 2, June 1, 2001, pp. 261-287. doi : 10.1128 / MMBR.65.2.261-287.2001 . PMID 11381102 . PMC 99027 (free full text).
  5. ↑ a b ICTV: ICTV Master Species List 2018b.v2
  6. ↑ a b c SIB: Salasvirus , on: ExPASy ViralZone
  7. ↑ See φ29 DNA polymerase # properties , Isothermal DNA amplification # properties
  8. ↑ EMBL-EBI: PDBe> 2pyj - Phi29 DNA polymerase complexed with primer-template DNA and incoming nucleotide substrates (ternary complex) , on: Protein Data Bank in Europe, 2012
  9. ↑ ICTV: ICTV Taxonomy history: Bacillus virus B103
  10. ↑ ICTV: ICTV Taxonomy history: Bacillus virus GA1
  11. ^ ICTV: ICTV Taxonomy history: Kurthia virus 6
  12. ↑ NCBI: unclassified Salasvirus
  13. ↑ NVBI: Salasvirus (genus)
  14. ↑ NCBI: Bacillus virus phi29 (species)
  15. ↑ P. Guo: Structure and function of phi29 hexameric RNA that drives the viral DNA packaging motor: Prog. Nucleic Acid Res. Mol. Biol. (Review)  (= Progress in Nucleic Acid Research and Molecular Biology), Volume 72 2002, ISBN 978-0-12-540072-5 , pp. 415-472, doi : 10.1016 / S0079-6603 (02) 72076-X . PMID 12206459
  16. ↑ M. C. Morais, Y. Tao, N. H. Olson et al .: Cryoelectron-microscopy image reconstruction of symmetry mismatches in bacteriophage phi29 . In: J. Struct. Biol . 135, No. 1, 2001, pp. 38-46. doi : 10.1006 / jsbi.2001.4379 . PMID 11562164 . PMC 5595366 (free full text).
  17. ^ A. A. Simpson, Y. Tao, P. G. Leiman et al .: Structure of the bacteriophage phi29 DNA packaging motor . In: Nature . 408, No. 6813, 2000, pp. 745-750. bibcode : 2000Natur.408..745S . doi : 10.1038 / 35047129 . PMID 11130079 . PMC 4151180 (free full text).
  18. ↑ a b M. O. Badasso, P. G. Leiman, Y. Tao et al .: Purification, crystallization and initial X-ray analysis of the head-tail connector of bacteriophage phi29 . In: Acta Crystallogr. D . 56, No. Pt 9, 2000, pp. 1187-1190. doi : 10.1107 / S0907444900009239 . PMID 10957642 .
  19. ↑ P. X. Guo, S. Erickson, D. Anderson: A small viral RNA is required for in vitro packaging of bacteriophage phi 29 DNA . In: Science . 236, No. 4802, 1987, pp. 690-694. bibcode : 1987Sci ... 236..690G . doi : 10.1126 / science.3107124 . PMID 3107124 .
  20. ↑ a b S. Bailey, J. Wichitendungkarn, D. Johnson, B. E. Reilly, D. L. Anderson, J. W. Bodley: Phylogenetic analysis and secondary structure of the Bacillus subtilis bacteriophage RNA required for DNA packaging . In: J. Biol. Chem. . 265, No. 36, 1990, pp. 22365-22370. PMID 2125049 .