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00.021.0.01.001. Pseudomonas Phage φ6

Cite this publication as: ICTVdB Management (2006). 00.021.0.01.001. Pseudomonas Phage φ6. In: ICTVdB - The Universal Virus Database, version 4. Büchen-Osmond, C. (Ed), Columbia University, New York, USA

Cite this site as: ICTVdB - The Universal Virus Database, version 4. http://www.ncbi.nlm.nih.gov/ICTVdb/ICTVdB/

Table of Contents

Classification

This is a description of a bacterial virus at the species level.

ICTVdB Virus Code: 00.021.0.01.001. Virus accession number: 21001001. Obsolete virus code: 21.0.1.0.001; superceded accession number: 21010001.
NCBI Taxon Identifier NCBI Taxonomy ID: 10879.

Name, Synonyms and Lineage

ICTV approved acronym: phi6. Virus is the type of the genus 00.021.0.01. Cystovirus in the family 00.021. Cystoviridae.

Virion Properties

Morphology

Phages consist of an envelope, a capsid, and a polymerase complex. Virus capsid is enveloped. Virions are spherical and measure 86 nm in diameter. Surface projections are distinctive spikes covering evenly the surface; comprise P3 adsorption proteins and fusion proteins (P6). Surface projections are composed of one type of protein. Surface projections are 8 nm long. Capsid/nucleocapsid is round and exhibits icosahedral symmetry. The nucleocapsid is isometric and has a diameter of 58 nm. Nucleocapsid contains a polymerase complex; that is dodecahedral in shape; has a diameter of about 43 nm.







































Electron micrograph of Cystoviridae, Cystovirus, Pseudomonas phage φ6: Electron Micrographs of Bacterial Viruses kindly provided by Dr Hans Ackermann, Department of Microbiology, Medical Faculty, Laval University, Quebec, Canada. 3D reconstruction by Sarah J. Butcher at the Division of Virology at Glasgow, UK.

Physicochemical and Physical Properties

The molecular mass (Mr) of virions is 99 x 106, or 40 x 106 (for nucleocapsid). Virions have a buoyant density in CsCl of 1.27 g cm-3; sucrose of 1.24 g cm-3. The sedimentation coefficient is about 405 S20w. Under in vitro conditions virions are stable in acid environment of pH 6; stable in alkaline environment of pH 9. Virions are sensitive to treatment with detergents, ether, and chloroform.

Nucleic Acid

The Mr of the genome constitutes 10% of the virion by weight. The genome is segmented and consists of three segments of linear, double -stranded RNA. The complete genome is 13379 nucleotides long. Sequence can be accessed from EBI-EMBL and GenBank. The RNA-L is fully sequenced. Complete sequence is 6374 nucleotides long and encodes P1, P2, P4, and P7 proteins. Sequence has the accession number [M17461]. RNA-M is fully sequenced, complete sequence is 4057 nucleotides long and has the accession number [M17462]. RNA-S is fully sequenced, complete sequence is 2948 nucleotides long and has the accession number [M12921]. The genome has a guanine + cytosine content of 55.2 %, or 56.7 %, or 55.5 % (for L, M and S, respectively). The multipartite genome is found in one type of particle only.

GenBank records for nucleotide sequences; complete genome sequences.

Proteins

Proteins constitute about about 70% of the particle weight.

The viral genome encodes structural proteins and non-structural proteins located in the envelope (P9, P10, and P13), peplomers (P3, and P6), nucleocapsid (P8 and P5), polymerase complex (P1, P2, P4, and P7).

Structural Proteins: Envelope protein P10 and P13. Envelope protein has a function assigned; is a membrane protein which possess(es) lytic activity (P10, during post-translational processing envelope protein modifications occur that include phosphorylation and myristylation. Envelope protein P3; is involved in absorption; which possess(es) receptor recognition activity; during post-translational processing envelope protein modifications occur that include phosphorylation. Envelope protein P6; is a membrane protein (and serves as anchor for P3, which possess(es) membrane fusion activity. Envelope protein P9; is involved in membrane assembly. Nucleocapsid protein P8; is binding to the genomic RNA. Nucleocapsid protein P5; which possess(es) lytic activity initiating the cell lysis during assembly. Nucleocapsid protein P1, P2, P4 and P7 are early proteins; is polymerase complex.

Non-Structural Proteins: One non-structural protein is found. The virus codes for membrane assembly proteins (envelopment of capsid, an RNA-dependent RNA polymerase. 4 internal protein(s) (P1, P2, P4, and P7). Non-structural protein P12. The protein is coded from genome segment S; a membrane assembly protein (needed inside the host cell).

Lipids

Lipids are present and located in the envelope. Virions are composed of 20% lipids by weight. The composition of viral lipids and host cell membranes are similar. The lipids are of host origin and are derived from plasma membranes. Viral membranes include phospholipids.

Carbohydrates

Carbohydrates have not been reported.

Genome Organization and Replication

Phages are adsorbed to specific receptors located on the pili which retract and bring the virion into contact with the host outer membrane, upon contact with the host cell wall virus membrane fuses with the host outer membrane followed by digestion with a lytic enzyme (associated with nucleocapsid locally digesting the peptidoglycan).

The process of intracellular uncoating of virions is understood. Virus uncoating occurs in the cell; the viral nucleocapsid is delivered to the cell cytoplasm; the release of the viral polymerase (activates it and the prodution of early transcripts starts).

Transcription: Virus transcription is temporally regulated; they are termed early and late. The viral genome is transcribed by virion-associated enzymes.

The viral genome is transcribed by a viral polymerase. The translated L transcripts produce the early proteins which assemble to polymerase complexes).

Coding Strategy of Segment 1: RNA-L has a unidirectional coding strategy, which is polycistronic, and encodes 4 structural proteins, constituting the polymerase complex.

Coding Strategy of Segment 2: RNA-M has a unidirectional coding strategy, has 5 genes that encode 4 structural proteins. The sequence encodes membranes and spikes.

Coding Strategy of Segment 3: RNA-S genome is polycistronic, encodes 3 structural proteins for the capsid (coat protein), membrane assembly protein and endopeptidase (lysis and entry) and encodes 1 non-structural protein for envelopment of capsid.

Translation: During the replication cycle early synthesis of viral protein is decreased during switch-over to late gene expression. Translation of structural and non-structural proteins occurs in the late stage of replication.

Replication cycle Virions accumulate in the cell cytoplasm.

Assembly and Egress: For assembly and packaging a virus specific nonstructural assembly factor is needed to form the nucleocapsid. Viruses assemble in the cytoplasm.

Maturation: Virions mature acquiring the membrane from hosts with plasma membranes.

Release: Infected cells produce virions. Virus is released from host cell upon death by lysis. The virus envelope is acquired from the host cell during the maturation process in the cytoplasm. Envelope lipids are derived from the host cell plasma membrane.

Biological Properties

Natural Host

Domain
Viral hosts belong to the Domain Bacteria.

Domain Bacteria
Phylum Proteobacteria.

Host Classification Virus infects Genus Pseudomonsas; Species pseudoalcalingenes strains and many pathogenic species.

Signs and Symptoms

Virus found in — Pseudomonsas.

References

The following generic references are cited in the most recent ICTV Report.

PubMed References.

Images

Taxon images: • EM by Hans Ackermann, Laval University, Quebec. • 3D reconstruction by Sarah J. Butcher at the Division of Virology at Glasgow, UK.



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DELTA - DEscription Language for TAxonomy developed by Dr Mike Dallwitz, Toni Paine and Eric Zurcher, CSIRO Entomology, Canberra, Australia. ICTVdB - The Universal Virus Database, developed for the International Committee on Taxonomy of Viruses by Dr Cornelia Büchen-Osmond is written in DELTA. The virus descriptions in ICTVdB are coded by, or using data from experts in the field of virology or members ICTV. The character list is the underlying code. All virus descriptions are based on the character list and natural language translations are automatically generated and formatted for display on the Web from the descriptions in DELTA-format. The description has been generated automatically from DELTA files. DELTA - DEscription Language for TAxonomy developed by Dr Mike Dallwitz, Toni Paine and Eric Zurcher, CSIRO Entomology, Canberra, Australia.

ICTVdB - The Universal Virus Database, developed for the International Committee on Taxonomy of Viruses (ICTV) by Dr Cornelia Büchen-Osmond, is written in DELTA. The virus descriptions in ICTVdB are coded by ICTV members and experts, or by the ICTVdB Management using data provided by the experts, the literature or the latest ICTV Report. The character list is the underlying code. All virus descriptions are based on the character list and natural language translations from the encoded descriptions are automatically generated and formatted for display on the Web.

Developer of the DELTA software: M. J. Dallwitz, T. Paine and E. Zurcher

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Last updated on 25 April 2006 by Cornelia Büchen-Osmond
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