Potyvirus

Potyvirus is a genus of viruses in the family Potyviridae. Plants serve as natural hosts. There are currently 183 species in this genus including the type species Potato virus Y.[1][2] The genus is named after the type virus (potato virus Y). Potyviruses account for ~30% of the currently known plant viruses. Like begomoviruses, members of this genus may cause significant losses in agricultural, pastoral, horticultural and ornamental crops. More than 200 species of aphids spread potyviruses and most are from the subfamily Aphidinae (genera Macrosiphum and Myzus).

Potyvirus
Plum pox virus genome with electron micrograph and model of virions
Virus classification
(unranked): Virus
Realm: Riboviria
Kingdom: Orthornavirae
Phylum: Pisuviricota
Class: Stelpaviricetes
Order: Patatavirales
Family: Potyviridae
Genus: Potyvirus
Type species
Potato virus Y
Species

See text

Virology
Genomic map of a typical member of the genus Potyvirus.

The virion is non-enveloped with a flexuous and filamentous nucleocapsid, 680 to 900 nanometers (nm) long and is 11–20 nm in diameter.[1] The nucleocapsid contains ~2000 copies of the capsid protein. The symmetry of the nucleocapsid is helical with a pitch of 3.4 nm.

The genome is a linear positive sense ssRNA ranging in size from 9000–12000 bases/nucleotides. Most potyviruses have non-segmented genomes,[1] though a number of species are bipartite. The base composition is: 21–23.51–26% G; 23–30.15–44% A; 14.9–22.41–28% C; 15.6–24.41–30.9% U.

GenusStructureSymmetryCapsidGenomic arrangementGenomic segmentation
PotyvirusFilamentousNon-envelopedLinearMonopartite

In the species with a single genome, at the 5' end a protein is covalently linked (the Vg protein). It encodes a single open reading frame (ORF) expressed as a 350kDa polyprotein precursor. This is processed into seven smaller proteins: P1, helper component (HC), P3, cylindrical inclusion (CI), nuclear inclusion A (NIa), nuclear inclusion B (NIb), capsid protein (CP) and two small putative proteins known as 6K1 and 6K2. The P3 cistron also encodes a second protein—P3N-PIPO—which is generated by a +2 frameshift.[3]

Molecular biology

Protein P1 (~33 kiloDaltons (kDa) in molecular weight) is a serine protease.

HC (~52 KDa) is a protease that is also involved in aphid transmission. As a protease it cleaves a glycine-glycine dipeptide at its own C terminus. It also interacts with eukaryotic initiation factor 4 (eIF4). It acts as a viral RNA silencing suppressor.

The function of P3 (~41 kDa) is not known. It interacts with large subunit of the ribulose-1,5-bisphosphate carboxylase/oxygenase.

CI (~71 kDa) is an RNA helicase with ATPase activity. It is also involved in membrane attachment.

NIa (~50 kDa) is cleaved into a protease (~27 kDa) and the VPg (~22 kDa) protein.

NIb (~59 kDa) is an RNA-dependent RNA polymerase.

The functions of the 6K1 (~6 kDa) is not known. 6K2 (~6 kDa) protein, having a single trans membrane domain, is accumulating in the host cellular membranes and is thought to play a role in forming the replication vesicles of the virus.

The function of the P3N-PIPO (~25 kDa) is not known but it appears to be essential. It interacts with both the large and small subunits of the ribulose-1,5-bisphosphate carboxylase/oxygenase.

The capsid protein ranges between 30 and 35 kDa in weight.

The VPg protein interacts with eukaryotic initiation factor 4E (eIF4E).[4] This interaction appears to be essential to viral infectivity.

Two proteinases, P1 and the helper component proteinase (HC) catalyse only autoproteolytic reactions at their respective C termini. The remaining cleavage reactions are catalysed by either trans-proteolytic or autoproteolytic mechanisms by the small nuclear inclusion protein (NIa-Pro). This latter protein is an evolutionary homology of the picornavirus 3C proteinase.

Life cycle
Replication and movement of soybean mosaic virus (SMV) within cell

Replication may occur in the cytoplasm,[1] nuclei, chloroplasts, Golgi apparatus, cell vacuoles or more rarely in unusual sites.

Potyviruses make proteinacous inclusions in infected plant cells. These may be crystals in either the cytoplasm or in the nucleus, as amorphous X-bodies, membranous bodies, viroplasms or pinwheels. The inclusions may or may not (depending on the species) contain virions. These inclusions can be seen in the light microscope in leaf strips of infected plant tissue stained with Orange-Green (protein stain) but not Azure A (nucleic acid stain).[5][6][7] There are four different kinds of Potyvirus inclusions.[8]

Replication follows the positive stranded RNA virus replication model. Positive-stranded RNA virus transcription is the method of transcription. Translation takes place by -1 ribosomal frameshifting. The virus exits the host cell by tubule-guided viral movement. Plants serve as the natural host. The virus is transmitted via a vector (insects). Transmission routes are vector and mechanical.[1]

GenusHost detailsTissue tropismEntry detailsRelease detailsReplication siteAssembly siteTransmission
PotyvirusPlantsNoneViral movement; mechanical inoculationViral movementCytoplasmCytoplasmMechanical inoculation: aphids

Evolution

The potyviruses evolved between 6,600 and 7,250 years ago.[9][10] They appear to have evolved in southwest Eurasia or north Africa. The estimated mutation rate is about 1.15×10−4 nucleotide substitutions/site/year.

Geographical spread

Agriculture was introduced into Australia in the 18th century. This introduction also included plant pathogens. Thirty eight potyvirus species have been isolated in Australia. Eighteen potyviruses have been found only in Australia and are presumed to be endemic there. The remaining twenty appear to have been introduced with agriculture.

Species

Potyvirus contains the following species:[11]

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gollark: Must be being ratelimited.
gollark: Or was it mode2? Anyway.
gollark: Oh, yes, mode8.
gollark: What?

References
  1. "Viral Zone". ExPASy. Retrieved 15 June 2015.
  2. ICTV. "Virus Taxonomy: 2014 Release". Retrieved 15 June 2015.
  3. Chung, BY; Miller, WA; Atkins, JF; Firth, AE (2008). "An overlapping essential gene in the Potyviridae". Proc Natl Acad Sci U S A. 105 (15): 5897–5902. Bibcode:2008PNAS..105.5897C. doi:10.1073/pnas.0800468105. PMC 2311343. PMID 18408156.
  4. Léonard, S; Plante, D; Wittmann, S; Daigneault, N; Fortin, MG; Laliberté, JF (2000). "Complex formation between potyvirus VPg and translation eukaryotic initiation factor 4E correlates with virus infectivity". J Virol. 74 (17): 7730–7737. doi:10.1128/jvi.74.17.7730-7737.2000. PMC 112301. PMID 10933678.
  5. "Materials and Methods for the Detection of Viral Inclusions". University of Florida - Institute of Food and Agricultural Sciences. Archived from the original on 19 February 2012.
  6. Christie, R.G. and Edwardson, J.R. (1977). Fla Agric. Exp. Stn Monog. No. 9, 150 pp.
  7. How do you diagnose a virus infection in a plant? Archived 4 August 2012 at Archive.today
  8. Florida Department of Agriculture and Consumer Services: Florida plant viruses and their inclusions—Potyvirus
  9. Gibbs, AJ; Ohshima, K; Phillips, MJ; Gibbs, MJ (2008). "The Prehistory of potyviruses: Their initial radiation was during the dawn of agriculture". PLoS ONE. 3 (6): e2523. Bibcode:2008PLoSO...3.2523G. doi:10.1371/journal.pone.0002523. PMC 2429970. PMID 18575612.
  10. Gibbs, A; Ohshima, K (2010). "Potyviruses and the digital revolution". Annu Rev Phytopathol. 48: 205–23. doi:10.1146/annurev-phyto-073009-114404. PMID 20438367.
  11. "Virus Taxonomy: 2019 Release" (html). International Committee on Taxonomy of Viruses (ICTV). March 2020. Retrieved 2 May 2020.

Bibliography
  • Ward, CW; Shukla, DD (1991). "Taxonomy of potyviruses: current problems and some solutions". Intervirology. 32 (5): 269–96. doi:10.1159/000150211. PMID 1657820.
  • King, Andrew M. Q.; et al., eds. (2012). "Potyvirus". Virus taxonomy : classification and nomenclature of viruses : ninth report of the International Committee on Taxonomy of Viruses. London: Academic Press. pp. 926–1072. ISBN 978-0123846846. Retrieved 9 December 2014.
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