Potyvirus

Structure

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 around 2000 copies of the capsid protein. The symmetry of the nucleocapsid is helical with a pitch of 3.4 nm.

Genome

Genomic map of a typical member of the genus Potyvirus.

The genome is a linear, positive-sense, single-stranded RNA ranging in size from 9,000–12,000 nucleotide bases. 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.

In the species with a single genome, at the 5' end a protein is covalently linked (the VPg protein). It encodes a single open reading frame (ORF) expressed as a 350 kDa polyprotein precursor. This is processed into ten smaller proteins: protein 1 protease (P1-Pro), helper component protease (HC-Pro), protein 3 (P3), cylindrical inclusion (CI), viral protein genome-linked (Vpg), 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]

Proteins

Diagram of potyvirus virion

Properties of the viral protein:

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

HC-Pro (~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.

P3 (~41 kDa) the function 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 NIa-Pro a protease (~27 kDa) and the VPg (~22 kDa) protein.

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

6K1 (~6 kDa) the function 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.

P3N-PIPO (~25 kDa) the function 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.

CP the capsid protein ranges between 30 and 35 kDa in weight.

VPg protein interacts with eukaryotic initiation factor 4E (eIF4E).^[4] This interaction appears to be essential to viral infectivity. Two proteases, P1 and the helper component protease (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 proteinaceous 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]

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 groups

Potyviruses were further divided into the PVY, SCMV, BYMV, BCMV species groups in 1992. Gibbs and Ohshima 2010 produced a more extensive molecular phylogeny with the same four, but also several new groups: the BtMV, ChVMV, DaMV, OYDV, PRSV, TEV, and TuMV.^[10]