Potyvirus

Potyvirus is a genus of positive-strand RNA viruses (named after its type species, Potato virus Y (PVY)) in the family Potyviridae. Plants serve as natural hosts. 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). The genus contains 190 species and potyviruses account for about thirty percent of all currently known plant viruses.

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. The nucleocapsid contains around 2000 copies of the capsid protein. The symmetry of the nucleocapsid is helical with a pitch of 3.4-3.5 nm.

Genome 

The genome is a linear, positive-sense, single-stranded RNA ranging in size from 9,000 to 12,000 nucleotide bases. Most potyviruses have non-segmented genomes, though a number of species are bipartite. The typical base compositions of some of the most common, non-recombinant strains of the type species, PVY, range between ~23.4-23.8 % G; ~31-31.6 % A; ~18.2-18.8 % C; and ~26.5-26.8 % U.

In the species with a monopartite genome, a genome-linked VPg protein is covalently bound to the 5' end and the 3' end is polyadenylated. The genome encodes a single open reading frame (ORF) expressed as a 350 kDa polyprotein precursor. This polyprotein 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 contains an overlapping reading frame called "Pretty interesting Potyviridae ORF" (PIPO). PIPO codes for an alternative C-terminus to the P3 protein, which is generated into a subset of transcripts by a +2 frameshift caused by a ribosome slippage mechanism at a conserved GA6 repeat sequence. The resulting protein is called P3N-PIPO. A similar mechanism is thought to produce an alternative reading frame within the P1 cistron, named "pretty interesting sweet potato potyvirus ORF" (PISPO), in a number of sweet potato-infecting potyviruses including sweet potato feathery mottle virus.

Proteome 

P1 (~33 kiloDaltons (kDa) in molecular weight) is a serine protease which facilitates its own cleavage from the polyprotein at the P1-HC-Pro junction. P1 consists of a conserved C-terminal protease domain and an N-terminal region which has a high level of variation in sequence and length between potyvirus species but exhibits conserved patterns of intrinsic disorder. P1 is also promotes viral RNA replication, though it is not required for it.

HC-Pro (~52 KDa) is a cysteine protease which 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 through its interactions with host AGO proteins. HC-Pro's activity is regulated by the adjacent P1 protein: before P1 cleaves itself off the P1-HC-Pro intermediate, the P1 terminus reduces HC-Pro's RNA silencing suppression activity. The rate of P1 cleavage therefore regulates the level of RNA interference suppression during infection. HC-Pro is also involved in aphid transmission. Though the exact mechanism is unknown, HC-Pro has been proposed to attach to host aphid mouth parts through its N-terminal zinc finger-like domain and anchor virions through its interactions with the capsid protein.

P3 (~41 kDa) is a membrane protein which is required for viral replication and accumulates in viral replication vesicles. It mediates the interactions between replication vesicles and movement complex proteins which may allow replication vesicles to be recruited to the movement complex for efficient intercellular movement. P3 also interacts with large subunit of the ribulose-1,5-bisphosphate carboxylase/oxygenase.

CI (~71 kDa) is an RNA helicase with ATPase activity. Its most unusual property is its ability to form large and highly symmetrical conical and cylindrical inclusions with a central hollow cylinder from which laminate sheets radiate outward and fold in on themselves in a pattern often described as "pinwheels".  These inclusions are easily seen in transmission electron micrographs of infected tissues and were historically used as a diagnostic criterion for potyvirus infections. CI inclusions are a major component of the potyviral movement complex which is assembled at plasmodesmata. CI is also required for viral replication and is present on replication membranes. Its exact contributions to replication are not clear but, as an RNA helicase, CI is likely facilitating replication by dismantling the secondary structures of viral RNA.

NIa (~50 kDa) forms crystalline inclusions in the host nucleus. It is cleaved into NIa-Pro and VPg.

NIa-Pro (~27 kDa) is a cysteine protease which processes most of the cleavage sites of the polyprotein. The only exceptions are the self-cleavages of P1 and HC-Pro. The high degree of cleavage sequence specificity and conservation has made NIa-Pro (often that of Tobacco etch virus) a valuable tool in biotechnology, especially in applications which require removing affinity tags from recombinant proteins after affinity purification. NIa-Pro has also shown to exhibit sequence-independent DNase activity and to interfere with host DNA methylation suggesting that NIa and/or NIa-Pro are altering in host gene expression. Potyviral NIa-Pro shares a high level of homology with the picornaviral 3C protease.

VPg (~22 kDa) is covalently attched to the 5' end of the viral genomic RNA through uridylation and is thought to act as a primer for viral genome replication similarly to the VPg proteins of picornaviridae. It is a highly disordered protein and its flexibility has been suggested to allow it to interact with many other viral proteins. VPg also interacts with various host proteins including eukaryotic initiation factor 4E (eIF4E), eukaryotic elongation factor 1A (eEF1A), and poly(A)-binding protein (PABP).

NIb (~59 kDa) is a superfamily II RNA-dependent RNA polymerase (RdRp) which polymerises viral RNA during replication. Like NIa, NIb forms inclusions in the host nucleus where it is transported due to its two nuclear localisation sequences. NIb has the three-domain "palm, thumb, and fingers" structure typical of RdRps.

6K1 (~6 kDa) the function is not known, but because it accumulates in replication vesicles and has a transmembrane domain, 6K1 is thought to contribute to virus-induced vesicle formation.

6K2 (~6 kDa) is a transmembrane protein which rearranges host membranes into virus-induced membrane structures. It interacts with various ER exit site proteins to produce vesicular and tubular extensions which eventually mature into replication vesicles. 6K2 has three main domains: the N-terminal domain which is required for cell-to-cell movement, the central hydrophobic transmembrane alpha helix, and the C terminal domain which is required for viral replication.

P3N-PIPO (~25 kDa) is a dedicated movement protein which anchors the movement complex to the plasmodesma. It may also modulate the plasmodesmatal size exclusion limit by interacting with host proteins which sever plasmodesmatal actin filaments and reduce callose deposition. It interacts with both the large and small subunits of the ribulose-1,5-bisphosphate carboxylase/oxygenase.

CP (~30 - 35 kDa) is the capsid protein. It has two terminal domains which are disordered and exposed at the surface of the virion. The central core domain contains an RNA-binding pocket which binds to viral RNA. The structure of the capsid protein is highly conserved in potyviruses, though there is a relatively high degree of sequence variability. In addition to encapsidating the virion, CP core domain is required for intercellular movement and contributes to seed transmission.

Certain atypical potyviruses code for additional proteins or protein domains, such as P1-PISPO, Alkylation B (AlkB), and inosine triphosphate pyrophosphatase (known as ITPase or HAM1). Such anomalies are often situated in the hypervariable P1-HC-Pro region.

Life cycle

Transmission 
Most potyviruses are trasmitted by aphids as they probe plant tissues with their stylet during feeding. They do not circulate or multiply within the aphid and typically only persist in the aphid for a few minutes. Certain potyviruses have been shown to alter the feeding patterns of their aphid vectors, which may manifest as longer periods of time spent on infected plants, reduced non-probing feeding time, and increased phloem sap ingestion.

Seed and pollen transmission has been documented in certain potyvirus species, for instance in PVY and Turnip mosaic virus (TUMV). Vegetative transmission by infected tubers or grafting material are of particular concern for certain agricultural crops, such as potato and fruit trees, respectively.

Transmission can also occur by physical contact with infected plants or with contaminated tools, clothes, or even water.

Translation 
After entry, potyvirus particles are uncoated and genomic RNA is released into host cytoplasm. Potyviral RNA mimicks host mRNA: the 5' VPg protein shares functional similarities with the 5' cap and the 3' end is polyadenylated. VPg and its interactions with eIF4E and eIF4(iso)E allow the virus to utilise host cap-dependent translation machinery for its translation. Similarly to eukaryotic translation, the VPg-eIF4E interaction assembles the eIF4F complex around viral RNA.

A number of weak internal ribosome entry sites (IRES) have been identified in many potyvirus species but it is not known whether cap-independent translation is an important translation mechanism for potyviruses.

Replication 
Like many other positive strand RNA viruses, potyvirus replication is heavily associated with host membranes. The viral 6K2 protein coordinates the rearrangement of host membranes into various infection-associated structures which, depending of the potyvirus species, can include anything from small round viral vesicles to complex globular structures with many cisternae or lobes. These structures are dotted with viral replication complexes and are often called "replication vesicles", "viroplasm" or "viral factories". Replication vesicle membranes are derived from a variety of host organelles and the sources differ between potyvirus species. Some membrane sources include the ER, chloroplasts, Golgi apparatus, and vacuoles.

The exact replication mechanism is not known but it involves a negative sense RNA intermediate and requires both viral and host proteins. Viral proteins detected in replication complexes include HC-Pro, P3, 6K1, 6K2, CI, VPg, NIa-Pro, and NIb. Host factors present in replication vesicles include eIF4A and several heat shock proteins.

Intercellular movement 
Like most plant viruses, potyviruses have evolved to move from one plant cell to another through plasmodesmata. However, unlike some well-studied plant viruses, such as the Tobacco mosaic virus, potyviruses do not have a single movement protein but instead assemble a movement complex around the plasmodesma. This complex is primarily composed of three viral proteins: CI, CP, P3N-PIPO. Conical CI inclusions are anchored to plasmodesmata by P3N-PIPO during the early stages of potyvirus infection. This allows the inclusion to funnel either viral particles or viral RNA-CP complexes through the plasmodesma. Replication vesicles are also recruited to the movement complex, suggesting that replication and movement are coupled. Replication vesicles are recruited by P3N-PIPO, which interacts with both CI and P3 through the shared P3N-domain. P3's interaction with 6K2 allows replication vesicles to be tethered to the movement complex.

Evolution

Potyviruses evolved between 6,600 and 7,250 years ago. They appear to have evolved in southwest Eurasia or north Africa. The estimated mutation rate is about 1.15 nucleotide substitutions/site/year.

Geographical distribution 
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.

Diagnostics 
Historically, potyvirus diagnostics relied on the detection of various proteinaceous inclusions in infected plant cells. These may appear as 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 by light microscopy in leaf strips of infected plant tissue stained with Orange-Green (protein stain) but not Azure A (nucleic acid stain).

Modern detection methods rely primarily on reverse transcription PCR.

Taxonomy

Potyvirus contains the following species:

 African eggplant mosaic virus
 Algerian watermelon mosaic virus
 Alstroemeria mosaic virus
 Alternanthera mild mosaic virus
 Amaranthus leaf mottle virus
 Amazon lily mosaic virus
 Angelica virus Y
 Apium virus Y
 Araujia mosaic virus
 Arracacha mottle virus
 Asparagus virus 1
 Banana bract mosaic virus
 Barbacena virus Y
 Basella rugose mosaic virus
 Bean common mosaic necrosis virus
 Bean common mosaic virus
 Bean yellow mosaic virus
 Beet mosaic virus
 Begonia flower breaking virus
 Bidens mosaic virus
 Bidens mottle virus
 Blue squill virus A
 Brugmansia mosaic virus
 Brugmansia suaveolens mottle virus
 Butterfly flower mosaic virus
 Calanthe mild mosaic virus
 Calla lily latent virus
 Callistephus mottle virus
 Canna yellow streak virus
 Carnation vein mottle virus
 Carrot thin leaf virus
 Carrot virus Y
 Catharanthus mosaic virus
 Celery mosaic virus
 Ceratobium mosaic virus
 Chilli ringspot virus
 Chilli veinal mottle virus
 Chinese artichoke mosaic virus
 Clitoria virus Y
 Clover yellow vein virus
 Cocksfoot streak virus
 Colombian datura virus
 Commelina mosaic virus
 Costus stripe mosaic virus
 Cowpea aphid-borne mosaic virus
 Cucurbit vein banding virus
 Cypripedium virus Y
 Cyrtanthus elatus virus A
 Daphne mosaic virus
 Daphne virus Y
 Dasheen mosaic virus
 Datura shoestring virus
 Dendrobium chlorotic mosaic virus
 Dioscorea mosaic virus
 Diuris virus Y
 Donkey orchid virus A
 East Asian Passiflora distortion virus
 East Asian Passiflora virus
 Endive necrotic mosaic virus
 Euphorbia ringspot virus
 Freesia mosaic virus
 Fritillary virus Y
 Gloriosa stripe mosaic virus
 Gomphocarpus mosaic virus
 Habenaria mosaic virus
 Hardenbergia mosaic virus
 Henbane mosaic virus
 Hibbertia virus Y
 Hippeastrum mosaic virus
 Hyacinth mosaic virus
 Impatiens flower break virus
 Iris fulva mosaic virus
 Iris mild mosaic virus
 Iris severe mosaic virus
 Japanese yam mosaic virus
 Jasmine virus T
 Johnsongrass mosaic virus
 Kalanchoe mosaic virus
 Keunjorong mosaic virus
 Konjac mosaic virus
 Leek yellow stripe virus
 Lettuce Italian necrotic virus
 Lettuce mosaic virus
 Lily mottle virus
 Lily virus Y
 Lupinus mosaic virus
 Lycoris mild mottle virus
 Maize dwarf mosaic virus
 Malva vein clearing virus
 Mashua virus Y
 Meadow saffron breaking virus
 Mediterranean ruda virus
 Moroccan watermelon mosaic virus
 Narcissus degeneration virus
 Narcissus late season yellows virus
 Narcissus yellow stripe virus
 Nerine yellow stripe virus
 Noni mosaic virus
 Nothoscordum mosaic virus
 Onion yellow dwarf virus
 Ornithogalum mosaic virus
 Ornithogalum virus 2
 Ornithogalum virus 3
 Panax virus Y
 Papaya leaf distortion mosaic virus
 Papaya ringspot virus
 Paris mosaic necrosis virus
 Paris virus 1
 Parsnip mosaic virus
 Passiflora chlorosis virus
 Passiflora mottle virus
 Passion fruit woodiness virus
 Pea seed-borne mosaic virus
 Peanut mottle virus
 Pecan mosaic-associated virus
 Pennisetum mosaic virus
 Pepper mottle virus
 Pepper severe mosaic virus
 Pepper veinal mottle virus
 Pepper yellow mosaic virus
 Peru tomato mosaic virus
 Pfaffia mosaic virus
 Platycodon mild mottle virus
 Pleione flower breaking virus
 Pleione virus Y
 Plum pox virus
 Pokeweed mosaic virus
 Potato virus A
 Potato virus V
 Potato virus Y
 Potato yellow blotch virus
 Ranunculus leaf distortion virus
 Ranunculus mild mosaic virus
 Ranunculus mosaic virus
 Rhopalanthe virus Y
 Saffron latent virus
 Sarcochilus virus Y
 Scallion mosaic virus
 Shallot yellow stripe virus
 Sorghum mosaic virus
 Soybean mosaic virus
 Spiranthes mosaic virus 3
 Sudan watermelon mosaic virus
 Sugarcane mosaic virus
 Sunflower chlorotic mottle virus
 Sunflower mild mosaic virus
 Sunflower mosaic virus
 Sunflower ring blotch virus
 Sweet potato feathery mottle virus
 Sweet potato latent virus
 Sweet potato mild speckling virus
 Sweet potato virus 2
 Sweet potato virus C
 Sweet potato virus G
 Tamarillo leaf malformation virus
 Telfairia mosaic virus
 Telosma mosaic virus
 Thunberg fritillary mosaic virus
 Tobacco etch virus
 Tobacco mosqueado virus
 Tobacco vein banding mosaic virus
 Tobacco vein mottling virus
 Tomato necrotic stunt virus
 Tradescantia mild mosaic virus
 Tuberose mild mosaic virus
 Tuberose mild mottle virus
 Tulip breaking virus
 Tulip mosaic virus
 Turnip mosaic virus
 Twisted-stalk chlorotic streak virus
 Ugandan passiflora virus
 Vallota mosaic virus
 Vanilla distortion mosaic virus
 Verbena virus Y
 Watermelon leaf mottle virus
 Watermelon mosaic virus
 Wild melon banding virus
 Wild onion symptomless virus
 Wild potato mosaic virus
 Wild tomato mosaic virus
 Wisteria vein mosaic virus
 Yam mild mosaic virus
 Yam mosaic virus
 Yambean mosaic virus
 Zantedeschia mild mosaic virus
 Zea mosaic virus
 Zucchini shoestring virus
 Zucchini tigre mosaic virus
 Zucchini yellow fleck virus
 Zucchini yellow mosaic virus

A further four viruses were previously classified as species in this genus but were abolished due to lack of genetic sequence information:

 Cowpea green vein banding virus
 Groundnut eyespot virus
 Helenium virus Y
 Tropaeolum mosaic virus

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.

PVY
Contains 16 species including the type species of the genus (potato virus Y). The primary hosts are: Nine Solanaceae, three Amaranthus, three Asteraceae, one Lilium, and one Amaryllis.

References

Bibliography

External links 
 UniProt taxonomy: Potyvirus
 Viralzone: Potyvirus
 ICTV

Virus genera
Potyviruses
Viral plant pathogens and diseases