Potyvirus

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Potyvirus
Viruses-04-02853-g002.png
Plum pox virus genome with electron micrograph and model of virions
Virus classification OOjs UI icon edit-ltr.svg
(unranked): Virus
Realm: Riboviria
Kingdom: Orthornavirae
Phylum: Pisuviricota
Class: Stelpaviricetes
Order: Patatavirales
Family: Potyviridae
Genus:Potyvirus
Species

See text

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 ).[ citation needed ] The genus contains 190 species and potyviruses account for about thirty percent of all currently known plant viruses. [1] [2]

Contents

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 3.4-3.5 nm. [1]

Genome

Genomic map of a typical member of the genus Potyvirus. OPSR.Pot.Fig2.v3.png
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 to 12,000 nucleotide bases. Most potyviruses have non-segmented genomes, [1] 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. [3]

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). [4] 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. [5] [6] 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. [7]

Proteome

Diagram of potyvirus virion OPSR.Pot.Fig1.v1-potyvirus (l) shema.png
Diagram of potyvirus virion

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. [8] 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. [9]

HC-Pro (~52 KDa) is a cysteine protease which cleaves a glycine-glycine dipeptide at its own C-terminus. [8] It also interacts with eukaryotic initiation factor 4 (eIF4). It acts as a viral RNA silencing suppressor through its interactions with host AGO proteins. [10] 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. [8] The rate of P1 cleavage therefore regulates the level of RNA interference suppression during infection. HC-Pro is also involved in aphid transmission. [11] 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. [12]

P3 (~41 kDa) is a membrane protein which is required for viral replication and accumulates in viral replication vesicles. [13] 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. [14] P3 also interacts with large subunit of the ribulose-1,5-bisphosphate carboxylase/oxygenase.[ citation needed ]

CI (~71 kDa) is an RNA helicase with ATPase activity. [15] 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. [16] 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. [17] Potyviral NIa-Pro shares a high level of homology with the picornaviral 3C protease. [18]

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. [19] 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). [20] [21]

NIb (~59 kDa) is a superfamily II RNA-dependent RNA polymerase (RdRp) which polymerises viral RNA during replication. [22] 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. [23]

6K2 (~6 kDa) is a transmembrane protein which rearranges host membranes into virus-induced membrane structures. [24] It interacts with various ER exit site proteins to produce vesicular and tubular extensions which eventually mature into replication vesicles. [25] 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. [26]

P3N-PIPO (~25 kDa) is a dedicated movement protein which anchors the movement complex to the plasmodesma. [27] It may also modulate the plasmodesmatal size exclusion limit by interacting with host proteins which sever plasmodesmatal actin filaments and reduce callose deposition. [28] [29] It interacts with both the large and small subunits of the ribulose-1,5-bisphosphate carboxylase/oxygenase.[ citation needed ]

CP (~30 - 35 kDa) is the capsid protein. It has two terminal domains which are disordered and exposed at the surface of the virion. [30] [31] 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. [32]

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). [33] Such anomalies are often situated in the hypervariable P1-HC-Pro region. [8]

Life cycle

Replication and movement of soybean mosaic virus (SMV) within cell Plants-09-00219-g001.png
Replication and movement of soybean mosaic virus (SMV) within cell

Transmission

Most potyviruses are trasmitted by aphids as they probe plant tissues with their stylet during feeding. [34] 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). [35] 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. [36]

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. [37] 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. [37]

Replication

Like many other positive strand RNA viruses, potyvirus replication is heavily associated with host membranes. [1] [38] 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. [39] 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. [40] 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. [14] 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. [41] [42] 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.[ citation needed ]

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.[ citation needed ]

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. [43] The inclusions may or may not (depending on the species) contain virions.[ citation needed ] 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). [44] [45] [46]

Modern detection methods rely primarily on reverse transcription PCR. [47]

Taxonomy

Potyvirus contains the following species: [2]

A further four viruses were previously classified as species in this genus but were abolished due to lack of genetic sequence information: [48]

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. [42]

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 . [42]

Related Research Articles

<span class="mw-page-title-main">Picornavirus</span> Family of viruses

Picornaviruses are a group of related nonenveloped RNA viruses which infect vertebrates including fish, mammals, and birds. They are viruses that represent a large family of small, positive-sense, single-stranded RNA viruses with a 30 nm icosahedral capsid. The viruses in this family can cause a range of diseases including the common cold, poliomyelitis, meningitis, hepatitis, and paralysis.

Cauliflower mosaic virus (CaMV) is a member of the genus Caulimovirus, one of the six genera in the family Caulimoviridae, which are pararetroviruses that infect plants. Pararetroviruses replicate through reverse transcription just like retroviruses, but the viral particles contain DNA instead of RNA.

<span class="mw-page-title-main">Satellite (biology)</span> Subviral agent which depends on a helper virus for its replication

A satellite is a subviral agent that depends on the coinfection of a host cell with a helper virus for its replication. Satellites can be divided into two major classes: satellite viruses and satellite nucleic acids. Satellite viruses, which are most commonly associated with plants, are also found in mammals, arthropods, and bacteria. They encode structural proteins to enclose their genetic material, which are therefore distinct from the structural proteins of their helper viruses. Satellite nucleic acids, in contrast, do not encode their own structural proteins, but instead are encapsulated by proteins encoded by their helper viruses. The genomes of satellites range upward from 359 nucleotides in length for satellite tobacco ringspot virus RNA (STobRV).

<i>Potyviridae</i> Family of viruses

Potyviridae is a family of positive-strand RNA viruses that encompasses more than 30% of known plant viruses, many of which are of great agricultural significance. The family has 12 genera and 235 species, three of which are unassigned to a genus.

<i>Tobamovirus</i> Genus of viruses

Tobamovirus is a genus of positive-strand RNA viruses in the family Virgaviridae. Many plants, including tobacco, potato, tomato, and squash, serve as natural hosts. Diseases associated with this genus include: necrotic lesions on leaves. The name Tobamovirus comes from the host and symptoms of the first virus discovered.

VPg is a protein that is covalently attached to the 5′ end of positive strand viral RNA and acts as a primer during RNA synthesis in a variety of virus families including Picornaviridae, Potyviridae and Caliciviridae. There are some studies showing that a possible VPg protein is also present in astroviridae, however, experimental evidence for this has not yet been provided and requires further study. The primer activity of VPg occurs when the protein becomes uridylated, providing a free hydroxyl that can be extended by the virally encoded RNA-dependent RNA polymerase. For some virus families, VPg also has a role in translation initiation by acting like a 5' mRNA cap.

AlkB (Alkylation B) is a protein found in E. coli, induced during an adaptive response and involved in the direct reversal of alkylation damage. AlkB specifically removes alkylation damage to single stranded (SS) DNA caused by SN2 type of chemical agents. It efficiently removes methyl groups from 1-methyl adenines, 3-methyl cytosines in SS DNA. AlkB is an alpha-ketoglutarate-dependent hydroxylase, a superfamily non-haem iron-containing proteins. It oxidatively demethylates the DNA substrate. Demethylation by AlkB is accompanied with release of CO2, succinate, and formaldehyde.

<i>Cowpea chlorotic mottle virus</i> Species of virus

Cowpea chlorotic mottle virus, known by the abbreviation CCMV, is a virus that specifically infects the cowpea plant, or black-eyed pea. The leaves of infected plants develop yellow spots, hence the name "chlorotic". Similar to its "brother" virus, Cowpea mosaic virus (CPMV), CCMV is produced in high yield in plants. In the natural host, viral particles can be produced at 1–2 mg per gram of infected leaf tissue. Belonging to the bromovirus genus, cowpea chlorotic mottle virus (CCMV) is a small spherical plant virus. Other members of this genus include the brome mosaic virus (BMV) and the broad bean mottle virus (BBMV).

<i>Alfalfa mosaic virus</i> Species of virus

Alfalfa mosaic virus (AMV), also known as Lucerne mosaic virus or Potato calico virus, is a worldwide distributed phytopathogen that can lead to necrosis and yellow mosaics on a large variety of plant species, including commercially important crops. It is the only Alfamovirus of the family Bromoviridae. In 1931 Weimer J.L. was the first to report AMV in alfalfa. Transmission of the virus occurs mainly by some aphids, by seeds or by pollen to the seed.

Asparagus virus 1 (AV-1) is one of the nine known viruses that infects asparagus plants. It is a member of the genus Potyvirus in the family Potyviridae. Initially reported by G. L Hein in 1960, it causes no distinct symptoms in asparagus plants. The only known natural plant host is the asparagus. It is spread by aphid vectors, which means that aphids do not cause the AV-1, but they do spread it.

<i>Bidens mottle virus</i> Species of virus

Bidens mottle virus (BiMoV) is a pathogenic plant virus in the plant virus family Potyviridae. BiMoV is a flexuous filamentous particle, 720 nm long, and belongs to the Potyviridae genus Potyvirus. Like other viruses in this genus, Bidens mottle virus is transmitted both mechanically by sap and by aphids in a stylet-borne fashion.

Pepper mottle virus (PepMoV) is a plant pathogenic virus in the genus Potyvirus and the virus family Potyviridae. Like other members of the Potyvirus genus, PepMV is a monopartite strand of positive-sense, single-stranded RNA surrounded by a capsid made for a single viral encoded protein. The virus is a filamentous particle that measures about 737 nm in length. Isolates of this virus has been completely sequenced and its RNA is 9640 nucleotides long. This virus is transmitted by several species of aphids in a nonpersitant manner and by mechanical inoculation.

Potato virus Y (PVY) is a plant pathogenic virus of the family Potyviridae, and one of the most important plant viruses affecting potato production.

<i>Tobacco etch virus</i> Species of virus

Tobacco etch virus (TEV) is a plant virus in the genus Potyvirus and family Potyviridae. Like other members of the genus Potyvirus, TEV has a monopartite positive-sense, single-stranded RNA genome surrounded by a capsid made from a single viral encoded protein. The virus is a filamentous particle that measures about 730 nm in length. It is transmissible in a non-persistent manner by more than 10 species of aphids including Myzus persicae. It also is easily transmitted by mechanical means but is not known to be transmitted by seeds.

Sweet potato feathery mottle virus (SPFMV) is a member of the genus Potyvirus in the family Potyviridae. It is most widely recognized as one of the most regularly occurring causal agents of sweet potato viral disease (SPVD) and is currently observed in every continent except Antarctica. The number of locations where it is found is still increasing; generally, it is assumed that the virus is present wherever its host is. The virus has four strains that are found in varying parts of the world.

<i>Sobemovirus</i> Genus of viruses

Sobemovirus is a genus of non-enveloped, positive-strand RNA viruses which infect plants.. Plants serve as natural hosts. There are 21 species in this genus. Diseases associated with this genus include: mosaics and mottles.

Commelina mosaic virus (CoMV) is a plant pathogenic virus in the genus Potyvirus and the virus family Potyviridae. Like other members of the Potyvirus genus, CoMV is a monopartite strand of positive-sense, single-stranded RNA surrounded by a capsid made for a single viral encoded protein. The virus is a filamentous particle that measures about 707-808 nm in length. This virus is transmitted by two species of aphids, Myzus persicae and Aphis gossypii, and by mechanical inoculation.

Ipomovirus is a genus of positive-strand RNA viruses in the family Potyviridae. Member viruses infect plants and are transmitted by whiteflies. The name of the genus is derived from Ipomoea – the generic name of sweet potato. There are seven species in this genus.

Cassava brown streak virus is a species of positive-strand RNA viruses in the genus Ipomovirus and family Potyviridae which infects plants. Member viruses are unique in their induction of pinwheel, or scroll-shaped inclusion bodies in the cytoplasm of infected cells. Cylindrical inclusion bodies include aggregations of virus-encoded helicase proteins. These inclusion bodies are thought to be sites of viral replication and assembly, making then an important factor in the viral lifecycle. Viruses from both the species Cassava brown streak virus and Ugandan cassava brown streak virus (UCBSV), lead to the development of Cassava Brown Streak Disease (CBSD) within cassava plants.

Carrot virus Y (CarVY) is a (+)ss-RNA virus that affects crops of the carrot family (Apiaceae), such as carrots, anise, chervil, coriander, cumin, dill and parsnip. Carrots are the only known crop to be infected in the field. Infection by the virus leads to deformed roots and discolored or mottled leaves. The virus is spread through insect vectors, and is currently only found in Australia.

References

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