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Potyvirus
Potyvirus is a genus of positive-strand RNA viruses (named after Potato virus Y (Potyvirus yituberosi, 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 216 species.
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.
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 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 (Potyvirus batataplumei).
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.[citation needed]
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.
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Potyvirus
Potyvirus is a genus of positive-strand RNA viruses (named after Potato virus Y (Potyvirus yituberosi, 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 216 species.
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.
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 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 (Potyvirus batataplumei).
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.[citation needed]
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.