Potyviridae


Potyviridae

Chapter Contents

Potyviridae: The Family

Potyviridae: Member Taxa

Potyviridae: Supporting Information

  • Authors - Corresponding author: Stephen J Wylie (s.wylie@murdoch.edu.au)
  • Resources - Sequence alignments and tree files
  • References - Literature cited

Citation

A summary of this ICTV online (10th) report chapter has been published as an ICTV Virus Taxonomy Profile article in the Journal of General Virology, and should be cited when referencing this online chapter as follows: Wylie, S.J., Adams, M., Chalam, C., Kreuze, J., López-Moya, J.J., Ohshima, K., Praveen, S., Rabenstein, F., Stenger, D., Wang, A., Zerbini, F.M., and ICTV Report Consortium, ICTV Virus Taxonomy Profile: Potyviridae, Journal of General Virology, 98: 352-354.

Summary

Members of family Potyviridae (termed potyvirids) consist of monopartite and bipartite plant viruses with a single stranded, positive sense RNA genome and flexuous, filamentous particles. Genomes have a VPg covalently linked to the 5′ end and the 3′ terminus is polyadenylated. Genomes encode a large polyprotein that is self-cleaved into a set of functional proteins. Gene order is generally conserved throughout the family (Adams et al., 2005).

Table 1.Potyviridae. Characteristics of the family Potyviridae.

Characteristic

Description

Typical member 

potato virus Y-O (U09509), species Potato virus Y, genus Potyvirus 

Virion 

Non-enveloped, flexuous and filamentous capsid, 680 to 900 nm long and 11–20 nm in diameter with a single core capsid protein

Genome 

8–11 kb of positive-sense, single-stranded, usually monopartite RNA (bipartite in genus Bymovirus 

Replication

Cytoplasmic, initiated in virus replication complexes on membranous vesicles at ER exit sites. Replication initiates at 6K2-induced ER-originated vesicles

Translation 

Directly from genomic RNA.

Host range 

Plants (all virus genera). Most members are arthropod-borne but those of genus Bymovirus are transmitted by plasmodiophorids

Taxonomy 

Currently 8 genera containing nearly 200 species 

Virion

Morphology

Virions are flexuous filaments with no envelope and are 11–20 nm in diameter, with a helical pitch of about 3.4 nm (Figure 1.Potyviridae). Particle lengths of members of some of the eight genera differ. Members of the genera Potyvirus, Poacevirus, Ipomovirus, Macluravirus, Rymovirus, Tritimovirus, Brambyvirus and the unassigned viruses are monopartite with particle modal lengths of 650–950 nm. Members of the genus Bymovirus are bipartite with particles of two modal lengths of 250–300 and 500–600 nm.

Figure 1.Potyviridae. (Left) Schematic diagram of a potyvirus particle. The N-terminal (ca. 30 aa; large rectangle) and C-terminal (ca.19 aa; small rectangle) of the CP molecules are exposed on the surface of the intact virus particle (from (Shukla and Ward 1989)). (Right) Negative contrast electron micrograph of particles of an isolate of Plum pox virus, stained with 1% PTA, pH 6.0. The bar represents 200 nm (Courtesy of I.M. Roberts.) 

Physicochemical and physical properties

Virions of viruses in the genera Potyvirus and Rymovirus have a density in CsCl of about 1.31 g cm−3 and Sedimentation coefficient S20,w of 137–160S. Those of the genus Bymovirus have a density in CsCl of about 1.29 g cm−3.

Nucleic acid

Viruses in all genera except Bymovirus have a single molecule of positive sense, ssRNA, 9.3–10.8 kb in size. Virions are infectious. A VPg of about 24 kDa is covalently linked to the 5′-terminal nt. A polyadenylate tract (20 to 160 adenosines) is present at the 3′ terminus. Bymoviruses have two positive sense, ssRNA molecules; RNA-1 is 7.3–7.6 kb in size and RNA-2 is 3.5–3.7 kb in size. Both RNAs have 3′-terminal polyadenylate tracts and probably a VPg at the 5′ termini.

Proteins

Virions contain one type of CP of 28.5–47 kDa. N- and C-terminal residues are positioned on the exterior of the virion. Mild trypsin treatment removes N- and C-terminal segments, leaving a trypsin-resistant core of about 24 kDa. Plant proteases may degrade the CP in vivo, as occurs in vitro during purification using some procedures or from certain hosts. All potyvirus CPs display significant aa sequence identity in the trypsin-resistant core, but little identity in their N and C-terminal segments.

Genome organization and replication

The genomic RNA (two RNAs for the genus Bymovirus) encodes a single major polyprotein. This then undergoes co- and post-translational proteolytic processing by three viral-encoded proteinases to form the mature proteins. Genomic RNA replicates via the production of a full-length negative sense RNA. While there are exceptions noted in the relevant genus descriptions, the polyprotein of the majority of monopartite viruses in the family is cleaved into ten products, which show conservation of sequence and organisation (Kekarainen et al., 2002). As shown in Figure 2.Potyviridae, these products are:

  • P1 (Protein 1): Of all the potyvirid proteins, P1 is the least conserved in sequence and the most variable in size. It plays a significant role in virus replication probably due to the stimulation of the gene silencing suppressor HC-Pro. A serine protease domain towards the C-terminus cleaves the P1 from the polyprotein, typically at Tyr/Phe-Ser (Valli et al., 2007).
  • HC-Pro (Helper Component-Protease): the HC-Pro protein has roles in suppression of gene silencing and in vector transmission. A cysteine protease domain towards the C-terminus cleaves it from the remainder of the downstream polyprotein, typically at Gly-Gly.
  • P3 (Protein 3): Involved in virus replication and appears to be significant in host range and symptom development.
  • 6K1 (6-kDa peptide 1): Although it is present in the replication complex and required for replication, the function of this small protein is not known.
  • CI (Cylindrical Inclusion protein): This protein has helicase activity and accumulates in inclusion bodies in the cytoplasm of infected plant cells.
  • 6K2 (6-kDa peptide 2): A small transmembrane protein probably anchoring the replication complex to the ER.
  • VPg (Viral Protein genome-linked): Attached to the 5′ terminus of the genome and belongs to a class of intrinsically disordered proteins. It plays multiple roles in the viral infection cycle. It is essential for virus replication and translation, interacting with one or several isoforms of the eIF4E translation initiation factor. It is involved in suppression of RNA silencing.
  • NIa-Pro (Nuclear inclusion A-protease): Serine-like cysteine protease responsible for cleavage of most sites in the polyprotein, typically at Gln/Glu-(Ser/Gly/Ala) (Adams et al., 2005).
  • NIb (Nuclear inclusion B): The RNA-dependent RNA polymerase.
  • CP (Coat (capsid) protein: Viral coat protein that also has roles in virus movement, genome amplification and vector transmission.
  • A short ORF (PIPO, Pretty Interesting Potyvirus ORF) embedded within the P3 cistron is expressed as the trans-frame P3N-PIPO protein by a polymerase slippage mechanism (Chung et al., 2008, Olspert et al., 2015, Rodamilans et al., 2015). PIPO has been identified throughout the family and has been shown to be essential for virus intercellular movement.

The polymerase slippage model for the production of P3N-PIPO is consistent with the theory that potyvirus intercellular movement is coupled to active virus gnome replication and translation. Potyvirus replication initiates at the 6K2-induced ER-originated vesicles. The cellular COPI and COPII coating machineries are involved in the biogenesis of the potyvirus 6K2 vesicles. The ER-derived 6K2 vesicles also target and are associated with chloroplasts for virus replication.

Figure 2.Potyviridae. Genomic map of a typical member of the genus Potyvirus. The ssRNA genome is represented by a line and an open box representing the ORF translated into a polyprotein. Names associated with the mature proteins proteolytically processed from the polyprotein are shown. VPg (viral protein genome-linked), genome-linked viral protein covalently attached to the 5′-terminal nt (represented by the hexagon at the 5′ end); P1-Pro (protein 1 protease), a protein with serine proteolytic activity responsible for cleavage at typically Tyr/Phe-Ser (O); HC-Pro (helper component protease), a protein with aphid transmission helper-component activity and cysteine proteolytic activity responsible for cleavage at typically Gly-Gly (♦); P3 (protein 3); PIPO (pretty interesting Potyviridae ORF); 6K (six kilodalton peptide); CI (cytoplasmic inclusion); NIa-Pro (nuclear inclusion A protease), cysteine-like proteolytic activity responsible for cleavage at Gln/Glu-(Ser/Gly/Ala) (↓); Nib (nuclear inclusion B), RNA-dependent RNA polymerase; CP (coat protein).

Antigenicity

The viral proteins are moderately immunogenic; there are serological relationships among members. An epitope of the CP in the conserved internal trypsin-resistant core has been identified that is similar in most members of the family.

Biology

Inclusion body formation

All members of the family Potyviridae form cytoplasmic cylindrical inclusion (CI) bodies during infection. The CI is an array of a 70 kDa viral protein that possesses ATPase and helicase activities. Some potyviruses induce nuclear inclusion bodies that are co-crystals of two viral-encoded proteins – NIa and NIb – present in equimolar amounts. The small nuclear inclusion (NIa) protein (49 kDa) is a polyprotein consisting of the VPg and proteinase. Amorphous inclusion bodies are also evident in the cytoplasm during certain potyvirus infections and represent aggregations of the protein HC-Pro and perhaps other non-structural proteins.

Host range

Some members have a narrow host range, most members infect an intermediate number of plants, and a few members infect species in up to 30 families. Transmission to most hosts is readily accomplished by mechanical inoculation. Many viruses are widely distributed. Distribution is aided by seed transmission in some cases.

Transmission

Potyvirids are vectored by a variety of organisms. Members of the genera Potyvirus and Macluravirus have aphid vectors that transmit in a non-persistent, non-circulative manner. A helper component and a particular CP aa triplet (i.e., DAG for some potyviruses) are required for aphid transmission. Rymoviruses, poaceviruses and tritimoviruses are transmitted by eriophyid mites in a semi-persistent manner. Bymoviruses are transmitted by root-infecting vectors in the order Plasmodiophorales, once described as fungi but now classified as Cercozoa. Ipomoviruses appear to be transmitted by whiteflies, and the vector of the one species within Brambyvirus is unknown.

Genus demarcation criteria

The eight genera are differentiated by biological criteria, mainly transmission by specific vectors, and by molecular data (Figure 3.Potyviridae) (Adams et al., 2005, Gibbs and Ohshima 2010). For the entire open reading frame, genus demarcation criteria are <46% nucleotide identity, but this does not separate rymoviruses from potyviruses, which are separated by their vectors.

Figure 3.Potyviridae. Mid-point rooted phylogenetic tree based on the codon-aligned nucleotide sequences of the polyproteins of fully-sequenced members of the family Potyviridae. Sequences were codon aligned using MUSCLE in MEGA. A Maximum Likelihood tree was then constructed using the General Time Reversible (+G+I) substitution model and 100 bootstrap replicates; only bootstrap values of 0.7 or above are shown for clarity. The Potyvirus, Rymovirus, Brambyvirus, Unassigned, Tritimovirus, Poacevirus, Ipomovirus, Macluravirus, and Bymovirus genera are highlighted in yellow, purple, black, grey, green, pink, orange, brown and blue, respectively, and labeled accordingly.

Species demarcation criteria

Species demarcation criteria for the complete ORF are <76% nucleotide identity and <82% amino acid identity. The thresholds for species demarcation using nucleotide identity values for the individual coding regions range from 58% for the P1 coding region to 74–78% for other regions. For the coat protein, the optimal species demarcation criterion is 76–77% nucleotide and 80% amino acid identity (Adams et al., 2005).

Derivation of names

The family is named after the type species of the genus Potyvirus, Potato virus Y. 

Similarity with other taxa

The family Potyviridae is related to viruses in the order Picornavirales in the genome structure, in particular the polyprotein strategy and the replication block (helicase, VPg, 3C-like protease and polymerase).  However, they differ from these viruses in the virion morphology, size of VPg and type of helicase.

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