title: Analysis of the RNA of Potato yellow vein virus: evidence for a tripartite genome and conserved 3'-terminal structures among members of the genus Crinivirus.
abstract: Double-stranded RNA preparations produced from potato plants graft-inoculated with a Peruvian isolate of Potato yellow vein virus (PYVV; genus Crinivirus, family Closteroviridae) contain five RNA species denoted RNA 1, RNA 2, RNA 3, x and y of approximately 8, 5.3, 3.8, 2.0 and 1.8 kbp, respectively. The complete nucleotide sequences of PYVV RNAs 1, 2 and 3 and Northern hybridization analysis showed that PYVV RNA 1 contained the replication module and an additional open reading frame (p7), while two distinct species, RNAs 2 and 3, contain the Closteroviridae hallmark gene array. Pairwise comparisons and phylogeny of genome-encoded proteins showed that PYVV shares significant homology with other criniviruses but is most closely related to the Trialeurodes vaporariorum-vectored Cucumber yellows virus. Secondary structure prediction of the 3'-untranslated regions of all three PYVV RNAs revealed four conserved stem-loop structures and a 3'-terminal pseudoknot structure, also predicted for all fully characterized members of the genus Crinivirus and some members of the genera Closterovirus and Ampelovirus.
authors.affiliation: Department of Biological Sciences, Imperial College London, Sir Alexander Fleming Building, Imperial College Road, London SW7 2AZ, UK.
authors.forename: I C
authors.initials: IC
authors.lastname: Livieratos
authors.affiliation: Department of Biological Sciences, Imperial College London, Sir Alexander Fleming Building, Imperial College Road, London SW7 2AZ, UK.
authors.forename: E
authors.initials: E
authors.lastname: Eliasco
authors.affiliation: The International Potato Center, Apartado 1558, Lima, Peru.
authors.forename: G
authors.initials: G
authors.lastname: Müller
authors.affiliation: Leiden Institute of Chemistry, Gorlaeus Laboratories, Einsteinweg 55, 2300 RA Leiden, The Netherlands.
authors.forename: R C L
authors.initials: RCL
authors.lastname: Olsthoorn
authors.affiliation: The International Potato Center, Apartado 1558, Lima, Peru.
authors.forename: L F
authors.initials: LF
authors.lastname: Salazar
authors.affiliation: Leiden Institute of Chemistry, Gorlaeus Laboratories, Einsteinweg 55, 2300 RA Leiden, The Netherlands.
authors.forename: C W A
authors.initials: CWA
authors.lastname: Pleij
authors.affiliation: Department of Biological Sciences, Imperial College London, Sir Alexander Fleming Building, Imperial College Road, London SW7 2AZ, UK.
authors.forename: R H A
authors.initials: RHA
authors.lastname: Coutts
mesh_terms: D020413:3' Untranslated Regions / Q000235:genetics; D000595:Amino Acid Sequence; D001483:Base Sequence; D017124:Conserved Sequence; D029383:Crinivirus / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification; D016679:Genome, Viral; D008969:Molecular Sequence Data; D016366:Open Reading Frames; D010802:Phylogeny; D017800:Potyvirus / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification; D012367:RNA, Viral / Q000737:chemistry / Q000235:genetics*; D011198:Solanum tuberosum / Q000821:virology*
chemical_list: D020413:3' Untranslated Regions; D012367:RNA, Viral