title: Nucleotide sequence and genomic organization of cacao swollen shoot virus.
abstract: Cacao swollen shoot virus is classified as a badnavirus based on its nonenveloped, bacilliform particle morphology and double-stranded DNA genome. A complete copy of the genome was cloned into a plasmid vector and the sequence was determined from 75 overlapping subclones covering both strands. The genome contains 7161 base pairs and possesses an intergenic region and five putative open reading frames (ORF) capable of coding for proteins > 10 kDa. All of the ORFs are present on the plus-strand. ORF 1 (17 kDa) and ORF 2 (14 kDa) encode proteins of unknown function. The large ORF 3 (211 kDa) encodes a polyprotein that can be divided into three regions. Based on distant homologies with viral movement proteins, region 1 may encode a protein involved in cell-to-cell spread, while region 2 encodes the viral capsid protein. Region 3 contains consensus sequences for viral aspartyl proteinase, reverse transcriptase, and ribonuclease H characteristic of pararetroviruses. The last two ORFs (13 and 14 kDa) overlap ORF 3 and are not present in the other badnaviruses described.
authors.affiliation: Station de Pathologie Végétale, INRA, Montfavet, France.
authors.forename: L S
authors.initials: LS
authors.lastname: Hagen
authors.forename: M
authors.initials: M
authors.lastname: Jacquemond
authors.forename: A
authors.initials: A
authors.lastname: Lepingle
authors.forename: H
authors.initials: H
authors.lastname: Lot
authors.forename: M
authors.initials: M
authors.lastname: Tepfer
mesh_terms: D000595:Amino Acid Sequence; D016282:Aspartic Acid Endopeptidases / Q000235:genetics; D001483:Base Sequence; D002099:Cacao / Q000382:microbiology*; D002213:Capsid / Q000235:genetics; D003001:Cloning, Molecular; D016679:Genome, Viral; D008969:Molecular Sequence Data; D016366:Open Reading Frames / Q000235:genetics; D053830:Plant Viral Movement Proteins; D010942:Plant Viruses / Q000235:genetics*; D017433:Protein Structure, Secondary; D012194:RNA-Directed DNA Polymerase / Q000235:genetics; D016914:Ribonuclease H / Q000235:genetics; D017422:Sequence Analysis, DNA; D017386:Sequence Homology, Amino Acid; D014764:Viral Proteins / Q000235:genetics
chemical_list: D053830:Plant Viral Movement Proteins; D014764:Viral Proteins; D012194:RNA-Directed DNA Polymerase; D016914:Ribonuclease H; D016282:Aspartic Acid Endopeptidases