title: RNA recombination between cucumoviruses: possible role of predicted stem-loop structures and an internal subgenomic promoter-like motif.
abstract: We previously analyzed hybrids of Cucumber mosaic virus (CMV) and Tomato aspermy virus (TAV) that contained CMV RNA2 with the 3'-terminal sequence from TAV RNA2. In this article, we scrutinized the RNA3 molecules in these hybrid viruses by Northern hybridization and RT-PCR and found some recombinant CMV RNA3 molecules and various recombinant RNA4 molecules whose 3'-termini were derived from TAV RNA1 or 2. Sequence analyses revealed that most of the crossover sites for recombination were located near putative stem-loop structures and an internal subgenomic promoter-like motif. We inoculated in vitro transcripts synthesized from cDNA clones of the recombinant RNA3 onto N. benthamiana along with either CMV RNA1 and 2 or TAV RNA1 and 2. Although all of the hybrids were infectious, many sequence deletions and nucleotide substitutions were found when RNA1 and 2 from TAV were used, which suggests that fidelity of TAV replicase was lower than that of CMV replicase. The possible role of secondary structures and an internal subgenomic promoter-like motif in RNA recombination is discussed.
authors.affiliation: Laboratory of Plant Pathology, Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, University of Tokyo, 113-8657, Tokyo, Japan. m-suzuki@ynu.ac.jp
authors.forename: Masashi
authors.initials: M
authors.lastname: Suzuki
authors.forename: Tadaaki
authors.initials: T
authors.lastname: Hibi
authors.forename: Chikara
authors.initials: C
authors.lastname: Masuta
mesh_terms: D001483:Base Sequence; D018553:Cucumis sativus / Q000821:virology*; D017799:Cucumovirus / Q000737:chemistry / Q000235:genetics*; D016679:Genome, Viral; D008969:Molecular Sequence Data; D010935:Plant Diseases / Q000821:virology; D018515:Plant Leaves / Q000821:virology; D011401:Promoter Regions, Genetic; D012367:RNA, Viral / Q000737:chemistry* / Q000235:genetics; D011995:Recombination, Genetic; D014026:Nicotiana / Q000821:virology
chemical_list: D012367:RNA, Viral