title: Nonhomologous RNA-RNA recombination events at the 3' nontranslated region of the Sindbis virus genome: hot spots and utilization of nonviral sequences.
abstract: The mechanism of RNA-RNA recombination at the 3' nontranslated region (3'NTR) of the Sindbis virus (SIN) genome was studied by using nonreplicative RNA precursors. The 11.7-kb SIN genome was transcribed in vitro as two nonoverlapping RNA fragments. RNA-1 contained the entire 11.4-kb protein coding sequence of SIN and also carried an additional 1.8-kb nonviral sequence at its 3' end. RNA-2 carried the remaining 0.26 or 0.3 kb of the SIN genome containing the 3'NTR. Transfection of these two fragments into BHK cells resulted in vivo RNA-RNA recombination and release of infectious SIN recombinants. Eighteen plaque-purified recombinant viruses were sequenced to precisely map the RNA-RNA crossover sites at the 3'NTR. Sixteen of the 18 recombinants were found to be genetically heterogeneous at the 3'NTR. Two major clustered sites within the 3'NTR of RNA-2 were found to be fused to multiple locations on the nonviral sequence of RNA-1, resulting in insertions of 10 to 1,085 nucleotides at the 3'NTR. Sequence analysis of crossover sites suggested only limited homology and heteroduplex-forming capability between substrate RNAs. Analysis of additional 23 recombinant viruses generated by mutagenized donor and acceptor templates supports the occurrence of recombination hot spots on donor templates. Introduction of a 17-nucleotide rudimentary replicase recognition signal in the acceptor template alone did not induce the polymerase to reinitiate at the 17-nucleotide signal. Interestingly, deletion of a 24-nucleotide hot spot locus on the donor template abolished crossover events at one of the two sites and allowed the polymerase to reinitiate at the 17-nucleotide replicase recognition signal inserted at the acceptor template. The possible roles of RNA-protein and RNA-RNA interactions in the differential regulation of apparent pausing, template selection, and reinitiation are discussed.
authors.affiliation: Department of Microbiology, School of Medicine, Meharry Medical College, Nashville, Tennessee 37208, USA.
authors.forename: M
authors.initials: M
authors.lastname: Hajjou
authors.forename: K R
authors.initials: KR
authors.lastname: Hill
authors.forename: S V
authors.initials: SV
authors.lastname: Subramaniam
authors.forename: J Y
authors.initials: JY
authors.lastname: Hu
authors.forename: R
authors.initials: R
authors.lastname: Raju
mesh_terms: D001483:Base Sequence; D002874:Chromosome Mapping; D016679:Genome, Viral; D008969:Molecular Sequence Data; D012367:RNA, Viral / Q000235:genetics*; D011995:Recombination, Genetic; D012845:Sindbis Virus / Q000235:genetics*; D014162:Transfection
chemical_list: D012367:RNA, Viral