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Mapping sequences active in homologous RNA recombination in brome mosaic virus: prediction of recombination hot spots
- Source :
- Virology. 254(1)
- Publication Year :
- 1999
-
Abstract
- The mechanism of homologous recombination has been studied previously in brome mosaic virus (BMV), a tricomponent, positive-stranded RNA virus of plants, by using artificial sequences (reviewed by J. J. BujarskiP. D. Nagy (1996). Semin. Virol. 7, 363–372). Here we extend these studies over BMV-derived sequences to obtain clues on prediction of homologous recombination hot spots. First, mismatch mutations, which reduced the AU content, were introduced into the common 60-nt recombination hot-spot sequence, either in the RNA2 or in both RNA2RNA3 components. This decreased the frequency of targeted homologous RNA2/RNA3 recombinationchanged the distribution of junction sites. Second, several short BMV RNA1- or RNA2-derived sequences were introduced into the RNA3 component,homologous recombination activity of these sequences was compared with that observed for previously characterized artificial sequences. Third, sequences at homologous recombinant junctions were compared among a large number of targetednontargeted recombinants. All these studies revealed several factors important for homologous recombination including the length of sequence identity, the extent of sequence identity, the AU content of the common sequences, the relative position of the AU-rich segment vs a GC-rich segment,the presence of GC-rich sequences. Based on this novel model, we suggest that recombination hot spots can be predicted by means of RNA sequence analysis. In addition, we show that recombination can occur between positivenegative strands of BMV RNAs. This provides further clues toward the mechanism of recombination processes in BMV.
- Subjects :
- bromoviruses
nontemplated nucleotides
viruses
misannealing
Molecular Sequence Data
law.invention
03 medical and health sciences
Brome mosaic virus
law
Virology
Homologous chromosome
template-switching
030304 developmental biology
Sequence (medicine)
Genetics
Recombination, Genetic
0303 health sciences
biology
Base Sequence
AU-rich sequences
030302 biochemistry & molecular biology
RNA
food and beverages
Chromosome Mapping
RNA virus
biology.organism_classification
Bromovirus
mapping recombination hot spots
Mutagenesis
Recombinant DNA
RNA, Viral
Homologous recombination
Recombination
Subjects
Details
- ISSN :
- 00426822
- Volume :
- 254
- Issue :
- 1
- Database :
- OpenAIRE
- Journal :
- Virology
- Accession number :
- edsair.doi.dedup.....b71d4d6ee1651b2951af581866522b31