New Insights into the Mechanisms of RNA Recombination

Abstract

RNA plays many different roles in biological systems. characteristic marker mutations from the parental RNAs. One of RNAs most intriguing features is the ability to Following the initial recombination event, detection of carry genetic information despite a labile nature. While recombinants required amplification in cells that imRNA genomes were presumably widespread in the priposed a selection for or against a particular recombinant mordial ‘‘RNA world,’’ only RNA viruses and viroids conbased on its ability to be amplified in vivo. Nevertheless, tinue to exploit RNA-based genetic materials. As with these data were used to group RNA recombination as DNA-based organisms, these entities must evolve and homologous or nonhomologous (King, 1988). Homoloadapt in order to survive. Genetic recombination, the forgous recombinants were those derived from parental mation of chimeric molecules from segments previously RNAs that were either very similar in the case of intraseparated on the same molecule or present on different typic recombination or somewhat less similar in the case parental molecules, is one of the most important mechaof intertypic recombination. Based on the precision of nisms for generating novel genomes that may have sethe event, Lai (1992) further divided this grouping of relective advantages over parental genomes. Recent studcombinants into homologous or aberrant homologous ies on the evolution of RNA viruses have revealed that recombinants. Homologous recombinants were newly RNA recombination is a widespread phenomenon that defined as containing no sequence alterations (except has shaped modern viruses by rearranging viral gethe existing marker mutations) when compared to the nomes or disseminating functional modules among difparental molecules while aberrant homologous recombiferent viruses (Strauss and Strauss, 1988; Dolja and Carnants contained modifications such as mismatch mutarington, 1992; Lai, 1992; Simon and Bujarski, 1994). In tions, deletions, or insertions at or close to the junction addition, an important short-term function of genetic resite. Recombinants were grouped as nonhomologous if combination may be the rescue of functional sequences they were generated by recombination between dissimifrom mutated parental molecules, which is of particular lar viral genomes or between a viral genome and host significance given the high mutation rates associated RNA. This classical genetic grouping of recombinants, with replication by RNA-dependent RNA polymerases however, did not take into account the mechanisms lead(RdRp) (Domingo et al., 1996). Depending on the preciing to their generation. Not surprisingly, recent studies sion of the repair mechanism, the repaired genome can have suggested similar recombinants can be formed by be similar to the parental genome, or it can contain furdifferent mechanisms. Moreover, similar mechanisms ther mutations. This illustrates that sequence diversity in have been postulated that lead to the formation of some RNA sequences generated by genetic recombination can recombinants that currently would be grouped as homolinvolve both gross changes and minor mutations. Moreogous or nonhomologous. over, the products of recombination can overlap with unThe most accepted models of RNA recombination are related phenomena, including mutagenesis and nonrethe replicase-driven template switching model, the RNA combination-based genome repair. breakage and ligation model, and the breakage-induced Early studies identified RNA recombination events intemplate switching model. Since all these recombination directly by isolating chimeric products that contained models can lead to the formation of similar recombinant RNAs, it is not possible to promote a particular mecha1 To whom correspondence and reprint requests should be adnism based only on the sequence of the recombination dressed to at Department of Biochemistry and Molecular Biology, Ledend-products. Rather, characterization of recombination erle Graduate Research Center, University of Massachusetts, Box intermediates and components of the recombination ma34505, Amherst, MA 01003-4505. Fax: 413-545-4529; E-mail: simon@ biochem.umass.edu. chinery is required. Below, we will summarize our current