Getting a handle on RNA virus recombination

The above model could not be supported without an in vitro assay. Although Simon's work is a promising early step in the dissection of recombination mechanisms, many questions remain. For example, what features on the donor template encourage dissociation of the replicase and nascent strand? Possibilities proposed for a variety of RNAs include a stable secondary structure, the 5′ end of the template itself or AU-rich regions that weaken the interaction between the nascent strand and the template. In coronaviruses, dissociation has been attributed to the nonprocessive nature of the replicase[2xLai, M.M.C. Semin. Virol. 1996; 7: 381–388Crossref | Scopus (45)See all References[2]. In BMV, the replication complex is initially highly abortive but then undergoes a modification allowing efficient elongation[13xSun, J-H. and Kao, C.C. Virology. 1997; 236: 348–353Crossref | PubMed | Scopus (31)See all References[13]. Perhaps, at some points of the RNA synthesis, the replication complex can revert to its loosely bound abortive state and subsequently dissociate.What is the nature of the protein that interacts with the bulged stem–loop? Presumably, it is a component of the viral replicase, but is it the virally encoded RNA-dependent RNA polymerase itself or a host factor that participates? How does acceptor recognition by the replication machinery compare with the specific recognition of the origins of replication at the 3′ ends of positive and negative strands and internally at subgenomic RNA promoters?More broadly speaking, how widely does this type of mechanism apply? Recognition of an internal structure on a negative strand, as described here, resembles subgenomic RNA synthesis. Subgenomic RNA synthesis may be primer dependent in coronaviruses[2xLai, M.M.C. Semin. Virol. 1996; 7: 381–388Crossref | Scopus (45)See all References[2]but is primer independent in plant viruses[14xMiller, W.A., Dreher, T.W., and Hall, T.C. Nature. 1985; 313: 68–70Crossref | PubMed | Scopus (181)See all References[14]. However, we propose that plant viral subgenomic RNA promoters can also be recognized by this donor-primed mechanism in the recombination events that generate variation in luteoviruses[5xMiller, W.A., Dinesh-Kumar, S.P., and Paul, C.P. Crit. Rev. Plant Sci. 1995; 14: 179–211Crossref | Scopus (118)See all References[5]. This may occur in other viruses that produce subgenomic mRNAs, including many plant viruses, coronaviruses and alphaviruses.In contrast to the above viruses, recombination has been detected in poliovirus at hot spots for which no replication origin or subgenomic promoter would normally be predicted[8xKirkegaard, K. and Baltimore, D. Cell. 1986; 47: 433–443Abstract | Full Text PDF | PubMed | Scopus (268)See all References, 15xDuggal, R. et al. Proc. Natl. Acad. Sci. U. S. A. 1997; 94: 13786–13791Crossref | PubMed | Scopus (37)See all References, 16xTang, R.S. et al. RNA. 1997; 3: 624–633PubMedSee all References]. What are the features of the RNA and replicase that promote picornaviral recombination at specific sites? The recent demonstration of poliovirus recombination in cell-free systems[15xDuggal, R. et al. Proc. Natl. Acad. Sci. U. S. A. 1997; 94: 13786–13791Crossref | PubMed | Scopus (37)See all References, 16xTang, R.S. et al. RNA. 1997; 3: 624–633PubMedSee all References]bodes well for elucidation of the mechanism in the near future. Now that recombination has been demonstrated in two such very different in vitro systems, TCV and poliovirus, and numerous other cell-free replication systems are available, the next few years should yield a bounty of detailed analyses of a variety of different RNA recombination mechanisms.