Although the bacteriophage Qbeta RNA replication system has been known for over 30 years, it today still is of unique interest, because it represents a prototypical enzyme assembly that allows the specific and efficient amplification of an active viral RNA in vitro by soluble and defined molecular components.
     Intriguingly, only one of the subunits of the replicase enzyme is coded for by the viral genome. The other three are the host proteins EF-Tu and EF-Ts and the ribosomal protein S1. In order to use Qbeta RNA as a template, replicase requires an additional RNA binding protein, the Qbeta host factor, which was recently reported to have a role in the regulation of the stationary phase of the host cell.
     Our own recent results indicate that, paradoxically, it is two host proteins, namely the S1 protein and host factor, that are responsible for mediating the recognition of the phage RNA as a template, by binding the RNA at two internal sites and at the 3'-end. This conclusion comes mainly from studies in which we observed the effects of deletions in the RNA on template activity, as well as on the structure of the RNA-protein complexes as visualized by electron microscopy.
     In another approach, we have recently been able to adapt Qbeta to an E. coli strain devoid of host factor. All host factor-independent isolates were found to contain the same four point mutations, three of which affect the 3'-terminal secondary structure. Interestingly, a long-range base-pairing interaction involving the nucleotides at the very 3'-end is disrupted in the adapted mutants. This suggests that the host factor might function on wild type RNA as an "RNA chaperone", making the 3'-end available to replicase by melting out its 3'-terminal base-pairing interaction.
     Recognition of the Qbeta minus strand by replicase takes place by a completely different mechanism, for which neither S1 protein nor host factor are required. We found that on the RNA two specific secondary structure elements were important, one near the 5'-, the other near the 3'-end.
     RNA-protein interactions are of fundamental importance for the processes involved in genetic information transfer, but today they may well be the least understood of the different classes of macromolecular interactions. In view of the fact that only few RNA-protein complexes have been resolved by structural techniques, we attempt to describe the processes involved in phage RNA/replicase recognition at the highest possible resolution by molecular genetic/biochemical methods.