Site-specific interaction of Qbeta host factor and ribosomal protein S1 with Qbeta and R17 bacteriophage RNAs.

We have studied the interaction of the host factor (HF) required for bacteriophage Qbeta RNA replication and of ribosomal protein S1, a subunit of Qbeta replicase, with Qbeta and R17 RNA. Both proteins bind to both Qbeta and R17 RNA; HF has a higher affinity than S1 for these phages RNAs. HF binds to a single site in R17 RNA located in the replicase cistron, and to two sites of Qbeta RNA, one of which is located approximately 60 nucleotides from the 6' end of Qbeta RNA. The three HF binding sites all have portions rich in adenylate residues; all are bound by HF when contained in oligonucleotides which are predicted to exist only in single-stranded form. S1 selects a single site in Qbeta RNA, also near the 6' end, but binds to a large number of sites in R17 RNA. These results suggest that HF and possibly S1, through their interaction with the 3'-terminal region of Qbeta RNA, are directly involved in the recognition of the 6' end of Qbeta RNA by Qbeta replicase. Under conditions where specific protein-R1M RNA complexes are formed, we have also tested host factor and S1 for cistron-specific interference with ribosome binding to R17 RNA. Although S1 and HF lower the efficiency of initiation complex formation as described previously, we detect no discrimination against any particular cistron. We therefore conclude that translational interference exhibited by the two proteins probably reflects simply their high affinity for RNA and certain defined polynucleotides.