Molecular insights into replication initiation by Qβ replicase using ribosomal protein S1

Ribosomal protein S1, consisting of six contiguous OB-folds, is the largest ribosomal protein and is essential for translation initiation in Escherichia coli. S1 is also one of the three essential host-derived subunits of Q beta replicase, together with EF-Tu and EF-Ts, for Q beta RNA replication in E. coli. We analyzed the crystal structure of Q beta replicase, consisting of the virus-encoded RNA-dependent RNA polymerase (beta-subunit), EF-Tu, EF-Ts and the N-terminal half of S1, which is capable of initiating Q beta RNA replication. Structural and biochemical studies revealed that the two N-terminal OB-folds of S1 anchor S1 onto the beta-subunit, and the third OB-fold is mobile and protrudes beyond the surface of the beta-subunit. The third OB-fold mainly interacts with a specific RNA fragment derived from the internal region of Q beta RNA, and its RNA-binding ability is required for replication initiation of Q beta RNA. Thus, the third mobile OB-fold of S1, which is spatially anchored near the surface of the beta-subunit, primarily recruits the Q beta RNA toward the beta-subunit, leading to the specific and efficient replication initiation of Q beta RNA, and S1 functions as a replication initiation factor, beyond its established function in protein synthesis.