Terminal structure mediates 5 S rRNA stability and integration during ribosome biogenesis

Formation of the eukaryotic ribosomal 5 S RNA-protein complex has been shown to be critical to ribosome biogenesis and has been speculated to contribute to a quality control mechanism that helps ensure that only normal precursors are processed and assembled into active ribosomes. To study the structural basis of these observations, the RNA-protein interface in the 5 S RNA-protein complex of the yeast (Saccharomyces cerevisiae) ribosome was examined based on a systematic introduction of targeted base substitutions in the RNA sequence. Most base substitutions had little or no effect on the efficiency of complex formation, but large effects were observed when changes disrupted helix I, the secondary structure formed between the interacting termini. Again, only modest effects were evident when the extended 3' end of the mature RNA molecule was altered, but essentially no complex was formed when the 5' end of the mature 5 S RNA sequence was artificially extended by one nucleotide. In vitro analyses demonstrated that this extension also dramatically altered the maturation of 5 S rRNA precursor molecules as well as the stability of the mature 5 S rRNA. Taken together, the results indicate that in the course of RNA maturation, the 5 S RNA-binding protein binds precisely over or "caps" the termini in a critical manner that protects the RNA from further degradation.