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Project Summary

In this Project we are investigating the folding and interactions of a fragment of rRNA with a fragment of a ribosomal protein (rProtein), both derived from T. thermophilus. The goal is to examine the granularity of rRNA-rProtein recognition, to determine if small RNA and protein components of the ribosome can recapitulate interactions observed in the native ribosome. We have assayed the in vitro and in vivo folding and interactions of an isolated subdomain of rRNA with an rProtein and with a peptide fragment of the rProtein. Chemical mapping shows that a 199-nucleotide fragment of Domain III of the 23S rRNA (defined here as Domain IIIcore) folds to a near-native state. This rRNA fragment binds to ribosomal protein L23 in a yeast three-hybrid assay, as predicted from interactions in the native ribosome. A peptide was designed based on the segment of the rProtein that penetrates deep into the core of the native ribosome and associates primarily with Domain IIIcore. A spectroscopic assay shows that the peptide forms a 1:1 complex with both Domain III and Domain IIIcore. The results indicate that rRNA-rProtein recognition is fine-grained, and can be directed by specific interactions between small rRNA and rProtein fragments.