Functional epitopes at the ribosome subunit interface

The ribosome is a 2.5-MDa molecular machine that synthesizes cellular proteins encoded in mRNAs(1). The 30S and 50S subunits of the ribosome associate through structurally defined intersubunit bridges(2-5) burying 6,000 angstrom(2), 80% of which is buried in conserved RNA-RNA interactions(6). Intersubunit bridges bind translation factors(7,8), may coordinate peptide bond formation and translocation(9-11) and may be actively remodeled in the post-termination complex(12,13), but the functional importance of numerous 30S bridge nucleotides had been unknown. We carried out large-scale combinatorial mutagenesis and in vivo selections on 30S nucleotides that form RNA-RNA intersubunit bridges in the Escherichia coli ribosome. We determined the covariation and functional importance of bridge nucleotides, allowing comparison of the structural interface and phylogenetic data to the functional epitope. Our results reveal how information for ribosome function is partitioned across bridges, and suggest a subset of nucleotides that may have measurable effects on individual steps of the translational cycle.