Protein-RNA sequence covariation in a ribosomal protein-rRNA complex

Comparative sequence analysis has successfully predicted secondary structure and tertiary interactions in ribosomal and other RNAs. Experiments presented here ask whether the scope of comparative sequence-based predictions can be extended to specific interactions between proteins and RNA, using as a system the well-characterized C-terminal RNA binding domain of ribosomal protein L11 (L11-C76) and its 58 nucleotide binding region in 23S rRNA. The surface of L11-C76 alpha-helix 3 is known to contact RNA; position 69 in this helix is conserved as serine in most organisms but varies to asparagine (all plastids) or glutamine (Mycoplasma). RNA sequence substitutions unique to these groups of organisms occur at base pairs 1062/1076 or 1058/1080, respectively. The possibility that rRNA base pair substitutions compensate for variants in L11 alpha-helix 3 has been tested by measuring binding affinities between sets of protein and RNA sequence variants. Stability of the RNA tertiary structure, as measured by UV melting experiments, was unexpectedly affected by a 1062/1076 base pair substitution; additional mutations were required to restore a stably folded structure to this RNA. The results show that the asparagine variant of L11-C76 residue 69 has been compensated by substitution of a 1062/1076 base pair, and plausibly suggest a direct contact between the amino acid and base pair. For some of the protein and RNA mutations studied, changes in binding affinity probably reflect longer-range adjustments of the protein-RNA contact surface.