Specific interactions of the L10(L12)4 ribosomal protein complex with mRNA, rRNA, and L11

Large ribosomal subunit proteins L10 and L12 forma pentameric protein complex, L10(L12)(4), that is intimately involved in the ribosome elongation cycle. Its contacts with rRNA or other ribosomal proteins have been only partially resolved by crystallography. In Escherichia coli, L10 and L 12 are encoded from a single operon for which L10(L 12)(4) is a translational repressor that recognizes a secondary structure in the mRNA leader. In this study, L10(L12)(4) was expressed from the moderate thermophile Bacillus stearothermophilus to quantitatively compare strategies for binding of the complex to mRNA and ribosome targets. The minimal mRNA recognition structure is widely distributed among bacteria and has the potential to form a kink-turn structure similar to one identified in the rRNA as part of the L10(L12)(4) binding site. Mutations in equivalent positions between the two sequences have similar effects on L10(L12)(4)-RNA binding affinity and identify the kink-turn motif and a loop AA sequence as important recognition elements. In contrast to the larger rRNA structure, the mRNA apparently positions the kink-turn motif and loop for protein recognition without the benefit of Mg2+-dependent tertiary structure. The mRNA and rRNA fragments bind L10(L12)(4) with similar affinity (similar to 10(8) M-1), but fluorescence binding studies show that a nearby protein in the ribosome, L11, enhances L10(L12)(4) binding similar to 100-fold. Thus, mRNA and ribosome targets use similar RNA features, held in different structural contexts, to recognize L10(L12)(4), and the ribosome ensures the saturation of its L10(L12)(4) binding site by means of an additional protein-protein interaction.