S16 throws a conformational switch during assembly of 30S 5′ domain

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Abstract
Ribosomal proteins are known to play an important role in determining rRNA structure. The body of the 30S ribosomal subunit is formed by the 16S rRNA 5′ domain. New data indicate that the assembly protein S16 discriminates between folding intermediates of the 5′ domain, increasing cooperative 30S assembly and stabilizing interactions at its decoding site. Rapid and accurate assembly of new ribosomal subunits is essential for cell growth. Here we show that the ribosomal proteins make assembly more cooperative by discriminating against non-native conformations of the Escherichia coli 16S ribosomal RNA. We used hydroxyl radical footprinting to measure how much the proteins stabilize individual ribosomal RNA tertiary interactions, revealing the free-energy landscape for assembly of the 16S 5′ domain. When ribosomal proteins S4, S17 and S20 bind the 5′ domain RNA, a native and a non-native assembly intermediate are equally populated. The secondary assembly protein S16 suppresses the non-native intermediate, smoothing the path to the native complex. In the final step of 5′ domain assembly, S16 drives a conformational switch at helix 3 that stabilizes pseudoknots in the 30S decoding center. Long-range communication between the S16 binding site and the decoding center helps to explain the crucial role of S16 in 30S assembly.