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Abstract
Formation of 100S ribosome dimer is generally associated with translation suppression in bacteria. Trans-acting factors ribosome modulation factor (RMF) and hibernating promoting factor (HPF) were shown to directly mediate this process in E. coli. Gram-positive S. aureus lacks an RMF homolog and the structural basis for its 100S formation was not known. Here we report the cryo-electron microscopy structure of the native 100S ribosome from S. aureus, revealing the molecular mechanism of its formation. The structure is distinct from previously reported analogs and relies on the HPF C-terminal extension forming the binding platform for the interactions between both of the small ribosomal subunits. The 100S dimer is formed through interactions between rRNA h26, h40, and protein uS2, involving conformational changes of the head as well as surface regions that could potentially prevent RNA polymerase from docking to the ribosome.
Highlights
Formation of 100S ribosome dimer is generally associated with translation suppression in bacteria
Suppressing the translation process under stress conditions is an adaptation mechanism, as protein synthesis is a highly energy-consuming function[1,2,3,4]. Gammaproteobacteria such as Escherichia coli possess three ribosome-silencing factors that bind to the small ribosomal subunit and block the binding pocket of messenger RNA and the anticodon region of A, P, and E-transfer RNA5, 6
The first 100 residues that form the N-terminal domain of HPFSA (N-HPFSA) were clearly identified and modeled using the masked 30S density map (Supplementary Fig. 5). This structure revealed that the N-HPFSA is involved in several interactions with the 16S rRNA (Fig. 2a) and it is bound between the head and the body of the small ribosomal subunit in a pocket that is composed of rRNA helices h18, h23, h25, h28-h31, h34, h44, and ribosomal proteins uS7, uS9, and uS11
Summary
Formation of 100S ribosome dimer is generally associated with translation suppression in bacteria. Suppressing the translation process under stress conditions is an adaptation mechanism, as protein synthesis is a highly energy-consuming function[1,2,3,4] Gammaproteobacteria such as Escherichia coli possess three ribosome-silencing factors that bind to the small ribosomal subunit and block the binding pocket of messenger RNA (mRNA) and the anticodon region of A-, P-, and E-transfer RNA (tRNA)[5, 6]. Ribosomes of Gram-positive bacteria such as Staphylococcus aureus form 100S dimers They can be found throughout all growth phases, even when nutrients are ample[15, 18,19,20,21]. Features of the ribosomes were readily identified in this map and coordinates of the 70S were fitted (Fig. 1)
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