Ribosomal protein S18e as a putative molecular staple for the 18S rRNA 3′-major domain core

Ribosomal protein S18e is a structural constituent of the 40S ribosomal subunit. We obtained recombinant human ribosomal protein S18e and studied its structural and functional properties. With the use of CD spectroscopy we showed that the protein secondary structure is mainly helical and stable in the neutral pH range and at low urea concentrations. Applying multiple sequence alignment, we revealed that the protein structure has characteristics of the eukaryotic members of the ribosomal protein S13p family with additional extensions in the N-terminal and central parts that contain α-helices according to our prediction. S18e binds specifically and independently to an RNA transcript corresponding to the evolutionary core of the 3′-major domain of 18S rRNA. Hydroxyl radical footprinting showed that the binding site of S18e on the 18S rRNA is similar in general to the binding site of S13p on the 16S rRNA in the 30S ribosomal subunit, albeit the rRNA regions attributed to binding of the eukaryote-specific extensions of S18e were also detected. With magnesium ion concentration close to cellular conditions (2 mM), protein binding caused substantial rearrangements in the rRNA transcript making it compact in such a manner that helices H29/H30 and H41–H43 form a bundle resembling their arrangement in the ribosome. Thus, S18e seems to act as a molecular staple fixing the 18S rRNA 3′-major domain core.

Research Highlights
► S18e binds specifically to 18S rRNA without assistance from other ribosomal proteins.
► S18e fixes the structure of the 18S rRNA 3′-major domain core acting as a staple.
► The eukaryote-specific extensions of S18e are involved in binding to the 18S rRNA.
► S18e is capable of folding the rRNA structure under a low Mg2+ concentration.