Abstract
The peptidyl transferase center of the modern ribosome has been found to encompass an area of twofold pseudosymmetry (SymR). This observation strongly suggests that the very core of the ribosome arose from a dimerization event between two modest-sized RNAs. It was previously shown that at least four non-standard interactions exist between the two halves of SymR. Herein, we verify that the structure of the SymR is highly conserved with respect to both ribosome transition state and phylogenetic diversity. These comparisons also reveal two additional sites of interaction between the two halves of SymR and refine our understanding of the previously known interactions. In addition, the possible role that magnesium may have in the coordination, stabilization, association, and evolutionary history of the two halves (A-region and P-region) was examined. Together, the results identify a likely site where structural elements and Mg2+ ions may have facilitated the ligation of two aboriginal RNAs into a single unit.
Highlights
Ribosomes are responsible for the coded synthesis of proteins one residue at a time in all living systems
Peptide bond synthesis occurs in the peptidyl transferase center (PTC), of the large ribosomal subunit, which is comprised exclusively of RNA [1,2]
SymR seems to be a stable structure that is well-conserved at the core of the large subunit (LSU) [17]
Summary
Ribosomes are responsible for the coded synthesis of proteins one residue at a time in all living systems. Peptide bond synthesis occurs in the peptidyl transferase center (PTC), of the large ribosomal subunit, which is comprised exclusively of RNA [1,2]. In order to make room for the synthesis cycle, the growing peptide enters an RNA cavity or pore [4,5] that over evolutionary time has grown to be the exit tunnel, from which the product peptide emerges [6,7,8]. The most widely accepted hypothesis on the evolution of the ribosome states that the most ancient part of it is represented by the PTC and the ribonucleotides that delineate it [9,10,11,12,13,14]
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