Nanometer scale pores similar in size to the entrance of the ribosomal exit cavity are a common feature of large RNAs

Abstract

The highly conserved peptidyl transferase center (PTC) of the ribosome contains an RNA pore that serves as the entrance to the exit tunnel. Analysis of available ribosome crystal structures has revealed the presence of multiple additional well-defined pores of comparable size in the ribosomal (rRNA) RNAs. These typically have dimensions of 1-2 nm, with a total area of ∼100 Å 2 or more, and most are associated with one or more ribosomal proteins. The PTC example and the other rRNA pores result from the packing of helices. However, in the non-PTC cases the nitrogenous bases do not protrude into the pore, thereby limiting the potential for hydrogen bonding within the pore. Instead, it is the RNA backbone that largely defines the pore likely resulting in a negatively charged environment. In many but not all cases, ribosomal proteins are associated with the pores to a greater or lesser extent. With the exception of the PTC case, the large subunit pores are not found in what are thought to be the evolutionarily oldest regions of the 23S rRNA. The unusual nature of the PTC pore may reflect a history of being created by hybridization between two or more RNAs early in evolution rather than simple folding of a single RNA. An initial survey of nonribosomal RNA crystal structures revealed additional pores, thereby showing that they are likely a general feature of RNA tertiary structure.

Further Characterization of the Pseudo-Symmetrical Ribosomal Region

“…The synthesis itself is facilitated by proper positioning of substrates [ 3 ]. In order to make room for the next 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 ].…”

The Emergence of Life

“…Thus, it is now generally accepted that the catalytic core of the ribosome is a ribozyme (Cech 2000;Muth et al 2000; and that such translation machinery is clearly very ancient (Hury et al 2006). Recent efforts have also successfully delineated the components of the ribosome in a systems approach exploring the cavities within the ribosome (Rivas et al 2013), as well as smaller motifs or centers of motion Fox 2015, 2016).…”