Features of 80S mammalian ribosome and its subunits

Abstract

It is generally believed that basic features of ribosomal functions are universally valid, but a systematic test still stands out for higher eukaryotic 80S ribosomes. Here we report: (i) differences in tRNA and mRNA binding capabilities of eukaryotic and bacterial ribosomes and their subunits. Eukaryotic 40S subunits bind mRNA exclusively in the presence of cognate tRNA, whereas bacterial 30S do bind mRNA already in the absence of tRNA. 80S ribosomes bind mRNA efficiently in the absence of tRNA. In contrast, bacterial 70S interact with mRNA more productively in the presence rather than in the absence of tRNA. (ii) States of initiation (Pi), pre-translocation (PRE) and post-translocation (POST) of the ribosome were checked and no significant functional differences to the prokaryotic counterpart were observed including the reciprocal linkage between A and E sites. (iii) Eukaryotic ribosomes bind tetracycline with an affinity 15 times lower than that of bacterial ribosomes (Kd 30 μM and 1–2 μM, respectively). The drug does not effect enzymatic A-site occupation of 80S ribosomes in contrast to non-enzymatic tRNA binding to the A-site. Both observations explain the relative resistance of eukaryotic ribosomes to this antibiotic.

Regulation of the Mammalian Elongation Cycle by Subunit Rolling: A Eukaryotic-Specific Ribosome Rearrangement

“…Both specimens were prepared in vitro from mammalian components (Budkevich et al, 2011; Budkevich et al, 2008). To yield the decoding complex the ternary complex Val-tRNA•eEF1A•GMPPNP was stalled by the non-hydrolyzable GTP analogue.…”

The Eukaryotic Ribosome: Current Status and Challenges

“…These failed efforts suggest that the biochemistry and physical complexity of eukaryotic ribosomes are significantly different from those of their bacterial counterparts. Indeed, recent biochemical analyses showing that salt rather than divalent ion concentrations are more important for subunit joining suggest that protein/protein and protein/RNA interactions are more widespread in eukaryotic as opposed to bacterial ribosomes (7). The strongest biochemistry has been developed in the field of translation initiation, where in vitro systems have existed for some time (reviewed in Ref.…”

Eukaryote-specific extensions in ribosomal proteins of the small subunit: Structure and function

“…1,2 Eukaryotic 80S ribosomes (composed of 60S and 40S subunits) have evolved to be much larger in size with more proteins and ribosomal RNA (rRNA) than their archeal, or bacterial counterparts, (70S ribosomes composed of 50S and 30S subunits). [3][4][5][6] Recent X-ray crystal structures of the yeast 80S ribosome at 3.0 A resolution permitted detailed analysis of the structural organization of the eukaryotic ribosome. 5,6 It became evident that bacterial and eukaryotic ribosomes evolved from a common structural (RNP) core with the majority of changes occurring on the outer shell of the ribosome.…”

“…5 Interestingly, despite general similarity in sequence and structure, many of the conserved ribosomal proteins have evolved eukaryote-specific extensions, the functional significance of which is largely unknown and/or just beginning to emerge. [4][5][6][7][8][9][10][11] These polypeptide extensions frequently appear to interact with each other, resulting in complex networks of ribosomal protein interactions on the outer shell of the ribosome in eukaryotes. 9,10 It has been hypothesized that eukaryote-specific extensions of the conserved ribosomal proteins evolved to accommodate specific features of the eukaryotic translational apparatus/mechanism such as the increased number of initiation factors (>12 in eukaryotes compared to only 3 in bacteria) ( Table 1).…”