scholarly journals A recent intermezzo at the Ribosome Club

2017 ◽  
Vol 372 (1716) ◽  
pp. 20160185 ◽  
Author(s):  
Michael Y. Pavlov ◽  
Anders Liljas ◽  
Måns Ehrenberg
Keyword(s):  
Messenger Rna ◽  
Ternary Complex ◽  
Elongation Factor ◽  
Transfer Rna ◽  
Elongation Factor Tu ◽  
Transfer Rnas ◽  
30S Subunit ◽  
Translation Accuracy ◽  
Codon Selection ◽  
Two Sides

Two sets of ribosome structures have recently led to two different interpretations of what limits the accuracy of codon translation by transfer RNAs. In this review, inspired by this intermezzo at the Ribosome Club, we briefly discuss accuracy amplification by energy driven proofreading and its implementation in genetic code translation. We further discuss general ways by which the monitoring bases of 16S rRNA may enhance the ultimate accuracy ( d -values) and how the codon translation accuracy is reduced by the actions of Mg 2+ ions and the presence of error inducing aminoglycoside antibiotics. We demonstrate that complete freezing-in of cognate-like tautomeric states of ribosome-bound nucleotide bases in transfer RNA or messenger RNA is not compatible with recent experiments on initial codon selection by transfer RNA in ternary complex with elongation factor Tu and GTP. From these considerations, we suggest that the sets of 30S subunit structures from the Ramakrishnan group and 70S structures from the Yusupov/Yusupova group may, after all, reflect two sides of the same coin and how the structurally based intermezzo at the Ribosome Club may be resolved simply by taking the dynamic aspects of ribosome function into account. This article is part of the themed issue ‘Perspectives on the ribosome’.

scholarly journals Accuracy mechanism of eukaryotic ribosome translocation

Nature ◽  
2021 ◽  
Author(s):  
Muminjon Djumagulov ◽  
Natalia Demeshkina ◽  
Lasse Jenner ◽  
Alexey Rozov ◽  
Marat Yusupov ◽  
...  
Keyword(s):  
Messenger Rna ◽  
Large Scale ◽  
Molecular Mechanisms ◽  
Elongation Factor ◽  
80S Ribosome ◽  
Reading Frame ◽  
Transfer Rnas ◽  
Elongation Factor 2 ◽  
Complex Process ◽  
Translation Accuracy

AbstractTranslation of the genetic code into proteins is realized through repetitions of synchronous translocation of messenger RNA (mRNA) and transfer RNAs (tRNA) through the ribosome. In eukaryotes translocation is ensured by elongation factor 2 (eEF2), which catalyses the process and actively contributes to its accuracy1. Although numerous studies point to critical roles for both the conserved eukaryotic posttranslational modification diphthamide in eEF2 and tRNA modifications in supporting the accuracy of translocation, detailed molecular mechanisms describing their specific functions are poorly understood. Here we report a high-resolution X-ray structure of the eukaryotic 80S ribosome in a translocation-intermediate state containing mRNA, naturally modified eEF2 and tRNAs. The crystal structure reveals a network of stabilization of codon–anticodon interactions involving diphthamide1 and the hypermodified nucleoside wybutosine at position 37 of phenylalanine tRNA, which is also known to enhance translation accuracy2. The model demonstrates how the decoding centre releases a codon–anticodon duplex, allowing its movement on the ribosome, and emphasizes the function of eEF2 as a ‘pawl’ defining the directionality of translocation3. This model suggests how eukaryote-specific elements of the 80S ribosome, eEF2 and tRNAs undergo large-scale molecular reorganizations to ensure maintenance of the mRNA reading frame during the complex process of translocation.

scholarly journals Two proofreading steps amplify the accuracy of genetic code translation

2016 ◽  
Vol 113 (48) ◽  
pp. 13744-13749 ◽  
Author(s):  
Ka-Weng Ieong ◽  
Ülkü Uzun ◽  
Maria Selmer ◽  
Måns Ehrenberg
Keyword(s):  
Protein Synthesis ◽  
Genetic Information ◽  
Molecular Basis ◽  
Messenger Rna ◽  
Ternary Complex ◽  
Elongation Factor ◽  
Elongation Factor Tu ◽  
Substrate Selection ◽  
Gtp Hydrolysis

Aminoacyl-tRNAs (aa-tRNAs) are selected by the messenger RNA programmed ribosome in ternary complex with elongation factor Tu (EF-Tu) and GTP and then, again, in a proofreading step after GTP hydrolysis on EF-Tu. We use tRNA mutants with different affinities for EF-Tu to demonstrate that proofreading of aa-tRNAs occurs in two consecutive steps. First, aa-tRNAs in ternary complex with EF-Tu·GDP are selected in a step where the accuracy increases linearly with increasing aa-tRNA affinity to EF-Tu. Then, following dissociation of EF-Tu·GDP from the ribosome, the accuracy is further increased in a second and apparently EF-Tu−independent step. Our findings identify the molecular basis of proofreading in bacteria, highlight the pivotal role of EF-Tu for fast and accurate protein synthesis, and illustrate the importance of multistep substrate selection in intracellular processing of genetic information.

scholarly journals EF-G–induced ribosome sliding along the noncoding mRNA

2019 ◽  
Vol 5 (6) ◽  
pp. eaaw9049 ◽  
Author(s):  
M. Klimova ◽  
T. Senyushkina ◽  
E. Samatova ◽  
B. Z. Peng ◽  
M. Pearson ◽  
...  
Keyword(s):  
Messenger Rna ◽  
Elongation Factor ◽  
Transfer Rna ◽  
Noncoding Region ◽  
Forward Movement ◽  
Stem Loop ◽  
A Site ◽  
Hydrolysis Of ◽  
Reading Frames ◽  
Factor G

Translational bypassing is a recoding event during which ribosomes slide over a noncoding region of the messenger RNA (mRNA) to synthesize one protein from two discontinuous reading frames. Structures in the mRNA orchestrate forward movement of the ribosome, but what causes ribosomes to start sliding remains unclear. Here, we show that elongation factor G (EF-G) triggers ribosome take-off by a pseudotranslocation event using a small mRNA stem-loop as an A-site transfer RNA mimic and requires hydrolysis of about two molecules of guanosine 5′-triphosphate per nucleotide of the noncoding gap. Bypassing ribosomes adopt a hyper-rotated conformation, also observed with ribosomes stalled by the SecM sequence, suggesting common ribosome dynamics during translation stalling. Our results demonstrate a new function of EF-G in promoting ribosome sliding along the mRNA, in contrast to codon-wise ribosome movement during canonical translation, and suggest a mechanism by which ribosomes could traverse untranslated parts of mRNAs.

scholarly journals Structure of a novel antibacterial toxin that exploits elongation factor Tu to cleave specific transfer RNAs

2017 ◽  
Vol 45 (17) ◽  
pp. 10306-10320 ◽  
Author(s):  
Karolina Michalska ◽  
Grant C. Gucinski ◽  
Fernando Garza-Sánchez ◽  
Parker M. Johnson ◽  
Lucy M. Stols ◽  
...  
Keyword(s):  
Elongation Factor ◽  
Elongation Factor Tu ◽  
Transfer Rnas
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