Peptide Release on the Ribosome: Mechanism and Implications for Translational Control

Abstract

Peptide release, the reaction that hydrolyzes a completed protein from the peptidyl-tRNA upon completion of translation, is catalyzed in the active site of the large subunit of the ribosome and requires a class I release factor protein. The ribosome and release factor protein cooperate to accomplish two tasks: recognition of the stop codon and catalysis of peptidyl-tRNA hydrolysis. Although many fundamental questions remain, substantial progress has been made in the past several years. This review summarizes those advances and presents current models for the mechanisms of stop codon specificity and catalysis of peptide release. Finally, we discuss how these views fit into a larger emerging theme in the translation field: the importance of induced fit and conformational changes for progression through the translation cycle.

In vitro incorporation of nonnatural amino acids into protein using tRNACys-derived opal, ochre, and amber suppressor tRNAs

“…Because these synthetic tRNAs are identical in every aspect with the exception of the anticodon, it seems unlikely that they would exhibit different rates of eEF1-a GTP hydrolysis or a different induced conformational fit upon codon-anticodon base pairing at the ribosome A-site (Rodnina et al 2005;Youngman et al 2008). Rather, our results suggest that eukaryotic release factors, eRF1/eRF3, terminate translation more efficiently at the opal and ochre codons as opposed to the amber codons.…”

RF3:GTP promotes rapid dissociation of the class 1 termination factor

“…Stop codons are decoded by class 1 release factor proteins (RFs) that act as bifunctional molecules to recognize stop codons with high fidelity and release the growing polypeptide chain in a hydrolytic reaction. Although the bifunctional nature of class 1 RFs is conserved from bacteria to eukaryotes, distinct proteins have evolved in these domains of life to accomplish this task (Youngman et al 2008). In bacteria, two related proteins, RF1 and RF2, recognize the three stop codons with overlapping specificity (UAA is recognized by both factors, while RF1 is specific for UAG and RF2 for UGA); in eukaryotes, a single factor, eRF1, recognizes all three stop codons.…”

Ribosome's mode of function: myths, facts and recent results

“…However, careful comparisons between the antibiotic-binding sites in ribosomes from the eubacterium D. Radiodurans and those from the archaeon H. marismortui highlighted a neat distinction in the nucleotide sequence and orientation, leading to substantial differences in macrolide binding modes [2,75,80]. Hence, it was concluded that although A2058 is the main macrolide binding 'anchor', it is not the sole nucleotide determining drug positioning and, therefore, effectiveness.…”

“…[1,2]) obtained after 20 years [3] of extensive systematic explorations of crystal growth, refinements of bacterial growth pathways [4], and ribosome separations (E. Zimmerman, data not shown) and requiring the development of innovative methodologies, such as bio-crystallography at cryogenic temperatures [5], and an unconventional use of multiheavy atom clusters [6][7][8][9]. Accompanied by advances in the cryo electron microscopy that revealed elements of ribosome's functional dynamics, e.g.…”