Introduction In Nature, the vast majority of polypeptides are synthesized through translation of the messenger RNA (mRNA) by the joint action of the ribosome and the transfer RNA (tRNA). The mRNA is a transcribed copy of the gene that carries genetic information in the form of series of three-nucleotide sequences referred as ‘codon’. Each codon corresponds to a specific amino acid or a terminat...

Translation termination is accomplished by proteins of the Class I release factor family (RF) that recognize stop codons and catalyze the ribosomal release of the newly synthesized peptide. Bacteria have two canonical RFs: RF1 recognizes UAA and UAG, RF2 recognizes UAA and UGA. Despite that these two release factor proteins are sufficient for de facto translation termination, the eukaryotic org...

Modified trinucleotides, 3MeU-A-G+, 3MeU-A-A, 5MeUA-G, 5MeU-A-A, BrU-A-G, hU-A-G, and U-A-I (see J. BioZ. Chem., 241, 527 (1966)), were synthesized by a combination of organic and enzymatic methods. The activity of each trinucleotide as a template for peptide chain termination was determined. The attachment of a methyl group to the NB position of uracil eliminates the template activity of termi...

Accumulating evidence shows that the repertoire of major histocompatibility complex class I-restricted epitopes extends beyond conventional translation reading frames. Previously, we reported that scanthrough translation, where the initiating AUG of a primary open reading frame is bypassed, is most likely to account for the presentation of cryptic epitopes from alternative reading frames within...

Protein synthesis follows the advice given in Alice in Wonderland: “‘Begin at the beginning,’ the King said gravely, ‘and go on till you come to the end: then stop.’” (1). For most protein synthesis, “the beginning” is the first methionine codon (AUG) encountered by the ribosome downstream of the cap, which is situated at the 5′ end of the mRNA (Fig. 1). “The end” is a signal that consists of o...

Assembly factors (AFs) prevent premature translation initiation on small (40S) ribosomal subunit assembly intermediates by blocking ligand binding. However, it is unclear how AFs are displaced from maturing 40S ribosomes, if or how maturing subunits are assessed for fidelity, and what prevents premature translation initiation once AFs dissociate. Here we show that maturation involves a translat...

Translational readthrough of premature termination codons (PTCs) induced by pharmacological compounds has proven to be an effective way of restoring functional protein expression and reducing symptoms in several genetic disorders. We tested the potential of different concentrations of several aminoglycosides (AAGs) for promoting PTC-readthrough in 5 genes involved in the pathogenesis of primary...

Ribosomes translating mRNA without an in-frame stop codon (non-stop mRNA) stall at its 3' end. In eubacteria, such ribosomes are rescued by SsrA-mediated trans-translation. Recently, we have shown that Escherichia coli ArfA (formerly YhdL) also rescues stalled ribosomes by a mechanism distinct from that of trans-translation. Synthetic lethality phenotype of ssrA arfA double mutants suggests tha...

Six diverse prokaryotic and five eukaryotic genomes were compared to deduce whether the protein synthesis termination signal has common determinants within and across both kingdoms. Four of the six prokaryotic and all of the eukaryotic genomes investigated demonstrated a similar pattern of nucleotide bias both 5' and 3' of the stop codon. A preferred core signal of 4 nt was evident, encompassin...