Abstract
Translation of mRNA into a polypeptide is terminated when the release factor eRF1 recognizes a UAA, UAG, or UGA stop codon in the ribosomal A site and stimulates nascent peptide release. However, stop codon readthrough can occur when a near-cognate tRNA outcompetes eRF1 in decoding the stop codon, resulting in the continuation of the elongation phase of protein synthesis. At the end of a conventional mRNA coding region, readthrough allows translation into the mRNA 3’-UTR. Previous studies with reporter systems have shown that the efficiency of termination or readthrough is modulated by cis-acting elements other than stop codon identity, including two nucleotides 5’ of the stop codon, six nucleotides 3’ of the stop codon in the ribosomal mRNA channel, and stem-loop structures in the mRNA 3’-UTR. It is unknown whether these elements are important at a genome-wide level and whether other mRNA features proximal to the stop codon significantly affect termination and readthrough efficiencies in vivo. Accordingly, we carried out ribosome profiling analyses of yeast cells expressing wild-type or temperature-sensitive eRF1 and developed bioinformatics strategies to calculate readthrough efficiency, and to identify mRNA and peptide features which influence that efficiency. We found that the stop codon (nt +1 to +3), the nucleotide after it (nt +4), the codon in the P site (nt -3 to -1), and 3’-UTR length are the most influential features in the control of readthrough efficiency, while nts +5 to +9 had milder effects. Additionally, we found low readthrough genes to have shorter 3’-UTRs compared to high readthrough genes in cells with thermally inactivated eRF1, while this trend was reversed in wild-type cells. Together, our results demonstrated the general roles of known regulatory elements in genome-wide regulation and identified several new mRNA or peptide features affecting the efficiency of translation termination and readthrough.
Highlights
Translation of an mRNA into a polypeptide is terminated when the release factor eRF1 interacts with a UAA, UAG, or UGA stop codon in the ribosomal A site and another release factor, eRF3, hydrolyzes GTP and stimulates the polypeptide release activity of eRF1 [1,2,3]
Of the 64 codons that exist for translation of the genetic code into a polypeptide chain, only UAA, UAG, and UGA signify termination of continued protein synthesis
Our results demonstrated the general roles of known regulatory elements, such as the identities of the stop codon and the surrounding nucleotides, in genome-wide regulation and identified several new mRNA features that appear to play a role in translation termination and readthrough, including the penultimate codon in the P site and the length of the 3’-UTR
Summary
Translation of an mRNA into a polypeptide is terminated when the release factor eRF1 interacts with a UAA, UAG, or UGA stop codon in the ribosomal A site and another release factor, eRF3, hydrolyzes GTP and stimulates the polypeptide release activity of eRF1 [1,2,3]. When the stop codon is located at its normal site at the end of an open reading frame (ORF) elongation will continue into the mRNA 3’-untranslated region (3’UTR), producing a C-terminally extended polypeptide product. Ribosome profiling and phylogenetic investigation of flies, humans, and yeast cells revealed that readthrough is more prevalent than previously anticipated, with efficiencies varying by more than 100-fold for distinct mRNAs [12,19,20,21] These observations indicate that the efficiency of translation termination can be subjected to transcript-specific regulation, and that a key to understanding this regulation may lie in specific cis-acting mRNA sequences
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