Transcriptome-wide investigation of stop codon readthrough in Saccharomyces cerevisiae


Autoři: Kotchaphorn Mangkalaphiban aff001;  Feng He aff001;  Robin Ganesan aff001;  Chan Wu aff001;  Richard Baker aff001;  Allan Jacobson aff001
Působiště autorů: Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America aff001
Vyšlo v časopise: Transcriptome-wide investigation of stop codon readthrough in Saccharomyces cerevisiae. PLoS Genet 17(4): e1009538. doi:10.1371/journal.pgen.1009538
Kategorie: Research Article
doi: https://doi.org/10.1371/journal.pgen.1009538

Souhrn

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.

Klíčová slova:

Gene expression – Genetic footprinting – Messenger RNA – Nucleotides – Ribosomes – Transfer RNA – Translation termination – Yeast


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