UMMS Affiliation

Department of Microbiology and Physiological Systems; Graduate School of Biomedical Sciences

Publication Date

2021-04-20

Document Type

Article

Disciplines

Amino Acids, Peptides, and Proteins | Biochemistry, Biophysics, and Structural Biology | Bioinformatics | Fungi | Genetics and Genomics | Microbiology | Nucleic Acids, Nucleotides, and Nucleosides

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.

Keywords

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

Rights and Permissions

Copyright © 2021 Mangkalaphiban et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

DOI of Published Version

10.1371/journal.pgen.1009538

Source

Mangkalaphiban K, He F, Ganesan R, Wu C, Baker R, Jacobson A. Transcriptome-wide investigation of stop codon readthrough in Saccharomyces cerevisiae. PLoS Genet. 2021 Apr 20;17(4):e1009538. doi: 10.1371/journal.pgen.1009538. PMID: 33878104; PMCID: PMC8087045. Link to article on publisher's site

Journal/Book/Conference Title

PLoS genetics

Related Resources

Link to Article in PubMed

PubMed ID

33878104

Creative Commons License

Creative Commons Attribution 4.0 License
This work is licensed under a Creative Commons Attribution 4.0 License.

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