UMMS Affiliation
Department of Microbiology and Physiological Systems; Graduate School of Biomedical Sciences
Publication Date
2020-10-26
Document Type
Poster
Disciplines
Biochemistry, Biophysics, and Structural Biology | Cellular and Molecular Physiology | Genetics and Genomics
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 elongation 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 remains to be determined 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. Our analyses revealed that the most influential features consist of 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, while nts +5 to +9 and mRNA secondary structure in the 3’-UTR 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 confirmed the general roles of known regulatory elements in genome-wide regulation and identified several new mRNA or peptide features important for translation termination and readthrough.
Keywords
mRNA, stop codon, translation, termination, readthrough
Rights and Permissions
Copyright © 2020 The Author(s). This is an open access document 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
10.13028/njar-gz64
Journal/Book/Conference Title
25th Annual University of Massachusetts Medical School Research Retreat 2020
Repository Citation
Mangkalaphiban K, He F, Ganesan R, Wu C, Baker RE, Jacobson AS. (2020). Transcriptome-wide investigation of stop codon readthrough in Saccharomyces cerevisiae. University of Massachusetts Medical School Publications. https://doi.org/10.13028/njar-gz64. Retrieved from https://escholarship.umassmed.edu/publications/52
Creative Commons License
This work is licensed under a Creative Commons Attribution 4.0 License.
Included in
Biochemistry, Biophysics, and Structural Biology Commons, Cellular and Molecular Physiology Commons, Genetics and Genomics Commons
Comments
Poster presented virtually at the 25th Annual University of Massachusetts Medical School Research Retreat 2020 on October 26, 2020.