University of Massachusetts Medical School Faculty Publications
Title
Transcriptome-wide investigation of stop codon readthrough in Saccharomyces cerevisiae [preprint]
UMMS Affiliation
Department of Microbiology and Physiological Systems; Graduate School of Biomedical Sciences
Publication Date
2020-12-15
Document Type
Article Preprint
Disciplines
Amino Acids, Peptides, and Proteins | Biochemistry, Biophysics, and Structural Biology | Cellular and Molecular Physiology | Genetics and Genomics | 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 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 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
mRNA, stop codon, translation, termination, readthrough
Rights and Permissions
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
DOI of Published Version
10.1101/2020.12.15.422930
Source
bioRxiv 2020.12.15.422930; doi: https://doi.org/10.1101/2020.12.15.422930. Link to preprint on bioRxiv.
Related Resources
This research was presented in a poster at the 25th Annual University of Massachusetts Medical School Research Retreat 2020 on October 26, 2020.
Journal/Book/Conference Title
bioRxiv
Repository Citation
Mangkalaphiban K, He F, Ganesan R, Wu C, Baker RE, Jacobson A. (2020). Transcriptome-wide investigation of stop codon readthrough in Saccharomyces cerevisiae [preprint]. University of Massachusetts Medical School Faculty Publications. https://doi.org/10.1101/2020.12.15.422930. Retrieved from https://escholarship.umassmed.edu/faculty_pubs/1873
Creative Commons License
This work is licensed under a Creative Commons Attribution-Noncommercial-No Derivative Works 4.0 License.
Included in
Amino Acids, Peptides, and Proteins Commons, Biochemistry, Biophysics, and Structural Biology Commons, Cellular and Molecular Physiology Commons, Genetics and Genomics Commons, Nucleic Acids, Nucleotides, and Nucleosides Commons
Comments
This article is a preprint. Preprints are preliminary reports of work that have not been certified by peer review.