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https://doi.org/10.21256/zhaw-4023| Publication type: | Conference poster |
| Type of review: | No review |
| Title: | Programmed ribosomal frameshifting and codon usage bias |
| Authors: | Garcia, Victor Zoller, Stefan Anisimova, Maria |
| DOI: | 10.21256/zhaw-4023 |
| Proceedings: | Life in Numbers 4.0 |
| Editors of the parent work: | Hirsch, Sven |
| Conference details: | Life in Numbers 4, Wädenswil, 4 October 2018 |
| Issue Date: | 4-Oct-2018 |
| Publisher / Ed. Institution: | ZHAW Zürcher Hochschule für Angewandte Wissenschaften |
| Language: | English |
| Subjects: | Codon usage bias; Programmed ribosomal frameshifting; mRNA translation; Genetics |
| Subject (DDC): | 572: Biochemistry |
| Abstract: | Experimental evidence shows that synonymous mutations can have important consequences on genetic fitness. Many organisms display codon usage bias (CUB), where synonymous codons that are translated into the same amino acid appear with distinct frequency. Within genomes, CUB is thought to arise from selection for translational efficiency and accuracy, termed the translational efficiency hypothesis (TEH). Indeed, CUB indices correlate with protein expression levels, which is widely interpreted as evidence for translational selection. However, these tests neglect -1 programmed ribosomal frameshifting (-1 PRF), an important translational disruption effect found across all organisms of the tree of life. Genes that contain -1 PRF signals should cost more to express than genes without. Thus, CUB indices that do not consider -1 PRF may overestimate genes’ true adaptation to translational efficiency and accuracy constraints. Here, we first investigate whether -1 PRF signals do indeed carry such translational cost. We then propose two corrections for CUB indices for genes containing -1 PRF signals. We retest the TEH in Saccharomyces cerevisiae under these corrections. We find that the correlation between corrected CUB index and protein expression remains intact for most levels of uniform -1 PRF efficiencies, and tends to increase when these efficiencies decline with protein expression. We conclude that the TEH is strengthened and that -1 PRF events constitute a promising and useful tool to examine the relationships between CUB and selection for translation efficiency and accuracy. |
| URI: | https://digitalcollection.zhaw.ch/handle/11475/11719 |
| Fulltext version: | Published version |
| License (according to publishing contract): | Licence according to publishing contract |
| Departement: | Life Sciences and Facility Management |
| Organisational Unit: | Institute of Computational Life Sciences (ICLS) |
| Appears in collections: | Publikationen Life Sciences und Facility Management |
Files in This Item:
| File | Description | Size | Format | |
|---|---|---|---|---|
| life_in_numbers_v1.pdf | Poster Life in Numbers 4.0 | 8.15 MB | Adobe PDF |  View/Open |
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Garcia, V., Zoller, S., & Anisimova, M. (2018). Programmed ribosomal frameshifting and codon usage bias [Conference poster]. In S. Hirsch (Ed.), Life in Numbers 4.0. ZHAW Zürcher Hochschule für Angewandte Wissenschaften. https://doi.org/10.21256/zhaw-4023
Garcia, V., Zoller, S. and Anisimova, M. (2018) ‘Programmed ribosomal frameshifting and codon usage bias’, in S. Hirsch (ed.) Life in Numbers 4.0. ZHAW Zürcher Hochschule für Angewandte Wissenschaften. Available at: https://doi.org/10.21256/zhaw-4023.
V. Garcia, S. Zoller, and M. Anisimova, “Programmed ribosomal frameshifting and codon usage bias,” in Life in Numbers 4.0, Oct. 2018. doi: 10.21256/zhaw-4023.
GARCIA, Victor, Stefan ZOLLER und Maria ANISIMOVA, 2018. Programmed ribosomal frameshifting and codon usage bias. In: Sven HIRSCH (Hrsg.), Life in Numbers 4.0. Conference poster. ZHAW Zürcher Hochschule für Angewandte Wissenschaften. 4 Oktober 2018
Garcia, Victor, Stefan Zoller, and Maria Anisimova. 2018. “Programmed Ribosomal Frameshifting and Codon Usage Bias.” Conference poster. In Life in Numbers 4.0, edited by Sven Hirsch. ZHAW Zürcher Hochschule für Angewandte Wissenschaften. https://doi.org/10.21256/zhaw-4023.
Garcia, Victor, et al. “Programmed Ribosomal Frameshifting and Codon Usage Bias.” Life in Numbers 4.0, edited by Sven Hirsch, ZHAW Zürcher Hochschule für Angewandte Wissenschaften, 2018, https://doi.org/10.21256/zhaw-4023.
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