Codon choice directs constitutive mRNA levels in trypanosomes
- University of Cambridge, United Kingdom
- University of Oxford, United Kingdom
Abstract
Selective transcription of individual protein coding genes does not occur in trypanosomes and the cellular copy number of each mRNA must be determined post-transcriptionally. Here, we provide evidence that codon choice directs the levels of constitutively expressed mRNAs. First, a novel codon usage metric, the gene expression codon adaptation index (geCAI), was developed that maximised the relationship between codon choice and the measured abundance for a transcriptome. Second, geCAI predictions of mRNA levels were tested using differently coded GFP transgenes and were successful over a 25-fold range, similar to the variation in endogenous mRNAs. Third, translation was necessary for the accelerated mRNA turnover resulting from codon choice. Thus, in trypanosomes, the information determining the levels of most mRNAs resides in the open reading frame and translation is required to access this information.
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Funding
Coordenação de Aperfeiçoamento de Pessoal de Nível Superior
- Janaina de Freitas Nascimento
Cambridge Overseas Trust
- Janaina de Freitas Nascimento
Wellcome (085956/Z/08/Z)
- Mark Carrington
Biotechnology and Biological Sciences Research Council
- Jack Sunter
Horizon 2020 Framework Programme (637765)
- Jack Sunter
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
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© 2018, de Freitas Nascimento et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
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Codon choice directs constitutive mRNA levels in trypanosomes
eLife 7:e32467.
https://doi.org/10.7554/eLife.32467
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