Codon usage bias controls mRNA and protein abundance in trypanosomatids

Abstract
Data availability
Article and author information

Abstract

Protein abundance differs from a few to millions of copies per cell. Trypanosoma brucei presents an excellent model for studies on codon bias and differential gene expression because transcription is broadly unregulated and uniform across the genome. T. brucei is also a major human and animal protozoal pathogen. Here, an experimental assessment, using synthetic reporter genes, revealed that GC3 codons have a major positive impact on both mRNA and protein abundance. Our estimates of relative expression, based on coding sequences alone (codon usage and sequence length), are within 2-fold of the observed values for the majority of measured cellular mRNAs (n>7000) and proteins (n>2000). Our estimates also correspond with expression measures from published transcriptome and proteome datasets from other trypanosomatids. We conclude that codon usage is a key factor affecting global relative mRNA and protein expression in trypanosomatids and that relative abundance can be effectively estimated using only protein coding sequences.

Data availability

The following data sets were generated

1. Jeacock L
2. Faria J
3. Horn D
(2018) T. brucei RNA-seq data
PRJEB22797.

https://www.ebi.ac.uk/ena

The following previously published data sets were used

(2012) SILAC proteome data
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http://www.proteomecommons.org

Article and author information

Author details

Laura Jeacock

Wellcome Trust Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dundee, United Kingdom

Competing interests
The authors declare that no competing interests exist.
Joana Faria

Wellcome Trust Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dundee, United Kingdom

Competing interests
The authors declare that no competing interests exist.
David Horn

Wellcome Trust Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dundee, United Kingdom

For correspondence
d.horn@dundee.ac.uk

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0001-5173-9284

Funding

Wellcome (100320/Z/12/Z)

David Horn

Wellcome (203134/Z/16/Z)

David Horn

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Copyright

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.