Codon usage bias controls mRNA and protein abundance in trypanosomatids

  1. Laura Jeacock
  2. Joana Faria
  3. David Horn  Is a corresponding author
  1. University of Dundee, United Kingdom

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
The following previously published data sets were used
    1. Urbaniak MD
    2. Guther MLS
    3. Ferguson MAJ
    (2012) SILAC proteome data
    #6nVGofIEQu6D4odoX8aAd- odoX8aAdpUngsx1fAv43g8UN2w23Bb/ dXd6zBwaqq7SQKQcH7Mf05dGtfye0vl8pnrH3mu- ce8eA67EAAAAAAAAcbw = = ).

Article and author information

Author details

  1. 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.
  2. 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.
  3. 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.
    ORCID icon "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.

Reviewing Editor

  1. Dominique Soldati-Favre, University of Geneva, Switzerland

Publication history

  1. Received: October 3, 2017
  2. Accepted: March 9, 2018
  3. Accepted Manuscript published: March 15, 2018 (version 1)
  4. Version of Record published: April 11, 2018 (version 2)

Copyright

© 2018, Jeacock 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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  1. Laura Jeacock
  2. Joana Faria
  3. David Horn
(2018)
Codon usage bias controls mRNA and protein abundance in trypanosomatids
eLife 7:e32496.
https://doi.org/10.7554/eLife.32496
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