Codon usage bias controls mRNA and protein abundance in trypanosomatids

Laura Jeacock, Joana Correia Faria, David Horn (Lead / Corresponding author)

Research output: Contribution to journalArticle

9 Citations (Scopus)
57 Downloads (Pure)

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.
Original languageEnglish
Article numbere32496
Number of pages20
JournaleLife
Volume7
Early online date15 Mar 2018
DOIs
Publication statusPublished - 15 Mar 2018

Fingerprint

Codon
Messenger RNA
Proteins
Genes
Synthetic Genes
Trypanosoma brucei brucei
Pathogens
Proteome
Transcription
Reporter Genes
Transcriptome
Gene expression
Animals
Genome
Gene Expression

Keywords

  • Leishmania
  • Post-transcription
  • Synonymous
  • Translation
  • Trypanosoma brucei
  • Trypanosoma vivas
  • Trypanosomes

Cite this

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title = "Codon usage bias controls mRNA and protein abundance in trypanosomatids",
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.",
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Codon usage bias controls mRNA and protein abundance in trypanosomatids. / Jeacock, Laura; Correia Faria, Joana; Horn, David (Lead / Corresponding author).

In: eLife, Vol. 7, e32496, 15.03.2018.

Research output: Contribution to journalArticle

TY - JOUR

T1 - Codon usage bias controls mRNA and protein abundance in trypanosomatids

AU - Jeacock, Laura

AU - Correia Faria, Joana

AU - Horn, David

N1 - Funding: Wellcome Trust 100320/Z/12/Z; Wellcome Trust 203134/Z/16/

PY - 2018/3/15

Y1 - 2018/3/15

N2 - 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.

AB - 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.

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KW - Post-transcription

KW - Synonymous

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