Codon usage bias controls mRNA and protein abundance in trypanosomatids.

Abstract

Protein abundance differs from a few to millions of copies per cell. <i>Trypanosoma brucei</i> presents an excellent model for studies on codon bias and differential gene expression because transcription is broadly unregulated and uniform across the genome. <i>T. brucei</i> 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.