Research digital skills training 2021
Determinants of translation efficiency in the evolutionarily-divergent protist Trichomonas vaginalis
Shuqi E. Wang, Anna E. S. Brooks, Anthony M. Poole & Augusto Simoes-Barbosa, School of Biological Sciences
Trichomonas vaginalis, the causative agent of a prevalent urogenital infection in humans, is an evolutionarily divergent protozoan. Protein-coding genes in T. vaginalis are largely controlled by two core promoter elements, producing mRNAs with short 5′ UTRs. The specific mechanisms adopted by T. vaginalis to fine-tune the translation efficiency (TE) of mRNAs remain largely unknown.
Using both computational and experimental approaches, this study investigated two key factors influencing TE in T. vaginalis: codon usage and mRNA secondary structure. Statistical dependence between TE and codon adaptation index (CAI) highlighted the impact of codon usage on mRNA translation in T. vaginalis. A genome-wide interrogation revealed that low structural complexity at the 5′ end of mRNA followed closely by a highly structured downstream region correlates with TE variation in this organism.
To validate these findings, a synthetic library of 15 synonymous iLOV genes was created, representing five mRNA folding profiles and three codon usage profiles. Fluorescence signals produced by the expression of these synonymous iLOV genes in T. vaginalis were consistent with and validated our in silico predictions.
Using complementary in silico and in vivo approaches, this study systematically investigated the impact of codon usage bias and mRNA secondary structure on TE of T. vaginalis mRNAs. In addition to guiding optimal gene expression in this parasite, the results here provide new information that leads to a more comprehensive understanding of the mechanisms by which gene expression is controlled in T. vaginalis. Despite having a translation machinery that is rather typical of eukaryotes, T. vaginalis and other evolutionarily divergent protozoans such as Giardia produce mRNAs with short 5′ UTRs. This study indicates that T. vaginalis mRNAs contain information at the level of both sequence and structure that impact their expression, adding a novel layer to our understanding of gene regulation in this divergent unicellular eukaryote.
Details of the synthetic iLOV gene library to be expressed in T. vaginalis.a Diagram of the iLOV genes showing 5′ and 3′ portions connected by the Nru I site.
Transient and stable expressions of the synonymous iLOV genes determined by flow cytometry.
We are grateful to the Centre for eResearch, the University of Auckland, for access to computing resources such as research virtual machines.