Determinants of translation efficiency in the evolutionarily-divergent protist Trichomonas vaginalis.

BMC Molecular and Cell Biology
Shuqi E WangAugusto Simoes-Barbosa

Abstract

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. This study demonstrates the role of cod...Continue Reading

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Methods Mentioned

BETA
flow cytometry
transfection

Software Mentioned

RNAfold
Python
TrichDB
CAIcal SERVER
nEST
OPTIMIZER
ViennaRNA Package
uclust
EMBOSS

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