Life cycle adapted upstream open reading frames (uORFs) in Trypanosoma congolense: A post-transcriptional approach to accurate gene regulation.

Philipp Fervers,Florian Fervers,Wojciech Makałowski,Marcin Jąkalski,Igor B Rogozin

doi:10.1371/journal.pone.0201461

Philipp Fervers, Florian Fervers + Show 3 more

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https://doi.org/10.1371/journal.pone.0201461

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Abstract

The presented work explores the regulatory influence of upstream open reading frames (uORFs) on gene expression in Trypanosoma congolense. More than 31,000 uORFs in total were identified and characterized here. We found evidence for the uORFs’ appearance in the transcriptome to be correlated with proteomic expression data, clearly indicating their repressive potential in T. congolense, which has to rely on post-transcriptional gene expression regulation due to its unique genomic organization. Our data show that uORF’s translation repressive potential does not only correlate with elemental sequence features such as length, position and quantity, but involves more subtle components, in particular the codon and amino acid profiles. This corresponds with the popular mechanistic model of a ribosome shedding initiation factors during the translation of a uORF, which can prevent reinitiation at the downstream start codon of the actual protein-coding sequence, due to the former extensive consumption of crucial translation components. We suggest that uORFs with uncommon codon and amino acid usage can slow down the translation elongation process in T. congolense, systematically deplete the limited factors, and restrict downstream reinitiation, setting up a bottleneck for subsequent translation of the protein-coding sequence. Additionally we conclude that uORFs dynamically influence the T. congolense life cycle. We found evidence that transition to epimastigote form could be supported by gain of uORFs due to alternative trans-splicing, which down-regulate housekeeping genes’ expression and render the trypanosome in a metabolically reduced state of endurance.

Highlights

Trypanosomes are flagellate, unicellular parasites, belonging to the class of Kinetoplastida [1]
Gene expression profiles derive from the high throughput transcriptome sequencing (Illumina RNA-seq) experiments of all four life cycle stages of T. congolense, in which the sequenced reads were mapped to the genes annotated in TriTrypDB 25 to estimate their mRNA abundance levels
Considering only the longest upstream open reading frames (uORFs) variant as the representative sequence for each stop codon, it leaves 15,348, 13,467, 15,920 and 15,920 non-redundant uORFs identified in BSF, PCF, EMF and MCF, respectively (18,511 unique uORFs in total)

Summary

Introduction

Trypanosomes are flagellate, unicellular parasites, belonging to the class of Kinetoplastida [1]. T. congolense is the infective agent of the animal African trypanosomiasis (AAT) and probably the most widespread pathogen of livestock in the sub-Saharan Africa [2]. In contrast to higher eukaryotes, the genome of kinetoplastids is organized in polycistronic transcription units (PTUs), each consisting of approximately 10 to 100 protein-coding genes. Such gene clusters generally comprise of functionally unrelated genes [3,4,5,6]. The alternative trans-splicing has been shown to be wide-spread in T. brucei and hypothesized to contribute to its stage specific gene regulation by gain or loss of UTR-embedded sequence features [8]

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