G-quadruplex RNA motifs influence gene expression in the malaria parasite Plasmodium falciparum.

Franck Dumetz,Mubarak I Umar,Ting Fung Chan,Betty Chung,Chun Kit Kwok,Shiau Wei Liew,Lynne M Harris,Eugene Yui-Ching Chow,Anders Jensen,Catherine J Merrick

doi:10.1093/nar/gkab1095

Abstract

G-quadruplexes are non-helical secondary structures that can fold in vivo in both DNA and RNA. In human cells, they can influence replication, transcription and telomere maintenance in DNA, or translation, transcript processing and stability of RNA. We have previously showed that G-quadruplexes are detectable in the DNA of the malaria parasite Plasmodium falciparum, despite a very highly A/T-biased genome with unusually few guanine-rich sequences. Here, we show that RNA G-quadruplexes can also form in P. falciparum RNA, using rG4-seq for transcriptome-wide structure-specific RNA probing. Many of the motifs, detected here via the rG4seeker pipeline, have non-canonical forms and would not be predicted by standard in silico algorithms. However, in vitro biophysical assays verified formation of non-canonical motifs. The G-quadruplexes in the P. falciparum transcriptome are frequently clustered in certain genes and associated with regions encoding low-complexity peptide repeats. They are overrepresented in particular classes of genes, notably those that encode PfEMP1 virulence factors, stress response genes and DNA binding proteins. In vitro translation experiments and in vivo measures of translation efficiency showed that G-quadruplexes can influence the translation of P. falciparum mRNAs. Thus, the G-quadruplex is a novel player in post-transcriptional regulation of gene expression in this major human pathogen.

Highlights

Protozoan Plasmodium parasites are the causative agents of human malaria, a disease responsible for widespread morbidity and almost half a million deaths each year [1]
A fluorescent signal was seen throughout the parasites and this appeared to be somewhat RNase-sensitive, but much of the signal was apparently nuclear and DNase-sensitive, suggesting that the QUMA-1 dye is not as RNA-specific in P. falciparum cells as it is in human cells
DNA G4s are likely to dominate in parasite nuclei, in telomeres, while rG4s, if present, are likely to be less abundant and more dispersed throughout the cytoplasm, so they may be difficult to detect via microscopy

Summary

Introduction

Protozoan Plasmodium parasites are the causative agents of human malaria, a disease responsible for widespread morbidity and almost half a million deaths each year [1]. The G-quadruplex is an important non-double-helical structure that can form in DNA and RNA [6]. ∼100 PQSs are found outside the inherently-G-rich telomeres: this is approximately one per 300 kb of the nontelomeric genome, compared to an average of one per kb in the human genome [9]. More modern algorithms such as G4Hunter [10], which can identify PQSs in ‘non-canonical’

Methods

Results

Conclusion