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RNA Biol. 2018;15(9):1206-1214. doi: 10.1080/15476286.2018.1517014. Epub 2018 Sep 20.

Disruption of the RNA exosome reveals the hidden face of the malaria parasite transcriptome.

Author information

1
a Unité Biologie des Interactions Hôte-Parasite, Département de Parasites et Insectes Vecteurs , Institut Pasteur , Paris , France.
2
b CNRS, ERL 9195 , Paris , France.
3
c INSERM, Unit U1201 , Paris , France.
4
d Research Center for Translational Medicine, Key Laboratory of Arrhythmias of the Ministry of Education of China, East Hospital , Tongji University School of Medicine , Shanghai , China.
5
e CAS Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology , Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences , Shanghai , China.

Abstract

Antisense transcription emerges as a key regulator of important biological processes in the human malaria parasite Plasmodium falciparum. RNA-processing factors, however, remain poorly characterized in this pathogen. Here, we purified the multiprotein RNA exosome complex of malaria parasites by affinity chromatography, using HA-tagged PfRrp4 and PfDis3 as the ligands. Seven distinct core exosome subunits (PfRrp41, PfMtr3, PfRrp42, PfRrp45, PfRrp4, PfRrp40, PfCsl4) and two exoribonuclease proteins PfRrp6 and PfDis3 are identified by mass spectrometry. Western blot analysis detects Dis3 and Rrp4 predominantly in the cytoplasmic fraction during asexual blood stage development. An inducible gene knock out of the PfDis3 subunit reveals the upregulation of structural and coding RNA, but the vast majority belongs to antisense RNA. Furthermore, we detect numerous types of cryptic unstable transcripts (CUTs) linked to virulence gene families including antisense RNA in the rif gene family. Our work highlights the limitations of steady-state RNA analysis to predict transcriptional activity and link the RNA surveillance machinery directly with post-transcriptional control and gene expression in malaria parasites.

KEYWORDS:

Dis3 knock out; Malaria; RNA exosome; antisense RNA; cryptic RNA

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