Malaria pathogenesis results from the asexual replication of Plasmodium falciparum within human red blood cells, which relies on a precisely timed cascade of gene expression over a 48-h life cycle. Although substantial post-transcriptional regulation of this hardwired program has been observed, it remains unclear how these processes are mediated on a transcriptome-wide level. To this end, we identified mRNA modifications in the P. falciparum transcriptome and performed a comprehensive characterization of N6-methyladenosine (m6A) over the course of blood-stage development. Using mass spectrometry and m6A RNA sequencing, we demonstrate that m6A is highly developmentally regulated, exceeding m6A levels known in any other eukaryote. We characterize a distinct m6A writer complex and show that knockdown of the putative m6A methyltransferase, PfMT-A70, by CRISPR interference leads to increased levels of transcripts that normally contain m6A. In accordance, we find an inverse correlation between m6A methylation and mRNA stability or translational efficiency. We further identify two putative m6A-binding YTH proteins that are likely to be involved in the regulation of these processes across the parasite’s life cycle. Our data demonstrate unique features of an extensive m6A mRNA methylation programme in malaria parasites and reveal its crucial role in dynamically fine-tuning the transcriptional cascade of a unicellular eukaryote.
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Nature Communications Open Access 27 May 2021
Cell Death & Disease Open Access 01 April 2021
N6-Adenosine methylation on mRNA is recognized by YTH2 domain protein of human malaria parasite Plasmodium falciparum
Epigenetics & Chromatin Open Access 31 August 2020
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All sequencing data are accessible on the Gene Expression Omnibus database (https://www.ncbi.nlm.nih.gov/geo) under study accession number GSE123839. Raw sequence data are accessible on the NCBI Sequence Read Archive (SRA) under BioProject accession number PRJNA473770. Proteomics and mRNA modification LC-MS/MS data are deposited at the Chorus database with accession number 1579.
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We thank A. Claës, C. Scheidig-Benatar and P. Chen for help with parasite culture. Protein mass-spectrometry was performed at the Biopolymers and Proteomics core of The Koch Institute Swanson Biotechnology Center. This work was supported by a European Research Council Advanced Grant (PlasmoSilencing 670301) and the French Parasitology consortium ParaFrap (ANR-11-LABX0024) to A.Scherf. Work in the labs of P.R.P. and P.C.D. was funded by the National Research Foundation Singapore under its Singapore-MIT Alliance for Research and Technology (SMART) Centre, Infectious Disease and Antimicrobial Resistance IRGs. S.B. and J.M.B. were supported by an EMBO fellowship (S.B.: ALTF 1444-2016; J.M.B.: ALTF 180-2015). A.Si. acknowledges financial support from the Singapore-MIT Alliance (SMA) Graduate Fellowships.
The authors declare no competing interests.
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Baumgarten, S., Bryant, J.M., Sinha, A. et al. Transcriptome-wide dynamics of extensive m6A mRNA methylation during Plasmodium falciparum blood-stage development. Nat Microbiol 4, 2246–2259 (2019). https://doi.org/10.1038/s41564-019-0521-7
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