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Transcriptome-wide dynamics of extensive m6A mRNA methylation during Plasmodium falciparum blood-stage development

Nature Microbiology volume 4, pages 2246–2259 (2019)Cite this article

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Abstract

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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Fig. 1: Global dynamics of mRNA modifications during the P. falciparum IDC.
Fig. 2: Characterization of the P. falciparum m6A writer complex.
Fig. 3: Knockdown of the PfMT-A70 m6A methyltransferase by CRISPRi.
Fig. 4: Differential m6A methylation during the P. falciparum IDC.
Fig. 5: PfMT-A70 knockdown leads to upregulation of m6A-methylated transcripts.
Fig. 6: Correlation of m6A with mRNA stability and translational efficiency.

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Data availability

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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Acknowledgements

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.

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  1. Thibaud Reyser

    Present address: Laboratoire de Chimie de Coordination, Toulouse, France

Authors and Affiliations

  1. Biology of Host–Parasite Interactions Unit, Department of Parasites and Insect Vectors, Institut Pasteur, Paris, France

    Sebastian Baumgarten, Jessica M. Bryant, Thibaud Reyser & Artur Scherf

  2. CNRS, ERL 9195, Paris, France

    Sebastian Baumgarten, Jessica M. Bryant, Thibaud Reyser & Artur Scherf

  3. INSERM, Unit U1201, Paris, France

    Sebastian Baumgarten, Jessica M. Bryant, Thibaud Reyser & Artur Scherf

  4. School of Biological Sciences, Nanyang Technological University Singapore, Singapore, Singapore

    Ameya Sinha & Peter R. Preiser

  5. Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore, Singapore

    Ameya Sinha, Peter R. Preiser & Peter C. Dedon

  6. Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA

    Peter C. Dedon

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Contributions

P.R.P, P.C.D. and A.Sc. conceptualized the project. S.B., J.M.B. and A.Sc. conceived experiments. J.M.B. developed and performed CRISPR interference and dCas9 ChIP-seq experiments. S.B. performed m6A-seq and RT-qPCR experiments. A.Si. performed and analysed LC-MS/MS and protein co-IP experiments. S.B., J.M.B. and T.R. generated constructs, transfectants and parasite material. S.B. performed bioinformatic analyses. P.R.P., P.C.D. and A.Sc. supervised and helped interpret analyses. All authors discussed and approved the manuscript.

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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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