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Evolutionary compaction and adaptation visualized by the structure of the dormant microsporidian ribosome

Abstract

Microsporidia are eukaryotic parasites that infect essentially all animal species, including many of agricultural importance1,2,3, and are significant opportunistic parasites of humans4. They are characterized by having a specialized infection apparatus, an obligate intracellular lifestyle5, rudimentary mitochondria and the smallest known eukaryotic genomes5,6,7. Extreme genome compaction led to minimal gene sizes affecting even conserved ancient complexes such as the ribosome8,9,10. In the present study, the cryo-electron microscopy structure of the ribosome from the microsporidium Vairimorpha necatrix is presented, which illustrates how genome compaction has resulted in the smallest known eukaryotic cytoplasmic ribosome. Selection pressure led to the loss of two ribosomal proteins and removal of essentially all eukaryote-specific ribosomal RNA (rRNA) expansion segments, reducing the rRNA to a functionally conserved core. The structure highlights how one microsporidia-specific and several repurposed existing ribosomal proteins compensate for the extensive rRNA reduction. The microsporidian ribosome is kept in an inactive state by two previously uncharacterized dormancy factors that specifically target the functionally important E-site, P-site and polypeptide exit tunnel. The present study illustrates the distinct effects of evolutionary pressure on RNA and protein-coding genes, provides a mechanism for ribosome inhibition and can serve as a structural basis for the development of inhibitors against microsporidian parasites.

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Fig. 1: Cryo-EM structure of the microsporidian ribosome reveals a prokaryotic-like rRNA core covered with eukaryotic ribosomal proteins.
Fig. 2: Extensive rRNA expansion segment loss in microsporidia.
Fig. 3: Dormancy factors blocking the E-site, the peptidyl-transferase centre and the polypeptide exit tunnel.
Fig. 4: MDF1 is a conserved eukaryotic protein.

Data availability

The data that support the findings of this study are available from the corresponding author on request. The cryo-EM density maps for the microsporidian ribosome have been deposited in the EM Data Bank with accession code EMD-4935 (overall state 1), EMD-4935—additional map 1—(overall state 2), EMD-4931 (LSU focused), EMD-4932 (SSU-body focused), EMD-4933 (SSU-head focused) and EMD-4934 (state 1, SSU-head focused). Coordinates for state 1 have been deposited in the Protein Data Bank under accession code 6RM3. Mass spectrometry data has been uploaded to PRIDE42 under project accession PXD013432.

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Acknowledgements

We thank M. Ebrahim and J. Sotiris for their support with data collection at the Evelyn Gruss Lipper Cryo-Electron Microscopy Resource Center, all members of the Klinge laboratory for helpful discussions and critical reading of this manuscript and H. Molina from the Rockefeller University Proteomics Resource Center for help with mass spectrometry analysis. The Rockefeller University Proteomics Resource Center acknowledges funding from the Leona M. and Harry B. Helmsley Charitable Trust and Sohn Conferences Foundation for mass spectrometer instrumentation. We thank B. Vossbrinck for her help in editing the manuscript. J.B. was supported by a Swiss National Science Foundation fellowship (155515) and is a SciLifeLab National Fellow at Umeå University. C.R.V. acknowledges funding from the Hatch Grant Project no. CONH00786 and R. Tyler Huning. S.K. is supported by the Robertson Foundation, the Alfred P. Sloan Foundation, the Irma T. Hirschl Trust, the Alexandrine and Alexander L. Sinsheimer Fund and the National Institutes of Health New Innovator Award (no. 1DP2GM123459).

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J.B., C.R.V. and M.H. conceived the study. C.R.V. cultivated microsporidia and purified ribosomes. J.B. and M.H. performed all EM work, determined the cryo-EM structures and built the model. S.K., J.B., C.R.V. and M.H. interpreted the results and wrote and edited the manuscript.

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Correspondence to Jonas Barandun.

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Supplementary Figs. 1–7, Supplementary Tables 1–3 and Supplementary References.

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Barandun, J., Hunziker, M., Vossbrinck, C.R. et al. Evolutionary compaction and adaptation visualized by the structure of the dormant microsporidian ribosome. Nat Microbiol 4, 1798–1804 (2019). https://doi.org/10.1038/s41564-019-0514-6

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