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High-resolution cryo-electron microscopy structure of the Trypanosoma brucei ribosome

Abstract

Ribosomes, the protein factories of living cells, translate genetic information carried by messenger RNAs into proteins, and are thus involved in virtually all aspects of cellular development and maintenance. The few available structures of the eukaryotic ribosome1,2,3,4,5,6 reveal that it is more complex than its prokaryotic counterpart7,8, owing mainly to the presence of eukaryote-specific ribosomal proteins and additional ribosomal RNA insertions, called expansion segments9. The structures also differ among species, partly in the size and arrangement of these expansion segments. Such differences are extreme in kinetoplastids, unicellular eukaryotic parasites often infectious to humans. Here we present a high-resolution cryo-electron microscopy structure of the ribosome of Trypanosoma brucei, the parasite that is transmitted by the tsetse fly and that causes African sleeping sickness. The atomic model reveals the unique features of this ribosome, characterized mainly by the presence of unusually large expansion segments and ribosomal-protein extensions leading to the formation of four additional inter-subunit bridges. We also find additional rRNA insertions, including one large rRNA domain that is not found in other eukaryotes. Furthermore, the structure reveals the five cleavage sites of the kinetoplastid large ribosomal subunit (LSU) rRNA chain, which is known to be cleaved uniquely into six pieces10,11,12, and suggests that the cleavage is important for the maintenance of the T. brucei ribosome in the observed structure. We discuss several possible implications of the large rRNA expansion segments for the translation-regulation process. The structure could serve as a basis for future experiments aimed at understanding the functional importance of these kinetoplastid-specific ribosomal features in protein-translation regulation, an essential step towards finding effective and safe kinetoplastid-specific drugs.

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Figure 1: High-resolution cryo-EM structure of the T. brucei ribosome.
Figure 2: Atomic model of the T. brucei ribosome.
Figure 3: Comparison between T. brucei and yeast ribosomes.
Figure 4: T. brucei srRNAs and protein extensions.

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Protein Data Bank

Data deposits

The electron microscopy map has been deposited in the European Molecular Biology Laboratory (EMBL) European Bioinformatics Institute Electron Microscopy Data Bank (EMDB) under accession code EMD-2239. Coordinates of electron-microscopy-based model have been deposited in the RCSB Protein Data Bank under accession numbers 3ZEQ, 3ZEX, 3ZEY and 3ZF7.

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Acknowledgements

This work is dedicated to the memory of Mariano Levin, who collaborated with J.F. and S.M.A. on the ribosomes from T. cruzi and T. brucei. We thank G. Cardone for assistance in the local resolution computation, and M. Thomas for her assistance with the preparation of figures. We wish to thank N. Williams for an useful discussion about the T. brucei LSU rRNA processing. This work was supported by the Howard Hughes Medical Institute (HHMI) and the National Institutes of Health (NIH) R01 GM29169 (to J.F.), L’Agence Nationale de la recherche (ANR) project AMIS ARN ANR-09-BLAN-0160 (E.W. and F.J.), as well as NIH R01-EB004873 and R01-GM074258 (to Q.Z. and C.B.). S.N.B. was supported by a Centers for Disease Control (CDC) Emerging Infectious Diseases (EID) fellowship program.

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Contributions

Y.H., A.d.G., S.N.B., F.J., Q.Z., C.B., S.M.-A., E.W. and J.F. interpreted the data and wrote the manuscript. S.N.B. purified the T. brucei ribosomes. Y.H., J. Fu and R.A.G. carried out the cryo-EM experiments. H.Y.L. performed the three-dimensional variance estimation. Y.H., A.J. and Q.Z. performed the density-map segmentations. Y.H., A.d.G., J. Fu, A.J. and H.Y.L. carried out the cryo-EM data processing. Y.H. and F.J. modelled the rRNA. Y.H. and Q.Z. modelled the ribosomal proteins. J.F. directed research.

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Correspondence to Joachim Frank.

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Hashem, Y., des Georges, A., Fu, J. et al. High-resolution cryo-electron microscopy structure of the Trypanosoma brucei ribosome. Nature 494, 385–389 (2013). https://doi.org/10.1038/nature11872

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