Structural basis of highly conserved ribosome recycling in eukaryotes and archaea

Abstract

Ribosome-driven protein biosynthesis is comprised of four phases: initiation, elongation, termination and recycling. In bacteria, ribosome recycling requires ribosome recycling factor and elongation factor G, and several structures of bacterial recycling complexes have been determined. In the eukaryotic and archaeal kingdoms, however, recycling involves the ABC-type ATPase ABCE1 and little is known about its structural basis. Here we present cryo-electron microscopy reconstructions of eukaryotic and archaeal ribosome recycling complexes containing ABCE1 and the termination factor paralogue Pelota. These structures reveal the overall binding mode of ABCE1 to be similar to canonical translation factors. Moreover, the iron–sulphur cluster domain of ABCE1 interacts with and stabilizes Pelota in a conformation that reaches towards the peptidyl transferase centre, thus explaining how ABCE1 may stimulate peptide-release activity of canonical termination factors. Using the mechanochemical properties of ABCE1, a conserved mechanism in archaea and eukaryotes is suggested that couples translation termination to recycling, and eventually to re-initiation.

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Figure 1: The ribosome-bound Pelota–ABCE1 complex.
Figure 2: Interaction of Pelota and ABCE1 with the ribosome.
Figure 3: Domain movements in Pelota and eRF1.
Figure 4: Mechanochemical activity of ABCE1 on the ribosome.
Figure 5: Scheme of archaeal and eukaryotic ribosome recycling bridging termination with initiation.

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Acknowledgements

We thank A. Schele and A. Gilmozzi for technical assistance, and D. Wilson for critical discussions. This work was supported by grants from the Deutsche Forschungsgemeinschaft, SFB594 (to R.B.), SFB646 (to T.B., R.B. and K.-P.H.), National Institutes of Health U19 AI083025 (to K.-P.H.) and by the Fonds der chemischen Industrie (to S.F.).

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Contributions

T.B. and R.B. designed the study, T.B. processed the yeast SL–RNC–Dom34–Rli1 complex and interpreted the cryo-EM structures, S.F. purified archaeal proteins and reconstituted the archaeal 70S–aPelota–aABCE1 sample, processed all archaeal data sets and interpreted the cryo-EM structures, S.W. developed an automated workflow for data processing from the Titan Krios microscope, C.J.S. purified yeast Rli1p, A.M.A. built the archaeal 70S ribosome rRNA model, J.-P.A. built the archaeal 70S ribosome protein models, H.S. reconstituted the SL–RNC–Dom34–Rli1 sample, C.U. prepared cryo-EM grids and assisted in data collection, O.B. optimized and performed cryo-EM data collection, I.D. implemented software for automated data collection on the Titan Krios microscope, A.K. purified archaeal ABCE1, M.T. provided P. furiosus and Thermococcus kodakaraensis cells, T.B., S.F., K.-P.H., R.G. and R.B. interpreted results.

Corresponding authors

Correspondence to Thomas Becker or Roland Beckmann.

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The authors declare no competing financial interests.

Additional information

EM density maps are deposited in the 3D-EM database (EMD-2008 and EMD-2010 for yeast maps, EMD-2009 for the archaeal map) and the coordinates for EM-based models are deposited in the Protein Data Bank (3J15 and 3J16).

Supplementary information

Supplementary Information

This file contains Supplementary Figures 1-5 with legends, Supplementary Tables 1-2, legends for Supplementary Movies 1-3 and additional references. (PDF 1939 kb)

Supplementary Movie 1

This movie shows the domain movement of Pelota central domain stabilized by ABCE1 – yeast (see Supplementary Information file for full legend). (MOV 14182 kb)

Supplementary Movie 2

This movie shows the domain movement of Pelota central domain stabilized by ABCE1 - archaea (see Supplementary Information file for full legend). (MOV 10126 kb)

Supplementary Movie 3

This move shows the conformational transition of ABCE1 (see Supplementary Information file for full legend). (MOV 14925 kb)

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Becker, T., Franckenberg, S., Wickles, S. et al. Structural basis of highly conserved ribosome recycling in eukaryotes and archaea. Nature 482, 501–506 (2012). https://doi.org/10.1038/nature10829

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