Translation factors direct intrinsic ribosome dynamics during translation termination and ribosome recycling

Abstract

Characterizing the structural dynamics of the translating ribosome remains a major goal in the study of protein synthesis. Deacylation of peptidyl-tRNA during translation elongation triggers fluctuations of the pretranslocation ribosomal complex between two global conformational states. Elongation factor G–mediated control of the resulting dynamic conformational equilibrium helps to coordinate ribosome and tRNA movements during elongation and is thus a crucial mechanistic feature of translation. Beyond elongation, deacylation of peptidyl-tRNA also occurs during translation termination, and this deacylated tRNA persists during ribosome recycling. Here we report that specific regulation of the analogous conformational equilibrium by translation release and ribosome recycling factors has a critical role in the termination and recycling mechanisms. Our results support the view that specific regulation of the global state of the ribosome is a fundamental characteristic of all translation factors and a unifying theme throughout protein synthesis.

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Figure 1: Experimental model and reaction schemes for termination and recycling.
Figure 2: RF1 binds stably to a release complex and prevents tRNA fluctuations.
Figure 3: RF1 blocks GS1 → GS2 transitions and stabilizes GS1.
Figure 4: RF1 domain 1 is dispensable for RF1-mediated blocking of GS1 → GS2 transitions.
Figure 5: RF3(GDP) interacts with an RF1-bound RC locked in GS1, and binding of GTP to RC-bound RF3 enables the GS1 → GS2 transition.
Figure 6: RRF preferentially binds GS2 and competes with GS2 → GS1 transitions within a fluctuating post-termination complex.
Figure 7: Mechanistic model for regulation of the GS1GS2 dynamic equilibrium by RF1, RF3 and RRF.

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Acknowledgements

This work was supported in part by start-up funds to R.L.G. from Columbia University, as well as grants to R.L.G. from the Burroughs Wellcome Fund (CABS 1004856), the US National Science Foundation (MCB 0644262) and the American Cancer Society (RSG GMC-117152). S.H.S. was supported, in part, by the Columbia University Langmuir Scholars Program, and N.P. was supported, in part, by the Columbia University Summer Undergraduate Research Fellowship (SURF) Program. We are indebted to S. Das for managing the Gonzalez laboratory. We thank J. Frank, E. Greene, N. Gao and the members of the Gonzalez laboratory for valuable discussions and for carefully reading the manuscript and providing comments.

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S.H.S. and R.L.G. designed the research; S.H.S. conducted the research, except for the release factor activity assays, which were conducted by S.H.S, N.P. and K.A.M., and purification of RRF, which was conducted by N.P.; J.F. provided L1(Cy5) ribosomes and offered critical discussions related to data analysis and interpretation; S.H.S. and R.L.G. wrote the manuscript; all authors approved the final manuscript.

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Correspondence to Ruben L Gonzalez Jr.

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Sternberg, S., Fei, J., Prywes, N. et al. Translation factors direct intrinsic ribosome dynamics during translation termination and ribosome recycling. Nat Struct Mol Biol 16, 861–868 (2009). https://doi.org/10.1038/nsmb.1622

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