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The Rrp4–exosome complex recruits and channels substrate RNA by a unique mechanism

Nature Chemical Biology volume 13, pages 522–528 (2017)Cite this article

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Abstract

The exosome is a large molecular machine involved in RNA degradation and processing. Here we address how the trimeric Rrp4 cap enhances the activity of the archaeal enzyme complex. Using methyl-TROSY NMR methods we identified a 50-Å long RNA binding path on each Rrp4 protomer. We show that the Rrp4 cap can thus simultaneously recruit three substrates, one of which is degraded in the core while the others are positioned for subsequent degradation rounds. The local interaction energy between the substrate and the Rrp4–exosome increases from the periphery of the complex toward the active sites. Notably, the intrinsic interaction strength between the cap and the substrate is weakened as soon as substrates enter the catalytic barrel, which provides a means to reduce friction during substrate movements toward the active sites. Our data thus reveal a sophisticated exosome–substrate interaction mechanism that enables efficient RNA degradation.

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Figure 1: Structure and NMR spectra of the Rrp4–exosome complex.
Figure 2: Methionine scanning identifies residues in Rrp4 that interact with substrate RNA.
Figure 3: Activity and RNA interaction surface of the Rrp4–exosome.
Figure 4: Quantification of RNA–exosome interactions.
Figure 5: Illustration of the Rrp4–modulated RNA degradation mechanism.

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Acknowledgements

We acknowledge all members of R.S.'s laboratory for discussions. We thank S. Wiesner for suggestions regarding the methionine scanning experiments, I. Holdermann and J. Petters for excellent technical assistance and V. Truffault for maintenance of the NMR infrastructure. M.A.C. and S.S. acknowledge funding from the International Max Planck Research School “From Molecules to Organisms”. This work was supported by the Max Planck Society and the European Research Council under the European Union's Seventh Framework Programme (FP7/2007–2013), ERC grant agreement 616052 (R.S.).

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Authors and Affiliations

  1. Max Planck Institute for Developmental Biology, Tübingen, Germany

    Milos A Cvetkovic, Jan Philip Wurm, Maxime J Audin, Stefan Schütz & Remco Sprangers

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  1. Milos A Cvetkovic
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Contributions

M.A.C. performed and analyzed NMR, binding and degradation experiments. J.P.W. assisted with the binding experiments, M.J.A. assisted with the degradation experiments and S.S. performed NMR assignment experiments. R.S. conceived the project, analyzed data and wrote the manuscript. All authors commented on the data, the analysis and the manuscript.

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Correspondence to Remco Sprangers.

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The authors declare no competing financial interests.

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Cvetkovic, M., Wurm, J., Audin, M. et al. The Rrp4–exosome complex recruits and channels substrate RNA by a unique mechanism. Nat Chem Biol 13, 522–528 (2017). https://doi.org/10.1038/nchembio.2328

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