Letter | Published:

Structural basis of co-translational quality control by ArfA and RF2 bound to ribosome

Nature volume 541, pages 554557 (26 January 2017) | Download Citation

Abstract

Quality control mechanisms intervene appropriately when defective translation events occur, in order to preserve the integrity of protein synthesis. Rescue of ribosomes translating on messenger RNAs that lack stop codons is one of the co-translational quality control pathways. In many bacteria, ArfA recognizes stalled ribosomes and recruits the release factor RF2, which catalyses the termination of protein synthesis1,2,3. Although an induced-fit mechanism of nonstop mRNA surveillance mediated by ArfA and RF2 has been reported4, the molecular interaction between ArfA and RF2 in the ribosome that is responsible for the mechanism is unknown. Here we report an electron cryo-microscopy structure of ArfA and RF2 in complex with the 70S ribosome bound to a nonstop mRNA. The structure, which is consistent with our kinetic and biochemical data, reveals the molecular interactions that enable ArfA to specifically recruit RF2, not RF1, into the ribosome and to enable RF2 to release the truncated protein product in this co-translational quality control pathway. The positively charged C-terminal domain of ArfA anchors in the mRNA entry channel of the ribosome. Furthermore, binding of ArfA and RF2 induces conformational changes in the ribosomal decoding centre that are similar to those seen in other protein-involved decoding processes. Specific interactions between residues in the N-terminal domain of ArfA and RF2 help RF2 to adopt a catalytically competent conformation for peptide release. Our findings provide a framework for understanding recognition of the translational state of the ribosome by new proteins, and expand our knowledge of the decoding potential of the ribosome.

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Acknowledgements

We thank J. Peng for scripting, W. Jiang, Y. He, J. Liu and T. H. D. Nguyen for suggestions on EM data collection and structural refinement, members of the Jin laboratory for discussions, the structural biology facility at Northwestern University for the use of the microscope and the Chicago Biomedical Consortium for the purchase of the Gatan K2 detector. H.J. acknowledges support from the National Institute of General Medical Sciences of the NIH (R01-GM120552). The computational part of the study was supported by the National Institute of General Medical Sciences (P41-GM104601 to J.C.P. and E.T.).

Author information

Affiliations

  1. Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA

    • Fuxing Zeng
    • , Yanbo Chen
    • , Emad Tajkhorshid
    •  & Hong Jin
  2. Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208-3500, USA

    • Jonathan Remis
  3. Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA

    • Mrinal Shekhar
    • , Emad Tajkhorshid
    •  & Hong Jin
  4. Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA

    • Mrinal Shekhar
    • , James C. Phillips
    •  & Emad Tajkhorshid

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Contributions

F.Z. and H.J. designed the study. F.Z. purified ribosomes, proteins and tRNAs, processed EM data and built the atomic model. Y.C. did the mutagenesis and purified ArfA mutants. F.Z. and Y.C. performed the peptide release assay. F.Z., Y.C., H.J. and J.R. collected EM data. M.S., J.C.P. and E.T. provided computational support. F.Z., Y.C. and H.J. analysed the data and refined the structure. F.Z. and Y.C. helped with manuscript preparation. H.J. wrote the paper. All authors discussed the final manuscript.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Hong Jin.

Reviewer Information Nature thanks Y. Hashem, K. Keiler and the other anonymous reviewer(s) for their contribution to the peer review of this work.

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https://doi.org/10.1038/nature21053

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