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Specific recognition and ubiquitination of translating ribosomes by mammalian CCR4–NOT

Nature Structural & Molecular Biology volume 30, pages 1314–1322 (2023)Cite this article

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Abstract

Translation affects messenger RNA stability and, in yeast, this is mediated by the Ccr4–Not deadenylation complex. The details of this process in mammals remain unclear. Here, we use cryogenic electron microscopy (cryo-EM) and crosslinking mass spectrometry to show that mammalian CCR4–NOT specifically recognizes ribosomes that are stalled during translation elongation in an in vitro reconstituted system with rabbit and human components. Similar to yeast, mammalian CCR4–NOT inserts a helical bundle of its CNOT3 subunit into the empty E site of the ribosome. Our cryo-EM structure shows that CNOT3 also locks the L1 stalk in an open conformation to inhibit further translation. CCR4–NOT is required for stable association of the nonconstitutive subunit CNOT4, which ubiquitinates the ribosome, likely to signal stalled translation elongation. Overall, our work shows that human CCR4–NOT not only detects but also enforces ribosomal stalling to couple translation and mRNA decay.

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Fig. 1: Human CCR4–NOT and CNOT4 recognize stalled ribosomes in an in vitro translation system.
Fig. 2: Structure of mammalian CNOT3-bound to the 80S ribosome.
Fig. 3: CNOT3 mutations in human disease.
Fig. 4: CCR4–NOT binds 80S ribosomes in the vicinity of the E site.
Fig. 5: The CNOT4 RRM and ZnF domains are required for association with the 80S ribosome and eS7 ubiquitination.
Fig. 6: Model for CCR4–NOT and CNOT4 recognition of mammalian ribosomes during slow elongation.

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Data availability

Cryo-EM maps and molecular models have been deposited in the Electron Microscopy Data Bank (accession code EMD-16052) and in the PDB (accession code 8BHF). We also analyzed previously reported structures (PDB 6TB3 and PDB 5LZV) and used PDB 6SGC for initial model building. EM micrographs are available from the EMPIAR database with accession code EMPIAR-11593. MS data have been deposited in jPOST (project ID JPST001798, PRIDE ID PXD035522). Cancer Hotspot mutations on CNOT3 were accessed from the COSMIC database (v.96). Source data are provided with this paper. All other data are available in the main text or as part of the Extended Data or supplementary materials. Original gels and blot images are provided in the source data. Correspondence and requests for materials should be addressed to L.A.P. or V.C. All unique materials are available upon request with completion of a standard Materials Transfer Agreement.

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Acknowledgements

We are grateful to members of the Passmore, Ramakrishnan and Rappsilber laboratories for assistance and advice; F. Schildhauer for assistance with modified Streptavidin bead preparation; R. Hegde for the stall mRNA plasmid template; the Medical Research Council (MRC) LMB Electron Microscopy Facility for access and support of EM sample preparation and data collection; J. Grimmett and T. Darling (LMB scientific computation) and J.G. Shi (baculovirus) for support. We acknowledge Diamond Light Source for access to eBIC (proposal no. BI23268) funded by the Wellcome Trust, MRC and Biotechnology and Biological Sciences Research Council. This work was supported by the MRC, as part of United Kingdom Research and Innovation (also known as UK Research and Innovation), MRC file reference number MC_U105192715 (L.A.P.); a postdoctoral fellowship of the Deutsche Forschungsgemeinschaft (the German Research Foundation, project no. 429892960) to E.A and the European Union’s Horizon 2020 research and innovation program (European Research Council Consolidator grant agreement no. 725685) (to L.A.P.). V.C. was supported by V. Ramakrishnan whose funding was from the MRC (grant no. MC_U105184332), the Wellcome Trust (grant no. WT096570), the Agouron Institute, and the Louis-Jeantet Foundation. The Wellcome Centre for Cell Biology (J.R.) is supported by core funding from the Wellcome Trust (grant no. 203149). For the purpose of open access, the MRC-LMB has applied a CC BY public copyright licence to any Author Accepted Manuscript version arising.

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Author notes

  1. Eva Absmeier

    Present address: Freie University of Berlin, Berlin, Germany

  2. These authors contributed equally to this work: Eva Absmeier, Viswanathan Chandrasekaran.

Authors and Affiliations

  1. MRC Laboratory of Molecular Biology (LMB), Cambridge, UK

    Eva Absmeier, Viswanathan Chandrasekaran, James A. W. Stowell & Lori A. Passmore

  2. Technical University of Berlin, Chair of Bioanalytics, Berlin, Germany

    Francis J. O’Reilly & Juri Rappsilber

  3. Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK

    Juri Rappsilber

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Contributions

E.A. designed CNOT4 mutants and truncations and purified all proteins (CCR4–NOT and CNOT4) used in this study. J.A.W.S. initially designed the CCR4–NOT expression and purification scheme. V.C. and E.A. designed and performed in vitro translation assays, cryo-EM sample preparation, cryo-EM data collection, processing and analysis. E.A. produced crosslinking MS sample and F.J.O’R. measured the crosslinked sample and analyzed it. L.A.P. and J.R. supervised the research. E.A., V.C. and L.A.P. wrote the manuscript with contributions from all the authors.

Corresponding authors

Correspondence to Viswanathan Chandrasekaran or Lori A. Passmore.

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Competing interests

L.A.P. is an inventor on a patent filed by the MRC for all-gold EM supports (PCT/GB2014/051896), licensed to Quantifoil under the trademark UltrAuFoil. The other authors declare no competing interests.

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Nature Structural & Molecular Biology thanks Mark Bartlam, Ariel Bazzini, and the other, anonymous, reviewer(s) for their contribution to the peer review of this work. Peer reviewer reports are available. Sara Osman and Dimitris Typas were the primary editors on this article and managed its editorial process and peer review in collaboration with the rest of the editorial team.

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Extended data

Extended Data Fig. 1 In vitro reconstitution of ribosome stalling during elongation, CCR4-NOT/CNOT4 binding and eS7 mono-ubiquitination.

(a) Autoradiogram of a sucrose gradient fractionation of stall mRNA in RRL shows that the majority of the radiolabeled 3x FLAG-β-VHP-(UUA)3 is on stalled monosomes (fractions 5-8; 200 µl gradient). * indicates a small amount of full-length protein product, released from the ribosome at the stop codon and therefore migrating in the supernatant (fractions 1-3). The band below the full-length protein product corresponds to released, shortened protein product, resulting from ribosomal stalling on the three UUA leucine codons of the stall mRNA. We note that unlike in the previous cryoEM structure of yeast Ccr4-Not bound to stalled RNCs, we observed mainly stalled monosomes. Multiple rounds of initiation are disfavored in the RRL and only <5% of mRNAs have two or more ribosomes translating on a single mRNA (compare signals in monosome fractions 6–8 and polysome fractions 9–11). Data are representative of experiments performed twice. (b) Autoradiogram visualizing that full-length protein (*) accumulates in the supernatant when stall mRNA is translated in RRL supplemented with total tRNA from pig liver. Data are representative of experiments performed twice. (c) Immunoblot of the 80S peak fractions from a sucrose gradient of a sample containing CCR4-NOT, CNOT4 and stall mRNA using antibodies against CNOT1, CNOT3, CNOT4, CNOT6, CNOT11 and CNOT9 (12 ml gradient). Data are representative of experiments performed twice. (d-f) Sucrose gradient fractions of non-radiolabeled translation reactions of stall mRNA in the presence of the indicated CCR4-NOT and/or CNOT4 proteins immunoblotted using antibodies against CNOT3, CNOT4 and eS7 (12 ml gradient). The mono-ubiquitinated eS7 band is also labeled. Data are representative of experiments performed six (d,e) or four (f) times. (g-i) Same experiments as in panels (d-f) but performed on ribosomes elongating on native α- and β-globin mRNA in RRL not treated with nuclease (12 ml gradient). Data are representative of experiments performed twice. In d-i, asterisks denote cross-reacting bands. We note that in previous studies in yeast, eS7 is mono-ubiquitinated in monosome fractions and poly-ubiquitinated in polysome fractions. We observe eS7 mono-ubiquitination in the monosome peak but no poly-ubiquitination. We conclude that poly-ubiquitination is not required for stable binding of CCR4-NOT and CNOT4.

Source data

Extended Data Fig. 2 RELION 3.1 processing workflow.

Two datasets were collected, processed separately and merged at the end to yield a final reconstruction at 3.1 Å resolution.

Extended Data Fig. 3 CryoEM analysis of 80S ribosomes bound to CNOT3.

(a) Representative micrograph used for single particle analysis. Scale bar: 50 nm. A total of 32,762 micrographs were used for this study. (b) Hand-picked two-dimensional class averages of 80S ribosomes (Table 1). (c) Gold-standard Fourier shell correlation (FSC) curve (blue) of the final map illustrating an overall resolution of 3.1 Å. The phase-randomized, masked FSC curve (orange) is also shown. (d) Final map segmented to show 60S (cyan), 40S (yellow), CNOT3 (red-orange) and the P-site tRNA (green). (e) Map from panel (d) colored according to the local resolution (cyan - high resolution; magenta - low resolution).

Extended Data Fig. 4 Details around the P-site tRNA in the cryoEM map of 80S CNOT3.

(a-b) The cryoEM map and atomic model are shown for the nascent chain (a) and the codon-anticodon in the P site (b). This map was calculated from two-fold downscaled particles (to a pixel size of 1.66 Å/pix) to improve interpretability. The P-site tRNA and nascent chain are contoured at 10 r.m.s.d. (c) Packing interactions between CNOT3 helical bundle a (red-orange) and the P-site tRNA (green). (d) Packing interactions between CNOT3 helical bundle a (red-orange) and the 28S rRNA (cyan). Salt-bridges are indicated with black, dashed lines.

Extended Data Fig. 5 Evolutionary conservation of the interaction between CNOT3 and the 80S ribosome.

(a) Multiple sequence alignments of the two helical bundles across representative eukaryotes (bundle a: 1-111, bundle b: 115-236). Numbering is according to the human sequence and frequently mutated residues in developmental disorders and cancer are indicated with red and orange asterisks, respectively. Helical bundle a has a sequence identity of 54.5% between yeast and human; helical bundle b (residues 120-213 in yeast Not5 and 115-236 in human CNOT3) has a sequence identity of 29.8%. High conservation, dark purple; lower conservation, lighter purple. (b) Superposition of budding yeast (Sc) Not5 helical bundle a (from PDB 6TB3) and helical bundle b (Alphafold2 model, residues 120-213) on human (Hs) CNOT3 helical bundles a and b (residues 1-236). Black lines indicate the extended helices in the human structure (residues 147-169), which are missing in yeast. Note that the cryoEM structure of the yeast complex only contains bundle a. Oc, Oryctolagus cuniculus. (c) Surface charge of helical bundle b of Hs CNOT3. (d) Surface charge of the AlphaFold2 prediction of helical bundle b of Sc Not5. Red- negative surface charge, blue- positive surface charge.

Extended Data Fig. 6 Crosslinking mass spectrometry of CCR4-NOT- and CNOT4-bound stalled 80S ribosomes.

(a-b) Circle diagrams of observed crosslinks (a) between selected CCR4-NOT subunits or CNOT4 and 80S ribosomal proteins or (b) within CCR4-NOT and CNOT4. Dashed lines indicate crosslinks between proteins that were not visible in the structure and therefore not modelled on the structure. In panels (a) and (b), the indicated subunits are highlighted. (c) Diagrams of observed crosslinks of CNOT3 to other CCR4-NOT subunits and CNOT4 when bound to 80S. CNOT3 is drawn to a larger scale than the other proteins.

Extended Data Fig. 7 Repetitions of experiments in Fig. 5.

The experimental repeats of data shown in Fig. 5 are shown. Note that sample 9 (*) is missing in the anti-CNOT4 Western blot of panel b.

Source data

Supplementary information

Reporting Summary

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Supplementary Video 1

Cryo-EM structure of a stalled ribosome bound to CNOT3. The atomic model of the cryo-EM structure is shown in cartoon form with 40S (yellow), 60S (cyan), L1 stalk (blue), P site tRNA (green), mRNA (salmon) and CNOT3 (red) indicated. The electrostatic surface charge of CNOT3 is also shown.

Supplementary Table 1

Table of oligonucleotides, antibodies and reagents.

Source data

Source Data Fig. 1

Unprocessed gels and western blots.

Source Data Fig. 5

Unprocessed gels and western blots.

Source Data Extended Data Fig. 1

Unprocessed gels and western blots.

Source Data Extended Data Fig. 7

Unprocessed gels and western blots.

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Absmeier, E., Chandrasekaran, V., O’Reilly, F.J. et al. Specific recognition and ubiquitination of translating ribosomes by mammalian CCR4–NOT. Nat Struct Mol Biol 30, 1314–1322 (2023). https://doi.org/10.1038/s41594-023-01075-8

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