K6-linked ubiquitylation marks formaldehyde-induced RNA-protein crosslinks for resolution
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Reactive aldehydes are produced by normal cellular metabolism or after alcohol consumption, and they accumulate in human tissues if aldehyde clearance mechanisms are impaired. Their toxicity has been attributed to the damage they cause to genomic DNA and the subsequent inhibition of transcription and replication. However, whether interference with other cellular processes contributes to aldehyde toxicity has not been investigated. We demonstrate that formaldehyde induces RNA-protein crosslinks (RPCs) that stall the ribosome and inhibit translation in human cells. RPCs in the messenger RNA (mRNA) are recognized by the translating ribosomes, marked by atypical K6-linked ubiquitylation catalyzed by the RING-in-between-RING (RBR) E3 ligase RNF14, and subsequently resolved by the ubiquitin- and ATP-dependent unfoldase VCP. Our findings uncover an evolutionary conserved formaldehyde-induced stress response pathway that protects cells against RPC accumulation in the cytoplasm, and they suggest that RPCs contribute to the cellular and tissue toxicity of reactive aldehydes.
| Originalsprog | Engelsk |
|---|---|
| Tidsskrift | Molecular Cell |
| Vol/bind | 83 |
| Udgave nummer | 23 |
| Sider (fra-til) | 4272-4289.e10 |
| Antal sider | 29 |
| ISSN | 1097-2765 |
| DOI | |
| Status | Udgivet - 2023 |
Bibliografisk note
Funding Information:
We thank Katharina Mayr for technical support, Amitkumar Fulzele for help with mass spectrometry, Sabine Heinen for help with recombinant protein purification, and Anke Busch for iCLIP data processing and help with the GEO submission. We thank Kazuhiro Maeshima (NIG, Japan) for gifting us the DLD-1-mAID-RPB1 cells and Julian Stingele (Gene Center Munich, Germany) for HAP1 RNF14- and HeLa ZNF598-knockout cells. Support from the IMB Microscopy, Flow Cytometry, Genomics and Bioinformatics Core Facilities is gratefully acknowledged. The research in the Beli lab is funded by the Deutsche Forschungsgemeinschaft (German Research Foundation, DFG) project-ID BE 5342/1-2; Emmy Noether Programme project-ID BE 5342/3-1, project-ID 393547839— SFB 1361 , and project-ID 464588647— SFB 1551 ; and the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie grant agreement no 860517 . B.A.S. has received funding from the Max Planck Society , the European Research Council under the European Union’s Horizon 2020 Research and Innovation Programme (grant agreement no. 789016 -NEDD8Activate), and the German Research Foundation DFG (Leibniz Prize SCHU 3196/1-1 ). The NNF Center for Protein research is financially supported by the Novo Nordisk Foundation ( NNF14CC0001 ).
Funding Information:
We thank Katharina Mayr for technical support, Amitkumar Fulzele for help with mass spectrometry, Sabine Heinen for help with recombinant protein purification, and Anke Busch for iCLIP data processing and help with the GEO submission. We thank Kazuhiro Maeshima (NIG, Japan) for gifting us the DLD-1-mAID-RPB1 cells and Julian Stingele (Gene Center Munich, Germany) for HAP1 RNF14- and HeLa ZNF598-knockout cells. Support from the IMB Microscopy, Flow Cytometry, Genomics and Bioinformatics Core Facilities is gratefully acknowledged. The research in the Beli lab is funded by the Deutsche Forschungsgemeinschaft (German Research Foundation, DFG) project-ID BE 5342/1-2; Emmy Noether Programme project-ID BE 5342/3-1, project-ID 393547839—SFB 1361, and project-ID 464588647—SFB 1551; and the European Union's Horizon 2020 research and innovation program under the Marie Skłodowska-Curie grant agreement no 860517. B.A.S. has received funding from the Max Planck Society, the European Research Council under the European Union's Horizon 2020 Research and Innovation Programme (grant agreement no. 789016-NEDD8Activate), and the German Research Foundation DFG (Leibniz Prize SCHU 3196/1-1). The NNF Center for Protein research is financially supported by the Novo Nordisk Foundation (NNF14CC0001). P.B. J.K. C.C. A.S.R. and C.J.B. designed the research. A.S.R. C.J.B. C.S. J.B.H. and M.M. performed the experiments and analyzed the data. I.M. M.O. N.D.S.F. and J.-X.C. established important assays, provided ideas, and helped with data analysis. J.F.G. analyzed the phosphoproteomics data. S.E. and J.K. analyzed CLIP datasets. R.H. and A.O. performed proteome-wide iCLIP. D.H.-G. purified RNF14, performed RNF14 E2 screening, and RNF14 in vitro ubiquitylation assays under the supervision of B.A.S. N.K. performed yeast experiments under the supervision of H.D.U. M.M.M. generated the biotin-tagged K6-ubiquitin affimer and LotA-N. A.M. and Y.Z. performed and analyzed nascent RNA sequencing under the supervision of A.P. P.B. wrote the manuscript. All authors read and commented on the manuscript. The authors declare no competing interests. We support inclusion, diversity, and equality in scientific research.
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© 2023 The Author(s)
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