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Published May 15, 2023 | Published + Supplemental Material
Journal Article Open

Coupled protein quality control during nonsense-mediated mRNA decay


Translation of mRNAs containing premature termination codons (PTCs) results in truncated protein products with deleterious effects. Nonsense-mediated decay (NMD) is a surveillance pathway responsible for detecting PTC containing transcripts. Although the molecular mechanisms governing mRNA degradation have been extensively studied, the fate of the nascent protein product remains largely uncharacterized. Here, we use a fluorescent reporter system in mammalian cells to reveal a selective degradation pathway specifically targeting the protein product of an NMD mRNA. We show that this process is post-translational and dependent on the ubiquitin proteasome system. To systematically uncover factors involved in NMD-linked protein quality control, we conducted genome-wide flow cytometry-based screens. Our screens recovered known NMD factors but suggested that protein degradation did not depend on the canonical ribosome-quality control (RQC) pathway. A subsequent arrayed screen demonstrated that protein and mRNA branches of NMD rely on a shared recognition event. Our results establish the existence of a targeted pathway for nascent protein degradation from PTC containing mRNAs, and provide a reference for the field to identify and characterize required factors.

Additional Information

© 2023. Published by The Company of Biologists Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution and reproduction in any medium provided that the original work is properly attributed. We thank Tino Pleiner, Joseph Replogle and the Voorhees lab for discussion. Flow cytometry experiments were performed at the Caltech flow cytometry facility. The Whitehead Institute Genome Technology core performed sequencing for genome-wide screens. This work was supported by the Heritage Medical Research Institute, the Kinship Foundation, the Pew-Stewart Foundation, the Howard Hughes Medical Institute (J.S.W.), the Center for Genome Editing and Recording (2RM1 HG009490-06 to J.S.W.) and by the Millard and Muriel Jacobs Genetics and Genomics Laboratory at California Institute of Technology. A.J.I. was supported by a Caltech BBE postdoctoral fellowship and a grant from the Larry L. Hillblom Foundation and A.G. by a Human Frontier Science Program post-doctoral fellowship. Open access funding provided by California Institute of Technology. Deposited in PMC for immediate release. Author contributions. Conceptualization: R.M.V., A.G.-M.; Methodology: H.R.K., E.M.F.; Validation: A.G., A.J.I.; Formal analysis: A.J.I., A.G., A.P.; Investigation: A.J.I., A.G., A.G.-M., A.P., T.K.E., H.R.K., R.O.; Resources: H.R.K., E.M.F.; Data curation: A.J.I., A.G.; Writing - original draft: R.M.V., A.J.I., A.G.; Writing - review & editing: R.M.V., A.J.I., A.G., A.G.-M., J.S.W.; Visualization: A.J.I., A.G.; Supervision: R.M.V., J.S.W.; Project administration: R.M.V.; Funding acquisition: R.M.V., J.S.W. Data availability. All the relevant data can be found within the article and its supplementary information. Competing interests. J.S.W. declares outside interest in 5 AM Venture, Amgen, Chroma Medicine, KSQ Therapeutics, Maze Therapeutics, Tenaya Therapeutics, Tessera Therapeutics, and Third Rock Ventures. R.M.V. declares outside interest in Gate Biosciences.

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Supplemental Material - jcs261216supp.pdf


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Additional details

August 22, 2023
December 22, 2023