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Coupled protein quality control during nonsense mediated mRNA decay

Inglis, Alison J. and Guna, Alina and Gálvez Merchán, Ángel and Pal, Akshaye and Esantsi, Theodore K. and Keys, Heather R. and Frenkel, Evgeni M. and Oania, Robert and Weissman, Jonathan S. and Voorhees, Rebecca M. (2021) Coupled protein quality control during nonsense mediated mRNA decay. . (Unpublished) https://resolver.caltech.edu/CaltechAUTHORS:20220104-663910700

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Abstract

Translation of mRNAs containing premature termination codons (PTCs) can result in truncated protein products with deleterious effects. Nonsense-mediated decay (NMD) is a surveillance path-way responsible for detecting and degrading PTC containing transcripts. While 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 an intact 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, and suggested a lack of dependence on the canonical ribosome-quality control (RQC) pathway. Finally, one of the strongest hits in our screens was the E3 ubiquitin ligase CNOT4, a member of the CCR4-NOT complex, which is involved in initiating mRNA degradation. We show that CNOT4 is involved in NMD coupled protein degradation, and its role depends on a functional RING ubiquitin ligase domain. Our results demonstrate the existence of a targeted pathway for nascent protein degradation from PTC containing mRNAs, and provide a framework for identifying and characterizing factors involved in this process.


Item Type:Report or Paper (Discussion Paper)
Related URLs:
URLURL TypeDescription
https://doi.org/10.1101/2021.12.22.473893DOIDiscussion Paper
ORCID:
AuthorORCID
Inglis, Alison J.0000-0002-9008-8565
Guna, Alina0000-0003-0757-1255
Gálvez Merchán, Ángel0000-0001-7420-8697
Keys, Heather R.0000-0003-1371-2288
Frenkel, Evgeni M.0000-0002-1199-2653
Oania, Robert0000-0003-4070-761X
Weissman, Jonathan S.0000-0003-2445-670X
Voorhees, Rebecca M.0000-0003-1640-2293
Additional Information:The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. Version 1 - December 23, 2021; Version 2 - December 24, 2021; Version 3 - January 3, 2022; Version 4 - March 30, 2022. We thank Tino Pleiner, Joseph Replogle and the Voorhees lab for discussion and Simon Byrne and Patrick Smyth for help with data processing. 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 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 fellowship. The three co-first authors are joint authors and as such they can prioritize their names when adding this paper to their resumes. The authors have declared no competing interest.
Group:Heritage Medical Research Institute, Millard and Muriel Jacobs Genetics and Genomics Laboratory
Funders:
Funding AgencyGrant Number
Heritage Medical Research InstituteUNSPECIFIED
Kinship FoundationUNSPECIFIED
Pew-Stewart FoundationUNSPECIFIED
Millard and Muriel Jacobs Genetics and Genomics LaboratoryUNSPECIFIED
Caltech Division of Biology and Biological EngineeringUNSPECIFIED
Larry L. Hillblom FoundationUNSPECIFIED
Human Frontier Science ProgramUNSPECIFIED
DOI:10.1101/2021.12.22.473893
Record Number:CaltechAUTHORS:20220104-663910700
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20220104-663910700
Official Citation:Coupled protein quality control during nonsense mediated mRNA decay. Alison J. Inglis, Alina Guna, Ángel Gálvez Merchán, Akshaye Pal, Theodore K. Esantsi, Heather R. Keys, Evgeni M. Frenkel, Robert Oania, Jonathan S. Weissman, Rebecca M. Voorhees. bioRxiv 2021.12.22.473893; doi: https://doi.org/10.1101/2021.12.22.473893
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:112655
Collection:CaltechAUTHORS
Deposited By: Tony Diaz
Deposited On:04 Jan 2022 17:11
Last Modified:06 Apr 2022 17:23

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