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Ribosome-nascent Chain Interaction Regulates N-terminal Protein Modification

Yang, Chien-I and Kim, Jiwoo and Shan, Shu-ou (2022) Ribosome-nascent Chain Interaction Regulates N-terminal Protein Modification. Journal of Molecular Biology, 434 (9). Art. No. 167535. ISSN 0022-2836. PMCID PMC9126151. doi:10.1016/j.jmb.2022.167535. https://resolver.caltech.edu/CaltechAUTHORS:20220310-121624000

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Abstract

Numerous proteins initiate their folding, localization, and modifications early during translation, and emerging data show that the ribosome actively participates in diverse protein biogenesis pathways. Here we show that the ribosome imposes an additional layer of substrate selection during N-terminal methionine excision (NME), an essential protein modification in bacteria. Biochemical analyses show that cotranslational NME is exquisitely sensitive to a hydrophobic signal sequence or transmembrane domain near the N terminus of the nascent polypeptide. The ability of the nascent chain to access the active site of NME enzymes dictates NME efficiency, which is inhibited by confinement of the nascent chain on the ribosome surface and exacerbated by signal recognition particle. In vivo measurements corroborate the inhibition of NME by an N-terminal hydrophobic sequence, suggesting the retention of formylmethionine on a substantial fraction of the secretory and membrane proteome. Our work demonstrates how molecular features of a protein regulate its cotranslational modification and highlights the active participation of the ribosome in protein biogenesis pathways via interactions of the ribosome surface with the nascent protein.


Item Type:Article
Related URLs:
URLURL TypeDescription
https://doi.org/10.1016/j.jmb.2022.167535DOIArticle
ORCID:
AuthorORCID
Yang, Chien-I0000-0001-8606-5013
Shan, Shu-ou0000-0002-6526-1733
Additional Information:© 2022 Published by Elsevier. Received 28 December 2021, Revised 1 March 2022, Accepted 4 March 2022, Available online 10 March 2022, Version of Record 17 March 2022. We thank members of the Shan lab for discussions and comments on the manuscript. The E. coli strains CAG12184 and KPS73, and the plasmids pHUE and pHUsp2-cc are generous gifts from A. Varshavsky. This work was supported by NIH grant R35 GM136321 to S.S. and Think Global Education Trust Fellowship to C.I.Y. CRediT authorship contribution statement: Chien-I Yang: Conceptualization, Investigation, Formal analysis, Writing – original draft, Writing – review & editing. Jiwoo Kim: Investigation. Shu-ou Shan: Supervision, Writing – review & editing. The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.
Funders:
Funding AgencyGrant Number
NIHGM136321
Think Global Education TrustUNSPECIFIED
Subject Keywords:N-terminal protein modification; ribosome; methionine aminopeptidase; peptide deformylase; cotranslational protein biogenesis
Issue or Number:9
PubMed Central ID:PMC9126151
DOI:10.1016/j.jmb.2022.167535
Record Number:CaltechAUTHORS:20220310-121624000
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20220310-121624000
Official Citation:Chien-I Yang, Jiwoo Kim, Shu-ou Shan, Ribosome-nascent Chain Interaction Regulates N-terminal Protein Modification, Journal of Molecular Biology, Volume 434, Issue 9, 2022, 167535, ISSN 0022-2836, https://doi.org/10.1016/j.jmb.2022.167535.
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:113868
Collection:CaltechAUTHORS
Deposited By: George Porter
Deposited On:11 Mar 2022 20:56
Last Modified:28 Jun 2022 21:37

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