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Published November 12, 2019 | Supplemental Material + Published
Journal Article Open

Timing and specificity of cotranslational nascent protein modification in bacteria


The nascent polypeptide exit site of the ribosome is a crowded environment where multiple ribosome-associated protein biogenesis factors (RPBs) compete for the nascent polypeptide to influence their localization, folding, or quality control. Here we address how N-terminal methionine excision (NME), a ubiquitous process crucial for the maturation of over 50% of the bacterial proteome, occurs in a timely and selective manner in this crowded environment. In bacteria, NME is mediated by 2 essential enzymes, peptide deformylase (PDF) and methionine aminopeptidase (MAP). We show that the reaction of MAP on ribosome-bound nascent chains approaches diffusion-limited rates, allowing immediate methionine excision of optimal substrates after deformylation. Specificity is achieved by kinetic competition of NME with translation elongation and by regulation from other RPBs, which selectively narrow the processing time window for suboptimal substrates. A mathematical model derived from the data accurately predicts cotranslational NME efficiency in the cytosol. Our results demonstrate how a fundamental enzymatic activity is reshaped by its associated macromolecular environment to optimize both efficiency and selectivity, and provides a platform to study other cotranslational protein biogenesis pathways.

Additional Information

© 2019. Published under the PNAS license. Edited by Gisela Storz, National Institute of Child Health and Human Development, Bethesda, MD, and approved October 6, 2019 (received for review July 16, 2019) We thank T. F. Miller, M. H. Zimmer, and Y. L. Ni for critical advice on the simulation and T. F. Miller, A. Varshavsky, and members of the S.-o.S. laboratory for discussions and comments on the manuscript. This work was supported by National Institutes of Health Grant GM078024 and a grant from the Weston Havens Foundation (to S.-o.S.) and a Think Global Education Trust Fellowship from Taiwan (to C.-I.Y.). Data Availability. Materials are available on request. Author contributions: C.-I.Y. and S.-o.S. designed research; C.-I.Y. performed research; H.-H.H. contributed new reagents/analytic tools; C.-I.Y. and S.-o.S. analyzed data; and C.-I.Y. and S.-o.S. wrote the paper. The authors declare no competing interest. This article is a PNAS Direct Submission. Data deposition: All data discussed in the paper will be made available to readers. This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10.1073/pnas.1912264116/-/DCSupplemental.

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Published - 23050.full.pdf

Supplemental Material - pnas.1912264116.sapp.pdf


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