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Published August 19, 2022 | Supplemental Material + Published
Journal Article Open

System-wide analyses reveal essential roles of N-terminal protein modification in bacterial membrane integrity


The removal of the N-terminal formyl group on nascent proteins by peptide deformylase (PDF) is the most prevalent protein modification in bacteria. PDF is a critical target of antibiotic development; however, its role in bacterial physiology remains a long-standing question. This work used the time-resolved analyses of the Escherichia coli translatome and proteome to investigate the consequences of PDF inhibition. Loss of PDF activity rapidly induces cellular stress responses, especially those associated with protein misfolding and membrane defects, followed by a global down-regulation of metabolic pathways. Rapid membrane hyperpolarization and impaired membrane integrity were observed shortly after PDF inhibition, suggesting that the plasma membrane disruption is the most immediate and primary consequence of formyl group retention on nascent proteins. This work resolves the physiological function of a ubiquitous protein modification and uncovers its crucial role in maintaining the structure and function of the bacterial membrane.

Additional Information

© 2022 The Authors. Under a Creative Commons license - Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0). Received 7 April 2022, Revised 20 June 2022, Accepted 7 July 2022, Available online 15 July 2022, Version of Record 31 July 2022. We thank D. Newman for critical discussions and members of the Shan lab for comments on the manuscript. The E. coli strains CAG12184 and KPS73 (Δfmt) are generous gifts from A. Varshavsky. We thank L. Shan, F. Wang, and C. Sanfiorenzo for the assistance in MS sample preparation, data analysis, and microscopy. Sequencing was performed at the Millard and Muriel Jacobs Genetics and Genomics Laboratory at California Institute of Technology. This work was supported by NIH grant R35 GM136321 to S.S. and Think Global Education Trust Fellowship to C.-I.Y. Author contributions. Conceptualization: C.-I.Y. and S.S.; Investigation: C.-I.Y., Z.Z., and B.L.; Formal analysis: C.-I.Y, Z.Z., and J.J.; Software: Z.Z. and J.J.; Writing – original draft: C.-I.Y; Writing – review & editing: C. -I.Y, Z.Z., J.J., B.L., T.-F.C, and S.S.; Supervision: T.-F.C, and S.S. Data and code availability: The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE (Perez-Riverol et al., 2022) partner, and the ribosome profiling data is available at GEO. The data are publicly available as of the date of publication. Accession numbers are listed in the key resources table. All original code has been deposited to the ProteomeXchange Consortium and is publicly available as of the date of publication. The accession number is listed in the key resources table. Any additional information required to reanalyze the data reported in this paper is available from the lead contact upon request. The authors declare no competing interests.

Attached Files

Published - 1-s2.0-S2589004222010288-main.pdf

Supplemental Material - 1-s2.0-S2589004222010288-mmc1.pdf

Supplemental Material - 1-s2.0-S2589004222010288-mmc2.xlsx

Supplemental Material - 1-s2.0-S2589004222010288-mmc3.xlsx

Supplemental Material - 1-s2.0-S2589004222010288-mmc4.xlsx

Supplemental Material - 1-s2.0-S2589004222010288-mmc5.xlsx


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August 22, 2023
December 22, 2023