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PBP-A, a cyanobacterial dd-peptidase with high specificity for amidated muropeptides, exhibits pH-dependent promiscuous activity harmful to Escherichia coli

Lookup NU author(s): Matthias Winkle, Dr Jacob BiboyORCiD, Dr Joseph Gray, Professor Waldemar Vollmer

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This work is licensed under a Creative Commons Attribution 4.0 International License (CC BY 4.0).

Abstract

© The Author(s) 2024. Penicillin binding proteins (PBPs) are involved in biosynthesis, remodeling and recycling of peptidoglycan (PG) in bacteria. PBP-A from Thermosynechococcus elongatus belongs to a cyanobacterial family of enzymes sharing close structural and phylogenetic proximity to class A β-lactamases. With the long-term aim of converting PBP-A into a β-lactamase by directed evolution, we simulated what may happen when an organism like Escherichia coli acquires such a new PBP and observed growth defect associated with the enzyme activity. To further explore the molecular origins of this harmful effect, we decided to characterize deeper the activity of PBP-A both in vitro and in vivo. We found that PBP-A is an enzyme endowed with dd-carboxypeptidase and dd-endopeptidase activities, featuring high specificity towards muropeptides amidated on the d-iso-glutamyl residue. We also show that a low promiscuous activity on non-amidated peptidoglycan deteriorates E. coli’s envelope, which is much higher under acidic conditions where substrate discrimination is mitigated. Besides expanding our knowledge of the biochemical activity of PBP-A, this work also highlights that promiscuity may depend on environmental conditions and how it may hinder rather than promote enzyme evolution in nature or in the laboratory.

Publication metadata

Author(s): Dorrazehi GM, Winkle M, Desmet M, Stroobant V, Tanriver G, Degand H, Evrard D, Desguin B, Morsomme P, Biboy J, Gray J, Mitusinska K, Gora A, Vollmer W, Soumillion P

Publication type: Article

Publication status: Published

Journal: Scientific Reports

Year: 2024

Volume: 14

Online publication date: 18/06/2024

Acceptance date: 13/06/2024

Date deposited: 24/06/2024

ISSN (electronic): 2045-2322

Publisher: Springer Nature

URL: https://doi.org/10.1038/s41598-024-64806-x

DOI: 10.1038/s41598-024-64806-x

Data Access Statement: Data is provided within the manuscript or supplementary information files.

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