Alamán-Zárate, M.G. orcid.org/0009-0007-0587-534X, Rady, B.J. orcid.org/0000-0003-4763-4070, Evans, C.A. orcid.org/0000-0003-4356-9216 et al. (8 more authors) (2024) Unusual 1-3 peptidoglycan cross-links in Acetobacteraceae are made by L,D-transpeptidases with a catalytic domain distantly related to YkuD domains. Journal of Biological Chemistry, 300 (1). 105494. ISSN 0021-9258
Abstract
Peptidoglycan is an essential component of the bacterial cell envelope that contains glycan chains substituted by short peptide stems. Peptide stems are polymerized by D,D-transpeptidases, which make bonds between the amino acid in position four of a donor stem and the third residue of an acceptor stem (4-3 cross-links). Some bacterial peptidoglycans also contain 3-3 cross-links that are formed by another class of enzymes called L,D-transpeptidases which contain a YkuD catalytic domain. In this work, we investigate the formation of unusual bacterial 1-3 peptidoglycan cross-links. We describe a version of the PGFinder software that can identify 1-3 cross-links and report the high-resolution peptidoglycan structure of Gluconobacter oxydans (a model organism within the Acetobacteraceae family). We reveal that G. oxydans peptidoglycan contains peptide stems made of a single alanine as well as several dipeptide stems with unusual amino acids at their C-terminus. Using a bioinformatics approach, we identified a G. oxydans mutant from a transposon library with a drastic reduction in 1-3 cross-links. Through complementation experiments in G. oxydans and recombinant protein production in a heterologous host, we identify an L,D-transpeptidase enzyme with a domain distantly related to the YkuD domain responsible for these non-canonical reactions. This work revisits the enzymatic capabilities of L,D-transpeptidases, a versatile family of enzymes that play a key role in bacterial peptidoglycan remodelling.
Metadata
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Copyright, Publisher and Additional Information: | © 2023 The Authors. Published by Elsevier Inc on behalf of American Society for Biochemistry and Molecular Biology. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/). | ||||
Keywords: | Gluconobacter oxydans; L,D-transpeptidase; PGFinder; bacterial cell envelope; crosslink; peptidoglycan; Peptidyl Transferases; Peptidoglycan; Catalytic Domain; Bacteria; Amino Acids; Bacterial Proteins | ||||
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Institution: | The University of Sheffield | ||||
Academic Units: | The University of Sheffield > Faculty of Science (Sheffield) > School of Biosciences (Sheffield) The University of Sheffield > Faculty of Engineering (Sheffield) > Department of Chemical and Biological Engineering (Sheffield) |
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Depositing User: | Symplectic Sheffield | ||||
Date Deposited: | 14 Feb 2024 11:08 | ||||
Last Modified: | 14 Feb 2024 11:08 | ||||
Status: | Published | ||||
Publisher: | Elsevier BV | ||||
Refereed: | Yes | ||||
Identification Number: | https://doi.org/10.1016/j.jbc.2023.105494 | ||||
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