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Unusual 1-3 peptidoglycan cross-links in Acetobacteraceae are made by L,D-transpeptidases with a catalytic domain distantly related to YkuD domains
Open accessPreprint — published as 10.1016/j.jbc.2023.105494
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 4 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. In this work, we investigate the formation of unusual bacterial 1-3 peptidoglycan cross-links. We describe a version of the PGFinder software which 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 Sudoku transposon library, we identified a G. oxydans mutant 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.
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Metadata
- Authors
- Alaman-Zarate, M. G., Rady, B. J., Evans, C. A., Pian, B., Greetham, D., Marecos-Ortiz, S., Dickman, M. J., Lidbury, I. D., Lovering, A. L., Barstow, B. M., & Mesnage, S.
- Affiliations
- University of Sheffield (GB)
- Cornell University (US)
- University of Birmingham (GB)
- Corresponding author
- Mesnage, Stéphane
- ORCID
- Venue
- Journal of Biological Chemistry
- Publisher
- openRxiv
- Published
- 2023-11-01
- Volume
- 300
- Issue
- 1
- Pages
- 105494-105494
- ISSN
- 0021-9258 (ISSN-L)
- PMC
- PMC10727944
- OpenAlex
- W4388943903
- Cited by
- 12
- References
- 1
- Citations by year
- 2026: 5 · 2025: 4 · 2024: 3
- FWCI
- 1.99
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- cc-by
- Locations
- Journal of Biological Chemistry (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- White Rose Research Online (University of Leeds, The University of Sheffield, University of York) (submittedVersion)
- Funders
- Burroughs Wellcome Fund
- Cornell University
- Advanced Research Projects Agency - Energy (DE-AR0001341)
- Advanced Research Projects Agency (DE-AR0001341)
- David R. Atkinson Center for a Sustainable Future , Cornell University
- Cornell Atkinson Center for Sustainability, Cornell University
- Medical Research Council (MR/S009272/1)
- Natural Environment Research Council (NE/S00713X, NE/S00713X/1)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Bacterial Genetics and Biotechnology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Biochemical and Structural Characterization
- Health Sciences › Medicine › Microbiology (medical) › Antibiotic Resistance in Bacteria
- Keywords
- L,D-transpeptidase, Gluconobacter oxydans, acetic acid bacteria, peptidoglycan structure, transposon mutant screen, complementation, cell envelope
- MeSH terms
- Amino Acids, Bacteria, Bacterial Proteins, Genetic Complementation Test, Models, Molecular, Peptidoglycan, Peptidyl Transferases, Software, Protein Structure, Tertiary, Computational Biology, Catalytic Domain, Gluconobacter oxydans
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