Involvement of penicillin-binding proteins in the metabolism of a bacterial peptidoglycan containing a non-canonical d-amino acid

Bacteria produce various d-amino acids, including non-canonical d-amino acids, to adapt to environmental changes and overcome a variety of threats. These d-amino acids are largely utilized as components of peptidoglycan, and they promote peptidoglycan remodeling and biofilm disassembly. The biosynthesis, maturation, and recycling of peptidoglycan are catalyzed by penicillin-binding proteins (PBPs). However, although non-canonical d-amino acids are known to be incorporated into peptidoglycan, the maturation and recycling of peptidoglycan containing such residues remain uncharacterized. Therefore, we investigated whether PBP4 and PBP5, low molecular mass (LMM) PBPs from Escherichia coli and Bacillus subtilis, are involved in these events of peptidoglycan metabolism. Enzyme assays using p-nitroaniline (pNA)-derivatized d-amino acids and peptidoglycan-mimicking peptides revealed that PBP4 and PBP5 from both species have peptidase activity toward substrates containing d-Asn, d-His, or d-Trp. These d-amino acids slowed the growth of dacA- or dacB-deficient E. coli ( increment dacA or increment dacB) relative to the wild-type strain. Additionally, these d-amino acids affected biofilm formation by the increment dacB strain. Collectively, PBP4 and PBP5 are involved in the cleavage of peptidoglycan containing non-canonical d-amino acids, and these properties affect growth and biofilm formation.