Unusual 1-3 peptidoglycan cross-links inAcetobacteraceaeare made by L,D-transpeptidases with a catalytic domain distantly related to YkuD domains

Abstract

AbstractPeptidoglycan 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 ofGluconobacter oxydans(a model organism within theAcetobacteraceaefamily). We reveal thatG. oxydanspeptidoglycan 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 aG. oxydansmutant with a drastic reduction in 1-3 cross-links. Through complementation experiments inG. oxydansand 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.