LD‐transpeptidases: the great unknown among the peptidoglycan cross‐linkers

Abstract

The peptidoglycan (PG) cell wall is an essential polymer for the shape and viability of bacteria. Its protective role is in great part provided by its mesh-like character. Therefore, PG-cross-linking enzymes like the penicillin-binding proteins (PBPs) are among the best targets for antibiotics. However, while PBPs have been in the spotlight for more than 50 years, another class of PG-cross-linking enzymes called LDtranspeptidases (LDTs) seemed to contribute less to PG synthesis and, thus, has kept an aura of mystery. In the last years, a number of studies have associated LDTs with cell wall adaptation to stress including blactam antibiotics, outer membrane stability, and toxin delivery, which has shed light onto the biological meaning of these proteins. Furthermore, as some species display a great abundance of LD-cross-links in their cell wall, it has been hypothesized that LDTs could also be the main synthetic PGtranspeptidases in some bacteria. In this review, we introduce these enzymes and their role in PG biosynthesis and we highlight the most recent advances in understanding their biological role in diverse species.

Unipolar Peptidoglycan Synthesis in the Rhizobiales Requires an Essential Class A Penicillin-Binding Protein

“…Traditional fluorescent d- amino acid (FDAA) probes are an exceptionally useful tool for investigating the patterning of cell wall synthesis in diverse microbes ( 33 ). However, FDAAs report on the activity of extracellular/periplasmic dd and ld transpeptidases and as a result can be incorporated into the PG in a growth-independent mechanism ( 6 , 20 ). Here, we have developed fluorescent d- amino acid dipeptide (FDAAD) probes to observe nascent sites of PG cross-linking in living cells, thus eliminating the need for click chemistry that is required when using traditional d- amino acid dipeptide (DAAD) probes ( 6 , 34 ).…”

“…Expanding our knowledge of the incorporation mechanisms of FDAA and FDAAD probes is critical for proper data interpretation of such labeling experiments and to unveil the molecular mechanisms of PG biosynthesis utilized by diverse bacteria. Several lines of evidence suggest that FDAAs are primarily incorporated into the cell wall extracellularly through remodeling by LDTs ( 20 , 39 , 42 , 60 , 61 ). In contrast, DAAD probes are incorporated into peptidoglycan precursors in vitro ( 6 , 35 ).…”

“…In addition, the genomes of Rhizobiales encode a large number of ld -transpeptidase (LDT) enzymes compared to most laterally growing species. LDTs are a class of cell wall synthesizing enzymes, which carry out transpeptidation reactions that result in a covalent cross-link between the mDAP at the third position of the donor strand and the mDAP at the third position of the acceptor strand, resulting in a 3-3 ( ld) cross-link ( 20 ). The cell wall of A. tumefaciens contains a high proportion (30%) of 3-3 cross-links ( 1 ), in contrast to laterally growing rod-shaped bacteria, where only 1 to 5% of the cell wall is cross-linked by LDTs ( 21 ).…”

A new class of cell wall-recycling L,D-carboxypeptidase determines β-lactam susceptibility and morphogenesis in Acinetobacter baumannii

“…Prominent among this group are two YkuD-domain proteins, which we have named ElsL (ACX60_RS03475) and Ldt Ab (ACX60_RS05685) (5) (referred to as LdtK and LdtJ in (8)). YkuD domains are found in secreted enzymes that modify the cell wall for a variety of purposes in other organisms (9). For example, many YkuD-domain proteins carry out L,D-transpeptidase (LDT) reactions that generate 3-3 cell wall cross-links.…”

“…For example, many YkuD-domain proteins carry out L,D-transpeptidase (LDT) reactions that generate 3-3 cell wall cross-links. These bonds are usually less abundant than the 4-3 cross-links catalyzed by DD-transpeptidases (PBPs) but may reinforce the wall against envelope stress (9). Unlike PBPs, LDTs are generally insensitive to β-lactam antibiotics (with the exception of carbapenems) and thus are potential sites of drug resistance (10, 11).…”