A conserved zinc-binding site in Acinetobacter baumannii PBP2 required for elongasome-directed bacterial cell shape

Abstract

Acinetobacter baumannii is a gram-negative bacterial pathogen that causes challenging nosocomial infections. β-lactam targeting of penicillin-binding protein (PBP)–mediated cell wall peptidoglycan (PG) formation is a well-established antimicrobial strategy. Exposure to carbapenems or zinc (Zn)-deprived growth conditions leads to a rod-to-sphere morphological transition in A. baumannii , an effect resembling that caused by deficiency in the RodA–PBP2 PG synthesis complex required for cell wall elongation. While it is recognized that carbapenems preferentially acylate PBP2 in A. baumannii and therefore block the transpeptidase function of the RodA–PBP2 system, the molecular details underpinning cell wall elongation inhibition upon Zn starvation remain undefined. Here, we report the X-ray crystal structure of A. baumannii PBP2, revealing an unexpected Zn coordination site in the transpeptidase domain required for protein stability. Mutations in the Zn-binding site of PBP2 cause a loss of bacterial rod shape and increase susceptibility to β-lactams, therefore providing a direct rationale for cell wall shape maintenance and Zn homeostasis in A. baumannii . Furthermore, the Zn-coordinating residues are conserved in various β- and γ-proteobacterial PBP2 orthologs, consistent with a widespread Zn-binding requirement for function that has been previously unknown. Due to the emergence of resistance to virtually all marketed antibiotic classes, alternative or complementary antimicrobial strategies need to be explored. These findings offer a perspective for dual inhibition of Zn-dependent PG synthases and metallo-β-lactamases by metal chelating agents, considered the most sought-after adjuvants to restore β-lactam potency against gram-negative bacteria.

Characterization of Acinetobacter baumannii core oligosaccharide synthesis reveals novel aspects of lipooligosaccharide assembly

“…Our analysis thus far suggested that strains lacking 2903 or lpsB —two mutants proposed to be involved in KdoIII residue addition to the core oligosaccharide—exhibited defects in cell division to varying extents. Cell division errors much like those observed here are often found in cells with underlying defects in peptidoglycan cell wall synthesis ( 35 – 37 ). It was unclear why this might be the case as there is no known overlap between core oligosaccharide synthesis and cell wall synthesis.…”

Rapid identification of key genes for the rod-shaped morphology in bacteria using multi-species genomes

“…In addition to validating the two genes, Pal and MreB, which influence rod-shaped bacterial morphology in this study, other genes known to affect bacterial morphology, such as RodZ and PBP [47,48], were not directly obtained. One possible reason is that the shapes obtained from online sources or through book references and extrapolation may still contain errors.…”

Drug Discovery in the Field of β-Lactams: An Academic Perspective

“…Whereas many β-lactamases are plasmid-borne and exhibit few variations among different bacteria, the peptidoglycan transpeptidases from each bacterial species may have unique features. Most recently, two groups reported the identification of highly conserved zinc-binding domains in C. difficile and A. baumannii PBP2, which in C. difficile was found to be an essential transpeptidase for cell growth [165,170]. This motif in PBP has never been observed in any other known PBP structures, but sequence analysis has suggested its prevalence in many bacteria, particularly the Firmicutes [165].…”