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.

• Authors: Carmina Micelli, Yunfei Dai, Nicole Raustad, Ralph R Isberg, Christopher G Dowson, Adrian J Lloyd, Edward Geisinger, Allister Crow, David I Roper
• Journal: Proceedings of the National Academy of Sciences of the United States of America (Proc Natl Acad Sci U S A) Vol. 120 Issue 8 Pg. e2215237120 (02 21 2023) ISSN: 1091-6490 [Electronic] United States
• PMID: 36787358 (Publication Type: Journal Article, Research Support, N.I.H., Extramural, Research Support, Non-U.S. Gov't)

Chemical References

• Peptidyl Transferases
• Zinc
• Anti-Bacterial Agents
• Penicillin-Binding Proteins
• beta-Lactams
• Carbapenems
• Chelating Agents
• Bacterial Proteins

Topics

• Acinetobacter baumannii (metabolism)
• Peptidyl Transferases (metabolism)
• Zinc (metabolism)
• Cell Shape
• Anti-Bacterial Agents (pharmacology, metabolism)
• Penicillin-Binding Proteins (metabolism)
• beta-Lactams (pharmacology)
• Carbapenems (pharmacology)
• Chelating Agents (pharmacology)
• Binding Sites
• Bacterial Proteins (metabolism)