DXP Synthase Function in a Bacterial Metabolic Adaptation and Implications for Antibacterial Strategies

Abstract

Pathogenic bacteria possess a remarkable ability to adapt to fluctuating host environments and cause infection. Disturbing bacterial central metabolism through inhibition of 1-deoxy-d-xylulose 5-phosphate synthase (DXPS) has the potential to hinder bacterial adaptation, representing a new antibacterial strategy. DXPS functions at a critical metabolic branchpoint to produce the metabolite DXP, a precursor to pyridoxal-5-phosphate (PLP), thiamin diphosphate (ThDP) and isoprenoids presumed essential for metabolic adaptation in nutrient-limited host environments. However, specific roles of DXPS in bacterial adaptations that rely on vitamins or isoprenoids have not been studied. Here we investigate DXPS function in an adaptation of uropathogenic E. coli (UPEC) to d-serine (d-Ser), a bacteriostatic host metabolite that is present at high concentrations in the urinary tract. UPEC adapt to d-Ser by producing a PLP-dependent deaminase, DsdA, that converts d-Ser to pyruvate, pointing to a role for DXPS-dependent PLP synthesis in this adaptation. Using a DXPS-selective probe, butyl acetylphosphonate (BAP), and leveraging the toxic effects of d-Ser, we reveal a link between DXPS activity and d-Ser catabolism. We find that UPEC are sensitized to d-Ser and produce sustained higher levels of DsdA to catabolize d-Ser in the presence of BAP. In addition, BAP activity in the presence of d-Ser is suppressed by β-alanine, the product of aspartate decarboxylase PanD targeted by d-Ser. This BAP-dependent sensitivity to d-Ser marks a metabolic vulnerability that can be exploited to design combination therapies. As a starting point, we show that combining inhibitors of DXPS and CoA biosynthesis displays synergy against UPEC grown in urine where there is increased dependence on the TCA cycle and gluconeogenesis from amino acids. Thus, this study provides the first evidence for a DXPS-dependent metabolic adaptation in a bacterial pathogen and demonstrates how this might be leveraged for development of antibacterial strategies against clinically relevant pathogens.

Disruption of an Active Site Network Leads to Activation of C2α-Lactylthiamin Diphosphate on the Antibacterial Target 1-Deoxy-d-xylulose-5-phosphate Synthase

“…The gated DXPS mechanism has important implications for developing DXPS as an antimicrobial target. The long-lived E-LThDP complex and E-LThDP-GAP ternary complex (Figure ) represent distinct DXPS states that can be selectively targeted. − ,− Furthermore, such a gated mechanism hints that DXPS senses and responds to, or is regulated by, its chemical environment, which could be important for pathogen metabolic adaptation to host environments during infection. − Elucidating the mechanism is fundamental to understand DXPS function in bacteria and fully appreciate its significance as a drug target.…”

Potent Inhibition of E. coli DXP Synthase by a gem-Diaryl Bisubstrate Analog

“…Antimicrobial resistance predates the discovery of antibiotics and is an unavoidable threat in the treatment of infectious diseases. To combat resistance, new antibacterial strategies are needed that are selective for pathogens and avoid toxicity to the host microbiome, which can negatively impact human health. − Agents that target central metabolic processes are increasingly sought − and have the potential to exert narrow-spectrum activities. ,− However, this target space is relatively underexploited owing to the complexities in developing central metabolism targets and the perceived difficulties in selectively targeting bacterial metabolism over host metabolism. ,,, Essential to bacterial central metabolism and absent in humans, 1-deoxy- d -xylulose 5-phosphate synthase (DXPS) emerged as a promising antibacterial target with the potential to offer opportunities for developing narrow spectrum approaches. ,− …”

“… 4 , 15 , 16 , 20 Essential to bacterial central metabolism and absent in humans, 1-deoxy- d -xylulose 5-phosphate synthase (DXPS) emerged as a promising antibacterial target with the potential to offer opportunities for developing narrow spectrum approaches. 5 , 21 − 31 …”

An activity-based probe for antimicrobial target DXP synthase, a thiamin diphosphate-dependent enzyme

“…1-Deoxy D-xylulose 5-phosphate synthase (DXPS) is an essential central metabolic enzyme that we hypothesize is critical for bacterial metabolic adaptation (Bartee D. and Freel Meyers CL. 2018;Sanders et al, 2017;E. C. Chen and Freel Meyers, 2023).…”

“…We have recently demonstrated such a role for DXPS in the adaptation of uropathogenic Escherichia coli (UPEC) to D-Ser, a bacteriostatic host metabolite present at high concentrations within the urinary tract (E. C. Chen and Freel Meyers, 2023). UPEC detoxify D-Ser through PLP-dependent conversion to pyruvate.…”