Transcriptome-guided metabolic network analysis reveals rearrangements of carbon flux distribution in Neisseria gonorrhoeae during neutrophil co-culture

Abstract

The ability of bacterial pathogens to metabolically adapt to the environmental conditions of their hosts is critical to both colonization and invasive disease. Infection with Neisseria gonorrhoeae (the gonococcus, Gc) is characterized by the influx of neutrophils [polymorphonuclear leukocytes (PMNs)], which fail to clear the bacteria and make antimicrobial products that can exacerbate tissue damage. The inability of the human host to clear Gc infection is particularly concerning in light of the emergence of strains that are resistant to all clinically recommended antibiotics. Bacterial metabolism represents a promising target for the development of new therapeutics against Gc. Here, we generated a curated genome-scale metabolic network reconstruction (GENRE) of Gc strain FA1090. This GENRE links genetic information to metabolic phenotypes and predicts Gc biomass synthesis and energy consumption. We validated this model with published data and in new results reported here. Contextualization of this model using the transcriptional profile of Gc exposed to PMNs revealed substantial rearrangements of Gc central metabolism and induction of Gc nutrient acquisition strategies for alternate carbon source use. These features enhanced the growth of Gc in the presence of neutrophils. From these results, we conclude that the metabolic interplay between Gc and PMNs helps define infection outcomes. The use of transcriptional profiling and metabolic modeling to reveal new mechanisms by which Gc persists in the presence of PMNs uncovers unique aspects of metabolism in this fastidious bacterium, which could be targeted to block infection and thereby reduce the burden of gonorrhea in the human population. IMPORTANCE The World Health Organization designated Gc as a high-priority pathogen for research and development of new antimicrobials. Bacterial metabolism is a promising target for new antimicrobials, as metabolic enzymes are widely conserved among bacterial strains and are critical for nutrient acquisition and survival within the human host. Here we used genome-scale metabolic modeling to characterize the core metabolic pathways of this fastidious bacterium and to uncover the pathways used by Gc during culture with primary human immune cells. These analyses revealed that Gc relies on different metabolic pathways during co-culture with human neutrophils than in rich media. Conditionally essential genes emerging from these analyses were validated experimentally. These results show that metabolic adaptation in the context of innate immunity is important to Gc pathogenesis. Identifying the metabolic pathways used by Gc during infection can highlight new therapeutic targets for drug-resistant gonorrhea.

Dual species transcriptomics reveals conserved metabolic and immunologic processes in interactions between human neutrophils and Neisseria gonorrhoeae

“…Strikingly, 30% of DE genes had roles in metabolism, including central metabolism, amino acid metabolism, cofactor synthesis, and nutrient transport ( S3 Dataset ). The metabolic adaptations Gc undergoes during PMN co-culture were assessed in depth in a corresponding study [ 27 ]. The 413 genes were compared to RNA-seq datasets interrogating other infection-related factors including iron, hydrogen peroxide (H 2 O 2 ), anaerobic growth, exposure to PMNs in suspension, and natural human infection ( Fig 3 and S3 Dataset ) [ 28 – 32 ].…”

Optimal Protein Allocation Controls the Inhibition of GltA and AcnB inNeisseria gonorrhoeae

“…The study utilized the previously published Ngo genome-scale metabolic model, iNgo_557 (Potter et al . 2023).…”

“…Molecular weights (MW) for these enzymes were also calculated using amino acid sequences derived from the KEGG database. Additionally, to accurately reflect the in vivo environment, reaction bounds were adjusted according to minimal defined medium (MDM) (Potter et al . 2023), ensuring that the simulated nutrient availabilities aligned with the physiological conditions under which N. gonorrhoeae thrives.…”

“…The study utilized the previously published Ngo genome-scale metabolic model, iNgo_557 (Potter et al 2023). Initial preparations involved adding pathway information and making the model irreversible (https://github.com/ssbio/Gc_protein_constrained).…”

Development and implementation of a Type I-C CRISPR-based programmable repression system for Neisseria gonorrhoeae

“…However, essential genes cannot be deleted and are important as possible targets for antimicrobials or vaccines. Gc is predicted to possess about 800 essential genes, of which 130 have no predicted function ( 12 , 13 ). It is possible to overcome the inability to delete essential genes by inactivating the gene of interest while regulating its expression at an ectopic locus ( 14 , 15 ).…”