Elucidating dynamic anaerobe metabolism with HRMAS 13C NMR and genome-scale modeling

Autor: Aidan Pavao, Brintha Girinathan, Johann Peltier, Pamela Altamirano Silva, Bruno Dupuy, Isabella H. Muti, Craig Malloy, Leo L. Cheng, Lynn Bry
Přispěvatelé: Harvard Medical School [Boston] (HMS), Pathogénèse des Bactéries Anaérobies / Pathogenesis of Bacterial Anaerobes (PBA (U-Pasteur_6)), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Universidad de Costa Rica (UCR), University of Texas Southwestern Medical Center [Dallas], This project was supported by the National Institutes of Health (L.B., grant nos. R01AI153653, R03AI174158 and P30DK056338, L.L.C., grant nos. S10OD023406, R21CA243255 and R01AG070257), the Brigham and Women’s Hospital Precision Medicine Institute and Presidential Scholar’s Award (L.B.), the MGH A. A. Martinos Center for Biomedical Imaging (L.B. and L.L.C.) and the Massachusetts Life Sciences Center (L.B. and L.L.C.).
Jazyk: angličtina
Rok vydání: 2023
Předmět:
Zdroj: Nature Chemical Biology
Nature Chemical Biology, 2023, 19 (5), pp.556-564. ⟨10.1038/s41589-023-01275-9⟩
ISSN: 1552-4450
1552-4469
DOI: 10.1038/s41589-023-01275-9⟩
Popis: Anaerobic microbial metabolism drives critical functions within global ecosystems, host–microbiota interactions, and industrial applications, yet remains ill-defined. Here we advance a versatile approach to elaborate cellular metabolism in obligate anaerobes using the pathogen Clostridioides difficile, an amino acid and carbohydrate-fermenting Clostridia. High-resolution magic angle spinning nuclear magnetic resonance (NMR) spectroscopy of C. difficile, grown with fermentable 13C substrates, informed dynamic flux balance analysis (dFBA) of the pathogen’s genome-scale metabolism. Analyses identified dynamic recruitment of oxidative and supporting reductive pathways, with integration of high-flux amino acid and glycolytic metabolism at alanine’s biosynthesis to support efficient energy generation, nitrogen handling and biomass generation. Model predictions informed an approach leveraging the sensitivity of 13C NMR spectroscopy to simultaneously track cellular carbon and nitrogen flow from [U-13C]glucose and [15N]leucine, confirming the formation of [13C,15N]alanine. Findings identify metabolic strategies used by C. difficile to support its rapid colonization and expansion in gut ecosystems.
Databáze: OpenAIRE
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