Mycobacterium tuberculosis partitions the Krebs cycle to persist under iron starvation

Abstract In this study, we investigated how iron limitation alters central metabolism in Mycobacterium tuberculosis using metabolomics and stable isotope tracing. Our findings reveal a well-orchestrated metabolic program to enable Krebs cycle activity despite the inefficient action of its iron-dependent enzymes. Under such conditions, carbon flux through the oxidative branch of the Krebs cycle is stalled, resulting in the accumulation of metabolites that are partially secreted. As a result, carbon flux from glycolysis is partially diverted to the reductive branch of the Krebs cycle to support the production of oxaloacetate and malate through the activity of phosphoenolpyruvate carboxykinase and pyruvate carboxylase. Both branches terminate with the synthesis of malate, which is secreted. This unprecedented split of the Krebs cycle and malate secretion in a bacterial pathogen facilitates the continuous flow of carbon through the core of carbon metabolism, overcoming the metabolic stalling triggered by iron starvation. Competing Interest Statement The authors have declared no competing interest. Footnotes This revised version of the manuscript has been improved through the incorporation of new experiments and additional metabolomic analyses, which have strengthened the overall conclusions and enabled us to propose a more mechanistic hypothesis on how Mycobacterium tuberculosis persists under iron-limiting conditions. Furthermore, the Discussion has been expanded to include a series of considerations on how the observed metabolic remodelling may contribute to the pathogenesis of Mycobacterium tuberculosis. Data availability Metabolomics data used on this study are available via Zenodo (DOI 10.5281/zenodo.18494375). Dataset title: Metabolomics data from Mycobacterium tuberculosis partitions the Krebs cycle under iron starvation.