Assessing Corynebacterium glutamicum as a surrogate of Mycobacterium tuberculosis for DNA gyrase inhibitor design.

Abstract

DNA gyrase is an essential bacterial enzyme and a clinically validated target for the treatment of tuberculosis. However, the discovery of new inhibitors remains limited by the many challenges regarding the manipulation on pathogenic mycobacteria. This study validates Corynebacterium glutamicum (Cglu) as a safe, non-pathogenic surrogate for Mycobacterium tuberculosis (Mtb) to investigate DNA gyrase and facilitate the identification of new inhibitors. Using Cglu as a target allows for fast whole-cell screening under safe conditions while ensuring efficient drug uptake. Cglu shares key physiological features with Mtb, including genome size, complex cell wall structure, and a single type I and type II topoisomerase. Structural and functional comparisons emphasize the similarity of Cglu and Mtb gyrases, which share 70% sequence identity and show comparable catalytic properties and responsiveness to known inhibitors. Thus, the cryo-EM structure of the Cglu gyrase-DNA complex at 3.2 [A] resolution reveals highly conserved drug-binding pockets for known anti-gyrase inhibitors and the genetic depletion of gyrA or gyrB in Cglu causes severe growth and morphological defects, mirroring the effects of chemical inhibition and allowing to link gyrase function to cellular phenotypes. Comparative imaging of different inhibitor classes (fluoroquinolones, aminocoumarins, NBTIs) uncovers distinct morphological signatures that reflect each compounds mode of action. Finally, cross-species complementation confirms functional conservation but also highlights subtle structural differences affecting efficiency. Together, these findings establish Cglu as a robust and biosafe model for dissecting gyrase function, visualizing DNA topology dynamics, and accelerating the discovery of gyrase-targeting antimicrobials. More generally, our studies demonstrate the feasibility of using Cglu as a cell-based screening platform to discover new anti-tuberculous compounds targeting conserved mechanisms, not only for validated TB drug targets such as DNA gyrase but also for new, yet to be identified, targets.