PE11 promotes intracellular persistence of Mycobacterium tuberculosis by inhibiting autophagy and lysosomal biogenesis by targeting the FLCN-lactate-TFEB signaling axis

Abstract

Mycobacterium tuberculosis (Mtb) employs multiple virulence factors, including cell wall-associated proteins, to evade host immune responses. PE11, a cell wall-localized esterase, contributes to Mtb persistence by facilitating cell wall remodelling and resistance to acidic and antibiotic stress. Herein we describe a novel role of PE11 in subverting host autophagy through disruption of TFEB-mediated lysosomal function. PE11 promotes FLCN-dependent depletion of intracellular lactate to destabilize TFEB and thereby downregulate genes essential for autophagic flux and lysosomal acidification. Using a PE11-deficient Mtb strain, we demonstrate that PE11 targets the FLCN-lactate axis to regulate TFEB stability. Exogenous lactate supplementation restored TFEB stability, enhanced lysosomal acidification, and significantly reduced intracellular bacterial burden. Lactate also synergized with frontline anti-tubercular drugs to improve Mtb clearance. These findings establish PE11 as a key immune evasion factor and highlight lactate as a promising host-directed therapeutic to enhance bacterial killing and reduce antibiotic-associated toxicity.