Dynamic Polyphosphate Metabolism Coordinating with Manganese Ions Defends against Oxidative Stress in the Extreme Bacterium Deinococcus radiodurans

Abstract

Deinococcus radiodurans is an extreme bacterium with unparalleled resistance to oxidative stresses. Accumulation of intracellular Mn²⁺ complexing with small metabolites is the key contributor to the tolerance of D. radiodurans against oxidative stress. However, the intracellular reservoir of Mn ions and homeostatic regulation of the Mn-complex in D. radiodurans remain unclear. We identified an evolutionarily ancient and negatively charged phosphate polymer (polyphosphate, PolyP) in D. radiodurans. We investigated the PolyP metabolism in the response of D. radiodurans to oxidative stress. The genes dr1939, encoding polyphosphatase kinase (PPK_Dr), and dra0185, encoding exopolyphosphatase (PPX_Dr), were identified. PPX_Dr is a novel exopolyphosphatase with a cofactor preference to Mn²⁺, which enhances the dimerization and activity of PPX_Dr to allow the effective cleavage of PolyP-Mn. PPK_Dr and PPX_Dr exhibited different dynamic expression profiles under oxidative stress. First, the ppk_Dr was upregulated leading to the accumulation of PolyP, which chelated large amounts of intracellular Mn ions. Subsequently, the expression level of ppk_Dr decreased while the ppx_Dr was substantially upregulated and effectively hydrolyzed inactive PolyP-Mn to release phosphate (Pi) and Mn²⁺, which could form into Mn-Pi complexes to scavenge O₂^- and protect proteins from oxidative damage. Hence, dynamic cellular PolyP metabolites complexed with free Mn ions highlight a defense strategy of D. radiodurans in response to oxidative stress. Importance Mn-phosphate complex (Mn-Pi) plays a key role in the cellular resistance of radioresistant bacteria. The evolutionarily ancient polyphosphate polymers (PolyP) could effectively chelate Mn²⁺ and donate phosphates. However, the intracellular reservoir of Mn ions and homeostatic regulation of the Mn-Pi complex remain unclear. Here, we investigated the relationship of PolyP metabolites and Mn²⁺ homeostasis, and how they function to defend against oxidative stress in the radioresistant bacterium Deinococcus radiodurans. We found that PPX_Dr is a novel exopolyphosphatase with a cofactor preference for Mn²⁺, mediating PolyP-Mn degradation into Pi and Mn ions. The formed Mn-Pi complexes effectively protect proteins. The dynamic PolyP metabolism coordinating with Mn ions is a defense strategy of D. radiodurans in response to oxidative stress. The findings not only provide new insights into the resistance mechanism of the extreme bacterium D. radiodurans but also broaden our understanding of the functions of PolyP metabolism in organisms.