Filamentation-driven peripheral clustering of the inducible lysine decarboxylase is crucial for E. coli acid stress response

Abstract

Bacteria have evolved numerous sophisticated acid stress response strategies to withstand fluctuating environmental pH, with enterobacterial inducible amino acid decarboxylases playing a major role. The lysine decarboxylase LdcI catalyses lysine-to-cadaverine conversion coupled to proton consumption and carbon dioxide release, thereby buffering cytoplasmic and extracellular pH. Our previous study showed that Escherichia coli LdcI forms intracellular patches under mild acid stress, and that at the corresponding acidic pH, purified LdcI polymerises into filaments, suggesting a potential role for polymerisation in its function. Here, we investigate the physiological relevance of LdcI filamentation in E. coli using 3D super-resolution fluorescence microscopy and a structure-based LdcI polymerisation-deficient E. coli mutant strain. We establish a semi-automated workflow for detection of clusters within a bacterial cell as well as quantitative analysis of their volume and localisation. We demonstrate that LdcI predominantly clusters at the cell periphery. We then show that disrupting LdcI polymerisation markedly reduces cluster size without significantly affecting localisation, suggesting that acid-stress induced LdcI clustering in vivo is driven by the enzymes filamentation. Growth and pH measurements reveal that the mutant strain exhibits reduced fitness and impaired extracellular buffering compared to the wild type, indicating that LdcI polymerisation enhances E. coli acid stress response. Our findings provide strong evidence that LdcI filamentation is a key regulatory feature of the E. coli capacity to counteract acid stress, optimising enzymatic activity by spatially organising LdcI within the cytoplasm. More broadly, this work adds to a growing body of evidence supporting the functional significance of metabolic enzyme self-assembly and its implications for bacterial stress adaptation. Author summaryAmino acid decarboxylases confer enterobacteria the ability to survive under acidic conditions. Kirchner et al. show that polymerisation of the acid-stress inducible lysine decarboxylase LdcI within E. coli cells leads to its peripheral intracellular clustering and fine-tunes its enzymatic activity in vivo.