Schnorr, W. E. | Search bioRxiv

bioRxiv2025

Bacterial Ribonucleoprotein bodies maintain an acidic pH environment as a mechanism of enzyme regulation

Phase separated biomolecular condensates create subcellular niches, yet their role in client regulation remains unclear. Here, we demonstrate that Bacterial Ribonucleoprotein bodies (BR-bodies) are acidic. Using ratiometric fluorescent probes in vivo, we find BR-bodies exhibit a dense-phase pH of [~]5.1, significantly lower than the near-neutral cytoplasm. Single-molecule localization microscopy and fluorescence lifetime imaging reveals that Caulobacter crescentus BR-bodies have spatially variable and acidic nanoscale RNase E clusters. These results question the notion of homogeneous condensates, suggesting that BR-bodies exhibit structural and biochemical diversity, which may facilitate RNA processing under stress. In vitro, pH gradients observed with C-SNARF-4F and RNase E CTD-pHluorin2 deteriorate with increasing buffer concentrations. Notably, the acidic microenvironment within BR-bodies enhances PNPase activity, highlighting the significance of condensate pH regulation. These findings suggest that pH modulation is intrinsic to condensates, directly influencing biochemical reactions and offering a new strategy for designing pH-sensitive drugs to target enzymes within condensates.

microbiology↗

bioRxiv2025

BR-Bodies Facilitate Adaptive Responses and Survival During Copper Stress in Caulobacter crescentus

Microbes must rapidly adapt to environmental stresses, including toxic heavy metals like copper, by sensing and mitigating their harmful effects. Here, we demonstrate that the phase separation properties of bacterial ribonucleoprotein bodies (BR-bodies) enhance Caulobacter crescentus fitness under copper stress. To uncover the underlying mechanism, we identified two key interactions between copper and the central scaffold of BR-bodies, RNase E. First, biochemical assays and fluorescence microscopy experiments show that reductive chelation of Cu{superscript 2} leads to cysteine oxidation, driving the transition of BR-bodies into more solid-like condensates. Second, tryptophan fluorescence and EPR assays reveal that RNase E binds Cu{superscript 2} at histidine sites, creating a protective microenvironment that prevents mismetallation and preserves PNPase activity. More broadly, this example highlights how metal-condensate interactions can regulate condensate material properties and establish specialized chemical environments that safeguard enzyme function.

microbiology↗