Bacterial ribonucleoprotein bodies create an internal acidic microenvironment with a pH of roughly 5.1, according to research published in Nature Communications. Researchers discovered that the low isoelectric point and negative charge of the scaffold protein drive this dense-phase acidification.
Using single-molecule localization microscopy and fluorescence lifetime imaging, the team examined Caulobacter crescentus BR-bodies. The imaging revealed spatially variable, acidic nanoscale clusters of the enzyme RNase E inside the condensates. In vivo measurements relied on ratiometric fluorescent probes to monitor internal conditions.
Experiments showed that altering the electrical charge of the scaffold shifts the internal chemical state. When researchers reduced the negative charge of RNase E, the BR-bodies became more neutral. This change triggered cellular morphological defects and viability loss during outgrowth from stationary phase, which researchers tied to altered pH and reduced condensation.
In vitro tests utilizing C-SNARF-4F and RNase E CTD-pHluorin2 reproduced the observed acidic gradient. The acidic microenvironment enhanced the activity of polynucleotide phosphorylase, known as PNPase, which operates at an optimal pH between 5.3 and 6.3.
Stationary-phase BR-bodies maintained an average pH of 4.8 ± 0.2, falling just below the optimal range for PNPase. This reading aligns with arrested RNA decay observed in laboratory assays and past findings on stationary-phase RNA storage.
The study was conducted by researchers from the University of Pittsburgh, New York University, and Indiana University, with Wade E. Schnorr, Moeka Sasazawa, and Kathryn G. Dzurik among the co-authors. The National Institutes of Health funded the work under grants R01GM136863, R35GM124733, and 1R35GM157103 alongside United States Department of Education GAANN award P200A240158.
