Rne-HupB interaction fosters mycobacterial single-cell homeostasis and fitness during drug treatment and infection

RNA turnover is a primary source of gene expression variation, in turn promoting cellular adaptation. Mycobacteria leverage reversible mRNA stabilization to endure hostile conditions. Although ribonuclease E is essential for RNA turnover in several species, its role in mycobacterial single cell physiology and functional phenotypic diversification remains unexplored. Here, by integrating live-single-cell and quantitative-mass-spectrometry approaches, we show that ribonuclease E forms dynamic foci, which are associated with cellular homeostasis and single-cell fate, and we discover a versatile molecular interactome. We prove the interaction between ribonuclease E and the nucleoid-associated protein HupB, which is particularly pronounced during drug treatment and intracellularly, where we also observed marked increase of phenotypic diversity. Disruption of ribonuclease E expression affects HupB levels, impairing Mycobacterium tuberculosis growth homeostasis during treatment, intracellular replication and host spread. Our work lays the foundation for rational drug design against Mycobacterium tuberculosis diversification capacity, undermining its cellular balance and fitness landscape.