RNase E-HupB Dynamic Interaction Fosters Mycobacterial Cell Homeostasis and Fitness

Abstract

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. In particular, we prove the interaction between ribonuclease E and the nucleoid-associated protein HupB, which is particularly pronounced during drug treatment and infection, where we also observed marked increase of cell-to-cell 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 targeting the ribonuclease E and its molecular partner HupB, aiming to undermine Mycobacterium tuberculosis cellular balance, diversification capacity and persistence.