RNA regulation associated with mcr11-abmR locus in M. tuberculosis

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Project summary Mycobacterium tuberculosis (Mtb) adapts to host-associated environments during infection by modulating gene expression. While transcription factors (TFs) are the most widely recognized regulators of bacterial gene expression, RNA-based factors that modulate gene expression in Mtb are less well understood. The long term goal of this project is to define fundamental mechanisms of gene regulation in Mtb, with a particular focus on the role of RNAs. The objective of this project is to define riboregulatory mechanisms associated with two products of the abmR-mcr11 gene locus in Mtb: the prototypical sRNA Mcr11 and the dual function RNA binding TF AbmR, which is required for stable mcr11 expression. We will test the hypothesis that multiple distinct regions of Mcr11 regulate gene expression by base pairing with target mRNA sequences, and characterize the impact of Mcr11 regulation in Mtb. Stable expression of Mcr11 requires AbmR, which binds ATP and contributes to central metabolism in Mtb by repressing expression of the menaquinone biosynthesis gene menE. We propose that RNA- mediated oligomerization of AbmR reduces its TF activity by converting it to a 39S complex with an alternate function. High resolution structural information regarding the nature of the RNA- AbmR complex interaction is critically needed to identify AbmR complex functions and its possible roles in Mtb biology. The specific aims of this research include: Aim 1: Define regulatory interactions of Mcr11 at the biological, molecular and genetic levels; and Aim 2: Characterize the roles of RNA-AbmR interactions at the structural and biochemical levels. These studies will combine high resolution cryo-electron microscopy with strategic mutagenesis, biochemical and biological approaches to define AbmR-RNA interactions while providing fundamental new insights into RNA-mediated regulatory mechanisms in Mtb.