Small RNA Mcr11 requires the transcription factor AbmR for stable expression and regulates genes involved in the central metabolism of Mycobacterium tuberculosis

• Published in: Molecular microbiology 2020-02, Vol.113 (2), p.504-520
• Main Authors: Girardin, Roxie C., McDonough, Kathleen A.
• Format: Article
• Language: English
• Subjects: Animals; Bacteria; Bacterial Proteins - metabolism; Computational Biology; Etiology; Fatty acids; Gene expression; Gene Expression Regulation, Bacterial - physiology; Gene regulation; Genes; Genes, Bacterial; Infections; lipoylation; Lipoylation - genetics; Metabolism; Mice; Mutation; Mycobacterium tuberculosis; Mycobacterium tuberculosis - genetics; Mycobacterium tuberculosis - metabolism; Nucleotides; Real-Time Polymerase Chain Reaction; Ribonucleic acid; RNA; RNA stability; RNA termination; RNA, Bacterial - genetics; RNA, Bacterial - metabolism; RNA, Small Untranslated - genetics; RNA, Small Untranslated - metabolism; sRNA targets; Target recognition; Transcription factors; Transcription Factors - metabolism; Tuberculosis
• ISSN: 0950-382X; 1365-2958
• DOI: 10.1111/mmi.14436

Mycobacterium tuberculosis (Mtb), the etiologic agent of tuberculosis, must adapt to host‐associated environments during infection by modulating gene expression. Small regulatory RNAs (sRNAs) are key regulators of bacterial gene expression, but their roles in Mtb are not well understood. Here, we address the expression and function of the Mtb sRNA Mcr11, which is associated with slow bacterial growth and chronic infections in mice. We found that stable expression of Mcr11 requires multiple factors specific to TB‐complex bacteria, including the AbmR transcription factor. Bioinformatic analyses used to predict regulatory targets of Mcr11 identified 7–11 nucleotide regions with potential for direct base‐pairing with Mcr11 immediately upstream of Rv3282, fadA3, and lipB. mcr11‐dependent regulation of these genes was demonstrated using qRT‐PCR and found to be responsive to the presence of fatty acids. Mutation of the putative Mcr11 base‐pairing site upstream of lipB in a promoter reporter strain resulted in significant de‐repression of lipB expression, similar to that observed in mcr11‐deleted Mtb. These studies establish Mcr11’s roles in regulating growth and central metabolism in Mtb. Our finding that multiple TB‐complex‐specific factors are required for production of stable Mcr11 also emphasizes the need to better understand mechanisms of sRNA expression and stability in TB. This study shows that the small non‐coding RNA Mcr11, which is highly expressed in slowly replicating Mtb and during mouse infection, directly regulates expression of target genes involved in central metabolism. Our unexpected finding that factors specific to TB complex mycobacteria are required for the stable production of Mcr11 further identifies sRNA stability as a new frontier for understanding gene expression in Mtb.