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

Abstract

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.

sncRNA-1 Is a Small Noncoding RNA Produced by Mycobacterium tuberculosis in Infected Cells That Positively Regulates Genes Coupled to Oleic Acid Biosynthesis

“…Small RNAs often regulate the expression of target transcripts by Watson–Crick base pairing through a 6–7 nts seed sequence ( Gerrick et al, 2018 ; Girardin and McDonough, 2019 ; Mai et al, 2019 ). For this reason, a homology search was done comparing the sncRNA-1 nucleotide sequences in different mycobacterial species.…”

“…One stress responsive sRNA, called MrsI (ncRV11846), reduces the expression of non-essential iron-containing proteins by using a seed sequence to bind the 5′ untranslated region (UTR) of the mRNA target ( Gerrick et al, 2018 ). A distinct sRNA, called Mcr11 (ncRv11264c), is required for Mtb growth in fatty acid depleted media, as it regulates targets involved in lipid production ( Girardin and McDonough, 2020 ). This regulation was proposed mediated by a base-pairing between the sRNA and multiple transcripts.…”

Small Noncoding RNAs MTS0997 and MTS1338 Affect the Adaptation and Virulence of Mycobacterium tuberculosis

“…Recent studies indicate an active role of mycobacterial small non-coding RNA in this process [25][26][27][28]. To study the effect of small mycobacterial RNAs MTS0997 and MTS1338 on the ability of M. tuberculosis to interact with the host, we created mutants of the H37Rv strain with deleted genes of these small RNAs.…”

“…Small RNAs MTS1338 and MTS0997 activate mycobacterial genes involved in the bacterial persistence within a macrophage [25,27], meaning that an increase in the concentration of these small RNAs contributes to the survival of the bacteria. These observations are consistent with our studies, where AMs more prominently inhibit the growth of mutant H37Rv-MTS1338KO and also H37Rv-MTS0997KO mycobacteria as compared with wild-type H37Rv strain.…”

Small RNAs Asserting Big Roles in Mycobacteria

“…MTS0997 (131 nts), later named Mcr11, regulates Mtb fatty acid metabolism (Figure 2D, Table 1) 37 . It positively regulates Rv3282, fadA3, and lipB translation by binding a 7-11 nucleotide region upstream of the start codon.…”