Mycobacterium tuberculosis Rv2179c Protein Establishes a New Exoribonuclease Family with Broad Phylogenetic Distribution

Abendroth, Jan; Ollodart, Anja R; Andrews, Emma S.V.; Myler, Peter J.; Staker, Bart L.; Edwards, Thomas E.; Arcus, Vickery L.; Grundner, Christoph

doi:10.1074/jbc.m113.525683

Cited by 16 publications

(16 citation statements)

References 26 publications

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“…Recent work has demonstrated that Rho terminated transcripts have processed 3′ ends immediately downstream of a stable stem‐loop (Dar & Sorek, ). While few RNA processing enzymes of mycobacteria have been well characterized, the Mtb genome encodes many known RNases with varying sequence specificities (Abendroth et al, ; Taverniti, Forti, Ghisotti, & Putzer, ; Uson, Ordonez, & Shuman, ; Zeller et al, ; Zhu et al, , ). We speculate that unidentified TB‐complex RNA chaperones and/or modifying enzymes contribute to Mcr11 stability, and that their absence in Msm results in Mcr11 degradation.…”

Section: Discussionmentioning

confidence: 99%

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

Girardin

McDonough

2019

Molecular Microbiology

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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.

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Section: Discussionmentioning

confidence: 99%

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

Girardin

McDonough

2019

Molecular Microbiology

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“…The processing of these discrete ends is dependent on the redundant action of the 3’ → 5’ exonucleases PNPase and RNase II, and it was speculated that the stem-loop promotes stabilization of the processed transcript (71). While few RNA processing enzymes of mycobacteria have been well characterized, the Mtb genome encodes many known RNases with varying sequence specificities (72-77). We speculate that unidentified TB-complex RNA chaperones and/or modifying enzymes contribute to Mcr11 stability, and that their absence in Msm results in Mcr11 degradation.…”

Section: Discussionmentioning

confidence: 99%

Small RNA Mcr11 regulates genes involved in the central metabolism ofMycobacterium tuberculosisand requires 3’ sequence along with the transcription factor AbmR for stable expression

2019

Preprint

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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 latent infections in mice. We found, by using biochemical and genetic approaches, that the AbmR transcription factor and an extended region of native sequence 3’ to the mcr11 gene enhance production of mature Mcr11. Additionally, we found that expression of Mcr11 was unstable in the saprophyte Mycobacterium smegmatis, which lacks an mcr11 orthologue. Bioinformatic analyses used to predict regulatory targets of Mcr11 identified 9-11 nucleotide regions immediately upstream of Rv3282 and lipB with potential for direct base-pairing with Mcr11. mcr11-dependent regulation of Rv3282, lipB, Rv2216 and pknA was demonstrated using qRT-PCR in wild type versus mcr11-deleted Mtb and found to be responsive to the presence of fatty acids. These studies establish that Mcr11 has roles in regulating growth and central metabolism in Mtb that warrant further investigation. In addition, our finding that multiple factors are required for production of stable, mature Mcr11 emphasizes the need to study mechanisms of sRNA expression and stability in TB complex mycobacteria to understand their roles in TB pathogenesis.Author SummaryBacterial pathogens must continuously modulate their gene expression in response to changing conditions to successfully infect and survive within their hosts. Transcription factors are well known regulators of gene expression, but there is growing recognition that small RNAs (sRNAs) also have critically important roles in bacterial gene regulation. Many sRNAs have been identified in M. tuberculosis (Mtb), but little is known about their expression, regulatory targets or roles in Mtb biology. In this study, we found that the Mtb sRNA Mcr11, which is expressed at high levels in slowly replicating Mtb and during mouse infection, regulates expression of several target genes involved in central metabolism. Importantly, we also discovered that mcr11 has unexpected requirements for stable expression in mycobacteria. In particular, we identified RNA sequence elements immediately downstream of mcr11 that enhance transcription termination and production of mature Mcr11 RNA in TB-complex mycobacteria. Meanwhile, ectopic expression of Mcr11 was unstable in a non-pathogenic strain of mycobacteria, suggesting that factors specific to pathogenic mycobacteria are required for the stable production of Mcr11. These studies identify sRNA stability as a new frontier for understanding gene expression in Mtb.

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“…Rather than targeting low-homology (unannotated) proteins to fill-out 'fold-space', the TBSGC has instead applied the concept of a highthroughput pipeline to determining the structures of functionally important proteins [107,108], to improve our understanding of metabolic pathways, and ultimately to facilitate the drug discovery process. [109][110][111], to assign functions to previously uncharacterized or "hypothetical" proteins [112][113][114],…”

Section: Accepted Manuscriptmentioning

confidence: 99%

Functional, structural and epitopic prediction of hypothetical proteins of Mycobacterium tuberculosis H37Rv: An in silico approach for prioritizing the targets

Gazi

Kibria

Mahfuz

et al. 2016

Gene

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Mycobacterium tuberculosis Rv2179c Protein Establishes a New Exoribonuclease Family with Broad Phylogenetic Distribution

Cited by 16 publications

References 26 publications

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

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

Small RNA Mcr11 regulates genes involved in the central metabolism ofMycobacterium tuberculosisand requires 3’ sequence along with the transcription factor AbmR for stable expression

Functional, structural and epitopic prediction of hypothetical proteins of Mycobacterium tuberculosis H37Rv: An in silico approach for prioritizing the targets

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