Structure and Function of AmtR in Mycobacterium smegmatis: Implications for Post-Transcriptional Regulation of Urea Metabolism through a Small Antisense RNA

Petridis, Michael; Vickers, Chelsea; Robson, Jennifer R.; McKenzie, Joanna Leigh; Bereza, Magdalena; Sharrock, Abigail V.; Aung, Htin; Arcus, Vickery L.; Cook, Gregory M.

doi:10.1016/j.jmb.2016.09.009

Cited by 9 publications

(7 citation statements)

References 36 publications

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“…As a control, the PPR protein was replaced by the M. smegmatis DNA‐binding protein (AmtR) that had been expressed and purified in the same manner as Pf PPR (Petridis et al, ). This showed no binding to the RNA transcripts, demonstrating that pull‐down of the Pf PPR1 is specific and is not an artefact of the experiment (Figure c).…”

Section: Resultsmentioning

confidence: 99%

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An essential pentatricopeptide repeat protein in the apicomplexan remnant chloroplast

Hicks

Lassadi

Carpenter

et al. 2019

Cellular Microbiology

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The malaria parasite Plasmodium and other apicomplexans such as Toxoplasma evolved from photosynthetic organisms and contain an essential, remnant plastid termed the apicoplast. Transcription of the apicoplast genome is polycistronic with extensive RNA processing. Yet little is known about the mechanism of apicoplast RNA processing. In plants, chloroplast RNA processing is controlled by multiple pentatricopeptide repeat (PPR) proteins. Here, we identify the single apicoplast PPR protein, PPR1. We show that the protein is essential and that it binds to RNA motifs corresponding with previously characterized processing sites. Additionally, PPR1 shields RNA transcripts from ribonuclease degradation. This is the first characterization of a PPR protein from a nonphotosynthetic plastid.

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Section: Resultsmentioning

confidence: 99%

“…Pf PPR1 was observed to bind to both transcripts (Figure a). As a control, PPR protein was replaced by a DNA‐binding protein from Mycobacterium smegmatis (AmtR), which had been expressed and isolated using the same procedure as Pf PPR1 (Petridis et al, ). No binding to AmtR was seen.…”

Section: Resultsmentioning

confidence: 99%

An essential pentatricopeptide repeat protein in the apicomplexan remnant chloroplast

Hicks

Lassadi

Carpenter

et al. 2019

Cellular Microbiology

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“…A number of AmtR crystal structures have now been deposited in the Protein Data Bank (Berman et al, 2000). These include crystal structures of AmtR from C. glutamicum in different space groups, namely PDB entries 5dy1 (termed AmtR tri in the current study; 2.65 Å resolution), 5dxz (2.25 Å resolution) and 5dy0 (3.0 Å resolution), which describes an AmtR-DNA complex (Palanca & Rubio, 2016), as well as the structure of AmtR from Mycobacterium segmatis (PDB entry 5e57; 1.98 Å resolution; Petridis et al, 2016). Interestingly, a molecular-packing assembly similar to AmtR orth is shared by AmtR tri (Palanca & Rubio, 2016).…”

Section: Resultsmentioning

confidence: 99%

Similarities in the structure of the transcriptional repressor AmtR in two different space groups suggest a model for the interaction with GlnK

et al. 2017

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AmtR belongs to the TetR family of transcription regulators and is a global nitrogen regulator that is induced under nitrogen-starvation conditions in Corynebacterium glutamicum. AmtR regulates the expression of transporters and enzymes for the assimilation of ammonium and alternative nitrogen sources, for example urea, amino acids etc. The recognition of operator DNA by homodimeric AmtR is not regulated by small-molecule effectors as in other TetR-family members but by a trimeric adenylylated P-type signal transduction protein named GlnK. The crystal structure of ligand-free AmtR (AmtR) has been solved at a resolution of 2.1 Å in space group P222. Comparison of its quaternary assembly with the previously solved native AmtR structure (PDB entry 5dy1) in a trigonal crystal system (AmtR) not only shows how a solvent-content reduction triggers a space-group switch but also suggests a model for how dimeric AmtR might stoichiometrically interact with trimeric adenylylated GlnK.

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“…However, in this study, urea was found elevated in Mtb treated with ciprofloxacin, indicating accumulation of ammonia and reduced recycling of nitrogen via glutamine and proline metabolism. This, in addition to a decreased degradation of urea by urease, also linked to the Mtb stress-response [127], retains ammonia from protein synthesis [128]. Inhibited protein formation has also been suggested in a proteomics study of Mtb treated with ciprofloxacin [129], as well as a metabolomics study of M. smegmatis treated with ciprofloxacin [48].…”

Section: Discussionmentioning

confidence: 99%

Elucidating the antimycobacterial mechanism of action of ciprofloxacin using metabolomics

Knoll¹,

Lindeque²,

Adetomiwa³

et al. 2021

Preprint

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In the interest of developing more effective and safer anti-Tuberculosis treatment, we aimed for a better understanding of the antimycobacterial action of ciprofloxacin against Mycobacterium tuberculosis (Mtb). We used GCxGC-TOF-MS and well described metabolomics statistical approaches, to investigate and compare the metabolic profiles of Mtb in the presence and absence of the drug. The metabolites that best describe the differences between the compared groups were identified as markers characterizing the changes induced by ciprofloxacin. Malic acid was ranked as the most significantly altered metabolite marker induced by ciprofloxacin, indicative of an inhibition of the tricarboxylic acid (TCA) and glyoxylate cycle of Mtb. The altered fatty acid, myo-inositol and triacylglycerol metabolism seen in this group, supports the previous observations of ciprofloxacin action on the Mtb cell wall. Furthermore, the altered pentose phosphate intermediates, glycerol metabolism markers, glucose accumulation, and the reduction in the glucogenic amino acids specifically, indicates a flux towards DNA (as well as cell wall) repair, also supporting previous findings of DNA damage caused by ciprofloxacin. This study further provides insights useful for designing network whole-system strategies for the identification of possible modes of actions of various drugs and possibly adaptations by Mtb resulting in resistance.

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Structure and Function of AmtR in Mycobacterium smegmatis: Implications for Post-Transcriptional Regulation of Urea Metabolism through a Small Antisense RNA

Cited by 9 publications

References 36 publications

An essential pentatricopeptide repeat protein in the apicomplexan remnant chloroplast

An essential pentatricopeptide repeat protein in the apicomplexan remnant chloroplast

Similarities in the structure of the transcriptional repressor AmtR in two different space groups suggest a model for the interaction with GlnK

Elucidating the antimycobacterial mechanism of action of ciprofloxacin using metabolomics

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