Molecular insights into effector binding by DgoR, a GntR/FadR family transcriptional repressor of D‐galactonate metabolism in <i>Escherichia coli</i>

Arya, Garima; Pal, Mohinder; Sharma, Monika; Singh, Bhupinder; Singh, Swati; Agrawal, Vishal; Chaba, Rachna

doi:10.1111/mmi.14625

Cited by 8 publications

(4 citation statements)

References 74 publications

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“…2i and 2j). These data support DmdR being autoregulatory, consistent with other GntR superfamily regulators [51][52][53] , and the DMSP and acrylate responsive transcriptional repressor of dmdA-acuI and dmdR.…”

Section: Dmdr Represses Dmda-acui Transcription In a Dmsp And Acrylat...supporting

confidence: 79%

Coordinated regulation of DMSP demethylation and cleavage in abundant marine bacteria

Todd,

Fu,

Wang

et al. 2023

Preprint

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Dimethylsulfoniopropionate (DMSP) catabolism by ubiquitous marine Roseobacters is important in global carbon and sulfur cycling, chemotaxis, and climate-active gas production. Many Roseobacters contain competing DMSP demethylation and cleavage pathways, the latter generating the climate-cooling gas dimethylsulfide (DMS). The mechanism partitioning flux through these pathways, referred to as “the switch”, is unknown. Here, we identify a FadR family transcriptional regulator “DmdR” in Roseobacters that represses transcription of the DMSP demethylation gene dmdA and acuI, central to DMSP cleavage pathways, under low intracellular DMSP levels. Increased DMSP levels induces DMSP cleavage and accumulation of the toxic intermediate and AcuI substrate acryloyl-CoA. DmdR binds acryloyl-CoA as its effector and derepresses dmdA-acuI transcription. Roseobacterial DmdR-dependent regulation, together with transcriptional and kinetic regulation of DMSP cleavage, likely ensures cellular DMSP concentrations that allow its antistress functions and accelerated DMSP demethylation and catabolism of toxic cleavage pathway intermediates at higher DMSP levels. In other abundant marine bacteria that lack dmdA, e.g., Oceanospirillales, DmdR is predicted to still regulate acuI transcription and, thus, acryloyl-CoA catabolism/detoxification. DmdR regulation is widespread in Earth’s oceans and their margins and is an important step in global biogeochemical cycling and climate-active gas production.

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Section: Dmdr Represses Dmda-acui Transcription In a Dmsp And Acrylat...supporting

confidence: 79%

Coordinated regulation of DMSP demethylation and cleavage in abundant marine bacteria

Todd,

Fu,

Wang

et al. 2023

Preprint

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“…Bioinformatic analysis showed that PA1520 was found to be another homologue of the FadR subfamily (Fig. S1) (Cronan Jr. and Subrahmanyam, 1998; Gao et al ., 2008; Arya et al ., 2020; Vigouroux et al ., 2021), which led us to investigate the role of PA1520 named UgmR (Uric acid and glyoxylate metabolism regulator) in P . aeruginosa .…”

Section: Resultsmentioning

confidence: 99%

Regulation of uric acid and glyoxylate metabolism by UgmR protein in Pseudomonas aeruginosa

Yan

Huang

et al. 2022

Environmental Microbiology

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Summary The opportunistic pathogen Pseudomonas aeruginosa has evolved several systems to adapt to complex environments. The GntR family proteins play important roles in the regulation of metabolic processes and bacterial pathogenesis. In this study, we uncovered that the gene clusters of PA1513‐PA1518 and PA1498‐PA1502 in P. aeruginosa are required for uric acid and glyoxylate metabolism respectively. We also identified a GntR family regulator UgmR that is involved in regulation of uric acid and glyoxylate metabolism. Promoter activity measurement and biochemical assays revealed that the UgmR directly represses the transcriptional activity of PA1513‐PA1518 and PA1498‐PA1502, and this inhibition was relieved by the addition of uric acid. Importantly, further experiments showed that UgmR also participates in the glyoxylate shunt. Collectively, these findings contribute to a better understanding of the UgmR factor involved in uric acid and glyoxylate metabolism, which provide insights into the complex metabolic pathways in P. aeruginosa.

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“…The metabolism of D-galactonate, a widely prevalent aldonic sugar acid, is considered to be important for the enteric bacterium E. coli. It metabolizes D-galactonate through the enzymes encoded by D-galactonate operon (dgo) and a modified Entner-Doudoroff pathway (Peekhaus and Conway, 1998), where D-galactonate is degraded into D-glyceraldehyde-3-phosphate and pyruvate, and then enter central metabolism (Singh et al, 2019;Arya et al, 2020). DgoR is encoded by the first gene of dgo operon and negatively regulates the whole operon.…”

Section: Introductionmentioning

confidence: 99%

“…DgoR is encoded by the first gene of dgo operon and negatively regulates the whole operon. DgoR was previously predicted to be a FadR family of transcription regulator, and repress the D-galactonate metabolic pathway by binding inverted repeats in the dgo cis-acting element using D-galactonate as a specific effector molecule (De Ley and Doudoroff, 1957;Deacon and Cooper, 1977;Cooper, 1978;Singh et al, 2019;Arya et al, 2020). Although several regulators of the FadR family have been well described at the molecular level, the binding pocket of Dgalactonate and its substrate specificity have not been investigated (Singh et al, 2019).…”

Section: Introductionmentioning

confidence: 99%

Structural and Functional Analyses of the Transcription Repressor DgoR From Escherichia coli Reveal a Divalent Metal-Containing D-Galactonate Binding Pocket

et al. 2020

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The transcription repressor of D-galactonate metabolism, DgoR, from Escherichia coli belongs to the FadR family of the GntR superfamily. In the presence of D-galactonate, DgoR binds to two inverted repeats overlapping the dgo cis-acting promoter repressing the expression of genes involved in D-galactonate metabolism. To further understand the structural and molecular details of ligand and effector interactions between Dgalactonate and this FadR family member, herein we solved the crystal structure of C-terminal domain of DgoR (DgoR_C), which revealed a unique divalent metalcontaining substrate binding pocket. The metal ion is required for D-galactonate binding, as evidenced by the dramatically decreased affinity between D-galactonate and DgoR in the presence of EDTA, which can be reverted by the addition of Zn 2+ , Mg 2+ , and Ca 2+. The key amino acid residues involved in the interactions between Dgalactonate and DgoR were revealed by molecular docking studies and further validated with biochemical studies by site-directed mutagenesis. It was found that changes to alanine in residues R102, W181, T191, and R224 resulted in significantly decreased binding affinities for D-galactonate, as determined by EMSA and MST assays. These results suggest that the molecular modifications induced by a D-galactonate and a metal binding in the DgoR are required for DNA binding activity and consequently, transcriptional inhibition.

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Molecular insights into effector binding by DgoR, a GntR/FadR family transcriptional repressor of D‐galactonate metabolism in Escherichia coli

Cited by 8 publications

References 74 publications

Coordinated regulation of DMSP demethylation and cleavage in abundant marine bacteria

Coordinated regulation of DMSP demethylation and cleavage in abundant marine bacteria

Regulation of uric acid and glyoxylate metabolism by UgmR protein in Pseudomonas aeruginosa

Structural and Functional Analyses of the Transcription Repressor DgoR From Escherichia coli Reveal a Divalent Metal-Containing D-Galactonate Binding Pocket

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