Structure study of MarR family protein from Paenisporosarcina sp.TG-14
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PROVIDER: PRJEB42800 | ENA |
REPOSITORIES: ENA
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Project description:Paenisporosarcina sp. TG-14 Genome sequencing and assembly
| PRJNA174754 | ENA
Project description: Not available
| S-EPMC8420766 | biostudies-literature
Project description:SlyA and its homologs are conserved essential transcription factors in enteric bacteria, including Salmonella enterica and Yersinia pestis, in which they upregulate horizontally-acquired virulence genes. As members of the MarR family of transcription factors, they possess a small molecule binding pocket that allows the protein to undergo a conformational change upon ligand interaction that abrogates DNA binding. Although the original discovery of MarR was based on its ability to recognize xenobiotic compounds and promote their efflux, the conservation of the MarR family throughout Bacteria and Archaea suggests a more general function. Because SlyA is known to bind xenobiotic aromatic carboxylates, we performed a targeted analysis of aromatic metabolic genes in S. Typhimurium to identify potential endogenous ligands, including genes involved in essential cellular processes including iron metabolism, respiration, and aromatic amino acid and folate biosynthesis. We found that SlyA is promiscuously inhibited by multiple aromatic carboxylates including 2,3-dihydroxybenzoate, a precursor of iron-scavenging catecholate siderophores, and 4-hydroxybenzoate, a precursor of quinone-based electron-carriers, which allows it to sense changes in iron availability, respiration and growth on succinate. We suggest that SlyA and other MarR proteins sense bacterial metabolic status via the flux of aromatic carboxylates in biosynthetic pathways, allowing SlyA to function as a counter-silencer of horizontally-acquired genes that is exquisitely responsive to the metabolic state of the cell.
2025-07-31 | GSE293030 | GEO
Project description:Chemical signaling in the plant microbiome can have drastic effects on microbial community structure, and on host growth and development. Previously, we demonstrated that the auxin metabolic signal interference performed by the bacterial genus Variovorax via a novel auxin degradation locus was essential for maintaining stereotypic root development in an ecologically-relevant bacterial synthetic community. Here, we dissect the Variovorax auxin degradation locus to define the genes necessary and sufficient for indole-3-acetic acid (IAA) degradation and signal interference. We determine the crystal structures and binding properties of the operon’s MarR-family repressor with IAA and other auxins. We identify auxin-degradation operons across the bacterial tree of life and define two distinct types based on gene content and metabolic products: iac-like and iad-like. We solve the structures of MarRs from representatives of each auxin degradation operon type, establishing that each have distinct IAA binding pockets. Comparison of representative IAA degrading strains from diverse bacterial genera show that while all degrade IAA, only strains containing iad-like auxin degrading operons interfere with auxin signaling in a complex synthetic community context. This suggests that iad-like operon containing strains, including Variovorax species, play a key ecological role in modulating auxins in the plant microbiome.
2022-08-11 | GSE210968 | GEO
Project description:Paenisporosarcina indica PN2 genome sequencing
| PRJNA334007 | ENA
Project description:Streptococcus pneumoniae D39 AdcR (adhesion competence repressor) is the first metal-sensing member of the MarR (multiple antibiotic resistance repressor) family to be characterized. Expression profiling of a ∆adcR strain grown in liquid culture under microaerobic conditions revealed that transcript amounts for 13 genes were up-regulated relative to the wild-type strain, among them adcR, adcCBA, encoding a high affinity ABC uptake system for zinc, and genes encoding cell-surface zinc-binding pneumococcal histidine triad (pht) and adcII (lmb, laminin binding) proteins. Down-regulated transcripts included those encoding two putative zinc-containing alcohol dehydrogenases.
2010-10-01 | GSE21506 | GEO
Project description:Paenisporosarcina sp. TG20 Genome sequencing and assembly
| PRJNA170891 | ENA
Project description:Paenisporosarcina sp. OV554 Genome sequencing and assembly
| PRJNA443365 | ENA
Project description:Streptococcus pneumoniae D39 AdcR (adhesion competence repressor) is the first metal-sensing member of the MarR (multiple antibiotic resistance repressor) family to be characterized. Expression profiling of a âadcR strain grown in liquid culture under microaerobic conditions revealed that transcript amounts for 13 genes were up-regulated relative to the wild-type strain, among them adcR, adcCBA, encoding a high affinity ABC uptake system for zinc, and genes encoding cell-surface zinc-binding pneumococcal histidine triad (pht) and adcII (lmb, laminin binding) proteins. Down-regulated transcripts included those encoding two putative zinc-containing alcohol dehydrogenases. Bacterial strains were grown exponentially in rich (BHI) media at 37C and an atmosphere of 5% CO2 to OD620~0.2, and were processed as described in the related Sample records. Samples were collected from three independent biological replicates and included one dye swap. Data were normalized using the Lowess (block) method without background subtraction. Changes in relative transcript amounts of positive or negative 2-fold with Bayesian P value of <0.001 were considered significant, and were included as supplementary material for the accompanying manuscript (The metalloregulatory site in Streptococcus pneumoniae AdcR, a zinc-activated MarR-family repressor; Reyes-Caballero, H. et al, manuscript in preparation).
2010-10-01 | E-GEOD-21506 | biostudies-arrayexpress