Synthetic metagenome
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA768850 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR21052300_1.fastq.gz | Fastqsanger.gz | |||
| SRR21052300_2.fastq.gz | Fastqsanger.gz | |||
| SRR21052301_1.fastq.gz | Fastqsanger.gz | |||
| SRR21052301_2.fastq.gz | Fastqsanger.gz | |||
| SRR21052302_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 168 |
Similar Datasets
Project description:Structure, function and microbial ecology of diverse MarR bacterial regulators of auxin catabolism
| PRJNA868387 | ENA
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:Sphingolipids are required for diverse biological functions and are degraded by specific catabolic enzymes. However, the mechanisms that regulate sphingolipid catabolism are not known. Here we characterize a transcriptional axis that regulates sphingolipid breakdown to control resistance against bacterial infection. From an RNAi screen for transcriptional regulators of pathogen resistance in the nematode C. elegans, we identified the nuclear hormone receptor nhr-66, a ligand-gated transcription factor homologous to human hepatocyte nuclear factor 4. Tandem chromatin immunoprecipitation-sequencing (ChIP-seq) and RNA sequencing (RNA-seq) experiments revealed that NHR-66 is a transcriptional repressor, which directly targets sphingolipid catabolism genes. Transcriptional de-repression of two sphingolipid catabolic enzymes in nhr-66 loss-of-function mutants drives the breakdown of sphingolipids, which enhances host susceptibility to infection with the bacterial pathogen Pseudomonas aeruginosa. These data define transcriptional control of sphingolipid catabolism in the regulation of cellular sphingolipids, a process that is necessary for pathogen resistance.
2023-09-08 | GSE240426 | GEO
Project description:Sphingolipids are required for diverse biological functions and are degraded by specific catabolic enzymes. However, the mechanisms that regulate sphingolipid catabolism are not known. Here we characterize a transcriptional axis that regulates sphingolipid breakdown to control resistance against bacterial infection. From an RNAi screen for transcriptional regulators of pathogen resistance in the nematode C. elegans, we identified the nuclear hormone receptor nhr-66, a ligand-gated transcription factor homologous to human hepatocyte nuclear factor 4. Tandem chromatin immunoprecipitation-sequencing (ChIP-seq) and RNA sequencing (RNA-seq) experiments revealed that NHR-66 is a transcriptional repressor, which directly targets sphingolipid catabolism genes. Transcriptional de-repression of two sphingolipid catabolic enzymes in nhr-66 loss-of-function mutants drives the breakdown of sphingolipids, which enhances host susceptibility to infection with the bacterial pathogen Pseudomonas aeruginosa. These data define transcriptional control of sphingolipid catabolism in the regulation of cellular sphingolipids, a process that is necessary for pathogen resistance.
2023-09-08 | GSE240425 | GEO
Project description:Transcription regulatory factors of MarR family play an important role in diverse bacterial physiologic functions, whereas the effect and its intrinsic regulatory mechanism on aquatic pathogenic bacteria Aeromonas hydrophila are still largely unknown. In this study, we firstly constructed a deletion strain of gene AHA_2124 (ΔAHA_2124) of a MarR family transcriptional regulator in A. hydrophila, and found that it had significantly enhanced hemolysis, extracellular protease, and motility activities. The differentially expressed proteins (DEPs) between wild-type and ΔAHA_2124 strain were compared by using the label-free based quantitative proteomics technology, and there were 178 DEPs including 80 proteins up-regulated and 98 proteins down-regulated. Bioinformatics analysis showed that the deletion of gene AHA_2124 led to some changes in the expression of proteins related to multiple biological processes, such as translation, peptide transport and oxidation reduction. These results provided a theoretical basis for better exploring the regulatory mechanism of transcriptional regulators of the MarR family of A. hydrophila on bacterial physiological functions.
2023-11-02 | PXD046625 |
Project description:How developmental signals program gene expression in space and time is still poorly understood. Here, we addressed this question for the plant master regulator, auxin. Transcriptional responses to auxin rely on a large multigenic transcription factor family, the auxin response factors (ARFs). We deconvoluted the complexity of ARF-regulated transcription using auxin-inducible synthetic promoters built from cis-element pair configurations differentially bound by ARFs. We demonstrate using cellular systems that ARF transcriptional properties are not only intrinsic but also depend on the cis-element pair configurations they bind to, thus identifying a bi-layer ARF/cis-element transcriptional code. Auxin-inducible synthetic promoters were expressed differentially in planta showing at single-cell resolution how this bi-layer code patterns transcriptional responses to auxin. Combining cis-element pair configurations in synthetic promoters created distinct patterns, demonstrating the combinatorial power of the auxin bi-layer code in generating diverse gene expression patterns that are not simply a direct translation of auxin distribution.
2025-07-31 | GSE241573 | GEO
Project description:Microbe-microbe interactions are critical for gut microbiome function. A challenging task to understand health and disease-related microbiome signatures is to move beyond descriptive community-level profiling towards disentangling microbial interaction networks. Here, we aimed to determine members taking on a keystone role in shaping the community ecology of a widely used synthetic bacterial community (OMM12).
2022-11-14 | MSV000090704 | MassIVE
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:Although RNA structures play important roles in regulating gene expression, the mechanism and function of mRNA folding in plant bacterial pathogens remain elusive. Therefore, we perform dimethyl sulfate sequencing (DMS-seq) on the Pseudomonas syringae under nutrition-rich and deficient conditions, revealing that the mRNA structure changes substantially in the minimal medium (MM) that tunes global translation efficiency (TE), thereby inducing virulence. This process is led by the increased expression of hfq, which is directly activated by transcription regulators RpoS and CysB. The co-occurrence of Hfq and RpoS in diverse bacteria and the deep conservation of Hfq Y25 is critical for RNA-mediated regulation and implicates the wider biological importance of mRNA structure and feedback loops in the control of global gene expression.
2024-07-02 | GSE216157 | GEO