PA3027, a novel AraC-type transcriptional regulator activating genes of glycerolipid metabolism in Pseudomonas aeruginosa (F-PA3027 ChIP-seq)
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA686674 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR13276979_1.fastq.gz | Fastqsanger.gz | |||
| SRR13276979_2.fastq.gz | Fastqsanger.gz | |||
| SRR13276980_1.fastq.gz | Fastqsanger.gz | |||
| SRR13276980_2.fastq.gz | Fastqsanger.gz | |||
| SRR13276981_1.fastq.gz | Fastqsanger.gz |
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Project description:Pseudomonas aeruginosa encodes a large set of transcriptional regulators which allow to modulate and manage cellular metabolism to survive in variable environmental conditions, including the human body. The AraC family regulators are an abundant group of transcriptional regulators in bacteria, mostly acting as gene expression activators controlling diverse cellular functions e.g. carbon metabolism, stress response and virulence. PA3027 protein from P. aeruginosa has been classified in silico as a putative AraC-type transcriptional regulator. Comparative transcriptome analysis of P. aeruginosa PAO1161 overexpressing PA3027 versus empty vector control revealed a spectacular over 15-fold up-regulation of expression of pa3026-pa3024, PA3464 and PA3342 genes potentially involved in glycerolipid metabolism. Concomitantly, the ChIP-seq analysis using FLAG-PA3027 under mild overproduction conditions revealed at least 22 PA3027 binding sites in the PAO1161 genome, including promoter regions of genes showing a major increase in expression in response to PA3027 excess. The presented data showed that PA3027 acts as the transcriptional regulator in P. aeruginosa activating genes engaged in glycerolipid metabolism.
2021-05-11 | GSE163555 | GEO
Project description:Pseudomonas aeruginosa encodes a large set of transcriptional regulators which allow to modulate and manage cellular metabolism to survive in variable environmental conditions, including the human body. The AraC family regulators are an abundant group of transcriptional regulators in bacteria, mostly acting as gene expression activators controlling diverse cellular functions e.g. carbon metabolism, stress response and virulence. PA3027 protein from P. aeruginosa has been classified in silico as a putative AraC-type transcriptional regulator. Comparative transcriptome analysis of P. aeruginosa PAO1161 overexpressing PA3027 versus empty vector control revealed a spectacular over 15-fold up-regulation of expression of pa3026-pa3024, PA3464 and PA3342 genes potentially involved in glycerolipid metabolism. Concomitantly, the ChIP-seq analysis using FLAG-PA3027 under mild overproduction conditions revealed at least 22 PA3027 binding sites in the PAO1161 genome, including promoter regions of genes showing a major increase in expression in response to PA3027 excess. The presented data showed that PA3027 acts as the transcriptional regulator in P. aeruginosa activating genes engaged in glycerolipid metabolism.
2021-05-11 | GSE163554 | GEO
Project description:PA3027, a novel AraC-type transcriptional regulator activating genes of glycerolipid metabolism in Pseudomonas aeruginosa (PA3027 overexpression RNA-seq)
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Project description:The AraC-type regulator encoded by locus tag BPSS1610 is overexpressed in Burkholderia pseudomallei to identify the genes it regulates.
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Project description:Francisella tularensis is a Gram-negative bacterium that causes a fatal human disease known as tularemia. The Centers for Disease Control have classified F. tularensis as Category A Tier-1 Select Agent. The virulence mechanisms of Francisella are not entirely understood. Francisella possesses very few transcription regulators, and most of these regulate the expression of genes involved in intracellular survival and virulence. The F. tularensis genome sequence analysis reveals an AraC (FTL_0689) transcriptional regulator homologous to the AraC/XylS family of transcriptional regulators. In Gram-negative bacteria, AraC activates genes required for L-arabinose utilization and catabolism. The role of the FTL_0689 regulator in F. tularensis is not known. In this study, we characterized the role of FTL_0689 in gene regulation of F. tularensis and investigated its contribution to intracellular survival and virulence. The results demonstrate that FTL_0689 in Francisella is not required for L-arabinose utilization. Instead, FTL_0689 specifically regulates the expression of the oxidative and global stress response, virulence, metabolism, and other key pathways genes required by Francisella when exposed to oxidative stress. The FTL_0689 mutant is attenuated for intramacrophage growth, and mice infected with the FTL_0689 mutant survive better than wild-type F. tularensis LVS infected mice. Based on the deletion mutant phenotype, FTL_0689 was termed osrR (oxidative stress response regulator). Altogether, this study elucidates the role of the osrR transcriptional regulator in tularemia pathogenesis.
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Project description:The Pseudomonas aeruginosa quorum-sensing (QS) systems contribute to bacterial homeostasis and pathogenicity. Although the AraC family transcription factor VqsM has been characterized to control the production of virulence factors and QS signaling molecules, its detailed regulatory mechanisms still remain elusive. Here, we report that VqsM directly binds to the lasI promoter region, and thus regulates its expression. To identify additional targets of VqsM in P. aeruginosa PAO1, we performed chromatin immunoprecipitation followed by high-throughput DNA sequencing (ChIP-seq) which detected 48 enriched loci harboring VqsM-binding peaks in P. aeruginosa genome. The direct regulation of these genes by VqsM has been confirmed by Electrophoretic mobility shift assays (EMSAs) and quantitative real-time polymerase chain reactions (qRT-PCR). A VqsM-binding motif is found by using MEME suite and verified by footprint assays in vitro. In addition, VqsM directly binds to the promoter regions of antibiotic resistance regulator NfxB and the master type III system regulator ExsA. Notably, the vqsM mutant displayed more resistance to two types of antibiotics and promoted bacterial survival in a mouse model, compared to the wild type PAO1 strain. Collectively, this work provides new cues to better understand the detailed regulatory networks of QS systems, T3SS, and antibiotic resistance. Pseudomonas aeruginosa MAPO1 containing empty pAK1900 or pAK1900-VqsM-VSV
2014-08-04 | E-GEOD-57284 | biostudies-arrayexpress
Project description:The Pseudomonas aeruginosa quorum-sensing (QS) systems contribute to bacterial homeostasis and pathogenicity. Although the AraC family transcription factor VqsM has been characterized to control the production of virulence factors and QS signaling molecules, its detailed regulatory mechanisms still remain elusive. Here, we report that VqsM directly binds to the lasI promoter region, and thus regulates its expression. To identify additional targets of VqsM in P. aeruginosa PAO1, we performed chromatin immunoprecipitation followed by high-throughput DNA sequencing (ChIP-seq) which detected 48 enriched loci harboring VqsM-binding peaks in P. aeruginosa genome. The direct regulation of these genes by VqsM has been confirmed by Electrophoretic mobility shift assays (EMSAs) and quantitative real-time polymerase chain reactions (qRT-PCR). A VqsM-binding motif is found by using MEME suite and verified by footprint assays in vitro. In addition, VqsM directly binds to the promoter regions of antibiotic resistance regulator NfxB and the master type III system regulator ExsA. Notably, the vqsM mutant displayed more resistance to two types of antibiotics and promoted bacterial survival in a mouse model, compared to the wild type PAO1 strain. Collectively, this work provides new cues to better understand the detailed regulatory networks of QS systems, T3SS, and antibiotic resistance.
2014-08-04 | GSE57284 | GEO
Project description:Pseudomonas aeruginosa encodes a large set of transcriptional regulators (TRs) that modulate and manage cellular metabolism to survive in variable environmental conditions including that of the human body. The AraC family regulators are an abundant group of TRs in bacteria, mostly acting as gene expression activators, controlling diverse cellular functions (e.g., carbon metabolism, stress response, and virulence). The PA3027 protein from P. aeruginosa has been classified in silico as a putative AraC-type TR. Transcriptional profiling of P. aeruginosa PAO1161 overexpressing PA3027 revealed a spectacular increase in the mRNA levels of PA3026-PA3024 (divergent to PA3027), PA3464, and PA3342 genes encoding proteins potentially involved in glycerolipid metabolism. Concomitantly, chromatin immunoprecipitation-sequencing (ChIP-seq) analysis revealed that at least 22 regions are bound by PA3027 in the PAO1161 genome. These encompass promoter regions of PA3026, PA3464, and PA3342, showing the major increase in expression in response to PA3027 excess. In Vitro DNA binding assay confirmed interactions of PA3027 with these regions. Furthermore, promoter-reporter assays in a heterologous host showed the PA3027-dependent activation of the promoter of the PA3026-PA3024 operon. Two motifs representing the preferred binding sites for PA3027, one localized upstream and one overlapping with the -35 promoter sequence, were identified in PA3026p and our data indicate that both motifs are required for full activation of this promoter by PA3027. Overall, the presented data show that PA3027 acts as a transcriptional regulator in P. aeruginosa, activating genes likely engaged in glycerolipid metabolism. The GliR name, from a glycerolipid metabolism regulator, is proposed for PA3027 of P. aeruginosa.
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Project description:The putative trancriptional regulator PA2449 was found to be essential for both glycine/serine metabolism and the production of phenazines in P. aeruignosa PAO1. We examined the regulon controlled by PA2449 via microarray analysis between wild-type P. aeruignosa PAO1 and the PA2449-null mutant P. aeruginosa PW5126. Both strains were obtained from the PA-two allele library (Univ. of Washington, Ref. Jacobs et al. 2003. PNAS 100, 14339).
2012-10-15 | GSE39044 | GEO
Project description:The putative trancriptional regulator PA2449 was found to be essential for both glycine/serine metabolism and the production of phenazines in P. aeruignosa PAO1. We examined the regulon controlled by PA2449 via microarray analysis between wild-type P. aeruignosa PAO1 and the PA2449-null mutant P. aeruginosa PW5126. Both strains were obtained from the PA-two allele library (Univ. of Washington, Ref. Jacobs et al. 2003. PNAS 100, 14339). Strains were grown under conditions known to induce phenazine biosynthesis (peptone broth), and their resulting transcriptomes were compared. Total RNA was isolated and prepped for Affymetrix GeneChips.
2012-10-15 | E-GEOD-39044 | biostudies-arrayexpress