Vibrio harveyi
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA356167 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR5074720.fastq.gz | Fastqsanger.gz | |||
| SRR5074721.fastq.gz | Fastqsanger.gz | |||
| SRR5074722.fastq.gz | Fastqsanger.gz | |||
| SRR5074723.fastq.gz | Fastqsanger.gz | |||
| SRR5074724.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 9 |
Similar Datasets
Project description:LuxR is the master quorum sensing regulator in Vibrio harveyi. This transcription factor controls the expression of over 600 genes to coordinate group behaviors. In order to understand how LuxR regulates transcription we identified a co-regulator, integration host factor (IHF). In this study we performed RNA-seq to show that the LuxR and IHF regulons overlap significantly.
2017-12-03 | GSE90845 | GEO
Project description:Quorum sensing controls hundreds of genes in vibrios required for cell density-specific behaviors, including bioluminescence, biofilm formation, competence, secretion, and motility. The central regulator in the quorum sensing pathway in vibrios is LuxR/HapR, which directly regulates >100 genes in the 625-gene regulon of Vibrio harveyi. Among these directly regulated genes are 15 transcription factors, which we predicted would comprise the second tier in the hierarchy of the quorum sensing regulon. To better study the mechanism of regulation of the quorum sensing network, we mapped all transcriptional start sites in V. harveyi using dRNA-seq. From these data, we determined the relative position of LuxR binding sites in the promoters of genes directly regulated by LuxR. We confirmed that LuxR directly binds to the promoters of the genes encoding transcription factors and quantified the extent of LuxR activation or repression of transcript levels. Finally, we determined the individual regulons for a subset of transcription factors that have not been previously studied. For regulators such as LysR- or AsnC/Lrp-type transcription factors, the regulons contained >100 genes that contained both unique and overlapping genes with the LuxR regulon. These data support a model in which LuxR directly regulates other transcription factors, which act to further alter the second tier of the gene expression cascade producing cell density behaviors in V. harveyi.
2020-05-15 | GSE144017 | GEO
Project description:Microarray data for study "The master regulators AphA and LuxR control the Vibrio harveyi quorum-sensing regulon: analysis of their individual and combined effects". Bacteria use a chemical communication process called quorum sensing to control transitions between individual and group behaviors. In the Vibrio harveyi quorum-sensing circuit, two master transcription factors AphA and LuxR coordinate the quorum-sensing response. Here we show that AphA regulates 167 genes, LuxR regulates 625 genes, and they co-regulate 77 genes. LuxR strongly controls genes both at low-cell-density and high-cell-density, suggesting it is the major quorum-sensing regulator. By contrast, AphA is absent at high-cell-density, and acts to fine-tune quorum-sensing gene expression at low-cell-density. We examined two loci as case studies of co-regulation by AphA and LuxR. First, AphA and LuxR directly regulate expression of the genes encoding the quorum regulatory small RNAs Qrr2, Qrr3, and Qrr4, the consequence of which is a specifically timed transition between the individual and the group lifestyle. Second, AphA and LuxR repress type III secretion system genes but at different times and to different extents. The consequence of this regulation is that type III secretion is restricted to a peak at mid-cell-density. Thus, asymmetric production of AphA and LuxR coupled with differences in their strength and timing of target gene regulation generates a precise temporal pattern of gene expression. Triplicate biological samples of Vibrio harveyi strains BB721 and JAF548 were hybridized to Agilent arrays (Amadid design ID: 037644), and one experiment was a control dye-swap, for a total of four experiments in this array set.
2013-02-08 | E-GEOD-44153 | biostudies-arrayexpress
Project description:Microarray data for study "The master regulators AphA and LuxR control the Vibrio harveyi quorum-sensing regulon: analysis of their individual and combined effects". Bacteria use a chemical communication process called quorum sensing to control transitions between individual and group behaviors. In the Vibrio harveyi quorum-sensing circuit, two master transcription factors AphA and LuxR coordinate the quorum-sensing response. Here we show that AphA regulates 167 genes, LuxR regulates 625 genes, and they co-regulate 77 genes. LuxR strongly controls genes both at low-cell-density and high-cell-density, suggesting it is the major quorum-sensing regulator. By contrast, AphA is absent at high-cell-density, and acts to fine-tune quorum-sensing gene expression at low-cell-density. We examined two loci as case studies of co-regulation by AphA and LuxR. First, AphA and LuxR directly regulate expression of the genes encoding the quorum regulatory small RNAs Qrr2, Qrr3, and Qrr4, the consequence of which is a specifically timed transition between the individual and the group lifestyle. Second, AphA and LuxR repress type III secretion system genes but at different times and to different extents. The consequence of this regulation is that type III secretion is restricted to a peak at mid-cell-density. Thus, asymmetric production of AphA and LuxR coupled with differences in their strength and timing of target gene regulation generates a precise temporal pattern of gene expression. Triplicate biological samples of Vibrio harveyi strains STR416 and JV55 were hybridized to Agilent arrays (Amadid design ID: 021087), and one experiment was a control dye-swap, for a total of four experiments in this array set.
2013-02-20 | E-GEOD-44197 | biostudies-arrayexpress
Project description:Microarray data for study "The master regulators AphA and LuxR control the Vibrio harveyi quorum-sensing regulon: analysis of their individual and combined effects". Bacteria use a chemical communication process called quorum sensing to control transitions between individual and group behaviors. In the Vibrio harveyi quorum-sensing circuit, two master transcription factors AphA and LuxR coordinate the quorum-sensing response. Here we show that AphA regulates 167 genes, LuxR regulates 625 genes, and they co-regulate 77 genes. LuxR strongly controls genes both at low-cell-density and high-cell-density, suggesting it is the major quorum-sensing regulator. By contrast, AphA is absent at high-cell-density, and acts to fine-tune quorum-sensing gene expression at low-cell-density. We examined two loci as case studies of co-regulation by AphA and LuxR. First, AphA and LuxR directly regulate expression of the genes encoding the quorum regulatory small RNAs Qrr2, Qrr3, and Qrr4, the consequence of which is a specifically timed transition between the individual and the group lifestyle. Second, AphA and LuxR repress type III secretion system genes but at different times and to different extents. The consequence of this regulation is that type III secretion is restricted to a peak at mid-cell-density. Thus, asymmetric production of AphA and LuxR coupled with differences in their strength and timing of target gene regulation generates a precise temporal pattern of gene expression. Triplicate biological samples of Vibrio harveyi strains STR415 and JV54 were hybridized to Agilent arrays (Amadid design ID: 021087), and one experiment was a control dye-swap, for a total of four experiments in this array set.
2013-02-20 | E-GEOD-44199 | biostudies-arrayexpress
Project description:Microarray data for study "The master regulators AphA and LuxR control the Vibrio harveyi quorum-sensing regulon: analysis of their individual and combined effects". Bacteria use a chemical communication process called quorum sensing to control transitions between individual and group behaviors. In the Vibrio harveyi quorum-sensing circuit, two master transcription factors AphA and LuxR coordinate the quorum-sensing response. Here we show that AphA regulates 167 genes, LuxR regulates 625 genes, and they co-regulate 77 genes. LuxR strongly controls genes both at low-cell-density and high-cell-density, suggesting it is the major quorum-sensing regulator. By contrast, AphA is absent at high-cell-density, and acts to fine-tune quorum-sensing gene expression at low-cell-density. We examined two loci as case studies of co-regulation by AphA and LuxR. First, AphA and LuxR directly regulate expression of the genes encoding the quorum regulatory small RNAs Qrr2, Qrr3, and Qrr4, the consequence of which is a specifically timed transition between the individual and the group lifestyle. Second, AphA and LuxR repress type III secretion system genes but at different times and to different extents. The consequence of this regulation is that type III secretion is restricted to a peak at mid-cell-density. Thus, asymmetric production of AphA and LuxR coupled with differences in their strength and timing of target gene regulation generates a precise temporal pattern of gene expression. Triplicate biological samples of Vibrio harveyi strains KM808 and JV54 were hybridized to Agilent arrays (Amadid design ID: 021087), and one experiment was a control dye-swap, for a total of four experiments in this array set.
2013-02-20 | E-GEOD-44198 | biostudies-arrayexpress
Project description:Microarray data for study "The master regulators AphA and LuxR control the Vibrio harveyi quorum-sensing regulon: analysis of their individual and combined effects". Bacteria use a chemical communication process called quorum sensing to control transitions between individual and group behaviors. In the Vibrio harveyi quorum-sensing circuit, two master transcription factors AphA and LuxR coordinate the quorum-sensing response. Here we show that AphA regulates 167 genes, LuxR regulates 625 genes, and they co-regulate 77 genes. LuxR strongly controls genes both at low-cell-density and high-cell-density, suggesting it is the major quorum-sensing regulator. By contrast, AphA is absent at high-cell-density, and acts to fine-tune quorum-sensing gene expression at low-cell-density. We examined two loci as case studies of co-regulation by AphA and LuxR. First, AphA and LuxR directly regulate expression of the genes encoding the quorum regulatory small RNAs Qrr2, Qrr3, and Qrr4, the consequence of which is a specifically timed transition between the individual and the group lifestyle. Second, AphA and LuxR repress type III secretion system genes but at different times and to different extents. The consequence of this regulation is that type III secretion is restricted to a peak at mid-cell-density. Thus, asymmetric production of AphA and LuxR coupled with differences in their strength and timing of target gene regulation generates a precise temporal pattern of gene expression. Triplicate biological samples of Vibrio harveyi strains KM810 and JV55 were hybridized to Agilent arrays (Amadid design ID: 021087), and one experiment was a control dye-swap, for a total of four experiments in this array set. KM810 contains a luxO D47E phosphomimic allele and a deletion in luxR; JV55 contains a luxO D47E phosphomimic allele and deletions in luxR and aphA.
2013-02-20 | E-GEOD-44196 | biostudies-arrayexpress
Project description:Microarray data for study "The master regulators AphA and LuxR control the Vibrio harveyi quorum-sensing regulon: analysis of their individual and combined effects". Bacteria use a chemical communication process called quorum sensing to control transitions between individual and group behaviors. In the Vibrio harveyi quorum-sensing circuit, two master transcription factors AphA and LuxR coordinate the quorum-sensing response. Here we show that AphA regulates 167 genes, LuxR regulates 625 genes, and they co-regulate 77 genes. LuxR strongly controls genes both at low-cell-density and high-cell-density, suggesting it is the major quorum-sensing regulator. By contrast, AphA is absent at high-cell-density, and acts to fine-tune quorum-sensing gene expression at low-cell-density. We examined two loci as case studies of co-regulation by AphA and LuxR. First, AphA and LuxR directly regulate expression of the genes encoding the quorum regulatory small RNAs Qrr2, Qrr3, and Qrr4, the consequence of which is a specifically timed transition between the individual and the group lifestyle. Second, AphA and LuxR repress type III secretion system genes but at different times and to different extents. The consequence of this regulation is that type III secretion is restricted to a peak at mid-cell-density. Thus, asymmetric production of AphA and LuxR coupled with differences in their strength and timing of target gene regulation generates a precise temporal pattern of gene expression.
2013-02-20 | GSE44348 | GEO
Project description:Microarray data for study "The master regulators AphA and LuxR control the Vibrio harveyi quorum-sensing regulon: analysis of their individual and combined effects". Bacteria use a chemical communication process called quorum sensing to control transitions between individual and group behaviors. In the Vibrio harveyi quorum-sensing circuit, two master transcription factors AphA and LuxR coordinate the quorum-sensing response. Here we show that AphA regulates 167 genes, LuxR regulates 625 genes, and they co-regulate 77 genes. LuxR strongly controls genes both at low-cell-density and high-cell-density, suggesting it is the major quorum-sensing regulator. By contrast, AphA is absent at high-cell-density, and acts to fine-tune quorum-sensing gene expression at low-cell-density. We examined two loci as case studies of co-regulation by AphA and LuxR. First, AphA and LuxR directly regulate expression of the genes encoding the quorum regulatory small RNAs Qrr2, Qrr3, and Qrr4, the consequence of which is a specifically timed transition between the individual and the group lifestyle. Second, AphA and LuxR repress type III secretion system genes but at different times and to different extents. The consequence of this regulation is that type III secretion is restricted to a peak at mid-cell-density. Thus, asymmetric production of AphA and LuxR coupled with differences in their strength and timing of target gene regulation generates a precise temporal pattern of gene expression.
2013-02-20 | GSE44199 | GEO
Project description:Microarray data for study "The master regulators AphA and LuxR control the Vibrio harveyi quorum-sensing regulon: analysis of their individual and combined effects". Bacteria use a chemical communication process called quorum sensing to control transitions between individual and group behaviors. In the Vibrio harveyi quorum-sensing circuit, two master transcription factors AphA and LuxR coordinate the quorum-sensing response. Here we show that AphA regulates 167 genes, LuxR regulates 625 genes, and they co-regulate 77 genes. LuxR strongly controls genes both at low-cell-density and high-cell-density, suggesting it is the major quorum-sensing regulator. By contrast, AphA is absent at high-cell-density, and acts to fine-tune quorum-sensing gene expression at low-cell-density. We examined two loci as case studies of co-regulation by AphA and LuxR. First, AphA and LuxR directly regulate expression of the genes encoding the quorum regulatory small RNAs Qrr2, Qrr3, and Qrr4, the consequence of which is a specifically timed transition between the individual and the group lifestyle. Second, AphA and LuxR repress type III secretion system genes but at different times and to different extents. The consequence of this regulation is that type III secretion is restricted to a peak at mid-cell-density. Thus, asymmetric production of AphA and LuxR coupled with differences in their strength and timing of target gene regulation generates a precise temporal pattern of gene expression.
2013-02-20 | GSE44195 | GEO