Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1216175 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR32150000_1.fastq.gz | Fastqsanger.gz | |||
| SRR32150000_2.fastq.gz | Fastqsanger.gz | |||
| SRR32150001_1.fastq.gz | Fastqsanger.gz | |||
| SRR32150001_2.fastq.gz | Fastqsanger.gz | |||
| SRR32149990_1.fastq.gz | Fastqsanger.gz |
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Project description:Aerobic methanotrophic bacteria use methane as their sole source of carbon and energy and serve as a major sink for the potent greenhouse gas methane in freshwater ecosystems. Despite this important environmental role, little is known about the molecular details of how these organisms interact in the environment. Many bacterial species use quorum sensing systems to regulate gene expression in a density-dependent manner. We have identified a quorum sensing system in the genome of Methylobacter tundripaludum, a dominant methane-oxidizer in methane enrichments of sediment from Lake Washington (Seattle, WA, USA). We determined that M. tundripaludum primarily produces N-3-hydroxydecanoyl-L-homoserine lactone (3-OH-C10-HSL) and that production is governed by a positive feedback loop. We then further characterized this system by determining which genes are regulated by quorum sensing in this methane-oxidizer using RNA-seq, and discovered this system regulates the expression of a novel nonribosomal peptide synthetase biosynthetic gene cluster. These results identify and characterize a mode of cellular communication in an aerobic methane-oxidizing bacterium.
2016-08-16 | GSE85617 | GEO
Project description:Aerobic methanotrophic bacteria use methane as their sole source of carbon and energy and serve as a major sink for the potent greenhouse gas methane in freshwater ecosystems. Despite this important environmental role, little is known about the molecular details of how these organisms interact in the environment. Many bacterial species use quorum sensing systems to regulate gene expression in a density-dependent manner. We have identified a quorum sensing system in the genome of Methylobacter tundripaludum, a dominant methane-oxidizer in methane enrichments of sediment from Lake Washington (Seattle, WA, USA). We determined that M. tundripaludum primarily produces N-3-hydroxydecanoyl-L-homoserine lactone (3-OH-CÂ10-HSL) and that production is governed by a positive feedback loop. We then further characterized this system by determining which genes are regulated by quorum sensing in this methane-oxidizer using RNA-seq, and discovered this system regulates the expression of a novel nonribosomal peptide synthetase biosynthetic gene cluster. These results identify and characterize a mode of cellular communication in an aerobic methane-oxidizing bacterium. Samples are 2 sets of biological replicates of a Methylobacter tundripaludum strain 21/22 mutant where the acyl-homoserine lactone (AHL) synthase gene mbaI (T451DRAFT_0796) has been deleted. The mutant strain was grown to log (48 hours) or stationary (68 hours) phase in the absence or presence of the AHL 3-OH-C10-HSL.
2016-08-16 | E-GEOD-85617 | biostudies-arrayexpress
Project description:Yersinia pestis, the etiological agent of plague, is able to sense cell density by quorum sensing. The function of quorum sensing in Y. pestis is not clear. Here, the process of AHL quorum sensing was investigated by comparing transcript profiles when two AHL quorum-sensing signals are added in. The strain Δpgm (pigmentation-negative) mutant was called wild type. The two AHLs signals are N-(3-Oxooctanoyl)-L-homoserine lactone and N-Hexanoyl-DL-homoserine lactone.The control consisted of cells grown and treated under the same conditions without added signals.
2016-01-01 | GSE30238 | GEO
Project description:Yersinia pestis, the etiological agent of plague, is able to sense cell density by quorum sensing. The function of quorum sensing in Y. pestis is not clear. Here, the process of AHL quorum sensing was investigated by comparing transcript profiles when two AHL quorum-sensing signals are added in. The strain ∆pgm (pigmentation-negative) mutant R88 was called wild type. The two AHLs signals are N-(3-Oxooctanoyl)-L-homoserine lactone and N-Hexanoyl-DL-homoserine lactone.The control consisted of cells grown and treated under the same conditions without added signals.
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Project description:Yersinia pestis, the etiological agent of plague, is able to sense cell density by quorum sensing. The function of quorum sensing in Y. pestis is not clear. Here, the process of quorum sensing was investigated by comparing transcript profiles when three quorum-sensing signals are added in. The strain ∆pgm (pigmentation-negative) mutant R88 was used as wild type. The three signals are AI-2, AHLs (N-(3-Oxooctanoyl)-L-homoserine lactone and N-Hexanoyl-DL-homoserine lactone).The control consisted of cells grown and treated under the same conditions without added signals.
2013-09-05 | GSE22846 | GEO
Project description:Yersinia pestis, the etiological agent of plague, is able to sense cell density by quorum sensing. The function of quorum sensing in Y. pestis is not clear. Here, the process of quorum sensing was investigated by comparing transcript profiles when three quorum-sensing signals are added in. The strain M-bM-^HM-^Fpgm (pigmentation-negative) mutant R88 was used as wild type. The three signals are AI-2, AHLs (N-(3-Oxooctanoyl)-L-homoserine lactone and N-Hexanoyl-DL-homoserine lactone).The control consisted of cells grown and treated under the same conditions without added signals. Six independent RNA samples from Y. pestis CO92 M-bM-^HM-^Fpgm cultures were paired with six independent RNA samples from 3 signals added cultures for hybridization to six two-color microarrays. A dye-swap design was used to remove the Cy5 and Cy3 dye bias.
2013-09-05 | E-GEOD-22846 | biostudies-arrayexpress
Project description:We show that ZS1 in the medium supplemented with YE (YE-medium) produces more cell biomass but less rhamnolipid than it does in Glc-medium. To elucidate the transcriptional regulation of genes that are involved in biosynthesis of rhamnolipids and its precursors, RNA-seq-based transcriptional profiling of ZS1 cells in response to reciprocal change of YEand Glc-media is performed. Based on the assembly of ZS1 transcriptome using the reference PAO1 genome, we show that genes involved in energy metabolic pathways in ZS1 strain are highly transcribed in YE medium but not in Glc-medium, in agreement with their cell mass production. Similarly, transcription of quorum sensing systems genes lasI-lasR, rhlI-rhlR, and pqsH-mvfR are downregulated in Glc-medium. On the other hand, we show that two of the three enzymes RhlB and RhlC essential for rhamnolipid biosynthesis are transcriptionally upregulated, independent of quorum sensing signals. Notably, three of the four enzymes involved in dTDP-L-rhamnose, a precursor for the rhamnolipid biosynthesis, are downregulated in Glc except for RmlD that catalyzes the last reaction in the pathway. Together, our results indicate that increased rhamnolipid production in ZS1 cells is independent of quorum sensing signals. We propose that quorum sensing-independent rhamnolipid production in ZS1 Glc-culture is achieved by transcriptional re-programming of the minimum number of genes involved in rhamnolipid biosynthesis.
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Project description:The etiologic agent of bubonic plague, Yersinia pestis, senses cell density-dependent chemical signals to synchronize transcription between cells of the population in a process named quorum sensing. Though the closely related enteric pathogen Y. pseudotuberculosis uses quorum sensing system to regulate motility, the role of YpeIR quorum sensing in Y. pestis has been unclear. YpeIR is one of the AHL quorum sensing system in Y. pestis. In this study we performed transcriptional profiling experiments to identify Y. pestis YpeIR quorum sensing regulated functions at 37°C.
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Project description:Yersinia pestis, the etiological agent of plague, is able to sense cell density by quorum sensing. The function of quorum sensing in Y. pestis is not clear. Here, the process of AHL quorum sensing was investigated by comparing transcript profiles when two AHL quorum-sensing signals are added in. The strain âpgm (pigmentation-negative) mutant R88 was called wild type. The two AHLs signals are N-(3-Oxooctanoyl)-L-homoserine lactone and N-Hexanoyl-DL-homoserine lactone.The control consisted of cells grown and treated under the same conditions without added signals. Six independent RNA samples from R88 cultures were paired with six independent RNA samples from two AHLs added cultures for hybridization to six two-color microarrays. A dye-swap design was used to remove the Cy5 and Cy3 dye bias.
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