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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Analysis of the Hfq regulon in Pseudomonas fluorescens SBW25.

ABSTRACT: Hfq is a transcriptional and translational pleiotropic regulator in several bacteria. RNA-Seq, Ribo-Seq and Proteomic analyses were carried out in the wild-type and a hfq deletion strain of Pseudomonas fluorescens SBW25 with the intention to separate the influence of Hfq on the transcript stability and translation. This submission relates to the RNA-Seq data only. RNA was extracted from two replicate cultures each of SBW25-WT and SBW25-Δhfq strains and, after removal of ribosomal RNA, subjected to RNA-Seq in an Illumina NextSeq500 machine. The resulting sequence data was analysed by mapping to the reference sequence of Pseudomonas fluorescens SBW25 as available in the Genbank accession NC_012660.

INSTRUMENT(S): Illumina MiSeq

ORGANISM(S): Pseudomonas fluorescens

SUBMITTER: Govind Chandra

PROVIDER: E-MTAB-5396 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Ribosome profiling of Pseudomonas fluorescens SBW25 and its hfq deletion mutant.

Project description:Hfq is a transcriptional and translational pleiotropic regulator in several bacteria. RNA-Seq, Ribo-Seq and Proteomic analyses were carried out in the wild-type and a hfq deletion strain of Pseudomonas fluorescens SBW25 with the intention to separate the influence of Hfq on the transcript stability and translation. This submission relates to the Ribosome profiling data only. Ribosomes were purified from MNase treated cell lysates by density gradient ultracentrifugation from two replicate cultures each of SBW25-WT and SBW25-hfq strains. RNA was extracted from the purified ribosomes and subjected to RNA-Seq in an Illumina HiSeq2000 machine. The resulting sequence data was analysed by mapping to the reference sequence of Pseudomonas fluorescens SBW25 as available in the Genbank accession NC_012660.

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Project description:Plasmids can affect expression of genes on the host chromosome. This experiment was carried out to determine the effect of the presence of the plasmid pQBR103 (with and without the rsmQ gene on it) on global gene expression in Pseudomonas fluorescens SBW25.

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Project description:Histidine is a good source of nutrient for many bacteria, but its utilization poses a significant challenge as it delivers excess nitrogen over carbon. The rate of histidine catabolism (hut) must thus be tightly regulated. Here, in Pseudomonas fluorescens SBW25, we show that the CbrAB two-component system directly activates the transcription of hut genes, while mediating succinate-induced carbon catabolite repression of hut at the translational level via the CbrAB-CrcYZ-Hfq/Crc regulatory cascade. When growing in minimal salt medium supplemented with histidine and succinate (the most preferred carbon source), the CbrAB-mediated promoter activity is weak; and the global nitrogen regulator NtrBC plays the dominant role in directly activating hut transcription.

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Expression analysis of the gacS mutant of Pseudomonas fluorescens SBW25

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Project description:pQBR103 is a naturally occurring plasmid known to alter the behaviour of its host, Pseudomonas fluorescens. This plasmid encodes a predicted translational regulator, rsmQ which is a homologue of known global regulators within Pseudomonas. Within this study we compared Pseudomonas fluorescens SBW25 plasmid free cells with cells carrying either WT pQBR103 or pQBR103 lacking rsmQ. Using comparative quantitative proteomics and RNAseq we showed that the loss of rsmQ leads to widespread proteomic changes in the absence of changes in mRNA abundance, suggesting RsmQ is a translational regulator of its host chromosome.

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