RNA-seq data showing the effects of rpoD mutation t1682c in Pseudomonas fluorescens
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ABSTRACT:
ORGANISM(S): Pseudomonas fluorescens SBW25
PROVIDER: GSE116490 | GEO | 2019/03/01
REPOSITORIES: GEO
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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 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.
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2022-12-02 | GSE196705 | GEO
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:Pseudomonas species are ubiquitous in plant-associated environments and produce an array of volatiles, enzymes and antimicrobials. The biosynthesis of many metabolites is regulated by the GacS/GacA two-component regulatory system. Transcriptome analysis of Pseudomonas fluorescens SBW25 revealed that 702 genes were differentially regulated (fold change>4, P<0.0001) in a gacS::Tn5 mutant, with 300 and 402 genes up- and down-regulated, respectively. Genes that were significantly down-regulated are involved in viscosin biosynthesis (viscABC), protease production (aprA), motility, biofilm formation, and secretory systems. Genes that were significantly up-regulated are involved in siderophore biosynthesis and oxidative stress. In contrast to previous studies with gac-mutants of other Pseudomonas species/strains, the gacS mutant of SBW25 inhibited growth of oomycete, fungal and bacterial pathogens significantly more than parental strain SBW25. A potential candidate for this enhanced antimicrobial activity was a large nonribosomal peptide synthetase (NRPS) gene cluster predicted to encode for an 8-amino-acid ornicorrugatin-like peptide. Site-directed mutagenesis of an NRPS gene in this cluster, however, did not lead to a reduction in the antimicrobial activity of the gacS mutant. Collectively these results indicate that a mutation in the GacS/GacA regulatory system causes major transcriptional changes in P. fluorescens SBW25 and significantly enhances its antimicrobial activities by yet unknown mechanisms. This expression study used total RNA recovered from four separate wild-type cultures of Pseudomonas fluorescens SBW25 and four separate cultures of the gacS mutant. Expression design was based on the updated genome sequence of Pseudomonas fluorescens SBW25, NC_012660.1 and associated plasmid pQBR0476 with nineteen 60-mer probe per gene. Each probe is replicated 3 times. The design includes random GC and other control probes.
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Project description:Pseudomonas species are ubiquitous in plant-associated environments and produce an array of volatiles, enzymes and antimicrobials. The biosynthesis of many metabolites is regulated by the GacS/GacA two-component regulatory system. Transcriptome analysis of Pseudomonas fluorescens SBW25 revealed that 702 genes were differentially regulated (fold change>4, P<0.0001) in a gacS::Tn5 mutant, with 300 and 402 genes up- and down-regulated, respectively. Genes that were significantly down-regulated are involved in viscosin biosynthesis (viscABC), protease production (aprA), motility, biofilm formation, and secretory systems. Genes that were significantly up-regulated are involved in siderophore biosynthesis and oxidative stress. In contrast to previous studies with gac-mutants of other Pseudomonas species/strains, the gacS mutant of SBW25 inhibited growth of oomycete, fungal and bacterial pathogens significantly more than parental strain SBW25. A potential candidate for this enhanced antimicrobial activity was a large nonribosomal peptide synthetase (NRPS) gene cluster predicted to encode for an 8-amino-acid ornicorrugatin-like peptide. Site-directed mutagenesis of an NRPS gene in this cluster, however, did not lead to a reduction in the antimicrobial activity of the gacS mutant. Collectively these results indicate that a mutation in the GacS/GacA regulatory system causes major transcriptional changes in P. fluorescens SBW25 and significantly enhances its antimicrobial activities by yet unknown mechanisms.
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Project description:RNA-seq data showing the effects of rpoD mutation t1682c in Pseudomonas fluorescens
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