YAMAT-seq of mature tRNA pools in the bacterium Pseudomonas fluorescens SBW25 and derivatives
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PROVIDER: PRJNA604919 | ENA |
REPOSITORIES: ENA
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Project description:Mature tRNA pools were measured using an adaptation of YAMAT-seq (Shigematsu et al., 2017; doi:10.1093/nar/gkx005 ) and further described in (Ayan et al., 2020; doi:10.7554/eLife.57947) in eight strains dervied from the model bacterium, Pseudomonas fluorescens SBW25. The aim of the experiment was to determine the effect on the mature tRNA pool of (i) removing multi-copy tRNA genes by genetic engineering, and (ii) duplicating tRNA genes during a subsequent, compensatory evolution experiment. We found that (i) results in a reduction in some tRNA isotypes in the mature tRNA pool, and (ii) results in an increase in a compensatory increase in their expression.
2022-12-02 | GSE196705 | GEO
Project description:Mature tRNA pools were measured using an adaptation of Y-shaped Adapter-ligated MAture tRNA sequencing (YAMAT-seq) (Shigematsu et al., 2017) in nine strains derived from the model bacterium, Pseudomonas fluorescens SBW25. The aim of the experiment was to determine the effect on the mature tRNA pool of (i) removing the single-copy serCGA gene by genetic engineering, and (ii) duplicating the serTGA gene during a subsequent, compensatory evolution experiment. We found that (i) results in the loss of tRNA-Ser(CGA) from the mature tRNA pool, and (ii) results in a 2-fold higher expression of tRNA-Ser(UGA). tRNA-Ser(UGA) presumably substitutes for tRNA-Ser(CGA) by wobble base pairing to translate codon 5'-UCG-3'.
2020-11-02 | GSE144791 | GEO
Project description:Mature tRNA pools were measured using an adaptation of YAMAT-seq (Shigematsu et al., 2017; doi:10.1093/nar/gkx005 ) and further described in (Ayan et al., 2020; doi:10.7554/eLife.57947) in 10 strain-medium combinations (all strains dervied from the model bacterium E. coli MG1655). The aim of the experiment was to investigate the effect of reducing tRNA gene copy number on mature tRNA pools in rich and poor media.
2022-12-02 | GSE198606 | 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 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.
2019-02-07 | E-MTAB-5396 | biostudies-arrayexpress
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.
2017-08-24 | E-MTAB-5408 | biostudies-arrayexpress
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.
2013-06-17 | E-GEOD-43443 | biostudies-arrayexpress
Project description:Pseudomonas fluorescens SBW25 cultures were inoculated into the rhizospheres of barley seedlings of the Chevallier and Tipple varieties growing in axenic cultures. Bacterial cells were collected from the rhizosphere one and five days after inculation and RNA extracted from them. Culture used for inoculation (but not exposed to the rhizospheres) were used as control. The aim of the experiment was to determine the changes in gene expression of P. fluorescens SBW25 upon exposure to barley rhizosphere and also to determine if the rhizospehres of the two varieties of Barley had different effects on gene expression of P. fluorescens SBW25.
2023-05-15 | E-MTAB-12918 | biostudies-arrayexpress
Project description:The goal of this study was to evaluate the molecular mechanisms by which Brachypodium distachyon grown with and without Pseudomonas fluorescens (P. fluorescens) strain SBW25 respond to Fe deprivation. Fe deprivation induced Brachypodium secretion of phytosiderophores and reduced biomass production while inoculation with P. fluorescens resulted in alterations of extracellular metabolite abundances. Results provide insight into the role of iron in interactions between a host plant and root associated bacteria.
2020-09-22 | GSE158273 | GEO
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.
2013-06-17 | GSE43443 | GEO
Project description:Pseudomonas fluorescens SBW25 transcriptome - SBW25b
| PRJNA439765 | ENA