Pseudomonas putida KT2440
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ABSTRACT:
PROVIDER: PRJNA231933 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Alginate, a major exopolysaccharide (EPS) produced by P. putida, is known to create hydrated environments and alleviate the effect of water limitation. In addition to alginate, P. putida is capable of producing cellulose (bcs), putida exopolysaccharide a (pea), and putida exopolysaccharide b (peb). However, unlike alginate, not much is known about their roles under water limitation. Hence, in this study we examined the role of different EPS under water stress. To create environmentally realistic water stress conditions as observed in soil, we used Pressurized Porous Surface Model (PPSM). Our main hypothesis was that under water stress, absence of alginate would be compensated by the other EPS. To test our hypothesis, we investigated colony morphologies and whole genome transcriptomes of P. putida KT2440 WT and its mutants deficient in either alginate or all known EPS A custom-made Nimblegen (WI, USA) whole genome one-color oligonucleotide expression array (12x135K with 45-60 mer probes) of P. putida KT2440 was used to investigate effect of water stress on the differential expression of the whole genome. In this study Pseudomonas putida KT2440 wild type (WT) and two of its mutants deficient either in alginate (Alg-), or all known EPS (EPS-) production were used and grown under dry (water stress) and wet (without water stress) conditions. (Deleted genes in Alg-: PP1277-PP128; in EPS-: PP1277-1288 (alg) + PP2634-2638 (bcs) + PP3132-3142 (pea) + PP1795-1788 (peb)) (Nilsson et al., 2011).39. Nilsson, M., Chiang, W.C., Fazli, M., Gjermansen, M., Givskov, M., and Tolker-Nielsen, T. (2011) Influence of putative exopolysaccharide genes on Pseudomonas putida KT2440 biofilm stability. Environ Microbiol. 13 (5):1 357-1369
2013-12-23 | E-GEOD-53407 | biostudies-arrayexpress
Project description:Alginate, a major exopolysaccharide (EPS) produced by P. putida, is known to create hydrated environments and alleviate the effect of water limitation. In addition to alginate, P. putida is capable of producing cellulose (bcs), putida exopolysaccharide a (pea), and putida exopolysaccharide b (peb). However, unlike alginate, not much is known about their roles under water limitation. Hence, in this study we examined the role of different EPS under water stress. To create environmentally realistic water stress conditions as observed in soil, we used Pressurized Porous Surface Model (PPSM). Our main hypothesis was that under water stress, absence of alginate would be compensated by the other EPS. To test our hypothesis, we investigated colony morphologies and whole genome transcriptomes of P. putida KT2440 WT and its mutants deficient in either alginate or all known EPS
2013-12-23 | GSE53407 | GEO
Project description:We used Progenika oligonucleotide arrays to monitor the gene expression after cold shock from 30°C to 10°C. The 10°C samples of the P. putida wild type were compared to those of the respective P. putida KT2440 Tn5 mutants affected in either cbrA (PP4695), cbrB (PP4696), pcnB (PP4697), vacB (PP4880) or bipA (PP5044).
2014-02-01 | GSE28257 | GEO
Project description:Our first aim was understand whole genome expression dynamics of Pseudomonas putida KT2440 surface colonies under water stress. Therefore, we wanted to identify significantly differentially expressed genes of at -0.4 MPa matric potential relative to the -0.5 kPa (near saturation condition) at different stress durations. Aliquots of overnight grown P. putida KT2440 cells were inoculated (approx. 100 µl and 1x107 cells) on the surface of ceramic plates. Prior to matric stress, the cells were incubated for 120, 116, 96, and 48 hr at-0.5 kPa to allow formation of a mature cell loan. -0.4 MPa matric potential was applied for the last 0 (control), 4, 24, and 72 hr of incubation periods, respectively, so that the total incubation time (at (-0.5 kPa) and (-0.4 MPa)) was kept constant as 5 days. Our second aim was to find out how the gene expression profile would change when we use PEG-8000 to simulate matric stress. To that effect, similar incubations were performed where the direct matric potential was -0.5 kPa, but supplemented with PEG-8000 to set a matric potential equivalent of -0.5 or -1.0 MPa. Incubations were again 5 days. In addition, we tested the effect of gas pressure on gene expression profile of cells in liquid medium. 20 ml of overnight grown KT2440 cells were exposed to 0.4 MPa (gauge) and 0.1 MPa (atmospheric) pressures.
2010-11-24 | GSE25512 | GEO
Project description:Pseudomonas putida KT2440 is a well-known model organism for the medium chain length (mcl) PHA accumulation. (R)-Specific enoyl-coenzyme A hydratase (PhaJ) was considered to be the main supplier of monomers for PHA synthesis by converting the -oxidation intermediate, trans-2-enoyl-CoA to (R)-3-hydroxyacyl-CoA when fatty acids (FA) are used. Three PhaJ homologues, PhaJ1, PhaJ4 and MaoC are annotated in P. putida KT2440. To investigate the relationship of fatty acids - PHA metabolism and the role of each PhaJ in PHA biosynthesis in P. putida KT2440, a series of P. putida KT2440 knockouts was obtained. PHA content and monomer composition in WT and mutants under different growth conditions were analysed. However, when all three PhaJ homologues were deleted, the mutant still accumulated PHA up to 10.7 % of the cell dry weight (CDW). To identify other potential PHA monomer suppliers by analysing the proteome of the phaJ1maoCphaJ4. The proteomes of the WT, phaJ1phaJ4 and phaJ1maoCphaJ4 strains in MSM medium with octanoate under nitrogen limited condition were detected. In addition, we found that the deletion of PhaJ1 in P. putida KT2440 has a negative impact on the PHA accumulation in cells cultivated on glucose with nitrogen limitation conditions. It seems PhaJ1 also mediates the synthesis of PHA when glucose was used as the carbon and energy source. To investigate the role of PhaJ1 in PHA accumulation with glucose, the proteomes of P. putida KT2440 wild type, phaJ1, phaJ1phaJ4 and phaJ1maoCphaJ4 mutant growing on glucose were detected and compared.
2023-05-10 | PXD037932 | Pride
Project description:Our first aim was understand whole genome expression dynamics of Pseudomonas putida KT2440 surface colonies under water stress. Therefore, we wanted to identify significantly differentially expressed genes of at -0.4 MPa matric potential relative to the -0.5 kPa (near saturation condition) at different stress durations. Aliquots of overnight grown P. putida KT2440 cells were inoculated (approx. 100 µl and 1x107 cells) on the surface of ceramic plates. Prior to matric stress, the cells were incubated for 120, 116, 96, and 48 hr at-0.5 kPa to allow formation of a mature cell loan. -0.4 MPa matric potential was applied for the last 0 (control), 4, 24, and 72 hr of incubation periods, respectively, so that the total incubation time (at (-0.5 kPa) and (-0.4 MPa)) was kept constant as 5 days. Our second aim was to find out how the gene expression profile would change when we use PEG-8000 to simulate matric stress. To that effect, similar incubations were performed where the direct matric potential was -0.5 kPa, but supplemented with PEG-8000 to set a matric potential equivalent of -0.5 or -1.0 MPa. Incubations were again 5 days. In addition, we tested the effect of gas pressure on gene expression profile of cells in liquid medium. 20 ml of overnight grown KT2440 cells were exposed to 0.4 MPa (gauge) and 0.1 MPa (atmospheric) pressures. Matric Stress Experiments: we had 3 to 4 replicates for each time point and controls (-0.5 kPa). These were kept under -0.4 MPa stress at 4 hr (P4), 24 hr (P24), 72 hr (P72), and controls kept at -0.5 kPa (C).
2010-11-24 | E-GEOD-25512 | biostudies-arrayexpress
Project description:We used Progenika oligonucleotide arrays to monitor the gene expression after cold shock from 30°C to 10°C. The 10°C samples of the P. putida wild type were compared to those of the respective P. putida KT2440 Tn5 mutants affected in either cbrA (PP4695), cbrB (PP4696), pcnB (PP4697), vacB (PP4880) or bipA (PP5044). Cultures were grown in minimal medium supplemented with succinate at 30°C. In mid-exponential phase, cells were cooled down to 10°C. Two hours after the medium had reached 10°C, cells were harvested for subsequent RNA extraction.
2014-02-01 | E-GEOD-28257 | biostudies-arrayexpress
Project description:Transcriptional profiling of P. putida KT2440 cells comparing control untreated cells with 1 mM indole treated cells
2012-10-02 | GSE41254 | GEO
Project description:Transcriptional profiling of P. putida KT2440 cells comparing control untreated wild type cells with untreated recG gene mutant cells or PQ treated recG gene mutant cells
2011-12-15 | GSE34410 | GEO
Project description:Transcriptome of the wildtype or evolved Pseudomonas putida KT2440
2020-07-08 | GSE149827 | GEO