Expression profile of Pseudomonas putida KT2440 growing in myristic acid
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ABSTRACT:
ORGANISM(S): Pseudomonas putida KT2440
PROVIDER: GSE116756 | GEO | 2018/12/31
REPOSITORIES: GEO
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Project description:In this study we exploited next-generation Illumina sequencing technology (Wang et al., 2009) to refine the current annotation of the KT2440 genome. Transcriptome sequencing data were queried for yet undescribed small RNAs and ORFs and employed to validate predicted operons and gene coordinates. Expression profiles were measured at 10°C and 30°C to cover the physiologic temperature profile of this mesophilic bacterium. Moreover we compared the sensitivity and specificity of transcriptome data by taking the same RNA preparations for cDNA sequencing and hybridization of Progenika and Affymetrix microarrays. This SuperSeries is composed of the SubSeries listed below. P. putida KT2440 (strain DSM6125) (Bagdasarian et al., 1981) was obtained from the German Resource Centre for Biological Material (DSMZ, (Braunschweig, Germany). Bacterial cultures were inoculated from a frozen stock culture of P. putida wild type, and incubated at 30°C for 8 hours at 250 rpm in LB medium. An aliquot of 0.2 mL was added to 20 mL M9 medium (Na2HPO4 33.9 g/L, KH2PO4 15.0 g/L, NaCl 2.5 g/L, NH4Cl 5.0 g/L, MgSO4 2 mM, CaCl2 0.1 mM, FeSO4 x 7 H2O 0.01 mM, pH 6.8) supplemented with 15 mM succinate as sole carbon source in a 100 mL flask and incubated overnight at 30°C. For RNA extraction, bacteria were grown in a 1.5 L batch culture (M9 + 15 mM succinate) using the BioFlo 110 Fermenter (New Brunswick Scientific Co., Edison, NJ) to ensure constant pH, aeration and agitation. When cultures reached mid-exponential phase (OD600 ~ 0.8) the temperature was decreased from 30°C to 10°C. Three samples, each for parallel RNA extraction, were subsequently taken immediately before temperature downshift (30°C) and two hours after the media had been cooled to 10°C. The gene expression profiles of P. putida KT2440 at 30°C and 10°C were analyzed using three different transcriptome platforms: RNA-Seq (Illumina cDNA sequencing), Affymetrix microarrays and Progenika oligonucleotide microarrays. For a detailed description of sample preparation (RNA, cDNA , labelling, hybridization etc.) refer to individual Series.
2011-03-25 | E-GEOD-24176 | biostudies-arrayexpress
Project description:The completely sequenced catabolic plasmid pCAR1 of Pseudomonas resinovorans CA10 confers the ability to degrade carbazole upon the recipient strain Pseudomonas putida KT2440. To study the coordinated expression of pCAR1 with its host chromosome, transcriptome of the transconjugant strain KT2440(pCAR1) was analyzed at growth with carbazole as the sole carbon source compared to succinate as an alternative carbon source. Next, horizontal gene transfer of a plasmid potentially alters the transcriptome of its host chromosome. Transcriptome of the transconjugant strain KT2440(pCAR1) was compared to the parental strain KT2440 at the same growth conditions. Furthermore, pCAR1 encodes a possible global regulator designated ORF70, which belongs to the MvaT family of H-NS-like nucleoid-associated proteins in Pseudomonas. To investigate the regulon under the control of ORF70, transcriptome of KT2440(pCAR1deltaORF70) was compared to the parental strain KT2440(pCAR1) at the same growth conditions. Keywords: Comparative transcriptome analysis
2007-05-01 | GSE7650 | GEO
Project description:DNA microarrays were carried out to compare the transcriptional profiles of P. putida KT2440 and its isogenic knock-out mutant in agmR gene (mut agmR) when grown in M9 medium with glucose as a sole carbon source and in absense of chloramphenicol or any other stressor compound.
2011-12-01 | E-MEXP-3203 | biostudies-arrayexpress
Project description:Pseudomonas putida is characterized by a versatile metabolism and stress tolerance traits that allow the bacterium to cope with different environmental conditions. In this work, the mechanisms that allow P. putida KT2440 to grow in the presence of four sole carbon sources (glucose, citrate, ferulic acid, serine) were investigated by RNA sequencing (RNA-seq) and genome-scale metabolic modeling. Transcriptomic data identified uptake systems for the four carbon sources, and candidates were subjected to preliminary experimental characterization by mutant strain growth to test their involvement in substrate assimilation. The OpdH and BenF-like porins were involved in citrate and ferulic acid uptake, respectively. The citrate transporter (encoded by PP_0147) and the TctABC system were important for supporting cell growth in citrate; PcaT and VanK were associated with ferulic acid uptake; and the ABC transporter AapJPQM was involved in serine transport. A genome-scale metabolic model of P. putida KT2440 was used to integrate and analyze the transcriptomic data, identifying and confirming the active catabolic pathways for each carbon source. This study reveals novel information about transporters that are essential for understanding bacterial adaptation to different environments.
2018-10-23 | GSE118554 | GEO
Project description:Genome-wide scanning of gene expression by microarray techniques was successfully performed on RNA extracted from a sterilized soil inoculated with Pseudomonas putida KT2440/pSL1, which contains a chloroaromatic degrading plasmid, in the presence or absence of 3-chlorobenzoic acid (3CB). The genes showing significant changes in their expression in both triplicate microarray analyses using amplified RNA and single microarray analysis using unamplified RNA were investigated. Pathway analysis revealed that the benzoate degradation pathway underwent the most significant changes following treatment with 3CB. Analysis based on categorization of differentially expressed genes against 3CB revealed new findings about the cellular responses of the bacteria to 3CB, including upregulation of the genes specifically involved in transport of 3CB, and induction of a K+/H+ antiporter complex, an universal stress protein, two cytochrome P450 proteins and an efflux transporter. Downregulated expression of some genes involved in carbon metabolism and the genes belong to a prophage in the presence of 3CB was observed. This study demonstrated the applicability of the method of soil RNA extraction for microarray analysis through a proof-of-concept experiment using a sterilized soil inoculated with Pseudomonas putida KT2440/pSL1. A study using total RNA extracted from soil cultures of Pseudomonas putida KT2440/pSL1. Each chip measures the expression level of 5,341 genes from the Pseudomonas putida KT2440 genome with two sets of six 60-mer probes per gene.
2011-03-29 | E-GEOD-28215 | biostudies-arrayexpress
Project description:P. putida KT2440-JD1 was derived from P. putida KT2440 after NTG-mutagenesis and exposure to 3-fluorobenzoate. The strain was no longer able to grow with benzoate as a single source of carbon and energy. Instead, benzoate was co-metabolized to cis, cis-muconate, which accumulated in the culture medium while grown on glucose. During continuous cultivations with glucose as a growth substrate, benzoate was co-metabolized to cis, cis-muconate with a molar product yield (Y(P/S)) of 0.88 ±0.01 mol cis, cis-muconate/ mol benzoate and a specific production rate (qpm) of 0.18 ±0.03 g cis, cis-muconate/ (gDCW* h). During wash-out cultivation a maximum growth rate of 0.6 h-1 and a maximum qpm of 1.4 g cis, cis-muconate/ (gDCW* h) were obtained. Analysis of the transcriptome revealed that the cat operon was no longer induced in P. putida KT2440-JD1 in the presence of 5 mM benzoate. This was also confirmed on the proteomic level for CatA and CatB. A point mutation in catR in P. putida KT2440-JD1 changed the highly conserved Arg50 in the DNA binding domain to Cys50, resulting in the inactivation of the transcriptional regulator of the cat operon. A catechol 1,2-dioxygenase that is encoded by gene PP_3166 (catA2) on the ben operon is likely to convert catechol to cis, cis-muconate in P. putida KT2440-JD1.
2013-05-15 | GSE25329 | GEO
Project description:The response of P. putida KT2440 (PB2440) to preferential carbon source and varying nitrogen levels was studied in this experiment. The culture was grown in minimal medium with 2mM glucose as carbon source and different concentration of ammonium chloride as nitrogen source. For nitrogen limiting condition 2mM ammonium chloride was used whereas, for nitrogen rich condition 20mM ammonium chloride was added in the medium. Overall it was seen that the strain could grow efficiently in varying nitrogen conditions by adapting or regulating their metabolism without compromising on the growth rate. To ascertain how the cells were coping with the nitrogen stress, gene expression by microarray was performed. RNA extraction was done using Qiagen RNeasy minikit (Germany). Standard Affymetrix protocol was followed for hybridization with GeneChip P. aeruginosa Genome Array supplied by Affymetrix as GeneChip for P. putida were not supplied by any company.
2014-04-24 | E-MTAB-2536 | 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: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:Expression profile of Pseudomonas putida KT2440 growing in myristic acid
| PRJNA480068 | ENA