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The glycolytic and gluconeogenic transcriptome of Pseudomonas putida KT2440

ABSTRACT: Pseudomonas putida KT2440 is a metabolically versatile soil bacterium useful both as a model biodegradative organism and as a host of catalytic activities of biotechnological interest. In this report, we present the high-resolution transcriptome of P. putida grown in different carbon sources as revealed by deep sequencing of the corresponding RNA pools. Examination of the data from growth on glycolytic (glucose, fructose) and gluconeogenic (succinate or glycerol) substrates revealed that > 20% of the P. putida genome is differentially expressed depending on the ensuing metabolic regime. Changes affected not only metabolic genes but also a suite of global regulators, e.g. the rpoS sigma subunit of RNAP, various cold-shock proteins and the three HU histone-like proteins. Specifically, the genes encoding HU subunit variants hupA, hupB and hupN drastically altered their expression levels (and thus their ability to form heterodimeric combinations) under the different growth conditions. Furthermore, we found that the two small RNAs crcZ and crcY, known to inhibit the Crc protein that mediates catabolite repression in P. putida, were both down-regulated by glucose.

ORGANISM(S): Pseudomonas putida KT2440

PROVIDER: GSE46491 | GEO | 2013/07/23

SECONDARY ACCESSION(S): PRJNA200633

REPOSITORIES: GEO

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The glycolytic and gluconeogenic transcriptome of Pseudomonas putida KT2440

Project description:Pseudomonas putida KT2440 is a metabolically versatile soil bacterium useful both as a model biodegradative organism and as a host of catalytic activities of biotechnological interest. In this report, we present the high-resolution transcriptome of P. putida grown in different carbon sources as revealed by deep sequencing of the corresponding RNA pools. Examination of the data from growth on glycolytic (glucose, fructose) and gluconeogenic (succinate or glycerol) substrates revealed that > 20% of the P. putida genome is differentially expressed depending on the ensuing metabolic regime. Changes affected not only metabolic genes but also a suite of global regulators, e.g. the rpoS sigma subunit of RNAP, various cold-shock proteins and the three HU histone-like proteins. Specifically, the genes encoding HU subunit variants hupA, hupB and hupN drastically altered their expression levels (and thus their ability to form heterodimeric combinations) under the different growth conditions. Furthermore, we found that the two small RNAs crcZ and crcY, known to inhibit the Crc protein that mediates catabolite repression in P. putida, were both down-regulated by glucose. cDNA libraries from Pseudomonas supplemented with different carbon sources (glucose, glycerol, fructose, succinate) were sequenced using HiSeq 2000 to yield 91 paired-end reads. Gene expression values were compared.

2013-07-23 | E-GEOD-46491 | biostudies-arrayexpress

Gluconeogenic/Glycolytic growth in P. putida KT2440 and C. testosteroni Kf1

Project description:Data comparing protein expression during gluconeogenic growth (on succinate) versus glycolytic growth (on gluconate) of P. putida KT2440 and C. testosteroni Kf1. Quantification by diDO-IPTL (Waldbauer et al. 2017 Analytical Chemistry).

2021-07-01 | MSV000087734 | MassIVE

KT2440 vs. KT2440 _NAH7 Naphthalene

Project description:Plasmid-free Pseudomonas putida KT2440 compared with the same strain harbouring NAH7 plasmid; all the cells were grown in minimal medium (M9 with glucose) saturated with naphthalene.

2012-07-27 | E-MEXP-3411 | biostudies-arrayexpress

KT2440 vs KT2440_NAH7

Project description:Plasmid-free Pseudomonas putida KT2440 compared with the same strain harbouring NAH7 plasmid; all the cells were grown in minimal medium M9 with glucose

2012-07-27 | E-MEXP-3412 | biostudies-arrayexpress

The Crc/CrcZ-CrcY global regulatory system helps integrating gluconeogenic and glycolytic metabolism in Pseudomonas putida

Project description:In metabolically versatile bacteria, carbon catabolite repression (CCR) facilitates the preferential assimilation of the most efficient carbon sources, improving growth rate and fitness. In Pseudomonas putida, the Crc protein and the CrcZ and CrcY small RNAs (sRNAs), which are believed to antagonise Crc, are key players in CCR. Contrary to what occurs in other bacterial species, succinate or glucose elicit a weak CCR in this bacterium. We combined metabolic, transcriptomics and constraints-based metabolic flux analyses to clarify whether P. putida prefers succinate or glucose, and the role of the Crc/CrcZ-CrcY regulatory system in their metabolization. Succinate was consumed faster than glucose and allowed a higher growth rate. However, both compounds were co-metabolised when provided simultaneously. The levels of CrcZ and CrcY were lower when both substrates were present than when only one of them was provided, suggesting a role for Crc in coordinating metabolism. Metabolic reconstructions suggested that, when both substrates are present, Crc works to organize a metabolism in which carbon compounds flow in two opposite directions: from glucose to pyruvate, and from succinate to pyruvate. Therefore, Crc serves not only to favour the assimilation of preferred compounds, but also to balance the carbon fluxes, optimising metabolism and growth.

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Pseudomonas putida KT2440

Project description:The glycolytic and gluconeogenic transcriptome of Pseudomonas putida KT2440

| PRJNA200633 | ENA

Production of cis, cis-muconate from benzoate at high rate and yield by a mutant of P. putida KT2440

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

The effect of multiple phaJ deletions Pseudomonas putida KT2440 on polyhydroxyalkanoates synthesis

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

Expression profile of Pseudomonas putida KT2440 growing in myristic acid

Project description:We report the application of a high-throughput technique, RNA-seq, to study the transcriptomic pattern of P. putida KT2440 cultures using myristic acid as the sole carbon source at the exponential phase of growth compared with cultures grown with glucose as the sole carbon source. Thus, we can explore the expression of genes involved in fatty acid degradation.

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Pseudomonas putida KT2440: Control vs. indole 1mM treated

Project description:Transcriptional profiling of P. putida KT2440 cells comparing control untreated cells with 1 mM indole treated cells

2012-10-02 | GSE41254 | GEO