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Pseudomonas putida KT2440

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

PROVIDER: PRJNA269721 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR1698422_1.fastq.gz	Fastqsanger.gz
	SRR1698422_2.fastq.gz	Fastqsanger.gz
	SRR1698423_1.fastq.gz	Fastqsanger.gz
	SRR1698423_2.fastq.gz	Fastqsanger.gz
	SRR1698424_1.fastq.gz	Fastqsanger.gz

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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.

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Pseudomonas putida KT2440

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

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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).

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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).

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Expression data from Pseudomonas putida KT2440 (Affymetrix data)

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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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