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Expression data from Pseudomonas putida KT2440: Fuelling the central metabolism with aromatic compounds

ABSTRACT: We used Progenika oligonucleotide arrays to monitore the gene expression of P. putida during carbon source stimulus experiments.

ORGANISM(S): Pseudomonas putida KT2440

PROVIDER: GSE26785 | GEO | 2014/02/01

SECONDARY ACCESSION(S): PRJNA136257

REPOSITORIES: GEO

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Expression data from Pseudomonas putida KT2440: Fuelling the central metabolism with aromatic compounds

Project description:We used Progenika oligonucleotide arrays to monitore the gene expression of P. putida during carbon source stimulus experiments. After ensuring steady state conditions on benzoate, the stimuli were introduced by changing the carbon source from benzoate to glucose, from glucose to fructose and from fructose to benzoate, respectively. The single stimuli were monitored over a time period from 10 to 120 minutes after changing the carbon source by three representative timepoints. Moreover, the steady state conditions were compared among each other. Supplementary file: Individual normalized signal intensity VALUES for each channel of each array are provided in the FullNormalizedMatrix.txt file.

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Expression data from Pseudomonas putida KT2440 (Affymetrix data)

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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 (RNA-Seq data)

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Expression data from Pseudomonas putida KT2440 Tn5 mutants

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Outer membrane vesicles catabolize lignin-derived aromatic compounds in Pseudomonas putida KT2440.

Project description:Lignin is an abundant and recalcitrant component of plant cell walls. While lignin degradation in nature is typically attributed to fungi, growing evidence suggests that bacteria also catabolize this complex biopolymer. However, the spatiotemporal mechanisms for lignin catabolism remain unclear. Improved understanding of this biological process would aid in our collective knowledge of both carbon cycling and microbial strategies to valorize lignin to value-added compounds. Here, we examine lignin modifications and the exoproteome of three aromatic-catabolic bacteria: Pseudomonas putida KT2440, Rhodoccocus jostii RHA1, and Amycolatopsis sp. ATCC 39116. P. putida cultivation in lignin-rich media is characterized by an abundant exoproteome that is dynamically and selectively packaged into outer membrane vesicles (OMVs). Interestingly, many enzymes known to exhibit activity toward lignin-derived aromatic compounds are enriched in OMVs from early to late stationary phase, corresponding to the shift from bioavailable carbon to oligomeric lignin as a carbon source. In vivo and in vitro experiments demonstrate that enzymes contained in the OMVs are active and catabolize aromatic compounds. Taken together, this work supports OMV-mediated catabolism of lignin-derived aromatic compounds as an extracellular strategy for nutrient acquisition by soil bacteria and suggests that OMVs could potentially be useful tools for synthetic biology and biotechnological applications.

| S-EPMC7196908 | biostudies-literature

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