Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Global gene expression analysis of (R)-1,3-butanediol catabolism in Pseudomonas putida KT2440

ABSTRACT: (R)-1,3-butanediol [(R)-1,3-BDO] is a chiral diol with potential applications in the chemical and pharmaceutical industries; however, its microbial degradation pathway remains poorly understood. In this study, we performed strand-specific, paired-end RNA-seq transcriptomic analysis of Pseudomonas putida KT2440 grown on (R)-1,3-BDO and (R)-3-hydroxybutyrate [(R)-3-HB] as sole carbon sources to elucidate the underlying degradation pathway. Gluconate was used as a reference carbon source. Differential gene expression analysis was performed to identify genes specifically induced during (R)-1,3-BDO and (R)-3-HB metabolism, providing insight into the enzymatic steps and regulatory mechanisms governing their catabolism in P. putida KT2440.

ORGANISM(S): Pseudomonas putida KT2440

PROVIDER: GSE333645 | GEO | 2026/05/28

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Understanding Isoprenol effect on Pseudomonas putida KT2440 grown on a minimal medium supplemented with glucose

Project description:Pseudomonas putida KT2440 (KT2440) has been established as an industrially relevant chassis for the production of the jet-fuel precursor isoprenol. However, the wild type KT2440 strain consumed isoprenol as sole carbon source and its growth is inhibited by isoprenol, which is an impediment to high titer, rate, yield production. In this study, we investigated genes responsible for isoprenol catabolism and the stress responses of Pseudomonas putida via RNA-seq.

2026-04-20 | GSE281392 | GEO

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

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

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.

2018-12-31 | GSE116756 | GEO

Transcriptional network between pCAR1 and KT2440 chromosome

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

Analysis of Pseudomonas putida growth on non-trivial carbon sources using transcriptomics and genome-scale modeling

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

3CB-induced gene expression of Pseudomonas putida KT2440/pSL1 in soil (with RNA amplification)

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

KT2440 wt vs. mut agmR -M9 plus glucose chloramphenicol-free medium

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

Generation of Ionic Liquid Tolerant Pseudomonas putida KT2440 Strains via Adaptive Laboratory Evolution

Project description:Transcriptome of the wildtype or evolved Pseudomonas putida KT2440

2020-07-08 | GSE149827 | 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

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data