Pseudomonas putida strain:NA-1
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ABSTRACT:
PROVIDER: PRJNA546965 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR11067106_subreads.fastq.gz | Fastqsanger.gz | |||
| SRR11067107_subreads.fastq.gz | Fastqsanger.gz |
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Project description:KaiC is the central cog of the circadian clock in Cyanobacteria. Close homologs of this protein are widespread among bacteria not known to have a circadian physiology. The function, interaction network, and mechanism of action of these KaiC homologs are still largely unknown. Here, we focus on KaiC homologs found in environmental Pseudomonas species. We characterize experimentally the only KaiC homolog present in Pseudomonas putida KT2440 and Pseudomonas protegens CHA0. Through phenotypic assays and transcriptomics, we show that KaiC is involved in osmotic and oxidative stress resistance in P. putida and in biofilm production in both P. putida and P. protegens.
2023-01-04 | GSE221044 | GEO
Project description:Transcription profiling of Pseudomonas putida PP3546 mutant
2013-04-02 | E-MEXP-3655 | biostudies-arrayexpress
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
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.
2013-07-23 | GSE46491 | GEO
Project description:Sohn2010 - Genome-scale metabolic network of
Pseudomonas putida (PpuMBEL1071)
This model is described in the article:
In silico genome-scale
metabolic analysis of Pseudomonas putida KT2440 for
polyhydroxyalkanoate synthesis, degradation of aromatics and
anaerobic survival.
Sohn SB, Kim TY, Park JM, Lee
SY.
Biotechnol J 2010 Jul; 5(7):
739-750
Abstract:
Genome-scale metabolic models have been appearing with
increasing frequency and have been employed in a wide range of
biotechnological applications as well as in biological studies.
With the metabolic model as a platform, engineering strategies
have become more systematic and focused, unlike the random
shotgun approach used in the past. Here we present the
genome-scale metabolic model of the versatile Gram-negative
bacterium Pseudomonas putida, which has gained widespread
interest for various biotechnological applications. With the
construction of the genome-scale metabolic model of P. putida
KT2440, PpuMBEL1071, we investigated various characteristics of
P. putida, such as its capacity for synthesizing
polyhydroxyalkanoates (PHA) and degrading aromatics. Although
P. putida has been characterized as a strict aerobic bacterium,
the physiological characteristics required to achieve anaerobic
survival were investigated. Through analysis of PpuMBEL1071,
extended survival of P. putida under anaerobic stress was
achieved by introducing the ackA gene from Pseudomonas
aeruginosa and Escherichia coli.
This model is hosted on
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and identified by:
MODEL1507180043.
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2015-07-30 | MODEL1507180043 | BioModels
Project description:Transcriptome of the wildtype or evolved Pseudomonas putida KT2440
2020-07-08 | GSE149827 | GEO