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Determination of ErfA regulon by DAP-seq in several Pseudomonas species

ABSTRACT: ErfA is a transcription factor of Pseudomonas aeruginosa. We here define the genome-wide binding sites of ErfA by DAP-seq in Pseudomonas aeruginosa PAO1 and IHMA87, Pseudomonas chlororaphis PA23, Pseudomonas protegens CHA0 and Pseudomonas putida KT2440.

ORGANISM(S): Pseudomonas putida Pseudomonas aeruginosa Pseudomonas protegens Pseudomonas chlororaphis

PROVIDER: GSE137648 | GEO | 2019/12/20

REPOSITORIES: GEO

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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 BioModels Database and identified by: MODEL1507180043. To cite BioModels Database, please use: BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to CC0 Public Domain Dedication for more information.

Dataset Information

Determination of ErfA regulon by DAP-seq in several Pseudomonas species

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