Dataset Information

Nogales2020 - Genome-scale metabolic network of Pseudomonas putida (iJN1462)

ABSTRACT: iJN1462 (i) incorporates several hundred additional genes and associated reactions resulting in new predictive capabilities, including new nutrients supporting growth; (ii) was validated by in vivo growth screens that included previously untested carbon (48) and nitrogen (41) sources; (iii) yielded gene essentiality predictions showing large accuracy when compared with a knock-out library and Bar-seq data; and (iv) allowed mapping of its network to 82 P. putida sequenced strains revealing functional core that reflect the large metabolic versatility of this species, including aromatic compounds derived from lignin.

SUBMITTER: David San León Granado

PROVIDER: MODEL2204040001 | BioModels | 2024-10-15

REPOSITORIES: BioModels

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			Action	DRS
	MODEL2204040001?filename=801611ee-d0a1-414a-86f6-f8f991a7eda6.omex	Other
	MODEL2204040001?filename=iJN1463.xml	Xml
	MODEL2204040001?filename=miniFROG%20Report_Juan_010422.xlsx	Xlsx

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Publications

High-quality genome-scale metabolic modelling of Pseudomonas putida highlights its broad metabolic capabilities.

Nogales Juan J Mueller Joshua J Gudmundsson Steinn S Canalejo Francisco J FJ Duque Estrella E Monk Jonathan J Feist Adam M AM Ramos Juan Luis JL Niu Wei W Palsson Bernhard O BO

Environmental microbiology 20191111 1

Genome-scale reconstructions of metabolism are computational species-specific knowledge bases able to compute systemic metabolic properties. We present a comprehensive and validated reconstruction of the biotechnologically relevant bacterium Pseudomonas putida KT2440 that greatly expands computable predictions of its metabolic states. The reconstruction represents a significant reactome expansion over available reconstructed bacterial metabolic networks. Specifically, iJN1462 (i) incorporates se ...[more]

PMID: 31657101

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Project description:In this study we exploited next-generation Illumina sequencing technology (Wang et al., 2009) to refine the current annotation of the KT2440 genome. Transcriptome sequencing data were queried for yet undescribed small RNAs and ORFs and employed to validate predicted operons and gene coordinates. Expression profiles were measured at 10Â°C and 30Â°C to cover the physiologic temperature profile of this mesophilic bacterium. Moreover we compared the sensitivity and specificity of transcriptome data by taking the same RNA preparations for cDNA sequencing and hybridization of Progenika and Affymetrix microarrays. This SuperSeries is composed of the SubSeries listed below. P. putida KT2440 (strain DSM6125) (Bagdasarian et al., 1981) was obtained from the German Resource Centre for Biological Material (DSMZ, (Braunschweig, Germany). Bacterial cultures were inoculated from a frozen stock culture of P. putida wild type, and incubated at 30Â°C for 8 hours at 250 rpm in LB medium. An aliquot of 0.2 mL was added to 20 mL M9 medium (Na2HPO4 33.9 g/L, KH2PO4 15.0 g/L, NaCl 2.5 g/L, NH4Cl 5.0 g/L, MgSO4 2 mM, CaCl2 0.1 mM, FeSO4 x 7 H2O 0.01 mM, pH 6.8) supplemented with 15 mM succinate as sole carbon source in a 100 mL flask and incubated overnight at 30Â°C. For RNA extraction, bacteria were grown in a 1.5 L batch culture (M9 + 15 mM succinate) using the BioFlo 110 Fermenter (New Brunswick Scientific Co., Edison, NJ) to ensure constant pH, aeration and agitation. When cultures reached mid-exponential phase (OD600 ~ 0.8) the temperature was decreased from 30Â°C to 10Â°C. Three samples, each for parallel RNA extraction, were subsequently taken immediately before temperature downshift (30Â°C) and two hours after the media had been cooled to 10Â°C. The gene expression profiles of P. putida KT2440 at 30Â°C and 10Â°C were analyzed using three different transcriptome platforms: RNA-Seq (Illumina cDNA sequencing), Affymetrix microarrays and Progenika oligonucleotide microarrays. For a detailed description of sample preparation (RNA, cDNA , labelling, hybridization etc.) refer to individual Series.