Dataset Information

Exploring the Glucose Fluxotype of the E. coli y-ome Using High-Resolution Fluxomics

ABSTRACT: We have developed a robust workflow to measure high-resolution fluxotypes (metabolic flux phenotypes) for large strain libraries under fully controlled growth conditions. This was achieved by optimizing and automating the whole high-throughput fluxomics process and integrating all relevant software tools. This workflow allowed us to obtain highly detailed maps of carbon fluxes in the central carbon metabolism in a fully automated manner. It was applied to investigate the glucose fluxotypes of 180 Escherichia coli strains deleted for y-genes. Since the products of these y-genes potentially play a role in a variety of metabolic processes, the experiments were designed to be agnostic as to their potential metabolic impact. The obtained data highlight the robustness of E. coli's central metabolism to y-gene deletion. For two y-genes, deletion resulted in significant changes in carbon and energy fluxes, demonstrating the involvement of the corresponding y-gene products in metabolic function or regulation. This work also introduces novel metrics to measure the actual scope and quality of high-throughput fluxomics investigations.

OTHER RELATED OMICS DATASETS IN: PRJNA100395PRJNA95591

INSTRUMENT(S): Nuclear Magnetic Resonance (NMR) -, Liquid Chromatography MS - positive - reverse phase

SUBMITTER: Cecilia Berges

PROVIDER: MTBLS2188 | MetaboLights | 2021-05-13

REPOSITORIES: MetaboLights

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			Action	DRS
	MTBLS2188	Other
	FILES	Other
	a_MTBLS2188_LC-MS_positive_reverse-phase_metabolite_profiling.txt	Txt
	a_MTBLS2188_NMR___metabolite_profiling.txt	Txt
	i_Investigation.txt	Txt

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Exploring the Glucose Fluxotype of the <i>E. coli</i> y-ome Using High-Resolution Fluxomics.

Bergès Cécilia C Cahoreau Edern E Millard Pierre P Enjalbert Brice B Dinclaux Mickael M Heuillet Maud M Kulyk Hanna H Gales Lara L Butin Noémie N Chazalviel Maxime M Palama Tony T Guionnet Matthieu M Sokol Sergueï S Peyriga Lindsay L Bellvert Floriant F Heux Stéphanie S Portais Jean-Charles JC

Metabolites 20210426 5

We have developed a robust workflow to measure high-resolution fluxotypes (metabolic flux phenotypes) for large strain libraries under fully controlled growth conditions. This was achieved by optimizing and automating the whole high-throughput fluxomics process and integrating all relevant software tools. This workflow allowed us to obtain highly detailed maps of carbon fluxes in the central carbon metabolism in a fully automated manner. It was applied to investigate the glucose fluxotypes of 18 ...[more]

PMID: 33926117

Similar Datasets

Project description:Transcription profiling of wild type E. coli MG1655, intestine-adapted E. coli MG1655star, and E. coli MG1655 flhD mutant grown on glucose, mannose, and mucus. We previously isolated a spontaneous mutant of E. coli K-12, strain MG1655, following passage through the streptomycin-treated mouse intestine, which has colonization traits superior to the wild-type parent strain (Leatham, et. al., 2005, Infect Immun 73:8039-49) The intestine-adapted strain (E. coli MG1655star) grew faster on several different carbon sources compared to the wild-type and was non-motile due to deletion of the flhD gene. To further characterize E. coli MG1655star, we used several high-throughput genomic approaches. Whole-genome pyrosequencing did not reveal any changes on its genome, aside from the deletion at the flhDC locus, that could explain the colonization advantage of E. coli MG1655star. Microarray analysis revealed modest, yet significant induction of catabolic gene systems across the genome in both E. coli MG1655star and the isogenic flhD mutant. Catabolome analysis with Biolog GN2 Microplates revealed an enhanced ability of both E. coli MG1655star and the isogenic flhD mutant to oxidize a wide variety of carbon sources. The results show that intestine-adapted E. coli MG1655star is more fit than the wild-type for intestinal colonization because loss of FlhD results in elevated expression of genes involved in carbon and energy metabolism, leading to more efficient carbon source utilization, which results in a higher population size in the intestine. Hence mutations that enhance metabolic efficiency confer a colonization advantage. Three strains were profiled: E. coli MG1655 wildtype, E. coli flhD, and an intestine adapted strain, MG1655star, derived from the wildtype and isolated from feces after 15 days in the streptomycin treated mouse intestine, which proved to be a better colonizer than the wildtype, were grown on MOPS minimal medium containing 0.2% glucose or mannose, or mucus (10 mg/ml) and RNA was extracted from logarithmic phase cultures, and also from mucus grown cells in late log phase.

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