Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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RNA-seq analysis of E. coli BW25113 during exponential growth on M9 minimal medium supplemented with either glucose, xylose or glucose+xylose (glucose exponential phase)

ABSTRACT: Escherichia coli strain BW25113 carying the plasmid [pBR322 PihfB-mTagBFP PxylA-mRFP1] was grown on minimal M9 medium with either glucose (15 mM), xylose (18 mM), or a mix of glucose (6 mM) and xylose (11 mM). The scope here was to observe transcriptomic differences on glucose versus xylose and to pinpoint putative effects of xylose in the medium during the growth on glucose. M9 medium contains 33.7 mM Na2HPO4, 22 mM KH2PO4, 8.55 mM NaCl, 9.35 mM NH4Cl, 1 mM MgSO4, 0.3 mM CaCl2, 13.4 mM EDTA, 3;1 mM FeCl3-6H2O, 0.62 mM ZnCl2, 76 μM CuCl2-2H2O, 42 μM CoCl2-2H2O, 162 μM H3BO3, 8.1 μM MnCl2-4H2O, 1 μg.L-1 thiamine and carbon sources as described above. M9 medium was supplemented with 20 mg.L-1 chloramphenicol to maintain the plasmid pBR322 PihfB-mTagBFP PxylA-mRFP1. This plasmid was used to slow down and monitor the glucose-xylose transition, hence it has no obvious effect on the proposed datasets since they concern exponential phases. Growths were performed in 1L bioreactors (pH 7, 37°C, pO2>20%). Inoculations were done at 0.03 OD 600 nm and sampling was performed between OD 0.5 and 1. Three independent repetitions led to three biological replicates per conditions. Cell samples were processed to extract RNA using trizol/phenol treatment. ERCCs were added as a control for normalization, before ribodepletion in order to eliminate ribosomal RNAs. RNAseq analysis was carried out in IonTorrent (Ion S5, Thermofischer) on the GETbiopuce platform. The data were normalized using the R package following the TMM_exact methodology developed in the team.

INSTRUMENT(S): Ion Torrent S5

ORGANISM(S): Escherichia coli K-12

SUBMITTER:

PROVIDER: E-MTAB-14542 | biostudies-arrayexpress |

SECONDARY ACCESSION(S): ERP166411

REPOSITORIES: biostudies-arrayexpress

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Project description:Xylose induced effects on metabolism and gene expression during anaerobic growth of an engineered Saccharomyces cerevisiae on mixed glucose-xylose medium were quantified. Gene expression of S. cerevisiae harbouring an XR-XDH pathway for xylose utilisation was analysed from early cultivation when mainly glucose was metabolised, to times when xylose was co-consumed in the presence of low glucose concentrations, and finally, to glucose depletion and solely xylose being consumed. Cultivations on glucose as a sole carbon source were used as a control. Genome-scale dynamic flux balance analysis models were developed and simulated to analyse the metabolic dynamics of S. cerevisiae in the cultivations. Model simulations quantitatively estimated xylose dependent dynamics of fluxes and challenges to the metabolic network utilisation. Increased relative xylose utilisation was predicted to induce two-directionality of glycolytic flux and a redox challenge already at low glucose concentrations. Xylose effects on gene expression were observed also when glucose was still abundant. Remarkably, xylose was observed to specifically delay the glucose-dependent repression of particular genes in mixed glucose-xylose cultures compared to glucose cultures. The delay occurred during similar metabolic flux activities in the both cultures. Xylose is abundantly present together with glucose in lignocellulosic streams that would be available for the valorisation to biochemicals or biofuels. Yeast S. cerevisiae has superior characteristics for a host of the bioconversion except that it strongly prefers glucose and the co-consumption of xylose is yet a challenge. Further, since xylose is not a natural substrate of S. cerevisiae, the regulatory response it induces in an engineered yeast strain cannot be expected to have evolved for its utilisation. Dynamic cultivation experiments on mixed glucose-xylose medium having glucose cultures as control integrated with mathematical modelling allowed to resolve specific effects of xylose on the gene expression and metabolism of engineered S. cerevisiae in the presence of varying amounts of glucose.

Dataset Information

RNA-seq analysis of E. coli BW25113 during exponential growth on M9 minimal medium supplemented with either glucose, xylose or glucose+xylose (glucose exponential phase)

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