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RNA expression for ethanologenic Escherichia coli strain LY180 in the absence and presence of 15 mM furfural for 15 min

ABSTRACT: The data explore the transcriptional response of strain LY180 to 15 mM furfural under anaerobic fermentation conditions. The expression differences of oxidoreductase in LY180 are described.

ORGANISM(S): Escherichia coli Escherichia coli str. K-12 substr. MG1655

PROVIDER: GSE34956 | GEO | 2012/01/10

SECONDARY ACCESSION(S): PRJNA150953

REPOSITORIES: GEO

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RNA expression for ethanologenic Escherichia coli strain LY180 in the absence and presence of 15 mM furfural for 15 min

Project description:The data explore the transcriptional response of strain LY180 to 15 mM furfural under anaerobic fermentation conditions. The expression differences of oxidoreductase in LY180 are described. Total RNA was prepared from cultures of LY180 immediately before and 15 min after addition of furfural to 15 mM. The NimbleGen TI83333 chip measures expression of 4,237 genes, with 5 replicates, and 18 probes average per gene.

2012-01-10 | E-GEOD-34956 | biostudies-arrayexpress

RNA expression for ethanologenic E coli strains LY180, EMFR9 and EMFR35 in the absence and presence of 5mM and 15 mM furfural for 15 min

2013-04-29 | GSE46442 | GEO

RNA expression for ethanologenic E coli strains LY180, EMFR9 and EMFR35 in the absence and presence of 5mM and 15 mM furfural for 15 min

Project description:The data explore the transcriptional response of strains LY180 and EMFR9 to 5 mM furfural under anaerobic fermentation condition The data explore the transcriptional response of strains LY180 and EMFR35 to 15 mM furfural under anaerobic fermentation condition The expression differences of polyamine transporters in LY180 vs EMFR9 and EMFR35 are further described in RD Geddes,X Wang, LP Yomano, EN Miller, H Zheng, KT Shanmugam, and LO Ingram. 2013. Selected Polyamines and Polyamine Transporters Increase Furfural Tolerance (in preparation for submission to Appl Env Microbiol) Total RNA was prepared from cultures of LY180, EMFR9 and EMFR35 immediately before and 15 min after addition of furfural (5mM and 15 mM). The Nimblegen TI83333 chip measures expression of 4,237 genes, with 5 replicates, and 18 probes average per gene. The complete dataset comprising 8 samples is linked below as a supplementary file.

2013-04-29 | E-GEOD-46442 | biostudies-arrayexpress

Response of ethanologenic E coli strains LY180 and EMFR9 to furfural

Project description:The data explore the transcriptional response of strain LY180 and the furfural-resistant derivative EMFR9 to 0.5 g/L furfural LY180 and EMFR9 and differences in their expression profiles are described in Miller, E. N., L. R. Jarboe, L. P. Yomano, S. W. York, K. T. Shanmugam, and L. O. Ingram. 2009. Silencing of NADPH-dependent oxidoreductase genes (yqhD and dkgA) in furfural-resistant ethanologenic Escherichia coli. Appl Environ Microbiol 75:4315-23. The response of LY180 to furfural is described in Miller, E. N., L. R. Jarboe, P. C. Turner, P. Pharkya, L. P. Yomano, S. W. York, D. Nunn, K. T. Shanmugam, and L. O. Ingram. 2009. Furfural Inhibits Growth by Limiting Sulfur Assimilation in Ethanologenic Escherichia coli strain LY180. Appl Environ Microbiol., 2009.

2009-08-25 | GSE17786 | GEO

Response of ethanologenic E coli strains LY180 and EMFR9 to furfural

2010-05-06 | E-GEOD-17786 | biostudies-arrayexpress

RNA expression for ethanologenic E coli strains LY180 and LY180 del yqhC in the absence and presence of furfural

2010-08-24 | GSE17788 | GEO

Genomic instability induced by furfural-treated in S. cerevisiae [whole genome]

Project description:Furfural is a key inhibitor in S. cerevisiae fermentation causing serious economic loss. To understand the toxic mechanisms of furfural-induced genomic instability and phenotypic evolution, we mapped chromosomal alterations in 21 furfural-treated yeast strains by whole genome SNP microarrays at a resolution about 1kb.

2017-10-13 | GSE104879 | GEO

RNA expression for ethanologenic E coli strains LY180 and LY180 del yqhC in the absence and presence of furfural

Project description:The data explore the transcription of strain LY180 and the yqhC deletion mutant LY180 del yqhC without and with 0.5 g/L furfural. LY180 and LY180 del yqhC are described in Turner, PC, EN Miller, LR Jarboe, P Pharkya, KT Shanmugam, and LO Ingram. 2009. Escherichia coli YqhC regulates transcription of the adjacent yqhD and dkgA genes, and mutations in yqhC contribute to furfural resistance in ethanologenic strains (in preparation for submission to Appl Env Microbiol) Total RNA was prepared from cultures of LY180 and LY180 del yqhC immediately before and 15 min after addition of furfural to 0.5 g/L. The Nimblegen TI83333 chip measures expression of 4,237 genes, with 5 replicates, and 18 probes average per gene.

2010-08-24 | E-GEOD-17788 | biostudies-arrayexpress

Effect of furfural on the Clostridium beijerinckii NCIMB 8052 transcriptome

Project description:Furfural is the prevalent microbial inhibitor generated during pretreatment and hydrolysis of lignocellulosic biomass to monomeric sugars, but the molecular response of Clostridium beijerinckii NCIMB 8052 to this compound is unknown. To discern the effect of furfural on C. beijerinckii and to gain insights into the molecular mechanisms of action and detoxification, we studied the physiological changes of furfural-stressed cultures during acetone-butanol-ethanol (ABE) fermentation, and profiled differentially expressed genes by genome-wide transcriptional analysis. C. beijerinckii exposed to furfural stress during the acidogenic growth phase produced 13% more ABE than the unstressed control. The growth and ABE by C. beijerinckii ceased following exposure to furfural stress during the solventogenic growth phase. By comparing gene expression of furfural-stressed cultures to that of the unstressed control, at both the acidogenic and solventogenic phases, we ascertained that furfural induces expression of several genes including those that code for heat shock proteins, redox enzymes and cofactor associated proteins, and ATP-binding cassette transporters, and represses genes belonging to the phosphotransferase system, two-component system, chemotaxis and cell motility. Based on these results, we discuss the underpinning for furfural-mediated change in ABE fermentation by the solventogenic Clostridium species.

2012-12-06 | GSE42597 | GEO

Saccharomyces cerevisiae stress responses to HMF and furfural

Project description:The inhibitors hydroxymethylfurfural (HMF) and furfural were added to the feed-medium of carbon-limited anaerobic chemostat cultures. Samples were taken for transcriptome analysis at steady-state from cultures with inhibitors and without inhibitors.

2012-10-18 | GSE41659 | GEO

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