Exposure of non-lethal doses of furfural drives genomic alterations and phenotypic evolution in Saccharomyces cerevisiae
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PROVIDER: PRJNA863622 | ENA |
REPOSITORIES: ENA
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Project description:Using multiple genetic screening assays and high-throughput analysis approaches, this study explored the genotoxic and evolutional effects of nonlethal dosages of furfural in yeast model.
2022-08-01 | GSE210078 | GEO
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
Project description:Cellular tolerance toward furfural is a complex phenotype involved many genes, and hard to be improved by manipulating individual genes. We previously established exogenous global regulator IrrE mutants that confer Escherichia coli with significantly enhanced tolerance to furfural stress. In order to elucidate the mechanism for enhancement of furfural tolerance in the mutants and to identify new genes and pathways that can be possible targets for engineering of furfural tolerance, we carried out comparative transcriptomic with the representative strains F1-37 and WT (harboring the furfural-tolerant mutant F1-37 of IrrE and the wild type IrrE, respectively). The data from transcriptome analyses were deposited here.
2012-01-28 | GSE35100 | GEO
Project description:Cellular tolerance toward furfural is a complex phenotype involved many genes, and hard to be improved by manipulating individual genes. We previously established exogenous global regulator IrrE mutants that confer Escherichia coli with significantly enhanced tolerance to furfural stress. In order to elucidate the mechanism for enhancement of furfural tolerance in the mutants and to identify new genes and pathways that can be possible targets for engineering of furfural tolerance, we carried out comparative transcriptomic with the representative strains F1-37 and WT (harboring the furfural-tolerant mutant F1-37 of IrrE and the wild type IrrE, respectively). The data from transcriptome analyses were deposited here. Cells of furfural-tolerant mutant F1-37 and wild-type strain WT were grown in LB medium supplemented with furfural, and the cells were harvested in the exponential phase. The samples for both of these two strains were prepared in triplicate with biological replicates.
2012-01-28 | E-GEOD-35100 | biostudies-arrayexpress
Project description:Furfural is a potential mutagenic agent. To explore the global effect of furfural on genomic intergrity, chromosomal alterations in 14 furfural-treated isolates of JSC25-1 strain were determined by whole genome SNP microarrays at a resolution about 1kb. Our results showed furfural exposure results in striking elevations of both mitotic recombination and aneuploidy events in yeast.
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Project description:Metabolic survival adaptations of Plasmodium falciparum exposed to sub-lethal doses of fosmidomycin
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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
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.
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Project description:Identification of the furfural detoxifying machinery in T. pseudoethanolicus (Tps) by LC-MS/MS based proteomics for engineering cellulolytic microbes involved in bioethanol production.
2018-10-19 | PXD001446 | Pride
Project description:This study investigated the responses of ZM532 and wild-type ZM4 to acetic acid and furfural using genomics, transcriptomics and label free quantitative proteome. By Sanger sequencing technology we re-verified of previously identified 19 mutations in ZM532, but we found a total of 23 single nucleotide polymorphisms (SNPs) in the coding sequence (CDS; 4) and intergenic region (19) in ZM532. Six SNPs were however novel in this study. We also identified a total of 1865 and 14 novel differentially expressed genes (DEGs) in ZM532 and wild-type ZM4. Further we identified 1,532 proteins by label free proteome. These proteins and genes are involved in amino acid biosynthesis, macromolecules repair, glycolysis, flagella assembly, ABC transporter, fermentation, and ATP synthesis pathways and stress response. The exclusively found genes and proteins in ZM532 confirmed and help to unravel the acetic acid and furfural tolerance mechanism between ZM532 and wild-type ZM4. May be these proteins and genes play key roles in ZM532 regulation with strong expressions under acids stress conditions. Furthermore, we knocked-out and overexpressed two differentially expressed genes (DEGs), ZMO_RS02740 up-regulated and ZMO_RS06525 down-regulated to investigate their roles in acetic acid and furfural tolerance. Our knockout and complementary experiments revealed that up-regulated expression gene ZMO RS02740 and the down-regulated expression gene ZMO-RS06525 play important roles in dealing with Furfural and acetic acid stress. ZM532 can be used to substitute ZM4 as a biocatalyst for bioethanol under acetic acid and furfural condition, with a shorter fermentation time and higher productivity.
2023-05-10 | PXD030417 | Pride