Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1009144 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR25758790_1.fastq.gz | Fastqsanger.gz | |||
| SRR25758790_2.fastq.gz | Fastqsanger.gz | |||
| SRR25758791_1.fastq.gz | Fastqsanger.gz | |||
| SRR25758791_2.fastq.gz | Fastqsanger.gz | |||
| SRR25758792_1.fastq.gz | Fastqsanger.gz |
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Project description:High concenHigh concentration acetic acid in the fermentation medium represses cell growth, metabolism and fermentation efficiency of Saccharomyces cerevisiae, which is widely used for cellulosic ethanol production. Our previous study proved that supplementation of zinc sulfate in the fermentation medium improved cell growth and ethanol fermentation performance of S. cerevisiae under acetic acid stress condition. However, the molecular mechanisms is still unclear. To explore the underlying mechanism of zinc sulfate protection against acetic acid stress, transcriptomic and proteomic analysis were performed. The changed genes and proteins are related to carbon metabolism, amino acid biosynthesis, energy metabolism, vitamin biosynthesis and stress responses. In a total, 28 genes showed same expression in transcriptomic and proteomic data, indicating that zinc sulfate affects gene expression at posttranscriptional and posttranslational levels.tration acetic acid in the fermentation medium represses cell growth, metabolism and fermentation efficiency of Saccharomyces cerevisiae, which is widely used for cellulosic ethanol production. Our previous study proved that supplementation of zinc sulfate in the fermentation medium improved cell growth and ethanol fermentation performance of S. cerevisiae under acetic acid stress condition. However, the molecular mechanisms is still unclear. To explore the underlying mechanism of zinc sulfate protection against acetic acid stress, transcriptomic and proteomic analysis were performed. The changed genes and proteins are related to carbon metabolism, amino acid biosynthesis, energy metabolism, vitamin biosynthesis and stress responses. In a total, 28 genes showed same expression in transcriptomic and proteomic data, indicating that zinc sulfate affects gene expression at posttranscriptional and posttranslational levels.
2022-05-19 | PXD015459 | 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
Project description:The non-conventional yeast species Zygosaccharomyces bailii is remarkably tolerant to acetic acid, a highly important microbial inhibitory compound in Food Industry and Biotechnology. ZbHaa1 is the functional homologue of S. cerevisiae Haa1 and a bifunctional transcription factor able to modulate Z. bailii adaptive response to both acetic acid and copper stresses. RNA-Seq was used to investigate genomic transcription changes in Z. bailii during early response to sublethal concentrations of acetic acid (140 mM, pH 4.0) or copper (0.08 mM), and uncover the regulatory network activated by these stresses under ZbHaa1 control.
2018-12-21 | GSE113552 | GEO
Project description:The modification of the The modification of the tolerance of xylose-fermenting yeast is an urgent issue for improving ethanol production. In this study, multiple genes involving in superoxide dismutase, glutathione biosynthesis, NADPH regeneration and acetic acid degradation were overexpressed using stress-induced promoters, which is selected from the transcriptome data. Stress-induced promoters were used to realize the feedback control of the tolerant genes, which can ultimately improve the tolerance and ethanol production. We reported the stress-induced promoters for overexpressing tolerant genes and increasing yeast tolerance in a feedback manner
2022-01-01 | GSE140075 | GEO
Project description:Comparative phenotype and transcriptome analyses were performed with Bacillus cereus ATCC 14579 exposed to acid down-shock to pH 5.5 set with different acidulants. When acidified with hydrochloric acid (HCl), growth was diminished, whereas 2 mM undissociated lactic acid (HL) or acetic acid (HAc) stopped growth without inactivation (bacteriostatic condition), and 15 mM undissociated HAc caused growth arrest and, finally, cell death, as reflected by a 3 to 4 log inactivation (bactericidal condition). Within the first 60 min after pH down-shock, the intracellular ATP levels of cultures shocked with HCl were increased. The bacteriostatic pH shocks did not result in increased nor decreased intracellular ATP levels, indicating that the high energy status within the stressed aerobically grown B. cereus cells could be maintained. In contrast, exposure to 15 mM undissociated HAc resulted in significant lower ATP levels, which was in accordance with the observed inactivation. The transcriptomic responses pH down-shocked cultures were studied in the same time frame. The analyses revealed general and specific responses coupled to the different phenotypes and the acidulant used. The general acid stress response, shown in all different pH shocks, involves modulation of pyruvate metabolism and an oxidative stress response. The shifts in pyruvate metabolism include induction dehydrogenases of a butanediol fermentation pathway under non-lethal acid stress conditions and of lactate, formate, and ethanol fermentation pathways under 15 mM HAc stress. Other 15 mM HAc-specific responses were induction of the alternative electron-transport systems, including cydAB, and fatty acid biosynthesis genes. Differences in gene expression for the bacteriostatic organic acid stress conditions compared to the growth-retarded inorganic stress condition indicated a more stringent oxidative stress response, including induction of an additional catalase gene and a gene encoding a Dps-like protein. Moreover, modulations in amino acid and oligopeptide transport were also found for the 2 mM HAc and HL shocks. HL-specific and HAc-specific responses both involve amino acid metabolism. Our study on the genome-wide responses of aerobically grown B. cereus pH 5.5 shocks provides a unique overview of the different responses induced by three acidulants relevant for food preservation. Per acid down-shock three exposure times (i.e., 10, 30 and 60 min) were each compared with non-exposed cells (i.e., t0). In total 4 different pH 5.5 acid down-shocks were applied. pH 5.5 was reached by adding different acidulants i.e., hydrochloric acid (HCl), lactic acid (HL) resulting in 2 mM undissociated HL, acetic acid (HAc) resulting in 15 mM undissociated HAc, and a combination of acetic acid and hydrochloric acid (HAc/HCl) resulting in 2 mM undissociated HAc. The experiments were performed in duplicate and the duplicate samples were hybridised with a dye-swap.
2010-06-25 | E-GEOD-15140 | biostudies-arrayexpress
Project description:Furfural, phenol and acetic acid, generated during the cellulosic material pretreatment, are the representative inhbitors to yeast used for ethanol production. The responses to multi-inhbitors in industrial yeast and the tolerant strain were analyzed. We analyzed the transcriptome of the parental and tolerant strains in the presence of multi-inhibitors.
2011-08-13 | GSE31366 | GEO
Project description:Transcript profiling was performed using a wild-type C. albicans strain (CaI8+CIp10). Cells were cultured in 50 ml SC-pH3.0 to a cell density of 1x10^7 cells per ml and then either treated with control (0 mM acetic acid) or stress inducing (20 mM acetic acid) doses. Cells from the same culture were harvested after 300 min treatment. Three independent biological replicates were obtained for each condition.
2008-07-31 | E-MEXP-1633 | biostudies-arrayexpress
Project description:Acetic acid stress Acididesulfobacillus acetoxydans
| PRJEB64580 | ENA