Allomuricauda
Ontology highlight
ABSTRACT:
PROVIDER: PRJDB15463 | ENA |
REPOSITORIES: ENA
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Project description:To obtain insight in the genome-wide response of heterologous carotenoid production in Saccharomyces cerevisiae, we have analyzed the transcriptome of S. cerevisiae strains overexpressing carotenogenic genes from the yeast Xanthophyllomyces dendrorhous. For this purpose, two strains producing different levels of carotenoids were grown in carbon-limited continuous cultures and genome-wide expression was analyzed. The strain producing low carotenoid levels did not exhibit a clear genome-wide transcriptional response, suggesting that low carotenoid levels do not result in cellular stress. Transcriptome analysis of a strain producing high carotenoid levels resulted in specific induction of genes involved in pleiotropic drug resistance (PDR). These genes encode ATP-binding cassette (ABC) type transporters and major facilitator transporters which are involved in secretion of toxic compounds out of cells. Our results suggest that production of high amounts of carotenoids in S. cerevisiae lead to toxicity and that these cells are prone to secrete carotenoids out of the cell. Indeed, secretion of beta-carotene into sunflower oil was observed upon addition of this hydrophobic solvent to the growth medium. Finally, it was observed that deletion of the ABC transporter pdr10, one of the induced PDR transporters, highly decreased the transformation efficiency of an episomal vector containing carotenogenic genes. The few colored transformants that were obtained had decreased growth rates and lower carotenoid production levels compared to control strains transformed with the same carotenogenic genes. These results indicate that Pdr10 might be specifically involved in carotenoid tolerance in S. cerevisiae strains. Keywords: dose response
2008-06-01 | GSE8451 | GEO
Project description:To obtain insight in the genome-wide response of heterologous carotenoid production in Saccharomyces cerevisiae, we have analyzed the transcriptome of S. cerevisiae strains overexpressing carotenogenic genes from the yeast Xanthophyllomyces dendrorhous. For this purpose, two strains producing different levels of carotenoids were grown in carbon-limited continuous cultures and genome-wide expression was analyzed. The strain producing low carotenoid levels did not exhibit a clear genome-wide transcriptional response, suggesting that low carotenoid levels do not result in cellular stress. Transcriptome analysis of a strain producing high carotenoid levels resulted in specific induction of genes involved in pleiotropic drug resistance (PDR). These genes encode ATP-binding cassette (ABC) type transporters and major facilitator transporters which are involved in secretion of toxic compounds out of cells. Our results suggest that production of high amounts of carotenoids in S. cerevisiae lead to toxicity and that these cells are prone to secrete carotenoids out of the cell. Indeed, secretion of ï¢-carotene into sunflower oil was observed upon addition of this hydrophobic solvent to the growth medium. Finally, it was observed that deletion of the ABC transporter pdr10, one of the induced PDR transporters, highly decreased the transformation efficiency of an episomal vector containing carotenogenic genes. The few colored transformants that were obtained had decreased growth rates and lower carotenoid production levels compared to control strains transformed with the same carotenogenic genes. These results indicate that Pdr10 might be specifically involved in carotenoid tolerance in S. cerevisiae strains. Experiment Overall Design: The genome wide transcriptional response of S. cerevisiae cells that heterologously produce carotenoids might provide information concerning the impact of carotenoid production on yeast physiology and might identify bottlenecks relevant for the production of these compounds. DNA microarray experiments have been proven to be a powerful tool to study the genome wide transcriptional response of S. cerevisiae to changes of the physiological state and the environment (for example 3,. Genomics approaches on cells producing heterologous metabolites to study their impact on yeast physiology have not been reported yet for S. cerevisiae. Additionally, most transcriptome studies with S. cerevisiae have been performed with cells grown in shake flasks cultures. The main drawback of shake flask cultivation is that the environment is continuously changing, which may be of high influence on carotenoid production, and interpretation of transcriptome data . Chemostat cultivation offers advantages for studies with DNA microarrays because it enables cultivation of microorganisms under tightly defined environmental conditions. An interlaboratory comparison of transcriptome data obtained in chemostat cultures has indeed demonstrated that the accuracy and reproducibility of this approach are superior to those obtained in previous studies with shake-flask cultures .
2008-06-18 | E-GEOD-8451 | biostudies-arrayexpress
Project description:Genome sequencing of two Muricauda strains isolated from deep sea
| PRJNA556639 | ENA
Project description:Carotenoids are a large family of health-beneficial compounds that have been widely used in the food and nutraceutical industries. There have been extensive studies to engineer Saccharomyces cerevisiae for the production of carotenoids, which already gained high level. However, it was difficult to discover new targets that were relevant to the accumulation of carotenoids. Herein, a new, ethanol-induced adaptive laboratory evolution was applied to boost carotenoid accumulation in a carotenoid producer BL03-D-4, subsequently, an evolved strain M3 was obtained with a 5.1-fold increase in carotenoid yield. Through whole-genome resequencing and reverse engineering, loss-of-function mutation of phosphofructokinase 1 (PFK1) was revealed as the major cause of increased carotenoid yield. Transcriptome analysis was conducted to reveal the potential mechanisms for improved yield, and strengthening of gluconeogenesis and downregulation of cell wall-related genes were observed in M3. This study provided a classic case where the appropriate selective pressure could be employed to improve carotenoid yield using adaptive evolution and elucidated the causal mutation of evolved strain.
2021-01-09 | GSE164470 | GEO
Project description:Among colicin producing E. coli, colicin M producing strains are the most frequently present in natural populations. Bacteria must be able to sense and respond to unfavourable conditions, resulting in adaptive responses. To gain insight into colicin M ecological role and the purposes related to antimicrobial therapy, the effects of subinhibitory concentrations of colicin M on E. coli whole genome transcription was investigated. We used microarray analysis to follow differential gene expression in E. coli upon colicin M exposure. Colicin M inhibits peptidoglycan synthesis altering expression of genes involved in envelope stress, osmotic and other stresses, exopolysaccharide prodoction, biofilm formation, and cell motility.
2012-11-26 | GSE37026 | GEO
Project description:Whole genome analysis of EPS-producing human commensal bacteria S. salivarius.
| PRJDB18286 | ENA
Project description:The tangerine2 mutant identified from Diepoxybutadiene (DEB) mutagenized population of Solanum lycopersicum and the biochemical studies revealed that mutant fruits accumulate prolycopene instead of lycopene in ripened fruits. We have developed whole genome microarray expression profiling as a discovery platform to identify differentially expressed genes in fruits tangerine2 mutant in comparison to Wild type. Tomato fruit tissue samples from different stages of fruit ripening like Mature green, Breaker, Turning and Ripening stages of tangerine2 mutant and wild type was used for microarray gene expression analysis. Carotenoid pathway analysis of both mutant and wild type reveals that the absence of expression of Carotenoid isomerase (CRTISO) gene in the tangerine2 mutant, the gene which is involved in the isomerisation of prolycopene to lycopene. Four genes (PSY, PDS, CRTISO, CYCB) of the carotenoid pathway was quantified in the same RNA samples by real-time PCR, confirming that the variation of the gene expression in Tangerine2 mutant.
2018-12-01 | GSE91045 | GEO