Transcriptome analysis of xylose metabolism in the methylotrophic yeast Hansenula polymopha
Ontology highlight
ABSTRACT:
ORGANISM(S): Ogataea angusta
PROVIDER: GSE43240 | GEO | 2016/01/01
SECONDARY ACCESSION(S): PRJNA185135
REPOSITORIES: GEO
Similar Datasets
Project description:The transcriptomes of H. polymorpha grown on xylose were compared with those of glucose-grown cells under both aerobic and microaerobic conditions The transcriptomes of H. polymorpha grown on xylose were compared with those of glucose-grown cells under both aerobic and microaerobic conditions
2016-07-03 | E-GEOD-43240 | biostudies-arrayexpress
Project description:In the present study transcriptome and proteome of recombinant, xylose-utilising S. cerevisiae grown in aerobic batch cultures on xylose were compared with glucose-grown cells both in glucose repressed and derepressed states. The aim was to study at genome-wide level how signalling and carbon catabolite repression differed in cells grown on either glucose or xylose. The more detailed knowledge about is xylose sensed as a fermentable carbon source, capable of catabolite repression like glucose, or is it rather recognised as a non-fermentable carbon source is important in achieving understanding for further engineering this yeast for more efficient anaerobic fermentation of xylose.
2008-09-24 | GSE12890 | GEO
Project description:In the present study transcriptome and proteome of recombinant, xylose-utilising S. cerevisiae grown in aerobic batch cultures on xylose were compared with glucose-grown cells both in glucose repressed and derepressed states. The aim was to study at genome-wide level how signalling and carbon catabolite repression differed in cells grown on either glucose or xylose. The more detailed knowledge about is xylose sensed as a fermentable carbon source, capable of catabolite repression like glucose, or is it rather recognised as a non-fermentable carbon source is important in achieving understanding for further engineering this yeast for more efficient anaerobic fermentation of xylose. Experiment Overall Design: Three aerobic batch fermentations were carried out both on 50 g l-1 glucose and on 50 g l-1 xylose to compare the yeast transcriptome and proteome of cells growing on xylose with that of glucose repressed and glucose derepressed cells. Samples of the xylose-grown cells were harvested at 72 h from the start of the xylose cultures with 32 g l-1 of residual xylose present. Samples of the glucose repressed cells were harvested at 5 h from the start of the glucose cultures with 37 g l-1 of residual glucose present. Samples of the glucose derepressed cells were harvested at 24 h from the start of the glucose cultures containing no glucose but 13 g l-1 of accumulated ethanol.
2008-10-26 | E-GEOD-12890 | biostudies-arrayexpress
Project description:A recombinant C. utilis strain expressing Candida shehatae xylose reductase K275R/N277D (NADH-preferring), C. shehatae xylitol dehydrogenase and Pichia stipitis xylulokinase produce ethanol from xylose. Here, we report the transcriptional-profiling in the engineered C. utilis strain grown on xylose using DNA microarray. Transcriptome analysis indicated that expression of genes encoding the tricarboxylic acid cycle, respiration enzymes and the ethanol consumption were increased significantly when cells were cultivated on xylose. Gene expression in Candida utilis cells grown on glucose or xylose was measured at 10.5 and 24 hours, respectively. Two or three independent experiments were performed at each time for each experiment.
2014-01-01 | E-GEOD-43514 | biostudies-arrayexpress
Project description:Our study is the first investigation of proteome of oleaginous yeast Rhotodorula toruloides during conversion of xylose into lipids. We performed comparative proteomics of R. toruloides during cultivation of two carbon sources: glucose and xylose. Proteome analysis revealed significantly lower levels of ribosomal proteins and translation associated factors in xylose-grown cells as compared to glucose-grown cells. We showed that proteins involved in sugar transport, phospholipid and leucine biosynthesis as well as peroxisomal beta-oxidation and oxidative stress response were differentially regulated in response to carbon source.
2019-08-08 | PXD012332 | Pride
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.
2016-05-24 | GSE69966 | GEO
Project description:Different genetic engineering strategies have been proposed to obtain E. coli strains that selectively consume xylose. In this study, a previously reported strategy for obtaining a xylose-selective strain in E. coli K12 was applied to E. coli BL21 (DE3). While this approach resulted in the expected xylose-selective phenotype, a low xylose consumption rate was recorded when the strain was grown on a mixture of xylose and glucose. To enhance xylose consumption, a variant of the transcriptional activator XylR was expressed. The resulting strain not only exhibited an improved capacity to consume xylose but also slightly recovered the ability to consume glucose. The aim of the microarray analysis was to identify the transcriptional changes associated with glucose assimilation in the BL21(DE3) derived xylose-selective strain.
2024-10-01 | GSE277741 | GEO
Project description:This SuperSeries is composed of the following subset Series: GSE24853: Expression analysis of Spathaspora passalidarum NRRL Y-27907 grown in glucose or xylose GSE24854: Expression analysis of Pichia stipitis CBS 6054 grown in glucose or xylose GSE24855: Expression analysis of Lodderomyces elongisporus NRRL YB-4239 grown in glucose or xylose GSE24856: Expression analysis of Candida tenuis NRRL Y-1498 grown in glucose or xylose GSE24857: Expression analysis of Candida albicans WO-1 grown in glucose or xylose Refer to individual Series
2011-10-19 | E-GEOD-24858 | biostudies-arrayexpress
Project description:To select candidate promoters that function in the presence of xylose, we performed comprehensive gene expression analyses using xylose-utilizing yeast strains both during xylose and glucose fermentation.
2017-04-11 | GSE97580 | GEO
Project description:Investigation of whole genome gene expression level changes in Candida albicans WO-1 grown aerobically in xylose, compared to the same strain grown aerobically in glucose.
2011-10-20 | GSE24857 | GEO