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Expression analysis of Pichia stipitis CBS 6054 grown in glucose or xylose

ABSTRACT: Investigation of whole genome gene expression level changes in Pichia stipitis CBS 6054 grown aerobically in xylose, compared to the same strain grown aerobically in glucose.

ORGANISM(S): Scheffersomyces stipitis CBS 6054

PROVIDER: GSE24854 | GEO | 2011/10/20

SECONDARY ACCESSION(S): PRJNA133443

REPOSITORIES: GEO

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Expression analysis of Pichia stipitis CBS 6054 grown in glucose or xylose

Project description:Investigation of whole genome gene expression level changes in Pichia stipitis CBS 6054 grown aerobically in xylose, compared to the same strain grown aerobically in glucose. A six array study using total RNA recovered from three separate cultures of Pichia stipitis CBS 6054 grown in glucose and three separate cultures of Pichia stipitis CBS 6054 grown in xylose. Each array measures the expression level of 374,100 probes (average probe length 53.6 +/- 4.1 nt) tiled across the Pichia stipitis CBS 6054 genome with a median spacing distance of 33 nt. During data processing, probes are filtered to include only those probes corresponding to annotated protein-coding genes.

2011-10-19 | E-GEOD-24854 | biostudies-arrayexpress

Expression analysis of various fungi grown in glucose or xylose

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

Xylose metabolism in Candida utilis

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

Expression analysis of Candida albicans WO-1 grown in glucose or xylose

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

Expression analysis of Candida tenuis NRRL Y-1498 grown in glucose or xylose

Project description:Investigation of whole genome gene expression level changes in Candida tenuis NRRL Y-1498 grown aerobically in xylose, compared to the same strain grown aerobically in glucose.

2011-10-20 | GSE24856 | GEO

Expression analysis of Lodderomyces elongisporus NRRL YB-4239 grown in glucose or xylose

Project description:Investigation of whole genome gene expression level changes in Lodderomyces elongisporus NRRL YB-4239 grown aerobically in xylose, compared to the same strain grown aerobically in glucose.

2011-10-20 | GSE24855 | GEO

Expression analysis of Spathaspora passalidarum NRRL Y-27907 grown in glucose or xylose

Project description:Investigation of whole genome gene expression level changes in Spathaspora passalidarum NRRL Y-27907 grown aerobically in xylose, compared to the same strain grown aerobically in glucose.

2011-10-20 | GSE24853 | GEO

Scheffersomyces stipitis CBS 6054

Project description:Expression analysis of Pichia stipitis CBS 6054 grown in glucose or xylose

| PRJNA133443 | ENA

Metabolomic and transcriptomic analysis for rate-limiting metabolic steps in xylose utilization by recombinant Candida utilis

Project description:We previously reported that a recombinant Candida utilis strain expressing a Candida shehatae xylose reductase K275R/N277D, a C. shehatae xylitol dehydrogenase, and xylulokinase from Pichia stipitis produced ethanol from xylose. However, its productivity was low. In this study, metabolomic (CE-TOF MS) and transcriptomic (microarray) analyses were performed to characterize xylose metabolism by the engineered C. utilis and to identify key genetic changes contributing to efficient xylose utilization. Metabolomic analysis revealed that the xylose-fermenting strain accumulated more pentose phosphate pathway intermediates, more NADH, and more glycolytic intermediates upstream of glyceraldehyde 3-phosphate than wild-type. Transcriptomic analysis of the strain grown on xylose indicated a significant increase in expression of genes encoding tricarboxylic acid cycle enzymes, respiratory enzymes, and enzymes involved in ethanol oxidation. To decrease the NADH/NAD+ ratio and increase ethanol yield from the fermentation of xylose, ADH1 encoding NADH-dependent alcohol dehydrogenase was overexpressed. The resultant strain exhibited a 17% increase in ethanol production and a 22% decrease in xylitol accumulation relative to the control.

2014-01-01 | GSE43514 | GEO

Expression analysis of Candida albicans WO-1 grown in glucose or xylose

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. A six array study using total RNA recovered from three separate cultures of Candida albicans WO-1 grown in glucose and three separate cultures of Candida albicans WO-1 grown in xylose. Each array measures the expression level of 373,067 probes (average probe length 55.2 +/- 4.0 nt) tiled across the Candida albicans WO-1 genome with a median spacing distance of 31 nt. During data processing, probes are filtered to include only those probes corresponding to annotated protein-coding genes.

2011-10-19 | E-GEOD-24857 | biostudies-arrayexpress

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