Scheffersomyces stipitis CBS 6054
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PROVIDER: PRJNA133443 | ENA |
REPOSITORIES: ENA
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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
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.
2011-10-20 | GSE24854 | 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:In Scheffersomyces stipitis and related fungal species the genes for L-rhamnose catabolism RHA1, LRA2, LRA3 and LRA4 but not LADH are clustered. We find that located next to the cluster is a transcription factor, TRC1, which is conserved among related species.Our transcriptome analysis shows that all the catabolic genes and all genes of the cluster are up-regulated on L-rhamnose. Among the genes that were also up-regulated on L-rhamnose were two transcription factors including the TRC1. In addition, in 16 out of the 32 analysed fungal species only RHA1, LRA2 and LRA3 are in a cluster. The clustering of RHA1, LRA3 and TRC1 is also conserved in species not closely related to S. stipitis. Since the LRA4 is often not part of the cluster and it has several paralogs in L-rhamnose utilising yeasts we analysed the function of one of the paralogs, RHA41 by heterologous expression and biochemical characterization. Rha41p has similar catalytic properties but the transcript was not up-regulated on L-rhamnose. The RHA1, LRA2, LRA4 and LADH genes were previously characterized in Sheffersomyces (Pichia) stipitis. We expressed the L-rhamnonate dehydratase, Rha3p, in S. cerevisiae, estimated the kinetic constants of the protein and showed that it indeed has activity with L-rhamnonate. A six chip study using total RNA recovered from three separate cultures of S. stipitis CBS 6054 grown glucose and respectively three separate cultures grown on rhamnose
2011-11-23 | E-GEOD-28557 | biostudies-arrayexpress
Project description:Mutational profiling of Scheffersomyces stipitis (previously known as Pichia stipitis Shi21)
| PRJNA32053 | ENA
Project description:In Scheffersomyces stipitis and related fungal species the genes for L-rhamnose catabolism RHA1, LRA2, LRA3 and LRA4 but not LADH are clustered. We find that located next to the cluster is a transcription factor, TRC1, which is conserved among related species.Our transcriptome analysis shows that all the catabolic genes and all genes of the cluster are up-regulated on L-rhamnose. Among the genes that were also up-regulated on L-rhamnose were two transcription factors including the TRC1. In addition, in 16 out of the 32 analysed fungal species only RHA1, LRA2 and LRA3 are in a cluster. The clustering of RHA1, LRA3 and TRC1 is also conserved in species not closely related to S. stipitis. Since the LRA4 is often not part of the cluster and it has several paralogs in L-rhamnose utilising yeasts we analysed the function of one of the paralogs, RHA41 by heterologous expression and biochemical characterization. Rha41p has similar catalytic properties but the transcript was not up-regulated on L-rhamnose. The RHA1, LRA2, LRA4 and LADH genes were previously characterized in Sheffersomyces (Pichia) stipitis. We expressed the L-rhamnonate dehydratase, Rha3p, in S. cerevisiae, estimated the kinetic constants of the protein and showed that it indeed has activity with L-rhamnonate.
2011-11-23 | GSE28557 | GEO
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:Expression analysis of L-rhamnose catabolism in the yeast Scheffersomyces stipitis
| PRJNA139073 | ENA
Project description:Scheffersomyces stipitis Genome sequencing and assembly
| PRJNA609885 | ENA
Project description:The ascomycetes Saccharomyces cerevisiae, Candida albicans and Scheffersomyces stipitis metabolize the pentose sugar xylose very differently. S. cerevisiae fails to grow on xylose, while C. albicans can grow, and S. stipitis can both grow and ferment xylose to ethanol. However, all three species contain highly similar genes that encode xylose reductase and xylitol dehydrogenase required to convert xylose to xylulose, on which all three fungi grow. We have created C. albicans strains deleted for either or both the xylose reductase gene GRE3, and the xylitol dehydrogenase gene XYL2. As expected, all the mutant strains cannot grow on xylose, while the gre3 mutant can grow on xylitol. The gre3 and xyl2 mutants are complemented efficiently by the XYL1 and XYL2 from S. stipitis respectively. Intriguingly, the S. cerevisiae GRE3 and SOR1 genes can complement the gre3 and xyl2 mutants respectively, showing that S. cerevisiae contains the enzymatic capacity for converting xylose to xylulose. In addition, the gre3 xyl2 double mutant is effectively rescued by the xylose isomerase (XI) gene of either Piromyces or Orpinomyces, suggesting that the XI provides an alternative to the missing oxido-reductase functions in the mutant required for the xylose-xylulose conversion. Overall this work establishes that C. albicans strains engineered to lack essential steps for xylose metabolism provide a platform for the analysis of xylose metabolism enzymes from a variety of species, and confirms that S. cerevisiae has the genetic potential to convert xylose to xylulose, although non-engineered strains cannot proliferate on xylose as the sole carbon source. Transcription profile of cells in xylose compared to glucose. Two sets: Candida albicans, 1 condition ; Saccharomyces cerevisiae 2 conditions / in xylose (SX) or no sugar (S) (replicates with dye-swap)
2013-10-30 | E-GEOD-50476 | biostudies-arrayexpress