To identify novel targets of a zinc finger transcription factor, Mxr1p in Pichia pastoris cultured in medium containing ethanol
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ABSTRACT:
PROVIDER: PRJNA713383 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR13928069_1.fastq.gz | Fastqsanger.gz | |||
| SRR13928069_2.fastq.gz | Fastqsanger.gz | |||
| SRR13928070_1.fastq.gz | Fastqsanger.gz | |||
| SRR13928070_2.fastq.gz | Fastqsanger.gz | |||
| SRR13928071_1.fastq.gz | Fastqsanger.gz |
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Project description:Comparison of transcription profile of Pichia pastoris cells grown on Glucose medium with Pichia pastoris cells grown on Methanol/Glycerol medium, the fermentations were done in a chemostat.
2015-08-31 | GSE67690 | GEO
Project description:We have identified a methanol- and biotin-starvation-inducible zinc finger protein named ROP [repressor of phosphoenolpyruvate carboxykinase (PEPCK)] in the methylotrophic yeast Pichia pastoris. When P.pastoris strain GS115 (wild-type, WT) is cultured in biotin-deficient, glucose ammonium (Bio-) medium, growth is suppressed due to the inhibition of anaplerotic synthesis of oxaloacetate, catalysed by the biotin-dependent enzyme pyruvate carboxylase (PC). Deletion of ROP results in a strain (∆ROP) that can grow under biotin-deficient conditions due to derepression of a biotin- and PC-independent pathway of anaplerotic synthesis of oxaloacetate. Northern analysis as well as microarray expression profiling of RNA isolated from WT and ∆ROP strains cultured in Bio(-) medium indicate that expression of the phosphoenolpyruvate carboxykinase gene (PEPCK) is induced in ∆ROP during biotin- or PC-deficiency even under glucose-abundant conditions. There is an excellent correlation between PEPCK expression and growth of ∆ROP in Bio(-) medium, suggesting that ROP-mediated regulation of PEPCK may have a crucial role in the biotin- and PC-independent growth of the ∆ROP strain. To our knowledge, ROP is the first example, of a zinc finger transcription factor involved in the catabolite repression of PEPCK in yeast cells cultured under biotin- or PC-deficient and glucose-abundant conditions. Agilent one-color experiment,Organism: Pichia pastoris ,Custom Pichia pastoris Gene Expression 8x15k array designed by Genotypic Technology Pvt. Ltd. (Agilent -AMADID: 25088 ) , Labeling kit: Agilent Quick-Amp labeling Kit (p/n5190-0442)
2011-10-13 | E-GEOD-32948 | biostudies-arrayexpress
Project description:Comparison of transcription profile of Pichia pastoris cells grown on Glucose medium with Pichia pastoris cells grown on Methanol/Glycerol medium, the fermentations were done in a chemostat. 2 color experiment in reference design. Pichia pastoris reference mix [mixed pool of Pichia pastoris cells sampled from various conditions including cells grown on glycerine, glucose and methanol, on full andminimal medium, in stationary and exponential growth phase, and in different stress states]
2015-08-31 | E-GEOD-67690 | biostudies-arrayexpress
Project description:Over the past three decades, due to the universal application of Pichia yeast in the fermentation industry as well as the establishment of Pichia pastoris fermentation process for more than 30 years, the technology of the whole process has become very mature and has now reached a stagnated period of growth. However, studies and research conducted on the genomics of the classic fermentation process and the uncovering of the biological phenomena in the fermentation process from the point of view of high-throughput gene or protein is still in its early stages, and there is still insufficient data within this field. First, in collaboration with Agilent Company, we designed and prepared an expression microarray that could be used for the detection of Pichia pastoris transcriptomics. The transcriptomic changes in the five key technology steps (time points), during the fermentation process of Pichia pastoris would then be detected with the aid of an expression microarray. The five key steps of technology described above formed two important biological processes, namely, the limiting carbon source replacement and secondly, the fermentative production of exogenous proteins. The biological phenomena involved in these two processes were displayed and analyzed at the transcriptional level. In addition to this, with regard to the most important function in the fermentation process of Pichia pastoris, oxid-reduction, the metabolic drift process was analyzed and the important genes that might dominate the changes in the metabolic flux were discovered creatively by using the function tree method in this paper. This study was undertaken from the point of view of the transcriptome and the biological phenomena in the fermemntation process of Pichia pastoris. Both of which, were thoroughly explained during this study. The hope is for many more researchers to optimize the strain fermentation process, to produce proteins at the genetic level, as well as providing and obtaining new perspectives and detailed scientific data for the continued development within this field.
2014-04-18 | GSE56873 | GEO
Project description:Transcriptional profiling of Pichia pastoris cultivated at different specific growth rates in carbon and energy-limited aerobic chemostats and retentostats
2016-05-10 | GSE81070 | GEO
Project description:Over the past three decades, due to the universal application of Pichia yeast in the fermentation industry as well as the establishment of Pichia pastoris fermentation process for more than 30 years, the technology of the whole process has become very mature and has now reached a stagnated period of growth. However, studies and research conducted on the genomics of the classic fermentation process and the uncovering of the biological phenomena in the fermentation process from the point of view of high-throughput gene or protein is still in its early stages, and there is still insufficient data within this field. First, in collaboration with Agilent Company, we designed and prepared an expression microarray that could be used for the detection of Pichia pastoris transcriptomics. The transcriptomic changes in the five key technology steps (time points), during the fermentation process of Pichia pastoris would then be detected with the aid of an expression microarray. The five key steps of technology described above formed two important biological processes, namely, the limiting carbon source replacement and secondly, the fermentative production of exogenous proteins. The biological phenomena involved in these two processes were displayed and analyzed at the transcriptional level. In addition to this, with regard to the most important function in the fermentation process of Pichia pastoris, oxid-reduction, the metabolic drift process was analyzed and the important genes that might dominate the changes in the metabolic flux were discovered creatively by using the function tree method in this paper. This study was undertaken from the point of view of the transcriptome and the biological phenomena in the fermemntation process of Pichia pastoris. Both of which, were thoroughly explained during this study. The hope is for many more researchers to optimize the strain fermentation process, to produce proteins at the genetic level, as well as providing and obtaining new perspectives and detailed scientific data for the continued development within this field. The transcriptomic changes in the five key technology steps (time points), during the fermentation process of Pichia pastoris would then be detected with the aid of an expression microarray.
2014-04-18 | E-GEOD-56873 | biostudies-arrayexpress
Project description:Pichia pastoris is widely used as a host for recombinant protein production. More than 500 proteins have been expressed in the organism at a variety of cultivation scales, from small shake flasks to large bioreactors. Large-scale fermentation strategies typically employ chemically-defined growth media because of its greater batch-to-batch consistency and in many cases, lower cost compared to complex media. For biopharmaceuticals, defined growth media may also simplify downstream purification and regulatory documentation. Standard formulations of defined media for Pichia are minimal ones that lack the metabolic intermediates provided by complex components such as peptone and yeast extract. As a result, growth rates and per-cell productivities are significantly lower than in complex media. We have designed an improved defined media for Pichia pastoris, rich defined medium (RDM), by systematically evaluating nutrients of increasing complexity and identifying those that are most critical for growth. We have also demonstrated the use of RDM for expression of three heterologous proteins, at titers comparable to or higher than in standard complex medium. Rich defined medium has the potential to improve productivity of Pichia pastoris fermentations and accelerate process development for new molecules.
2019-05-22 | GSE99613 | GEO
Project description:The regulation of gene expression in Pichia pastoris has so far involved study of transcription factors. However, there are factors other than transcription factors affecting mRNA synthesis such as coactivators, enhancers, and chromatin modifiers. This study is a first ever report on epigenetic regulation in Pichia pastoris where, a histone acetyltransferase is reported to regulate transcription of genes involved in utilization of alternate carbon sources. We employed RNA Seq to identify new targets of Gcn5 in methanol medium.
2022-12-31 | GSE150467 | GEO
Project description:We have identified a methanol- and biotin-starvation-inducible zinc finger protein named ROP [repressor of phosphoenolpyruvate carboxykinase (PEPCK)] in the methylotrophic yeast Pichia pastoris. When P.pastoris strain GS115 (wild-type, WT) is cultured in biotin-deficient, glucose ammonium (Bio-) medium, growth is suppressed due to the inhibition of anaplerotic synthesis of oxaloacetate, catalysed by the biotin-dependent enzyme pyruvate carboxylase (PC). Deletion of ROP results in a strain (∆ROP) that can grow under biotin-deficient conditions due to derepression of a biotin- and PC-independent pathway of anaplerotic synthesis of oxaloacetate. Northern analysis as well as microarray expression profiling of RNA isolated from WT and ∆ROP strains cultured in Bio(-) medium indicate that expression of the phosphoenolpyruvate carboxykinase gene (PEPCK) is induced in ∆ROP during biotin- or PC-deficiency even under glucose-abundant conditions. There is an excellent correlation between PEPCK expression and growth of ∆ROP in Bio(-) medium, suggesting that ROP-mediated regulation of PEPCK may have a crucial role in the biotin- and PC-independent growth of the ∆ROP strain. To our knowledge, ROP is the first example, of a zinc finger transcription factor involved in the catabolite repression of PEPCK in yeast cells cultured under biotin- or PC-deficient and glucose-abundant conditions.
2011-10-14 | GSE32948 | GEO
Project description:Pichia pastoris is extensively employed as a host for expressing foreign proteins, and its secretion system is especially advantageous for efficient protein purification. Ulp1 is essential for the cell cycle. In Saccharomyces cerevisiae, the absence of Ulp1 leads to G2/M cell cycle arrest. Similarly, in Pichia pastoris, we also observed G2 phase stalling in Ulp1 knockout cells. RNA-seq data revealed significant changes in seven genes, including INO1. Interestingly, overexpressing INO1 in Ulp1 knockout cells restored cell proliferation, suggesting that Ulp1 regulates cell proliferation through INO1. However, adding extra inositol to Ulp1 knockout cells was not able to restore cell proliferation, indicating that the enzyme activity of INO1 is not essential for cell proliferation. Our data provide new insights into Ulp1 functions in the cell cycle and raise new questions about yeast cell cycle regulation.
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