Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1222576 | ENA |
REPOSITORIES: ENA
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Project description:We analyzed the chromatin accessibility and nucleosome positioning by ATAC-seq of both null and transgene-expressing strains of Komagataella phaffii (Pichia pastoris) under different growth conditions. These data enabled identification of the features that determine performance of various integration sites for transgene expression. Understanding chromatin accessibility and nucleosome positioning can provide further clarity into gene regulation and expression broadly in this organism.
2020-10-02 | GSE154330 | GEO
Project description:In order to investigate the specific mechanism of maltose on the production of recombinant type III collagen by Komagataella phaffii GS115, Two groups were set up, control group C using BMMY medium and experimental group M using BMMY + 1% maltose.
2025-02-01 | GSE225749 | GEO
Project description:The protein production host Komagataella phaffii has possess the ability to differentiate into pseudohyphal form when cultivated at slow growth rates (µ=0.05 h-1) in glucose-limited chemostats. In this study, we investigated the K. phaffii FLO gene family in the context of pseudohyphae formation. Transcriptional analysis helped us identify 3 possible responsible genes, FLO11, FLO400 and FLO5-1, all of which are under control of Flo8, a transcription factor whose disruption prevents pseudohyphae formation. Knocking out FLO11 revealed that this is not the sole protein responsible for this phenotype. Strikingly, the expression of FLO400 and FLO5-1 was negatively correlated with pseudohyphae formation, and shown to be under epigenetic control by FAIRE-Seq analysis. Knock outs of these two genes completely inhibited the appearance of pseudohyphal cells and prevented the expression of FLO11. Even though the mechanism is unclear at present, we propose that in K. phaffii Flo400 and/or Flo5-1 act as upstream signals that lead to the induction of FLO11 expression upon severe glucose limitation in chemostats at slow growth rate, and that the expression of FLO400 and FLO5-1 is controlled by epigenetic silencing, which acts independently from the general activation of FLO gene expression by the transcriptional regulator Flo8.
2020-08-19 | GSE131290 | GEO
Project description:Recombinant TLP (rTLP) and CHI (rCHI), expressed by Komagataella phaffii, were used as as haze-protein models, for having similar characteristics (aggregation potential, melting point, functionality, glycosylation levels and bentonite adsorption) to the native-haze proteins from Vitis vinifera.
2023-03-11 | PXD035796 | Pride
Project description:The yeast Komagataella phaffii (syn. Pichia pastoris) is a highly effective and well-established host for the production of recombinant proteins. The redox balance of its secretory pathway, which is multi-organelle dependent, is of high importance for producing secretory proteins. Redox imbalance and oxidative stress an significantly influence protein folding and secretion. Glutathione serves as the main redox buffer of the cell and cellular redox conditions can be assessed through the status of the glutathione redox couple (GSH-GSSG). Previous research often focused on the redox potential of the endoplasmic reticulum (ER), where oxidative protein folding and disulfide bond formation occur. In this study, in vivo measurements of the glutathione redox potential were extended to different subcellular compartments by targeting genetically encoded redox sensitive fluorescent proteins (roGFPs) to the cytosol, ER, mitochondria and peroxisomes. Using these biosensors, the impact of oxygen availability on the redox potentials of the different organelles was investigated in non-producing and producing K. phaffii strains in glucose-limited chemostat cultures. It was found that the transition from normoxic to hypoxic conditions affected the redox potentials of all investigated organelles, while the exposure to hyperoxic conditions did not impact them. Also, as reported previously, hypoxic conditions led to increased recombinant protein secretion. Finally, transcriptome and proteome analyses provided novel insights into the short-term adaptation of the cells from normoxic to hypoxic conditions.
2025-02-10 | GSE277464 | GEO
Project description:Non-conventional methylotrophic yeast Komagataella phaffii is an important production host in biotechnology and an emerging model organism. In this work, we studied K. phaffii response to nitrogen starvation during cultivation in media with methanol as the sole carbon source. The results were compared with well-established model yeast Saccharomyces cerevisiae. Some of the observed effects of nitrogen starvation in K. phaffii were similar to those in S. cerevisiae, despite this yeast does not have metabolic pathway for methanol utilization. The effects include activation of autophagy, transport and catabolism of nitrogen-containing compounds, interconversions of amino acids, and biosynthesis of fatty acids. K. phaffii cells also demonstrated specific response to nitrogen starvation including suppression of genes involved in methanol metabolism and other peroxisomal processes and activation of purine catabolism genes.
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