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Transcriptomic profiling of the yeast Komagataella phaffii in response to environmental alkalinization

ABSTRACT: Transcriptomic profiling of the yeast Komagataella phaffii in response to environmental alkalinization

PROVIDER: PRJNA931229 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR23330437.fastq.gz	Fastqsanger.gz
	SRR23330438.fastq.gz	Fastqsanger.gz
	SRR23330439.fastq.gz	Fastqsanger.gz
	SRR23330440.fastq.gz	Fastqsanger.gz
	SRR23330441.fastq.gz	Fastqsanger.gz

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Transcriptomic profiling of the yeast Komagataella phaffii in response to environmental alkalinization

Project description:Adaptation to alkalinization of the medium in fungi involves an extensive remodeling of gene expression. Komagataella phaffii is an ascomycetous yeast that has become an organism widely used for heterologous protein expression. We explore here the transcriptional impact of moderate alkalinization in this yeast. In spite of a minor effect on growth, shifting the cultures from pH 5.5 to 8.0 or 8.2 provokes significant changes in the mRNA levels of over 700 genes. Functional categories such as arginine and methionine biosynthesis, non-reductive iron uptake and phosphate metabolism are enriched in induced genes, whereas many genes encoding iron-sulfur proteins or members of the respirasome were repressed. We also show that alkalinization is accompanied by oxidative stress and we propose this circumstance as a common trigger of a subset of the observed changes. PHO89, encoding a Na+/Pi cotransporter, appears among the most potently induced genes by high pH. We demonstrate that this response is mainly based on two calcineurin-dependent response elements located in its promoter, thus indicating that alkalinization triggers a calcium-mediated signal in K. phaffii. Further characterization of alkaline pH responsive promoters may lead to developing novel pH-controlled systems for heterologous protein expression in this fungus.

2023-04-12 | GSE224427 | GEO

Specific features of the transcriptomic response to nitrogen starvation in methylotrophic yeast Komagataella phaffi

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.

2024-10-06 | GSE278110 | GEO

Komagataella phaffii

Project description:Komagataella phaffii SNP analysis

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Project description:Komagataella phaffii Raw sequence reads

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Komagataella phaffii

Project description:Komagataella phaffii Raw sequence reads

| PRJNA930494 | ENA

Komagataella phaffii

Project description:Komagataella phaffii Raw sequence reads

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CRISPR-Cas9 knockout screen informs efficient reduction of the Komagataella phaffii secretome

Project description:The yeast Komagataella phaffii is a promising alternative host for manufacturing of therapeutic proteins. Deletion of unneeded endogenous proteins could increase the secreted titer of recombinant proteins by redirecting cellular resources. Genetic engineering in non-model hosts is hampered by limited annotation of genes, especially essential genes. In this study, we identified the set of endogenous secreted proteins in K. phaffii and attempted to disrupt these genes. We designed, transformed, and sequenced a pooled CRISPR-Cas9 knockout library to determine which genes are essential. With this knowledge, we rapidly disrupted up to 9 consecutive genes in K. phaffii. Engineered strains exhibited a ~20x increase in the production of human serum albumin and a 2x increase in the production of a monoclonal antibody. The pooled CRISPR-Cas9 library and knowledge of gene essentiality reported here will facilitate future efforts to engineer K. phaffii for production of other recombinant therapeutic proteins and enzymes.

2024-08-08 | GSE252605 | GEO

Komagataella phaffii

Project description:Komagataella phaffii Transcriptome or Gene expression

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Komagataella phaffii GS115

Project description:Ribosome profiling in Komagataella phaffii

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A single Gal4-like transcription factor activates the Crabtree effect in Komagataella phaffii

Project description:The Crabtree phenotype defines whether a yeast can perform simultaneous respiration and fermentation under aerobic conditions at high growth rates, a phenomenon that resembles the Warburg effect in cancer cells. Whole genome duplication, global promoter rewiring and loss of respiratory complex I are the main molecular events that contributed to the evolution of Crabtree effect. Here we show that overexpression of a single Gal4-like transcription factor is sufficient to convert Crabtree-negative Komagataella phaffii (Pichia pastoris) into a Crabtree positive yeast. We report the transcriptome profile (RNASeq) of the Δgal4-like and Gal4-like overexpression K. phaffii strains. Upregulation of the glycolytic genes and a significant increase in glucose uptake rate due to the overexpression of the Gal4-like transcription factor caused an overflow metabolism, triggering both short-term and long-term Crabtree phenotypes. This indicates that a single mutation leading to overexpression of one gene may have been sufficient as a first molecular event towards respiro-fermentative metabolism in the course of yeast evolution.

2018-10-19 | GSE110624 | GEO

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