Ogataea polymorpha
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA170212 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| SRR12403033_1.fastq.gz | Fastqsanger.gz | |||
| SRR12403033_2.fastq.gz | Fastqsanger.gz | |||
| SRR12403034_1.fastq.gz | Fastqsanger.gz |
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Project description:Methylotrophic ascomycetous yeast used in research and industry
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Project description:To gain insight into the basic mechanism of Hydrogen peroxide detoxification in the methylotrophic yeast, H. polymorpha, we analyzed changes in transcriptional profiles in response to hydrogen peroxide exposure.
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Project description:To gain insight into the basic mechanism of Cd detoxification in the methylotrophic yeast, H. polymorpha, we analyzed temporal changes in transcriptional profiles in response to Cd exposure. We used H. polymorpha whole-genome cDNA microarrays, which contain 98% of all H. polymorpha ORFs in duplicate or triplicate. Keywords: time course, cadmium
2007-08-30 | GSE6989 | GEO
Project description:To gain insight into the basic mechanism of Hydrogen peroxide detoxification in the methylotrophic yeast, H. polymorpha, we analyzed changes in transcriptional profiles in response to hydrogen peroxide exposure. Total RNA samples were collected from H. polymorpha cells after 30 min incubation with 0.5mM hydrogen peroxide. Using the RNA sample obtained prior to hydrogen peroxide addition as a reference, the differential fluorescence intensities of each RNA sample prepared at the indicated time was measured after labeling with Cy3 or Cy5 fluorochromes. For all analyses, we performed dye swapping experiments to avoid dye bias.
2015-02-28 | E-GEOD-43048 | biostudies-arrayexpress
Project description:BackgroundOgataea polymorpha is a thermotolerant, methylotrophic yeast with significant industrial applications. While previously mainly used for protein synthesis, it also holds promise for producing platform chemicals. O. polymorpha has the distinct advantage of using methanol as a substrate, which could be potentially derived from carbon capture and utilization streams. Full development of the organism into a production strain and estimation of the metabolic capabilities require additional strain design, guided by metabolic modeling with a genome-scale metabolic model. However, to date, no genome-scale metabolic model is available for O. polymorpha.ResultsTo overcome this limitation, we used a published reconstruction of the closely related yeast Komagataella phaffii as a reference and corrected reactions based on KEGG and MGOB annotation. Additionally, we conducted phenotype microarray experiments to test the suitability of 190 substrates as carbon sources. Over three-quarter of the substrate use was correctly reproduced by the model and 27 new substrates were added, that were not present in the K. phaffii reference model.ConclusionThe developed genome-scale metabolic model of O. polymorpha will support the engineering of synthetic metabolic capabilities and enable the optimization of production processes, thereby supporting a sustainable future methanol economy.
| S-EPMC7962355 | biostudies-literature
Project description:Bio-manufacturing via microbial cell factory requires large promoter library for fine-tuned metabolic engineering. Ogataea polymorpha, one of the methylotrophic yeasts, possesses advantages in broad substrate spectrum, thermal-tolerance, and capacity to achieve high-density fermentation. However, a limited number of available promoters hinders the engineering of O. polymorpha for bio-productions. Here, we systematically characterized native promoters in O. polymorpha by both GFP fluorescence and fatty alcohol biosynthesis. Ten constitutive promoters (P PDH , P PYK , P FBA , P PGM , P GLK , P TRI , P GPI , P ADH1 , P TEF1 and P GCW14 ) were obtained with the activity range of 13%-130% of the common promoter P GAP (the promoter of glyceraldehyde-3-phosphate dehydrogenase), among which P PDH and P GCW14 were further verified by biosynthesis of fatty alcohol. Furthermore, the inducible promoters, including ethanol-induced P ICL1 , rhamnose-induced P LRA3 and P LRA4 , and a bidirectional promoter (P Mal -P Per ) that is strongly induced by sucrose, further expanded the promoter toolbox in O. polymorpha. Finally, a series of hybrid promoters were constructed via engineering upstream activation sequence (UAS), which increased the activity of native promoter P LRA3 by 4.7-10.4 times without obvious leakage expression. Therefore, this study provided a group of constitutive, inducible, and hybrid promoters for metabolic engineering of O. polymorpha, and also a feasible strategy for rationally regulating the promoter strength.
| S-EPMC8685918 | biostudies-literature
Project description:BackgroundOgataea polymorpha, a non-conventional methylotrophic yeast, has demonstrated significant potential for heterologous protein expression and the production of high-value chemicals and biopharmaceuticals. However, the lack of precise and efficient genome editing tools severely hinders the construction of cell factories. Although the CARISP-Cas9 system has been established in Ogataea polymorpha, the gene editing efficiency, especially for multiple genes edition, needs to be further improved.ResultsIn this study, we developed an efficient CRISPR-Cpf1-mediated genome editing system in O. polymorpha that exhibited high editing efficiency for single gene (98.1 ± 1.7%), duplex genes (93.9 ± 2.4%), and triplex genes (94.0 ± 6.0%). Additionally, by knocking out non-homologous end joining (NHEJ) related genes, homologous recombination (HR) efficiency was increased from less than 30% to 90 ~ 100%, significantly enhancing precise genome editing capabilities. The increased HR rates enabled over 90% integration efficiency of triplex genes, as well as over 90% deletion rates of large DNA fragments up to 20 kb. Furthermore, using this developed CRISPR-Cpf1 system, triple genes were precisely integrated into the genome by one-step, enabling lycopene production in O. polymorpha.ConclusionsThis novel multiplexed genome-editing tool mediated by CRISPR-Cpf1 can realize the deletion and integration of multiple genes, which holds great promise for accelerating engineering efforts on this non-conventional methylotrophic yeast for metabolic engineering and genomic evolution towards its application as an industrial cell factory.
| S-EPMC11748851 | biostudies-literature
Project description:Methylotrophic yeast Ogataea polymorpha is capable to utilize multiple carbon feedstocks especially methanol as sole carbon source and energy, making it an ideal host for bio-manufacturing. However, the lack of gene integration sites limits its systems metabolic engineering, in particular construction of genome-integrated pathway. We here screened the genomic neutral sites for gene integration without affecting cellular fitness, by genomic integration of an enhanced green fluorescent protein (eGFP) gene via CRISPR-Cas9 technique. After profiling the growth and fluorescent intensity in various media, 17 genome positions were finally identified as potential neutral sites. Finally, integration of fatty alcohol synthetic pathway genes into neutral sites NS2 and NS3, enabled the production of 4.5 mg/L fatty alcohols, indicating that these neutral sites can be used for streamline metabolic engineering in O. polymorpha. We can anticipate that the neutral sites screening method described here can be easily adopted to other eukaryotes.
| S-EPMC8040119 | biostudies-literature