Ontology highlight
ABSTRACT:
PROVIDER: PRJNA418298 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR6289230.fastq.gz | Fastqsanger.gz | |||
| SRR6289221.fastq.gz | Fastqsanger.gz | |||
| SRR6289222.fastq.gz | Fastqsanger.gz | |||
| SRR6289223.fastq.gz | Fastqsanger.gz | |||
| SRR6289224.fastq.gz | Fastqsanger.gz |
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Project description:The methylotrophic, thermotolerant yeast Ogataea parapolymorpha (formerly Hansenula polymorpha) is an industrially relevant production host and exhibits a respiratory metabolism in the presence of oxygen. It possesses a branched respiratory chain with multiple entry points for NADH-derived electrons that differ in complexity and degree of energy conservation: proton-translocating respiratory Complex I and three putative alternative NADH dehydrogenases. To investigate the physiological importance of Complex I, wild type O. parapolymorpha and a Complex I-disrupted mutant were cultured in glucose-grown bioreactor experiments in batch, chemostat and retentostat cultivations which allowed quantitative characterization of the strains over a wide range of growth rates in the presence and absence of excess substrate.
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Project description:WT and rme1 KO K. lactis cells (a, alpha, and a/alpha) were grown in YEPD, phosphate starvation and phosphate starvation with the addition of alpha pheromone. The goal was to identify cell-type regulated genes and to determine the effects of growth media on the regulation of cell-type regulated genes
2010-12-01 | GSE24874 | GEO
Project description:Calcium deficiency response in liverwort, Arabidopsis and lettuce: (1) Marchantia polymorpha: M. polymorpha wildtype and Gβ-null mutant plants (Tak-1, gpb1-2) were grown in control liquid Yamagami media (2 mM Ca) for 6 days. For RNA-seq experiments, 6 day old gemmalings were transferred to calcium deficiency (0 mM Ca) media. Samples were collected at 48 h after the transfer. The transcriptomic profiles were collected from two independent batches. In total four biological replicates were used for each condition and each genotype for a total of 16 samples. (2) Arabidopsis thaliana: For Arabidopsis RNA-seq experiment, 6-day old seedlings grown on ½ strength MS media with sucrose were transferred to Yamagami media with 2 mM or 0 mM CaCl2 and treated for 7 days. (3) Lactuca Sativa: For lettuce RNA-seq, 4-day old seedlings grown on water agar (1%) were transferred to Yamagami media with 2 mM or 0.15 mM CaCl2 and treated for 7 days. In total four and three biological replicates were used for each condition for a total of 8 and 6 samples respectively for Arabidopsis and lettuce.
2023-08-03 | GSE189793 | GEO
Project description:ChIP-chip to determine the regulation of the K. lactis hsgs (ChIP of MATa1, MATalpha2, and RME1). The MATa1 and MATalpha2 ChIPs were performed in an a/alpha cell using N-terminally HA-tagged proteins and the RME1 ChIPs were perfomed in an a cell using C-terminally myc-tagged protein. For the RME1 ChIPs, the cells grown with out phosphate. For the MATa1 andMATalpha2 ChIPs the cells were grown in YEPD.
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Project description:Ogataea polymorpha draft genome sequencing
| PRJDB3035 | ENA
Project description:This is genome-scale metabolic model of Komagataella pastoris as the representative yeast species for the clade Pichiaceae. This model was generated through homology search using a fungal pan-GEM largely based on Yeast8 for Saccharomyces cerevisiae, in addition to manual curation. This model has been produced by the Yeast-Species-GEMs project from Sysbio (www.sysbio.se). This is model version 1.0.0 accompanying the publication (DOI: 10.15252/msb.202110427), currently hosted on BioModels Database and identified by MODEL2109130009. Further curations of this model will be tracked in the GitHub repository: https://github.com/SysBioChalmers/Yeast-Species-GEMs Models for species of the same clade includes: Ambrosiozyma kashinagacola; Ambrosiozyma monospora; Brettanomyces anomalus; Candida arabinofermentans; Candida boidinii; Candida sorboxylosa; Candida succiphila; Brettanomyces bruxellensis; Komagataella pastoris; Kuraishia capsulata; Ogataea methanolica; Ogataea parapolymorpha; Ogataea polymorpha; Pichia membranifaciens; Ogataea henricii; Ambrosiozyma ambrosiae; Citeromyces matritensis; Ambrosiozyma vanderkliftii; Brettanomyces custersianus; Komagataella populi; Saturnispora hagleri; Saturnispora mendoncae; Saturnispora saitoi; Saturnispora serradocipensis; Saturnispora silvae; Saturnispora zaruensis; Pichia occidentalis; Pichia norvegensis; Pichia nakasei; Pichia kudriavzevii; Pichia heedii; Pichia exigua; Martiniozyma abiesophila; Ogataea nitratoaversa; Ogataea populialbae; Ogataea zsoltii; Ogataea trehalophila; Ogataea trehaloabstinens; Ogataea ramenticola; Ogataea pini; Ogataea pilisensis; Ogataea philodendri; Ogataea glucozyma; Ogataea kodamae; Ogataea methylivora; Ogataea minuta; Ogataea naganishii; Ogataea nonfermentans; Kuraishia ogatae; Kuraishia molischiana; Komagataella pseudopastoris; Ambrosiozyma oregonensis; Ambrosiozyma philentoma; Citeromyces hawaiiensis; Citeromyces siamensis; Ambrosiozyma maleeae; Ambrosiozyma pseudovanderkliftii; Pichia terricola; Saturnispora dispora; Kregervanrija delftensis; Kregervanrija fluxuum. These models are available in the zip file. To cite BioModels, please use: V Chelliah et al; BioModels: ten-year anniversary. Nucleic Acids Res 2015; 43 (D1): D542-D548. To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to MIT License for more information.
2021-11-01 | MODEL2109130009 | BioModels
Project description:Previously, it has been demonstrated that formate can be utilized by Saccharomyces cerevisiae as additional energy source using cells grown in a glucose-limited chemostat. Here, we investigated utilization of formaldehyde as co-substrate. Since endogenous formaldehyde dehydrogenase activities were insufficient to allow co-feeding of formaldehyde, the Hansenula polymorpha FLD1, encoding formaldehyde dehydrogenase, was introduced in S. cerevisiae. Chemostat cultivations revealed that formaldehyde was co-utilized with glucose, but the yield was lower than predicted. Moreover, formate was secreted by the cells. Upon co-expression of the H. polymorpha gene encoding formate dehydrogenase, FMD, the levels of secreted formate decreased, but the biomass yield was still lower than anticipated. Transcriptome comparisons of cells of the engineered FLD1/FMD-expressing S. cerevisiae strain grown with or without formaldehyde feed, suggested that the cells experienced biotin limitation, possibly due to inactivation of biotin by formaldehyde in the feed. When separate feeds were used for formaldehyde and biotin, the engineered S. cerevisiae strain was able to efficiently utilize formaldehyde as additional energy source. Experiment Overall Design: In industrial biotechnology, the cost of feedstocks (often sugars) are crucial for production of both biomass related products, such as proteins, or for the production of commodity chemicals. In many such processes a large fraction of the sugars is dissimilated to either provide free-energy (in the form of ATP) or to provide electrons (in the form of NADH). Co-consumption of methanol, which can be derived from fossil sources (via natural gas) or from biomass (via syngas) , via the above mentioned route can provide NADH and/or ATP, thereby creating the possibility to utilise the sugars more efficiently. It would therefore be advantageous to co-feed S. cerevisiae with methanol during fermentations since it is a cheap alternative to sugars as energy source. Experiment Overall Design: Efficient dissimilation of the intermediate formaldehyde is a crucial first step for utilisation of methanol by S. cerevisiae. Therefore, his study analyses the effect of co-expression of H. polymorpha FLD1 encoding NAD+-dependent formaldehyde and FMD encoding formate dehydrogenases, on tolerance to formaldehyde and co-consumption of formaldehyde by S. cerevisiae.
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Project description:Ogataea polymorpha species complex population genomics
| PRJNA706707 | ENA