Phaeodactylum tricornutum
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA13153 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| ABQD01.dat.gz | Other | |||
| ABQD01.fasta.gz | Fasta.gz | |||
| ABQD01.master.dat | Other | |||
| SRR10168442_1.fastq.gz | Fastqsanger.gz |
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Project description:Microalgae being used as a model diatom species for genome analysis
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Project description:Diatoms are prominent marine microalgae, interesting not only from an ecological point of view, but also for their possible use for biotechnology applications. They can be cultivated in phototrophic conditions, using sunlight as the only energy source. Some diatoms, however, can also grow in mixotrophic mode, where both light and external reduced carbon contribute to biomass accumulation. In this study, we investigated the consequences of mixotrophy on the growth and metabolism of the pennate diatom Phaeodactylum tricornutum, using glycerol as a source of reduced carbon. Transcriptomic, metabolomic and physiological data indicate that glycerol affects the central-carbon, carbon-storage and lipid metabolism of the diatom. In particular, glycerol addition mimics some typical responses of nitrogen limitation on lipid metabolism at the level of TAG accumulation and fatty acid composition. However, this compound does not diminish photosynthetic activity and cell growth, at variance with nutrient limitation, revealing essential aspects of the metabolic flexibility of these microalgae and suggesting possible biotechnological applications of mixotrophy.
2017-03-31 | GSE91004 | GEO
Project description:Here we use a transcriptomic approach to investigate the molecular underpinnings of thermal acclimation in the model diatom species Phaeodactylum tricornutum by comparing the differential gene expression in cultures acclimated to sub-optimal, optimal, and supra-optimal temperatures (10, 20 and 26.5 °C, respectively).
2021-10-20 | GSE186035 | GEO
Project description:Investigating mixotrophic metabolism in the model diatom Phaeodactylum tricornutum.
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Project description:Here we use a transcriptomic approach to investigate the molecular underpinnings of thermal stress in the model diatom species Phaeodactylum tricornutum. We expose cultures to high temperature (optimal +8°C) and follow changes in gene expression through time (over a 12 hour period) in comparison to optimal conditions (20 °C).
2021-10-20 | GSE186033 | GEO
Project description:Diatoms are eukaryotic microalgae that contain genes from various sources, including bacteria and the secondary endosymbiotic host. Due to this unique combination of genes, diatoms are taxonomically and functionally distinct from other algae and vascular plants and confer novel metabolic capabilities. Based on the genome annotation, we performed a genome-scale metabolic network reconstruction for the marine diatom Phaeodactylum tricornutum. Due to their endosymbiotic origin, diatoms possess a complex chloroplast structure which complicates the prediction of subcellular protein localization. Based on previous work we implemented a pipeline that exploits a series of bioinformatics tools to predict protein localization. The manually curated reconstructed metabolic network iLB1027_lipid accounts for 1,027 genes associated with 4,456 reactions and 2,172 metabolites distributed across six compartments. To constrain the genome-scale model, we determined the organism specific biomass composition in terms of lipids, carbohydrates, and proteins using Fourier transform infrared spectrometry. Our simulations indicate the presence of a yet unknown glutamine-ornithine shunt that could be used to transfer reducing equivalents generated by photosynthesis to the mitochondria. The model reflects the known biochemical composition of P. tricornutum in defined culture conditions and enables metabolic engineering strategies to improve the use of P. tricornutum for biotechnological applications.
2023-03-10 | MODEL2204200002 | BioModels
Project description:A study to investigate redox reactions in Phaeodactylum tricornutum diatom using OxiCAT method.Diatoms are ubiquitous marine photosynthetic eukaryotes that are responsible for about 20% of photosynthesis on Earth and therefore are an important component of the large biogeochemical cycles in the ocean. Very little is known about the molecular mechanisms that mediate cellular stress responses and are therefore responsible for their ecological success. Recent evidences suggest that diatoms may possess a surveillance system based on induction of reactive oxygen species (ROS) which have been implicated in response to various environmental stresses. Here we explored diatom mechanisms of perception of oxidative stress by combining in vivo imaging of organelle-specific redox response with quantification of the whole redox proteome in the model diatom Phaeodactylum tricornutum. Subcellular measurements of the glutathione redox potential using the redox-sensitive GFP (roGFP) sensor revealed distinct compartmentalization in the redox microenvironments. In vivo quantification of the whole thiol-proteome elucidated significant differential oxidation of around 300 redox-sensitive proteins (redoxome) under oxidative stress conditions. Functional assignment of this redoxome revealed involvement of a wide range of cellular functions that include signaling, transcription and translation machinery. We identified a high proportion of redox-sensitive enzymes that regulate key metabolic pathways in diatom biology such as photosynthesis, the urea cycle, photorespiration and lipid biosynthesis. The redoxome analysis revealed enrichment of chloroplast-targeted proteins and their high reactivity under reducing chloroplast microenvironment as determined by the roGFP sensor. Comparative analysis of the diatom redoxome across 48 genomes revealed evolutionary conserved cysteines responsive to oxidative stress across kingdoms. We propose that redox regulation may provide diatoms with important machinery for rapid and reversible responses to multiple environmental cues; therefore this mechanism would be essential for their ecological success in the marine ecosystem. Data Processing, Searching and Analysis: Raw data processing and database searching was performed using Proteinlynx Global Server (IdentityE) version 2.5.2. Database searching was carried out using the Ion Accounting algorithm. Data were searched against a combined target and reversed (decoy) database and the CRAP list of common laboratory contaminants. Trypsin was set as the protease, one missed cleavage was allowed. Each raw data file was searched 4 times with the following modification settings: heavy or light ICAT as fixed modifications; then with heavy or light ICAT as variable modifications. Feature Detection and alignment: Raw data were imported into Rosetta Elucidator System, version 3.3 (Rosetta Biosoftware, Seattle, WA, USA). Elucidator was used for alignment of raw MS1 data in RT and m/z dimensions. Aligned features were extracted and quantitative measurements obtained by integration of three-dimensional volumes (time, m/z, intensity) of each feature as detected in the MS1 scans. Detection of light and heavy pairs: The detection of light and heavy pairs from the MS1 channel in each raw data file was conducted using Rosetta Biosoftware’s Elucidator system, allowing 4 modified cysteines per peptide, with the heavy peak having a mass shift of 9.03 Da. Criteria for the unbiased detection of light and heavy pairs included ±0.2 minutes in the time domain and ±15ppm in the mass domain. Following detection of the pairs, the search results were imported for annotation and the minimum identification score was set to achieve a maximum global false discovery rate of 1%.
2014-01-23 | PXD000191 | Pride
Project description:In multicellular organisms, tri-methylation of lysine 27 of histone H3 (H3K27me3) was shown to be deposited by Polycomb Repressive Complex 2 (PRC2) to establish and maintain silencing, critical for cell fate and developmentally regulated processes. PRC2 complex is absent in both yeast Saccharomyces cerevisiae and S. pombe which initially suggested that PRC2 arose with the emergence of multicellularity. However, its discovery in several microalgae questions its role in this important class of organisms. Here, we show using mutants of the homologue of catalytic unit of PRC2, enhancer of zeste E(z) in the model diatom P. tricornutum (Pt), which presents different morphotypes (fusiform, triradiate, oval and cruciform) that Pt E(z) is responsible of di and tri-methylation of lysine 27. Indeed, H3K27me3 depletion causes the distortion of the morphology providing evidence for a role of H3K27me3 in cell differentiation in unicellular species. H3K27me3 genome wide profiling in fusiform and triradiate further revealed genes important for cell identity. These results suggest a role of PRC2 and its associated mark in cell fate in unicellular species and their ancestral function in a broad evolutionary context.
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Project description:An integrated analysis of phosphorus starvation responses in the diatom Pheaodactylum tricornutum
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Project description:Whole genome McrBC-chip on DNA methylation of diatom Phaeodactylum tricornutum
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