Phaeodactylum tricornutum
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA278661 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR1917250.fastq.gz | Fastqsanger.gz | |||
| SRR1917241.fastq.gz | Fastqsanger.gz | |||
| SRR1917242.fastq.gz | Fastqsanger.gz | |||
| SRR1917243.fastq.gz | Fastqsanger.gz | |||
| SRR1917244.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:Phosphate (Pi) is an essential element to all living cells yet fluctuations in Pi concentrations are recurrent in the marine environment. Diatoms are amongst the most successful phytoplankton clade living in the worldâs oceans adapting to and surviving long periods of sub-optimal conditions and resuming growth as soon as nutrient concentrations permit. The knowledge of the molecular underpinnings of diatom ecological success is, however, still very incomplete. Using high-throughput RNA sequencing we have identified the dynamics of the model diatom Phaeodactylum tricornutum global transcriptome in response to Pi fluctuations. We report genes encoding previously unidentified putative Pi transporters that, together with the alkaline phosphatases genes highly expressed under Pi depletion, are probably accountable for a very efficient Pi scavenging system. Our data also reveal the complexity of the P. tricornutum responsive sensory and signaling system that combines bacterial two-component systems with more complex pathways reminiscent of metazoans. This intricate set of membrane receptors and signal-transduction related proteins is likely responsible for the detection of environmental nutrient fluctuations, triggering a multitude of signaling cascades leading to gene regulatory events that define new adaptive physiological states. This together with the novel detection of a multitude of long non-coding intergenic RNAs specifically expressed under Pi stress, begins to provide insights into the complex molecular regulatory program involved in the resilience and ecological success of diatoms. Examination of Pi-responsive transcriptoms in diatoms.
2016-07-03 | E-GEOD-66997 | biostudies-arrayexpress
Project description:Unicellular organisms living in a marine environment sometimes have to cope with massive fluctuations in inorganic phosphate (Pi) availability. We studied phosphatases and phosphate transporters of the diatom Phaeodactylum tricornutum with respect to the extracellular Pi-concentration depending expression as well as their extra- or intracellular localization. These studies, which add a further level of knowledge to already existing transcriptomic data, highlight the capacity of the diatom to distribute Pi intracellularly and to mobilize Pi from extra- and intracellular resources
2020-04-30 | PXD016456 | Pride
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:Phosphate (Pi) is an essential element to all living cells yet fluctuations in Pi concentrations are recurrent in the marine environment. Diatoms are amongst the most successful phytoplankton clade living in the world’s oceans adapting to and surviving long periods of sub-optimal conditions and resuming growth as soon as nutrient concentrations permit. The knowledge of the molecular underpinnings of diatom ecological success is, however, still very incomplete. Using high-throughput RNA sequencing we have identified the dynamics of the model diatom Phaeodactylum tricornutum global transcriptome in response to Pi fluctuations. We report genes encoding previously unidentified putative Pi transporters that, together with the alkaline phosphatases genes highly expressed under Pi depletion, are probably accountable for a very efficient Pi scavenging system. Our data also reveal the complexity of the P. tricornutum responsive sensory and signaling system that combines bacterial two-component systems with more complex pathways reminiscent of metazoans. This intricate set of membrane receptors and signal-transduction related proteins is likely responsible for the detection of environmental nutrient fluctuations, triggering a multitude of signaling cascades leading to gene regulatory events that define new adaptive physiological states. This together with the novel detection of a multitude of long non-coding intergenic RNAs specifically expressed under Pi stress, begins to provide insights into the complex molecular regulatory program involved in the resilience and ecological success of diatoms.
2016-01-01 | GSE66997 | GEO
Project description:An experiment was performed to determine the similarities on the RNA level between different conditions where cell division stops in the diatom Phaeodactylum tricornutum. Many of these conditions also increase the accumulation of lipids within the cell or impair photosynthesis. The different metabolic responses were evaluated and the dataset was mined for potential transcriptional regulators of these changes. The experimental setup was as follows: Cells from the pennate diatom Phaeodactylum tricornutum were grown in ESAW medium under continous fluorescent light at 21C in baffled shakeflasks. Exponentially growing cells were harvested by centrifugation and washed twice in 21gr/L NaCL to remove nutrients. Cells were subsequently resuspended in the five different media/conditions (control, darkness, no nitrate, no phosphate, nocodazole).
2015-12-07 | E-MTAB-4096 | biostudies-arrayexpress
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:Nucleosomes are the building blocks of chromatin where gene regulation takes place. Chromatin landscapes have been profiled for several species, providing insights into the understanding of fundamental mechanisms of chromatin-mediated transcriptional regulation of gene expression. However, knowledge is missing from several major and deep-branching eukaryotic groups, such as the marine model diatom Phaeodactylum tricornutum. Diatoms are highly diverse and ubiquitous species of phytoplankton that play a key role in global biogeochemical cycles. Dissecting chromatin-mediated regulation of genes in diatoms will help understand the ecological success of these organisms in contemporary oceans. Here, we use high resolution mass spectrometry to identify a full repertoire of post-translational modifications on P. tricornutum histones, including eight novel modifications. We map five histone marks coupled with expression data and show that P. tricornutum displays both unique and broadly conserved chromatin features, reflecting the chimeric nature of its genome. Combinatorial analysis of histone marks and DNA methylation demonstrates the presence of an epigenetic code defining active or repressive chromatin states. We further profile three specific histone marks under conditions of nitrate depletion and show that the histone code is dynamic and targets specific sets of genes. This study is the first genome-wide characterization of the histone code from a Stramenopile and a marine phytoplankton. The work represents an important initial step for understanding the evolutionary history of chromatin and how epigenetic modifications affect gene expression in response to environmental cues in marine environments.
2015-05-08 | PXD002148 | Pride
Project description:Histone modifications in the marine diatom Phaeodactylum tricornutum
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Project description:Investigating mixotrophic metabolism in the model diatom Phaeodactylum tricornutum.
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Project description:Whole genome McrBC-chip on DNA methylation of diatom Phaeodactylum tricornutum
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