Phaeodactylum tricornutum
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PROVIDER: PRJNA298540 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:The absorption of visible light in aquatic environments has led to the common assumption that aquatic organisms sense and adapt to penetrative blue/green light wavelengths, but show little or no response to the more attenuated red/far-red wavelengths. Here we show that two marine diatom species, Phaeodactylum tricornutum and Thalassiosira pseudonana, possess a bona fide red/far-red light sensing phytochrome (DPH) that uses biliverdin as a chromophore and displays accentuated red-shifted absorbance peaks compared to other characterized plant and algal phytochromes. Exposure to both red and far-red light causes changes in gene expression in P. tricornutum and the responses to far-red light disappear in DPH knockout cells, demonstrating that P. tricornutum DPH mediates far-red light signaling. The identification of DPH genes in diverse diatom species widely distributed along the water column further emphasizes the ecological significance of far-red light sensing, raising questions about the sources of far-red light. Our analyses indicate that, although far-red wavelengths from sunlight are only detectable at the ocean surface, chlorophyll fluorescence and Raman scattering can generate red/far-red photons in deeper layers. This study opens up novel perspectives on phytochrome-mediated far-red light signaling in the ocean and on the light sensing and adaptive capabilities of marine phototrophs.
2016-05-09 | GSE73915 | GEO
Project description:Analysis of etiolated seedlings exposed for 1hr to red light. Phytochromes are red/far-red light receptors, palying important roles in photomorphogenesis. Results suggest that red light and phytochromes regulate a set of genes' expression in seedlings.
2021-03-01 | GSE111380 | GEO
Project description:We have studied the transcriptional, metabolic and photo-physiological responses to light of different spectral quality in the marine diatom Phaeodactylum tricornutum through time-series studies of cultures exposed to equal doses of photosynthetically usable radiation of blue, green and red light. The experiments showed that short-term differences in gene expression and profiles are mainly light quality-dependent. Transcription of photosynthesis-associated nuclear genes was activated mainly through a light quality-independent mechanism likely to rely on chloroplast-to-nucleus signaling. In contrast, genes encoding proteins important for photoprotection and PSII repair were highly dependent on a blue light receptor-mediated signal. Changes in energy transfer efficiency by light-harvesting pigments were spectrally dependent; furthermore, a declining trend in photosynthetic efficiency was observed in red light. The combined results suggest that diatoms possess a light quality-dependent ability to activate photoprotection and efficient repair of photodamaged PSII. In spite of approximately equal numbers of PSII-absorbed quanta in blue, green and red light, the spectral quality of light is important for diatom responses to ambient light conditions.
2014-12-22 | GSE55959 | GEO
Project description:The red/far-red light photoreceptor phytochrome mediates photomorphological responses in plants. For light sensing and signaling, phytochromes need to associate with open-chain tetrapyrrole molecules as the chromophore. Biosynthesis of tetrapyrrole chromophores requires members of ferredoxin-dependent bilin reductases (FDBRs). There are two FDBRs in Physcomitrella patens, HY2 and PUBS. Knocking out both generates the phytochrome-deficient mutant. Datasets here provides the transcriptome profiling of Physcomitrella protonema grown in the dark and exposed to one hour red light. Wild type and the hy2 pubs double mutant were used to dissect the regulated genes of moss phytochromes. For details, please see PMID: .
2012-05-08 | GSE36274 | GEO
Project description:Phytochromes are red/far-red light photoreceptors. We sought to test at the transcriptomic level if Arabidopsis mutants lacking all phytochromes (from phyA to phyE), or just retaining trace levels of phyC, had transcriptional response to red light exposure.
2012-04-01 | GSE31587 | GEO
Project description:System responses to equal doses of photosynthetically usable radiation of blue, green, and red light in the marine diatom Phaeodactylum tricornutum.
| PRJNA241436 | ENA
Project description:The red/far-red light photoreceptor phytochrome mediates photomorphological responses in plants. For light sensing and signaling, phytochromes need to associate with open-chain tetrapyrrole molecules as the chromophore. Biosynthesis of tetrapyrrole chromophores requires members of ferredoxin-dependent bilin reductases (FDBRs). There are two FDBRs in Physcomitrella patens, HY2 and PUBS. Knocking out both generates the phytochrome-deficient mutant. Datasets here provides the transcriptome profiling of Physcomitrella protonema grown in the dark and exposed to one hour red light. Wild type and the hy2 pubs double mutant were used to dissect the regulated genes of moss phytochromes. 4 samples, dark-grown wild-type and pubs hy2 protonema as time 0 control, followed by red light irradiation for one hour respectively
2012-05-08 | E-GEOD-36274 | biostudies-arrayexpress
Project description:An Integrated Analysis of Molecular Acclimation to High Light in the Marine Diatom Phaeodactylum tricornutum
| PRJNA119115 | ENA
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:We have studied the transcriptional, metabolic and photo-physiological responses to light of different spectral quality in the marine diatom Phaeodactylum tricornutum through time-series studies of cultures exposed to equal doses of photosynthetically usable radiation of blue, green and red light. The experiments showed that short-term differences in gene expression and profiles are mainly light quality-dependent. Transcription of photosynthesis-associated nuclear genes was activated mainly through a light quality-independent mechanism likely to rely on chloroplast-to-nucleus signaling. In contrast, genes encoding proteins important for photoprotection and PSII repair were highly dependent on a blue light receptor-mediated signal. Changes in energy transfer efficiency by light-harvesting pigments were spectrally dependent; furthermore, a declining trend in photosynthetic efficiency was observed in red light. The combined results suggest that diatoms possess a light quality-dependent ability to activate photoprotection and efficient repair of photodamaged PSII. In spite of approximately equal numbers of PSII-absorbed quanta in blue, green and red light, the spectral quality of light is important for diatom responses to ambient light conditions. Continuous, axenic culturing of P. tricornutum was done as described in Nymark et al. (2009). The cultures were incubated at 15M-BM-0C under cool white fluorescent light (Philips TLD 36W/96) providing a scalar irradiance (EPAR) of 100 M-NM-<mol m-2 s-1 under continuous white light (CWL) conditions. Upon the onset of the experiment the cultures were synchronized by 48 h dark-treatment (D48). Thereafter the algae were exposed to blue light (BL), green light (GL) or red light (RL) provided by a waveband specific LED panel (SL3500, Photon Systems Instruments). The algae were exposed to 0.5 h, 6 h or 24 h of: 1) 230 M-NM-<mol m-2 s-1 of RL, 2) 100 M-NM-<mol m-2 s-1 of GL, 3) 50 M-NM-<mol m-2 s-1 of BL or 4) 100 M-NM-<mol m-2 s-1 of WL respectively. Three biological replicas for each of the treatments were harvested. Data for the white light exposure and 48h dark treatment is described in GSE42039, PMID: 23520530.
2014-12-22 | E-GEOD-55959 | biostudies-arrayexpress