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Phaeodactylum tricornutum

ABSTRACT: Infleunce of carbon and nitrogen availability on patterns of transcription in P. tricornutum and Alteromonas macleodii co-cultures

PROVIDER: PRJNA319251 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR3466320_1.fastq.gz	Fastqsanger.gz
	SRR3466320_2.fastq.gz	Fastqsanger.gz
	SRR3466340_1.fastq.gz	Fastqsanger.gz
	SRR3466340_2.fastq.gz	Fastqsanger.gz
	SRR3466360_1.fastq.gz	Fastqsanger.gz

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Next generation sequencing of Phaeodactylum tricornutum grown with and without nitrogen

2015-01-02 | GSE56346 | GEO

Whole cell response to nitrogen deprivation in the diatom Phaeodactylum tricornutum

Project description:We combined transcriptional and metabolite analyses to monitor the effect of N deficiency at different molecular levels in order to get better insight on the acclimation strategies P. tricornutum employs under nitrogen limitation. Physiological data like neutral lipid measurement, cell growth and other cell chemistry measurements further complemented our molecular data. We showed that P. tricornutum is able to remobilize nitrogen through catabolism of various internal nitrogen-containing resources such as amino acids and proteins. N starvation was also accompanied by reduction in pigment pools as well as photosynthetic capacity. The global expression data showed that majority of metabolic changes were related to carbon and lipid metabolism. Decreased levels of carbon skeletons due to suppression of the Calvin cycle was compensated by breakdown of chrysolaminaran leading to up-regulation of OPPP, glycolysis, pyruvate metabolism and TCA cycle. These pathways provide precursors for fatty acid biosynthesis. In addition, remodeling of membrane lipids and up-regulation of the de novo TAG biosynthetic pathway was further supported by physiological measurements of neutral lipids, indicating TAG accumulation under N limitation. Our study gives a detailed image of adaptation of P. tricornutum to N starvation, and can be used for future metabolic manipulations to increase TAG production.

2015-06-01 | GSE58946 | GEO

Next generation sequencing of Phaeodactylum tricornutum grown with and without nitrogen

Project description:We have done next generation sequencing of optically thin, exponentialy growing Phaeodactylum tricornutum cultures grown with and without nitrogen source to improve our undestanding of the pathways regulation under conditions that promote lipid accumulation (N-starvation). 3 biologically independent exponentially growing culture of Phaeodactylum tricornutum were pelleted and washed several times with N-free media. Each culture was devided to 2 replicates with initial cell concentration of 2X105 cells/mL, one with NaNO3 as nitrogen source and the other without any nitrogen source. The cuture were bubbled foro 48 hours and sampled for transcriptome together with other physiological parameters and lipid analysis.

2015-01-02 | E-GEOD-56346 | biostudies-arrayexpress

Investigating mixotrophic metabolism in the model diatom Phaeodactylum tricornutum.

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

Next generation sequencing for understading the role of nitrate reductase in remodeling intermediate metabolism in Phaeodactylum tricornutum

Project description:We have done next generation sequencing of optically thin, exponentialy growing WT Phaeodactylum tricornutum and our ~50% nitrate reductase knock-down cultures. Culture were grown with and without nitrogen source to improve our undestanding of the pathways regulation under conditions that promote lipid accumulation (N-starvation).

2016-03-31 | GSE67449 | GEO

Phaeodactylum tricornutum

Project description:Transcriptome of nitrogen starved and normal cultured Phaeodactylum tricornutum

| PRJNA235975 | ENA

Regulatory mechanism of diurnal fluctuated laminarin in diatom Phaeodactylum tricornutum

Project description:Diatoms played an essential role in marine primary productivity. Polysaccharide chrysolaminarin and neutral lipid, mainly TAG, were necessary carbon fixation in diatom Phaeodactylum tricornutum. Our study speculated on the metabolism pathway of chrysolaminarin, fatty acid, fatty acid β-oxidation and TAG. Transcriptional levels coordinated with carbon fixation metabolism pathway were conjoint analysis in this study.

2022-08-03 | GSE210141 | GEO

Transcriptional response of the marine pennate diatom Phaeodactylum tricornutum to Fe limitation

Project description:Diatoms, which are responsible for up to 40% of the 45 to 50 billion metric tons of organic carbon production each year in the sea, are particularly sensitive to Fe stress. Here we describe the transcriptional response of the pennate diatom Phaeodactylum tricornutum to Fe limitation using a partial genome microarray based on EST and genome sequence data. Processes carried out by components rich in Fe, such as photosynthesis, mitochondrial electron transport and nitrate assimilation are down-regulated to cope with the reduced cellular iron quota. This retrenchment is compensated by nitrogen (N) and carbon (C) reallocation from protein and storage carbohydrate degradation, adaptations to chlorophyll biosynthesis and pigment metabolism, removal of excess electron s by mitochondrial alternative oxidase (AOX), augmented Fe-independent oxidative stress responses, and sensitized iron capture mechanisms. Keywords: Marine phytoplankton, pinnate diatom Wild-type Phaeodactylum tricornutum was grown under Fe replete (10,000 nM) and Fe limiting (5nM) conditions. Partial genome gene expression analysis of iron-inducible genes was conducted using a two-color competitive hybridization microarray.

2010-05-27 | E-GEOD-8675 | biostudies-arrayexpress

Gene regulation of carbon fixation, storage and utilization in the diatom Phaeodactylum tricornutum acclimated to light/dark cycles

Project description:Regulation of carbon metabolism in the diatom Phaeodactylum tricornutum at cell, metabolite and gene expression level in exponential fed-batch cultures is reported. Transcriptional profiles and cell chemistry sampled simultaneously at all time-points provide a comprehensive data set on carbon incorporation, fate and regulation. More than 4,500 transcripts that were differentially regulated during the light/dark cycle are identified, many of which were associated with carbohydrate and lipid metabolism. Genes not previously described in algae and their regulation in response to light were integrated in this analysis together with proposed roles in metabolic processes. Some very fast light responding genes in e.g. fatty acid biosynthesis were identified. Transcripts and cell chemistry data reflect the link between light energy availability and light energy consuming metabolic processes. Our data confirm spatial localization of processes in carbon metabolism to e.g. either plastids or mitochondria, or glycolysis/gluconeogenesis which are localized to the cytosol, chloroplast and to mitochondria. Localization and diel expression pattern may be of help to determine the roles of different isoenzymes, and mining of genes involved in light responses and circadian rhythms. Gene regulation in Phaeodactylum tricornutum was examined in cultures acclimatized to growth cycles of 16/8 hour photoperiods (16 hour light, 8 hour dark). Two biological replicas were harvested at each of the eight time points, spaning a 27 hour period. 5 of the time points (0.5 h, 3 h, 6 h, 10.5 h and 15.5 h) were harvested in the light phase, while 3 time points were harvested during the dark phase (0.5 h, 4 h and 7.5 h darkness).

2013-03-01 | E-GEOD-42514 | biostudies-arrayexpress

Phaeodactylum tricornutum

Project description:Whole cell response to nitrogen deprivation in the diatom Phaeodactylum tricornutum

| PRJNA253958 | ENA