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Phaeodactylum tricornutum

ABSTRACT: Circadian rhythm and differential gene expression in Phaeodactylum tricornutum under continuous light and day/night cycle

PROVIDER: PRJNA922714 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR23703100_1.fastq.gz	Fastqsanger.gz
	SRR23703100_2.fastq.gz	Fastqsanger.gz
	SRR23703101_1.fastq.gz	Fastqsanger.gz
	SRR23703101_2.fastq.gz	Fastqsanger.gz
	SRR23703102_1.fastq.gz	Fastqsanger.gz

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bHLH-PAS protein RITMO1 regulates diel biological rhythms in the marine diatom Phaeodactylum tricornutum

Project description:Periodic light–dark cycles govern the timing of basic biological processes in organisms inhabiting land as well as the sea, where life evolved. Although prominent marine phytoplanktonic organisms such as diatoms show robust diel rhythms, the mechanisms regulating these processes are still obscure. By characterizing a Phaeodactylum tricornutum bHLH-PAS nuclear protein, hereby named RITMO1, we shed light on the regulation of the daily life of diatoms. Alteration of RITMO1 expression levels and timing by ectopic overexpression results in lines with deregulated diurnal gene expression profiles compared with the wild-type cells. Reduced gene expression oscillations are also observed in these lines in continuous darkness, showing that the regulation of rhythmicity by RITMO1 is not directly dependent on light inputs. We also describe strong diurnal rhythms of cellular fluorescence in wild-type cells, which persist in continuous light conditions, indicating the existence of an endogenous circadian clock in diatoms. The altered rhythmicity observed in RITMO1 overexpression lines in continuous light supports the involvement of this protein in circadian rhythm regulation. Phylogenetic analysis reveals a wide distribution of RITMO1-like proteins in the genomes of diatoms as well as in other marine algae, which may indicate a common function in these phototrophs. This study adds elements to our understanding of diatom biology and offers perspectives to elucidate timekeeping mechanisms in marine organisms belonging to a major, but under-investigated, branch of the tree of life.

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bHLH-PAS protein RITMO1 regulates diel biological rhythms in the marine diatom Phaeodactylum tricornutum

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Mapping of H3K4me3 in the model diatom Phaeodactylum tricornutum

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Project description:Phaeodactylum tricornutum transcriptome

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Early nutrient starvation response of the diatom Phaeodactylum tricornutum

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).

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Molecular responses to prolonged darkness and subsequent acclimation to re-illumination in the diatom Phaeodactylum tricornutum

Project description:We have investigated both the response to prolonged darkness and the re-acclimation to “moderate intensity” white irradiance (E = 100 µmol m-2 s-1) in the diatom Phaeodactylum tricornutum, using an integrated approach involving global transcriptional profiling, pigment analyses, imaging and photo-physiological measurements. The responses were studied during continuous white light, after 48 h of dark treatment and after 0.5 h, 6 h, and 24 h of re-exposure to the initial irradiance.

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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

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