Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

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

ABSTRACT: 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).

ORGANISM(S): Phaeodactylum tricornutum

SUBMITTER: Per Winge

PROVIDER: E-GEOD-42514 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

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

Chauton Matilde Skogen MS Winge Per P Brembu Tore T Vadstein Olav O Bones Atle M AM

Plant physiology 20121203 2

The regulation of carbon metabolism in the diatom Phaeodactylum tricornutum at the cell, metabolite, and gene expression levels 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. An increase in Nile Red fluorescence (a proxy for cellular neutral lipids) was observed throughout the light period, and water-soluble glucans increased rapidl ...[more]

PMID: 23209127

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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.

Project description:Photosynthetic diatoms are exposed to rapid and unpredictable changes in irradiance and spectral quality, and must be able to adapt their light harvesting systems to varying light conditions. Molecular mechanisms behind light acclimation in diatoms are largely unknown. We set out to investigate the mechanisms of high light acclimation in Phaeodactylum tricornutum using an integrated approach involving global transcriptional profiling, metabolite profiling and variable fluorescence technique. Algae cultures were acclimated to low light (LL), after which the cultures were transferred to high light (HL). Molecular, metabolic and physiological responses were studied at time points 0.5 h, 3 h, 6 h, 12 h, 24 h and 48 h after transfer to HL conditions. The integrated results indicate that the acclimation mechanisms in diatoms can be divided into an initial response phase (0.5 h), an intermediate acclimation phase (3-12 h) and a late acclimation phase (12-48 h). The initial phase is recognized by strong and rapid regulation of genes encoding proteins involved in photosynthesis, pigment metabolism and reactive oxygen species (ROS) scavenging systems. A significant increase in light protecting metabolites occur together with the induction of transcriptional processes involved in protection of cellular structures at this early phase. During the following phases, the metabolite profiling display a pronounced decrease in light harvesting pigments, whereas the variable fluorescence measurements show that the photosynthetic capacity increases strongly during the late acclimation phase. We show that P. tricornutum is capable of swift and efficient execution of photoprotective mechanisms, followed by changes in the composition of the photosynthetic machinery that enable the diatoms to utilize the excess energy available in HL. Central molecular players in light protection and acclimation to high irradiances have been identified. The experiment was designed as a time series, with diatom cultures were harvested at time points 0.5 h, 3 h, 6 h, 12 h, 24 h and 48 h after transfer to high light conditions. The reference samples were kept at low light and harvested in parallel with the treated samples. Three biological replicates were harvested for all samples.

Dataset Information

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

Publications

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

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