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Fe limitation decreases transcriptional regulation over the diel cycle in the model diatom Thalassiosira pseudonana

ABSTRACT: Fe limitation decreases transcriptional regulation over the diel cycle in the model diatom Thalassiosira pseudonana

PROVIDER: PRJNA542375 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR9042870_1.fastq.gz	Fastqsanger.gz
	SRR9042870_2.fastq.gz	Fastqsanger.gz
	SRR9042880_1.fastq.gz	Fastqsanger.gz
	SRR9042880_2.fastq.gz	Fastqsanger.gz
	SRR9042890_1.fastq.gz	Fastqsanger.gz

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Fe limitation decreases transcriptional regulation over the diel cycle in the model diatom Thalassiosira pseudonana

Project description:Iron (Fe) is an important growth limiting factor for diatoms and its availability is further restricted by changes in the carbonate chemistry of the water. We investigated the physiological attributes and transcriptional profiles of the diatom Thalassiosira pseudonana grown on a day:night cycle under different CO2/pH and iron concentrations, that in combination generated available iron (Fe’) concentrations of 1160, 233, 58 and 12 pM. We found the light-dark conditions to be the main driver of transcriptional patterns, followed by Fe’ concentration and CO2 availability, respectively. At the highest Fe’ (1160 pM), 55% of the transcribed genes were differentially expressed between day and night, whereas at the lowest Fe’ (12 pM), only 28% of the transcribed genes displayed comparable patterns. While Fe limitation disrupts the diel transcriptional patterns for genes in most central metabolism pathways, the diel periodicity of light- signaling molecules and glycolytic genes, was relatively robust in response to reduced Fe’. Moreover, we identified a non-canonical splicing of transcripts encoding triose-phosphate isomerase, a key-enzyme of glycolysis, generating transcript isoforms that would encode proteins with and without an active site. Transcripts that encoded an active enzyme maintained a diel pattern at low Fe’, while transcripts that encoded the non-active enzyme lost the diel pattern. This work illustrates the interplay between nutrient limitation and transcriptional regulation over the diel cycle. Considering that future ocean conditions will reduce the availability of Fe in many parts of the oceans, our work identifies some of the regulatory mechanisms that may shape future ecological communities.

2019-09-12 | GSE131042 | GEO

Fe limitation decreases transcriptional regulation over the diel cycle in the model diatom Thalassiosira pseudonana.

Project description:Iron (Fe) is an important growth factor for diatoms and its availability is further restricted by changes in the carbonate chemistry of seawater. We investigated the physiological attributes and transcriptional profiles of the diatom Thalassiosira pseudonana grown on a day: night cycle under different CO2/pH and iron concentrations, that in combination generated available iron (Fe') concentrations of 1160, 233, 58 and 12 pM. We found the light-dark conditions to be the main driver of transcriptional patterns, followed by Fe' concentration and CO2 availability, respectively. At the highest Fe' (1160 pM), 55% of the transcribed genes were differentially expressed between day and night, whereas at the lowest Fe' (12 pM), only 28% of the transcribed genes displayed comparable patterns. While Fe limitation disrupts the diel expression patterns for genes in most central metabolism pathways, the diel expression of light- signaling molecules and glycolytic genes was relatively robust in response to reduced Fe'. Moreover, we identified a non-canonical splicing of transcripts encoding triose-phosphate isomerase, a key-enzyme of glycolysis, generating transcript isoforms that would encode proteins with and without an active site. Transcripts that encoded an active enzyme maintained a diel expression at low Fe', while transcripts that encoded the non-active enzyme lost the diel expression. This work illustrates the interplay between nutrient limitation and transcriptional regulation over the diel cycle. Considering that future ocean conditions will reduce the availability of Fe in many parts of the oceans, our work identifies some of the regulatory mechanisms that may shape future ecological communities.

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Thalassiosira pseudonana CCMP1335

Project description:Diel growth of Thalassiosira pseudonana

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Synchronous cell cycle progression in the diatom Thalassiosira pseudonana

Project description:To identify the molecular components involved in diatom cell division, global transcript level changes were monitored over the silicon-synchronized cell cycle the model diatom Thalassiosira pseudonana.

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Project description:Transcript levels of all T. pseudonana genes was measured every twelve hours throughout the batch (non-chemostatic) growth of axenic cells grown in large glass bioreactors on a 12hr:12hr dark:light cycle for five days. The data were analyzed to reveal the physiological and regulatory changes that recurred in this diatom when transitioning between dark and light conditions, as well as from exponential phase to stationary, nutrient limited conditions. The longitudinal experiment was performed with two replicates, at 400 and 800ppm CO2. Two growth experiments were conducted, with 10 and 9 longitudinal samples collected from each experiment, respectively. Two-color arrays were used with dye flips for labeling. A common internal reference sample was used for one channel on each array. Expression changes for longitudinal analysis were calculated as the difference from the mean log2 expression ratio for each to the common reference sample, for each gene, over all samples within an experiment. For the analysis of diel states in T. pseudonana, samples from the two series were matched according to the time from innoculation, and divided into four classes: dawn samples (taken at the end of each dark phase), dusk samples (taken at the end of each light phase), exponential samples (the first five samples in each series prior to a drop in growth rate on Day 3), and stationary samples (all samples including following the drop in growth rate on Day 3).

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Project description:To test whether elevated CO2 , which drives seawater below pH 7.9, would shift the dynamical expression patterns diatoms in a more natural environment, we designed a controlled mesocosm study at Friday Harbor Laboratories (FHL) Ocean Acidification Environmental Laboratory (OAEL). Briefly, four independent mesocosm tanks were set up with continuous flow (10-12 mL/min) of filtered seawater from the Puget Sound to simulate mid-century (pH 7.9) and acidified oceanic conditions (pH 7.6) in duplicate. Mesocosm reservoirs were supplemented with nutrients and inoculated with T. pseudonana acclimated in FHL seawater. Mesocosms were outfitted with custom enclosures to simulate a 12:12 light:dark diel cycle. Cells for RNA extraction were sampled in the middle of the light and dark cycle and sequenced on Illumina NextSeq 500 platform.

2021-03-13 | GSE168812 | GEO

The diatom Thalassiosira pseudonana grown at [normal and elevated CO2] x [normal and elevated light]

Project description:Transcriptomic profiling of the diatom Thalassiosira pseudonana at normal and elevated CO2 levels and at normal and elevated light levels. Common reference total RNA (Agilent Quick-Amp Cy3-labeled) was used in all arrays as an internal standard.

2015-11-06 | GSE57737 | GEO

Thalassiosira pseudonana

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Project description:Thalassiosira pseudonana TAG accumulation Project

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Gene profiling of Thalassiosira pseudonana under various growth conditions

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