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Thalassiosira pseudonana

ABSTRACT: Diatoms are photosynthetic unicellular algae and this species has served as a model for diatom physiology studies

PROVIDER: PRJNA9562 | ENA |

REPOSITORIES: ENA

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			Action	DRS
		Other
	SRR077494.fastq.gz	Fastqsanger.gz
	SRR077760.fastq.gz	Fastqsanger.gz
	SRR077761.fastq.gz	Fastqsanger.gz
	SRR081270.fastq.gz	Fastqsanger.gz

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Similar Datasets

Transcript level coordination of carbon pathways during silicon starvation induced lipid accumulation in the diatom Thalassiosira pseudonana

2015-12-31 | GSE75651 | GEO

Flavobacterial exudates disrupt cell cycle progression and metabolism of the diatom Thalassiosira pseudonana

Project description:Phytoplankton and bacteria form the base of marine ecosystems and their interactions drive global biogeochemical cycles. The effect of bacteria and bacteria-produced compounds on diatoms range from synergistic to pathogenic and can affect the physiology and transcriptional patterns of the interacting diatom. Here, we investigate physiological and transcriptional changes in the marine diatom Thalassiosira pseudonana induced by extracellular metabolites of a known antagonistic bacterium Croceibacter atlanticus. Mono-cultures of C. atlanticus released compounds that inhibited diatom cell division and elicited a distinctive phenotype of enlarged cells with multiple plastids and nuclei, similar to what was observed when the diatom was co-cultured with the live bacteria. The extracellular C. atlanticus metabolites induced transcriptional changes in diatom pathways that include recognition and signaling pathways, cell cycle regulation, carbohydrate and amino acid production, as well as cell wall stability. Phenotypic analysis showed a disruption in the diatom cell cycle progression and an increase in both intra- and extracellular carbohydrates in diatom cultures after bacterial exudate treatment. The transcriptional changes and corresponding phenotypes suggest that extracellular bacterial metabolites, produced independently of direct bacterial-diatom interaction, may modulate diatom metabolism in ways that support bacterial growth.

2022-06-24 | GSE197934 | GEO

Subcellular proteomics for determining iron limited remodeling of plastids in the model diatom Thalassiosira pseudonana

Project description:Diatoms are important primary producers in the world’s oceans, yet their growth is constrained in large regions by low bioavailable iron (Fe). Low Fe-induced limitation of primary production is due to requirements for Fe in components of essential metabolic pathways including photosynthesis and other chloroplast plastid functions. Studies have shown that under Fe-limited stress, diatoms alter plastid-specific processes, including components of electron transport. These physiological changes suggest changes of protein content and their abundance within the diatom plastid. While in-silico predictions provide putative information on plastid-localized proteins, knowledge of diatom plastid proteins remains limited in comparison to model photosynthetic organisms. To characterize proteins enriched in diatom plastids we have used shotgun proteomics to assess the proteome of subcellular plastid-enriched fractions from Thalassiosira pseudonana. To improve our understanding of how the plastid proteome is remodeled in response to Fe limitation, proteome sequencing has been performed on T. pseudonana grown under Fe replete and limited conditions. These analyses have shown that Fe limitation regulates major metabolic pathways in the plastid, including the Calvin cycle, as well as changes in light harvesting protein expression. In-silico localization predictions of proteins identified in this plastid-enriched proteome allowed for an in-depth comparison of theoretical vs observed plastid-localization, providing evidence for the potential of additional protein import pathways into the diatom plastid.

2023-08-04 | PXD040824 | Pride

Transcript level coordination of carbon pathways during silicon starvation induced lipid accumulation in the diatom Thalassiosira pseudonana

Project description:Nutrient-starvation induced lipid accumulation has been reported in diverse algae, including diatoms. Molecular mechanisms underlying lipid accumulation in nutrient-starved algae are of interest to inform genetic engineering strategies aimed at improving lipid productivity. Diatom cell walls are made of nanostructured silica which is a unique feature of the group and silicon deprivation induces both growth arrest and lipid accumulation. In this work, we report the whole cell transcript level response during silicon starvation induced lipid accumulation. Analyzed mRNA from cells after 0, 4, 8, 12, 18, and 24 hr of silicon starvation using the Affymetrix GeneChip whole genome tiling array. Initial analysis of gene level expression was performed using the Affymetrix Expression Console Software, version 1.1. No biological replicates were performed. 0 hr is used as a reference point.

2015-12-31 | E-GEOD-75651 | biostudies-arrayexpress

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.

2022-05-19 | GSE203136 | GEO

Thalassiosira pseudonana

Project description:Diatoms EST project

| PRJNA13883 | ENA

Transcript level coordination of carbon pathways during silicon-starvation induced lipid accumulation in the diatom Thalassiosira pseudonana

Project description:To characterize the transcript level component of metabolic regulation, genome-wide transcript level changes were documented in the model diatom Thalassiosira pseudonana over a time-course of silicon starvation. Growth, cell cycle progression, chloroplast replication, fatty acid composition, pigmentation, and photosynthetic parameters were characterized alongside lipid accumulation. Extensive coordination of large suites of genes was observed, highlighting the existence of clusters of co-regulated genes as a key feature of global gene regulation in T. pseudonana. The identity of key enzymes for carbon metabolic pathway inputs (photosynthesis) and outputs (growth and storage) reveals these clusters are organized to synchronize these processes.

2015-11-30 | GSE75460 | GEO

Diel growth of Thalassiosira pseudonana

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.

2013-04-18 | GSE45252 | GEO

Contrasting Effects of Acclimated Copper Limitation on the Photosynthetic Apparatus in Two Strains of the open ocean diatom Thalassiosira oceanica

Project description:The physiological adaptations of diatoms to cope with Cu limitation are largely unknown. In the present study we investigated the response to Cu limitation in two strains of the model open ocean diatom T. oceanica (CCMP 1003 and CCMP 1005), focusing on physiological and proteomic changes in the photosynthetic apparatus. Our results show remarkable differences between the adaptations of TO05 and TO03 to low Cu, highlighting significant intra specific variations.

2017-08-15 | PXD006237 | Pride

Coordination in the transcriptome and proteome of the diatom Thalassiosira pseudonana reveals a diverse phosphorus stress response

Project description:Phosphorus (P) is a critical driver of phytoplankton growth and ecosystem structure and function in the ocean. Diatoms are an abundant and widespread functional group of phytoplankton that are responsible for significant amounts of primary production in the ocean, however there has not been a comprehensive study of diatom physiological responses to P deficiency. Here, we coupled deep sequencing of transcript tags and quantitative proteomic analysis from the diatom Thalassiosira pseudonana grown under P-replete and P-deficient conditions. The reads (tags) were mapped to the T. pseudonana genome sequence, confirming expression of 91% of the modeled gene set. A total of 318 genes were differentially regulated with a false discovery rate of p<0.05. A total of 1264 proteins were detected, and of those 136 were differentially expressed with a false discovery rate of p<0.05. Significant changes in the abundance of transcripts and proteins were observed and these changes were coordinated for glycolysis, translation, and multiple biochemical responses to P deficiency. These data demonstrate that diatom P deficiency results in changes in cellular P allocation through polyphosphate production, increased P transport, a switch to utilization of dissolved organic P (DOP) through increased production of alkaline phosphatase metalloenzymes and a diesterase, and a remodeling of the cell surface through production of sulfolipids. Together, these findings reveal that T. pseudonana has evolved a sophisticated response to P deficiency involving multiple biochemical strategies that are likely critical to its ability to rapidly respond to variations in environmental P availability.

2013-08-03 | GSE28134 | GEO

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