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

ABSTRACT: 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.

ORGANISM(S): Thalassiosira pseudonana

PROVIDER: GSE75651 | GEO | 2015/12/31

SECONDARY ACCESSION(S): PRJNA304974

REPOSITORIES: GEO

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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

Thalassiosira pseudonana

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

| PRJNA304974 | ENA

Thalassiosira pseudonana

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

| PRJNA304348 | 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

Profiling the transcriptome of Thalassiosira pseudonana under silicon replete and deplete growth.

Project description:T. pseudonana tiling arrays were used to validate gene models and to predict new genes in the genome of this diatom. The tiling array data validated transcription of about 41% (4,653) of the 11,390 computationally predicted genes. An additional 1,132 transcripts were identified that did not correspond to modeled genes with few of these transcripts (<17%) predicted to encode proteins with homology (e-value < 10-05) to publicly available proteins. These newly identified transcripts have an average length of 1,549 bp, comparable to the average length of the computationally derived genes. Whole genome tiling arrays were conducted under silicon replete and deplete growth conditions to identify new genes involved in the synthesis of the diatom silica cell wall. Keywords: silicon, stress response, cell wall

2008-01-09 | GSE9661 | GEO

Profiling the transcriptome of Thalassiosira pseudonana under silicon replete and deplete growth.

2010-05-26 | E-GEOD-9661 | biostudies-arrayexpress

Profiling the transcriptome of Thalassiosira pseudonana under environmentally relevant growth conditions

Project description:T. pseudonana gene-specific arrays were used for differential gene expression. Seven hundred nine genes were differentially expressed by more than 2-fold (Bayesian t-test, p< 0.001) under at least one growth-limiting condition relative to nutrient-replete conditions. A striking result of the hierarchical cluster analysis was the identification of a common set of genes that were upregulated by both iron and silicon limitation, but no other treatment. Together, these two treatments accounted for about one fourth of all differentially expressed genes but almost two thirds of the differentially expressed novel genes, further emphasizing the distinctive aspects of silicon manipulation in diatoms. Keywords: silicon, stress response, cell wall, iron, temperature, carbon dioxide

2008-01-09 | GSE9660 | GEO

Thalassiosira pseudonana CCMP1335

Project description:Distinct genome-wide alternative polyadenylation during silicon starvation response of marine diatom Thalassiosira pseudonana

| PRJNA417734 | ENA

Whole Transcriptome Analysis of the Silicon Response of the Diatom Thalassiosira pseudonana

Project description:Diatom cell walls, made of nanostructured silica, are of interest in diverse areas ranging from cellular structure, to hierarchical organization in biomineralization, to nanotechnology. Thus far, only cell surface proteins and proteins tightly associated with silica matrix have been characterized, and essential components of the silica deposition vesicle (SDV) are unknown, including components of the SDV membrane, cytoskeletal-interacting proteins, and proteins involved in trafficking associated with the SDV. Thus, an understanding of most of the molecular components and the dynamics of cellular processes involved in cell wall synthesis is lacking. In this work we report the first whole-cell response analysis using whole genome microarrays to identify genes potentially involved in diverse aspects of diatom cell division or cell wall synthesis. Thalassiosira pseudonana transcript profiles from precise time points, known to be associated with specific cell wall formation processes in cell-cycle synchronized cultures, suggests that this gene set includes extracellular proteins, silica matrix proteins, and proteins involved in signal transduction, vesicle trafficking, and transport. Protein localization experiments further confirm the first discovery of proteins associated with the SDV membrane. We propose that these proteins provide the interface between extra-SDV organization by the cytoskeleton and intra-SDV organization of silica polymerization determinants, which lead to the higher order organization of diatom silica structure.

2012-10-01 | GSE37081 | GEO

Whole Transcriptome Analysis of the Silicon Response of the Diatom Thalassiosira pseudonana

2012-10-01 | E-GEOD-37081 | biostudies-arrayexpress

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