Synchronous cell cycle progression in the diatom Thalassiosira pseudonana
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PROVIDER: PRJNA838632 | ENA |
REPOSITORIES: ENA
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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
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
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
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
Project description:Transcriptomic profiling of the diatom Thalassiosira pseudonana at normal and elevlated 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. Triplicate batch cultures grown at normal (~400ppm) and elevated (~800ppm) CO2 levels, both at i) normal or ii) elevated light levels. Samples were taken during a) exponential and b) stationary growth during all growth experiments. Result: 48 total transcriptomic measurements: [3 parallel replicates] x [400ppm, 800ppm] x [normal light, high light] x [exponential, stationary] x [2 serial replicates]
2015-11-06 | E-GEOD-57737 | biostudies-arrayexpress
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
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
Project description:This SuperSeries is composed of the following subset Series: GSE9660: Profiling the transcriptome of Thalassiosira pseudonana under environmentally relevant growth conditions GSE9661: Profiling the transcriptome of Thalassiosira pseudonana under silicon replete and deplete growth Refer to individual Series
2010-05-26 | E-GEOD-9697 | biostudies-arrayexpress
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. Analyzed mRNA from 0, 2, 4, 7, 8 and 9 hr of synchronized cell cycle using the Affymetrix GeneChip whole genome tiling array. Initial analysis of gene level expression was performed using Affymetrix Expression Console Software, version 1.1. No biological replicates were performed. 0 hr is used as reference point.
2012-10-01 | E-GEOD-37081 | biostudies-arrayexpress
Project description:Flavobacterial exudates disrupt cell cycle progression and metabolism of the diatom Thalassiosira pseudonana
| PRJNA812899 | ENA