The transcriptome of Tetraselmis suecica reveals new insights on green algae response to nitrogen starvation
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ABSTRACT:
ORGANISM(S): Tetraselmis suecica
PROVIDER: GSE109461 | GEO | 2018/12/01
REPOSITORIES: GEO
Similar Datasets
Project description:Limited systems-level understanding of oil synthesis in wild oleaginous algae has hindered the development of microalgal feedstock. Nannochloropsis is a small unicellular microalgae widely distributed in oceans and fresh water. In many large-scale and pilot-scale outdoor cultivation facilities, Nannochloropsis strains have been found to be capable of robust growth when supplied with flue gases, naturally accumulating large quantities of oils in a stationary phase, and exhibiting resistance to environmental contaminants. The rich genomic resources, compact genomes, resistance to foreign DNA invasion, wide ecological adaptation, large collections of natural strains and the demonstrated ability to grow on a large scale suggested Nannochloropsis can serve as research models and platform strains for economical and scalable photosynthetic production of fuels and chemicals. To untangle the intricate genome-wide networks underlying the robust biomass accumulation and oil production in Nannochloropsis, we applied high-throughput mRNA-sequencing and reconstructed the structure and dynamics of the genome-wide functional network underlying robust microalgal triacylglycerol (TAG) production in Nannochloropsis oceanica, by tracking the genome-wide, single-base-resolutiontranscript change for the complete time-courses of nitrogen-depletion-induced TAG synthesis.
2014-05-14 | GSE42508 | GEO
Project description:The transcriptome of Tetraselmis suecica reveals new insights on green algae response to nitrogen starvation
| PRJNA430950 | ENA
Project description:Algal biofuel production requires an input of synthetic nitrogen fertilizer. Fertilizer synthesized via the Haber-Bosch process produces CO2 as a waste by-product and represents a substantial financial and energy investment. Reliance on synthetic fertilizer attenuates the environmental significance and economic viability of algae production systems. To lower fertilizer input, the waste streams of algal production systems can be recycled to provide alternative sources of nitrogen such as amino acids to the algae. The halophytic green alga Dunaliella viridis can use ammonium (NH4+) derived from the abiotic degradation of amino acids, and previously, supplementation of NH4+ from glutamine (GLN) degradation was shown to support acceptable levels of growth and increased neutral lipid production compared to nitrate. To understand the effect of glutamine-released NH4+ on algae growth and physiology, metabolite levels, growth parameters, and transcript profiles of D. viridis cultures were observed in a time course after transition from media containing nitrate as a sole N source to medium containing GLN, glutamate (GLU), or a N-depleted medium. Growth parameters were similar between GLN (NH4+) and nitrate supplemented cultures, however, metabolite data showed that the GLN supplemented cultures (NH4+) more closely resembled cultures under nitrogen starvation (N-depleted and GLU supplementation). Neutral lipid accumulation was the same in nitrate and glutamine-derived NH4+ cultures. However, glutamine-derived NH4+ caused a transcriptional response in the immediate hours after inoculation of the culture. The strong initial response of cultures to NH4+ changed over the course of days to closely resemble that of nitrogen starvation. These observations suggest that release of NH4+ from glutamine was sufficient to maintain growth, but not high enough to trigger a cell transition to a nitrogen replete state. Comparative transcript profiling of the nitrogen-starved and nitrate-supplied cultures show an overall downregulation of fatty acid synthesis and a shift to starch synthesis and accumulation. The results indicate that a continuous, amino acid derived slow release of NH4+ to algae cultures could reduce the amount of synthetic nitrogen needed for growth, but optimization is needed to balance nitrogen starvation and cell division.
2018-03-30 | GSE111548 | GEO
Project description:Alga-derived lipids represent an attractive potential source of biofuels. However, lipid accumulation in algae is a stress response tightly coupled to growth arrest, thereby imposing a major limitation on productivity. To identify master regulators of lipid accumulation and decipher the regulation of lipid biosynthetic pathway, we performed an integrative chromatin signature and transcriptomic analysis in the alga Chlamydomonas reinhardtii. Genome-wide histone modification profiling revealed remarkable differences in functional chromatin states between algae and higher eukaryotes and uncovered regulatory components at the core of lipid accumulation pathways. We identified the transcription factor PSR1 as a pivotal master switch that triggers cytosolic lipid hyper-accumulation an order of magnitude higher than stress regimens have achieved. Dissection of the PSR1 target network corroborates its central role in coordinating multiple stress responses. The comprehensive maps of functional chromatin signatures in a major clade of eukaryotic life and the discovery of a central regulator of algal lipid metabolism will facilitate targeted engineering strategies in microalgae. 1. Genome-wide H3K4me3 time series profiling (at 0 hr, 10 min, 30 min, 1 hr, 2hr, 6 hr, 8 hr, 24 hr and 48 hr after nitrogen starvation) was performed to determine time point to capture maximal chromatin changes. 2. Genome-wide H3K4me3, H3K27ac, H3K9me3, H3K27me3, H3K36me3 and Pol II profiling were performed at 0 hr, 1 hr after nitrogen starvation and 1 hr after sulfur starvation to determine chromatin signatures. Genome-wide H3K4me2 profiling was performed at 0 hr before starvation. 3. Transcriptome time series profiling (at 0 hr, 10 min, 30 min, 1 hr, 2hr, 6 hr, 8 hr, 24 hr and 48 hr after nitrogen and sulfur starvation separately) for chromatin signature characterization and integrative analysis. 4. Genome-wide PSR1 binding profiling was performed with polyclonal antibody against PSR1 peptide A region and PSR1 peptide B region individually. (At 30 min and 1 hr after nitrogen starvation, and 1 hr, 2 hr and 6 hr after sulfur starvation.) Please note that the following reference genome and gene models used in these experiments are linked below; C.reinhardtii_v5.3_genomic_scaffold_plastids.fasta.gz reference_gene_model.gtf.gz These are based off Phytozome (http://www.phytozome.net/) which does not provide access to earlier version data.
2015-07-28 | E-GEOD-59629 | biostudies-arrayexpress
Project description:Dinoflagellates are phytoplanktonic organisms found in both freshwater and marine habitats. They are often studied because related to harmful algal blooms responsible for impacts on ecosystem functioning, economic damages for aquaculture and fishery industries and/or deleterious impacts for human health. In addition they are also known to produce bioactive compounds, such as for the treatment of cancer or beneficial effects for the treatment of Alzheimer’s disease. The dinoflagellate Amphidinium sp. is a cosmopolitan dinoflagellate species known to produce both cytotoxic and beneficial compounds. However, several studies reported that environmental changes (e.g. nutrient starvation, UV radiation and ocean acidification) may alter this production. The aim of this study was to sequence the full transcriptome of the dinoflagellate Amphidinium carterae in both nitrogen- starved and -repleted culturing conditions (1) to evaluated its response to nitrogen starvation, (2) to look for possible polyketide synthases (PKSs), involved in the synthesis of various compounds, in this studied clone, (3) if present, to evaluate if nutrient starvation can influence PKS activity, (4) to test strain cytotoxicity on human cells and (5) to look for other possible enzymes/proteins of biotechnological interest.
2017-12-01 | GSE94355 | GEO
Project description:Like many microalgae unicellular green alga, Chlamydomonas reinhardtii also accumulates energy rich storage lipid and starch under nutrient-limited conditions, such as phosphorus (P) and nitrogen (N) limitation. To dissect the transcriptional regulation of lipid and starch biosynthesis in response to nutrient limitation, we have characterized the biological role of a candidate regulator: the MYB family transcription factor, PSR1 (phosphorus starvation response 1). Genetically modified (psr1 compromised) and wild-type lines were grown under P limiting and sufficient conditions and assayed at two time points by SOLiD RNA-seq.
2016-01-08 | E-MTAB-2556 | biostudies-arrayexpress
Project description:Limited systems-level understanding of CO2 concentrating mechanism (CCM) and metabolic adaption in response to different CO2-level in wild oleaginous algae has hindered the development of microalgal feedstock and the knowledge of its role in global warming and oceanic acidification. Nannochloropsis are a group of small unicellular microalgae widely distributed in oceans and fresh water, which implies that it plays a crucial role in biogeochemical cycles impinged on global climate change. In addition, Nannochloropsis has been used for flue gas fixation in many large-scale and pilot-scale outdoor cultivation facilities for photosynthetic production of fuels and chemicals. To untangle the intricate genome-wide networks underlying CCM and metabolic adjustment under different CO2 concentrations in Nannochloropsis, we applied high-throughput mRNA-sequencing and reconstructed the structure and dynamics of the genome-wide functional network underlying robust microalgal CCM and in Nannochloropsis oceanica, by tracking the genome-wide, single-base-resolution transcript change for the complete time-courses of different CO2 concentrations.
2019-07-16 | GSE55861 | GEO
Project description:The oleaginous green microalga Neochloris oleoabundans accumulates both starch and lipids to high levels under stress conditions such as nitrogen starvation. In order to steer the metabolism towards starch or lipids only, it is important to understand the mechanisms behind it. In this study physiological changes and gene expression upon nitrogen starvation were analysed in controlled flat-panel photobioreactors over both short- and long-term time-scales. Starch accumulation is transient and occurs rapidly within 24 hrs upon starvation, while lipid accumulation lasts longer and reaches a maximum after 4 days. The major fraction of accumulated lipids is composed of de novo synthesized neutral lipids - triacylglycerides (TAG) - and is characterized by a decreased composition of the polyunsaturated fatty acids (PUFAs) C18:3 and C16:3 and an increased composition of the mono-unsaturated and saturated fatty acids C18:1/C16:1 and C18:0/C16:0, respectively. RNA-sequencing revealed that genes related to starch biosynthesis and degradation show different temporal expression dynamics compared to those of lipid biosynthesis. An immediate rapid increase in starch synthesis gene expression is followed by an increase in starch degradation and decrease in starch synthesis gene expression. In contrast, increased gene expression for fatty acid and TAG synthesis is initiated later and occurs more gradually. Expression of several fatty acid desaturase (FAD) genes was decreased upon starvation, which corresponds to the observed changes to higher levels of mono-unsaturated and saturated fatty acids. Moreover, several homologs of transcription regulators that were implicated in controlling starch and lipid metabolism in other microalgae showed differential gene expression and might be key regulators of starch and lipid metabolism in N. oleoabundans as well. Promising candidates for future metabolic engineering are a DYRKP homolog that in Chlamydomonas acts as a negative regulator of carbon storage and photosynthetic efficiency under N-starvation, and two bZIP-type regulators that have been implicated to control several steps in microalgal TAG synthesis. Our data for the first time show the temporal dynamics of storage compound accumulation and transcriptional changes on a short- and long-term time-scale during nitrogen starvation in N. oleoabundans, and increases insight into the genetic foundation for starch and lipid metabolism in this microalga. This information and the identified target genes can now be used for metabolic engineering strategies towards tailored N. oleoabundans strains for industrial applications with increased lipid production and altered fatty acid composition.
2018-10-11 | GSE104807 | GEO
Project description:Limited systems-level understanding of oil synthesis in wild oleaginous algae has hindered the development of microalgal feedstock. Nannochloropsis is a small unicellular microalgae widely distributed in oceans and fresh water. In many large-scale and pilot-scale outdoor cultivation facilities, Nannochloropsis strains have been found to be capable of robust growth when supplied with flue gases, naturally accumulating large quantities of oils in a stationary phase, and exhibiting resistance to environmental contaminants. The rich genomic resources, compact genomes, resistance to foreign DNA invasion, wide ecological adaptation, large collections of natural strains and the demonstrated ability to grow on a large scale suggested Nannochloropsis can serve as research models and platform strains for economical and scalable photosynthetic production of fuels and chemicals. To untangle the intricate genome-wide networks underlying the robust biomass accumulation and oil production in Nannochloropsis, we applied high-throughput mRNA-sequencing and reconstructed the structure and dynamics of the genome-wide functional network underlying robust microalgal triacylglycerol (TAG) production in Nannochloropsis oceanica, by tracking the genome-wide, single-base-resolutiontranscript change for the complete time-courses of nitrogen-depletion-induced TAG synthesis. Nannochloropsis oceanica IMET1 cells were grown in liquid cultures under continuous light (approximately 50 M-BM-5mol photons m-2 s-1) at 25M-bM-^DM-^C and aerated by bubbling with a mixture of 1.5% CO2 in air. Mid-logarithmic phase algal cells were collected and washed three times with axenic seawater. Equal numbers of cells were re-inoculated in nitrogen replete medium (Control condition or C, i.e. N+) and nitrogen deprived medium (N deficiency or N, i.e. N-) with 50M-BM-5mol m-2 s-1 light intensity, respectively. Cell aliquots were collected for RNA isolation after being transferred to the designated conditions for 3h, 4h, 6h, 12h, 24h and 48h. Three biological replicates of algal cultures were established under each of the above M-bM-^@M-^\CM-bM-^@M-^] (i.e. N+) and M-bM-^@M-^\NM-bM-^@M-^] (i.e. N-) conditions, respectively. In total, 36 samples collected at six time points (3h,4h,6h,12h,24h and 48h) were used for mRNA-Seq library preparation and then submitted to Illumina HiSeq 2000 for sequencing.
2014-05-14 | E-GEOD-42508 | biostudies-arrayexpress