Diatom transcriptomics under nitrate limitation
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA242525 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR1202311.fastq.gz | Fastqsanger.gz | |||
| SRR1202311_1.fastq.gz | Fastqsanger.gz | |||
| SRR1202311_2.fastq.gz | Fastqsanger.gz | |||
| SRR1202321_1.fastq.gz | Fastqsanger.gz | |||
| SRR1202321_2.fastq.gz | Fastqsanger.gz |
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Project description:Here, we examined the ramifications of between-species diversity by documenting the transcriptional response of three marine diatoms - Thalassiosira pseudonana, Fragilariopsis cylindrus, and Pseudo-nitzschia multiseries - to the onset of nitrate limitation of growth, a common limiting nutrient in the ocean. Less than 5% of orthologous genes, shared across the three diatoms, displayed the same transcriptional responses across species when growth was limited by nitrate availability. Orthologs, such as those involved in nitrogen uptake and assimilation, as well as carbon metabolism, were differently expressed across the three species. The two pennate diatoms, F. cylindrus and P. multiseries, shared 3,839 clusters without orthologs in the genome of the centric diatom T. pseudonana. A majority of these pennate-clustered genes, as well as the non-orthologous genes in each species, had minimal annotation information, but were often significantly differentially expressed under nitrate limitation, indicating their potential importance in the response to nitrogen availability. Despite these variations in the specific transcriptional response of each diatom, overall transcriptional patterns suggested that all three diatoms displayed a common physiological response to nitrate limitation that consisted of a general reduction in carbon fixation and carbohydrate and fatty acid metabolism and an increase in nitrogen recycling.
2014-03-25 | GSE56132 | GEO
Project description:Here, we examined the ramifications of between-species diversity by documenting the transcriptional response of three marine diatoms - Thalassiosira pseudonana, Fragilariopsis cylindrus, and Pseudo-nitzschia multiseries - to the onset of nitrate limitation of growth, a common limiting nutrient in the ocean. Less than 5% of orthologous genes, shared across the three diatoms, displayed the same transcriptional responses across species when growth was limited by nitrate availability. Orthologs, such as those involved in nitrogen uptake and assimilation, as well as carbon metabolism, were differently expressed across the three species. The two pennate diatoms, F. cylindrus and P. multiseries, shared 3,839 clusters without orthologs in the genome of the centric diatom T. pseudonana. A majority of these pennate-clustered genes, as well as the non-orthologous genes in each species, had minimal annotation information, but were often significantly differentially expressed under nitrate limitation, indicating their potential importance in the response to nitrogen availability. Despite these variations in the specific transcriptional response of each diatom, overall transcriptional patterns suggested that all three diatoms displayed a common physiological response to nitrate limitation that consisted of a general reduction in carbon fixation and carbohydrate and fatty acid metabolism and an increase in nitrogen recycling. Transcriptomes were collected for diatom cultures harvested at the onset of stationary phase in low nitrate media (55 M-NM-<M NaNO3, 212 M-NM-<M Na2SiO3, 72.4 M-NM-<M NaH2PO4) or during mid-exponential growth in nutrient-replete media (882 M-NM-<M NaNO3, 106 M-NM-<M Na2SiO3, 36.2 M-NM-<M NaH2PO4) in artificial seawater, maintaining three biological replicates per condition and per diatom (N=18). The SOLiD sequencer (version 4) was used to generate the transcriptomes and the SEAStAR software package was used to process the SOLiD reads and to calculate gene counts. Pooled counts for the nitrate-limited treatment were normalized to pooled counts for the nutrient-replete M-bM-^@M-^\controlM-bM-^@M-^] treatment to generate log fold changes in gene transcription using the R software package edgeR from Bioconductor.
2014-03-25 | E-GEOD-56132 | biostudies-arrayexpress
Project description:ngs2020_19_arimnet-barley responses to nitrate limitation-What are the molecular mechanisms taking place in barley under nitrate limitation?-Barley were grown on sand under 0.5 mM nitrate (Low nitrate= LN) or 5 mM nitrate (high nitrate = HN)
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Project description:Diatoms, which are responsible for up to 40% of the 45 to 50 billion metric tons of organic carbon production each year in the sea, are particularly sensitive to Fe stress. Here we describe the transcriptional response of the pennate diatom Phaeodactylum tricornutum to Fe limitation using a partial genome microarray based on EST and genome sequence data. Processes carried out by components rich in Fe, such as photosynthesis, mitochondrial electron transport and nitrate assimilation are down-regulated to cope with the reduced cellular iron quota. This retrenchment is compensated by nitrogen (N) and carbon (C) reallocation from protein and storage carbohydrate degradation, adaptations to chlorophyll biosynthesis and pigment metabolism, removal of excess electron s by mitochondrial alternative oxidase (AOX), augmented Fe-independent oxidative stress responses, and sensitized iron capture mechanisms. Keywords: Marine phytoplankton, pinnate diatom Wild-type Phaeodactylum tricornutum was grown under Fe replete (10,000 nM) and Fe limiting (5nM) conditions. Partial genome gene expression analysis of iron-inducible genes was conducted using a two-color competitive hybridization microarray.
2010-05-27 | E-GEOD-8675 | biostudies-arrayexpress
Project description:Diatoms, which are responsible for up to 40% of the 45 to 50 billion metric tons of organic carbon production each year in the sea, are particularly sensitive to Fe stress. Here we describe the transcriptional response of the pennate diatom Phaeodactylum tricornutum to Fe limitation using a partial genome microarray based on EST and genome sequence data. Processes carried out by components rich in Fe, such as photosynthesis, mitochondrial electron transport and nitrate assimilation are down-regulated to cope with the reduced cellular iron quota. This retrenchment is compensated by nitrogen (N) and carbon (C) reallocation from protein and storage carbohydrate degradation, adaptations to chlorophyll biosynthesis and pigment metabolism, removal of excess electron s by mitochondrial alternative oxidase (AOX), augmented Fe-independent oxidative stress responses, and sensitized iron capture mechanisms. Keywords: Marine phytoplankton, pinnate diatom
2008-01-01 | GSE8675 | GEO
Project description:Chemostats have been used for decades in studying cell growth under controlled environments. Whole transcriptome sequencing by RNA-seq is a relatively new method for gene expression analysis. We utilized both tools for expression analysis of Pseudomonas aeruginosa growing slowly in synthetic cystic fibrosis medium under growth-limiting nitrate and oxygen levels. We established steady-state cultures under two divergent growth rates and found that during slower growth at a doubling time of 9.8 h, 76 known quorum genes were up-expressed while just 11 were down-expressed. Quorum-controlled genes were also more expressed in response to oxygen limitation. 21% of up-expressed genes under slow, oxygen-limited growth are quorum controlled while just 6% are up-expressed under slow, nitrate-limited growth. We found that the autoinducer for regulator RhlR, C4-HSL, is ~3.4 times higher when cells are growing slowly under oxygen limitation while the concentration of the autoinducer for LasR remained unchanged. Experiments with deletion mutants show the importance of rhlR for expression of quorum-controlled genes under slow, oxygen-limited conditions. This is an intriguing observation since P. aeruginosa is likely growing in similar environments in the cystic fibrosis lung, and lasR mutations are known to arise during chronic infection.
2016-12-01 | GSE71880 | GEO
Project description:Diatoms are responsible for ~40% of marine primary productivity1, fueling the oceanic carbon cycle and contributing to natural carbon sequestration in the deep ocean2. Diatoms rely on energetically expensive carbon concentrating mechanisms (CCMs) to fix carbon efficiently at modern levels of CO23–5. How diatoms may respond over the short and long-term to rising atmospheric CO2 remains an open question. Here we use nitrate-limited chemostats to show that the model diatom Thalassiosira pseudonana rapidly responds to increasing CO2 by differentially expressing gene clusters that regulate transcription and chromosome folding and subsequently reduces transcription of photosynthesis and respiration gene clusters under steady-state elevated CO2. These results suggest that exposure to elevated CO2 first causes a shift in regulation and then a metabolic rearrangement. Genes in one CO2-responsive cluster included CCM and photorespiration genes that share a putative cyclic-AMP responsive cis-regulatory sequence, implying these genes are co-regulated in response to CO2 with cAMP as an intermediate messenger. We verified cAMP-induced down-regulation of CCM gene ?-CA3 in nutrient-replete diatom cultures by inhibiting the hydrolysis of cAMP. These results indicate an important role for cAMP in down-regulating CCM and photorespiration genes under elevated CO2 and provide insights into mechanisms of diatom acclimation in response to climate change. In steady-state experiments: axenic T. pseudonana cells in four biological replicates (duplicate chemostats x 2 experimental runs) were acclimated to nitrate-limitation at 70% (1.5 day-1) of max growth rate for >10 days (>15 generations) under continuous light of 80 µmol photons·m?2·s?1. Cell biomass was maintained at ~2 x 105 cells·mL?1 by 10 ?M nitrate and carbonate chemistry stabilized to 300, 475 or 800 ?atm CO2, verified by pH and DIC measurements. Transition samples and carbonate chemistry were collected daily from chemostat cultures as CO2 levels were increased from ~300-800 ?atm at a rate ? 0.2 ?atm·min?1 over four consecutive days (6 generations) after pre-acclimation to 300 ?atm CO2 and nitrate-limitation.
2015-04-17 | E-GEOD-67971 | biostudies-arrayexpress
Project description:This SuperSeries is composed of the following subset Series:; GSE14515: Comparative transcriptomics analysis of Populus leaves under nitrogen limitation: clone 1979; GSE14893: Comparative transcriptomics analysis of Populus leaves under nitrogen limitation: clone 3200 Experiment Overall Design: Refer to individual Series
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