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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Genome-wide profiling of responses to cadmium in the diatom Phaeodactylum tricornutum

ABSTRACT: The only group of organisms in which a biological function for cadmium has been shown is the diatoms, which are unicellular phytoplankton. Yet diatoms exhibit similar sensitivity to Cd as other groups of phytoplankton. We have investigated responses of Cd on molecular, metabolic and physiological levels in the diatom Phaeodactylum tricornutum. P. tricornutum apparently has a high tolerance to Cd; only minor responses were observed on growth, pigment and transcriptional changes at cadmium concentrations of 123 µg/l. No significant changes in chlorophyll and xanthophyll levels were observed, and the very few transcripts affected strongly indicate that the cells were able to respond to the increased Cd2+ levels without changing proteins levels. At 10 times this concentration, 1230 µg/l, a much clearer response was observed, including transcripts encoding proteins involved in metal transport, cell signalling and detoxification processes. Our results point towards putative pathways for the removal or detoxification of Cd and its metabolites, as well as a possible Cd uptake mechanism. We predict that ATPase5-1B is involved in removal of Cd by pumping Cd2+ ions out of the cell, whereas VIT1/CCC1 sequesters Cd2+ in the vacuole. Cultures of Phaeodactylum tricornutum were treated with two concentrations of Cd2+, 123 µg/l and 1230 µg/l. The reference samples were grown in artificial seawater base AK modified with added f/2-medium nutrients. Three biological replicates were harvested for all samples.

ORGANISM(S): Phaeodactylum tricornutum

SUBMITTER: Per Winge

PROVIDER: E-GEOD-31131 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Genome-wide profiling of responses to cadmium in the diatom Phaeodactylum tricornutum

Project description:The only group of organisms in which a biological function for cadmium has been shown is the diatoms, which are unicellular phytoplankton. Yet diatoms exhibit similar sensitivity to Cd as other groups of phytoplankton. We have investigated responses of Cd on molecular, metabolic and physiological levels in the diatom Phaeodactylum tricornutum. P. tricornutum apparently has a high tolerance to Cd; only minor responses were observed on growth, pigment and transcriptional changes at cadmium concentrations of 123 µg/l. No significant changes in chlorophyll and xanthophyll levels were observed, and the very few transcripts affected strongly indicate that the cells were able to respond to the increased Cd2+ levels without changing proteins levels. At 10 times this concentration, 1230 µg/l, a much clearer response was observed, including transcripts encoding proteins involved in metal transport, cell signalling and detoxification processes. Our results point towards putative pathways for the removal or detoxification of Cd and its metabolites, as well as a possible Cd uptake mechanism. We predict that ATPase5-1B is involved in removal of Cd by pumping Cd2+ ions out of the cell, whereas VIT1/CCC1 sequesters Cd2+ in the vacuole.

2011-08-02 | GSE31131 | GEO

Transcriptional response of the marine pennate diatom Phaeodactylum tricornutum to Fe limitation

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

Global transcriptome responses of a marine diatom to phosphate fluctuations provides insights into its ecological success

Project description:Phosphate (Pi) is an essential element to all living cells yet fluctuations in Pi concentrations are recurrent in the marine environment. Diatoms are amongst the most successful phytoplankton clade living in the worldâs oceans adapting to and surviving long periods of sub-optimal conditions and resuming growth as soon as nutrient concentrations permit. The knowledge of the molecular underpinnings of diatom ecological success is, however, still very incomplete. Using high-throughput RNA sequencing we have identified the dynamics of the model diatom Phaeodactylum tricornutum global transcriptome in response to Pi fluctuations. We report genes encoding previously unidentified putative Pi transporters that, together with the alkaline phosphatases genes highly expressed under Pi depletion, are probably accountable for a very efficient Pi scavenging system. Our data also reveal the complexity of the P. tricornutum responsive sensory and signaling system that combines bacterial two-component systems with more complex pathways reminiscent of metazoans. This intricate set of membrane receptors and signal-transduction related proteins is likely responsible for the detection of environmental nutrient fluctuations, triggering a multitude of signaling cascades leading to gene regulatory events that define new adaptive physiological states. This together with the novel detection of a multitude of long non-coding intergenic RNAs specifically expressed under Pi stress, begins to provide insights into the complex molecular regulatory program involved in the resilience and ecological success of diatoms. Examination of Pi-responsive transcriptoms in diatoms.

2016-07-03 | E-GEOD-66997 | biostudies-arrayexpress

Quantitative proteomic analyses reveal the impact of nitrogen shortage on the proteome of the model diatom Phaeodactylum tricornutum

Project description:Diatoms represent one of the largest groups of Stramenopiles. In the phytoplankton biodiversity, they dominate oceanic and freshwater ecosystems, and contribute significantly to biogeochemical cycles. They are primary producers at the base of food webs, capturing dissolved CO2, inorganic nitrogen, phosphorus, sulfur, etc., and are important carriers of carbon and silicon to the ocean interior. Whereas extensive studies of P. tricornutum response to a lack of nitrogen have been reported from transcriptomics to metabolomics and lipidomics, changes occurring at the proteome level are still missing. Here we aimed at providing a reference dataset, corresponding to the proteomic changes occurring when Phaeodactylum tricornutum cells were cultivated in either a nitrogen-rich or a nitrogen-poor medium.

2022-09-29 | PXD033328 | Pride

Identification and Characterization of MicroRNAs from Phaeodactylum tricornutum by High-throughput Sequencing and Bioinformatics Analysis

Project description:Diatoms, which are important planktons widespread in various aquatic environments, are believed to play a vital role in primary production as well as silica cycling. The genomes of the pennate diatom Phaeodactylum tricornutum and the centric diatom Thalassiosira pseudonana have been sequenced, revealing some characteristics of the diatomsâ mosaic genome as well as some features of their fatty acid metabolism and urea cycle, and indicating their unusual properties. To identify microRNAs (miRNAs) from P. tricornutum and to study their probable roles in nitrogen and silicon metabolism, we constructed and sequenced small RNA (sRNA) libraries from P. tricornutum under normal (PT1), nitrogen-limited (PT2) and silicon-limited (PT3) conditions. A total of 13 miRNAs were identified. They were probable P. tricornutum-specific novel miRNAs. These miRNAs were differentially expressed in PT1, PT2 and PT3, and their potential targets were involved in various processes. Our results indicated that P. tricornutum contained novel miRNAs that differed from miRNAs of other organisms and that they might play important regulator roles in P. tricornutum metabolism. Constructing and sequencing small RNA (sRNA) libraries from P. tricornutum under normal (PT1), nitrogen-limited (PT2) and silicon-limited (PT3) conditions

2011-08-08 | E-GEOD-29321 | biostudies-arrayexpress

Evolutionary and functional analysis of DNA methyltransferases in micro-eukaryotes: Insights from the model diatom Phaeodactylum tricornutum [RNA-seq]

Project description:Loss of DNA methylation is traditionally associated with transcriptional up-regulation of transposable elements. Here we describe for the first time expression changes upon loss of DNA methylation in diatoms using Phaeodactylum tricornutum as a model species. The loss of DNA methylation was obtained by generation of DNMT5 KOs, a divergent DNMT with SNF-like domains. Expression analysis confirm the loss of DNA methylation is associated with de-repression of transposable elements in Phaeodactylum tricornutum with indirect effects on protein coding genes.

2023-03-15 | GSE186856 | GEO

Next generation sequencing of Phaeodactylum tricornutum grown with and without nitrogen

Project description:We have done next generation sequencing of optically thin, exponentialy growing Phaeodactylum tricornutum cultures grown with and without nitrogen source to improve our undestanding of the pathways regulation under conditions that promote lipid accumulation (N-starvation). 3 biologically independent exponentially growing culture of Phaeodactylum tricornutum were pelleted and washed several times with N-free media. Each culture was devided to 2 replicates with initial cell concentration of 2X105 cells/mL, one with NaNO3 as nitrogen source and the other without any nitrogen source. The cuture were bubbled foro 48 hours and sampled for transcriptome together with other physiological parameters and lipid analysis.

2015-01-02 | E-GEOD-56346 | biostudies-arrayexpress

Whole genome McrBC-chip on DNA methylation of diatom Phaeodactylum tricornutum

Project description:Extensive gene methylation correlated strongly with transcriptional silencing and differential expression under specific conditions. DNA methylation and its role in gene regulation is conserved in stramenopile. Methylome of the whole genome of diatom phaeodactylum tricornutum.

2013-06-15 | E-GEOD-47947 | biostudies-arrayexpress

Regulatory mechanism of diurnal fluctuated laminarin in diatom Phaeodactylum tricornutum

Project description:Diatoms played an essential role in marine primary productivity. Polysaccharide chrysolaminarin and neutral lipid, mainly TAG, were necessary carbon fixation in diatom Phaeodactylum tricornutum. Our study speculated on the metabolism pathway of chrysolaminarin, fatty acid, fatty acid β-oxidation and TAG. Transcriptional levels coordinated with carbon fixation metabolism pathway were conjoint analysis in this study.

2022-08-03 | GSE210141 | GEO

Chronic iron limitation induces resistance to ROS

Project description:Diatoms are single celled photosynthetic bloom-forming algae that are responsible for at least 20% of global primary production. Nevertheless, more than 30% of the oceans are considered “ocean deserts” due to iron limitation. We used the diatom Phaeodactylum tricornutum as a model system to explore diatom’s response to iron limitation and its interplay with susceptibility to oxidative stress. By analyzing physiological parameters and proteome profiling, we defined two distinct phases: short-term (< 3 days, phase I) and chronic (> 5 days, phase II) iron limitation. While at phase I no changes in physiological parameters were observed, molecular markers for iron starvation, such as ISIP and flavodoxin, were highly upregulated. At phase II, down regulation of numerous iron-containing proteins was detected in parallel to reduction in growth rate, chlorophyll content, photosynthetic activity, respiration rate and antioxidant capacity. Intriguingly, while application of oxidative stress to phase I and II iron limited cells similarly oxidized the GSH pool, phase II iron limitation exhibited transient resistance to oxidative stress, despite the down regulation of many antioxidant proteins. By comparing proteomic profiles of P. tricornutum under iron limitation and metatranscriptomic data of an iron enrichment experiment conducted in the Pacific Ocean, we propose that iron limited cells in the natural environment resemble the phase II metabolic state. These results provide insights into the trade-off between maximal growth rate and susceptibility to oxidative stress as a possible key determinant in the response of diatoms to iron quota in the marine environment.

2017-01-16 | PXD004694 | Pride

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