Five diatoms transcriptomes under iron limitation and oxidative stress
Ontology highlight
ABSTRACT:
ORGANISM(S): Thalassiosira oceanica Chaetoceros sp. CCMP199 Thalassiosira pseudonana Amphora coffeiformis Cylindrotheca closterium
PROVIDER: GSE217467 | GEO | 2022/11/07
REPOSITORIES: GEO
Similar Datasets
Project description:Proteins associated with diatom silica are likely involved in the biogenesis of the complex, species-specific morphologies of the biomineral, but only very few such proteins have been identified. In this project we extracted and identified proteins from three related, but morphologically distinct, species of centric diatoms: Thalassiosira pseudonana, Thalassiosira oceanica and Cyclotella cryptica.
2022-05-30 | PXD026496 | Pride
Project description:Background: Marine phytoplankton are responsible for 50% of the CO2 that is fixed annually worldwide and contribute massively to other biogeochemical cycles in the oceans. Diatoms and coccolithophores play a significant role as the base of the marine food web and they sequester carbon due to their ability to form blooms and to biomineralise. To discover the presence and regulation of short non-coding RNAs (sRNAs) in these two important phytoplankton groups, we sequenced short RNA transcriptomes of two diatom species (Thalassiosira pseudonana, Fragilariopsis cylindrus) and validated them by Northern blots along with the coccolithophore Emiliania huxleyi. Results: Despite an exhaustive search, we did not find canonical miRNAs in diatoms. The most prominent classes of sRNAs in diatoms were repeat-associated sRNAs and tRNA-derived sRNAs. The latter were also present in E. huxleyi. tRNA-derived sRNAs in diatoms were induced under important environmental stress conditions (iron and silicate limitation, oxidative stress, alkaline pH), and they were very abundant especially in the polar diatom F. cylindrus (20.7% of all sRNAs) even under optimal growth conditions. Conclusions: This study provides first experimental evidence for the existence of short non-coding RNAs in marine microalgae. Our data suggest that canonical miRNAs are absent from diatoms. However, the group of tRNA-derived sRNAs seems to be very prominent in diatoms and coccolithophores and may be used for acclimation to environmental conditions. RNA-seq study of sRNA populations in two species of diatoms using Illumina GAII high-throughput sequencing
2015-03-06 | E-GEOD-57987 | biostudies-arrayexpress
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:Background: Marine phytoplankton are responsible for 50% of the CO2 that is fixed annually worldwide and contribute massively to other biogeochemical cycles in the oceans. Diatoms and coccolithophores play a significant role as the base of the marine food web and they sequester carbon due to their ability to form blooms and to biomineralise. To discover the presence and regulation of short non-coding RNAs (sRNAs) in these two important phytoplankton groups, we sequenced short RNA transcriptomes of two diatom species (Thalassiosira pseudonana, Fragilariopsis cylindrus) and validated them by Northern blots along with the coccolithophore Emiliania huxleyi. Results: Despite an exhaustive search, we did not find canonical miRNAs in diatoms. The most prominent classes of sRNAs in diatoms were repeat-associated sRNAs and tRNA-derived sRNAs. The latter were also present in E. huxleyi. tRNA-derived sRNAs in diatoms were induced under important environmental stress conditions (iron and silicate limitation, oxidative stress, alkaline pH), and they were very abundant especially in the polar diatom F. cylindrus (20.7% of all sRNAs) even under optimal growth conditions. Conclusions: This study provides first experimental evidence for the existence of short non-coding RNAs in marine microalgae. Our data suggest that canonical miRNAs are absent from diatoms. However, the group of tRNA-derived sRNAs seems to be very prominent in diatoms and coccolithophores and may be used for acclimation to environmental conditions.
2015-03-06 | GSE57987 | GEO
Project description:<p>Diatoms perform about 20% of photosynthesis on earth, play a crucial role in forming the base of the marine food web, and sequester anthropogenic carbon into the deep ocean through the biological pump. In some areas of the ocean, diatom growth is limited by the organic micronutrient cobalamin (vitamin B12). Cobalamin affects phytoplankton growth rate and biomass yield, though the consequences of cobalamin limitation are not well understood on the biochemical level. In a controlled laboratory setting, we grew two diatoms, Thalassiosira pseudonana and Navicula pelliculosa, under cobalamin limited and replete conditions to elucidate changes in metabolite pools under cobalamin limitation. Using targeted and untargeted metabolomics, we show that the cobalamin-dependent T. pseudonana experienced a metabolic cascade under cobalamin limitation that a ects the central methionine cycle, the transsulfuration pathway, and the composition of its osmolyte pools. N. pelliculosa, a cobalamin-independent diatom, also showed evidence for changes in the methionine cycle when grown without cobalamin, though to a lesser extent than what we observed in T. pseudonana. In both diatoms the concentration of 5'-methylthioadenosine decreased when limited for cobalamin, suggesting a disruption in the diatoms' polyamine biosynthesis. Furthermore, two acylcarnitines and adenosyl cobalamin accumulated in T. pseudonana under cobalamin limitation, suggesting the use of an adenosylcobalamin-dependent enzyme, methylmalonyl CoA mutase. Overall, these changes in metabolite pools yield insight into the metabolic consequences of cobalamin limitation in diatoms and suggest that cobalamin starvation may have consequences for microbial interactions that are based on metabolite production by phytoplankton. </p><p><br></p><p> <strong>Navicula pelliculosa</strong> protocols and data are reported in the current study <a href='https://www.ebi.ac.uk/metabolights/MTBLS708' rel='noopener noreferrer' target='_blank'><strong>MTBLS708</strong></a>. </p><p> <strong>Thalassiosira pseudonana</strong> protocols and data are reported in <a href='https://www.ebi.ac.uk/metabolights/MTBLS703' rel='noopener noreferrer' target='_blank'><strong>MTBLS703</strong></a>.</p>
2019-06-04 | MTBLS708 | MetaboLights
Project description:<p>Diatoms perform about 20% of photosynthesis on earth, play a crucial role in forming the base of the marine food web, and sequester anthropogenic carbon into the deep ocean through the biological pump. In some areas of the ocean, diatom growth is limited by the organic micronutrient cobalamin (vitamin B12). Cobalamin affects phytoplankton growth rate and biomass yield, though the consequences of cobalamin limitation are not well understood on the biochemical level. In a controlled laboratory setting, we grew two diatoms, Thalassiosira pseudonana and Navicula pelliculosa, under cobalamin limited and replete conditions to elucidate changes in metabolite pools under cobalamin limitation. Using targeted and untargeted metabolomics, we show that the cobalamin-dependent T. pseudonana experienced a metabolic cascade under cobalamin limitation that a ects the central methionine cycle, the transsulfuration pathway, and the composition of its osmolyte pools. N. pelliculosa, a cobalamin-independent diatom, also showed evidence for changes in the methionine cycle when grown without cobalamin, though to a lesser extent than what we observed in T. pseudonana. In both diatoms the concentration of 5'-methylthioadenosine decreased when limited for cobalamin, suggesting a disruption in the diatoms' polyamine biosynthesis. Furthermore, two acylcarnitines and adenosyl cobalamin accumulated in T. pseudonana under cobalamin limitation, suggesting the use of an adenosylcobalamin-dependent enzyme, methylmalonyl CoA mutase. Overall, these changes in metabolite pools yield insight into the metabolic consequences of cobalamin limitation in diatoms and suggest that cobalamin starvation may have consequences for microbial interactions that are based on metabolite production by phytoplankton. </p><p><br></p><p> <strong>Thalassiosira pseudonana</strong> protocols and data are reported in the current study <a href='https://www.ebi.ac.uk/metabolights/MTBLS703' rel='noopener noreferrer' target='_blank'><strong>MTBLS703</strong></a>. </p><p> <strong>Navicula pelliculosa</strong> protocols and data are reported in <a href='https://www.ebi.ac.uk/metabolights/MTBLS708' rel='noopener noreferrer' target='_blank'><strong>MTBLS708</strong></a>.</p>
2019-06-04 | MTBLS703 | MetaboLights
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
Project description:Diatoms are important primary producers in the world’s oceans, yet their growth is constrained in large regions by low bioavailable iron (Fe). Low Fe-induced limitation of primary production is due to requirements for Fe in components of essential metabolic pathways including photosynthesis and other chloroplast plastid functions. Studies have shown that under Fe-limited stress, diatoms alter plastid-specific processes, including components of electron transport. These physiological changes suggest changes of protein content and their abundance within the diatom plastid. While in-silico predictions provide putative information on plastid-localized proteins, knowledge of diatom plastid proteins remains limited in comparison to model photosynthetic organisms. To characterize proteins enriched in diatom plastids we have used shotgun proteomics to assess the proteome of subcellular plastid-enriched fractions from Thalassiosira pseudonana. To improve our understanding of how the plastid proteome is remodeled in response to Fe limitation, proteome sequencing has been performed on T. pseudonana grown under Fe replete and limited conditions. These analyses have shown that Fe limitation regulates major metabolic pathways in the plastid, including the Calvin cycle, as well as changes in light harvesting protein expression. In-silico localization predictions of proteins identified in this plastid-enriched proteome allowed for an in-depth comparison of theoretical vs observed plastid-localization, providing evidence for the potential of additional protein import pathways into the diatom plastid.
2023-08-04 | PXD040824 | Pride
Project description:Thalassiosira weissflogii, Thalassiosira pseudonana, and Cyclotella striata strains isolated from marine samples (RNAseq/Transcriptomics)
| PRJNA835115 | ENA
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