A Protein Blue-Print of the Diatom CO2-Fixing Organelle
Ontology highlight
ABSTRACT:
INSTRUMENT(S): timsTOF, Orbitrap Fusion
ORGANISM(S): Thalassiosira Pseudonana (ncbitaxon:35128)
SUBMITTER: 
Luke Mackinder
PROVIDER: MSV000092867 | MassIVE |
SECONDARY ACCESSION(S): PXD045418
REPOSITORIES: MassIVE
Similar Datasets
Project description:Raw mass spectromety data, DIA-NN search files and results relating to A Protein Blueprint of the Diatom CO2-Fixing Organelle.
2024-05-23 | MSV000094846 | MassIVE
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 δ-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.
2015-04-17 | GSE67971 | 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:Diatoms are a major primary producer accounting for 20% of the global primary production. Their massive carbon fixation is driven by the CO2-concentrating mechanisms (CCM), in which CO2 is actively supplied to the Rubisco localized in the pyrenoid, a membrane-less organelle of the plastid. To promote CO2 fixation, CO2 concentration in the pyrenoid matrix is assumed to be elevated while leakage of CO2 is minimized. However, due to the lack of information on the structural basis of diatom pyrenoid, the mechanism allowing efficient CO2 supply in conjunction with pyrenoid structure remains to be elucidated. While isolation of diatom pyrenoid is technically difficult due to structural instability, here we applied in vivo crosslinking using photo amino acids (pAA) which enabled us to obtain Rubisco enriched fractions. Based on LC-MS/MS analysis of the RbcL-enriched fraction, we identified a novel protein that surrounds the pyrenoid like a shell and hence named a Pyshell (Pyrenoid shell). Using genome-edited mutants, Pyshell was demonstrated to be a critical component required for growth under CO2-limiting conditions. The comprehensive analysis and identification of the pyrenoid component gave an important insight into the molecular basis driving the oceanic primary production.
2024-05-04 | PXD041920 | JPOST Repository
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:We have studied the transcriptional, metabolic and photo-physiological responses to light of different spectral quality in the marine diatom Phaeodactylum tricornutum through time-series studies of cultures exposed to equal doses of photosynthetically usable radiation of blue, green and red light. The experiments showed that short-term differences in gene expression and profiles are mainly light quality-dependent. Transcription of photosynthesis-associated nuclear genes was activated mainly through a light quality-independent mechanism likely to rely on chloroplast-to-nucleus signaling. In contrast, genes encoding proteins important for photoprotection and PSII repair were highly dependent on a blue light receptor-mediated signal. Changes in energy transfer efficiency by light-harvesting pigments were spectrally dependent; furthermore, a declining trend in photosynthetic efficiency was observed in red light. The combined results suggest that diatoms possess a light quality-dependent ability to activate photoprotection and efficient repair of photodamaged PSII. In spite of approximately equal numbers of PSII-absorbed quanta in blue, green and red light, the spectral quality of light is important for diatom responses to ambient light conditions.
2014-12-22 | GSE55959 | GEO
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: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