Rhodophyta, marine red-algae
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PROVIDER: PRJNA742114 | ENA |
REPOSITORIES: ENA
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Project description:The study of macroalgae capacity to acclimate and recover in environments contaminated with Cu and Cd could prove a promising way to understand the tolerance mechanisms of these seaweeds against different pollutants. This study used as a model organism Gracilaria tenuistipitata (Rhodophyta), a macroalga with economic and ecological importance. The partial transcriptome of G. tenuistipitata was profiled using cDNA microarrays in the sixth day of exposition to EC50 metals. Genes involved in Cu and Cd chronic stress belonging to various functional categories suffered shallow modifications. This possibly indicates that G. tenuistipitata would be in the acclimatization process. In addition, the expression of nine stress genes accompanied by analysis of the photosynthetic rate of seaweed to both metals in three different time frames was analyzed. Genetic variation linked to the mechanism of resistance of the algae, determined from EC50 culture conditions established for two metals, occurred in the early hours of treatment. It was found that G. tenuistipitata was able to accumulate these two metals and to resist and acclimate to the negative effects produced by these elements. The temporal analysis from the nine specific genes showed some specific transcriptional responses of the G. tenuistipitata, exposed to Cu and Cd. Three-condition experiment, control cells cultivated in seawater enriched with von Stosch solution vs. copper and cadmium (indepedent) treated cells. Biological replicates: 4 control, 2 copper treated, 2 cadmium treated. All independently grown and harvested. Four replicates per array.
2013-06-01 | E-GEOD-42988 | biostudies-arrayexpress
Project description:The study of macroalgae capacity to acclimate and recover in environments contaminated with Cu and Cd could prove a promising way to understand the tolerance mechanisms of these seaweeds against different pollutants. This study used as a model organism Gracilaria tenuistipitata (Rhodophyta), a macroalga with economic and ecological importance. The partial transcriptome of G. tenuistipitata was profiled using cDNA microarrays in the sixth day of exposition to EC50 metals. Genes involved in Cu and Cd chronic stress belonging to various functional categories suffered shallow modifications. This possibly indicates that G. tenuistipitata would be in the acclimatization process. In addition, the expression of nine stress genes accompanied by analysis of the photosynthetic rate of seaweed to both metals in three different time frames was analyzed. Genetic variation linked to the mechanism of resistance of the algae, determined from EC50 culture conditions established for two metals, occurred in the early hours of treatment. It was found that G. tenuistipitata was able to accumulate these two metals and to resist and acclimate to the negative effects produced by these elements. The temporal analysis from the nine specific genes showed some specific transcriptional responses of the G. tenuistipitata, exposed to Cu and Cd.
2013-06-01 | GSE42988 | GEO
Project description:The study of macroalgae capacity to acclimate and recover in environments contaminated with Cu and Cd could prove a promising way to understand the tolerance mechanisms of these seaweeds against different pollutants. This study used as a model organism Gracilaria tenuistipitata (Rhodophyta), a macroalga with economic and ecological importance. The partial transcriptome of G. tenuistipitata was profiled using cDNA microarrays in the sixth day of exposition to EC50 metals. Genes involved in Cu and Cd chronic stress belonging to various functional categories suffered shallow modifications. This possibly indicates that G. tenuistipitata would be in the acclimatization process. In addition, the expression of nine stress genes accompanied by analysis of the photosynthetic rate of seaweed to both metals in three different time frames was analyzed. Genetic variation linked to the mechanism of resistance of the algae, determined from EC50 culture conditions established for two metals, occurred in the early hours of treatment. It was found that G. tenuistipitata was able to accumulate these two metals and to resist and acclimate to the negative effects produced by these elements. The temporal analysis from the nine specific genes showed some specific transcriptional responses of the G. tenuistipitata, exposed to Cu and Cd.
2013-06-01 | GSE42988 | GEO
Project description:Colonization of land from marine environments was a major transition for biological life on Earth, and intertidal adaptation was a key evolutionary event in the transition from marine- to land-based lifestyles. Multicellular intertidal red algae exhibit the earliest, systematic, and successful adaptation to intertidal environments, with Porphyra sensu lato (Bangiales, Rhodophyta) being a typical example. We used proteomic analyse to reveal the complex regulation of rapid responses to intertidal dehydration/rehydration cycling within Neoporphyra haitanensis. These adaptations include rapid regulation of its photosynthetic system, a readily available capacity to utilize ribosomal stores, an excess of methylation supply to rapidly synthesize proteins, and a strong anti-oxidation system to dissipate excess redox energy upon exposure to air. These novel insights into the unique adaptations of red algae to intertidal lifestyles inform our understanding of adaptations to intertidal ecosystems and the unique evolutionary steps required for intertidal colonization by biological life.
2022-02-16 | PXD028649 | Pride
Project description:We investigated light dependent gene expression changes in the marine ochrophyte Nannochloropsis oceanica CCMP1779. These algae have several putative blue light photoreceptors but appear to lack red light photoreceptors. To study early light signaling in N. oceanica and avoid as much as possible secondary downstream events, we quantified gene expression changes in dark-adapted cells after a short blue or red light pulse. More genes were differentially expressed under blue than under red light. In addition, fold change in expression was smaller for the red light-treated samples. For example, the median fold change of induced genes was 3 for blue light and 2.5 for red light. Moreover, hierarchical cluster analysis showed that gene expression after red light treatment was more similar to the dark control than after blue light treatment.
2022-01-05 | GSE164714 | GEO
Project description:Plastid genome sequencing of 'basal' mesophilic non-seaweed red algae
| PRJNA376227 | ENA
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. Continuous, axenic culturing of P. tricornutum was done as described in Nymark et al. (2009). The cultures were incubated at 15M-BM-0C under cool white fluorescent light (Philips TLD 36W/96) providing a scalar irradiance (EPAR) of 100 M-NM-<mol m-2 s-1 under continuous white light (CWL) conditions. Upon the onset of the experiment the cultures were synchronized by 48 h dark-treatment (D48). Thereafter the algae were exposed to blue light (BL), green light (GL) or red light (RL) provided by a waveband specific LED panel (SL3500, Photon Systems Instruments). The algae were exposed to 0.5 h, 6 h or 24 h of: 1) 230 M-NM-<mol m-2 s-1 of RL, 2) 100 M-NM-<mol m-2 s-1 of GL, 3) 50 M-NM-<mol m-2 s-1 of BL or 4) 100 M-NM-<mol m-2 s-1 of WL respectively. Three biological replicas for each of the treatments were harvested. Data for the white light exposure and 48h dark treatment is described in GSE42039, PMID: 23520530.
2014-12-22 | E-GEOD-55959 | biostudies-arrayexpress
Project description:About one half of the global, biogenic carbon dioxide fixation into organic matter is driven by microscopic algae in the surface oceans. These microalgal activities generate, among other molecules, polysaccharides that are food for and recycled by bacteria with polysaccharide utilization loci (PULs). These genetic clusters of co-evolved genes, which work together in recognition, depolymerizing and uptake of one type of polysaccharide. However, we rarely know the substrates of PULs present in marine bacteria. Here we investigated the proteomic and physiological response of mannan PULs from marine Flavobacteriia isolated in the North Sea. The genomic clusters of these marine Bacteroidetes are related to PULs of human gut Bacteroides strains, which are known to digest α- and β-mannans from yeasts and plants respectively. Proteomics and defined growth experiments with these types of mannans as sole carbon source confirmed the functional prediction. Our data suggest that biochemical principles established for gut or terrestrial microbes apply to marine bacteria even though the PULs are evolutionary distant. Moreover, our data support discoveries from the 60th reporting mannans in microalgae suggesting that these polysaccharides play an important role in the marine carbon cycle.
2018-10-17 | PXD009080 | Pride
Project description:About one half of the global, biogenic carbon dioxide fixation into organic matter is driven by microscopic algae in the surface oceans. These microalgal activities generate, among other molecules, polysaccharides that are food for and recycled by bacteria with polysaccharide utilization loci (PULs). These genetic clusters of co-evolved genes, which work together in recognition, depolymerizing and uptake of one type of polysaccharide. However, we rarely know the substrates of PULs present in marine bacteria. Here we investigated the proteomic and physiological response of mannan PULs from marine Flavobacteriia isolated in the North Sea. The genomic clusters of these marine Bacteroidetes are related to PULs of human gut Bacteroides strains, which are known to digest α- and β-mannans from yeasts and plants respectively. Proteomics and defined growth experiments with these types of mannans as sole carbon source confirmed the functional prediction. Our data suggest that biochemical principles established for gut or terrestrial microbes apply to marine bacteria even though the PULs are evolutionary distant. Moreover, our data support discoveries from the 60th reporting mannans in microalgae suggesting that these polysaccharides play an important role in the marine carbon cycle.
2018-10-17 | PXD009066 | Pride
Project description:Light is one of the main environmental cues that affects the physiology and behavior of many organisms. The effect of light on genome-wide transcriptional regulation has been well-studied in green algae and plants, but not in red algae. Cyanidioschyzon merolae is used as a model red algae, and is suitable for studies on transcriptomics because of its compact genome with a relatively small number of genes. In addition, complete genome sequences of the nucleus, mitochondrion, and chloroplast of this organism have been determined. Together, these attributes make C. merolae an ideal model organism to study the response to light stimuli at the transcriptional and the systems biology levels. Previous studies have shown that light significantly affects cell signaling in this organism, but there are no reports on its blue light- and red light-mediated transcriptional responses. We investigated the direct effects of blue and red light at the transcriptional level using RNA-seq. Blue and red light were found to regulate 35% of the total genes in C. merolae. Blue light affected the transcription of genes involved protein synthesis while red light specifically regulated the transcription of genes involved in photosynthesis and DNA repair. Blue or red light regulated genes involved in carbon metabolism and pigment biosynthesis. Overall, our data showed that red and blue light regulate the majority of the cellular, cell division, and repair processes in C. merolae.
2016-09-10 | GSE83828 | GEO