Ontology highlight
ABSTRACT:
PROVIDER: PRJEB44682 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
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| ERR5451065.fasta.gz | Fasta.gz | |||
| ERR5451052.fasta.gz | Fasta.gz | |||
| ERR5451066.fasta.gz | Fasta.gz | |||
| ERR5451044.fasta.gz | Fasta.gz | |||
| ERR5451067.fasta.gz | Fasta.gz |
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Similar Datasets
Project description:Nitrogen fixation rates and cyanobacteria cover in a subarctic biological soil crust are enhanced by warming, wetting and light
| PRJEB43502 | ENA
Project description:Biological soil crusts (BSCs) are cyanobacteria-dominated microbial communities that cover extensive portions of the world’s arid and semi-arid deserts. The infrequent periods of hydration are often too short to allow for dormancy strategies based on sporulation; consequently, survival is based on the unique capabilities of vegetative cells to resuscitate from and re-enter a stress resistant dormant state, one of which is migration within the crust layers in response to hydration. In this study, we sought to characterize the events that govern the emergence of the dominant cyanobacterium from dormancy, its subsequent growth, and the events triggered by re-desiccation and a transition back to dormant state. We performed a 48 hour laboratory wetting experiment of a desert BSC and tracked the response of Microcoleus vaginatus using a whole genome transcriptional time-course including night/day periods. This allowed the identification of genes with a diel expression pattern, genes involved uniquely in the signaling after hydration and those that contribute primarily to desiccation preparation.
2012-10-30 | GSE40188 | GEO
Project description:Biological soil crusts (BSCs) are cyanobacteria-dominated microbial communities that cover extensive portions of the world’s arid and semi-arid deserts. The infrequent periods of hydration are often too short to allow for dormancy strategies based on sporulation; consequently, survival is based on the unique capabilities of vegetative cells to resuscitate from and re-enter a stress resistant dormant state, one of which is migration within the crust layers in response to hydration. In this study, we sought to characterize the events that govern the emergence of the dominant cyanobacterium from dormancy, its subsequent growth, and the events triggered by re-desiccation and a transition back to dormant state. We performed a 48 hour laboratory wetting experiment of a desert BSC and tracked the response of Microcoleus vaginatus using a whole genome transcriptional time-course including night/day periods. This allowed the identification of genes with a diel expression pattern, genes involved uniquely in the signaling after hydration and those that contribute primarily to desiccation preparation. Desert BSC samples collected from Moab, UT, were hydrated over a period of 48 hours followed by drying induced by removal of water. At periodic times soil samples were harvested and used for RNA extraction and whole genome expression analysis using an expression array representing genes from two strains of M. vaginatus (PCC 9802 and FGP-2)
2012-10-30 | E-GEOD-40188 | biostudies-arrayexpress
Project description:The daily light-dark cycle is a recurrent and predictable environmental phenomenon to which many organisms, including cyanobacteria, have evolved to adapt. Understanding how cyanobacteria alter their metabolic attributes in response to subjective light or dark growth may provide key features for developing strains with an improved photosynthetic efficiency as well as for applications in enhanced carbon sequestration and renewable energy. Here, we undertook a label free proteomic approach to investigate the effect of extended light (LL) or extended dark (DD) conditions on the unicellular cyanobacterium Crocosphaera subtropica ATCC 51142. We quantified 2287 proteins, of which 603 proteins were significantly different between the two growth conditions. These proteins represent several biological processes, including photosynthetic electron transport, carbon fixation, stress responses, translation, and protein degradation. Results highlight the regulation of proteases including ATP dependent Clp-proteases (endopeptidases) and metalloproteases and may suggest dynamic responses of proteases to extended light or dark exposure to regulate protein turnover or protein quality control mechanisms. The results enhance our understanding of how Crocosphaera subtropica ATCC51142 adjusts its molecular machinery in response to extended light or dark growth conditions.
2024-04-11 | MSV000094518 | MassIVE
Project description:Regulation of CO2 fixation in cyanobacteria is important both for the organism and the global carbon balance. Here we show that phosphoketolase in Synechococcus elongatus PCC7942 (SeXPK) possesses a distinct ATP sensing mechanism, which upon ATP drops, allows SeXPK to divert precursors of the RuBisCO substrate away from the Calvin-Benson-Bassham (CBB) cycle. Deleting the SeXPK gene increased CO2 fixation particularly during light-dark transitions. In high-density cultures, the xpk strain showed a 60% increase in carbon fixation, and unexpectedly resulted in sucrose secretion without any pathway engineering. Using cryo-EM analysis, we discovered that these functions were enabled by a unique allosteric regulatory site involving two subunits jointly binding two ATP, which constantly suppresses the activity of SeXPK until the ATP level drops. This magnesium-independent ATP allosteric site is present in many species across all three domains of life, where it may also play important regulatory functions.
2023-08-08 | GSE227397 | GEO
Project description:Clipping (i.e., harvesting aboveground plant biomass) is common in agriculture and for bioenergy production. However, microbial responses to clipping in the context of climate warming are poorly understood. We investigated the interactive effects of grassland warming and clipping on soil properties, plant and microbial communities, in particular microbial functional genes. Clipping alone did not change the plant biomass production, but warming and clipping combined increased the C4 peak biomass by 47% and belowground net primary production by 110%. Clipping alone and in combination with warming decreased the soil carbon input from litter by 81% and 75%, respectively. With less carbon input, the abundances of genes involved in degrading relatively recalcitrant carbon increased by 38-137% in response to either clipping or the combined treatment, which could weaken the long-term soil carbon stability and trigger a positive feedback to warming. Clipping alone also increased the abundance of genes for nitrogen fixation, mineralization and denitrification by 32-39%. The potentially stimulated nitrogen fixation could help compensate for the 20% decline in soil ammonium caused by clipping alone, and contribute to unchanged plant biomass. Moreover, clipping tended to interact antagonistically with warming, especially on nitrogen cycling genes, demonstrating that single factor studies cannot predict multifactorial changes. These results revealed that clipping alone or in combination with warming altered soil and plant properties, as well as the abundance and structure of soil microbial functional genes. The aboveground biomass removal for biofuel production needs to be re-considered as the long-term soil carbon stability may be weakened.
2016-09-27 | GSE86527 | GEO
Project description:Cyanobacteria fix atmospheric CO2 to biomass and through metabolic engineering can also act as photosynthetic cell factories for sustainable productions of fuels and chemicals. The Calvin cycle is the primary pathway for CO2 fixation in cyanobacteria, algae and C3 plants, and several studies have shown that overexpression of a cyanobacterial Calvin cycle enzyme, bifunctional sedoheptulose-1,7-bisphosphatase/fructose-1,6-bisphosphatase (hereafter BiBPase), enhances CO2 fixation in both plants and algae, although its impact on cyanobacteria has not yet been rigorously studied. Here, we show that overexpression of BiBPase enhanced growth, cell size, and photosynthetic O2 evolution of the cyanobacterium Synechococcus sp. PCC 7002 in an environment with elevated CO2 concentration. Biochemical analysis, immunodetection, and proteomic analysis revealed that overexpression of BiBPase considerably elevated the cellular activities of two rate-limiting enzymes in the Calvin cycle, namely ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) and aldolase, while it repressed several enzymes involved in the respiratory carbon metabolism (e.g. glycolysis and the oxidative pentose phosphate pathway) including glucose-6-phosphate dehydrogenase. Concomitantly, the content of glycogen was significantly reduced while the extracellular carbohydrate content increased. These results indicate that overexpression of BiBPase leads to global reprogramming of carbon metabolism in Synechococcus sp. PCC 7002, promoting photosynthetic carbon fixation and repressing the respiratory carbon catabolism, while altering carbohydrate partitioning.
2019-01-17 | PXD007963 | Pride
Project description:We used RNA sequencing to measure genome-wide gene expression in the cyanobacterium Synechococcus elongatus PCC 7942 grown under dynamic light regimes that mimic the variation in light intensity seen on a Clear Day in nature, or the rapid changes in light intensity that accompany changes in shading We compare these gene expression dynamics to those of a culture grown under a Low Light condition that mimics the standard laboratory conditions used for study of cyanobacteria. Our analysis reveals that naturally relevant light conditions drastically modify gene expression dynamics in cyanobacteria Notably, the expression of circadian clock-controlled genes is responsive to changes in light intensity, showing modulated dynamics that can allow cyanobacteria to adapt their metabolism to changing environmental conditions
2017-12-16 | GSE104203 | GEO
Project description:<p><strong>BACKGROUND:</strong> Converting carbon dioxide (CO2) into value-added chemicals using engineered cyanobacteria is a promising strategy to tackle the global warming and energy shortage issues. However, most cyanobacteria are autotrophic and use CO2 as a sole carbon source, which makes it hard to compete with heterotrophic hosts in either growth or productivity. One strategy to overcome this bottleneck is to introduce sugar utilization pathways to enable photomixotrophic growth with CO2 and sugar (e.g., glucose and xylose). Advances in engineering mixotrophic cyanobacteria have been obtained, while a systematic interrogation of these engineered strains is missing. This work aimed to fill the gap at omics level.</p><p><strong>RESULTS:</strong> We first constructed two engineered <em>Synechococcus elongatus</em> YQ2-gal and YQ3-xyl capable of utilizing glucose and xylose, respectively. To investigate the metabolic mechanism, transcriptomic and metabolomic analysis were then performed in the engineered photomixotrophic strains YQ2-gal and YQ3-xyl. Transcriptome and metabolome of wild-type <em>S. elongatus</em> were set as baselines. Increased abundance of metabolites in glycolysis or pentose phosphate pathway indicated that efficient sugar utilization significantly enhanced carbon flux in <em>S. elongatus</em> as expected. However, carbon flux was redirected in strain YQ2-gal as more flowed into fatty acids biosynthesis but less into amino acids. In strain YQ3-xyl, more carbon flux was directed into synthesis of sucrose, glucosamine and acetaldehyde, while less into fatty acids and amino acids. Moreover, photosynthesis and bicarbonate transport could be affected by upregulated genes, while nitrogen transport and assimilation were regulated by less transcript abundance of related genes in strain YQ3-xyl with utilization of xylose.</p><p><strong>CONCLUSIONS:</strong> Our work identified metabolic mechanism in engineered <em>S. elongatus</em> during photomixotrophic growth, where regulations of fatty acids metabolism, photosynthesis, bicarbonate transport, nitrogen assimilation and transport are dependent on different sugar utilization. Since photomixotrophic cyanobacteria is regarded as a promising cell factory for bioproduction, this comprehensive understanding of metabolic mechanism of engineered <em>S. elongatus</em> during photomixotrophic growth would shed light on the engineering of more efficient and controllable bioproduction systems based on this potential chassis.</p>
2022-03-21 | MTBLS2825 | MetaboLights