Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1229585 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR32543244_1.fastq.gz | Fastqsanger.gz | |||
| SRR32543244_2.fastq.gz | Fastqsanger.gz |
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Project description:Seven carbon autotrophic fixation pathways were described so far. However, it is not common to find the co-existence of more than one cycle in a single cell. Here, we describe a thermophilic bacterium Carbonactinospora thermoautotrophica StC with a unique and versatile carbon metabolism. StC was isolated from a consortium found in a burning organic pile that exhibits an optimal growth temperature between 55° and 65° C. The genome analyses suggested that the strain StC potentially performs two-carbon fixation pathways, Calvin-Benson-Bassham (CBB) cycle and the Reductive citrate cycle (rTCA) and preserve a microcompartment related with CO2 concentration. To better understand the carbon fixation in StC strain, the expression of the genes of bacterial cells grown autotrophically and heterotrophically were analyzed. For our surprise the data showed the co-existing of the both carbon fixation pathways - CBB and rTCA cycles - in a cultivable thermophilic chemoautotrophic bacterium Carbonactinospora thermoautotrophica strain StC, based on integrated omics of genomics, transcriptomics, and proteomics. These two cycles working together may help microorganisms to improve the CO2 fixation. The knowledge about the co-occurrence of carbon cycle in a single cell leads open a question ‘why microorganisms use multiple pathways to fix carbon and what the advantage for this strategy?’. Advancing on this is a key to better understand the biological carbon fixation mechanism in thermophiles and prospecting the repurposing of enzymes in synthetic biology for biotechnological applications.
2024-04-09 | GSE263135 | GEO
Project description:Marine microalgae (phytoplankton) mediate almost half of the worldwide photosynthetic carbon dioxide fixation and therefore play a pivotal role in global carbon cycling, most prominently during massive phytoplankton blooms. Phytoplankton biomass consists of considerable proportions of polysaccharides, substantial parts of which are rapidly remineralized by heterotrophic bacteria. We analyzed the diversity, activity and functional potential of such polysaccharide-degrading bacteria in different size fractions during a diverse spring phytoplankton bloom at Helgoland Roads (southern North Sea) at high temporal resolution using microscopic, physicochemical, biodiversity, metagenome and metaproteome analyses.
2024-01-15 | PXD046705 | Pride
Project description:Metallosphaera sedula is an extremely thermoacidophilic archaeon that grows heterotrophically on peptides, and chemolithoautotrophically on hydrogen, sulfur, or reduced metals as energy sources. During autotrophic growth, carbon dioxide is incorporated into cellular carbon via the 3-hydroxypropionate /4-hydroxybutyrate cycle (3HP/4HB). To date, all of the steps in the pathway have been connected to enzymes encoded in specific ORFs, except for the one responsible for ligation of coenzyme A (CoA) to 4-hydroxybutyrate (4HB). While several candidates for this step have been identified through bioinformatic analysis of the M. sedula genome, none have been shown to catalyze this biotransformation. Transcriptomic analysis of cells grown under strict H2-CO2 autotrophy was used elucidate additional candidate genes involved in carbon fixation and identify the genes which encode for 4HB-CoA synthetase. Three slide loop for Mse cells includes 3 conditions tested in duplicate (biological repeats from tandem fermentors): autotrophic carbon limited (ACL), autotrophic carbon rich (ACR), and heterotrophic (HTR). Half of an RNA sample for one condition was labeled with Cy3 while the other half was labeled with Cy5. The two differently labeled samples were run on different slides. Each probe is spotted on each slide 5 times (5 replicates; spot intensities for all replicates on slide provided in associated raw data file).
2013-03-05 | E-GEOD-39944 | biostudies-arrayexpress
Project description:The unicellular microalga Dunaliella salina is one of the halotolerant and cell wall-less green microalgae in Dunaliella genus. The ability of halotolerance in Dunaliella is attributed to the accumulation of glycerol. Both sugar made by photosynthesis and starch serve as carbon sources for glycerol biosynthesis. Quantitative PCR-based analyses concluded no apparent transcriptional regulation of glycerol, carbon fixation, and starch metabolisms upon salinity stresses. To examine whether or not transcriptional regulation is involved at the transcriptomic level, we assembled a de novo deep sequencing transcriptome. By using a pathway-based approach, we show that low- and high-salt (i.e., 0.5M versus 2M NaCl) adapted cells share a common transcriptomic profile and that subsets of ESTs associated with energy metabolisms are less affected upon salinity stress. We find that enzymes involved in glycerol, carbon fixation, and starch metabolisms are encoded by multiple EST isoforms. We show that EST isoforms encoding dihydroacetone reductase in glycerol metabolism, phosphoglycerate kinase in carbon fixation, and beta-amylase and fructobiphosphate aldolase in starch metabolism display a correlated transcriptional level change to the alteration of glycerol and starch contents upon salinity stresses. Taken together, our results demonstrate that some enzymes involved in glycerol, carbon fixation, and starch metabolisms are regulated at the transcriptional level upon salinity stresses. Furthermore, our analyses indicate that energy metabolisms are not drastically affected upon salinity stresses, consistent with its ability to adapt to a wide range of salinities.
2017-02-22 | GSE74466 | GEO
Project description:Metallosphaera sedula is an extremely thermoacidophilic archaeon that grows heterotrophically on peptides, and chemolithoautotrophically on hydrogen, sulfur, or reduced metals as energy sources. During autotrophic growth, carbon dioxide is incorporated into cellular carbon via the 3-hydroxypropionate /4-hydroxybutyrate cycle (3HP/4HB). To date, all of the steps in the pathway have been connected to enzymes encoded in specific ORFs, except for the one responsible for ligation of coenzyme A (CoA) to 4-hydroxybutyrate (4HB). While several candidates for this step have been identified through bioinformatic analysis of the M. sedula genome, none have been shown to catalyze this biotransformation. Transcriptomic analysis of cells grown under strict H2-CO2 autotrophy was used elucidate additional candidate genes involved in carbon fixation and identify the genes which encode for 4HB-CoA synthetase.
2013-03-05 | GSE39944 | GEO
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: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