Ontology highlight
ABSTRACT:
PROVIDER: PRJNA607234 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR11100095_1.fastq.gz | Fastqsanger.gz | |||
| SRR11100095_2.fastq.gz | Fastqsanger.gz | |||
| SRR11100096_1.fastq.gz | Fastqsanger.gz | |||
| SRR11100096_2.fastq.gz | Fastqsanger.gz |
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Project description:Acetate is a simple carboxylic acid that is synthesized in various microorganisms. Although acetate toxicity and tolerance have been studied in many microorganisms, little is known about the effects of exogenous acetate on the cell growth of acetogenic bacteria. In this study, we report the phenotypic changes that occurred in the acetogenic bacterium Clostridium sp. AWRP as a result of an adaptive laboratory evolution under acetate challenge. When compared with the wild-type strain, the acetate-adapted strain displayed a tolerance to acetate up to 10 g L-1 and higher biomass yields in batch cultures, although the metabolite profiles greatly varied depending on culture conditions. Interestingly, genome sequencing revealed that the adapted strain harbored three point mutations in the genes encoding an electron-bifurcating hydrogenase, which is crucial to its autotrophic growth on CO2 + H2, in addition to one in the dnaK gene. Transcriptome analysis revealed the global change in the gene expression profile of the acetate-adapted strain. Strikingly, most genes involved in CO2-fixing Wood-Ljungdahl pathway and auxiliary pathways for energy conservation (e.g., Rnf complex, Nfn, etc.) were significantly down-regulated. In addition, we observed that a couple of metabolic pathways associated with dissimilation of nucleosides and carbohydrates were significantly up-regulated in the acetate-adapted strain as well as several amino acid biosynthetic pathways, indicating that the strain might increase its fitness by utilizing organic substrates in response to the down-regulation of carbon fixation. Further investigation into the carbon fixation degeneration of the acetate-adapted strain will provide practical implications in CO2 + H2 fermentation using acetogenic bacteria for long-term continuous fermentation. The transcriptome profiles of the wild-type Clostridium sp. AWRP and its acetate-tolerant derivative 46T-a were compared.
2022-06-26 | GSE206757 | GEO
Project description:Elevated atmospheric CO2 can influence the structure and function of rhizosphere microorganisms by altering root growth and the quality and quantity of compounds released into the rhizosphere via root exudation. In these studies we investigated the transcriptional responses of Bradyrhizobium japonicum cells growing in the rhizosphere of soybean plants exposed to elevated atmospheric CO2. The results of microarray analyses indicated that atmospheric elevated CO2 concentration indirectly influences on expression of large number of Bradyrhizobium genes through soybean roots. In addition, genes involved in C1 metabolism, denitrification and FixK2-associated genes, including those involved in nitrogen fixation, microanaerobic respiration, respiratory nitrite reductase, and heme biosynthesis, were significantly up-regulated under conditions of elevated CO2 in the rhizosphere, relative to plants and bacteria grown under ambient CO2 growth conditions. The expression profile of genes involved in lipochitinoligosaccharide Nod factor biosynthesis and negative transcriptional regulators of nodulation genes, nolA and nodD2, were also influenced by plant growth under conditions of elevated CO2. Taken together, results of these studies indicate that growth of soybeans under conditions of elevated atmospheric CO2 influences gene expressions in B. japonicum in the soybean rhizosphere, resulting in changes to carbon/nitrogen metabolism, respiration, and nodulation efficiency.
2010-07-29 | GSE23296 | GEO
Project description:To investigate the effect that biological nitrogen fixation will have on plant responses to nitrogen dose at elevated CO2, alfalfa (Medicago sativa) lines were grown at three nitrogen doses and ambient or elevated CO2. Four lines were used in the study, two lines that can form nodules capable of fixing nitrogen (effective lines) and two lines that can not form nodules capable of nitrogen fixation (ineffective lines). The ineffective lines are the result of a complementary mutation in the same gene.
2024-02-26 | GSE244008 | GEO
Project description:To study mixotrophy, it is desirable to have an organism capable of growth in the presence and absence of both organic and inorganic carbon sources, as well as organic and inorganic energy sources. Metallosphaera sedula is an extremely thermoacidophilic archaeon which has been shown to grow in the presence of inorganic carbon and energy source supplements (autotrophy), organic carbon and energy source supplements (heterotrophy), and in the presence of organic carbon and inorganic energy source supplements. The recent elucidation of M. sedula’s inorganic carbon fixation cycle and its genome sequence further facilitate its use in mixotrophic studies. In this study, we grow M. sedula heterotrophically in the presence of organic carbon and energy sources (0.1% tryptone), autotrophically in the presence of inorganic carbon and energy sources (H2 + CO2), and “mixotrophically” in the presence of both organic and inorganic carbon and energy sources (0.1% tryptone + H2 + CO2 ) to characterize the nature of mixotrophy exhibited.
2009-11-01 | GSE14978 | GEO
Project description:The pyrenoid, a single microcompartment of the chloroplasts of most algae and hornworts, is the major site of CO2 fixation. To compensate the limited availability of CO2 in aquatic environments due to slower CO2 diffusion in water than air, the RubisCO-containing pyrenoid is involved in a carbon concentrating mechanism (CCM) and promotes the carboxylase activity rather than the oxygenase activity of RubisCO, the Calvin-Benson cycle enzyme catalyzing the first step of CO2 fixation. Data in the literature suggest that pyrenoid can have other functions in addition to CO2 fixation. To decipher its functions, the characterization of the pyrenoid proteome in the microalga Chlamydomonas reinhardtii was undertaken. Pyrenoid-enriched fractions from two independent biological cultures (sample1 and sample2) were obtained from cells (WT-cell) or isolated chloroplasts (WT-cp) either from the wild-type (WT) strain or from pyrenoid-deficient Chlamydomonas strains (MX-CW15 and SS-AT) and analyzed by nLC-MS/MS. Substractive proteomic analysis allowed the identification of contaminant proteins and the characterization of the pyrenoid proteome.
2018-02-28 | PXD004509 | 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.
2013-03-05 | GSE39944 | GEO
Project description:Conversion of biomass-derived syngas (gaseous mixture of mainly H2, CO and CO2) to methane might be a sustainable alternative for the biofuel industry. Via the syngas route more methane can be produced from biomass than via conventional anaerobic digestion. Methanogenic archaea are key players in syngas conversion, but only a few are known to utilize CO (or syngas). Methanothermobacter thermoautotrophicus is one of the few hydrogenotrophic methanogens which has been observed to grow on CO. However, carboxydotrophic growth is slow and is reported to be readily inhibited above 50 kPa CO. The aim of this work was to get more insight of the CO metabolism in hydrogenotrophic archaea and to assess the potential toxic effects of CO towards these microorganisms. Archaeal genomic databases were searched for putative homologues of the Methanothermobacter thermoautotrophicus CODH alpha subunit (containing the catalytic site): the highest scores were for the CODH subunits of Methamothermobacter marburgensis (93% identity) and Methanococcus maripaludis (71%). M. thermoautotrophicus and the other two potential carboxydotrophic strains were incubated with CO and CO + H2 as sole substrates. In addition to M. thermoautotrophicus, M. marburgensis was able to grow methanogenically on CO alone and on CO + H2. In contrast to M. thermoautotrophicus, M. marburgensis was not as strongly inhibited when grown in presence of CO alone and was able to adapt its metabolism, shifting its lag phase from ~500 to ~100 hours. It was observed for both strains that presence of hydrogen stimulates the carbon monoxide metabolism. To gain further insight, the proteome of M. marburgensis culture grown on H2 + CO2 and H2 + CO2 + CO were analysed. Cultures grown with H2 + CO showed relative higher abundance of enzymes involved in CODH/ACS associated reactions and reactions involved in redox metabolism. Overall, the data suggests the strong reducing capacity of CO inhibits the hydrogenotrophic methanogen, making growth on CO as a sole substrate difficult for these organisms.
2016-08-03 | PXD003661 | Pride
Project description:To study mixotrophy, it is desirable to have an organism capable of growth in the presence and absence of both organic and inorganic carbon sources, as well as organic and inorganic energy sources. Metallosphaera sedula is an extremely thermoacidophilic archaeon which has been shown to grow in the presence of inorganic carbon and energy source supplements (autotrophy), organic carbon and energy source supplements (heterotrophy), and in the presence of organic carbon and inorganic energy source supplements. The recent elucidation of M. sedulaâ??s inorganic carbon fixation cycle and its genome sequence further facilitate its use in mixotrophic studies. In this study, we grow M. sedula heterotrophically in the presence of organic carbon and energy sources (0.1% tryptone), autotrophically in the presence of inorganic carbon and energy sources (H2 + CO2), and â??mixotrophicallyâ?? in the presence of both organic and inorganic carbon and energy sources (0.1% tryptone + H2 + CO2 ) to characterize the nature of mixotrophy exhibited. Two 3 slide loops joined at equivalent conditions (8 slides total) for Mse cells includes 3 conditions tested in duplicate (biological repeats): heterotrophy (H1 and H2), autotrophy (A1 and A2), and mixotrophy (M1 and M2). 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).
2010-06-20 | E-GEOD-14978 | biostudies-arrayexpress