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PROVIDER: PRJEB22958 | ENA |
REPOSITORIES: ENA
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Project description:Escherichia coli culture was subjected to two different types of nutritional scenarios, abundant carbon/ nitrogen sources and scarce carbon/nitrogen medium. Study revealed that scarce medium adapted culture were more tolerant to hydrogen peroxide than abundant medium.
2013-01-08 | E-MEXP-3799 | biostudies-arrayexpress
Project description:Photosynthetic microbes can produce the clean-burning fuel hydrogen using one of nature’s most plentiful resources, sunlight 1,2. Anoxygenic photosynthetic bacteria generate hydrogen and ammonia during a process known as biological nitrogen fixation. This reaction is catalyzed by the enzyme nitrogenase and consumes nitrogen gas, ATP and electrons 3. One bacterium, Rhodopseudomonas palustris, has a remarkable ability to obtain electrons from green plant-derived material 4,5 and to efficiently absorb both high and low intensity light energy to form ATP 6. Manipulating R. palustris or a similar organism to produce hydrogen commercially will require us to identify all its genes that contribute to hydrogen production and to understand how this process is regulated in cells. Here we describe mutant strains in which metabolism is redirected such that hydrogen production is uncoupled from nitrogen fixation. Our data indicate that three different single amino acid changes in the transcriptional regulator NifA each yielded strains that produced hydrogen even in the presence of the repressing nitrogen source ammonium and in the absence of specific inducing metabolic signals. We used the mutants to show that, in addition to nitrogenase genes, 18 genes outside of the nitrogenase gene cluster may contribute to hydrogen production. Some of these genes are likely involved in efficient ATP acquisition and in channeling electrons to nitrogenase for reduction of protons to molecular hydrogen. Our results demonstrate that photosynthetic bacteria can be genetically manipulated for sustained production of pure hydrogen in a variety of cultivation conditions in the absence of oxygen, nitrogen or other gases as long as light and an electron donor are supplied. Keywords: Comparison of transcriptome profiles
2007-06-29 | GSE5194 | GEO
Project description:Photosynthetic microbes can produce the clean-burning fuel hydrogen using one of natureâ??s most plentiful resources, sunlight 1,2. Anoxygenic photosynthetic bacteria generate hydrogen and ammonia during a process known as biological nitrogen fixation. This reaction is catalyzed by the enzyme nitrogenase and consumes nitrogen gas, ATP and electrons 3. One bacterium, Rhodopseudomonas palustris, has a remarkable ability to obtain electrons from green plant-derived material 4,5 and to efficiently absorb both high and low intensity light energy to form ATP 6. Manipulating R. palustris or a similar organism to produce hydrogen commercially will require us to identify all its genes that contribute to hydrogen production and to understand how this process is regulated in cells. Here we describe mutant strains in which metabolism is redirected such that hydrogen production is uncoupled from nitrogen fixation. Our data indicate that three different single amino acid changes in the transcriptional regulator NifA each yielded strains that produced hydrogen even in the presence of the repressing nitrogen source ammonium and in the absence of specific inducing metabolic signals. We used the mutants to show that, in addition to nitrogenase genes, 18 genes outside of the nitrogenase gene cluster may contribute to hydrogen production. Some of these genes are likely involved in efficient ATP acquisition and in channeling electrons to nitrogenase for reduction of protons to molecular hydrogen. Our results demonstrate that photosynthetic bacteria can be genetically manipulated for sustained production of pure hydrogen in a variety of cultivation conditions in the absence of oxygen, nitrogen or other gases as long as light and an electron donor are supplied. Transcriptome profile of wild type (CGA009) growing photosynthetically in the presence of amonium an acetate was compare with that of 4 different mutants (CGA570, CGA571, CGA572 and CGA574). We did 2 biological replicates per strain.
2010-06-10 | E-GEOD-5194 | biostudies-arrayexpress
Project description:Nitrogen fixation is an important metabolic process carried out by microorganisms, which converts molecular nitrogen into inorganic nitrogenous compounds such as ammonia (NH3). These nitrogenous compounds are crucial for biogeochemical cycles and for the synthesis of essential biomolecules, i.e. nucleic acids, amino acids and proteins. Azotobacter vinelandii is a bacterial non-photosynthetic model organism to study aerobic nitrogen fixation (diazotrophy) and hydrogen production. Moreover, the diazotroph can produce biopolymers like alginate and polyhydroxybutyrate (PHB) that have important industrial applications. However, many metabolic processes such as partitioning of carbon and nitrogen metabolism in A. vinelandii remain unknown to date.
Genome-scale metabolic models (M-models) represent reliable tools to unravel and optimize metabolic functions at genome-scale. M-models are mathematical representations that contain information about genes, reactions, metabolites and their associations. M-models can simulate optimal reaction fluxes under a wide variety of conditions using experimentally determined constraints. Here we report on the development of a M-model of the wild type bacterium A. vinelandii DJ (iDT1278) which consists of 2,003 metabolites, 2,469 reactions, and 1,278 genes. We validated the model using high-throughput phenotypic and physiological data, testing 180 carbon sources and 95 nitrogen sources. iDT1278 was able to achieve an accuracy of 89% and 91% for growth with carbon sources and nitrogen source, respectively. This comprehensive M-model will help to comprehend metabolic processes associated with nitrogen fixation, ammonium assimilation, and production of organic nitrogen in an environmentally important microorganism.
2023-03-10 | MODEL2204190001 | BioModels
Project description:Comparative proteomic study of the chemolithoautotroph Ghiorsea bivora strain TAG-1. This strain was grown under two different conditions: hydrogen-oxidizing (H2 as electron donor) and iron-oxidizing (ferrous iron as electron donor). TAG-1 was grown in microaerobic conditions.
2020-05-27 | MSV000085471 | MassIVE
Project description:hydrogen-oxidizing bacteria enrichment for microbial protein production
| PRJNA580512 | ENA
Project description:Aerobic methanotrophic bacteria can use methane as their sole energy source. The discovery of ‘Ca. Methylacidiphilum fumariolicum’ strain SolV and other verrucomicrobial methanotrophs has revealed that the ability of bacteria to oxidize CH4 is much more diverse than has previously been assumed in terms of ecology, phylogeny and physiology. A remarkable characteristic of the methane-oxidizing Verrucomicrobia is their extremely acidophilic phenotype, growing even below pH 1. In this study we used RNA-Seq to analyze the metabolic regulation of ‘Ca. M. fumariolicum’ SolV cells growing at μmax in batch culture or under nitrogen fixing or oxygen limited conditions in chemostats, all at pH 2. The analysis showed that two of the three pmoCAB operons each encoding particulate methane monoxygenases were differentially expressed, probably regulated by the available oxygen. The hydrogen produced during N2 fixation is apparently recycled as demonstrated by the upregulation of the genes encoding a Ni/Fe-dependent hydrogenase. These hydrogenase genes were also upregulated under low oxygen conditions. Handling of nitrosative stress was shown by the expression of the nitric oxide reductase encoding genes norB and norC under all conditions tested, the upregulation of nitrite reductase nirK under oxygen limitation and of hydroxylamine oxidoreductase hao in the presence of ammonium. Unraveling the gene regulation of carbon and nitrogen metabolism helps to understand the underlying physiological adaptations of strain SolV in view of the harsh conditions of its natural ecosystem. Cells grown under 3 different conditions were harvested by centrifugation and 3.1 mg dry weight cells were used for isolation of mRNA, and subsequent synthesis of cDNA (328 ng). The cDNA was used for Illumina sequencing on a Illumina Genome.Analyser II
2012-09-01 | E-GEOD-40528 | biostudies-arrayexpress
Project description:Assimilation of nitrogen is an essential process in bacteria. The nitrogen regulation stress response is an adaptive mechanism used by nitrogen-starved Escherichia coli to scavenge for alternative nitrogen sources and requires the global transcriptional regulator NtrC.
2014-06-17 | E-MTAB-2612 | biostudies-arrayexpress
Project description:Aerobic, glucose-limited chemostat cultures of Saccharomyces cerevisiae grown with six different nitrogen sources were subjected to transcriptome analysis. The use of chemostats enabled an analysis of nitrogen-source-dependent transcriptional regulation at a fixed specific growth rate. A selection of preferred (ammonium and asparagine) and non-preferred (leucine, phenylalanine, methionine and proline) nitrogen sources was investigated. For each nitrogen source, distinct sets of genes were induced or repressed relative to the other five nitrogen sources. A total number of 131 of such ‘signature transcripts’ were identified in this study. In addition to signature transcripts, genes were identified that showed a transcriptional co-response to two or more of the six nitrogen sources. For example, 33 genes were transcriptionally up-regulated in leucine-, phenylalanine- and methionine-grown cultures, which was partly attributed to the involvement of common enzymes in the dissimilation of these amino acids. In addition to specific transcriptional responses elicited by individual nitrogen sources, their impact on global regulatory mechanisms such as nitrogen catabolite repression (NCR) could be monitored. NCR-sensitive gene expression in the chemostat cultures showed that, ammonia and asparagine were ‘rich’ nitrogen sources. By this criterion, leucine, proline and methionine were ‘poor’ nitrogen sources and phenylalanine showed an ‘intermediate’ NCR response. Keywords: Response to growth on various nitrogen source transcriptome
2007-02-28 | GSE6405 | GEO
Project description:Here we have compared adult wildtype (N2) C. elegans gene expression when grown on different bacterial environments/fod sources in an effort to model naturally occuring nematode-bacteria interactions at the Konza Prairie. We hypothesize that human-induced changes to natural environments, such as the addition of nitrogen fertalizer, have effects on the bacterial community in soils and this drives downstream changes in the structure on soil bacterial-feeding nematode community structure. Here we have used transcriptional profiling to identify candidate genes involved in the interaction of nematodes and bacteria in nature.
2009-05-02 | GSE15923 | GEO