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PROVIDER: PRJDB20123 | ENA |
REPOSITORIES: ENA
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Project description:Comparison of Azotobacter vinelandii str. DJ transcriptomes using either ammonium or dinitrogen as sole nitrogen source. Transcriptomes from cells in early stages of nitrogenase derepression (10 min and 30 min) and at the peak of nitrogenase derepression (4 hours) were compared against the corresponding controls from cells using ammonium as nitrogen source. Kinetics of the nitrogen fixation (nif) genes expression profiles resemble those previously published (Poza-Carrion, 2013; doi: 10.1128/jb.00942-13).
2023-10-10 | GSE244772 | GEO
Project description:The enhancer binding protein VnfA1 of Azotobacter vinelandii has two paralogs as well VnfA2 and VnfA3. This experiment was carried out to compare the binding sites of VnfA1 and VnfA3 under conditions of vanadium availability and its absence. This is important for the regulation of expression of alternative nitrogenase isoenzymes in response to metal availability.
2022-06-23 | E-MTAB-11716 | biostudies-arrayexpress
Project description:Biological nitrogen fixation, the microbial reduction of atmospheric nitrogen to bioavailable ammonia, represents both a major limitation on biological productivity and a highly desirable engineering target for synthetic biology. However, the engineering of nitrogen fixation requires an integrated understanding of how the gene regulatory dynamics of host diazotrophs respond across sequence-function space of its central catalytic metalloenzyme, nitrogenase. Here, we interrogate this relationship by analyzing the transcriptome of Azotobacter vinelandii engineered with a phylogenetically inferred ancestral nitrogenase protein variant. The engineered strain exhibits reduced cellular nitrogenase activity but recovers wild-type growth rates following an extended lag period. We find that expression of genes within the immediate nitrogen fixation network is resilient to the introduced nitrogenase sequence-level perturbations. Rather the sustained physiological compatibility with the ancestral nitrogenase variant is accompanied by reduced expression of genes that support trace metal and electron resource allocation to nitrogenase. Our results spotlight gene expression changes in cellular processes adjacent to nitrogen fixation as productive engineering considerations to improve compatibility between remodeled nitrogenase proteins and engineered host diazotrophs. IMPORTANCE Azotobacter vinelandii is a key model bacterium for the study of biological nitrogen fixation, an important metabolic process catalyzed by nitrogenase enzymes. Here, we demonstrate that compatibilities between engineered A. vinelandii strains and nitrogenase variants can be modulated at the regulatory level. The engineered strain studied here responds by adjusting the expression of proteins involved in cellular processes adjacent to nitrogen fixation, rather than that of nitrogenase proteins themselves. These insights can inform future strategies to transfer nitrogenase variants to non-native hosts.
2023-06-07 | GSE234075 | GEO
Project description:Biological nitrogen fixation (BNF) is an essential source of new nitrogen for terrestrial ecosystems. The abiotic factors regulating BNF have been extensively studied in various ecosystems and laboratory settings. Despite this, our understanding of the impact of neighbouring bacteria on N2 fixer activity remains limited. Here, we explored this question using a coculture of the free-living diazotroph Azotobacter vinelandii and the non-fixing plant growth-promoting rhizobacteria Bacillus subtilis. We assessed the interaction between the two bacteria under low N availability.
2024-10-15 | PXD056293 | Pride
Project description:All diazotrophic bacteria and archaea isolated so far utilise a nitrogenase enzyme containing molybdenum in the active site co-factor to fix atmospheric dinitrogen to ammonia. However, in addition to the Mo-dependent nitrogenase, some nitrogen-fixing prokaryotes also express genetically distinct alternative nitrogenase isoenzymes, namely the V-dependent and Fe-only nitrogenases respectively. Nitrogenase isoenzymes are expressed hierarchically according to metal availability and catalytic efficiency. In proteobacteria, this hierarchy is maintained via stringent transcriptional regulation of gene clusters by dedicated bacterial enhancer binding proteins (bEBPs). The model diazotroph Azotobacter vinelandii contains two paralogs of the vanadium nitrogenase activator VnfA (henceforth, VnfA1), designated VnfA2 and VnfA3, with unknown functions. Here we demonstrate that the VnfA1 and VnfA3 bEBPs bind to the same target promoters in the Azotobacter vinelandii genome and co-activate a subset of genes in the absence of V, including the structural genes for the Fe only nitrogenase. Co-activation is inhibited by the presence of V and is dependent on an accessory protein VnfZ that is co-expressed with VnfA3. Our studies uncover a plethora of interactions between bEBPs required for nitrogen fixation, revealing unprecedented potential for fine tuning expression of alternative nitrogenases in response to metal availability.
2022-06-23 | PXD033387 | Pride
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:Azotobacter vinelandii CA6 Genome sequencing
| PRJNA186699 | ENA
Project description:Azotobacter vinelandii strain:AEIV Genome sequencing
| PRJNA809843 | ENA
Project description:Azotobacter vinelandii DSM 279 Genome sequencing
| PRJNA296715 | ENA