Ontology highlight
ABSTRACT:
PROVIDER: PRJNA560244 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR9967750_1.fastq.gz | Fastqsanger.gz | |||
| SRR9967750_2.fastq.gz | Fastqsanger.gz | |||
| SRR9968290_1.fastq.gz | Fastqsanger.gz | |||
| SRR9968290_2.fastq.gz | Fastqsanger.gz | |||
| SRR9967751_1.fastq.gz | Fastqsanger.gz |
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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.
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Project description:We designed a new specific mRNA microarray targeting a subset of genes (956) of the diazotrophs Richelia intracellularis and Calothrix rhizosoleniae (genomes RintRC01, RintHH01, RintHM01 and CalSC01) which associate with diatom hosts. The aim was to be able to describe the gene expressions of genes related to several metabolic pathways, specifically nitrogen fixation and how they possibly differed between the closely related strains based on environment and host association. In this study we focused on the RintRC01 and RintHH01. To better understand how the gene expression of nitrogen fixation genes relates to nitrogen fixation rates both gene expression and rate measurements were done in parallell.
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Project description:Sustainable production of switchgrass (Panicum virgatum) as a bioenergy crop hinges in part on efficient use of soil macronutrients, especially nitrogen (N). This study investigated the physiological, metabolic and transcriptomic responses of switchgrass to N limitation. Moderate N limitation marked a tipping point for large changes in plant growth, root-to-shoot ratio, root system architecture and total nitrogen content. Integration of transcriptomic and metabolic data revealed that N limitation reduced switchgrass photosynthetic capacity and carbon(C)-fixation activities. Switchgrass balanced C-fixation with N-assimilation, transport and recycling of N compounds by rerouting C-flux from glycolysis, the oxidative branch of the pentose phosphate pathway (OPPP) and from the tricarboxylic acid (TCA) cycle in an organ specific manner. The energy and reduction power so generated, and C-skeletons appear to be directed towards N uptake, biosynthesis of energy storage compounds with high C/N ratio such as sucrose, non-N-containing lipids, and various branches of secondary metabolism.
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Project description:Nitrogen fixation is a highly energy-demanding process and highly regulated at multiple levels. The two major signals that regulate nitrogen fixation in most diazotrophs are oxygen and ammonia. In order to study the complex regulated mechanism and to highlight the complete nitrogen fixing system in genome level, here we present the transcriptional profiles of the nitrogen fixation genes of P.stutzeri A1501 in different growth conditions with a genome-wide DNA microarray. In this study, the three samples of "P.stutzeri A1501 treated with 0.1mM ammonia and 0.5% Oxygen tension","P.stutzeri A1501 treated with 0.1mM ammonia and 0.5% Oxygen tension-2" and "P.stutzeri A1501 treated with 0.1mM ammonia and 0.5% Oxygen tension-3" were three repeat experiments, while, the other three samples of "P.stutzeri A1501 treated with 20mM ammonia and 0.5% Oxygen tension-1", "P.stutzeri A1501 treated with 20mM ammonia and 0.5% Oxygen tension-2" and "P.stutzeri A1501 treated with 20mM ammonia and 0.5% Oxygen tension-3" were three repeat experiments. The gene expressions under these two growth phases were compared to investigate which genes' expression were effected by different ammonia concentrations. Keywords: nitrogen fixation, nitrogen repression
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Project description:The global significance of marine non-cyanobacterial diazotrophs, notably heterotrophic bacterial diazotrophs (HBDs), has become increasingly clear. Understanding N2 fixation rates for these largely uncultured organisms poses a challenge due to uncertain growth requirements and complex nitrogenase regulation. We identified Candidatus Thalassolituus haligoni as an Oceanospirillales member, closely related to other significant γ-proteobacterial HBDs. Pangenome analysis reinforces this classification, indicating the isolate belongs to the same species as the uncultured metagenome-assembled genome Arc-Gamma-03. Analysis of the nifH gene in amplicon sequencing libraries reveals the extensive distribution of Cand. T. haligoni across the Pacific, Atlantic and Arctic Oceans. Through combined proteomic analysis and N2 fixation rate measurements, we confirmed the isolate’s capacity for nitrate independent N2 fixation, although a clear understanding of nitrogenase regulation remains unclear. Overall, our study highlights the significance of Cand. T. haligoni as the first globally distributed, cultured model species within the understudied group of Oceanospirillales, and γ-HBDs in general.
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Project description:Our study revealed a synergistic effect between biological nitrogen fixation and current generation by G. sulfurreducens, providing a green nitrogen fixation alternative through shifting the nitrogen fixation field from energy consumption to energy production and having implications for N-deficient wastewater treatment.
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Project description:Several studies have shown that plant hormones play key roles during legume-rhizobia symbiosis. For instance, auxins can induce formation of nodule-like structures (NLS) on legume roots in the absence of rhizobia. Furthermore, these NLS can be colonized by nitrogen-fixing bacteria, which favor nitrogen fixation compared to regular roots and subsequently increase plant yield. Interestingly, auxin also induces similar NLS in cereal roots. While several genetic studies have identified plant genes controlling NLS formation in legumes, no studies have investigated the genes involved in NLS formation in cereals. In this study, we performed a comprehensive RNA sequencing experiment to identify genes differentially expressed during NLS formation in rice at different stages and identified several promising genes for control of NLS based on their biological and molecular functions.
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