Project description:Analysis of microbial community composition in arctic tundra and boreal forest soils using serial analysis of ribosomal sequence tags (SARST). Keywords: other
Project description:Protein phosphorylation is an important post translational modification that plays a major role in cellular regulatory processes in both eukaryotes and prokaryotes. In recent years, aided by advancements in mass spectrometry techniques, there has been a growing interest in studying protein phosphorylation in prokaryotic model organisms. There are, however, only a limited number of phosphoproteomics reports on non-model organisms. Here, using mass spectrometry, we performed a genome wide investigation of protein phosphorylation in the non-model organism and biofuel producer Zymomonas mobilis under anaerobic, aerobic, and N2-fixing conditions. Our phosphoproteome analysis revealed 125 unique phosphorylated proteins and 172 unique phosphopeptides across these three growth conditions. The phosphoproteins identified belonged to major pathways, including glycolysis, TCA cycle, protein biosynthesis, electron transport, and nitrogen fixation. Quantitative analysis revealed significant and widespread changes in protein phosphorylation across anaerobic, aerobic, and N2-fixing growth conditions. For example, two different serine residues of KDPG aldolase, an Entner-Doudoroff pathway enzyme, were differentially phosphorylated under aerobic and N2-fixing conditions. On the other hand, the final enzyme in the ethanol fermentation pathway, alcohol dehydrogenase, showed phosphorylation on its Ser99 only under N2-fixing condition while its Ser126 was only phosphorylated under anaerobic condition. Moreover, nitrogenases and nitrogen regulatory proteins were differentially phosphorylated at multiple sites under aerobic and N2-fixing conditions. Altogether, this study provides new knowledge regarding potential phosphorylation regulatory sites of specific proteins in pathways relevant to ethanol production and overall physiology and establishes new ground for future engineering of Z. mobilis for advanced biofuel production.
Project description:Regulation of nitrogenase, which converts nitrogen gas (N2) into ammonium (NH4+), typically involves a conserved set of regulatory proteins across diverse N2-fixing (diazotrophic) bacteria. However, the interactions and relative influence of these regulators can vary between species. Thus, one cannot make assumptions about nitrogenase regulation when working with uncharacterized diazotrophs like Vibrio natriegens, a γ-proteobacterium of growing interest for synthetic biology. Here, we characterized the roles of several annotated V. natriegens nitrogenase regulatory proteins in response to NH4+ versus N2. This data set describes the NtrC binding sites in Vibrio natrigens grown with NH4+ versus N2 using chromatin immunopreiciptation combined with combined with massively parallel sequencing (ChIP-seq).
2026-06-01 | GSE333729 | GEO
Project description:Active Methanotrophs in tidal mangrove forest soils.
Project description:For the filamentous cyanobacterium Anabaena variabilis to grow without combined nitrogen, certain cells differentiate into heterocysts that fix N2, while vegetative cells perform photosynthesis. Much remains unknown on how heterocysts differ from vegetative cells in terms of carbon and energy metabolisms. Microarrays were used to investigate gene transcription patterns in vegetative cells, heterocysts, and filaments of N2-fixing phototrophic, mixotrophic, and heterotrophic cultures.
2013-11-01 | GSE46076 | GEO
Project description:Response mechanisms of nitrogen-fixing microorganisms in biochar-amended soils
Project description:We herein conducted high throughput analyses of proteome and protein acetylation in Z. mobilis under N2-fixing conditions, and established its first acetylome.
Project description:Regulation of nitrogenase, which converts nitrogen gas (N2) into ammonium (NH4+), typically involves a conserved set of regulatory proteins across diverse N2-fixing (diazotrophic) bacteria. However, the interactions and relative influence of these regulators can vary between species. Thus, one cannot make assumptions about nitrogenase regulation when working with uncharacterized diazotrophs like Vibrio natriegens, a γ-proteobacterium of growing interest for synthetic biology. Here, we characterized the roles of several annotated V. natriegens nitrogenase regulatory proteins in response to NH4+ versus N2. This data set describes global transcript levels for a parent strain ntrBC and nifA deletion mutants in non-growing cell suspensions where nitrogenase is expressed.
Project description:Model endophyte Azoarcus sp. BH72 is known to contribute fixed nitrogen to its host Kallar grass by nitrogen fixation and also expresses nitrogenase genes endophytically in rice seedlings in gnotobiotic culture. Availability of fixed nitrogen is one of the important signals regulating the transcription of nitrogenase genes and hence nitrogen fixing activity. Therefore, we analysed global transcription in response to differences in the nitrogen source. Transcription profiles of cells grown microaerobically (0.6% oxygen) on minimal medium with nitrogen (N2-fixing) versus ammonium (combined nitrogen) were compared using a genome-wide microarray approach and differences in the gene expression profile were monitored.