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PROVIDER: PRJNA524633 | ENA |
REPOSITORIES: ENA
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Project description:Uranium reducing microbial consortia, under alkaline conditions relevent to geological disposal
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Project description:Mature Fine Tailings under sulfate-reducing and methanogenic conditions Targeted Locus (Loci)
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Project description:In the methanogenic pathway from CO2 and H2, low potential electrons for CO2 reduction are generated by a flavin-based electron branching reaction catalysed by heterodisulphide reductase (Hdr) in complex with [NiFe]-hydrogenase (Mvh). The F420-reducing [NiFe]-hydrogenase (Frh) provides electrons for the methane formation pathway via the electron carrier F420. The production of both [NiFe]-hydrogenases in Methanothermobacter marburgensis is strongly down-regulated under strictly nickel-limited conditions. The Frh reaction is replaced by a coupled reaction with [Fe]-hydrogenase (Hmd), and the role of Mvh is taken over by F420-dependent electron donating proteins (Elp). Thus, Hmd provides all electrons for the reducing metabolism under these nickel-limited conditions.
2025-08-18 | PXD063936 | Pride
Project description:In the methanogenic pathway from CO2 and H2, low potential electrons for CO2 reduction are generated by a flavin-based electron branching reaction catalysed by heterodisulphide reductase (Hdr) in complex with [NiFe]-hydrogenase (Mvh). The F420-reducing [NiFe]-hydrogenase (Frh) provides electrons for the methane formation pathway via the electron carrier F420. The production of both [NiFe]-hydrogenases in Methanothermobacter marburgensis is strongly down-regulated under strictly nickel-limited conditions. The Frh reaction is replaced by a coupled reaction with [Fe]-hydrogenase (Hmd), and the role of Mvh is taken over by F420-dependent electron donating proteins (Elp). Thus, Hmd provides all electrons for the reducing metabolism under these nickel-limited conditions.
2025-08-18 | PXD063927 | Pride
Project description:Microbial degradation of coumarin under methanogenic conditions
| PRJEB41563 | ENA
Project description:Bacillus subtilis adapts to fluctuating environmental stress, such as membrane perturbation or alkaline conditions, using membrane-associated regulatory complexes. Here, we rename the previously termed pspA-ydjGHI operon to pspA-samGHI (for starvation and motility) to reflect its functional roles in membrane envelope stress signalling. The SamG–SamH membrane proteins recruit SamI, a cytosolic SPFH protein, which stabilizes focal membrane localization and recruitment of PspA, an ESCRT-III homolog. Under normal conditions, this system transiently assembles at the membrane, stabilizing it and allowing proper motility, secretion, and biofilm formation. Loss of SamI (ΔsamI/ΔydjI) leads to unbalanced SamG–SamH activity leading to a constitutive stress signalling, and global transcriptional changes reminiscent of starvation situations. This, in turn, blocks secretion of the matrix protein BslA, preventing biofilm formation, and reducing motility. Deletion of samH in combination with ΔsamI restores biofilm formation, while ΔpspA mutants form biofilms normally, indicating that PspA is dispensable for the developmental phenotype. Our findings reveal that beside membrane integrity SamGHI coordinates transcriptional homeostasis and multicellular development through formation of a membrane integral stress sensor complex.
2026-04-20 | GSE327651 | GEO
Project description:To investigate how Methanothermobacter marburgensis adapts to nickel limitation, we performed transcriptomic profiling under 50 nM and 5000 nM nickel conditions. RNA-seq revealed differential expression of hydrogenase-related genes, suggesting a shift in methanogenic electron flow under nickel limitation, with increased reliance on [Fe]-hydrogenase and associated pathways.
2026-01-06 | GSE311913 | GEO
Project description:【Objective】 The objective of this study is to study the transcriptome regulation mechanism of F. graminearum under different pH stress conditions, analyze the gene expression level and its differences, and explore the metabolic pathways related to the anti-stress response of F. graminearum cells under acidic or alkaline conditions, and reveal how F. graminearum actively regulates intracellular metabolism and synthesis processes to adapt to the changes of extracellular pH environment. 【Method】 F. graminearum was cultured in PDB (potato dextrose broth) medium with initial pH of 4.5, 6.5 and 8.0 for 48 h, and the total RNA of the strain was extracted to construct a cDNA library. Transcriptome sequencing and bioinformatics techniques were used to identify the related differentially expressed genes (DEGs), and the metabolic pathways involved were further analyzed. 【Result】 A total of 4283 DEGs were detected under acidic conditions, of which 2232 were up-regulated and 2252 were down-regulated. Under alkaline conditions, there were a total of 498 DEGs, of which 269 were up-regulated and 229 were down-regulated. The results of Gene Ontology (GO) functional enrichment analysis showed that 211 GO terms were significantly enriched and 72 were down-regulated under acidic conditions. There were 33 GO terms that were revised upwards and 40 downwards under alkaline conditions. The results of KEGG encyclopedia of genes and Genomes (Kyoto Encyclopedia of Genes and Genomes) enrichment analysis showed that 22 pathways were significantly enriched and 32 pathways were down-regulated under acidic conditions. There were 8 up-regulated pathways and 13 down-regulated pathways under alkaline conditions. The expression of membrane transporters and hydrolysis of carbohydrate compounds and other related genes were up-regulated, and the expression of genes related to protein metabolism was down-regulated, which assisted F. graminearum cells to adapt to changes in the external environment. At the same time, F. graminearum maintained the internal environment balance of its own cells by reducing secondary metabolism and amino acid metabolism under acidic and alkaline conditions, respectively, so as to resist extracellular pH stress. 【Conclusion】 In the acidic environment, Fusarium graminearum adapts to the changes in the extracellular environment by promoting the production of riboprotein complexes and secondary metabolism. In an alkaline environment, Fusarium graminearum cells respond to and sense external stresses through amino acid metabolism. The analysis of the metabolic pathways of F. graminearum cells provides important gene expression data for the response of F. graminearum to different pH environments, and the results of this study are helpful to understand the pathogenesis of F. graminearum.
2025-05-01 | GSE267311 | GEO