Ontology highlight
ABSTRACT:
PROVIDER: PRJNA846499 | ENA |
REPOSITORIES: ENA
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Project description:Meta-proteomics analysis approach in the application of biogas production from anaerobic digestion has many advantages that has not been fully uncovered yet. This study aims to investigate biogas production from a stable 2-stage chicken manure fermentation system in chemical and biological perspective. The diversity and functional protein changes from the 1st stage to 2nd stage is a good indication to expose the differential metabolic processes in anaerobic digestion. The highlight of identified functional proteins explain the causation of accumulated ammonia and carbon sources for methane production. Due to the ammonia stress and nutrient limitation, the hydrogenotrophic methanogenic pathway is adopted as indicative of meta-proteomics data involving the key methanogenic substrates (formate and acetate). Unlike traditional meta-genomic analysis, this study could provide both species names of microorganism and enzymes to directly point the generation pathway of methane and carbon dioxide in investigating biogas production of chicken manure.
2021-02-08 | PXD022498 | Pride
Project description:Efficient microbial conversion of lignocellulosic hydrolysates to biofuels is a key barrier to the economically viable deployment of lignocellulosic biofuels. A chief contributor to this barrier is the impact on microbial processes and energy metabolism of lignocellulose-derived inhibitors, including phenolic carboxylates, phenolic amides (for ammonia-pretreated biomass), phenolic aldehydes, and furfurals. To understand the bacterial pathways induced by inhibitors present in ammonia-pretreated biomass hydrolysates, which are less well studied than acid-pretreated biomass hydrolysates, we developed and exploited synthetic mimics of ammonia-pretreated corn stover hydrolysate (ACSH). To determine regulatory responses to the inhibitors normally present in ACSH, we measured transcript and protein levels in an Escherichia coli ethanologen using RNA-seq and quantitative proteomics during fermentation to ethanol of synthetic hydrolysates containing or lacking the inhibitors. Our study identified four major regulators mediating these responses, the MarA/SoxS/Rob network, AaeR, FrmR, and YqhC. Induction of these regulons was correlated with a reduced rate of ethanol production, buildup of pyruvate, depletion of ATP and NAD(P)H, and an inhibition of xylose conversion. The aromatic aldehyde inhibitor 5M-bM-^@M-^Qhydroxymethylfurfural appeared to be reduced to its alcohol form by the ethanologen during fermentation, whereas phenolic acid and amide inhibitors were not metabolized. Together, our findings establish that the major regulatory responses to lignocellulose-derived inhibitors are mediated by transcriptional rather than translational regulators, suggest that energy consumed for inhibitor efflux and detoxification may limit biofuel production, and identify a network of regulators for future synthetic biology efforts. Fermentations were carried out in 0.5L bioreactors (Sartorius) containing 0.3L of SynH, SynH lacking osmoprotectants, SynH+LT, or SynH lacking osmoprotectants but containing lignotoxins and cultures were diluted into SynH with initial OD at 0.2, grown anaerobically overnight, and then inoculated into bioreactors to a starting OD600 of 0.2. Two biological replicates (independent cultures) were grown in each medium. RNA samples were obtained at 4 time points, corresponding to exponential (Exp), transitional (Trans), early stationary (Stat1), and late stationary (Stat2) growth phases.
2014-07-18 | E-GEOD-58976 | biostudies-arrayexpress
Project description:Ammonia is a ubiquitous, toxic by-product of cell metabolism. Its high membrane permeability and proton affinity causes ammonia to accumulate inside acidic lysosomes in its poorly membrane-permeant form: ammonium (NH4+). Ammonium buildup compromises lysosomal function, suggesting the existence of mechanisms that protect cells from ammonium toxicity. Here, we identified SLC12A9 as a lysosomal regulator of ammonium export that preserves lysosomal homeostasis. SLC12A9 knockout cells showed grossly enlarged lysosomes and elevated ammonium content. These phenotypes were reversed upon removal of the metabolic source of ammonium or dissipation of the lysosomal pH gradient. Lysosomal chloride increased in SLC12A9 knockout cells and chloride binding by SLC12A9 was required for ammonium transport. Our data indicate that SLC12A9 function is central for the handling of lysosomal ammonium and chloride, an unappreciated, fundamental mechanism of lysosomal physiology that may have special relevance in tissues with elevated ammonia, such as tumors.
2024-09-12 | GSE276655 | GEO
Project description:The faecal indicator bacterium Escherichia coli K12 was used to study the cellular events that take place at the transcription level using the microarray technology during short-term (physiological) and long-term (genetic) adaptation to slow growth under limited nutrient supply. Short-term and long-term adaptation were assessed by comparing the mRNA levels isolated after 40 or 500 hours of glucose-limited continuous culture at a dilution rate of 0.3 h-1 with those from batch culture with glucose excess. Keywords: glucose-limited continuous culture, adaptation, microarray, high affinity transport systems, transcriptome, Escherichia coli
2006-04-26 | GSE4706 | GEO
Project description:Investigation of rapid evolutionary adaptation events of Magnaporthe oryzae of HOG1 deficient mutants. Osmosensitive mutants adapt and re-gain osmoregulatory capabilities. Proteomics and phosphoproteomics were analyzed to shed light on the underlying processes.
2023-04-13 | PXD034481 | JPOST Repository
Project description:Ammonia production via glutamate dehydrogenase is inhibited by SIRT4, a sirtuin that displays both amidase and non-amidase activities. The processes underlying the regulation of ammonia removal by amino acids remain unclear. Here, we report that SIRT4 acts as a decarbamylase that responds to amino acid sufficiency and regulates ammonia removal. Amino acids promote lysine 307 carbamylation (OTCCP-K307) of ornithine transcarbamylase (OTC), which activates OTC and the urea cycle. Proteomic and interactome screening identified OTC as a substrate of SIRT4. SIRT4 decarbamylates OTCCP-K307 and inactivates OTC in a NAD+-dependent manner. SIRT4 expression was transcriptionally upregulated by the amino acid insufficiency-activated GCN2–eIF2a–ATF4 axis. SIRT4 knockout in cultured cells caused higher OTCCP-K307 levels, activated OTC, elevated urea cycle intermediates, and urea production via amino acid catabolism. Sirt4 ablation decreased mouse blood ammonia levels and ameliorated CCl4-induced hepatic encephalopathy phenotypes. We reveal that SIRT4 safeguards cellular ammonia toxicity during amino acid catabolism.
2023-03-29 | PXD037101 | Pride
Project description:Addition of zeolites to boost continuous bio-hydrogen production
| PRJEB23747 | ENA