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D-Glutamate Utilization in Pseudomonas aeruginosa PAO1

ABSTRACT: D-Glutamate (D-Glu), an essential component of peptidoglycans, can be utilized as carbon and nitrogen source by Pseudomonas aeruginosa. DNA microarrays were employed to identify genes involved in D-Glu catabolism. Through gene knockout and growth phenotype analysis, the divergent dguR-dguABC (D-glutamate utilization) gene cluster was shown to participate in D-Glu catabolism and regulation. The dguA gene encodes a FAD-dependent D-amino acid dehydrogenase with D-Glu as its preferred substrate, and its promoter was specifically induced by exogenous D-Glu and D-Gln. The function of DguR as transcriptional activator of the dguABC operon was demonstrated by promoter activity measurements in vivo and by mobility shift assays with purified His-tagged DguR in vitro. Although the DNA-binding activity of DguR did not require D-Glu, the presence of D-Glu in the binding reaction was found to stabilize a preferred nucleoprotein complex. The dguB gene encodes a putative enamine/imine deaminase of the RidA family, but its role in D-Glu catabolism remained to be determined. While a lesion in dguC encoding a periplasmic solute binding protein did not affect growth on D-Glu, the AatJMQP transporter for acidic amino acid uptake was found essential for D-Glu and L-Glu utilization. Expression of this uptake system was subjected to induction by exogenous DL-Glu, most likely via the AauSR two-component system. In summary, DguA was identified in this study as a new member of the FAD-dependent amino acid dehydrogenase family for D-amino acid catabolism. DguR serves as a D-Glu sensor and transcriptional activator of the dguA promoter.

ORGANISM(S): Pseudomonas aeruginosa PAO1 Pseudomonas aeruginosa

PROVIDER: GSE46603 | GEO | 2013/05/03

SECONDARY ACCESSION(S): PRJNA201067

REPOSITORIES: GEO

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D-Glutamate Utilization in Pseudomonas aeruginosa PAO1

Project description:D-Glutamate (D-Glu), an essential component of peptidoglycans, can be utilized as carbon and nitrogen source by Pseudomonas aeruginosa. DNA microarrays were employed to identify genes involved in D-Glu catabolism. Through gene knockout and growth phenotype analysis, the divergent dguR-dguABC (D-glutamate utilization) gene cluster was shown to participate in D-Glu catabolism and regulation. The dguA gene encodes a FAD-dependent D-amino acid dehydrogenase with D-Glu as its preferred substrate, and its promoter was specifically induced by exogenous D-Glu and D-Gln. The function of DguR as transcriptional activator of the dguABC operon was demonstrated by promoter activity measurements in vivo and by mobility shift assays with purified His-tagged DguR in vitro. Although the DNA-binding activity of DguR did not require D-Glu, the presence of D-Glu in the binding reaction was found to stabilize a preferred nucleoprotein complex. The dguB gene encodes a putative enamine/imine deaminase of the RidA family, but its role in D-Glu catabolism remained to be determined. While a lesion in dguC encoding a periplasmic solute binding protein did not affect growth on D-Glu, the AatJMQP transporter for acidic amino acid uptake was found essential for D-Glu and L-Glu utilization. Expression of this uptake system was subjected to induction by exogenous DL-Glu, most likely via the AauSR two-component system. In summary, DguA was identified in this study as a new member of the FAD-dependent amino acid dehydrogenase family for D-amino acid catabolism. DguR serves as a D-Glu sensor and transcriptional activator of the dguA promoter. Pseudomonas aeruginosa PAO1 was chosen as model to study gene response with different D-amino acids.

2013-05-03 | E-GEOD-46603 | biostudies-arrayexpress

RNA-Seq of Arabidopsis Col-0 and sid2 seedlings treated with L-Glu and urea

Project description:Plant resistance inducers (PRIs) are compounds that protect crops from diseases by activating plant immunity. The exogenous treatment with glutamate (Glu), an important amino acid for living organisms, was shown to induce resistance against fungal pathogen in rice and tomato. To understand the molecular mechanism of Glu-induced immunity, we developed a model system using Arabidopsis thaliana. Here, we found that exogenous treatment with Glu to Arabidopsis enhances resistance against Pseudomonas syringae pv. tomato DC3000 and Colletotrichum higginsianum. Consistently, transcriptome analyses of Arabidopsis seedlings treated with Glu showed that Glu significantly induces the expression of wound, defense, and stress related genes. Interestingly, Glu activates the expression of pathogen or damage associated molecular patterns (PAMP or DAMP)–inducible genes at much later time points than PAMP/DAMPs normally do. Moreover, expression of Glu-inducible genes does not require known components of PAMP receptor complex, glutamate receptors, salicylic acid-biosynthesis enzyme, or glutamate decarboxylase. In addition, Glu also enhances PAMP-inducible immune responses, such as production of reactive oxygen species and mitogen-activated protein kinase activation. These results show that Glu activates PAMP/DAMP-triggered immunity signaling pathway in a novel manner.

2019-12-06 | GSE123621 | GEO

RNA-Seq of Arabidopsis Col-0 seedlings treated with L-Glu, urea, SA, and distilled water.

2019-12-06 | GSE123620 | GEO

Quantification of global gene expression control by growth rate and metabolic cues

Project description:We performed a series of 14 steady-state chemostat cultures of S. cerevisiae in biological triplicates, which orthogonally modulated either the growth rate under nitrogen limitation, or the amino acid metabolism of the cell under nitrogen or carbon limitation. The nitrogen sources in the AA subset were chosen to represent those that are preferred (NH4 and Glu) and non-preferred (Phe and Ile). This dataset allows us to account for gene expression changes that arise from changing growth rate and metabolism, which is necessary for a complete understanding of gene regulation.

2021-03-16 | E-MTAB-9117 | biostudies-arrayexpress

B. subtilis: temporal expression response to amino acid treatment

Project description:Microorganisms can restructure their transcriptional output to adapt to environmental conditions by sensing endogenous metabolite pool. In this study, an Agilent customized microarray representing approximately 4,106 genes was used to study temporal transcript profiles of Bacillus subtilis in response to valine, glutamate and glutamine pulses. Amino-acid-regulated genes were identified having significantly changed expression at one or more time points in response to pulses of valine, glutamate, and glutamine, respectively, and Val-, Glu and Gln-specific genes were further distinguished from them. Different amino acid treatments were compared in terms of both the global temporal profiles and the 5-minute quick regulations, and between-experiment differential genes were identified. The highlighted genes were analyzed based on diverse sources of gene functions using a variety of computational tools, including T-profiler analysis, hierarchical clustering and enrichment of functional categories. The results revealed the common and distinct modes of action of these three amino acids, and should help to elucidate the specific signaling mechanism of each amino acid as an effector. Three amino acids (Glutamate, Glutamine, and Valine) were adopted to perturb the culture of subtilis. Four time-points were investigated for each perturbation. There are two replicates for the first time-point of Valine-treatment experiment.

2010-05-05 | E-GEOD-17243 | biostudies-arrayexpress

Amino Acids Downregulate SIRT4 to Detoxify Ammonia through the Urea Cycle

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

B. subtilis: temporal expression response to amino acid treatment

2009-09-09 | GSE17243 | GEO

B. subtilis: temporal expression response to amino acid treatment

2009-09-09 | GSE17243 | GEO

Dunaliella tertiolecta UTEX 'LB 999'

Project description:Amino acid catabolism fuels microalgal lipogenesis

| PRJNA324164 | ENA

Improved Fermentative Production of Gamma-Aminobutyric Acid via the Putrescine Route: Systems Metabolic Engineering for Production From Glucose, Amino Sugars, and Xylose

Project description:Gamma-aminobutyric acid (GABA) is a non-protein amino acid widespread in Nature. Among the various uses of GABA, its lactam form 2-pyrrolidone can be chemically converted to the biodegradable plastic polyamide-4. In metabolism, GABA can be synthesized either by decarboxylation of L-glutamate or by a pathway that starts with the transamination of putrescine. Fermentative production of GABA from glucose by recombinant Corynebacterium glutamicum has been described via both routes. Putrescine-based GABA production was characterized by accumulation of by-products such as N-acetyl-putrescine. Their formation was abolished by deletion of the spermi(di)ne N-acetyl-transferase gene snaA. To improve provision of L-glutamate as precursor 2-oxoglutarate dehydrogenase activity was reduced by changing the translational start codon of the chromosomal gene for 2-oxoglutarate dehydrogenase subunit E1o to the less preferred TTG and by maintaining the inhibitory protein OdhI in its inhibitory formby changing amino acid residue 15 from threonine to alanine. Putrescine-based GABA production by the strains described here led to GABA titers up to 63.2 g L-1 in fed-batch cultivation at maximum volumetric productivities up to 1.34 g L-11 h1-1, the highest volumetric productivity for fermentative GABA production reported to date. Moreover, GABA production from the carbon sources xylose, glucosamine, and N-acetyl-glucosamine that do not have competing uses in the food or feed industries was established.

2016-05-21 | GSE81695 | GEO

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