Protein sequence
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ABSTRACT:
PROVIDER: PRJEB52857 | ENA |
REPOSITORIES: ENA
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Project description:The genomic response to low levels of nitrate was studied in Arabidopsis using the Affymetrix ATH1 chip containing more than 22,500 probe sets. Arabidopsis plants were grown hydroponically in sterile liquid culture on ammonium as the sole source of nitrogen for 10 d, then treated with 250 um nitrate for 20 min. The response to nitrate was much stronger in roots (1,176 genes showing increased or decreased mRNA levels) than in shoots (183 responding genes). In addition to known nitrate-responsive genes (e.g. those encoding nitrate transporters, nitrate reductase, nitrite reductase, ferredoxin reductase, and enzymes in the pentose phosphate pathway), genes encoding novel metabolic and potential regulatory proteins were found. These genes encode enzymes in glycolysis (glucose-6-phosphate isomerase and phosphoglycerate mutase), in trehalose-6-P metabolism (trehalose-6-P synthase and trehalose-6-P phosphatase), in iron transport/metabolism (nicotianamine synthase), and in sulfate uptake/reduction. In many cases, only a few select genes out of several in small gene families were induced by nitrate. These results show that the effect of nitrate on gene expression is substantial (affecting almost 10% of the genes with detectable mRNA levels) yet selective and affects many genes involved in carbon and nutrient metabolism. Keywords: Expression profilling by array
2009-11-18 | GSE18984 | GEO
Project description:The genomic response to low levels of nitrate was studied in Arabidopsis using the Affymetrix ATH1 chip containing more than 22,500 probe sets. Arabidopsis plants were grown hydroponically in sterile liquid culture on ammonium as the sole source of nitrogen for 10 d, then treated with 250 um nitrate for 20 min. The response to nitrate was much stronger in roots (1,176 genes showing increased or decreased mRNA levels) than in shoots (183 responding genes). In addition to known nitrate-responsive genes (e.g. those encoding nitrate transporters, nitrate reductase, nitrite reductase, ferredoxin reductase, and enzymes in the pentose phosphate pathway), genes encoding novel metabolic and potential regulatory proteins were found. These genes encode enzymes in glycolysis (glucose-6-phosphate isomerase and phosphoglycerate mutase), in trehalose-6-P metabolism (trehalose-6-P synthase and trehalose-6-P phosphatase), in iron transport/metabolism (nicotianamine synthase), and in sulfate uptake/reduction. In many cases, only a few select genes out of several in small gene families were induced by nitrate. These results show that the effect of nitrate on gene expression is substantial (affecting almost 10% of the genes with detectable mRNA levels) yet selective and affects many genes involved in carbon and nutrient metabolism. Keywords: Expression profilling by array 8 samples were used in this experiment
2009-11-17 | E-GEOD-18984 | biostudies-arrayexpress
Project description:Nitrogen metabolism in Aspergillus nidulans is subject to regulation by the GATA transcription factor AreA which is required for the utilization of a wide range of nitrogen sources other than glutamine or ammonium. The level of AreA activity is regulated by intracellular glutamine levels that vary in response to nitrogen supplementation. For nitrate assimilation, which involves two transporters (CrnA, CrnB), nitrate reductase (NiaD) and nitrite reductase (NiiA), the respective genes are subject to regulation at the level of transcription, including nitrogen metabolite repression mediated by AreA and induction mediated by nitrite or nitrate, mediated by a second transcription factor, NirA. Both transcription factors act synergistically to regulate the expression of all four structural genes when nitrogen is limiting or either nitrate or nitrite is available. In this study we dissect the nitrogen limitation effect mediated by AreA form the nitrate/nitrite specific effect mediated by NirA on the transcriptome level. Keywords: Nitrate/nitrogen limitation response
2009-01-01 | GSE10475 | GEO
Project description:Shewanella spp. possess a broad respiratory versatility, which contributes to the occupation of hypoxic/anoxic environmental or host-associated niches. Here we observed a strain-specific induction of biofilm formation in response to supplementation with the anaerobic electron acceptors dimethyl sulfoxide (DMSO) and nitrate in a panel of Shewanella algae isolates. The respiration-driven biofilm response is not observed in DMSO and nitrate reductase deletion mutants of the type strain S. algae CECT 5071, and can be restored upon complementation with the corresponding reductase operon(s) but not by an operon containing a catalytically inactive nitrate reductase. The distinct transcriptional changes, proportional to the effect of these compounds on biofilm formation, include cyclic di-GMP (c-di-GMP) turnover genes. In support, ectopic expression of the c-di-GMP phosphodiesterase YhjH of Salmonella Typhimurium but not its catalytically inactive variant decreased biofilm formation. The respiration-dependent biofilm response of S. algae may permit differential colonization of environmental or host niches.
2020-12-05 | GSE133627 | GEO
Project description:Nitrate regulates plant growth and development and acts as a potent signal to control gene expression in Arabidopsis. Using an integrative bioinformatics approach we identified TGA1 and TGA4 as putative regulatory factors that mediate nitrate responses in Arabidopsis thaliana roots. We showed that both TGA1 and TGA4 mRNAs accumulate strongly and quickly after nitrate treatments in root organs in a tissue-specific manner. Phenotypic analysis of tga1/tga4 double mutant plants indicated that TGA1 and TGA4 are necessary for nitrate modulation of both primary and lateral root growth. Global gene expression analysis revealed that 97% of the genes with altered expression in tga1/tga4 double mutant plants are regulated by nitrate treatments indicating these transcription factors have a specific role in nitrate responses in Arabidopsis root organs. Among the nitrate-responsive genes that depend on TGA1/TGA4 for normal regulation of gene expression, we found nitrate transporters NRT2.1, NRT2.2 and nitrite reductase (NIR) genes. Specific binding of TGA1 to its cognate DNA sequence on the target gene promoters was confirmed by chromatin immunoprecipitation assays. These results identify TGA1 and TGA4 as important regulatory factors of the nitrate response in Arabidopsis roots.
2013-03-31 | GSE43011 | GEO
Project description:Alicycliphilus denitrificans is a versatile, ubiquitous, facultative anaerobic bacterium. A. denitrificans strain BC can use chlorate, nitrate and oxygen as electron acceptor for growth. Cells display a prolonged lag-phase when transferred from nitrate to chlorate and vice versa. Furthermore, cells adapted to aerobic growth do not easily use nitrate or chlorate as electron acceptor. We further investigated these responses of strain BC by differential proteomics, transcript analysis and enzyme activity assays. In nitrate-adapted cells transferred to chlorate and vice versa, appropriate electron acceptor reduction pathways need to be activated. In oxygen-adapted cells, adaptation to the use of chlorate or nitrate is likely difficult due to the poorly active nitrate reduction pathway and low active chlorate reduction pathway. We deduce that the Nar-type nitrate reductase of strain BC also reduces chlorate, which may result in toxic levels of chlorite if cells are transferred to chlorate. Furthermore, the activities of nitrate reductase and nitrite reductase appear to be not balanced when oxygen-adapted cells a shifted to nitrate as electron acceptor, leading to the production of a toxic amount of nitrite. These data suggest that strain BC encounters metabolic challenges in environments with fluctuations in the availability of electron acceptors. Proteomic samples were prepared from Alicycliphilus denitrificans grown in the presence of different electron acceptors: chlorate, nitrate and oxygen. Proteins were separated by a short SDS gel and for each sample 4 in-gel digest slices were prepared. Peptide samples were measured by nLC LTQ-Orbitrap and the data were analysed with MaxQuant using default settings (1% FDR on peptide and protein level) and filtered extra to keep only proteins identified with at least 2 peptides and 1 unique and 1 unmodified peptide.
2013-08-12 | PXD000258 | Pride
Project description:We have done next generation sequencing of optically thin, exponentialy growing WT Phaeodactylum tricornutum and our ~50% nitrate reductase knock-down cultures. Culture were grown with and without nitrogen source to improve our undestanding of the pathways regulation under conditions that promote lipid accumulation (N-starvation).
2016-03-31 | GSE67449 | GEO
Project description:In plants, nitrate is suggested to act as an indicator of nitrogen (N) status that modulates N responses under steady-state conditions. Our preceding study suggested that shoot nitrate accumulation alone represses expression of N starvation-inducible genes in shoots and roots. Notably, we observed that shoot nitrate accumulation was accompanied by increases in shoot expression of ISOPENTENYL TRANSFERASE 3 (IPT3) and shoot levels of N6-(Δ2-isopentenyl) adenine (iP)-type CK. IPT3 expression is localized primarily in phloem companion cells, and iP-type CKs, which are synthesized by IPT3, are phloem-mobile. Hence, both local and systemic responses to shoot nitrate status may be regulated by IPT3-synthesized iP-type CKs. Thus, the present study aims to dissect the local/systemic responses to shoot nitrate status and their dependence on shoot IPT3. To achieve this, we developed a novel experimental system to manipulate nitrate levels and IPT3 expression in a shoot-specific manner using grafted plants derived from the plants lacking nitrate reductase and/or IPT3. Using shoots and roots from the grafted plants, RNA-seq analysis was performed.
2024-08-31 | E-MTAB-14302 | biostudies-arrayexpress
Project description:Acididesulfobacillus acetoxydans is an acidophilic sulfate reducer that can dissimilatory reduce nitrate to ammonia (DNRA). However, no known nitrite reductase is encoded. This study was performed to investigate how A. acetoxydans reduces nitrate to nitrite and elucidated a novel DNRA mechanism and potential nitrosative stress resistance mechanisms in acidophiles.
2024-01-26 | PXD045135 | Pride
Project description:Nitrate metabolism is an adaptation mechanism used by many bacteria for survival under anaerobic environments. As a by-product of inflammation, nitrate is used by the intestinal bacterial pathogens to enable gut infection. However, the responses of bacterial respiratory pathogens to nitrate are less well understood. Actinobacillus pleuropneumoniae is an important bacterial respiratory pathogen of swine. Previous studies have suggested that adaptation of A. pleuropneumoniae to anaerobiosis is important for infection. In this work, A. pleuropneumoniae growth and pathogenesis in response to the nitrate were investigated. Nitrate significantly promoted A. pleuropneumoniae growth under anaerobic condition in vitro and lethality in mice. By using narQ and narP deletion mutants, and single-residue mutation complementary strains of ΔnarQ, the two-component system NarQ/P were confirmed to be critical for nitrate induced growth, with Arg50 in NarQ as an essential functional residue. Transcriptome analysis showed that nitrate up-regulated multiple energy-generating pathways, including nitrate metabolism, mannose and pentose metabolism and glycerolipid metabolism via the regulation of NarQ/P. Furthermore, narQ, narP and its target gene encoding the nitrate reductase Nap contributed to the pathogenicity of A. pleuropneumoniae. The Nap inhibitor tungstate significantly reduced the survival of A. pleuropneumoniae in vivo, suggesting that Nap is a potential drug target. These results give new insights into how the respiratory pathogen A. pleuropneumoniae utilizes alternative electron acceptor nitrate to overcome the hypoxia microenvironment, which can occur in the inflammatory or necrotic infected tissues.
2022-07-29 | GSE207497 | GEO