Ontology highlight
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PROVIDER: PRJNA1023363 | ENA |
REPOSITORIES: ENA
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Project description:Nitrification, the oxidation of ammonia via nitrite to nitrate, has always been considered to be a two-step process catalysed by chemolithoautotrophic microorganisms oxidizing either ammonia or nitrite. No known nitrifier carries out both steps, although complete nitrification should be energetically advantageous. This functional separation has puzzled microbiologists for a century. Here we report on the discovery and cultivation of a completely nitrifying bacterium from the genus Nitrospira, a globally distributed group of nitrite oxidizers. The genome of this chemolithoautotrophic organism encodes the pathways both for ammonia and nitrite oxidation, which are concomitantly activated during growth by ammonia oxidation to nitrate. Genes affiliated with the phylogenetically distinct ammonia monooxygenase and hydroxylamine dehydrogenase genes of Nitrospira are present in many environments and were retrieved on Nitrospira contigs in new metagenomes from engineered systems. These findings fundamentally change our picture of nitrification and point to completely nitrifying Nitrospira as key components of nitrogen-cycling microbial communities.
2019-03-15 | PXD013103 | Pride
Project description:Nitrite-oxidizing bacteria are vital players in the global nitrogen cycle that convert nitrite to nitrate during the 2nd step of nitrification. Within this functional guild, the genus Nitrospira is among the most widespread and phylogenetically and physiologically diverse nitrite oxidizers and its members drive nitrite oxidation in many natural and biotechnological ecosystems. Despite their ecological and biotechnological importance, our understanding of Nitrospira’s energy metabolism is still limited. The main bottleneck for a detailed biochemical characterization of Nitrospira is biomass production, since they are slow-growing organisms and fastidious to culture. In this study, we cultured Nitrospira moscoviensis in a continuous stirred tank reactor system (CSTR) allowing constant biomass harvesting. Additionally, this cultivation setup enabled accurate control of physicochemical parameters and thus avoided fluctuating levels of nitrite and accumulation of nitrate. We performed transcriptome analysis and confirmed constant gene expression profiles in the chemostat culture over a period of two weeks. The transcriptomic data supports the predicted core metabolism of N. moscoviensis, including the reductive TCA cycle as a CO2 fixation pathway, the novel bd-like oxidase as terminal oxidase and the octaheme nitrite reductase involved in nitrogen assimilation. Additionally, the expression of multiple copies of respiratory complexes suggests functional differentiation of these copies within the respiratory chain. Transcriptome analysis also suggests a soluble and a membrane-bound gamma subunit as part of the nitrite oxidoreductase (NXR), the enzyme catalyzing nitrite oxidation. Overall, the transcriptome data provided novel insights into the metabolism of Nitrospira supporting the genome-based prediction of key pathways. Moreover, the application of a CSTR to cultivate Nitrospira is an important foundation for future proteomic and biochemical characterizations, which are crucial for a better understanding of canonical and complete nitrifying microorganisms.
2019-07-03 | GSE123406 | GEO
Project description:In this project, we identified an uncharted subcompartment of the C. elegans germ granule, which we termed the E granule. We show that the E granule is required for the synthesis of a specialized class of 22G-RNAs.
2024-06-21 | PXD053319 |
Project description:This RNA-Seq experiment aims at unraveling the sets of genes that may be deregulated in a specific subset of sensory neurons (the C-Low Threshold MechanoReceptors or C-LTMRs), in absence of transcription factor bhlha9. In this study, we show that the transcription factor bhlha9 is expressed in a subset of adult C-LTMRs. Moreover, we show that bhlha9 KO males but not female displayed impaired thermotaxis behavior in the temperature gradient paradigm and exhibited exacerbated pain hypersensitivity in the formalin test. To address this question, we FACS-sorted C-LTMRs from adult WT and bhlha9 KO males and females and extracted the total RNA. Further RNA-deep sequencing is a major step to pin-point the sets of genes deregulated selectively in these neurons, in absence of bhlha9.
2020-01-21 | GSE138245 | GEO
Project description:Global expression profiling of epileptogenesis has been confounded by variability across laboratories, epilepsy models, tissue sampled and experimental platforms, with the result that very few genes demonstrate consistent expression changes. The present study minimizes these confounds by combining Affymetrix microarray datasets from seven laboratories, using three status epilepticus (SE) models of epilepsy in rats (pilocarpine, kainate, self-sustained SE or SSSE) and the rat kindling model. Total RNA was harvested from laser-captured dentate granule cells from 6 rats at three times during the early-to-mid latent phase that precedes epilepsy symptoms in the SE models (1, 3 and 10 days after SE), or 24 hr after the first stage 2, stage 4 and stage 5 seizure in the kindling model. Each epilepsy model was studied in two independent laboratories except SSSE. The initial goals of this study were to a) identify model-independent transcriptional changes in dentate granule cells that could point to novel intervention targets for epileptogenesis, b) characterize the basal transcriptional profile of dentate granule cells, and c) identify genes that have highly variable expression. Each experimental group consists of 6 rats (biological replicates) from one laboratory at a single time point, except for the SSSE group (6 at day 1 after SSSE, 5 controls and at day 3 after SSSE, 4 at day 10). Thus granule cells were harvested from 164 rats.
2013-06-08 | E-GEOD-47752 | biostudies-arrayexpress
Project description:D6 PROTEIN KINASE (D6PK) is a polarly localized plasma membrane-associated kinase from Arabidopsis thaliana that activates polarly distributed PIN-FORMED (PIN) auxin transporters. D6PK traffics rapidly to and from the plasma membrane, independently from its PIN targets. D6PK plasma membrane association is dependent on the middle domain, an insertion between kinase subdomains VII and VIII. How D6PK polar plasma membrane targeting is established and maintained remains to be understood. Here, we show that cysteines of repeated CXX(X)P motifs in the middle domain are S-acylated and required for D6PK membrane association. While D6PK S-acylation is not detectably regulated during intracellular trafficking, the phosphorylation of adjacent serine residues, in dependence of the upstream regulatory 3-PHOSPHOINOSITIDE-DEPENDENT PROTEIN KINASES1, regulates D6PK residence time at the plasma membrane, lateral diffusion, and trafficking. We describe a mechanism for the regulation of D6PK plasma membrane interaction and polarity, which may also explain the polarity regulation of related kinases.
2024-05-23 | PXD037885 | Pride
Project description:genome sequence of Nardonella Pin
| PRJDB5646 | ENA
Project description:Disruption of either the auxin transporter PIN-FORMED 1 (PIN1) or the protein kinase PINOID (PID) leads to the development of pin-like inflorescences. Previous studies suggested that PID phosphorylates and activates PIN1. Here we report unexpected findings about the genetic interactions between the two genes. We deleted the first 2/3 of the PIN1 coding sequence using CRISPR/Cas9 and the resulting pin1 mutant (pin1-27) was a strong allele. Surprisingly, heterozygous pin1-27 suppressed three independent pid null mutants whereas homozygous pin1-27 enhanced the phenotypes of the pid mutants during embryogenesis. Furthermore, we show that deletion of either the hydrophilic loop or the second half of PIN1 also abolished PIN1 function, yet those heterozygous pin1 mutants were also capable of rescuing pid nulls. Moreover, we inserted GFP into the hydrophilic loop of PIN1 through CRISPR-mediated homology-directed repair (HDR). The GFP signal and pattern in the PIN1-GFP HDR line are similar to those in the previously reported PIN1-GFP transgenic lines. Interestingly, the PIN1-GFP HDR line also rescued various pid null mutants in a semi-dominant fashion. In addition, the previously reported key phosphorylation sites in PIN1 were still phosphorylated in PIN1-GFP pid plants. We conclude that PID is not directly required for phosphorylation and activation of PIN1.
2023-07-07 | MSV000092373 | MassIVE
Project description:Peroxiredoxins are modulators of aging in yeast and multicellular organisms. The mechanisms by which peroxiredoxins stimulate H2O2 resistance and slow down aging are, however, unclear. Here we show that the yeast peroxiredoxin Tsa1 boosts H2O2 resistance and prevents aging independent of cellular H2O2 levels, but in a manner dependent on H2O2 signaling. More specifically, we pin-point a role of Tsa1 in repressing nutrient signaling via protein kinase A (PKA) that governs both H2O2 resistance and longevity. Tsa1 controls PKA activity at the level of the catalytic subunits and Tpk1 is redox-modified by Tsa1 on a conserved cysteine residue (Cys243) in Tpk1 upon H2O2 addition boosting cellular H2O2 resistance. Tpk1 redox modification dephosphorylates a conserved threonine 241 in the activation loop reducing enzyme activity. We discuss these results in the context of an integrative view on aging where nutrient signaling pathways constitute hubs integrating information from multiple aging-related conduits.
2020-07-27 | PXD012617 | Pride