Soil metagenome
Ontology highlight
ABSTRACT:
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| DRR014314.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:Information on the files related to the respective experiments can be found in the metadata file titled “Metadata_for_Nviennensis_Experiments.xlsx”. The data found here encompasses three related mass spectrometry experiments: 1.) BN-PAGE: Biomass of Nitrososphaera viennensis grown in a bioreactor was lysed and membrane fractions were harvested using an ultracentrifuge. Membrane proteins were extracted using n-dodecyl-beta-D-maltoside (DDM) and loaded on a 3-12% gradient blue native PAGE gel. Selected bands were cut out and analyzed via mass spectrometry. 2.) SDS-Tricine-PAGE of AMO Band: A band containing a large amount of the ammonia monooxygenase complex (AMO) was denatured and run on a 15% SDS-Tricine-PAGE gel to identify individual subunits. 3.) AmoC from SDS-Tricine-PAGE: A band containing a high amount of AmoC from the SDS-Tricine-PAGE gel was processed with three separate digestive enzymes (trypsin, chymotrypsin, or GluC) to identify unique peptides among the six AmoC homologs found in the genome of N. viennensis.
2023-02-13 | PXD035349 | Pride
Project description:Ammonia-oxidizing archaea (AOA) are among the most abundant microorganisms and key players in the global nitrogen and carbon cycles. They share a common energy metabolism but represent a heterogeneous group with respect to their environmental distri- bution and adaptions, growth requirements, and genome contents. We report here the genome and proteome of Nitrososphaera viennensis EN76, the type species of the archaeal class Nitrososphaeria of the phylum Thaumarchaeota encompassing all known AOA. N. viennensis is a soil organism with a 2.52-Mb genome and 3,123 predicted protein-coding genes. Proteomic analysis revealed that nearly 50% of the predicted genes were translated under standard laboratory growth conditions. Comparison with genomes of closely related species of the predominantly terrestrial Nitrososphaerales as well as the more streamlined marine Nitrosopumilales (Candidatus order) and the acidophile Nitrosotalea devanaterra revealed a core genome of AOA comprising 860 genes, which allowed for the reconstruction of central metabolic pathways common to all known AOA and expressed in the N. viennensis and Nitrosopelagicus brevis proteomes. Concomitantly, we were able to identify candidate proteins for as yet unidentified crucial steps in central metabolisms. In addition to unraveling aspects of core AOA metabolism, we identified specific metabolic innovations associated with the Nitrososphaerales mediating growth and survival in the soil milieu, including the capacity for biofilm formation, cell surface modifications and cell adhesion, and carbohydrate conversions as well as detoxification of aromatic compounds and drugs.
2017-05-03 | PXD005297 | Pride
Project description:Nitrososphaera viennensis EN76 Genome sequencing
| PRJEA60103 | ENA
Project description:Marine sponges represent one of the few eukaryotic groups that ubiquitously harbor symbiotic members of the Thaumarchaeota, which are important chemoautotrophic ammonia-oxidizers in many environments. However in most studies, direct demonstration of ammonia-oxidation by these archaea within sponges is lacking, and little is known about sponge-specific adaptations of archaeal ammonia oxidizers (AOA). In this study, we characterized the thaumarchaeal symbiont of the marine sponge Ianthella basta using metaproteogenomics, fluorescence in situ hybridization, qPCR and direct isotope-based functional assays. We demonstrate that the I. basta symbiont is not closely related to other genomically sequenced sponge AOA and is a member of a new genus. “Candidatus Nitrosospongia bastadiensis” is an abundant symbiont that is solely responsible for nitrite formation from ammonia in I. basta that surprisingly does not harbor nitrite-oxidizing microbes. Consistently, Ca N. bastadiensis encodes and expresses the genetic repertoire required for chemolithoautotrophic ammonia oxidation. Furthermore, we show that this AOA is equipped with an expanded set of extracellular subtilisin-like proteases, a metalloprotease unique among archaea, as well as a putative branched-chain amino acid ABC transporter. This repertoire is strongly indicative of a mixotrophic lifestyle and is (with slight variations) also found in other sponge-associated, but not in free-living AOA. We predict that this feature as well as an expanded and unique set of secreted serpins (protease inhibitors), a unique array of eukaryotic-like proteins, and a DNA-phosporothioation system likely involved in defense against foreign DNA, represent important adaptations of AOA to life within these ancient filter-feeding animals.
2019-11-13 | PXD012484 | Pride
Project description:Nitrososphaera viennensis EN76 Raw sequence reads
| PRJNA895715 | ENA
Project description:Ammonia-oxidizing archaea (AOA) play a significant role in global nitrogen and carbon cycling. AOA can survive under fluctuating environmental conditions by modulating gene expression. Little is known about how AOA regulate gene expression to adapt environmental stress. Here, we report a chromatin-driven mechanism of transcription in Nitrososphaera Viennensis (EN76) to adapt to temperature stress. Using computational and biochemical assays, we found EN76 contains an archaeasome structure. We found that several residues, including G20, K57, and T58 of histone, are important to form archaea chromatin structures. In vitro transcription assays revealed that AOA chromatin efficiently controls gene expression, similar to eukaryote chromatin. Furthermore, we identified AOA histone acetylation, which activates gene expression. Moreover, by integrating chromatin-based gene expression analyses, we revealed that AOA differentially regulate gene expression in response to temperature stress by altering archaeasome occupancy. Our study provides unprecedented documentation that AOA fine-tunes gene expression through a chromatin-driven epigenetic mechanism.
2024-06-30 | GSE249032 | GEO
Project description:Ammonia-oxidizing archaea (AOA) play a significant role in global nitrogen and carbon cycling. AOA can survive under fluctuating environmental conditions by modulating gene expression. Little is known about how AOA regulate gene expression to adapt environmental stress. Here, we report a chromatin-driven mechanism of transcription in Nitrososphaera Viennensis (EN76) to adapt to temperature stress. Using computational and biochemical assays, we found EN76 contains an archaeasome structure. We found that several residues, including G20, K57, and T58 of histone, are important to form archaea chromatin structures. In vitro transcription assays revealed that AOA chromatin efficiently controls gene expression, similar to eukaryote chromatin. Furthermore, we identified AOA histone acetylation, which activates gene expression. Moreover, by integrating chromatin-based gene expression analyses, we revealed that AOA differentially regulate gene expression in response to temperature stress by altering archaeasome occupancy. Our study provides unprecedented documentation that AOA fine-tunes gene expression through a chromatin-driven epigenetic mechanism.
2024-06-30 | GSE249031 | GEO
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:Nitrososphaera viennensis strain:PLX03 | isolate:PLX03 Genome sequencing
| PRJNA870303 | ENA