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11 results for “Methanosarcina”
Nature and nurture: Enabling formate-dependent growth in Methanosarcina acetivorans
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The novel regulator HdrR controls the transcription of the heterodisulfide reductase operon hdrBCA in Methanosarcina barkeri
<p><span>RNA-seq raw data and processed data are accessible at Zenodo.</span></p>
Data from: Horizontal gene transfer and genome evolution in Methanosarcina
Background: Genomes of Methanosarcina spp. are among the largest archaeal genomes. One suggested reason for that is massive horizontal gene transfer (HGT) from bacteria. Genes of bacterial origin may be involved in the central metabolism and solute transport, in particular sugar synthesis, sulfur metabolism, phosphate metabolism, DNA repair, transport of small molecules etc. Horizontally transferred (HT) genes are considered to play the key role in the ability of Methanosarcina spp. to inhabit diverse environments. At the moment, genomes of three Methanosarcina spp. have been sequenced, and while these genomes vary in length and number of protein-coding genes, they all have been shown to accumulate HT genes. However, previous estimates had been made when fewer archaeal genomes were known. Moreover, several Methanosarcinaceae genomes from other genera have been sequenced recently. Here, we revise the census of genes of bacterial origin in Methanosarcinaceae. Results: About 5 % of Methanosarcina genes have been shown to be horizontally transferred from various bacterial groups to the last common ancestor either of Methanosarcinaceae, or Methanosarcina, or later in the evolution. Simulation of the composition of the NCBI protein non-redundant database for different years demonstrates that the estimates of the HGT rate have decreased drastically since 2002, the year of publication of the first Methanosarcina genome. The phylogenetic distribution of HT gene donors is non-uniform. Most HT genes were transferred from Firmicutes and Proteobacteria, while no HGT events from Actinobacteria to the common ancestor of Methanosarcinaceae were found. About 50 % of HT genes are involved in metabolism. Horizontal transfer of transcription factors is not common, while 46 % of horizontally transferred genes have demonstrated differential expression in a variety of conditions. HGT of complete operons is relatively infrequent and half of HT genes do not belong to operons. Conclusions: While genes of bacterial origin are still more frequent in Methanosarcinaceae than in other Archaea, most HGT events described earlier as Methanosarcina-specific seem to have occurred before the divergence of Methanosarcinaceae. Genes horizontally transferred from bacteria to archaea neither tend to be transferred with their regulators, nor in long operons.
Data from: Horizontal gene transfer and genome evolution in Methanosarcina
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MM_0565 orchestrates CRISPR-based immunity in Methanosarcina mazei by transcriptional regulation of components essential for the adaptation
GEO Series GSE151372. Methanosarcina mazei Go1. 4 samples. Type: Expression profiling by high throughput sequencing.
In vivo structure probing of RNA in Archaea: Novel insights into the ribosome structure of Methanosarcina acetivorans
GEO Series GSE229536. Methanosarcina acetivorans C2A. 12 samples. Type: Other.
Transcriptional response of Methanosarcina acetivorans to repression of the energy-conserving methanophenazine: CoM-CoB heterodisulfide reductase enzyme HdrED
GEO Series GSE263381. Methanosarcina acetivorans; Methanosarcina acetivorans C2A. 16 samples. Type: Expression profiling by array.
Genetic, Biochemical, and Molecular Characterization of Methanosarcina barkeri Mutants Lacking Three Distinct Classes of Hydrogenase
GEO Series GSE98441. Methanosarcina barkeri str. Fusaro. 27 samples. Type: Expression profiling by high throughput sequencing.
Small proteome of Methanosarcina mazei: Insights from Ribo-seq and peptidomics under different nitrogen conditions
GEO Series GSE240615. Methanosarcina mazei Go1. 8 samples. Type: Expression profiling by high throughput sequencing; Other.
High-throughput RNA sequencing of methanosarcina grown on methylated sulfur compounds
GEO Series GSE64349. Methanosarcina acetivorans C2A. 15 samples. Type: Expression profiling by high throughput sequencing.
sRNA154 a newly identified regulator of nitrogen fixation in Methanosarcina mazei strain Gö1
GEO Series GSE85456. Methanosarcina mazei Go1. 4 samples. Type: Expression profiling by high throughput sequencing.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
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DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.