Archaeon
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ABSTRACT:
PROVIDER: PRJDB17443 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:uncultured methanogenic archaeon overview
| PRJNA851135 | ENA
Project description:Genome analysis of archaeal strain Heim1 and methanogenic archaeon Methanocalculs sp. strain HC2
| PRJDB16865 | ENA
Project description:A hyperthermophilic archaeon Thermococcus onnurineus NA1 can grow and produce H2 on a variety of CO-containing feed stocks such as by-product gas generated from steel-mill process. In this study we applied a long-term adaptive evolution to enhance H2 productivity. Through serial transfer of cell cultures with carbon monoxide (CO) as an energy source, we observed physiological changes in cell density, CO consumption rate and H2 production rate. To understand the underlying mechanism for the changes, we performed systems analysis of genomic, transcriptomic and epigenomic data. Genomic analysis of an evolved strain, designated as 156T, revealed that single or multiple bases were substituted, deleted or inserted in the sequence of the parental strain. A single point mutation in a putative transcriptional regulator (TON_1525) seemed to play a pivotal role in changing cellular phenotypes by increasing the expression level of genes of a CO dehydrogenase-hydrogenase gene cluster. Additionally, a mutation in an aromatic amino acid permease (TON_0820) contributed to increasing cell growth. Transcriptomic analysis revealed that genes belonging to the categories of transcription, translation and energy metabolism in archaeal Clusters of Orthologous Genes (arCOGs) were significantly changed. In particular, genes involved in energy conservation via CO oxidation were highly upregulated. Epigenomic analysis suggested that methylation change might be a way of gene regulation in a hyperthermophilic archaeon. The evolved 156T strain showed highly enhanced hydrogen productivity with CO at high flow rates of 800 ml min-1 and above, indicating the adaptation rendered the strain less sensitive to high CO. The 156T strain was demonstrated to be appropriate for H2 production by using synthetic gas obtained by coal gasification. This study is the first example to show that evolutionary engineering is very effective in enhancing H2 productivity of a hyperthermophilic archaeon on CO
2017-02-09 | GSE73031 | GEO
Project description:Biogenic methane formation, methanogenesis, a key process in the global carbon cycle is the only energy metabolism known to sustain growth of the microorganisms employing it, the methanogenic archaea. All known methanogenic pathways converge at the methane-liberating step where also the terminal electron acceptor of methanogenic respiration, the heterodisulfide of coenzyme M and coenzyme B is formed. Carbon monoxide (CO) utilization of Methanosarcina acetivorans is unique in that the organism can shift from methanogenesis towards acetogenesis. Here, we show that M. acetivorans can dispense of methanogenesis for energy conservation completely. By disrupting the methanogenic pathway through targeted mutagenesis, followed by adaptive evolution, a strain capable of sustained growth by CO-dependent acetogenesis was created. Still, a minute flux through the methane-liberating reaction remained essential, which was attributed to the involvement of the heterodisulfide in at least one essential anabolic reaction. Genomic and proteomic analysis showed that substantial metabolic rewiring had occurred in the strain. Most notably, heterodisulfide reductase, the terminal respiratory oxidoreductase was eliminated to funnel the heterodisulfide towards anabolism. These results suggest that the metabolic flexibility of “methanogenic” archaea is much greater than anticipated and open avenues for probing the mechanism of energetic coupling and the crosstalk between catabolism and anabolism.
2021-10-05 | PXD022016 | Pride
Project description:As part of a comprehensive post-genomic investigation of the model archaeon Halobacterium sp. NRC-1, we used whole genome DNA microarrays to compare transcriptional profiles of cells grown anaerobically via arginine fermentation versus cells either respiring aerobically in the presence of oxygen or anaerobically using trimethylamine N-oxide (TMAO) as a terminal electron acceptor.
2012-11-06 | GSE38374 | GEO
Project description:Transcriptomics of Candidatus Hodarchales strain SC1
| PRJDB19601 | ENA
Project description:Methanococcus maripaludis is a methanogenic archaeon. Within its genome, there are two operons for membrane associated hydrogenases, eha and ehb. To investigate the regulation of ehb on the cell, an S40 mutant was constructed in such a way that a portion of the ehb operon was replaced by pac cassette in the wild type parental strain S2 (done by Whitman's group at the University of Georgia). Four samples of each strain were grown in batch culture. Differences in transcriptional expression between S40 and S2 were measured using cDNA arrays, with flip dye experiments for each biological replicate. Keywords: mutant, archaea, carbon, hydrogenase, methanogen
2005-09-20 | GSE2745 | GEO
Project description:Methanogenic archaeon ISO4-G1 genome sequencing and assembly
| PRJNA305317 | ENA
Project description:Histones are a principal constituent of chromatin in eukaryotes and fundamental to our understanding of eukaryotic gene regulation. In archaea, histones are phylogenetically widespread but not universal: several archaeal lineages have independently lost histone genes. What prompted or facilitated these losses and how archaea without histones organize their chromatin remains largely unknown. Here, we use micrococcal nuclease digestion of native and reconstituted chromatin to elucidate primary chromatin architecture in an archaeon without histones, the acido-thermophilic archaeon Thermoplasma acidophilum. We confirm and extend prior results showing that T. acidophilum harbours a HU family protein, HTa, that protects part of the genome from MNase digestion. Charting HTa-based chromatin architecture in vitro, in vivo and in an HTa-expressing E. coli strain, we present evidence that HTa is an archaeal histone analog. HTa-protected fragments are GC-rich, display histone-like mono- and dinucleotide patterns around a conspicuous dyad, exhibit relatively invariant positioning throughout the growth cycle, and show archaeal histone-like oligomerization behaviour. Our results suggest that HTa, a DNA-binding protein of bacterial origin, has converged onto an architectural role filled by histones in other archaea.
2019-10-08 | GSE138576 | GEO
Project description:Thermococcus gammatolerans, the most radioresistant archaeon known to date, is an anaerobic and hyperthermophilic sulfur-reducing organism living in deep-sea hydrothermal vents. Knowledge of mechanisms underlying archaeal metal tolerance in such metal-rich ecosystem is still poorly documented. We showed that T. gammatolerans exhibits high resistance to cadmium (Cd), cobalt (Co) and zinc (Zn), a weaker tolerance to nickel (Ni), copper (Cu) and arsenate (AsO4) and that cells exposed to 1mM Cd exhibit a cellular Cd concentration of 67µM. A time-dependent transcriptomic analysis using microarrays was performed at a non-toxic (100μM) and a toxic (1mM) Cd dose. The reliability of microarray data was strengthened by real time RT-PCR validations. Altogether, 114 Cd responsive genes were revealed and a substantial subset of genes is related to metal homeostasis, drug detoxification, re-oxidization of cofactors and ATP production. This first genome-wide expression profiling study of archaeal cells challenged with Cd showed that T. gammatolerans withstands induced stress through pathways observed in both prokaryotes and eukaryotes but also through new and original strategies. T. gammatolerans cells challenged with 1mM Cd basically promote: 1) the induction of several transporter/permease encoding genes, probably to detoxify the cell; 2) the upregulation of Fe transporters encoding genes to likely compensate Cd damages in iron-containing proteins; 3) the induction of membrane-bound hydrogenase (Mbh) and membrane-bound hydrogenlyase (Mhy2) subunits encoding genes involved in recycling reduced cofactors and/or in proton translocation for energy production. By contrast to other organisms, redox homeostasis genes appear constitutively expressed and only a few genes encoding DNA repair proteins are regulated. We compared the expression of 27 Cd responsive genes in other stress conditions (Zn, Ni, heat shock, γ-rays), and showed that the Cd transcriptional pattern is comparable to other metal stress transcriptional responses (Cd, Zn, Ni) but not to a general stress response.
2012-08-01 | GSE13546 | GEO