Caldalkalibacillus thermarum
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA63121 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| AFCE01.dat.gz | Other | |||
| AFCE01.fasta.gz | Fasta.gz | |||
| AFCE01.master.dat | Other | |||
| SRR12283457_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 7 |
Similar Datasets
Project description:Alkaliphilic microorganisms are similar to mesophilic counterparts with exception to membrane proteins. Detection of membrane proteins is difficult due to hydrophobicity and low absolute abundance. Caldalkalibacillus thermarum TA2.A1 is of interest due to growth from pH 7.5 to pH 10. Combination of whole cell lysate proteomics and membrane extracts solubilized with either SDS or FOS-choline-12 detected 158 membrane proteins, including a complete electron transport chain. Additionally, transporters for osmolytes ectoine and glycine betaine were observed.
2023-07-11 | PXD042369 | Pride
Project description:Caldalkalibacillus thermarum TA2.A1 Genome sequencing project
| PRJNA63105 | ENA
Project description:Caldalkalibacillus thermarum TA2.A1 Genome sequencing and assembly
| PRJNA638815 | ENA
Project description:The crystal structure has been determined of the F1-catalytic domain of the F-ATPase from Caldalkalibacillus thermarum, which hydrolyzes adenosine triphosphate (ATP) poorly. It is very similar to those of active mitochondrial and bacterial F1-ATPases. In the F-ATPase from Geobacillus stearothermophilus, conformational changes in the ?-subunit are influenced by intracellular ATP concentration and membrane potential. When ATP is plentiful, the ?-subunit assumes a "down" state, with an ATP molecule bound to its two C-terminal ?-helices; when ATP is scarce, the ?-helices are proposed to inhibit ATP hydrolysis by assuming an "up" state, where the ?-helices, devoid of ATP, enter the ?3?3-catalytic region. However, in the Escherichia coli enzyme, there is no evidence that such ATP binding to the ?-subunit is mechanistically important for modulating the enzyme's hydrolytic activity. In the structure of the F1-ATPase from C. thermarum, ATP and a magnesium ion are bound to the ?-helices in the down state. In a form with a mutated ?-subunit unable to bind ATP, the enzyme remains inactive and the ?-subunit is down. Therefore, neither the ?-subunit nor the regulatory ATP bound to the ?-subunit is involved in the inhibitory mechanism of this particular enzyme. The structure of the ?3?3-catalytic domain is likewise closely similar to those of active F1-ATPases. However, although the ?E-catalytic site is in the usual "open" conformation, it is occupied by the unique combination of an ADP molecule with no magnesium ion and a phosphate ion. These bound hydrolytic products are likely to be the basis of inhibition of ATP hydrolysis.
| S-EPMC5047172 | biostudies-literature
Project description:Nymphaea thermarum Seed Development Transcriptome
| PRJNA718528 | ENA
Project description:Nymphaea thermarum Genome sequencing and assembly
| PRJNA508901 | ENA
Project description:Type II NADH:quinone oxidoreductase (NDH-2) is a respiratory enzyme found in the electron-transport chain of many species, with the exception of mammals. It is a 40-70?kDa single-subunit monotopic membrane protein that catalyses the oxidation of NADH and the reduction of quinone molecules via the cofactor FAD. NDH-2 is a promising new target for drug development given its essential role in many bacterial species and intracellular parasites. Only two bacterial NDH-2 structures have been reported and these structures are at moderate resolution (2.3-2.5?Å). In this communication, a new crystallization platform is reported that produced high-quality NDH-2 crystals that diffracted to high resolution (2.15?Å). The high-resolution NDH-2 structure was used for in silico quinone substrate-docking studies to investigate the binding poses of menadione and ubiquinone molecules. These studies revealed that a very limited number of molecular interactions occur at the quinone-binding site of NDH-2. Given that the conformation of the active site is well defined, this high-resolution structure is potentially suitable for in silico inhibitor-compound screening and ligand-docking applications.
| S-EPMC5633920 | biostudies-literature
Project description:Thermotoga thermarum DSM 5069 genome sequencing project
| PRJNA41517 | ENA
Project description:The aerobic thermoalkaliphile Caldalkalibacillus thermarum strain TA2.A1 is a member of a separate order of alkaliphilic bacteria closely related to the Bacillales order. Efforts to relate the genomic information of this evolutionary ancient organism to environmental adaptation have been thwarted by the inability to construct a complete genome. The existing draft genome is highly fragmented due to repetitive regions, and gaps between and over repetitive regions were unbridgeable. To address this, Oxford Nanopore Technology's MinION allowed us to span these repeats through long reads, with over 6000-fold coverage. This resulted in a single 3.34 Mb circular chromosome. The profile of transporters and central metabolism gives insight into why the organism prefers glutamate over sucrose as carbon source. We propose that the deamination of glutamate allows alkalization of the immediate environment, an excellent example of how an extremophile modulates environmental conditions to suit its own requirements. Curiously, plant-like hallmark electron transfer enzymes and transporters are found throughout the genome, such as a cytochrome b6c1 complex and a CO2-concentrating transporter. In addition, multiple self-splicing group II intron-encoded proteins closely aligning to those of a telomerase reverse transcriptase in Arabidopsis thaliana were revealed. Collectively, these features suggest an evolutionary relationship to plant life.
| S-EPMC7561548 | biostudies-literature