Caldalkalibacillus thermarum TA2.A1
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA638815 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| SRR12283457_1.fastq.gz | Fastqsanger.gz | |||
| SRR12283458_1.fastq.gz | Fastqsanger.gz | |||
| SRR12283458_2.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 4 of 4 |
Similar Datasets
Project description:Caldalkalibacillus thermarum TA2.A1 Genome sequencing project
| PRJNA63105 | ENA
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 overview
| PRJNA63121 | ENA
Project description:Proteomics has greatly advanced the understanding of the cellular biochemistry of microorganisms. The thermoalkaliphile Caldalkalibacillus thermarum TA2.A1 is an organism of interest for studies into how alkaliphiles adapt to their extreme lifestyles, as it can grow from pH 7.5 to pH 11. Within most classes of microbes, the membrane-bound electron transport chain (ETC) enables a great degree of adaptability and is a key part of metabolic adaptation. Knowing what membrane proteins are generally expressed is crucial as a benchmark for further studies. Unfortunately, membrane proteins are the category of proteins hardest to detect using conventional cellular proteomics protocols. In part, this is due to the hydrophobicity of membrane proteins as well as their general lower absolute abundance, which hinders detection. Here, we performed a combination of whole cell lysate proteomics and proteomics of membrane extracts solubilised with either SDS or FOS-choline-12 at various temperatures. The combined methods led to the detection of 158 membrane proteins containing at least a single transmembrane helix (TMH). Within this data set we revealed a full oxidative phosphorylation pathway as well as an alternative NADH dehydrogenase type II (Ndh-2) and a microaerophilic cytochrome oxidase ba3. We also observed C. thermarum TA2.A1 expressing transporters for ectoine and glycine betaine, compounds that are known osmolytes that may assist in maintaining a near neutral internal pH when the external pH is highly alkaline.
| S-EPMC10416648 | biostudies-literature
Project description:Nymphaea thermarum Genome sequencing and assembly
| PRJNA508901 | ENA
Project description:Nymphaea thermarum genome sequencing and assembly, and offspring epigenome
| PRJNA1085992 | 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 Reorganized Genome sequencing and assembly
| PRJNA1086863 | ENA
Project description:Caldalkalibacillus salinus strain:YIM B00319 Genome sequencing and assembly
| PRJNA692084 | 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