Thermus thermophilus HB8
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA215364 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR11140732_1.fastq.gz | Fastqsanger.gz | |||
| SRR11140732_2.fastq.gz | Fastqsanger.gz |
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Project description:Thermus thermophilus small crRNAs isolated from the T. thermophilus CMR complex
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Project description:We observed the expression profile of the total mRNA of crp (TTHA1437) deletion mutant of Thermus thermophilus HB8 strain grown in a rich (TT) medium at 70 degC
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Project description:We observed the expression profile of the total mRNA of wild-type and TTHA1559 disrupted Thermus thermophilus HB8 strain at 70°C.
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Project description:We observed the expression profile of the total mRNA of TTHB212-deficient of Thermus thermophilus HB8 strain grown in a rich medium at 70°C for 7 and 8 hours
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Project description:The CRISPR-Cas system represents an RNA-based adaptive immune response system in prokaryotes. CRISPRs (Clustered Regularly Interspaced Short Palindromic Repeats) consist of arrays of short repeat sequences interspaced by non-repetitive short spacers, some of which show sequence similarity to foreign phage genetic elements. Their cistronic transcripts are processed to produce the mature CRISPR RNAs (crRNAs), the elements that confer immunity by base-pairing with exogenous nucleic acids. We characterized the expression and processing patterns of Thermus thermophilus HB8 CRISPRs using differential deep-sequencing, which differentiates between 5’ monophosphate and 5’ non-monophosphate-containing RNAs, and/or between 3’ hydroxyl and 3’ non-hydroxyl-containing RNAs. The genome of T. thermophilus HB8 encodes 11 CRISPRs, classified into three distinct repeat sequence types, all of which were constitutively expressed without deliberately infecting the bacteria with phage. Analysis of the differential deep sequencing data suggested that crRNAs are generated by endonucleolytic cleavage, leaving fragments with 5’ hydroxyl and 3’ phosphate or 2’,3’-cyclic phosphate termini. The 5’ ends of all crRNAs are generated by site-specific cleavage eight nucleotides upstream of the spacer start position, however, the 3’ ends, are generated by two alternative, repeat-sequence-type-dependent mechanisms. These observations are consistent with the operation of multiple crRNA processing systems within a bacterial strain.
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Project description:Thermus thermophilus HB8 Raw sequence reads
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Project description:Lysine acetylation in proteins has recently been globally identified in bacteria and eukaryotes. Even though acetylproteins are known to be involved in various cellular processes, its physiological significance has not yet been resolved. Using a proteomics approach in combination with immunoprecipitation, we identified 197 lysine acetylation sites and 4 N-terminal acetylation sites from 128 proteins in Thermus thermophilus HB8, an extremely thermophilic eubacterium. Our analyses revealed that identified acetylproteins are well conserved across all three domains of life and are mainly involved in central metabolism and translation. To further characterize functional significance, we successfully mapped 113 acetylation sites on their 54 authentic and 59 homologous protein structures. The acetylation in the majority of proteins occurs in ordered structures and the sites were situated near the negatively charged glutamic acid residues. In addition, 59 of 103 acetylations were located within considerable distance that can disrupt electrostatic interactions and hydrogen bonding networks on protein surface, demonstrating the physiological significances of the acetylations. Finally, we further summarized 22 critical acetylation sites related to Schiff-base formation, ligand binding, protein-RNA and protein-protein interaction. The structural information of 113 acetylation sites provides new molecular insight into the role of lysine acetylation in the proteins. Data processing, bioinformatics: MS and MS/MS spectral data were processed by DataAnalysis 4.0 software (Bruker Daltonics). The peak lists containing m/z of precursor ions with that of their product ions were generated by the Compound-Auto MS(n) option of the DataAnalysis 4.0 software. Fifty non-deconvoluted peaks over the intensity threshold 150 and charge deconvoluted peaks in each MS/MS spectrum were exported into peak list files. The spectra were searched against our in-house T. thermophilus HB8 database, containing 2,238 protein sequence entries from the complete genome sequence using Mascot search engine (version 2.3; Matrix Science, London, UK). The acetylated peptides were identified using a mass tolerance of ±0.05 Da for precursor and product ions and allowed a maximum of 6 mis-cleavage sites for trypsin. The carbamidomethylation of cysteine was selected as a fixed modification. The oxidation of methionine, deamidation of asparagine and glutamine, acetylation of lysine and acetylation of protein N-terminus were selected as variable modifications. Only peptides in the confidence range of 99% probability (P value < 0.01) in Mascot ion score were assumed to be identified.
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Project description:Expression profile of TTHA1438-deficient Thermus thermophilus HB8 strain
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Project description:Expression profile of crp-deficient Thermus thermophilus HB8 strain
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