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Acidobacterium capsulatum

ABSTRACT: Acidophilic bacterium

PROVIDER: PRJNA35211 | ENA |

REPOSITORIES: ENA

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			Action	DRS
		Other
	SRR16973006_1.fastq.gz	Fastqsanger.gz
	SRR16973006_2.fastq.gz	Fastqsanger.gz
	SRR16973007_1.fastq.gz	Fastqsanger.gz
	SRR16973007_2.fastq.gz	Fastqsanger.gz

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Acidobacterium capsulatum ATCC 51196

Project description:An acidophilic chemoorganotrophic bacterium isolated from an acidic mineral environment

| PRJNA28085 | ENA

Discovery of a novel (R)-selective bacterial hydroxynitrile lyase from Acidobacterium capsulatum.

Project description:Hydroxynitrile lyases (HNLs) are powerful carbon-carbon bond forming enzymes. The reverse of their natural reaction - the stereoselective addition of hydrogen cyanide (HCN) to carbonyls - yields chiral cyanohydrins, versatile building blocks for the pharmaceutical and chemical industry. Recently, bacterial HNLs have been discovered, which represent a completely new type: HNLs with a cupin fold. Due to various benefits of cupins (e.g. high yield recombinant expression in Escherichia coli), the class of cupin HNLs provides a new source for interesting, powerful hydroxynitrile lyases in the ongoing search for HNLs with improved activity, enantioselectivity, stability and substrate scope. In this study, database mining revealed a novel cupin HNL from Acidobacterium capsulatum ATCC 51196 (AcHNL), which was able to catalyse the (R)-selective synthesis of mandelonitrile with significantly better conversion (97%) and enantioselectivity (96.7%) than other cupin HNLs.

| S-EPMC4151996 | biostudies-literature

Acidobacterium capsulatum ATCC 51196

Project description:Acidobacterium capsulatum ATCC 51196 Raw sequence reads

| PRJNA667213 | ENA

Structural and biochemical characterization of glycoside hydrolase family 79 β-glucuronidase from Acidobacterium capsulatum.

Project description:We present the first structure of a glycoside hydrolase family 79 β-glucuronidase from Acidobacterium capsulatum, both as a product complex with β-D-glucuronic acid (GlcA) and as its trapped covalent 2-fluoroglucuronyl intermediate. This enzyme consists of a catalytic (β/α)(8)-barrel domain and a β-domain with irregular Greek key motifs that is of unknown function. The enzyme showed β-glucuronidase activity and trace levels of β-glucosidase and β-xylosidase activities. In conjunction with mutagenesis studies, these structures identify the catalytic residues as Glu(173) (acid base) and Glu(287) (nucleophile), consistent with the retaining mechanism demonstrated by (1)H NMR analysis. Glu(45), Tyr(243), Tyr(292)-Gly(294), and Tyr(334) form the catalytic pocket and provide substrate discrimination. Consistent with this, the Y292A mutation, which affects the interaction between the main chains of Gln(293) and Gly(294) and the GlcA carboxyl group, resulted in significant loss of β-glucuronidase activity while retaining the side activities at wild-type levels. Likewise, although the β-glucuronidase activity of the Y334F mutant is ~200-fold lower (k(cat)/K(m)) than that of the wild-type enzyme, the β-glucosidase activity is actually 3 times higher and the β-xylosidase activity is only 2.5-fold lower than the equivalent parameters for wild type, consistent with a role for Tyr(334) in recognition of the C6 position of GlcA. The involvement of Glu(45) in discriminating against binding of the O-methyl group at the C4 position of GlcA is revealed in the fact that the E45D mutant hydrolyzes PNP-β-GlcA approximately 300-fold slower (k(cat)/K(m)) than does the wild-type enzyme, whereas 4-O-methyl-GlcA-containing oligosaccharides are hydrolyzed only 7-fold slower.

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Terriglobus saanensis

Project description:Acidophilic bacterium

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Desulfosporosinus acidiphilus

Project description:Acidophilic bacterium

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Low base-substitution mutation rate and predominance of insertion-deletion events in the acidophilic bacterium <i>Acidobacterium capsulatum</i>.

Project description:Analyses of spontaneous mutation have shown that total genome-wide mutation rates are quantitatively similar for most prokaryotic organisms. However, this view is mainly based on organisms that grow best around neutral pH values (6.0-8.0). In particular, the whole-genome mutation rate has not been determined for an acidophilic organism. Here, we have determined the genome-wide rate of spontaneous mutation in the acidophilic Acidobacterium capsulatum using a direct and unbiased method: a mutation-accumulation experiment followed by whole-genome sequencing. Evaluation of 69 mutation accumulation lines of A. capsulatum after an average of ~2900 cell divisions yielded a base-substitution mutation rate of 1.22 × 10-10 per site per generation or 4 × 10-4 per genome per generation, which is significantly lower than the consensus value (2.5-4.6 × 10-3) of mesothermophilic (~15-40°C) and neutrophilic (pH 6-8) prokaryotic organisms. However, the insertion-deletion rate (0.43 × 10-10 per site per generation) is high relative to the base-substitution mutation rate. Organisms with a similar effective population size and a similar expected effect of genetic drift should have similar mutation rates. Because selection operates on the total mutation rate, it is suggested that the relatively high insertion-deletion rate may be balanced by a low base-substitution rate in A. capsulatum, with selection operating on the total mutation rate.

| S-EPMC8717266 | biostudies-literature

Alicyclobacillus acidocaldarius subsp. acidocaldarius DSM 446

Project description:Thermophilic, acidophilic bacterium

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Ferroplasma acidarmanus

Project description:Acidophilic iron-oxidizing bacterium

| PRJNA35151 | ENA

Kyrpidia tusciae DSM 2912

Project description:Thermophilic and acidophilic bacterium

| PRJNA31345 | ENA