Metabolism of halophilic archaea

In spite of their common hypersaline environment, halophilic archaea are surprisingly different in their nutritional demands and metabolic pathways. The metabolic diversity of halophilic archaea was investigated at the genomic level through systematic metabolic reconstruction and comparative analysis of four completely sequenced species: Halobacterium salinarum, Haloarcula marismortui, Haloquadratum walsbyi, and the haloalkaliphile Natronomonas pharaonis. The comparative study reveals different sets of enzyme genes amongst halophilic archaea, e.g. in glycerol degradation, pentose metabolism, and folate synthesis. The carefully assessed metabolic data represent a reliable resource for future system biology approaches as it also links to current experimental data on (halo)archaea from the literature

Mevalonic acid is partially synthesized from amino acids in Halobacterium cutirubrum: a 13C nuclear magnetic resonance study.

13C nuclear magnetic resonance revealed an unusual pathway for the biosynthesis of lipids in Halobacterium cutirubrum and H. halobium. Mevalonic acid was not synthesized from three acetyl-coenzyme A molecules, as has been suggested previously, and the branch-methyl and methine carbons in phytanyl chains were derived from neither acetate nor glycerol. Instead, they were supplied by the degradation of amino acids, in particular of lysine. Presumably, two different types of two-carbon fragments were used simultaneously by halobacteria for the biosynthesis of mevalonate. The labeling pattern of squalene supported the above conclusions. Based on these data, a general scheme is proposed to account for the contribution of lysine-to-lipid biosynthesis

Biosynthetic pathways in Methanospirillum hungatei as determined by 13C nuclear magnetic resonance.

The main metabolic pathways in Methanospirillum hungatei GP1 were followed by using 13C nuclear magnetic resonance, with 13C-labeled acetate and CO2 as carbon sources. The labeling patterns found in carbohydrates, amino acids, lipids, and nucleosides were consistent with the formation of pyruvate from acetate and CO2 as the first step in biosynthesis. Carbohydrates are formed by the glucogenic pathway, and no scrambling of label was observed, indicating that the oxidative or reductive pentose phosphate pathways are not functioning at significant rates. The pathways for amino acid biosynthesis are the usual ones, with the exception of that for isoleucine. The tricarboxylic acid pathway is incomplete and operates in a reductive direction to form alpha-ketoglutarate. The phytanyl chains of lipids are synthesized from acetate via mevalonic acid

Coiled-coil helix rotation selects repressing or activating state of transcriptional regulator DhaR

Escherichia coli dihydroxyacetone (Dha) kinase consists of two subunits, DhaK and DhaL. Transcription of dha operon is regulated by the DhaR transcription factor and its action is under control of the kinase subunits. DhaR is activated by interaction with DhaL while it is repressed by DhaK. We have determined the structures of DhaK and DhaL bound to the tandem GAF-like and PAS domains of the DhaR, providing an architectural model for how GAF/PAS tandem domains work together in binding protein partners. The structures reveal a mechanism of opposite transcriptional regulation by the DhaK and DhaL subunits. The kinase subunits interface with DhaR through surfaces that partially overlap with their active sites, allowing sensing of ATP- versus ADP-loaded DhaL subunit and also precluding a ternary complex between DhaK-DhaL and DhaR. The rotation of helices within the DhaR coiled-coil linker upon DhaL binding provides the mechanism for transmitting the binding signal from the GAF/PAS domains to the C-terminal DNA-binding domain. \ua9 2014 Elsevier Ltd. All rights reserved.Peer reviewed: YesNRC publication: Ye

Metabolic pathways in deep sea, thermophilic Methanococcus jannaschii, and other methanogenic bacteria

Peer reviewed: YesNRC publication: Ye

Acetate and CO2 assimilation by Methanothrix concilii.

Biosynthetic pathways in Methanothrix concilii, a recently isolated aceticlastic methanogen, were studied by 13C-nuclear magnetic resonance spectroscopy. Labeling patterns of amino acids, lipids, and carbohydrates were determined. Similar to other methanogens, acetate was carboxylated to pyruvate, which was further converted to amino acids by various biosynthetic pathways. The origin of carbon atoms in glutamate, proline, and arginine clearly showed that an incomplete tricarboxylic acid cycle operating in the oxidative direction was used for their biosynthesis. Isoleucine was synthesized via citramalate, which is a typical route for methanogens. As with Methanosarcina barkeri, an extensive exchange of the label between the carboxyl group of acetate and CO2 was observed. Lipids predominantly contained diphytanyl chains, the labeling of which indicated that biosynthesis proceeded through mevalonic acid. Labeling of the C-1,6 of glucose from [2-13C]acetate is consistent with a glucogenic route for carbohydrate biosynthesis. Except for the different origins of the methyl group of methionine, the metabolic properties of Methanothrix concilii are closely related to those of Methanosarcina barkeri