Genetic Examination of Initial Amino Acid Oxidation and Glutamate Catabolism in the Hyperthermophilic Archaeon Thermococcus kodakarensis

Yokooji, Yuusuke; Sato, Takaaki; Fujiwara, Shinsuke; Imanaka, Tadayuki; Atomi, Haruyuki

doi:10.1128/jb.01979-12

Cited by 26 publications

(35 citation statements)

References 58 publications

(55 reference statements)

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“…KGOR from Thermococcus litoralis has been shown to be specific to 2-oxoglutarate, indicating its role in the metabolism of Glu/Gln (7). KGOR from T. kodakarensis has been genetically shown to be the major 2-oxo acid:ferredoxin oxidoreductase in Glu/Gln metabolism, as succinate generation was no longer observed in its disruption strain (2). As a whole, the amino acids for which a 2-oxo acid:ferredoxin oxidoreductase is present correspond well to those suggested to be metabolized by the five groups of NDP-forming acyl-CoA synthetases.…”

Section: Discussionmentioning

confidence: 67%

“…Among the five groups of NDP-forming acyl-CoA synthetase ␣ subunits of the Thermococcales (Fig. 1), at least one member of groups 1 to 3 has been biochemically examined with enzymes from either P. furiosus or T. kodakarensis (2,(9)(10)(11)(12)(13)(14)(15)19). In this study, we set out to determine the biochemical properties of enzymes that are composed of the group 4 and group 5 ␣ subunits from T. kodakarensis.…”

Section: Resultsmentioning

confidence: 99%

“…One group is represented by ACS I Pf (␣ subunit; PF1540), and another group includes ACS II Pf (␣ subunit; PF0532) and ACS II Tk (␣ subunit; TK0139), while a third group includes the ␣ subunit of an ADPforming acyl-CoA synthetase specific to succinate/succinyl-CoA (succinyl-CoA synthetase [SCS Tk ]) (␣ subunit; TK1880) from T. kodakarensis (19). The enzyme has recently been shown to be involved in Glu catabolism and succinate generation (2).…”

mentioning

confidence: 99%

“…Step i is catalyzed by either glutamate dehydrogenase (GDH) in the case of Glu or multiple aminotransferases coupled with GDH for other amino acids (2)…”

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confidence: 99%

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Characterization of Two Members among the Five ADP-Forming Acyl Coenzyme A (Acyl-CoA) Synthetases Reveals the Presence of a 2-(Imidazol-4-yl)Acetyl-CoA Synthetase in Thermococcus kodakarensis

Awano¹,

Wilming²,

Tomita³

et al. 2013

Journal of Bacteriology

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eThe genome of Thermococcus kodakarensis, along with those of most Thermococcus and Pyrococcus species, harbors five paralogous genes encoding putative ␣ subunits of nucleoside diphosphate (NDP)-forming acyl coenzyme A (acyl-CoA) synthetases. The substrate specificities of the protein products for three of these paralogs have been clarified through studies on the individual enzymes from Pyrococcus furiosus and T. kodakarensis. Here we have examined the biochemical properties of the remaining two acyl-CoA synthetase proteins from T. kodakarensis. The TK0944 and TK2127 genes encoding the two ␣ subunits were each coexpressed with the ␤ subunit-encoding TK0943 gene. In both cases, soluble proteins with an ␣ 2 ␤ 2 structure were obtained and their activities toward various acids in the ADP-forming reaction were examined. The purified TK0944/TK0943 protein (ACS III Tk ) accommodated a broad range of acids that corresponded to those generated in the oxidative metabolism of Ala, Val, Leu, Ile, Met, Phe, and Cys. In contrast, the TK2127/TK0943 protein exhibited relevant levels of activity only toward 2-(imidazol-4-yl)acetate, a metabolite of His degradation, and was thus designated 2-(imidazol-4-yl)acetyl-CoA synthetase (ICS Tk ), a novel enzyme. Kinetic analyses were performed on both proteins with their respective substrates. In T. kodakarensis, we found that the addition of histidine to the medium led to increases in intracellular ADP-forming 2-(imidazol-4-yl)acetyl-CoA synthetase activity, and 2-(imidazol-4-yl)acetate was detected in the culture medium, suggesting that ICS Tk participates in histidine catabolism. The results presented here, together with those of previous studies, have clarified the substrate specificities of all five known NDP-forming acyl-CoA synthetase proteins in the Thermococcales.

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Section: Discussionmentioning

confidence: 67%

Section: Resultsmentioning

confidence: 99%

mentioning

confidence: 99%

“…Step i is catalyzed by either glutamate dehydrogenase (GDH) in the case of Glu or multiple aminotransferases coupled with GDH for other amino acids (2)…”

mentioning

confidence: 99%

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Characterization of Two Members among the Five ADP-Forming Acyl Coenzyme A (Acyl-CoA) Synthetases Reveals the Presence of a 2-(Imidazol-4-yl)Acetyl-CoA Synthetase in Thermococcus kodakarensis

Awano¹,

Wilming²,

Tomita³

et al. 2013

Journal of Bacteriology

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“…Glutamate formed by the transamination is regenerated to 2-oxoglutarate by alanine aminotransferasemediated transfer of the amino group to pyruvate (15), resulting in the formation of alanine as one of the end products (15,16). Although it is also possible that glutamate dehydrogenase (GDH) participates in the regeneration of 2-oxoglutarate through oxidative deamination of glutamate, GDH was suggested to act in the direction of glutamate formation when T. kodakarensis was grown with excess pyruvate (17). The amino acid-derived 2-oxoacids then are oxidized to acyl-CoAs by a set of 2-oxoacid (2-ketoacid):Fd oxidoreductases (KORs), followed by conversion to the corresponding carboxylic acids concomitant with ATP synthesis.…”

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Genetic Examination and Mass Balance Analysis of Pyruvate/Amino Acid Oxidation Pathways in the Hyperthermophilic Archaeon Thermococcus kodakarensis

et al. 2014

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bThe present study investigated the simultaneous oxidation of pyruvate and amino acids during H 2 -evolving growth of the hyperthermophilic archaeon Thermococcus kodakarensis. The comparison of mass balance between a cytosolic hydrogenase (HYH)-deficient strain (the ⌬hyhBGSL strain) and the parent strain indicated that NADPH generated via H 2 uptake by HYH was consumed by reductive amination of 2-oxoglutarate catalyzed by glutamate dehydrogenase. Further examinations were done to elucidate functions of three enzymes potentially involved in pyruvate oxidation: pyruvate formate-lyase (PFL), pyruvate:ferredoxin oxidoreductase (POR), and 2-oxoisovalerate:ferredoxin oxidoreductase (VOR) under the HYH-deficient background in T. kodakarensis. No significant change was observed by deletion of pflDA, suggesting that PFL had no critical role in pyruvate oxidation. The growth properties and mass balances of ⌬porDAB and ⌬vorDAB strains indicated that POR and VOR specifically functioned in oxidation of pyruvate and branched-chain amino acids, respectively, and the lack of POR or VOR was compensated for by promoting the oxidation of another substrate driven by the remaining oxidoreductase. The H 2 yields from the consumed pyruvate and amino acids were increased from 31% by the parent strain to 67% and 82% by the deletion of hyhBGSL and double deletion of hyhBGSL and vorDAB, respectively. Significant discrepancies in the mass balances were observed in excess formation of acetate and NH 3 , suggesting the presence of unknown metabolisms in T. kodakarensis grown in the rich medium containing pyruvate.T he euryarchaeal order Thermococcales, composed of two major genera, Thermococcus and Pyrococcus, comprises hyperthermophiles capable of growing at temperatures around 100°C (1, 2). Many members of the Thermococcales are anaerobic sulfur-reducing heterotrophs preferring proteinaceous substrates and utilize elemental sulfur (S 0 ) as a terminal electron acceptor evolving H 2 S. In the absence of S 0 , some of these hyperthermophiles can grow on carbohydrates and related compounds, evolving hydrogen gas (H 2 ) by using protons as a terminal electron acceptor (3).The energy-conserving metabolism of carbohydrates associated with H 2 evolution in the order Thermococcales has been well studied for Thermococcus kodakarensis and Pyrococcus furiosus (4). Pyruvate, added into the medium or generated from carbohydrates, is oxidized to acetyl coenzyme A (acetyl-CoA) by pyruvate: ferredoxin (Fd) oxidoreductase (POR) (5-8) and subsequently is converted to acetate concomitant with ATP synthesis by ADPforming acetyl-CoA synthetases (9, 10). In addition to pyruvate oxidation, peptides and amino acids also are dissimilated simultaneously (11). Amino acids, which are directly incorporated into the cells or formed by degradation of peptides, are deaminated to the corresponding 2-oxoacids using 2-oxoglutarate as an amino acceptor by a number of aminotransferases with different substrate specificities (12)(13)(14)(15). Glutamate formed by the transamina...

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Fervidicoccus

Perevalova¹,

Lebedinsky²,

Bonch-Osmolovskaya³

2016

Bergey's Manual of Systematics of Archaea and Bacteria

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Fer.vi.do.coc'cus L. adj. fervidus hot; L. masc. n. coccus a berry and, in biology, a coccoid cell; N.L. masc. n. Fervidicoccus coccus that grows at high temperatures. Crenarchaeota / Thermoprotei / Fervidicoccales / Fervidicoccaceae / Fervidicoccus Members of the genus Fervidicoccus are extremely thermophilic, obligately anaerobic, and organotrophic microorganisms of the phylum Crenarchaeota . 16S rRNA genes of closely related microorganisms were found in environmental DNA samples from terrestrial hot springs of Kamchatka and Kuril Islands (Russia), Iceland, Yellowstone National Park (USA), and New Zealand with temperatures of 55–84°C, where they can make up a significant fraction of the microbial community. At present, the only cultivated representative of the Fervidicoccus genus is Fervidicoccus fontis, isolated from the Treshchinnyi hot spring of Uzon Caldera, Kamchatka. It is an anaerobic organotroph growing optimally on peptides in the presence of 20–50 mg/l yeast extract at 65–70°C and pH 6.0. Elemental sulfur, if present, is reduced to H 2 S; however, it is not obligately required for growth. H 2 partially inhibits the growth of Fervidicoccus fontis . Thus, phenotypically Fervidicoccus fontis resembles other anaerobic organotrophic archaea of the phyla Crenarchaeota and Euryarchaeota , such as desulfurococci and thermococci, but differs from them by its lower growth temperature. Complete genome analysis of Fervidicoccus fontis confirmed a distinct phylogenetic position of this group. DNA G + C content (mol%) : 37.5 (genome). Type species : Fervidicoccus fontis Perevalova, Bidzhieva, Kublanov, Hinrichs, Liu, Kolganova, Lebedinsky and Bonch‐Osmolovskaya 2010, 2086.

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Genetic Examination of Initial Amino Acid Oxidation and Glutamate Catabolism in the Hyperthermophilic Archaeon Thermococcus kodakarensis

Cited by 26 publications

References 58 publications

Characterization of Two Members among the Five ADP-Forming Acyl Coenzyme A (Acyl-CoA) Synthetases Reveals the Presence of a 2-(Imidazol-4-yl)Acetyl-CoA Synthetase in Thermococcus kodakarensis

Characterization of Two Members among the Five ADP-Forming Acyl Coenzyme A (Acyl-CoA) Synthetases Reveals the Presence of a 2-(Imidazol-4-yl)Acetyl-CoA Synthetase in Thermococcus kodakarensis

Genetic Examination and Mass Balance Analysis of Pyruvate/Amino Acid Oxidation Pathways in the Hyperthermophilic Archaeon Thermococcus kodakarensis

Fervidicoccus

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