Proteome analysis of Thermococcus onnurineus NA1 reveals the expression of hydrogen gene cluster under carboxydotrophic growth

Yun, Sung-Ho; Kwon, Sang Oh; Park, Gun Wook; Kim, Jin Young; Kang, Sung Gyun; Lee, Jung-Hyun; Chung, Young‐Ho; Kim, Soohyun; Choi, Jong‐Soon; Kim, Kyung Sik

doi:10.1016/j.jprot.2011.05.010

Cited by 13 publications

(14 citation statements)

References 38 publications

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“…CO-responsive Hydrogenase and Other Membrane-bound Hydrogenases-Previous studies revealed the presence of CO-dependent hydrogenase gene clusters in T. onnurineus NA1 (8,18). In accordance with these studies, our proteomic analysis showed marked expression of hydrogenase gene clusters belonging to Hyg4_II during growth on CO (Table II and Fig.…”

Section: Analysis Of One-carbon Metabolism In T Onnurineus Na1supporting

confidence: 88%

“…This study demonstrated that T. gammatolerans utilizes various metabolic pathways during growth in nutrient-rich medium (15). However, few studies have examined changes in the protein expression profile of T. onnurineus NA1 (17,18). A previous 2-DE/MS-MS proteome analysis provided the first global view of the metabolic pathways of T. onnurineus NA1 during heterotrophic growth (17).…”

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confidence: 86%

“…A previous 2-DE/MS-MS proteome analysis provided the first global view of the metabolic pathways of T. onnurineus NA1 during heterotrophic growth (17). Using an SDS-PAGE/LC-MS/MS shotgun proteomic approach, we recently made significant progress in identifying the metabolic enzymes specific for hydrogen production under carboxydotrophic culture conditions (18). Although recent genome analyses and proteomic characterizations have revealed general genomic features and metabolic pathways, a comprehensive understanding of the overall metabolism of T. onnurineus NA1 is lacking.…”

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confidence: 99%

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Proteome Analyses of Hydrogen-producing Hyperthermophilic Archaeon Thermococcus onnurineus NA1 in Different One-carbon Substrate Culture Conditions

Moon

Kwon

Yun

et al. 2012

Molecular & Cellular Proteomics

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Thermococcus onnurineus NA1, a sulfur-reducing hyperthermophilic archaeon, is capable of H 2 -producing growth, considered to be hydrogenogenic carboxydotrophy. Utilization of formate as a sole energy source has been well studied in T. onnurineus NA1. However, whether formate can be used as its carbon source remains unknown. To obtain a global view of the metabolic characteristics of H 2 -producing growth, a quantitative proteome analysis of T. onnurineus NA1 grown on formate, CO, and starch was performed by combining one-dimensional SDS-PAGE with nano UPLC-MS E . A total of 587 proteins corresponding to 29.7% of the encoding genes were identified, and the major metabolic pathways (especially energy metabolism) were characterized at the protein level. Expression of glycolytic enzymes was common but more highly induced in starch-grown cells. In contrast, enzymes involved in key steps of the gluconeogenesis and pentose phosphate pathways were strongly up-regulated in formate-grown cells, suggesting that formate could be utilized as a carbon source by T. onnurineus NA1. In accordance with the genomic analysis, comprehensive proteomic analysis also revealed a number of hydrogenase clusters apparently associated with formate metabolism. On the other hand, CODH and CO-induced hydrogenases belonging to the Hyg4-II cluster, as well as sulfhydrogenase-I and Mbx, were prominently expressed during CO culture. Our data suggest that CO can be utilized as a sole energy source for H 2 production via an electron transport mechanism and that CO 2 produced from catabolism or CO oxidation by CODH and CO-induced hydrogenases may subsequently be assimilated into the organic carbon. Hyperthermophilic archaea can use a wide variety of carbon and energy sources. Hyperthermophiles are widely distributed in extreme habitats such as deep-sea thermal vents, hot springs, and deep oil reservoirs (1-3). So far, the most frequently studied hyperthermophiles are from the genera Thermococcus and Pyrococcus, which belong to the order Thermococcales (4). These are ecologically important hyperthermophilic archaea for understanding the physiology and metabolic activity of microbial consortia within marine hotwater ecosystems. Members of the order Thermococcales are anaerobic heterotrophs that utilize various complex substrates with elemental sulfur (S 0 ) or protons as electron acceptors (4 -6). Unlike other Thermococcales, Thermococcus strain AM4 (7) and Thermococcus onnurineus NA1 (8) are capable of lithotrophic carbon monoxide-dependent hydrogenogenic growth. These Thermococcus strains use CO as a carbon and energy source by converting it into carbon dioxide (CO 2 ). In addition, several hyperthermophilic archaea of the genus Thermococcus can grow with formate as an electron donor, producing hydrogen gas (9). T. onnurineus NA1 is a sulfur-reducing hyperthermophilic archaeon isolated from a deep sea hydrothermal vent area in the Eastern Manus Basin of Papua New Guinea (10). It is one of the more metabolically versatile hyperthermophiles in that it...

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Section: Analysis Of One-carbon Metabolism In T Onnurineus Na1supporting

confidence: 88%

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confidence: 86%

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confidence: 99%

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Proteome Analyses of Hydrogen-producing Hyperthermophilic Archaeon Thermococcus onnurineus NA1 in Different One-carbon Substrate Culture Conditions

Moon

Kwon

Yun

et al. 2012

Molecular & Cellular Proteomics

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“…Using a bacterial artificial chromosome, we genetically inserted into the chromosome of P. furiosus strain A the 16-gene operon encoding the complete carbon monoxide dehydrogenase/membrane-bound hydrogenase complex (CODH; SI Appendix, Fig. S5) of the carboxydotrophic thermophile Thermococcus onnurineus, which oxidizes CO to H 2 and CO 2 at 80°C (23,24). Remarkably, engineered P. furiosus strain A/Codh was able to use the strong reducing power of CO to produce high concentrations of the alcohol from the corresponding acid at 72°C.…”

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Single gene insertion drives bioalcohol production by a thermophilic archaeon

Basen

Schut

Nguyen

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

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Bioethanol production is achieved by only two metabolic pathways and only at moderate temperatures. Herein a fundamentally different synthetic pathway for bioalcohol production at 70°C was constructed by insertion of the gene for bacterial alcohol dehydrogenase (AdhA) into the archaeon Pyrococcus furiosus. The engineered strain converted glucose to ethanol via acetate and acetaldehyde, catalyzed by the host-encoded aldehyde ferredoxin oxidoreductase (AOR) and heterologously expressed AdhA, in an energy-conserving, redox-balanced pathway. Furthermore, the AOR/AdhA pathway also converted exogenously added aliphatic and aromatic carboxylic acids to the corresponding alcohol using glucose, pyruvate, and/or hydrogen as the source of reductant. By heterologous coexpression of a membrane-bound carbon monoxide dehydrogenase, CO was used as a reductant for converting carboxylic acids to alcohols. Redirecting the fermentative metabolism of P. furiosus through strategic insertion of foreign genes creates unprecedented opportunities for thermophilic bioalcohol production. Moreover, the AOR/AdhA pathway is a potentially game-changing strategy for syngas fermentation, especially in combination with carbon chain elongation pathways.Archaea | metabolic engineering | hyperthermophile | carbon monoxide | aldehydes

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“…T was chosen for further examination as an EV producer in the present study because the parent microorganism had already been taxonomically identified and studied by genomic and proteomic approaches (17,22,23). TEM images of negatively stained cells appeared to show that the vesicles budded from the surfaces of parent cells (Fig.…”

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Extracellular Vesicles of the Hyperthermophilic Archaeon “Thermococcus onnurineus” NA1 ^T

Choi

Kwon

Chiura

et al. 2015

Appl Environ Microbiol

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, were separately purified and counted using a qNano particle analyzer. These EVs, showing different buoyant densities, were identically spherical in shape, and their sizes varied from 80 to 210 nm in diameter, with 120-and 190-nm sizes predominant. The average size of DNA packaged into EVs was about 14 kb. The DNA of the EVs in band C was sequenced and assembled. Mapping of the T. onnurineus NA1 T EV (ToEV) DNA sequences onto the reference genome of the parent archaeon revealed that most genes of T. onnurineus NA1 T were packaged into EVs, except for an ϳ9.4-kb region from TON_0536 to TON_0544. The absence of this specific region of the genome in the EVs was confirmed from band B of the same culture and from bands B and C purified from a different batch culture. The presence of the 3=-terminal sequence and the absence of the 5=-terminal sequence of TON_0536 were repeatedly confirmed. On the basis of these results, we hypothesize that the unpackaged part of the T. onnurineus NA1 T genome might be related to the process that delivers DNA into ToEVs and/or the mechanism generating the ToEVs themselves.

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Proteome analysis of Thermococcus onnurineus NA1 reveals the expression of hydrogen gene cluster under carboxydotrophic growth

Cited by 13 publications

References 38 publications

Proteome Analyses of Hydrogen-producing Hyperthermophilic Archaeon Thermococcus onnurineus NA1 in Different One-carbon Substrate Culture Conditions

Proteome Analyses of Hydrogen-producing Hyperthermophilic Archaeon Thermococcus onnurineus NA1 in Different One-carbon Substrate Culture Conditions

Single gene insertion drives bioalcohol production by a thermophilic archaeon

Extracellular Vesicles of the Hyperthermophilic Archaeon “Thermococcus onnurineus” NA1 ^T

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Proteome analysis of Thermococcus onnurineus NA1 reveals the expression of hydrogen gene cluster under carboxydotrophic growth

Cited by 13 publications

References 38 publications

Proteome Analyses of Hydrogen-producing Hyperthermophilic Archaeon Thermococcus onnurineus NA1 in Different One-carbon Substrate Culture Conditions

Proteome Analyses of Hydrogen-producing Hyperthermophilic Archaeon Thermococcus onnurineus NA1 in Different One-carbon Substrate Culture Conditions

Single gene insertion drives bioalcohol production by a thermophilic archaeon

Extracellular Vesicles of the Hyperthermophilic Archaeon “Thermococcus onnurineus” NA1 T

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Extracellular Vesicles of the Hyperthermophilic Archaeon “Thermococcus onnurineus” NA1 ^T