• KSBB Journal
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• v.20 no.5 s.94
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• pp.387-391
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• 2005

Totally 16,299 conservative genes, commonly found in 13 thermophilic and hyperthermophilic bacteria, were analyzed. All genes were belong to W 67 COGs (clusters of orthologous groups of proteins). COGs related to protein metabolism were 80 among 167 COGs. Conservative genes were not limited only thermophiles and hyperthermophiles, meaning thermal stability is independent of specific protein. However reverse gyrase was only found in all hyperthermophilic archaebacteria and eubacteria, meaning DNA stability is important in hyperthermophiles. Hyperthermophilic eubacteria and thermophilic archaebacteria had different position between phylogenetic tree of gene content and 165 rRNA gene. Thermophilic archaebacteria hyperthermophilic eubacteria and archaebacteria had similar values by the statistical analysis of distance values with 167 COGs in each organism.

• KOGO NEWS
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• v.6 no.4
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• pp.29-33
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• 2006

• Journal of Hydrogen and New Energy
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• v.22 no.5
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• pp.671-677
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• 2011

A hyperthermophilic archaeon, $Thermococcus$ $onnurineus$ NA1 was studied to investigate its fermentation characteristics using various carbon sources including formate, maltose and carbon monoxide during the anaerobic batch cultivation at $80^{\circ}C$. Formate was the best carbon source for cell growth and hydrogen production among others. In the batch culture on formate, it was found that the cell concentration increased exponentially by 12 hrs of culture, after which the cell growth and formate consumption was retarded. Hydrogen production was continued more than 24 hrs although the cell growth was ceased at 18 hrs. Hydrogen production rate was directly correlated with the cell growth and formate degradation up to 18 hrs, and the average hydrogen production yield was 1.05 mole-$H_2$/mole-formate. Cell growth and hydrogen production were optimized at the initial pH 6-7, while inhibited at the initial pH lower than 5 and higher than 9.

• Microbiology and Biotechnology Letters
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• v.43 no.3
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• pp.236-240
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• 2015

Previously we reported that the hyperthermophilic archaeon, Thermococcus onnurineus NA1 is capable of producing hydrogen (H₂) from formate, CO or starch. In this study, we describe the immobilization of T. onnurineus NA1 as an alternative means of H₂ production. Amine-coated silica particles were effective in immobilizing T. onnurineus NA1 by electrostatic interaction, showing a maximum cell adsorption capacity of 71.7 mg-dried cells per g of particle. In three cycles of repeated-batch cultivation using sodium formate as the sole energy source, immobilized cells showed reproducible H₂ production with a considerable increase in the initial production rate from 2.3 to 4.0 mmol l⁻¹ h⁻¹, mainly due to the increase in the immobilized cell concentration as the batch culture was repeated. Thus, the immobilized-cell system of T. onnurineus NA1 was demonstrated to be feasible for H₂ production. This study is the first example of immobilized cells of hyperthermophilic archaea being used for the production of H₂.

• Journal of Life Science
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• v.26 no.6
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• pp.711-720
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• 2016

To determine the degree of common genes and the phylogenetic relationships among genome-sequenced 680 prokaryotes, the similarities among 4,631 clusters of orthologous groups of protein (COGs)’ presence/ absence and gene content trees were analyzed. The number of COGs was in the range of 103–2,199 (mean 1377.1) among 680 prokaryotes. Candidatus Nasuia deltocephalinicola str. NAS-ALF, an obligate symbiont with insects, showed the minimum COG, while Pseudomonas aeruginosa PAO1, an opportunistic pathogen, represented the maximum COG. The similarities between two prokaryotes were 49.30–99.78 % (mean 72.65%). Methanocaldococcus jannaschii DSM 2661 (hyperthermophilic and autotrophic, Euryarchaeota phylum) and Mesorhizobium loti MAFF303099 (mesophilic and symbiotic, alpha-Proteobacteria class) had the minimum amount of similarities. As gene content may represent the potential for an organism to adapt to each habitat, this may represent the history of prokaryotic evolution or the range of prokaryotic habitats at present on earth. COG content trees represented the following. First, two members of Chloroflexi phylum (Dehalogenimonas lykanthroporepellens BL-DC-9 and Dehalococcoides mccartyi 195) showed a greater relationship with Archaea than other Eubacteria. Second, members of the same phylum or class in the 16S rRNA gene were separated in the COG content tree. Finally, delta- and epsilon-Proteobacteria were in different lineages with other Proteobacteria classes in neighbor-joining (NJ) and maximum likelihood (ML) trees. The results of this study would be valuable to identifying the origins of organisms, functional relationships, and useful genes.

• Ocean and Polar Research
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• v.39 no.4
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• pp.269-277
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• 2017

Medium compositions for the hyperthermophilic archaeon, Thermococcus onnurineus NA1 was statistically optimized to enhance formate-driven hydrogen ($H_2$) production by using response surface methodology. From the Plackett-Burman design-based experiment, it was confirmed that among the minor components of medium such as KCl, $MgSO_4$, $NH_4Cl$, Cystein-HCl, trace elements, Fe-EDTA and $CaCl_2$, the trace elements were screened as the only positively effective components with respect to $H_2$ production. Subsequently, the optimal concentrations of the trace elements and the major components of a medium such as NaCl, yeast extract and sodium formate were determined from the five-level central composite design (CCD)-based experiment. The resulting quadratic model predicted the maximum $H_2$ production of 46.6 mmol/L in serum bottle and it was validated experimentally using the optimal medium initially supplemented with 26.70 g/L of NaCl, 9.81 g/L of sodium formate, 3.50 g/L of yeast extract and 4.59 mL/L of trace elements. From the duplicate batch cultivations in the fermentor using the optimized medium, the a maximum $H_2$ production rate up to 71.8 mmol/L/h could be obtained, which was a 65% enhanced value compared with that obtained using the control medium, showing the high efficiency of the optimized medium.

• Korean Journal of Air-Conditioning and Refrigeration Engineering
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• v.29 no.5
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• pp.259-268
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• 2017

This paper proposes a hydrogen-based social economy derived from fuel cells capable of replacing fossil fuels and resolving global warming, It thus provides an entry for developing economically feasible social configurations to make use of bio-hydrogen production systems. Bio-hydrogen production works from the principle that microorganisms decompose water in the process of converting CO to $CO_2$, thereby producing hydrogen. This study parts from an analysis of an existing 157-ton class NA1 bio-hydrogen reactor that identifies the state of feedstock and reactor conditions. Based on this analysis, we designed a 1-ton class bio-hydrogen reactor process simulator. We carried out thermal analyses of biological heat reactions, sensible heat, and heat radiation in order to calculate the thermal load of each system element. The reactor temperature changes were determined by modeling the feed mixing tank capacity, heat exchange, and heat storage tank. An analysis was carried out to confirm the condition of the feed mixing tank, heat exchanger, heat storage tank capacity as well as the operating conditions of the system so as to maintain the target reactor temperature.

• Journal of Life Science
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• v.28 no.3
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• pp.369-375
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• 2018

Mycoplasma genitalium has 367 conserved genes and the smallest genome among mono-culturable prokaryotes. Conservative metabolic pathways were examined among M. genitalium and 14 prokaryotes, one hyperthermophilic exosymbiotic archaeon Nanoarchaeum equitans and 13 intracellular eubacteria of plants or insects, with fewer conserved genes than M. genitalium. They have 11 to 71 metabolic pathways, however complete metabolic pathways ranged from 1 to 24. Totally, metabolic pathway hole is very high due to the lack of 45.8% of the enzymes required for the whole metabolic pathways and it could be suggested that the shared metabolic pathway with the host's enzyme would work or the essential substances are host dependent. The number of genes necessary for mass transfer through the cell membrane is also very low, and it may be considered that the simple diffusion or the protein of the host will function in the cell membrane of these prokaryotes. Although the tRNA charging pathway was distributed in all 15 prokaryotes, each has 5-20 tRNA charging genes. This study would give clues to the understanding of the metabolic pathways of intracellular parasitic bacteria of plant and endosymbiotic bacteria of insects, and could provide basic data for prevention of crop damage, development of insect pests and human medicines.

• Journal of Life Science
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• v.27 no.6
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• pp.694-701
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• 2017

Mycoplasma genitalium represents the smallest genome among mono-cultivable prokaryotes. To discover and compare the orthologs (conservative genes) among M. genitalium and 14 prokaryotes that are uncultivable and have less orthologs than M. genitalium, COG (clusters of orthologous groups of protein) analyses were applied. The analyzed prokaryotes were M. genitalium, one hyperthermophilic exosymbiotic archaeon Nanoarchaeum equitans, four intracellular plant pathogenic eubacteria of Candidatus Phytoplasma genus, and nine endosymbiotic eubacteria of phloem- and xylem-feeding insects. Among 367 orthologs of M. genitalium, 284 orthologs were conservative between M. genitalium and at least one other prokaryote. All 15 prokaryotes commonly have 29 orthologs, representing the significance of proteins in life. They belong to 25 translation-related, including 22 ribosomal proteins, 3 subunits of RNA polymerase, and 1 protein-folding-related. Among the 15 prokaryotes, 40 orthologs were only found in all four Candidatus Phytoplasma. The other nine Candidatus, all endosymbionts with insects, showed only a single common COG0539 (ribosomal protein S1), representing the diversity of orthologs among them. These results might provide clues to understand conservative genes in uncultivable prokaryotes, and may be helpful in industrial areas, such as handling prokaryotes producing amino acids and antibiotics, and as precursors of organic synthesis.