• Journal of Microbiology and Biotechnology
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• v.26 no.5
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• pp.867-875
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• 2016

Archaea substantially contribute to global geochemical cycling and energy cycling and are impacted by land-use change. However, the response of archaeal communities to a change from upland field to paddy field has been poorly characterized. Here, soil samples were collected at two depths (0-20 cm and 20-40 cm) from one upland field and six paddy fields that were established on former upland fields at different times (1, 5, 10, 20, 30, and 40 years before the study). Barcoded pyrosequencing was employed to assess the archaeal communities from the samples at taxonomic resolutions from phylum to genus levels. The total archaeal operational taxonomic unit (OTU) richness showed a significant positive correlation with the land-use change duration. Two phyla, Euryarchaeota and Crenarchaeota, were recorded throughout the study. Both the relative abundance and OTU richness of Euryarchaeota increased at both depths but increased more steadily at the subsurface rather than at the surface. However, these data of Crenarchaeota were the opposite. Additionally, the archaeal composition exhibited a significant relationship with C/N ratios, total phosphorus, soil pH, Olsen phosphorus, and the land-use change duration at several taxonomic resolutions. Our results emphasize that after a change from upland fields to paddy fields, the archaeal diversity and composition changed, and the duration is an important factor in addition to the soil chemical properties.

• The Journal of the Korea Contents Association
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• v.20 no.8
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• pp.674-684
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• 2020

To investigate the differences of bacterial- and archaeal communities depending on kind of wastewater (municipal/livestock) and on treating conditions of basins, sludges were sampled from 10 basins of 3 municipal wastewater treatment plants(WWTP) with A2O and a activated sludge sample from a livestock WWTP. The metagenomic DNAs of the sludge samples were extracted and amplified with primers, 27F/518R for bacteria and Arch519F/A958R for archaea, and pyrosequenced with Roche 454 GS-FLX Titanium. As results, the bacterial communities in basins of municipal WWTPs were quite different from those of livestock WWTP, but within the same municipal WWTP their community structures were similar to each other regardless of different environmental conditions such as O₂. And their archaeal communities resulted from anaerobic·anoxic basins were clustered only within communities originated from the same WWTP. Furthermore Seo-bu WWTP with high bacterial diversity and species richness performed better N/P-removal compared to the orther WWTPs.

• Journal of Microbiology and Biotechnology
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• v.16 no.11
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• pp.1826-1831
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• 2006

A novel hyperthermophilic, anaerobic, heterotrophic archaeon, designated strain $NA1^T$, was isolated from a deep-sea hydrothermal vent area (depth, 1,650 m) within the Papua New Guinea-Australia-Canada-Manus (PACMANUS) field. Cells of this strain were motile by means of polar flagella, coccoid-shaped with a diameter of approximately $0.5-1.0{\mu}m$, and occurred as single cells. Optimal temperature, pH, and NaCl concentration for growth were $80^{\circ}C$, 8.5, and 3.5%, respectively. The new isolate was an obligate heterotroph that utilized yeast extract, beef extract, tryptone, peptone, casein, and starch as carbon and energy sources. Elemental sulfur was required for growth and was reduced to hydrogen sulfide. The G+C content of the genomic DNA was 52.0 mol%. Phylogenetic analysis of the 16S rRNA gene indicated that strain $NA1^T$ belongs to the genus Thermococcus, and the organism is most closely related to T. gorgonarius, T. peptonophilus, and T. celer; however, no significant homology was observed among species by DNA-DNA hybridization. Strain $NA1^T$ therefore represents a novel species for which the name Thermococcus onnurineus sp. novo is proposed. The type strain is $NA1^T$ (=KCTC 10859, =JCM 13517).

• Journal of Microbiology and Biotechnology
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• v.17 no.3
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• pp.454-460
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• 2007

Enzymatic properties and substrate specificity of recombinant $\beta-glycosidases$ from a hyperthermophilic archaeon, Sulfolobus shibatae (rSSG), were analyzed. rSSG showed its optimum temperature and pH at $95^{\circ}C$ and pH 5.0, respectively. Thermal inactivation of rSSG showed that its half-life of enzymatic activity at $75^{\circ}C$ was 15 h whereas it drastically decreased to 3.9 min at $95^{\circ}C$. The addition of 10 mM of $MnCl_2$ enhanced the hydrolysis activity of rSSG up to 23% whereas most metal ions did not show any considerable effect. Dithiothreitol (DTT) and 2-mercaptoethanol exhibited significant influence on the increase of the hydrolysis activity of rSSG rSSG apparently preferred laminaribiose $(\beta1\rightarrow3Glc)$, followed by sophorose $(\beta1\rightarrow2Glc)$, gentiobiose $(\beta1\rightarrow6Glc)$, and cellobiose $(\beta1\rightarrow4Glc)$. Various. intermolecular transfer products were formed by rSSG in the lactose reaction, indicating that rSSG prefers lactose as a good acceptor as well as a donor. The strong intermolecular transglycosylation activity of rSSG can be applied in making functional oligosaccharides.

• Journal of Microbiology and Biotechnology
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• v.23 no.8
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• pp.1060-1069
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• 2013

Genome organization near cyclomaltodextrinases (CDases) was analyzed and compared for four different hyperthermophilic archaea: Thermococcus, Pyrococcus, Staphylothermus, and Thermofilum. A gene (CL1_0884) encoding a putative CDase from Thermococcus sp. CL1 (tccd) was cloned and expressed in Escherichia coli. TcCD was confirmed to be highly thermostable, with optimal activity at $85^{\circ}C$. The melting temperature of TcCD was determined to be $93^{\circ}C$ by both differential scanning calorimetry and differential scanning fluorimetry. A size-exclusion chromatography experiment showed that TcCD exists as a monomer. TcCD preferentially hydrolyzed ${\alpha}$-cyclodextrin (${\alpha}$-CD), and at the initial stage catalyzed a ring-opening reaction by cleaving one ${\alpha}$-1,4-glycosidic linkage of the CD ring to produce the corresponding single maltooligosaccharide. Furthermore, TcCD could hydrolyze branched CDs (G1-${\alpha}$-CD, G1-${\beta}$-CD, and G2-${\beta}$-CD) to yield significant amounts (45%, 40%, and 46%) of isomaltooligosaccharides (panose and $6^2$-${\alpha}$-maltosylmaltose) in addition to glucose and maltose. This enzyme is one of the most thermostable maltogenic amylases reported, and might be of potential value in the production of isomaltooligosaccharides in the food industry.

• Journal of Microbiology and Biotechnology
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• v.25 no.2
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• pp.196-205
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• 2015

A Sulfolobus-E. coli shuttle vector for an efficient expression of the target gene in S. acidocaldarius strain was constructed. The plasmid-based vector pSM21 and its derivative pSM21N were generated based on the pUC18 and Sulfolobus cryptic plasmid pRN1. They carried the S. solfataricus P2 pyrEF gene for the selection marker, a multiple cloning site (MCS) with C-terminal histidine tag, and a constitutive promoter of the S. acidocaldarius gdhA gene for strong expression of the target gene, as well as the pBR322 origin and ampicillin-resistant gene for E. coli propagation. The advantage of pSM21 over other Sulfolobus shuttle vectors is that it contains a MCS and a histidine tag for the simple and easy cloning of a target gene as well as one-step purification by histidine affinity chromatography. For successful expression of the foreign genes, two genes from archaeal origins (PH0193 and Ta0298) were cloned into pSM21N and the functional expression was examined by enzyme activity assay. The recombinant PH0193 was successfully expressed under the control of the gdhA promoter and purified from the cultures by His-tag affinity chromatography. The yield was approximately 1 mg of protein per liter of cultures. The enzyme activity measurements of PH0913 and Ta0298 revealed that both proteins were expressed as an active form in S. acidocaldarius. These results indicate that the pSM21N shuttle vector can be used for the functional expression of foreign archaeal genes that form insoluble aggregates in the E. coli system.

• Bulletin of the Korean Chemical Society
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• v.28 no.12
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• pp.2261-2265
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• 2007

Prevention of thermal aggregation of the denatured protein by the group II chaperonin from the aerobic hyperthermophilic crenarchaeon Aeropyrum pernix K1 (ApcpnA) has been investigated. ApcpnA exists as a homo-oligomer in a ring structure, which protects thermal aggregation of the chemically denatured bovine rhodanese at 50 oC. ApcpnA alone is not sufficient for chaperonin activity, but the chaperonin activity is greatly enhanced in the presence of manganese ion and ATP. Compared to the mesophilic chaperonin GroEL/GroES, ApcpnA is more activated at a higher temperature and protects the aggregation-prone unfolded state of the denatured rhodanese from thermal aggregation. Binding of ATP is sufficient for ApcpnA to perform the chaperonin function in vitro, but hydrolysis of ATP is not necessarily required. We propose that utilization of Mn2+ and adenosine nucleotide regardless of ATP hydrolysis may be one of peculiar properties of archaeal chaperonins.

• Journal of Life Science
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• v.18 no.11
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• pp.1617-1624
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• 2008

Chitin and chitosan, which is deacetylated form of chitin, are one of the most abundant biomass on the earth. They showed various biological activities including antimicrobial activity, heavy metal chelating, immune system activation, and have very diverse applications in food, pharmaceutical, medicinal, and environmental industry. There have been reported many chitin/chitosan-hydrolyzing enzymes, their structures and genes from three domains, archaea, bacteria, and eukarya. Carbohydrate hydrolyzing enzymes are classified in CAZy (Carbohydrate Active Enzymes) database according to their amino acid sequence similarity. Interestingly, chitinases and chitosanases are classified in various glycosyl hydrolase(GH) families, GH2, GH5, GH7, GH8, GH18, GH19, GH20, GH46, GH48, GH73, GH75, GH80, GH84, and GH85. Here, we review characteristics and structures of chitin/chitosan hydrolyzing enzymes according to glycosyl hydrolase families in order to provide information about gene mining.

• BMB Reports
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• v.44 no.11
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• pp.719-724
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• 2011

The $Sec61{\alpha}$ subunit is the core subunit of the protein conducting channel which is required for protein translocation in eukaryotes and prokaryotes. In this study, we cloned a $Sec61{\alpha}$ subunit from Penicillium ochrochloron ($PoSec61{\alpha}$). Sequence and 3D structural model analysis showed that $PoSec61{\alpha}$ conserved the typical characteristics of eukaryotic and prokaryotic $Sec61{\alpha}$ subunit homologues. The pore ring known as the constriction point of the channel is formed by seven hydrophobic amino acids. Two methionine residues from transmembrane ${\alpha}$-helice 7 (TM7) contribute to the pore ring formation and projected notably to the pore area and narrowed the pore compared with the superposed residues at the corresponding positions in the crystal structures or the 3D models of the $Sec61{\alpha}$ subunit homologues in archaea or other eukaryotes, respectively. Results reported herein indicate that the pore ring residues differ among $Sec61{\alpha}$ subunit homologues and two hydrophobic residues in the TM7 contribute to the pore ring formation.

• Ocean and Polar Research
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• v.27 no.2
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• pp.205-214
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• 2005

From ancient Antarctic glacier ice, we extracted total genomic DNA that was suitable for prokaryotic 16S rDNA gene cloning and sequencing, and bacterial artificial chromosome (BAC) library and end-sequencing. The ice samples were from the Dry Valley region. Age dating by $^{40}Ar/^{39}Ar$ analysis on the volcanic ashes deposited in situ indicated the ice samples are minimum 100,000-300,000 yr (sample DLE) and 8 million years (sample EME) old. Further assay proved the ice survived freeze-thaw cycles or other re-working processes. EME, which was from a small lobe of the basal Taylor glacier, is the oldest known ice on Earth. Microorganisms, preserved frozen in glacier ice and isolated from the rest of the world over a geological time scale, can provide valuable data or insight for the diversity, distribution, survival strategy, and evolutionary relationships to the extant relatives. From the 16S gene cloning study, we detected no PCR amplicons with Archaea-specific primers, however we found many phylotypes belonging to Bacteria divisions, such as Actinobacteria, Acidobacteria, Proteobacteria $({\alpha},\;{\beta},\;and\;{\gamma})$, Firmicutes, and Cytophaga-Flavobacterium-Bacteroid$. BAC cloning and sequencing revealed protein codings highly identical to phenylacetic acid degradation protein paaA, chromosome segregation ATPases, or cold shock protein B of present day bacteria. Throughput sequencing of the BAC clones is underway. Viable and culturable cells were recovered from the DLE sample, and characterized by their 16S rDNA sequences. Further investigation on the survivorship and functional genes from the past should help unveil the evolution of life on Earth, or elsewhere, if any.