• Proceedings of the Korean Society for Bioinformatics Conference
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• 2000.11a
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• pp.17-20
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• 2000

Structural genomics aims to provide a good experimental structure or computational model of every tractable protein in a complete genome. Underlying this goal is the immense value of protein structure, especially in permitting recognition of distant evolutionary relationships for proteins whose sequence analysis has failed to find any significant homolog. A considerable fraction of the genes in all sequenced genomes have no known function, and structure determination provides a direct means of revealing homology that may be used to infer their putative molecular function. The solved structures will be similarly useful for elucidating the biochemical or biophysical role of proteins that have been previously ascribed only phenotypic functions. More generally, knowledge of an increasingly complete repertoire of protein structures will aid structure prediction methods, improve understanding of protein structure, and ultimately lend insight into molecular interactions and pathways. We use computational methods to select families whose structures cannot be predicted and which are likely to be amenable to experimental characterization. Methods to be employed included modern sequence analysis and clustering algorithms. A critical component is consultation of the presage database for structural genomics, which records the community's experimental work underway and computational predictions. The protein families are ranked according to several criteria including taxonomic diversity and known functional information. Individual proteins, often homologs from hyperthermophiles, are selected from these families as targets for structure determination. The solved structures are examined for structural similarity to other proteins of known structure. Homologous proteins in sequence databases are computationally modeled, to provide a resource of protein structure models complementing the experimentally solved protein structures.

• Journal of Microbiology and Biotechnology
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• v.19 no.1
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• pp.99-107
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• 2009

Strain PUPC1 produces an antifungal protease as well as plant growth promoting enzymes such as 1-aminocyclopropane-1-carboxylate (ACC) deaminase and phosphatase. Morphological, cultural, and physiological characteristics as well as 16S rRNA gene-sequence-based phylogenetic analysis confirmed the taxonomic affiliation of PUPC1 as Chryseobacterium aquaticum. The optimum growth of PUPC1 was observed at pH 6.0 and $30^{\circ}C$, and maximum protease production was observed in medium B amended with 1% tryptone, 0.5% sucrose, and 0.005% $MnCl_2$. The protease was purified by ammonium sulfate precipitation, Sephadex G-75 gel filtration chromatography, and electroelution from preparative SDS-PAGE. The protease had a molecular mass of 18.5 kDa. The optimum pH and temperature stability of the protease were pH 5.0-10.0 and temperature $40-70^{\circ}C$. Chryseobacterium aquaticum PUPC1 and its protease showed a broad-spectrum antifungal activity against phytopathogenic fungi. Strain PUPC1 also exhibited plant growth promoting traits. The objective of the present investigation was to isolate a strain for agricultural application for plant growth promotion and biocontrol of fungal diseases.

• Journal of Species Research
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• v.5 no.2
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• pp.235-240
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• 2016

To investigate the indigenous prokaryotic species diversity in Korea, various environmental samples from diverse ecosystems were examined taxonomically. The isolated bacterial strains were identified based on 16S rRNA gene sequences, and those exhibiting at least 98.7% sequence similarity with known bacterial species but never reported in Korea were selected as unrecorded species. As an outcome of this study, 10 unrecorded bacterial species belonging to the phylum Firmicutes were discovered from various sources such as soil, tidal flat, fresh water, sea water, kimchi and gut of Fulvia mutica. The unrecorded species were assigned to 7 different genera of 5 families, namely Bacillus and Ornithinibacillus of Bacillaceae, Exiguobacterium of Exiguobacteriaceae, Brevibacillus and Paenibacillus of Paenibacillaceae, Staphylococcus of Staphylococcaceae, and Lactococcus of Streptococcaceae. The selected isolates were subjected to further taxonomic characterization including the analysis of Gram reaction, cellular and colonial morphology, biochemical activities, and phylogenetic trees. The descriptive information on the 10 unrecorded species are provided.

• The Plant Pathology Journal
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• v.38 no.4
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• pp.304-312
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• 2022

Boxwood is a representative ornamental shrub that is widely used in landscaping horticulture. After pruning, damaged leaves or stems of boxwoods are unavoidably vulnerable to infection by various plant pathogens. Several boxwood diseases caused by fungi, such as Volutella blight and Macrophoma leaf spot, have been reported worldwide including Republic of Korea. In this study, we isolated and identified fungal pathogens of boxwood diseases that occurred in Korea and characterized their morphological and taxonomic characteristics. Boxwood samples showing blight symptoms were collected in Seoul, Republic of Korea, and the putative fungal pathogens Pseudonectria buxi, P. foliicola, and Neofusicoccum buxi were successfully identified. Investigation of the morphological features of the field isolates, including mycelial growth and conidial morphology, and phylogenetic analysis of multiple DNA barcode loci revealed that there were some morphological and genetic variations among isolates, but all of the analyzed isolates were closely related to the corresponding reference strains. We also found that P. foliicola strains were more virulent than P. buxi, and the N. buxi strains isolated in this study were weak pathogens or saprophytes. The results of our study will contribute to the development of control strategies for boxwood diseases caused by fungi and accelerate research on the complex ecology of boxwood diseases.

• Korean Journal of Environmental Biology
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• v.41 no.4
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• pp.657-665
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• 2023

The root-lesion nematode Pratylenchus spp. is the most important plantparasitic nematode due to its worldwide distribution, wide host ranges, and migratory endoparasitic characteristics. One population of Pratylenchus collected from the giant pussy willow (Salix chaenomeloides Kimura) in the Andong area as part of a nematode survey in Korea was characterized morphologically and by molecular methods. The analysis of morphological measurements and morphometric characteristics, as well as DNA sequencing of the rRNA large subunit (LSU) D2/D3 expansion segments and the internal transcribed spacer (ITS) gene sequence, confirmed the identity of this population as P. hippeastri. This study is the first report of P. hippeastri associated with Salix chaenomeloides in Korea and worldwide. Further studies on distribution and pathogenicity in different P. hippeastri host crops, such as grapevines, strawberries, and apples, are necessary. The taxonomic keys to 16 Pratylenchus species in Korea are provided.

• The Korean Journal of Mycology
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• v.52 no.1
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• pp.35-54
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• 2024

With a history spanning 9,000 years, yeast has played a central role in the traditional production of fermented foods, particularly alcohol and bakery. Recent research has highlighted the versatility of yeast in various industries, including the production of bioactive compounds, bioethanol, pigments, and enzymes, and as a host for molecular biology studies. In Korea, yeast isolation has traditionally focused on traditional fermented foods such as soybean paste. However, there is a growing trend in the isolation and characterization of yeasts from natural environments such as flowers and fruits for industrial applications. In this study, we isolated and identified 12 yeasts from various natural environments in Korea, including botanical gardens and parks that are not listed on the National Species List of Korea (NSLK). These newly discovered species included Sakaguchia oryzae, Cystobasidium raffinophilum, Meira argovae, Kazachstania humilis, Meyerozyma smithsonii, Anthracocystis trispicatae, Naganishia brisbanensis, Tremella yokohamensis, Kwoniella shandongensis, Kwoniella newhampshirensis, Aureobasidium proteae, and Rhodotorula dairenensis.

• Journal of Species Research
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• v.13 no.3
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• pp.310-317
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• 2024

Various samples from island and coastal ecosystems in South Korea were investigated to discover unrecorded bacterial species. Soils from these areas, along with seawater samples, were plated on marine agar and R2A agar (containing 3% sea salt). From these samples, approximately 1,070 bacterial strains were isolated as single colonies and identified using 16S rRNA gene sequences. A total of 20 strains, which exhibited at least 98.7% similarity in their 16S rRNA gene sequences to those of validly published bacterial species not yet reported in Korea, were identified as unrecorded bacterial species. These strains belonged to three phyla, six classes, 10 orders, 14 families, and 16 genera. These were assigned as follows: Thioclava, Breoghania, Acidovorax, Erythrobacter, Paracoccus, Jiella, Aurantimonas, and Qipengyuania within the class Alphaproteobacteria; Pseudomonas, Cobetia, and Rheinheimera within the class Gammaproteobacteria; Aequorivita, Leeuwenhoekiella, and Polaribacter within the class Flavobacteriia; Algoriphagus within the class Cytophagia; and Microbacterium within the class Actinobacteria. The unreported species underwent further taxonomic characterization, which included assessments of Gram reaction, colony and cell morphology, biochemical and phylogenetic characteristics.

• The Korean Journal of Mycology
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• v.43 no.3
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• pp.149-157
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• 2015

We examined taxonomic characteristics and safety of eight Nuruk molds that are widely used for making soybean paste, soy sauce and alcoholic beverages in Korea. HK1 from Hakyeong Fermentation Co., SW101 from Suwon Fermentation Co., CF1001, CF1002, CF1003 from Chungmoo Fermaentation Co. and KACC 93210 are yellow-Nuruk molds, and SW201 from Suwon Fermentation Co. and CF1005 from Chungmoo Fermentation Co. are white-Nuruk molds. Six strains of yellow-Nuruk molds were identified as Aspergillus oryzae. HK1, SW101, CF1001 and CF1003 of yellow-Nuruk molds have middle length of stipes ($711{\sim}1,121{\mu}m$), and CF1003 (for sake) produced less conidia and more hyphae than HK1, SW101 and CF1001 (for soybean paste). CF 1002 used for soy sauce has shorter stipes ($543{\mu}m$) and is clustered into IBLB-group based on omtA gene analysis although the other yellow-Nuruk molds are clustered into ICAo group. KACC 93210 isolated from traditional Korean Meju has very short stipes (average $270{\mu}m$), and showed velvety colonies although the others showed floccose colonies. The strain has different DNA sequences of omtA gene from other strains in NCBI GenBank as well as strains used in Korea, suggesting that it is unique from other strains published. SW201 and CF1005 of white-Nuruk molds were identified as Aspergillus luchuensis or A. luchuensis mut. Kawachii that is known as safe, non-toxigenic fungus. The six strains of yellow-Nuruk molds did not produce mycotoxins including aflatoxin, cyclopiazonic acid, and sterigmatocystin. Therefore, eight strains of Nuruk molds used for making soy sauce, soybean paste and alcoholic beverages in Korea were proved to be safe in this study.

• Microbiology and Biotechnology Letters
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• v.18 no.5
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• pp.511-516
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• 1990

A high-alcohol producing yeast strain had sugar and alcohol tolerance was isolated from soil and identified as Saccharomyces cerevisiae Dl according to the Lodder's yeast taxonomic studies. On investigation of the characteristics of the strain, it could grow in 60% glucose, within 15% ethanol and in the YPD medium containing 2.0 mM copper. It had 39.1% the inhibition rate of fermentation efficiency and 8% viability after 2 days in the YPD medium containing 15% ethanol. Its optimum initial pH, growth temperature, initial glucose concentration for the production of alcohol showed pH 4.5, $30^{\circ}C$, and 30%, respectively. Saa:hwomyce8 mvisiae Dl produced 14.0% (wlv) alcohol when incubated at $30^{\circ}C$, with orbital shaking 150 rpm for 72 h in a medium (pH 4.5) containing 30% (wfv) glucose.

• Journal of Environmental Science International
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• v.8 no.4
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• pp.451-456
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• 1999

Microorganisms utilizing petroleum as substrate were screened from the seawater in Pusan coastal area. Among them, fifty strains utilized bunker-A oil as a sole carbon and energy source. Five of these fifty strains were selected to experiment this study. According to the taxonomic characteristics of its morphological, cultural and biochemical properties, the selected stains were named Pseudomonas sp. EL-12, Flavobacterium sp. EL-15, Acinetobacter sp. EL-18, Enterobacter sp. EL-27 and Micrococcus sp. EL-43, respectively. The optimal medium compositions and cultural conditions for assimilation of bunker-A oil by the selected strains were 1.5-2% bunker-A oil, 0.1% $NH_4NO_3$, 1-1.5% $MgSO_4$.$7H_2O$, 0.05-0.15% KCl, 0.1-0.15% $CaCl_2$.$2H_2O$, 2.5-3.5% NaCl, initial pH 8-9, temperature 3$0^{\circ}C$ and aeration, respectively. The utilization and degradation characteristics on the various hydrocarbons by the selected stains were showed that bunker oil, n-alkane and branched alkane compounds were highly activity than cyclic alkane and aromatic hydrocarbon compounds.