• Microbiology and Biotechnology Letters
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• v.44 no.2
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• pp.156-162
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• 2016

In this study, we isolated a new agar-degrading marine bacterium and characterized its agarase. An agardegrading marine bacterium SH-1 was isolated from seawater, collected from the seashore of Namhae in Gyeongnam province, Korea, and cultured in marine agar 2216 media. It was identified as Maribacter. sp. SH-1 by phylogenetic analyses, based on 16S rRNA gene sequence. The extracellular agarase was extracted from culture media of Maribacter sp. SH-1 and characterized. Its relative activities were 56, 62, 94, 100, and 8% at 20, 30, 40, 50, and 60℃, respectively, whereas 15, 100, 60, and 21% relative activities were observed at pH 5, 6, 7, and 8, respectively. Its extracellular agarase exhibited maximum activity (231 units/l) at pH 6.0 and 50℃, in 20 mM Tris-HCl buffer. Therefore, this agarase would be applicable as it showed the maximum activity at the temperature at which the agar is in a sol state. Furthermore, the agarase activities remained over 90% at 20, 30, and 40℃ after 0.5 h exposure at these temperatures. Thin layer chromatography analysis suggested that Maribacter sp. SH-1 produces extracellular β-agarase, as it hydrolyzes agarose to produce neoagarooligosaccharides, such as neoagarohexaose (34.8%), neoagarotetraose (52.2%), and neoagarobiose (13.0%). Maribacter sp. SH-1 and its β-agarase would be useful for the production of neoagarooligosaccharides, which shows functional properties, like skin moisturizing, skin whitening, inhibition of bacterial growth, and delay in starch degradation.

• Journal of Plant Biotechnology
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• v.35 no.4
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• pp.317-327
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• 2008

Phytocystatins, which are inhibitors of plant cysteine peptidases, are involved in the regulation of protein turnover and in the defense against insect pests and pathogens. Extensive searches in the Brassica rapa genome allowed the prediction of at least eight different phytocystatin genes on seven chromosomes in the B. rapa genome. Structure comparisons based on alignments of the all BrCYS ($\underline{B}$. $\underline{r}apa$ $phyto{\underline{cys}}tatin$) proteins using the CLUSTALW program revealed conservation of the three consensus motifs known to interact with the active site of cysteine peptidases. According to the phylogenetic analysis based on the deduced amino acid sequences, the eight BrCYS proteins were divided into several clusters related to the orthologous phytocystatin. The predicted three-dimensional structure models of the eight BrCYS proteins demonstrate that all of these proteins are similar to the reported crystal structure of oryzacystatin-I (OC-I). Digital northern and RT-PCR analyses indicated that the eight BrCYS genes exhibit different expression patterns in B. rapa tissues and respond differently to abiotic stimuli. The differences in gene structure and expression between the eight BrCYS genes suggest that these proteins may play diverse physiological roles in B. rapa and may interact with cysteine peptidases through different mechanisms.

• Journal of Life Science
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• v.28 no.6
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• pp.639-647
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• 2018

A new heat shock protein 70 was identified in red-spotted grouper (Epinephelus akaara) based on an expression analysis. The cDNA of red-spotted grouper Hsp70 (designated RgHsp70) was cloned by the rapid amplification of cDNA ends (RACE) techniques. The full-length of RgHsp70 cDNA was 2,152 bp, consisting of a 5'-terminal untranslated region (UTR) of 105 bp, a 3'-terminal UTR of 274 bp, and an open reading frame (ORF) of 1,773 bp that encode a polypeptide of 590 amino acids with a theoretical molecular weight of 64.9 kDa and an estimated isoelectric point of 5.2. Multiple alignment and phylogenetic analyses revealed that the RgHsp70 gene shares a high similarity with other Hsp70 fish genes. RgHsp70 contained all three classical Hsp70 family signatures. The results indicated the RgHsp70 is a member of the heat shock protein 70 family. RgHsp70 mRNA was predominately expressed in the liver, with reduced expression noted in the head-kidney tissues. The expression analysis of different water temperatures (21, 18, 15 and $12^{\circ}C$) for sampled livers revealed that expression gradually increased at $12^{\circ}C$ compared to $21^{\circ}C$. In this study, the effects of water temperature lowering on the physiological conditions were investigated, and the results revealed that novel RgHsp70 may be an important molecule involved in stress responses.

• The Plant Pathology Journal
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• v.33 no.5
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• pp.478-487
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• 2017

Soybean is the most important legume crop in the world. Several diseases in soybean lead to serious yield losses in major soybean-producing countries. Moreover, soybean can be infected by diverse viruses. Recently, we carried out a large-scale screening to identify viruses infecting soybean using available soybean transcriptome data. Of the screened transcriptomes, a soybean transcriptome for soybean seed development analysis contains several virus-associated sequences. In this study, we identified five viruses, including soybean mosaic virus (SMV), infecting soybean by de novo transcriptome assembly followed by blast search. We assembled a nearly complete consensus genome sequence of SMV China using transcriptome data. Based on phylogenetic analysis, the consensus genome sequence of SMV China was closely related to SMV isolates from South Korea. We examined single nucleotide variations (SNVs) for SMVs in the soybean seed transcriptome revealing 780 SNVs, which were evenly distributed on the SMV genome. Four SNVs, C-U, U-C, A-G, and G-A, were frequently identified. This result demonstrated the quasispecies variation of the SMV genome. Taken together, this study carried out bioinformatics analyses to identify viruses using soybean transcriptome data. In addition, we demonstrated the application of soybean transcriptome data for virus genome assembly and SNV analysis.

• Korean Journal of Microbiology
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• v.43 no.1
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• pp.47-53
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• 2007

The DY1 strain of Gram-positive, rod-shaped bacteria was isolated from the soil sample collected from Daeam mountain, Korea. The culture filtrate of DY1 strain showed a broad spectrum of antimicrobial activity on various pathogenic and food poisoning enteric bacterial species tested in vitro. It showed significant growth-inhibitory effect on Salmonella enterica sp., Shigella sp., pathogenic Escherichia coli, Vibrio cholerae, Vibrio parahemolyticus, and Yersinia enterocolitica. For the identification of the DY1 strain, morphological, biochemical and molecular phylogenetic approaches were performed. The DY1 strain was found to be a member of the genus Paenibacillus on the basis of morphological and biochemical analyses. The 16S rDNA of DY1 showed the highest pairwise identity with Paenibacillus polymyxa with 99.79% (1,413 bp/1,416 bp). The antimicrobial entity from DY1 looked different from preciously reported ones and seems to have a great potential to be further studied as a candidate of new antibiotics to control multi-drug resistant pathogens.

• Research in Plant Disease
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• v.21 no.4
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• pp.337-340
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• 2015

During July to November 2014, severe rust infection was consistently found on Peucedanum japonicum growing farm in Yeosu, Korea. The rust was observed mainly on lower leaf surfaces. Symptoms of typical plants included yellow-orange rust pustules were observed on the petiole and leaf surface with small yellowish to chlorotic lesions on the upper surface. No symptom was observed on flowers. Uredinia were occurred amphigenous on leaf surface, and occasionally caulicolous, scattered or loosely aggregate, rounded to oblong, 0.4 to 4 mm in diameter, covered by epidermis, then naked, surrounded by ruptured epidermis, pulverulent, and brown. Urediniospores were ovate-ellipsoid, ellipsoid or subglobose, light brown, 20 to $45{\times}15$ to $35{\mu}m$, walls 2 to $4{\mu}m$ thick. The resulting sequences were deposited in GenBank with accession No. KT778808, KT778809, and KT778810, respectively. Since this was the first accession of 28S sequence Puccinia jogashimensis, there was no exact match in GenBank nucleotide database. On the basis of the morphological characteristics and phylogenetic analyses of 28S rDNA, the fungus was identified as P. jogashimensis. To our knowledge, this is the first confirmed report on the occurrence of P. jogashimensis on P. japonicum in Korea.

• Research in Plant Disease
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• v.21 no.1
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• pp.27-31
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• 2015

In April 2014, Fusarium wilt was found on kohlrabi seedlings in Iksan, Korea. Symptoms included wilting of foliage, drying and withering of older leaves, and stunting of the plants. The infected plants eventually died during growth. Colonies on potato dextrose agar were pinkish white, and felted with cottony and aerial mycelium. Macroconidia were falcate to almost straight, thin walled and usually 3-septate. Microconidia were usually formed abundantly in false-heads on short monophialides on the hyphae and were hyaline, smooth, oval to ellipsoidal, aseptate or medianly 1-septate, very occasionally 2-septate, slightly constricted at the septa, $4-11{\times}2.5-5{\mu}m$. On the basis of the morphological characteristics and phylogenetic analyses of molecular markers (internal transcribed spacer rDNA and translation elongation factor $1{\alpha}$), the fungus was identified as Fusarium oxysporum. Pathogenicity of a representative isolate was proved by artificial inoculation, fulfilling Koch's postulates. To our knowledge, this is the first report on the occurrence of Fusarium oxysporum on kohlrabi in Korea.

• Research in Plant Disease
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• v.21 no.1
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• pp.36-39
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• 2015

In June 2012 and 2013, a destructive stem rot symptoms of Ligularia fischeri occurred sporadically in Hoengseong-gun and Pyeongchang-gun Gangwon-do, Korea. The typical symptom included water-soaking on the main stem, rotting, wilting and blighting, which eventually leads to death of the plant. White mycelial mats were spread over lesions and brown sclerotia were formed on stems and near soil surface. The sclerotia were white to brown, spherical or irregular, 1-3 mm in size on potato dextrose agar (PDA), The optimum temperature range of hyphal growth was $25-30^{\circ}C$ and the hyphal diameter was $4-10{\mu}m$. The typical clamp connections were observed in the hyphae of the fungus grown on PDA. The resulting sequence of 695 bp was deposited in GenBank. A BLAST search revealed that sequences of the this isolates showed >99% identity with those of Sclerotium rolfsii. On the basis of the morphological characteristics and phylogenetic analyses of molecular markers ITS rDNA, the fungi were identified as S. rolfsii. A pathogenicity test was carried out to fulfill Koch's postulates. To our knowledge, this is the first report of S. rolfsii on Ligularia fischeri in Korea.

• Journal of Microbiology and Biotechnology
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• v.25 no.9
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• pp.1467-1475
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• 2015

The use of microbial extracts containing plant hormones is a promising technique to improve crop growth. Little is known about the effect of bacterial cell-free extracts on plant growth promotion. This study, based on phytohormonal analyses, aimed at exploring the potential mechanisms by which Enterococcus faecium LKE12 enhances plant growth in oriental melon. A bacterial strain, LKE12, was isolated from soil, and further identified as E. faecium by 16S rDNA sequencing and phylogenetic analysis. The plant growth-promoting ability of an LKE12 bacterial culture was tested in a gibberellin (GA)-deficient rice dwarf mutant (waito-C) and a normal GA biosynthesis rice cultivar (Hwayongbyeo). E. faecium LKE12 significantly improved the length and biomass of rice shoots in both normal and dwarf cultivars through the secretion of an array of gibberellins (GA₁, GA₃, GA₇, GA₈, GA₉, GA₁₂, GA₁₉, GA₂₀, GA₂₄, and GA₅₃), as well as indole-3-acetic acid (IAA). To the best of our knowledge, this is the first study indicating that E. faecium can produce GAs. Increases in shoot and root lengths, plant fresh weight, and chlorophyll content promoted by E. faecium LKE12 and its cell-free extract inoculated in oriental melon plants revealed a favorable interaction of E. faecium LKE12 with plants. Higher plant growth rates and nutrient contents of magnesium, calcium, sodium, iron, manganese, silicon, zinc, and nitrogen were found in cell-free extract-treated plants than in control plants. The results of the current study suggest that E. faecium LKE12 promotes plant growth by producing GAs and IAA; interestingly, the exogenous application of its cell-free culture extract can be a potential strategy to accelerate plant growth.

• Journal of Microbiology and Biotechnology
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• v.30 no.4
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• pp.526-532
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• 2020

A bacterial strain, designated B301^T and isolated from raw chicken meat obtained from a local market in Korea, was characterized and identified using a polyphasic taxonomic approach. Cells were gram-negative, non-motile, obligate-aerobic coccobacilli that were catalase-positive and oxidase-negative. The optimum growth conditions were 30℃, pH 7.0, and 0% NaCl in tryptic soy broth. Colonies were round, convex, smooth, and cream-colored on tryptic soy agar. Strain B301^T has a genome size of 3,102,684 bp, with 2,840 protein-coding genes and 102 RNA genes. The 16S rRNA gene analysis revealed that strain B301^T belongs to the genus Acinetobacter and shares highest sequence similarity (97.12%) with A. celticus ANC 4603^T and A. sichuanensis WCHAc060041^T. The average nucleotide identity and digital DNA-DNA hybridization values for closely related species were below the cutoff values for species delineation (95-96% and 70%, respectively). The DNA G+C content of strain B301^T was 37.0%. The major respiratory quinone was Q-9, and the cellular fatty acids were primarily summed feature 3 (C_16:1 ω6c/C_16:1 ω7c), C_16:0, and C_18:1 ω9c. The major polar lipids were phosphatidylethanolamine, diphosphatidyl-glycerol, phosphatidylglycerol, and phosphatidyl-serine. The antimicrobial resistance profile of strain B301^T revealed the absence of antibiotic-resistance genes. Susceptibility to a wide range of antimicrobials, including imipenem, minocycline, ampicillin, and tetracycline, was also observed. The results of the phenotypic, chemotaxonomic, and phylogenetic analyses indicate that strain B301^T represents a novel species of the genus Acinetobacter, for which the name Acinetobacter pullorum sp. nov. is proposed. The type strain is B301^T (=KACC 21653^T = JCM 33942^T).