• Journal of Microbiology and Biotechnology
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• 제17권6호
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• pp.897-904
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• 2007

The aim of this paper is to discuss the methodology of our investigation of the dynamics of protein degradation and the total in situ protealytic activity in meso/eutrophic, eutrophic, and hypereutrophic freshwater environments. Analysis of the kinetics and rates of enzymatic release of amino acids in water samples preserved with sodium azide allows determination of the concentrations of labile proteins $(C_{LAB})$, and their half-life time $(T_{1/2})$. Moreover, it gives more realistic information on resultant activity in situ $(V_{T1/2})$ of ecto- and extracellular proteases that are responsible for the biological degradation of these compounds. Although the results provided by the proposed method are general y well correlated with those obtained by classical procedures, they better characterize the dynamics of protein degradation processes, especially in eutrophic or hypereutrophic lakes. In these environments, processes of protein decomposition occur mainly on the particles and depend primarily on a metabolic activity of seston-attached bacteria. The method was tested in three lakes. The different degree of eutrophication of these lakes was clearly demonstrated by the measured real proteolytic pattern and confirmed by conventional trophic state determinants.

• 한국미생물학회:학술대회논문집
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• 한국미생물학회 2003년도 International Meeting of the Microbiological Society of Korea
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• pp.26-33
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• 2003

We isolated and identifed culturable Arctic bacteria that have inhabited around Korean Arctic Research Station Dasan located at Ny-Alsund, Svalbard, Norway $(79^{\circ}N,\;12^{\circ}E)$. The pure colonies were inoculated into nutrient liquid media, genomic DNA was extracted, and phylogenetic analysis was performed on the basis of 16S rDNA sequences. Out of total 227 strains, 198 strains were overlapped or unidentified, and 43 bacteria were finally identified: 31 strains belonged to Pseudomonas, 7 strains Arthrobacter, two Flavobacterium sp., an Achromobacter sp., a Pedobacter sp., and a Psychrobacter sp. For isolation of diverse bacteria, we need more effective transport method than 3M petri-films, which were used for convenience of transportation that was restricted by volume. We also need to use other culture media than nutrient media. We expect these Arctic bacteria can be used for screening to develop new antibiotics or industrial enzymes that are active at low temperature.

• 미생물학회지
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• 제42권1호
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• pp.59-61
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• 2006

먹물버섯의 하나인 Coprinellus congregatus를 대상으로 유전자의 도입을 위한 형질전환실험에서 원형질체를 생성하지 않고 분열자 (oidium)를 사용하는 방법을 확립하였다. 분열자는 20일 이상된 CKMM 한천배지에서 생성되며, 이를 밤샘배양으로 발아를 촉진시킨 상태에서 전기천공방법으로 항생물질 basta에 대한 형질전환을 수행한 결과 10-20 형질전환체/${\mu}g$ DNA의 수율로 형질전환체를 확보할 수 있었다. 이 형질전환체들은 도입된 벡터가 염색체 상에 삽입되어 유전적으로 안정된 상태를 유지하였다.

• Journal of Microbiology and Biotechnology
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• 제26권12호
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• pp.2127-2137
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• 2016

A mangrove microbial community was analyzed at the gene and protein levels using metagenomic and proteomic methods with the green macroalgae Enteromorpha prolifera as the substrate. Total DNA was sequenced on the Illumina HiSeq 2000 PE-100 platform. Two-dimensional gel electrophoresis in combination with liquid chromatography tandem mass spectrometry was used for proteomic analysis. The metagenomic data revealed that the orders Pseudomonadales, Rhizobiales, and Sphingomonadales were the most prevalent in the mangrove microbial community. By monitoring changes at the functional level, proteomic analyses detected ATP synthase and transporter proteins, which were expressed mainly by members of the phyla Proteobacteria and Bacteroidetes. Members of the phylum Proteobacteria expressed a high number of sugar transporters and demonstrated specialized and efficient digestion of various glycans. A few glycoside hydrolases were detected in members of the phylum Firmicutes, which appeared to be the main cellulose-degrading bacteria. This is the first report of multiple "omics" analysis of E. prolifera degradation. These results support the fact that key enzymes of glycoside hydrolase family were expressed in large quantities, indicating the high metabolic activity of the community.

• Journal of Microbiology and Biotechnology
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• 제24권4호
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• pp.447-452
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• 2014

To isolate novel and useful microbial enzymes from uncultured gastrointestinal microorganisms, a fecal microbial metagenomic library of the pygmy loris was constructed. The library was screened for amylolytic activity, and 8 of 50,000 recombinant clones showed amylolytic activity. Subcloning and sequence analysis of a positive clone led to the identification a novel gene (amyPL) coding for ${\alpha}$-amylase. AmyPL was expressed in Escherichia coli BL21 (DE3) and the purified AmyPL was enzymatically characterized. This study is the first to report the molecular and biochemical characterization of a novel ${\alpha}$-amylase from a gastrointestinal metagenomic library.

• 한국미생물학회:학술대회논문집
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• 한국미생물학회 2004년도 International Meeting of the Microbiological Society of Korea
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• pp.39-41
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• 2004

• 생약학회지
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• 제24권2호
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• pp.116-123
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• 1993

The genus Ganoderma is typical wood-rotting fungi and its fruiting body has been used as an important herb in oriental medicine. Recent research discovered antitumor components from Ganoderma lncidum. Various Ganoderma species are being cultivated in Korea. However, taxonomic system of the genus Ganoderma has been based mainly on the macromorphology of fruiting bodies and the ultrastructural characteristics of basidiospores. Since there are similar characteristics in Ganoderma mycelia grown on the same artificial media, it is suggested that the compatibility of the fungi by di-mon mating be used as an aid to determine the identity of species in addition to the conventional characterization. In this study, we examined physiological and genetical properties such as growth temperature, pH, compatibility and enzyme or protein patterns of laccase, esterase and cellular proteins of G. lucidum RZ, G. tsugae and Ganoderma species cultivated in Korea by electrophoresis for characterization of the isolates. We found that compatibility test and isozyme patterns of laccase and esterase of the mycelia could be used for the differentiation of the isolates. These results showed that Ganoderma species cultivated in Korea is genetically similar to G. lucidum but physiologically closer to G. tsugae than to G. lucidum.

• Journal of Microbiology and Biotechnology
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• 제15권1호
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• pp.155-160
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• 2005

Abstract A direct approach was used to retrieve active lipases from Paenibacillus polymyxa genome databases. Twelve putative lipase genes were tested using a typical lipase sequence rule built on the basis of a consensus sequence of a catalytic triad and oxyanion hole. Among them, six genes satisfied the sequence rule and had similarity (about 25%) with known bacterial lipases. To obtain the six lipase proteins, lipase genes were expressed in E. coli cells and lipolytic activities were measured by using tributyrin plate and pnitrophenyl caproate. One of them, contig 160-26, was expressed as a soluble and active form in E. coli cell. After purifying on Ni-NTA column, its detailed biochemical properties were characterized. It had a maximum hydrolytic activity at $30^{\circ}C$ and pH 7- 8, and was stable up to $40^{\circ}C$ and in the range of pH 5- 8. It most rapidly hydrolyzed pNPC$_6$ among various PNPesters. The other contigs were expressed more or less as soluble forms, although no lipolytic activities were detected. As they have many conserved regions with lipase 160-26 as well as other bacterial lipases throughout their equence, they are suggested as true lipase genes.

• 한국식품영양과학회지
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• 제39권4호
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• pp.587-594
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• 2010

다양한 기능적 특성을 가지는 단백질 가수분해물의 개발을 위하여, casein, ISP, wheat gluten, gelatin의 4종류 단백질 기질을 alcalase, bromelain, papain, neutrase, trypsin 등의 효소를 이용하여 가수분해물을 제조하였다. 각 단백질에 대한 효소 분해과정을 확인하기 위하여 pH-stat 방법을 이용하여 시간에 따른 단백질 가수분해도(DH)를 측정하였고, 단백질 종류와 효소 종류에 의한 쓴맛 정도와 단백질 가수분해물의 용해성을 검토하고자 DH 10%에서 가수분해를 종결짓고, pH 6.5에서 각각의 용해성과 쓴맛을 NSI(nitrogen soluble index) 측정과 관능검사로 비교하였다. 시간에 따른 가수분해도는 단백질에 따라 다양하게 나타났으며, Casein, ISP, wheat gluten, gelatin의 순으로 높게 나타났다. 모든 단백질에서 alcalase의 가수분해도가 가장 높았으며, neutrase, bromelain, papain의 가수분해도는 비슷한 정도를 보였다. 그러나 trypsin의 경우는 casein에서는 매우 높았지만, ISP에서는 가장 낮았다. DH 10%에서 casein은 trypsin 가수분해물이, ISP와 gluten은 brolmelain과 neutrase 가수분해물이, gelatin의 경우 사용된 모든 효소 가수분해물이 쓴맛이 약하고 용해도가 높아 좋은 기질-효소 조합으로 선택될 수 있었다. 따라서 쓴맛이 적고 용해도가 높은 단백질 가수분해물은 가수분해도의 조절과 단백질과 효소 조합의 선택, 단백질 가수분해물의 농도 조절 등으로 얻을 수 있었다.

• 한국균학회소식:학술대회논문집
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• 한국균학회 2014년도 추계학술대회 및 정기총회
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• pp.11-11
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• 2014

Fungal pathogens have huge impact on health and economic wellbeing of human by causing life-threatening mycoses in immune-compromised patients or by destroying crop plants. A key determinant of fungal pathogenesis is their ability to undergo developmental change in response to host or environmental factors. Genetic pathways that regulate such morphological transitions and adaptation are therefore extensively studied during the last few decades. Given that epigenetic as well as genetic components play pivotal roles in development of plants and mammals, contribution of microbial epigenetic counterparts to this morphogenetic process is intriguing yet nearly unappreciated question to date. To bridge this gap in our knowledge, we set out to investigate histone modifications among epigenetic mechanisms that possibly regulate fungal adaptation and processes involved in pathogenesis of a model plant pathogenic fungus, Magnaporthe oryzae. M. oryzae is a causal agent of rice blast disease, which destroys 10 to 30% of the rice crop annually. Since the rice is the staple food for more than half of human population, the disease is a major threat to global food security. In addition to the socioeconomic impact of the disease it causes, the fungus is genetically tractable and can undergo well-defined morphological transitions including asexual spore production and appressorium (a specialized infection structure) formation in vitro, making it a model to study fungal development and pathogenicity. For functional and comparative analysis of histone modifications, a web-based database (dbHiMo) was constructed to archive and analyze histone modifying enzymes from eukaryotic species whose genome sequences are available. Histone modifying enzymes were identified applying a search pipeline built upon profile hidden Markov model (HMM) to proteomes. The database incorporates 22,169 histone-modifying enzymes identified from 342 species including 214 fungal, 33 plants, and 77 metazoan species. The dbHiMo provides users with web-based personalized data browsing and analysis tools, supporting comparative and evolutionary genomics. Based on the database entries, functional analysis of genes encoding histone acetyltransferases and histone demethylases is under way. Here I provide examples of such analyses that show how histone acetylation and methylation is implicated in regulating important aspects of fungal pathogenesis. Current analysis of histone modifying enzymes will be followed by ChIP-Seq and RNA-seq experiments to pinpoint the genes that are controlled by particular histone modifications. We anticipate that our work will provide not only the significant advances in our understanding of epigenetic mechanisms operating in microbial eukaryotes but also basis to expand our perspective on regulation of development in fungal pathogens.