• Journal of Microbiology and Biotechnology
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• v.31 no.1
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• pp.8-15
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• 2021

More and more available fungal genome sequence data reveal a large amount of secondary metabolite (SM) biosynthetic 'dark matter' to be discovered. Heterogeneous expression is one of the most effective approaches to exploit these novel natural products, but it is limited by having to clone entire biosynthetic gene clusters (BGCs) without errors. So far, few effective technologies have been developed to manipulate the specific large DNA fragments in filamentous fungi. Here, we developed a fungal BGC-capturing system based on CRISPR/Cas9 cleavage in vitro. In our system, Cas9 protein was purified and CRISPR guide sequences in combination with in vivo yeast assembly were rationally designed. Using targeted cleavages of plasmid DNAs with linear (8.5 kb) or circular (8.5 kb and 28 kb) states, we were able to cleave the plasmids precisely, demonstrating the high efficiency of this system. Furthermore, we successfully captured the entire Nrc gene cluster from the genomic DNA of Neosartorya fischeri. Our results provide an easy and efficient approach to manipulate fungal genomic DNA based on the in vitro application of Cas9 endonuclease. Our methodology will lay a foundation for capturing entire groups of BGCs in filamentous fungi and accelerate fungal SMs mining.

• Asian-Australasian Journal of Animal Sciences
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• v.24 no.1
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• pp.65-72
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• 2011

Twenty-four Holstein dairy cows were used to evaluate the single and combined effects of different levels of crude protein (CP) and monensin treatment during early lactation on blood metabolites, milk yield and digestion of dairy cows. The experiment was designed as a completely randomized block with a $3{\times}2$ factorial arrangement of treatments. The factors were three concentrations of CP supplement (19.5, 21.4, and 23.4% of dry matter) and two levels of monensin (0 and 350 mg per cow per day). The experiment consisted of three phases and each phase was 3 wk in length. Monensin did not affect milk yield, lactose, solids-non-fat (SNF), blood glucose, triglyceride and DMI, but increased blood cholesterol, blood urea nitrogen (BUN), insulin and reduced blood ${\beta}$-hydroxybutyrate (BHBA), milk fat and protein percentage. Monensin premix significantly decreased rumen ammonia, but rumen pH and microbial protein synthesis were not affected by monensin treatment. Increasing dietary CP improved milk and protein production, but did not alter the other components of milk. Digestibility of NDF, ADF, CP were improved by increasing dietary CP. Increasing dietary CP from 19.5 to 21.4% had no significant effect on ruminal ammonia, but increasing CP to 23.4% significantly increased ruminal ammonia. There was a linear relationship between level of crude protein in the diet and volume of urine excretion. Microbial protein synthesis was affected by increasing CP level; in this way maximum protein synthesis was achieved at 23.4% CP.

• Journal of Ginseng Research
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• v.42 no.2
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• pp.199-207
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• 2018

Background: Ginseng is a well-known traditional Chinese medicine that has been widely used in a range of therapeutic and healthcare applications in East Asian countries. Microbial transformation is regarded as an effective and useful technology in modification of nature products for finding new chemical derivatives with potent bioactivities. In this study, three minor derivatives of ginsenoside compound K were isolated and the inducing effects in the Wingless-type MMTV integration site (Wnt) signaling pathway were also investigated. Methods: New compounds were purified from scale-up fermentation of ginsenoside Rb1 by Paecilomyces bainier sp. 229 through repeated silica gel column chromatography and high pressure liquid chromatography. Their structures were determined based on spectral data and X-ray diffraction. The inductive activities of these compounds on the Wnt signaling pathway were conducted on MC3T3-E1 cells by quantitative real-time polymerase chain reaction analysis. Results: The structures of a known 3-keto derivative and two new dehydrogenated metabolites were elucidated. The crystal structure of the 3-keto derivative was reported for the first time and its conformation was compared with that of ginsenoside compound K. The inductive effects of these compounds on osteogenic differentiation by activating the Wnt/b-catenin signaling pathway were explained for the first time. Conclusion: This study may provide a new insight into the metabolic pathway of ginsenoside by microbial transformation. In addition, the results might provide a reasonable explanation for the activity of ginseng in treating osteoporosis and supply good monomer ginsenoside resources for nutraceutical or pharmaceutical development.

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2000.11a
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• pp.13-16
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• 2000

Microorganisms have been widely employed for the production of useful bioproducts including primary metabolites such as ethanol, succinic acid, acetone and butanol, secondary metabolites represented by antibiotics, proteins, polysaccharides, lipids and many others. Since these products can be obtained in small quantities under natural condition, mutation and selection processes have been employed for the improvement of strains. Recently, metabolic engineering strategies have been employed for more efficient production of these bioproducts. Metabolic engineering can be defined as purposeful modification of cellular metabolic pathways by introducing new pathways, deleting or modifying the existing pathways for the enhanced production of a desired product or modified/new product, degradation of xenobiotics, and utilization of inexpensive raw materials. Metabolic flux analysis and metabolic control analysis along with recombinant DNA techniques are three important components in designing optimized metabolic pathways, This powerful technology is being further improved by the genomics, proteomics, metabolomics and bioinformatics. Complete genome sequences are providing us with the possibility of addressing complex biological questions including metabolic control, regulation and flux. In silico analysis of microbial metabolic pathways is possible from the completed genome sequences. Transcriptome analysis by employing ONA chip allows us to examine the global pattern of gene expression at mRNA level. Two dimensional gel electrophoresis of cellular proteins can be used to examine the global proteome content, which provides us with the information on gene expression at protein level. Bioinformatics can help us to understand the results obtained with these new techniques, and further provides us with a wide range of information contained in the genome sequences. The strategies taken in our lab for the production of pharmaceutical proteins, polyhydroxyalkanoate (a family of completely biodegradable polymer), succinic acid and me chemicals by employing metabolic engineering powered by genomics, proteomics, metabolomics and bioinformatics will be presented.

• Asian-Australasian Journal of Animal Sciences
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• v.31 no.8
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• pp.1205-1212
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• 2018

Objective: The aim of this experiment was to evaluate the effects of different dietary ratio of metabolizable glucose (MG) to metabolizable protein (MP) on growth performance, blood metabolites, rumen fermentation parameters and the ruminal microbial community of 8 to 10-month-old heifers. Methods: A total of 24 Holstein heifers weighing an average of 282.90 kg (8 month of age) were randomly assigned to four groups of six. The heifers were fed one of four diets of different dietary MG/MP (0.97, 1.07, 1.13, and 1.26). Results: The results showed that the ratio of MG/MP affected the growth performance, blood metabolites, rumen fermentation parameters and the ruminal microbial community of heifers. The average daily gain of heifers was enhanced by increasing the ratio of MG/MP (p<0.05). The concentration of blood urea nitrogen, cholesterol, and low density lipoprotein cholesterol as well as the concentration of total volatile fatty acid in the rumen fluid of heifers decreased with the improvement in the ratio of dietary MG/MP (p<0.05). However, the relative amount of Ruminococcus albus and Butyrivibrio fibrisolvens in the rumen of heifers was increased significantly (p<0.05) when the dietary MG/MP increased. At the same time, with the improvement in dietary MG/MP, the amount of Fibrobacter succinogenes increased (p = 0.08). Conclusion: A diet with an optimal ratio (1.13) of MG/MP was beneficial for the improvement of growth, rumen fermentation, dietary protein and energy utilization of 8 to 10-month-old dairy heifers in this experiment.

• Mycobiology
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• v.48 no.4
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• pp.326-329
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• 2020

Valuable natural compounds produced by a variety of microorganisms can be used as lead molecules for development of new agrochemicals. Furthermore, high-throughput in vitro screening systems with specific modes of action can increase the probability of discovery of new fungicides. In the current study, a rapid assay tested with various microbes was developed to determine the degree of respiratory inhibition of Saccharomyces cerevisiae in two different liquid media, YG (containing a fermentable carbon source) and NFYG (containing a non-fermentable carbon source). Based on this system, we screened 100 fungal isolates that were classified into basidiomycetes, to find microbial secondary metabolites that act as respiratory inhibitors. Consequently, of the 100 fungal species tested, the culture broth of an IUM04881 isolate inhibited growth of S. cerevisiae in NFYG medium, but not in YG medium. The result is comparable to that from treatment with kresoxim-methyl used as a control, suggesting that the culture broth of IUM04881 isolate might contain active compounds showing the inhibition activity for respiratory chain. Based on the assay developed in this study and spectroscopic analysis, we isolated and identified an antifungal compound (-)-oudemansin A from culture broth of IUM04881 that is identified as Oudemansiella venosolamellata. This is the first report that (-)-oudemansin A is identified from O. venosolamellata in Korea. Taken together, the development of this assay will accelerate efforts to find and identify natural respiratory inhibitors from various microbes.

• Microbiology and Biotechnology Letters
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• v.29 no.3
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• pp.149-154
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• 2001

We have investigated the secondary metabolites from the mushroom Suillus granulatus. The methanolic extract of fruit body was separated by silica gel and Sephadex LH-20 column chromatographies. TLC and HPLC were also used for the further purification on compounds from the extracts, Nine compounds were finally isolated and their structures were assigned as 4-hydroxyphenylacetic acid 4-hydroxybenzaldehyde 2,5-dihydroxybenzoic acid methyl ester 5'-deoxy-5'methylthioadenosine. indole-3- carboxlic acid methyl ester indole 3-carboxaldehyde 1,3,5-trihydroxy 7-methylanthraquinone nicotinamide and 3-geranylgeranyl-4-hydroxybenzoic acid on the basis of NMR studies.

• Proceedings of the Korean Society of Plant Biotechnology Conference
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• 2005.11a
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• pp.88-94
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• 2005

Plant tissue culture studies have been done for the preservation of medicinal plant resources and efficient production of pharmaceutically important secondary metabolites. Micropropagation methods for Cephaelis ipecacuanha have been established and these methods enabled much more efficient propagation of the plants than the conventional methods using seedling or layering. The C. ipecacuanha plants derived from tissue culture grew uniformly in the field and they showed higher alkaloid contents compared to the plants grown from seedlings. Hairy root cultures of C. ipecacuanha and Panax ginseng have been established by infection with Agrobacterium rhizogenes, and the production of important pharmaceuticals by these cultures have been successfully demonstrated. In the case of C. ipecacuanha, the highest alkaloid yields from the hairy roots cultured for 8 weeks were 2.75-fold cephaeline (5.5 mg) and one third emetine (0.7 mg) compared with those from the roots of one-year old plant propagated through shoot-tip culture and cultivated in a greenhouse (2.0 mg cephaeline and 2.0 mg emetine). In the case of P. ginseng, ginsenoside contents in the hairy roots optimally cultured for 4 weeks were much higher than those in the roots of 4-year old field-grown plant. Thus our medicinal plant tissue cultures demonstrate desirable properties. However, they are always exposed to danger of microbial contamination or unexpected trouble of culture facilities. Cryopreservation of plant tissue cultures is a reliable method for long-term preservation. Cryopreservation studies on these cultures are also presented.

• Journal of Microbiology and Biotechnology
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• v.31 no.1
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• pp.70-78
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• 2021

Identifying the extracellular metabolites of microorganisms in fresh vegetables is industrially useful for assessing the quality of processed foods. Pectobacterium carotovorum subsp. carotovorum (PCC) is a plant pathogenic bacterium that causes soft rot disease in cabbages. This microbial species in plant tissues can emit specific volatile molecules with odors that are characteristic of the host cell tissues and PCC species. In this study, we used headspace solid-phase microextraction followed by gas chromatography coupled with mass spectrometry (HS-SPME-GC-MS) to identify volatile compounds (VCs) in PCC-inoculated cabbage at different storage temperatures. HS-SPME-GC-MS allowed for recognition of extracellular metabolites in PCC-infected cabbages by identifying specific volatile metabolic markers. We identified 4-ethyl-5-methylthiazole and 3-butenyl isothiocyanate as markers of fresh cabbages, whereas 2,3-butanediol and ethyl acetate were identified as markers of soft rot in PCC-infected cabbages. These analytical results demonstrate a suitable approach for establishing non-destructive plant pathogen-diagnosis techniques as alternatives to standard methods, within the framework of developing rapid and efficient analytical techniques for monitoring plant-borne bacterial pathogens. Moreover, our techniques could have promising applications in managing the freshness and quality control of cabbages.

• Korean Journal of Soil Science and Fertilizer
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• v.45 no.6
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• pp.1065-1072
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• 2012

Crop productivity decreases globally as a result of salinization. However, salinity impact on greenhouse-grown crops is much higher than on field-grown crops due to the overall concentrations of nutrients in greenhouse soils. Therefore, this study was performed to determine the short-term changes in growth, photosynthesis, and metabolites of tomato plants grown in greenhouse under heavily input of fertilizers evaluated by microbial activity and chemical properties of soils. The soils (< 3, 3.01~6, 6.01~10 and > 10.01 dS $m^{-1}$) from farmer's greenhouse fields having different fertilization practices were used. Results showed that the salt-accumulated soil affected adversely the growth of tomato plants. Tomato plants were seldom to complete their growth against > 10.0 dS $m^{-1}$ level of EC. The assimilation rate of $CO_2$ from the upper fully expanded leaves of tomato plants is reduced under increasing soil EC levels at 14 days, however; it was the highest in moderate or high EC-subjected (3.0 ~ 10.0 dS $m^{-1}$) at 28 days. In our experiment, soluble sugars and starch were sensitive markers for salt stress and thus might assume the status of crops against various salt conditions. Taken together, tomato plants found to have tolerance against moderate soil EC stress. Various EC levels (< 3.0 ~ 10.0 dS $m^{-1}$) led to a slight decrease in organic matter (OM) contents in soils at 28 days. Salinity stress led to higher microbial activity in soils, followed by a decomposition of OM in soils as indicated by the changes in soil chemical properties.