• 한국생물공학회:학술대회논문집
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• 2005.10a
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• pp.739-740
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• 2005

• Journal of Applied Biological Chemistry
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• v.56 no.1
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• pp.37-42
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• 2013

In eukaryotes, most of the genome are transcribed, however only a small proportion of total transcripts encodes for protein, thus resulting in many of noncoding RNAs. In order to recover DNA damage including DNA double-strand breaks (DSBs) eukaryotes have evolved complex mechanisms and these are processed through coordinated mechanisms of protein sensors, transducers, and effectors including RNAs. During recent years, small RNAs have been increasingly studied and gradually considered as key regulators in various aspects of biology. Upon DNA damage, small RNAs including diRNAs (DSB induced RNA) are generated in both plant and human cell lines. Inhibition of their biogenesis has severe influence on DSB repair system.

• 한국생물공학회:학술대회논문집
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• 2005.04a
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• pp.584-584
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• 2005

• Journal of Applied Biological Chemistry
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• v.58 no.3
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• pp.201-208
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• 2015

The role of RNA-binding proteins (RBPs) to regulate expression of genes seems to be very important. RBPs play important roles in RNA related bioprocess such as transcription, pre-mRNA splicing, polyadenylation, transport, localization, translation, turn over and maintenance of structure. Despite of many researches on RNA binding proteins, detailed mechanisms of these proteins have not been fully understood. It seems that many parts of RBPs remains unknown and should be characterized for the better understanding of gene expression. Recently, genetic, biochemical, and bioinformatic analysis of genomes revealed a vast array of RBPs and many parts are interesting to understand bioprocessing including gene expression.

• Journal of Life Science
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• v.32 no.3
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• pp.249-255
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• 2022

Metabolism is essential for survival and reproduction, and there is a metabolic pathways entry in the clusters of orthologous groups of proteins (COGs) database, updated in 2020. In this study, the metabolic pathways of 1309 prokaryotes were analyzed using COGs. There were 822 COGs associated with 63 metabolic pathways, and the mean for each taxon was between 200.50 (mollicutes) and 527.07 (cyanobacteria) COGs. The metabolic pathway composition ratio (MPCR) was defined as the number of COGs present in one genome in relation to the total number of COGs constituting each metabolic pathway, and the number of pathways with 100% MPCR ranged from 0 to 26 in each prokaryote. Among 1309 species, the 100% MPCR pathways included murein biosynthesis associated with cell wall synthesis (922 species); glycine cleavage (918); and ribosomal 30S subunit synthesis (903). The metabolic pathways with 0% MPCR were those involving photosystem I (1263 species); archaea/vacuolar-type ATP synthase (1028); and Na⁺-translocation NADH dehydrogenase (976). Depending on the prokaryote, three to 49 metabolic pathways could not be performed at all. The sequence of most highly conserved metabolic pathways was ribosome 30S subunit synthesis (96.1% of 1309 species); murein biosynthesis (86.8%); arginine biosynthesis (80.4%); serine biosynthesis (80.3%); and aminoacyl-tRNA synthesis (82.2%). Protein and cell wall synthesis have been shown to be important metabolic pathways in prokaryotes, and the results of this study of COGs related to such pathways can be utilized in, for example, the development of antibiotics and artificial cells.

• Journal of Plant Biotechnology
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• v.29 no.4
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• pp.265-275
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• 2002

Flavonoid biosynthesis is one of the most extensively studied areas in the secondary metabolism. Due to the study of flavonoid metabolism in diverse plant system, the pathways become the best characterized secondary metabolites and can be excellent targets for metabolic engineering. These flavonoid-derived secondary metabolites have been considerably divergent functional roles: floral pigment, anticancer, antiviral, antitoxin, and hepatoprotective. Three species have been significant for elucidating the flavonoid metabolism and isolating the genes controlling the flavonoid genes: maize (Zea mays), snapdragon (Antirrhinum majus) and petunia (Prtunia hybrida). Recently, many genes involved in biosynthesis of flavonoid have been isolated and characterized using mutation and recombinant DNA technologies including transposon tagging and T-DNA tagging which are novel approaches for the discovery of uncharacterized genes. Metabolic engineering of flavonoid biosynthesis was approached by sense or antisense manipulation of the genes related with flavonoid pathway, or by modified expression of regulatory genes. So, the use of a variety of experimental tools and metabolic engineering facilitated the characterization of the flavonoid metabolism. Here we review recent progresses in flavonoid metabolism: confirmation of genes, metabolic engineering, and applications in the industrial use.

• Journal of Microbiology and Biotechnology
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• v.25 no.7
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• pp.999-1006
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• 2015

The endo-polygalacturonase gene (endo-pgaA) was cloned from DNA of Aspergillus niger SC323 using the cDNA synthesized by overlapping PCR, and successfully expressed in Saccharomyces cerevisiae EBY100 through fusing the α-factor signal peptide of yeast. The fulllength cDNA consists of 1,113 bp and encodes a protein of 370 amino acids with a calculated molecular mass of 38.8 kDa. After induction by galactose for 48 h, the activity of recombinant endo-PgaA in the culture supernatant can reach up to 1,448.48 U/mg. The recombinant protein was purified to homogeneity by ammonium sulfate precipitation and gel filtration column chromatography and subsequently characterized. The optimal pH and temperature of the purified recombinant enzyme were 5.0 and 50℃, respectively. The Michaelis-Menten constant (K_m) and maximal velocity (V_max) of the enzyme for pectin were 88.54 μmol/ml and 175.44 μmol/mg/min, respectively. The enzyme activity was enhanced by Ca²⁺, Cu²⁺, and Na⁺, and strongly inhibited by Pb²⁺ and Mn²⁺. The pectin hydrolysates were mainly galacturonic acid and other oligo-galacturonates. Therefore, these characteristics suggest that the recombinant endo-PgaA may be of potential use in the food and feed industries.

• KSBB Journal
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• v.32 no.3
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• pp.169-173
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• 2017

Butyric acid (C4 carboxylic acid) is used as an important compound in food, pharmaceutical, and chemical industries. Currently, butyric acid is mainly produced at the industrial scale through the petrochemical processes. Bio-based butyric acid has also gained attention, because the consumer prefers the food and pharmaceutical ingredients that are produced through fermentation. Clostridia is one of the well-known butyric acid producers, and massively engineered for enhanced production of butyric acid. In this paper, we reviewed the metabolic pathway of clostridia, especially Clostridium acetobutylicum and Clostridium tyrobutyricum, and summarized the metabolic engineering strategies of the strains for enhanced production of butyric acid.

• Proceedings of the Korean Society for Applied Microbiology Conference
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• 2005.06a
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• pp.233-244
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• 2005

Guanosine fermentation process can be well predicted and analyzed by the proposed state equations describing the dynamic change of a bioreactor. Pyruvate and alanine were found to be characteristically accumulated along with the decline of the guanosine formation rate during the mid-late phase of the process. The enzymological study of the main pathways in glucose catabolism and the quantitative stoichiometric calculation of metabolic flux distribution revealed that it was entirely attributed to the shift of metabolic flux from hexose monophosphate (HMP) pathway to glycolysis pathway. The process optimization by focusing on the restore of the shift of metabolic flux was conducted and the overcoming the decrease of oxygen uptake rate (OUR) was taken as the relevant factor of the trans-scale operation. As a result, the production of guanosinewas increased from 17 g/L to over 34 g/I.

• Korean Chemical Engineering Research
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• v.45 no.6
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• pp.529-535
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• 2007

Recently, an attempt to analyze and modify metabolic networks of living organisms in global level emerged with the benefit of development of high-throughput techniques, and it is generally called systems biology. Various systems biology studies have been carried out for the development of enhanced metabolite production systems. By modification of metabolic characteristics of microorganisms, metabolite productivities and yields obtained with metabolically engineered bacteria increased significantly compare with that obtained with wild type bacteria.