• Genomics & Informatics
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• v.4 no.4
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• pp.182-187
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• 2006

6-Phosphogluconolactonase (6PGL) is one of the key enzymes in the ubiquitous pathways of central carbon metabolism, but bacterial 6PGL had been long known as a missing enzyme even after complete bacterial genome sequence information became available. Although recent experimental characterization suggests that there are two types of 6PGLs (DevB and YbhE), their phylogenetic distribution is severely biased. Here we present that proteins in COG group previously described as 3-oarboxymuconate cyclase (COG2706) are actually the YbhE-type 6PGLs, which are widely distributed in Proteobacteria and Fimicutes. This case exemplifies how erroneous functional description of a member in the reference database commonly used in transitive genome annotation cause systematic problem in the prediction of genes even with universal cellular functions.

• Korean Journal of Pharmacognosy
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• v.20 no.2
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• pp.110-116
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• 1989

This study was conducted to purify and characterize a polysaccharide fraction from whole parts of Duchesnea indica (Andr.) Focke, which was previously reported to show an antitumor activity by us. The plant was extracted with 5% ethanol for 3 days in the room temperature. The extract was dialyzed by 5% ethanol, and then concentrated by extraction with $excess\;_N-butanol$, followed by gel filtration named Fr. a and b. Each was composed of gallic acid, hexose, pentose, uronic acid and protein, indicating that both fractions were tannic polysaccharide containing protein. Heat treatment of them yielded gallic acid less polysaccharides. They showed a colony stimulating factor activity.

• Journal of Microbiology
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• v.35 no.1
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• pp.15-20
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• 1997

Kinetic studies were done to elucidate the reaction mechanism of purine nucleoside phosphorylase (PNP) in Micrococcus Luteus. PNP catalyzes the reversible phosphorolysis of ribonucleosides to their respective base. The effect of alternative competing substrates suggested that a single enzyme was involved in binding to the active site for all purine nucleosides, inosine, deoxyiosine, guanosine, deoxyguanosine, adenosine and deoxyadenosine. Affinity studies showed that pentose moiety reduced the binding capacity and methylation of ring N-1 of inosine and guanosine had little effect on binding to bacterial enzyme, whereas these compounds did not bind to the mammalian enzymes. The initial velocity and product inhibition studies demonstrated that the predominant mechanism of reaction was an ordered bi, bi reaction. The nucleoside bound to the enzyme first, followed by phosphate. Ribose 1-phosphate was the first product to leave, followed by base.

• Journal of Microbiology and Biotechnology
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• v.29 no.3
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• pp.339-346
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• 2019

L-Arabinose, a five carbon sugar, has not been considered as an important bioresource because most studies have focused on D-xylose, another type of five-carbon sugar that is prevalent as a monomeric structure of hemicellulose. In fact, L-arabinose is also an important monomer of hemicellulose, but its content is much more significant in pectin (3-22%, g/g pectin), which is considered an alternative biomass due to its low lignin content and mass production as juice-processing waste. This review presents native and engineered microorganisms that can ferment L-arabinose. Saccharomyces cerevisiae is highlighted as the most preferred engineering host for expressing a heterologous arabinose pathway for producing ethanol. Because metabolic engineering efforts have been limited so far, with this review as momentum, more attention to research is needed on the fermentation of L-arabinose as well as the utilization of pectin-rich biomass.

• KOREAN JOURNAL OF CROP SCIENCE
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• v.37 no.5
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• pp.468-475
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• 1992

In order to understand more clearly the integration between N-assmilation and C-metabolism in relation to N fertilization, a pot experiment with 5 different level of N fertilization(0, 5, 10, 25, 50 mM NO$_3$$_{[-10]}$ ) was conducted in Manchester, U.K. The peas (Pisum sativum L., cv. Early Onward) were sown in vermiculate (5 cm depth) and cultivated for 6 days under temperature controlled dark room conditions ($25^{\circ}C$). The plants received frequent irrigation with a nutrient solution: it was fertilized every 2 days, 3 times a day at 10h, 13h, 16h respectively. Elevated NO$_3$$^{[-10]}$ concentration, the activity levels of NR, NiR, total GS(crude extract), GS$_2$(plastid) in both root and shoot were increased and reached the peak in 5～25 mM, except NiR specific activity which increased its activity continually until 50 mM NO$_3$$^{[-10]}$ treatment. Total activities of GS (crude extract) in both root and shoot became higher than those of GS$_2$(Plastid), and the activity ratios of total GS in the crude extract and GS$_2$ in the plastids were 3.0 to 4.3 in root, but 3.2 to 10.6 in shoot. It was concluded that the reductants and A TP from OPPP itself should be enough to achieve the high rate of NR, NiR, GS$_1$, GS$_2$ in plant root and shoot for reduction or assimilation of nitrogen, but these enzyme activities might be inhibited by an excess of NO$_3$$^{[-10]}$ influx over the reduction capacity.

• Clinical and Experimental Reproductive Medicine
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• v.34 no.2
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• pp.95-106
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• 2007

Objective: We previously identified differentially expressed genes (DEGs) between germinal vesicle (GV) and metaphase II (MII) mouse oocyte. The present study was accomplished as a preliminary study to elucidate the role of ribose 5-phosphate isomerase A (Rpia), the essential enzyme of the pentose phosphate pathway (PPP), in oocyte maturation. We observed expression of Rpia in the mouse and porcine oocytes. Methods: Expression pattern of the 11 MII-selective DEGs in various tissues was evaluated using RT-PCR and selected 4 genes highly expressed in the ovary. According to the oocyte-selective expression profile, we selected Rpia as a target for this study. We identified the porcine Rpia sequence using EST clustering technique, since it is not yet registered in public databases. Results: The extended porcine Rpia nucleotide sequence was submitted and registered to GenBank (accession number EF213106). We prepared primers for porcine Rpia according to this sequence. In contrast to the oocyte-specific expression in the mouse, Rpia was expressed in porcine cumulus and granulosa cells as well as in oocytes. Conclusion: This is the first report on the characterization of the Rpia gene in the mouse and porcine ovarian cells. Results of the present study suggest that the mouse and porcine COCs employ different mechanism of glucose metabolism. Therefore, the different metabolic pathways during in vitro oocyte maturation (IVM) in different species may lead different maturation rates. It is required to study further regarding the role of Rpia in glucose metabolism of oocytes and follicular cell fore exploring the regulatory mechanism of oocyte maturation as well as for finding the finest culture conditions for in vitro maturation.

• Journal of Life Science
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• v.34 no.7
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• pp.465-475
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• 2024

Lactiplantibacillus plantarum K9 is a probiotic strain that can be utilized from various bioactive substances isolated from Protaetia brevitarsis seulensis larvae. In this study, a genetic analysis of L. plantarum K9 revealed the existence of a bacterial chromosome and three plasmids. The glycolysis pathway and pentose phosphate pathway were examined for their normal functioning via an analysis of the core metabolic pathways of L. plantarum K9. Since the key enzymes, fluctose-1,6-bisphospatase (EC: 3.1.3.11) and 6-phosphogluconate dehydratase (EC: 4.2.1.12)/2-keto-deoxy-6-phosphogluconate (KDPG) aldolase (EC: 4.2.1.55), of gluconeogenesis and the ED pathway were not identified from the L. plantarum K9 genome, we suggest that gluconeogenesis and the ED pathway are not performed in L. plantarum K9. Additionally, while some enzymes, related to fumarate and malate biosyntheses, involved in the TCA cycle were identified from L. plantarum K9, the enzymes associated with the remaining TCA cycle were absent, indicating that the TCA cycle cannot proceed. Meanwhile, based on our findings, we propose that the oxidative electron transport system performs class IIB-type (bd-type) electron transfer. In summary, we assert that L. plantarum K9 performs homolactic fermentation, executes gluconeogenesis and the pentose phosphate pathway, and carries out energy metabolism through the class IIB-type oxidative electron transport system. Therefore, we suggest that L. plantarum K9 has relatively high lactic acid production, and that it has excellent antibacterial activity, as a result, compared to other lactic acid bacterial strains. Moreover, we speculate that L. plantarum K9 has an oxidative electron transport capability, indicating that it is highly resistant to oxygen and suggesting that it has fine cultivation characteristics, which collectively make it highly suitable for use as a probiotic.

• Korean Journal of Soil Science and Fertilizer
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• v.21 no.4
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• pp.434-442
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• 1988

This study has been made to investigate the influences of organic matter on the soil composition, nitrogen fixing organism, soil enzyme activity and nitrogen fixing activity in the paddy rice rhizosphere when rice and barley straw were applied. The results are summarized as follows: 1. The pH in the submerged soil was increased from ear formation stage to harvesting. 2. In the rhizosphere, $Fe^{{+}{+}}$ content was decreased according to the growing stage, while increased in the nonrhizosphere. 3. In the initial stage, rhizosphere was higher than nonrhizosphere but in the late stage nonrhizosphere was higher than rhizosphere on the $NH_4-N$ content. 4. In the submerged soil, rhizosphere was higher than nonrhizosphere, on the concentration of glucose and pentose. 5. Changes of the number of nitrogen fixing organism in whole soil was not high. 6. Generally, rhizosphere was higher than nonrhizosphere on the soil enzyme activity such as phosphatase, ${\beta}$-glucosidase, and protease. 7. Acetylene-reducing activity was the highest in the tillering stage, and rhizosphere, Samgang (high-yielding variety) were higher than nonrhizosphere. Dongjin (general variety) respectively. 8. In the submerged soil applied barley straw, acetylene-reducing activity was slightly higher than rice straw in the initial stage.

• Applied Chemistry for Engineering
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• v.19 no.2
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• pp.199-204
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• 2008

Hemicellulose, consisteing of pentose as xylose and mannose, is usable as high octane fuels and heavy oil additives if depolymerized to monomer unit. In this study, thermochemical degradation by pyrolysis-liquefaction of hemicellulose, the effects of reaction temperature, conversion yield, degradation properties and degradation products were investigated. Experiments were performed in a tube reactor by varying reaction temperatures from $200^{\circ}C$ to $400^{\circ}C$ at 40 min of reaction time. The liquid products from pyrolysis-liquefaction of hemicellulose contained various kinds of ketones. Ketones, as 2,3-dimethyl-2-cyclopenten-1-one, 2,3,4-trimethyl-2-cyclopentan-1-one, and 2-methyl-cyclopentanone, could be used as high-octane-value fuels and fuel additives. However, phenols are not valuable as fuels. Combustion heating value of liquid products obtained from thermochemical conversion processes of hemicellulose was in the range of 6,680~7,170 cal/g. After 40 min of reaction at $400^{\circ}C$ in pyrolysis-liquefaction of hemicellulose, the energy yield and mass yield were as high as 72.2% and 41.2 g oil/100 g raw material, respectively.

• Journal of Life Science
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• v.25 no.5
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• pp.507-514
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• 2015

D-Xylulose is phosphorylated to D-xylulose-5-phosphate by D-xylulose kinase before it enters glycolysis via the nonoxidative pentose phosphate pathway. A gene encoding a novel D-xylulose kinase (XK) from K. gwangalliensis strain SJ2 was sequenced and expressed in E. coli. The sequence of the isolated XK gene was 1,419 bp, encoding 472 amino acids. The XK protein was more closely related to the Arthrobacter phenanthrenivorans XK than to the Bifidobacterium catenulatum one, as reflected in the sequence identity (54.9% vs. 38.7%). The XK gene was subcloned into the pCold-II expression vector. The resulting plasmid was transformed into E. coli strain BL21 (DE3) cells and the expression of the recombinant XK protein was induced by the addition of IPTG. The resulting protein was expressed as a fusion protein of approximately 48 kDa containing a N-terminal six-histidine extension that was derived from the expression vector. The expressed protein was homogenized by affinity chromatography and showed enzymatic activity corresponding to D-xylulose kinase. XK enzyme kinetic studies with D-xylulose and ATP showed a Km of 250±20 μM and 1,300±50 μM, respectively. The results obtained from this study will provide a wider knowledge base for the characterization of D-xylulose kinase at the molecular level.