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Tracing Metabolite Footsteps of Escherichia coli Along the Time Course of Recombinant Protein Expression by Two-Dimensional NMR Spectroscopy

  • Chae, Young Kee;Kim, Seol Hyun;Ellinger, James J.;Markley, John L.
    • Bulletin of the Korean Chemical Society
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    • v.33 no.12
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    • pp.4041-4046
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    • 2012
  • The recombinant expression of proteins has been the method of choice to meet the demands from proteomics and structural genomics studies. Despite its successful production of many heterologous proteins, Escherichia coli failed to produce many other proteins in their native forms. This may be related to the fact that the stresses resulting from the overproduction interfere with cellular processes. To better understand the physiological change during the overproduction phase, we profiled the metabolites along the time course of the recombinant protein expression. We identified 32 metabolites collected from different time points in the protein production phase. The stress induced by protein production can be characterized by (A) the increased usage of aspartic acid, choline, glycerol, and N-acetyllysine; and (B) the accumulation of adenosine, alanine, oxidized glutathione, glycine, N-acetylputrescine, and uracil. We envision that this work can be used to create a strategy for the production of usable proteins in large quantities.

Synthesis of 1-(4'-Thio-${\alpha},{\beta}$-D-ribofuransyl)-5-halogeno Uracils (I) (5-할로겐 치환 uracil 들의 4-Thiosugar Nucleosides의 합성 (제 1 보))

  • Kim Jack C.;Lee Euk-suck;Kim Chang-bae;Bobek Miroslav;Whistlee Roy L.
    • Journal of the Korean Chemical Society
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    • v.19 no.2
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    • pp.130-133
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    • 1975
  • The 4'-thio analogs of the 5-bromo-and 5-iodo-pyrimidine nucleosides were prepared by condensation of 2,3,5-tri-O-acetyl-4-thio-${\alpha},{\beta}$-D-ribofuranosyl chloride with the chloromercury derivatives of 5-halogeno-2,4-bis(trimethylsiloxy)pyrimidine, followed by the removal of the protecting groups. Although the biological activities of the 4'-thio derivatives are not greatly different from the corresponding 4'-oxygen analogs in this preliminary test, the fact that the 4'-thio analogs have comparableihigh activities, is of interest, and indicates the value of further biochemical examinations.

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A Case of Long-Term Complete Remission of Advanced Gastric Adenocarcinoma with Liver Metastasis

  • Rim, Ch'angbum;Lee, Jung-Ae;Gong, Soojung;Kang, Dong Wook;Yang, Heebum;Han, Hyun Young;Kim, Nae Yu
    • Journal of Gastric Cancer
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    • v.16 no.2
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    • pp.115-119
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    • 2016
  • We report the case of a patient with gastric adenocarcinoma with multiple liver metastases. This patient showed complete remission for more than 68 months after S-1/cisplatin combination chemotherapy and radical total gastrectomy. The patient, a 63-year-old man, presented with dyspepsia and difficulty in swallowing. Endoscopic findings showed a huge ulcero-infiltrative mass at the lesser curvature of the mid-body, extending to the distal esophagus. Biopsy revealed a poorly differentiated tubular adenocarcinoma. An abdominal computed tomography scan demonstrated multiple hepatic metastases. S-1/cisplatin combination chemotherapy was initiated, and following completion of six cycles of chemotherapy, the gastric masses and hepatic metastatic lesions had disappeared on abdominal computed tomography. Radical total gastrectomy and D2 lymphadenectomy combined with splenectomy were performed. The patient underwent three cycles of S-1/cisplatin combination chemotherapy followed by tegafur-uracil therapy for 1 year. He remained in complete remission for more than 68 months after surgery.

Chemical Constituents of Lathyrus davidii

  • Park, Su-Yeon;Kim, Ju-Sun;Lee, So-Young;Bae, Ki-Hwan;Kang, Sam-Sik
    • Natural Product Sciences
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    • v.14 no.4
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    • pp.281-288
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    • 2008
  • From the MeOH extract of the whole plants of Lathyrus davidii (Fabaceae), thirteen constituents were isolated and identified as the flavonoids astragalin, isoquercitrin, nicotiflorin, and rutin, as the saponins soyasapogenol B 3-O-${\beta}$-D-glucuronopyranoside, azukisaponins II and V, soyasaponins II and V and as 4-O-${\beta}$-Dglucopyranosyl syringic acid, uracil and n-hexacosanol. Five saponins and 4-O-${\beta}$-D-glucopyranosyl syringic acid were isolated from the BuOH fraction as their methyl esters. Ombuoside (rutin 7,4'-di-O-methyl ether) was also isolated from the methylated BuOH-soluble fraction. However, no ombuoside was detected in the HPLC analysis of the nonmethylated BuOH fraction. Therefore, ombuoside is an artifact derived from methylation of rutin. All of these compounds were isolated for the first time from this plant.

Establishment of HPLC-UV Analysis Method Validation for Simultaneous Analysis of Standard Compounds of Oplopanax elatus Nakai Stem (HPLC-UV를 이용한 땃두릅나무 줄기의 지표 성분 동시 분석법 확립)

  • Yoo, Nam Ho;Kwon, Yongsoo;Kim, Myong Jo
    • Korean Journal of Pharmacognosy
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    • v.50 no.2
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    • pp.133-140
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    • 2019
  • In our previous study, we found uracil, adenosine, protocatechuic acid, syringin (eleutheroside B) and scoparone (6, 7-dimethoxycoumarin) in the Oplopanax elatus Nakai Stem. High-performance liquid chromatography (HPLC) -UV was used to quality and quantify the internal marker compounds in the O. elatus extract after validation of method with linearity, limit of detection (LOD), limit of quantitation (LOQ), accuracy and precision. The specificity assessment visually confirmed that the substance was detected without the introduction of other substances. The established method showed high linearity of the calibration curve and coefficient of correlation ($R^2$) of over the 0.999. HPLC was reported as five standard compounds equivalent using the following linear equation based on the calibration curve. The accuracy of measurement was 84.34 ~ 119.74% and the relative standard deviation (RSD) value was 0.28 ~ 1.60%. In addition, our established method showed high repeatability. The RSD value was 1.10 ~ 6.81%. So, we found the amount of the internal marker compounds in the O. elatus extract. These results demonstrated that can be used to quality evaluation of the O. elatus.

Metabolite Chemical Composition of the Bletilla striata (Thunb.) Reichb. f. Endophyte Penicillium oxalicum

  • Ran Liu;Xuehua Han;Jing Gao;Min Luo;Dale Guo;Guangzhi Wang
    • Mycobiology
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    • v.51 no.3
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    • pp.148-156
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    • 2023
  • Penicillium oxalicum strain can be isolated from the Bletilla striata (Thunb.) Reichb. f. tubers. Its solid-state fermentation products are concentrated by percolation extraction. Separation and purification have been conducted to the ethyl acetate extracts by preparative HPLC. Based on the use of spectrometry, we have determined 17 known compounds, 12,13-dihydroxy-fumitremorgin C (1), pseurotin A (2), tyrosol (3), cyclo-(L-Pro-L-Val) (4), cis-4-hydroxy-8-O-methylmellein (5), uracil (6), cyclo-(L-Pro-L-Ala) (7), 1,2,3,4-tetrahydro-4-hydroxy-4-quinolin carboxylic acid (8), cyclo-(Gly-L-Pro) (9), 2'-deoxyuridine (10), 1-(b-D-ribofuranosyl)thymine (11), cyclo-(L-Val-Gly) (12), 2'-deoxythymidine (13), cyclo-(Gly-D-Phe) (14), cyclo-L-(4-hydroxyprolinyl)-D-leucine (15), cyclo-(L)-4-hydroxy-Pro-(L)-Phe (16), uridine (17). Here, we report compounds 1-3, 5, 7-8, 11-12, 14-17 are first found and isolated from this endophyte.

Phenolic Compounds from the Leaves of Nelumbo nucifera Showing DPPH Radical Scavenging Effect (연잎에서 DPPH 라디칼 소거활성을 가지는 페놀성 화합물의 분리)

  • Park, Chan-Hum;Hur, Jong-Moon;Song, Kyong-Sik;Park, Jong-Cheol
    • Korean Journal of Pharmacognosy
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    • v.38 no.3 s.150
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    • pp.263-269
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    • 2007
  • Nelumbo nucifera (Nymphaeaceae) has been widely used in a traditional oriental medicine to treat bleeding, fever, diarrhea, hemorrhoid, sunstroke, dysentery and dizziness. The leaves of this plant were refluxed with methanol, and then fractionated with organic solvents to screen the antioxidant activity using DPPH radical. Ethyl acetate and n-butanol fractions showed good DPPH radical scavenging effects and were carried out column chromatographies to isolate nine compounds. Their chemical structures were characterized as p-hydroxybenzoic acid (1), uracil (2), luteolin (3), quercetin $3-O-{\beta}-D-glucopyranoside$ (4), $rhamnetin 3-O-{\beta}-D-glucopyranoside$ (5), $isorhamnetin 3-O-{\beta}-D-glucopyranoside$ (6), $quercetin 3-O-{\beta}-D-glucuropyranoside$ (7), $quercetin 3-O-{\beta}β-D-xylofuranosyl(1{\rightarrow}2)-{\beta}-D-galactopyranoside$ (8), and adenine (9) by comparison NMR spectral data and with those in references. Compounds 1, 2, 5 and 9 were firstly isolated from this plant. Compounds 1, 3 and 4 showed potent DPPH radical scavenging activity. Especially, compound 3, luteolin showed the higher effect than ascorbic acid used as a positive control.

Purification and Properties of Intracellular Cytosine Deaminase from Chromobacterium violaceum YK 391

  • KIM , JUNG;YU, TAE-SHICK
    • Journal of Microbiology and Biotechnology
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    • v.14 no.6
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    • pp.1182-1189
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    • 2004
  • Cytosine deaminase (cytosine aminohydrolase, EC 3.5.4.1) stoichiometrically catalyzes the hydrolytic deamination of cytosine and 5-fluorocytosine to uracil and 5-fluorouracil, respectively. The intracellular cytosine deaminase from Chromobacterium violaceum YK 391 was purified to apparent homogeneity with 272.9-fold purification with an overall yield of $13.8\%$. The enzyme consisted of dimeric polypeptides of 63 kDa, and the total molecular mass was calculated to be approximately 126 kDa. Besides cytosine, the enzyme deaminated 5-fluorocytosine, cytidine, 6-azacytosine, and 5-methylcytosine, but not 5-azacytosine. Optimum pH and temperature for the enzyme reaction were 7.5 and $30^{\circ}C$, respectively. The enzyme was stable at pH 6.0 to 8.0, and at 30T for a week. About $70\%$ of the enzyme activity was retained at $60^{\circ}C$ for 5 min. The apparent $K_{m}$ values for cytosine, 5-fluorocytosine, and 5-methylcytosine were calculated to be 0.38 mM, 0.87 mM, and 2.32 mM, respectively. The enzyme activity was strongly inhibited by 1 mM $Hg^{2+},\;Zn^{2+},\;Cu^{2+},\;Pb^{2+},\;and\;Fe^{3+}$, and by o-phenanthroline, $\alpha,\;{\alpha}'$-dipyridyl, p-choromercuribenzoate, N-bromosuccinimide, and cWoramine­T. In addition, the enzyme activity was strongly inhibited by I mM 2-thiouracil, and weakly inhibited by 2-thiocytosine, or 5-azacytosine. Finally, intracellular and extracellular cytosine deaminases from Chromobacterium violaceum YK 391 were found to have a different optimum temperature, apparent $K_{m}$ value, and molecular mass.

Inulooligosaccharide Production from Inulin by Saccharomyces cerevisiae Strain Displaying Cell-Surface Endoinulinase

  • Kim Hyun-Chul;Kim Hyun-Jin;Choi Woo-Bong;Nam Soo-Wan
    • Journal of Microbiology and Biotechnology
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    • v.16 no.3
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    • pp.360-367
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    • 2006
  • The endoinulinase gene (inu1) from Pseudomonas mucidolens was expressed on the cell surface of Saccharomyces cerevisiae by fusing with Aga2p linked to the membrane anchored protein, Aga1p. The inu1 gene of P. mucidolens was subcloned into the surface display vector, pCTcon (GAL1 promoter). The constructed plasmid, pCTENIU (8.5kb), was then introduced to S. cerevisiae EBY100 cells and the yeast transformants selected on synthetic defined media lacking uracil and inulin-containing media. The inu1 gene under the control of the GAL1 promoter was successfully expressed in the yeast transformants, and the surface display of endoinulinase confirmed by immunofluorescence microscopy, along with its enzymatic ability to form inulooligosaccharides (IOSs) from inulin. The total endoinulinase activity reached about 2.31 units/ml when the yeast transform ants were cultivated on a YPDG medium. To efficiently hydrolyze the inulin, various reaction conditions were examined, including the pH, temperature, and inulin source. The optimized conditions were then determined as follows: pH, 7.0; temperature, $50^{\circ}C$; inulin source, Jerusalem artichoke. Under the optimized condition and 46 units of endoinulinase per g of inulin, IOSs started to be produced after 10 min of enzymatic reaction. The highest yield, 71.2% of IOSs, was achieved after 30 h of reaction without any significant loss of the initial enzyme activity. As a result of the reaction with inulin, IOSs consisting of inulobiose (F2), inulotriose (F3), inulotetraose (F4), and inulopentaose (F5) were produced, and F4 was the major product.

Enhanced Activity of Cytidine Deaminase by Gene Family Shuffling. (Gene Family Shuffling을 이용한 Cytidine Deaminase 활성 증가)

  • Hong, Sik;Kim, Kyung-Dong;Song, Bang-Ho;Jung, Kyung-Hwa;Kim, Sa-Yeol
    • Microbiology and Biotechnology Letters
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    • v.30 no.4
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    • pp.298-304
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    • 2002
  • A family shuffling associating PCR-based and in vitro recombination and expression in Escherichia coli cdd mutant was carried out. Two cdd genes encoding cytidine deaminases (CDase) from thermophilic Bacillus caldolyticus and B. stearothermophilus were shuffled. Around 150 viable mutant colonies screened on AB minimal medium without uracil by E. coli cdd complementation were selected for cytidine deaminase assay and 4 candidates (SH1067, SH1077, SH1086, and SH1118) were chosen for the detailed study. The nucleotide sequence analyses of 4 selected mutants revealed that they have several point mutations and recombinations. Surprisingly, the SH 1067 showed 770 fold more specific CDase activity at $80^{\circ}C$ than that of T101 from parental B. stearothermophilus.