Jongkeun Choi

Structural insights into the molecular mechanism of Escherichia coli SdiA, a quorum-sensing receptor

Escherichia coli SdiA is a quorum-sensing (QS) receptor that responds to autoinducers produced by other bacterial species to control cell division and virulence. Crystal structures reveal that E. coli SdiA, which is composed of an N-terminal ligand-binding domain and a C-terminal DNA-binding domain (DBD), forms a symmetrical dimer. Although each domain shows structural similarity to other QS receptors, SdiA differs from them in the relative orientation of the two domains, suggesting that its ligand-binding and DNA-binding functions are independent. Consistently, in DNA gel-shift assays the binding affinity of SdiA for the ftsQP2 promoter appeared to be insensitive to the presence of autoinducers. These results suggest that autoinducers increase the functionality of SdiA by enhancing the protein stability rather than by directly affecting the DNA-binding affinity. Structural analyses of the ligand-binding pocket showed that SdiA cannot accommodate ligands with long acyl chains, which was corroborated by isothermal titration calorimetry and thermal stability analyses. The formation of an intersubunit disulfide bond that might be relevant to modulation of the DNA-binding activity was predicted from the proximal position of two Cys residues in the DBDs of dimeric SdiA. It was confirmed that the binding affinity of SdiA for the uvrY promoter was reduced under oxidizing conditions, which suggested the possibility of regulation of SdiA by multiple independent signals such as quorum-sensing inducers and the oxidation state of the cell.

Discovery and characterization of the tuberculosis drug lead ecumicin.

The new tuberculosis (TB) lead ecumicin (1), a cyclic tridecapeptide, was isolated from Nonomuraea sp. MJM5123, following a high-throughput campaign for anti-TB activity. The large molecular weight of 1599 amu detected by LC-HR-MS precluded the initial inference of its molecular formula. The individual building blocks were identified by extensive NMR experiments. The resulting two possible planar structures were distinguished by LC-MS(2). Determination of absolute configuration and unambiguous structural confirmation were carried out by X-ray crystallography and Marfeys analysis.

Ameliorative Effects of Monascus pilosus-Fermented Black Soybean (Glycine max L. Merrill) on High-Fat Diet-Induced Obesity

The purpose of this study was to examine the antiobesity effects of Monascus pilosus-fermented black soybean (F-BS) in C57BL/6 mice with high-fat diet (HFD)-induced obesity. F-BS (oral, 0.5 and 1.0 g/kg per body weight, twice per day) ameliorated obesity by reducing body and liver weight increases, and regulating blood glucose and cholesterol levels in C57BL/6 mice fed a control or HFD with oral administration of F-BS for 12 weeks. F-BS suppressed the growth of epididymal, retroperitoneal, and perirenal fat pads by preventing increases in the adipocyte size. Moreover, the levels of blood glucose, total cholesterol, and leptin were significantly lowered by F-BS administration in a dose-dependent manner. These results indicated that F-BS is a beneficial food supplement for preventing obesity, controlling blood glucose, and lowering cholesterol. Future research strategies should address the mechanisms that selectively regulate obesity, including hyperglycemia and hypercholesterolemia.

Structural Studies on the Extracellular Domain of Sensor Histidine Kinase YycG from Staphylococcus aureus and Its Functional Implications

Bacterial two-component signal transduction systems are used to adapt to fluctuations in the environment. YycG, a key two-component histidine kinase in Staphylococcus aureus, plays an essential role in cell viability and regulates cell wall metabolism, biofilm formation, virulence, and antibiotic resistance. For these reasons, YycG is considered a compelling target for the development of novel antibiotics. However, to date, the signaling mechanism of YycG and its stimulus are poorly understood mainly because of a lack of structural information on YycG. To address this deficiency, we determined the crystal structure of the extracellular domain of S. aureus YycG (YycGex) at 2.0-Å resolution. The crystal structure indicated two subunits with an extracellular Per-Arnt-Sim (PAS) topology packed into a dimer with interloop interactions. Disulfide scanning using cysteine-substituted mutants revealed that YycGex possessed dimeric interfaces not only in the loop but also in the helix α1. Cross-linking studies using intact YycG demonstrated that it was capable of forming high molecular weight oligomers on the cell membrane. Furthermore, we also observed that two auxiliary proteins of YycG, YycH and YycI, cooperatively interfered with the multimerization of YycG. From these results, we propose that signaling through YycG is regulated by multimerization and binding of YycH and YycI. These structural studies, combined with biochemical analyses, provide a better understanding of the signaling mechanism of YycG, which is necessary for developing novel antibacterial drugs targeting S. aureus.

Anti-inflammatory effects of KOTMIN13: A mixed herbal medicine in LPS-stimulated RAW 264.7 cells and mouse edema models

Background: A Korean herbal medicine, KOTMIN13, composed of Inula japonica Thunberg, Trichosanthes kirilowii Maximowicz var. japonica kitamura, Peucedanum praeruptorum Dunn, and Allium macrostemon Bge, has been used for anti-allergic and anti-asthmatic treatment in oriental clinics, but its activity has not been investigated. Materials and Methods: To evaluate the anti-inflammatory activity of KOTMIN13 for in vitro study, LPS-stimulated RAW 264.7 cells were used to induce the production and expression of inflammatory mediators and its mechanisms. 12-O-Tetradecanoylphorobol-13 aceate (TPA)-induced ear edema and carrageenan-induced paw edema models were also used to evaluate the effect of KOTMIN13 on acute inflammation in vivo. Results: KOTMIN13 reduced the release of inflammatory mediators [nitric oxide, prostaglandin E2, interleukin (IL)-1β, and IL-6] and the protein expression of inducible nitric oxide synthase and cyclooxygenase-2 in LPS-stimulated RAW 264.7 cells. Mechanism studies showed the attenuation of LPS-induced NF-κB activation by KOTMIN13 via IκBα degradation abrogation and a subsequent decrease in nuclear p65 levels. Activation of mitogen-activated protein kinases (ERK, JNK, and p38) was also suppressed. Furthermore, KOTMIN13 ameliorated the development of TPA-induced ear edema and carrageenan-induced paw edema in acute inflammatory edema mouse models. Conclusion: Our study demonstrates that KOTMIN13 inhibits inflammatory mediators through the inhibitions of NF-κB and MAPK activities in LPS-induced RAW 264.7 cells, as well as acute inflammation in edema models, indicating that KOTMIN13 is an effective suppressor for anti-inflammatory activities. Abbreviations used: NO: nitric oxide; PGE2: prostaglandin E2; iNOS: inducible NO synthase; COX-2: cyclooxygenase-2; TNF-α: tumor necrosis factor-α; IL: interleukin; NF-κB: nuclear factor kappaB; MAPK: mitogen-activated protein kinases; ERK: extracellular signal regulated kinase; JNK: c-jun N terminal kinase; TPA: 12-O-tetradecanoylphorbol-13-acetate

Effects of Hot-Water Extract of Mulberry Leaf Tea Fermented by Monascus pilosus on Body Weight and Hepatic Antioxidant Enzyme Activities in Mouse Fed a Normal Diet

Abstract In this study, to evaluate the anti-obesity effects of mulberry leaf tea and its fermented product by Monascus pilosus , we investigated body and organ weight, blood and liver biomarkers in mice fed 1% tea infusionsinstead of water for 8 weeks. Mice were divided into three groups such as a normal control (NC), unfermented mulberry leaf tea infusion (UMI) and fermented mulberry leaf tea infusion (FMI). Although it is not significant, teainfusion groups showed reduction of body weight gains compared with NC group. Moreover, contents of LDL-cholesterol and lipid peroxide (LPO), altherogenic index, and xanthin oxidase (XO) activity were significantlydecreased, and glutathione S-transferase (GST) activity was significantly elevated. The results from this study suggested that UMI and FMI may have an anti-obesity activity, upregulate antioxidant enzymes and reduce levelsof oxidants related to liver damage. Key Words : Antiobese, Fermentation, Monascus pilosuss, Mulberry leaf tea, ROS-scavenging enzymes

Determination of Formaldehyde in Cosmetics Using a Convenient DNPH Derivatization Procedure Followed by HPLC Analysis

대한민국 식품의약품안전처(식약처)는 포름알데하이드 분석법으로 2,4-dinitrophenylhydrazine(DNPH) 유도체화-고성능액체크로마토그래프법(HPLC)을 고시하고 있다. 본 연구는 고시법의 복잡한 시료 전처리 과정을 개선하여 화장품 분석에 편리하게 사용할 수 있는 유도체화법을 개발하고자 수행되었다. 전처리법을 간단하게 하기 위하여 pH, 시간 및 온도 등 반응조건을 최적화하였다. 이 전처리법은 초산염 완충액(pH 5.0)을 사용한 검액의 pH 조정, 디클로로메탄을 사용한 액-액 분획 그리고 감압농축기를 사용한 증발건조와 같이 식약처 고시법의 복잡한 과정이 필요 없다. 유도체화 과정을 통하여 생성된 formaldehyde dinitrophenylhydrazone(formaldehyde-DNP)는 식약처의 시험방법을 약간 변형한 역상 HPLC법으로 분리하고 정량하였다. 2 ~ 40 ppm 농도 범위의 표준액들을 가지고 수행한 검량선 작성 결과, 본 시험법은 상관계수 값이 0.9999로 좋은 직선성을 보여주었다. 본 실험의 최소검출한계(LOD)와 최소정량한계(LOQ)는 각각 0.2 ppm과 0.5 ppm이었다. 또한 회수율 실험결과는 실험방법이 매우 정확하고 재현성이 높음을 보여주었다. 따라서 본 연구에서 제안된 시험법은 화장품 중 포름알데하이드를 신속하게 분석하는데 적용될 수 있을 것이다. 【Korea Food and Drug Administration (KFDA) has officially announced 2,4-dinitrophenylhydrazine (DNPH) derivatization - high performance liquid chromatography (HPLC) methods for analysis of formaldehyde. This study was conducted to develop a convenient derivatization method for cosmetics by improving complex pre-treatment procedures included in KFDA method. To simplify pre-treatment procedures of KFDA method, reaction conditions including pH, time and temperature were optimized. This pre-treatment method does not require complicate pre-treatment steps of KFDA method such as pH adjustment of test solution with acetate buffer (pH 5.0), solvent-solvent partitioning with dichloromethane and concentrating procedure with vacuum evaporator. Formaldehyde-dinitrophenylhydrazone (formaldehyde-DNP) product produced by derivatization reaction was separated and quantified with a reversed-phase HPLC, which was slightly modified with KFDA method. The linearity test showed good results with 0.9999 of correlation coefficient (

Crystal structure analysis of c4763, a uropathogenic Escherichia coli-specific protein

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Characterization and Culture Optimization of an Glucosidase Inhibitor-producing Bacteria, Gluconobactor oxydans CK-2165

) in the range of 2 ~ 40 ppm of standard solutions. In this method, limit of detection (LOD) and limit of quantitation (LOQ) values for formaldehyde were 0.2 ppm and 0.5 ppm, respectively. In addition, recovery test demonstrated that the method was also accurate and reproducible. Therefore, the proposed method can be applicable to rapid analysis of formaldehyde in cosmetics.】

KOTMIN13, a Korean herbal medicine alleviates allergic inflammation in vivo and in vitro

Urinary-tract infections (UTIs), which are some of the most common infectious diseases in humans, can cause sepsis and death without proper treatment. Therefore, it is necessary to understand their pathogenicity for proper diagnosis and therapeutics. Uropathogenic Escherichia coli, the major causative agents of UTIs, contain several genes that are absent in nonpathogenic strains and are therefore considered to be relevant to UTI pathogenicity. c4763 is one of the uropathogenic E. coli-specific proteins, but its function is unknown. To investigate the function of c4763 and its possible role in UTI pathogenicity, its crystal structure was determined at a resolution of 1.45 Å by a multiple-wavelength anomalous diffraction method. c4763 is a homodimer with 129 residues in one subunit that contains a GGCT-like domain with five α-helices and seven β-strands. c4763 shows structural similarity to the C-terminal domain of allophanate hydrolase from Kluyveromyces lactis, which is involved in the degradation of urea. These results suggest that c4763 might be involved in the utilization of urea, which is necessary for bacterial survival in the urinary tract. Further biochemical and physiological investigation will elucidate its functional relevance in UTIs.