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Novosphingobium ginsenosidimutans sp. nov., with the Ability to Convert Ginsenoside
( Jin Kwang Kim ),( Dan He ),( Qing Mei Liu ),( Hye Yoon Park ),( Mi Sun Jung ),( Min Ho Yoon ),( Sun Chang Kim ),( Wan Taek Im ) 한국미생물 · 생명공학회 2013 Journal of microbiology and biotechnology Vol.23 No.4
A Gram-negative, strictly aerobic, non-motile, non-sporeforming, and rod-shaped bacterial strain designated FW-6T was isolated from a freshwater sample and its taxonomic position was investigated by using a polyphasic approach. Strain FW-6T grew optimally at 10-42oC and at pH 7.0 on nutrient and R2A agar. Strain FW-6T displayed β- glucosidase activity that was responsible for its ability to transform ginsenoside Rb1 (one of the dominant active components of ginseng) to Rd. On the basis of 16S rRNA gene sequence similarity, strain FW-6T was shown to belong to the family Sphingomonadaceae and was related to Novosphingobium aromaticivorans DSM 12444T (98.1% sequence similarity) and N. subterraneum IFO 16086T (98.0%). The G+C content of the genomic DNA was 64.4%. The major menaquinone was Q-10 and the major fatty acids were summed feature 7 (comprising C18:1 ω9c/ ω12t/ω7c), summed feature 4 (comprising C16:1 ω7c/iso- C15:0 2OH), C16:0, and C14:0 2OH. DNA and chemotaxonomic data supported the affiliation of strain FW-6T to the genus Novosphingobium. Strain FW-6T could be differentiated genotypically and phenotypically from the recognized species of the genus Novosphingobium. The isolate that has ginsenoside converting ability therefore represents a novel species, for which the name Novosphingobium ginsenosidimutans sp. nov. is proposed, with the type strain FW-6T (= KACC 16615T = JCM 18202T).
전사체와 대사물질 구조분석을 통한 Novosphingobium pentaromativorans US6-1의 dibenzofuran 분해 경로 해석
나혜윤,권개경,Na, Hyeyun,Kwon, KaeKyoung 한국미생물학회 2018 미생물학회지 Vol.54 No.1
다환 방향족 탄화수소(polycyclic aromatic hydrocarbon, PAH) 우수 분해균주인 Novosphingobium pentaromativorans US6-1의 dibenzofuran (DBF) 분해경로를 밝히기 위하여 중간대사물질 분석과 전사체 분석을 진행하였다. GC/MS로 중간대사물질을 분석한 결과, 3(2H)-벤조퓨라논이 검출되었는데 이 화합물은 측면 이산소화에 의해 생성된 중간대사산물들의 기본 골격이 되는 물질로써 균주 US6-1에 의한 DBF의 분해가 측면 이산소화로 진행될 가능성을 시사한다. RNA-Seq 분석 결과, 균주 US6-1이 DBF에 노출되었을 때 발현되는 유전자들의 대부분이 lateral dioxygenation과 관련이 있다는 것을 확인하였다. 이상의 결과로부터N. pentaromativorans US6-1에 의해 일어나는 측면 이산소화를통한 DBF 분해경로와 관련 유전자들을 제시하였다. Biodegradation pathway of dibenzofuran (DBF) of Novosphingobium pentaromativorans US6-1, a high-molecular-weight polycyclic aromatic hydrocarbons degrading strain, was investigated via analysis of metabolic intermediates and transcriptome. As a result, 3(2H)-benzofuranone, a basic skeleton of the metabolic intermediates produced by lateral dioxygenation process, was detected as an intermediate. RNA-Seq analysis confirmed that most of the expressed genes upon exposure to DBF were related to the lateral degradation pathway. Based on these results, the biodegradation pathway of DBF by N. pentaromativorans US6-1 was proposed.
류청매,이병희,이기은,김상용,위지향,임완택 한국미생물학회 2020 미생물학회지 Vol.56 No.1
According to the previous study, a Gram-stain-negative, rodshaped, non-spore-forming, non-motile bacterium, Novosphingobium ginsenosidimutans FW-6 T was isolated from fresh water. Strain FW-6 T possessed β-glucosidase activity, which was responsible for its ability to convert ginsenoside Rb1 to ginsenoside Rd. In this study the whole genome of Novosphingobium ginsenosidimutans FW-6 T was sequenced, which consisted of one circular chromosome of 3,118,872 bp, with a DNA G + C content of 64.3%. Of the 3,073 predicted genes, 2,996 proteincoding genes, 50 RNA genes and 27 pseudogenes were identified. The whole genome analysis of strain FW-6 T showed several genes including glycoside hydrolase, antitoxin genes, and DNA repair genes.
Novosphingobium sp. PP1Y as a novel source of outer membrane vesicles
Federica De Lise,Francesca Mensitieri,Giulia Rusciano,Fabrizio Dal Piaz,Giovanni Forte,Flaviana Di Lorenzo,Antonio Molinaro,Armando Zarrelli,Valeria Romanucci,Valeria Cafaro,Antonio Sasso,Amelia Filip 한국미생물학회 2019 The journal of microbiology Vol.57 No.6
Outer membrane vesicles (OMVs) are nanostructures of 20– 200 nm diameter deriving from the surface of several Gramnegative bacteria. OMVs are emerging as shuttles involved in several mechanisms of communication and environmental adaptation. In this work, OMVs were isolated and characterized from Novosphingobium sp. PP1Y, a Gram-negative non-pathogenic microorganism lacking LPS on the outer membrane surface and whose genome was sequenced and annotated. Scanning electron microscopy performed on samples obtained from a culture in minimal medium highlighted the presence of PP1Y cells embedded in an extracellular matrix rich in vesicular structures. OMVs were collected from the exhausted growth medium during the mid-exponential phase, and purified by ultracentrifugation on a sucrose gradient. Atomic force microscopy, dynamic light scattering and nanoparticle tracking analysis showed that purified PP1Y OMVs had a spherical morphology with a diameter of ca. 150 nm and were homogenous in size and shape. Moreover, proteomic and fatty acid analysis of purified OMVs revealed a specific biochemical “fingerprint”, suggesting interesting details concerning their biogenesis and physiological role. Moreover, these extracellular nanostructures do not appear to be cytotoxic on HaCaT cell line, thus paving the way to their future use as novel drug delivery systems.
윤성호,이상엽,최치원,이하영,노현주,전상미,권용민,권개경,김상진,김건화,김승일 한국미생물학회 2017 The journal of microbiology Vol.55 No.1
Novosphingobium pentaromativorans US6-1 is a Gram-negative halophilic marine bacterium able to utilize several polycyclic aromatic hydrocarbons such as phenanthrene, pyrene, and benzo[a]pyrene. In this study, using transmission electron microscopy, we confirmed that N. pentaromativorans US6-1 produces outer membrane vesicles (OMVs). N. pentaromativorans OMVs (hereafter OMVNovo) are spherical in shape, and the average diameter of OMVNovo is 25–70 nm. Proteomic analysis revealed that outer membrane proteins and periplasmic proteins of N. pentaromativorans are the major protein components of OMVNovo. Comparative proteomic analysis with the membrane-associated protein fraction and correlation analysis demonstrated that the outer membrane proteins of OMVNovo originated from the membrane- associated protein fraction. To the best of our knowledge, this study is the first to characterize OMV purified from halophilic marine bacteria.
주베르,박혜윤,김가련,Chang-Hao Cui,조영준,김선창,임완택 한국생물공학회 2021 Biotechnology and Bioprocess Engineering Vol.26 No.6
Background: The minor ginsenosides such as F2, C-K, Rh2, and Rg3 make up less than 1% of the total ginseng extract; however, many studies have shown that ginsenoside F2 has anti-cancer and antioxidant effects and improves dementia and atopic dermatitis. Therefore, the enhanced production of this minor ginsenoside is a promising approach for the pharmaceutical industry. In this study, we found and cloned a novel glycoside hydrolase gene for the gram-scale production of ginsenoside F2. Methods and Results: Novosphingobium aromaticivorans, which was isolated from deep-terrestrial-subsurface sediments, has shown ginsenoside-converting ability. From this bacterium, a novel glycoside hydrolase, named BglNar, was found that can efficiently biotransform the protopanaxatriol (PPD-mix-type) major ginsenosides (Rb1, Rb2, Rc, and Rd) into the minor ginsenoside F2. This enzyme was cloned, expressed in Escherichia coli BL21, and characterized. The BglNar comprises 439 amino acid and belongs to the glycoside hydrolase family 1. The Km value of p-nitrophenyl- β-D-glucopyranoside was 9.06 ± 0.28 and the Vmax value was 24.0 ± 0.34 μmol/min/mg of protein. For gram-scale production of minor ginsenoside F2, crude PPD-mix-type ginsenosides (2 g/400 mL) were treated with BglNar and 1.14 g of F2 with final purity of 82.5 ± 1.3%, was obtained after purification using a column packed with HP20 resin. Conclusion: Our preliminary data demonstrate that the gram production of ginsenoside F2 using a recombinant enzyme will enhance the health benefits of Panax ginseng. This is the first study describing the gram-scale production of F2 from PPD-mix using a single novel ginsenosidetransforming β-glucosidase of the GH family 1. Significance and Impact of Study: In most of the previous studies, researchers have been used the combination of enzymes for production of F2, while in this study we found the possibility of gram-scale production of F2 from PPD-mixtype major ginsenosides using a single recombinant enzyme, thus simplifying the production and reducing the cost.
Xiaobin Liao,Chao Chen,Chih-Hsiang Chang,Zhao Wang,Xiaojian Zhang,Shuguang Xie 한국생물공학회 2012 Biotechnology and Bioprocess Engineering Vol.17 No.4
Filtration using biological activated carbon (BAC) performs well in the removal of biodegradable dissolved organic carbon from water sources. The application of ozonation followed by up-flow BAC filtration has gained increasing attention in the world scale. In this study, a pilotscale up-flow BAC filtration system was constructed for the treatment of polluted lake water. The operational results indicated that this BAC filtration system could effectively remove organic matter. Spatial heterogeneity of the microbial community structure inside the BAC filtration system was identified using bacterial 16S rRNA clone library analysis. A marked decrease of microbial diversity in the BAC filtration system was observed along the flow path. Alphaproteobacteria,Gammaproteobacteria and Acidobacteria were found to be the major bacterial groups in the BAC filters. Moreover, Novosphingobium aromaticivorans-like microorganisms were detected. This work might add some new insights towards microbial communities in regards to BAC filtration for the treatment of drinking water.
강지현(Ji-Hyun Kang),이희순(Hee Sun Lee),이숙영(Suk Young Lee),권개경(Kae Kyoung Kwon),김상진(Sang-Jin Kim) 한국해양환경·에너지학회 2004 한국해양환경공학회 학술대회논문집 Vol.2004 No.-
In the previous work we reported that 1,2-hydroxypropyl-β-cyclodextrin (β-HPCD) could accelerate the biodegradation rate of PAHs by increasing the solubility of PAHs through detaining of PAHs in the cavity of β-HPCD. The aim of this study is to screen for chiefer material which could substitute the β-HPCD, because the β-HPCD is too expensive for bulk usage. Low molecular weight PAHs, saturated hydrocarbons, metabolites of PAHs, several plant terpenoids, β-cyclodextrin and mixed form of cyclodextrin were tested for the enhancement of PAHs biodegradation. As a result, most of the tested materials could enhance the biodegradation rate of benzo[a]pvrene, more or less, except hexadecane, β-cyclodextrin and thymol. The enhancement was not affected by the concentration of additives. Among the additives, the addition of 1% mixed form of cyclodextrin could enhance the BaP degradation rate comparable to that of β-HPCD. Therefore, mixed form of cyclodextrin could substitute the β-HPCD to increase the degradation rate of HMW - PAHs by N. pentaromativorans US6-1.