Journal of Microbiology

Journal Article

Mutation of the cyclic di-GMP phosphodiesterase gene in Burkholderia lata SK875 attenuates virulence and enhances biofilm formation: Hae-In Jung , Yun-Jung Kim , Yun-Jung Lee , Hee-Soo Lee , Jung-Kee Lee , Soo-Ki Kim; J. Microbiol. 2017;55(10):800-808. Published online September 28, 2017; DOI: https://doi.org/10.1007/s12275-017-7374-7

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Burkholderia sp. is a gram-negative bacterium that commonly exists in the environment, and can cause diseases in plants, animals, and humans. Here, a transposon mutant library of a Burkholderia lata isolate from a pig with swine respiratory disease in Korea was screened for strains showing attenuated virulence in Caenorhabditis elegans. One such mutant was obtained, and the Tn5 insertion junction was mapped to rpfR, a gene encoding a cyclic di-GMP phosphodiesterase that functions as a receptor. Mutation of rpfR caused a reduction in growth on CPG agar and swimming motility as well as a rough colony morphology on Congo red agar. TLC analysis showed reduced AHL secretion, which was in agreement with the results from plate-based and bioluminescence assays. The mutant strain produced significantly more biofilm detected by crystal violet staining than the parent strain. SEM of the mutant strain clearly showed that the overproduced biofilm contained a filamentous structure. These results suggest that the cyclic di-GMP phosphodiesterase RpfR plays an important role in quorum sensing modulation of the bacterial virulence and biofilm formation.

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Biocontrol of bacterial wilt disease in tomato using Bacillus subtilis strain R31
Yunhao Sun, Yutong Su, Zhen Meng, Jie Zhang, Li Zheng, Shuang Miao, Di Qin, Yulan Ruan, Yanhui Wu, Lina Xiong, Xun Yan, Zhangyong Dong, Ping Cheng, Mingwei Shao, Guohui Yu
Frontiers in Microbiology.2023;[Epub] CrossRef
Comprehensive genome analysis of Burkholderia contaminans SK875, a quorum-sensing strain isolated from the swine
Eiseul Kim, Hae-In Jung, Si Hong Park, Hae-Yeong Kim, Soo-Ki Kim
AMB Express.2023;[Epub] CrossRef
Comparative genomics and transcriptomic response to root exudates of six rice root-associated Burkholderia sensu lato species
Adrian Wallner, Agnieszka Klonowska, Ludivine Guigard, Eoghan King, Isabelle Rimbault, Eddy Ngonkeu, Phuong Nguyen, Gilles Béna, Lionel Moulin
Peer Community Journal.2023;[Epub] CrossRef
The cis -2-Dodecenoic Acid (BDSF) Quorum Sensing System in Burkholderia cenocepacia
Mingfang Wang, Xia Li, Shihao Song, Chaoyu Cui, Lian-Hui Zhang, Yinyue Deng, Gladys Alexandre
Applied and Environmental Microbiology.2022;[Epub] CrossRef
A c-di-GMP Signaling Cascade Controls Motility, Biofilm Formation, and Virulence in Burkholderia thailandensis
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Applied and Environmental Microbiology.2022;[Epub] CrossRef
Methodological tools to study species of the genus Burkholderia
Viola Camilla Scoffone, Gabriele Trespidi, Giulia Barbieri, Samuele Irudal, Aygun Israyilova, Silvia Buroni
Applied Microbiology and Biotechnology.2021; 105(24): 9019. CrossRef
Complete Genome Sequence of Burkholderia contaminans SK875, Isolated from the Respiratory Tract of a Pig in the Republic of Korea
Hae-In Jung, Sang-Won Lee, Soo-Ki Kim, Irene L. G. Newton
Microbiology Resource Announcements.2020;[Epub] CrossRef
Key Players and Individualists of Cyclic-di-GMP Signaling in Burkholderia cenocepacia
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Frontiers in Microbiology.2019;[Epub] CrossRef
In silico comparative analysis of GGDEF and EAL domain signaling proteins from the Azospirillum genomes
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BMC Microbiology.2018;[Epub] CrossRef

Research Support, Non-U.S. Gov'ts

Isolation and Characterization of a Family VII Esterase Derived from Alluvial Soil Metagenomic Library: Weixin Tao , Myung Hwan Lee , Jing Wu , Nam Hee Kim , Seon-Woo Lee; J. Microbiol. 2011;49(2):178-185. Published online May 3, 2011; DOI: https://doi.org/10.1007/s12275-011-1102-5

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Abstract: A novel esterase gene, estDL30, was isolated from an alluvial metagenomic library using function-driven screening. estDL30 consisted of 1,524 nucleotides and encoded a 507-amino acid protein. Sequence analysis revealed that EstDL30 is similar to many type B carboxylesterases, containing a G-E-S-A-G pentapeptide with a catalytic Ser residue. Phylogenetic analysis suggested that EstDL30 belongs to the family VII lipases, together with esterases from Bacillus subtilis (P37967), Streptomyces coelicolor A3(2) (CAA22794), and Arthrobacter oxydans (Q01470). Purified EstDL30 showed its highest catalytic efficiency toward p-nitrophenyl butyrate, with a kcat of 229.3 s-1 and kcat/Km of 176.4 s-1mM-1; however, little activity was detected when the acyl chain length exceeded C8. Biochemical characterization of EstDL30 revealed that it is an alkaline esterase that possesses maximal activity at pH 8 and 40°C. The effects of denaturants and divalent cations were also investigated. EstDL30 tolerated well the presence of methanol and Tween 20. Its activity was strongly inhibited by 1 mM Cu2+ and Zn2+, but stimulated by Fe2+. The unique properties of EstDL30, its high activity under alkaline conditions and stability in the presence of organic solvents, may render it applicable to organic synthesis.

Screening and Identification of a Novel Esterase EstPE from a Metagenomic DNA Library: So-Youn Park , Hyun-Jae Shin , Geun-Joong Kim; J. Microbiol. 2011;49(1):7-14. Published online March 3, 2011; DOI: https://doi.org/10.1007/s12275-011-0201-7

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Abstract: Esterases represent a large family of hydrolases with broad substrate specificity and functional sequence space. Although many attempts to screen new esterases have been conducted, there have been few reports conducted to discriminate unique enzymes from typical ones based on novel structure and function. In this study, we discovered an esterase and a novel family through a successive assay of whole cells and crude lysates (oxidative open condition). The screened putative esterases from the metagenomic DNA of salted shrimp consisted of 753 bp encoding 27 kDa of polypeptide, namely PE esterase. Sequence analyses revealed that an identical gene was reported from whole genome sequencing of Stenotrophomonas maltophilia K279a. However, its biochemical and phylogenetic characteristics have not yet been evaluated. PE esterase was overexpressed only by the MBP fusion state in E. coli and was easily purified using an affinity column. This enzyme showed a typical spectrum of substrate specificity and possessed the consensus motifs, Ser-Asp-His and GXSXG, which are essential for most esterase/lipase superfamilies. Interestingly, the entire organization of the ORF and consensus sequence around the active site were distinct from the related enzymes, and its structure could be affected by a reducing agent, DTT.

Effect of Fungal Pellet Morphology on Enzyme Activities Involved in Phthalate Degradation: Young-Mi Kim , Hong-Gyu Song; J. Microbiol. 2009;47(4):420-424. Published online September 9, 2009; DOI: https://doi.org/10.1007/s12275-009-0051-8

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Abstract: Pellet size of white rot fungus, Pleurotus ostreatus may affect the secretion of its degradative enzymes and accompanying biodegrading capability, but could be controlled by several physical culture conditions in liquid culture. The pellet size of P. ostreatus was affected by the volume of inoculum, flask, and medium, but the agitation speed was the most important control factor. At the lower agitation speed of 100 rpm, the large pellets were formed and the laccase activity was higher than that of small pelleted culture at 150 rpm, which might be due to loose intrapellet structure. However, the biodegradation rates of benzylbutylphthalate and dimethylphthalate were higher in the small pelleted culture, which indicated the involvement of other degradative enzyme rather than laccase. The activity of esterase which catalyzes the nonphenolic compounds before the reaction of ligninolytic enzymes was higher in the small pelleted culture, and coincided with the degradation pattern of phthalates. This study suggests the optimization of pellet morphology and subsequent secretion of degradative enzymes is necessary for the efficient removal of recalcitrants by white rot fungi.

Cloning and Analysis of a Type II Polyketide Synthase Gene Cluster from Streptomyces toxytricini NRRL 15,443: Anna Yoo , Atanas V. Demirev , Ji Seon Lee , Sang Dal Kim , Doo Hyun Nam; J. Microbiol. 2006;44(6):649-654.; DOI: https://doi.org/2462 [pii]

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Abstract: A standard type II polyketide synthase (PKS) gene cluster was isolated while attempting to clone the biosynthetic gene for lipstatin from Streptomyces toxytricini NRRL 15,443. This result was observed using a Southern blot of a PstI-digested S. toxytricini chromosomal DNA library with a 444 bp amplified probe of a ketosynthase (KS) gene fragment. Four open reading frames [thioesterase (TE), β-ketoacyl systhase (KAS), chain length factor (CLF), and acyl carrier protein (ACP)], were identified through the nucleotide sequence determination and analysis of a 4.5 kb cloned DNA fragment. In order to confirm the involvement of a cloned gene in lipstatin biosynthesis, a gene disruption experiment for the KS gene was performed. However, the resulting gene disruptant did not show any significant difference in lipstatin production when compared to wild-type S. toxytricini. This result suggests that lipstatin may not be synthesized by a type II PKS.

Journal Article

Effect of Mycelial Extract of Clavicorona pyxidata on Acetylcholinesterase and β-Secretase Activity in vitro: Tae-Hee Lee , Young-Il Park , Yeong-Hwan Han; J. Microbiol. 2006;44(5):502-507.; DOI: https://doi.org/2448 [pii]

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Abstract: In a previous study, an extract of Clavicorona pyxidata DGUM 29005 mycelia demonstrated an inhibitory effect against enzyme-associated perceptual disorders. We have attempted to determine whether this mycelial extract is also capable of inhibiting the activities of acetylcholinesterase (AChE) and β-secretase (BACE) activity. Butanol, ethanol, and water extracts of C. pyxidata DGUM 29005 mycelia were shown to inhibit AChE activity by 99.3%, 93.7%, and 91.7%, respectively. The inhibitory value of the butanol extract was more profound than that of tacrine (95.4%). The ethanol extract also exerted an inhibitory effect against BACE activity; this fraction may harbor the potential for development into a pharmocotherapeutic modality for the treatment of Alzheimer''s disease (AD) patients. Rat pheochromocytoma PC12 cells in culture were not determined to be susceptible to the cytotoxic activity evidenced by the mycelial extract. The ethanol extract inhibited endogenous AChE activity in PC12 cellular homogenates, with an IC50 of 67.5 μg/ml, after incubation with intact cells, and also inhibited BACE activity in a dose-dependent fashion. These results suggest that the C. pyxidata mycelial extract has the potential to enhance cholinergic function and, therefore, may perform a function in the amelioration of the cholinergic deficit observed in cases of AD, as well as other types of age-associated memory impairment.

Research Support, Non-U.S. Gov't

Cloning and Characterization of Thermostable Esterase from Archaeoglobus fulgidus: Seung-Bum Kim , Wonkyu Lee , Yeon-Woo Ryu; J. Microbiol. 2008;46(1):100-107.; DOI: https://doi.org/10.1007/s12275-007-0185-5

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34 Scopus

Abstract: Thermostable esterase gene was cloned (Est-AF) from extremophilic microorganisms, Archaeoglobus fulgidus DSM 4304. The protein analysis result showed that Est-AF is monomer with total 247 amino acids and molecular weight of estimated 27.5 kDa. It also showed repeating units G-X-S-X-G (GHSLG) (residues 86~90) which is reported as active site of known esterases, and the putative catalytic triad composed of Ser88, Asp198 and His226. The esterase activity test with various acyl chain length of ρ-nitrophenol resulted that Est-AF showed highest specific activity with ρ-nitrophenylbutyrate (pNPC4) and rapidly decrease with ρ-nitrophenyl ester contain more than 8 carbon chain. These results represent that cloned enzyme is verified as a carboxylesterase but not a lipase because esterase activity is decreased with ρ-nitrophenyl ester contains more than 8 carbon chains but lipase activity does not affected with carbon chain length. Optimum temperature of esterase reaction with ρ-nitrophenylbutyrate (pNPC4) was 80°C. When ketoprofen ethyl ester was used as a substrate, activity of Est-AF showed the highest value at 70°C, and 10% of activity still remains after 3 h of incubation at 90°C. This result represents Est-AF has high thermostability with comparison of other esterases that have been reported. However, Est-AF showed low enantioselectivity with ketoprofen ethyl ester. Optimum pH of Est-AF is between pH 7.0 and pH 8.0. Km value of ketoprofen ethyl ester is 1.6 mM and, Vmax is 1.7 μmole/mg protein/min. Est-AF showed similar substrate affinity but slower reaction with ketoprofen ethyl ester compare with esterase from mesophilic strain P. fluorescens.

Pleiotrohpic effect of a gene fragment conferring H₂O₂resistance in streptomyces coelicolor: Um, Tae Han , Oh, Chung Hun , Lee, Jong Soo , Park, Yong Doo , Roe, Jung Hye , Kim, Jae Heon; J. Microbiol. 1995;33(4):339-343.

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Abstract: We isolated a 10 kb Bam HI fragment originated from the chromosome of a H₂O₂-resistant mutant strain of Streptomyces coelicolor, which confer H₂O₂-resistance to S. lividance upon transformation. Among various subclones ot 10kb Bam HI fragment tested for their H₂O₂-resistant phenotype in S. lividans, a subclone containing 5.2 kb Bam HI-BglII fragment was found to be responsible for H₂O₂-resistance. The plasmid containing this 5.2 kb fragment was then transformed into S. coellicolor A3(2) at early and tested for their phenotype of H₂O₂-resistance and the change in various enzymes whose activity can be stained in the gel. We found out that the 5.2 kb insert DNA conferred H₂O₂-resisstance in S. coelicolor A3(2) at early phase of cell growth. The presence of this DNA also resulted in higher level of peroxidase compared with the wild type cell containing parental vector (pIJ702) only. Esterase activity was also higher in this clone. However, alcohol dehydrogenase activity decreased compared with the wild type. These results suggest that the presence of a gene in 5.2 kb BamHI-BglII DNA fragment causes multiple changes in S. coelicolor related to its response against hydrogen peroxide. The result also implies that not only peroxidase but also esterase may function in the defencse meahsnism agianst H₂O₂.

Isolation of a Medium Chain Length Polyhydroxyalkanoic Acids Degrading Bacterium, Janthinobacterium lividum: Jin-Seo Park , Jeong-Youl Choi , Pil-Mun Joung , Seong Joo Park , Young Ha Rhe e , Kwang-Soo Shin; J. Microbiol. 2001;39(2):139-141.

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Abstract: Medium-chain length polyhydroxyalkanoic acids (MCL-PHAs) degrading bacterium was isolated from the soil. The bacterium was identified as Janthinobacterium lividum by its biochemical properties, cell membrane fatty acids composition, and 16S rDNA sequence analysis. The bacterium showed a similarity of 0.911 with J. lividum according to the cell membrane fatty acids analysis and a similarity of 97% in the 16S rDNA sequence analysis. Culture supernatant of the bacterium showed the highest depolymerase activity toward polyhydroxynonanoic acid (PHN) that did not degrade the poly-[beta]-hydroxybutyric acid (PHB). The esterase activity was also detected with p-nitrophenyl (PNP) esters of fatty acids such as PNP-octanoic acid, PNP-dodecanoic acid, PNP-decanoic acid, and PNP-hexanoic acid.

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