Journal of Microbiology

Journal Articles

Genetic changes in plaque-purified varicella vaccine strain Suduvax during in vitro propagation in cell culture: Hye Rim Hwang , Se Hwan Kang , Chan Hee Lee; J. Microbiol. 2021;59(7):702-707. Published online June 1, 2021; DOI: https://doi.org/10.1007/s12275-021-1062-3

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Abstract: Infection by varicella-zoster virus (VZV) can be prevented by using live attenuated vaccines. VZV vaccine strains are known to evolve rapidly in vivo, however, their genetic and biological effects are not known. In this study, the plaque-purified vaccine strain Suduvax (PPS) was used to understand the genetic changes that occur during the process of propagation in in vitro cell culture. Full genome sequences of three different passages (p4, p30, and p60) of PPS were determined and compared for genetic changes. Mutations were found at 59 positions. The number of genetically polymorphic sites (GPS) and the average of minor allele frequency (MAF) at GPSs were not significantly altered after passaging in cell culture up to p60. The number of variant nucleotide positions (VNPs), wherein GPS was found in at least one passage of PPS, was 149. Overall, MAF changed by less than 5% at 52 VNPs, increased by more than 5% at 42 VNPs, and decreased by more than 5% at 55 VNPs in p60, compared with that seen in p4. More complicated patterns of changes in MAF were observed when genetic polymorphism at 149 VNPs was analyzed among the three passages. However, MAF decreased and mixed genotypes became unequivocally fixed to vaccine type in 23 vaccine-specific positions in higher passages of PPS. Plaque-purified Suduvax appeared to adapt to better replication during in vitro cell culture. Further studies with other vaccine strains and in vivo studies will help to understand the evolution of the VZV vaccine.

Intervention with kimchi microbial community ameliorates obesity by regulating gut microbiota: Seong-Eun Park , Sun Jae Kwon , Kwang-Moon Cho , Seung-Ho Seo , Eun-Ju Kim , Tatsuya Unno , So-Hyeon Bok , Dae-Hun Park , Hong-Seok Son; J. Microbiol. 2020;58(10):859-867. Published online September 2, 2020; DOI: https://doi.org/10.1007/s12275-020-0266-2

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The objective of this study was to evaluate anti-obesity effects of kimchi microbial community (KMC) on obesity and gut microbiota using a high fat diet-induced mouse model compared to effects of a single strain. Administration of KMC decreased body weight, adipose tissue, and liver weight gains. Relative content of Muribaculaceae in the gut of the KMCtreated group was higher than that in the high-fat diet (HFD) group whereas relative contents of Akkermansiaceae, Coriobacteriaceae, and Erysipelotrichaceae were lower in KMCtreated group. Metabolic profile of blood was found to change differently according to the administration of KMC and a single strain of Lactobacillus plantarum. Serum metabolites significantly increased in the HFD group but decreased in the KMC-treated group included arachidic acid, stearic acid, fumaric acid, and glucose, suggesting that the administration of KMC could influence energy metabolism. The main genus in KMC was not detected in guts of mice in KMC-treated group. Since the use of KMC has advantages in terms of safety, it has potential to improve gut microbial community for obese people.

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Review

[Minireivew]Microbial consortia including methanotrophs: some benefits of living together: Rajendra Singh , Jaewon Ryu , Si Wouk Kim; J. Microbiol. 2019;57(11):939-952. Published online October 28, 2019; DOI: https://doi.org/10.1007/s12275-019-9328-8

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Abstract

With the progress of biotechnological research and improvements made in bioprocessing with pure cultures, microbial consortia have gained recognition for accomplishing biological processes with improved effectiveness. Microbes are indispensable tool in developing bioprocesses for the production of bioenergy and biochemicals while utilizing renewable resources due to technical, economic and environmental advantages. They communicate with specific cohorts in close proximity to promote metabolic cooperation. Use of positive microbial associations has been recognized widely, especially in food industries and bioremediation of toxic compounds and waste materials. Role of microbial associations in developing sustainable energy sources and substitutes for conventional fuels is highly promising with many commercial prospects. Detoxification of chemical contaminants sourced from domestic, agricultural and industrial wastes has also been achieved through microbial catalysis in pure and co-culture systems. Methanotrophs, the sole biological sink of greenhouse gas methane, catalyze the methane monooxygenasemediated oxidation of methane to methanol, a high energy density liquid and key platform chemical to produce commodity chemical compounds and their derivatives. Constructed microbial consortia have positive effects, such as improved biomass, biocatalytic potential, stability etc. In a methanotroph- heterotroph consortium, non-methanotrophs provide key nutrient factors and alleviate the toxicity from the culture. Non-methanotrophic organisms biologically stimulate the growth and activity of methanotrophs via production of growth stimulators. However, methanotrophs in association with cocultured microorganisms are in need of further exploration and thorough investigation to study their interaction mode and application with improved effectiveness.

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Journal Articles

The crystal structure of methanol dehydrogenase, a quinoprotein from the marine methylotrophic bacterium Methylophaga aminisulfidivorans MPT: Thinh-Phat Cao , Jin Myung Choi , Si Wouk Kim , Sung Haeng Lee; J. Microbiol. 2018;56(4):246-254. Published online February 28, 2018; DOI: https://doi.org/10.1007/s12275-018-7483-y

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Abstract

The first crystal structure of a pyrroloquinoline quinone (PQQ)-dependent methanol dehydrogenase (MDH) from a marine methylotrophic bacterium, Methylophaga aminisulfidivorans MPT (MDHMas), was determined at 1.7 Å resolution. The active form of MDHMas (or MDHIMas) is a heterotetrameric α2β2, where each β-subunit assembles on one side of each of the α-subunits, in a symmetrical fashion, so that two β-subunits surround the two PQQ-binding pockets on the α-subunits. The active site consists of a PQQ molecule surrounded by a β-propeller fold for each α-subunit. Interestingly, the PQQ molecules are coordinated by a Mg2+ ion, instead of the Ca2+ ion that is commonly found in the terrestrial MDHI, indicating the efficiency of osmotic balance regulation in the high salt environment. The overall interaction of the β-subunits with the α-subunits appears tighter than that of terrestrial homologues, suggesting the efficient maintenance of MDHIMas integrity in the sea water environment to provide a firm basis for complex formation with MxaJMas or Cyt cL. With the help of the features mentioned above, our research may enable the elucidation of the full molecular mechanism of methanol oxidation by taking advantage of marine bacterium-originated proteins in the methanol oxidizing system (mox), including MxaJ, as the attainment of these proteins from terrestrial bacteria for structural studies has not been successful.

Citations

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Computational insights into the molecular dynamics of the binding of ligands in the methanol dehydrogenase
One-Sun Lee, Sung Haeng Lee
Chemistry Letters.2024;[Epub] CrossRef
Formaldehyde: An Essential Intermediate for C1 Metabolism and Bioconversion
Mengshi Jia, Mengge Liu, Jiawen Li, Wankui Jiang, Fengxue Xin, Wenming Zhang, Yujia Jiang, Min Jiang
ACS Synthetic Biology.2024; 13(11): 3507. CrossRef
Unveiling the Secrets of Calcium-Dependent Proteins in Plant Growth-Promoting Rhizobacteria: An Abundance of Discoveries Awaits
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The biochemistry of lanthanide acquisition, trafficking, and utilization
Emily R. Featherston, Joseph A. Cotruvo
Biochimica et Biophysica Acta (BBA) - Molecular Cell Research.2021; 1868(1): 118864. CrossRef
Bioinorganic insights of the PQQ-dependent alcohol dehydrogenases
Pedro D. Sarmiento-Pavía, Martha E. Sosa-Torres
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Bioinformatic analysis of subfamily-specific regions in 3D-structures of homologs to study functional diversity and conformational plasticity in protein superfamilies
Daria Timonina, Yana Sharapova, Vytas Švedas, Dmitry Suplatov
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Methanol Dehydrogenases as a Key Biocatalysts for Synthetic Methylotrophy
Thien-Kim Le, Yu-Jin Lee, Gui Hwan Han, Soo-Jin Yeom
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Lanthanide-dependent alcohol dehydrogenases require an essential aspartate residue for metal coordination and enzymatic function
Nathan M. Good, Matthias Fellner, Kemal Demirer, Jian Hu, Robert P. Hausinger, N. Cecilia Martinez-Gomez
Journal of Biological Chemistry.2020; 295(24): 8272. CrossRef
Zebra2: advanced and easy-to-use web-server for bioinformatic analysis of subfamily-specific and conserved positions in diverse protein superfamilies
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Crystal structure of Cytochrome cL from the aquatic methylotrophic bacterium Methylophaga aminisulfidivorans MPT
Suparna Ghosh, Immanuel Dhanasingh, Jaewon Ryu, Si Wouk Kim, Sung Haeng Lee
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New metal cofactors and recent metallocofactor insights
Robert P Hausinger
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Characterization of Trichoderma reesei Endoglucanase II Expressed Heterologously in Pichia pastoris for Better Biofinishing and Biostoning: Sutanu Samanta , Asitava Basu , Umesh Chandra Halder , Soumitra Kumar Sen; J. Microbiol. 2012;50(3):518-525. Published online June 30, 2012; DOI: https://doi.org/10.1007/s12275-012-1207-5

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Abstract: The endoglucanase II of Trichoderma reesei is considered the most effective enzyme for biofinishing cotton fabrics and biostoning denim garments. However, the commercially available preparation of endoglucanase II is usually mixed with other cellulase components, especially endoglucanase I, resulting in hydrolysis and weight loss of garments during biofinishing and biostoning. We thus isolated the endoglucanase II gene from T. reesei to express this in Pichia pastoris, under the control of a methanol-inducible AOX1 promoter, to avoid the presence of other cellulase components. A highly expressible Mut+ transformant was selected and its expression in BMMH medium was found most suitable for the production of large amounts of the recombinant protein. Recombinant endoglucanase II was purified to electrophoretic homogeneity, and functionally characterized by activity staining. The specific activity of recombinant endoglucanase II was found to be 220.57 EU/mg of protein. Purified recombinant endoglucanase II was estimated to have a molecular mass of 52.8 kDa. The increase in molecular mass was likely due to hyperglycosylation. Hyperglycosylation of recombinant endoglucanase II secreted by P. pastoris did not change the temperature or pH optima as compared to the native protein, but did result in increased thermostability. Kinetic analysis showed that recombinant endoglucanase was most active against amorphous cellulose, such as carboxymethyl cellulose, for which it also had a high affinity.

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

Characterization of Methylophaga sp. strain SK1 Cytochrome cL Expressed in Escherichia coli: Hee Gon Kim , Trong Nhat Phan , Tae Sa Jang , Moonjoo Koh , Si Wouk Kim; J. Microbiol. 2005;43(6):499-502.; DOI: https://doi.org/2299 [pii]

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Abstract: Methylophaga sp. strain SK1 is a new restricted facultative methanol-oxidizing bacterium that was isolated from seawater. The aim of this study was to characterize the electron carriers involved in the methanol oxidation process in Methylophaga sp. strain SK1. The gene encoding cytochrome cL (mxaG) was cloned and the recombinant gene was expressed in Escherichia coli DH5 under strict anaerobic conditions. The recombinant cytochrome cL had the same molecular weight and absorption spectra as the wild-type cytochrome cL both in the reduced and oxidized forms. The electron flow rate from methanol dehydrogenase (MDH) to the recombinant cytochrome cL was similar to that from MDH to the wild-type cytochrome cL. These results suggest that recombinant cytochrome cL acts as a physiological primary electron acceptor for MDH.

Effect of copper on the growth and methanol dehydrogenase activity of methylobacillusd sp. strain SK1 DSM 8269: Kim, Si W. , Kim, Young M.; J. Microbiol. 1996;34(2):172-178.

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Abstract: Methylobacillus sp. strain SK1, which grows only on methanol, was found to grow in the absence of added copper. The doubling time (t_d = 1.3 h) of the bacterium growing at the exponential growth phase at 30℃ in the absence of copper was the same as that of the cell growing in the presence of copper. The bacterium growing after the exponential phase in the absence of copper, however, grew faster than the cell growing in the presence of copper. Cells harvested after thee early stationary phase in the presence of copper were found to exhibit no methanol dehydrogenase (MDH) activity, but the amount and subunit structure of the enzyme in the cells were almost the same as that in cells harboring active MDH. Pellets of the cells harvested after the early stationary phase in the presence of copper were pale green. Cell-free extracts prepared from cells harvested at the early stationary phase in the presence of copper were pink and exhibited MDH activity, but it turned dark-green rapidly from the surface under air. The green-colored portions of the extracts showed no MDH activity and contained c-type cytochromes that were oxidized completely. The inactive MDH activity and contained c-type cytochromes that were oxidized completely. The inactive MDH proteins in the green portions were found to have antigenic sites identical to those of the active one as the inactive MDHs in cells grown in the presence of copper. The bacterium was found to accumulate copper actively during the exponential growth phase. MDH prepared from cells grown in the presence or absence of copper was found to be more stable under nitrogen gas than under air. Methanol at 10 mM was found to enhance the stability of the MDH under air.

Growth on methanol of a carboxydobacterium, acinetobacter sp. strain JC1 DSM 3803: Ro, Young Tae , Seo, Jae Goo , Lee, Joo Hun , Kim, Dae Myung , Chung, In Kwon , Kim, Tae Ue , Kim, Young Min; J. Microbiol. 1997;35(1):30-39.

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Abstract: Acinetobacter sp. strain JC1 DSM 3803, a carboxydobacterium, was found to grow methylotrophically at the expense of methanol and methlamine, but not of methane, formaldehyde, formate, dimethylamine, or trimethylamine, as the sole source of carbon and energy. The doubling times of the bacterium growing on methanol (0.5% v/v) and methylamine (0.5% w/v) at 30℃ and pH 6.8 were 4.8 h and 5.7 h respectively. Cells grown on methanol, however, failed to show typical methanol dehydrogenase and oxidase activities. The cell was found to contain no c-type cytochromes. Cells grown on methanol exhibited higher catalase activity than those grown on pyruvate or glucose. The catalase present in the cells also exhibited peroxidase activity. The catalase activity, growth on methanol of the cell, and oxygen consumption by methanol-grown maldehyde dehydrogenase, formaldehyde reductase, glucose-6-phosphate dehydrogenase, and 6-phosphogluconate dehydrogenase activities were detected from cells grown on methanol.

Kinetic and spectral investigations on Ca^2+ and Sr^2+ containing methanol dehydrogenases: Kim, Si Wouk , Kim, Chung, Sung , Lee, Jung Sup , Koh, Moon Joo , Yang, Song Suk , Duine, Johannis A. , Kim, Young Min; J. Microbiol. 1997;35(3):200-205.

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Abstract: Both Ca^2+ and Sr^2+ containing methanol dehydrogenases (MDH) were purified to homogeneity with yields of 48% and 42%, respectively, from Methylabacillus methanolovorus sp. strain SK5. Most of the biochemical and structural properties were similar to each other. However, some differences were found: (1) although the overall shape of the absorption spectrum of Sr^2+ MDH was very similar to that of Ca^2+ MDH, the absorption intensity originating from the cofactor in Sr^2+. MDH was higher than that in Ca^2+-MDH. Small blue shift of the maximum was also observed. These are probably due to a difference in redox state of the cofactors in Ca^2+ and Sr^2+ -MDH; (2)Sr^2+ -MDH was more heat-stable than Ca^2+-MDH above 56℃; (3) the V_max values for the methanol-dependent activities of Sr^2+ Ca^2+ -MDH in the presence of 3 mM KCN were 2.038 and 808 nmol/mg protein/min, respectively. In addition, the K_m values of Sr^2+ and Ca^2+ MDH for methanol were 12 and 21 uM, respectively; (4) the endogenous activity of Ca^2+ -MDH was more sensitive than that of Sr^2+ -MDH in the presence of cyanide; (5) Diethyl pyrocarbonate treatment increased the enzyme activities of Ca^2+ and Sr^2+ MDH 4.2 and 1.4 folds, respectively. These results indicate that Sr^2+ stabilizes the structural conformation and enhances the activity of MDH more than Ca^2+.

Enzyme Activities Related to the Methanol Oxidation of Mycobacterium sp. strain JC1 DSM 3803: Youngtae Ro , Eungbin Kim , Youngmin Kim; J. Microbiol. 2000;38(4):209-217.

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Abstract: Mycobacterium sp. strain JC1 DSM 3803 grown in methanol showed no methanol dehydrogenase or oxidase activities found in most methylotrophic bacteria and yeasts, respectively. Even though the methanol-grown cells exhibited a little methanol-dependent oxidation by cytochrome c-dependent methanol dehydrogenase and alcohol dehydrogenase, they were not the key enzymes responsible for the methanol oxidation of the cells, in that the cells contained no c-type cytochrome and the methanol oxidizing activity from the partially purified alcohol dehydrogenase was too low, respectively. In substrate switching experiments, we found that only a catalase-peroxidase among the three types of catalase found in glucose-grown cells was highly expressed in the methanol-grown cells and that its activity was relatively high during the exponential growth phase in Mycobacterium sp. JC1. Therefore, we propose that catalase-peroxidase is an essential enzyme responsible for the methanol metabolism directly or indirectly in Mycobacterium sp. JC1.

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