Journal Articles
- Genetic changes in plaque-purified varicella vaccine strain Suduvax during in vitro propagation in cell culture
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Hye Rim Hwang , Se Hwan Kang , Chan Hee Lee
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J. Microbiol. 2021;59(7):702-707. Published online June 1, 2021
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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
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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
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J. Microbiol. 2020;58(10):859-867. Published online September 2, 2020
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DOI: https://doi.org/10.1007/s12275-020-0266-2
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Abstract
- 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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Citations
Citations to this article as recorded by

- Anti-obesogenic effects of plant natural products: A focus on Korean traditional foods
Gitishree Das, Luis Alfonso Jiménez Ortega, Sandra Gonçalves, J. Basilio Heredia, Maria de Lourdes Gomes Pereira, Anabela Romano, Han-Seung Shin, Jayanta Kumar Patra
Trends in Food Science & Technology.2024; 148: 104470. CrossRef - Anti-obesity activity of lactic acid bacteria-starter-based kimchi in high-fat diet-induced obese mice
Ye-Rang Yun, Min-Sung Kwon, Ho-Jae Lee, Wooje Lee, Ji-Eun Lee, Sung Wook Hong
Journal of Functional Foods.2024; 112: 105966. CrossRef - Effects of Kimchi Intake on the Gut Microbiota and Metabolite Profiles of High-Fat-Induced Obese Rats
Dong-Wook Kim, Quynh-An Nguyen, Saoraya Chanmuang, Sang-Bong Lee, Bo-Min Kim, Hyeon-Jeong Lee, Gwang-Ju Jang, Hyun-Jin Kim
Nutrients.2024; 16(18): 3095. CrossRef - Does kimchi deserve the status of a probiotic food?
Jeongmin Cha, Yeon Bee Kim, Seong-Eun Park, Se Hee Lee, Seong Woon Roh, Hong-Seok Son, Tae Woong Whon
Critical Reviews in Food Science and Nutrition.2024; 64(19): 6512. CrossRef - Revisiting the potential anti-obesity effects of kimchi and lactic acid bacteria isolated from kimchi: a lustrum of evidence
Anshul Sharma, Hae-Jeung Lee
Journal of Ethnic Foods.2024;[Epub] CrossRef - Metabolites of Kimchi Lactic Acid Bacteria, Indole-3-Lactic Acid, Phenyllactic Acid, and Leucic Acid, Inhibit Obesity-Related Inflammation in Human Mesenchymal Stem Cells
Moeun Lee, Daun Kim, Ji Yoon Chang
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+
neutrophils on intraepithelial lymphocytes exacerbates gut inflammation via decreasing microbiota-derived DMF
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Ya‐Ling Yang, Ying‐Hsien Huang, Feng‐Sheng Wang, Ming‐Chao Tsai, Chien‐Hung Chen, Wei‐Shiung Lian
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Ye-Rang Yun, Moeun Lee, Jung Hee Song, Eun Ji Choi, Ji Yoon Chang
Journal of Functional Foods.2022; 90: 104969. CrossRef - Interaction between the PNPLA3 Gene and Nutritional Factors on NAFLD Development: The Korean Genome and Epidemiology Study
Sooyeon Oh, Jooho Lee, Sukyung Chun, Ja-Eun Choi, Mi Na Kim, Young Eun Chon, Yeonjung Ha, Seong-Gyu Hwang, Sang-Woon Choi, Kyung-Won Hong
Nutrients.2022; 15(1): 152. CrossRef -
Acids produced by lactobacilli inhibit the growth of commensal
Lachnospiraceae
and S24-7 bacteria
Emma J. E. Brownlie, Danica Chaharlangi, Erin Oi-Yan Wong, Deanna Kim, William Wiley Navarre
Gut Microbes.2022;[Epub] CrossRef - The Role of Gut Microbiota Modulation Strategies in Obesity: The Applications and Mechanisms
Lingyue Shan, Akanksha Tyagi, Umair Shabbir, Xiuqin Chen, Selvakumar Vijayalakshmi, Pianpian Yan, Deog-Hwan Oh
Fermentation.2022; 8(8): 376. CrossRef - Fermented rice bran supplementation ameliorates obesity via gut microbiota and metabolism modification in female mice
Shiro Tochitani, Yoshiteru Maehara, Takahiro Kawase, Takamitsu Tsukahara, Ryoichi Shimizu, Taizo Watanabe, Kazuo Maehara, Kenji Asaoka, Hideo Matsuzaki
Journal of Clinical Biochemistry and Nutrition.2022; 70(2): 160. CrossRef - Bifidobacterium longum 070103 Fermented Milk Improve Glucose and Lipid Metabolism Disorders by Regulating Gut Microbiota in Mice
Tong Jiang, Ying Li, Longyan Li, Tingting Liang, Mingzhu Du, Lingshuang Yang, Juan Yang, Runshi Yang, Hui Zhao, Moutong Chen, Yu Ding, Jumei Zhang, Juan Wang, Xinqiang Xie, Qingping Wu
Nutrients.2022; 14(19): 4050. CrossRef - What Is the Role of Gut Microbiota in Obesity Prevalence? A Few Words about Gut Microbiota and Its Association with Obesity and Related Diseases
Julita Tokarek, Joanna Gadzinowska, Ewelina Młynarska, Beata Franczyk, Jacek Rysz
Microorganisms.2021; 10(1): 52. CrossRef - Eating Fermented: Health Benefits of LAB-Fermented Foods
Vincenzo Castellone, Elena Bancalari, Josep Rubert, Monica Gatti, Erasmo Neviani, Benedetta Bottari
Foods.2021; 10(11): 2639. CrossRef - Anti-Inflammatory and Immunomodulatory Properties of Fermented Plant Foods
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Review
- [Minireivew]Microbial consortia including methanotrophs: some benefits of living together
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Rajendra Singh , Jaewon Ryu , Si Wouk Kim
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J. Microbiol. 2019;57(11):939-952. Published online October 28, 2019
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DOI: https://doi.org/10.1007/s12275-019-9328-8
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26
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28
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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
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Thinh-Phat Cao , Jin Myung Choi , Si Wouk Kim , Sung Haeng Lee
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J. Microbiol. 2018;56(4):246-254. Published online February 28, 2018
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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.
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Citations
Citations to this article as recorded by

- 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
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Dmitry Suplatov, Yana Sharapova, Elizaveta Geraseva, Vytas Švedas
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Suparna Ghosh, Immanuel Dhanasingh, Jaewon Ryu, Si Wouk Kim, Sung Haeng Lee
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Robert P Hausinger
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Giovanna De Simone, Fabio Polticelli, Silvio Aime, Paolo Ascenzi
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- Characterization of Trichoderma reesei Endoglucanase II Expressed Heterologously in Pichia pastoris for Better Biofinishing and Biostoning
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Sutanu Samanta , Asitava Basu , Umesh Chandra Halder , Soumitra Kumar Sen
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J. Microbiol. 2012;50(3):518-525. Published online June 30, 2012
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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
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Hee Gon Kim , Trong Nhat Phan , Tae Sa Jang , Moonjoo Koh , Si Wouk Kim
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J. Microbiol. 2005;43(6):499-502.
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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
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Kim, Si W. , Kim, Young M.
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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
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Ro, Young Tae , Seo, Jae Goo , Lee, Joo Hun , Kim, Dae Myung , Chung, In Kwon , Kim, Tae Ue , Kim, Young Min
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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
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Kim, Si Wouk , Kim, Chung, Sung , Lee, Jung Sup , Koh, Moon Joo , Yang, Song Suk , Duine, Johannis A. , Kim, Young Min
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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
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Youngtae Ro , Eungbin Kim , Youngmin Kim
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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.