- Fibroblast Growth Factor 11 Inhibits Hepatitis B Virus Gene Expression Through FXRα Suppression
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Mi So Seong , Jeong Ah Jang , Ye Rim Jeong , Ye Bin Kim , Yi Yi Kyaw , Hee Jeong Kong , Jung-Hyun Lee , JaeHun Cheong
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J. Microbiol. 2023;61(7): 693-702.
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DOI: https://doi.org/10.1007/s12275-023-00065-1
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 Abstract
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Fibroblast growth factor 11 (FGF11) is a member of the intracellular FGF family, which shows different signal transmission
compared with other FGF superfamily members. The molecular function of FGF11 is not clearly understood. In this study,
we identified the inhibitory effect of FGF11 on hepatitis B virus (HBV) gene expression through transcriptional suppression.
FGF11 decreased the mRNA and protein expression of HBV genes in liver cells. While the nuclear receptor FXRα1
increased HBV promoter transactivation, FGF11 decreased the FXRα-mediated gene induction of the HBV promoter by
the FXRα agonist. Reduced endogenous levels of FXRα by siRNA and the dominant negative mutant protein (aa 1–187
without ligand binding domain) of FXRα expression indicated that HBV gene suppression by FGF11 is dependent on FXRα
inhibition. In addition, FGF11 interacts with FXRα protein and reduces FXRα protein stability. These results indicate that
FGF11 inhibits HBV replicative expression through the liver cell-specific transcription factor, FXRα, and suppresses HBV
promoter activity. Our findings may contribute to the establishment of better regimens for the treatment of chronic HBV
infections by including FGF11 to alter the bile acid mediated FXR pathway.
- Expression and purification of intracrine human FGF 11 and study of its FGFR-dependent biological activity
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Kyeong Won Lee , Young Jun An , Janet Lee , Ye-Eun Jung , In Young Ko , Jonghwa Jin , Ji Hoon Park , Won Kyu Lee , Kiweon Cha , Sun-Shin Cha , Jung-Hyun Lee , Hyung-Soon Yim
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J. Microbiol. 2022;60(11):1086-1094. Published online November 1, 2022
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DOI: https://doi.org/10.1007/s12275-022-2406-3
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3
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Abstract
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Fibroblast growth factor 11 (FGF11) is one of intracrine FGFs
(iFGFs), which function within cells. Unlike canonical FGFs,
FGF11 remains intracellularly and plays biological roles in
FGF receptor (FGFR)-independent manner. Here, we established
an expression system of recombinant FGF11 proteins
in E. coli and investigated whether the extracellular administration
of FGF11 can activate cellular signaling. Human
FGF11 has two isoforms, FGF11a and FGF11b, depending
on the presence of nuclear localization sequences (NLSs) in
the N-terminus. Because these two isoforms are unstable, we
prepared an FGF11a-Mut by substituting three cysteine residues
in the NLS with serine and FGF11b-ΔC with C-terminal
truncation. The introduction of mutation in the NLS improved
the solubility of FGF11 prepared from E. coli. Exogenous
addition of FGF11b and FGF11b-ΔC to BALB3T3
increased cell proliferation, while FGF11a-Mut exerted no
effect. FGF11b-ΔC showed higher cell proliferation activity
and FGFR signaling than FGF11b. The cell-proliferating activities
of FGF11b and FGF11b-ΔC were blocked by an FGFR1
inhibitor or a recombinant FGFR1, confirming the FGFR1-
dependent extracellular activity of FGF11b. The analysis of
circular dichroism suggested that the C-terminus of FGF11
has an α-helical structure, which may affect its interaction
with FGFR1. These results suggest that the N-and C-terminus
of recombinant FGF11 are involved in the activation of
FGFR1. The above results provide novel insights into the function
and mechanism of FGF11 that may aid the development
of useful ligands for FGFR regulation.
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Citations
Citations to this article as recorded by  - Glycosylation of FGF/FGFR: An underrated sweet code regulating cellular signaling programs
Aleksandra Gędaj, Paulina Gregorczyk, Dominika Żukowska, Aleksandra Chorążewska, Krzysztof Ciura, Marta Kalka, Natalia Porębska, Łukasz Opaliński
Cytokine & Growth Factor Reviews.2024; 77: 39. CrossRef - FGF homologous factors are secreted from cells to induce FGFR‐mediated anti‐apoptotic response
Martyna Biadun, Martyna Sochacka, Radoslaw Karelus, Karolina Baran, Aleksandra Czyrek, Jacek Otlewski, Daniel Krowarsch, Lukasz Opalinski, Malgorzata Zakrzewska
The FASEB Journal.2023;[Epub] CrossRef - FGF/FGFR1 system in paired breast tumor-adjacent and tumor tissues, associations with mammographic breast density and tumor characteristics
Öykü Boraka, Marie Klintman, Johan Vallon-Christersson, Sophia Zackrisson, Per Hall, Signe Borgquist, Ann H. Rosendahl
Frontiers in Oncology.2023;[Epub] CrossRef
- Thermococcus indicus sp. nov., a Fe(III)-reducing hyperthermophilic archaeon isolated from the Onnuri Vent Field of the Central Indian Ocean ridge
-
Jae Kyu Lim , Yun Jae Kim , Jhung-Ahn Yang , Teddy Namirimu , Sung-Hyun Yang , Mi-Jeong Park , Yong Min Kwon , Hyun Sook Lee , Sung Gyun Kang , Jung-Hyun Lee , Kae Kyoung Kwon
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J. Microbiol. 2020;58(4):260-267. Published online April 1, 2020
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DOI: https://doi.org/10.1007/s12275-020-9424-9
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67
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8
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9
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Abstract
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A strictly anaerobic, dissimilatory Fe(III)-reducing hyperthermophilic
archaeon, designated as strain IOH1T, was isolated
from a new deep-sea hydrothermal vent (Onnuri Vent Field)
area in the Central Indian Ocean ridge. Strain IOH1T showed
> 99% 16S rRNA gene sequence similarity with Thermococcus
celericrescens TS2T (99.4%) and T. siculi DSM 12349T (99.2%).
Additional three species T. barossii SHCK-94T (99.0%), T. celer
Vu13T (98.8%), and T. piezophilus (98.6%) showed > 98.6%
of 16S rRNA gene sequence similarity, however, the maximum
OrthoANI value is 89.8% for the genome of T. celericrescens
TS2T. Strain IOH1T cells are coccoid, 1.2–1.8 μm
in diameter, and motile by flagella. Growth was at 70–82°C
(optimum 80°C), pH 5.4–8.0 (optimum pH 6.0) with 2–4%
(optimum 3%) NaCl. Growth of strain IOH1T was enhanced
by starch, pyruvate, D(+)-maltose and maltodextrin as a carbon
sources, and elemental sulfur as an electron acceptor;
clearly different from those of related species T. celecrescens
DSM 17994T and T. siculi DSM 12349T. Strain IOH1T, T. celercrescence
DSM 17994T, and T. siculi DSM 12349T reduced
soluble Fe(III)-citrate present in the medium, whereas the
amount of total cellular proteins increased with the concomitant
accumulation of Fe(II). We determined a circular chromosome
of 2,234 kb with an extra-chromosomal archaeal
plasmid, pTI1, of 7.7 kb and predicted 2,425 genes. The DNA
G + C content was 54.9 mol%. Based on physiological properties,
phylogenetic, and genome analysis, we proposed that
strain IOH1T (= KCTC 15844T = JCM 39077T) is assigned to
a new species in the genus Thermococcus and named Thermococcus
indicus sp. nov.
-
Citations
Citations to this article as recorded by - Macrobenthic communities in the polymetallic nodule field, Indian Ocean, based on multicore and box core analysis
Santosh Gaikwad, Sabyasachi Sautya, Samir Damare, Maria Brenda Luzia Mascarenhas-Pereira, Vijayshree Gawas, Jayesh Patil, Mandar Nanajkar, Sadiq Bukhari
Frontiers in Marine Science.2024;[Epub] CrossRef -
Thermococcus argininiproducens sp. nov., an arginine biosynthesis archaeal species isolated from the Central Indian Ocean ridge
Yeong-Jun Park, Jae Kyu Lim, Yun Jae Kim, Sung-Hyun Yang, Hyun Sook Lee, Sung Gyun Kang, Jung-Hyun Lee, Youngik Yang, Kae Kyoung Kwon
International Journal of Systematic and Evolutionary Microbiology
.2023;[Epub] CrossRef - Spatial comparison and temporal evolution of two marine iron-rich microbial mats from the Lucky Strike Hydrothermal Field, related to environmental variations
Aina Astorch-Cardona, Mathilde Guerre, Alain Dolla, Valérie Chavagnac, Céline Rommevaux
Frontiers in Marine Science.2023;[Epub] CrossRef - Formate and hydrogen in hydrothermal vents and their use by extremely thermophilic methanogens and heterotrophs
James F. Holden, Harita Sistu
Frontiers in Microbiology.2023;[Epub] CrossRef - Microbiome and environmental adaption mechanisms in deep-sea hydrothermal vents
WeiShu ZHAO, Xiang XIAO
SCIENTIA SINICA Vitae.2022;[Epub] CrossRef - Limitations of microbial iron reduction under extreme conditions
Sophie L Nixon, Emily Bonsall, Charles S Cockell
FEMS Microbiology Reviews.2022;[Epub] CrossRef - Valid publication of new names and new combinations effectively published outside the IJSEM
Aharon Oren, George M. Garrity
International Journal of Systematic and Evolutionary Microbiology
.2021;[Epub] CrossRef - Thermococcus aciditolerans sp. nov., a piezotolerant, hyperthermophilic archaeon isolated from a deep-sea hydrothermal vent chimney in the Southwest Indian Ridge
Xue-Gong Li, Hong-Zhi Tang, Wei-Jia Zhang, Xiao-Qing Qi, Zhi-Guo Qu, Jun Xu, Long-Fei Wu
International Journal of Systematic and Evolutionary Microbiology.2021;[Epub] CrossRef - Microorganisms from deep-sea hydrothermal vents
Xiang Zeng, Karine Alain, Zongze Shao
Marine Life Science & Technology.2021; 3(2): 204. CrossRef
- Paradesulfovibrio onnuriensis gen. nov., sp. nov., a chemolithoautotrophic sulfate-reducing bacterium isolated from the Onnuri vent field of the Indian Ocean and reclassification of Desulfovibrio senegalensis as Paradesulfovibrio senegalensis comb. nov.
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Yun Jae Kim , Jhung-Ahn Yang , Jae Kyu Lim , Mi-Jeong Park , Sung-Hyun Yang , Hyun Sook Lee , Sung Gyun Kang , Jung-Hyun Lee , Kae Kyoung Kwon
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J. Microbiol. 2020;58(4):252-259. Published online February 27, 2020
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DOI: https://doi.org/10.1007/s12275-020-9376-0
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72
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8
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7
Crossref
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Abstract
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An anaerobic, rod-shaped, mesophilic, chemolithoautotrophic,
sulfate-reducing bacterial strain IOR2T was isolated from
a newly found deep-sea hydrothermal vent (OVF, Onnuri
Vent Field) area in the central Indian Ocean ridge (11°2488
S 66°2542E, 2021 m water depth). The 16S rRNA gene sequence
analysis revealed that the strain IOR2T was most closely
related to Desulfovibrio senegalensis BLaC1T (96.7%).
However, it showed low similarity with the members of the
family Desulfovibrionaceae, such as Desulfovibrio tunisiensis
RB22T (94.0%), D. brasiliensis LVform1T (93.9%), D. halophilus
DSM 5663T (93.7%), and Pseudodesulfovibrio aespoeensis
Aspo-2T (93.2%). The strain IOR2T could grow at 23–
42°C (optimum 37°C), pH 5.0–8.0 (optimum pH 7.0) and
with 0.5–6.5% (optimum 3.0%) NaCl. The strain could use
lactate, pyruvate, H2, and glycerol as electron donors and sulfate,
thiosulfate, and sulfite as electron acceptors. The major
fatty acids of the strain IOR2T were iso-C15:0, iso-C17:0, anteiso-
C15:0, and summed feature 9 (C16:0 methyl/iso-C17:1ω9c).
Both the strains IOR2T and BLaC1T could grow with CO2 and
H2 as the sole sources of carbon and energy, respectively. Genomic
evidence for the Wood-Ljungdahl pathway in both
the strains reflects chemolithoautotrophic growth. The DNA
G + C content of the strain IOR2T and BLaC1T was 58.1–60.5
mol%. Based on the results of the phylogenetic and physiologic
studies, Paradesulfovibrio onnuriensis gen. nov., sp.
nov. with the type strain IOR2T (= KCTC 15845T = MCCC
1K04559T) was proposed to be a member of the family Desulfovibrionaceae.
We have also proposed the reclassification
of D. senegalensis as Paradesulfovibrio senegalensis comb. nov.
-
Citations
Citations to this article as recorded by - Sulfate-Reducing Bacteria Isolated from an Oil Field in Kazakhstan and a Description of Pseudodesulfovibrio karagichevae sp. nov.
Salimat K. Bidzhieva, Tatyana P. Tourova, Denis S. Grouzdev, Salima R. Samigullina, Diyana S. Sokolova, Andrey B. Poltaraus, Alexander N. Avtukh, Vera M. Tereshina, Andrey V. Mardanov, Nurlan S. Zhaparov, Tamara N. Nazina
Microorganisms.2024; 12(12): 2552. CrossRef - Sulfur fertilization integrated with soil redox conditions reduces Cd accumulation in rice through microbial induced Cd immobilization
Quan Zhang, Hai-Fei Chen, Dao-You Huang, Xiao-Bin Guo, Chao Xu, Han-Hua Zhu, Bo Li, Tong-Tong Liu, Ren-Wei Feng, Qi-Hong Zhu
Science of The Total Environment.2022; 824: 153868. CrossRef - Pseudodesulfovibrio sediminis sp. nov., a mesophilic and neutrophilic sulfate-reducing bacterium isolated from sediment of a brackish lake
Ayaka Takahashi, Hisaya Kojima, Miho Watanabe, Manabu Fukui
Archives of Microbiology.2022;[Epub] CrossRef - Diversity and biogenesis contribution of sulfate-reducing bacteria in arsenic-contaminated soils from realgar deposits
Xianbin Zhu, Liyuan Chen, Hongzhong Pan, Lei Wang, Xun Zhang, Dan Wang
Environmental Science and Pollution Research.2022; 29(21): 31110. CrossRef - A sulfate-reducing bacterial genus, Desulfosediminicola gen. nov., comprising two novel species cultivated from tidal-flat sediments
Jaeho Song, Juchan Hwang, Ilnam Kang, Jang-Cheon Cho
Scientific Reports.2021;[Epub] CrossRef - Desulfomarina profundi gen. nov., sp. nov., a novel mesophilic, hydrogen-oxidizing, sulphate-reducing chemolithoautotroph isolated from a deep-sea hydrothermal vent chimney
Yurina Hashimoto, Akihiro Tame, Shigeki Sawayama, Junichi Miyazaki, Ken Takai, Satoshi Nakagawa
International Journal of Systematic and Evolutionary Microbiology.2021;[Epub] CrossRef -
Pseudodesulfovibrio mercurii sp. nov., a mercury-methylating bacterium isolated from sediment
Cynthia C. Gilmour, Ally Bullock Soren, Caitlin M. Gionfriddo, Mircea Podar, Judy D. Wall, Steven D. Brown, Joshua K. Michener, Maria Soledad Goñi Urriza, Dwayne A. Elias
International Journal of Systematic and Evolutionary Microbiology
.2019;[Epub] CrossRef
- Isolation, cultivation, and genome analysis of proteorhodopsincontaining SAR116-clade strain Candidatus Puniceispirillum marinum IMCC1322
-
Junhak Lee , Kae Kyoung Kwon , Seung-Il Lim , Jaeho Song , Ah Reum Choi , Sung-Hyun Yang , Kwang-Hwan Jung , Jung-Hyun Lee , Sung Gyun Kang , Hyun-Myung Oh , Jang-Cheon Cho
-
J. Microbiol. 2019;57(8):676-687. Published online June 14, 2019
-
DOI: https://doi.org/10.1007/s12275-019-9001-2
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82
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12
Web of Science
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11
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Abstract
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Strain IMCC1322 was isolated from a surface water sample
from the East Sea of Korea. Based on 16S rRNA analysis,
IMCC1322 was found to belong to the OCS28 sub-clade of
SAR116. The cells appeared as short vibrioids in logarithmicphase
culture, and elongated spirals during incubation with
mitomycin or in aged culture. Growth characteristics of strain
IMCC1322 were further evaluated based on genomic information;
proteorhodopsin (PR), carbon monoxide dehydrogenase,
and dimethylsulfoniopropionate (DMSP)-utilizing
enzymes. IMCC1322 PR was characterized as a functional
retinylidene protein that acts as a light-driven proton pump
in the cytoplasmic membrane. However, the PR-dependent
phototrophic potential of strain IMCC1322 was only observed
under CO-inhibited and nutrient-limited culture conditions.
A DMSP-enhanced growth response was observed in addition
to cultures grown on C1 compounds like methanol, formate,
and methane sulfonate. Strain IMCC1322 cultivation
analysis revealed biogeochemical processes characteristic of
the SAR116 group, a dominant member of the microbial community
in euphotic regions of the ocean. The polyphasic taxonomy
of strain IMCC1322 is given as Candidatus Puniceispirillum
marinum, and was confirmed by chemotaxonomic
tests, in addition to 16S rRNA phylogeny and cultivation
analyses.
-
Citations
Citations to this article as recorded by - Effects of Light and Dark Conditions on the Transcriptome of Aging Cultures of Candidatus Puniceispirillum marinum IMCC1322
Ji Hyen Lee, Hyun-Myung Oh
Journal of Microbiology.2024; 62(4): 297. CrossRef - Identification of Structural and Morphogenesis Genes of Sulfitobacter Phage ΦGT1 and Placement within the Evolutionary History of the Podoviruses
Stephen C. Hardies, Byung Cheol Cho, Gwang Il Jang, Zhiqing Wang, Chung Yeon Hwang
Viruses.2023; 15(7): 1475. CrossRef - Seasonal niche differentiation among closely related marine bacteria
Adrià Auladell, Albert Barberán, Ramiro Logares, Esther Garcés, Josep M Gasol, Isabel Ferrera
The ISME Journal.2022; 16(1): 178. CrossRef - Cultivation of Dominant Freshwater Bacterioplankton Lineages Using a High-Throughput Dilution-to-Extinction Culturing Approach Over a 1-Year Period
Suhyun Kim, Md. Rashedul Islam, Ilnam Kang, Jang-Cheon Cho
Frontiers in Microbiology.2021;[Epub] CrossRef - Towards culturing the microbe of your choice
J. Cameron Thrash
Environmental Microbiology Reports.2021; 13(1): 36. CrossRef - Seasonal and annual changes in the microbial communities of Ofunato Bay, Japan, based on metagenomics
Atsushi Kobiyama, Jonaira Rashid, Md. Shaheed Reza, Yuri Ikeda, Yuichiro Yamada, Toshiaki Kudo, Nanami Mizusawa, Saki Yanagisawa, Daisuke Ikeda, Shigeru Sato, Takehiko Ogata, Kazuho Ikeo, Shinnosuke Kaga, Shiho Watanabe, Kimiaki Naiki, Yoshimasa Kaga, Sat
Scientific Reports.2021;[Epub] CrossRef - Aequoribacter fuscus gen. nov., sp. nov., a new member of the family Halieaceae, isolated from coastal seawater
Shan-Hui Li, Jaeho Song, Ilnam Kang, Juchan Hwang, Jang-Cheon Cho
Journal of Microbiology.2020; 58(6): 463. CrossRef - Functional Seasonality of Free-Living and Particle-Associated Prokaryotic Communities in the Coastal Adriatic Sea
Paul A. Steiner, Javier Geijo, Eduard Fadeev, Aleix Obiol, Eva Sintes, Thomas Rattei, Gerhard J. Herndl
Frontiers in Microbiology.2020;[Epub] CrossRef - High-throughput cultivation based on dilution-to-extinction with catalase supplementation and a case study of cultivating acI bacteria from Lake Soyang
Suhyun Kim, Miri S. Park, Jaeho Song, Ilnam Kang, Jang-Cheon Cho
Journal of Microbiology.2020; 58(11): 893. CrossRef - Advantages outweigh concerns about using genome sequence as type material for prokaryotic taxonomy
Konstantinos T. Konstantinidis, Ramon Rosselló‐Móra, Rudolf Amann
Environmental Microbiology.2020; 22(3): 819. CrossRef - Expanding the Diversity of Bacterioplankton Isolates and Modeling Isolation Efficacy with Large-Scale Dilution-to-Extinction Cultivation
Michael W. Henson, V. Celeste Lanclos, David M. Pitre, Jessica Lee Weckhorst, Anna M. Lucchesi, Chuankai Cheng, Ben Temperton, J. Cameron Thrash, Robert M. Kelly
Applied and Environmental Microbiology.2020;[Epub] CrossRef
- Metagenomic analysis reveals the contribution of anaerobic methanotroph-1b in the oxidation of methane at the Ulleung Basin, East Sea of Korea
-
Jin-Woo Lee , Kae Kyoung Kwon , Jang-Jun Bahk , Dong-Hun Lee , Hyun Sook Lee , Sung Gyun Kang , Jung-Hyun Lee
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J. Microbiol. 2016;54(12):814-822. Published online November 26, 2016
-
DOI: https://doi.org/10.1007/s12275-016-6379-y
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74
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4
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Abstract
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We have previously identified a sulfate methane transition
zone (SMTZ) within the methane hydrate-bearing sediment
in the Ulleung Basin, East Sea of Korea, and the presence of
ANME-1b group in the sediment has been shown by phylogenetic
analysis of a 16S rRNA gene. Herein, we describe
taxonomic and functional profiling in the SMTZ sample by
metagenomic analysis, comparing with that of surface sediment.
Metagenomic sequences of 115 Mbp and 252 Mbp
were obtained from SMTZ and surface sediments, respectively.
The taxonomic profiling using BLASTX against the
SEED within MG-RAST showed the prevalence of methanogens
(19.1%), such as Methanosarcinales (12.0%) and
Methanomicrobiales (4.1%) predominated within the SMTZ
metagenome. A number of 185,200 SMTZ reads (38.9%) and
438,484 surface reads (62.5%) were assigned to functional
categories, and methanogenesis-related reads were statistically
significantly overrepresented in the SMTZ metagenome.
However, the mapping analysis of metagenome reads to the
reference genomes, most of the sequences of the SMTZ metagenome
were mapped to ANME-1 draft genomes, rather
than those of methanogens. Furthermore, the two copies of
the methyl-coenzyme M reductase gene (mcrA) segments
of the SMTZ metagenome were clustered with ANME-1b in
the phylogenetic cluster. These results indicate that ANME-
1b reads were miss-annotated to methanogens due to limitation
of database. Many of key genes necessary for reverse
methanogenesis were present in the SMTZ metagenome,
except for N5,N10-methenyl-H4MPT reductase (mer) and CoBCoM
heterodisulfide reductase subunits D and E (hdrDE). These data suggest that the ANME-1b represents the primary
player the anaerobic methane oxidation in the SMTZ,
of the methane hydrate-bearing sediment at the Ulleung
Basin, East Sea of Korea.
-
Citations
Citations to this article as recorded by - Methane seepage intensity distinguish microbial communities in sediments at the Mid-Okinawa Trough
Youzhi Xin, Nengyou Wu, Zhilei Sun, Hongmei Wang, Ye Chen, Cuiling Xu, Wei Geng, Hong Cao, Xilin Zhang, Bin Zhai, Dawei Yan
Science of The Total Environment.2022; 851: 158213. CrossRef - Anthropogenic and Environmental Constraints on the Microbial Methane Cycle in Coastal Sediments
Anna J. Wallenius, Paula Dalcin Martins, Caroline P. Slomp, Mike S. M. Jetten
Frontiers in Microbiology.2021;[Epub] CrossRef -
Roles of Organohalide-Respiring
Dehalococcoidia
in Carbon Cycling
Yi Yang, Robert Sanford, Jun Yan, Gao Chen, Natalie L. Cápiro, Xiuying Li, Frank E. Löffler, Nick Bouskill
mSystems.2020;[Epub] CrossRef - Community structure and distribution of benthic Bacteria and Archaea in a stratified coastal lagoon in the Southern Gulf of Mexico
Santiago Cadena, M. Leopoldina Aguirre-Macedo, Daniel Cerqueda-García, Francisco J. Cervantes, Jorge A. Herrera-Silveira, José Q. García-Maldonado
Estuarine, Coastal and Shelf Science.2019; 230: 106433. CrossRef
- Abyssisolibacter fermentans gen. nov. sp. nov., isolated from deep sub-seafloor sediment
-
Wonduck Kim , Jung-Hyun Lee , Kae Kyoung Kwon
-
J. Microbiol. 2016;54(5):347-352. Published online April 20, 2016
-
DOI: https://doi.org/10.1007/s12275-016-6048-1
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64
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Abstract
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A Gram-staining-negative, thin rod-shaped, anaerobic bacterium
designated MCWD3T was isolated from sediment of
the deep sea in Ulleung Basin, East Sea, Korea. The ranges of
temperature, pH and NaCl for growth of this strain were 15–
40°C (optimum 29°C), 5.0–10.0 (optimum pH 6.5), and 1–5%,
respectively. The major fatty acids were iso-C15:0 (30%) and
iso-C15:0 dimethyl acetal (17%). The major polar lipids were
diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine,
and unidentified aminophospholipids, phospholipids,
and aminolipids. The fermentation product from
yeast extract was acetate. Phylogenetic analysis based on 16S
rRNA genes indicated that the isolate was related to Sporosalibacterium
faouarense (92.8% sequence identity), Clostridiisalibacter
paucivorans (92.6%), and Brassicibacter mesophilus
(92.4%). However, the isolate was differentiated from these
genera by both physiological and chemotaxonomical properties.
On the basis of a polyphasic taxonomic analysis, we
propose that MCWD3T represents a novel taxon with the
name Abyssisolibacter fermentans gen. nov. sp. nov.
-
Citations
Citations to this article as recorded by - Validation List no. 220. Valid publication of new names and new combinations effectively published outside the IJSEM
Aharon Oren, Markus Göker
International Journal of Systematic and Evolutionary Microbiology
.2024;[Epub] CrossRef - The Phylogeny, Metabolic Potentials, and Environmental Adaptation of an Anaerobe, Abyssisolibacter sp. M8S5, Isolated from Cold Seep Sediments of the South China Sea
Ying Liu, Songze Chen, Jiahua Wang, Baoying Shao, Jiasong Fang, Junwei Cao
Microorganisms.2023; 11(9): 2156. CrossRef - Description of Fervidibacillus gen. nov. with Two Species, Fervidibacillus albus sp. nov., and Fervidibacillus halotolerans sp. nov., Isolated from Tidal Flat Sediments and Emendation of Misclassificed Taxa in the Genus Caldibacillus
Sung-Hyun Yang, Mi-Jeong Park, Hyun-Myung Oh, Kae Kyoung Kwon
Journal of Microbiology.2023; 61(2): 175. CrossRef -
Vibrio ostreae sp. nov., a novel gut bacterium isolated from a Yellow Sea oyster
Neak Muhammad, Tra T.H. Nguyen, Yong-Jae Lee, Jaeho Ko, Forbes Avila, Song-Gun Kim
International Journal of Systematic and Evolutionary Microbiology
.2022;[Epub] CrossRef - A Deep-Sea Sediment Sampling System: Design, Analysis and Experimental Verification
Guangping Liu, Yongping Jin, Youduo Peng, Buyan Wan, Kun Xie
Journal of Pressure Vessel Technology.2022;[Epub] CrossRef -
Alkalibacter rhizosphaerae sp. nov., a CO-utilizing bacterium isolated from tidal flat sediment, and emended description of the genus Alkalibacter
Teddy Namirimu, Jihyun Yu, Jhung-Ahn Yang, Sung-Hyun Yang, Yun Jae Kim, Kae Kyoung Kwon
International Journal of Systematic and Evolutionary Microbiology
.2022;[Epub] CrossRef -
Anaerosacchariphilus polymeriproducens gen. nov., sp. nov., an anaerobic bacterium isolated from a salt field
Wonduck Kim, Sung-Hyun Yang, Mi-Jeong Park, Jihye Oh, Jung-Hyun Lee, Kae Kyoung Kwon
International Journal of Systematic and Evolutionary Microbiology
.2019; 69(7): 1934. CrossRef - Isolation and characterization of anaerobic microbes from marine environments in Korea
Wonduck Kim, Jung-Hyun Lee, Kae Kyoung Kwon
The Korean Journal of Microbiology.2016; 52(2): 183. CrossRef
- Characterization of Hyperthermostable Fructose-1,6-Bisphosphatase from Thermococcus onnurineus NA1
-
Yeol Gyun Lee , Sung Gyun Kang , Jung-Hyun Lee , Seung Il Kim , Young-Ho Chung
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J. Microbiol. 2010;48(6):803-807. Published online January 9, 2011
-
DOI: https://doi.org/10.1007/s12275-010-0377-2
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57
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3
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Abstract
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To understand the physiological functions of thermostable fructose-1,6-bisphosphatase (TNA1-Fbp) from Thermococcus onnurineus NA1, its recombinant enzyme was overexpressed in Escherichia coli, purified, and the enzymatic properties were characterized. The enzyme showed maximal activity for fructose-1,6-
bisphosphate at 95°C and pH 8.0 with a half-life (t1/2) of about 8 h. TNA1-Fbp had broad substrate specificities for fructose-1,6-bisphosphate and its analogues including fructose-1-phosphate, glucose-1-phosphate, and phosphoenolpyruvate. In addition, its enzyme activity was increased five-fold by addition of 1 mM Mg2+, while Li+ did not enhance enzymatic activity. TNA1-Fbp activity was inhibited by ATP, ADP, and phosphoenolpyruvate, but AMP up to 100 mM did not have any effect. TNA1-Fbp is currently defined as a class V fructose-1,6-bisphosphatase (FBPase) because it is very similar to FBPase of Thermococcus kodakaraensis KOD1 based on sequence homology. However, this enzyme shows a different range of substrate specificities. These results suggest that TNA1-Fbp can establish new criterion for class V FBPases.
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Citations
Citations to this article as recorded by - Pcal_0111, a highly thermostable bifunctional fructose-1,6-bisphosphate aldolase/phosphatase from Pyrobaculum calidifontis
Iram Aziz, Naeem Rashid, Raza Ashraf, Qamar Bashir, Tadayuki Imanaka, Muhammad Akhtar
Extremophiles.2017; 21(3): 513. CrossRef - Identification of a novel ligand binding site in phosphoserine phosphatase from the hyperthermophilic archaeon Thermococcus onnurineus
Tae‐Yang Jung, Yae‐Sel Kim, Byoung‐Ha Oh, Euijeon Woo
Proteins: Structure, Function, and Bioinformatics.2013; 81(5): 819. CrossRef - Proteome Analyses of Hydrogen-producing Hyperthermophilic Archaeon Thermococcus onnurineus NA1 in Different One-carbon Substrate Culture Conditions
Yoon-Jung Moon, Joseph Kwon, Sung-Ho Yun, Hye Li Lim, Min-Sik Kim, Sung Gyun Kang, Jung-Hyun Lee, Jong-Soon Choi, Seung Il Kim, Young-Ho Chung
Molecular & Cellular Proteomics.2012; 11(6): M111.015420. CrossRef
- NOTE] Nomenclature of ISCR1 Elements Capable of Mobilizing Antibiotic Resistance Genes Present in Complex Class 1 Integrons
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Seung Ghyu Sohn , Jae Jin Lee , Jae Seok Song , Jung Hun Lee , Ha Ik Sun , Kwang Seung Park , Il Kwon Bae , Jung-Hyun Lee , Byeong Chul Jeong , Sang Hee Lee
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J. Microbiol. 2009;47(4):514-516. Published online September 9, 2009
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DOI: https://doi.org/10.1007/s12275-009-0054-5
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Abstract
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The dissemination of many antibiotic resistance genes has arisen among members of the family Enterobacteriaceae. The dissemination mechanism of these antibiotic resistance genes is closely linked with insertion sequence common region 1 (ISCR1). Thus, caution must be taken in clinical settings to prevent further dissemination of these antibiotic resistance genes. A nomenclature system of ISCR1 variants, important for the antibiotic resistance dissemination, was proposed. The proposed system can designate all ISCR1 variants on the basis of the detection time and by considering amino-acid substitution(s) compared with ISCR1a. This nomenclature system of ISCR1 variants can be applied to 19 groups (ISCR1 to ISCR19) of the ISCR family and help some researchers to correctly designate new ISCR subgroups.
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Citations
Citations to this article as recorded by - Molecular Characteristics of Carbapenem-Resistant Gram-Negative Bacteria in Southern China
Fen Zheng, Jingjing Sun, Cancan Cheng, Yongyu Rui
Microbial Drug Resistance.2015; 21(2): 178. CrossRef - Novel ISCR1-linked resistance genes found in multidrug-resistant Gram-negative bacteria in southern China
Fengping Wang, Kuihai Wu, Jingjing Sun, Qian Wang, Qing Chen, Shouyi Yu, Yongyu Rui
International Journal of Antimicrobial Agents.2012; 40(5): 404. CrossRef - Gene flow, mobile genetic elements and the recruitment of antibiotic resistance genes into Gram-negative pathogens
Hatch W. Stokes, Michael R. Gillings
FEMS Microbiology Reviews.2011; 35(5): 790. CrossRef
- Monitoring Nutrient Impact on Bacterial Community Composition during Bioremediation of Anoxic PAH-Contaminated Sediment
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Myungsu Kim , Seung Seob Bae , Mijin Seol , Jung-Hyun Lee , Young-Sook Oh
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J. Microbiol. 2008;46(6):615-623. Published online December 24, 2008
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DOI: https://doi.org/10.1007/s12275-008-0097-z
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98
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Abstract
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Marine harbor sediments are frequently polluted with significant amount of polycyclic aromatic hydrocarbons (PAHs) some of which are naturally toxic, recalcitrant, mutagenic, and carcinogenic. To stimulate biodegradation of PAHs in PAH-contaminated sediments collected from near Gwangyang Bay, Korea, lactate was chosen as a supplementary carbonaceous substrate. Sediment packed into 600 ml air-tight jar was either under no treatment condition or lactate amended condition (1%, w/v). Microbial community composition was monitored by bacteria-specific and archaea-specific PCR-terminal restriction fragment length polymorphism (T-RFLP), in addition to measuring the residual PAH concentration. Results showed that lactate amendment enhanced biodegradation rate of PAHs in the sediment by 4 to 8 times, and caused a significant shift in archaebacterial community in terms of structure and diversity with time. Phylogenetic analysis of 23 archaeal clones with distinctive RFLP patterns among 288 archaeal clones indicated that majority of the archaeal members were closest to unculturable environmental rDNA clones from hydrocarbon-contaminated and/or methanogenesis-bearing sediments. Lactate amendment led to the enrichment of some clones that were most closely related to PAH-degrading Methanosarcina species. These results suggest a possible contribution of methanogenic community to PAH degradation and give us more insights on how to effectively remediate PAH-contaminated sediments.
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Citations
Citations to this article as recorded by - Effects of electron acceptors and donors on anaerobic biodegradation of PAHs in marine sediments
Qingguo Chen, Zhenzhen Li, Yu Chen, Mei Liu, Qiao Yang, Baikang Zhu, Jun Mu, Lijuan Feng, Zhi Chen
Marine Pollution Bulletin.2024; 199: 115925. CrossRef - Electrical current generation from a continuous flow macrophyte biocathode sediment microbial fuel cell (mSMFC) during the degradation of pollutants in urban river sediment
Felix Tetteh Kabutey, Jing Ding, Qingliang Zhao, Philip Antwi, Frank Koblah Quashie
Environmental Science and Pollution Research.2020; 27(28): 35364. CrossRef - Application of in situ Solid-Phase Microextraction on Mediterranean Sponges for Untargeted Exometabolome Screening and Environmental Monitoring
Barbara Bojko, Bora Onat, Ezel Boyaci, Eleftheria Psillakis, Thanos Dailianis, Janusz Pawliszyn
Frontiers in Marine Science.2019;[Epub] CrossRef - Effect of carbonyl cyanide m-chlorophenylhydrazone (CCCP) on microbial activity and polycyclic aromatic hydrocarbons (PAH) degradation in contaminated river sediments
G. Patricia Johnston, Z. Kalik, C. G. Johnston
Environmental Earth Sciences.2016;[Epub] CrossRef - Effects of polycyclic aromatic hydrocarbons on microbial community structure and PAH ring hydroxylating dioxygenase gene abundance in soil
Przemyslaw Sawulski, Nicholas Clipson, Evelyn Doyle
Biodegradation.2014; 25(6): 835. CrossRef - Anthracene biodegradation under nitrate-reducing condition and associated microbial community changes
Ying Wang, Rui Wan, Shuying Zhang, Shuguang Xie
Biotechnology and Bioprocess Engineering.2012; 17(2): 371. CrossRef - Molecular characterization of phenanthrene-degrading methanogenic communities in leachate-contaminated aquifer sediment
S. Y. Zhang, Q. F. Wang, S. G. Xie
International Journal of Environmental Science and Technology.2012; 9(4): 705. CrossRef - Increment in Anaerobic Hydrocarbon Degradation Activity of Halic Bay Sediments via Nutrient Amendment
Mustafa Kolukirik, Orhan Ince, Bahar K. Ince
Microbial Ecology.2011; 61(4): 871. CrossRef - Revealing archaeal diversity patterns and methane fluxes in Admiralty Bay, King George Island, and their association to Brazilian Antarctic Station activities
C.R. Nakayama, E. Kuhn, A.C.V. Araújo, P.C. Alvalá, W.J. Ferreira, R.F. Vazoller, V.H. Pellizari
Deep Sea Research Part II: Topical Studies in Oceanography.2011; 58(1-2): 128. CrossRef - Bioremediation of marine sediments contaminated by hydrocarbons: Experimental analysis and kinetic modeling
Francesca Beolchini, Laura Rocchetti, Francesco Regoli, Antonio Dell’Anno
Journal of Hazardous Materials.2010; 182(1-3): 403. CrossRef
- Removal of Contaminating TEM-la β-Lactamase Gene from Removal of Contaminating TEM-la β-Lactamase Gene from
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Jae Seok Song , Jung Hun Lee , Jung-Hyun Lee , Byeong Chul Jeong , Won-Keun Lee , Sang Hee Lee
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J. Microbiol. 2006;44(1):126-128.
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DOI: https://doi.org/2326 [pii]
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Abstract
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This study confirms that Taq DNA polymerase could be contaminated with the blaTEM-1a gene.
It also proposes two different methods that could be used to overcome DNA contamination: (i)
DNase I treatment prior to PCR amplification; and (ii) the use of a highly purified Taq DNA polymerase
which was devoid of detectable contamination.
- Molecular Characterization of TEM-type [beta]-Lactamases Identified in Cold-Seep Sediments of Edison Seamount (South of Lihir Island, Papua New Guinea)
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Jae Seok Song , Jeong Ho Jeon , Jung Hun Lee , Seok Hoon Jeong , Byeong Chul Jeong , Sang-Jin Kim , Jung-Hyun Lee , Sang Hee Lee
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J. Microbiol. 2005;43(2):172-178.
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DOI: https://doi.org/2165 [pii]
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Abstract
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To determine the prevalence and genotypes of [beta]-lactamases among clones of a metagenomic library from the cold-seep sediments of Edison seamount (10,000 years old), we performed pulse-field gel electrophoresis, antibiotic susceptibility testing, pI determination, and DNA sequencing analysis. Among the 8,823 clones of the library, thirty clones produced [beta]-lactamases and had high levels of genetic diversity. Consistent with minimum inhibitory concentration patterns, we found that five (16.7%) of thirty clones produced an extended-spectrum [beta]-lactamase. 837- and 259-bp fragments specific to bla_TEM genes were amplified, as determined by banding patterns of PCR amplification with designed primers. TEM-1 was the most prevalent [beta]-lactamase and conferred resistance to ampicillin, piperacillin, and cephalothin. TEM-116 had a spectrum that was extended to ceftazidime, cefotaxime, and aztreonam. The resistance levels conferred by the pre-antibiotic era alleles of TEM-type [beta]-lactamases were essentially the same as the resistance levels conferred by the TEM-type alleles which had been isolated from clinically resistant strains of bacteria of the antibiotic era. Our first report on TEM-type [beta]-lactamases of the pre-antibiotic era indicates that TEM-type [beta]-lactamases paint a picture in which most of the diversity of the enzymes may not be the result of recent evolution, but that of ancient evolution.
- Purification and Characterization of NADPH-Dependent Cr(VI) Reductase from Escherichia coli ATCC 33456
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Woo-Chul Bae , Han-Ki Lee , Young-Chool Choe , Deok-Jin Jahng , Sang-Hee Lee , Sang-Jin Kim , Jung-Hyun Lee , Byeong-Chul Jeong
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J. Microbiol. 2005;43(1):21-27.
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DOI: https://doi.org/2143 [pii]
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Abstract
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A soluble Cr(VI) reductase was purified from the cytoplasm of Escherichia coli ATCC 33456. The molecular mass was estimated to be 84 and 42 kDa by gel filtration and SDS-polyacrylamide gel electrophoresis, respectively, indicating a dimeric structure. The pI was 4.66, and optimal enzyme activity was obtained at pH 6.5 and 37^oC. The most stable condition existed at pH 7.0. The purified enzyme used both NADPH and NADH as electron donors for Cr(VI) reduction, while NADPH was the better, conferring 61% higher activity than NADH. The K_m values for NADPH and NADH were determined to be 47.5 and 17.2 umol, and the V_max values 322.2 and 130.7 umol Cr(VI) min^-1mg^-1 protein, respectively. The activity was strongly inhibited by N-ethylmalemide, Ag^2+, Cd^2+, Hg^2+, and Zn^2+. The antibody against the enzyme showed no immunological cross reaction with those of other Cr(VI) reducing strains.
- Isolation and Identification of Biofilm-Forming Marine Bacteria on Glass Surfaces in Dae-Ho Dike, Korea
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Kae Kyoung Kwon , Hyun Sang Lee , Sung-Young Jung , Joung-Han Yim , Jung-Hyun Lee , Hong Kum Lee
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J. Microbiol. 2002;40(4):260-266.
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Abstract
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Bacterial strains were isolated from biofilms formed on glass slides submerged in seawater in Dae-Ho Dike. Eight strains showing fast attaching ability were selected and identified. Their exopolysaccharide(EPS)-producing ability and EPS properties were characterized. Based on Microlog System, 4 among the 8 strains were identified as Micrococcus luteus and the rest were Bacillus thuringiensis, Bacillus megaterium, Staphylococcus saprophyticus and Agrobacterium vitis. A. vitis was reidentified as Sulfitobacter pontiacus based on 16S rDNA sequence data. The amount of water-soluble EPS produced by the 8 strains ranged from 0.114 to 1.329 g·l^-1 and the productivity was negatively correlated with the cell biomass. The molecular weight of the produced EPS ranged from 0.38 to 25.19x 10^4 Da. Glucose and galactose were ubiquitous sugar components. Mannose, ribose, and xylose were also major sugar components. The molecular weight and composition of the EPS showed strain-specific variation.
- Microbial Symbiosis in Marine Sponges
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Yoo Kyung Lee , Jung-Hyun Lee , Hong Kum Lee
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J. Microbiol. 2001;39(4):254-264.
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Abstract
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Sponges are host organisms for various symbiotic microorganisms such as archaea, bacteria, cyanobacteria and microalgae. Sponges are also sources of a wide variety of useful natural products like cytotoxins, antifouling agents, antibiotics, and anti-inflammatory and antiviral compounds. Symbiotic microorganisms in sponges can be sources of various natural products, because metabolites previously ascribed to sponges have recently been demonstrated to be biosynthesized by symbionts. If a symbiotic microorganism from which some natural products are derived can be cultured, the microorganism could be used in a mass production of the bioactive compounds. We summarize recent research on isolation and cultivation of sponge-symbiotic microorganisms and the symbiotic relationship.
- Purification and Characterization of Chitinase from a Marine Bacterium, Vibrio sp. 98CJ11027
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Shin Hye Park , Jung-Hyun Lee , Hong Kum Lee
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J. Microbiol. 2000;38(4):224-229.
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Abstract
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Chitin-degrading marine bacterial strain 98CJ11027 was isolated from bryozoa from the coastal area of Cheju Island, Korea, and identified as a member of the genus Vibrio. The molecular mass of the main extracellular chitinase (chitinase I), purified from strain 98CJ11027, was estimated to be 98 kDa. The optimal condition for chitinase I activity is pH 6.0 and 45 C. The activity was inhibited by Fe^+2 and Cu^+2. Chitinase I displayed the hydrolysis type of chitobiosidase and catalyzed reversed hydrolysis leading to the synthesis of tetraacetylchitotetraose.
- Bacterial Diversity of Culturable Isolates from Seawater and a Marine Coral, Plexauridae sp., near Mun-Sum, Cheju-Island
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Jung-Hyun Lee , Hyun-Hee Shin , Deuk-Soo Lee , Kae Kyung Kwon , Sang-Jin Kim , Hong Kum Lee
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J. Microbiol. 1999;37(4):193-199.
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Abstract
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Fifty-eight strains showing different colony morphological characteristics on various media were isolated from marine coral (Plexauridae sp.) and ambient seawater near Mun-Sum, Cheju-Island in 1998. Bacterial diversity was studies by phylogenetic analysis of the partial 16S rRNA gene sequences. All isolates representing the bacterial domain included affiliates of the high G+C (59%) and los G+C (3%) subdivision of Gram positive bacteria, and the alpha (33%) and gamma (5%) subdivision of the Proteobacteria. The 16S rDNA sequence similarity of the isolates was in the 88.3 to 100% range (average, 95.6%) to reported sequence data. In the comparison of the isolates from marine coarl and ambient seawater, more diverse groups belonging to alpha-proteobacteria were preferentially obtained from seawater.
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