Journal of Microbiology

Journal Article

Those Nematode‑Trapping Fungi That are not Everywhere: Hints Towards Soil Microbial Biogeography: Wei Deng , Fa Zhang , Davide Fornacca , Xiao-Yan Yang , Wen Xiao; J. Microbiol. 2023;61(5):511-523. Published online April 6, 2023; DOI: https://doi.org/10.1007/s12275-023-00043-7

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The existence of biogeography for microorganisms is a raising topic in ecology and researchers are employing better distinctions between single species, including the most rare ones, to reveal potential hidden patterns. An important volume of evidence supporting heterogeneous distributions for bacteria, archaea and protists is accumulating, and more recently a few efforts have targeted microscopic fungi. We propose an insight into this latter kingdom by looking at a group of soil nematode-trapping fungi whose species are well-known and easily recognizable. We chose a pure culture approach because of its reliable isolation procedures for this specific group. After morphologically and molecularly identifying all species collected from 2250 samples distributed in 228 locations across Yunnan province of China, we analyzed occurrence frequencies and mapped species, genera, and richness. Results showed an apparent cosmopolitan tendency for this group of fungi, including species richness among sites. However, only four species were widespread across the region, while nonrandom heterogeneous distributions were observed for the remaining 40 species, both in terms of statistical distribution of species richness reflected by a significant variance-to-mean ratio, as well as in terms of visually discernible spatial clusters of rare species and genera on the map. Moreover, several species were restricted to only one location, raising the question of whether endemicity exists for this microbial group. Finally, environmental heterogeneity showed a marginal contribution in explaining restricted distributions, suggesting that other factors such as geographical isolation and dispersal capabilities should be explored. These findings contribute to our understanding of the cryptic geographic distribution of microorganisms and encourage further research in this direction.

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Linking watershed formation with the phylogenetic distribution of a soil microscopic fungus in Yunnan Province, China
Davide Fornacca, Wei Deng, Yaoquan Yang, Fa Zhang, Xiaoyan Yang, Wen Xiao
BMC Microbiology.2024;[Epub] CrossRef
Analysis of Nuclear Dynamics in Nematode-Trapping Fungi Based on Fluorescent Protein Labeling
Liang Zhou, Zhiwei He, Keqin Zhang, Xin Wang
Journal of Fungi.2023; 9(12): 1183. CrossRef

Review

[Minireview]Potential roles of condensin in genome organization and beyond in fission yeast: Kyoung-Dong Kim; J. Microbiol. 2021;59(5):449-459. Published online April 20, 2021; DOI: https://doi.org/10.1007/s12275-021-1039-2

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Abstract

The genome is highly organized hierarchically by the function of structural maintenance of chromosomes (SMC) complex proteins such as condensin and cohesin from bacteria to humans. Although the roles of SMC complex proteins have been well characterized, their specialized roles in nuclear processes remain unclear. Condensin and cohesin have distinct binding sites and mediate long-range and short-range genomic associations, respectively, to form cell cycle-specific genome organization. Condensin can be recruited to highly expressed genes as well as dispersed repeat genetic elements, such as Pol III-transcribed genes, LTR retrotransposon, and rDNA repeat. In particular, mitotic transcription factors Ace2 and Ams2 recruit condensin to their target genes, forming centromeric clustering during mitosis. Condensin is potentially involved in various chromosomal processes such as the mobility of chromosomes, chromosome territories, DNA reannealing, and transcription factories. The current knowledge of condensin in fission yeast summarized in this review can help us understand how condensin mediates genome organization and participates in chromosomal processes in other organisms.

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Brewing COFFEE: A Sequence-Specific Coarse-Grained Energy Function for Simulations of DNA−Protein Complexes
Debayan Chakraborty, Balaka Mondal, D. Thirumalai
Journal of Chemical Theory and Computation.2024; 20(3): 1398. CrossRef
Contributions of transcriptional noise to leukaemia evolution: KAT2A as a case-study
Cristina Pina
Philosophical Transactions of the Royal Society B: Biological Sciences.2024;[Epub] CrossRef
Viral remodeling of the 4D nucleome
Kyoung-Dong Kim, Paul M. Lieberman
Experimental & Molecular Medicine.2024; 56(4): 799. CrossRef
BiFCo: visualizing cohesin assembly/disassembly cycle in living cells
Emilio González-Martín, Juan Jiménez, Víctor A Tallada
Life Science Alliance.2023; 6(7): e202301945. CrossRef

Journal Article

Temporal and spatial impact of Spartina alterniflora invasion on methanogens community in Chongming Island, China: Xue Ping Chen , Jing Sun , Yi Wang , Heng Yang Zhang , Chi Quan He , Xiao Yan Liu , Nai Shun Bu , Xi-En Long; J. Microbiol. 2018;56(7):507-515. Published online June 14, 2018; DOI: https://doi.org/10.1007/s12275-018-8062-y

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Abstract

Methane production by methanogens in wetland is recognized as a significant contributor to global warming. Spartina alterniflora (S. alterniflora), which is an invasion plant in China’s wetland, was reported to have enormous effects on methane production. But studies on shifts in the methanogen community in response to S. alterniflora invasion at temporal and spatial scales in the initial invasion years are rare. Sediments derived from the invasive species S. alterniflora and the native species Phragmites australis (P. australis) in pairwise sites and an invasion chronosequence patch (4 years) were analyzed to investigate the abundance and community structure of methanogens using quantitative real-time PCR (qPCR) and Denaturing gradient gel electrophoresis (DGGE) cloning of the methyl-coenzyme M reductase A (mcrA) gene. For the pairwise sites, the abundance of methanogens in S. alterniflora soils was lower than that of P. australis soils. For the chronosequence patch, the abundance and diversity of methanogens was highest in the soil subjected to two years invasion, in which we detected some rare groups including Methanocellales and Methanococcales. These results indicated a priming effect at the initial invasion stages of S. alterniflora for microorganisms in the soil, which was also supported by the diverse root exudates. The shifts of methanogen communities after S. alterniflora invasion were due to changes in pH, salinity and sulfate. The results indicate that root exudates from S. alterniflora have a priming effect on methanogens in the initial years after invasion, and the predominate methylotrophic groups (Methanosarcinales) may adapt to the availability of diverse substrates and reflects the potential for high methane production after invasion by S. alterniflora.

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Stronger increase of methane emissions from coastal wetlands by non‐native Spartina alterniflora than non‐native Phragmites australis
Andrea Fuchs, Ian C. Davidson, J. Patrick Megonigal, John L. Devaney, Christina Simkanin, Genevieve L. Noyce, Meng Lu, Grace M. Cott
PLANTS, PEOPLE, PLANET.2025; 7(1): 62. CrossRef
Predictions of Spartina alterniflora leaf functional traits based on hyperspectral data and machine learning models
Wei Li, Xueyan Zuo, Zhijun Liu, Leichao Nie, Huazhe Li, Junjie Wang, Zhiguo Dou, Yang Cai, Xiajie Zhai, Lijuan Cui
European Journal of Remote Sensing.2024;[Epub] CrossRef
Salt marsh soil organic carbon is regulated by drivers of microbial activity
Hailey Erb, Ashley Keiser, Kristen M DeAngelis
Sustainable Microbiology.2024;[Epub] CrossRef
Asymmetric responses of functional microbes in methane and nitrous oxide emissions to plant invasion: A meta-analysis
Yanzhong Yao, Youtao Song, Pinjie Su, Jing Wang, Congke Miao, Yifu Luo, Qiqi Sun, Jiale Wang, Guohui Zhang, Naishun Bu, Zhaolei Li
Soil Biology and Biochemistry.2023; 178: 108931. CrossRef
Increasing coastal reclamation by Invasive alien plants and coastal armoring threatens the ecological sustainability of coastal wetlands
Jian Li, Zhanrui Leng, Taitiya Kenneth Yuguda, Lili Wei, Jiaojiao Xia, Chongyu Zhuo, Ziying Nie, Daolin Du
Frontiers in Marine Science.2023;[Epub] CrossRef
Spartina alterniflora Invaded Coastal Wetlands by Raising Soil Sulfur Contents: A Meta-Analysis
Zhenzhen Zhao, Liyu Cheng, Chiquan He, Feifei Wang, Jialin Liu, Yuanhang Li, Xueping Chen, Xiaoyan Liu, Gaoming Lv, Daoyuan Wang
Water.2022; 14(10): 1633. CrossRef
Exogenous nitrogen from riverine exports promotes soil methane production in saltmarshes in China
Chenhao Zhou, Yan Zhang, Songshuo Li, Qiuyue Jiang, Hongyang Chen, Ting Zhu, Xiao Xu, Hao Liu, Shiyun Qiu, Jihua Wu, Ming Nie, Bo Li
Science of The Total Environment.2022; 838: 156203. CrossRef
Exogenous Nitrogen from Riverine Exports Promotes Soil Methane Production in Saltmarshes in China
Chenhao Zhou, Yan Zhang, Songshuo Li, Qiuyue Jiang, Hongyang Chen, Ting Zhu, Xiao Xu, Hao Liu, Shi-Yun Qiu, Jihua Wu, Ming Nie, Bo Li
SSRN Electronic Journal .2021;[Epub] CrossRef
Spartina alterniflora raised soil sulfide content by regulating sulfur cycle-associated bacteria in the Jiuduansha Wetland of China
Chiquan He, Liyu Cheng, Daoyuan Wang, Zhenzhen Zhao, Zhengyu Wang, Feifei Wang, Xiaoxi Wang, Pu Zhang, Xueping Chen, Xiaoyan Liu
Plant and Soil.2021; 469(1-2): 107. CrossRef
The linkage between methane production activity and prokaryotic community structure in the soil within a shale gas field in China
Yan-Qin Wang, Guang-Quan Xiao, Yong-Yi Cheng, Ming-Xia Wang, Bo-Ya Sun, Zhi-Feng Zhou
Environmental Science and Pollution Research.2020; 27(7): 7453. CrossRef

Review

MINIREVIEW] Hydroxylation of methane through component interactions in soluble methane monooxygenases: Seung Jae Lee; J. Microbiol. 2016;54(4):277-282. Published online April 1, 2016; DOI: https://doi.org/10.1007/s12275-016-5642-6

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Abstract

Methane hydroxylation through methane monooxygenases (MMOs) is a key aspect due to their control of the carbon cycle in the ecology system and recent applications of methane gas in the field of bioenergy and bioremediation. Methanotropic bacteria perform a specific microbial conversion from methane, one of the most stable carbon compounds, to methanol through elaborate mechanisms. MMOs express particulate methane monooxygenase (pMMO) in most strains and soluble methane monooxygenase (sMMO) under copper-limited conditions. The mechanisms of MMO have been widely studied from sMMO belonging to the bacterial multicomponent monooxygenase (BMM) superfamily. This enzyme has diiron active sites where different types of hydrocarbons are oxidized through orchestrated hydroxylase, regulatory and reductase components for precise control of hydrocarbons, oxygen, protons, and electrons. Recent advances in biophysical studies, including structural and enzymatic achievements for sMMO, have explained component interactions, substrate pathways, and intermediates of sMMO. In this account, oxidation of methane in sMMO is discussed with recent progress that is critical for understanding the microbial applications of C-H activation in one-carbon substrates.

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Complete genome sequences of Methylococcus capsulatus (Norfolk) and Methylocaldum szegediense (Norfolk) isolated from a landfill methane biofilter
David Pearce, Elliot Brooks, Charles Wright, Daniel Rankin, Andrew T. Crombie, J. Colin Murrell, Elinne Becket
Microbiology Resource Announcements.2024;[Epub] CrossRef
Effect of monodentate heterocycle co-ligands on the μ-1,2-peroxo-diiron(III) mediated aldehyde deformylation reactions
Patrik Török, Dóra Lakk-Bogáth, Duenpen Unjaroen, Wesley R. Browne, József Kaizer
Journal of Inorganic Biochemistry.2024; 258: 112620. CrossRef
Crucial Role of the Chaperonin GroES/EL for Heterologous Production of the Soluble Methane Monooxygenase from Methylomonas methanica MC09
Domenic Zill, Elisabeth Lettau, Christian Lorent, Franziska Seifert, Praveen K. Singh, Lars Lauterbach
ChemBioChem.2022;[Epub] CrossRef
Bioinspired Oxidation of Methane: From Academic Models of Methane Monooxygenases to Direct Conversion of Methane to Methanol
A. A. Shteinman
Kinetics and Catalysis.2020; 61(3): 339. CrossRef
Effect of the Nuclearity and Coordination of Cu and Fe Sites in β Zeolites on the Oxidation of Hydrocarbons
Petr Sazama, Jaroslava Moravkova, Stepan Sklenak, Alena Vondrova, Edyta Tabor, Galina Sadovska, Radim Pilar
ACS Catalysis.2020; 10(7): 3984. CrossRef
Enrichment culture and identification of endophytic methanotrophs isolated from peatland plants
Zofia Stępniewska, Weronika Goraj, Agnieszka Kuźniar, Natalia Łopacka, Magdalena Małysza
Folia Microbiologica.2017; 62(5): 381. CrossRef
A growing family of O2 activating dinuclear iron enzymes with key catalytic diiron(III)-peroxo intermediates: Biological systems and chemical models
Alexandre Trehoux, Jean-Pierre Mahy, Frédéric Avenier
Coordination Chemistry Reviews.2016; 322: 142. CrossRef

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

Dimethyl sulfoxide reduction by a hyperhermophilic archaeon Thermococcus onnurineus NA1 via a cysteine-cystine redox shuttle: Ae Ran Choi , Min-Sik Kim , Sung Gyun Kang , Hyun Sook Lee; J. Microbiol. 2016;54(1):31-38. Published online January 5, 2016; DOI: https://doi.org/10.1007/s12275-016-5574-1

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Abstract

A variety of microbes grow by respiration with dimethyl sulfoxide (DMSO) as an electron acceptor, and several distinct DMSO respiratory systems, consisting of electron carriers and a terminal DMSO reductase, have been characterized. The heterotrophic growth of a hyperthermophilic archaeon Thermococcus onnurineus NA1 was enhanced by the addition of DMSO, but the archaeon was not capable of reducing DMSO to DMS directly using a DMSO reductase. Instead, the archaeon reduced DMSO via a cysteine-cystine redox shuttle through a mechanism whereby cystine is microbially reduced to cysteine, which is then reoxidized by DMSO reduction. A thioredoxin reductase-protein disulfide oxidoreductase redox couple was identified to have intracellular cystine-reducing activity, permitting recycle of cysteine. This study presents the first example of DMSO reduction via an electron shuttle. Several Thermococcales species also exhibited enhanced growth coupled with DMSO reduction, probably by disposing of excess reducing power rather than conserving energy.

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Heavy Metal-Resistant Biohybrid System Boosts Dissimilatory Nitrate Reduction to Ammonium for Agronomic Sustainability
Jialin Chi, Shiyin Wu, Liping Fang, Kai Liu, Shaochen Huang, Wenjun Zhang, Fangbai Li
ACS Sustainable Chemistry & Engineering.2024; 12(44): 16444. CrossRef
Phenotypic and genomic characterization of Bathyarchaeum tardum gen. nov., sp. nov., a cultivated representative of the archaeal class Bathyarchaeia
Maria A. Khomyakova, Alexander Y. Merkel, Dana D. Mamiy, Alexandra A. Klyukina, Alexander I. Slobodkin
Frontiers in Microbiology.2023;[Epub] CrossRef
Direct Electron Transfer between the frhAGB -Encoded Hydrogenase and Thioredoxin Reductase in the Nonmethanogenic Archaeon Thermococcus onnurineus NA1
Hae-Chang Jung, Jae Kyu Lim, Tae-Jun Yang, Sung Gyun Kang, Hyun Sook Lee, Haruyuki Atomi
Applied and Environmental Microbiology.2020;[Epub] CrossRef
A peroxiredoxin of Thermus thermophilus HB27: Biochemical characterization of a new player in the antioxidant defence
Gabriella Fiorentino, Patrizia Contursi, Giovanni Gallo, Simonetta Bartolucci, Danila Limauro
International Journal of Biological Macromolecules.2020; 153: 608. CrossRef
A Reexamination of Thioredoxin Reductase from Thermoplasma acidophilum, a Thermoacidophilic Euryarchaeon, Identifies It as an NADH-Dependent Enzyme
Dwi Susanti, Usha Loganathan, Austin Compton, Biswarup Mukhopadhyay
ACS Omega.2017; 2(8): 4180. CrossRef
Redox regulation of SurR by protein disulfide oxidoreductase in Thermococcus onnurineus NA1
Jae Kyu Lim, Hae-Chang Jung, Sung Gyun Kang, Hyun Sook Lee
Extremophiles.2017; 21(3): 491. CrossRef
Exploring membrane respiratory chains
Bruno C. Marreiros, Filipa Calisto, Paulo J. Castro, Afonso M. Duarte, Filipa V. Sena, Andreia F. Silva, Filipe M. Sousa, Miguel Teixeira, Patrícia N. Refojo, Manuela M. Pereira
Biochimica et Biophysica Acta (BBA) - Bioenergetics.2016; 1857(8): 1039. CrossRef

Pseudomonas aeruginosa MdaB and WrbA are Water-soluble Two-electron Quinone Oxidoreductases with the Potential to Defend against Oxidative Stress: Laura K Green , Anne C La Flamme , David F Ackerley; J. Microbiol. 2014;52(9):771-777. Published online August 2, 2014; DOI: https://doi.org/10.1007/s12275-014-4208-8

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Abstract

Water-soluble quinone oxidoreductases capable of reducing quinone substrates via a concerted two-electron mechanism have been implicated in bacterial antioxidant defence. Twoelectron transfer avoids formation of dangerously reactive semi-quinone intermediates, moreover previous work in Pseudomonas putida indicated a direct protective effect for the quinols generated by an over-expressed oxidoreductase. Here, the Pseudomonas aeruginosa orthologs of five quinone oxidoreductases – MdaB, ChrR, WrbA, NfsB, and NQO1 – were tested for their possible role in defending P. aeruginosa against H2O2 challenge. In in vitro assays, each enzyme was shown to reduce quinone substrates with only minimal semiquinone formation. However, when each was individually over-expressed in P. aeruginosa no overt H2O2-protective phenotype was observed. It was shown that this was due to a masking effect of the P. aeruginosa catalase, KatA; in a katA mutant, H2O2 challenged strains over-expressing the WrbA and MdaB orthologs grew significantly better than the empty plasmid control. A growth advantage was also observed for H2O2 challenged P. putida strains over-expressing P. aeruginosa wrbA, mdaB or katA. Despite not conferring a growth advantage to wild type P. aeruginosa, it is possible that these quinone oxidoreductases defend against H2O2 toxicity at lower concentrations.

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Plants.2024; 13(20): 2897. CrossRef
Effects of the Quinone Oxidoreductase WrbA on Escherichia coli Biofilm Formation and Oxidative Stress
Federico Rossi, Cristina Cattò, Gianmarco Mugnai, Federica Villa, Fabio Forlani
Antioxidants.2021; 10(6): 919. CrossRef
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Abhijeet Singh, Anna Schnürer, Maria Westerholm
Environmental Microbiology.2021; 23(3): 1620. CrossRef
Plasma Membrane MCC/Eisosome Domains Promote Stress Resistance in Fungi
Carla E. Lanze, Rafael M. Gandra, Jenna E. Foderaro, Kara A. Swenson, Lois M. Douglas, James B. Konopka
Microbiology and Molecular Biology Reviews.2020;[Epub] CrossRef
Diazaquinomycin Biosynthetic Gene Clusters from Marine and Freshwater Actinomycetes
Jana Braesel, Jung-Ho Lee, Benoit Arnould, Brian T. Murphy, Alessandra S. Eustáquio
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Kinetic Investigation of a Presumed Nitronate Monooxygenase from Pseudomonas aeruginosa PAO1 Establishes a New Class of NAD(P)H:Quinone Reductases
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Mohammed O. Suraju, Sloan Lalinde-Barnes, Sachindra Sanamvenkata, Mahsa Esmaeili, Shishir Shishodia, Jason A. Rosenzweig
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NOTE] A Protective Role of Methionine-R-Sulfoxide Reductase against Cadmium in Schizosaccharomyces pombe: Chang-Jin Lim , Hannah Jo , Kyunghoon Kim; J. Microbiol. 2014;52(11):976-981. Published online May 30, 2014; DOI: https://doi.org/10.1007/s12275-014-3512-7

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Abstract

The Schizosaccharomyces pombe cells harboring the methionine- R-sulfoxide reductase (MsrB)-overexpressing recombinant plasmid pFMetSO exhibited better growth than vector control cells, when shifted into fresh medium containing cadmium chloride (abbreviated as Cd). Although both groups of cells contained enhanced reactive oxygen species (ROS) and nitric oxide (NO) levels in the presence of Cd, ROS and NO levels were significantly lower in the S. pombe cells harboring pFMetSO than in vector control cells. Conversely, the S. pombe cells harboring pFMetSO possessed higher total glutathione (GSH) levels and a greater reduced/oxidized GSH ratio than vector control cells under the same conditions.

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Pleurotus pulmonarius Strain: Arsenic(III)/Cadmium(II) Accumulation, Tolerance, and Simulation Application in Environmental Remediation
Yuhui Zhang, Xiaohong Chen, Ling Xie
International Journal of Environmental Research and Public Health.2023; 20(6): 5056. CrossRef
Impact of cadmium and nickel on ion homeostasis in the yeast Schizosaccharomyces pombe
Miroslava Pozgajova, Alica Navratilova, Julius Arvay, Hana Duranova, Anna Trakovicka
Journal of Environmental Science and Health, Part B.2020; 55(2): 166. CrossRef
A methionine-R-sulfoxide reductase, OsMSRB5, is required for rice defense against copper toxicity
Tengwei Xiao, Mengmeng Mi, Changyong Wang, Meng Qian, Yahua Chen, Luqing Zheng, Hongsheng Zhang, Zhubing Hu, Zhenguo Shen, Yan Xia
Environmental and Experimental Botany.2018; 153: 45. CrossRef
Identification and Characterization of a Novel Methionine Sulfoxide Reductase B Gene (AccMsrB) fromApis cerana cerana(Hymenoptera: Apidae)
Feng Liu, Zhihong Gong, Weixing Zhang, Ying Wang, Lanting Ma, Hongfang Wang, Xingqi Guo, Baohua Xu
Annals of the Entomological Society of America.2015; 108(4): 575. CrossRef

NOTE] Glyoxal Detoxification in Escherichia coli K-12 by NADPH Dependent Aldo-keto Reductases: Changhan Lee , Insook Kim , Chankyu Park; J. Microbiol. 2013;51(4):527-530. Published online August 30, 2013; DOI: https://doi.org/10.1007/s12275-013-3087-8

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Abstract: Glyoxal (GO) and methylglyoxal (MG) are reactive carbonyl compounds that are accumulated in vivo through various pathways. They are presumably detoxified through multiple pathways including glutathione (GSH)-dependent/independent glyoxalase systems and NAD(P)H dependent reductases. Previously, we reported an involvement of aldo-ketoreductases (AKRs) in MG detoxification. Here, we investigated the role of various AKRs (YqhE, YafB, YghZ, YeaE, and YajO) in GO metabolism. Enzyme activities of the AKRs to GO were measured, and GO sensitivities of the corresponding mutants were compared. In addition, we examined inductions of the AKR genes by GO. The results indicate that AKRs efficiently detoxify GO, among which YafB, YghZ, and YeaE are major players.

Characterization, Metabolites and Gas Formation of Fumarate Reducing Bacteria Isolated from Korean Native Goat (Capra hircus coreanae): Lovelia L. Mamuad , Seon Ho Kim , Sung Sil Lee , Kwang Keun Cho , Che Ok Jeon , Sang-Suk Lee; J. Microbiol. 2012;50(6):925-931. Published online December 30, 2012; DOI: https://doi.org/10.1007/s12275-012-2497-3

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Abstract: Fumarate reducing bacteria, able to convert fumarate to succinate, are possible to use for the methane reduction in rumen because they can compete for H2 with methanogens. In this, we isolated fumarate reducing bacteria from a rumen of Korean native goat and characterized their molecular properties [fumarate reductase A gene (frdA)], fumarate reductase activities, and productions of volatile fatty acids and gas. Eight fumarate reducing bacteria belonging to Firmicutes were isolated from rumen fluid samples of slaughtered Korean black goats and characterized their phylogenetic positions based on 16S rRNA gene sequences. PCR based analyses showed that only one strain, closely related to Mitsuokella jalaludinii, harbored frdA. The growths of M. jalaludinii and Veillonella parvula strains were tested for different media. Interestingly, M. jalaludinii grew very well in the presence of hydrogen alone, while V. parvula grew well in response of fumarate and fumarate plus hydrogen. M. jalaludinii produced higher levels of lactate (P≤0.05) than did V. parvula. Additionally, M. jalaludinii produced acetate, but not butyrate, whereas V. parvula produced butyrate, not acetate. The fumarate reductase activities of M. jalaludinii and V. parvula were 16.8 ± 0.34 and 16.9 ± 1.21 mmol NADH oxidized/min/mg of cellular N, respectively. In conclusion, this showed that M. jalaludinii can be used as an efficient methane reducing agent in rumen.

DsbM, a Novel Disulfide Oxidoreductase Affects Aminoglycoside Resistance in Pseudomonas aeruginosa by OxyR-Regulated Response: Xuehan Wang , Mingxuan Li , Liwei Liu , Rui Mou , Xiuming Zhang , Yanling Bai , Haijin Xu , Mingqiang Qiao; J. Microbiol. 2012;50(6):932-938. Published online December 30, 2012; DOI: https://doi.org/10.1007/s12275-012-2177-3

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Abstract: A Pseudomonas aeruginosa mutant strain M122 was isolated from a Mu transposon insertion mutant library. In our prophase research, we have found that PA0058, a novel gene encodes a 234-residue conserved protein, was disrupted in the M122 mutant. In this study, the bacteriostatic experiment in vitro indicates that M122 has abnormally high aminoglycoside resistance. We expressed PA0058 in E. coli and found that PA0058 oxidizes and reduces disulfide. This biochemical characterization suggests that PA0058 is a novel disulfide oxidoreductase. Hence, the protein was designated as DsbM. Microarray analysis of the M122 mutant showed its unusual phenotype might be related to the bacterial antioxidant defense system mediated by the oxyR regulon. Meanwhile, we detected –SH content in the periplasm of M122 and wild strain and found a lower –SH/S–S ratio in M122. Therefore, we consider that the loss of dsbM function decreased the –SH/S–S ratio, which then prolongs the OxyR-regulated response, thereby conferring high aminoglycoside resistance to the M122 mutant strain. Our findings have important implications for understanding the mechanisms underlying aminoglycoside resistance in P. aeruginosa.

NOTE] Biosynthetic Pathway for Poly(3-Hydroxypropionate) in Recombinant Escherichia coli: Qi Wang , Changshui Liu , Mo Xian , Yongguang Zhang , Guang Zhao; J. Microbiol. 2012;50(4):693-697. Published online August 25, 2012; DOI: https://doi.org/10.1007/s12275-012-2234-y

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Abstract: Poly(3-hydroxypropionate) (P3HP) is a biodegradable and biocompatible thermoplastic. In this study, we engineered a P3HP biosynthetic pathway in recombinant Escherichia coli. The genes for malonyl-CoA reductase (mcr, from Chloroflexus aurantiacus), propionyl-CoA synthetase (prpE, from E. coli), and polyhydroxyalkanoate synthase (phaC1, from Ralstonia eutropha) were cloned and expressed in E. coli. The E. coli genes accABCD encoding acetyl-CoA carboxylase were used to channel the carbon into the P3HP pathway. Using glucose as a sole carbon source, the cell yield and P3HP content were 1.32 g/L and 0.98% (wt/wt [cell dry weight]), respectively. Although the yield is relatively low, our study shows the feasibility of engineering a P3HP biosynthetic pathway using a structurally unrelated carbon source in bacteria.

A Quantitative and Direct PCR Assay for the Subspecies-Specific Detection of Clavibacter michiganensis subsp. michiganensis Based on a Ferredoxin Reductase Gene: Min Seok Cho , Jang Ha Lee , Nam Han Her , ChangKug Kim , Young-Joo Seol , Jang Ho Hahn , Ji Hyoun Baeg , Hong Gi Kim , Dong Suk Park; J. Microbiol. 2012;50(3):496-501. Published online June 30, 2012; DOI: https://doi.org/10.1007/s12275-012-1611-x

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Abstract: The Gram-positive bacterium Clavibacter michiganensis subsp. michiganensis is the causal agent of canker disease in tomato. Because it is very important to control newly introduced inoculum sources from commercial materials, the specific detection of this pathogen in seeds and seedlings is essential for effective disease control. In this study, a novel and efficient assay for the detection and quantitation of C. michiganensis subsp. michiganensis in symptomless tomato and red pepper seeds was developed. A pair of polymerase chain reaction (PCR) primers (Cmm141F/R) was designed to amplify a specific 141 bp fragment on the basis of a ferredoxin reductase gene of C. michiganensis subsp. michiganensis NCPPB 382. The specificity of the primer set was evaluated using purified DNA from 16 isolates of five C. michiganensis subspecies, one other Clavibacter species, and 17 other reference bacteria. The primer set amplified a single band of expected size from the genomic DNA obtained from the C. michiganensis subsp. michiganensis strains but not from the other C. michiganensis subspecies or from other Clavibacter species. The detection limit was a single cloned copy of the ferredoxin reductase gene of C. michiganensis subsp. michiganensis. In conclusion, this quantitative direct PCR assay can be applied as a practical diagnostic method for epidemiological research and the sanitary management of seeds and seedlings with a low level or latent infection of C. michiganensis subsp. michiganensis.

Research Support, N.I.H., Extramural

Phenotypes Associated with Saccharomyces cerevisiae Hug1 Protein, a Putative Negative Regulator of dNTP Levels, Reveal Similarities and Differences with Sequence-Related Dif1: Eunmi Kim# , Wolfram Siede; J. Microbiol. 2011;49(1):78-85. Published online March 3, 2011; DOI: https://doi.org/10.1007/s12275-011-0200-8

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Abstract: Saccharomyces cerevisiae Hug1 is a small protein of unknown function that is highly inducible following replication stress and DNA damage. Its deletion suppresses the lethality of deletion of checkpoint kinase Mec1. Although DNA damage responses were largely normal in the HUG1 deletion mutant, we found enhanced resistance towards heat in logarithmic phase. In response to simultaneous carbon and replication stress, overall growth delay and less pseudohyphal filament formation were evident. These novel phenotypes are shared with deletion mutants of the negative regulators of ribonucleotide reductase, Dif1 and Sml1. Microarray analysis showed the influence of Hug1 on the expression of a large number of transcripts, including stress-related transcripts. Elevated dNTP levels in hug1Δ cells may result in a stress response reflected by the observed phenotypes and transcript profiles. However, in contrast to a deletion of structurally related Dif1, Rnr2-Rnr4 subcellular localization is not grossly altered in a Hug1 deletion mutant. Thus, although Hug1 appears to be derived from the Rnr2-Rnr4 binding region of Dif1, its mechanism of action must be independent of determining the localization of Rnr2-Rnr4.

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

Metagenomic Assessment of a Sulfur-Oxidizing Enrichment Culture Derived from Marine Sediment: Man-Young Jung , VinhHoa Pham , Soo-Je Park , So-Jeong Kim , Jong-Chan Chae , Yul Roh , Sung-Keun Rhee; J. Microbiol. 2010;48(6):739-747. Published online January 9, 2011; DOI: https://doi.org/10.1007/s12275-010-0257-9

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Abstract: The biological oxidation of reduced sulfur compounds is a critically important process in global sulfur biogeochemistry. In this study, we enriched from marine sediments under denitrifying conditions, chemolithotrophic sulfur oxidizers that could oxidize a variety of reduced sulfur compounds: thiosulfate, tetrathionate, sulfide, and polysulfide. Two major phylotypes of 16S rRNA gene (>99% identity in each phylotype) were detected in this enrichment culture. In order to characterize sulfide oxidation, we sequenced and characterized one fosmid clone (43.6 kb) containing the group I sulfide-quinone reductase (sqr) gene. Interestingly, four putative rhodanese genes were found in this clone. Furthermore, comparative alignment with the closest genome of Thiomicrospira crunogena XCL2 revealed that three homologous genes were located within the vicinity of the sqr gene. Fosmid clones harboring carbon fixation (cbbL and cbbM) and denitrification (narG) genes were screened, and the phylogeny of the functional genes was analyzed. Along with the comparison between the sqr-containing fosmid clones and the relevant gamma-proteobacteria, our phylogenetic study based on the 16S rRNA gene and carbon fixation genes suggest the prevalence of chemolithotrophic gamma-proteobacteria in the denitrifying cultures. The findings of this study imply that a combination of cultivation and metagenomic approaches might provide us with a glimpse into the characteristics of sulfur oxidizers in marine sediments.

Characterization of Deinococcus radiophilus Thioredoxin Reductase Active with Both NADH and NADPH: Hee-Jeong Seo , Young Nam Lee; J. Microbiol. 2010;48(5):637-643. Published online November 3, 2010; DOI: https://doi.org/10.1007/s12275-010-0283-7

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Abstract: Thioredoxin reductase (TrxR, EC 1.6.4.5) of Deinococcus radiophilus was purified by steps of sonication, ammonium sulfate fractionation, 2'5' ADP Sepharose 4B affinity chromatography, and Sephadex G-100 gel filtration. The purified TrxR, which was active with both NADPH and NADH, gave a 368 U/mg protein of specific activity with 478-fold purification and 18% recovery from the cell-free extract. An isoelectric point of the purified enzymes was ca. 4.5. The molecular weights of the purified TrxR estimated by PAGE and gel filtration were about 63.1 and 72.2 kDa, respectively. The molecular mass of a TrxR subunit is 37 kDa. This suggests that TrxR definitely belongs to low molecular weight TrxR (L-TrxR). The Km and Vmax of TrxR for NADPH are 12.5 μM and 25 μM/min, whereas those for NADH are 30.2 μM and 192 μ M/min. The Km and Vmax for 5, 5'-dithio-bis-2-nitrobenzoic acid (DTNB, a substituted substrate for thioredoxin) are 463 μM and 756 μM/min, respectively. The presence of FAD in TrxR was confirmed with the absorbance peaks at 385 and 460 nm. The purified TrxR was quite stable from pH 3 to 9, and was thermo-stable up to 70°C. TrxR activity was drastically reduced (ca. 70%) by Cu2+, Zn2+, Hg2+, and Cd2+, but moderately reduced (ca. 50%) by Ag+. A significant inhibition of TrxR by N ethylmaleimide suggests an occurrence of cysteine at its active sites. Amino acid sequences at the N-terminus of purified TrxR are H2N-Ser-Glu-Gln-Ala-Gln-Met-Tyr-Asp-Val-Ile-Ile-Val-Gly-Gly-Gly-Pro-Ala-Gly-Leu-Thr-Ala-COOH. These sequences show high similarity with TrxRs reported in Archaea, such as Methanosarcina mazei, Archaeoglobus fulgidus etc.

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