Journal of Microbiology

Volume 54(9); September 2016

Review

MINIREVIEW] Multilayered regulations of RIG-I in the anti-viral signaling pathway: Nari Kim , Hesung Now , Nhung T.H. Nguyen , Joo-Yeon Yoo; J. Microbiol. 2016;54(9):583-587. Published online August 31, 2016; DOI: https://doi.org/10.1007/s12275-016-6322-2

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RIG-I is a cytosolic receptor recognizing virus-specific RNA structures and initiates an antiviral signaling that induces the production of interferons and proinflammatory cytokines. Because inappropriate RIG-I signaling affects either viral clearance or immune toxicity, multiple regulations of RIG-I have been investigated since its discovery as the viral RNA detector. In this review, we describe the recent progress in research on the regulation of RIG-I activity or abundance. Specifically, we focus on the mechanism that modulates RIGI- dependent antiviral response through post-translational modifications of or protein-protein interactions with RIG-I.

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Military Medical Research.2024;[Epub] CrossRef
ZNF205 positively regulates RLR antiviral signaling by targeting RIG-I
Ni Zhong, Chen Wang, Guangxiu Weng, Ting Ling, Liangguo Xu
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Identification of Vital Hub Genes and Potential Molecular Pathways of Dermatomyositis by Bioinformatics Analysis
Xueren Ouyang, Yuning Zeng, Xiaotao Jiang, Hua Xu, Yile Ning, Ming Yi
BioMed Research International.2021; 2021: 1. CrossRef
HSPBP1 facilitates cellular RLR-mediated antiviral response by inhibiting the K48-linked ubiquitination of RIG-I
Ya-Xian Yang, Jing-Ping Huang, Sheng-Na Li, Jing Li, Ting Ling, Tao Xie, Liang-Guo Xu
Molecular Immunology.2021; 134: 62. CrossRef
Investigation of Human IFITM3 Polymorphisms rs34481144A and rs12252C and Risk for Influenza A(H1N1)pdm09 Severity in a Brazilian Cohort
Jéssica S. C. Martins, Maria L. A. Oliveira, Cristiana C. Garcia, Marilda M. Siqueira, Aline R. Matos
Frontiers in Cellular and Infection Microbiology.2020;[Epub] CrossRef
Radiation Attenuates Prostate Tumor Antiviral Responses to Vesicular Stomatitis Virus Containing IFNβ, Resulting in Pronounced Antitumor Systemic Immune Responses
Thirupandiyur S. Udayakumar, Dillon M. Betancourt, Anis Ahmad, Wensi Tao, Tulasigeri M. Totiger, Mausam Patel, Brian Marples, Glen Barber, Alan Pollack
Molecular Cancer Research.2020; 18(8): 1232. CrossRef
Antiviral potential of human IFN-α subtypes against influenza A H3N2 infection in human lung explants reveals subtype-specific activities
Aline da Rocha Matos, Katharina Wunderlich, Sebastian Schloer, Klaus Schughart, Robert Geffers, Martine Seders, Marlous de Witt, Anmari Christersson, Rainer Wiewrodt, Karsten Wiebe, Peter Barth, Andreas Hocke, Stefan Hippenstiel, Katja Hönzke, Ulf Dittmer
Emerging Microbes & Infections.2019; 8(1): 1763. CrossRef
Discovery of Key Genes in Dermatomyositis Based on the Gene Expression Omnibus Database
Shuoshan Xie, Hui Luo, Huali Zhang, Honglin Zhu, Xiaoxia Zuo, Sijia Liu
DNA and Cell Biology.2018; 37(12): 982. CrossRef
Change in the immune function of porcine iliac artery endothelial cells infected with porcine circovirus type 2 and its inhibition on monocyte derived dendritic cells maturation
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Journal Articles

Gracilibacillus kimchii sp. nov., a halophilic bacterium isolated from kimchi§: Young Joon Oh , Hae-Won Lee , Seul Ki Lim , Min-Sung Kwon , Jieun Lee , Ja-Young Jang , Hae Woong Park , Young-Do Nam , Myung-Ji Seo , Hak-Jong Choi; J. Microbiol. 2016;54(9):588-593. Published online August 31, 2016; DOI: https://doi.org/10.1007/s12275-016-6349-4

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Abstract

A novel halophilic bacterium, strain K7T, was isolated from kimchi, a traditional Korean fermented food. The strain is Gram-positive, motile, and produces terminal endospores. The isolate is facultative aerobic and grows at salinities of 0.0–25.0% (w/v) NaCl (optimum 10–15% NaCl), pH 5.5–8.5 (optimum pH 7.0–7.5), and 15–42°C (optimum 37°C). The predominant isoprenoid quinone in the strain is menaquinone- 7 and the peptidoglycan of the strain is meso-diaminopimelic acid. The major fatty acids of the strain are anteisio- C15:0, iso-C15:0, and, C16:0 (other components were < 10.0%), while the major polar lipids are diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, and three unidentified lipids. A phylogenetic analysis of 16S rRNA gene sequence similarity showed that the isolated strain was a cluster of the genus Gracilibacillus. High levels of gene sequence similarity were observed between strain K7T and Gracilibacillus orientalis XH-63T (96.5%), and between the present strain and Gracilibacillus xinjiangensis (96.5%). The DNA G+C content of this strain is 37.7 mol%. Based on these findings, strain K7T is proposed as a novel species: Gracilibacillus kimchii sp. nov. The type strain is K7T (KACC 18669T; JCM 31344T).

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Synergistic improvement of humus formation in compost residue by fenton-like and effective microorganism composite agents
Jun Zhuo Cai, Ying Lan Yu, Zhan Biao Yang, Xiao Xun Xu, Guo Chun Lv, Chang Lian Xu, Gui Yin Wang, Xin Qi, Ting Li, Yu Bon Man, Ming Hung Wong, Zhang Cheng
Bioresource Technology.2024; 400: 130703. CrossRef
Gracilibacillus salinarum sp. nov. and Gracilibacillus caseinilyticus sp. nov., halotolerant bacteria isolated from a saltern environment
Parthiban Subramanian, Yiseul Kim, Hanako Naito, Tomomi Asano, Moriyuki Hamada, Hang-Yeon Weon, Soon-Wo Kwon, Jun Heo
International Journal of Systematic and Evolutionary Microbiology .2023;[Epub] CrossRef
Investigation on Structural Prediction of Pectate Lyase Enzymes from Different Microbes and Comparative Docking Studies with Pectin: The Economical Waste from Food Industry
Swati Sudeshna Panda, Jyotirmayee Dey, Soumya Ranjan Mahapatra, Gajraj Singh Kushwaha, Namrata Misra, Mrutyunjay Suar, Mrinmoy Ghosh
Geomicrobiology Journal.2022; 39(3-5): 294. CrossRef
Salicibibacter cibarius sp. nov. and Salicibibacter cibi sp. nov., two novel species of the family Bacillaceae isolated from kimchi
Young Joon Oh, Joon Yong Kim, Seul Ki Lim, Min-Sung Kwon, Hak-Jong Choi
Journal of Microbiology.2021; 59(5): 460. CrossRef
Characterization of β-galactosidase and α-galactosidase activities from the halophilic bacterium Gracilibacillus dipsosauri
Charles E. Deutch, Amy M. Farden, Emily S. DiCesare
Annals of Microbiology.2021;[Epub] CrossRef
Gracilibacillus suaedae sp. nov., an indole acetic acid-producing endophyte isolated from a root of Suaeda salsa
Xiao-Xian Huang, Lian Xu, Ji-Quan Sun
International Journal of Systematic and Evolutionary Microbiology .2021;[Epub] CrossRef
Genomic sequencing of Gracilibacillus dipsosauri reveals key properties of a salt-tolerant α-amylase
Charles E. Deutch, Shanshan Yang
Antonie van Leeuwenhoek.2020; 113(7): 1049. CrossRef
Lentibacillus cibarius sp. nov., isolated from kimchi, a Korean fermented food
Young Joon Oh, Joon Yong Kim, Hee Eun Jo, Hyo Kyeong Park, Seul Ki Lim, Min-Sung Kwon, Hak-Jong Choi
Journal of Microbiology.2020; 58(5): 387. CrossRef
Salicibibacter halophilus sp. nov., a moderately halophilic bacterium isolated from kimchi
Young Joon Oh, Joon Yong Kim, Hyo Kyeong Park, Ja-Young Jang, Seul Ki Lim, Min-Sung Kwon, Hak-Jong Choi
Journal of Microbiology.2019; 57(11): 997. CrossRef
List of new names and new combinations that have appeared in effective publications outside of the IJSEM and are submitted for valid publication
Aharon Oren, George M. Garrity
International Journal of Systematic and Evolutionary Microbiology .2019;[Epub] CrossRef
Salicibibacter kimchii gen. nov., sp. nov., a moderately halophilic and alkalitolerant bacterium in the family Bacillaceae, isolated from kimchi
Ja-Young Jang, Young Joon Oh, Seul Ki Lim, Hyo Kyeong Park, Changsu Lee, Joon Yong Kim, Mi-Ai Lee, Hak-Jong Choi
Journal of Microbiology.2018; 56(12): 880. CrossRef
Virgibacillus kimchii sp. nov., a halophilic bacterium isolated from kimchi
Young Joon Oh, Ja-Young Jang, Seul Ki Lim, Min-Sung Kwon, Jieun Lee, NamHee Kim, Mi-Young Shin, Hyo Kyeong Park, Myung-Ji Seo, Hak-Jong Choi
Journal of Microbiology.2017; 55(12): 933. CrossRef

Intestinal Lactobacillus community structure and its correlation with diet of Southern Chinese elderly subjects§: Yuanyuan Pan , Da-Wen Sun , Quanyang Li; J. Microbiol. 2016;54(9):594-601. Published online August 31, 2016; DOI: https://doi.org/10.1007/s12275-016-6131-7

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Abstract

This study aimed to investigate the relationship between the intestinal Lactobacillus species and diet of elderly subjects in a longevity area in Southern China. Healthy elderly subjects ranging from 80 to 99 years old were respectively selected from the regions of Bama and Nanning, Guangxi, China. The nested polymerase chain reaction and denaturing gradient gel electrophoresis (PCR-DGGE) technology was used to analyze the intestinal Lactobacillus community structure.
Results
showed that Weissella confusa, L. mucosae, L. crispatus, L. salivarius, and L. delbrueckii were the representative Lactobacillus of elderly subjects. Among them, L. crispatus and L. delbrueckii were the dominant Lactobacillus of all species. In comparison to Nanning elderly subjects, the detection frequencies of W. confusa and L. salivarius were significantly increased in Bama elderly subjects (P < 0.01), whereas L. mucosae was significantly decreased (P < 0.01). Interestingly, it was also found that there were 4 kinds of representative Lactobacillus, which were significantly correlated with dietary fiber. W. confusa (P < 0.01) and L. salivarius (P < 0.05) were significantly positively correlated with the intake of dietary fiber, while L. mucosae (P < 0.01) and L. crispatus (P < 0.05) were significantly negatively correlated with the intake of dietary fiber, respectively. Results confirmed that different diets had obvious effects on the intestinal Lactobacillus community structure of elderly subjects in Southern China, which may provide a certain theoretical basis for the elderly’s healthy food strategic design and probiotics product development.

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Cr(VI) removal from aqueous solution by thermophilic denitrifying bacterium Chelatococcus daeguensis TAD1 in the presence of single and multiple heavy metals: Han Li , Shaobin Huang , Yongqing Zhang; J. Microbiol. 2016;54(9):602-610. Published online August 31, 2016; DOI: https://doi.org/10.1007/s12275-016-5295-5

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Abstract

Cr(VI) pollution is increasing continuously as a result of ongoing industrialization. In this study, we investigated the thermophilic denitrifying bacterium Chelatococcus daeguensis TAD1, isolated from the biofilm of a biotrickling filter used in nitrogen oxides (NOX) removal, with respect to its ability to remove Cr(VI) from an aqueous solution. TAD1 was capable of reducing Cr(VI) from an initial concentration of 10 mg/L to non-detectable levels over a pH range of 7–9 and at a temperature range of 30–50°C. TAD1 simultaneously removed both Cr(VI) and NO3 −-N at 50°C, when the pH was 7 and the initial Cr(VI) concentration was 15 mg/L. The reduction of Cr(VI) to Cr(III) correlated with the growth metabolic activity of TAD1. The presence of other heavy metals (Cu, Zn, and Ni) inhibited the ability of TAD1 to remove Cr(VI). The metals each individually inhibited Cr(VI) removal, and the extent of inhibition increased in a cooperative manner in the presence of a combination of the metals. The addition of biodegradable cellulose acetate microspheres (an adsorption material) weakened the toxicity of the heavy metals; in their presence, the Cr(VI) removal efficiency returned to a high level. The feasibility and applicability of simultaneous nitrate removal and Cr(VI) reduction by strain TAD1 is promising, and may be an effective biological method for the clean-up of wastewater.

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Dong-Wook Hyun, Hojun Sung, Pil Soo Kim, Ji-Hyun Yun, Jin-Woo Bae
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Iron oxide minerals promote simultaneous bio-reduction of Cr(VI) and nitrate: Implications for understanding natural attenuation
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Cr(VI) reductase activity locates in the cytoplasm of Aeribacillus pallidus BK1, a novel Cr(VI)-reducing thermophile isolated from Tengchong geothermal region, China
Yan Ma, Hui Zhong, Zhiguo He
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Long-term organic-inorganic fertilization ensures great soil productivity and bacterial diversity after natural-to-agricultural ecosystem conversion: Weibing Xun , Zhihui Xu , Wei Li , Yi Ren , Ting Huang , Wei Ran , Boren Wang , Qirong Shen , Ruifu Zhang; J. Microbiol. 2016;54(9):611-617. Published online August 31, 2016; DOI: https://doi.org/10.1007/s12275-016-6143-3

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Abstract

Natural ecosystems comprise the planet’s wild plant and animal resources, but large tracts of land have been converted to agroecosystems to support the demand for agricultural products. This conversion limits the number of plant species and decreases the soil biological diversity. Here we used highthroughput 16S rRNA gene sequencing to evaluate the responses of soil bacterial communities in long-term converted and fertilized red soils (a type of Ferralic Cambisol). We observed that soil bacterial diversity was strongly affected by different types of fertilization management. Oligotrophic bacterial taxa demonstrated large relative abundances in chemically fertilized soil, whereas copiotrophic bacterial taxa were found in large relative abundances in organically fertilized and fallow management soils. Only organic-inorganic fertilization exhibited the same local taxonomic and phylogenetic diversity as that of a natural ecosystem. However, the independent use of organic or inorganic fertilizer reduced local taxonomic and phylogenetic diversity and caused biotic homogenization. This study demonstrated that the homogenization of bacterial communities caused by natural-to-agricultural ecosystem conversion can be mitigated by employing rational organic-inorganic fertilization managemen

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Jinshan Lian, Huiying Wang, Ye Deng, Minggang Xu, Shutang Liu, Baoku Zhou, Kamlesh Jangid, Yinghua Duan
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Li Xiao, Yimei Huang, Junfeng Zhao, Junying Zhou, Fakher Abbas
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Eight years of manure fertilization favor copiotrophic traits in paddy soil microbiomes
Hang Wang, Xiang He, Zhongfu Zhang, Minggang Li, Qing Zhang, Hongye Zhu, Shengtao Xu, Peiwen Yang
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Wen Xing Li, Chao Wang, Man Man Zheng, Ze Jiang Cai, Bo Ren Wang, Ren Fang Shen
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Application of high-resolution melting analysis for differentiation of spoilage yeasts: Mine Erdem , Zülal Kesmen , Esra Özbekar , Bülent Çetin , Hasan Yetim; J. Microbiol. 2016;54(9):618-625. Published online August 31, 2016; DOI: https://doi.org/10.1007/s12275-016-6017-8

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Abstract

A new method based on high resolution melting (HRM) analysis was developed for the differentiation and classification of the yeast species that cause food spoilage. A total 134 strains belonging to 21 different yeast species were examined to evaluate the discriminative power of HRM analysis. Two different highly variable DNA regions on the 26 rRNA gene were targeted to produce the HRM profiles of each strain. HRMbased grouping was compared and confirmed by (GTG)5 rep- PCR fingerprinting analysis. All of the yeast species belonging to the genera Pichia, Candida, Kazachstania, Kluyveromyces, Debaryomyces, Dekkera, Saccharomyces, Torulaspora, Ustilago, and Yarrowia, which were produced as species-specific HRM profiles, allowed discrimination at species and/or strain level. The HRM analysis of both target regions provided successful discrimination that correlated with rep-PCR fingerprinting analysis. Consequently, the HRM analysis has the potential for use in the rapid and accurate classification and typing of yeast species isolated from different foods to determine their sources and routes as well as to prevent contamination.

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Molecular characterization of SCO0765 as a cellotriose releasing endo-β-1,4-cellulase from Streptomyces coelicolor A(3): Joo-Bin Hong , Vijayalakshmi Dhakshnamoorthy , Chang-Ro Lee; J. Microbiol. 2016;54(9):626-631. Published online August 31, 2016; DOI: https://doi.org/10.1007/s12275-016-6271-9

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Abstract

The sco0765 gene was annotated as a glycosyl hydrolase family 5 endoglucanase from the genomic sequence of Streptomyces coelicolor A3(2) and consisted of 2,241 bp encoding a polypeptide of 747 amino acids (molecular weight of 80.5 kDa) with a 29-amino acid signal peptide for secretion. The SCO0765 recombinant protein was heterogeneously overexpressed in Streptomyces lividans TK24 under the control of a strong ermE* promoter. The purified SCO0765 protein showed the expected molecular weight of the mature form (718 aa, 77.6 kDa) on sodium dodecyl sulfate-polyacryl amide gel electrophoresis. SCO0765 showed high activity toward β-glucan and carboxymethyl cellulose (CMC) and negligible activity to Avicel, xylan, and xyloglucan. The SCO0765 cellulase had a maximum activity at pH 6.0 and 40°C toward CMC and at pH 9.0 and 50–60°C toward β-glucan. Thin layer chromatography of the hydrolyzed products of CMC and β-glucan by SCO0765 gave cellotriose as the major product and cellotetraose, cellopentaose, and longer oligosaccharides as the minor products. These results clearly demonstrate that SCO0765 is an endo-β-1,4-cellulase, hydrolyzing the β-1,4 glycosidic bond of cellulose into cellotriose.

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Cellulase Promotes Mycobacterial Biofilm Dispersal in Response to a Decrease in the Bacterial Metabolite Gamma-Aminobutyric Acid
Jiaqi Zhang, Yingying Liu, Junxing Hu, Guangxian Leng, Xining Liu, Zailin Cui, Wenzhen Wang, Yufang Ma, Shanshan Sha
International Journal of Molecular Sciences.2024; 25(2): 1051. CrossRef
Haloferax sulfurifontis GUMFAZ2 producing xylanase‐free cellulase retrieved from Haliclona sp. inhabiting rocky shore of Anjuna, Goa‐India
Alisha D. Malik, Irene J. Furtado
Journal of Basic Microbiology.2019; 59(7): 692. CrossRef
Biochemical characterization of a novel cold-adapted agarotetraose-producing α-agarase, AgaWS5, from Catenovulum sediminis WS1-A
Choong Hyun Lee, Chang-Ro Lee, Soon-Kwang Hong
Applied Microbiology and Biotechnology.2019; 103(20): 8403. CrossRef

D-Galactose as an autoinducer 2 inhibitor to control the biofilm formation of periodontopathogens: Eun-Ju Ryu , Jaehyun Sim , Jun Sim , Julian Lee , Bong-Kyu Choi; J. Microbiol. 2016;54(9):632-637. Published online August 31, 2016; DOI: https://doi.org/10.1007/s12275-016-6345-8

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Abstract

Autoinducer 2 (AI-2) is a quorum sensing molecule to which bacteria respond to regulate various phenotypes, including virulence and biofilm formation. AI-2 plays an important role in the formation of a subgingival biofilm composed mostly of Gram-negative anaerobes, by which periodontitis is initiated. The aim of this study was to evaluate D-galactose as an inhibitor of AI-2 activity and thus of the biofilm formation of periodontopathogens. In a search for an AI-2 receptor of Fusobacterium nucleatum, D-galactose binding protein (Gbp, Gene ID FN1165) showed high sequence similarity with the ribose binding protein (RbsB), a known AI-2 receptor of Aggregatibacter actinomycetemcomitans. D-Galactose was evaluated for its inhibitory effect on the AI-2 activity of Vibrio harveyi BB152 and F. nucleatum, the major coaggregation bridge organism, which connects early colonizing commensals and late pathogenic colonizers in dental biofilms. The inhibitory effect of D-galactose on the biofilm formation of periodontopathogens was assessed by crystal violet staining and confocal laser scanning microscopy in the absence or presence of AI-2 and secreted molecules of F. nucleatum. D-Galactose significantly inhibited the AI-2 activity of V. harveyi and F. nucleatum. In addition, D-galactose markedly inhibited the biofilm formation of F. nucleatum, Porphyromonas gingivalis, and Tannerella forsythia induced by the AI-2 of F. nucleatum without affecting bacterial growth. Our
results
demonstrate that the Gbp may function as an AI-2 receptor and that galactose may be used for prevention of the biofilm formation of periodontopathogens by targeting AI-2 activity.

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