Journal of Microbiology

Volume 51(2); April 2013

Review

Minireview] The Unique Metabolism of SAR11 Aquatic Bacteria: H. James Tripp; J. Microbiol. 2013;51(2):147-153. Published online April 27, 2013; DOI: https://doi.org/10.1007/s12275-013-2671-2

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The deeply branching clade of abundant, globally distributed aquatic α-Proteobacteria known as “SAR11”, are adapted to nutrient-poor environments such as the surface waters of the open ocean. Unknown prior to 1990, uncultured until 2002, members of the SAR11 clade can now be cultured in artificial, defined media to densities three orders of magnitude higher than in unamended natural media. Cultivation in natural and defined media has confirmed genomic and metagenomic predictions such as an inability to reduce sulfate to sulfide, a requirement for pyruvate, an ability to oxidize a wide variety of methylated and one-carbon compounds for energy, and an unusual form of conditional glycine auxotrophy. Here we describe the metabolism of the SAR11 type strain Candidatus “Pelagibacter ubique” str. HTCC1062, as revealed by genomeassisted studies of laboratory cultures. We also describe the discovery of SAR11 and field studies that have been done on natural populations.

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

The α-Barrel Tip Region of Escherichia coli TolC Homologs of Vibrio vulnificus Interacts with the MacA Protein to Form the Functional Macrolide-Specific Efflux Pump MacAB-TolC: Minho Lee , Hyun-Lee Kim , Saemee Song , Minju Joo , Seunghwa Lee , Daeyoung Kim , Yoonsoo Hahn , Nam-Chul Ha , Kangseok Lee; J. Microbiol. 2013;51(2):154-159. Published online April 27, 2013; DOI: https://doi.org/10.1007/s12275-013-2699-3

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Abstract PDF: TolC and its homologous family of proteins are outer membrane factors that are essential for exporting small molecules and toxins across the outer membrane in Gram-negative bacteria. Two open reading frames in the Vibrio vulnificus genome that encode proteins homologous to Escherichia coli TolC, designated TolCV1 and TolCV2, have 51.3% and 29.6% amino acid identity to TolC, respectively. In this study, we show that TolCV1 and TolCV2 functionally and physically interacted with the membrane fusion protein, MacA, a component of the macrolide-specific MacAB-TolC pump of E. coli. We further show that the conserved residues located at the aperture tip region of the α-hairpin of TolCV1 and TolCV2 played an essential role in the formation of the functional MacAB-TolC pump using site-directed mutational analyses. Our findings suggest that these outer membrane factors have conserved tip-to-tip interaction with the MacA membrane fusion protein for action of the drug efflux pump in Gramnegative bacteria.

Prevalence of Amino Acid Changes in the yvqF, vraSR, graSR, and tcaRAB Genes from Vancomycin Intermediate Resistant Staphylococcus aureus: Jae Il Yoo , Jung Wook Kim , Gi Su Kang , Hwa Su Kim , Jung Sik Yoo , Yeong Seon Lee; J. Microbiol. 2013;51(2):160-165. Published online April 27, 2013; DOI: https://doi.org/10.1007/s12275-013-3088-7

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Abstract PDF

Vancomycin intermediate Staphylococcus aureus (VISA) strains are increasingly prevalent in the hospital setting, and are of major concern in the treatment of methicillin-resistant S. aureus infections. Multiple mutations in vancomycinsusceptible S. aureus (VSSA) strains likely led to the emergence of VISA, and point mutations in the agr, orf1, yvqF, vraSR, graSR, and tcaRAB genes of VISA strains have been shown to contribute to glycopeptide resistance. Therefore, we investigated point mutations in these genes from 87 VISA and 27 VSSA clinical strains isolated from Korean hospitals. All strains were assigned an agr type (I, II, or III) on the basis of multiplex PCR, with the majority of VISA strains belonging to agr groups I and II. Sequencing revealed amino acid changes in vraS from VISA strains which were not present in the VSSA strains. The E59D substitution in the vraR gene occurred in 36.3% of VSSA/agrI and 92.7% of VISA/agrI strains, suggesting that this mutation associated with emergence of VISA/agrI strains. VISA strains were classified into 31 mutation patterns according to mutations in the yvqF, vraSR, graSR, and tcaRAB genes. In addition, the mutation patterns were correlated with agr and sequence type (ST). The most prevalent pattern included agr type I (ST 72) strains with E59D (vraR), L26F and T224I (graS), D148Q (graR), and L218P, R283H and G312D (tcaA) amino acid substitutions. The minimum inhibitory concentration (MIC) range of mutation pattern 5 toward oxacillin and imipenem was much lower than that of patterns 6 and 24. These results improve our understanding of emergence of VISA strains.

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Construction of a Streptomyces lydicus A01 Transformant with a chit42 Gene from Trichoderma harzianum P1 and Evaluation of Its Biocontrol Activity against Botrytis cinerea: Qiong Wu , Linquan Bai , Weicheng Liu , Yingying Li , Caige Lu , Yaqian Li , Kehe Fu , Chuanjin Yu , Jie Chen; J. Microbiol. 2013;51(2):166-173. Published online April 27, 2013; DOI: https://doi.org/10.1007/s12275-013-2321-8

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Abstract PDF

Streptomyces lydicus A01 and Trichoderma harzianum P1 are potential biocontrol agents of fungal diseases in plants. S. lydicus A01 produces natamycin to bind the ergosterol of the fungal cell membrane and inhibits the growth of Botrytis cinerea. T. harzianum P1, on the other hand, features high chitinase activity and decomposes the chitin in the cell wall of B. cinerea. To obtain the synergistic biocontrol effects of chitinase and natamycin on Botrytis cinerea, this study transformed the chit42 gene from T. harzianum P1 to S. lydicus A01. The conjugal transformant (CT) of S. lydicus A01 with the chit42 gene was detected using polymerase chain reaction (PCR). Associated chitinase activity and natamycin production were examined using the 3, 5-dinitrosalicylic acid (DNS) method and ultraviolet spectrophotometry, respectively. The S. lydicus A01-chit42 CT showed substantially higher chitinase activity and natamycin production than its wild type strain (WT). Consequently, the biocontrol effects of S. lydicus A01-chit42 CT on B. cinerea, including inhibition to spore germination and mycelial growth, were highly improved compared with those of the WT. Our research indicates that the biocontrol effect of Streptomyces can be highly improved by transforming the exogenous resistance gene, i.e. chit42 from Trichoderma, which not only enhances the production of antibiotics, but also provides a supplementary function by degrading the cell walls of the pathogens.

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Enzyme and Microbial Technology.2015; 81: 80. CrossRef
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Jinjin Li, Weicheng Liu, Lijin Luo, Dan Dong, Ting Liu, Taotao Zhang, Caige Lu, Dewen Liu, Dianpeng Zhang, Huiling Wu
Biological Control.2015; 90: 141. CrossRef

Cloning, Annotation and Expression Analysis of Mycoparasitism-Related Genes in Trichoderma harzianum 88: Lin Yao , Qian Yang , Jinzhu Song , Chong Tan , Changhong Guo , Li Wang , Lianhai Qu , Yun Wang; J. Microbiol. 2013;51(2):174-182. Published online April 27, 2013; DOI: https://doi.org/10.1007/s12275-013-2545-7

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Abstract PDF: Trichoderma harzianum 88, a filamentous soil fungus, is an effective biocontrol agent against several plant pathogens. High-throughput sequencing was used here to study the mycoparasitism mechanisms of T. harzianum 88. Plate confrontation tests of T. harzianum 88 against plant pathogens were conducted, and a cDNA library was constructed from T. harzianum 88 mycelia in the presence of plant pathogen cell walls. Randomly selected transcripts from the cDNA library were compared with eukaryotic plant and fungal genomes. Of the 1,386 transcripts sequenced, the most abundant Gene Ontology (GO) classification group was “physiological process”. Differential expression of 19 genes was confirmed by real-time RT-PCR at different mycoparasitism stages against plant pathogens. Gene expression analysis revealed the transcription of various genes involved in mycoparasitism of T. harzianum 88. Our study provides helpful insights into the mechanisms of T. harzianum 88-plant pathogen interactions.

Lactobacillus salivarius Strain FDB89 Induced Longevity in Caenorhabditis elegans by Dietary Restriction: Yang Zhao , Liang Zhao , Xiaonan Zheng , Tianjiao Fu , Huiyuan Guo , Fazheng Ren; J. Microbiol. 2013;51(2):183-188. Published online April 27, 2013; DOI: https://doi.org/10.1007/s12275-013-2076-2

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Abstract PDF: In this study, we utilized the nematode Caenorhabditis elegans to assess potential life-expanding effect of Lactobacillus salivarius strain FDB89 (FDB89) isolated from feces of centenarians in Bama County (Guangxi, China). This study showed that feeding FDB89 extended the mean life span in C. elegans by up to 11.9% compared to that of control nematodes. The reduced reproductive capacities, pharyngeal pumping rate, growth, and increased superoxide dismutase (SOD) activity and XTT reduction capacity were also observed in FDB89 feeding worms. To probe the anti-aging mechanism further, we incorporated a food gradient feeding assay and assayed the life span of eat-2 mutant. The results demonstrated that the maximal life span of C. elegans fed on FDB89 was achieved at the concentration of 1.0 mg bacterial cells/plate, which was 10-fold greater than that of C. elegans fed on E. coli OP50 (0.1 mg bacterial cells/plate). However, feeding FDB89 could not further extend the life span of eat-2 mutant. These results indicated that FDB89 modulated the longevity of C. elegans in a dietary restriction-dependent manner and expanded the understanding of anti-aging effect of probiotics.

Journal Article

Biochemical Characterization of Chitinase 2 Expressed during the Autolytic Phase of the Inky Cap, Coprinellus congregatus: Yuri Kang , Hyewon Kim , Hyoung T. Choi; J. Microbiol. 2013;51(2):189-193. Published online April 27, 2013; DOI: https://doi.org/10.1007/s12275-013-2535-9

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Abstract PDF: Fungal cell walls consist of various glucans and chitin. The inky cap, Coprinellus congregatus, produces mushrooms at 25°C in a regime of 15 h light/9 h dark, and then the mushroom is autolyzed rapidly to generate black liquid droplets in which no cell walls are detected by microscopy. Chitinase cDNA from the mature mushroom tissues of C. congregatus, which consisted of 1,622 nucleotides (chi2), was successfully cloned using the rapid amplification of cDNA ends polymerase chain reaction technique. The deduced 498 amino acid sequence of Chi2 had a conserved catalytic domain as in other fungal chitinase family 18 enzymes. The Chi2 enzyme was purified from the Pichia pastoris expression system, and its estimated molecular weight was 68 kDa. The optimum pH and temperature of Chi2 was pH 4.0 and 35°C, respectively when 4-nitrophenyl N,N’-diacetyl-β-D-chitobioside was used as the substrate. The Km value and Vmax for the substrate A, 4-nitrophenyl N,N’-diacetyl-β-D-chitobioside, was 0.175 mM and 0.16 OD min-1unit-1, respectively.

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

Pneumolysin-Mediated Expression of β-Defensin 2 Is Coordinated by p38 MAP Kinase-MKP1 in Human Airway Cells: Yong-Jae Kim , Hee-Sung Shin , Jung-Hoon Lee , Yong Woo Jung , Hyong-Bai Kim , Un-Hwan Ha; J. Microbiol. 2013;51(2):194-199. Published online April 27, 2013; DOI: https://doi.org/10.1007/s12275-013-2579-x

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Abstract PDF

Antimicrobial peptides act as important innate immune defense mediators against invading microbes such as Streptococcus pneumoniae. Among a number of antimicrobial peptides, β-defensin 2 (BD2) has strong antimicrobial activity against S. pneumoniae. However, little is known about the molecular signaling mechanisms leading to the BD2 expression. Here, we report that BD2 is strongly induced by S. pneumoniae in human airway cells including human middle-ear cells. Among diverse pneumococcal virulence factors, pneumolysin is required for inducing BD2 whose expression is under the control of p38 mitogen-activated protein kinase (MAPK). Pneumolysin also selectively regulates the expression of MAPK phosphatase 1 (MKP1), which inhibits the p38 signaling pathway, thereby leading to upregulation of BD2 to mount an effective defense against S. pneumoniae infection. These results provide novel insights into the molecular mechanisms underlying the coordinative regulation of BD2 expression via p38-MKP1 in the pathogenesis of airway infectious diseases.

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The Yin and Yang of Pneumolysin During Pneumococcal Infection
Joana M. Pereira, Shuying Xu, John M. Leong, Sandra Sousa
Frontiers in Immunology.2022;[Epub] CrossRef
Streptococcus pneumoniae and Its Virulence Factors H2O2 and Pneumolysin Are Potent Mediators of the Acute Chest Syndrome in Sickle Cell Disease
Joyce Gonzales, Trinad Chakraborty, Maritza Romero, Mobarak Abu Mraheil, Abdullah Kutlar, Betty Pace, Rudolf Lucas
Toxins.2021; 13(2): 157. CrossRef
Toll-like receptor 2-mediated induction of avian β -defensin 9 by Lactobacillus rhamnosus and its cellular components in chicken intestinal epithelial cells
Yongjie Jia, Wei Si, Zhimin Hong, Mingren Qu, Nianhua Zhu, Siguo Liu, Guanhong Li
Food and Agricultural Immunology.2019; 30(1): 398. CrossRef
Effector triggered immunity
Rajmohan Rajamuthiah, Eleftherios Mylonakis
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Paeoniflorin Upregulates β-Defensin-2 Expression in Human Bronchial Epithelial Cell Through the p38 MAPK, ERK, and NF-κB Signaling Pathways
Yuying Gan, Xuefan Cui, Ting Ma, Yanliang Liu, Amin Li, Mao Huang
Inflammation.2014; 37(5): 1468. CrossRef

The Intracellular Mechanism of Action on Escherichia coli of BF2-A/C, Two Analogues of the Antimicrobial Peptide Buforin 2: Gang Hao , Yong-Hui Shi , Ya-Li Tang , Guo-Wei Le; J. Microbiol. 2013;51(2):200-206. Published online April 27, 2013; DOI: https://doi.org/10.1007/s12275-013-2441-1

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Abstract PDF: In the present study, the antimicrobial peptides BF2-A and BF2-C, two analogues of Buforin 2, were chemically synthesized and the activities were assayed. To elucidate the bactericidal mechanism of BF2-A/C and their different antimicrobial activities, the influence of peptides to E. coli cell membrane and targets of intracellular action were researched. Obviously, BF2-A and BF2-C did not induce the influx of PI into the E. coli cells, indicating nonmemebrane permeabilizing killing action. The FITC-labeled BF2-A/C could penetrate the E. coli cell membrane and BF2-C penetrated the cells more efficiently. Furthermore, BF2-A/C could bind to DNA and RNA respectively, and the affinity of BF2-C to DNA was powerful at least over 4 times than that of BF2-A. The present results implied that BF2-A and BF2-C inhibited the cellular functions by binding to DNA and RNA of cells after penetrating the cell membranes, resulting in the rapid cell death. The structure-activity relationship analysis of BF2-A/C revealed that the cell-penetrating efficiency and the affinity ability to DNA were critical factors for determining the antimicrobial potency of both peptides. The more efficient cellpenetrating and stronger affinity to DNA caused that BF2-C displayed more excellent antimicrobial activity and rapid killing kinetics than BF2-A.

An Aqueous Extract of Yunnan Baiyao Inhibits the Quorum-Sensing-Related Virulence of Pseudomonas aeruginosa: Zu-Guo Zhao , Shuang-Shuang Yan , Yun-Mei Yu , Na Mi , La-Xi Zhang , Jun Liu , Xiao-Ling Li , Fang Liu , Jun-Fa Xu , Wei-Qing Yang , Guo-Ming Li; J. Microbiol. 2013;51(2):207-212. Published online April 27, 2013; DOI: https://doi.org/10.1007/s12275-013-2595-x

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Abstract PDF: Yunnan Baiyao is a famous Chinese medicine that has long been directly applied to wounds to reduce bleeding, pain, and swelling without causing infection. However, little is known about its ability to prevent infection. The present study aimed to assess in vitro the anti-virulence activity of an aqueous extract of Yunnan Baiyao (YBX) using Pseudomonas aeruginosa as a pathogenic model. We found that a sub-MIC (2.5 mg/ml) of YBX can efficiently interfere with the quorum-sensing (QS) signaling circuit. Real-time polymerase chain reaction analysis showed that a sub-MIC of YBX downregulated the transcriptions of lasR, lasI, rhlR, and rhlI, which resulted in global attenuation of QS-regulated virulence activities, such as biofilm formation, and secretion of LasA protease, LasB elastase and pyocyanin. Further, YBX reduced the motility of P. aeruginosa related to QS, and impaired the formation of biofilms. These results suggest that YBX may possess global inhibitory activity against the virulence of P. aeruginosa and that YBX may also exhibit antimicrobial activity in vivo. The present study suggests that Yunnan Baiyao represents a potential source for isolating novel, safe, and efficacious antimicrobial agents.

Low-Scale Expression and Purification of an Active Putative Iduronate 2-Sulfate Sulfatase-Like Enzyme from Escherichia coli K12: Edwin David Morales-Álvarez , Claudia Marcela Rivera-Hoyos , Angélica María Baena-Moncada , Patricia Landázuri , Raúl A. Poutou-Piñales , Homero Sáenz-Suárez , Luis A. Barrera , Olga Y. Echeverri-Peña; J. Microbiol. 2013;51(2):213-221. Published online April 27, 2013; DOI: https://doi.org/10.1007/s12275-013-2416-2

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Abstract PDF

The sulfatase family involves a group of enzymes with a large degree of similarity. Until now, sixteen human sulfatases have been identified, most of them found in lysosomes. Human deficiency of sulfatases generates various genetic disorders characterized by abnormal accumulation of sulfated intermediate compounds. Mucopolysaccharidosis type II is characterized by the deficiency of iduronate 2-sulfate sulfatase (IDS), causing the lysosomal accumulation of heparan and dermatan sulfates. Currently, there are several cases of genetic diseases treated with enzyme replacement therapy, which have generated a great interest in the development of systems for recombinant protein expression. In this work we expressed the human recombinant IDS-Like enzyme (hrIDS-Like) in Escherichia coli DH5α. The enzyme concentration revealed by ELISA varied from 78.13 to 94.35 ng/ml and the specific activity varied from 34.20 to 25.97 nmol/h/mg. Western blotting done after affinity chromatography purification showed a single band of approximately 40 kDa, which was recognized by an IgY polyclonal antibody that was developed against the specific peptide of the native protein. Our 100 ml-shake-flask assays allowed us to improve the enzyme activity seven fold, compared to the E. coli JM109/pUC13-hrIDS-Like system. Additionally, the results obtained in the present study were equal to those obtained with the Pichia pastoris GS1115/ pPIC-9-hrIDS-Like system (3 L bioreactor scale). The system used in this work (E. coli DH5α/pGEX-3X-hrIDS-Like) emerges as a strategy for improving protein expression and purification, aimed at recombinant protein chemical characterization, future laboratory assays for enzyme replacement therapy, and as new evidence of active putative sulfatase production in E. coli.

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A review on computational models for predicting protein solubility
Teerapat Pimtawong, Jun Ren, Jingyu Lee, Hyang-Mi Lee, Dokyun Na
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Jun Ren, Suhee Hwang, Junhao Shen, Hyeongwoo Kim, Hyunjoo Kim, Jieun Kim, Soyoung Ahn, Min-gyun Kim, Seung Ho Lee, Dokyun Na
Journal of Microbiology.2022; 60(9): 960. CrossRef
Characterization of mouse di-N-acetylchitobiase that can degrade chitin-oligosaccharides
Misa Ohno, Masao Miyazaki, Masahiro Kimura, Yusaku Minowa, Masayoshi Sakaguchi, Fumitaka Oyama, Tetsuro Yamashita
Bioscience, Biotechnology, and Biochemistry.2020; 84(12): 2499. CrossRef
Lysosomal sulfatases: a growing family
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Therapeutic Options for Mucopolysaccharidoses: Current and Emerging Treatments
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Production and characterization of a human lysosomal recombinant iduronate‐2‐sulfatase produced inPichia pastoris
Natalia Pimentel, Alexander Rodríguez‐Lopez, Sergio Díaz, Juan C. Losada, Dennis J. Díaz‐Rincón, Carolina Cardona, Ángela J. Espejo‐Mojica, Aura M. Ramírez, Fredy Ruiz, Patricia Landázuri, Raúl A. Poutou‐Piñales, Henry A. Cordoba‐Ruiz, Carlos J. Alméciga‐
Biotechnology and Applied Biochemistry.2018; 65(5): 655. CrossRef
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Orphanet Journal of Rare Diseases.2018;[Epub] CrossRef
Anaerobic sulfatase maturase AslB from Escherichia coli activates human recombinant iduronate-2-sulfate sulfatase (IDS) and N -acetylgalactosamine-6-sulfate sulfatase (GALNS)
Carlos Javier Alméciga-Díaz, Andrés Dario Tolosa-Díaz, Luisa Natalia Pimentel, Yahir Andres Bonilla, Alexander Rodríguez-López, Angela J. Espejo-Mojica, Juan D. Patiño, Oscar F. Sánchez, Janneth Gonzalez-Santos
Gene.2017; 634: 53. CrossRef
Prediction of glycation sites: new insights from protein structural analysis
Homero SÁENZ-SUÁREZ, Raúl A. POUTOU-PIÑALES, Janneth GONZÁLEZ-SANTOS, George E. BARRETO, Lynda P. RIETO-NAVARRERA, José A. SÁENZ-MORENO, Patricia LANDÁZURI, Luis A. BARRERA-AVELLANEDA
TURKISH JOURNAL OF BIOLOGY.2016; 40: 12. CrossRef
Bioinformatic Analysis of the Human Recombinant Iduronate 2-Sulfate Sulfatase
Edwin D. Morales-Álvarez, Claudia M. Rivera-Hoyos, Patricia Landázuri, Raúl A. Poutou-Piñales, Aura M. Pedroza-Rodríguez
The Open Microbiology Journal.2016; 10(1): 124. CrossRef
Human recombinant lysosomal enzymes produced in microorganisms
Ángela J. Espejo-Mojica, Carlos J. Alméciga-Díaz, Alexander Rodríguez, Ángela Mosquera, Dennis Díaz, Laura Beltrán, Sergio Díaz, Natalia Pimentel, Jefferson Moreno, Jhonnathan Sánchez, Oscar F. Sánchez, Henry Córdoba, Raúl A. Poutou-Piñales, Luis A. Barre
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Expression, Purification, and Biochemical Properties of Arginase from Bacillus subtilis 168: Jin-Ju Yu , Ki-Bum Park , Su-Gon Kim , Suk-Heung Oh; J. Microbiol. 2013;51(2):222-228. Published online April 27, 2013; DOI: https://doi.org/10.1007/s12275-013-2669-9

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Abstract PDF: The arginine-degrading and ornithine-producing enzymes arginase has been used to treat arginine-dependent cancers. This study was carried out to obtain the microbial arginase from Bacillus subtilis, one of major microorganisms found in fermented foods such as Cheonggukjang. The gene encoding arginase was isolated from B. subtilis 168 and cloned into E. coli expression plasmid pET32a. The enzyme activity was detected in the supernatant of the transformed and IPTG induced cell-extract. Arginase was purified for homogeneity from the supernatant by affinity chromatography. The specific activity of the purified arginase was 150 U/mg protein. SDS-PAGE analysis revealed the molecular size to be 49 kDa (Trix·Tag, 6×His·Tag added size). The optimum pH and temperature of the purified enzyme with arginine as the substrate were pH 8.4 and 45°C, respectively. The Km and Vmax values of arginine for the enzyme were 4.6 mM and 133.0 mM/min/mg protein respectively. These findings can contribute in the development of functional fermented foods such as Cheonggukjang with an enhanced level of ornithine and pharmaceutical products by providing the key enzyme in arginine-degradation and ornithine-production.

A Real-Time qPCR Assay to Quantify Ophiocordyceps sinensis Biomass in Thitarodes Larvae: Wei Lei , Shaosong Li , Qingyun Peng , Guren Zhang , Xin Liu; J. Microbiol. 2013;51(2):229-233. Published online April 27, 2013; DOI: https://doi.org/10.1007/s12275-013-2241-7

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Abstract PDF

Ophiocordyceps sinensis, an entomogenous fungus parasitic in the larvae of moths (Lepidoptera), is one of the most valuable medicinal fungi, and it only distributed naturally on the Tibetan Plateau. The parasitical amount of O. sinensis in various tissues of the host Thitarodes larvae has an important role in study the occurrence and developmental mechanisms of O. sinensis, but there no an effective method to detect the fungal anamorph. A real-time quantitative PCR (qPCR) system, including a pair of species-specific ITS primers and its related program, was developed for O. sinensis assay with high reliability and efficiency. A calibration curve was established and exhibited a very good linear correlation between the fungal biomass and the CT values (R2=0.999419) by the qPCR system. Based on this method, O. sinensis was detected rapidly in four tissues of its host caterpillars, and the results were shown as following: the maximum content of O. sinensis parasitized in the fat-body, and next came bodywall; both of them were much larger than that observed in the haemolymph and intestinal-wall. Taken together, these
results
show that qPCR assays may become useful tools for study on developmental mechanism of O. sinensis.

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Ophiocordyceps sinensis-induced changes in Thitarodes xiaojinensis: from intestinal barrier destruction, microbiome dysbiosis to immune responses at the molecular level
Xiu-wen Bao, Qing-he Wang, Ting Li, Yong Li, Zhi-ying Bian, Si-jing Liu, Li-ying He, Shu-qi Niu, Jin-lin Guo
BMC Biology.2025;[Epub] CrossRef
Histopathological observations and comparative transcriptome analysis of Ophiocordyceps sinensis infection of Hepialus xiaojinensis in the early stage
Xiuwen Bao, Haoran Song, Liying He, Yong Li, Shuqi Niu, Jinlin Guo
Developmental & Comparative Immunology.2024; 150: 105067. CrossRef
Use of electrical penetration graphs (EPG) and quantitative PCR to evaluate the relationship between feeding behaviour and Pandora neoaphidis infection levels in green peach aphid, Myzus persicae
Chun Chen, Sudan Ye, Huajun Hu, Chengmei Xue, Xiaoping Yu
Journal of Insect Physiology.2018; 104: 9. CrossRef
Establishment of a PCR Assay for the Detection and Discrimination of Authentic Cordyceps and Adulterant Species in Food and Herbal Medicines
Byeong Cheol Moon, Wook Jin Kim, Inkyu Park, Gi-Ho Sung, Pureum Noh
Molecules.2018; 23(8): 1932. CrossRef
Antimicrobial peptide repertoire of Thitarodes armoricanus, a host species of Ophiocordyceps sinensis, predicted based on de novo transcriptome sequencing and analysis
Min Wang, Xianda Hu
Infection, Genetics and Evolution.2017; 54: 238. CrossRef
Morphological Observations and Fatty Acid Composition of Indoor-Cultivated Cordyceps sinensis at a High-Altitude Laboratory on Sejila Mountain, Tibet
Lian-Xian Guo, Xiao-Ming Xu, Fu-Rui Liang, Jian-Ping Yuan, Juan Peng, Chou-Fei Wu, Jiang-Hai Wang, Rita Grosch
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Wei Lei, Guren Zhang, Qingyun Peng, Xin Liu
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Shiwei Zhang, Xintian Lai, Bifang Li, Cong Wu, Shifeng Wang, Xuejian Chen, Jingmin Huang, Guowu Yang
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Secretion of Truncated Recombinant Rabies Virus Glycoprotein with Preserved Antigenic Properties Using a Co-Expression System in Hansenula polymorpha: Weidong Qian , Frank Aguilar , Ting Wang , Bingsheng Qiu; J. Microbiol. 2013;51(2):234-240. Published online April 27, 2013; DOI: https://doi.org/10.1007/s12275-013-2337-0

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Abstract PDF

Rabies virus infection remains a serious public health threat in the developing world, where cost-concerns make widescale public health interventions impractical. The development of novel and inexpensive ELISA diagnostic antigens is critical in early detection and prevention of complications. The transmembrane glycoprotein (G) of rabies virus (RV) contains an external domain capable of inducing the synthesis of anti-rabies, virus-neutralizing antibodies, in infected or immunized hosts. In our study, the external G domain was synthesized and fused in-frame with a polyhistidine-tag coding sequence present in the expression plasmid. Soluble truncated recombinant G was secreted in Hansenula polymorpha (H. polymorpha) using H. polymorpha-derived calnexin (HpCNE1) overproduction and found to be correctly N-glycosylated. The truncated recombinant G was purified from cell culture supernatant by Ni-agarose affinity chromatography and when compared with the full-length glycoprotein, found to be similarly immunogenic in vaccinated rabbits. These results subsequently led us to explore the potential of truncated recombinant G as a diagnostic antigen in ELISA. Our results show that the truncated recombinant G can detect antibodies directed to both whole virion and native glycoprotein. More sophisticated applications of truncated recombinant G would profit from the correctly N-glycosylated and soluble monomer.

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Ogataea polymorpha as a next-generation chassis for industrial biotechnology
Linfeng Xie, Wei Yu, Jiaoqi Gao, Haoyu Wang, Yongjin J. Zhou
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Sara Brachelente, Alvaro Galli, Tiziana Cervelli
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Advances in Using Hansenula polymorpha as Chassis for Recombinant Protein Production
João Heitor Colombelli Manfrão-Netto, Antônio Milton Vieira Gomes, Nádia Skorupa Parachin
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Highly efficient production of rabies virus glycoprotein G ectodomain in Sf9 insect cells
Alexandra Marisa Targovnik, Alejandro Ferrari, Gregorio Juan Mc Callum, Mariana Bernadett Arregui, Ignacio Smith, Lautaro Fidel Bracco, Victoria Alfonso, María Gabriela López, María Martínez-Solís, Salvador Herrero, María Victoria Miranda
3 Biotech.2019;[Epub] CrossRef
Comparison of the protective efficacy between single and combination of recombinant adenoviruses expressing complete and truncated glycoprotein, and nucleoprotein of the pathogenic street rabies virus in mice
Ha-Hyun Kim, Dong-Kun Yang, Jin-Ju Nah, Jae-Young Song, In-Soo Cho
Virology Journal.2017;[Epub] CrossRef
Development of a Time and Cost Benefit Antibody Binding Test-Based Method for Determination of Rabies Vaccine Potency
Vahid Asgary, Nazanin Mojtabavi, Alireza Janani, Tahereh Mousavi, Jamshid Hadjati, Mohammad Sadeq Khosravy, Reza Ahangari Cohan
Viral Immunology.2017; 30(3): 204. CrossRef
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Renato Mancini Astray, Soraia Attie Calil Jorge, Carlos Augusto Pereira
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Allelic MHC Class I Chain Related B (MICB) Molecules Affect the Binding to the Human Cytomegalovirus (HCMV) Unique Long 16 (UL16) Protein: Implications for Immune Surveillance: Kanya Klumkrathok , Amonrat Jumnainsong , Chanvit Leelayuwat; J. Microbiol. 2013;51(2):241-246. Published online April 27, 2013; DOI: https://doi.org/10.1007/s12275-013-2514-1

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Abstract PDF: Unique long 16 (UL16) is a viral glycoprotein produced in a host cell infected with human cytomegalovirus (HCMV). It down regulates surface expression of MICB, one of the NKG2D ligands, by forming stable intracellular complexes and retained in the endoplasmic reticulum. Down expression of MICB renders cells less susceptible to NK cell lysis via the NKG2D receptor. Diverse UL16 sequences were identified from different strains of HCMV. MICB is known to be polymorphic. It is not known whether these polymorphisms affect the interactions between these molecules leading to alteration of the immune surveillance of HCMV. The soluble Fc fusion variant UL16 proteins from four laboratory and clinical isolates (AD169, Toledo, PH, and TR) were produced. Four allelic MICB alleles (008, 003, 004, and 00502) were cloned and stable cell lines expressing these MICB alleles were produced. The binding activities of variant UL16 to allelic MICB proteins were determined by flow cytometry. The variants of UL16 proteins did not affect the binding activities to allelic MICB proteins. However, diverse MICB alleles differentially bound UL16. We found that MICB*008 which contains methionine and asparagine at the amino acid positions 98 and 113, respectively, in the alpha 2 domain showed decreased binding activities to UL16 when compared to MICB*003, 004, and MICB*00502 containing isoleucine and aspartic acid, respectively. This finding may imply that MICB*008 is a protective allele and involved in the immune surveillance of HCMV infected patients.

Phenotypic Characteristics of Natural Killer Cells in Acute Hepatitis: Hyosun Cho; J. Microbiol. 2013;51(2):247-251. Published online April 27, 2013; DOI: https://doi.org/10.1007/s12275-013-2522-1

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Abstract PDF

Natural killer (NK) cells are the principal effector cell population in innate immune defense against many types of infections. These cells are enriched in the liver, where they comprise approximately 40% to 60% of the intrahepatic lymphocyte pool compared to the peripheral blood compartment. In chronic HBV and HCV infection, NK cells were reported to be partially dysfunctional due to impaired IFN-γ secretion. Few studies have examined phenotypic features of NK cells in acute hepatitis. We identified NK (CD56+CD3-) cell populations in patients with acute hepatitis by examining the expressions of phenotypic NK cell markers (CD16, NKG2A, and NKG2D). Peripheral blood mononuclear cells were isolated from patients with acute hepatitis A (7) and patients with non-viral acute toxic hepatitis (6) during the symptomatic and convalescent phases. Expressions of NK (CD56+CD3-) cell markers, CD16, NKG2A, and NKG2D, were measured by flow cytometry. Symptomatic acute hepatitis including non-viral hepatitis and HAV infection showed significant increases of NKG2A expression compared to healthy controls. Interestingly, there was a direct correlation between the proportion of NK cell populations and liver function parameters (AST, ALT) in HAV infection. The strong correlation was also observed between the expression of NKG2A+NK cells and ALT, which suggests that most of NK cells in severe phase of disease express high level of NKG2A on their surface. In addition, decreased number of NK cells (CD56+CD3-) in symptomatic phase began to increase in the convalescent phase of acute hepatitis A. However, the expression of NKG2A tended to be reduced, which indicates that NKG2A, the inhibitory receptor on NK cells, can be a severity parameter in acute hepatitis.

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Ichiro Misumi, You Li, Takayoshi Shirasaki, Lixin Yang, Maryna Kapustina, Stanley M. Lemon, Jason K. Whitmire, Guangxiang George Luo
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Natural Killer p46 Controls Hepatitis B Virus Replication and Modulates Liver Inflammation
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Development and Evaluation of Multiplex Real-time RT-PCR Assays for Seasonal, Pandemic A/H1pdm09 and Avian A/H5 Influenza Viruses Detection: Jang-Hoon Choi , Mi-Seon Kim , Joo-Yeon Lee , Nam-Joo Lee , Donghyok Kwon , Min Gu Kang , Chun Kang; J. Microbiol. 2013;51(2):252-257. Published online April 27, 2013; DOI: https://doi.org/10.1007/s12275-013-2452-y

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Abstract PDF: Since the pandemic influenza A (H1N1) 2009 ((H1N1)pdm09) virus spread all over the world, the (H1N1)pdm09 virus has been circulating with seasonal influenza viruses. We developed rapid and sensitive one-step multiplex real-time RTPCR assays (rRT-PCR) for simultaneous detection of influenza viruses currently circulating in humans, and the avian A/H5 virus. The detection limit of each assay was 4.8 to 1 copies per reaction and no cross-reactivity with other major respiratory pathogens was found. Analytical positive predictive value (PPV), negative predictive value (NPV) sensitivity and specificity were 100%, 94.1%, 93.7% and 100%, respectively. Clinical evaluation revealed that 1,976 (16.5%) of 11,963 throat swabs from patients with respiratory symptoms were confirmed as 1,651 (83.6%) A/H1pdm09, 308 (15.6%) A/H3 and 17 (0.8%) B virus during the 2010-2011 influenza season. Collectively, the multiplex rRT-PCR assays described here provide a practical tool for reliable implementation of influenza surveillance and diagnosis.

NOTE] Rhodanobacter umsongensis sp. nov., Isolated from a Korean Ginseng Field: Yi-Seul Kim , Soo-Jin Kim , Rangasamy Anandham , Hang-Yeon Weon , Soon-Wo Kwon; J. Microbiol. 2013;51(2):258-261. Published online April 27, 2013; DOI: https://doi.org/10.1007/s12275-013-2516-z

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Abstract PDF

A bacterial isolate designated GR24-2T was isolated from Korean soil used for cultivating ginseng (Panax ginseng C. A. Meyer). The strain was aerobic, Gram-negative, motile, and rod-shaped. It grew optimally at 28–30°C, pH 7.0, and in a range of 0–1% NaCl. Phylogenetically, the strain clustered with members of the genus Rhodanobacter. The strain exhibited the highest sequence similarities (>98%) with R. panaciterrae LnR5-47T (98.4%), R. soli DCY45T (98.2%), and R. ginsengisoli GR17-7T (98.0%). However, it also showed high sequence similarities (>97%) with some other Rhodanobacter and Dyella species. The strain contained Q-8 as the predominant respiratory quinone. The major fatty acids (greater than 10% of the total fatty acids) were iso-C17:1 ω9c (24.5%), iso-C16:0 (22.8%), anteiso-C15:0 (10.5%), and iso-C15:0 (10.1%). Its major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, and an unknown aminophospholipid. The DNA G+C content of strain GR24-2T was 65.6 mol%. The strain showed less than 70% DNA relatedness values between the closely related Rhodanobacter and Dyella species. The phylogeny, phenotype, DNA–DNA hybridization, and chemotaxonomic data generated in this study reveal that the isolate is a novel species of the genus Rhodanobacter. The name proposed for this strain is Rhodanobacter umsongensis sp. nov. (type strain GR24-2T =KACC 12917T =DSM 21300T).

Citations

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List of new names and new combinations previously effectively, but not validly, published

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NOTE] Paraherbaspirillum soli gen. nov., sp. nov. Isolated from Soil: Rangasamy Anandham , Soo-Jin Kim , Ji Young Moon , Hang-Yeon Weon , Soon-Wo Kwon; J. Microbiol. 2013;51(2):262-267. Published online April 27, 2013; DOI: https://doi.org/10.1007/s12275-013-2563-5

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Abstract PDF: A bacterial strain, designated JS5-2T, was isolated from soil collected from Jeju Island, Republic of Korea. The cells of the strain were Gram-negative, nonspore forming, catalaseand oxidase-positive, aerobic, nonmotile and rod-shaped. Strain JS5-2T exhibited 96.2–97.2, 95.1–96.3, and 95.4–95.8% 16S rRNA gene sequence similarities to the genera Herbaspirillum, Oxalicibacterium, and Herminiimonas, respectively. The highest sequence similarities were with Herbaspirillum autotrophicum IAM 14942T (97.2%) and Herbaspirillum frisingense GSF30T (97.1%). The major fatty acids of strain JS5-2T were C16:0 (35.0%), C17:0 cyclo (19.9%), C18:1 ω7c (11.4%), and summed feature 3 (C16:1 ω7c/C15:0 iso 2-OH) (15.2%), and the major polar lipids of strain JS5-2T were diphosphatidylglycerol and an unknown aminophospholipid. The strain contained Q-8 as the predominant ubiquinone. DNA-DNA relatedness values between strain JS5-2T and H. autotrophicum IAM 14942T, and H. frisingense GSF30T were 32 and 35%, respectively. The DNA G+C content of strain JS5-2T was 59.0 mol%. On the basis of phenotypic, genotypic, and physiological evidence, strain JS5-2T represents a novel species of a new genus, for which the name Paraherbaspirillum soli gen. nov., sp. nov. is proposed. The type strain JS5-2T (=KACC 12633T =NBRC 106496T) is proposed.

NOTE] Rummeliibacillus suwonensis sp. nov., Isolated from Soil Collected in a Mountain Area of South Korea: Jihee Her , Jaisoo Kim; J. Microbiol. 2013;51(2):268-272. Published online April 27, 2013; DOI: https://doi.org/10.1007/s12275-013-3126-5

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Abstract PDF: A Gram-positive, facultatively aerobic, rod-shaped, nonmotile, terminal spore-forming bacterium, designated strain G20T, was isolated from soil collected in a mountain region of Suwon, South Korea. On the basis of 16S rRNA gene sequence similarity, this strain was shown to be related to Rummeliibacillus pycnus NBRC 101231T (97.4%) and Rummeliibacillus stabekisii KSC-SF6gT (95.7%). DNA-DNA hybridization studies showed 42% and 50% similarity of strain G20T with R. pycnus NBRC 101231Tand R. stabekisii KSCSF6gT, respectively. The DNA G+C content of G20T was 37.8 mol%, the major cellular fatty acids were iso-C15:0 and anteiso-C15:0, and the predominant menaquinones were MK-7 and MK-8. On the basis of phylogenetic, chemotaxonomic, and phenotypic characteristics, we propose this strain to be a novel species and the third member of genus Rummeliibacillus. We suggest the name Rummeliibacillus suwonensis sp. nov. The type strain is G20T (KACC 17316T =KEMB 9005-003T =JCM 19065T).

Retraction of Publication

Retraction] Identification and Characterization of a Novel Antibacterial Peptide, Avian β-Defensin 2 from Ducks: Deying Ma , Ruiqin Wang , Wenyan Liao , Zongxi Han , Shengwang Liu; J. Microbiol. 2013;51(2):273-273.; DOI: https://doi.org/10.1007/s12275-013-0722-3

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Abstract PDF: The article by Ma et al. that appears in the Journal of Microbiology (2009, 47: 610-618) is a redundant publication of the paper published in Scientia Agricultura Sinica (2009, 42: 3685-3692). Therefore, we, the JM committee, decided to retract the article from JM. We regret any inconvenience that the retraction may have caused to readers.

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