Journal of Microbiology

Volume 55(5); May 2017

Review

[Minireview] Primary lymphocyte infection models for KSHV and its putative tumorigenesis mechanisms in B cell lymphomas: Sangmin Kang , Jinjong Myoung; J. Microbiol. 2017;55(5):319-329. Published online April 29, 2017; DOI: https://doi.org/10.1007/s12275-017-7075-2

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22 Citations

Abstract: Kaposi’s sarcoma-associated herpesvirus (KSHV) is the latest addition to the human herpesvirus family. Unlike alpha- and beta-herpesvirus subfamily members, gamma-herpesviruses, including Epstein-Barr virus (EBV) and KSHV, cause vari-ous tumors in humans. KSHV primarily infects endothelial and B cells in vivo, and is associated with at least three malig-nancies: Kaposi’s sarcoma and two B cell lymphomas, res-pectively. Although KSHV readily infects endothelial cells in vitro and thus its pathogenic mechanisms have been exten-sively studied, B cells had been refractory to KSHV infection. As such, functions of KSHV genes have mostly been eluci-dated in endothelial cells in the context of viral infection but not in B cells. Whether KSHV oncogenes, defined in endo-thelial cells, play the same roles in the tumorigenesis of B cells remains an open question. Only recently, through a few ground-breaking studies, B cell infection models have been established. In this review, those models will be compared and contrasted and putative mechanisms of KSHV-induced B cell transformation will be discussed.

Journal Articles

Azohydromonas riparia sp. nov. and Azohydromonas ureilytica sp. nov. isolated from a riverside soil in South Korea: Tuan Manh Nguyen , Jaisoo Kim; J. Microbiol. 2017;55(5):330-336. Published online January 26, 2017; DOI: https://doi.org/10.1007/s12275-017-6519-z

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16 Citations

Abstract: White and pale yellow coloured bacteria were isolated from the riverside soil, Daejeon, South Korea, and were designated UCM-11T, UCM-F25, and UCM-80T. We found that all strains were able to reduce nitrate, and the cells were aerobic and motile. The DNA G+C contents of UCM-11T, UCM-F25, and UCM-80T were between 68.9 to 71.2 mol% and the main ubiquinone was observed as Q-8. Based on16S rRNA gene sequences, strains UCM-11T and UCM-F25 were found to closely match with Azohydromonas australica IAM 12664T (98.48–98.55%), and the strain UCM-80T was the closest match with Azohydromonas lata IAM 12599T (98.34%). The presence of summed feature 3 (C16:1ω7c and/or C16:1ω6c), C16:0, summed feature 8 (C18:1ω7c and/or C18:1ω6c) as well as twokinds of hydroxyfatty acids consisting of C10:0 3-OH and C12:0 2-OH, and branched fatty acids containing C16:0 iso and C17:0 cyclo were detected in all the strains. Phosphatidy-lethanolamine was a major polar lipid. DNA–DNA related-ness confirmed UCM-11T, UCM-F25 and UCM-80T as novel members of the genus Azohydromonas. Based on the mor-phological, physiological, biochemical and genotypic char-acteristics, we suggest that strains UCM-11T, UCM-F25, and UCM-80T represent novel species within the genus Azohy-dromonas. The names Azohydromonas riparia sp. nov., and Azohydromonas ureilytica sp. nov. are proposed for the type strains UCM-11T (=KACC 18570T =NBRC 111646T) and UCM-80T (=KACC 18576T =NBRC 111658T), respectively.

A diversity study of Saccharomycopsis fibuligera in rice wine starter nuruk, reveals the evolutionary process associated with its interspecies hybrid: Mohamed El-Agamy Farh , Yunjoo Cho , Jae Yun Lim , Jeong-Ah Seo; J. Microbiol. 2017;55(5):337-343. Published online April 29, 2017; DOI: https://doi.org/10.1007/s12275-017-7115-y

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12 Citations

Abstract: The amylolytic yeast Saccharomycopsis fibuligera is the pre-dominant yeast in the starter product, nuruk, which is utilized for rice wine production in South Korea. Latest molecular studies explore a recently developed interspecific hybridiza-tion among stains of S. fibuligera with a unique genetic fea-ture. However, the origin of the natural hybridization occur-rence is still unclear. Thus, to respectively distinguish paren-tal and hybrid strains, specific primer sets were applied on 141 yeast strains isolated from different nuruk samples fer-mented in different provinces. Sixty-seven strains were de-fined accordingly as parental species with genome A while 8 strains were defined as hybrid strains. Unexpectedly, another parental species with genome B could not be found among the strain pools yet. Furthermore, it was observed that hybrid strains are phenotypically different from A genome strains; asci containing tetrad ascospores were observed in A genome strains more frequent than in hybrid strains. Nevertheless, hybrid strains were slightly more thermotolerant than A ge-nome strains. Interestingly, all hybrid strains were located only in Jeju province. Based on these sets of data, we specu-lated that the unique climate of Jeju province might play an evolutionary role in the interspecific hybridization between A genome strains, as well as the unculturable allopatric B ge-nome strains.

Wild birds and urban pigeons as reservoirs for diarrheagenic Escherichia coli with zoonotic potential: Clarissa A. Borges , Marita V. Cardozo , Livia G. Beraldo , Elisabete S. Oliveira , Renato P. Maluta , Kaline B. Barboza , Karin Werther , Fernando A. Ávila; J. Microbiol. 2017;55(5):344-348. Published online March 9, 2017; DOI: https://doi.org/10.1007/s12275-017-6523-3

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47 Citations

Abstract: In order to describe the role of wild birds and pigeons in the transmission of shiga toxigenic Escherichia coli (STEC) and enteropathogenic Escherichia coli (EPEC) to humans and other animals, samples were collected from cloacae and oropharynx of free-living wild birds and free-living pigeons. Two STEC (0.8%) and five EPEC strains (2.0%) were isolated from wild birds and four EPEC strains (2.0%) were recovered from pi-geons. Serogroups, sequence types (STs) and virulence genes, such as saa, iha, lpfAO113, ehxA, espA, nleB and nleE, detected in this study had already been implicated in human and ani-mal diseases. Multidrug resistance (MDR) was found in 25.0% of the pigeon strains and in 57.0% of the wild bird strains; the wild birds also yielded one isolate carrying extended-spec-trum β-lactamases (ESBLs) gene blaCTX-M-8. The high varia-bility shown by PFGE demonstrates that there are no preva-lent E. coli clones from these avian hosts. Wild birds and pi-geons could act as carriers of multidrug-resistant STEC and EPEC and therefore may constitute a considerable hazard to human and animal health by transmission of these strains to the environment.

Impact of tillage practices on soil bacterial diversity and composition under the tobacco-rice rotation in China: Yanping Lei , Yongliang Xiao , Lifeng Li , Chaoqiang Jiang , Chaolong Zu , Tian Li , Hui Cao; J. Microbiol. 2017;55(5):349-356. Published online March 1, 2017; DOI: https://doi.org/10.1007/s12275-017-6242-9

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27 Citations

Abstract: Tobacco-rice rotation is a common farming system in south China, and many tillage practices such as straw mulching, do-lomite dust, and quicklime application have been adopted to improve crop production. These agricultural management practices alter soil physical and chemical properties and affect microbial life environment and community composition. In this research, six tillage practices including no tobacco and rice straw mulching (CK), tobacco and rice straw mulching (TrSr), rice straw returning fire (TrSc), tobacco and rice straw mulching with dolomite dust (TSD), rice straw returning fire and quicklime (TSQ), and rice straw returning fire, quicklime and reduced fertilizer (TSQf) were conducted to detect changes in soil bacterial diversity and composition using Illumina se-quencing. The results showed that the total number of opera-tional taxonomic units (OTUs) from the six treatments was 2030, and the number of mutual OTUs among all samples was 550. The TrSc treatment had the highest diversity and richness, while TSQf had the lowest. Soil physio-chemical properties and microbial diversity can influence each other. Proteobacteria and Actinobacteria had the greatest propor-tion in all treatments. The abundance of Nitrospirae was the highest in the TrSc treatment. The TSQf treatment had the highest abundance of Firmicutes. The abundance of Nitrospira in the TrSc treatment was 2.29-fold over CK. Streptomyces affiliated with Firmicutes improved by 37.33% in TSQf com-pared to TSQ. TSQf treatment was considered to be the most important factor in determining the relative abundance at the genus level.

Comprehensive analysis of fungal diversity and enzyme activity in nuruk, a Korean fermenting starter, for acquiring useful fungi: Emily Carroll , Tran Ngoc Trinh , Hokyoung Son , Yin-Won Lee , Jeong-Ah Seo; J. Microbiol. 2017;55(5):357-365. Published online April 29, 2017; DOI: https://doi.org/10.1007/s12275-017-7114-z

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34 Citations

Abstract: Nuruk is a fermenting starter that is involved in the pro-duction of alcoholic beverages, and has been used in South Korea for a very long time. To analyze the fungal diversity, we collected a total of 59 nuruk samples from several com-panies and persons in 2013 to 2014, and obtained 364 iso-lates. All of the single isolated fungi were identified, both morphologically and molecularly, based on the sequences of ribosomal RNA gene [18S, ITS1-5.8S-ITS2, and 26S (D1/D2 region)]. In 46 nuruk samples out of 59 (78%), Saccharo-mycopsis fibuligera, a dimorphic yeast, was most frequently isolated. Among the filamentous fungi, Aspergillus and Lich-theimia were found in more than 50% of the samples with lower colony forming unit (CFU/g of sample) than those of yeasts. The yeasts S. fibuligera and Wickerhamomyces ano-malus were counted with maximum 1.3 – 1.8 × 108 CFU/g. Among Mucorales fungi, Lichtheimia and Mucor were iso-lated in much higher numbers than Rhizopus and Rhizo-mucor. Overall, the home-made nuruks tend to contain more diverse filamentous fungi than the commercial nuruks. To acquire industrially useful filamentous fungi and yeasts, we analyzed the enzyme activities of α-amylase, glucoamylase and acid protease associated with brewing properties for 131 strains. Aspergillus oryzae and S. fibuligera had high α- and glucoamylase activities and most isolates of Lichtheimia ramosa had high acid protease activity. For further applica-tions, 27 fungal strains were chosen based on isolation fre-quencies from nuruk, and the ability to produce useful en-zyme.

Minimal amino acids in the I/LWEQ domain required for anterior/posterior localization in Dictyostelium: Hyeseon Kim , Dong-Yeop Shin , Taeck Joong Jeon; J. Microbiol. 2017;55(5):366-372. Published online January 26, 2017; DOI: https://doi.org/10.1007/s12275-017-6550-0

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1 Citations

Abstract: Establishment of cell polarity is mediated by a series of signal-ing molecules that are asymmetrically activated or localized in the cell upon extracellular stimulation. To understand the mechanism that mediates anterior/posterior asymmetric localization of RapGAP3 during migration, we determined the minimally required amino acids in the I/LWEQ domain that cause posterior localization and found that the minimal region of the F-actin binding domain for posterior localiza-tion could, with some additional deletion at the C-terminal, localize to the anterior. Analysis of the localization and trans-location kinetics to the cell cortex of the truncated proteins suggests that the required regions for anterior/posterior lo-calization might have a preferential binding affinity to pre- existing F-actins at the rear and lateral sides of the cell or newly formed F-actins at the front of the cell, leading to dis-tinct differential sites of the cell.

Mutational analysis of the RNA helicase Dhh1 in Ste12 expression and yeast mating: Daehee Jung , Jihye Ahn , Boram Rhee , Jinmi Kim; J. Microbiol. 2017;55(5):373-378. Published online April 29, 2017; DOI: https://doi.org/10.1007/s12275-017-7020-4

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5 Citations

Abstract: Dhh1 and Dhh1 homologues (RCK/p54/DDX6) are mem-bers of the DEAD-box protein family of RNA helicases. These proteins display conserved sequence motifs for ATPase and RNA binding activities. Dhh1 is a component of the P-bodies (processing bodies) of mRNA granules and functions as an mRNA decapping activator in Saccharomyces cerevisiae. Dhh1 also contributes to gene-specific regulation during yeast mating. The dhh1 deletion mutation results in a significant decrease in the expression of Ste12, a mating-specific trans-cription factor, showing severe mating defects. Here, we in-troduced amino-acid substitution mutations in the ATPase and RNA binding domains of Dhh1 and also constructed a deletion of 79 amino acids at the Q/P-rich C-terminal region. The mutations in ATPase A and B motif (K96R, D195A) and C-terminus deletion showed reduced levels of mating effi-ciency as well as Ste12 protein expression. The Q/P-rich C- terminal region of Dhh1 was dispensable for growth at non- permissive temperature 37°C but appeared to play an im-portant role in regulating the Ste12 protein expression and mating processes. The P-body accumulation induced by treatment with α-mating factor required ATPase, RNA-bind-ing and the Q/P-rich C-terminal domains of Dhh1.

The hyperthermophilic α-amylase from Thermococcus sp. HJ21 does not require exogenous calcium for thermostability because of high-binding affinity to calcium: Huaixu Cheng , Zhidan Luo , Mingsheng Lu , Song Gao , Shujun Wang; J. Microbiol. 2017;55(5):379-387. Published online March 1, 2017; DOI: https://doi.org/10.1007/s12275-017-6416-5

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11 Citations

Abstract: The hyperthermophilic α-amylase from Thermococcus sp. HJ21 does not require exogenous calcium ions for thermo-stability, and is a promising alternative to commercially avail-able α-amylases to increase the efficiency of industrial pro-cesses like the liquefaction of starch. We analyzed the amino acid sequence of this α-amylase by sequence alignments and structural modeling, and found that this α-amylase closely resembles the α-amylase from Pyrococcus woesei. The gene of this α-amylase was cloned in Escherichia coli and the re-combinant α-amylase was overexpressed and purified with a combined renaturation-purification procedure. We con-firmed thermostability and exogenous calcium ion indepen-dency of the recombinant α-amylase and further investigated the mechanism of the independency using biochemical ap-proaches. The results suggested that the α-amylase has a high calcium ion binding affinity that traps a calcium ion that would not dissociate at high temperatures, providing a direct expla-nation as to why the addition of calcium ions is not required for thermostability. Understanding of the mechanism offers a strong base on which to further engineer properties of this α-amylase for better potential applications in industrial pro-cesses.

Crystal structure of Streptomyces coelicolor RraAS2, an unusual member of the RNase E inhibitor RraA protein family: Nohra Park , Jihune Heo , Saemee Song , Inseong Jo , Kangseok Lee , Nam-Chul Ha; J. Microbiol. 2017;55(5):388-395. Published online April 29, 2017; DOI: https://doi.org/10.1007/s12275-017-7053-8

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5 Citations

Abstract: Bacterial ribonuclease E (RNase E) plays a crucial role in the processing and decay of RNAs. A small protein named RraA negatively regulates the activity of RNase E via protein-protein interaction in various bacteria. Recently, RraAS1 and RraAS2, which are functional homologs of RraA from Escherichia coli, were identified in the Gram-positive species Streptomyces coelicolor. RraAS1 and RraAS2 inhibit RNase ES ribonuclease activity in S. coelicolor. RraAS1 and RraAS2 have a C-termi-nal extension region unlike typical bacterial RraA proteins. In this study, we present the crystal structure of RraAS2, ex-hibiting a hexamer arranged in a dimer of trimers, consistent with size exclusion chromatographic results. Importantly, the C-terminal extension region formed a long α-helix at the junction of the neighboring subunit, which is similar to the trimeric RraA orthologs from Saccharomyces cerevisiae. Trun-cation of the C-terminal extension region resulted in loss of RNase ES inhibition, demonstrating its crucial role. Our find-ings present the first bacterial RraA that has a hexameric assembly with a C-terminal extension α-helical region, which plays an essential role in the regulation of RNase ES activity in S. coelicolor.

N-acetylcysteine prevents the development of gastritis induced by Helicobacter pylori infection: Sungil Jang , Eun-Jung Bak , Jeong-Heon Cha; J. Microbiol. 2017;55(5):396-402. Published online April 29, 2017; DOI: https://doi.org/10.1007/s12275-017-7089-9

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Abstract: Helicobacter pylori (H. pylori) is a human gastric pathogen, causing various gastric diseases ranging from gastritis to gas-tric adenocarcinoma. It has been reported that combining N-acetylcysteine (NAC) with conventional antibiotic therapy increases the success rate of H. pylori eradication. We evalu-ated the effect of NAC itself on the growth and coloniza-tion of H. pylori, and development of gastritis, using in vitro liquid culture system and in vivo animal models. H. pylori growth was evaluated in broth culture containing NAC. The H. pylori load and histopathological scores of stomachs were measured in Mongolian gerbils infected with H. pylori strain 7.13, and fed with NAC-containing diet. In liquid culture, NAC inhibited H. pylori growth in a concentration-depen-dent manner. In the animal model, 3-day administration of NAC after 1 week from infection reduced the H. pylori load; 6-week administration of NAC after 1 week from infection prevented the development of gastritis and reduced H. pylori colonization. However, no reduction in the bacterial load or degree of gastritis was observed with a 6-week administ-ration of NAC following 6-week infection period. Our results indicate that NAC may exert a beneficial effect on reduction of bacterial colonization, and prevents the development of severe inflammation, in people with initial asymptomatic or mild H. pylori infection.

The antibacterial activity of E. coli bacteriophage lysin lysep3 is enhanced by fusing the Bacillus amyloliquefaciens bacteriophage endolysin binding domain D8 to the C-terminal region: Shuang Wang , Jingmin Gu , Meng Lv , Zhimin Guo , Guangmou Yan , Ling Yu , Chongtao Du , Xin Feng , Wenyu Han , Changjiang Sun , Liancheng Lei; J. Microbiol. 2017;55(5):403-408. Published online January 26, 2017; DOI: https://doi.org/10.1007/s12275-017-6431-6

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28 Citations

Abstract: Bacteriophage endolysin is one of the most promising anti-biotic substitutes, but in Gram-negative bacteria, the outer membrane prevents the lysin from hydrolyzing peptidogly-cans and blocks the development of lysin applications. The prime strategy for new antibiotic substitutes is allowing lysin to access the peptidoglycan from outside of the bacteria by reformation of the lysin. In this study, the novel Escherichia coli (E. coli) phage lyase lysep3, which lacks outside-in cata-lytic ability, was fused with the N-terminal region of the Bacillus amyloliquefaciens lysin including its cell wall bind-ing domain D8 through the best manner of protein fusion based on the predicted tertiary structure of lysep3-D8 to ob-tain an engineered lysin that can lyse bacteria from the out-side. Our results showed that lysep3-D8 could lyse both Gram- negative and Gram-positive bacteria, whereas lysep3 and D8 have no impact on bacterial growth. The MIC of lysep3-D8 on E. coli CVCC1418 is 60 μg/ml; lysep3-D8 can inhibit the growth of bacteria up to 12 h at this concentration. The bac-tericidal spectrum of lysep3-D8 is broad, as it can lyse of all of 14 E. coli strains, 3 P. aeruginosa strains, 1 Acinetobacter baumannii strain, and 1 Streptococcus strain. Lysep3-D8 has sufficient bactericidal effects on the 14 E. coli strains tested at the concentration of 100 μg/ml. The cell wall binding do-main of the engineered lysin can destroy the integrity of the outer membrane of bacteria, thus allowing the catalytic do-main to reach its target, peptidoglycan, to lyse the bacteria. Lysep3-D8 can be used as a preservative in fodder to benefit the health of animals. The method we used here proved to be a successful exploration of the reformation of phage lysin.

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