Journal of Microbiology

Volume 53(6); June 2015

Review

MINIREVIEW] Molecular architecture of the bacterial tripartite multidrug efflux pump focusing on the adaptor bridging model: Saemee Song , Jin-Sik Kim , Kangseok Lee , Nam-Chul Ha; J. Microbiol. 2015;53(6):355-364. Published online May 30, 2015; DOI: https://doi.org/10.1007/s12275-015-5248-4

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Gram-negative bacteria expel a wide range of toxic substances through tripartite drug efflux pumps consisting of an inner membrane transporter, an outer membrane channel protein, and a periplasmic adaptor protein. These pumps form tripartite assemblies which can span the entire cell envelope, including the inner and outer membranes. There have been controversial findings regarding the assembly of the individual components in tripartite drug efflux pumps. Recent structural and functional studies have advanced our understanding of the assembly and working mechanisms of the pumps. Here, we re-evaluate the assembly models based on recent structural and functional studies. In particular, this study focuses on the ‘adaptor bridging model’, highlighting the intermeshing cogwheel-like interactions between the tip regions of the outer membrane channel protein and the periplasmic adaptor protein in the hexameric assembly.

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Recent paradigm shift in the assembly of bacterial tripartite efflux pumps and the type I secretion system
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Genetic identification of factors for extracellular cellulose accumulation in the thermophilic cyanobacterium Thermosynechococcus vulcanus: proposal of a novel tripartite secretion system
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Switch Loop Flexibility Affects Substrate Transport of the AcrB Efflux Pump
Reinke T. Müller, Timothy Travers, Hi-jea Cha, Joshua L. Phillips, S. Gnanakaran, Klaas M. Pos
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Venkata Krishnan Ramaswamy, Attilio V. Vargiu, Giuliano Malloci, Jürg Dreier, Paolo Ruggerone
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Structure of the MacAB–TolC ABC-type tripartite multidrug efflux pump
Anthony W. P. Fitzpatrick, Salomé Llabrés, Arthur Neuberger, James N. Blaza, Xiao-Chen Bai, Ui Okada, Satoshi Murakami, Hendrik W. van Veen, Ulrich Zachariae, Sjors H. W. Scheres, Ben F. Luisi, Dijun Du
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Structural Basis for the Serratia marcescens Lipase Secretion System: Crystal Structures of the Membrane Fusion Protein and Nucleotide-Binding Domain
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The Crystal Structure of the YknZ Extracellular Domain of ABC Transporter YknWXYZ from Bacillus amyloliquefaciens
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Journal Article

Lysobacter tyrosinelyticus sp. nov. isolated from Gyeryongsan national park soil: Juan Du , Hina Singh , Hien T.T. Ngo , KyungHwa Won , Ki-Young Kim , Tae-Hoo Yi; J. Microbiol. 2015;53(6):365-370. Published online May 30, 2015; DOI: https://doi.org/10.1007/s12275-015-4729-9

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Abstract

A novel Gram-negative, rod-shaped (0.2-0.5 um x 1.5-2.5 um), aerobic, non-motile bacterium was isolated from Gyeryongsan national park soil, Republic of Korea. The novel isolate was designated as THG-DN8.2T. The strain grows optimally at 28oC, at pH 7 and in the absence of NaCl. Phylogenetic analysis based on 16S rRNA gene sequence showed that the novel isolate shared the highest sequence similarity with Lysobacter oryzae KCTC 22249T followed by Lysobacter yangpyeongensis KACC 11407T and Lysobacter niabensis KACC 11587T. The DNA G+C content of strain THG-DN8.2T is 66.0 mol% and ubiquinone Q-8 is the main isoprenoid quinone. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, and phosphatidyl-N-methylethanolamine. The major fatty acids of strain THG-DN8.2T were identified as iso-C15:0, iso-C16:0, and C16:1w7c alcohol. The phylogenetic distinctiveness and phenotypic characteristics differentiated strain THG-DN8.2T from closely related Lysobacter species. The results of polyphasic taxonomic analysis suggest that strain THG-DN8.2T represents a novel species of the genus Lysobacter, for which the name Lysobacter tyrosinelyticus sp. nov. is proposed. The type strain is THG-DN8.2T (=KCTC 42235T =JCM 30320T).

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

Microbial communities inhabiting oil-contaminated soils from two major oilfields in Northern China: Implications for active petroleum-degrading capacity: Weimin Sun , Yiran Dong , Pin Gao , Meiyan Fu , Kaiwen Ta , Jiwei Li; J. Microbiol. 2015;53(6):371-378. Published online May 30, 2015; DOI: https://doi.org/10.1007/s12275-015-5023-6

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Abstract

Although oilfields harbor a wide diversity of microorganisms with various metabolic potentials, our current knowledge about oil-degrading bacteria is limited because the vast majority of oil-degrading bacteria remain uncultured. In the present study, microbial communities in nine oil-contaminated soils collected from Daqing and Changqing, two of the largest oil fields in China, were characterized through highthroughput sequencing of 16S rRNA genes. Bacteria related to the phyla Proteobacteria and Actinobacteria were dominant in four and three samples, respectively. At the genus level, Alkanindiges, Arthrobacter, Pseudomonas, Mycobacterium, and Rhodococcus were frequently detected in nine soil samples. Many of the dominant genera were phylogenetically related to the known oil-degrading species. The correlation between physiochemical parameters within the microbial communities was also investigated. Canonical correspondence analysis revealed that soil moisture, nitrate, TOC, and pH had an important impact in shaping the microbial communities of the hydrocarbon-contaminated soil. This study provided an in-depth analysis of microbial communities in oilcontaminated soil and useful information for future bioremediation of oil contamination.

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The complete genome sequence of the cold adapted crude-oil degrader: Pedobacter steynii DX4
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Soil fungal communities of montane natural secondary forest types in China: Fei Cheng , Xin Wei , Lin Hou , Zhengchun Shang , Xiaobang Peng , Peng Zhao , Zhaoxue Fei , Shuoxin Zhang; J. Microbiol. 2015;53(6):379-389. Published online May 30, 2015; DOI: https://doi.org/10.1007/s12275-015-4722-3

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Abstract

Distinctive plant communities may provide specific physical and chemical properties with soils by specific litters and root exudates to exert effects on soil microorganisms. Past logging activities in the Qinling Mountains induced diverse natural secondary forest types (NSFTs). How these recovered NSFTs regulate patterns of soil microbial communities remain limited. In the study, we used terminal-restriction fragment length polymorphism (T-RFLP) to precisely determine forest type-specific soil fungal diversity and composition in five NSFTs. Our results indicated that NSFTs had significant impacts on the soil fungal communities. The most diverse fungal species were found in the Armand pine (Pinus armandi) and Chinese pine (Pinus tabulaeformis) forest soils, followed by sharptooth oak (Quercus aliena var. acuteserrata) and Chinese pine-sharptooth oak forest soils, the wilson spruce (Picea wilsonii) forests had the lowest soil fungal diversity. The analyses of community composition suggested that the fungal communities of Armand pine forest soils were similar to those of Chinese pine forest soils, while other communities prominently differed from each other. Stepwise multiple regression analysis revealed that soil silt, clay, pH, and ammonium nitrogen had intimate linkages with soil fungal diversity. Furthermore, the patterns of soil fungal communites were strongly governed by the specific soil environments of the tested NSFTs, as described by canonical correspondence analysis (CCA). Finally, our study showed that soil fungal communities may be mediated by NSFTs via specific soil edaphic status. Hence, such a comparable study may provide fundamental information for fungal diversity and community structure of natural forests and assist with better prediction and understanding how soil fungal composition and function alter with forest type transformation.

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An endophytic Coniochaeta velutina producing broad spectrum antimycotics: Jie Xie , Gary A. Strobel , Tao Feng , Huishuang Ren , Morgan T. Mends , Zeyang Zhou , Brad Geary; J. Microbiol. 2015;53(6):390-397. Published online May 30, 2015; DOI: https://doi.org/10.1007/s12275-015-5105-5

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Abstract

An endophyte (PC27-5) was isolated from stem tissue of Western hemlock (Tsuga heterophylla) in a Pacific Northwest temperate rainforest. Phylogenetic analyses, based on ITS- 5.8S rDNA and 18S rDNA sequence data, combined with cultural and morphological analysis showed that endophyte PC27-5 exhibited all characteristics of a fungus identical to Coniochaeta velutina. Furthermore, wide spectrum antimycotics were produced by this endophyte that were active against such plant pathogens as Sclerotinia sclerotiorum, Pythium ultimum, and Verticillium dahliae and lethal to Phythophthora cinnamomi, Pythium ultimum, and Phytophthora palmivora in plate tests. The bioactive components were purified through organic solvent extraction, followed by silica column chromatography, and finally preparative HPLC. The minimum inhibitory concentration of the active fraction to Pythium ultimum, which was gained from preparative HPLC, was 11 ?/ml. UPLC-HRMS analysis showed there were two similar components in the antimycotic fraction. Their molecular formulae were established as C30H22O11 (compound I) and C30H22O10 (compound II) respectively, and preliminary spectral results indicate that they are anthroquinone glycosides. Other non ?biologically active compounds were identified in culture fluids of this fungus by spectral means as emodin and chrysophanol - anthroquinone derivatives. This is the first report that Coniochaeta velutina as an endophyte produces bioactive antifungal components.

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Effects of Lactobacillus salivarius Ren on cancer prevention and intestinal microbiota in 1, 2-dimethylhydrazine-induced rat model: Ming Zhang , Xing Fan , Bing Fang , Chengzhen Zhu , Jun Zhu , Fazheng Ren; J. Microbiol. 2015;53(6):398-405. Published online May 30, 2015; DOI: https://doi.org/10.1007/s12275-015-5046-z

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Abstract

Probiotics have been suggested as a prophylactic measure in colon cancer. The aim of this study was to investigate the impact of Lactobacillus salivarius Ren (Ren) in modulating colonic microbiota structure and colon cancer incidence in a rat model after injection with 1,2-dimethyl hydrazine (DMH). The results indicated that oral administration of Ren could effectively suppress DMH-induced colonic carcinogenesis. A significant decrease in cancer incidence (87.5% to 25%) was detected in rats fed with a dose of 5 × 1010 CFU/kg bodyweight per day. Using denaturing gradient gel electrophoresis and Real-time PCR combined with multivariate statistical methods, we demonstrated that injection with DMH significantly altered the rat gut microbiota, while Ren counteracted these DMH-induced adverse effects and promoted reversion of the gut microbiota close to the healthy state. Tvalue biplots followed by band sequencing identified 21 bacterial strains as critical variables affected by DMH and Ren. Injection of DMH significantly increased the amount of Ruminococcus species (sp.) and Clostridiales bacteria, as well as decreasing the Prevotella sp. Administration of Ren reduced the amount of Ruminococcus sp., Clostridiales bacteria, and Bacteroides dorei, and increased the amount of Prevotella. Real-time PCR results were consistent with the results derived by t-value biplots. These findings suggested that Ren is a potential agent for colon cancer prevention. In conclusion, the
results
in the present study suggest a potential therapeutic approach based on the modulation of intestinal microflora by probiotics may be beneficial in the prevention of colorectal carcinogenesis.

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Morphological changes in human gastric epithelial cells induced by nuclear targeting of Helicobacter pylori urease subunit A: Jung Hwa Lee , So Hyun Jun , Jung-Min Kim , Seung Chul Baik , Je Chul Lee; J. Microbiol. 2015;53(6):406-414. Published online May 30, 2015; DOI: https://doi.org/10.1007/s12275-015-5085-5

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Abstract

Nuclear targeting of bacterial proteins and their pathological effects on host cells are an emerging pathogenic mechanism in bacteria. We have previously reported that urease subunit A (UreA) of Helicobacter pylori targets the nuclei of COS-7 cells through nuclear localization signals (NLSs). This study further investigated whether UreA of H. pylori targets the nuclei of gastric epithelial cells and then induces molecular and cellular changes in the host cells. H. pylori 26695 strain produced and secreted outer membrane vesicles (OMVs). UreA was translocated into gastric epithelial AGS cells through outer membrane vesicles (OMVs) and then targeted the nuclei of AGS cells. Nuclear targeting of rUreA did not induce host cell death, but resulted in morphological changes, such as cellular elongation, in AGS cells. In contrast, AGS cells treated with rUreAΔNLS proteins did not show this morphological change. Next generation sequencing revealed that nuclear targeting of UreA differentially regulated 102 morphogenesis- related genes, of which 67 and 35 were up-regulated and down-regulated, respectively. Our results suggest that nuclear targeting of H. pylori UreA induces both molecular and cellular changes in gastric epithelial cells.

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Therapeutic potential of an AcHERV-HPV L1 DNA vaccine: Hee-Jung Lee , Jong Kwang Yoon , Yoonki Heo , Hansam Cho , Yeondong Cho , Yongdae Gwon , Kang Chang Kim , Jiwon Choi , Jae Sung Lee , Yu-Kyoung Oh , Young Bong Kim; J. Microbiol. 2015;53(6):415-420. Published online May 30, 2015; DOI: https://doi.org/10.1007/s12275-015-5150-0

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Abstract

Cervical cancer is strongly associated with chronic human papillomavirus infections, among which HPV16 is the most common. Two commercial HPV vaccines, Gardasil and Cervarix are effective for preventing HPV infection, but cannot be used to treat existing HPV infections. Previously, we developed a human endogenous retrovirus (HERV)-enveloped recombinant baculovirus capable of delivering the L1 genes of HPV types 16, 18, and 58 (AcHERV-HP16/18/58L1, AcHERV-HPV). Intramuscular administration of AcHERVHPV vaccines induced a strong cellular immune response as well as a humoral immune response. In this study, to examine the therapeutic effect of AcHERV-HPV in a mouse model, we established an HPV16 L1 expressing tumor cell line. Compared to Cervarix, immunization with AcHERVHPV greatly enhanced HPV16 L1-specific cytotoxic T lymphocytes (CTL) in C57BL/6 mice. Although vaccination could not remove preexisting tumors, strong CTL activity retarded the growth of inoculated tumor cells. These results indicate that AcHERV-HPV could serve as a potential therapeutic DNA vaccine against concurrent infection with HPV 16, 18, and 58.

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