Journal of Microbiology

Volume 53(10); October 2015

Review

MINIREVIEW] Regulation and function of the Salmonella MgtC virulence protein: Jang-Woo Lee , Eun-Jin Lee; J. Microbiol. 2015;53(10):667-672. Published online August 1, 2015; DOI: https://doi.org/10.1007/s12275-015-5283-1

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25 Citations

Abstract: Salmonella enterica serovar Typhimurium produces many virulence proteins to cause diseases. The Salmonella MgtC protein is one of such virulence proteins specially required for intracellular proliferation inside macrophages and mouse virulence. In this review, we will cover how the mgtC gene is turned on or off and what the signals required for mgtC expression are. Later in this review, we will discuss a recent understanding of MgtC function in Salmonella pathogenesis by identifying its target proteins.

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

Sphingomonas parvus sp. nov. isolated from a ginseng-cultivated soil: Jae-Hyung Ahn , Byoung-chan Kim , Soo-Jin Kim , Geun-Hey Lee , Jaekyeong Song , Soon-Wo Kwon , Hang-Yeon Weon; J. Microbiol. 2015;53(10):673-677. Published online October 2, 2015; DOI: https://doi.org/10.1007/s12275-015-5132-2

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Abstract: Strain GP20-2T was isolated from a soil cultivated with ginseng in Korea. The 16S rRNA gene sequence of this strain showed the highest sequence similarity with Sphingomonas daechungensis CH15-11T (96.7%) and Sphingomonas sediminicola Dae 20T (96.2%) among the type strains. The strain GP20-2T was a strictly aerobic, Gram-negative, non-motile, rod-shaped bacterium that formed very tiny colonies, less than 0.3 mm in diameter after 10 days on R2A agar. The strain grew at 10–35°C (optimum, 35°C), at a pH of 5.0–8.0 (optimum, pH 6.0), and in the absence of NaCl. The DNA G+C content of strain GP20-2T was 67.2 mol%. It contained ubiquinone Q-10 as the major isoprenoid quinone, and summed feature 8 (C18:1ω6c and/or C18:1ω7c, 49.8%) and C16:0 (17.0%) as the major fatty acids. On the basis of evidence from our polyphasic taxonomic study, we concluded that strain GP20-2T should be classified as a novel species of the genus Sphingomonas, for which the name Sphingomonas parvus sp. nov. is proposed. The type strain is GP20-2T (=KACC 12865T =DSM 100456T).

Illumina-based analysis of bacterial diversity related to halophytes Salicornia europaea and Sueada aralocaspica: Ying-wu Shi , Kai Lou , Chun Li , Lei Wang , Zhen-yong Zhao , Shuai Zhao , Chang-yan Tian; J. Microbiol. 2015;53(10):678-685. Published online October 2, 2015; DOI: https://doi.org/10.1007/s12275-015-5080-x

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37 Citations

Abstract: We used Illumina-based 16S rRNA V3 amplicon pyrosequencing to investigate the community structure of soil bacteria from the rhizosphere surrounding Salicornia europaea, and endophytic bacteria living in Salicornia europaea plants and Sueada aralocaspica seeds growing at the Fukang Desert Ecosystem Observation and Experimental Station (FDEOES) in Xinjiang Province, China, using an Illumina genome analyzer. A total of 89.23 M effective sequences of the 16S rRNA gene V3 region were obtained from the two halophyte species. These sequences revealed a number of operational taxonomic units (OTUs) in the halophytes. There were between 22–2,206 OTUs in the halophyte plant sample, at the 3% cutoff level, and a sequencing depth of 30,000 sequences. We identified 25 different phyla, 39 classes and 141 genera from the resulting 134,435 sequences. The most dominant phylum in all the samples was Proteobacteria (41.61%–99.26%; average, 43.30%). The other large phyla were Firmicutes (0%– 7.19%; average, 1.15%), Bacteroidetes (0%–1.64%; average, 0.44%) and Actinobacteria (0%–0.46%; average, 0.24%). This
result
suggested that the diversity of bacteria is abundant in the rhizosphere soil, while the diversity of bacteria was poor within Salicornia europaea plant samples. To the extent of our knowledge, this study is the first to characterize and compare the endophytic bacteria found within different halophytic plant species roots using PCR-based Illumina pyrosequencing
method
.

Performance of PCR-reverse blot hybridization assay for detection of rifampicin-resistant Mycobacterium leprae: Hye-young Wang , Hyunjung Kim , Yeun Kim , Hyeeun Bang , Jong-Pill Kim , Joo Hwan Hwang , Sang-Nae Cho , Tae Ue Kim , Hyeyoung Lee; J. Microbiol. 2015;53(10):686-693. Published online October 2, 2015; DOI: https://doi.org/10.1007/s12275-015-5057-9

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Abstract: Drug resistance in Mycobacterium leprae is a significant problem in countries where leprosy is endemic. A sensitive, specific, and high-throughput reverse blot hybridization assay (REBA) for the detection of genotypic resistance to rifampicin (RIF) was designed and evaluated. It has been shown that resistance to RIF in M. leprae involves mutations in the rpoB gene encoding the β-subunit of the RNA polymerase. The PCR-REBA simultaneously detects both 6 wild-type regions and 5 different mutations (507AGC, 513GTG, 516TAT, 531ATG, and 531TTC) including the most prevalent mutations at positions 507 and 531. Thirty-one clinical isolates provided by Korea Institute of Hansen’s Disease were analyzed by PCR-REBA with RIF resistance of rpoB gene. As a
result
, missense mutations at codons 507 AGC and 531ATG with 2-nucleotide substitutions were found in one sample, and a missense mutation at codon 516 TAT and ΔWT6 (deletion of 530-534) was found in another sample. These cases were confirmed by DNA sequence analysis. This rapid, simple, and highly sensitive assay provides a practical alternative to sequencing for genotypic evaluation of RIF resistance in M. leprae.

Antifungal activity of violacein purified from a novel strain of Chromobacterium sp. NIIST (MTCC 5522): Anju Sasidharan , Nishanth Kumar Sasidharan , Dileepkumar Bhaskaran Nair Saraswathy Amma , Radhakrishnan Kokkuvayil Vasu , Anupama Vijaya Nataraja , Krishnakumar Bhaskaran; J. Microbiol. 2015;53(10):694-701. Published online October 2, 2015; DOI: https://doi.org/10.1007/s12275-015-5173-6

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45 Citations

Abstract: A novel strain of Chromobacterium sp. NIIST (MTCC 5522) producing high level of purple blue bioactive compound violacein was isolated from clay mine acidic sediment. During 24 h aerobic incubation in modified Luria Bertani medium, around 0.6 g crude violacein was produced per gram of dry weight biomass. An inexpensive method for preparing crystalline, pure violacein from crude pigment was developed (12.8 mg violacein/L) and the pure compound was characterized by different spectrometric methods. The violacein prepared was found effective against a number of plant and human pathogenic fungi and yeast species such as Cryptococcus gastricus, Trichophyton rubrum, Fusarium oxysporum, Rhizoctonia solani, Aspergillus flavus, Penicillium expansum, and Candida albicans. The best activity was recorded against Trichophyton rubrum (2 μg/ml), a human pathogen responsible for causing athlete’s foot infection. This is the first report of antifungal activity of purified violacein against pathogenic fungi and yeast.

Relationships between the use of Embden Meyerhof pathway (EMP) or Phosphoketolase pathway (PKP) and lactate production capabilities of diverse Lactobacillus reuteri strains: Grégoire Burgé , Claire Saulou-Bérion , Marwen Moussa , Florent Allais , Violaine Athes , Henry-Eric Spinnler; J. Microbiol. 2015;53(10):702-710. Published online October 2, 2015; DOI: https://doi.org/10.1007/s12275-015-5056-x

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24 Citations

Abstract: The aims of this study is to compare the growth and glucose metabolism of three Lactobacillus reuteri strains (i.e. DSM 20016, DSM 17938, and ATCC 53608) which are lactic acid bacteria of interest used for diverse applications such as probiotics implying the production of biomass, or for the production of valuable chemicals (3-hydroxypropionaldehyde, 3-hydroxypropionic acid, 1,3-propanediol). However, the physiological diversity inside the species, even for basic metabolisms, like its capacity of acidification or glucose metabolism, has not been studied yet. In the present work, the growth and metabolism of three strains representative of the species diversity have been studied in batch mode. The strains were compared through characterization of growth kinetics and evaluation of acidification kinetics, substrate consumption and product formation. The results showed significant differences between the three strains which may be explained, at least in part, by variations in the distribution of carbon source between two glycolytic pathways during the bacterial growth: the phosphoketolase or heterolactic pathway (PKP) and the Embden-Meyerhof pathway (EMP). It was also shown that, in the context of obtaining a large amount of biomass, DSM 20016 and DSM 17938 strains were the most effective in terms of growth kinetics. The DSM 17938 strain, which shows the more significant metabolic shift from EMP to PKP when the pH decreases, is more effective for lactate production.

Structural basis for the ATP-independent proteolytic activity of LonB proteases and reclassification of their AAA+ modules: Young Jun An , Jung-Hyun Na , Myung-Il Kim , Sun-Shin Cha; J. Microbiol. 2015;53(10):711-717. Published online October 2, 2015; DOI: https://doi.org/10.1007/s12275-015-5417-5

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Abstract: Lon proteases degrade defective or denature proteins as well as some folded proteins for the control of cellular protein quality. There are two types of Lon proteases, LonA and LonB. Each consists of two functional components: a protease component and an ATPase associated with various cellular activities (AAA+ module). Here, we report the 2.03 Å-resolution crystal structure of the isolated AAA+ module (iAAA+ module) of LonB from Thermococcus onnurineus NA1 (TonLonB). The iAAA+ module, having no bound nucleotide, adopts a conformation virtually identical to the ADP-bound conformation of AAA+ modules in the hexameric structure of TonLonB; this provides insights into the ATP-independent proteolytic activity observed in a LonB protease. Structural comparison of AAA+ modules between LonA and LonB revealed that the AAA+ modules of Lon proteases are separated into two distinct clades depending on their structural features. The AAA+ module of LonB belongs to the ‘H2 & Ins1 insert clade (HINS clade)’ defined for the first time in this study, while the AAA+ module of LonA is a member of the HCLR clade.

Journal Article

Regulation of HBV-specific CD8+ T cell-mediated inflammation is diversified in different clinical presentations of HBV infection: Colin M. Dinney , Lu-Dong Zhao , Charles D. Conrad , Jay M. Duker , Richard O. Karas , Zhibin Hu , Michele A. Hamilton , Thomas R. Gillis , Thomas M. Parker , Bing Fan , Andrew H. Advani , Fred B. Poordad , Paulette L. Fauceglia , Kathrin M. Kirsch , Peter T. Munk , Marc P. Ladanyi , Bernard A. Bochner , Justin A. Bekelman , Carla M. Grandori , James C. Olson , Ronald D. Lechan , Ghassan M.A. Abou , Mark A. Goodarzi; J. Microbiol. 2015;53(10):718-724. Published online October 2, 2015; DOI: https://doi.org/10.1007/s12275-015-5314-y

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Abstract: Chronic HBV infection is the leading cause of liver cirrhosis and hepatic cancer, but the individual responses toward HBV infection are highly variable, ranging from asymptomatic to chronic active hepatitis B inflammation. In this study, we hypothesized that the different individual responses to HBV infection was associated with differences in HBV-specific CD8+ T cell-mediated inflammation and cytotoxicity. Blood samples were collected from subjects with asymptomatic HBV-infection, subjects undergoing active chronic HBV flares (active CHB), and subjects with HBV-infected hepatocellular carcinoma (HBV-HCC). By tetramer staining, we found that all three groups had similar frequencies of HBVspecific CD8+ T cells. However, after HBV peptide stimulation, the HBV-specific CD8+ T cells in asymptomatic subjects had significantly stronger interferon gamma (IFN-γ), tumor necrosis factor alpha (TNF-α), and CD107a expression than those in active CHB and HBV-HCC patients. Examination of surface marker expression revealed that the PD-1-Tim-3- double-negative cell population was the main contributor to HBV-specific inflammation. In active CHB patients and HBV-HCC patients, however, the frequencies of activated PD-1-Tim-3- cells were significantly reduced. Moreover, the serum HBV DNA titer was not correlated with the frequencies of HBV-specific CD8+ T cells but was inversely correlated with the frequencies of IFN-g-expressing and CD107a-express cells in response to HBV stimulation. Together, our data demonstrated that the status of HBVspecific CD8+ T cell exhaustion was associated with different clinical outcomes of chronic HBV infection.

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

The hrp pathogenicity island of Pseudomonas syringae pv. tomato DC3000 is induced by plant phenolic acids: Jun Seung Lee , Hye Ryun Ryu , Ji Young Cha , Hyung Suk Baik; J. Microbiol. 2015;53(10):725-731. Published online October 2, 2015; DOI: https://doi.org/10.1007/s12275-015-5256-4

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6 Citations

Abstract: Plants produce a wide array of antimicrobial compounds, such as phenolic compounds, to combat microbial pathogens. The hrp PAI is one of the major virulence factors in the plant pathogen, Pseudomonas syringae. A major role of hrp PAI is to disable the plant defense system during bacterial invasion. We examined the influence of phenolic compounds on hrp PAI gene expression at low and high concentrations. There was approximately 2.5 times more hrpA and hrpZ mRNA in PtoDC3000 that was grown in minimal media (MM) supplemented with 10 μM of ortho-coumaric acid than in PtoDC3000 grown in MM alone. On the other hand, a significantly lower amount of hrpA mRNA was observed in bacteria grown in MM supplemented with a high concentration of phenolic compounds. To determine the regulation pathway for hrp PAI gene expression, we performed qRTPCR using gacS, gacA, and hrpS deletion mutants.

Characterization of the rapamycin-inducible EBV LMP1 activation system: Sang Yong Kim , Jung-Eun Kim , Jiyeon Won , Yoon-Jae Song; J. Microbiol. 2015;53(10):732-738. Published online October 2, 2015; DOI: https://doi.org/10.1007/s12275-015-5455-z

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Abstract: Epstein-Barr virus (EBV) latent infection membrane protein 1 (LMP1) is required for EBV-mediated B lymphocyte transformation into proliferating lymphoblastoid cell lines (LCL). LMP1 oligomerizes spontaneously in membrane lipid rafts via its transmembrane domain and constitutively activates signal transduction pathways, including NF-κB, p38 Mitogen-Activated Protein Kinase (MAPK), and c-Jun N-terminal Kinase (JNK). Since LMP1 mimics the tumor necrosis factor receptor (TNFR), CD40, it may be effectively utilized to study the effects of constitutive activation of signal transduction pathways on cellular physiology. On the other hand, LMP1 presents a disadvantage in terms of determining the sequential events and factors involved in signaling pathways. A CD40-LMP1 chimeric molecule has been generated to overcome this limitation but does not represent the authentic and physiological nature of LMP1. In the current study, a ligand-dependent activation system for LMP1 using rapamycin-inducible dimerization was generated to delineate the LMP1 signaling pathway.

Published Erratum

Erratum] Identification of the Vibrio vulnificus htpG Gene and Its Influence on Cold Shock Recovery: Slae Choi , Kyungku Jang , Seulah Choi , Hee-jee Yun , Dong-Hyun Kang; J. Microbiol. 2015;53(10):739-739.; DOI: https://doi.org/10.1007/s12275-015-0740-4

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Abstract: In the article by Choi et al. published in Journal of Microbiology 2012; 50, 707-711. The 2nd author name of this paper should be corrected as Kyung Ku Jang. The authors should be Slae Choi1†, Kyung Ku Jang1†, Seulah Choi2, Hee-jee Yun2, and Dong-Hyun Kang1*

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