Journal of Microbiology

Volume 53(5); May 2015

Reviews

MINIREVIEW] Unraveling interactions in microbial communities - from co-cultures to microbiomes: Justin Tan , Cristal Zuniga , Karsten Zengler; J. Microbiol. 2015;53(5):295-305. Published online May 3, 2015; DOI: https://doi.org/10.1007/s12275-015-5060-1

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Microorganisms do not exist in isolation in the environment. Instead, they form complex communities among themselves as well as with their hosts. Different forms of interactions not only shape the composition of these communities but also define how these communities are established and maintained. The kinds of interaction a bacterium can employ are largely encoded in its genome. This allows us to deploy a genomescale modeling approach to understand, and ultimately predict, the complex and intertwined relationships in which microorganisms engage. So far, most studies on microbial communities have been focused on synthetic co-cultures and simple communities. However, recent advances in molecular and computational biology now enable bottom up methods to be deployed for complex microbial communities from the environment to provide insight into the intricate and dynamic interactions in which microorganisms are engaged. These methods will be applicable for a wide range of microbial communities involved in industrial processes, as well as understanding, preserving and reconditioning natural microbial communities present in soil, water, and the human microbiome.

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MINIREVIEW] Two stress sensor proteins for the expression of sigmaE regulon: DegS and RseB: Dong Young Kim; J. Microbiol. 2015;53(5):306-310. Published online May 3, 2015; DOI: https://doi.org/10.1007/s12275-015-5112-6

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Abstract

In E. coli, sigmaE-dependent transcription is controlled by regulated-proteolysis of RseA. RseA, which holds sigmaE as an anti-sigma factor, is sequentially digested by DegS, RseP and cytoplasmic proteases to liberate sigmaE in response to dysfunction in outer-membrane biogenesis. Additionally, the sequential proteolysis is regulated by RseB binding to RseA (Fig. 1A). Direct interaction between RseA and RseB inhibits RseA-cleavage by DegS. Both proteolytic activation of DegS and binding disruption of RseB are thus required to initiate sigmaE-stress response. For the induction of sigmaEstress response, DegS and RseB recognize the states of OMP and LPS for outer-membrane biogenesis. DegS is activated by binding of unfolded OMPs and RseB binding to RseA is antagonized by LPS accumulated in periplasm. In this regard, DegS and RseB are proposed to be stress sensor proteins for sigmaE signal transduction. Interestingly, biogenesis of OMP and LPS appears to cross-talk with each other, indicating that dysfunction of either OMP or LPS can initiate RseA proteolysis. This review aims to briefly introduce two stress sensor proteins, DegS and RseB, which regulate sigmaEdependent transcription.

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

Communities of ammonia oxidizers at different stages of Spartina alterniflora invasion in salt marshes of Yangtze River estuary: Fei Xia , Jemaneh Zeleke , Qiang Sheng , Ji-Hua Wu , Zhe-Xue Quan; J. Microbiol. 2015;53(5):311-320. Published online May 3, 2015; DOI: https://doi.org/10.1007/s12275-015-4660-0

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Abstract

Spartina alterniflora, an aggressive invasive plant species at the estuarine wetlands of China’s coasts, has become a major threat to the natural ecosystems. To understand its potential influence on nitrification processes, the community structures and abundance of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) were investigated using 454-pyrosequencing and quantitative real-time PCR (qPCR) in S. alterniflora invading salt marsh sediments at the Yangtze River estuary in Chongming island, Shanghai, China. Copy numbers of archaeal and bacterial ammonia monooxygenase subunit A (amoA) genes did not show accordant shifts with S. alterniflora invasion in the two sampling sites. However, the copy numbers of archaeal amoA gene were higher in summer than in spring. Phylogenetic analysis indicated that more than 90% of the archaeal and 92% of the bacterial amoA gene sequences were closely related to marine group I.1a and the clusters 13 and 15 in Nitrosospira lineage, respectively. The effect of different seasons (spring and summer) was important for the abundance variation of AOA, while different stages of S. alterniflora invasion did not show significant effect for both AOA and AOB. Variation of AOA community was significantly related to total carbon (TC) and sulfate concentration (P < 0.05), whereas the AOB community was significantly related to sulfate concentration, total nitrogen (TN), TC and pH (P < 0.05). In conclusion, the abundance and diversity of ammonia oxidizing microbial communities were not strongly affected by S. alterniflora invasion.

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In vitro effects of N-acetyl cysteine alone and in combination with antibiotics on Prevotella intermedia: Ji-Hoi Moon , Eun-Young Jang , Kyu Sang Shim , Jin-Yong Lee; J. Microbiol. 2015;53(5):321-329. Published online May 3, 2015; DOI: https://doi.org/10.1007/s12275-015-4500-2

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Abstract

N-acetyl cysteine (NAC) is an antioxidant that possesses anti-inflammatory activities in tissues. In the field of dentistry, NAC was demonstrated to prevent the expression of LPS-induced inflammatory mediators in phagocytic cells and gingival fibroblasts during the inflammatory process, but the effect of NAC on oral pathogens has been rarely studied. Here, we examined the effect of NAC against planktonic and biofilm cells of Prevotella intermedia, a major oral pathogen. NAC showed antibacterial activity against the planktonic P. intermedia with MIC value of 3 mg/ml and significantly decreased biofilm formation by the bacterium even at sub MIC. NAC did not affect the antibiotic susceptibility of planktonic P. intermedia, showing indifference (fractional inhibitory concentration index of 0.5?) results against the bacterium in combination with ampicillin, ciprofloxacin, tetracycline or metronidazole. On the other hand, viability of the pre-established bacterial biofilm exposed to the antibiotics except metronidazole was increased in the presence of NAC. Collectively, NAC may be used for prevention of the biofilm formation by P. intermedia rather than eradication of the pre-established bacterial biofilm. Further studies are required to explore antibacterial and anti-biofilm activity of NAC against mixed population of oral bacteria and its modulatory effect on antibiotics used for oral infectious diseases.

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Biological Activities and Potential Oral Applications of N‐Acetylcysteine: Progress and Prospects
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Identification of seven novel virulence genes from Xanthomonas citri subsp. citri by Tn5-based random mutagenesis: Xue Song , Jing Guo , Wen-xiu Ma , Zhi-yuan Ji , Li-fang Zou , Gong-you Chen , Hua-song Zou; J. Microbiol. 2015;53(5):330-336. Published online May 3, 2015; DOI: https://doi.org/10.1007/s12275-015-4589-3

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Abstract

To identify novel virulence genes, a mutant library of Xanthomonas citri subsp. citri 29-1 was produced using EZ-Tn5 transposon and the mutants were inoculated into susceptible grapefruit. Forty mutants with altered virulence phenotypes were identified. Nine of the mutants showed a complete loss of citrus canker induction, and the other 31 mutants resulted in attenuated canker symptoms. Southern blot analysis revealed that each of the mutants carried a single copy of Tn5. The flanking sequence was identified by plasmid rescue and 18 different ORFs were identified in the genome sequence. Of these 18 ORFs, seven had not been previously associated with the virulence of X. citri subsp. citri and were therefore confirmed by complementation analysis. Real-time PCR analysis showed that the seven genes were upregulated when the bacteria were grown in citrus plants, suggesting that the expression of these genes was essential for canker development.

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Xanthomonas citri subsp. citri type III effector PthA4 directs the dynamical expression of a putative citrus carbohydrate-binding protein gene for canker formation
Xinyu Chen, Huasong Zou, Tao Zhuo, Wei Rou, Wei Wu, Xiaojing Fan
eLife.2024;[Epub] CrossRef
The Methyltransferase HemK Regulates the Virulence and Nutrient Utilization of the Phytopathogenic Bacterium Xanthomonas citri Subsp. citri
Yu Shi, Xiaobei Yang, Xiaoxin Ye, Jiaying Feng, Tianfang Cheng, Xiaofan Zhou, Ding Xiang Liu, Linghui Xu, Junxia Wang
International Journal of Molecular Sciences.2022; 23(7): 3931. CrossRef
A Comprehensive Overview of the Genes and Functions Required for Lettuce Infection by the Hemibiotrophic Phytopathogen Xanthomonas hortorum pv. vitians
Lucas Morinière, Laurène Mirabel, Erwan Gueguen, Franck Bertolla, Christopher W. Schadt, Steven Lindow
mSystems.2022;[Epub] CrossRef
Identification of Essential Genes Associated With Prodigiosin Production in Serratia marcescens FZSF02
Xianbo Jia, Fangchen Liu, Ke Zhao, Junjie Lin, Yu Fang, Shouping Cai, Chenqiang Lin, Hui Zhang, Longjun Chen, Jichen Chen
Frontiers in Microbiology.2021;[Epub] CrossRef
An inducible transposon mutagenesis approach for the intracellular human pathogen Chlamydia trachomatis
Colette E. O'Neill, Rachel J. Skilton, Jade Forster, David W. Cleary, Sarah A. Pearson, David J. Lampe, Nicholas R. Thomson, Ian N. Clarke
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Yanfei Xia, Shen Li, Guohui Xu, Shanshan Xie, Xueting Liu, Xiaomin Lin, Huijun Wu, Xuewen Gao
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Comparing bacterial properties in relation to the virulence factors of Xanthomonas citri subsp. citri strains and evaluating resistance of subtribe Citrinae cultivars to the most virulent strain
Hossein Mirzaei-Najafgholi, Milad Aeini, Saeed Tarighi, Morteza Golmohammadi
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Inhibition of the Citrus Canker Pathogen Using a Photosensitizer Assisted by Sunlight Irradiation
Libin Jiang, Yurong Liu, Xianyuan Xu, Dan Su, Huasong Zou, Jianyong Liu, Cai Yuan, Mingdong Huang
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Tn5 Transposase Applied in Genomics Research
Niannian Li, Kairang Jin, Yanmin Bai, Haifeng Fu, Lin Liu, Bin Liu
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Global Regulator PhoP is Necessary for Motility, Biofilm Formation, Exoenzyme Production, and Virulence of Xanthomonas citri Subsp. citri on Citrus Plants
Chudan Wei, Tian Ding, Changqing Chang, Chengpeng Yu, Xingwei Li, Qiongguang Liu
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The ColRS-Regulated Membrane Protein Gene XAC1347 Is Involved in Copper Homeostasis and hrp Gene Expression in Xanthomonas citri subsp. citri
Xiaojing Fan, Jing Guo, Yinghui Zhou, Tao Zhuo, Xun Hu, Huasong Zou
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Identification of New Genes Related to Virulence of <i>Xanthomonas axonopodis</i> Pv. <i>Citri</i> during Citrus Host Interactions
Cristiano B. Ferreira, Leandro M. Moreira, Joice B. Brigati, Lonjoré L. Lima, Jesus A. Ferro, Maria I. T. Ferro, Julio C. F. de Oliveira
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Identification of an Extracellular Endoglucanase That Is Required for Full Virulence in Xanthomonas citri subsp. citri
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The sigma 54 genes rpoN1 and rpoN2 of Xanthomonas citri subsp. citri play different roles in virulence, nutrient utilization and cell motility
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Genome sequence analysis of potential probiotic strain Leuconostoc lactis EFEL005 isolated from kimchi: Jin Seok Moon , Hye Sun Choi , So Yeon Shin , Sol Ji Noh , Che Ok Jeon , Nam Soo Han; J. Microbiol. 2015;53(5):337-342. Published online May 3, 2015; DOI: https://doi.org/10.1007/s12275-015-5090-8

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Abstract

Leuconostoc lactis EFEL005 (KACC 91922) isolated from kimchi showed promising probiotic attributes; resistance against acid and bile salts, absence of transferable genes for antibiotic resistance, broad utilization of prebiotics, and no hemolytic activity. To expand our understanding of the species, we generated a draft genome sequence of the strain and analyzed its genomic features related to the aforementioned probiotic properties. Genome assembly resulted in 35 contigs, and the draft genome has 1,688,202 base pairs (bp) with a G+C content of 43.43%, containing 1,644 protein-coding genes and 50 RNA genes. The average nucleotide identity analysis showed high homology (≥ 96%) to the type strain L. lactis KCTC3528, but low homology (≤ 95%) to L. lactis KCTC3773 (formerly L. argentinum). Genomic analysis revealed the presence of various genes for sucrose metabolism (glucansucrases, invertases, sucrose phosphorylases, and mannitol dehydrogenase), acid tolerance (F1F0 ATPases, cation transport ATPase, branched-chain amino acid permease, and lysine decarboxylase), vancomycin response regulator, and antibacterial peptide (Lactacin F). No gene for production of biogenic amines (histamine and tyramine) was found. This report will facilitate the understanding of probiotic properties of this strain as a starter for fermented foods.

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ODFM, an omics data resource from microorganisms associated with fermented foods
Tae Woong Whon, Seung Woo Ahn, Sungjin Yang, Joon Yong Kim, Yeon Bee Kim, Yujin Kim, Ji-Man Hong, Hojin Jung, Yoon-E Choi, Se Hee Lee, Seong Woon Roh
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Se Hee Lee, Tae Woong Whon, Seong Woon Roh, Che Ok Jeon
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Bao Le, Seung-Hwan Yang
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Diana De Santis, Giuseppina Giacinti, Giulia Chemello, Maria Teresa Frangipane
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Lactobacillus allii sp. nov. isolated from scallion kimchi
Min Young Jung, Se Hee Lee, Moeun Lee, Jung Hee Song, Ji Yoon Chang
International Journal of Systematic and Evolutionary Microbiology .2017; 67(12): 4936. CrossRef
Genomic Analysis of Vulcanisaeta thermophila Type Strain CBA1501T Isolated from Solfataric Soil
Joon Yong Kim, Kyung June Yim, Hye Seon Song, Yeon Bee Kim, Dong-Gi Lee, Joseph Kwon, Kyung-Seo Oh, Seong Woon Roh
Frontiers in Microbiology.2016;[Epub] CrossRef
Immunomodulatory effects of Leuconostoc citreum EFEL2061 isolated from kimchi, a traditional Korean food, on the Th2 type-dominant immune response in vitro and in vivo
Hee Kang, Jin Seok Moon, Mi-Gi Lee, Nam Soo Han
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Ozlem Ates
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Phosphorylation of the nucleocapsid protein of Hantaan virus by casein kinase II: Jeong-Joong Yoon , Yun-Tai Lee , Hin Chu , Seung-yeol Son , Manbok Kim; J. Microbiol. 2015;53(5):343-347. Published online May 3, 2015; DOI: https://doi.org/10.1007/s12275-015-5095-3

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Abstract

Hantaanvirus (HTNV) is the prototype of the genus Hantavirus, which belongs to the family Bunyaviridae. Hantaviruses are carried and transmitted by rodents and are known to cause two serious disease syndromes in humans i.e., hemorrhagic fever with renal syndrome (HFRS) and the hantavirus pulmonary syndrome (HPS). HTNV is an enveloped virus that contains a tripartite genome consisting of three negative-sense RNA segments (L, M, S), and the S and M segment of HTNV, respectively, encode the viral nucleocapsid protein (NP) and envelope glycoproteins. Possible phosphorylation motifs of casein kinase II (CKII) and protein kinase C (PKC) were identified in HTNV NP through bioinformatics searches. Sucrose gradient SDS-PAGE analysis indicated that dephosphorylated HTNV NP migrated faster than non-dephosphorylated NP, suggesting that HTNV NP is phosphorylated in infected Vero E6 cells. Immunoblot anaylsis of HTNV particles with anti-phosphoserine antibody and anti-phosphothreonine antibody after immunoprecipitation showed that viral particles are readily phosphorylated at threonine residues. In vitro kinase assay further showed that HTNV NP is phosphorylated by CK II, but not by PKC. Full length or truncated HTNV NPs expressed in E. coli were phosphorylated in vitro by CKII suggesting that phosphorylation may occur in vivo at multiple sites. Site specific mutagenesis studies suggest that HTNV NP phosphorylation might occur at unknown sites excluding the site-directly mutagenized locations. Taken together, HTNV NP can be phosphorylated mainly at threonine residues in vivo by CK II treatment.

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Protein kinase CK2: a potential therapeutic target for diverse human diseases
Christian Borgo, Claudio D’Amore, Stefania Sarno, Mauro Salvi, Maria Ruzzene
Signal Transduction and Targeted Therapy.2021;[Epub] CrossRef
Unique Interferon Pathway Regulation by the Andes Virus Nucleocapsid Protein Is Conferred by Phosphorylation of Serine 386
Matthew J. Simons, Elena E. Gorbunova, Erich R. Mackow, Susana López
Journal of Virology.2019;[Epub] CrossRef

Identification of Porcine Endogenous Retrovirus (PERV) packaging sequence and development of PERV packaging viral vector system: Jiwon Choi , Hoon-mi Kim , Jong Kwang Yoon , Yeondong Cho , Hee-Jung Lee , Kang Chang Kim , Chang-Kyu Kim , Gye-Woong Kim , Young Bong Kim; J. Microbiol. 2015;53(5):348-353. Published online May 3, 2015; DOI: https://doi.org/10.1007/s12275-015-5134-0

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Abstract

Studies of the retroviruses have focused on the specific interaction of the nucleocapsid protein with a packaging signal in the viral RNA as important for this selectivity, but the packaging signal in porcine endogenous retrovirus (PERV) has not been defined. Herein, we identified and analyzed this packaging signal in PERV and found hairpin structures with conserved tetranucleotides in their loops and nucleocapsid recognition sequences; both of which are key elements in the viral packaging signal of MLV. We evaluated packaging efficiency of sequence variants isolated from viral and proviral integrated genomes. All viral packaging sequences (Ψ) were identical, while five distinct packaging sequences were identified from proviral sources. One proviral sequence (Ψ1) was identical to that of the viral Ψ and had the highest packaging efficiency. Three variants (Ψ2, Ψ3, Ψ4) maintained key elements of the viral packaging signal, but had nucleotide replacements and consequently demonstrated reduced packaging efficiency. Despite of the same overall hairpin structure, the proviral variant (Ψ5) had only one GACG sequence in the hairpin loop and showed the lowest packaging efficiency other than ΔΨ, in which the essential packaging sequence was removed. This result, thus, defined the packaging sequences in PERV and emphasized the importance of nucleotide sequence and RNA structure in the determination of packaging efficiency. In addition, we demonstrate efficient infection and gene expression from the PERVbased viral vector, which may serve as a novel alternative to current retroviral expression systems.

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Porcine Endogenous Retrovirus (PERV) – Molecular Structure and Replication Strategy in the Context of Retroviral Infection Risk of Human Cells
Krzysztof Łopata, Emilia Wojdas, Roman Nowak, Paweł Łopata, Urszula Mazurek
Frontiers in Microbiology.2018;[Epub] CrossRef

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