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Pycnogenol reduces the expression of P. aeruginosa T3SS and inflammatory response in NCI-H292 cells
Seung-Ho Kim, Da Yun Seo, Sang-Bae Han, Un-Hwan Ha, Ji-Won Park, Kyung-Seop Ahn
J. Microbiol. 2025;63(10):2503004.   Published online September 19, 2025
DOI: https://doi.org/10.71150/jm.2503004
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AbstractAbstract PDFSupplementary Material

Nosocomial infections caused by Pseudomonas aeruginosa (P. aeruginosa) have become increasingly common, particularly among immunocompromised individuals, who experience high mortality rates and prolonged treatment durations due to the limited availability of effective therapies. In this study, we screened for anti-ExoS compounds targeting P. aeruginosa and identified pycnogenol (PYC) as a potent inhibitor of the type III secretion system (T3SS), a major virulence mechanism responsible for the translocation of effectors such as ExoS. Using ELISA, western blotting, and real-time PCR analyses in both P. aeruginosa and infected H292 cells, we found that PYC significantly reduced T3SS activity. Mechanistically, PYC suppressed the transcription of T3SS-related genes by downregulating exsA expression in P. aeruginosa. Furthermore, pretreatment with PYC attenuated the cytotoxic effects and reduced the expression of proinflammatory cytokines, including interleukin-1β (IL-1β), interleukin-6 (IL-6), interleukin-8 (IL-8), and interleukin-18 (IL-18), in P. aeruginosa-infected H292 cells. These effects were associated with the inhibition of NF-κB signaling and inflammasome activation. Taken together, our findings suggest that PYC may serve as a promising therapeutic candidate against P. aeruginosa infections by targeting T3SS-mediated virulence and modulating host inflammatory responses.

Alizarin, which reduces ExoS, attenuates inflammation by P. aeruginosa in H292 cells
Seung-Ho Kim, Hye In Ahn, Jae-Hoon Oh, Da Yun Seo, Jung-Hee Kim, Ok-kyoung Kwon, Ji-Won Park, Kyung-Seop Ahn
J. Microbiol. 2025;63(5):e2411012.   Published online May 27, 2025
DOI: https://doi.org/10.71150/jm.2411012
  • 1,440 View
  • 31 Download
  • 1 Web of Science
  • 1 Crossref
AbstractAbstract PDF

Pseudomonas aeruginosa (P. aeruginosa) is resistant to several drugs as well as antibiotics and is thus classified as multidrug resistant and extensively drug resistant. These bacteria have a secretion system called the "type 3 secretion system (T3SS)", which facilitates infection by delivering an effector protein. ExoenzymeS (ExoS) is known to induce cell death and activate caspase-1. In particular, patients infected with P. aeruginosa develop diseases associated with high mortality, such as pneumonia, because no drug targets an ExoS or T3SS. We selected natural compounds to treat T3SS-mediated pneumonia and chose alizarin, a red dye. We confirmed the effects of alizarin on T3SS by bacterial PCR and ELISA. It was confirmed that alizarin regulates ExoS by inhibiting exsA but also popD and pscF. Furthermore, in infected H292 cells, it not only attenuates inflammation by inhibiting lipopolysaccharide (LPS)-induced phosphorylation of nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) p65 but also interferes with the level of ExoS delivered into the host and modulates caspase-1. We confirmed this result and determined that it led to decreases in proinflammatory cytokines such as Interleukin-1beta (IL-1β), Interleukin-6 (IL-6), and Interleukin-18 (IL-18). Therefore, we suggest that alizarin is a suitable drug for treating pneumonia caused by P. aeruginosa because it helps to attenuate inflammation by regulating T3SS and NF-κB signaling.

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  • Beyond pathogenicity: applications of the type III secretion system (T3SS) of Pseudomonas aeruginosa
    Tianqi Su, Lin Zhang, Jie Shen, Danyu Qian, Yulei Guo, Zhenpeng Li
    Frontiers in Microbiology.2025;[Epub]     CrossRef
Protocol
A guide to genome mining and genetic manipulation of biosynthetic gene clusters in Streptomyces
Heonjun Jeong, YeonU Choe, Jiyoon Nam, Yeon Hee Ban
J. Microbiol. 2025;63(4):e2409026.   Published online April 29, 2025
DOI: https://doi.org/10.71150/jm.2409026
  • 8,573 View
  • 270 Download
  • 1 Crossref
AbstractAbstract PDF

Streptomyces are a crucial source of bioactive secondary metabolites with significant clinical applications. Recent studies of bacterial and metagenome-assembled genomes have revealed that Streptomyces harbors a substantial number of uncharacterized silent secondary metabolite biosynthetic gene clusters (BGCs). These BGCs represent a vast diversity of biosynthetic pathways for natural product synthesis, indicating significant untapped potential for discovering new metabolites. To exploit this potential, genome mining using comprehensive strategies that leverage extensive genomic databases can be conducted. By linking BGCs to their encoded products and integrating genetic manipulation techniques, researchers can greatly enhance the identification of new secondary metabolites with therapeutic relevance. In this context, we present a step-by-step guide for using the antiSMASH pipeline to identify secondary metabolite-coding BGCs within the complete genome of a novel Streptomyces strain. This protocol also outlines gene manipulation methods that can be applied to Streptomyces to activate cryptic clusters of interest and validate the functions of biosynthetic genes. By following these guidelines, researchers can pave the way for discovering and characterizing valuable natural products.

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  • A review of geomicrobial bioprospecting strategies for novel therapeutic discovery from Earth’s extreme environments
    Trideep Saikia, Sandipan Das
    Discover Geoscience.2025;[Epub]     CrossRef
Research Article
Enoxacin adversely affects Salmonella enterica virulence and host pathogenesis through interference with type III secretion system type II (T3SS-II) and disruption of translocation of Salmonella Pathogenicity Island-2 (SPI2) effectors
El-Sayed Khafagy, Gamal A. Soliman, Maged S. Abdel-Kader, Mahmoud M. Bendary, Wael A. H. Hegazy, Momen Askoura
J. Microbiol. 2025;63(2):e2410015.   Published online February 27, 2025
DOI: https://doi.org/10.71150/jm.2410015
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AbstractAbstract PDF

Salmonella enterica is a clinically significant oro-fecal pathogen that causes a wide variety of illnesses and can lead to epidemics. S. enterica expresses a lot of virulence factors that enhance its pathogenesis in host. For instance, S. enterica employs a type three secretion system (T3SS) to translocate a wide array of effector proteins that could change the surrounding niche ensuring suitable conditions for the thrive of Salmonella infection. Many antimicrobials have been recently introduced to overcome the annoying bacterial resistance to antibiotics. Enoxacin is member of the second-generation quinolones that possesses a considerable activity against S. enterica. The present study aimed to evaluate the effect of enoxacin at sub-minimum inhibitory concentration (sub-MIC) on S. enterica virulence capability and pathogenesis in host. Enoxacin at sub-MIC significantly diminished both Salmonella invasion and intracellular replication within the host cells. The observed inhibitory effect of enoxacin on S. enterica internalization could be attributed to its ability to interfere with translocation of the T3SS effector proteins. These results were further confirmed by the finding that enoxacin at sub-MIC down-regulated the expression of the genes encoding for T3SS-type II (T3SS-II). Moreover, enoxacin at sub-MIC lessened bacterial adhesion to abiotic surface and biofilm formation which indicates a potential anti-virulence activity. Importantly, in vivo results showed a significant ability of enoxacin to protect mice against S. enterica infection and decreased bacterial colonization within animal tissues. In nutshell, current findings shed light on an additional mechanism of enoxacin at sub-MIC by interfering with Salmonella intracellular replication. The outcomes presented herein could be further invested in conquering bacterial resistance and open the door for additional effective clinical applications.

Journal Articles
Comparative Secretory Efficiency of Two Chitosanase Signal Peptides from Bacillus subtilis in Escherichia coli
Tae-Yang Eom, Yehui Gang, Youngdeuk Lee, Yoon-Hyeok Kang, Eunyoung Jo, Svini Dileepa Marasinghe, Heung Sik Park, Gun-Hoo Park, Chulhong Oh
J. Microbiol. 2024;62(12):1155-1164.   Published online November 25, 2024
DOI: https://doi.org/10.1007/s12275-024-00186-1
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  • 1 Web of Science
  • 1 Crossref
AbstractAbstract PDF
The production of recombinant proteins in Escherichia coli is often challenged by cytoplasmic expression due to proteolytic degradation and inclusion body formation. Extracellular expression can overcome these problems by simplifying downstream processing and improving protein yields. This study aims to compare the efficiency of two Bacillus subtilis chitosanase signal peptides in mediating extracellular secretion in E. coli. We identified a naturally occurring mutant signal peptide (mCsn2-SP) from B. subtilis CH2 chitosanase (CH2CSN), which is characterized by a deletion of six amino acids in the N-region relative to the signal peptide (Csn1-SP) from B. subtilis CH1 chitosanase (CH1CSN). The CH1CSN and CH2CSN genes were cloned into the pET-11a vector and protein secretion was evaluated in E. coli BL21(DE3) host cells. Expression was induced with 0.1 mM and 1 mM isopropyl β-D-1-thiogalactopyranoside (IPTG) at 30 °C for one and three days. CH2CSN showed higher secretion levels compared to CH1CSN under all experimental conditions, especially with 0.1 mM IPTG induction for 3 days, which resulted in a 2.37-fold increase in secretion. Furthermore, it was demonstrated that mCsn2-SP is capable of secreting human Cu,Zn-superoxide dismutase (hSOD) in E. coli BL21(DE3) and successfully translocating it to the periplasmic region. This study represents the inaugural investigation into the utilisation of a naturally modified signal peptide, thereby corroborating the assertion that signal peptide deletion variants can influence protein secretion efficiency. Furthermore, the findings substantiate the proposition that such variants can serve as a viable alternative for the secretion of heterologous proteins in E. coli.

Citations

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  • Signal Peptides: From Molecular Mechanisms to Applications in Protein and Vaccine Engineering
    Shuai Zhang, Zhihui He, Hui Wang, Jingbo Zhai
    Biomolecules.2025; 15(6): 897.     CrossRef
Deletion of IRC19 Causes Defects in DNA Double-Strand Break Repair Pathways in Saccharomyces cerevisiae
Ju-Hee Choi, Oyungoo Bayarmagnai, Sung-Ho Bae
J. Microbiol. 2024;62(9):749-758.   Published online July 12, 2024
DOI: https://doi.org/10.1007/s12275-024-00152-x
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AbstractAbstract PDF
DNA double-strand break (DSB) repair is a fundamental cellular process crucial for maintaining genome stability, with homologous recombination and non-homologous end joining as the primary mechanisms, and various alternative pathways such as single-strand annealing (SSA) and microhomology-mediated end joining also playing significant roles under specific conditions. IRC genes were previously identified as part of a group of genes associated with increased levels of Rad52 foci in Saccharomyces cerevisiae. In this study, we investigated the effects of IRC gene mutations on DSB repair, focusing on uncharacterized IRC10, 19, 21, 22, 23, and 24. Gene conversion (GC) assay revealed that irc10Δ, 22Δ, 23Δ, and 24Δ mutants displayed modest increases in GC frequencies, while irc19Δ and irc21Δ mutants exhibited significant reductions. Further investigation revealed that deletion mutations in URA3 were not generated in irc19Δ mutant cells following HO-induced DSBs. Additionally, irc19Δ significantly reduced frequency of SSA, and a synergistic interaction between irc19Δ and rad52Δ was observed in DSB repair via SSA. Assays to determine the choice of DSB repair pathways indicated that Irc19 is necessary for generating both GC and deletion products. Overall, these results suggest a potential role of Irc19 in DSB repair pathways, particularly in end resection process.
Vaccine Development for Severe Fever with Thrombocytopenia Syndrome Virus in Dogs
Seok-Chan Park, Da-Eun Jeong, Sun-Woo Han, Joon-Seok Chae, Joo-Yong Lee, Hyun-Sook Kim, Bumseok Kim, Jun-Gu Kang
J. Microbiol. 2024;62(4):327-335.   Published online April 18, 2024
DOI: https://doi.org/10.1007/s12275-024-00119-y
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  • 5 Web of Science
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AbstractAbstract PDF
Severe fever with thrombocytopenia syndrome (SFTS) is a life-threatening viral zoonosis. The causative agent of this disease is the Dabie bandavirus, which is usually known as the SFTS virus (SFTSV). Although the role of vertebrates in SFTSV transmission to humans remains uncertain, some reports have suggested that dogs could potentially transmit SFTSV to humans. Consequently, preventive measures against SFTSV in dogs are urgently needed. In the present study, dogs were immunized three times at two-week intervals with formaldehyde-inactivated SFTSV with two types of adjuvants. SFTSV (KCD46) was injected into all dogs two weeks after the final immunization. Control dogs showed viremia from 2 to 4 days post infection (dpi), and displayed white pulp atrophy in the spleen, along with a high level of terminal deoxynucleotidyl transferase-mediated dUTP nick-end labelling assay (TUNEL) positive area. However, the inactivated SFTSV vaccine groups exhibited rare pathological changes and significantly reduced TUNEL positive areas in the spleen. Furthermore, SFTSV viral loads were not detected at any of the tested dpi. Our results indicate that both adjuvants can be safely used in combination with an inactivated SFTSV formulation to induce strong neutralizing antibodies. Inactivated SFTSV vaccines effectively prevent pathogenicity and viremia in dogs infected with SFTSV. In conclusion, our study highlighted the potential of inactivated SFTSV vaccination for SFTSV control in dogs.

Citations

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  • The immunogenicity and protection efficacy evaluation of mRNA vaccine candidate for severe fever with thrombocytopenia syndrome in mice
    Da-Eun Jeong, Jack Yoon, Baek Kim, Jun-Gu Kang, Abdallah M. Samy
    PLOS Neglected Tropical Diseases.2025; 19(4): e0012999.     CrossRef
  • Efficient and modular reverse genetics system for rapid generation of recombinant severe acute respiratory syndrome coronavirus 2
    Sojung Bae, Jinjong Myoung
    Journal of Microbiology.2025; 63(7): e2504015.     CrossRef
  • Current status of severe fever with thrombocytopenia syndrome in China (Review)
    Hao Sun, Quanman Hu, Saiwei Lu, Yanyan Yang, Li Zhang, Jinzhao Long, Yuefei Jin, Haiyan Yang, Shuaiyin Chen, Guangcai Duan
    International Journal of Molecular Medicine.2025; 56(5): 1.     CrossRef
  • Domain-Specific Impacts of Spike Protein Mutations on Infectivity and Antibody Escape in SARS-CoV-2 Omicron BA.1
    Tae-Hun Kim, Sojung Bae, Jinjong Myoung
    Journal of Microbiology and Biotechnology.2025;[Epub]     CrossRef
Review
Temperature Matters: Bacterial Response to Temperature Change
Seongjoon Moon , Soojeong Ham , Juwon Jeong , Heechan Ku , Hyunhee Kim , Changhan Lee
J. Microbiol. 2023;61(3):343-357.   Published online April 3, 2023
DOI: https://doi.org/10.1007/s12275-023-00031-x
  • 1,355 View
  • 10 Download
  • 47 Web of Science
  • 49 Crossref
AbstractAbstract PDF
Temperature is one of the most important factors in all living organisms for survival. Being a unicellular organism, bacterium requires sensitive sensing and defense mechanisms to tolerate changes in temperature. During a temperature shift, the structure and composition of various cellular molecules including nucleic acids, proteins, and membranes are affected. In addition, numerous genes are induced during heat or cold shocks to overcome the cellular stresses, which are known as heat- and cold-shock proteins. In this review, we describe the cellular phenomena that occur with temperature change and bacterial responses from a molecular perspective, mainly in Escherichia coli.

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    A. Lara-Moreno, A. Vargas-Ordóñez, J. Villaverde, F. Madrid, J.D. Carlier, J.L. Santos, E. Alonso, E. Morillo
    Journal of Hazardous Materials.2024; 480: 136128.     CrossRef
  • Dietary supplementation with host-associated low-temperature potential probiotics improves the growth, immunity, digestive enzyme activity, and intestinal microbial population of olive flounder (Paralichthys olivaceus)
    Su-Jeong Lee, Young-Sun Lee, Da-In Noh, Md Tawheed Hasan, Sang Woo Hur, Seunghan Lee, Seong-Mok Jeong, Kang-Woong Kim, Jong Min Lee, Eun-Woo Lee, Won Je Jang
    Aquaculture Reports.2024; 36: 102128.     CrossRef
  • Global biochemical profiling of fast-growing Antarctic bacteria isolated from meltwater ponds by high-throughput FTIR spectroscopy
    Volha Akulava, Valeria Tafintseva, Uladzislau Blazhko, Achim Kohler, Uladzislau Miamin, Leonid Valentovich, Volha Shapaval, Marcos Pileggi
    PLOS ONE.2024; 19(6): e0303298.     CrossRef
  • Phyletic patterns of bacterial growth temperature in Pseudomonas and Paenibacillus reveal gradual and sporadic evolution towards cold adaptation
    Kihyun Lee, Seong-Hyeon Kim, Seongjoon Moon, Sangha Kim, Changhan Lee
    ISME Communications.2024;[Epub]     CrossRef
  • Bacterial Regulatory Mechanisms for the Control of Cellular Processes: Simple Organisms’ Complex Regulation
    Jin-Won Lee
    Journal of Microbiology.2023; 61(3): 273.     CrossRef
Journal Article
Relaxed Cleavage Specificity of Hyperactive Variants of Escherichia coli RNase E on RNA I
Dayeong Bae , Hana Hyeon , Eunkyoung Shin , Ji&# , Kangseok Lee
J. Microbiol. 2023;61(2):211-220.   Published online February 22, 2023
DOI: https://doi.org/10.1007/s12275-023-00013-z
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AbstractAbstract PDF
RNase E is an essential enzyme in Escherichia coli. The cleavage site of this single-stranded specific endoribonuclease is well-characterized in many RNA substrates. Here, we report that the upregulation of RNase E cleavage activity by a mutation that affects either RNA binding (Q36R) or enzyme multimerization (E429G) was accompanied by relaxed cleavage specificity. Both mutations led to enhanced RNase E cleavage in RNA I, an antisense RNA of ColE1-type plasmid replication, at a major site and other cryptic sites. Expression of a truncated RNA I with a major RNase E cleavage site deletion at the 5′-end (RNA I- 5) resulted in an approximately twofold increase in the steady-state levels of RNA I- 5 and the copy number of ColE1-type plasmid in E. coli cells expressing wild-type or variant RNase E compared to those expressing RNA I. These
results
indicate that RNA I- 5 does not efficiently function as an antisense RNA despite having a triphosphate group at the 5′-end, which protects the RNA from ribonuclease attack. Our study suggests that increased cleavage rates of RNase E lead to relaxed cleavage specificity on RNA I and the inability of the cleavage product of RNA I as an antisense regulator in vivo does not stem from its instability by having 5′-monophosphorylated end.

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  • Engineering an Escherichia coli based in vivo mRNA manufacturing platform
    Edward Curry, George Muir, Jixin Qu, Zoltán Kis, Martyn Hulley, Adam Brown
    Biotechnology and Bioengineering.2024; 121(6): 1912.     CrossRef
Meta-Analysis
Proposal of a health gut microbiome index based on a meta-analysis of Korean and global population datasets
Hyun-Seok Oh , Uigi Min , Hyejin Jang , Namil Kim , Jeongmin Lim , Mauricio Chalita , Jongsik Chun
J. Microbiol. 2022;60(5):533-549.   Published online March 31, 2022
DOI: https://doi.org/10.1007/s12275-022-1526-0
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AbstractAbstract PDF
The disruption of the human gut microbiota has been linked to host health conditions, including various diseases. However, no reliable index for measuring and predicting a healthy microbiome is currently available. Here, the sequencing data of 1,663 Koreans were obtained from three independent studies. Furthermore, we pooled 3,490 samples from public databases and analyzed a total of 5,153 fecal samples. First, we analyzed Korean gut microbiome covariates to determine the influence of lifestyle on variation in the gut microbiota. Next, patterns of microbiota variations across geographical locations and disease statuses were confirmed using a global cohort and disease data. Based on comprehensive comparative analysis, we were able to define three enterotypes among Korean cohorts, namely, Prevotella type, Bacteroides type, and outlier type. By a thorough categorization of dysbiosis and the evaluation of microbial characteristics using multiple datasets, we identified a wide spectrum of accuracy levels in classifying health and disease states. Using the observed microbiome patterns, we devised an index named the gut microbiome index (GMI) that could consistently predict health conditions from human gut microbiome data. Compared to ecological metrics, the microbial marker index, and machine learning approaches, GMI distinguished between healthy and non-healthy individuals with a higher accuracy across various datasets. Thus, this study proposes a potential index to measure health status of gut microbiome that is verified from multiethnic data of various diseases, and we expect this model to facilitate further clinical application of gut microbiota data in future.

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  • Methodology for Assessing Patient Centricity and Data Integrity in Clinical Trials With Decentralized Elements: A Pilot Trial on Mastic Gum
    Jiyeon Park, Ki Young Huh, Jae‐Yong Chung, Kyung‐Sang Yu
    Clinical and Translational Science.2025;[Epub]     CrossRef
  • A comparison of the prevalence of respiratory pathogens and opportunistic respiratory pathogenic profile of ‘clean’ and ‘unclean’ removable dental prostheses
    Tong Wah Lim, Shi Huang, Yufeng Zhang, Michael Francis Burrow, Colman McGrath
    Journal of Dentistry.2024; 145: 104968.     CrossRef
  • Characterization of pathogenic microbiome on removable prostheses with different levels of cleanliness using 2bRAD-M metagenomic sequencing
    Tong Wah Lim, Shi Huang, Yuesong Jiang, Yufeng Zhang, Michael Francis Burrow, Colman McGrath
    Journal of Oral Microbiology.2024;[Epub]     CrossRef
  • Gut microbial signatures in clinically stable ulcerative colitis according to the mucosal state and associated symptoms
    Soyoung Kim, Yeonjae Jung, Seung Bum Lee, Hyun‐Seok Oh, Sung Noh Hong
    Journal of Gastroenterology and Hepatology.2024; 39(2): 319.     CrossRef
  • Difference in gut microbial dysbiotic patterns between body-first and brain-first Parkinson's disease
    Don Gueu Park, Woorim Kang, In-Ja Shin, Mauricio Chalita, Hyun-Seok Oh, Dong-Wook Hyun, Hyun Kim, Jongsik Chun, Young-Sil An, Eun Jeong Lee, Jung Han Yoon
    Neurobiology of Disease.2024; 201: 106655.     CrossRef
  • Should Routine Diagnostics Implement Gut Microbiota Analysis?
    Giuseppe Guido Maria Scarlata, Ludovico Abenavoli
    The International Journal of Gastroenterology and Hepatology Diseases.2024;[Epub]     CrossRef
  • Feasibility study for a fully decentralized clinical trial in participants with functional constipation symptoms
    Ki Young Huh, Woo Kyung Chung, Jiyeon Park, SeungHwan Lee, Min‐Gul Kim, Jaeseong Oh, Kyung‐Sang Yu
    Clinical and Translational Science.2023; 16(11): 2177.     CrossRef
  • Predicting Personalized Responses to Dietary Fiber Interventions: Opportunities for Modulation of the Gut Microbiome to Improve Health
    Car Reen Kok, Devin Rose, Robert Hutkins
    Annual Review of Food Science and Technology.2023; 14(1): 157.     CrossRef
  • Effects of the multidomain intervention with nutritional supplements on cognition and gut microbiome in early symptomatic Alzheimer’s disease: a randomized controlled trial
    Eun Hye Lee, Geon Ha Kim, Hee Kyung Park, Hae Jin Kang, Yoo Kyoung Park, Hye Ah Lee, Chang Hyung Hong, So Young Moon, Woorim Kang, Hyun-Seok Oh, Hai-Jeon Yoon, Seong Hye Choi, Jee Hyang Jeong
    Frontiers in Aging Neuroscience.2023;[Epub]     CrossRef
  • Fecal microbial signatures of healthy Han individuals from three bio-geographical zones in Guangdong
    Litao Huang, Liting Deng, Changhui Liu, Enping Huang, Xiaolong Han, Cheng Xiao, Xiaomin Liang, Huilin Sun, Chao Liu, Ling Chen
    Frontiers in Microbiology.2022;[Epub]     CrossRef
Journal Articles
The novel antifungal agent AB-22 displays in vitro activity against hyphal growth and biofilm formation in Candida albicans and potency for treating systemic candidiasis
Kyung-Tae Lee , Dong-Gi Lee , Ji Won Choi , Jong-Hyun Park , Ki Duk Park , Jong-Seung Lee , Yong-Sun Bahn
J. Microbiol. 2022;60(4):438-443.   Published online March 14, 2022
DOI: https://doi.org/10.1007/s12275-022-2016-0
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AbstractAbstract PDF
Systemic candidiasis, which is mainly caused by Candida albicans, is a serious acute fungal infection in the clinical setting. In a previous study, we reported that compound 22h (designated as AB-22 in this study), a vinyl sulfate compound, is a fast-acting fungicidal agent against a broad spectrum of fungal pathogens. In this study, we aimed to further analyze the in vitro and in vivo efficacy of AB-22 against filamentation, biofilm formation, and virulence of C. albicans. Under in vitro hyphal growth-inducing condition, AB-22 effectively inhibited germ tube formation and hyphal growth, which are required for the initiation of biofilm formation. Indeed, AB-22 significantly suppressed C. albicans biofilm formation in a dose-dependent manner. Moreover, AB-22 treatment inhibited the normal induction of ALS3, HWP1, and ECE1, which are all required for hyphal transition in C. albicans. Furthermore, AB-22 treatment increased the survival of mice systemically infected with C. albicans. In conclusion, in addition to its fungicidal activity, AB-22 inhibits filamentation and biofilm formation in C. albicans, which could collectively contribute to its potent in vivo efficacy against systemic candidiasis.

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  • Preparation and analysis of quinoa active protein (QAP) and its mechanism of inhibiting Candida albicans from a transcriptome perspective
    Xufei Zhang, Chunmei Zheng, Wenxuan Ge, Xueying Li, Xiuzhang Wang, Yanxia Sun, Xiaoyong Wu
    PeerJ.2025; 13: e18961.     CrossRef
  • Inhibition of candidalysin production by methoxy-apo-enterobactin from Streptomyces ambofaciens CJD34 as a novel antifungal strategy against Candida albicans
    Eui-Seong Kim, Hyeongju Jeong, Mustansir Abbas, Soohyun Um, Juntack Oh, Kyuho Moon, Kyung-Tae Lee
    Journal of Microbiology.2025; 63(6): e2504019.     CrossRef
The role of Jacalin-related lectin gene AOL_s00083g511 in the development and pathogenicity of the nematophagous fungus Arthrobotrys oligospora
Xinyuan Dong , Jiali Si , Guanghui Zhang , Zhen Shen , Li Zhang , Kangliang Sheng , Jingmin Wang , Xiaowei Kong , Xiangdong Zha , Yongzhong Wang
J. Microbiol. 2021;59(8):736-745.   Published online July 5, 2021
DOI: https://doi.org/10.1007/s12275-021-1029-4
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AbstractAbstract PDF
Arthrobotrys oligospora is a model species of nematophagous fungi and has great potential for the biological control of nematode diseases. Lectin is a protein that binds to carbohydrates and their complexes with high specificity, which mediates recognition events in various physiological and pathological processes. This study aimed to investigate the role of the Jacalin-related lectin (JRL) gene, AOL_s00083g511, in A. oligospora development. Through a homology recombination approach, we obtained the AOL_s00083g511 knockout mutant strain (Δg511). Next, the biological characteristics of the Δg511 mutant strain, including growth rate, conidia germination rate, adaptation to environmental stresses, and nematocidal activity, were compared with those of the wild-type (WT) strain. The results showed that the JRL gene AOL_ s00083g511 did not affect fungal growth, conidia germination, 3D-trap formation, and the ability of A. oligospora to prey on nematodes significantly. We speculate that this phenomenon may be caused by a loss of the key β1–β2 loops in the AOL_ s00083g511-encoded JRL domain and an intrinsic genetic compensation of AOL_s00083g511 in this fungus. The growth rates of both strains on high salt or surfactant media were similar; however, in the strong oxidation medium, the growth rate of the Δg511 mutant was significantly lower than that of the WT strain, indicating that AOL_s00083g511 might play a role in oxidative stress resistance. These findings provide a basis for further analysis of the related functions of the JRL gene in A. oligospora and their potential roles in the biological control of nematodes in the future.

Citations

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  • Function discovery of a non-ribosomal peptide synthetase-like encoding gene in the nematode-trapping fungus Arthrobotrys oligospora
    Tiantian Gu, Hengqian Lu, Huiwen Liu, Guanghui Zhang, Yongzhong Wang
    Frontiers in Microbiology.2023;[Epub]     CrossRef
  • The fucose-specific lectin gene AOL_s00054g276 affects trap formation and nematocidal activity of the nematophagous fungus Arthrobotrys oligospora
    Jiali Si, Xinyuan Dong, Guanghui Zhang, Hengqian Lu, Kaijing Tang, Li Zhang, Xiaowei Kong, Kangliang Sheng, Jingmin Wang, Xiangdong Zha, Yongzhong Wang
    FEMS Microbiology Letters.2022;[Epub]     CrossRef
  • Phospholipase C (AoPLC2) regulates mycelial development, trap morphogenesis, and pathogenicity of the nematode-trapping fungus Arthrobotrys oligospora
    Meihua Xie, Ni Ma, Na Bai, Meichen Zhu, Ke-Qin Zhang, Jinkui Yang
    Journal of Applied Microbiology.2022; 132(3): 2144.     CrossRef
Inferences in microbial structural signatures of acne microbiome and mycobiome
Jubin Kim , Taehun Park , Hye-Jin Kim , Susun An , Woo Jun Sul
J. Microbiol. 2021;59(4):369-375.   Published online February 10, 2021
DOI: https://doi.org/10.1007/s12275-021-0647-1
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AbstractAbstract PDF
Acne vulgaris, commonly known as acne, is the most common skin disorder and a multifactorial disease of the sebaceous gland. Although the pathophysiology of acne is still unclear, bacterial and fungal factors are known to be involved in. This study aimed to investigate whether the microbiomes and mycobiomes of acne patients are distinct from those of healthy subjects and to identify the structural signatures of microbiomes related to acne vulgaris. A total of 33 Korean female subjects were recruited (Acne group, n = 17; Healthy group, n = 16), and microbiome samples were collected swabbing the forehead and right cheek. To characterize the fungal and bacterial communities, 16S rRNA V4–V5 and ITS1 region, respectively, were sequenced and analysed using Qiime2. There were no significant differences in alpha and beta diversities of microbiomes between the Acne and Healthy groups. In comparison with the ratio of Cutibacterium to Staphylococcus, the acne patients had higher abundance of Staphylococcus compared to Cutibacterium than the healthy individuals. In network analysis with the dominant microorganism amplicon sequence variants (ASV) (Cutibacterium, Staphylococcus, Malassezia globosa, and Malassezia restricta) Cutibacterium acnes was identified to have hostile interactions with Staphylococcus and Malassezia globosa. Accordingly, this
results
suggest an insight into the differences in the skin microbiome and mycobiome between acne patients and healthy controls and provide possible microorganism candidates that modulate the microbiomes associated to acne vulgaris.

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  • Acne due to JAK inhibitors in inflammatory bowel disease
    Andrew Awad, Britt Christensen, Jonathan P Segal, Gayle Ross
    Frontline Gastroenterology.2025; 16(2): 166.     CrossRef
  • Amplicon-based analysis reveals link between adolescent acne and altered facial skin microbiome induced by negative emotional states
    Yu Chen, Lixia Peng, Yueying Li, Yusheng Peng, Siqi Dai, Kai Han, Jinge Xin
    Frontiers in Cellular and Infection Microbiology.2025;[Epub]     CrossRef
  • Cyclodextrin-based supramolecular dissolving microneedles for enhanced transdermal delivery of azelaic acid in acne vulgaris treatment
    Yuxu Chen, Yuanyu Xu, Jingqing Zhang, Xinjun Xu
    Journal of Drug Delivery Science and Technology.2025; 111: 107108.     CrossRef
  • Analysis of Skin Microbiome in Facial and Back Acne Patients Based on High‐Throughput Sequencing
    YiJie Du, BenYue Li, Jie Yang, YeXiang Zhang, FengWei Qi, Hong Meng
    Journal of Cosmetic Dermatology.2025;[Epub]     CrossRef
  • Yanomami skin microbiome complexity challenges prevailing concepts of healthy skin
    Juliana Durack, Yvette Piceno, Hoang Vuong, Brian Fanelli, David A. Good, Nur A. Hasan, Manoj Dadlani, Larry Weiss, Julia Oh, Aleksandar D. Kostic, Thomas L. Dawson, Hortensia Caballero-Arias, Rita R. Colwell
    Nature Communications.2025;[Epub]     CrossRef
  • The Mechanism and Research Progress of Skin Microbiota in Pathogenesis of Acne
    Xinwei Li, Juan Jin, Craig G. Burkhart
    Dermatology Research and Practice.2025;[Epub]     CrossRef
  • Unveiling acne microbiome signatures: the role of the microbiome and the impact of a facewash formula containing plant-derived monoterpenes
    Yi-Ning Xu, Neha Salgaonkar, Mingming Pu, Stacy Hawkins, Kevin Hermanson, Yaping Du, Chandraprabha Doraiswamy, Yimei Tan, Chao Yuan, Anindya Dasgupta, Chung-Ching Chu
    British Journal of Dermatology.2025; 193(Supplement): ii15.     CrossRef
  • Interações entre malassezia restricta e o micobioma humano: uma perspectiva abrangente
    Maria Vitória Cavalheiro Berlofa, Ana Carolina de Oliveira Ramos Siqueira, Yara Natércia Lima Faustino de Maria, Rafaela de Campos Oliveira, Paulo Salarrola Takao, Ana Clara da Silva, Milena Coutinho Natucci, Fabiano Bezerra Menegidio, Daniela Leite Jabes
    Revista Científica Multidisciplinar Núcleo do Conhecimento.2024; : 21.     CrossRef
  • Guidelines of care for the management of acne vulgaris
    Rachel V. Reynolds, Howa Yeung, Carol E. Cheng, Fran Cook-Bolden, Seemal R. Desai, Kelly M. Druby, Esther E. Freeman, Jonette E. Keri, Linda F. Stein Gold, Jerry K.L. Tan, Megha M. Tollefson, Jonathan S. Weiss, Peggy A. Wu, Andrea L. Zaenglein, Jung Min H
    Journal of the American Academy of Dermatology.2024; 90(5): 1006.e1.     CrossRef
  • Microenvironmental host–microbe interactions in chronic inflammatory skin diseases
    Lene Bay, Gregor Borut Jemec, Hans Christian Ring
    APMIS.2024; 132(12): 974.     CrossRef
  • Microbiome: Role in Inflammatory Skin Diseases
    Xue-Er Zhang, Pai Zheng, Sheng-Zhen Ye, Xiao Ma, E Liu, Yao-Bin Pang, Qing-Ying He, Yu-Xiao Zhang, Wen-Quan Li, Jin-Hao Zeng, Jing Guo
    Journal of Inflammation Research.2024; Volume 17: 1057.     CrossRef
  • Evaluation of the Effects of Age, Sex, and Dexpanthenol-Containing Skin Care on the Facial and Body Skin Microbiome
    Zainab Qaizar, Raffaella de Salvo, Gregor Bieri, Katrin Unbereit, Shannon Montgomery, Erwan Peltier
    Cosmetics.2024; 11(6): 213.     CrossRef
  • New insights into the characteristic skin microorganisms in different grades of acne and different acne sites
    Zitao Guo, Yuliang Yang, Qianjie Wu, Meng Liu, Leyuan Zhou, Liang Zhang, Dake Dong
    Frontiers in Microbiology.2023;[Epub]     CrossRef
  • Distinct skin microbiome modulation following different topical acne treatments in mild acne vulgaris patients: A randomized, investigator‐blinded exploratory study
    Chanidapa Wongtada, Pinidphon Prombutara, Pravit Asawanonda, Nopadon Noppakun, Chanat Kumtornrut, Tanittha Chatsuwan
    Experimental Dermatology.2023; 32(6): 906.     CrossRef
  • A cross‐sectional cohort study on the skin microbiota in patients with different acne durations
    Lang Sun, Qingqun Wang, Huan Wang, Jing Huang, Zheng Yu
    Experimental Dermatology.2023; 32(12): 2102.     CrossRef
  • Truncal acne following JAK inhibitor use in vitiligo with rare opportunistic fungal infections: Two case reports
    Jee Yun Doh, Piyapat Rintarhat, Won Hee Jung, Hei Sung Kim
    JAAD Case Reports.2023; 37: 123.     CrossRef
  • New Normal Mask-Wearing and Its Impact on Underneath Skin Microbiome: A Cross-Sectional Study in Mild Acne Vulgaris Patients
    Chanidapa Wongtada, Thanaporn Puaratana-arunkon, Pinidphon Prombutara, Pravit Asawanonda, Nopadon Noppakun, Chanat Kumtornrut, Tanittha Chatsuwan
    Skin Appendage Disorders.2022; 8(5): 376.     CrossRef
  • Truncal Acne: An Overview
    Yu Ri Woo, Hei Sung Kim
    Journal of Clinical Medicine.2022; 11(13): 3660.     CrossRef
  • Skin microbiome in acne vulgaris, skin aging, and rosacea
    Yu-Ching Weng, Yi-Ju Chen
    Dermatologica Sinica.2022; 40(3): 129.     CrossRef
  • Infant Mode of Delivery Shapes the Skin Mycobiome of Prepubescent Children
    Yan-Ren Wang, Ting Zhu, Fan-Qi Kong, Yuan-Yuan Duan, Carlos Galzote, Zhe-Xue Quan, Jan Claesen, Laura Tipton
    Microbiology Spectrum.2022;[Epub]     CrossRef
  • A split face study on the effect of an anti-acne product containing fermentation products of Enterococcus faecalis CBT SL-5 on skin microbiome modification and acne improvement
    Hye Sung Han, Sun Hye Shin, Bo-Yun Choi, Nayeon Koo, Sanghyun Lim, Dooheon Son, Myung Jun Chung, Kui Young Park, Woo Jun Sul
    Journal of Microbiology.2022; 60(5): 488.     CrossRef
  • Genome of Malassezia arunalokei and Its Distribution on Facial Skin
    Yong-Joon Cho, Taeyune Kim, Daniel Croll, Minji Park, Donghyeun Kim, Hye Lim Keum, Woo Jun Sul, Won Hee Jung, Teresa R. O'Meara
    Microbiology Spectrum.2022;[Epub]     CrossRef
  • Features of the Skin Microbiota in Common Inflammatory Skin Diseases
    Iva Ferček, Liborija Lugović-Mihić, Arjana Tambić-Andrašević, Diana Ćesić, Ana Gverić Grginić, Iva Bešlić, Marinka Mravak-Stipetić, Iva Mihatov-Štefanović, Ana-Marija Buntić, Rok Čivljak
    Life.2021; 11(9): 962.     CrossRef
Comparative genomic analysis of selenium utilization traits in different marine environments
Muhammad Farukh
J. Microbiol. 2020;58(2):113-122.   Published online January 29, 2020
DOI: https://doi.org/10.1007/s12275-020-9250-0
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AbstractAbstract PDF
Selenium (Se) is an essential trace element for many organisms, which is required in the biosynthesis of proteins with selenocysteine, tRNAs with selenouridine, and certain enzymes with Se as a cofactor. Recent large-scale metagenomics projects provide a unique opportunity for studying the global trends of Se utilization in marine environments. Here, we analyzed samples from different marine microbial communities, revealed by the Tara Oceans project, to characterize the Se utilization traits. We found that the selenophosphate synthetase gene, which defines the overall Se utilization, and Se utilization traits are present in all samples. Regions with samples rich and poor in Se utilization traits were categorized. From the analysis of environmental factors, the mesopelagic zone and high temperature (> 15°C) of water are favorable, while geographical location has little influence on Se utilization. All Se utilization traits showed a relatively independent occurrence. The taxonomic classification of Se traits shows that most of the sequences corresponding to Se utilization traits belong to the phylum Proteobacteria. Overall, our study provides useful insights into the general features of Se utilization in ocean samples and may help to understand the evolutionary dynamics of Se utilization in different marine environments.

Citations

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  • The selenophosphate synthetase family: A review
    Bruno Manta, Nadezhda E Makarova, Marco Mariotti
    Free Radical Biology and Medicine.2022; 192: 63.     CrossRef
  • Selenium Metabolism and Selenoproteins in Prokaryotes: A Bioinformatics Perspective
    Yan Zhang, Jiao Jin, Biyan Huang, Huimin Ying, Jie He, Liang Jiang
    Biomolecules.2022; 12(7): 917.     CrossRef
  • Uses of Selenium Nanoparticles in the Plant Production
    Iqra Bano, Sylvie Skalickova, Hira Sajjad, Jiri Skladanka, Pavel Horky
    Agronomy.2021; 11(11): 2229.     CrossRef
Novosphingobium sp. PP1Y as a novel source of outer membrane vesicles
Federica De Lise , Francesca Mensitieri , Giulia Rusciano , Fabrizio Dal Piaz , Giovanni Forte , Flaviana Di Lorenzo , Antonio Molinaro , Armando Zarrelli , Valeria Romanucci , Valeria Cafaro , Antonio Sasso , Amelia Filippelli , Alberto Di Donato , Viviana Izzo
J. Microbiol. 2019;57(6):498-508.   Published online May 27, 2019
DOI: https://doi.org/10.1007/s12275-019-8483-2
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AbstractAbstract PDF
Outer membrane vesicles (OMVs) are nanostructures of 20– 200 nm diameter deriving from the surface of several Gramnegative bacteria. OMVs are emerging as shuttles involved in several mechanisms of communication and environmental adaptation. In this work, OMVs were isolated and characterized from Novosphingobium sp. PP1Y, a Gram-negative non-pathogenic microorganism lacking LPS on the outer membrane surface and whose genome was sequenced and annotated. Scanning electron microscopy performed on samples obtained from a culture in minimal medium highlighted the presence of PP1Y cells embedded in an extracellular matrix rich in vesicular structures. OMVs were collected from the exhausted growth medium during the mid-exponential phase, and purified by ultracentrifugation on a sucrose gradient. Atomic force microscopy, dynamic light scattering and nanoparticle tracking analysis showed that purified PP1Y OMVs had a spherical morphology with a diameter of ca. 150 nm and were homogenous in size and shape. Moreover, proteomic and fatty acid analysis of purified OMVs revealed a specific biochemical “fingerprint”, suggesting interesting details concerning their biogenesis and physiological role. Moreover, these extracellular nanostructures do not appear to be cytotoxic on HaCaT cell line, thus paving the way to their future use as novel drug delivery systems.

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  • Outer membrane vesicles from Escherichia coli as a presentation platform for AR-23 antiviral peptide
    Francesca Mensitieri, Federica Dell’Annunziata, Giulia Gaudino, Veronica Folliero, Gianluigi Franci, Fabrizio Dal Piaz, Viviana Izzo
    Frontiers in Molecular Biosciences.2025;[Epub]     CrossRef
  • Proteomic analysis of meropenem-induced outer membrane vesicles released by carbapenem-resistant Klebsiella pneumoniae
    Fangfang Fan, Guangzhang Chen, Siqian Deng, Li Wei, Mariola J. Ferraro
    Microbiology Spectrum.2024;[Epub]     CrossRef
  • LuxR402 of Novosphingobium sp. HR1a regulates the correct configuration of cell envelopes
    Ana Segura, Lázaro Molina
    Frontiers in Microbiology.2023;[Epub]     CrossRef
  • Genomic and physiological characterization of Novosphingobium terrae sp. nov., an alphaproteobacterium isolated from Cerrado soil containing a mega-sized chromid
    Aline Belmok, Felipe Marques de Almeida, Rodrigo Theodoro Rocha, Carla Simone Vizzotto, Marcos Rogério Tótola, Marcelo Henrique Soller Ramada, Ricardo Henrique Krüger, Cynthia Maria Kyaw, Georgios J. Pappas
    Brazilian Journal of Microbiology.2023; 54(1): 239.     CrossRef
  • Outer Membrane Vesicles Derived from Klebsiella pneumoniae Are a Driving Force for Horizontal Gene Transfer
    Federica Dell’Annunziata, Carmela Dell’Aversana, Nunzianna Doti, Giuliana Donadio, Fabrizio Dal Piaz, Viviana Izzo, Anna De Filippis, Marilena Galdiero, Lucia Altucci, Giovanni Boccia, Massimiliano Galdiero, Veronica Folliero, Gianluigi Franci
    International Journal of Molecular Sciences.2021; 22(16): 8732.     CrossRef
Proteome analysis reveals global response to deletion of mrflbA in Monascus ruber
Qingqing Yan , Zhouwei Zhang , Yishan Yang , Fusheng Chen , Yanchun Shao
J. Microbiol. 2018;56(4):255-263.   Published online February 28, 2018
DOI: https://doi.org/10.1007/s12275-018-7425-8
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AbstractAbstract PDF
Monascus spp. are commonly used for a wide variety of applications in the food and pharmaceutical industries. In previous studies, the knock-out of mrflbA (a putative regulator of the G protein α subunit) in M. ruber led to autolysis of the mycelia, decreased pigmentation and lowered mycotoxin production. Therefore, we aimed to obtain a comprehensive overview of the underlying mechanism of mrflbA deletion at the proteome level. A two-dimensional gel electrophoresis analysis of mycelial proteins indicated that the abundance of 178 proteins was altered in the ΔmrflbA strain, 33 of which were identified with high confidence. The identified proteins are involved in a range of activities, including carbohydrate and amino acid metabolism, hyphal development and the oxidative stress response, protein modification, and the regulation of cell signaling. Consistent with these findings, the activity of antioxidative enzymes and chitinase was elevated in the supernatant of the ΔmrflbA strain. Furthermore, deletion of mrflbA resulted in the transcriptional reduction of secondary metabolites (pigment and mycotoxin). In short, the mutant phenotypes induced by the deletion of mrflbA were consistent with changes in the expression levels of associated proteins, providing direct evidence of the regulatory functions mediated by mrflbA in M. ruber.

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  • Histone deacetylase MrHos3 negatively regulates the production of citrinin and pigments in Monascus ruber
    Qianrui Liu, Yunfan Zheng, Baixue Liu, Fufang Tang, Yanchun Shao
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Variations in bacterial and fungal communities through soil depth profiles in a Betula albosinensis forest
Can Du , Zengchao Geng , Qiang Wang , Tongtong Zhang , Wenxiang He , Lin Hou , Yueling Wang
J. Microbiol. 2017;55(9):684-693.   Published online September 2, 2017
DOI: https://doi.org/10.1007/s12275-017-6466-8
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AbstractAbstract PDF
Microbial communities in subsurface soil are specialized for their environment, which is distinct from that of the surface communities. However, little is known about the microbial communities (bacteria and fungi) that exist in the deeper soil horizons. Vertical changes in microbial alpha-diversity (Chao1 and Shannon indices) and community composition were investigated at four soil depths (0–10, 10–20, 20–40, and 40–60 cm) in a natural secondary forest of Betula albosinensis by high-throughput sequencing of the 16S and internal transcribed spacer rDNA regions. The numbers of operational taxonomic units (OTUs), and the Chao1 and Shannon indices decreased in the deeper soil layers. Each soil layer contained both mutual and specific OTUs. In the 40–60 cm soil layer, 175 and 235 specific bacterial and fungal OTUs were identified, respectively. Acidobacteria was the most dominant bacterial group in all four soil layers, but reached its maximum at 40–60 cm (62.88%). In particular, the 40–60 cm soil layer typically showed the highest abundance of the fungal genus Inocybe (47.46%). The Chao1 and Shannon indices were significantly correlated with the soil organic carbon content. Redundancy analysis indicated that the bacterial communities were closely correlated with soil organic carbon content (P = 0.001). Collectively, these results indicate that soil nutrients alter the microbial diversity and relative abundance and affect the microbial composition.

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Comparative and bioinformatics analyses of pathogenic bacterial secretomes identified by mass spectrometry in Burkholderia species
Thao Thi Nguyen , Tae-Soo Chon , Jaehan Kim , Young-Su Seo , Muyoung Heo
J. Microbiol. 2017;55(7):568-582.   Published online June 30, 2017
DOI: https://doi.org/10.1007/s12275-017-7085-0
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AbstractAbstract PDF
Secreted proteins (secretomes) play crucial roles during bacterial pathogenesis in both plant and human hosts. The identification and characterization of secretomes in the two plant pathogens Burkholderia glumae BGR1 and B. gladioli BSR3, which cause diseases in rice such as seedling blight, panicle blight, and grain rot, are important steps to not only understand the disease-causing mechanisms but also find remedies for the diseases. Here, we identified two datasets of secretomes in B. glumae BGR1 and B. gladioli BSR3, which consist of 118 and 111 proteins, respectively, using mass spectrometry approach and literature curation. Next, we characterized the functional properties, potential secretion pathways and sequence information properties of secretomes of two plant pathogens in a comparative analysis by various computational approaches. The ratio of potential non-classically secreted proteins (NCSPs) to classically secreted proteins (CSPs) in B. glumae BGR1 was greater than that in B. gladioli BSR3. For CSPs, the putative hydrophobic regions (PHRs) which are essential for secretion process of CSPs were screened in detail at their N-terminal sequences using hidden Markov model (HMM) – based method. Total 31 pairs of homologous proteins in two bacterial secretomes were indicated based on the global alignment (identity ≥ 70%). Our results may facilitate the understanding of the species-specific features of secretomes in two plant pathogenic Burkholderia species.

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  • Proteomics approaches: A review regarding an importance of proteome analyses in understanding the pathogens and diseases
    Muhammad Zubair, Jia Wang, Yanfei Yu, Muhammad Faisal, Mingpu Qi, Abid Ullah Shah, Zhixin Feng, Guoqing Shao, Yu Wang, Qiyan Xiong
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ZntR positively regulates T6SS4 expression in Yersinia pseudotuberculosis
Tietao Wang , Keqi Chen , Fen Gao , Yiwen Kang , Muhammad Tausif Chaudhry , Zhuo Wang , Yao Wang , Xihui Shen
J. Microbiol. 2017;55(6):448-456.   Published online March 10, 2017
DOI: https://doi.org/10.1007/s12275-017-6540-2
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  • 21 Crossref
AbstractAbstract PDF
The type VI secretion system (T6SS) is a widespread and versatile protein secretion system found in most Gram- negative bacteria. Studies of T6SS have mainly focused on its role in virulence toward host cells and inter-bacterial inter-actions, but studies have also shown that T6SS4 in Yersinia pseudotuberculosis participates in the acquisition of zinc ions to alleviate the accumulation of hydroxyl radicals induced by multiple stressors. Here, by comparing the gene expression patterns of wild-type and zntR mutant Y. pseudotubercu-losis cells using RNA-seq analysis, T6SS4 and 17 other bio-logical processes were found to be regulated by ZntR. T6SS4 was positively regulated by ZntR in Y. pseudotuberculosis, and further investigation demonstrated that ZntR regulates T6SS4 by directly binding to its promoter region. T6SS4 ex-pression is regulated by zinc via ZntR, which maintains in-tracellular zinc homeostasis and controls the concentration of reactive oxygen species to prevent bacterial death under oxidative stress. This study provides new insights into the regulation of T6SS4 by a zinc-dependent transcriptional regu-lator, and it provides a foundation for further investigation of the mechanism of zinc transport by T6SS.

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    Mengsi Zhang, Mingming Yang, Xiaoxue Zhang, Shuying Li, Shuaiwu Wang, Alex Muremi Fulano, Yongting Meng, Xihui Shen, Li-li Huang, Yao Wang
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    Changfu Li, Zhiyan Wei, Xinquan He, Haiyang He, Yuqi Liu, Yuxin Zuo, He Xiao, Yao Wang, Xihui Shen, Lingfang Zhu, Olaya Rendueles
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    Jialin Wu, Yutao Liu, Wendi Li, Fan Li, Ruiying Liu, Hao Sun, Jingliang Qin, Xiaohui Feng, Di Huang, Bin Liu
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    Caitlin C. Murdoch, Eric P. Skaar
    Nature Reviews Microbiology.2022; 20(11): 657.     CrossRef
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    Ran Cai, Fen Gao, Junfeng Pan, Xinwei Hao, Zonglan Yu, Yichen Qu, Jialin Li, Dandan Wang, Yao Wang, Xihui Shen, Xingyu Liu, Yantao Yang
    Microbiological Research.2021; 249: 126787.     CrossRef
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    Kai-Wei Yu, Peng Xue, Yang Fu, Liang Yang
    International Journal of Molecular Sciences.2021; 22(2): 478.     CrossRef
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    Sarah L. Price, Viveka Vadyvaloo, Jennifer K. DeMarco, Amanda Brady, Phoenix A. Gray, Thomas E. Kehl-Fie, Sylvie Garneau-Tsodikova, Robert D. Perry, Matthew B. Lawrenz
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    Xiaobing Yang, Hai Liu, Yanxiong Zhang, Xihui Shen
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    Jinshui Lin, Lei Xu, Jianshe Yang, Zhuo Wang, Xihui Shen
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    Vanessa Knittel, Pooja Sadana, Stephanie Seekircher, Anne-Sophie Stolle, Britta Körner, Marcel Volk, Cy M. Jeffries, Dmitri I. Svergun, Ann Kathrin Heroven, Andrea Scrima, Petra Dersch, Joan Mecsas
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    Lei Li, Yi-Nuo Wang, Hong-Bing Jia, Ping Wang, Jun-Fang Dong, Juan Deng, Feng-Min Lu, Qing-Hua Zou
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    Can Chen, Xiaobing Yang, Xihui Shen
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    Microbiological Research.2019; 220: 32.     CrossRef
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    Xiaobing Yang, Junfeng Pan, Yao Wang, Xihui Shen
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Identification of essential genes of Pseudomonas aeruginosa for its growth in airway mucus
Mohammed Abd Alrahman , Sang Sun Yoon
J. Microbiol. 2017;55(1):68-74.   Published online December 30, 2016
DOI: https://doi.org/10.1007/s12275-017-6515-3
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AbstractAbstract PDF
Pseudomonas aeruginosa has been identified as an important causative agent of airway infection, mainly in cystic fibrosis. This disease is characterized by defective mucociliary clearance induced in part by mucus hyper-production. Mucin is a major component of airway mucus and is heavily O-glycosylated, with a protein backbone. Airway infection is known to be established with bacterial adhesion to mucin. However, the genes involved in mucin degradation or utilization remain elusive. In this study, we sought to provide a genetic basis of P. aeruginosa airway growth by identifying those genes. First, using RNASeq analyses, we compared genome-wide expression profiles of PAO1, a prototype P. aeruginosa laboratory strain, grown in M9-mucin (M9M) and M9-glucose (M9G) media. Additionally, a PAO1 transposon (Tn) insertion mutants library was screened for mutants defective in growth in M9M medium. One mutant with a Tn insertion in the xcpU gene (PA3100) was determined to exhibit faulty growth in M9M medium. This gene contributes to the type II secretion system, suggesting that P. aeruginosa uses this secretion system to produce a number of proteins to break down and assimilate the mucin molecule. Furthermore, we screened the PAO1 genome for genes with protease activity. Of 13 mutants, one with mutation in PA3247 gene exhibited defective growth in M9M, suggesting that the PA3247-encoded protease plays a role in mucin utilization. Further mechanistic dissection of this particular process will reveal new drug targets, the inhibition of which could control recalcitrant P. aeruginosa infections.

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A computationally simplistic poly-phasic approach to explore microbial communities from the Yucatan aquifer as a potential sources of novel natural products
Marfil-Santana Miguel David , O’Connor-Sánchez Aileen , Ramírez-Prado Jorge Humberto , De los Santos-Briones Cesar , López- Aguiar , Lluvia Korynthia , Rojas-Herrera Rafael , Lago-Lestón Asunción , Prieto-Davó Alejandra
J. Microbiol. 2016;54(11):774-781.   Published online October 29, 2016
DOI: https://doi.org/10.1007/s12275-016-6092-x
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AbstractAbstract PDF
The need for new antibiotics has sparked a search for the microbes that might potentially produce them. Current sequencing technologies allow us to explore the biotechnological potential of microbial communities in diverse environments without the need for cultivation, benefitting natural product discovery in diverse ways. A relatively recent method to search for the possible production of novel compounds includes studying the diverse genes belonging to polyketide synthase pathways (PKS), as these complex enzymes are an important source of novel therapeutics. In order to explore the biotechnological potential of the microbial community from the largest underground aquifer in the world located in the Yucatan, we used a polyphasic approach in which a simple, non-computationally intensive method was coupled with direct amplification of environmental DNA to assess the diversity and novelty of PKS type I ketosynthase (KS) domains. Our results suggest that the bioinformatic method proposed can indeed be used to assess the novelty of KS enzymes; nevertheless, this in silico study did not identify some of the KS diversity due to primer bias and stringency criteria outlined by the metagenomics pipeline. Therefore, additionally implementing a method involving the direct cloning of KS domains enhanced our results. Compared to other freshwater environments, the aquifer was characterized by considerably less diversity in relation to known ketosynthase domains; however, the metagenome included a family of KS type I domains phylogenetically related, but not identical, to those found in the curamycin pathway, as well as an outstanding number of thiolases. Over all, this first look into the microbial community found in this large Yucatan aquifer and other fresh water free living microbial communities highlights the potential of these previously overlooked environments as a source of novel natural products.

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    Pablo Suárez‐Moo, Alejandra Prieto‐Davó
    MicrobiologyOpen.2024;[Epub]     CrossRef
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    Pablo Suárez-Moo, Claudia A. Remes-Rodríguez, Norma A. Márquez-Velázquez, Luisa I. Falcón, José Q. García-Maldonado, Alejandra Prieto-Davó
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    Carlos A. Fajardo-Hernández, Firoz Shah Tuglak Khan, Laura Flores-Bocanegra, Alejandra Prieto-Davó, Baojie Wan, Rui Ma, Mallique Qader, Rodrigo Villanueva-Silva, Anahí Martínez-Cárdenas, Marian A. López-Lobato, Shabnam Hematian, Scott G. Franzblau, Huzefa
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Research Support, Non-U.S. Gov'ts
In silico analysis and experimental validation of lipoprotein and novel Tat signal peptides processing in Anabaena sp. PCC7120
Sonika Kumari , Akhilesh Kumar Chaurasia
J. Microbiol. 2015;53(12):837-846.   Published online December 2, 2015
DOI: https://doi.org/10.1007/s12275-015-5281-3
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AbstractAbstract
Signal peptide (SP) plays a pivotal role in protein translocation. Lipoprotein- and twin arginine translocase (Tat) dependent signal peptides were studied in All3087, a homolog of competence protein of Synechocystis PCC6803 and in two putative alkaline phosphatases (ALPs, Alr2234 and Alr4976), respectively. In silico analysis of All3087 is shown to possess the characteristics feature of competence proteins such as helix-hairpin-helix, N and C-terminal HKD endonuclease domain, calcium binding domain and N-terminal lipoprotein signal peptide. The SP recognition-cleavage site in All3087 was predicted (AIA-AC) using SignalP while further in-depth analysis using Pred-Lipo and WebLogo analysis for consensus sequence showed it as IAA-C. Activities of putative ALPs were confirmed by heterologous overexpression, activity assessment and zymogram analysis. ALP activity in Anabaena remains cell bound in log-phase, but during late log/stationary phase, an enhanced ALP activity was detected in extracellular milieu. The enhancement of ALP activity during stationary phase was not only due to inorganic phosphate limitation but also contributed by the presence of novel bipartite Tat-SP. The Tat signal transported the folded active ALPs to the membrane, followed by anchoring into the membrane and successive cleavage enabling transportation of the ALPs to the extracellular milieu, because of bipartite architecture and processing of transit Tat-SP.

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    Y. Wang, M.J.O. Wakelam, V.A. Bankaitis, M.I. McDermott
    Advances in Biological Regulation.2024; 91: 101000.     CrossRef
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    Shiva Mohammadi, Zohreh Mostafavi-Pour, Younes Ghasemi, Mahdi Barazesh, Soudabeh Kavousi Pour, Amir Atapour, Pooneh Mokarram, Mohammad Hossein Morowvat
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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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AbstractAbstract
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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    Freddy Villanueva-Cotrina, Guillermo García-Effron, Soledad Gamarra, Julieta Mariana Rojas, Heli Barron-Pastor, Melina Lorenzini, Gustavo Giusiano
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    Dungang Wang, Shaojun Deng, Han Yang, Na Li, Qiuhong Feng, Jia Liu, Huajun Yin
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    Fei Cheng, Mingman Li, Yihua Ren, Lei Hou, Tan Gao, Peng He, Xiangsheng Deng, Jie Lu
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    Yonghua Zhao, Yujie Zhou, Xia Jia, Lei Han, Li Liu, Kun Ren, Xuan Ye, Zhi Qu, Yuanjie Pei
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    Yujie Zhou, Xia Jia, Lei Han, Ge Tian, Shuaizhi Kang, Yonghua Zhao
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    Maria M. Hernandez, Cristina M. Menéndez
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    Can Du, Zengchao Geng, Qiang Wang, Tongtong Zhang, Wenxiang He, Lin Hou, Yueling Wang
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New record and enzyme activity of four species in Penicillium section Citrina from marine environments in Korea
Myung Soo Park , Ji Eun Eom , Jonathan J. Fong , Young Woon Lim
J. Microbiol. 2015;53(4):219-225.   Published online April 8, 2015
DOI: https://doi.org/10.1007/s12275-015-4700-9
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AbstractAbstract PDF
Several strains of Penicillium section Citrina were isolated during a survey of fungi from marine environments along the southern coast of Korea. Based on multigene phylogenetic analyses (?tubulin and calmodulin) and morphological characteristics, the 11 strains were identified as P. citrinum, P. hetheringtonii, P. paxilli, P. sumatrense, P. terrigenum, and P. westlingii. To understand the ecological role of these species, we tested all strains for extracellular enzyme activity; six strains representing four species showed ?glucosidase activity. Four of the identified species ?P. hetheringtonii, P. paxilli, P. terrigenum, and P. westlingii ?are new records for Korea. For these new species records, we describe morphological characteristics of the strains and compare results to published data of type strains.

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    Xin-Cun Wang, Zhi-Kang Zhang, Wen-Ying Zhuang
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    Jun Won Lee, Chang Wan Seo, Wonjun Lee, Ji Seon Kim, Ki Hyeong Park, Yoonhee Cho, Young Woon Lim
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    Micael F. M. Gonçalves, Liliana Santos, Bruno M. V. Silva, Alberto C. Abreu, Tânia F. L. Vicente, Ana C. Esteves, Artur Alves
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Review
Against friend and foe: Type 6 effectors in plant-associated bacteria
Choong-Min Ryu
J. Microbiol. 2015;53(3):201-208.   Published online March 3, 2015
DOI: https://doi.org/10.1007/s12275-015-5055-y
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AbstractAbstract PDF
Bacterial secretion systems play critical roles in communication with neighboring bacteria and in the modulation of host immune responses via the secretion of small proteins called effectors. Several secretion systems have been identified and these are denoted types I-II. Of these, the type VI secretion system (T6SS) and its effectors were only recently elucidated. Most studies on the role and significance of the T6SS and its effectors have focused on human pathogens. In this review, type 6 effectors from plant-associated beneficial and pathogenic bacteria are discussed, including effectors from Agrobacterium tumefaciens, Dickeya dadanti, Rhizobium leguminosarum, Pectobacterium atroseptium, Ralstonia solanacearum, Pseudomonas syringae, Pseudomonas fluorescens, and Pseudomonas protegens. Type 6 effectors act in symbiosis, biofilm formation, virulence, and interbacterial competition. Understanding the impact of type 6 effectors on pathogenesis will contribute to the management of bacterial pathogens in crop plants by allowing the manipulation of intra and inter-specific interactions.

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Research Support, U.S. Gov't, Non-P.H.S.
Multiple cellular roles of Neurospora crassa plc-1, splA2, and cpe-1 in regulation of cytosolic free calcium, carotenoid accumulation, stress responses, and acquisition of thermotolerance§
Ananya Barman , Ranjan Tamuli
J. Microbiol. 2015;53(4):226-235.   Published online January 31, 2015
DOI: https://doi.org/10.1007/s12275-015-4465-1
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  • 21 Crossref
AbstractAbstract PDF
Phospholipase C1 (PLC1), secretory phospholipase A2 (sPLA2) and Ca2+/H+ exchanger proteins regulate calcium signaling and homeostasis in eukaryotes. In this study, we investigate functions for phospholipase C1 (plc-1), sPLA2 (splA2) and a Ca2+/H+ exchanger (cpe-1) in the filamentous fungus Neurospora crassa. The Δplc-1, ΔsplA2, and Δcpe-1 mutants exhibited a growth defect on medium supplemented with the divalent ionophore A23187, suggesting that these genes might play a role in regulation of cytosolic free Ca2+ concentration ([Ca2+]c) in N. crassa. The strains lacking plc-1, splA2, and cpe-1 possessed higher carotenoid content than wild type at 8°C, 22°C, and 30°C, and showed increased ultraviolet (UV)- survival under conditions that induced carotenoid accumulation. Moreover, Δplc-1, ΔsplA2, and Δcpe-1 mutants showed reduced survival rate under hydrogen peroxide-induced oxidative stress and induced thermotolerance after exposure to heat shock temperatures. Thus, this study revealed multiple cellular roles for plc-1, splA2, and cpe-1 genes in regulation of [Ca2+]c, carotenoid accumulation, survival under stress conditions, and acquisition of thermotolerance induced by heat shock.

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Research Support, Non-U.S. Gov'ts
Benzaldehyde as an insecticidal, antimicrobial, and antioxidant compound produced by Photorhabdus temperata M1021
Ihsan Ullah , Abdul Latif Khan , Liaqat Ali , Abdur Rahim Khan , Muhammad Waqas , Javid Hussain , In-Jung Lee , Jae-Ho Shin
J. Microbiol. 2015;53(2):127-133.   Published online January 28, 2015
DOI: https://doi.org/10.1007/s12275-015-4632-4
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AbstractAbstract
The Photorhabdus temperata M1021 secretes toxic compounds that kill their insect hosts by arresting immune responses. Present study was aimed to purify the insecticidal and antimicrobial compound(s) from the culture extract of P. temperata M1021 through bioassay guided fractionation. An ethyl acetate (EtOAc) extract of the P. temperata M1021 exhibited 100% mortality in Galleria mellonella larvae within 72 h. In addition, EtOAc extract and bioactive compound 1 purified form the extract through to column chromatography, showed phenol oxidase inhibition up to 60% and 80% respectively. The analysis of 1H and 13C NMR spectra revealed the identity of pure compound as "benzaldehyde". The benzaldehyde showed insecticidal activity against G. mellonella in a dose-dependent manner and 100% insect mortality was observed at 108 h after injection of 8 mM benzaldehyde. In a PO inhibition assay, 4, 6, and 8 mM concentrations of benzaldehyde were found to inhibit PO activity about 15%, 42%, and 80% respectively. In addition, nodule formation was significantly (P < 0.05) inhibited by 4, 6, and 8 mM of benzaldehyde as compare to control. Moreover, benzaldehyde was found to have great antioxidant activity and maximum antioxidant activity was 52.9% at 8 mM benzaldehyde as compare to control. Antimicrobial activity was assessed by MIC values ranged from 6 mM 10 mM for bacterial strains and 8 mM to 10 mM for fungal strains. The
results
suggest that benzaldehyde could be applicable for developing novel insecticide for agriculture use.

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Crystal structure of the bacterial type VI secretion system component TssL from Vibrio cholerae
Jeong Ho Chang , Yeon-Gil Kim
J. Microbiol. 2015;53(1):32-37.   Published online December 4, 2014
DOI: https://doi.org/10.1007/s12275-015-4539-0
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AbstractAbstract PDF
The type VI secretion system (T6SS), commonly found in Gram-negative bacteria, is responsible for exporting effector proteins. The T6SS has been reported to be cytotoxic to host cells. While the components and assembly of the T6SS complex have been largely assessed, structural data on T6SS components from virulent bacteria is remarkably insufficient. Here, we report the crystal structure of Vibrio cholerae TssL (VcTssL), a core component of T6SS. In spite of a relatively low sequence identity, the overall structure of VcTssL is largely similar to those from other bacterial homologs except for several differences found in local structural elements. A unique feature attributed to the C-terminal fragment of Vc- TssL is a crystallographic artifact. This incidental feature of VcTssL may provide insights into screening of molecular partners for the cytoplasmic domain of TssL. Additionally, our results may help in the design of molecular probes for a detailed understanding of the functional relationship between TssL and other T6SS components.

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The Identification of Six Novel Proteins with Fibronectin or Collagen Type І Binding Activity from Streptococcus suis Serotype 2
Hui Zhang , Junxi Zheng , Li Yi , Yue Li , Zhe Ma , Hongjie Fan , Chengping Lu
J. Microbiol. 2014;52(11):963-969.   Published online October 31, 2014
DOI: https://doi.org/10.1007/s12275-014-4311-x
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AbstractAbstract PDF
Streptococcus suis, a major swine pathogen, is an emerging zoonotic agent that causes meningitis and septic shock. Bacterial cell wall and secreted proteins are often involved in interactions with extracellular matrix proteins (ECMs), which play important roles in the initial steps of pathogenesis. In this study, 2D SDS-PAGE, western blotting-based binding affinity measurements, and microtiter plate binding assays were used to identify cell wall and secreted proteins from S. suis that interact with fibronectin and collagen type І. We identified six proteins from S. suis, including three proteins (translation elongation factor G, oligopeptide-binding protein OppA precursor, and phosphoglycerate mutase) that show both fibronectin and collagen type І binding activity. To the best of our knowledge, these three newly identified proteins had no previously reported fibronectin or collagen type І binding activity. Overall, the aim in this study was to identify proteins with ECM binding activity from S. suis and it represents the first report of six new proteins from S. suis that interact with fibronectin or collagen type І.

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Function of VP2 Protein in the Stability of the Secondary Structure of Virus-like Particles of Genogroup II Norovirus at Different pH Levels: Function of VP2 Protein in the Stability of NoV VLPs
Yao Lin , Li Fengling , Wang Lianzhu , Zhai Yuxiu , Jiang Yanhua
J. Microbiol. 2014;52(11):970-975.   Published online October 3, 2014
DOI: https://doi.org/10.1007/s12275-014-4323-6
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AbstractAbstract PDF
VP2 is the minor structural protein of noroviruses (NoV) and may function in NoV particle stability. To determine the function of VP2 in the stability of the NoV particle, we constructed and purified two kinds of virus-like particles (VLPs), namely, VLPs (VP1) and VLPs (VP1+VP2), from Sf9 cells infected with recombinant baculoviruses by using a Bac-to-Bac? baculovirus expression system. The two kinds of VLPs were treated with different phosphate buffers (pH 2 to pH 8); the secondary structure was then analyzed by far UV circular dichroism (CD) spectroscopy. Results showed that significant disruptions of the secondary structure of proteins were not observed at pH 2 to pH 7. At pH 8, the percentages of α-helix, β-sheet, and β-turn in VLPs (VP1) were decreased from 11% to 8%, from 37% to 32%, and from 20% to 16%, respectively. The percentage of coil was increased from 32% to 44%. By contrast, the percentages of α-helix, β-sheet, and β-turn in VLPs (VP1+VP2) were decreased from 11% to 10%, from 37% to 35%, and from 20% to 19%, respectively. The percentage of coil was increased from 32% to 36%. VLPs (VP1+VP2) was likely more stable than VLPs (VP1), as indicated by the percentage of the secondary structures analyzed by CD. These results suggested that VP2 could stabilize the secondary structure of VLPs under alkaline pH conditions. This study provided novel insights into the molecular mechanism of the function of VP2 in the stability of NoV particles.

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Journal Article
Aeration Effects on Metabolic Events during Sporulation of Bacillus thuringiensis
Mohammad H. Sarrafzadeh , Sabine Schorr-Galindo , Hyun-Joon La , Hee-Mock Oh
J. Microbiol. 2014;52(7):597-603.   Published online June 28, 2014
DOI: https://doi.org/10.1007/s12275-014-3547-9
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AbstractAbstract PDF
The metabolism of Bacillus thuringiensis during its sporulation process was investigated under different concentrations of oxygen. At the beginning of sporulation, the aeration conditions were regulated to obtain different oxygen transfer rates (OTR) in four separate fermentations, representing interrupted, limited, non-limited, and saturated oxygenation, respectively. A higher OTR resulted in a higher pH, up to about 9 in the case of saturated oxygenation, while the interrupted oxygenation resulted in a significantly acidic culture. In contrast, the absence of oxygen resulted in rapid sporangia lysis and caused acidification of the medium, indicating a distinctly different sporangia composition and different metabolism. The bacterium also showed different CO2 production rates during sporulation, although amaximum point was observed in every case.With a higher OTR, the maximal value was observed after a longer time and at a lower value (40, 26, and 13 mmol/L/h for limited, non-limited, and saturated cases, respectively). Despite the exhaustion of glucose prior to the sporulation phase, the interrupted oxygenation resulted in acetate, lactate, and citrate in the medium with a maximum concentration of 4.8, 1.3, and 5.0 g/L, respectively. Notwithstanding, while the metabolic events differed visibly in the absence of oxygen, once sporulation was triggered, it was completed, even in the case of an interrupted oxygen supply.

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  • The Sporulation Process of Bacillus thuringiensis as an Adaptive Response in Different Culture Systems: Analysis of the Respiratory Activity, spoIIA/cry1Ac Expression and Cell Aggregation
    J. Lima-Pérez, M. López-Pérez, D. G. Pérez-Solís, J. G. Rocha-Estrada, G. Viniegra-González, O. Loera
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    Túlio Alexandre Freire da Silva, Lívia Santos de Freitas, Larita Veruska José Bezerra da Silva, José Manoel Wanderley Duarte Neto, Gilvanda Ribeiro da Silva, Liane Maria de Almeida Castro Maranhão, Cynthia Araújo de Lacerda, José de Paula Oliveira, Raquel
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  • Solid-state fermentation of Bacillus thuringiensis var kurstaki HD-73 maintains higher biomass and spore yields as compared to submerged fermentation using the same media
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Research Support, Non-U.S. Gov'ts
Comparative Phylogenetic Relationships and Genetic Structure of the Caterpillar Fungus Ophiocordyceps sinensis and Its Host Insects Inferred from Multiple Gene Sequences
Qing-Mei Quan , Qing-Xia Wang , Xue-Li Zhou , Shan Li , Xiao-Ling Yang , Yun-Guo Zhu , Zhou Cheng
J. Microbiol. 2014;52(2):99-105.   Published online February 1, 2014
DOI: https://doi.org/10.1007/s12275-014-3391-y
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AbstractAbstract PDF
Ophiocordyceps sinensis (Ascomycota: Ophiocordycipitaceae) is a native fungal parasite of Hepialidae caterpillars and one of the most economically important medicinal caterpillar fungi in China. However, little is known about the phylogenetic and evolutionary relationships between O. sinensis and its host insects. In this study, nuclear ITS and β-tubulin sequences from O. sinensis and mitochondrial COI, COII, and Cytb sequences from its hosts were analyzed across 33 populations sampled from five regions in China. Phylogenetically, both O. sinensis and its hosts were divided into three geographically correlated clades, and their phylogenies were congruent. Analysis of molecular variance and calculated coefficients of genetic differentiation revealed significant genetic divergence among the clades within both O. sinensis (FST=0.878, NST=0.842) and its hosts (FST=0.861, NST=0.816). Estimated gene flow was very low for O. sinensis (Nm=0.04) and the host insects (Nm=0.04) among these three clades. Mantel tests demonstrated a significant correlation (P<0.01) between the genetic distances for O. sinensis and its hosts, as well as a significant association (P<0.05) between geographic and genetic distances in both. The similar phylogenetic relationships, geographic distributions, and genetic structure and differentiation between O. sinensis and its hosts imply that they have coevolved.

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Sequential Immunosuppressive Activities of Bacterial Secondary Metabolites from the Entomopahogenic Bacterium Xenorhabdus nematophila
Seonghyeon Eom , Youngjin Park , Yonggyun Kim
J. Microbiol. 2014;52(2):161-168.   Published online February 1, 2014
DOI: https://doi.org/10.1007/s12275-014-3251-9
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AbstractAbstract PDF
The entomopathogenic bacterium Xenorhabdus nematophila secretes at least eight bacterial metabolites that play crucial roles suppressing target insect immune responses by inhibiting eicosanoid biosynthesis. We analyzed sequential changes in bacterial metabolite production during bacterial growth and analyzed their individual immunosuppressive activities against the insect host, Spodoptera exigua. X. nematophila exhibited a typical bacterial growth pattern in both insect host and culture medium, and eight metabolites were secreted at different time points. At the early growth phase (6–12 h), Ac-FGV and PHPP were detected in significant amounts in the culture broth. At this early phase, both Ac-FGV (18 μg/ml) and oxindole (110 μg/ml) levels significantly inhibited phenoloxidase and phospholipase A2 activities in S. exigua hemolymph. At the late growth phase (12–36 h), all eight metabolites were detected at significant levels (10–140 μg/ml) in the culture broth and were sufficient to induce hemocyte toxicity. These results suggest that X. nematophila sequentially produces immunosuppressive metabolites that might sequentially and cooperatively inhibit different steps of insect immune responses.

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Characterization of Streptococcus pneumoniae N-Acetylglucosamine-6-Phosphate Deacetylase as a Novel Diagnostic Marker
Chi-Won Choi , Hee-Young An , Yong Ju Lee , Yeol Gyun Lee , Sung Ho Yun , Edmond Changkyun Park , Yeonhee Hong , Gun-Hwa Kim , Jae-Eun Park , Sun Jong Baek , Hyun Sik Kim , Seung Il Kim
J. Microbiol. 2013;51(5):659-664.   Published online October 31, 2013
DOI: https://doi.org/10.1007/s12275-013-3451-8
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AbstractAbstract PDF
The identification of novel diagnostic markers of pathogenic bacteria is essential for improving the accuracy of diagnoses and for developing targeted vaccines. Streptococcus pneumoniae is a significant human pathogenic bacterium that causes pneumonia. N-acetylglucosamine-6-phosphate deacetylase (NagA) was identified in a protein mixture secreted by S. pneumoniae and its strong immunogenicity was confirmed in an immuno-proteomic assay against the anti-serum of the secreted protein mixture. In this study, recombinant S. pneumoniae NagA protein was expressed and purified to analyze its protein characteristics, immunospecificity, and immunogenicity, thereby facilitating its evaluation as a novel diagnostic marker for S. pneumoniae. Mass spectrometry analysis showed that S. pneumoniae NagA contains four internal disulfide bonds and that it does not undergo posttranslational modification. S. pneumoniae NagA antibodies successfully detected NagA from different S. pneumoniae strains, whereas NagA from other pathogenic bacteria species was not detected. In addition, mice infected with S. pneumoniae generated NagA antibodies in an effective manner. These results suggest that NagA has potential as a novel diagnostic marker for S. pneumoniae because of its high immunogenicity and immunospecificity.

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    Irene Jiménez-Munguía, Mónica Calderón-Santiago, Antonio Rodríguez-Franco, Feliciano Priego-Capote, Manuel J. Rodríguez-Ortega
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NOTE] Comparative Assessment of the Intracellular Survival of the Burkholderia pseudomallei bopC Mutant
Varintip Srinon , Sunsiree Muangman , Nithima Imyaem , Veerachat Muangsombut , Natalie R. Lazar Adler , Edouard E. Galyov , Sunee Korbsrisate
J. Microbiol. 2013;51(4):522-526.   Published online August 30, 2013
DOI: https://doi.org/10.1007/s12275-013-2557-3
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AbstractAbstract PDF
Burkholderia pseudomallei, the causative agent of melioidosis, is a Gram-negative saprophytic bacterium capable of surviving within phagocytic cells. To assess the role of BopC (a type III secreted effector protein) in the pathogenesis of B. pseudomallei, a B. pseudomallei bopC mutant was used to infect J774A.1 macrophage-like cells. The bopC mutant showed significantly reduced intracellular survival in infected macrophages compared to wild-type B. pseudomallei. In addition, the bopC mutant displayed delayed escape from endocytic vesicles compared with the wild-type strain. This indicates that BopC is important, and at least in part, needed for intracellular survival of B. pseudomallei.

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    Jua Iwasaki, Nicole M. Bzdyl, Dion J. M. Lin-Sullivan, Nicolas J. Scheuplein, Maria Emilia Dueñas, Emma de Jong, Nicholas J. Harmer, Ulrike Holzgrabe, Mitali Sarkar-Tyson
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    Jennifer Chua, Jeffrey L. Senft, Stephen J. Lockett, Paul J. Brett, Mary N. Burtnick, David DeShazer, Arthur M. Friedlander, Shelley M. Payne
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Saccharomyces cerevisiae Can Secrete Sapp1p Proteinase of Candida parapsilosis But Cannot Use It for Efficient Nitrogen Acquisition
Zuzana Vinterová , Václava Bauerová , Ji&# , Hana Sychrová , Olga Hru&# , Iva Pichová
J. Microbiol. 2013;51(3):336-344.   Published online June 28, 2013
DOI: https://doi.org/10.1007/s12275-013-2422-4
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AbstractAbstract PDF
Secreted aspartic proteinase Sapp1p of Candida parapsilosis represents one of the factors contributing to the pathogenicity of the fungus. The proteinase is synthesized as an inactive pre-pro-enzyme, but only processed Sapp1p is secreted into extracellular space. We constructed a plasmid containing the SAPP1 coding sequence under control of the ScGAL1 promoter and used it for proteinase expression in a Saccharomyces cerevisiae kex2Δ mutant. Because Sapp1p maturation depends on cleavage by Kex2p proteinase, the kex2Δ mutant secreted only the pro-form of Sapp1p. Characterization of this secreted proteinase form revealed that the Sapp1p signal peptide consists of 23 amino acids. Additionally, we prepared a plasmid with the SAPP1 coding sequence under control of its authentic CpSAPP1 promoter, which contains two GATAA motifs. While in C. parapsilosis SAPP1 expression is repressed by good low molecular weight nitrogen sources (e.g., ammonium ions), S. cerevisiae cells harboring this plasmid secreted a low concentration of active proteinase regardless of the type of nitrogen source used. Quantitative real-time PCR analysis of a set of genes related to nitrogen metabolism and uptake (GAT1, GLN3, STP2, GAP1, OPT1, and PTR2) obtained from S. cerevisiae cells transformed with either plasmid encoding SAPP1 under control of its own promoter or empty vector and cultivated in media containing various nitrogen sources also suggested that SAPP1 expression can be connected with the S. cerevisiae regulatory network. However, this regulation occurs in a different manner than in C. parapsilosis.

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    Xiufang Liu, Mulin Lian, Mouming Zhao, Mingtao Huang
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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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AbstractAbstract 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.

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    Yue Gong, Chunxia Liu, Xin Tian, Young Ran Kim
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    Yue Gong, Rui Hong Guo, Joon Haeng Rhee, Young Ran Kim
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    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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    Seunghwa Lee, Saemee Song, Kangseok Lee
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    Seunghwa Lee, Saemee Song, Minho Lee, Soonhye Hwang, Ji-Sun Kim, Nam-Chul Ha, Kangseok Lee
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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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AbstractAbstract 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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Review
REVIEW] The Role of Type III Secretion System 2 in Vibrio parahaemolyticus Pathogenicity
Hyeilin Ham , Kim Orth
J. Microbiol. 2012;50(5):719-725.   Published online November 4, 2012
DOI: https://doi.org/10.1007/s12275-012-2550-2
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AbstractAbstract
Vibrio parahaemolyticus, a Gram-negative marine bacterial pathogen, is emerging as a major cause of food-borne illnesses worldwide due to the consumption of raw seafood leading to diseases including gastroenteritis, wound infection, and septicemia. The bacteria utilize toxins and type III secretion system (T3SS) to trigger virulence. T3SS is a multi-subunit needle-like apparatus used to deliver bacterial proteins, termed effectors, into the host cytoplasm which then target various eukaryotic signaling pathways. V. parahaemolyticus carries two T3SSs in each of its two chromosomes, named T3SS1 and T3SS2, both of which play crucial yet distinct roles during infection: T3SS1 causes cytotoxicity whereas T3SS2 is mainly associated with enterotoxicity. Each T3SS secretes a unique set of effectors that contribute to virulence by acting on different host targets and serving different functions. Emerging studies on T3SS2 of V. parahaemolyticus, reveal its regulation, translocation, discovery, characterization of its effectors, and development of animal models to understand the enterotoxicity. This review on recent findings for T3SS2 of V. parahaemolyticus highlights a novel mechanism of invasion that appears to be conserved by other marine bacteria.

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Research Support, Non-U.S. Gov't
NOTE] Construction and Characterisation of an Antifungal Recombinant Bacillus thuringiensis with an Expanded Host Spectrum
Qin Liu , Jong Yul Roh , Yong Wang , Jae Young Choi , Xue Ying Tao , Jae Su Kim , Yeon Ho Je
J. Microbiol. 2012;50(5):874-877.   Published online November 4, 2012
DOI: https://doi.org/10.1007/s12275-012-2201-7
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AbstractAbstract
A novel antifungal Bacillus thuringiensis strain 19–22, ssp. kurstaki (H3a3b3c), was characterised. This strain included cry1Aa, cry1Ab, cry1Ac, and cry1D, which have high insecticidal activities against lepidopteran larvae other than Spodoptera exigua. To expand the host spectrum, a cry1E gene whose product is active against S. exigua was introduced into the isolate. The transformant successfully expressed the Cry1E protein without any loss of its original antifungal activities. These results indicate that this recombinant strain exhibits dual activities and may be used as an integrated control agent to control plant diseases and insect pests.
Journal Article
Disruption of SCO5461 Gene Coding for a Mono-ADP-Ribosyltransferase Enzyme Produces a Conditional Pleiotropic Phenotype Affecting Morphological Differentiation and Antibiotic Production in Streptomyces coelicolor
Krisztina Szirák , Judit Keser&# , Sándor Biró , Iván Schmelczer , György Barabás , András Penyige
J. Microbiol. 2012;50(3):409-418.   Published online June 30, 2012
DOI: https://doi.org/10.1007/s12275-012-1440-y
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  • 9 Scopus
AbstractAbstract PDF
The SCO5461 gene of Streptomyces coelicolor A3(2) codes for an ADP-ribosyltransferase enzyme that is predicted to be a transmembrane protein with an extracellular catalytic domain. PCR-targeted disruption of the gene resulted in a mutant that differentiated normally on complex SFM medium; however, morphological differentiation in minimal medium was significantly delayed and this phenotype was even more pronounced on osmotically enhanced minimal medium. The mutant did not sporulate when it was grown on R5 medium, however the normal morphological differentiation was restored when the strain was cultivated beside the wild-type S. coelicolor M145 strain. Comparison of the pattern of ADP-ribosylated proteins showed a difference between the mutant and the wild type, fewer modified proteins were present in the cellular crude extract of the mutant strain. These results support our previous suggestions that protein ADP-ribosylation is involved in the regulation of differentiation and antibiotic production and secretion in Streptomyces.
Review
REVIEW] Recent Findings about the Yersinia enterocolitica Phage Shock Protein Response
Saori Yamaguchi , Andrew J. Darwin
J. Microbiol. 2012;50(1):1-7.   Published online February 27, 2012
DOI: https://doi.org/10.1007/s12275-012-1578-7
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AbstractAbstract PDF
The phage shock protein (Psp) system is a conserved extracytoplasmic stress response in bacteria that is essential for virulence of the human pathogen Yersinia enterocolitica. This article summarizes some recent findings about Y. enterocolitica Psp system function. Increased psp gene expression requires the transcription factor PspF, but under non-inducing conditions PspF is inhibited by an interaction with another protein, PspA, in the cytoplasm. A Psp-inducing stimulus causes PspA to relocate to the cytoplasmic membrane, freeing PspF to induce psp gene expression. This PspA relocation requires the integral cytoplasmic membrane proteins, PspB and PspC, which might sense an inducing trigger and sequester PspA by direct interaction. The subsequent induction of psp gene expression increases the PspA concentration, which also allows it to contact the membrane directly, perhaps for its physiological function. Mutational analysis of the PspB and PspC proteins has revealed that they both positively and negatively regulate psp gene expression and has also identified PspC domains associated with each function. We also compare the contrasting physiological roles of the Psp system in the virulence of Y. enterocolitica and Salmonella enterica sv. Typhimurium (S. Typhimurium). In S. Typhimurium, PspA maintains the proton motive force, which provides the energy needed to drive ion importers required for survival within macrophages. In contrast, in the extracellular pathogen Y. enterocolitica, PspB and PspC, but not PspA, are the Psp components needed for virulence. PspBC protect Y. enterocolitica from damage caused by the secretin component of its type 3 secretion system, an essential virulence factor.
Research Support, Non-U.S. Gov'ts
Evaluation of Insecticidal Activity of a Bacterial Strain, Serratia sp. EML-SE1 against Diamondback Moth
Hyung Uk Jeong , Hye Yeon Mun , Hyung Keun Oh , Seung Bum Kim , Kwang Yeol Yang , Iksoo Kim , Hyang Burm Lee
J. Microbiol. 2010;48(4):541-545.   Published online August 20, 2010
DOI: https://doi.org/10.1007/s12275-010-0221-9
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  • 1 Download
  • 21 Crossref
AbstractAbstract PDF
To identify novel bioinsecticidal agents, a bacterial strain, Serratia sp. EML-SE1, was isolated from a dead larva of the lepidopteran diamondback moth (Plutella xylostella) collected from a cabbage field in Korea. In this study, the insecticidal activity of liquid cultures in Luria-Bertani broth (LBB) and nutrient broth (NB) of a bacterial strain, Serratia sp. EML-SE1 against thirty 3rd and 4th instar larvae of the diamondback moth was investigated on a Chinese cabbage leaf housed in a round plastic cage (Ø 10×6 cm). 72 h after spraying the cabbage leaf with LBB and NB cultures containing the bacterial strain, the mortalities of the larvae were determined to be 91.7% and 88.3%, respectively. In addition, the insecticidal activity on potted cabbage containing 14 leaves in a growth cage (165×83×124 cm) was found to be similar to that of the plastic cage experiment. The results of this study provided valuable information on the insecticidal activity of the liquid culture of a Serratia species against the diamondback moth.

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    Suryawanshi Rahul, Patil Chandrashekhar, Borase Hemant, Narkhede Chandrakant, Shinde Laxmikant, Patil Satish
    Natural Product Research.2014; 28(17): 1399.     CrossRef
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    Anaïs Castagnola, S. Stock
    Insects.2014; 5(1): 139.     CrossRef
  • Effect of wax degrading bacteria on life cycle of the pink hibiscus mealybug, Maconellicoccus hirsutus (Green) (Hemiptera: Pseudococcidae)
    Rahul B. Salunkhe, Chandrashekhar D. Patil, Bipinchandra K. Salunke, Ninfa M. Rosas-García, Satish V. Patil
    BioControl.2013; 58(4): 535.     CrossRef
  • Insecticidal potency of bacterial species Bacillus thuringiensis SV2 and Serratia nematodiphila SV6 against larvae of mosquito species Aedes aegypti, Anopheles stephensi, and Culex quinquefasciatus
    Chandrashekhar D. Patil, Satish V. Patil, Bipinchandra K. Salunke, Rahul B. Salunkhe
    Parasitology Research.2012; 110(5): 1841.     CrossRef
  • Prodigiosin produced by Serratia marcescens NMCC46 as a mosquito larvicidal agent against Aedes aegypti and Anopheles stephensi
    Chandrashekhar D. Patil, Satish V. Patil, Bipinchandra K. Salunke, Rahul B. Salunkhe
    Parasitology Research.2011; 109(4): 1179.     CrossRef
  • Entomopathogenicity of endophytic Serratia marcescens strain SRM against larvae of Helicoverpa armigera (Noctuidae: Lepidoptera)
    Muthugounder Mohan, Govindan Selvakumar, Satya Nand Sushil, Jagdish Chandra Bhatt, Hari Shankar Gupta
    World Journal of Microbiology and Biotechnology.2011; 27(11): 2545.     CrossRef
Effect of Acidic pH on the Invasion Efficiency and the Type III Secretion System of Burkholderia thailandensis
Siroj Jitprasutwit , Wisansanee Thaewpia , Veerachat Muangsombut , Aroonlug Lulitanond , Chanvit Leelayuwat , Ganjana Lertmemongkolchai , Sunee Korbsrisate
J. Microbiol. 2010;48(4):526-532.   Published online August 20, 2010
DOI: https://doi.org/10.1007/s12275-010-0078-x
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AbstractAbstract PDF
Burkholderia thailandensis is a close relative of Burkholderia pseudomallei. These organisms are very similar, but B. thailandensis is far less virulent than B. pseudomallei. Nucleotide sequencing and analysis of 14 B. thailandensis isolates revealed variation in the regions coding for the type III secreted BipD protein. The degree of B. thailandensis BipD sequence variation was greater than that found in B. pseudomallei. Western blot analysis indicated that, unlike B. pseudomallei, B. thailandensis type III secreted proteins including BipD and BopE could not be detected in the supernatant of culture medium unless induced by acidic conditions. In addition, culturing B. thailandensis under acidic growth conditions (pH 4.5) can induce the ability of this bacterium to invade human respiratory epithelial cells A549. The identification of an environmental stimulus that increases the invasion capability of B. thailandensis invasion is of value for those who would like to use this bacterium as a model to study B. pseudomallei virulence.
NOTE] Biosynthesis of Poly(3-Hydroxybutyrate-co-3-Hydroxyvalerate) Copolyesters with a High Molar Fraction of 3-Hydroxyvalerate by an Insect-Symbiotic Burkholderia sp. IS-01
Do Young Kim , Doo-Sang Park , Soon Bum Kwon , Moon Gyu Chung , Kyung Sook Bae , Ho-Yong Park , Young Ha Rhee
J. Microbiol. 2009;47(5):651-656.   Published online October 24, 2009
DOI: https://doi.org/10.1007/s12275-009-0109-7
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AbstractAbstract PDF
Burkholderia sp. IS-01 capable of biosynthesizing poly(3-hydroxybutyrate-co-3-hydroxyvalerate) [poly(3HB- co-3HV)] copolyesters with a high molar fraction of 3HV was isolated from the gut of the adult longicorn beetle, Moechotypa diphysis. The strain IS-01 was relatively tolerant to high concentrations of levulinic acid and accumulated a poly(13.5 mol% 3HB-co-86.5 mol% 3HV) copolyester when cultivated on a mixture of gluconate (20 g/L) and levulinic acid (12.5 g/L). In this case, the content of the copolyester in the cells was approximately 60.0%. The compositions of the copolyesters were easily regulated by altering the molar ratio of gluconate and levulinic acid in the medium. The organism was found to possess a class I PHA synthase (PhaC) gene (1,881 bp) that encodes a protein with a deduced molecular mass of 68,538 Da that consists of 626 amino acids. The PhaC of this organism was most similar to that of B. cenocepacia PC184 (92% similarity).
Gene Expression Analysis of Phanerochaete chrysosporium During the Transition Time from Primary Growth to Secondary Metabolism
Mingfeng Jiang , Xiao Li , Liang Zhang , Hong Feng , Yizheng Zhang
J. Microbiol. 2009;47(3):308-318.   Published online June 26, 2009
DOI: https://doi.org/10.1007/s12275-008-0275-z
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AbstractAbstract PDF
In order to identify the secondary metabolism-related genes of Phanerochaete chrysosporium growing under pure O2 and nitrogen-limited conditions, 2322 ESTs fragments originated from two suppression-subtractive libraries were analyzed using the cDNA microarray technique. Ten significantly upregulated and 22 significantly downregulated genes were identified in the 72 h cultured mycelia RNA samples (secondary metabolism). According to qPCR, 16 out of the 32 genes were expressed differently in secondary metabolism. Transcripts of secondary metabolism up-regulation genes exhibited homologies to aryl-alcohol dehydrogenase (SSh1554), ABC transporter gene (SSH624), chitinase (SSH963), heat shock protein (SSH1193), catalase (SSH317), cytochrome P450 (SSH331), glucosamine-6-phosphate isomerase (SSH611), and alkyl hydroperoxide reductase (SSH362) genes. Ninety-three genes could be classified by Eukaryotic Orthologous Groups (KOG). Among the genes assigned a function, gene expression patterns were different in both secondary metabolism and primary metabolism. In the group of “Cellular Processes and Signaling,” most of the genes were from the primary metabolism library. On the other hand, genes from the secondary metabolism library were found mainly in the “Information Storage” and “Processing and Poorly Characterized” groups. Based on the KOG functional assignments, six genes belong to the ubiquitin system, and all of them were from primary metabolism phase. The presence of the H2O2-relevant genes suggested that parts of the genes expressed in 72 h might be involved in the ligninolytic process during secondary metabolism of P. chrysosporium.

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    Hans Mattila, Janina Österman-Udd, Tuulia Mali, Taina Lundell
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    Zhixin Jing, Hong Feng
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    M. L. Meijueiro, F. Santoyo, L. Ramirez, A. G. Pisabarro
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    Amber Vanden Wymelenberg, Jill Gaskell, Michael Mozuch, Grzegorz Sabat, John Ralph, Oleksandr Skyba, Shawn D. Mansfield, Robert A. Blanchette, Diego Martinez, Igor Grigoriev, Philip J. Kersten, Dan Cullen
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    Jin-Ming Wu, Yi-zheng Zhang
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Stable Expression and Secretion of Polyhydroxybutyrate Depolymerase of Paucimonas lemoignei in Escherichia coli
Se Whan Park , Moon Gyu Chung , Hwa Young Lee , Jeong Yoon Kim , Young Ha Rhee
J. Microbiol. 2008;46(6):662-669.   Published online December 24, 2008
DOI: https://doi.org/10.1007/s12275-008-0283-z
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AbstractAbstract PDF
An efficient strategy for the expression and secretion of extracellular polyhydroxybutyrate depolymerase (PhaZ1) of Paucimonas lemoignei in Escherichia coli was developed by employing the signal peptide of PhaZ1 and a truncated ice nucleation protein anchoring motif (INPNC). Directly synthesized mature form of PhaZ1 was present in the cytoplasm of host cells as inclusion bodies, while a construct containing PhaZ1 and its own N-terminal signal peptide (PrePhaZ1) enabled the secretion of active PhaZ1 into the extracellular medium. However, the PrePhaZ1 construct was harmful to the host cell and resulted in atypical growth and instability of the plasmid during the cultivation. In contrast, INPNC-PhaZ1 and INPNCPrePhaZ1 fusion constructs did not affect growth of host cells. INPNC-PhaZ1 was successfully displayed on the cell surface with its fusion form, but did not retain PhaZ1 activity. In the case of INPNC-PrePhaZ1, the initially synthesized fusion form was separated by precise cleavage of the signal peptide, and active PhaZ1 was consequently released into the culture medium. The amount of PhaZ1 derived from E. coli (INPNC-PrePhaZ1) was almost twice as great as that directly expressed from E. coli (PrePhaZ1), and was predominantly (approximately 85%) located in the periplasm when cultivated at 22°C but was efficiently secreted into the extracellular medium when cultivated at 37°C.
Taxonomic Revision of the Nematode-Trapping Fungus Arthrobotrys multisecundaria
Juan Li , Jinkui Yang , Lianming Liang , Ke-Qin Zhang
J. Microbiol. 2008;46(5):513-518.   Published online October 31, 2008
DOI: https://doi.org/10.1007/s12275-007-0115-6
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AbstractAbstract PDF
The gene encoding an extracellular serine protease was cloned from Arthrobotrys multisecundaria using degenerate primers. The gene was highly similar (99.26%) to protease Mlx from Monacrosporium microscaphoides. To clarify the taxonomic relationship between these species, genes encoding the internal transcribed spacer (ITS) and β-tubulin were also cloned and sequenced from A. multisecundaria and M. microscaphoides, respectively. Homologous analysis of the nuclear (ITS) and protein (β-tubulin) encoding genes showed that the two species of nematode-trapping fungi also shared extensive identity (99.82 and 99.63%, respectively), although they exhibited obvious differences in secondary conidia morphology. Accordingly, a taxonomic revision is recommended, with A. multisecundaria being revised as A. microscaphoides var. multisecundaria. In addition, the identified mutation may better facilitate the study of the sporulation of nematode-trapping fungi.

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Two Forms of Vibrio vulnificus Metalloprotease VvpE are Secreted via the Type II General Secretion System
Jong Park , So-Yeon Ryu , Choon-Mee Kim , Sung-Heui Shin
J. Microbiol. 2008;46(3):338-343.   Published online July 5, 2008
DOI: https://doi.org/10.1007/s12275-008-0058-6
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AbstractAbstract PDF
Vibrio vulnificus has been known to secrete one form of metalloprotease VvpE (45 kDa) that is cleaved to 34 kDa-VvpE and 11 kDa-C-terminal propeptide via extracellular autoproteolysis. However, we found that extracellular secretion of both the 34 and 45 kDa forms of VvpE began in the early growth phase; moreover, 34 kDa-VvpE existed as the major form in V. vulnificus cell lysates and culture supernatants. In addition, extracellular secretion of both 34 and 45 kDa-VvpE was blocked by mutation of the pilD gene, which encodes for the type IV leader peptidase/N-methyltransferase of the type II general secretion system, and the blocked VvpE secretion was recovered by in trans-complementation of the wild-type pilD gene. These results indicate that 34 kDa-VvpE is the major form secreted along with 45 kDa-VvpE from the early growth phase via the PilD-mediated type II general secretion system.

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Characterization of an Extracellular Lipase in Burkholderia sp. HY-10 Isolated from a Longicorn Beetle
Doo-Sang Park , Hyun-Woo Oh , Sun-Yeon Heo , Woo-Jin Jeong , Dong Ha Shin , Kyung Sook Bae , Ho-Young Park
J. Microbiol. 2007;45(5):409-417.
DOI: https://doi.org/2596 [pii]
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Burkholderia sp. HY-10 isolated from the digestive tracts of the longicorn beetle, Prionus insularis, produced an extracellular lipase with a molecular weight of 33.5 kDa estimated by SDS-PAGE. The lipase was purified from the culture supernatant to near electrophoretic homogenity by a one-step adsorption-desorption procedure using a polypropylene matrix followed by a concentration step. The purified lipase exhibited highest activities at pH 8.5 and 60°C. A broad range of lipase substrates, from C4 to C18 ρ-nitrophenyl esters, were hydrolyzed efficiently by the lipase. The most efficient substrate was ρ-nitrophenyl caproate (C6). A 2485 bp DNA fragment was isolated by PCR amplification and chromosomal walking which encoded two polypeptides of 364 and 346 amino acids, identified as a lipase and a lipase foldase, respectively. The N-terminal amino acid sequence of the purified lipase and nucleotide sequence analysis predicted that the precursor lipase was proteolytically modified through the secretion step and produced a catalytically active 33.5 kDa protein. The deduced amino acid sequence for the lipase shared extensive similarity with those of the lipase family I.2 of lipases from other bacteria. The deduced amino acid sequence contained two Cystein residues forming a disulfide bond in the molecule and three, well-conserved amino acid residues, Ser131, His330, and Asp308, which composed the catalytic triad of the enzyme.

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