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- Microbiome therapeutic PMC72 through reverse translational research in gout
- Mohammed Solayman Hossain, Hoonhee Seo, Kyung-Ann Lee, Asad ul-Haq, Sukyung Kim, Sujin Jo, Md Abdur Rahim, Hanieh Tajdozian, Fatemeh Ghorbanian, Youjin Yoon, Indrajeet Barman, Md Sarower Hossen Shuvo, Hyun-Sook Kim, Ho-Yeon Song
- J. Microbiol. 2025;63(5):e2501002. Published online May 27, 2025
- DOI: https://doi.org/10.71150/jm.2501002
- 2,236 View
- 78 Download
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- 2 Crossref
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Supplementary Material -
Gout is an inflammatory arthritis resulting from the deposition of monosodium urate crystals. Urate-lowering therapies for gout have limitations, including side effects and limited efficacy, highlighting the need for novel therapeutic approaches to improve patient outcomes. In this context, our research team conducted a microbiome analysis of fecal samples from healthy individuals and gout patients, identifying Bifidobacterium as a key biomarker. Subsequently, we isolated and identified this strain, B. longum PMC72, and demonstrated its efficacy in a gout mouse model. In potassium oxonate (PO)-induced hyperuricemia mice, PMC72 significantly alleviated nausea, gait disturbances, ankle inflammation, and improved renal health. These effects were associated with marked reductions in oxidative stress markers, including serum uric acid, blood urea nitrogen, hepatic xanthine oxidase, and malondialdehyde (MDA) levels in serum, liver, and joint samples, as well as the downregulation of inflammation and uric acid transport-related gene expression in kidney samples. These benefits were comparable to those treated with Febuxostat, a standard urate-lowering therapy for gout. Furthermore, gut microbiome analysis revealed that PMC72 restored dysbiosis induced by hyperuricemia, contrasting with the reduced microbial diversity observed with febuxostat alone, and showed a complete recovery to eubiosis when combined with Febuxostat. These findings position PMC72 as a promising microbial therapeutic candidate for gout management, demonstrating significant development potential and serving as a benchmark for reverse translational microbiome-based therapeutic research.
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Citations
Citations to this article as recorded by
- Characterization of Gut Microbiota of Honey Bees in Korea
Md Sarower Hossen Shuvo, Sukyung Kim, Sujin Jo, Md Abdur Rahim, Indrajeet Barman, Mohammed Solayman Hossain, Yoonkyoung Jeong, Hwasik Jeong, Sangrim Kim, Hoonhee Seo, Ho-Yeon Song
Polish Journal of Microbiology.2025;[Epub] CrossRef - Quantitative assessment of microbial dynamics in livestock manure and municipal wastewater treatment plants
Geon Choi, Hokyung Song, Tatsuya Unno
Applied Biological Chemistry.2025;[Epub] CrossRef
- Characterization of Gut Microbiota of Honey Bees in Korea
Journal Articles
- Heterologous Production and Structure Determination of a New Lanthipeptide Sinosporapeptin Using a Cryptic Gene Cluster in an Actinobacterium Sinosporangium siamense
- Keita Saito , Keiichiro Mukai , Issara Kaweewan , Hiroyuki Nakagawa , Takeshi Hosaka , Shinya Kodani
- J. Microbiol. 2023;61(6):641-648. Published online June 12, 2023
- DOI: https://doi.org/10.1007/s12275-023-00059-z
- 314 View
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- 6 Web of Science
- 5 Crossref
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- Lipolanthine is a subclass of lanthipeptide that has the modification of lipid moiety at the N-terminus. A cryptic biosynthetic gene cluster comprising four genes (sinA, sinKC, sinD, and sinE) involved in the biosynthesis of lipolanthine was identified in the genome of an actinobacterium Sinosporangium siamense. Heterologous coexpression of a precursor peptide coding gene sinA and lanthipeptide synthetase coding gene sinKC in the host Escherichia coli strain BL21(DE3) resulted in the synthesis of a new lanthipeptide, sinosporapeptin. It contained unusual amino acids, including one labionin and two dehydrobutyrine residues, as determined using NMR and MS analyses. Another coexpression experiment with two additional genes of decarboxylase (sinD) and N-acetyl transferase (sinE) resulted in the production of a lipolanthine-like modified sinosporapeptin.
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Citations
Citations to this article as recorded by- BGC heteroexpression strategy for production of novel microbial secondary metabolites
Yuanyuan Liu, Yuqi Tang, Zhiyang Fu, Wangjie Zhu, Hong Wang, Huawei Zhang
Metabolic Engineering.2025; 91: 1. CrossRef - Isolation and structure determination of a new antibacterial lanthipeptide derived from the marine derived bacterium Lysinibacillus sp.CTST325
Chanaphat Thetsana, Ryota Moriuchi, Shinya Kodani
World Journal of Microbiology and Biotechnology.2025;[Epub] CrossRef - Heterologous biosynthesis of myxobacterial lanthipeptides melittapeptins
Issara Kaweewan, Keiichiro Mukai, Pratchaya Rukthanapitak, Hiroyuki Nakagawa, Takeshi Hosaka, Shinya Kodani
Applied Microbiology and Biotechnology.2024;[Epub] CrossRef - Facile Method for Determining Lanthipeptide Stereochemistry
Youran Luo, Shuyun Xu, Autumn M. Frerk, Wilfred A. van der Donk
Analytical Chemistry.2024; 96(4): 1767. CrossRef - Antimicrobial Peptides Derived from Bacteria: Classification, Sources, and Mechanism of Action against Multidrug-Resistant Bacteria
Raynichka Mihaylova-Garnizova, Slavena Davidova, Yordan Hodzhev, Galina Satchanska
International Journal of Molecular Sciences.2024; 25(19): 10788. CrossRef
- BGC heteroexpression strategy for production of novel microbial secondary metabolites
- Transcriptome‑based Mining of the Constitutive Promoters for Tuning Gene Expression in Aspergillus oryzae
- Kobkul Laoteng , Jutamas Anantayanon , Chanikul Chutrakul , Sarocha Panchanawaporn , Sukanya Jeennor
- J. Microbiol. 2023;61(2):199-210. Published online February 6, 2023
- DOI: https://doi.org/10.1007/s12275-023-00020-0
- 351 View
- 0 Download
- 7 Web of Science
- 7 Crossref
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- Transcriptional regulation has been adopted for developing metabolic engineering tools. The regulatory promoter is a crucial genetic element for strain optimization. In this study, a gene set of Aspergillus oryzae with highly constitutive expression across different growth stages was identified through transcriptome data analysis. The candidate promoters were functionally characterized in A. oryzae by transcriptional control of β-glucuronidase (GUS) as a reporter. The results showed that the glyceraldehyde triphosphate dehydrogenase promoter (PgpdA1) of A. oryzae with a unique structure displayed the most robust strength in constitutively controlling the expression compared to the PgpdA2 and other putative promoters tested. In addition, the ubiquitin promoter (Pubi) of A. oryzae exhibited a moderate expression strength. The deletion analysis revealed that the 5' untranslated regions of gpdA1 and ubi with the length of 1028 and 811 nucleotides, counted from the putative translation start site (ATG), respectively, could efficiently drive the GUS expression. Interestingly, both promoters could function on various carbon sources for cell growth. Glucose was the best fermentable carbon source for allocating high constitutive expressions during cell growth, and the high concentrations (6–8% glucose, w/v) did not repress their functions. It was also demonstrated that the secondary metabolite gene coding for indigoidine could express under the control of PgpdA1 or Pubi promoter. These strong and moderate promoters of A. oryzae provided beneficial options in tuning the transcriptional expression for leveraging the metabolic control towards the targeted products.
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Citations
Citations to this article as recorded by- Construction of an Aspergillus oryzae △nptB△pyrG Host for Homologous Expression of Lipase and Catalytic Property Characterization of Recombinant Lipase
Yueting Zhang, Hongmei Nie, Fei Zhang, Mengmeng Jin, Zhao Wang, Jianyong Zheng
Applied Biochemistry and Biotechnology.2025; 197(2): 873. CrossRef - Transcriptome-Based Mining of the Strong Promoters for Hyperproduction of Gibberellin GA3 in Fusarium fujikuroi
Qi Guo, Yue-Feng Zhong, Xin-Yu Chen, Ya-Wen Li, Yu-Xin Yang, Zhi-Kui Nie, Tian-Qiong Shi
Journal of Agricultural and Food Chemistry.2025; 73(14): 8440. CrossRef - Promoter engineering of filamentous fungi for novel natural product discovery
Xiangzhou Gong, Jing Tian, Huawei Zhang
Bioorganic Chemistry.2025; 163: 108798. CrossRef - Mining and Understanding of New Transcriptional Regulatory Elements from Licorice-Derived Endophyte Serratia Rubidaea W12-1
Ying Zhang, Yunyang Ma, Bing Hu, H.M. Zabed, A.K. Singh, M.A. Ibrahim, N. Chen
BIO Web of Conferences.2024; 142: 03018. CrossRef - Development of Aspergillus oryzae BCC7051 as a Robust Cell Factory Towards the Transcriptional Regulation of Protease-Encoding Genes for Industrial Applications
Sarocha Panchanawaporn, Chanikul Chutrakul, Sukanya Jeennor, Jutamas Anantayanon, Kobkul Laoteng
Journal of Fungi.2024; 11(1): 6. CrossRef - Exploring and Engineering Novel Strong Promoters for High-Level Protein Expression in Bacillus subtilis DB104 through Transcriptome Analysis
Ji-Su Jun, Hyang-Eun Jeong, Kwang-Won Hong
Microorganisms.2023; 11(12): 2929. CrossRef - Efficient de novo production of bioactive cordycepin by Aspergillus oryzae using a food-grade expression platform
Sukanya Jeennor, Jutamas Anantayanon, Sarocha Panchanawaporn, Chanikul Chutrakul, Wanwipa Vongsangnak, Kobkul Laoteng
Microbial Cell Factories.2023;[Epub] CrossRef
- Construction of an Aspergillus oryzae △nptB△pyrG Host for Homologous Expression of Lipase and Catalytic Property Characterization of Recombinant Lipase
- Zinc-binding domain mediates pleiotropic functions of Yvh1 in Cryptococcus neoformans
- Jae-Hyung Jin , Myung Kyung Choi , Hyun-Soo Cho , Yong-Sun Bahn
- J. Microbiol. 2021;59(7):658-665. Published online July 1, 2021
- DOI: https://doi.org/10.1007/s12275-021-1287-1
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- Yvh1 is a dual-specificity phosphatase (DUSP) that is evolutionarily conserved in eukaryotes, including yeasts and humans. Yvh1 is involved in the vegetative growth, differentiation, and virulence of animal and plant fungal pathogens. All Yvh1 orthologs have a conserved DUSP catalytic domain at the N-terminus and a zinc-binding (ZB) domain with two zinc fingers (ZFs) at the C-terminus. Although the DUSP domain is implicated in the regulation of MAPK signaling in humans, only the ZB domain is essential for most cellular functions of Yvh1 in fungi. This study aimed to analyze the functions of the DUSP and ZB domains of Yvh1 in the human fungal pathogen Cryptococcus neoformans, whose Yvh1 (CnYvh1) contains a DUSP domain at the C-terminus and a ZB domain at the N-terminus. Notably, CnYvh1 has an extended internal domain between the two ZF motifs in the ZB domain. To elucidate the function of each domain, we constructed individual domain deletions and swapping strains by complementing the yvh1Δ mutant with wild-type (WT) or mutated YVH1 alleles and examined their Yvh1-dependent phenotypes, including growth under varying stress conditions, mating, and virulence factor production. Here, we found that the complementation of the yvh1Δ mutant with the mutated YVH1 alleles having two ZFs of the ZB domain, but not the DUSP and extended internal domains, restored the WT phenotypic traits in the yvh1Δ mutant. In conclusion, the ZB domain, but not the N-terminal DUSP domain, plays a pivotal role in the pathobiological functions of cryptococcal Yvh1.
- Extracellular products-mediated interspecific interaction between Pseudomonas aeruginosa and Escherichia coli
- Yang Yuan , Jing Li , Jiafu Lin , Wenjuan Pan , Yiwen Chu , Balakrishnan Prithiviraj , Yidong Guo , Xinrong Wang , Kelei Zhao
- J. Microbiol. 2021;59(1):29-40. Published online December 23, 2020
- DOI: https://doi.org/10.1007/s12275-021-0478-0
- 333 View
- 0 Download
- 7 Web of Science
- 3 Crossref
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Abstract
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- The Gram-negative pathogen Pseudomonas aeruginosa adopts several elaborate strategies to colonize a wide range of natural or clinical niches and to overcome the neighboring bacterial competitors in polymicrobial communities. However, the relationship and interaction mechanism of P. aeruginosa with other bacterial pathogens remains largely unexplored. Here we explore the interaction dynamics of P. aeruginosa and Escherichia coli, which frequently coinfect the lungs of immunocompromised hosts, by using a series of on-plate proximity assays and RNA-sequencing. We show that the extracellular products of P. aeruginosa can inhibit the growth of neighboring E. coli and induce a large-scale of transcriptional reprogramming of E. coli, especially in terms of cellular respiration- related primary metabolisms and membrane components. In contrast, the presence of E. coli has no significant effect on the growth of P. aeruginosa in short-term culture, but causes a dysregulated expression of genes positively controlled by the quorum-sensing (QS) system of P. aeruginosa during subsequent pairwise culture. We further demonstrate that the divergent QS-regulation of P. aeruginosa may be related to the function of the transcriptional regulator PqsR, which can be enhanced by E. coli culture supernatant to increase the pyocyanin production by P. aeruginosa in the absence of the central las-QS system. Moreover, the extracellular products of E. coli promote the proliferation and lethality of P. aeruginosa in infecting the Caenorhabditis elegans model. The current study provides a general characterization of the extracellular products-mediated interactions between P. aeruginosa and E. coli, and may facilitate the understanding of polymicrobial infections.
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Citations
Citations to this article as recorded by- Pigments from pathogenic bacteria: a comprehensive update on recent advances
Kusumita Acharya, Swarna Shaw, Sudipta Paul Bhattacharya, Shatarupa Biswas, Suman Bhandary, Arijit Bhattacharya
World Journal of Microbiology and Biotechnology.2024;[Epub] CrossRef - Selective detection of two bacterial species in a single collision system targeting metabolic products
Jun Lin, Qingwen Wang, Huike Tian, Qing Xin, Dong Zhang
Microchemical Journal.2024; 206: 111572. CrossRef - Effect of the Type VI Secretion System Secreted Protein Hcp on the Virulence of Aeromonas salmonicida
Hongyan Cai, Jiaying Yu, Ying Qiao, Ying Ma, Jiang Zheng, Mao Lin, Qingpi Yan, Lixing Huang
Microorganisms.2022; 10(12): 2307. CrossRef
- Pigments from pathogenic bacteria: a comprehensive update on recent advances
- A histone deacetylase, MoHOS2 regulates asexual development and virulence in the rice blast fungus
- Jongjune Lee , Jae-Joon Lee , Junhyun Jeon
- J. Microbiol. 2019;57(12):1115-1125. Published online November 22, 2019
- DOI: https://doi.org/10.1007/s12275-019-9363-5
- 337 View
- 0 Download
- 17 Web of Science
- 18 Crossref
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Abstract
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- Histone acetylation/deacetylation represent a general and efficient epigenetic mechanism through which fungal cells control gene expression. Here we report developmental requirement of MoHOS2-mediated histone deacetylation (HDAC) for the rice blast fungus, Magnaporthe oryzae. Structural similarity and nuclear localization indicated that MoHOS2 is an ortholog of Saccharomyces cerevisiae Hos2, which is a member of class I histone deacetylases and subunit of Set3 complex. Deletion of MoHOS2 led to 25% reduction in HDAC activity, compared to the wild-type, confirming that it is a bona-fide HDAC. Lack of MoHOS2 caused decrease in radial growth and impinged dramatically on asexual sporulation. Such reduction in HDAC activity and phenotypic defects of ΔMohos2 were recapitulated by a single amino acid change in conserved motif that is known to be important for HDAC activity. Expression analysis revealed up-regulation of MoHOS2 and concomitant down-regulation of some of the key genes involved in asexual reproduction under sporulation-promoting condition. In addition, the deletion mutant exhibited defect in appressorium formation from both germ tube tip and hyphae. As a result, ΔMohos2 was not able to cause disease symptoms. Wound-inoculation showed that the mutant is compromised in its ability to grow inside host plants as well. We found that some of ROS detoxifying genes and known effector genes are de-regulated in the mutant. Taken together, our data suggest that MoHOS2-dependent histone deacetylation is pivotal for proper timing and induction of transcription of the genes that coordinate developmental changes and host infection in M. oryzae.
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Citations
Citations to this article as recorded by- FolSas2 is a regulator of early effector gene expression during Fusarium oxysporum infection
Limin Song, Yalei Wang, Fahui Qiu, Xiaoxia Li, Jingtao Li, Wenxing Liang
New Phytologist.2025; 245(4): 1688. CrossRef - The role of Penicillium expansum histone deacetylases HosA and HosB in growth, development, and patulin production
Belén Llobregat, Antonio Abad-Fuentes, Josep V. Mercader, Luis González-Candelas, Ana-Rosa Ballester
Microbiological Research.2025; 297: 128181. CrossRef - Genome-wide identification of the lysine deacetylases gene and its dynamic expression profile during adversity stress and infestation in Arthrinium phaeospermum
Sijia Liu, Ziqi Ye, Jia Song, Yutong Liu, Shujiang Li
World Journal of Microbiology and Biotechnology.2025;[Epub] CrossRef - Glsirt1-mediated deacetylation of GlCAT regulates intracellular ROS levels, affecting ganoderic acid biosynthesis in Ganoderma lucidum
Jing Han, Lingshuai Wang, Xin Tang, Rui Liu, Liang Shi, Jing Zhu, Mingwen Zhao
Free Radical Biology and Medicine.2024; 216: 1. CrossRef - Histone (de)acetylation in epigenetic regulation of Phytophthora pathobiology
Yufeng Guan, Joanna Gajewska, Jolanta Floryszak‐Wieczorek, Umesh Kumar Tanwar, Ewa Sobieszczuk‐Nowicka, Magdalena Arasimowicz‐Jelonek
Molecular Plant Pathology.2024;[Epub] CrossRef - Regulatory roles of epigenetic modifications in plant-phytopathogen interactions
Zeng Tao, Fei Yan, Matthias Hahn, Zhonghua Ma
Crop Health.2023;[Epub] CrossRef - The additional PRC2 subunit and Sin3 histone deacetylase complex are required for the normal distribution of H3K27me3 occupancy and transcriptional silencing in Magnaporthe oryzae
Chuyu Lin, Zhongling Wu, Huanbin Shi, Jinwei Yu, Mengting Xu, Fucheng Lin, Yanjun Kou, Zeng Tao
New Phytologist.2022; 236(2): 576. CrossRef - Regulatory Roles of Histone Modifications in Filamentous Fungal Pathogens
Yiling Lai, Lili Wang, Weilu Zheng, Sibao Wang
Journal of Fungi.2022; 8(6): 565. CrossRef - Polycomb Repressive Complex 2-Mediated H3K27 Trimethylation Is Required for Pathogenicity in Magnaporthe oryzae
Zhongling Wu, Jiehua Qiu, Huanbin Shi, Chuyu Lin, Jiangnan Yue, Zhiquan Liu, Wei Xie, Naweed I. Naqvi, Yanjun Kou, Zeng Tao
Rice Science.2022; 29(4): 363. CrossRef - Protein acetylation and deacetylation in plant‐pathogen interactions
Jing Wang, Chao Liu, Yun Chen, Youfu Zhao, Zhonghua Ma
Environmental Microbiology.2021; 23(9): 4841. CrossRef - Emerging Roles of Posttranslational Modifications in Plant-Pathogenic Fungi and Bacteria
Wende Liu, Lindsay Triplett, Xiao-Lin Chen
Annual Review of Phytopathology.2021; 59(1): 99. CrossRef - Fungal Lysine Deacetylases in Virulence, Resistance, and Production of Small Bioactive Compounds
Ingo Bauer, Stefan Graessle
Genes.2021; 12(10): 1470. CrossRef - A Histone Deacetylase, Magnaporthe oryzae RPD3, Regulates Reproduction and Pathogenic Development in the Rice Blast Fungus
Song Hee Lee, Mohamed El-Agamy Farh, Jaejoon Lee, Young Taek Oh, Eunbyeol Cho, Jiyeun Park, Hokyoung Son, Junhyun Jeon, Antonio Di Pietro
mBio.2021;[Epub] CrossRef - The Histone Deacetylases MoRpd3 and MoHst4 Regulate Growth, Conidiation, and Pathogenicity in the Rice Blast Fungus Magnaporthe oryzae
Chaoxiang Lin, Xue Cao, Ziwei Qu, Shulin Zhang, Naweed I. Naqvi, Yi Zhen Deng, Aaron P. Mitchell
mSphere.2021;[Epub] CrossRef - Histone Acetyltransferases and Deacetylases Are Required for Virulence, Conidiation, DNA Damage Repair, and Multiple Stresses Resistance of Alternaria alternata
Haijie Ma, Lei Li, Yunpeng Gai, Xiaoyan Zhang, Yanan Chen, Xiaokang Zhuo, Yingzi Cao, Chen Jiao, Fred G. Gmitter, Hongye Li
Frontiers in Microbiology.2021;[Epub] CrossRef - Function of PoLAE2, a laeA homolog, in appressorium formation and cAMP signal transduction in Pyricularia oryzae
Pradabrat Prajanket, Kim-Chi Thi Vu, Jun Arai, Worawan Sornkom, Ayumi Abe, Teruo Sone
Bioscience, Biotechnology, and Biochemistry.2020; 84(11): 2401. CrossRef - A Histone Deacetylase, MoHDA1 Regulates Asexual Development and Virulence in the Rice Blast Fungus
Taehyun Kim, Song Hee Lee, Young Taek Oh, Junhyun Jeon
The Plant Pathology Journal.2020; 36(4): 314. CrossRef - Protein Acetylation/Deacetylation: A Potential Strategy for Fungal Infection Control
Junzhu Chen, Qiong Liu, Lingbing Zeng, Xiaotian Huang
Frontiers in Microbiology.2020;[Epub] CrossRef
- FolSas2 is a regulator of early effector gene expression during Fusarium oxysporum infection
- Increase in the genetic polymorphism of varicella-zoster virus after passaging in in vitro cell culture
- Hye Rim Hwang , Seok Cheon Kim , Se Hwan Kang , Chan Hee Lee
- J. Microbiol. 2019;57(11):1033-1039. Published online October 28, 2019
- DOI: https://doi.org/10.1007/s12275-019-9429-4
- 318 View
- 0 Download
- 3 Web of Science
- 2 Crossref
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Abstract
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- Primary infections with the varicella-zoster virus (VZV) result in varicella, while latent reactivation leads to herpes zoster. Both varicella and zoster can be prevented by live attenuated vaccines. There have been reports suggesting that both clinical VZV strains and those in vaccine preparations are genetically polymorphic, containing mixtures of both wild-type and vaccine-type sequences at certain vaccine-specific sites. In this study, the genetic polymorphism of the VZV genome was examined by analyzing the frequencies of minor alleles at each nucleotide position. Next-generation sequencing of the clinical VZV strain YC02 passaged in an in vitro cell culture was used to identify genetically polymorphic sites (GPS), where the minor allele frequency (MAF) exceeded 5%. The number of GPS increased by 7.3-fold at high passages (p100) when compared to low passages (p17), although the average MAF remained similar. GPS were found in 6 open reading frames (ORFs) in p17, 35, and 54 ORFs in p60 and p100, respectively. GPS were found more frequently in the dispensable gene group than the essential gene group, but the average MAF was greater in the essential gene group. The most common two major/minor base pairs were A/g and T/c. GPS were found in all three passages at 16 positions, all located in the reiterated (R) region. The population diversity as measured by Shannon entropy increased in p60 and p100. However, the entropy remained unchanged in the R regions.
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Citations
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Hye Rim Hwang, Se Hwan Kang, Chan Hee Lee
Journal of Microbiology.2021; 59(7): 702. CrossRef - Genetic diversity through social heterosis can increase virulence in RNA viral infections and cancer progression
Saba Ebrahimi, Peter Nonacs
Royal Society Open Science.2021;[Epub] CrossRef
- Genetic changes in plaque-purified varicella vaccine strain Suduvax during in vitro propagation in cell culture
- Anti-varicella-zoster virus activity of cephalotaxine esters in vitro
- Jung-Eun Kim , Yoon-Jae Song
- J. Microbiol. 2019;57(1):74-79. Published online November 19, 2018
- DOI: https://doi.org/10.1007/s12275-019-8514-z
- 366 View
- 0 Download
- 34 Web of Science
- 34 Crossref
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Abstract
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- Harringtonine (HT) and homoharringtonine (HHT), alkaloid esters isolated from the genus Cephalotaxus, exhibit antitumor activity. A semisynthetic HHT has been approved for treatment of chronic myelogenous leukemia. In addition to antileukemic activity, HT and HHT are reported to possess potent antiviral activity. In this study, we investigated the effects of HT and HHT on replication of varicella-zoster virus (VZV) in vitro. HT and HHT, but not their biologically inactive parental alkaloid cephalotaxine (CET), significantly inhibited replication of recombinant VZV-pOka luciferase. Furthermore, HT and HHT, but not CET, strongly induced down-regulation of VZV lytic genes and exerted potent antiviral effects against a VZV clinical isolate. The collective data support the utility of HT and HHT as effective antiviral candidates for treatment of VZV-associated diseases.
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Citations
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Jinhong Cai, Shenghong Guan, Xueli Hu, Xuezhao Chen, Xiaosun Liu, Shouxin Li, Jingkui Tian, Ping Wang, Hua Gu, Xiaoyong Zhang
Journal of AOAC International.2025; 108(1): 62. CrossRef - Recent Total Syntheses of Cephalotaxine‐Type Alkaloids and Their Structural Diversification (2021–2024): An Update
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Asian Journal of Organic Chemistry.2025;[Epub] CrossRef - Inhibitory effect of Alantolactone against varicella-zoster virus in vitro
Xinna Wu, Yunchuang Chang, Chengcheng Kong, Zhiwei Ding, Dongli Pan, Ping Lin, Sanying Wang, Genxiang Mao
Virology Journal.2025;[Epub] CrossRef - Alkaloids in the <italic>Cephalotaxus</italic> plants and the biosynthesis of phenethylisoquinolines: a review
Hao Yan, Wei Li, Hao Wang, Shengzhuo Huang, Pengwei Chen, Jun Zeng, Jiahong Zhu, Yuji Li, Wenli Mei, Haofu Dai
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Frontiers in Veterinary Science.2025;[Epub] CrossRef - Homoharringtonine: updated insights into its efficacy in hematological malignancies, diverse cancers and other biomedical applications
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Yang Xu, Junming Liang, Yushu Yan, Dejuan Sun, Hua Li, Lixia Chen
Phytochemistry Reviews.2024; 23(3): 657. CrossRef - Molecular insights into the inhibition mechanism of harringtonine against essential proteins associated with SARS-CoV-2 entry
Zhiwei Yang, Xinyue Fu, Yizhen Zhao, Xuhua Li, Jiangang Long, Lei Zhang
International Journal of Biological Macromolecules.2023; 240: 124352. CrossRef - The Transmembrane Protease TMPRSS2 as a Therapeutic Target for COVID-19 Treatment
Lukas Wettstein, Frank Kirchhoff, Jan Münch
International Journal of Molecular Sciences.2022; 23(3): 1351. CrossRef - Disease Markers and Therapeutic Targets for Rheumatoid Arthritis Identified by Integrating Bioinformatics Analysis with Virtual Screening of Traditional Chinese Medicine
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Frontiers in Bioscience-Landmark.2022;[Epub] CrossRef - Harringtonine Ester Derivatives with Enhanced Antiproliferative Activities against HL-60 and HeLa Cells
Akihiro Ochi, Makoto Yoritate, Tomofumi Miyamoto, Kazuteru Usui, Gorawit Yusakul, Waraporn Putalun, Hiroyuki Tanaka, Go Hirai, Satoshi Morimoto, Seiichi Sakamoto
Journal of Natural Products.2022; 85(2): 345. CrossRef - Clinical Management of Herpes Simplex Virus Keratitis
Bisant A. Labib, DeGaulle I. Chigbu
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Planta Medica.2022; 88(12): 1047. CrossRef - Rapid classification and identification of chemical constituents in Epimedium koreanum Nakai by UPLC‐Q‐TOF‐MS combined with data post‐processing techniques
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- An Integrated Strategy for Establishing the Chemical Profile of Premna Microphylla Turcz. Leaves and Metabolites in Vivo
- Analysis of IE62 mutations found in Varicella-Zoster virus vaccine strains for transactivation activity
- Hyemin Ko , Gwang Myeong Lee , Ok Sarah Shin , Moon Jung Song , Chan Hee Lee , Young Eui Kim , Jin-Hyun Ahn
- J. Microbiol. 2018;56(6):441-448. Published online June 1, 2018
- DOI: https://doi.org/10.1007/s12275-018-8144-x
- 315 View
- 0 Download
- 2 Crossref
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Abstract
PDF
- Live attenuated vaccine strains have been developed for Varicella- Zoster virus (VZV). Compared to clinically isolated strains, the vaccine strains contain several non-synonymous mutations in open reading frames (ORFs) 0, 6, 31, 39, 55, 62, and 64. In particular, ORF62, encoding an immediate-early (IE) 62 protein that acts as a transactivator for viral gene expression, contains six non-synonymous mutations, but whether these mutations affect transactivation activity of IE62 is not understood. In this study, we investigated the role of non-synonymous vaccine-type mutations (M99T, S628G, R958G, V1197A, I1260V, and L1275S) of IE62 in Suduvax, a vaccine strain isolated in Korea, for transactivation activity. In reporter assays, Suduvax IE62 showed 2- to 4-fold lower transactivation activity toward ORF4, ORF28, ORF29, and ORF68 promoters than wild-type IE62. Introduction of individual M99T, S628G, R958G, or V1197A/ I1260V/L1275S mutations into wild-type IE62 did not affect transactivation activity. However, the combination of M99T within the N-terminal Sp transcription factor binding region and V1197A/I1260V/L1275S within the C-terminal serineenriched acidic domain (SEAD) significantly reduced the transactivation activity of IE62. The M99T/V1197A/I1260V/ L1275S mutant IE62 did not show considerable alterations in intracellular distribution and Sp3 binding compared to wild-type IE62, suggesting that other alteration(s) may be responsible for the reduced transactivation activity. Collectively, our results suggest that acquisition of mutations in both Met 99 and the SEAD of IE62 is responsible for the reduced transactivation activity found in IE62 of the VZV vaccine strains and contributes to attenuation of the virus.
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Citations
Citations to this article as recorded by- Heightened incidence of adverse events associated with a live attenuated varicella vaccine strain that lacks critical genetic polymorphisms in open reading frame 62
Ye Ji Kim, Doyeop Oh, Jaehoon Kim, Jeongtae Son, Jae Yun Moon, Ye Kyung Kim, Bin Ahn, Kyu Ri Kang, Daechan Park, Hyun Mi Kang
Clinical Microbiology and Infection.2024; 30(11): 1466. CrossRef - Whole Transcriptome Analyses Reveal Differential mRNA and microRNA Expression Profiles in Primary Human Dermal Fibroblasts Infected with Clinical or Vaccine Strains of Varicella Zoster Virus
Soo-Jin Oh, Sooyeon Lim, Moon Jung Song, Jin Hyun Ahn, Chan Hee Lee, Ok Sarah Shin
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- Promising cellulolytic fungi isolates for rice straw degradation
- Diana Catalina Pedraza-Zapata , Andrea Melissa Sánchez-Garibello , Balkys Quevedo-Hidalgo , Nubia Moreno-Sarmiento , Ivonne Gutiérrez-Rojas
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- 335 View
- 0 Download
- 19 Crossref
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Abstract
PDF
- The objective of this study was to evaluate the potential of eight fungal isolates obtained from soils in rice crops for straw degradation in situ. From the initial eight isolates, Pleurotus ostreatus T1.1 and Penicillium sp. HC1 were selected for further characterization based on qualitative cellulolytic enzyme production and capacity to use rice straw as a sole carbon source. Subsequently, cellulolytic, xylanolytic, and lignolytic (Pleurotus ostreatus) activity on carboxymethyl cellulose, oat xylan, and rice straw with different nitrogen sources was evaluated. From the results obtained it was concluded both isolates are capable to produce enzymes necessary for rice straw degradation. However, their production is dependent upon carbon and nitrogen source. Last, it was established that Pleurotus ostreatus T1.1 and Penicillium sp. HC1 capability to colonize and mineralize rice straw, in mono-and co-culture, without affecting nitrogen soil content.
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Citations
Citations to this article as recorded by- Recent developments in microbial degradation of crop residues: a comprehensive review
K. S. Sruthy, S. Puranik, V. Kumar, A. Kaushik, K. V. Vikram, M. Manoj, L. Shukla, S. K. Singh, A. Kumar
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Meenakshi Verma, Pooja Singh, Manikprabhu Dhanorkar
Paddy and Water Environment.2024; 22(1): 1. CrossRef - Crop residue heterogeneity: Decomposition by potential indigenous ligno-cellulolytic microbes and enzymatic profiling
Sandeep Sharma, Kailash Chand Kumawat, Paawan Kaur, Sukhjinder Kaur, Nihar Gupta
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Jie Zhou, Yanling Li, Jiawen Lou, Yuekai Wang, Zhengrong Kan, Reinhard W. Neugschwandtner, Fengmin Li, Jian Liu, Ke Dong, Yaguang Xue, Haishui Yang, Lingling Shi
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Kunvar Gyanendra Kumar, Raja Husain, Anurag Mishra, Nitin Vikram, Devendra Kumar Dwivedi, Saurabh Pandey, Ashutosh Singh
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Shir Nee Ong, Chin Mei Lee
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Ayumi Shikata, Junjarus Sermsathanaswadi, Phakhinee Thianheng, Sirilak Baramee, Chakrit Tachaapaikoon, Rattiya Waeonukul, Patthra Pason, Khanok Ratanakhanokchai, Akihiko Kosugi
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- Characterization and phylogenetic analysis of Varicella-zoster virus strains isolated from Korean patients
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- DOI: https://doi.org/10.1007/s12275-017-7171-3
- 348 View
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- 6 Crossref
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Abstract
PDF
- Varicella-zoster virus (VZV) is a causative agent of chickenpox in primary infection and shingles after its reactivation from latency. Complete or almost-complete genomic DNA sequences for various VZV strains have been reported. Recently, clinical VZV strains were isolated from Korean patients whose genome was sequenced using high-throughput sequencing technology. In this study, we analyzed single nucleotide polymorphism (SNP) of VZV strains to genetically characterize Korean clinical isolates. Phylogenetic analyses revealed that three Korean strains, YC01, YC02, and YC03, were linked to clade 2. Comprehensive SNP analysis identified 86 sites specific for the 5 VZV clades. VZV strains isolated from Korea did not form a phylogenetic cluster. Rather, YC02 and YC03 clustered strongly with Chinese strain 84-7 within clade 2, more specifically cluster 2a. Signature sequences for the cluster 2a were identified and found to play an important role in the separation of cluster 2a strains from other clade 2 strains, as shown in substitution studies. Further genetic analysis with additional strains isolated from Japan, China, and other Asian countries would provide a novel insight into the significance of two distinct subclades within clade 2.
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Eun-Jeong Jang, Sivilay Xayaheuang, Ji-Young Hwang, Yunhwa Kim, Kyung-Min Lee, Seok-Tae Choi, Hye Won Kwak, Jae-Hwan Nam, Keunea Kim, Boomi Yoon, Jae Hyang Lim, Ho Seong Seo, Chang-Hoon Woo, Hosun Park
Human Vaccines & Immunotherapeutics.2025;[Epub] CrossRef - Cross-reactive humoral immunity of clade 2 Oka and MAV/06 strain-based varicella vaccines against different clades of varicella–zoster virus
Ji-Young Hwang, Yunhwa Kim, Kyung-Min Lee, Ok Sarah Shin, Jeong-An Gim, Younchul Shin, Hosun Park
Human Vaccines & Immunotherapeutics.2023;[Epub] CrossRef - Assessment of attenuation of varicella‐zoster virus vaccines based on genomic comparison
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Journal of Medical Virology.2023;[Epub] CrossRef - Immunological characteristics of MAV/06 strain of varicella-zoster virus vaccine in an animal model
Duckhyang Shin, Younchul Shin, Eunmi Kim, Hyojung Nam, Haiyan Nan, Jaewoo Lee
BMC Immunology.2022;[Epub] CrossRef - Human herpesvirus diversity is altered in HLA class I binding peptides
William H. Palmer, Marco Telford, Arcadi Navarro, Gabriel Santpere, Paul J. Norman
Proceedings of the National Academy of Sciences.2022;[Epub] CrossRef - Genetic Change of Varicella-Zoster Virus Propagated in Cell Culture in Non-Natural Conditions
Sang Hoon Yeon, Ji Seon Park, Se Hwan Kang, Chan Hee Lee
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- Impact of tillage practices on soil bacterial diversity and composition under the tobacco-rice rotation in China
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- 378 View
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- 29 Crossref
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Abstract
PDF
- Tobacco-rice rotation is a common farming system in south China, and many tillage practices such as straw mulching, do-lomite dust, and quicklime application have been adopted to improve crop production. These agricultural management practices alter soil physical and chemical properties and affect microbial life environment and community composition. In this research, six tillage practices including no tobacco and rice straw mulching (CK), tobacco and rice straw mulching (TrSr), rice straw returning fire (TrSc), tobacco and rice straw mulching with dolomite dust (TSD), rice straw returning fire and quicklime (TSQ), and rice straw returning fire, quicklime and reduced fertilizer (TSQf) were conducted to detect changes in soil bacterial diversity and composition using Illumina se-quencing. The results showed that the total number of opera-tional taxonomic units (OTUs) from the six treatments was 2030, and the number of mutual OTUs among all samples was 550. The TrSc treatment had the highest diversity and richness, while TSQf had the lowest. Soil physio-chemical properties and microbial diversity can influence each other. Proteobacteria and Actinobacteria had the greatest propor-tion in all treatments. The abundance of Nitrospirae was the highest in the TrSc treatment. The TSQf treatment had the highest abundance of Firmicutes. The abundance of Nitrospira in the TrSc treatment was 2.29-fold over CK. Streptomyces affiliated with Firmicutes improved by 37.33% in TSQf com-pared to TSQ. TSQf treatment was considered to be the most important factor in determining the relative abundance at the genus level.
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Scientific Reports.2024;[Epub] CrossRef - Microbial community change and quality improve via endophytic colonization of tobacco by Saccharomyces cerevisiae
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PLOS ONE.2023; 18(1): e0270944. CrossRef - Soil bacterial community composition in rice-turtle coculture systems with different planting years
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Frontiers in Environmental Science.2018;[Epub] CrossRef
- Investigation into the impact of chloride ion uptake inhibitors on tobacco plants
- Dynamics of bacterial communities in rice field soils as affected by different long-term fertilization practices
- Jae-Hyung Ahn , Shin Ae Lee , Jeong Myeong Kim , Myung-Sook Kim , Jaekyeong Song , Hang-Yeon Weon
- J. Microbiol. 2016;54(11):724-731. Published online October 29, 2016
- DOI: https://doi.org/10.1007/s12275-016-6463-3
- 338 View
- 0 Download
- 28 Crossref
-
Abstract
PDF
- Fertilization and the response of the soil microbial community to the process significantly affect crop yield and the environment. In this study, the seasonal variation in the bacterial communities in rice field soil subjected to different fertilization treatments for more than 50 years was investigated using 16S rRNA sequencing. The simultaneous application of inorganic fertilizers and rice straw compost (CAPK) maintained the species richness of the bacterial communities at levels higher than that in the case of non-fertilization (NF) and application of inorganic fertilizers only (APK) in the initial period of rice growth. The seasonal variation in the bacterial community structure in the NF and APK plots showed cyclic behavior, suggesting that the effect of season was important; however, no such trend was observed in the CAPK plot. In the CAPK plot, the relative abundances of putative copiotrophs such as Bacteroidetes, Firmicutes, and Proteobacteria were higher and those of putative oligotrophs such as Acidobacteria and Plactomycetes were lower than those in the other plots. The relative abundances of organotrophs with respiratory metabolism, such as Actinobacteria, were lower and those of chemoautotrophs that oxidize reduced iron and sulfur compounds were higher in the CAPK plot, suggesting greater carbon storage in this plot. Increased methane emission and nitrogen deficiency, which were inferred from the higher abundances of Methylocystis and Bradyrhizobium in the CAPK plot, may be a negative effect of rice straw application; thus, a solution for these should be considered to increase the use of renewable resources in agricultural lands.
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Citations
Citations to this article as recorded by- Straw return enhances the global warming potential in paddy soil under the regulation of functional genes
Ziying Cui, Jingli Wei, Yukun Pan, Wen Zhang, Jialong Lv, Yajun Yang
Environmental Technology & Innovation.2025; 39: 104293. CrossRef - Ramifications of crop residue loading for soil microbial community composition, activity and nutrient supply
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Xiran Zhao, Jun Li, Xin Hu, Baowei Hu, Guixin Chu, Rui Tao
Journal of Soils and Sediments.2023; 23(5): 2175. CrossRef - A 40 % paddy surface soil organic carbon increase after 5-year no-tillage is linked with shifts in soil bacterial composition and functions
Jian-Ying Qi, Xiang-Bin Yao, Jian Lu, Long-Xin He, Jun-Li Cao, Zheng-Rong Kan, Xing Wang, Sheng-Gang Pan, Xiang-Ru Tang
Science of The Total Environment.2023; 859: 160206. CrossRef - Bacterial community of agricultural soils used for potato cultivation in Sverdlovsk region
E. P. Shanina, G. A. Lihodeevskiy
Agricultural Science Euro-North-East.2023; 24(6): 989. CrossRef - Ratio of carbon and nitrogen in fertilizer treatment drives distinct rhizosphere microbial community composition and co-occurrence networks
Ruifen Zhu, Chang Liu, Yuan Dong Xu, Wei He, Jielin Liu, Jishan Chen, Yajun An, Shangli Shi
Frontiers in Microbiology.2022;[Epub] CrossRef - The effect of environmental parameters and fertilization practices on yield and soil microbial diversity in a Kenyan paddy rice field
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Applied Soil Ecology.2022; 176: 104495. CrossRef - Bacterial Diversity and Potential Functions in Response to Long-Term Nitrogen Fertilizer on the Semiarid Loess Plateau
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Microorganisms.2022; 10(8): 1579. CrossRef - Continental-Scale Paddy Soil Bacterial Community Structure, Function, and Biotic Interaction
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mSystems.2021;[Epub] CrossRef - Methanogenesis and Methane Oxidation in Paddy Fields under Organic Fertilization
Chungwoo Kim, Denver I. Walitang, Tongmin Sa
Korean Journal of Environmental Agriculture.2021; 40(4): 295. CrossRef - Insights into endophytic bacterial diversity of rice grown across the different agro-ecological regions of West Bengal, India
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World Journal of Microbiology and Biotechnology.2021;[Epub] CrossRef - Response of root nutrient resorption strategies to rhizosphere soil microbial nutrient utilization along Robinia pseudoacacia plantation chronosequence
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Forest Ecology and Management.2021; 489: 119053. CrossRef - Organic Manure Management Increases Soil Microbial Community Structure and Diversity in the Double-cropping Rice Paddy Field of Southern China
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Organic Agriculture.2021; 11(4): 553. CrossRef - Profiles of wheat rhizobacterial communities in response to repeated glyphosate applications, crop rotation, and tillage
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X. C. Zhu, L. Y. Sun, F. B. Song, S. Q. Liu, F. L. Liu, X. N. Li
European Journal of Soil Science.2018; 69(5): 924. CrossRef - Pyrosequencing reveals profiles of soil bacterial communities after 12 years of conservation management on irrigated crop rotations
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Applied Soil Ecology.2017; 121: 65. CrossRef
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Research Support, Non-U.S. Gov'ts
- Enhanced Production of Carboxymethylcellulase by a Marine Bacterium, Bacillus velezensis A-68, by Using Rice Hulls in Pilot-scale Bioreactor under Optimized Conditions for Dissolved Oxygen
- Wa Gao , Hye-Jin Kim , Chung-Han Chung , Jin-Woo Lee
- J. Microbiol. 2014;52(9):755-761. Published online July 30, 2014
- DOI: https://doi.org/10.1007/s12275-014-4156-3
- 282 View
- 0 Download
- 8 Crossref
-
Abstract
PDF
- The optimal conditions for the production of carboxymethylcellulase (CMCase) by Bacillus velezensis A-68 at a flask scale have been previously reported. In this study, the parameters involved in dissolved oxygen in 7 and 100 L bioreactors were optimized for the pilot-scale production of CMCase. The optimal agitation speed and aeration rate for cell growth of B. velezensis A-68 were 323 rpm and 1.46 vvm in a 7 L bioreactor, whereas those for the production of CMCase were 380 rpm and 0.54 vvm, respectively. The analysis of variance (ANOVA) implied that the highly significant factor for cell growth was the aeration rate, whereas that for the production of CMCase was the agitation speed. The optimal inner pressures for cell growth and the production of CMCase by B. velezensis A-68 in a 100 L bioreactor were 0.00 and 0.04 MPa, respectively. The maximal production of CMCase in a 100 L bioreactor under optimized conditions using rice hulls was 108.1 U/ml, which was 1.8 times higher than that at a flask scale under previously optimized conditions.
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Environmental Research.2021; 200: 111455. CrossRef - Biochemical and Molecular Characterization of Five Bacillus Isolates Displaying Remarkable Carboxymethyl Cellulase Activities
Esraa Abd Elhameed, Alaa R. M. Sayed, Tharwat E. E. Radwan, Gamal Hassan
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Chung-Il Park, Jae-Hong Lee, Jianhong Li, Jin-Woo Lee
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Miao Ye, Xiangfang Tang, Ru Yang, Hongfu Zhang, Fangshu Li, Fangzheng Tao, Fei Li, Zaigui Wang
ACS Chemical Biology.2018; 13(3): 500. CrossRef - Comparison of optimal conditions for mass production of carboxymethylcellulase by Escherichia coli JM109/A-68 with other recombinants in pilot-scale bioreactor
Myung-Hwan Kim, Wa Gao, Chung-Han Chung, Jin-Woo Lee
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Myung-Hwan Kim, Duk-Un Kang, Jin-Woo Lee
Biotechnology and Bioprocess Engineering.2016; 21(5): 601. CrossRef
- Utilization of shrimp heads for scaling up of production of Bacillus velezensis EB.KN15, its bioactive compounds and novel anti-fungal effect against durian pathogen fungi
- Diversity of the Bacterial Community in the Rice Rhizosphere Managed Under Conventional and No-tillage Practices
- Zubair Aslam , Muhammad Yasir , Hwan Sik Yoon , Che Ok Jeon , Young Ryun Chung
- J. Microbiol. 2013;51(6):747-756. Published online December 19, 2013
- DOI: https://doi.org/10.1007/s12275-013-2528-8
- 381 View
- 0 Download
- 27 Crossref
-
Abstract
PDF
-
Bacterial diversity in the rice rhizosphere at different rice
growth stages, managed under conventional and no-tillage
practices, was explored using a culture-based approach.
Actinobacteria are among the bacterial phyla abundant in
the rice rhizosphere. Their diversity was further examined by
constructing metagenomic libraries based on the 16S rRNA
gene, using actinobacterial- and streptomycete-specific polymerase
chain reaction (PCR) primers. The study included
132 culturable strains and 125 clones from the 16S rRNA gene
libraries. In conventional tillage, there were 38% Proteobacteria,
22% Actinobacteria, 33% Firmicutes, 5% Bacteroidetes,
and 2% Acidobacteria, whereas with no-tillage management
there were 63% Proteobacteria, 24% Actinobacteria, 6% Firmicutes,
and 8% Bacteroidetes as estimated using the culturedependent
method
during the four stages of rice cultivation. Principal coordinates analysis was used to cluster the bacterial communities along axes of maximal variance. The different growth stages of rice appeared to influence the rhizosphere bacterial profile for both cultivation practices. Novel clones with low similarities (89–97%) to Actinobacteria and Streptomyces were retrieved from both rice fields by screening the 16S rRNA gene libraries using actinobacterial- and streptomycete-specific primers. By comparing the actinobacterial community retrieved by culture-dependent and molecular methods, it was clear that a more comprehensive assessment of microbial diversity in the rice rhizosphere can be obtained using a combination of both techniques than by using either method alone. We also succeeded in culturing a number of bacteria that were previously described as unculturable. These were in a phylogenetically deep lineage when compared with related cultivable genera. -
Citations
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Chemical and Biological Technologies in Agriculture.2024;[Epub] CrossRef - Soil and Phytomicrobiome for Plant Disease Suppression and Management under Climate Change: A Review
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PLOS ONE.2021; 16(9): e0256970. CrossRef - Soil Bacterial Diversity and Potential Functions Are Regulated by Long-Term Conservation Tillage and Straw Mulching
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Jorge R. Osman, Gustavo Fernandes, Michael S. DuBow
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Jean Weissenbach, Abdelghani Sghir
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Mohammad Tofajjal Hossain, Ajmal Khan, Eu Jin Chung, Md. Harun-Or Rashid, Young Ryun Chung
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A. Tkacz, P. Poole
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Shyamalina Haldar, Sanghamitra Sengupta
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- Synergistic interplay of microbial probiotics in rice rhizosphere: A sustainable strategy for bacterial blight management through microbiome engineering
- Quantification of Rice Sheath Blight Progression Caused by Rhizoctonia solani
- Mukhamad Su’udi , Jong-Mi Park , Woo-Ri Kang , Duk-Ju Hwang , Soonok Kim , Il-Pyung Ahn
- J. Microbiol. 2013;51(3):380-388. Published online June 28, 2013
- DOI: https://doi.org/10.1007/s12275-013-3274-7
- 183 View
- 0 Download
- 9 Scopus
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Abstract
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- Rhizoctonia solani has a wide host range, including almost all cultivated crops and its subgroup anastomosis group (AG)-1 IA causes sheath blight in rice. An accurate measurement of pathogen’s biomass is a convincing tool for enumeration of this disease. Mycological characteristics and molecular diagnosis simultaneously supported that all six strains in this study were R. solani AG-1 IA. Heterokaryons between strains Rs40104, Rs40105, and Rs45811 were stable and viable, whereas Rs40103 and Rs40106 did not form viable fused cells, except for the combination of Rs40106 and Rs40104. A primer pair was highly specific to RsAROM gene of R. solani strains and the amplified fragment exists as double copies within fungal genome. The relationship between crossing point (CP) values and the amount of fungal DNA was reliable (R2>0.99). Based on these results, we determined R. solani’s proliferation within infected stems through real time PCR using a primer pair and a Taqman probe specific to the RsAROM gene. The amount of fungal DNA within the 250 ng of tissue DNA from rice cv. Dongjin infected with Rs40104, Rs40105, and Rs45811 were 7.436, 5.830, and 5.085 ng, respectively. In contrast, the fungal DNAs within the stems inoculated with Rs40103 and Rs40106 were 0.091 and 0.842 ng. The sheath blight symptom progression approximately coincided with the amount of fungal DNA within the symptoms. In summary, our quantitative evaluation method provided reliable and objective results reflecting the amount of fungal biomass within the infected tissues and would be useful for evaluation of resistance germplasm or fungicides and estimation of inoculum potential.
- Quantification of Rice Brown Leaf Spot through Taqman Real-Time PCR Specific to the Unigene Encoding Cochliobolus miyabeanus SCYTALONE DEHYDRATASE1 Involved in Fungal Melanin Biosynthesis
- Mukhamad Su’udi , Jong-Mi Park , Woo-Ri Kang , Sang-Ryeol Park , Duk-Ju Hwang , Il-Pyung Ahn
- J. Microbiol. 2012;50(6):947-954. Published online December 30, 2012
- DOI: https://doi.org/10.1007/s12275-012-2538-y
- 271 View
- 0 Download
- 5 Crossref
-
Abstract
PDF
- Rice brown leaf spot is a major disease in the rice paddy field. The causal agent Cochliobolus miyabeanus is an ascomycete fungus and a representative necrotrophic pathogen in the investigation of rice-microbe interactions. The aims of this research were to identify a quantitative evaluation method to determine the amount of C. miyabeanus proliferation in planta and determine the method’s sensitivity. Real-time polymerase chain reaction (PCR) was employed in combination with the primer pair and Taqman probe specific to CmSCD1, a C. miyabeanus unigene encoding SCYTALONE DEHYDRATASE, which is involved in fungal melanin biosynthesis. Comparative analysis of the nucleotide sequences of CmSCD1 from Korean strains with those from the Japanese and Taiwanese strains revealed some sequence differences. Based on the crossing point (CP) values from Taqman realtime PCR containing a series of increasing concentrations of cloned amplicon or fungal genomic DNA, linear regressions with a high level of reliability (R2>0.997) were constructed. This system was able to estimate fungal genomic DNA at the picogram level. The reliability of this equation was further confirmed using DNA samples from both resistant and susceptible cultivars infected with C. miyabeanus. In summary, our quantitative system is a powerful alternative in brown leaf spot forecasting and in the consistent evaluation of disease progression.
-
Citations
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Everlyne M. Nganga, Martina Kyallo, Philemon Orwa, Felix Rotich, Emily Gichuhi, John M. Kimani, David Mwongera, Bernice Waweru, Phoebe Sikuku, David M. Musyimi, Samuel K. Mutiga, Cathrine Ziyomo, Rosemary Murori, Lusike Wasilwa, James C. Correll, Nicholas
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Journal of Microbiology.2013; 51(6): 858. CrossRef
- Foliar Diseases and the Associated Fungi in Rice Cultivated in Kenya
- Characterization of the Bacterial and Archaeal Communities in Rice Field Soils Subjected to Long-Term Fertilization Practices
- Jae-Hyung Ahn , Jaekyeong Song , Byung-Yong Kim , Myung-Sook Kim , Jae-Ho Joa , Hang-Yeon Weon
- J. Microbiol. 2012;50(5):754-765. Published online November 4, 2012
- DOI: https://doi.org/10.1007/s12275-012-2409-6
- 185 View
- 0 Download
- 115 Scopus
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Abstract
- The bacterial and archaeal communities in rice field soils subjected to different fertilization regimes for 57 years were investigated in two different seasons, a non-planted, drained season (April) and a rice-growing, flooded season (August), by performing soil dehydrogenase assay, real-time PCR assay and pyrosequencing analysis. All fertilization regimes increased the soil dehydrogenase activity while the abundances of bacteria and archaea increased in the plots receiving inorganic fertilizers plus compost and not in those receiving inorganic fertilizers only. Rice-growing and flooding decreased the soil dehydrogenase activity while they increased the bacterial diversity in rice field soils. The bacterial communities were dominated by Chloroflexi, Proteobacteria, and Actinobacteria and the archaeal communities by Crenarchaeota at the phylum level. In principal coordinates analysis based on the weighted Fast UniFrac metric, the bacterial and archaeal communities were separated primarily by season, and generally distributed along with soil pH, the variation of which had been caused by long-term fertilization. Variations in the relative abundance according to the season or soil pH were observed for many bacterial and archaeal groups. In conclusion, the microbial activity, prokaryotic abundance and diversity, and prokaryotic community structure in the rice field soils were changed by season and long-term fertilization.
- Antifungal Activity of Leuconostoc citreum and Weissella confusa in Rice Cakes
- Eunjong Baek , Hyojin Kim , Hyejung Choi , Sun Yoon , Jeongho Kim
- J. Microbiol. 2012;50(5):842-848. Published online November 4, 2012
- DOI: https://doi.org/10.1007/s12275-012-2153-y
- 249 View
- 0 Download
- 39 Crossref
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Abstract
- The antifungal activity of organic acids greatly improves the shelf life of bread and bakery products. However, little is known about the effect of lactic acid fermentation on fungal contamination in rice cakes. Here, we show that lactic acid fermentation in rice dough can greatly retard the growth of three fungal species when present in rice cakes, namely Cladosporium sp. YS1, Neurospora sp. YS3, and Penicillium crustosum YS2. The antifungal activity of the lactic acid bacteria against these fungi was much better than that of 0.3% calcium propionate. We found that organic acids including lactic and acetic acid, which are byproducts of lactic fermentation or can be artificially added, were the main antifungal substances. We also found that some Leuconostoc citreum and Weissella confusa strains could be good starter species for rice dough fermentation. These results imply that these lactic acid bacteria can be applicable to improve the preservation of rice cakes.
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- Characterization and Screening of Plant Probiotic Traits of Bacteria Isolated from Rice Seeds Cultivated in Argentina
- Dante Ruiza , Betina Agaras , Patrice de Werrab , Luis G. Wall , Claudio Valverde
- J. Microbiol. 2011;49(6):902-912. Published online December 28, 2011
- DOI: https://doi.org/10.1007/s12275-011-1073-6
- 376 View
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- 49 Crossref
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Abstract
PDF
- Many seeds carry endophytes, which ensure good chances of seedling colonization. In this work, we have studied the seed-borne bacterial flora of rice varieties cultivated in the northeast of Argentina. Surface-sterilized husked seeds of the rice cultivars CT6919, El Paso 144, CAMBA, and IRGA 417 contained an average of 5×106 CFU/g of mesophilic and copiotrophic bacteria. Microbiological, physiological, and molecular characterization of a set of 39 fast-growing isolates from the CT6919 seeds revealed an important diversity of seed-borne mesophiles and potential plant probiotic activities, including diazotrophy and antagonism of fungal pathogens. In fact, the seed-borne bacterial flora protected the rice seedlings against Curvularia sp. infection. The root colonization pattern of 2 Pantoea isolates from the seeds was studied by fluorescence microscopy of the inoculated axenic rice seedlings. Both isolates strongly colonized the site of emergence of the lateral roots and lenticels, which may represent the entry sites for endophytic spreading. These findings suggest that rice plants allow grain colonization by bacterial species that may act as natural biofertilizers and bioprotectives early from seed germination.
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- Sequence and Phylogenetic Analyses of Novel Glucosyltransferase Genes of Mutans Streptococci Isolated from Pig Oral Cavity
- Noriko Shinozaki-Kuwahara , Kazuko Takada , Masatomo Hirasawa
- J. Microbiol. 2008;46(2):202-208. Published online June 11, 2008
- DOI: https://doi.org/10.1007/s12275-007-0199-z
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- Nucleotide sequences of water-insoluble glucan-producing glucosyltransferase (gtf) genes of new mutans streptococci isolated from pig oral cavity, Streptococcus orisuis JCM14035, and of Streptococcus criceti HS-6 were determined. The gtf gene of S. orisuis JCM14035 consisted of a 4,401 bp ORF encoding for a 1,466 amino acids, and was revealed to belong to the gtfI group. The percent homology of amino acid sequence of the GTF-I from S. orisuis and S. criceti are 95.0%, however, this score ranges from 77.0% to 78.0% when compared to Streptococcus sobrinus 6715. The deduced N-terminal amino acid sequence was considered responsible for the secretion of GTF-I in S. orisuis JCM14035 and S. criceti HS-6 with high similarity to known GTF proteins from other streptococci. In addition, two other conserved regions, i.e., N-terminal putative catalytic-site and C-terminal glucan binding domain, were also found in GTF-Is of S. orisuis JCM14035 and S. criceti HS-6. Phylogenetic analysis suggested that S. orisuis JCM14035 and S. criceti HS-6, closely related to each other, resemble S. sobrinus and S. downei based on the amino acid sequences of the GTFs.
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Citations
Citations to this article as recorded by- Bacterial α-Glucan and Branching Sucrases from GH70 Family: Discovery, Structure–Function Relationship Studies and Engineering
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Microbiology and Immunology.2013; 57(5): 359. CrossRef - Sequence and phylogenetic analyses of the water‐soluble glucan synthesizing‐glucosyltransferase genes of Streptococcus dentirousetti
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Microbiology and Immunology.2013; 57(5): 386. CrossRef -
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orisasini sp. nov. and
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dentasini sp. nov., isolated from the o
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International Journal of Systematic and Evolutionary Microbiology .2013; 63(Pt_8): 2782. CrossRef - gbpC Gene Repertoire Variation among Mutans Streptococci
Yuki Kojima, Kazuko Okamoto-Shibayama, Yutaka Sato, Toshifumi Azuma
The Bulletin of Tokyo Dental College.2012; 53(2): 51. CrossRef - Phylogenetic Analyses of the Water-Insoluble Glucan Synthesizing Glucosyltransferase Gene of Streptococcus ratti
Ryotaro Hirata
International Journal of Oral-Medical Sciences.2011; 9(3): 167. CrossRef -
Streptococcus dentapri sp. nov., isolated from the wild boar oral cavity
Kazuko Takada, Kazuhiko Hayashi, Yutaka Sato, Masatomo Hirasawa
International Journal of Systematic and Evolutionary Microbiology .2010; 60(4): 820. CrossRef - Comparative evaluation of antioxidant, nitrite scavenging, and antitumor effects of Antrodia camphorata extract
Wol-Suk Cha, Ji-Lu Ding, DuBok Choi
Biotechnology and Bioprocess Engineering.2009; 14(2): 232. CrossRef - Sequence and Phylogenetic Analyses of the Glucosyltransferase Gene of Mutans Streptococci Isolated from the Fruit Bat Oral Cavity
Noriko Shinozaki-Kuwahara, Kazuko Takada, Hiroyuki Kawabe, Koichiro Shida, Masatomo Hirasawa
International Journal of Oral-Medical Sciences.2009; 7(3): 176. CrossRef - Cariogenicity of Three Kinds of Mutans Streptococci from Pig Oral Cavity
Yasutaka Yamaguchi
International Journal of Oral-Medical Sciences.2008; 7(2): 67. CrossRef
- Bacterial α-Glucan and Branching Sucrases from GH70 Family: Discovery, Structure–Function Relationship Studies and Engineering
- Purification and Characterization of Poly(3-hydroxybutyrate) Depolymerase from a Fungal Isolate, Emericellopsis minima W2
- Do Young Kim , Ji Hye Yun , Hyung Woo Kim , Kyung Sook Bae , Young Ha Rhee
- J. Microbiol. 2002;40(2):129-133.
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- The fungus, Emericellopsis minima W2, capable of degrading poly(3-hydroxybutyrate) (PHB) was isolated from a waste water sample. Production of the PHB depolymerase from E. minima W2 (PhaZ_Emi ) was significantly repressed in the presence of glucose. PhaZ_Emi was purified by column chromatography on Octyl-Sepharose CL-4B and Sephadex G-100. The molecular mass of the PhaZ_Emi , which consisted of a single polypeptide chain, was estimated to be 48.0 kDa by SDS-PAGE and its pI value was 4.4. The maximum activity of the PhaZ_Emi was observed at pH 9.0 and 55 C. It was significantly inactivated by 1 mM dithiothreitol, 2 mM diisopropyl fluorophosphate, 0.1 mM Tween 80, and 0.1 mM Triton X-100, but insensitive to phenylmethylsulfonyl fluoride and N-ethylmaleimide. The PhaZ_Emi efficiently hydrolyzed PHB and its copolyester with 30 mol% 3-hydroxyvalerate, but did not act on poly(3-hydroxyoctanoate). It also hydrolyzed p-nitrophenylacetate and p-nitrophenylbutyrate but hardly affected the longer-chain forms. The main hydrolysis product of PHB was identified as a dimer of 3-hydroxybutyrate.
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