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- The photosensitizer DH-I-180-3 regulates intracellular bacterial growth by increasing the secretion of proinflammatory cytokines via the NF-κB- and MAPK-mediated signaling pathways and promoting phagosome maturation in Salmonella-infected mouse macrophages
- Hyo-Jung Kim, Eui-Kwon Jeong, Hyo-Ji Lee, Yu-Jin Jung
- Received February 6, 2025 Accepted April 3, 2025 Published online June 4, 2025
- DOI: https://doi.org/10.71150/jm.2502003 [Epub ahead of print]
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Abstract
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Photodynamic therapy (PDT) is a known strategy for treating cancer; in PDT, photosensitizers are activated by light stimulation and then induce reactive oxygen species (ROS) production to damage cancer tissues. Recently evidence has shown that PDT can also be used as a novel treatment strategy to control pathogenic bacteria. In previous studies, the photosensitizer DH-I-180-3 was reported to effectively regulate multidrug-resistant Mycobacterium tuberculosis growth. Here, we confirmed the effects of DH-I-180-3 on the antibacterial activity and inflammatory response of macrophages to Salmonella. Photoactivated DH-I-180-3 regulated intracellular bacterial growth in Salmonella-infected macrophages. Moreover, DH-I-180-3 increased intracellular ROS levels in Salmonella-infected macrophages. The phosphorylation of the intracellular signaling proteins IκBα and JNK1/2 was increased in DH-I-180-3-treated Salmonella-infected macrophages. Additionally, we observed that DH-I-180-3 significantly increased the mRNA expression and protein secretion of the proinflammatory cytokine TNF-α and promoted phagosome maturation by upregulating EEA1, LAMP1, and Cathepsin D in Salmonella-infected macrophages. Overall, these results demonstrate that photoactivated DH-I-180-3 enhances the bactericidal response to intracellular bacterial infection by promoting inflammatory signaling pathways and phagosome maturation. Therefore, DH-I-180-3 has the potential to be developed into PDT for treating bacterial-infection.
- Antiviral effects of heme oxygenase-1 against canine coronavirus and canine influenza virus in vitro
- Jae-Hyeong Kim, Dong-Hwi Kim, Kyu-Beom Lim, Joong-Bok Lee, Seung-Yong Park, Chang-Seon Song, Sang-Won Lee, Dong-Hun Lee, Do-Geun Kim, Hun-Young Yoon, In-Soo Choi
- J. Microbiol. 2025;63(5):e2501029. Published online May 27, 2025
- DOI: https://doi.org/10.71150/jm.2501029
- 144 View
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Abstract
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Supplementary Material -
Heme oxygenase-1 (HO-1) has antioxidant, anti-apoptotic, and anti-inflammatory properties. Emerging evidence shows that HO-1 also exhibits antiviral activity against severe acute respiratory syndrome coronavirus 2, human immunodeficiency virus, hepatitis B virus, and Ebola virus. Its antiviral effects are mediated not only by its enzymatic function but also through the modulation of interferon-related pathways, thereby inhibiting viral replication. In this study, we investigated the antiviral effects of HO-1 on canine coronavirus (CCoV) and canine influenza virus (CIV) H3N2 using cell-based assays. To determine whether HO-1 suppresses CCoV and CIV, cells were treated with hemin to induce HO-1 expression. Hemin treatment successfully induced HO-1 expression in A72 and Madin-Darby canine kidney cells, resulting in the suppression of CCoV and CIV replication. The canine HO-1 gene was cloned into an expression vector and transfected into cells to achieve transient overexpression. Recombinant canine HO-1 protein was expressed in Escherichia coli and purified using an expression vector. HO-1 overexpression suppressed CCoV and CIV replication in cells. Following viral infection, treatment with purified HO-1 protein led to a reduction in viral protein levels. Therefore, both HO-1 expression and exogenous protein treatment effectively inhibited CCoV and CIV replication. Elevated HO-1 protein levels consistently reduced viral RNA and protein expression in vitro. These findings suggest that HO-1 could serve as a potential therapeutic agent for managing viral infections in dogs.
Journal Articles
- Genome Sequencing Highlights the Plant Cell Wall Degrading Capacity of Edible Mushroom Stropharia rugosoannulata
- Mengpei Guo , Xiaolong Ma , Yan Zhou , Yinbing Bian , Gaolei Liu , Yingli Cai , Tianji Huang , Hongxia Dong , Dingjun Cai , Xueji Wan , Zhihong Wang , Yang Xiao , Heng Kang
- J. Microbiol. 2023;61(1):83-93. Published online February 1, 2023
- DOI: https://doi.org/10.1007/s12275-022-00003-7
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Abstract
- The basidiomycetous edible mushroom Stropharia rugosoannulata has excellent nutrition, medicine, bioremediation, and biocontrol properties. S. rugosoannulata has been widely and easily cultivated using agricultural by-products showing strong lignocellulose degradation capacity. However, the unavailable high-quality genome information has hindered the research on gene function and molecular breeding of S. rugosoannulata. This study provided a high-quality genome assembly and annotation from S. rugosoannulata monokaryotic strain QGU27 based on combined Illumina-Nanopore data. The genome size was about 47.97 Mb and consisted of 20 scaffolds, with an N50 of 3.73 Mb and a GC content of 47.9%. The repetitive sequences accounted for 17.41% of the genome, mostly long terminal repeats (LTRs). A total of 15,726 coding gene sequences were putatively identified with the BUSCO score of 98.7%. There are 142 genes encoding plant cell wall degrading enzymes (PCWDEs) in the genome, and 52, 39, 30, 11, 8, and 2 genes related to lignin, cellulose, hemicellulose, pectin, chitin, and cutin degradation, respectively. Comparative genomic analysis revealed that S. rugosoannulata is superior in utilizing aldehyde-containing lignins and is possible to utilize algae during the cultivation.
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Citations
Citations to this article as recorded by
- Analysis of Gene Regulatory Network and Transcription Factors in Different Tissues of the Stropharia rugosoannulata Fruiting Body
Jia Lu, Jing Yan, Na Lu, Jiling Song, Jiayao Lin, Xiaohua Zhou, Xuebing Ying, Zhen Li, Zufa Zhou, Fangjie Yao
Journal of Fungi.2025; 11(2): 123. CrossRef - Evaluation of Genetic Diversity and Agronomic Traits of Germplasm Resources of Stropharia rugosoannulata
Miao Gu, Qiang Chen, Yan Zhang, Yongchang Zhao, Li Wang, Xiangli Wu, Mengran Zhao, Wei Gao
Horticulturae.2024; 10(3): 213. CrossRef - Molecular Profiling of Rice Straw Degradability Discrepancy in Stropharia rugosoannulata Core Germplasm
Wenbing Gong, Yuyu Zeng, Xinru Li, Zhidong Zhao, Nan Shen, Yan Zhou, Yinbing Bian, Yang Xiao
Journal of Agricultural and Food Chemistry.2024; 72(45): 25379. CrossRef - Genome assembly of M. spongiola and comparative genomics of the genus Morchella provide initial insights into taxonomy and adaptive evolution
Qing Meng, Zhanling Xie, Hongyan Xu, Jing Guo, Qingqing Peng, Yanyan Li, Jiabao Yang, Deyu Dong, Taizhen Gao, Fan Zhang
BMC Genomics.2024;[Epub] CrossRef
- Analysis of Gene Regulatory Network and Transcription Factors in Different Tissues of the Stropharia rugosoannulata Fruiting Body
- Regulatory role of cysteines in (2R, 3R)-butanediol dehydrogenase BdhA of Bacillus velezensis strain GH1-13
- Yunhee Choi , Yong-Hak Kim
- J. Microbiol. 2022;60(4):411-418. Published online March 14, 2022
- DOI: https://doi.org/10.1007/s12275-022-2018-y
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- 3 Web of Science
- 3 Crossref
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Abstract
- Bacillus velezensis strain GH1-13 contains a (2R,3R)-butanediol dehydrogenase (R-BDH) BdhA which converts acetoin to R-BD reversibly, however, little is known about its regulatory cysteine and biological significance. We performed sitedirected mutation of three cysteines in BdhA. The C37S mutant had no enzyme activity and the C34S and C177S mutants differed from each other and wild type (WT). After zinc affinity chromatography, 1 mM ZnCl2 treatment resulted in a 3-fold enhancement of the WT activity, but reduced activity of the C34S mutant by more than 2 folds compared to the untreated ones. However, ZnCl2 treatment did not affect the activity of the C177S mutant. Most of the double and triple mutant proteins (C34S/C37S, C34S/C177S, C37S/C177S, and C34S/C37S/C177S) were aggregated in zinc resins, likely due to the decreased protein stability. All of the purified WT and single mutant proteins increased multiple intermolecular disulfide bonds in the presence of H2O2 as the buffer pH decreased from 7.5 to 5.5, whereas an intramolecular disulfide bond of cysteine 177 and another cysteine in the CGIC motif region was likely formed at pH higher than pKa of 7.5. When pH varied, WT and its C34S or C177S mutants reduced acetoin to R-BD at the optimum pH 5.5 and oxidized R-BD to acetoin at the optimum pH 10. This study demonstrated that cysteine residues in BdhA play a regulatory role for the production of acetoin and R-BD depending on pH as well as metal binding and oxidative stress.
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Citations
Citations to this article as recorded by- Significantly enhanced specific activity of Bacillus subtilis (2,3)-butanediol dehydrogenase through computer-aided refinement of its substrate-binding pocket
Bochun Hu, Xiaoqi Xi, Fugang Xiao, Xiaomeng Bai, Yuanyuan Gong, Yifan Li, Xueqin Qiao, Cunduo Tang, Jihong Huang
International Journal of Biological Macromolecules.2024; 281: 136443. CrossRef - Structural and enzymatic characterization of Bacillus subtilis R,R-2,3-butanediol dehydrogenase
Xiaofei Wang, Lingyun Jia, Fangling Ji
Biochimica et Biophysica Acta (BBA) - General Subjects.2023; 1867(4): 130326. CrossRef - Engineering a BsBDHA substrate-binding pocket entrance for the improvement in catalytic performance toward (R)-phenyl-1,2-ethanediol based on the computer-aided design
Bo-Chun Hu, Meng-Ran Li, Ying-Ying Li, Xin-Shuang Yuan, Yu-Ye Hu, Fu-Gang Xiao
Biochemical Engineering Journal.2023; 194: 108907. CrossRef
- Significantly enhanced specific activity of Bacillus subtilis (2,3)-butanediol dehydrogenase through computer-aided refinement of its substrate-binding pocket
Review
- [Minireview]Potential roles of condensin in genome organization and beyond in fission yeast
- Kyoung-Dong Kim
- J. Microbiol. 2021;59(5):449-459. Published online April 20, 2021
- DOI: https://doi.org/10.1007/s12275-021-1039-2
- 64 View
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- 6 Web of Science
- 6 Crossref
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Abstract
- The genome is highly organized hierarchically by the function of structural maintenance of chromosomes (SMC) complex proteins such as condensin and cohesin from bacteria to humans. Although the roles of SMC complex proteins have been well characterized, their specialized roles in nuclear processes remain unclear. Condensin and cohesin have distinct binding sites and mediate long-range and short-range genomic associations, respectively, to form cell cycle-specific genome organization. Condensin can be recruited to highly expressed genes as well as dispersed repeat genetic elements, such as Pol III-transcribed genes, LTR retrotransposon, and rDNA repeat. In particular, mitotic transcription factors Ace2 and Ams2 recruit condensin to their target genes, forming centromeric clustering during mitosis. Condensin is potentially involved in various chromosomal processes such as the mobility of chromosomes, chromosome territories, DNA reannealing, and transcription factories. The current knowledge of condensin in fission yeast summarized in this review can help us understand how condensin mediates genome organization and participates in chromosomal processes in other organisms.
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Citations
Citations to this article as recorded by- Unveiling nucleosome dynamics: A comparative study using all-atom and coarse-grained simulations enhanced by principal component analysis
Abhik Ghosh Moulick, Rutika Patel, Augustine Onyema, Sharon M. Loverde
The Journal of Chemical Physics.2025;[Epub] CrossRef - BMI1s interact with condensin complexes to regulate chromatin 3D structure and gene expression in Arabidopsis
Lingxiao Luo, Minqi Yang, Yue Zhou
aBIOTECH.2025;[Epub] CrossRef - Brewing COFFEE: A Sequence-Specific Coarse-Grained Energy Function for Simulations of DNA−Protein Complexes
Debayan Chakraborty, Balaka Mondal, D. Thirumalai
Journal of Chemical Theory and Computation.2024; 20(3): 1398. CrossRef - Contributions of transcriptional noise to leukaemia evolution: KAT2A as a case-study
Cristina Pina
Philosophical Transactions of the Royal Society B: Biological Sciences.2024;[Epub] CrossRef - Viral remodeling of the 4D nucleome
Kyoung-Dong Kim, Paul M. Lieberman
Experimental & Molecular Medicine.2024; 56(4): 799. CrossRef - BiFCo: visualizing cohesin assembly/disassembly cycle in living cells
Emilio González-Martín, Juan Jiménez, Víctor A Tallada
Life Science Alliance.2023; 6(7): e202301945. CrossRef
- Unveiling nucleosome dynamics: A comparative study using all-atom and coarse-grained simulations enhanced by principal component analysis
Journal Article
- Effects of digested Cheonggukjang on human microbiota assessed by in vitro fecal fermentation
- Vineet Singh , Nakwon Hwang , Gwangpyo Ko , Unno Tatsuya
- J. Microbiol. 2021;59(2):217-227. Published online February 1, 2021
- DOI: https://doi.org/10.1007/s12275-021-0525-x
- 88 View
- 0 Download
- 14 Web of Science
- 14 Crossref
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Abstract
- In vitro fecal fermentation is an assay that uses fecal microbes to ferment foods, the results of which can be used to evaluate the potential of prebiotic candidates. To date, there have been various protocols used for in vitro fecal fermentation- based assessments of food substances. In this study, we investigated how personal gut microbiota differences and external factors affect the results of in vitro fecal fermentation assays. We used Cheonggukjang (CGJ), a Korean traditional fermented soybean soup that is acknowledged as healthy functional diet. CGJ was digested in vitro using acids and enzymes, and then fermented with human feces anaerobically. After fecal fermentation, the microbiota was analyzed using MiSeq, and the amount of short chain fatty acids (SCFAs) were measured using GC-MS. Our results suggest that CGJ was effectively metabolized by fecal bacteria to produce SCFAs, and this process resulted in an increase in the abundance of Coprococcus, Ruminococcus, and Bifidobacterium and a reduction in the growth of Sutterella, an opportunistic pathogen. The metabolic activities predicted from the microbiota shifts indicated enhanced metabolism linked to methionine biosynthesis and depleted chondroitin sulfate degradation. Moreover, the amount of SCFAs and microbiota shifts varied depending on personal microbiota differences. Our findings also suggest that in vitro fecal fermentation of CGJ for longer durations may partially affect certain fecal microbes. Overall, the study discusses the usability of in vitro gastrointestinal digestion and fecal fermentation (GIDFF) to imitate the effects of diet-induced microbiome modulation and its impact on the host.
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Citations
Citations to this article as recorded by- Seeds for Gut Health: Prebiotic potential of seed mucilages from Chia, Fenugreek, Basil, Mustard, and Flaxseed and their impact on adult and toddler's gut microbiome
Kanika Mahra, Vineet Singh, Justina Klingate, Jae-Ho Shin
Future Foods.2025; : 100628. CrossRef - Significance of Soy-Based Fermented Food and Their Bioactive Compounds Against Obesity, Diabetes, and Cardiovascular Diseases
Sushmita Dwivedi, Vineet Singh, Kritika Sharma, Amani Sliti, Mamta Baunthiyal, Jae-Ho Shin
Plant Foods for Human Nutrition.2024; 79(1): 1. CrossRef - Fermented foods: Harnessing their potential to modulate the microbiota-gut-brain axis for mental health
Ramya Balasubramanian, Elizabeth Schneider, Eoin Gunnigle, Paul D. Cotter, John F. Cryan
Neuroscience & Biobehavioral Reviews.2024; 158: 105562. CrossRef - The nutrition and therapeutic potential of millets: an updated narrative review
Jinu Jacob, Veda Krishnan, Chris Antony, Masimukka Bhavyasri, C. Aruna, Kiran Mishra, Thirunavukkarasu Nepolean, Chellapilla Tara Satyavathi, Kurella B. R. S. Visarada
Frontiers in Nutrition.2024;[Epub] CrossRef - Effects of OsomeFood Clean Label plant-based meals on the gut microbiome
Dwiyanto Jacky, Chia Bibi, Look Melvin Chee Meng, Fong Jason, Tan Gwendoline, Lim Jeremy, Chong Chun Wie
BMC Microbiology.2023;[Epub] CrossRef - Fermented soybean foods and diabetes
Yoshitaka Hashimoto, Masahide Hamaguchi, Michiaki Fukui
Journal of Diabetes Investigation.2023; 14(12): 1329. CrossRef - Early response of the gut microbiome and serum metabolites to Cheonggukjang intake in healthy Korean subjects
Eun-Ji Song, Min Jung Kim, Chang Hwa Jung, Won-Hyong Chung, Young-Do Nam, Mi Young Lim
Journal of Functional Foods.2023; 101: 105420. CrossRef - Role, relevance, and possibilities of in vitro fermentation models in human dietary, and gut‐microbial studies
Vineet Singh, HyunWoo Son, GyuDae Lee, Sunwoo Lee, Tatsuya Unno, Jae‐Ho Shin
Biotechnology and Bioengineering.2022; 119(11): 3044. CrossRef - Evaluation of Prebiotics through an In Vitro Gastrointestinal Digestion and Fecal Fermentation Experiment: Further Idea on the Implementation of Machine Learning Technique
Hokyung Song, Dabin Jeon, Tatsuya Unno
Foods.2022; 11(16): 2490. CrossRef - Anti-diabetic prospects of dietary bio-actives of millets and the significance of the gut microbiota: A case of finger millet
Vineet Singh, GyuDae Lee, HyunWoo Son, Sliti Amani, Mamta Baunthiyal, Jae-Ho Shin
Frontiers in Nutrition.2022;[Epub] CrossRef - Current Perspectives on the Physiological Activities of Fermented Soybean-Derived Cheonggukjang
Il-Sup Kim, Cher-Won Hwang, Woong-Suk Yang, Cheorl-Ho Kim
International Journal of Molecular Sciences.2021; 22(11): 5746. CrossRef - Alleviation of Neuronal Cell Death and Memory Deficit with Chungkookjang Made with Bacillus amyloliquefaciens and Bacillus subtilis Potentially through Promoting Gut–Brain Axis in Artery-Occluded Gerbils
Ting Zhang, Myeong-Seon Ryu, Xuangao Wu, Hee-Jong Yang, Su Ji Jeong, Ji-Won Seo, Do-Yeon Jeong, Sunmin Park
Foods.2021; 10(11): 2697. CrossRef - The final fate of food: On the establishment of in vitro colon models
Saartje Hernalsteens, Song Huang, Hai Hua Cong, Xiao Dong Chen
Food Research International.2021; 150: 110743. CrossRef - In Vitro Simulation of Human Colonic Fermentation: A Practical Approach towards Models’ Design and Analytical Tools
Elena Veintimilla-Gozalbo, Andrea Asensio-Grau, Joaquim Calvo-Lerma, Ana Heredia, Ana Andrés
Applied Sciences.2021; 11(17): 8135. CrossRef
- Seeds for Gut Health: Prebiotic potential of seed mucilages from Chia, Fenugreek, Basil, Mustard, and Flaxseed and their impact on adult and toddler's gut microbiome
Reviews
- Functional interplay between the oxidative stress response and DNA damage checkpoint signaling for genome maintenance in aerobic organisms
- Ji Eun Choi , Woo-Hyun Chung
- J. Microbiol. 2020;58(2):81-91. Published online December 23, 2019
- DOI: https://doi.org/10.1007/s12275-020-9520-x
- 71 View
- 0 Download
- 10 Web of Science
- 9 Crossref
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Abstract
- The DNA damage checkpoint signaling pathway is a highly conserved surveillance mechanism that ensures genome integrity by sequential activation of protein kinase cascades. In mammals, the main pathway is orchestrated by two central sensor kinases, ATM and ATR, that are activated in response to DNA damage and DNA replication stress. Patients lacking functional ATM or ATR suffer from ataxia-telangiectasia (A-T) or Seckel syndrome, respectively, with pleiotropic degenerative phenotypes. In addition to DNA strand breaks, ATM and ATR also respond to oxidative DNA damage and reactive oxygen species (ROS), suggesting an unconventional function as regulators of intracellular redox status. Here, we summarize the multiple roles of ATM and ATR, and of their orthologs in Saccharomyces cerevisiae, Tel1 and Mec1, in DNA damage checkpoint signaling and the oxidative stress response, and discuss emerging ideas regarding the possible mechanisms underlying the elaborate crosstalk between those pathways. This review may provide new insights into the integrated cellular strategies responsible for maintaining genome stability in eukaryotes with a focus on the yeast model organism.
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Citations
Citations to this article as recorded by- Effects of Stress on Biological Characteristics and Metabolism of Periodontal Ligament Stem Cells of Deciduous Teeth
Zhengyang Li, Jinyi Li, Shanshan Dai, Xuelong Su, Meiyue Ren, Shuyang He, Qingyu Guo, Fei Liu
International Dental Journal.2025; 75(2): 908. CrossRef - DSB-induced oxidative stress: Uncovering crosstalk between DNA damage response and cellular metabolism
Xinyu Li, Caini Yang, Hengyu Wu, Hongran Chen, Xing Gao, Sa Zhou, Tong-Cun Zhang, Wenjian Ma
DNA Repair.2024; 141: 103730. CrossRef - Signification and Application of Mutator and Antimutator Phenotype-Induced Genetic Variations in Evolutionary Adaptation and Cancer Therapeutics
Woo-Hyun Chung
Journal of Microbiology.2023; 61(12): 1013. CrossRef - Metabolic Stress and Mitochondrial Dysfunction in Ataxia-Telangiectasia
Goutham Narayanan Subramanian, Abrey Jie Yeo, Magtouf Hnaidi Gatei, David John Coman, Martin Francis Lavin
Antioxidants.2022; 11(4): 653. CrossRef - The Rad9–Rad1–Hus1 DNA Repair Clamp is Found in Microsporidia
Anne Caroline Mascarenhas dos Santos, Alexander Thomas Julian, Jean-François Pombert, Emmanuelle Lerat
Genome Biology and Evolution.2022;[Epub] CrossRef - Novel insights into the mechanism of cell cycle kinases Mec1(ATR) and Tel1(ATM)
Elias A. Tannous, Peter M. Burgers
Critical Reviews in Biochemistry and Molecular Biology.2021; 56(5): 441. CrossRef - DNA damage checkpoint and repair: From the budding yeast Saccharomyces cerevisiae to the pathogenic fungus Candida albicans
Shuangyan Yao, Yuting Feng, Yan Zhang, Jinrong Feng
Computational and Structural Biotechnology Journal.2021; 19: 6343. CrossRef - Acute Toxicity and DNA Instability Induced by Exposure to Low Doses of Triclosan and Phthalate DEHP, and Their Combinations, in vitro
Nathalia de Assis Aguilar Duarte, Lindiane Eloisa de Lima, Flora Troina Maraslis, Michael Kundi, Emilene Arusievicz Nunes, Gustavo Rafael Mazzaron Barcelos
Frontiers in Genetics.2021;[Epub] CrossRef - The mechanism and prevention of mitochondrial injury after exercise
Mingzhe Li, Baoan Ning, Tianhui Wang
Journal of Physiology and Biochemistry.2021; 77(2): 215. CrossRef
- Effects of Stress on Biological Characteristics and Metabolism of Periodontal Ligament Stem Cells of Deciduous Teeth
- REVIEW] Antibacterial strategies inspired by the oxidative stress and response networks
- So Youn Kim , Chanseop Park , Hye-Jeong Jang , Bi-o Kim , Hee-Won Bae , In-Young Chung , Eun Sook Kim , You-Hee Cho
- J. Microbiol. 2019;57(3):203-212. Published online February 26, 2019
- DOI: https://doi.org/10.1007/s12275-019-8711-9
- 137 View
- 0 Download
- 124 Web of Science
- 114 Crossref
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Abstract
- Oxidative stress arises from an imbalance between the excessive accumulation of reactive oxygen species (ROS) and a cell’s capability to readily detoxify them. Although ROS are spontaneously generated during the normal oxygen respiration and metabolism, the ROS generation is usually augmented by redox-cycling agents, membrane disrupters, and bactericidal antibiotics, which contributes their antimicrobial bioactivity. It is noted that all the bacteria deploy an arsenal of inducible antioxidant defense systems to cope with the devastating effect exerted by the oxidative stress: these systems include the antioxidant effectors such as catalases and the master regulators such as OxyR. The oxidative stress response is not essential for normal growth, but critical to survive the oxidative stress conditions that the bacterial pathogens may encounter due to the host immune response and/or the antibiotic treatment. Based on these, we here define the ROS-inspired antibacterial strategies to enhance the oxidative stress of ROS generation and/or to compromise the bacterial response of ROS detoxification, by delineating the ROSgenerating antimicrobials and the core concept of the bacterial response against the oxidative stress.
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Citations
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Journal Articles
- Oxygen-mediated growth enhancement of an obligate anaerobic archaeon Thermococcus onnurineus NA1
- Seong Hyuk Lee , Hwan Youn , Sung Gyun Kang , Hyun Sook Lee
- J. Microbiol. 2019;57(2):138-142. Published online January 31, 2019
- DOI: https://doi.org/10.1007/s12275-019-8592-y
- 72 View
- 0 Download
- 3 Web of Science
- 2 Crossref
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Abstract
- Thermococcus onnurineus NA1, an obligate anaerobic hyperthermophilic archaeon, showed variable oxygen (O2) sensitivity depending on the types of substrate employed as an energy source. Unexpectedly, the culture with yeast extract as a sole energy source showed enhanced growth by 2-fold in the presence of O2. Genome-wide transcriptome analysis revealed the upregulation of several antioxidant-related genes encoding thioredoxin peroxidase (TON_0862), rubrerythrin (TON_0864), rubrerythrin-related protein (TON_0873), NAD(P)H rubredoxin oxidoreductase (TON_0865), or thioredoxin reductase (TON_1603), which can couple the detoxification of reactive oxygen species with the regeneration of NAD(P)+ from NAD(P)H. We present a plausible mechanism by which O2 serves to maintain the intracellular redox balance. This study demonstrates an unusual strategy of an obligate anaerobe underlying O2-mediated growth enhancement despite not having heme-based or cytochrome-type proteins.
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Citations
Citations to this article as recorded by- How low can they go? Aerobic respiration by microorganisms under apparent anoxia
Jasmine S Berg, Soeren Ahmerkamp, Petra Pjevac, Bela Hausmann, Jana Milucka, Marcel M M Kuypers
FEMS Microbiology Reviews.2022;[Epub] CrossRef - Reductive evolution and unique predatory mode in the CPR bacterium Vampirococcus lugosii
David Moreira, Yvan Zivanovic, Ana I. López-Archilla, Miguel Iniesto, Purificación López-García
Nature Communications.2021;[Epub] CrossRef
- How low can they go? Aerobic respiration by microorganisms under apparent anoxia
- Gentic overexpression increases production of hypocrellin A in Shiraia bambusicola S4201
- Dan Li , Ning Zhao , Bing-Jing Guo , Xi Lin , Shuang-Lin Chen , Shu-Zhen Yan
- J. Microbiol. 2019;57(2):154-162. Published online January 31, 2019
- DOI: https://doi.org/10.1007/s12275-019-8259-8
- 79 View
- 0 Download
- 19 Web of Science
- 19 Crossref
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Abstract
- Hypocrellin A (HA) is a perylenequinone (PQ) isolated from Shiraia bambusicola that shows antiviral and antitumor activities, but its application is limited by the low production from wild fruiting body. A gene overexpressing method was expected to augment the production rate of HA in S. bambusicola. However, the application of this molecular biology technology in S. bambusicola was impeded by a low genetic transformation efficiency and little genomic information. To enhance the plasmid transformant ratio, the Polyethylene Glycol-mediated transformation system was established and optimized. The following green fluorescent protein (GFP) analysis showed that the gene fusion expression system we constructed with a GAPDH promoter Pgpd1 and a rapid 2A peptide was successfully expressed in the S. bambusicola S4201 strain. We successfully obtained the HA high-producing strains by overexpressing O-methyltransferase/FAD-dependent monooxygenase gene (mono) and the hydroxylase gene (hyd), which were the essential genes involved in our putative HA biosynthetic pathway. The overexpression of these two genes increased the production of HA by about 200% and 100%, respectively. In general, this study will provide a basis to identify the genes involved in the hypocrellin A biosynthesis. This improved transformation method can also be used in genetic transformation studies of other fungi.
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Citations
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Optimisation of hypocrellin production in
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Zi-Min Lu, Run-Tong Zhang, Xiao-Bo Huang, Xue-Ting Cao, Xiao-Ye Shen, Li Fan, Cheng-Lin Hou
Mycology.2024; 15(2): 272. CrossRef - Production of fungal hypocrellin photosensitizers: Exploiting bambusicolous fungi and elicitation strategies in mycelium cultures
Xin Ping Li, Wen Hao Shen, Jian Wen Wang, Li Ping Zheng
Mycology.2024; : 1. CrossRef - Urea-Induced Enhancement of Hypocrellin A Synthesis in Shiraia bambusicola GDMCC 60438: Strategies and Mechanisms
Yanbo Tang, Yongdi Wen, Xiang Zhang, Qian Gao, Fuqiang Yu, Zhenqiang Wu, Xiaofei Tian
Fermentation.2024; 10(8): 381. CrossRef - Advancements and Future Prospects in Hypocrellins Production and Modification for Photodynamic Therapy
Xiang Zhang, Qiulin Wei, Liwen Tian, Zhixian Huang, Yanbo Tang, Yongdi Wen, Fuqiang Yu, Xiaoxiao Yan, Yunchun Zhao, Zhenqiang Wu, Xiaofei Tian
Fermentation.2024; 10(11): 559. CrossRef - Biosynthesis of Natural and Unnatural Perylenequinones for Drug Development
Zengping Su, Yan Zhang, Zhenbo Yuan, Yijian Rao
ChemMedChem.2024;[Epub] CrossRef - Heat stress enhanced perylenequinones biosynthesis of Shiraia sp. Slf14(w) through nitric oxide formation
Chenglong Xu, Wenxi Lin, Yunni Chen, Boliang Gao, Zhibin Zhang, Du Zhu
Applied Microbiology and Biotechnology.2023; 107(11): 3745. CrossRef - Biotechnological production and potential applications of hypocrellins
Zhuanying Bao, Yunchang Xie, Chenglong Xu, Zhibin Zhang, Du Zhu
Applied Microbiology and Biotechnology.2023; 107(21): 6421. CrossRef - L-Arginine enhanced perylenequinone production in the endophytic fungus Shiraia sp. Slf14(w) via NO signaling pathway
Yunni Chen, Chenglong Xu, Huilin Yang, Zhenying Liu, Zhibin Zhang, Riming Yan, Du Zhu
Applied Microbiology and Biotechnology.2022; 106(7): 2619. CrossRef - Advances and perspectives on perylenequinone biosynthesis
Huaxiang Deng, Xinxin Liang, Jinbin Liu, Xiaohui Zheng, Tai-Ping Fan, Yujie Cai
Frontiers in Microbiology.2022;[Epub] CrossRef - Temperature-responsive regulation of the fermentation of hypocrellin A by Shiraia bambusicola (GDMCC 60438)
Yongdi Wen, Baosheng Liao, Xiaoxiao Yan, Zhenqiang Wu, Xiaofei Tian
Microbial Cell Factories.2022;[Epub] CrossRef - Microbial production of nematicidal agents for controlling plant-parasitic nematodes
Jaemin Seong, Jongoh Shin, Kangsan Kim, Byung-Kwan Cho
Process Biochemistry.2021; 108: 69. CrossRef - Nitric oxide donor sodium nitroprusside-induced transcriptional changes and hypocrellin biosynthesis of Shiraia sp. S9
Yan Jun Ma, Xin Ping Li, Yue Wang, Jian Wen Wang
Microbial Cell Factories.2021;[Epub] CrossRef - Nitric oxide regulates perylenequinones biosynthesis in Shiraia bambusicola S4201 induced by hydrogen peroxide
Ning Zhao, Yingying Yu, Yunxia Yue, Mingzhu Dou, Bingjing Guo, Shuzhen Yan, Shuanglin Chen
Scientific Reports.2021;[Epub] CrossRef - Current State and Future Directions of Genetics and Genomics of Endophytic Fungi for Bioprospecting Efforts
Rosa Sagita, Wim J. Quax, Kristina Haslinger
Frontiers in Bioengineering and Biotechnology.2021;[Epub] CrossRef - Global identification of alternative splicing in Shiraia bambusicola and analysis of its regulation in hypocrellin biosynthesis
Xin-Yao Liu, Li Fan, Jian Gao, Xiao-Ye Shen, Cheng-Lin Hou
Applied Microbiology and Biotechnology.2020; 104(1): 211. CrossRef - Improved A40926 production from Nonomuraea gerenzanensis using the promoter engineering and the co-expression of crucial genes
Huijun Dong, Xue Yue, Bingyu Yan, Wen Gao, Shuai Wang, Yongquan Li
Journal of Biotechnology.2020; 324: 28. CrossRef - Adding bamboo charcoal powder to Shiraia bambusicola preculture improves hypocrellin A production
Xin Ping Li, Yan Jun Ma, Jian Wen Wang
Sustainable Chemistry and Pharmacy.2019; 14: 100191. CrossRef - Efficient agrobacterium-mediated transformation ofShiraia bambusicolaand activation of a specific transcription factor for hypocrellin production
Tong Li, Cheng-Lin Hou, Xiao-Ye Shen
Biotechnology & Biotechnological Equipment.2019; 33(1): 1365. CrossRef - Response mechanism of hypocrellin colorants biosynthesis by Shiraia bambusicola to elicitor PB90
Wen Du, Chunlong Sun, Baogui Wang, Yanmei Wang, Bin Dong, Junhua Liu, Jiangbao Xia, Wenjun Xie, Jun Wang, Jingkuan Sun, Xuehong Liu, Hongguo Wang
AMB Express.2019;[Epub] CrossRef
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Optimisation of hypocrellin production in
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- Comparative genomic analysis of pyrene-degrading Mycobacterium species: Genomic islands and ring-hydroxylating dioxygenases involved in pyrene degradation
- Dae-Wi Kim , Kihyun Lee , Do-Hoon Lee , Chang-Jun Cha
- J. Microbiol. 2018;56(11):798-804. Published online October 24, 2018
- DOI: https://doi.org/10.1007/s12275-018-8372-0
- 60 View
- 0 Download
- 21 Crossref
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Abstract
- The genome sequences of two pyrene-degrading bacterial strains of Mycobacterium spp. PYR10 and PYR15, isolated from the estuarine wetland of the Han river, South Korea, were determined using the PacBio RS II sequencing platform. The complete genome of strain PYR15 was 6,037,017 bp in length with a GC content of 66.5%, and contained 5,933 protein- coding genes. The genome of strain PYR10 was 5,999,427 bp in length with a GC content of 67.7%, and contained 5,767 protein-coding genes. Based on the average nucleotide identity values, these strains were designated as M. gilvum PYR10 and M. pallens PYR15. A genomic comparison of these pyrene-degrading Mycobacterium strains with pyrene- non-degrading strains revealed that the genomes of pyrene-degrading strains possessed similar repertoires of ringhydroxylating dioxygenases (RHDs), including the pyrenehydroxylating dioxygenases encoded by nidA and nidA3, which could be readily distinguished from those of pyrenenon- degraders. Furthermore, genomic islands, containing catabolic gene clusters, were shared only among the pyrenedegrading Mycobacterium strains and these gene clusters contained RHD genes, including nidAB and nidA3B3. Our genome data should facilitate further studies on the evolution of the polycyclic aromatic hydrocarbon-degradation pathways in the genus Mycobacterium.
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Natalia Maria Silva, Camila Lopes Romagnoli, Caio Rafael do Nascimento Santiago, João Paulo Amorim de de Lacerda, Sylvia Cardoso Leão, Luciano Antonio Digiampietri, Cristina Viana-Niero
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- The NADPH oxidase AoNoxA in Arthrobotrys oligospora functions as an initial factor in the infection of Caenorhabditis elegans
- Xin Li , Ying-Qian Kang , Yan-Lu Luo , Ke-Qin Zhang , Cheng-Gang Zou , Lian-Ming Liang
- J. Microbiol. 2017;55(11):885-891. Published online October 27, 2017
- DOI: https://doi.org/10.1007/s12275-017-7169-x
- 71 View
- 0 Download
- 15 Crossref
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Abstract
- Reactive oxygen species (ROS) produced by NADPH oxidases can serve as signaling molecules to regulate a variety of physiological processes in multi-cellular organisms. In the nematophagous fungus Arthrobotrys oligospora, we found that ROS were produced during conidial germination, hyphal extension, and trap formation in the presence of nematodes. Generation of an AoNoxA knockout strain demonstrated the crucial role of NADPH oxidase in the production of ROS in A. oligospora, with trap formation impaired in the AoNoxA mutant, even in the presence of the nematode host. In addition, the expression of virulence factor serine protease P186 was up-regulated in the wild-type strain, but not in the mutant strain, in the presence of Caenorhabditis elegans. These results indicate that ROS derived from AoNoxA are essential for full virulence of A. oligospora in nematodes.
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Journal of Fungi.2024; 10(2): 110. CrossRef - Tools and basic procedures of gene manipulation in nematode-trapping fungi
Shunxian Wang, Xingzhong Liu
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Huijie Zhang, Weirong Zeng, Ming‐Ming Zhao, Jiali Wang, Qiquan Wang, Ting Chen, Yuyan Zhang, Wenhui Lee, Shenghan Chen, Yun Zhang, Xinqiang Lan, Yang Xiang
The FASEB Journal.2023;[Epub] CrossRef - Key processes required for the different stages of fungal carnivory by a nematode-trapping fungus
Hung-Che Lin, Guillermo Vidal-Diez de Ulzurrun, Sheng-An Chen, Ching-Ting Yang, Rebecca J. Tay, Tomoyo Iizuka, Tsung-Yu Huang, Chih-Yen Kuo, A. Pedro Gonçalves, Siou-Ying Lin, Yu-Chu Chang, Jason E. Stajich, Erich M. Schwarz, Yen-Ping Hsueh, Aaron P. Mitc
PLOS Biology.2023; 21(11): e3002400. CrossRef - Recent Advances in Life History Transition with Nematode-Trapping Fungus Arthrobotrys oligospora and Its Application in Sustainable Agriculture
Da Wang, Nan Ma, Wanqin Rao, Ying Zhang
Pathogens.2023; 12(3): 367. CrossRef - Aolatg1 and Aolatg13 Regulate Autophagy and Play Different Roles in Conidiation, Trap Formation, and Pathogenicity in the Nematode-Trapping Fungus Arthrobotrys oligospora
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Frontiers in Cellular and Infection Microbiology.2022;[Epub] CrossRef - Regulatory Mechanism of Trap Formation in the Nematode-Trapping Fungi
Mei-Chen Zhu, Xue-Mei Li, Na Zhao, Le Yang, Ke-Qin Zhang, Jin-Kui Yang
Journal of Fungi.2022; 8(4): 406. CrossRef -
Transcriptomic Analysis Reveals That Rho GTPases Regulate Trap Development and Lifestyle Transition of the Nematode-Trapping Fungus
Arthrobotrys oligospora
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Vasileios Vangalis, Ioannis A. Papaioannou, Emmanouil A. Markakis, Michael Knop, Milton A. Typas
Journal of Fungi.2021; 7(9): 740. CrossRef - DdaSTE12 is involved in trap formation, ring inflation, conidiation, and vegetative growth in the nematode-trapping fungus Drechslerella dactyloides
Yani Fan, Weiwei Zhang, Yue Chen, Meichun Xiang, Xingzhong Liu
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Jian Zhang, Youzhi Miao, Mohammad Javad Rahimi, Hong Zhu, Andrei Steindorff, Sabine Schiessler, Feng Cai, Guan Pang, Komal Chenthamara, Yu Xu, Christian P. Kubicek, Qirong Shen, Irina S. Druzhinina
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- AoPrdx2 Regulates Oxidative Stress, Reactive Oxygen Species, Trap Formation, and Secondary Metabolism in Arthrobotrys oligospora
- A novel methanotroph in the genus Methylomonas that contains a distinct clade of soluble methane monooxygenase
- Ngoc-Loi Nguyen , Woon-Jong Yu , Hye-Young Yang , Jong-Geol Kim , Man-Young Jung , Soo-Je Park , Seong-Woon Roh , Sung-Keun Rhee
- J. Microbiol. 2017;55(10):775-782. Published online September 28, 2017
- DOI: https://doi.org/10.1007/s12275-017-7317-3
- 64 View
- 0 Download
- 15 Crossref
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Abstract
- Aerobic methane oxidation is a key process in the global carbon cycle that acts as a major sink of methane. In this study, we describe a novel methanotroph designated EMGL16-1 that was isolated from a freshwater lake using the floating filter culture technique. Based on a phylogenetic analysis of 16S rRNA gene sequences, the isolate was found to be closely related to the genus Methylomonas in the family Methylococcaceae of the class Gammaproteobacteria with 94.2–97.4% 16S rRNA gene similarity to Methylomonas type strains. Comparison of chemotaxonomic and physiological properties further suggested that strain EMGL16-1 was taxonomically distinct from other species in the genus Methylomonas. The isolate was versatile in utilizing nitrogen sources such as molecular nitrogen, nitrate, nitrite, urea, and ammonium. The genes coding for subunit of the particulate form methane monooxygenase (pmoA), soluble methane monooxygenase (mmoX), and methanol dehydrogenase (mxaF) were detected in strain EMGL16-1. Phylogenetic analysis of mmoX indicated that mmoX of strain EMGL16-1 is distinct from those of other strains in the genus Methylomonas. This isolate probably represents a novel species in the genus. Our study provides new insights into the diversity of species in the genus Methylomonas and their environmental adaptations.
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Reviews
- Minireview] Microbial radiation-resistance mechanisms
- Kwang-Woo Jung , Sangyong Lim , Yong-Sun Bahn
- J. Microbiol. 2017;55(7):499-507. Published online June 30, 2017
- DOI: https://doi.org/10.1007/s12275-017-7242-5
- 75 View
- 0 Download
- 40 Crossref
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Abstract
- Organisms living in extreme environments have evolved a wide range of survival strategies by changing biochemical and physiological features depending on their biological niches. Interestingly, organisms exhibiting high radiation resistance have been discovered in the three domains of life (Bacteria, Archaea, and Eukarya), even though a naturally radiationintensive environment has not been found. To counteract the deleterious effects caused by radiation exposure, radiation- resistant organisms employ a series of defensive systems, such as changes in intracellular cation concentration, excellent DNA repair systems, and efficient enzymatic and non-enzymatic antioxidant systems. Here, we overview past and recent findings about radiation-resistance mechanisms in the three domains of life for potential usage of such radiationresistant microbes in the biotechnology industry.
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- J. Microbiol. 2017;55(6):409-416. Published online March 9, 2017
- DOI: https://doi.org/10.1007/s12275-017-6647-5
- 74 View
- 0 Download
- 40 Crossref
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Abstract
- To deal with chemically reactive oxygen molecules constantly threatening aerobic life, cells are readily equipped with elabo-rate biological antioxidant systems. Superoxide dismutase is a metalloenzyme catalytically eliminating superoxide radi-cal as a first-line defense mechanism against oxidative stress. Multiple different SOD isoforms have been developed through-out evolution to play distinct roles in separate subcellular com-partments. SOD is not essential for viability of most aerobic organisms and intriguingly found even in strictly anaerobic bacteria. Sod1 has recently been known to play important roles as a nuclear transcription factor, an RNA binding pro-tein, a synthetic lethal interactor, and a signal modulator in glucose metabolism, most of which are independent of its canonical function as an antioxidant enzyme. In this review, recent advances in understanding the unconventional role of Sod1 are highlighted and discussed with an emphasis on its genetic crosstalk with DNA damage repair/checkpoint path-ways. The budding yeast Saccharomyces cerevisiae has been successfully used as an efficient tool and a model organism to investigate a number of novel functions of Sod1.
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