Journal of Microbiology

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Functional characterization of HigBA toxin-antitoxin system in an Arctic bacterium, Bosea sp. PAMC 26642: Eunsil Choi , Ahhyun Huh , Changmin Oh , Jeong-Il Oh , Ho Young Kang , Jihwan Hwang; J. Microbiol. 2022;60(2):192-206. Published online February 1, 2022; DOI: https://doi.org/10.1007/s12275-022-1619-9

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Toxin-antitoxin (TA) systems are growth-controlling genetic elements consisting of an intracellular toxin protein and its cognate antitoxin. TA systems have been spread among microbial genomes through horizontal gene transfer and are now prevalent in most bacterial and archaeal genomes. Under normal growth conditions, antitoxins tightly counteract the activity of the toxins. Upon stresses, antitoxins are inactivated, releasing activated toxins, which induce growth arrest or cell death. In this study, among nine functional TA modules in Bosea sp. PAMC 26642 living in Arctic lichen, we investigated the functionality of BoHigBA2. BohigBA2 is located close to a genomic island and adjacent to flagellar gene clusters. The expression of BohigB2 induced the inhibition of E. coli growth at 37°C, which was more manifest at 18°C, and this growth defect was reversed when BohigA2 was co-expressed, suggesting that this BoHigBA2 module might be an active TA module in Bosea sp. PAMC 26642. Live/dead staining and viable count analyses revealed that the BoHigB2 toxin had a bactericidal effect, causing cell death. Furthermore, we demonstrated that BoHigB2 possessed mRNA-specific ribonuclease activity on various mRNAs and cleaved only mRNAs being translated, which might impede overall translation and consequently lead to cell death. Our study provides the insight to understand the cold adaptation of Bosea sp. PAMC 26642 living in the Arctic.

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Evaluating the Contribution of the Predicted Toxin–Antitoxin System HigBA to Persistence, Biofilm Formation, and Virulence in Burkholderia pseudomallei
Itziar Chapartegui-González, Nittaya Khakhum, Jacob L. Stockton, Alfredo G. Torres, Igor E. Brodsky
Infection and Immunity.2022;[Epub] CrossRef
Chronicle of Research into Lichen-Associated Bacteria
Zichen He, Takeshi Naganuma
Microorganisms.2022; 10(11): 2111. CrossRef
Degradation of amoxicillin by newly isolated Bosea sp. Ads-6
Lei Yan, Ning Yan, Xi-Yan Gao, Ying Liu, Zhi-Pei Liu
Science of The Total Environment.2022; 828: 154411. CrossRef

Transposon insertion site sequencing (TIS) of Pseudomonas aeruginosa: Hongbaek Cho; J. Microbiol. 2021;59(12):1067-1074. Published online December 4, 2021; DOI: https://doi.org/10.1007/s12275-021-1565-y

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Abstract

Transposon insertion site sequencing (TIS) is a technique that determines the insertion profile of a transposon mutant library by massive parallel sequencing of transposon-genomic DNA junctions. Because the transposon insertion profile reflects the abundance of each mutant in the library, it provides information to assess the fitness contribution of each genetic locus of a bacterial genome in a specific growth condition or strain background. Although introduced only about a dozen years ago, TIS has become an important tool in bacterial genetics that provides clues to study biological functions and regulatory mechanisms. Here, I describe a protocol for generating high density transposon insertion mutant libraries and preparing Illumina sequencing samples for mapping the transposon junctions of the transposon mutant libraries using Pseudomonas aeruginosa as an example.

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Transposon insertion sequencing analysis reveals conditional essential genes for infection in Pseudomonas plecoglossicida
Haoyuan Ding, Peherden Ahat, Wei Song, Yuanxing Zhang, Sang Ho Choi, Yibei Zhang, Qiyao Wang
Aquaculture.2025; 607: 742655. CrossRef
Optimizing phage-based mutant recovery and minimizing heat effect in the construction of transposon libraries in Staphylococcus aureus
Sally W. Yousief, Nader Abdelmalek, Bianca Paglietti
Scientific Reports.2024;[Epub] CrossRef
The biological essence of synthetic lethality: Bringing new opportunities for cancer therapy
Meiyi Ge, Jian Luo, Yi Wu, Guobo Shen, Xi Kuang
MedComm – Oncology.2024;[Epub] CrossRef
Optimization of Transposon Mutagenesis Methods in Pseudomonas antarctica
Sangha Kim, Changhan Lee
Microorganisms.2023; 11(1): 118. CrossRef
Construction of high-density transposon mutant library of Staphylococcus aureus using bacteriophage ϕ11
Wonsik Lee
Journal of Microbiology.2022; 60(12): 1123. CrossRef

Lactiplantibacillus plantarum LRCC5314 includes a gene for serotonin biosynthesis via the tryptophan metabolic pathway: Jiseon Jeong , Yunjeong Lee , Seokmin Yoon , Jong-Hwa Kim , Wonyong Kim; J. Microbiol. 2021;59(12):1092-1103. Published online December 4, 2021; DOI: https://doi.org/10.1007/s12275-021-1472-2

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Abstract

As the functions of probiotics within the same species may not be shared, it is important to analyze the genetic characteristics of strains to determine their safety and usefulness before industrial applications. Hence the present study was undertaken to determine functional genes, and beneficial activities of strain LRCC5314, a bacterial strain isolated from kimchi through comparative genomic analysis. Phylogenetic analysis based on the 16S rRNA gene sequence showed that strain LRCC5314 was a member of the species L. plantarum. Whole genome size of strain LRCC5314 was sequence was 3.25 Mb long, with a G + C content of 44.5 mol% and 3,031 predicted genes. Strain LRCC5314 could metabolize hexoses through homofermentation, which produces only lactic acid from hexoses. According to gene annotation, strain LRCC- 5314 contained genes of EPS production and CRISPR. Moreover, the strain contained genes that could encode a complete biosynthetic pathway for the production of tryptophan, which can be used as a precursor of serotonin. Notably, the tryptophan and serotonin activities strain LRCC5314 were higher than those of reference strains, L. plantarum ATCC 14917T, DSM 20246, DSM 2601, and ATCC 8014, which reach tryptophan amount of 0.784 ± 0.045 μM/ml in MRS broth and serotonin concentration of 19.075 ± 0.295 ng/ml in HT-22 cells. These findings indicated that L. plantarum LRCC5314 could provide a source for serotonin production and could be used as a functional probiotic for stress regulation.

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Psychobiotics and the gut-brain axis: advances in metabolite quantification and their implications for mental health
Vincent Owusu Kyei-Baffour, Akshay Kumar Vijaya, Aurelijus Burokas, Eric Banan-Mwine Daliri
Critical Reviews in Food Science and Nutrition.2025; : 1. CrossRef
From in silico screening to in vivo validation in zebrafish – a framework for reeling in the right psychobiotics
Benjamin Valderrama, Isabelle Daly, Eoin Gunnigle, Kenneth J. O'Riordan, Maciej Chichlowski, Sagarika Banerjee, Alicja A. Skowronski, Neeraj Pandey, John F. Cryan, Gerard Clarke, Jatin Nagpal
Food & Function.2025; 16(5): 2018. 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
Effect of postbiotic Lactiplantibacillus plantarum LRCC5314 supplemented in powdered milk on type 2 diabetes in mice
J.-H. Kim, W. Kwak, Y. Nam, J. Baek, Y. Lee, S. Yoon, W. Kim
Journal of Dairy Science.2024; 107(8): 5301. CrossRef
The role of pharmacomicrobiomics in HIV prevention, treatment, and women’s health
Erik C. Swanson, Christopher M. Basting, Nichole R. Klatt
Microbiome.2024;[Epub] CrossRef
Whole-Genome Sequence of Lactococcus lactis Subsp. lactis LL16 Confirms Safety, Probiotic Potential, and Reveals Functional Traits
Justina Mileriene, Jurgita Aksomaitiene, Kristina Kondrotiene, Tora Asledottir, Gerd Elisabeth Vegarud, Loreta Serniene, Mindaugas Malakauskas
Microorganisms.2023; 11(4): 1034. CrossRef
Probiotic Incorporation into Yogurt and Various Novel Yogurt-Based Products
Douglas W. Olson, Kayanush J. Aryana
Applied Sciences.2022; 12(24): 12607. CrossRef

A Novel Ribonuclease with Potent HIV-1 Reverse Transcriptase Inhibitory Activity from Cultured Mushroom Schizophyllum commune: Yong-Chang Zhao , Guo-Qing Zhang , Tzi-Bun Ng , He-Xiang Wang; J. Microbiol. 2011;49(5):803-808. Published online November 9, 2011; DOI: https://doi.org/10.1007/s12275-011-1098-x

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Abstract

A 20-kDa ribonuclease (RNase) was purified from fresh fruiting bodies of cultured Schizophyllum commune mushrooms. The RNase was not adsorbed on Affi-gel blue gel but adsorbed on DEAE-cellulose and CM-cellulose. It exhibited maximal RNase activity at pH 6.0 and 70°C. It demonstrated the highest ribonucleolytic activity toward poly (U) (379.5 μ/mg), the second highest activity toward poly (C) (244.7 μ/mg), less activity toward poly (A) (167.4 μ/mg), and much weaker activity toward poly (G) (114.5 μ/mg). The RNase inhibited HIV-1 reverse transcriptase with an IC50 of 65 μM. No effect on [3H-methyl]-thymidine uptake by lymphoma MBL2 cells and leukemia L1210 cells was observed at 100 μM concentration of the RNase. A comparison of RNases from S. commune and Volvariella volvacea revealed that they demonstrated some similarities in N-terminal amino acid sequence, optimum pH and polyhomoribonucleotide specificity. However, some differences in chromatographic behavior and molecular mass were observed.

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Schizophyllum commune, an underrated edible and medicinal mushroom: farm to industry
Disha Dasgupta, Pranjali Basu, Anamika Paul, Krishnendu Acharya, Nilanjan Chakraborty
Studies in Fungi.2025;[Epub] CrossRef
Investigation of the inhibition of respiratory bacterial pathogens and HIV-1 enzymes by twenty-one South African mushroom species
Jenske Didloff, Gerhardt J. Boukes, Maryna van de Venter, Bennie Viljoen, Michael Lee, Candice Blom, Rebecca A. Dwyer, Sharlene Govender
South African Journal of Botany.2024; 166: 375. CrossRef
The Health-promoting Potential of Edible Mushroom Proteins
Ana Sofia Sousa, Helena Araújo-Rodrigues, Manuela Estevez Pintado
Current Pharmaceutical Design.2023; 29(11): 804. CrossRef
Evidence for the Presence of Hyphae and Fruiting Body Calcium Oxalate Crystallites in the Split Gill Medicinal Mushroom Schizophyllum commune (Agaricomycetes)
Xiangyue Xiao, Tianji Huang, Jingyi Zhang, Wei Liu, Hong Ji, Nemat O. Keyhani, Hui Chen, Weijie Wu, Chi Song
International Journal of Medicinal Mushrooms.2022; 24(10): 83. CrossRef
Medicinal Fungi with Antiviral Effect
Yu Zhang, Guoying Zhang, Jianya Ling
Molecules.2022; 27(14): 4457. CrossRef
Narrative Review: Bioactive Potential of Various Mushrooms as the Treasure of Versatile Therapeutic Natural Product
Hitesh Chopra, Awdhesh Kumar Mishra, Atif Amin Baig, Tapan Kumar Mohanta, Yugal Kishore Mohanta, Kwang-Hyun Baek
Journal of Fungi.2021; 7(9): 728. CrossRef
Lectins purified from medicinal and edible mushrooms: Insights into their antiviral activity against pathogenic viruses
Yousra A. El-Maradny, Esmail M. El-Fakharany, Marwa M. Abu-Serie, Mona H. Hashish, Heba S. Selim
International Journal of Biological Macromolecules.2021; 179: 239. CrossRef
Research Progress of Bioactive Proteins from the Edible and Medicinal Mushrooms
Rong Zhou, Zhao Kun Liu, Ye Ni Zhang, Jack Ho Wong, Tzi Bun Ng, Fang Liu
Current Protein & Peptide Science.2019; 20(3): 196. CrossRef
A novel ribonuclease with antiproliferative activity toward leukemia and lymphoma cells and HIV-1 reverse transcriptase inhibitory activity from the mushroom, Hohenbuehelia serotina
RUI ZHANG, LIYAN ZHAO, HEXIANG WANG, TZI BUN NG
International Journal of Molecular Medicine.2014; 33(1): 209. CrossRef
A Novel Ribonuclease with HIV-1 Reverse Transcriptase Inhibitory Activity from the Edible Mushroom Hygrophorus russula
Mengjuan Zhu, Lijing Xu, Xiao Chen, Zengqiang Ma, Hexiang Wang, T. B. Ng
Applied Biochemistry and Biotechnology.2013; 170(1): 219. CrossRef
Purification and characterization of a novel acid phosphatase from the split gill mushroom Schizophyllum commune
Guo‐Qing Zhang, Qing‐Jun Chen, Jian Sun, He‐Xiang Wang, Chun‐Hua Han
Journal of Basic Microbiology.2013; 53(10): 868. CrossRef
Purification and characterization of a protein with antifungal, antiproliferative, and HIV‐1 reverse transcriptase inhibitory activities from small brown‐eyed cowpea seeds
Guo‐Ting Tian, Meng Juan Zhu, Ying Ying Wu, Qin Liu, He Xiang Wang, Tzi Bun Ng
Biotechnology and Applied Biochemistry.2013; 60(4): 393. CrossRef

Cloning and Sequencing of the rph Gene Encoding RNase PH from Legionella pneumophila: Se Jin Kim , Jong-Seok Lim , Nicholas P. Cianciotto , Yong-Kyung Choe; J. Microbiol. 1999;37(4):218-223.

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Abstract: Legionella pneumophila, the cause of Legionnaires disease, is able to survive intracellularily in eukaryotic cells such as monocytes, macorphages, and protozoan ogranisms. During protein biosynthesis, the rph gene encodes ribonuclease (RNase) PH which functions as a phosphorolytic nuclease that removes nucleotides following the CCA terminus of tRNA and as a nucleotidyl-transferase which adds nucleotides to the ends of RNA molecules by usingnucelside diohosphates as substrates.In this sutdy, the rph gene was screened in pUC19 library employing a DNA probe whcich was constructed from PCR based on a consensus pattern of multiple alignment of RNas PH. The encoded protein consists of 235 amino acid residues with a calculated molecualr weight of 26,112 Daltons. The RNase PH signature domains are completely conserved.

Mutational Analysis of an Essential RNA Stem-loop Structure in a Minimal RNA Substrate Specifically Cleaved by Leishmania RNA Virus 1-4 (LRV1-4) Capsid Endoribonuclease: Youngtae Ro , Jean L. Patterson; J. Microbiol. 2003;41(3):239-247.

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Abstract: The LRV1-4 capsid protein possesses an endoribonuclease activity that is responsible for the single sitespecific cleavage in the 5’ untranslated region (UTR) of its own viral RNA genome and the formation of a conserved stem-loop structure (stem-loop IV) in the UTR is essential for the accurate RNA cleavage by the capsid protein. To delineate the nucleotide sequences, which are essential for the correct formation of the stem-loop structure for the accurate RNA cleavage by the viral capsid protein, a wildtype minimal RNA transcript (RNA 5’ 249-342) and several synthetic RNA transcripts encoding pointmutations in the stem-loop region were generated in an in vitro transcription system, and used as substrates for the RNA cleavage assay and RNase mapping studies. When the RNA 5’ 249-342 transcript was subjected to RNase T1 and A mapping studies, the results showed that the predicted RNA secondary structure in the stem-loop region using FOLD analysis only existed in the presence of Mg2+ ions, suggesting that the metal ion stabilizes the stem-loop structure of the substrate RNA in solution. When point-mutated RNA substrates were used in the RNA cleavage assay and RNase T1 mapping study, the specific nucleotide sequences in the stem-loop region were not required for the accurate RNA cleavage by the viral capsid protein, but the formation of a stem-loop like structure in a region (nucleotides from 267 to 287) stabilized by Mg_2^+ ions was critical for the accurate RNA cleavage. The RNase T1 mapping and EMSA studies revealed that the Ca2+ and Mn2+ ions, among the reagents tested, could change the mobility of the substrate RNA 5’ 249-342 on a gel similarly to that of Mg_2^+ ions, but only Ca_2^+ ions identically showed the stabilizing effect of Mg_2^+ ions on the stem-loop structure, suggesting that binding of the metal ions (Mg_2^+ or Ca_2^+) onto the RNA substrate in solution causes change and stabilization of the RNA stem-loop structure, and only the substrate RNA with a rigid stem-loop structure in the essential region can be accurately cleaved by the LRV1-4 viral capsid protein.

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