Journal of Microbiology

Review

Proteostasis-targeted antibacterial strategies: Yoon Chae Jeong, Seong-Hyeon Kim, Seongjoon Moon, Hyunhee Kim, Changhan Lee; Received November 6, 2025 Accepted November 26, 2025 Published online February 12, 2026; DOI: https://doi.org/10.71150/jm.2511007 [Epub ahead of print]

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Abstract PDF: Protein quality control systems are increasingly recognized as a critical determinant of bacterial survival and antibiotic tolerance. Conventional antibiotics predominantly target nucleic acids, protein synthesis, or cell wall synthesis, yet bacterial adaptation and resistance emergence remain major challenges. Targeting the bacterial protein quality control machineries including molecular chaperones and proteases offers a promising strategy to overcome these limitations. Recent advances include small molecules and adaptor/degron mimetics that modulate the activities of chaperones and proteases, aggregation-prone peptides (APPs) that induce proteotoxic stress, and bacterial PROTAC (BacPROTAC) strategies that redirect endogenous proteases. Notably, persister and viable-but-non-culturable (VBNC) cells, which tolerate conventional antibiotics, remain susceptible to proteostasis-targeted approaches, thereby enabling killing in both actively dividing and dormant populations. Furthermore, synergistic strategies combining chaperone inhibition or protease activation with conventional antibiotics enhance bactericidal efficacy, suggesting a potential avenue to mitigate antimicrobial resistance. This review summarizes the mechanistic basis, recent developments, and translational potential of proteostasis-centered antibacterial strategies.

Journal Article

Enhancing Seed Germination of Cremastra appendiculata: Screening and Identification of Four New Symbiotic Fungi in the Psathyrellaceae Family: Zhangneng Pan, Jing Wang, Shanshan He, Haiyang Zhao, Xinyue Dong, Tao Feng, Yanyan Meng, Xiaojun Li; J. Microbiol. 2024;62(8):671-682. Published online June 28, 2024; DOI: https://doi.org/10.1007/s12275-024-00148-7

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Several coprinoid fungi have been identified as promotors of Cremastra appendiculata seed germination, while others appear ineffective. This study aimed to discern which genera within the Psathyrellaceae family exhibit this capability and to identify the most effective coprinoid fungi for the cultivation of C. appendiculata. We collected 21 coprinoid fungi from diverse sources and symbiotically cultured them with C. appendiculata seeds. 9 fungi were found to induce seed germination and support seed development, specifically within the genera Coprinellus, Tulosesus, and Candolleomyces. In contrast, fungi that failed to promote germination predominantly belonged to the genera Coprinopsis and Parasola. Notably, four fungi-Coprinellus xanthothrix, Coprinellus pseudodisseminatus, Psathyrella singeri, and Psathyrella candolleana-were documented for the first time as capable of enhancing C. appendiculata seed germination. Strain 218LXJ-10, identified as Coprinellus radians, demonstrated the most significant effect and has been implemented in large-scale production, underscoring its considerable practical value. These findings contribute vital scientific insights for the conservation and sustainable use of C. appendiculata resources.

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Non-targeted metabolomic profiling of Cremastra appendiculata providing insights for phytochemical analyses
Rui Guan, Yuxin Shan, Hamizah Shahirah Hamezah, Somnuk Bunsupa, Hong To Quyen Duong, Yadong Zhou, Rongchun Han, Xiaohui Tong
PeerJ.2026; 14: e20592. CrossRef
Culture conditions of symbiotic fungus Coprinellus radians and its effects on seedlings of Cremastra appendiculata (D.Don.) Makino (Orchidaceae)
Liqin Wang, Jingyi Zhang, Qiuyu Lv, Gonggu Lv, Guangquan Lv, Xin Xiao, Fulin Yan, Miao Liu, Mingsheng Zhang
Canadian Journal of Plant Science.2025; 105: 1. CrossRef
Solid vermicompost and its liquid derivative exhibit strong biocontrol properties against Myzus persicae aphids on sweet pepper
Mey Jerbi-Elayed, Stefan Brandl, Grégory Sempo, John Riviere, Deborah Lanterbecq, Marie Annet, Leidy Grawez Demoulin, Muriel Quinet, Stanley Lutts, Thierry Hance, François Renoz
Journal of Pest Science.2025; 98(4): 2265. CrossRef

Review

Reverse Zoonotic Transmission of SARS-CoV-2 and Monkeypox Virus: A Comprehensive Review: Chiranjib Chakraborty, Manojit Bhattacharya, Md Aminul Islam, Hatem Zayed, Elijah Ige Ohimain, Sang-Soo Lee, Prosun Bhattacharya, Kuldeep Dhama; J. Microbiol. 2024;62(5):337-354. Published online May 23, 2024; DOI: https://doi.org/10.1007/s12275-024-00138-9

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Reverse zoonosis reveals the process of transmission of a pathogen through the human-animal interface and the spillback of the zoonotic pathogen. In this article, we methodically demonstrate various aspects of reverse zoonosis, with a comprehensive discussion of SARS-CoV-2 and MPXV reverse zoonosis. First, different components of reverse zoonosis, such as humans, different pathogens, and numerous animals (poultry, livestock, pets, wild animals, and zoo animals), have been demonstrated. Second, it explains the present status of reverse zoonosis with different pathogens during previous occurrences of various outbreaks, epidemics, and pandemics. Here, we present 25 examples from literature. Third, using several examples, we comprehensively illustrate the present status of the reverse zoonosis of SARS-CoV-2 and MPXV. Here, we have provided 17 examples of SARS-CoV-2 reverse zoonosis and two examples of MPXV reverse zoonosis. Fourth, we have described two significant aspects of reverse zoonosis: understanding the fundamental aspects of spillback and awareness. These two aspects are required to prevent reverse zoonosis from the current infection with two significant viruses. Finally, the One Health approach was discussed vividly, where we urge scientists from different areas to work collaboratively to solve the issue of reverse zoonosis.

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Journal Articles

[Protocol] Use of Cas9 Targeting and Red Recombination for Designer Phage Engineering: Shin-Yae Choi , Danitza Xiomara Romero-Calle , Han-Gyu Cho , Hee-Won Bae , You-Hee Cho; J. Microbiol. 2024;62(1):1-10. Published online February 1, 2024; DOI: https://doi.org/10.1007/s12275-024-00107-2

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Bacteriophages (phages) are natural antibiotics and biological nanoparticles, whose application is significantly boosted by recent advances of synthetic biology tools. Designer phages are synthetic phages created by genome engineering in a way to increase the benefits or decrease the drawbacks of natural phages. Here we report the development of a straightforward genome engineering method to efficiently obtain engineered phages in a model bacterial pathogen, Pseudomonas aeruginosa. This was achieved by eliminating the wild type phages based on the Streptococcus pyogenes Cas9 (SpCas9) and facilitating the recombinant generation based on the Red recombination system of the coliphage λ (λRed). The producer (PD) cells of P. aeruginosa strain PAO1 was created by miniTn7-based chromosomal integration of the genes for SpCas9 and λRed under an inducible promoter. To validate the efficiency of the recombinant generation, we created the fluorescent phages from a temperate phage MP29. A plasmid bearing the single guide RNA (sgRNA) gene for selectively targeting the wild type gp35 gene and the editing template for tagging the Gp35 with superfolder green fluorescent protein (sfGFP) was introduced into the PD cells by electroporation. We found that the targeting efficiency was affected by the position and number of sgRNA. The fluorescent phage particles were efficiently recovered from the culture of the PD cells expressing dual sgRNA molecules. This protocol can be used to create designer phages in P. aeruginosa for both application and research purposes.

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Ola Alessa, Yoshifumi Aiba, Mahmoud Arbaah, Yuya Hidaka, Shinya Watanabe, Kazuhiko Miyanaga, Dhammika Leshan Wannigama, Longzhu Cui
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The β‑Lactamase Activity at the Community Level Confers β‑Lactam Resistance to Bloom‑Forming Microcystis aeruginosa Ce: Yerim Park , Wonjae Kim , Minkyung Kim , Woojun Park; J. Microbiol. 2023;61(9):807-820. Published online October 18, 2023; DOI: https://doi.org/10.1007/s12275-023-00082-0

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Abstract PDF

Many freshwater cyanobacteria, including Microcystis aeruginosa, lack several known antibiotic resistance genes; however, both axenic and xenic M. aeruginosa strains exhibited high antibiotic resistance against many antibiotics under our tested concentrations, including colistin, trimethoprim, and kanamycin. Interestingly, axenic PCC7806, although not the xenic NIBR18 and NIBR452 strains, displayed susceptibility to ampicillin and amoxicillin, indicating that the associated bacteria in the phycosphere could confer such antibiotic resistance to xenic strains. Fluorescence and scanning electron microscopic observations revealed their tight association, leading to possible community-level β-lactamase activity. Combinatory treatment of ampicillin with a β-lactamase inhibitor, sulbactam, abolished the ampicillin resistance in the xenic stains. The nitrocefin-based assay confirmed the presence of significant community-level β-lactamase activity. Our tested low ampicillin concentration and high β-lactamase activity could potentially balance the competitive advantage of these dominant species and provide opportunities for the less competitive species, thereby resulting in higher bacterial diversity under ampicillin treatment conditions. Non-PCR-based metagenome data from xenic NIBR18 cultures revealed the dominance of blaOXArelated antibiotic resistance genes followed by other class A β-lactamase genes (AST-1 and FAR-1). Alleviation of ampicillin toxicity could be observed only in axenic PCC7806, which had been cocultured with β-lactamase from other freshwater bacteria. Our study suggested M. aeruginosa develops resistance to old-class β-lactam antibiotics through altruism, where associated bacteria protect axenic M. aeruginosa cells.

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Rapid and selective disruption of photosystem I in toxic cyanobacteria protects aquatic ecosystem health
Wonjae Kim, Yerim Park, Yongjun Son, Nayeon Yoo, Eui-Hwan Chung, Woojun Park
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Public goods-mediated bacterial interplay in aquatic ecosystems
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Selective cyanobactericidal activity of Nocardioides convexus MS16 against Microcystis aeruginosa, mediated by direct attack
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Sustainable control of Microcystis aeruginosa, a harmful cyanobacterium, using Selaginella tamariscina extracts
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Microcystis abundance is predictable through ambient bacterial communities: A data-oriented approach
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Journal of Microbiology.2024; 62(11): 933. CrossRef
Biological and Chemical Approaches for Controlling Harmful Microcystis Blooms
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Review

The “Cins” of Our Fathers: Rejuvenated Interest in Colicins to Combat Drug Resistance: Sumudu Upatissa , Robert J. Mitchell; J. Microbiol. 2023;61(2):145-158. Published online February 8, 2023; DOI: https://doi.org/10.1007/s12275-023-00023-x

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With the growing threat of antibiotic resistance, researchers around the globe are seeking alternatives to stem bacterial pathogenesis. One such alternative is bacteriocins, proteins produced by bacterial species to inhibit the growth and viability of related bacterial species. With their diverse mechanisms, which include pore formation and nuclease activities, and narrow spectrum of activities, which limit their impact to only certain bacterial species, unlike many chemical antibiotics, bacteriocins offer intriguing possibilities to selectively control individual bacterial populations. Within this review, therefore, we highlight current research exploring the application of colicins and microcins, a subset of bacteriocins, with an emphasis on their activities against drug-resistant pathogens, both in in vitro and in vivo settings.

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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 PDF

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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Jia Lu, Jing Yan, Na Lu, Jiling Song, Jiayao Lin, Xiaohua Zhou, Xuebing Ying, Zhen Li, Zufa Zhou, Fangjie Yao
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Dong Liu, Yousif Abdelrahman Yousif Abdellah, Tingting Dou, Katharina Maria Keiblinger, Ziyan Zhou, Parag Bhople, Jishao Jiang, Xiaofei Shi, Fengming Zhang, Fuqiang Yu, Baoshan Xing
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Isolation and Structural Characterization of Melanins from Red and Yellow Varieties of Stropharia rugosoannulata
Zhen-Fei Xie, Wei-Wei Zhang, Shun-Yin Zhao, Xiao-Han Zhang, Shu-Ning You, Chun-Mei Liu, Guo-Qing Zhang
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Lei Huang, Can Si, Chun-mei He, Xun-cheng Liu, Jun Duan
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Paenibacillus lycopersici sp. nov. and Paenibacillus rhizovicinus sp. nov., isolated from the rhizosphere of tomato (Solanum lycopersicum): Shin Ae Lee , Tae-Wan Kim , Mee-Kyung Sang , Jaekyeong Song , Soon-Wo Kwon , Hang-Yeon Weon; J. Microbiol. 2020;58(10):832-840. Published online September 29, 2020; DOI: https://doi.org/10.1007/s12275-020-0258-2

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Two Gram-stain-positive, rod-shaped, endospore-forming bacteria, designated 12200R-189T and 14171R-81T were isolated from the rhizosphere of tomato plants. The 16S rRNA gene sequence similarity between strains 12200R-189T and 14171R-81T were 97.2%. Both strains showed the highest 16S rRNA gene sequence similarities to Paenibacillus sacheonensis SY01T (96.3% and 98.0%, respectively). The genome of strain 12200R-189T was approximately 6.7 Mb in size with 5,750 protein-coding genes (CDSs) and the G + C content was 58.1 mol%, whereas that of strain 14171R-81T comprised one chromosome of 7.0 Mb and two plasmids (0.2 Mb each) with 6,595 CDSs and the G + C content was 54.5 mol%. Comparative genome analysis revealed that average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values among 12200R-189T, 14171R-81T, and other closely related species were below the cut-off levels 95% and 70%, respectively. Strain 12200R-189T grew at a temperature range of 15–40°C, pH 6.0–9.0, and 0–3% NaCl (w/v), whereas strain 14171R-81T grew at a temperature range of 10–37°C, pH 6.0– 8.0, and 0–1% NaCl (w/v). Menaquinone-7 (MK-7) was the only isoprenoid quinone detected in both strains. The predominant cellular fatty acids (> 10%) were iso-C15:0, anteiso- C15:0, and iso-C16:0. The polar lipids of strain 12200R- 189T were diphosphatidylglycerol (DPG), phosphatidylglycerol (PG), phosphatidylethanolamine (PE), aminophospholipid (APL), phospholipid (PL), phosphatidylglycolipid (PGL), and four aminophosphoglycolipids (APGLs) and those of strain 14171R-81T were DPG, PG, PE, APL, three PLs, two PGLs, and three APGLs. Based on phylogenetic, genomic, phenotypic, and chemotaxonomic analyses, strains 12200R- 189T and 14171R-81T represent two novel species of the genus Paenibacillus, for which the names Paenibacillus lycopersici sp. nov. and Paenibacillus rhizovicinus sp. nov. are proposed. The type strains are 12200R-189T (= KACC 19916T = CCTCC AB 2020027T) and 14171R-81T (= KACC 19915T = CCTCC AB 2020026T).

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Ming-Sheng Chen, Xiu-Long Pu, Ming-Dan Weng, Li Chen, Lan-Ying Zhu, Li Tuo
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Minh Hong Nguyen, Mai Thi Ngoc Dinh, Keun Chul Lee, Ji-Sun Kim, Thao Kim Nu Nguyen, Jung-Sook Lee
International Journal of Systematic and Evolutionary Microbiology .2022;[Epub] CrossRef
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Brevibacillus antibioticus sp. nov., with a broad range of antibacterial activity, isolated from soil in the Nakdong River: Ahyoung Choi , Young Ho Nam , Kiwoon Baek , Eu Jin Chung; J. Microbiol. 2019;57(11):991-996. Published online October 28, 2019; DOI: https://doi.org/10.1007/s12275-019-9325-y

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A Gram-stain-positive, aerobic, motile, and rod-shaped bacterial strain designated TGS2-1T was isolated from sediment soil in the Nakdong River, Republic of Korea. The optimal growth of strain TGS2-1T was observed at 28°C and pH 7.0 without NaCl supplementation. Strain TGS2-1T revealed antibiosis against various bacteria, including Staphylococcus aureus KCCM 4051, CCARM 3089 (methicillin resistant strains), Enterococcus faecalis KCCM 11814, Escherichia coli KCTC 2443, Candida albicans KACC 7270, and Filobasidium neoformans KCTC 7902. Phylogenetic analyses based on the 16S rRNA gene sequences indicated that strain TGS2-1T belonged to the genus Brevibacillus and shared 93.8–99.7% sequence similarity with Brevibacillus species. Whole-genome sequencing of strain TGS2-1T revealed a genome size of 6.2 Mbp and DNA G + C content of 47.0 mol%. The TGS2-1T genome shared an average nucleotide identity and digital DNA-DNA hybridization of 74.6–93.3% and 18.6–67.1%, respectively, with six related Brevibacillus genomes. The major fatty acid constituents of strain TGS2-1T were anteiso-C15:0 (62.3%) and anteiso-C17:0 (10.8%). Cells of strain TGS2-1T contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, seven unidentified aminophospholipids, and five unidentified lipids. The isoprenoid quinone detected in the strain was menaquinone-7 (MK-7). Based on data obtained from this polyphasic taxonomic study, strain TGS2-1T represents a novel species belonging to genus Brevibacillus, for which the name B. antibioticus sp. nov. is proposed. The type strain is TGS2-1T (= KCCM 90326T = NBRC 113840T = FBCC-B2501).

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Traditional processing increases biological activities of Dendrobium offificinale Kimura et. Migo in Southeast Yunnan, China
Di Zhou, Ying Zhao, Zhilin Chen, Xiuxiang Yan, Yanqiang Zhao, Lu Gao, Lixin Yang
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Martelella lutilitoris sp. nov., isolated from a tidal mudflat: Young-Ju Kim , Soon Dong Lee; J. Microbiol. 2019;57(11):976-981. Published online September 25, 2019; DOI: https://doi.org/10.1007/s12275-019-9259-4

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A novel, Gram-stain-negative, marine bacterium, designated GH2-6T, was isolated from a rhizosphere mudflat of a halophyte (Carex scabrifolia) collected in Gangwha Island, the Republic of Korea. The cells of the organism were strictly aerobic, oxidase- and catalase-positive, non-flagellated rods. Growth occurred at 20–45°C, pH 5–10, and 0.5–9 (w/v) NaCl. The requirement of Na+ for growth (0.5–3%) was observed. The major respiratory quinone was Q-10. The major polar lipids were phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, an aminolipid and a glycolipid. The predominant fatty acids were C18:1 ω7c, C18:0, C16:0, C19:0 cyclo ω8c, C18:1 ω7c 11-methyl and summed feature 2 (C14:0 3-OH and/or C16:1 iso I). The genome size was 4.45 Mb and the G+C content of the genomic DNA was 61.9 mol%. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain GH2-6T belonged to genus Martelella and formed a tight cluster with M. radicis BM5-7T and M. endophytica YC6887T. Levels of 16S rRNA gene sequence similarity between the novel isolate and members of the genus were 99.3–95.5%, but strain GH2-6T possessed an extended loop (49 nucleotides in length) between positions 187 and 213 of the 16S rRNA gene sequence (E. coli numbering). DDH values in vitro between the novel isolate and the closest relatives were 23.2±12.8 – 46.3±5.2%. On the basis of polyphasic data presented in this study, the type strain GH2-6T (= KACC 19403T = KCTC 62125T = NBRC 113212T) represents a novel species of the genus Martelella for which the name Martelella lutilitoris sp. nov. is proposed.

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Review

MINIREVIEW] Fungi in salterns: Dawoon Chung† , Haryun Kim† , Hyun Seok Choi; J. Microbiol. 2019;57(9):717-724. Published online August 27, 2019; DOI: https://doi.org/10.1007/s12275-019-9195-3

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Abstract PDF

Salterns are hypersaline extreme environments with unique physicochemical properties such as a salinity gradient. Although the investigation of microbiota in salterns has focused on archaea and bacteria, diverse fungi also thrive in the brine and soil of salterns. Fungi isolated from salterns are represented by black yeasts (Hortaea werneckii, Phaeotheca triangularis, Aureobasidium pullulans, and Trimmatostroma salinum), Cladosporium, Aspergillus, and Penicillium species. Most studies on saltern-derived fungi gave attention to black yeasts and their physiological characteristics, including growth under various culture conditions. Since then, biochemical and molecular tools have been employed to explore adaptation of these fungi to salt stress. Genome databases of several fungi in salterns are now publicly available and being used to elucidate salt tolerance mechanisms and discover the target genes for agricultural and industrial applications. Notably, the number of enzymes and novel metabolites known to be produced by diverse saltern-derived fungi has increased significantly. Therefore, fungi in salterns are not only interesting and important subjects to study fungal biodiversity and adaptive mechanisms in extreme environments, but also valuable bioresources with potential for biotechnological applications.

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Journal Article

Fulvimarina endophytica sp. nov., a novel endophytic bacterium isolated from bark of Sonneratia caseolaris: Li Tuo , Xiao-Rui Yan; J. Microbiol. 2019;57(8):655-660. Published online June 11, 2019; DOI: https://doi.org/10.1007/s12275-019-8627-4

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Abstract PDF

A Gram-negative, aerobic, short-rod-shaped, motile (with a terminal flagellum), non-spore-forming bacterium, designated strain 85T, was isolated from a surface-sterilized bark of Sonneratia caseolaris collected from Qinzhou in Guangxi, China and was analyzed using a polyphasic approach to determine its taxonomic position. Strain 85T grew optimally in the presence of 1–2% (w/v) NaCl at 30°C and pH 6.0–7.0. Phylogenetic analysis based on 16S rRNA gene sequence suggested that strain 85T belonged to the genus Fulvimarina and shared the highest 16S rRNA gene sequence similarity with Fulvimarina pelagi HTCC2506T (96.16%). The cell-wall peptidoglycan contained meso-diaminopimelic acid and ubiquinone Q-10 was the predominant respiratory lipoquinone. The polar lipids comprised diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, an unidentified amino lipid, three unidentified phospholipids and six unidentified lipids. The major fatty acid was C18:1 ω7c. The DNA G+C content of strain 85T was 65.4 mol%, and the average nucleotide identity and estimated DDH values between strain 85T and the type strain of Fulvimarina pelagi HTCC2506T were 77.3% and 21.7%, respectively. Based on the phylogenetic, phenotypic, and chemotaxonomic analyses, strain 85T should be considered as a novel species of the genus Fulvimarina with the proposed name Fulvimarina endophytica sp. nov., and its type strain is 85T (= KCTC 62717T = CGMCC 1.13665T).

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Review

Minireview] Electron microscopic observations of prokaryotic surface appendages: Ki Woo Kim; J. Microbiol. 2017;55(12):919-926. Published online December 7, 2017; DOI: https://doi.org/10.1007/s12275-017-7369-4

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Prokaryotic microbes possess a variety of appendages on their cell surfaces. The most commonly known surface appendages of bacteria include flagella, pili, curli, and spinae. Although archaea have archaella (archaeal flagella) and various types of pili that resemble those in bacteria, cannulae, and hami are unique to archaea. Typically involved in cell motility, flagella, the thickest appendages, are 20–26 nm and 10–14 nm wide in bacteria and archaea, respectively. Bacterial and archaeal pili are distinguished by their thin, short, hair-like structures. Curli appear as coiled and aggregative thin fibers, whereas spinae are tubular structures 50–70 nm in diameter in bacteria. Cannulae are characterized by ~25 nm-wide tubules that enter periplasmic spaces and connect neighboring archaeal cells. Hami are 1–3 μm in length and similar to barbed grappling hooks for attachment to bacteria. Recent advances in specimen preparation methods and image processing techniques have made cryo-transmission electron microscopy an essential tool for in situ structural analysis of microbes and their extracellular structures.

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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

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Abstract PDF

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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Comprehensive analysis of fungal diversity and enzyme activity in nuruk, a Korean fermenting starter, for acquiring useful fungi: Emily Carroll , Tran Ngoc Trinh , Hokyoung Son , Yin-Won Lee , Jeong-Ah Seo; J. Microbiol. 2017;55(5):357-365. Published online April 29, 2017; DOI: https://doi.org/10.1007/s12275-017-7114-z

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Nuruk is a fermenting starter that is involved in the pro-duction of alcoholic beverages, and has been used in South Korea for a very long time. To analyze the fungal diversity, we collected a total of 59 nuruk samples from several com-panies and persons in 2013 to 2014, and obtained 364 iso-lates. All of the single isolated fungi were identified, both morphologically and molecularly, based on the sequences of ribosomal RNA gene [18S, ITS1-5.8S-ITS2, and 26S (D1/D2 region)]. In 46 nuruk samples out of 59 (78%), Saccharo-mycopsis fibuligera, a dimorphic yeast, was most frequently isolated. Among the filamentous fungi, Aspergillus and Lich-theimia were found in more than 50% of the samples with lower colony forming unit (CFU/g of sample) than those of yeasts. The yeasts S. fibuligera and Wickerhamomyces ano-malus were counted with maximum 1.3 – 1.8 × 108 CFU/g. Among Mucorales fungi, Lichtheimia and Mucor were iso-lated in much higher numbers than Rhizopus and Rhizo-mucor. Overall, the home-made nuruks tend to contain more diverse filamentous fungi than the commercial nuruks. To acquire industrially useful filamentous fungi and yeasts, we analyzed the enzyme activities of α-amylase, glucoamylase and acid protease associated with brewing properties for 131 strains. Aspergillus oryzae and S. fibuligera had high α- and glucoamylase activities and most isolates of Lichtheimia ramosa had high acid protease activity. For further applica-tions, 27 fungal strains were chosen based on isolation fre-quencies from nuruk, and the ability to produce useful en-zyme.

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Review

REVIEW] H5 influenza, a global update: Rhodri Harfoot , Richard J. Webby; J. Microbiol. 2017;55(3):196-203. Published online February 28, 2017; DOI: https://doi.org/10.1007/s12275-017-7062-7

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Abstract PDF

H5 influenza viruses have caused much alarm globally due to their high pathogenic potential. As yet we have not seen sustained spread of the virus amongst humans despite a high prevalence of the virus in avian populations. Nevertheless, isolated human cases of infection have demonstrated high mortality and there are substantial efforts being taken to monitor the evolution of the virus and to undertake preparedness activities. Here we review and discuss the evolution of the A/goose/Guangdong/1/96 (H5N1) virus with emphasis on recent events.

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Journal Articles

Candida krusei isolated from fruit juices ultrafiltration membranes promotes colonization of Escherichia coli O157:H7 and Salmonella enterica on stainless steel surfaces: María Clara Tarifa , Jorge Enrique Lozano , Lorena Inés Brugnoni; J. Microbiol. 2017;55(2):96-103. Published online January 26, 2017; DOI: https://doi.org/10.1007/s12275-017-6300-3

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To clarify the interactions between a common food spoilage yeast and two pathogenic bacteria involved in outbreaks associated with fruit juices, the present paper studies the effect of the interplay of Candida krusei, collected from UF membranes, with Escherichia coli O157:H7 and Salmonella enterica in the overall process of adhesion and colonization of abiotic surfaces. Two different cases were tested: a) co-adhesion by pathogenic bacteria and yeasts, and b) incorporation of bacteria to pre-adhered C. krusei cells. Cultures were made on stainless steel at 25°C using apple juice as culture medium. After 24 h of co-adhesion with C. krusei, both E. coli O157:H7 and S. enterica increased their counts 1.05 and 1.11 log CFU cm2, respectively. Similar increases were obtained when incorporating bacteria to pre-adhered cells of Candida. Nevertheless C. krusei counts decreased in both experimental conditions, in a) 0.40 log CFU cm2 and 0.55 log CFU cm2 when exposed to E. coli O157:H7 and S. enterica and in b) 0.18 and 0.68 log CFU cm2, respectively. This suggests that C. krusei, E. coli O157:H7, and S. enterica have a complex relationship involving physical and chemical interactions on food contact surfaces. This study supports the possibility that pathogen interactions with members of spoilage microbiota, such as C. krusei, might play an important role for the survival and dissemination of E. coli O157:H7 and Salmonella enterica in food-processing environments. Based on the data obtained from the present study, much more attention should be given to prevent the contamination of these pathogens in acidic drinks.

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What We Still Don’t Know About Biofilms—Current Overview and Key Research Information
Tsvetozara Damyanova, Tsvetelina Paunova-Krasteva
Microbiology Research.2025; 16(2): 46. CrossRef
Efficacy of natamycin to reduce adhesion and biofilm formation of multispecies yeast biofilms on variable flow conditions
María del Rosario Agustín, Diego Bautista Genovese, Manuel Alejandro Palencia Díaz, Lorena Inés Brugnoni
Biofouling.2025; 41(6): 573. CrossRef
Effectiveness of sodium hypochlorite and benzalkonium chloride in reducing spoilage yeast biofilms on food contact surfaces
Manuel Alejandro Palencia Díaz, María Clara Tarifa, Patricia Liliana Marucci, Diego Bautista Genovese, Lorena Inés Brugnoni
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Application of natamycin and farnesol as bioprotection agents to inhibit biofilm formation of yeasts and foodborne bacterial pathogens in apple juice processing lines
María del Rosario Agustín, María Clara Tarifa, María Soledad Vela-Gurovic, Lorena Inés Brugnoni
Food Microbiology.2023; 109: 104123. CrossRef
Candida krusei is the major contaminant of ultrafiltration and reverse osmosis membranes used for cranberry juice production
Sherazade Fikri, Marie-Hélène Lessard, Véronique Perreault, Alain Doyen, Steve Labrie
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Application of Natamycin and Farnesol as Biocontrol Agents of Multi-Species Biofilms on Industrial Surfaces in Apple Juice
María del Rosario Agustín, Maria Clara Tarifa, Maria Soledad Vela-Gurovic, Lorena Ines Brugnoni
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María C. Tarifa, Jorge E. Lozano, Lorena I. Brugnoni
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GPH1 is involved in glycerol accumulation in the three-dimensional networks of the nematode-trapping fungus Arthrobotrys oligospora: Qin-Yi Wu , Yue-Yan Zhu , Cheng-Gang Zou , Ying-Qian Kang , Lian-Ming Liang; J. Microbiol. 2016;54(11):768-773. Published online October 29, 2016; DOI: https://doi.org/10.1007/s12275-016-6272-8

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Turgor is very important for the invasive growth of fungal pathogens. Glycerol, a highly osmotic solvent, is considered to play an important role in turgor generation. The nematophagous fungus Arthrobotrys oligospora mainly lives as a saprophyte. In the presence of nematodes, A. oligospora enters the parasitic stage by forming three-dimensional networks (traps) to capture nematodes. In A. oligospora, we found that glycerol accumulated during nematode-induced trap formation. We demonstrated that deleting gph1, which encodes glycogen phosphorylase, decreased the glycerol content, compared with that of a wild-type strain. Although the number of traps induced by nematodes was not affected in the Δgph1 mutant, the capture rate was lower. Meanwhile, deleting gph1 also affected the growth rate and conidiation capacity of the fungus. These results indicate that glycerol derived from GPH1 is essential for the full virulence of A. oligospora against nematodes.

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Increased production of pullulan in Aureobasidium pullulans YQ65 through reduction of intracellular glycogen content
Kai Zhang, Lei Yue, Jingxian Cong, Jianlong Zhang, Zhibin Feng, Qian Yang, Xuechun Lu
Carbohydrate Polymers.2025; 352: 123196. CrossRef
Glycerol as a potential solution for rotifer protection against predatory fungi in wastewater treatment
Agnieszka Pajdak-Stós, Yuliia Korzh, Edyta Fiałkowska
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Comparisons of soil microbial compositions in rhizospheres of sugarcane cultivars with different abilities to resist smut
Siyu Chen, Xinyan Zhou, Xinni Li, Yufei Wei, Zhongliang Chen, Shangdong Yang
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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
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Tools and basic procedures of gene manipulation in nematode-trapping fungi
Shunxian Wang, Xingzhong Liu
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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
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Aminotransferase SsAro8 Regulates Tryptophan Metabolism Essential for Filamentous Growth of Sugarcane Smut Fungus Sporisorium scitamineum
Guobing Cui, Chengwei Huang, Xinping Bi, Yixu Wang, Kai Yin, Luyuan Zhu, Zide Jiang, Baoshan Chen, Yi Zhen Deng, Slavena Vylkova
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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
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Natural diversity in the predatory behavior facilitates the establishment of a robust model strain for nematode-trapping fungi
Ching-Ting Yang, Guillermo Vidal-Diez de Ulzurrun, A. Pedro Gonçalves, Hung-Che Lin, Ching-Wen Chang, Tsung-Yu Huang, Sheng-An Chen, Cheng-Kuo Lai, Isheng J. Tsai, Frank C. Schroeder, Jason E. Stajich, Yen-Ping Hsueh
Proceedings of the National Academy of Sciences.2020; 117(12): 6762. CrossRef

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

Directed analysis of cyanobacterial membrane phosphoproteome using stained phosphoproteins and titanium-enriched phosphopeptides§: Dong-Gi Lee , Joseph Kwon , Chi-Yong Eom , Young-Moon Kang , Seong Woon Roh , Kyung-Bok Lee , Jong-Soon Choi; J. Microbiol. 2015;53(4):279-287. Published online April 8, 2015; DOI: https://doi.org/10.1007/s12275-015-5021-8

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Gel-free shotgun phosphoproteomics of unicellular cyanobacterium Synechocystis sp. PCC 6803 has not been reported up to now. The purpose of this study is to develop directed membrane phosphoproteomic method in Synechocystis sp. Total Synechocystis membrane proteins were separated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and phosphoprotein-stained gel bands were selectively subjected to in-gel trypsin digestion. The phosphorylation sites of the resulting peptides were determined by assigning the neutral loss of [M-H3PO4] to Ser, Thr, and Tyr residues using nano-liquid chromatography 7 Tesla Fourier transform mass spectrometry. As an initial application, 111 proteins and 33 phosphoproteins were identified containing 11 integral membrane proteins. Identified four unknown phosphoproteins with transmembrane helices were suggested to be involved in membrane migration or transporters based on BLASTP search annotations. The overall distribution of hydrophobic amino acids in pTyr was lower in frequency than that of pSer or pThr. Positively charged amino acids were abundantly revealed in the surrounding amino acids centered on pTyr. A directed shotgun membrane phosphoproteomic strategy provided insight into understanding the fundamental regulatory processes underlying Ser, Thr, and Tyr phosphorylation in multi-layered membranous cyanobacteria.

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Global Profiling of Protein Phosphorylation, Acetylation, and β-Hydroxybutyrylation in Nannochloropsis oceanica
Lingyu Ouyang, Wuxin You, Ansgar Poetsch, Li Wei
Journal of Agricultural and Food Chemistry.2024; 72(47): 26248. CrossRef
Post-translational Modifications of Serine/Threonine and Histidine Kinases and Their Roles in Signal Transductions in Synechocystis Sp. PCC 6803
Wu Xu, Yingchun Wang
Applied Biochemistry and Biotechnology.2021; 193(3): 687. CrossRef
Comprehensive Phosphoproteomic Analysis of Nostoc flagelliforme in Response to Dehydration Provides Insights into Plant ROS Signaling Transduction
Wenyu Liang, Fengkun Yan, Meng Wang, Xiaoxu Li, Zheng Zhang, Xiaorong Ma, Jinhong Hu, Jun Wang, Lingxia Wang
ACS Omega.2021; 6(21): 13554. CrossRef
Metaproteomic analysis of harmful algal bloom in the Daechung reservoir, Korea
Jong-Soon Choi, Yun Hwan Park, Soo Hyeon Kim, Ju Seong Park, Yoon-E Choi
Environmental Biology Research.2020; 38(3): 424. CrossRef
Efficient profiling of detergent-assisted membrane proteome in cyanobacteria
Jong-Soon Choi, Yun Hwan Park, Jeong Hyun Oh, Sooyong Kim, Joseph Kwon, Yoon-E Choi
Journal of Applied Phycology.2020; 32(2): 1177. CrossRef
Assessment of Protein Content and Phosphorylation Level in Synechocystis sp. PCC 6803 under Various Growth Conditions Using Quantitative Phosphoproteomic Analysis
Masakazu Toyoshima, Yuma Tokumaru, Fumio Matsuda, Hiroshi Shimizu
Molecules.2020; 25(16): 3582. CrossRef
Proteomic De-Regulation in Cyanobacteria in Response to Abiotic Stresses
Piyoosh Kumar Babele, Jay Kumar, Venkatesh Chaturvedi
Frontiers in Microbiology.2019;[Epub] CrossRef
The S-layer biogenesis system of Synechocystis 6803: Role of Sll1180 and Sll1181 (E. coli HlyB and HlyD analogs) as type-I secretion components for Sll1951 export
Rachna Agarwal, Julian P. Whitelegge, Sanjay Saini, Amit Prakash Shrivastav
Biochimica et Biophysica Acta (BBA) - Biomembranes.2018; 1860(7): 1436. CrossRef
Proteomics of cyanobacteria: current horizons
Natalia Battchikova, Dorota Muth-Pawlak, Eva-Mari Aro
Current Opinion in Biotechnology.2018; 54: 65. CrossRef
Determination of the Role of Microcystis aeruginosa in Toxin Generation Based on Phosphoproteomic Profiles
Jiangqi Qu, Liping Shen, Meng Zhao, Wentong Li, Chengxia Jia, Hua Zhu, Qingjing Zhang
Toxins.2018; 10(7): 304. CrossRef
Functional Diversity of Transcriptional Regulators in the Cyanobacterium Synechocystis sp. PCC 6803
Mengliang Shi, Xiaoqing Zhang, Guangsheng Pei, Lei Chen, Weiwen Zhang
Frontiers in Microbiology.2017;[Epub] CrossRef
Proteomic analysis of post translational modifications in cyanobacteria
Qian Xiong, Zhuo Chen, Feng Ge
Journal of Proteomics.2016; 134: 57. CrossRef
Proteomic and metabolomic analyses reveal metabolic responses to 3-hydroxypropionic acid synthesized internally in cyanobacterium Synechocystis sp. PCC 6803
Yunpeng Wang, Lei Chen, Weiwen Zhang
Biotechnology for Biofuels.2016;[Epub] CrossRef

Deletion analysis of LSm, FDF, and YjeF domains of Candida albicans Edc3 in hyphal growth and oxidative-stress response: Eung-Chul Kim , Jinmi Kim; J. Microbiol. 2015;53(2):111-115. Published online January 28, 2015; DOI: https://doi.org/10.1007/s12275-015-4727-y

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Candida albicans is an opportunistic fungal pathogen whose responses to environmental changes are associated with the virulence attributes. Edc3 is known to be an enhancer of the mRNA decapping reactions and a scaffold protein of cytoplasmic processing bodies (P-bodies). Recent studies of C. albicans Edc3 suggested its critical roles in filamentous growth and stress-induced apoptotic cell death. The edc3/edc3 deletion mutant strain showed increased cell survival and less ROS accumulation upon treatment with hydrogen peroxide. To investigate the diverse involvement of Edc3 in the cellular processes, deletion mutations of LSm, FDF, or YjeF domain of Edc3 were constructed. The edc3-LSmΔ or edc3-YjeFΔ mutation showed the filamentation defect, resistance to oxidative stress, and decreased ROS accumulation. In contrast, the edc3-FDFΔ mutation exhibited a wild-type level of filamentous growth and a mild defect in ROS accumulation. These results suggest that Lsm and YjeF domains of Edc3 are critical in hyphal growth and oxidative stress response.

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Roles of P-body factors in Candida albicans filamentation and stress response
Melissa A. Tosiano, Frederick Lanni, Aaron P. Mitchell, C. Joel McManus, Guilhem Janbon
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The FomYjeF Protein Influences the Sporulation and Virulence of Fusarium oxysporum f. sp. momordicae
Chenxing Wei, Caiyi Wen, Yuanyuan Zhang, Hongyan Du, Rongrong Zhong, Zhengzhe Guan, Mengjiao Wang, Yanhong Qin, Fei Wang, Luyang Song, Ying Zhao
International Journal of Molecular Sciences.2023; 24(8): 7260. CrossRef
Intersection of phosphate transport, oxidative stress and TOR signalling in Candida albicans virulence
Ning-Ning Liu, Priya Uppuluri, Achille Broggi, Angelique Besold, Kicki Ryman, Hiroto Kambara, Norma Solis, Viola Lorenz, Wanjun Qi, Maikel Acosta-Zaldívar, S. Noushin Emami, Bin Bao, Dingding An, Francisco A. Bonilla, Martha Sola-Visner, Scott G. Filler,
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Mutational analysis of metacaspase CaMca1 and decapping activator Edc3 in the pathogenicity of Candida albicans
Jeong-Hoon Jeong, Seok-Eui Lee, Jinmi Kim
Fungal Genetics and Biology.2016; 97: 18. CrossRef

Saccharomyces cerevisiae Can Secrete Sapp1p Proteinase of Candida parapsilosis But Cannot Use It for Efficient Nitrogen Acquisition: Zuzana Vinterová , Václava Bauerová , Ji&# , Hana Sychrová , Olga Hru&# , Iva Pichová; J. Microbiol. 2013;51(3):336-344. Published online June 28, 2013; DOI: https://doi.org/10.1007/s12275-013-2422-4

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Secreted aspartic proteinase Sapp1p of Candida parapsilosis represents one of the factors contributing to the pathogenicity of the fungus. The proteinase is synthesized as an inactive pre-pro-enzyme, but only processed Sapp1p is secreted into extracellular space. We constructed a plasmid containing the SAPP1 coding sequence under control of the ScGAL1 promoter and used it for proteinase expression in a Saccharomyces cerevisiae kex2Δ mutant. Because Sapp1p maturation depends on cleavage by Kex2p proteinase, the kex2Δ mutant secreted only the pro-form of Sapp1p. Characterization of this secreted proteinase form revealed that the Sapp1p signal peptide consists of 23 amino acids. Additionally, we prepared a plasmid with the SAPP1 coding sequence under control of its authentic CpSAPP1 promoter, which contains two GATAA motifs. While in C. parapsilosis SAPP1 expression is repressed by good low molecular weight nitrogen sources (e.g., ammonium ions), S. cerevisiae cells harboring this plasmid secreted a low concentration of active proteinase regardless of the type of nitrogen source used. Quantitative real-time PCR analysis of a set of genes related to nitrogen metabolism and uptake (GAT1, GLN3, STP2, GAP1, OPT1, and PTR2) obtained from S. cerevisiae cells transformed with either plasmid encoding SAPP1 under control of its own promoter or empty vector and cultivated in media containing various nitrogen sources also suggested that SAPP1 expression can be connected with the S. cerevisiae regulatory network. However, this regulation occurs in a different manner than in C. parapsilosis.

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Advances in recombinant protease production: current state and perspectives
Xiufang Liu, Mulin Lian, Mouming Zhao, Mingtao Huang
World Journal of Microbiology and Biotechnology.2024;[Epub] CrossRef
Pathogenic Candida species differ in the ability to grow at limiting potassium concentrations
B. Hušeková, H. Elicharová, H. Sychrová
Canadian Journal of Microbiology.2016; 62(5): 394. CrossRef

Extracellular Stress and Lipopolysaccharide Modulate Acinetobacter baumannii Surface-Associated Motility: Christin N. McQueary , Benjamin C. Kirkup , Yuanzheng Si , Miriam Barlow , Luis A. Actis , David W. Craft , Daniel V. Zurawski; J. Microbiol. 2012;50(3):434-443. Published online June 30, 2012; DOI: https://doi.org/10.1007/s12275-012-1555-1

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Abstract PDF

Acinetobacter baumannii is a nosocomial bacterial pathogen, and infections attributed to this species are further complicated by a remarkable ability to acquire antimicrobial resistance genes and to survive in a desiccated state. While the antibiotic resistance and biofilm formation of A. baumannii is well-documented, less is known about the virulence attributes of this organism. Recent studies reported A. baumannii strains display a motility phenotype, which appears to be partially dependent upon Type IV pili, autoinducer molecules, and the response to blue light. In this study, we wanted to determine the prevalence of this trait in genetically diverse clinical isolates, and any additional required factors, and environmental cues that regulate motility. When strains are subjected to a wide array of stress conditions, A. baumannii motility is significantly reduced. In contrast, when extracellular iron is provided or salinity is reduced, motility is significantly enhanced. We further investigated whether the genes required for the production of lipopolysaccharide (lpsB) and K1 capsule (epsA/ptk) are required for motility as demonstrated in other Gram-negative bacteria. Transposon mutagenesis resulted in reduced motility by the insertion derivatives of each of these genes. The presence of the parental allele provided in trans, in the insertion mutant background, could only restore motility in the lpsB mutant. The production of core LPS directly contributes to the motility phenotype, while capsular polysaccharide may have an indirect effect. Further, the data suggest motility is regulated by extracellular conditions, indicating that A. baumannii is actively sensing the environment and responding accordingly.

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Fine Mapping of a Foot-and-Mouth Disease Virus Epitope Recognized by Serotype-Independent Monoclonal Antibody 4B2: Yongzhong Yu , Haiwei Wang , Lei Zhao , Chunyuan Zhang , Zhigang Jiang , Li Yu; J. Microbiol. 2011;49(1):94-101. Published online March 3, 2011; DOI: https://doi.org/10.1007/s12275-011-0134-1

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Abstract PDF

VP2 is a structural protein of the foot-and-mouth disease virus (FMDV). In this study, a FMDV serotype-independent monoclonal antibody (MAb), 4B2, was generated. By screening a phage-displayed random 12-peptide library, we found positive phages displaying the consensus motif ETTXLE (X is any amino acid (aa)), which is highly homologous to 6ETTLLE11 at the N-terminus of the VP2 protein. Subsequently, a series of GST-fusion proteins expressing a truncated N-terminus of VP2 were examined by western blot analysis using the MAb 4B2. The results indicated that the motif 6ETTLLE11 of VP2 may be the minimal requirement of the epitope recognized by 4B2. Moreover, a 12-aa peptide 2KKTEETTLLEDR13 was shown to be the minimal unit of the epitope with maximal binding activity to 4B2. Alanine-scanning analysis demonstrated thatThr7, Thr8, and Leu10 are the functional residues of the 4B2 epitope Glu6 and Leu9 are required residues, and Glu11 plays a crucial role in the binding of MAb 4B2. The fine mapping of the epitope indicated that MAb 4B2 has the potential to be used in FMDV diagnosis.

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Research in Veterinary Science.2013; 94(3): 796. CrossRef
Assembly and characterization of foot-and-mouth disease virus empty capsid particles expressed within mammalian cells
Maria Gullberg, Bartosz Muszynski, Lindsey J. Organtini, Robert E. Ashley, Susan L. Hafenstein, Graham J. Belsham, Charlotta Polacek
Journal of General Virology .2013; 94(8): 1769. CrossRef
Insertion of type O-conserved neutralizing epitope into the foot-and-mouth disease virus type Asia1 VP1 G-H loop: effect on viral replication and neutralization phenotype
Haiwei Wang, Mei Xue, Decheng Yang, Guohui Zhou, Donglai Wu, Li Yu
Journal of General Virology .2012; 93(7): 1442. CrossRef
Effects of amino acid substitutions in the VP2 B-C loop on antigenicity and pathogenicity of serotype Asia1 foot-and-mouth disease virus
Mei Xue, Haiwei Wang, Wan Li, Guohui Zhou, Yabin Tu, Li Yu
Virology Journal.2012;[Epub] CrossRef

Identification of a Novel Linear B-Cell Epitope in the M Protein of Avian Infectious Bronchitis Coronaviruses: Junji Xing , Shengwang Liu , Zongxi Han , Yuhao Shao , Huixin Li , Xiangang Kong; J. Microbiol. 2009;47(5):589-599. Published online October 24, 2009; DOI: https://doi.org/10.1007/s12275-009-0104-z

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This report describes the identification of a novel linear B-cell epitope at the C-terminus of the membrane (M) protein of avian infectious bronchitis virus (IBV). A monoclonal antibody (MAb) (designated as 15E2) against the IBV M protein was prepared and a series of 14 partially-overlapping fragments of the IBV M gene were expressed with a GST tag. These peptides were subjected to enzyme-linked immunosorbent assay (ELISA) and western blotting analysis using MAb 15E2 to identify the epitope. A linear motif, 199FATFVYAK206, which was located at the C-terminus of the M protein, was identified by MAb 15E2. ELISA and western blotting also showed that this epitope could be recognized by IBV-positive serum from chicken. Given that 15E2 showed reactivity with the 199FATFVYAK206 motif, expressed as a GST fusion protein, in both western blotting and in an ELISA, we proposed that this motif represented a linear B-cell epitope of the M protein. The 199FATFVYAK206 motif was the minimal requirement for reactivity as demonstrated by analysis of the reactivity of 15E2 with several truncated peptides that were derived from the motif. Alignment and comparison of the 15E2-defined epitope sequence with the sequences of other coronaviruses indicated that the epitope is well conserved among chicken and turkey coronaviruses. The identified epitope should be useful in clinical applications and as a tool for the further study of the structure and function of the M protein of IBV.

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A Candidate Antigen of the Recombinant Membrane Protein Derived from the Porcine Deltacoronavirus Synthetic Gene to Detect Seropositive Pigs
Francisco Jesus Castañeda-Montes, José Luis Cerriteño-Sánchez, María Azucena Castañeda-Montes, Julieta Sandra Cuevas-Romero, Susana Mendoza-Elvira
Viruses.2023; 15(5): 1049. CrossRef
Predicted 3D model of the M protein of Porcine Epidemic Diarrhea Virus and analysis of its immunogenic potential
Alan Rodríguez-Enríquez, Irma Herrera-Camacho, Lourdes Millán-Pérez-Peña, Julio Reyes-Leyva, Gerardo Santos-López, José Francisco Rivera-Benítez, Nora Hilda Rosas-Murrieta, Claude Krummenacher
PLOS ONE.2022; 17(2): e0263582. CrossRef
Genetic and antigenic heterogeneity of infectious bronchitis virus in South America: implications for control programmes
Ana Marandino, Ariel Vagnozzi, María Isabel Craig, Gonzalo Tomás, Claudia Techera, Yanina Panzera, Federico Vera, Ruben Pérez
Avian Pathology.2019; 48(3): 270. CrossRef
Prediction and identification of novel IBV S1 protein derived CTL epitopes in chicken
Lei Tan, Ying Liao, Jin Fan, Yuqiang Zhang, Xiang Mao, Yingjie Sun, Cuiping Song, Xusheng Qiu, Chunchun Meng, Chan Ding
Vaccine.2016; 34(3): 380. CrossRef
Infectious bronchitis virus poly-epitope-based vaccine protects chickens from acute infection
Lei Tan, Yuqiang Zhang, Fang Liu, Yanmei Yuan, Yuan Zhan, Yingjie Sun, Xusheng Qiu, Chunchun Meng, Cuiping Song, Chan Ding
Vaccine.2016; 34(44): 5209. CrossRef
Characterization of an Immunodominant Epitope in the Endodomain of the Coronavirus Membrane Protein
Hui Dong, Xin Zhang, Hongyan Shi, Jianfei Chen, Da Shi, Yunnuan Zhu, Li Feng
Viruses.2016; 8(12): 327. CrossRef
Development of an ELISA based on a multi-fragment antigen of infectious bronchitis virus for antibodies detection
Meng-die Ding, Xin Yang, Hong-ning Wang, An-yun Zhang, Zhi-kun Zhang, Wen-qiao Fan, Hai-peng Cao
Biotechnology Letters.2015; 37(12): 2453. CrossRef
Two novel neutralizing antigenic epitopes of the s1 subunit protein of a QX-like avian infectious bronchitis virus strain Sczy3 as revealed using a phage display peptide library
Nianli Zou, Jing Xia, Fuyan Wang, Zhenzhen Duan, Dan Miao, Qigui Yan, Sanjie Cao, Xintian Wen, Ping Liu, Yong Huang
Veterinary Immunology and Immunopathology.2015; 168(1-2): 49. CrossRef
Adaptation and Attenuation of Duck Tembusu Virus Strain Du/CH/LSD/110128 following Serial Passage in Chicken Embryos
Ling Sun, Yunxia Li, Yue Zhang, Zongxi Han, Yang Xu, Xiangang Kong, Shengwang Liu, R. L. Hodinka
Clinical and Vaccine Immunology.2014; 21(8): 1046. CrossRef
Identification of a conserved linear B-cell epitope in the M protein of porcine epidemic diarrhea virus
Zhibang Zhang, Jianfei Chen, Hongyan Shi, Xiaojin Chen, Da Shi, Li Feng, Bin Yang
Virology Journal.2012;[Epub] CrossRef
Identification of a novel linear B-cell epitope in the UL26 and UL26.5 proteins of Duck Enteritis Virus
Xiaoli Liu, Zongxi Han, Yuhao Shao, Dan Yu, Huixin Li, Yu Wang, Xiangang Kong, Shengwang Liu
Virology Journal.2010;[Epub] CrossRef

Transformation and Mutagenesis of the Nematode-trapping Fungus Monacrosporium sphaeroides by Restriction Enzyme-mediated Integration (REMI): Xu Jin , Ming-He Mo , Zhou Wei , Xiao-Wei Huang , Ke-Qin Zhang; J. Microbiol. 2005;43(5):417-423.; DOI: https://doi.org/2281 [pii]

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Abstract PDF: In this study, the nematode-trapping fungus, Monacrosporium sphaeroides, was transformed with a plasmid harboring the hygromycin B phosphotransferase gene, via restriction enzyme-mediated integration (REMI). Frequencies of up to 94 transformants g-1 per linearized plasmid DNA were obtained by optimizing the PEG concentration, as well as the category and quantity of the added restriction enzyme. 90% of the transformants were determined to be stable for drug resistance when 20 randomly selected transformants were tested. Southern analyses revealed that the transforming DNA was integrated into the M. sphaeroides genome either with or without rearrangement. Five mitotic stable mutant strains were obtained using this approach, all of which had been altered with regard to sporulation capacity and pathogenicity toward nematodes. Southern blot analyses of the five mutants revealed that foreign plasmid DNA had integrated into the genome. Three of the mutants, Tms2316, Tms3583 and Tms1536, exhibited integration at a single location, whereas the remaining two, Tms32 and Tms1913, manifested integration at double or multiple locations. Our results suggest that the transformation of M. sphaeroides via REMI will facilitate insertional mutagenesis, the functional analysis of a variety of genes, and the tagging or cloning of genes of interest.

Diversity and Metal Tolerance of Nematode-Trapping Fungi in Pb-Polluted Soils: Ming-He Mo , Wei-Min Chen , Hao-Ran Yang , Ke-Qin Zhang; J. Microbiol. 2008;46(1):16-22.; DOI: https://doi.org/10.1007/s12275-007-0174-8

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The diversity of nematode-trapping fungi (NTF) in two lead (Pb) mines in Yunnan Province, China was investigated in 2004. In total, 20 species belonging to five genera were identified from 500 samples collected at the Lanping and the Huize mines. Pb concentrations ranged from 216~7,150 mg/kg for the former and 132~13,380 mg/kg for the latter, respectively. The fungi were divided into five groups based on different trapping mechanisms. The trapping-net producer group contained the largest number of species, with nine. Two predators, Dactylellina ellipsosporum and Arthrobotrys oligospora, were found at frequencies of 32.85% and 15.41%, respectively. The diversity indexes of NTF were positively correlated with Pb pollution levels in both the Lanping Mine (r=0.66) and the Huize Mine (r=0.72), suggesting that the distribution of NTF was not negatively affected by Pb contamination. For most strains of a given species, there was no significant difference (P>0.01) in the Pb tolerance between the strains isolated from habitats with low or high Pb concentrations. However, Pb toxicity exerted adverse effects on trap formation and predacious capability of fungi. We discuss the possible metal tolerance mechanisms and their relationships to the survival strategy of NTF in Pb-polluted environments.

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Lead (Pb) tolerance in the ectomycorrhizal fungi Suillus brevipes and S. tomentosus
William Leary, Matthew Johnson, Jessica Fletcher, Sara Branco
Mycorrhiza.2025;[Epub] CrossRef
Multilocus Phylogeny and Characterization of Five Undescribed Aquatic Carnivorous Fungi (Orbiliomycetes)
Fa Zhang, Yao-Quan Yang, Fa-Ping Zhou, Wen Xiao, Saranyaphat Boonmee, Xiao-Yan Yang
Journal of Fungi.2024; 10(1): 81. CrossRef
Independence Effects of Heat and Ash on Forest Soil Nematode-Trapping Fungi Communities
Rong She, Hai-Qing Wang, Davide Fornacca, Fei-Teng Li, Fa Zhang, Yao-Quan Yang, Fa-Ping Zhou, Xiao-Yan Yang, Wen Xiao
Fire.2023; 6(1): 27. CrossRef
Recent Advances in Life History Transition with Nematode-Trapping Fungus Arthrobotrys oligospora and Its Application in Sustainable Agriculture
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Pathogens.2023; 12(3): 367. CrossRef
Natural recovery from fire disturbance is more favorable than assisted recovery for the restoration of soil nematode-trapping fungi
Rong She, Xin-Juan Zhou, Hai-Qing Wang, Fa Zhang, Xiao-Yan Yang, Wen Xiao
Canadian Journal of Microbiology.2022; 68(5): 329. CrossRef
New Arthrobotrys Nematode-Trapping Species (Orbiliaceae) from Terrestrial Soils and Freshwater Sediments in China
Fa Zhang, Saranyaphat Boonmee, Jayarama D. Bhat, Wen Xiao, Xiao-Yan Yang
Journal of Fungi.2022; 8(7): 671. CrossRef
Drechslerella daliensis and D. xiaguanensis (Orbiliales, Orbiliaceae), two new nematode-trapping fungi from Yunnan, China
Fa Zhang, Saranyaphat Boonmee, Jutamart Monkai, Xiao-Yan Yang, Wen Xiao
Biodiversity Data Journal.2022;[Epub] CrossRef
Independence and Synergy Effects of Heat and Ash on Forest Soil Nematode-Trapping Fungi Communities
She Rong, Wang Hai-qing, David Fornacca, Li Fei-teng, Zhang Fa, Yang Yao-quan, Zhou Fa-ping, Yang Xiao-yan, Xiao Wen
SSRN Electronic Journal.2022;[Epub] CrossRef
Isolation of nematophagous fungi from soil samples collected from three different agro-ecologies of Ethiopia
Maradona Berhanu, Hika Waktole, Gezahegne Mamo, Getachew Terefe
BMC Microbiology.2022;[Epub] CrossRef
Succession of soil nematode-trapping fungi following fire disturbance in forest
She Rong, Zhou Xin-Juan, Wang Hai-Qing, Zhang Fa, Yang Xiao-Yan, Xiao Wen
Journal of Forest Research.2020; 25(6): 433. CrossRef
Isolation and selection ofArthrobotrysnematophagous fungi to control the nematodes on coffee and black pepper plants in Vietnam
Nguyen Viet Hiep, Nguyen Thu Ha, Tran Thi Thanh Thuy, Pham Van Toan
Archives of Phytopathology and Plant Protection.2019; 52(7-8): 825. CrossRef
Nematode-Trapping Fungi
Xiangzhi Jiang, Meichun Xiang, Xingzhong Liu, Joseph Heitman, Pedro W. Crous, Timothy Y. James
Microbiology Spectrum.2017;[Epub] CrossRef
Arthrobotrys oligospora: a model organism for understanding the interaction between fungi and nematodes
Xue-Mei Niu, Ke-Qin Zhang
Mycology.2011; 2(2): 59. CrossRef

Cloning and expression of pseudomonas cepacia catB gene in pseudomonas putida: Song, Seung Yeon , Jung, Young Hee , Lee, Myeong Sok , Lee, Ki Sung , Kim, Young Soo , Kim, Chi Kyung , Choi, Sang Ho , Min, Kyung Hee; J. Microbiol. 1996;34(4):334-340.

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Abstract PDF: The enzyme, cis,cis-muconate lactonizing enzyme has been proposed to play a key role in the β-ketoadipate pathway of benzoate degradation. A 3.2-kb EcoRI fragment termed as pRSU2, isolated from a Pseudomonas cepacia genomic library was able to complement the catB defective mutant. Several relevant restriction enzyme sites were determined within the cloned fragment. In Pseudomonas putida SUC2 carrying pRSU2, the enzyme activity was relatively higher than those of the induced or partially induced state of wild type P. putida PRS2000. It was probably due to higher expression of P. cepacia catB in P. putida PRS2000. It was probably due to higher expression of P. cepacia catB in P. putida. One possible interpretation of these results is that the catB promoter in P. cepacia is recognized within P. putida, resulting in the almost same expression level.

Deletion Analysis of the Major NF-[kappa]B Activation Domain in Latent Membrane Protein 1 of Epstein-Barr Virus: Shin Cho , Won-Keun Lee; J. Microbiol. 1999;37(4):256-262.

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Abstract PDF: Latent membrane protein 1 (LMP1) of the Epstein-Barr virus (EBV) is an integral membrane protein with six transmembrane domains, which is essential for EBV-induced B cell transformation. LMP1 functions as a constitutively active tumor necrosis factor receptor (TNFR) like membrane receptor, whose signaling requires recruitment of TNFR-associated factors (TRAFs) and leads to NF-[kappa]B activation. NF-[kappa]B activation by LMP1 is critical for B cell transformation and has been linked to many phenotypic changes associated with EBV-induced B cell transformation. Deletion analysis has identified two NF-[kappa]B activation regions in the carboxy terminal cytoplasmic domains of LMP1, termed CTAR1 (residues 194-232) and CTAR2 (351-386). The membrane proximal C-terminal domain was precisely mapped to a PXQXT motif (residues 204-208) involved in TRAF binding as well as NF-[kappa]B activation. In this study, we dissected the CTAR2 region, which is the major NF-[kappa]B signaling effector of LMP1, to determine a minimal functional sequence. A series of LMP1 mutant constructs systematically deleted for the CTAR2 region were prepared, and NF-[kappa]B activation activity of these mutants were assessed by transiently expressing them in 293 cells and Jurkat T cells. The NF-[kappa]B activation domain of CTAR2 appears to reside in a stretch of 6 amino acids (residues 379-384) at the end of the carboxy terminus.

Use of the Yeast 1.5-Hybrid System to Detect DNA-Protein-Protein Interactions: Sook-Kyung Kim , Jin Hee Han; J. Microbiol. 2000;38(2):113-116.

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Abstract PDF: Escherichia coli F plasmid partition apparatus is composed of two trans-acting proteins (SopA and SopB) and one cis-acting DNA sequence (sopC). The SopB-sopC complex has been suggested to serve a centromere-like function through its interaction with chromosomally encoded proteins which remain to be identified. In this paper, we are introducing a new yeast 1.5-hybrid system which assembles the two-hybrid and one-hybrid system as a mean to find an additional component of the F plasmid partition system, interacting with DNA (sopC)-bound SopB protein. The result indicates that this system is a promising one, capable of selecting an interacting component.

Genomic Organization of Penicillium chrysogenum chs4, a Class III Chitin Synthase Gene: Yoon-Dong Park , Myung-Sook Lee , Ji-Hoon Kim , Jun Namgung , Bum Chan Park , Kyung Sook Bae , Hee-Moon Park; J. Microbiol. 2000;38(4):230-238.

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Abstract PDF: Class III chitin synthases in filamentous fungi are important for hyphal growth and differentiation of several filamentous fungi. A genomic clone containing the full gene encoding Chs4, a class III chitin synthase in Penicillium chrysogenum, was cloned by PCR screening and colony hybridization from the genomic library. Nucleotide sequence analysis and transcript mapping of chs4 revealed an open reading frame (ORF) that consisted of 5 exons and 4 introns and encoded a putative protein of 915 amino acids. Nucleotide sequence analysis of the 5?lanking region of the ORF revealed a potential TATA box and several binding sites for transcription activators. The putative transcription initiation site at ?6 position was identified by primer extension and the expression of the chs4 during the vegetative growth was confirmed by Northern blot analysis. Amino acid sequence analysis of the Chs4 revealed at least 5 transmembrane helices and several sites for post-translational modifications. Comparison of the amino acid sequence of Chs4 with those of other fungi showed a close relationship between P. chr ysogenum and genus Aspergillus.

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