Journal of Microbiology

Research Article

Efficiency of reverse genetics methods for rescuing severe acute respiratory syndrome coronavirus 2: Chang-Joo Park, Taehun Kim, Seung-Min Yoo, Myung-Shin Lee, Nam-Hyuk Cho, Changhoon Park; J. Microbiol. 2025;63(2):e2411023. Published online February 27, 2025; DOI: https://doi.org/10.71150/jm.2411023

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Abstract PDF: Bacteria-free reverse genetics techniques are crucial for the efficient generation of recombinant viruses, bypassing the need for labor-intensive bacterial cloning. These methods are particularly relevant for studying the pathogenesis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of COVID-19. This study compared the efficiency of three bacteria-free approaches—circular polymerase extension reaction (CPER) with and without nick sealing and infectious sub-genomic amplicons (ISA)—to bacterial artificial chromosome (BAC)-based technology for rescuing SARS-CoV-2. Significant differences in viral titers following transfection were observed between methods. CPER with nick sealing generated virus titers comparable to those of the BAC-based method and 10 times higher than those of the standard CPER. In contrast, ISA demonstrated extremely low efficiency, as cytopathic effects were detected only after two passages. All rescued viruses exhibited replication kinetics consistent with those of the original strain, with no significant deviation in replication capacity. Furthermore, the utility of CPER and ISA in genetically modifying SARS-CoV-2 was demonstrated by successfully inserting the gene encoding green fluorescent protein into the genome. Overall, this study underscores the potential of bacteria-free methods, such as CPER and ISA, in advancing SARS-CoV-2 research while highlighting their significant differences in efficiency.

Journal Articles

Fleagrass (Adenosma buchneroides Bonati) Acts as a Fungicide Against Candida albicans by Damaging Its Cell Wall: Youwei Wu, Hongxia Zhang, Hongjie Chen, Zhizhi Du, Qin Li, Ruirui Wang; J. Microbiol. 2024;62(8):661-670. Published online July 3, 2024; DOI: https://doi.org/10.1007/s12275-024-00146-9

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Abstract: Fleagrass, a herb known for its pleasant aroma, is widely used as a mosquito repellent, antibacterial agent, and for treating colds, reducing swelling, and alleviating pain. The antifungal effects of the essential oils of fleagrass and carvacrol against Candida albicans were investigated by evaluating the growth and the mycelial and biofilm development of C. albicans. Transmission electron microscopy was used to evaluate the integrity of the cell membrane and cell wall of C. albicans. Fleagrass exhibited high fungicidal activity against C. albicans at concentrations of 0.5% v/v (via the Ras1/cAMP/PKA pathway). Furthermore, transmission electron microscopy revealed damage to the cell wall and membrane after treatment with the essential oil, which was further confirmed by the increased levels of β-1,3-glucan and chitin in the cell wall. This study showed that fleagrass exerts good fungicidal and hyphal growth inhibition activity against C. albicans by disrupting its cell wall, and thus, fleagrass may be a potential antifungal drug.

RapB Regulates Cell Adhesion and Migration in Dictyostelium, Similar to RapA: Uri Han, Nara Han, Byeonggyu Park, Taeck Joong Jeon; J. Microbiol. 2024;62(8):627-637. Published online June 17, 2024; DOI: https://doi.org/10.1007/s12275-024-00143-y

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Abstract: Ras small GTPases act as molecular switches in various cellular signaling pathways, including cell migration, proliferation, and differentiation. Three Rap proteins are present in Dictyostelium; RapA, RapB, and RapC. RapA and RapC have been reported to have opposing functions in the control of cell adhesion and migration. Here, we investigated the role of RapB, a member of the Ras GTPase subfamily in Dictyostelium, focusing on its involvement in cell adhesion, migration, and developmental processes. This study revealed that RapB, similar to RapA, played a crucial role in regulating cell morphology, adhesion, and migration. rapB null cells, which were generated by CRISPR/Cas9 gene editing, displayed altered cell size, reduced cell-substrate adhesion, and increased migration speed during chemotaxis. These phenotypes of rapB null cells were restored by the expression of RapB and RapA, but not RapC. Consistent with these results, RapB, similar to RapA, failed to rescue the phenotypes of rapC null cells, spread morphology, increased cell adhesion, and decreased migration speed during chemotaxis. Multicellular development of rapB null cells remained unaffected. These results suggest that RapB is involved in controlling cell morphology and cell adhesion. Importantly, RapB appears to play an inhibitory role in regulating the migration speed during chemotaxis, possibly by controlling cell-substrate adhesion, resembling the functions of RapA. These findings contribute to the understanding of the functional relationships among Ras subfamily proteins.

miR-135b Aggravates Fusobacterium nucleatum-Induced Cisplatin Resistance in Colorectal Cancer by Targeting KLF13: Wei Zeng , Jia Pan , Guannan Ye; J. Microbiol. 2024;62(2):63-73. Published online February 24, 2024; DOI: https://doi.org/10.1007/s12275-023-00100-1

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Abstract

Cisplatin resistance is the main cause of colorectal cancer (CRC) treatment failure, and the cause has been reported to be related to Fusobacterium nucleatum (Fn) infection. In this study, we explored the role of Fn in regulating cisplatin resistance of CRC cells and its underlying mechanism involved. The mRNA and protein expressions were examined by qRT-PCR and western blot. Cell proliferation and cell apoptosis were assessed using CCK8 and flow cytometry assays, respectively. Dual-luciferase reporter gene assay was adopted to analyze the molecular interactions. Herein, our results revealed that Fn abundance and miR-135b expression were markedly elevated in CRC tissues, with a favorable association between the two. Moreover, Fn infection could increase miR-135b expression via a concentration-dependent manner, and it also enhanced cell proliferation but reduced apoptosis and cisplatin sensitivity by upregulating miR-135b. Moreover, KLF13 was proved as a downstream target of miR-135b, of which overexpression greatly diminished the promoting effect of miR-135b or Fn-mediated cisplatin resistance in CRC cells. In addition, it was observed that upstream 2.5 kb fragment of miR-135b promoter could be interacted by β-catenin/TCF4 complex, which was proved as an effector signaling of Fn. LF3, a blocker of β-catenin/TCF4 complex, was confirmed to diminish the promoting role of Fn on miR-135b expression. Thus, it could be concluded that Fn activated miR-135b expression through TCF4/β-catenin complex, thereby inhibiting KLF13 expression and promoting cisplatin resistance in CRC.

Citations

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miR-135b: A key role in cancer biology and therapeutic targets
Yingchun Shao, Shuangshuang Zhang, Yuxin Pan, Zhan Peng, Yinying Dong
Non-coding RNA Research.2025; 12: 67. CrossRef
miR‐135b: A Potential Biomarker for Pathological Diagnosis and Biological Therapy
Dezhi Yan, Qingliu He, Chunjian Wang, Tian Li, Xueping Yi, Haisheng Yu, Wenfei Wu, Hanyun Yang, Wenzhao Wang, Liang Ma
WIREs RNA.2025;[Epub] CrossRef
Emerging roles of intratumor microbiota in cancer: tumorigenesis and management strategies
Zhuangzhuang Shi, Zhaoming Li, Mingzhi Zhang
Journal of Translational Medicine.2024;[Epub] CrossRef
Fusobacterium nucleatum: a novel regulator of antitumor immune checkpoint blockade therapy in colorectal cancer
Mengjie Luo
American Journal of Cancer Research.2024; 14(8): 3962. CrossRef
Antioxidant Role of Probiotics in Inflammation-Induced Colorectal Cancer
Sevag Hamamah, Andrei Lobiuc, Mihai Covasa
International Journal of Molecular Sciences.2024; 25(16): 9026. CrossRef
Identification of Penexanthone A as a Novel Chemosensitizer to Induce Ferroptosis by Targeting Nrf2 in Human Colorectal Cancer Cells
Genshi Zhao, Yanying Liu, Xia Wei, Chunxia Yang, Junfei Lu, Shihuan Yan, Xiaolin Ma, Xue Cheng, Zhengliang You, Yue Ding, Hongwei Guo, Zhiheng Su, Shangping Xing, Dan Zhu
Marine Drugs.2024; 22(8): 357. CrossRef

Lactobacillus acidophilus KBL409 Ameliorates Atopic Dermatitis in a Mouse Model: Woon-ki Kim , You Jin Jang , SungJun Park , Sung-gyu Min , Heeun Kwon , Min Jung Jo , GwangPyo Ko; J. Microbiol. 2024;62(2):91-99. Published online February 22, 2024; DOI: https://doi.org/10.1007/s12275-024-00104-5

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Abstract

Atopic dermatitis (AD) is a chronic inflammatory skin disease with repeated exacerbations of eczema and pruritus. Probiotics can prevent or treat AD appropriately via modulation of immune responses and gut microbiota. In this study, we evaluated effects of Lactobacillus acidophilus (L. acidophilus) KBL409 using a house dust mite (Dermatophagoides farinae)-induced in vivo AD model. Oral administration of L. acidophilus KBL409 significantly reduced dermatitis scores and decreased infiltration of immune cells in skin tissues. L. acidophilus KBL409 reduced in serum immunoglobulin E and mRNA levels of T helper (Th)1 (Interferon-γ), Th2 (Interleukin [IL]-4, IL-5, IL-13, and IL-31), and Th17 (IL-17A) cytokines in skin tissues. The anti-inflammatory cytokine IL-10 was increased and Foxp3 expression was up-regulated in AD-induced mice with L. acidophilus KBL409. Furthermore, L. acidophilus KBL409 significantly modulated gut microbiota and concentrations of short-chain fatty acids and amino acids, which could explain its effects on AD. Our results suggest that L. acidophilus KBL409 is the potential probiotic for AD treatment by modulating of immune responses and gut microbiota of host.

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The Skin Histopathology of Pro- and Parabiotics in a Mouse Model of Atopic Dermatitis
Hun Hwan Kim, Se Hyo Jeong, Min Yeong Park, Pritam Bhagwan Bhosale, Abuyaseer Abusaliya, Jeong Doo Heo, Hyun Wook Kim, Je Kyung Seong, Tae Yang Kim, Jeong Woo Park, Byeong Soo Kim, Gon Sup Kim
Nutrients.2024; 16(17): 2903. CrossRef
Limosilactobacillus fermentum KBL674 Alleviates Vaginal Candidiasis
Sung Jae Jang, Eun Jung Jo, Cheonghoon Lee, Bo-Ram Cho, Yun Jeong Shin, Jun Soo Song, Woon-Ki Kim, Nanhee Lee, Hyungjin Lee, SungJun Park, GwangPyo Ko
Probiotics and Antimicrobial Proteins.2024;[Epub] CrossRef

[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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Abstract

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.

Citations

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Pilin regions that select for the small RNA phages in Pseudomonas aeruginosa type IV pilus
Hee-Won Bae, Hyeong-Jun Ki, Shin-Yae Choi, You-Hee Cho, Kristin N. Parent
Journal of Virology.2025;[Epub] CrossRef
Characteristics of bioaerosols under high-ozone periods, haze episodes, dust storms, and normal days in Xi’an, China
Yiming Yang, Liu Yang, Xiaoyan Hu, Zhenxing Shen
Particuology.2024; 90: 140. CrossRef
Airborne desert dust and aeromicrobiology over the Turkish Mediterranean coastline
Dale W. Griffin, Nilgün Kubilay, Mustafa Koçak, Mike A. Gray, Timothy C. Borden, Eugene A. Shinn
Atmospheric Environment.2007; 41(19): 4050. CrossRef

Transcriptomic Insights into Archaeal Nitrification in the Amundsen Sea Polynya, Antarctica: Joo-Han Gwak , Samuel Imisi Awala , So-Jeong Kim , Sang-Hoon Lee , Eun-Jin Yang , Jisoo Park , Jinyoung Jung , Sung-Keun Rhee; J. Microbiol. 2023;61(11):967-980. Published online December 7, 2023; DOI: https://doi.org/10.1007/s12275-023-00090-0

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Abstract

Antarctic polynyas have the highest Southern Ocean summer primary productivity, and due to anthropogenic climate change, these areas have formed faster recently. Ammonia-oxidizing archaea (AOA) are among the most ubiquitous and abundant microorganisms in the ocean and play a primary role in the global nitrogen cycle. We utilized metagenomics and metatranscriptomics to gain insights into the physiology and metabolism of AOA in polar oceans, which are associated with ecosystem functioning. A polar-specific ecotype of AOA, from the “Candidatus Nitrosomarinus”-like group, was observed to be dominant in the Amundsen Sea Polynya (ASP), West Antarctica, during a succession of summer phytoplankton blooms. AOA had the highest transcriptional activity among prokaryotes during the bloom decline phase (DC). Metatranscriptomic analysis of key genes involved in ammonia oxidation, carbon fixation, transport, and cell division indicated that this polar AOA ecotype was actively involved in nitrification in the bloom DC in the ASP. This study revealed the physiological and metabolic traits of this key polar-type AOA in response to phytoplankton blooms in the ASP and provided insights into AOA functions in polar oceans.

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Alleviated photoinhibition on nitrification in the Indian Sector of the Southern Ocean
Lingfang Fan, Min Chen, Zifei Yang, Minfang Zheng, Yusheng Qiu
Acta Oceanologica Sinica.2024; 43(7): 52. CrossRef

Vaginal Microbiome Dysbiosis is Associated with the Different Cervical Disease Status: Yingying Ma , Yanpeng Li , Yanmei Liu , Le Cao , Xiao Han , Shujun Gao , Chiyu Zhang; J. Microbiol. 2023;61(4):423-432. Published online April 3, 2023; DOI: https://doi.org/10.1007/s12275-023-00039-3

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Abstract

Vaginal microbiome composition was demonstrated to be associated with cervical disease. The colonization characteristics of vaginal microbes and their association with the different cervical disease status, especially cervical cancer (CC), are rarely investigated. In this cross-sectional study, we characterized the vaginal microbiome of women with different status of cervical diseases, including 22 NV + (normal tissue with HPV infection), low-grade squamous intraepithelial lesion (LSIL, n = 45), high-grade squamous intraepithelial lesion (HSIL, n = 36) and CC (n = 27) using bacterial 16S DNA sequencing. Thirty HPV-negative women with normal tissue were used as the control group. We found that higher diversity of microbiome with gradual depletion of Lactobacillus, especially L. crispatus, was associated with the severity of cervical disease. High-risk HPV16 infection was associated with higher microbiome diversity and depletion of Lactobacillus in high-grade cervical diseases (i.e. HSIL and CC). The CC group was characterized by higher levels of Fannyhessea vaginae, Prevotella, Bacteroides, Finegoldia, Vibrio, Veillonella, Peptostreptococcus, and Dialister. Co-occurrence network analyses showed that negative correlations were exclusively observed between Lactobacillus and other bacteria, and almost all non-Lactobacillus bacteria were positively correlated with each other. In particular, the most diverse and complex co-occurrence network of vaginal bacteria, as well as a complete loss of L. crispatus, was observed in women with CC. Logistic regression model identified HPV16 and Lactobacillus as significant risk and protective factors for CC, respectively. These results suggest that specific Lactobacillus species (e.g. L. crispatus and L. iners) can be used as important markers to target prevention measures prioritizing HPV16-infected women and other hrHPV-infected women for test, vaccination and treat initiatives.

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Vaginal Microbiome and Pregnancy Complications: A Review
Angeliki Gerede, Konstantinos Nikolettos, Eleftherios Vavoulidis, Chrysoula Margioula-Siarkou, Stamatios Petousis, Maria Giourga, Panagiotis Fotinopoulos, Maria Salagianni, Sofoklis Stavros, Konstantinos Dinas, Nikolaos Nikolettos, Ekaterini Domali
Journal of Clinical Medicine.2024; 13(13): 3875. CrossRef
Advancements in the Vaginal Microenvironment and Regression of High-Risk Human Papillomavirus
Na He, Cunjian Yi, Qingsong Zeng, Wumei Jing, Wenrong He
Indian Journal of Microbiology.2024;[Epub] CrossRef
Research Progress on Related Factors of Cervical High-Grade Squamous Intraepithelial Lesions
红颖王
Advances in Clinical Medicine.2023; 13(12): 20536. CrossRef
Role of the vaginal microbiome in miscarriage: exploring the relationship
Marwa Saadaoui, Parul Singh, Osman Ortashi, Souhaila Al Khodor
Frontiers in Cellular and Infection Microbiology.2023;[Epub] CrossRef

Rhizosphere Microbial Community and Metabolites of Susceptible and Resistant Tobacco Cultivars to Bacterial Wilt: Wan Zhao , Yanyan Li , Chunlei Yang , Yong Yang , Yun Hu; J. Microbiol. 2023;61(4):389-402. Published online March 7, 2023; DOI: https://doi.org/10.1007/s12275-023-00012-0

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Abstract

Soil-borne diseases are closely related to rhizosphere microecosystem. While, plant species and genotypes are important factors affected rhizosphere microecosystem. In this study, the rhizosphere soil microbial community and metabolites of susceptible and resistant tobacco cultivars were investigated. The results showed that there were significant differences in the rhizosphere microbial community and metabolites between susceptible cultivar Yunyan87 and resistant cultivar Fandi3. Furthermore, the rhizosphere soil of Fandi3 showed a higher microbial diversity than that of Yunyan87. The abundance of R. solanacearum was much higher in the rhizosphere soil of Yunyan87 than in the rhizosphere soil of Fandi3, resulting in a higher disease incidence and index. While the abundance of beneficial bacteria in the rhizosphere soil of Fandi3 were higher than that of Yunyan87. Additionally, there were significant differences in metabolites between Yunyan87 and Fandi3 cultivars, and 4-hydroxybenzaldehyde, 3-hydroxy-4-methoxybenzoic acid, vamillic aldehyde, benzoic acid, 4-hydroxybenzyl alcohol, p-hydroxybenzoic acid and phthalic acid were notably high in Yunyan87. Redundancy analysis (RDA) indicated that the rhizosphere microbial community of Fandi3 and Yunyan87 were highly correlated with various environmental factors and metabolites. Overall, susceptible and resistant tobacco cultivars had different impact on rhizosphere microbial community and metabolites. The results expand our understanding of the roles of tobacco cultivars in plant-micro-ecosystem interactions, and provide a basis for the control of tobacco bacterial wilt.

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MAPK Cascades in Plant Microbiota Structure and Functioning
Thijs Van Gerrewey, Hoo Sun Chung
Journal of Microbiology.2024; 62(3): 231. CrossRef
Response of Soil Microorganisms and Phenolic to Pseudostelariae heterophylla Cultivation in Different Soil Types
Yingying Liu, Dan Wu, Yongjun Kan, Li Zhao, Chang Jiang, Wensheng Pang, Juan Hu, Meilan Zhou
Eurasian Soil Science.2024; 57(3): 446. CrossRef
Response of bacterial community metabolites to bacterial wilt caused by Ralstonia solanacearum: a multi-omics analysis
Chengjian Wei, Jinchang Liang, Rui Wang, Luping Chi, Wenjing Wang, Jun Tan, Heli Shi, Xueru Song, Zhenzhen Cui, Qiang Xie, Dejie Cheng, Xiaoqiang Wang
Frontiers in Plant Science.2024;[Epub] CrossRef
The Composition and Function of the Rhizosphere Bacterial Community of Paeonia lactiflora Varies with the Cultivar
Liping Yang, Xin Wan, Runyang Zhou, Yingdan Yuan
Biology.2023; 12(11): 1363. CrossRef
Analysis of the response mechanisms of Pinellia ternata to terahertz wave stresses using transcriptome and metabolic data
Dongdong Wang, Surendra Sarsaiya, Xu Qian, Leilei Jin, Fuxing Shu, Chuanyou Zhang, Jishuang Chen
Frontiers in Plant Science.2023;[Epub] CrossRef

Description of Corynebacterium poyangense sp. nov., isolated from the feces of the greater white-fronted geese (Anser albifrons): Qian Liu , Guoying Fan , Kui Wu , Xiangning Bai , Xi Yang , Wentao Song , Shengen Chen , Yanwen Xiong , Haiying Chen; J. Microbiol. 2022;60(7):668-677. Published online May 25, 2022; DOI: https://doi.org/10.1007/s12275-022-2089-9

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Abstract

Two novel Gram-positive, non-spore-forming, facultatively anaerobic, non-motile, and short rods to coccoid strains were isolated from the feces of the greater white-fronted geese (Anser albifrons) at Poyang Lake. The 16S rRNA gene sequences of strains 4H37-19T and 3HC-13 shared highest identity to that of Corynebacterium uropygiale Iso10T (97.8%). Phylogenetic and phylogenomic analyses indicated that strains 4H37-19T and 3HC-13 formed an independent clade within genus Corynebacterium and clustered with Corynebacterium uropygiale Iso10T. The average nucleotide identity and digital DNA-DNA hybridization value between strains 4H37-19T and 3HC-13 and members within genus Corynebacterium were all below 95% and 70%, respectively. The genomic G + C content of strains 4H37-19T and 3HC-13 was 52.5%. Diphosphatidylglycerol (DPG), phosphatidylglycerol (PG), phosphatidylinositol (PI), phosphatidylcholine, and phosphatidyl inositol mannosides (PIM) were the major polar lipids, with C18:1ω9c, C16:0, and C18:0 as the major fatty acids, and MK-8 (H4), MK-8(H2), and MK-9(H2) as the predominant respiratory quinones. The major whole cell sugar was arabinose, and the cell wall included mycolic acids. The cell wall peptidoglycan contained meso-diaminopimelic acid (meso-DAP). The polyphasic taxonomic data shows that these two strains represent a novel species of the genus Corynebacterium, for which the name Corynebacterium poyangense sp. nov. is proposed. The type strain of Corynebacterium poyangense is 4H37-19T (=GDMCC 1.1738T = KACC 21671T).

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Valid and accepted novel bacterial taxa isolated from non-domestic animals and taxonomic revisions published in 2023
Erik Munson, Claire R. Burbick, Sara D. Lawhon, Trinity Krueger, Elena Ruiz-Reyes, Romney M. Humphries
Journal of Clinical Microbiology.2024;[Epub] CrossRef
Validation List no. 212. Valid publication of new names and new combinations effectively published outside the IJSEM
Aharon Oren, Markus Göker
International Journal of Systematic and Evolutionary Microbiology .2023;[Epub] CrossRef
Keratokonjunktivitisli bir tavuktan Corynebacterium spp. ve Arcanobacterium spp. izolasyonu
Hüban GÖÇMEN, Banur BOYNUKARA
Veteriner Hekimler Derneği Dergisi.2023; 94(2): 161. CrossRef

Gamma-glutamyltransferase of Helicobacter pylori alters the proliferation, migration, and pluripotency of mesenchymal stem cells by affecting metabolism and methylation status: Zeyu Wang , Weijun Wang , Huiying Shi , Lingjun Meng , Xin Jiang , Suya Pang , Mengke Fan , Rong Lin; J. Microbiol. 2022;60(6):627-639. Published online April 18, 2022; DOI: https://doi.org/10.1007/s12275-022-1575-4

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Abstract

Virulence factor gamma-glutamyltransferase (GGT) of H. pylori consumes glutamine (Gln) in the stomach to decrease the tricarboxylic acid metabolite alpha-ketoglutarate (α-kg) and alter the downstream regulation of α-kg as well as cellular biological characteristics. Our previous research indicated that under H. pylori infection, mesenchymal stem cells (MSCs) migrated to the stomach and participated in gastric cancer (GC) development either by differentiating into epithelial cells or promoting angiogenesis. However, how MSCs themselves participate in H. pylori-indicated GC remains unclear. Therefore, a GGT knockout H. pylori strain (Hp- KS-1) was constructed, and downstream histone H3K9 and H3K27 methylation and the PI3K/AKT signaling pathway of α-kg were detected using Western blotting. The biological characteristics of MSCs were also examined. An additive α-kg supplement was also added to H. pylori-treated MSCs to investigate alterations in these aspects. Compared to the control and Hp-KS-1 groups, H. pylori-treated MSCs reduced Gln and α-kg, increased H3K9me3 and H3K27me3, activated the PI3K-AKT signaling pathway, and promoted the proliferation, migration, self-renewal, and pluripotency of MSCs. The addition of α-kg rescued the H. pylori-induced alterations. Injection of MSCs to nude mice resulted in the largest tumors in the H. pylori group and significantly reduced tumor sizes in the Hp-KS-1 and α-kg groups. In summary, GGT of H. pylori affected MSCs by interfering with the metabolite α-kg to increase trimethylation of histone H3K9 and H3K27, activating the PI3K/AKT signaling pathway, and promoting proliferation, migration, self-renewal, and pluripotency in tumorigenesis, elucidating the mechanisms of MSCs in GC development.

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Gamma-glutamyl transferase secreted by Helicobacter pylori promotes the development of gastric cancer by affecting the energy metabolism and histone methylation status of gastric epithelial cells
Xin Jiang, Weijun Wang, Zeyu Wang, Zhe Wang, Huiying Shi, Lingjun Meng, Suya Pang, Mengke Fan, Rong Lin
Cell Communication and Signaling.2024;[Epub] CrossRef
Design of a Helicobacter pylori multi-epitope vaccine based on immunoinformatics
Man Cui, Xiaohui Ji, Fengtao Guan, Guimin Su, Lin Du
Frontiers in Immunology.2024;[Epub] CrossRef
Gastric cancer and mesenchymal stem cell-derived exosomes: from pro-tumorigenic effects to anti-cancer vehicles
Maryam Dolatshahi, Ahmad Reza Bahrami, Qaiser Iftikhar Sheikh, Mohsen Ghanbari, Maryam M. Matin
Archives of Pharmacal Research.2024; 47(1): 1. CrossRef
Mesenchymal Stem Cell-Derived Exosomes Modulate Angiogenesis in Gastric Cancer
Fawzy Akad, Veronica Mocanu, Sorin Nicolae Peiu, Viorel Scripcariu, Bogdan Filip, Daniel Timofte, Florin Zugun-Eloae, Magdalena Cuciureanu, Monica Hancianu, Teodor Oboroceanu, Laura Condur, Radu Florin Popa
Biomedicines.2023; 11(4): 1031. CrossRef
Helicobacter pylori and Its Role in Gastric Cancer
Victor E. Reyes
Microorganisms.2023; 11(5): 1312. CrossRef

Review

SARS-CoV-2-mediated evasion strategies for antiviral interferon pathways: Soo-Jin Oh , Ok Sarah Shin; J. Microbiol. 2022;60(3):290-299. Published online February 5, 2022; DOI: https://doi.org/10.1007/s12275-022-1525-1

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Abstract

With global expansion of the COVID-19 pandemic and the emergence of new variants, extensive efforts have been made to develop highly effective antiviral drugs and vaccines against SARS-CoV-2. The interactions of coronaviruses with host antiviral interferon pathways ultimately determine successful viral replication and SARS-CoV-2-induced pathogenesis. Innate immune receptors play an essential role in host defense against SARS-CoV-2 via the induction of IFN production and signaling. Here, we summarize the recent advances in innate immune sensing mechanisms of SARS-CoV-2 and various strategies by which SARS-CoV-2 antagonizes antiviral innate immune signaling pathways, with a particular focus on mechanisms utilized by multiple SARS-CoV-2 proteins to evade interferon induction and signaling in host cell. Understanding the underlying immune evasion mechanisms of SARS-CoV-2 is essential for the improvement of vaccines and therapeutic strategies.

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Overview of the SARS-CoV-2 nucleocapsid protein
Ahmed Eltayeb, Faisal Al-Sarraj, Mona Alharbi, Raed Albiheyri, Ehab Mattar, Isam M. Abu Zeid, Thamer A. Bouback, Atif Bamagoos, Bassam O. Aljohny, Vladimir N. Uversky, Elrashdy M. Redwan
International Journal of Biological Macromolecules.2024; 260: 129523. CrossRef
Does SARS-CoV-2 Induce IgG4 Synthesis to Evade the Immune System?
Alberto Rubio-Casillas, Elrashdy Redwan, Vladimir Uversky
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Inhibition of p38 signaling curtails the SARS-CoV-2 induced inflammatory response but retains the IFN-dependent antiviral defense of the lung epithelial barrier
Aileen Faist, Sebastian Schloer, Angeles Mecate-Zambrano, Josua Janowski, André Schreiber, Yvonne Boergeling, Beate C.G. Conrad, Sriram Kumar, Leonie Toebben, Klaus Schughart, Morris Baumgardt, Mirjana Kessler, Katja Hoenzke, Andreas Hocke, Marcel Trautma
Antiviral Research.2023; 209: 105475. CrossRef
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Journal Articles

Structural and biochemical analysis of the PTPN4 PDZ domain bound to the C-terminal tail of the human papillomavirus E6 oncoprotein: Hye Seon Lee , Hye-Yeoung Yun , Eun-Woo Lee , Ho-Chul Shin , Seung Jun Kim , Bonsu Ku; J. Microbiol. 2022;60(4):395-401. Published online January 28, 2022; DOI: https://doi.org/10.1007/s12275-022-1606-1

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Abstract

High-risk genotypes of human papillomaviruses (HPVs) are directly implicated in various abnormalities associated with cellular hyperproliferation, including cervical cancer. E6 is one of two oncoproteins encoded in the HPV genome, which recruits diverse PSD-95/Dlg/ZO-1 (PDZ) domain-containing human proteins through its C-terminal PDZ-binding motif (PBM) to be degraded by means of the proteasome pathway. Among the three PDZ domain-containing protein tyrosine phosphatases, protein tyrosine phosphatase non-receptor type 3 (PTPN3) and PTPN13 were identified to be recognized by HPV E6 in a PBM-dependent manner. However, whether HPV E6 associates with PTPN4, which also has a PDZ domain and functions as an apoptosis regulator, remains undetermined. Herein, we present structural and biochemical evidence demonstrating the direct interaction between the PBM of HPV16 E6 and the PDZ domain of human PTPN4 for the first time. X-ray crystallographic structure determination and binding measurements using isothermal titration calorimetry demonstrated that hydrophobic interactions in which Leu158 of HPV16 E6 plays a key role and a network of intermolecular hydrogen bonds sustain the complex formation between PTPN4 PDZ and the PBM of HPV16 E6. In addition, it was verified that the corresponding motifs from several other highrisk HPV genotypes, including HPV18, HPV31, HPV33, and HPV45, bind to PTPN4 PDZ with comparable affinities, suggesting that PTPN4 is a common target of various pathogenic HPV genotypes.

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Bioinformatics Analysis of Human Papillomavirus 16 Integration in Cervical Cancer: Changes in MAGI-1 Expression in Premalignant Lesions and Invasive Carcinoma
Oscar Catalán-Castorena, Olga Lilia Garibay-Cerdenares, Berenice Illades-Aguiar, Rocio Castillo-Sánchez, Ma. Isabel Zubillaga-Guerrero, Marco Antonio Leyva-Vazquez, Sergio Encarnacion-Guevara, Eugenia Flores-Alfaro, Mónica Ramirez-Ruano, Luz del Carmen Al
Cancers.2024; 16(12): 2225. CrossRef
Comparative structural studies on Bovine papillomavirus E6 oncoproteins: Novel insights into viral infection and cell transformation from homology modeling and molecular dynamics simulations
Lucas Alexandre Barbosa de Oliveira Santos, Tales de Albuquerque Leite Feitosa, Marcus Vinicius de Aragão Batista
Genetics and Molecular Biology.2024;[Epub] CrossRef
Crystal Structures of Plk1 Polo-Box Domain Bound to the Human Papillomavirus Minor Capsid Protein L2-Derived Peptide
Sujin Jung, Hye Seon Lee, Ho-Chul Shin, Joon Sig Choi, Seung Jun Kim, Bonsu Ku
Journal of Microbiology.2023; 61(8): 755. CrossRef
The effects of HPV oncoproteins on host communication networks: Therapeutic connotations
Josipa Skelin, Ho Yin Luk, Dražan Butorac, Siaw Shi Boon, Vjekoslav Tomaić
Journal of Medical Virology.2023;[Epub] CrossRef
Structural analysis of human papillomavirus E6 interactions with Scribble PDZ domains
Bryce Z. Stewart, Sofia Caria, Patrick O. Humbert, Marc Kvansakul
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Viral manipulation of cell polarity signalling
Airah Javorsky, Patrick O. Humbert, Marc Kvansakul
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Critical Reviews in Oncology/Hematology.2022; 174: 103675. CrossRef

Description of Ornithinimicrobium ciconiae sp. nov., and Ornithinimicrobium avium sp. nov., isolated from the faeces of the endangered and near-threatened birds: So-Yeon Lee , Hojun Sung , Pil Soo Kim , Hyun Sik Kim , Jae-Yun Lee , June-Young Lee , Yun-Seok Jeong , Euon Jung Tak , Jeong Eun Han , Dong-Wook Hyun , Jin-Woo Bae; J. Microbiol. 2021;59(11):978-987. Published online September 27, 2021; DOI: https://doi.org/10.1007/s12275-021-1323-1

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Abstract

Phenotypic and genomic analyses were performed to characterize two novel species, H23M54T and AMA3305T, isolated from the faeces of the Oriental stork (Ciconia boyciana) and the cinereous vulture (Aegypius monachus), respectively. Strains H23M54T and AMA3305T showed the highest similarities of 16S rRNA gene sequences and complete genome sequences with Ornithinimicrobium cavernae CFH 30183T (98.5% of 16S rRNA gene sequence similarity and 82.1% of average nucleotide identity, ANI) and O. pekingense DSM 21552T (98.5% of 16S rRNA gene sequence similarity and 82.3% of ANI), respectively. Both strains were Gram-stain-positive, obligate aerobes, non-motile, non-spore-forming, and coccoid- and rodshaped. Strain H23M54T grew optimally at 25–30°C and pH 8.0 and in the presence of 1.5–2% (wt/vol) NaCl, while strain AMA3305T grew optimally at 30°C and pH 7.0 and in the presence of 1–3% (wt/vol) NaCl. Both strains had iso-C15:0, iso- C16:0, and summed feature 9 (iso-C17:1 ω9c and/or C16:0 10- methyl) as major cellular fatty acids. MK-8 (H4) was identified as the primary respiratory quinone in both strains. Strains H23M54T and AMA3305T possessed diphosphatidylglycerol and phosphatidylglycerol as major polar lipids. Moreover, strains H23M54T and AMA3305T commonly contained ribose and glucose as major sugars and L-ornithine, L-alanine, glycine, and aspartic acid as major amino acids. The polyphasic taxonomic data indicate that strains H23M54T and AMA3305T represent novel species of the genus Ornithinimicrobium. We propose the names Ornithinimicrobium ciconiae sp. nov. and Ornithinimicrobium avium sp. nov. for strains H23M54T (= KCTC 49151T = JCM 33221T) and AMA3305T (= KCTC 49180T = JCM 32873T), respectively.

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Morphological and genomic characteristics of two novel actinomycetes, Ornithinimicrobium sufpigmenti sp. nov. and Ornithinimicrobium faecis sp. nov. isolated from bat faeces (Rousettus leschenaultia and Taphozous perforates)
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Lysobacter ciconiae sp. nov., and Lysobacter avium sp. nov., isolated from the faeces of an Oriental stork
So-Yeon Lee, Pil Soo Kim, Hojun Sung, Dong-Wook Hyun, Jin-Woo Bae
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Brevibacterium limosum sp. nov., Brevibacterium pigmenatum sp. nov., and Brevibacterium atlanticum sp. nov., three novel dye decolorizing actinobacteria isolated from ocean sediments: Shengxiang Pei , Siwen Niu , Fuquan Xie , Wenjing Wang , Shuang Zhang , Gaiyun Zhang; J. Microbiol. 2021;59(10):898-910. Published online September 7, 2021; DOI: https://doi.org/10.1007/s12275-021-1235-0

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Abstract

During a study of the marine actinobacterial biodiversity, a large number of Brevibacterium strains were isolated. Of these, five that have relatively low 16S rRNA gene similarity (98.5– 99.3%) with validly published Brevibacterium species, were chosen to determine taxonomic positions. On the basis of 16S rRNA gene sequence analysis and BOX-PCR fingerprinting, strains o2T, YB235T, and WO024T were selected as representative strains. Genomic analyses, including average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH), clearly differentiated the three strains from each other and from their closest relatives, with values ranging from 82.8% to 91.5% for ANI and from 26.7% to 46.5% for dDDH that below the threshold for species delineation. Strains YB235T, WO024T, and o2T all exhibited strong and efficient decolorization activity in congo red (CR) dyes, moderate decolorization activity in toluidine blue (TB) dyes and poor decolorization in reactive blue (RB) dyes. Genes coding for peroxidases and laccases were identified and accounted for these strains’ ability to effectively oxidize a variety of dyes with different chemical structures. Mining of the whole genome for secondary metabolite biosynthesis gene clusters revealed the presence of gene clusters encoding for bacteriocin, ectoine, NRPS, siderophore, T3PKS, terpene, and thiopeptide. Based on the phylogenetic, genotypic and phenotypic data, strains o2T, YB235T and WO024T clearly represent three novel taxa within the genus Brevibacterium, for which the names Brevibacterium limosum sp. nov. (type strain o2T = JCM 33844T = MCCC 1A09961T), Brevibacterium pigmenatum sp. nov. (type strain YB235T = JCM 33843T = MCCC 1A09842T) and Brevibacterium atlanticum sp. nov. (type strain WO024T = JCM 33846T = MCCC 1A16743T) are proposed.

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