Journal of Microbiology

Full articles

Inhibition of cardiolipin biosynthesis partially suppresses the sensitivity of an Escherichia coli mutant lacking OmpC to envelope stress: Dae-Beom Ryu, Umji Choi, Gyubin Han, Chang-Ro Lee; J. Microbiol. 2025;63(11):e2507004. Published online November 30, 2025; DOI: https://doi.org/10.71150/jm.2507004

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Abstract PDF Supplementary Material: Porins in the outer membrane (OM) of Gram-negative bacteria play two main functions: passage of various extracellular molecules and maintenance of membrane integrity. OmpC, a non-specific porin, is involved in both functions; however, the exact mechanism of maintenance of membrane integrity remains unknown. In this study, we found that inhibiting cardiolipin biosynthesis partially restored the growth defect of the ompC mutant under envelope stress. Among the three enzymes involved in cardiolipin biosynthesis, ClsABC, this effect is primarily associated with ClsA. Notably, the deletion of ClsA also suppressed the similar phenotypes of an Escherichia coli mutant lacking YhdP, a transmembrane protein involved in phospholipid transport from the inner membrane to the OM. Collectively, these results imply that OmpC may contribute to membrane integrity, partially through mechanisms linked to transport or biosynthesis of phospholipids such as cardiolipin.

Genomic profiling of soil nitrifying microorganisms enriched on floating membrane filter: Christiana Abiola, Joo-Han Gwak, Ui-Ju Lee, Aderonke Odunayo Adigun, Sung-Keun Rhee; J. Microbiol. 2025;63(4):e2502002. Published online April 29, 2025; DOI: https://doi.org/10.71150/jm.2502002

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Abstract PDF Supplementary Material: Recently, floating membrane filter cultivation was adopted to simulate solid surface and enrich surface-adapted soil ammonia-oxidizing archaea (AOA) communities from agricultural soil, as opposed to the conventional liquid medium. Here, we conducted metagenomic sequencing to recover nitrifier bins from the floating membrane filter cultures and reveal their genomic properties. Phylogenomic analysis showed that AOA bins recovered from this study, designated FF_bin01 and FF_bin02, are affiliated with the Nitrososphaeraceae family, while the third bin, FF_bin03, is a nitrite-oxidizing bacterium affiliated with the Nitrospiraceae family. Based on the ANI/AAI analysis, FF_bin01 and FF_bin02 are identified as novel species within the genera “Candidatus Nitrosocosmicus” and Nitrososphaera, respectively, while FF_bin03 represents a novel species within the genus Nitrospira. The pan and core genome analysis for the 29 AOA genomes considered in this study revealed 5,784 orthologous clusters, out of which 653 were core orthologous clusters. Additionally, 90 unique orthologous clusters were conserved among the Nitrososphaeraceae family, suggesting their potential role in enhancing culturability and adaptation to diverse environmental conditions. Intriguingly, FF_bin01 and FF_bin02 harbor a gene encoding manganese catalase and FF_bin03 also possesses a heme catalase gene, which might enhance their growth on the floating membrane filter. Overall, the floating membrane filter cultivation has proven to be a promising approach for isolating distinct soil AOA, and further modifications to this technique could stimulate the growth of a broader range of uncultivated nitrifiers from diverse soil environments.

Journal Article

The Salmonella enterica EnvE is an Outer Membrane Lipoprotein and Its Gene Expression Leads to Transcriptional Repression of the Virulence Gene msgA: Sinyeon Kim, Yong Heon Lee; J. Microbiol. 2024;62(11):1013-1022. Published online November 15, 2024; DOI: https://doi.org/10.1007/s12275-024-00183-4

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Abstract PDF: The envE gene of Salmonella enterica serovar Typhimurium is encoded within Salmonella Pathogenicity Island-11 (SPI-11) and is located immediately upstream of the virulence gene msgA (macrophage survival gene A) in the same transcriptional orientation. To date, the characteristics and roles of envE remain largely unexplored. In this study, we show that EnvE, a predicted lipoprotein, is localized on the outer membrane using sucrose gradient ultracentrifugation. Under oxidative stress conditions, envE transcription is suppressed, while msgA transcription is induced, indicating an inverse correlation between the mRNA levels of the two neighboring genes. Importantly, inactivation of envE leads to constitutive transcription of msgA regardless of the presence of oxidative stress. Moreover, trans-complementation of the envE mutant with a plasmid-borne envE fails to prevent the induction of msgA transcription, suggesting that envE functions as a cis-regulatory element rather than a trans-acting factor. We further show that both inactivation and complementation of envE confer wild-type levels of resistance to oxidative stress by ensuring the expression of msgA. Our data suggest that the S. enterica envE gene encodes an outer membrane lipoprotein, and its transcription represses msgA expression in a cis-acting manner, probably by transcriptional interference, although the exact molecular details are yet unclear.

Review

Structural Insights into the Lipopolysaccharide Transport (Lpt) System as a Novel Antibiotic Target: Yurim Yoon, Saemee Song; J. Microbiol. 2024;62(4):261-275. Published online May 31, 2024; DOI: https://doi.org/10.1007/s12275-024-00137-w

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Abstract PDF

Lipopolysaccharide (LPS) is a critical component of the extracellular leaflet within the bacterial outer membrane, forming an effective physical barrier against environmental threats in Gram-negative bacteria. After LPS is synthesized and matured in the bacterial cytoplasm and the inner membrane (IM), LPS is inserted into the outer membrane (OM) through the ATP-driven LPS transport (Lpt) pathway, which is an energy-intensive process. A trans-envelope complex that contains seven Lpt proteins (LptA-LptG) is crucial for extracting LPS from the IM and transporting it across the periplasm to the OM. The last step in LPS transport involves the mediation of the LptDE complex, facilitating the insertion of LPS into the outer leaflet of the OM. As the Lpt system plays an essential role in maintaining the impermeability of the OM via LPS decoration, the interactions between these interconnected subunits, which are meticulously regulated, may be potential targets for the development of new antibiotics to combat multidrug-resistant Gram-negative bacteria. In this review, we aimed to provide an overview of current research concerning the structural interactions within the Lpt system and their implications to clarify the function and regulation of LPS transport in the overall process of OM biogenesis. Additionally, we explored studies on the development of therapeutic inhibitors of LPS transport, the factors that limit success, and future prospects.

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Boosting the Antimicrobial Activity of Quaternary Ammonium Photosensitizers by Janus‐Type AIE Luminogens
Dongyang Fan, Meng Li, Zipeng Shen, Ying Li, Jingjing Guo, Dong Wang, Ting Han, Ben Zhong Tang
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Annabelle Mathieu-Denoncourt, Marylise Duperthuy
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Emmanuel Tope Oluwabusola, Stephen A. Jackson, Cristina Brunati, Stefanie Gackstatter, Hannah Vedder, Marianna Iorio, Gargee Chawande, Lekha Menon Margassery, Giang-Son Nguyen, David J. Clarke, Rainer Ebel, Marcel Jaspars, Alan D. W. Dobson
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Journal Articles

Genetic Characteristics and Phylogeographic Dynamics of Echovirus: Yan Wang , Pir Tariq Shah , Yue Liu , Amina Nawal Bahoussi , Li Xing; J. Microbiol. 2023;61(9):865-877. Published online September 15, 2023; DOI: https://doi.org/10.1007/s12275-023-00078-w

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Echoviruses belong to the genus Enterovirus in the Picornaviridae family, forming a large group of Enterovirus B (EVB) within the Enteroviruses. Previously, Echoviruses were classified based on the coding sequence of VP1. In this study, we performed a reliable phylogenetic classification of 277 sequences isolated from 1992 to 2019 based on the full-length genomes of Echovirus. In this report, phylogenetic, phylogeographic, recombination, and amino acid variability landscape analyses were performed to reveal the evolutional characteristics of Echovirus worldwide. Echoviruses were clustered into nine major clades, e.g., G1–G9. Phylogeographic analysis showed that branches G2–G9 were linked to common strains, while the branch G1 was only linked to G5. In contrast, strains E12, E14, and E16 clustered separately from their G3 and G7 clades respectively, and became a separate branch. In addition, we identified a total of 93 recombination events, where most of the events occurred within the VP1-VP4 coding regions. Analysis of amino acid variation showed high variability in the a positions of VP2, VP1, and VP3. This study updates the phylogenetic and phylogeographic information of Echovirus and indicates that extensive recombination and significant amino acid variation in the capsid proteins drove the emergence of new strains.

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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
Unraveling the Potential Antiviral Activity of Isoxazoline-Carbocyclic Monophosphate Nucleotides Against Echovirus 11
Emilia Palazzotto, Valeria Stefanizzi, Floriana Bonura, Federica Cacioppo, Marco Leusciatti, Paolo Quadrelli, Annalisa Chianese, Carla Zannella, Anna De Filippis, Antonio Mastino, Francesca Marino Merlo, Simona De Grazia
Microorganisms.2025; 13(12): 2662. CrossRef

Silver Nanoparticles Modified with Polygonatum sibiricum Polysaccharide Improve Biocompatibility and Infected Wound Bacteriostasis: Ruonan Wang , Rongyu Li , Peng Zheng , Zicheng Yang , Cheng Qian , Zhou Wang , Senhe Qian; J. Microbiol. 2023;61(5):543-558. Published online April 13, 2023; DOI: https://doi.org/10.1007/s12275-023-00042-8

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Abstract PDF

Silver nanoparticles (AgNPs) exhibit strong antibacterial activity and do not easily induce drug resistance; however, the poor stability and biocompatibility in solution limit their widespread application. In this study, AgNPs were modified with Polygonatum sibiricum Polysaccharide (PSP) to synthesize PSP@AgNPs with good stability, biocompatibility, and antibacterial activity. When PSP@AgNP synthesis was performed under a reaction time of 70 min, a reaction temperature of 35 °C, and an AgNO3- to-PSP volume ratio of 1:1, the synthesized PSP@AgNPs were more regular and uniform than AgNPs, and their particle size was around 10 nm. PSP@AgNPs exhibited lower cytotoxicity and hemolysis, and stronger bacteriostatic activity. PSP@AgNPs damage the integrity and internal structure of cells, resulting in the leakage of intracellular nucleic acids and proteins. The rate of cell membrane damage in Escherichia coli and Staphylococcus aureus treated with PSP@ AgNPs increased by 38.52% and 43.75%, respectively, compared with that of AgNPs. PSP@AgNPs inhibit the activities of key enzymes related to antioxidant, energy and substance metabolism in cells. The inhibitory effects on the activities of superoxide dismutase (SOD), catalase (CAT), adenosine triphosphate enzyme (ATPase), malate dehydrogenase (MDH), and succinate dehydrogenase (SDH) in E. coli and S. aureus cells were significantly higher than those of AgNPs. In addition, compared with AgNPs, PSP@AgNPs promote faster healing of infected wounds. Therefore, PSP@AgNPs represent potential antibacterial agents against wound infections.

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Fabrication of Highly Stable Polyurushiol-Decorated Silver Nanoparticles and Evaluation of Their Antibacterial and Anti-Microalgae Activities
Lu Zheng, Jide Zhu, Jipeng Chen, Yanlian Xu, Lilong Jiang
Journal of Inorganic and Organometallic Polymers and Materials.2025; 35(1): 570. CrossRef
Preparation, Structure, Function, and Application of Dietary Polysaccharides from Polygonatum sibiricum in the Food Industry: A Review
Peilin Li, Huimin Yao, Hao Yue, Jiali Huang, Qi Wang, Chuanbo Ding, Lina Ma, Xinglong Liu, Min Yang
Molecules.2025; 30(5): 1098. CrossRef
Transcriptomic and metabolomic analyses of the antimicrobial activity of phenoxyethanol against phylotype IA1 and II Cutibacterium acnes
Li Shao, Lizhuang Wang, Yan Li, Laiji Ma, Hong Jiang, Fei Liu, Shanshan Jiang, Tianming Bai, Suzhen Yang
Journal of Applied Microbiology.2025;[Epub] CrossRef
Extraction, purification, structural characterization, biological activity, structure-activity relationship, and applications of polysaccharides derived from Polygonatum sibiricum: A review
Jiasu Wu, Chang Tan, Hongye Li, Siya Wang, Xingkui Wang, Shan Wang, Chong Ning, Weixuan Li, Chongting Guo
Trends in Food Science & Technology.2025; 161: 105038. CrossRef
Study on the structural characterization and biological activities of polysaccharides from Dictyophora rubrovolvata and its silver nanoparticles
Xiaonan Du, Junhui Wang, Li Gao, Jishun Zheng, Lei Zhang
International Journal of Biological Macromolecules.2025; 328: 147632. CrossRef
Elucidating the effects of nine-steaming-nine-drying on the morphology, metabolomic profile, and active ingredients of Polygonatum sibiricum Redouté
Rui Wang, Ping Li, Siyao Chen, Jinchao Guo, Yongling Liu, Huizhen Shen, Siyu Wang, Haiyan Li
Frontiers in Food Science and Technology.2025;[Epub] CrossRef
Improving the biocompatibility and antibacterial efficacy of silver nanoparticles functionalized with (LLRR)3 antimicrobial peptide
Rongyu Li, Jiaqing Mao, Peng Zheng, Ruonan Wang, Zicheng Yang, Senhe Qian
World Journal of Microbiology and Biotechnology.2024;[Epub] CrossRef
Advancing engineered approaches for sustainable wound regeneration and repair: Harnessing the potential of green synthesized silver nanoparticles
J. Nandhini, E. Karthikeyan, E. Elizabeth Rani, V.S. Karthikha, D. Sakthi Sanjana, H. Jeevitha, S. Rajeshkumar, Vijayan Venugopal, A. Priyadharshan
Engineered Regeneration.2024; 5(3): 306. CrossRef
Effect of Polygonatum sibiricum on biological toxicity of zinc oxide nanoparticles during respiratory exposure
Jingjing Yao, Wanqing Yang, Liang Tang, Dicheng Yang, Yan Xu, Shenmin Zhu, Jun Zhu
RSC Advances.2024; 14(43): 31360. CrossRef
Enhancing Healing of Infected Wounds with Glycerin‐Modified Sodium Alginate/Silk Sericin Composite Film Functionalized with Polygonatum sibiricum Polysaccharide‐Capped Silver Nanoparticles
Zicheng Yang, Rongyu Li, Ruonan Wang, Senhe Qian
ChemistrySelect.2024;[Epub] CrossRef
Host Defense Peptides: Exploiting an Innate Immune Component Against Infectious Diseases and Cancer
Taiwo Scholes Adewole, Oladiran Boniface Oladokun, Adenike Kuku
International Journal of Peptide Research and Therapeutics.2024;[Epub] CrossRef
Research progress on medicinal components and pharmacological activities of polygonatum sibiricum
Ruilian Liu, Xili Zhang, Yuhan Cai, Shuang Xu, Qian Xu, Chengli Ling, Xin Li, Wenjiao Li, Pingan Liu, Wenlong Liu
Journal of Ethnopharmacology.2024; 328: 118024. CrossRef
A comprehensive review on the potential applications of medicine Polygonatum species in the food sector
Mi Li, Bingzong Xie, Lewen Li, Yunge Zhang, Qingmin Chen, Jian Ju, Yanli Ma
Food Bioscience.2024; 60: 104116. CrossRef
Metallic elements combine with herbal compounds upload in microneedles to promote wound healing: a review
Xiao Tang, Li Li, Gehang You, Xinyi Li, Jian Kang
Frontiers in Bioengineering and Biotechnology.2023;[Epub] CrossRef

Observational Study

Early gut microbiota in very low and extremely low birth weight preterm infants with feeding intolerance: a prospective case-control study: Ling Liu , Dang Ao , Xiangsheng Cai , Peiyi Huang , Nali Cai , Shaozhu Lin , Benqing Wu; J. Microbiol. 2022;60(10):1021-1031. Published online August 19, 2022; DOI: https://doi.org/10.1007/s12275-022-2180-2

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The potential role of the gut microbiota in the pathogenesis of feeding intolerance (FI) remains unclear. Understanding the role of the gut microbiota could provide a new avenue for microbiota-targeted therapeutics. This study aimed to explore the associations between aberrant gut microbiota and FI in very low or extremely low birth weight (VLBW/ELBW) preterm infants. In this observational case-control study, VLBW/ ELBW infants were divided into two groups: FI group and feeding tolerance (FT) group. 16S rRNA gene sequencing was performed to analyze the gut microbial diversity and composition of the infants. The differences in the gut microbiota of the two groups were compared. In total, 165 stool samples were obtained from 44 infants, among which, 31 developed FI and 13 served as controls. Alpha diversity was the highest in the meconium samples of the two groups. LEfSe analysis revealed that the abundances of Peptostreptococcaceae, Clostridiales and Clostridia in the FT group were significantly higher than in the FI group. At the phylum level, the FI group was dominated by Proteobacteria, and the FT group was dominated by Firmicutes. The meconium samples of the FI group had higher proportions of γ-proteobacteria and Escherichia-Shigella and a lower proportion of Bacteroides compared with the FT group. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis demonstrated that aberrant gut bacteria in the FI group were strongly associated with dysregulation of C5-Brancheddibasic- acid-metabolism, protein kinases, and sporulation. These findings reveal candidate microbial markers to prevent FI. Increased relative abundances of γ-proteobacteria and Escherichia-Shigella and decreased abundance of Bacteroides in meconium were associated with an increased risk of FI, while Peptostreptococcaceae, Clostridiales and Clostridia reduced the risk of FI in VLBW/ELBW infants.

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Use of Macrogol to Accelerate Feeding Advancement in Extremely Preterm Infants
Kirstin Barbara Faust, Mariia Lupatsii, Frederike Römer , Simon Graspeuntner, Silvio Waschina, Sina Zimmermann, Alexander Humberg, Mats Ingmar Fortmann, Kathrin Hanke, Kai Böckenholt, Johannes Dirks, Christine Silwedel, Jan Rupp, Egbert Herting, Wolfga
Neonatology.2025; 122(3): 350. CrossRef
Clinical Characteristics and Influencing Factors of Feeding Intolerance After Surgery for Neonatal Necrotizing Enterocolitis
Mengting Hu, Fan Wu, Zhikai Fu, Yasi Zhang, Xinmin Ju, Zheng Chen, Xiaolu Ma, Yuanyuan Zhang, Wei Shi
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Bo Kyeong Jin, Hyunsu Kim, Cho Ae Lee, Hye-Rim Kim
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Reduced Gut Bacterial Diversity in Early Life Predicts Feeding Intolerance in Preterm Neonates
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Calorie restriction during gestation impacts maternal and offspring fecal microbiome in mice
Stephanie P. Gilley, Meghan L. Ruebel, Sree V. Chintapalli, Clyde J. Wright, Paul J. Rozance, Kartik Shankar
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Ling Liu, Chaohong Chen, YeShan Li, Dang Ao, Jiayuan Wu, Nali Cai, Wen Li, Min Xiang
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Nicholas Sizemore, Kaitlyn Oliphant, Ruolin Zheng, Camilia R. Martin, Erika C. Claud, Ishanu Chattopadhyay
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Investigating prenatal and perinatal factors on meconium microbiota: a systematic review and cohort study
Jenni Turunen, Mysore V. Tejesvi, Niko Paalanne, Tytti Pokka, Sajeen Bahadur Amatya, Surbhi Mishra, Anna Kaisanlahti, Justus Reunanen, Terhi Tapiainen
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Dynamics and Crosstalk between Gut Microbiota, Metabolome, and Fecal Calprotectin in Very Preterm Infants: Insights into Feeding Intolerance
Luyang Hong, Yihuang Huang, Junyan Han, Shujuan Li, Lan Zhang, Siyuan Jiang, Qi Zhou, Xincheng Cao, Weiyin Yu, Yi Yang, Shangyu Hong, Yufeng Zhou, Weili Yan, Yun Cao
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Hyun Mi Kang, Sol Kim, Seok Hwang-Bo, In Hyuk Yoo, Yu-Mi Seo, Moon Yeon Oh, Soo-Ah Im, Young-Ah Youn
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Journal Articles

Differences in the methanogen community between the nearshore and offshore sediments of the South Yellow Sea: Ye Chen , Yu Zhen , Jili Wan , Siqi Li , Jiayin Liu , Guodong Zhang , Tiezhu Mi; J. Microbiol. 2022;60(8):814-822. Published online July 14, 2022; DOI: https://doi.org/10.1007/s12275-022-2022-2

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The differences in methanogen abundance and community composition were investigated between nearshore and offshore sediments in the South Yellow Sea (SYS). Shannon, Simpson, and Chao1 indices revealed a higher diversity of methanogens in the nearshore sediments than in the offshore sediments. The Mann–Whitney U test demonstrated that the relative abundance of Methanococcoides was significantly higher in the offshore sediments, while the relative abundances of Methanogenium, Methanosarcina, Methanosaeta, Methanolinea, and Methanomassiliicoccus were significantly higher in the nearshore sediments (P < 0.05). The abundance of the mcrA gene in the nearshore sediments was significantly higher than that in the offshore sediments. Furthermore, a similar vertical distribution of the methanogen and sulfatereducing bacteria (SRB) abundances was observed in the SYS sediments, implying there is potential cooperation between these two functional microbes in this environment. Finally, total organic carbon (TOC) was significantly correlated with methanogen community composition.

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Methylmercury cycling in the Bohai Sea and Yellow Sea: Reasons for the low system efficiency of methylmercury production
Lufeng Chen, Guoyi Cheng, Zhengwen Zhou, Yong Liang, Zhijia Ci, Yongguang Yin, Guangliang Liu, Yong Cai, Yanbin Li
Water Research.2024; 258: 121792. CrossRef
Diversity, composition, metabolic characteristics, and assembly process of the microbial community in sewer system at the early stage
Yiming Yuan, Guangyi Zhang, Hongyuan Fang, Haifeng Guo, Yongkang Li, Zezhuang Li, Siwei Peng, Fuming Wang
Environmental Science and Pollution Research.2024; 31(9): 13075. CrossRef
Improved Quantitative Real-Time PCR Protocol for Detection and Quantification of Methanogenic Archaea in Stool Samples
Agata Anna Cisek, Iwona Bąk, Bożena Cukrowska
Microorganisms.2023; 11(3): 660. CrossRef

Assessing the microcystins concentration through optimized protein phosphatase inhibition assay in environmental samples: Kyoung-Hee Oh , Kung-Min Beak , Yuna Shin , Young-Cheol Cho; J. Microbiol. 2022;60(6):602-609. Published online April 30, 2022; DOI: https://doi.org/10.1007/s12275-022-2020-4

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Protein phosphatase (PPase) inhibition assay (PPIA) is widely used to analyze the concentration of microcystins (MCs) because it is comparatively less expensive and faster than other assays. This study aimed to optimize the PPIA by determining a suitable reaction terminator and an optimal methanol concentration in the sample. The most suitable reaction time was 90 min, with the corresponding methanol concentration in the sample being 15% or less. When p-nitrophenyl phosphate (pNPP) was used as a substrate, copper chloride solution was suitably used as a reaction terminator, and when 4- methylumbelliferyl phosphate (MUP) was used, a glycine buffer not only increased the measurement sensitivity of the reaction product but also terminated the enzymatic reaction. When PPase 1 and MUP were used as an enzyme and a substrate, respectively, the limit of quantitation for MC-leucine/ arginine (LR) was 0.02 μg/L, whereas it was 0.1 μg/L when pNPP was used as a substrate. The proposed method facilitated the measurement of MC-LR concentration without additional pretreatments, such as concentration or purification; therefore, this method was suitable and feasible for the continuous monitoring of MCs in drinking water.

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Acid phosphatase detection using a colorimetric probe based on azo compound toward forensic applications for seminal fluid identification
Jéssica Raimundo da Rocha, Marcone Gomes dos Santos Alcântara, Verônica Diniz da Silva, Dimas José da Paz Lima, Josué Carinhanha Caldas Santos
Dyes and Pigments.2025; 239: 112806. CrossRef
Analyzing MC-LR distribution characteristics in natural lakes by a novel fluorescence technology
Xiangyu Hu, Zhaomin Wang, Xiao Ye, Ping Xie, Yong Liu
Environmental Pollution.2024; 342: 123123. CrossRef
Magnetic solid phase extraction coupled with high-performance liquid chromatography-diode array detection based on assembled magnetic covalent organic frameworks for selective extraction and detection of microcystins in aquatic foods
Tianliang Wang, Hongzhen Xie, Yuting Cao, Qing Xu, Ning Gan
Journal of Chromatography A.2022; 1685: 463614. CrossRef

Activity of Lactobacillus crispatus isolated from vaginal microbiota against Mycobacterium tuberculosis: Youngkyoung Lee , Hoonhee Seo , Sukyung Kim Abdur Rahim , Youjin Yoon , Jehee Jung , Saebim Lee , Chang Beom Ryu , Ho-Yeon Song; J. Microbiol. 2021;59(11):1019-1030. Published online November 1, 2021; DOI: https://doi.org/10.1007/s12275-021-1332-0

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Abstract PDF

Tuberculosis, an infectious disease, is caused by Mycobacterium tuberculosis. It remains a significant public health issue around the globe, causing about 1.8 million deaths every year. Drug-resistant M. tuberculosis, including multi-drug-resistant (MDR), extremely-drug-resistant (XDR), and totally drugresistant (TDR) M. tuberculosis, continues to be a threat to public health. In the case of antibiotic-resistant tuberculosis, the treatment effect of conventional antibiotics is low. Side effects caused by high doses over a long period are causing severe problems. To overcome these problems, there is an urgent need to develop a new anti-tuberculosis drug that is different from the existing compound-based antibiotics. Probiotics are defined as live microorganisms conferring health benefits. They can be potential therapeutic agents in this context as the effectiveness of probiotics against different infectious diseases has been well established. Here, we report that Lactobacillus crispatus PMC201 shows a promising effect on tuberculosis isolated from vaginal fluids of healthy Korean women. Lactobacillus crispatus PMC201 reduced M. tuberculosis H37Rv under co-culture conditions in broth and reduced M. tuberculosis H37Rv and XDR M. tuberculosis in macrophages. Lactobacillus crispatus PMC201 was not toxic to a guinea pig model and did not induce dysbiosis in a human intestinal microbial ecosystem simulator. Taken together, these
results
indicate that L. crispatus PMC201 can be a promising alternative drug candidate in the current tuberculosis drug regime. Further study is warranted to assess the in vivo efficacy and confirm the mode of action of L. crispatus PMC201.

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Effect of Probiotics Supplementation on Clinical, Humanistic, and Safety Outcomes in Patients With Tuberculosis: A Prospective Cohort Study in a Tertiary Healthcare Facility in South India
Tejaswini Baral, Varun Kumar Sudha Gururaj, Mohan K. Manu, Chandrashekar Udyavara Kudru, Jitendra Singh, Chiranjay Mukhopadhyay, Mahadev Rao, Kavitha Saravu, Sonal Sekhar Miraj
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Md Abdur Rahim, Hoonhee Seo, Indrajeet Barman, Mohammed Solayman Hossain, Md Sarower Hossen Shuvo, Ho-Yeon Song
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Hamed Memariani, Mojtaba Memariani, Seyed Ebrahim Eskandari, Abdolmajid Ghasemian, Ali Nour Neamatollahi
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Yinghui Chai, Min Li, Xianping Deng, Congcong Ma, Nannan Zhou, Yanan Chen, Yushan Yao, Kang Li, Wenping Gong, Hong Lei
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The putative sensor histidine kinase VadJ coordinates development and sterigmatocystin production in Aspergillus nidulans: Yanxia Zhao , Mi-Kyung Lee , Jieyin Lim , Heungyun Moon , Hee-Soo Park , Weifa Zheng , Jae-Hyuk Yu; J. Microbiol. 2021;59(8):746-752. Published online July 5, 2021; DOI: https://doi.org/10.1007/s12275-021-1055-2

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The VosA-VelB heterocomplex governs expression of several genes associated with fungal development and secondary metabolism. In this study, we have investigated the functions of one of the VosA-VelB-activated developmental genes vadJ in development and production of the mycotoxin sterigmatocystin in the model fungus Aspergillus nidulans. The vadJ gene is predicted to encode a 957-amino acid length protein containing a highly conserved sensor histidine kinase domain. The deletion of vosA or velB resulted in decreased mRNA levels of vadJ throughout the life cycle, suggesting that VosA and VelB are necessary for proper expression of vadJ. Nullifying vadJ led to highly restricted colony growth, lowered formation of asexual spores, and about two-fold reduction in conidial viability. Conversely, the deletion of vadJ resulted in elevated production of sexual fruiting bodies and sterigmatocystin. These suggest that VadJ is necessary for proper coordination of asexual and sexual development, and sterigmatocystin production. In accordance with this idea, the deletion of vadJ led to elevated mRNA levels of the two key sexual developmental activators esdC and nsdD. In summary, the putative sensor histidine kinase VadJ represses sexual development and sterigmatocystin production, but activates asexual development in A. nidulans.

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Xiaomeng Wang, Juan Xi, Pengxu Chen, Yingying Chen, Keyu Chen, Weifa Zheng, Yanxia Zhao
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Involvement of LaeA and Velvet Proteins in Regulating the Production of Mycotoxins and Other Fungal Secondary Metabolites
Xuwen Hou, Liyao Liu, Dan Xu, Daowan Lai, Ligang Zhou
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Influence of dragon bamboo with different planting patterns on microbial community and physicochemical property of soil on sunny and shady slopes: Weiyi Liu , Fang Wang , Yanmei Sun , Lei Yang , Huihai Chen , Weijie Liu , Bin Zhu , Chaomao Hui , Shiwei Wang; J. Microbiol. 2020;58(11):906-914. Published online October 30, 2020; DOI: https://doi.org/10.1007/s12275-020-0082-8

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Dragon bamboo (Dendrocalamus giganteus) is a giant sympodial bamboo species widely distributed in Asia. However, it remains unclear how dragon bamboo and soil microbes interact to affect soil properties. In this study, we investigated the planting patterns (semi-natural and artificial) on different slopes (sunny and shady) to determine the effects on soil properties and microbial community. The results showed that the soil in which dragon bamboo was grown was acidic, with a pH value of ~5. Also, the soil organic matter content, nitrogen hydrolysate concentration, total nitrogen, available potassium, and total potassium of the dragon bamboo seminatural forest significantly improved, especially on the sunny slope. In contrast, the available phosphorus level was higher in the artificial bamboo forest, probably owing to the phosphate fertilizer application. The bacterial and fungal diversity and the bacterial abundance were all higher on the sunny slope of the semi-natural forest than those in the other samples. The microbial operational taxonomic units (OTUs) shared between the shady and sunny slopes accounted for 47.8–62.2%, but the core OTUs of all samples were only 24.4– 30.4% of each sample, suggesting that the slope type had a significant effect on the microbial community. Some acidophilic microbes, such as Acidobacteria groups, Streptomyces and Mortierella, became dominant in dragon bamboo forest soil. A PICRUSt analysis of the bacterial functional groups revealed that post-translational modification, cell division, and coenzyme transport and metabolism were abundant in the semi-natural forest. However, some microorganisms with strong stress resistance might be activated in the artificial forest. Taken together, these results illustrated the influence of dragon bamboo growth on soil physicochemical property and microbial community, which might help understand the growth status of dragon bamboo under different planting patterns.

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The relationship between bacterial diversity and organic carbon mineralization in soft rock and sand compound soil: Zhen Guo , Juan Li , Lei Ge , Chenxi Yang , Jichang Han; J. Microbiol. 2020;58(9):750-760. Published online July 24, 2020; DOI: https://doi.org/10.1007/s12275-020-0130-4

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The soil organic carbon (SOC) mineralization rate in sandy soil plays an important role in improving soil quality, and a research is needed to determine management practices that optimize the mineralization rate. When sandy soil is improved by adding soft rock, the specific promotion process of bacterium to SOC mineralization remain unclear. To investigate these mechanisms, we selected four treatments with soft rock to sand volume ratios of 0:1 (CK), 1:5 (C1), 1:2 (C2) and 1:1 (C3) to study. The mineralization rate of organic carbon was measured using the lye absorption method. Highthroughput sequencing and scanning electron microscopy were used to determine the bacterial community structure and soil microstructure, respectively. The results showed that the organic carbon content of the sandy soil increased significantly (182.22–276.43%) after using the soft rock treatments. The SOC mineralization rate could be divided into two stages: a rapid decline during days 1–8 and a slow decline during days 8–60. With increased incubation time, the intensity of the cumulative release of organic carbon gradually weakened. Compared with the CK treatment, the SOC mineralization accumulation (Ct) and the potential mineralizable organic carbon content (C0) in the C1, C2, and C3 treatments increased significantly, by 106.98–225.94% and 112.22– 254.08%, respectively. The cumulative mineralization rate (Cr) was 18.11% and 21.38% smaller with treatments C2 and C3, respectively. The SOC mineralization rate constant (k) decreased significantly after the addition of soft rock, while the half-turnover period (Th) changed inversely with k. Compared with the CK treatment, the number of gene copies of the soil bacteria increased by 15.38–272.53% after adding soft rock, with the most significant increase in treatment C3. The bacterial diversity index also increased significantly under treatment C3. The three dominant bacteria were Proteobacteria, Actinobacteria, and Chloroflexi. The correlation between Cr and one of the non-dominant bacteria, Firmicutes, was large, and the bacteria had a significant positive correlation with k. At the same time, the abundance of Firmicutes under treatments C2 and C3 was small. As the proportion of soft rock increased, the soil particles changed from point contact to surface contact, and the adhesion on the surface of the particles gradually increased. Results from this study show that the retention time of SOC can be increased and the carbon sequestration effect is better when the ratio of soft rock to sand is set to 1:2.

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Response of soil structure and crop yield to soft rock in Mu Us sandy land, China
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Novosphingobium sp. PP1Y as a novel source of outer membrane vesicles: Federica De Lise , Francesca Mensitieri , Giulia Rusciano , Fabrizio Dal Piaz , Giovanni Forte , Flaviana Di Lorenzo , Antonio Molinaro , Armando Zarrelli , Valeria Romanucci , Valeria Cafaro , Antonio Sasso , Amelia Filippelli , Alberto Di Donato , Viviana Izzo; J. Microbiol. 2019;57(6):498-508. Published online May 27, 2019; DOI: https://doi.org/10.1007/s12275-019-8483-2

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Outer membrane vesicles (OMVs) are nanostructures of 20– 200 nm diameter deriving from the surface of several Gramnegative bacteria. OMVs are emerging as shuttles involved in several mechanisms of communication and environmental adaptation. In this work, OMVs were isolated and characterized from Novosphingobium sp. PP1Y, a Gram-negative non-pathogenic microorganism lacking LPS on the outer membrane surface and whose genome was sequenced and annotated. Scanning electron microscopy performed on samples obtained from a culture in minimal medium highlighted the presence of PP1Y cells embedded in an extracellular matrix rich in vesicular structures. OMVs were collected from the exhausted growth medium during the mid-exponential phase, and purified by ultracentrifugation on a sucrose gradient. Atomic force microscopy, dynamic light scattering and nanoparticle tracking analysis showed that purified PP1Y OMVs had a spherical morphology with a diameter of ca. 150 nm and were homogenous in size and shape. Moreover, proteomic and fatty acid analysis of purified OMVs revealed a specific biochemical “fingerprint”, suggesting interesting details concerning their biogenesis and physiological role. Moreover, these extracellular nanostructures do not appear to be cytotoxic on HaCaT cell line, thus paving the way to their future use as novel drug delivery systems.

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Antimicrobial effect and proposed action mechanism of cordycepin against Escherichia coli and Bacillus subtilis: Qi Jiang , Zaixiang Lou , Hongxin Wang , Chen Chen; J. Microbiol. 2019;57(4):288-297. Published online March 30, 2019; DOI: https://doi.org/10.1007/s12275-019-8113-z

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The detailed antibacterial mechanism of cordycepin efficacy against food-borne germs remains ambiguous. In this study, the antibacterial activity and action mechanism of cordycepin were assessed. The results showed that cordycepin effectively inhibited the growth of seven bacterial pathogens including both Gram-positive and Gram-negative bacterial pathogens; the minimum inhibitory concentrations (MIC) were 2.5 and 1.25 mg/ml against Escherichia coli and Bacillus subtilis, respectively. Scanning electron microscope and transmission electron microscope examination confirmed that cordycepin caused obvious damages in the cytoplasmatic membranes of both E. coli and B. subtilis. Outer membrane permeability assessment indicated the loss of barrier function and the leakage of cytoplasmic contents. Propidium iodide and carboxyfluorescein diacetate double staining approach coupled with flow cytometry analysis indicated that the integrity of cell membrane was severely damaged during a short time, while the intracellular enzyme system still remained active. This clearly suggested that membrane damage was one of the reasons for cordycepin efficacy against bacteria. Additionally, results from circular dichroism and fluorescence analysis indicated cordycepin could insert to genome DNA base and double strand, which disordered the structure of genomic DNA. Basis on these results, the mode of bactericidal action of cordycepin against E. coli and B. subtilis was found to be a dual mechanism, disrupting bacterial cell membranes and binding to bacterial genomic DNA to interfere in cellular functions, ultimately leading to cell death.

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Review

[Minireview] Antibiotic resistance of pathogenic Acinetobacter species and emerging combination therapy: Bora Shin , Woojun Park; J. Microbiol. 2017;55(11):837-849. Published online October 27, 2017; DOI: https://doi.org/10.1007/s12275-017-7288-4

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Abstract PDF

The increasing antibiotic resistance of Acinetobacter species in both natural and hospital environments has become a serious problem worldwide in recent decades. Because of both intrinsic and acquired antimicrobial resistance (AMR) against last-resort antibiotics such as carbapenems, novel therapeutics are urgently required to treat Acinetobacter-associated infectious diseases. Among the many pathogenic Acinetobacter species, A. baumannii has been reported to be resistant to all classes of antibiotics and contains many AMR genes, such as blaADC (Acinetobacter-derived cephalosporinase). The AMR of pathogenic Acinetobacter species is the result of several different mechanisms, including active efflux pumps, mutations in antibiotic targets, antibiotic modification, and low antibiotic membrane permeability. To overcome the limitations of existing drugs, combination theraphy that can increase the activity of antibiotics should be considered in the treatment of Acinetobacter infections. Understanding the molecular mechanisms behind Acinetobacter AMR resistance will provide vital information for drug development and therapeutic strategies using combination treatment. Here, we summarize the classic mechanisms of Acinetobacter AMR, along with newly-discovered genetic AMR factors and currently available antimicrobial adjuvants that can enhance drug efficacy in the treatment of A. baumannii infections.

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Journal Article

Proteomic characterization of the outer membrane vesicle of the halophilic marine bacterium Novosphingobium pentaromativorans US6-1: Sung Ho Yun , Sang-Yeop Lee , Chi-Won Choi , Hayoung Lee , Hyun-Joo Ro , Sangmi Jun , Yong Min Kwon , Kae Kyoung Kwon , Sang-Jin Kim , Gun-Hwa Kim , Seung Il Kim; J. Microbiol. 2017;55(1):56-62. Published online December 30, 2016; DOI: https://doi.org/10.1007/s12275-017-6581-6

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Abstract PDF

Novosphingobium pentaromativorans US6-1 is a Gram-negative halophilic marine bacterium able to utilize several polycyclic aromatic hydrocarbons such as phenanthrene, pyrene, and benzo[a]pyrene. In this study, using transmission electron microscopy, we confirmed that N. pentaromativorans US6-1 produces outer membrane vesicles (OMVs). N. pentaromativorans OMVs (hereafter OMVNovo) are spherical in shape, and the average diameter of OMVNovo is 25–70 nm. Proteomic analysis revealed that outer membrane proteins and periplasmic proteins of N. pentaromativorans are the major protein components of OMVNovo. Comparative proteomic analysis with the membrane-associated protein fraction and correlation analysis demonstrated that the outer membrane proteins of OMVNovo originated from the membrane- associated protein fraction. To the best of our knowledge, this study is the first to characterize OMV purified from halophilic marine bacteria.

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Review

REVIEW] Plasma membrane organization promotes virulence of the human fungal pathogen Candida albicans: Lois M. Douglas , James B. Konopka; J. Microbiol. 2016;54(3):178-191. Published online February 27, 2016; DOI: https://doi.org/10.1007/s12275-016-5621-y

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Abstract PDF

Candida albicans is a human fungal pathogen capable of causing lethal systemic infections. The plasma membrane plays key roles in virulence because it not only functions as a protective barrier, it also mediates dynamic functions including secretion of virulence factors, cell wall synthesis, invasive hyphal morphogenesis, endocytosis, and nutrient uptake. Consistent with this functional complexity, the plasma membrane is composed of a wide array of lipids and proteins. These components are organized into distinct domains that will be the topic of this review. Some of the plasma membrane domains that will be described are known to act as scaffolds or barriers to diffusion, such as MCC/eisosomes, septins, and sites of contact with the endoplasmic reticulum. Other zones mediate dynamic processes, including secretion, endocytosis, and a special region at hyphal tips that facilitates rapid growth. The highly organized architecture of the plasma membrane facilitates the coordination of diverse functions and promotes the pathogenesis of C. albicans.

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Characterization of the rapamycin-inducible EBV LMP1 activation system: Sang Yong Kim , Jung-Eun Kim , Jiyeon Won , Yoon-Jae Song; J. Microbiol. 2015;53(10):732-738. Published online October 2, 2015; DOI: https://doi.org/10.1007/s12275-015-5455-z

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Abstract

Epstein-Barr virus (EBV) latent infection membrane protein 1 (LMP1) is required for EBV-mediated B lymphocyte transformation into proliferating lymphoblastoid cell lines (LCL). LMP1 oligomerizes spontaneously in membrane lipid rafts via its transmembrane domain and constitutively activates signal transduction pathways, including NF-κB, p38 Mitogen-Activated Protein Kinase (MAPK), and c-Jun N-terminal Kinase (JNK). Since LMP1 mimics the tumor necrosis factor receptor (TNFR), CD40, it may be effectively utilized to study the effects of constitutive activation of signal transduction pathways on cellular physiology. On the other hand, LMP1 presents a disadvantage in terms of determining the sequential events and factors involved in signaling pathways. A CD40-LMP1 chimeric molecule has been generated to overcome this limitation but does not represent the authentic and physiological nature of LMP1. In the current study, a ligand-dependent activation system for LMP1 using rapamycin-inducible dimerization was generated to delineate the LMP1 signaling pathway.

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Functional properties of the major outer membrane protein in Stenotrophomonas maltophilia: Yih-Yuan Chen , Han-Chiang Wu , Juey-Wen Lin , Shu-Fen Weng; J. Microbiol. 2015;53(8):535-543. Published online July 31, 2015; DOI: https://doi.org/10.1007/s12275-015-5202-5

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Abstract

Stenotrophomonas maltophilia is an opportunistic pathogen that is closely associated with high morbidity and mortality in debilitated and immunocompromised individuals. Therefore, to investigate the pathogenesis mechanism is urgently required. However, there are very few studies to evaluate the functional properties of outer membrane protein, which may contribute to the pathogenesis in S. maltophilia. In this study, three abundant proteins in the outer membrane fraction of S. maltophilia were identified by liquid chromatography- tandem mass spectrometry as OmpW1, MopB, and a hypothetical protein. MopB, a member of the OmpA family, was firstly chosen for functional investigation in this study because many OmpA-family proteins are known to be involved in pathogenesis and offer potential as vaccines. Membrane fractionation analyses demonstrated that MopB was indeed the most abundant outer membrane protein (OMP) in S. maltophilia. For functional studies, the mopB mutant of S. maltophilia (SmMopB) was constructed by insertional mutation. MopB deficiency resulted in a change in the protein composition of OMPs and altered the architecture of the outer membrane. The SmMopB strain exhibited reduced cytotoxicity toward L929 fibroblasts and was more sensitive to numerous stresses, including human serum, sodium dodecyl sulfate, and hydrogen peroxide compared with wildtype S. maltophilia. These results suggest that MopB may be a good candidate for the design of vaccines or anti-MopB drugs for controlling serious nosocomial infections of multidrug- resistant S. maltophilia, especially in immunosuppressed patients.

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Recombinant Ax21 protein is a promising subunit vaccine candidate against Stenotrophomonas maltophilia in a murine infection model
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Intranasal immunization with recombinant outer membrane protein A induces protective immune response against Stenotrophomonas maltophilia infection
Yan Li, Xueping Tang, Zunquan Zhao, Hui Wang, Xin Wang, Xueyi Shang, Peng Liu, Zhihua Kou, Yongqiang Jiang, Yan Li, Daniela Flavia Hozbor
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Morphological changes in human gastric epithelial cells induced by nuclear targeting of Helicobacter pylori urease subunit A: Jung Hwa Lee , So Hyun Jun , Jung-Min Kim , Seung Chul Baik , Je Chul Lee; J. Microbiol. 2015;53(6):406-414. Published online May 30, 2015; DOI: https://doi.org/10.1007/s12275-015-5085-5

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Abstract

Nuclear targeting of bacterial proteins and their pathological effects on host cells are an emerging pathogenic mechanism in bacteria. We have previously reported that urease subunit A (UreA) of Helicobacter pylori targets the nuclei of COS-7 cells through nuclear localization signals (NLSs). This study further investigated whether UreA of H. pylori targets the nuclei of gastric epithelial cells and then induces molecular and cellular changes in the host cells. H. pylori 26695 strain produced and secreted outer membrane vesicles (OMVs). UreA was translocated into gastric epithelial AGS cells through outer membrane vesicles (OMVs) and then targeted the nuclei of AGS cells. Nuclear targeting of rUreA did not induce host cell death, but resulted in morphological changes, such as cellular elongation, in AGS cells. In contrast, AGS cells treated with rUreAΔNLS proteins did not show this morphological change. Next generation sequencing revealed that nuclear targeting of UreA differentially regulated 102 morphogenesis- related genes, of which 67 and 35 were up-regulated and down-regulated, respectively. Our results suggest that nuclear targeting of H. pylori UreA induces both molecular and cellular changes in gastric epithelial cells.

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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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Proteomic and Functional Analyses of a Novel Porin-like Protein in Xanthomonas oryzae pv. oryzae: Hye-Jee Park , Sang-Won Lee , Sang-Wook Han; J. Microbiol. 2014;52(12):1030-1035. Published online November 29, 2014; DOI: https://doi.org/10.1007/s12275-014-4442-0

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Abstract PDF

Proteomic analysis is a useful technique for postulating and elucidating protein functions. In the present work, a shotgun proteomic analysis was used to identify functions of the PXO_03968 gene (previously known as the ax21) from Xanthomonas oryzae pv. oryzae (Xoo), a causal agent for bacterial blight disease in rice. Structural prediction performed on the protein sequence encoded by PXO_03968 reveals that it encodes a putative porin-like protein, possessing a β-barrel domain with 10 β-strands and a signal peptide at the Nterminus. We renamed the gene as an omp1X (outer membrane protein 1 in Xoo), generated its knock out mutant (XooΔomp1X), and compared the protein expression level in the mutant to that in the wild type. A total of 106 proteins displayed more than 1.5-fold difference in expression between the mutant and the wild type strains. COG analysis revealed that these proteins are involved in cell motility as well as signal transduction. In addition, phenotypic analysis demonstrated that motility and biofilm formation in XooΔomp1X are lower than the wild type. These results provide new insights into the functions of outer membrane proteins in Gram-negative bacteria.

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Journal Article

Comparative Proteomics Analysis of Sarcosine Insoluble Outer Membrane Proteins from Clarithromycin Resistant and Sensitive Strains of Helicobacter pylori: Rebecca Smiley , James Bailey , Mahadevan Sethuraman , Norberto Posecion , M. Showkat Ali; J. Microbiol. 2013;51(5):612-618. Published online October 31, 2013; DOI: https://doi.org/10.1007/s12275-013-3029-5

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Helicobacter pylori causes disease manifestations in humans including chronic gastric and peptic ulcers, gastric cancer, and lymphoid tissue lymphoma. Increasing rates of H. pylori clarithromycin resistance has led to higher rates of disease development. Because antibiotic resistance involves modifications of outer membrane proteins (OMP) in other Gram-negative bacteria, this study focuses on identification of H. pylori OMP’s using comparative proteomic analyses of clarithromycin-susceptible and -resistant H. pylori strains. Comparative proteomics analyses of isolated sarcosine-insoluble OMP fractions from clarithromycin-susceptible and -resistant H. pylori strains were performed by 1) one dimensional sodium dodecyl sulphate-polyacrylamide gel electrophoresis protein separation and 2) in-gel digestion of the isolated proteins and mass spectrometry analysis by Matrix Assisted Laser Desorption Ionization-tandem mass spectrometry. Iron-regulated membrane protein, UreaseB, EF-Tu, and putative OMP were down-regulated; HopT (BabB) transmembrane protein, HofC, and OMP31 were up-regulated in clarithromycin-resistant H. pylori. Western blotting and real time PCR, respectively, validated UreaseB subunit and EF-Tu changes at the protein level, and mRNA expression of HofC and HopT. This limited proteomic study provides evidence that alteration of the outer membrane proteins’ profile may be a novel mechanism involved in clarithromycin resistance in H. pylori.

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

Identification of Conserved Surface Proteins as Novel Antigenic Vaccine Candidates of Actinobacillus pleuropneumoniae: Xiabing Chen , Zhuofei Xu , Lu Li , Huanchun Chen , Rui Zhou; J. Microbiol. 2012;50(6):978-986. Published online December 30, 2012; DOI: https://doi.org/10.1007/s12275-012-2214-2

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Actinobacillus pleuropneumoniae is an important swine respiratory pathogen causing great economic losses worldwide. Identification of conserved surface antigenic proteins is helpful for developing effective vaccines. In this study, a genome-wide strategy combined with bioinformatic and experimental approaches, was applied to discover and characterize surface-associated immunogenic proteins of A. pleuropneumoniae. Thirty nine genes encoding outer membrane proteins (OMPs) and lipoproteins were identified by comparative genomics and gene expression profiling as beinghighly conserved and stably transcribed in the different serotypes of A. pleuropneumoniae reference strains. Twelve of these conserved proteins were successfully expressed in Escherichia coli and their immunogenicity was estimated by homologous challenge in the mouse model, and then three of these proteins (APJL_0126, HbpA and OmpW) were further tested in the natural host (swine) by homologous and heterologous challenges. The results showed that these proteins could induce high titers of antibodies, but vaccination with each protein individually elicited low protective immunity against A. pleuropneumoniae. This study gives novel insights into immunogenicity of the conserved OMPs and lipoproteins of A. pleuropneumoniae. Although none of the surface proteins characterized in this study could individually induce effective protective immunity against A. pleuropneumoniae, they are potential candidates for subunit vaccines in combination with Apx toxins.

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Identification of candidate vaccine antigens using 2-D gel electrophoresis and immunoproteomics for cross protection against Glaesserella parasuis
Samantha J. Hau, Kirsten C. Eberle, Jarlath E. Nally, Daniel W. Nielsen, John D. Lippolis, Susan L. Brockmeier
Veterinary Microbiology.2025; 307: 110594. CrossRef
Review of advanced research on swine Actinobacillus pleuropneumoniae vaccine development strategy
Adehanom Baraki Tesfaye, Rui Han, Zhengyu Tao, Liuchao You, Jiayao Zhu, Pengcheng Gao, Lei Fu, Yuefeng Chu
Frontiers in Immunology.2025;[Epub] CrossRef
De novo identification of bacterial antigens of a clinical isolate by combining use of proteosurfaceomics, secretomics, and BacScan technologies
Jinyue Yang, Xueting Zhang, Junhua Dong, Qian Zhang, Erchao Sun, Cen Chen, Zhuangxia Miao, Yifei Zheng, Nan Zhang, Pan Tao
Frontiers in Immunology.2023;[Epub] CrossRef
Identification of a Novel Linear B-Cell Epitope of HbpA Protein from Glaesserella parasuis Using Monoclonal Antibody
Geyan Liu, Kang Wang, Zhen Yang, Xiaoyu Tang, Yung-Fu Chang, Ke Dai, Xinwei Tang, Bangdi Hu, Yiwen Zhang, Sanjie Cao, Xiaobo Huang, Qigui Yan, Rui Wu, Qin Zhao, Senyan Du, Xintian Wen, Yiping Wen
International Journal of Molecular Sciences.2023; 24(10): 8638. CrossRef
Proteomic and immunoproteomic insights into the exoproteome of Actinobacillus pleuropneumoniae, the causative agent of porcine pleuropneumonia
Stelli G. Stancheva, Janna Frömbling, Elena L. Sassu, Isabel Hennig-Pauka, Andrea Ladinig, Wilhelm Gerner, Tom Grunert, Monika Ehling-Schulz
Microbial Pathogenesis.2022; 172: 105759. CrossRef
Genome-wide screening of lipoproteins in Actinobacillus pleuropneumoniae identifies three antigens that confer protection against virulent challenge
Yurou Cao, Lulu Gao, Li Zhang, Lixiang Zhou, Jihong Yang, Lingfu Deng, Jin Zhao, Chao Qi, Jinlin Liu
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The roles of flp1 and tadD in Actinobacillus pleuropneumoniae pilus biosynthesis and pathogenicity
Tingting Li, Qiuhong Zhang, Rong Wang, Sihua Zhang, Jie Pei, Yaokun Li, Lu Li, Rui Zhou
Microbial Pathogenesis.2019; 126: 310. CrossRef
Recombinant ApxIV protein enhances protective efficacy againstActinobacillus pleuropneumoniaein mice and pigs
H.-C. Wu, P.-H. Yeh, K.-J. Hsueh, W.-J. Yang, C.-Y. Chu
Journal of Applied Microbiology.2018; 124(6): 1366. CrossRef
New trends in innovative vaccine development against Actinobacillus pleuropneumoniae
Abraham Loera-Muro, Carlos Angulo
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A trivalent Apx-fusion protein delivered by E. coli outer membrane vesicles induce protection against Actinobacillus pleuropneumoniae of serotype 1 and 7 challenge in a murine model
Kui Xu, Qin Zhao, Xintian Wen, Rui Wu, Yiping Wen, Xiaobo Huang, Yong Huang, Qigui Yan, Xinfeng Han, Xiaoping Ma, Yung-Fu Chang, Sanjie Cao, Utpal Pal
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Structural and Functional Importance of Outer Membrane Proteins in Vibrio cholerae Flagellum: Wasimul Bari , Kang-Mu Lee , Sang Sun Yoon; J. Microbiol. 2012;50(4):631-637. Published online August 25, 2012; DOI: https://doi.org/10.1007/s12275-012-2116-3

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Vibrio cholerae has a sheath-covered monotrichous flagellum that is known to contribute to virulence. Although the structural organization of the V. cholerae flagellum has been extensively studied, the involvement of outer membrane proteins as integral components in the flagellum still remains elusive. Here we show that flagella produced by V. cholerae O1 El Tor strain C6706 were two times thicker than those from two other Gram-negative bacteria. A C6706 mutant strain (SSY11) devoid of two outer membrane proteins (OMPs), OmpU and OmpT, produced thinner flagella. SSY11 showed significant defects in the flagella-mediated motility as compared to its parental strain. Moreover, increased shedding of the flagella-associated proteins was observed in the culture supernatant of SSY11. This finding was also supported by the observation that culture supernatants of the SSY11 strain induced the production of a significantly higher level of IL-8 in human colon carcinoma HT29 and alveolar epithelial A549 cells than those of the wild-type C6706 strain. These results further suggest a definite role of these two OMPs in providing the structural integrity of the V. cholerae flagellum as part of the surrounding sheath.

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Acinetobacter baumannii Outer Membrane Protein A Modulates the Biogenesis of Outer Membrane Vesicles: Dong Chan Moon , Chul Hee Choi , Jung Hwa Lee , Chi-Won Choi , Hye-Yeon Kim , Jeong Soon Park , Seung Il Kim , Je Chul Lee; J. Microbiol. 2012;50(1):155-160. Published online February 27, 2012; DOI: https://doi.org/10.1007/s12275-012-1589-4

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Acinetobacter baumannii secretes outer membrane vesicles (OMVs) during both in vitro and in vivo growth, but the biogenesis mechanism by which A. baumannii produces OMVs remains undefined. Outer membrane protein A of A. baumannii (AbOmpA) is a major protein in the outer membrane and the C-terminus of AbOmpA interacts with diaminopimelate of peptidoglycan. This study investigated the role of AbOmpA in the biogenesis of A. baumannii OMVs. Quantitative and qualitative approaches were used to analyze OMV biogenesis in A. baumannii ATCC 19606T and an isogenic ΔAbOmpA mutant. OMV production was significantly increased in the ΔAbOmpA mutant compared to wild-type bacteria as demonstrated by quantitation of proteins and lipopolysaccharides (LPS) packaged in OMVs. LPS profiles prepared from OMVs from wild-type bacteria and the ΔAbOmpA mutant had identical patterns, but proteomic analysis showed different protein constituents in OMVs from wild-type bacteria compared to the ΔAbOmpA mutant. In conclusion, AbOmpA influences OMV biogenesis by controlling OMV production and protein composition.

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Review

REVIEW] Recent Findings about the Yersinia enterocolitica Phage Shock Protein Response: Saori Yamaguchi , Andrew J. Darwin; J. Microbiol. 2012;50(1):1-7. Published online February 27, 2012; DOI: https://doi.org/10.1007/s12275-012-1578-7

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Abstract PDF: The phage shock protein (Psp) system is a conserved extracytoplasmic stress response in bacteria that is essential for virulence of the human pathogen Yersinia enterocolitica. This article summarizes some recent findings about Y. enterocolitica Psp system function. Increased psp gene expression requires the transcription factor PspF, but under non-inducing conditions PspF is inhibited by an interaction with another protein, PspA, in the cytoplasm. A Psp-inducing stimulus causes PspA to relocate to the cytoplasmic membrane, freeing PspF to induce psp gene expression. This PspA relocation requires the integral cytoplasmic membrane proteins, PspB and PspC, which might sense an inducing trigger and sequester PspA by direct interaction. The subsequent induction of psp gene expression increases the PspA concentration, which also allows it to contact the membrane directly, perhaps for its physiological function. Mutational analysis of the PspB and PspC proteins has revealed that they both positively and negatively regulate psp gene expression and has also identified PspC domains associated with each function. We also compare the contrasting physiological roles of the Psp system in the virulence of Y. enterocolitica and Salmonella enterica sv. Typhimurium (S. Typhimurium). In S. Typhimurium, PspA maintains the proton motive force, which provides the energy needed to drive ion importers required for survival within macrophages. In contrast, in the extracellular pathogen Y. enterocolitica, PspB and PspC, but not PspA, are the Psp components needed for virulence. PspBC protect Y. enterocolitica from damage caused by the secretin component of its type 3 secretion system, an essential virulence factor.

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

Immunostimulatory Activity of Dendritic Cells Pulsed with Carbonic Anhydrase IX and Acinetobacter baumannii Outer Membrane Protein A for Renal Cell Carcinoma: Bo Ra Kim , Eun Kyoung Yang , Sun Hee Kim , Dong Chan Moon , Hwa Jung Kim , Je Chul Lee , Duk Yoon Kim; J. Microbiol. 2011;49(1):115-120. Published online March 3, 2011; DOI: https://doi.org/10.1007/s12275-011-1037-x

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Abstract PDF

Dendritic cell (DC)-based immunotherapy is a potent therapeutic modality for treating renal cell carcinoma (RCC), but development of antigens specific for tumor-targeting and anti-tumor immunity is of great interest for clinical trials. The present study investigated the ability of DCs pulsed with a combination of carbonic anhydrase IX (CA9) as an RCC-specific biomarker and Acinetobacter baumannii outer membrane protein A (AbOmpA) as an immunoadjuvant to induce anti-tumor immunity against murine renal cell carcinoma (RENCA) in a murine model. Murine bone-marrow-derived DCs pulsed with a combination of RENCA lysates and AbOmpA were tested for their capacity to induce DC maturation and T cell responses in vitro. A combination of RENCA lysates and AbOmpA up-regulated the surface expression of co-stimulatory molecules, CD80 and CD86, and the antigen presenting molecules, major histocompatibility (MHC) class I and class II, in DCs. A combination of RENCA lysates and AbOmpA also induced interleukin-12 (IL-12) production in DCs. Next, the immunostimulatory activity of DCs pulsed with a combination of CA9 and AbOmpA was determined. A combination of CA9 and AbOmpA up-regulated the surface expression of co-stimulatory molecules and antigen presenting molecules in DCs. DCs pulsed with a combination of CA9 and AbOmpA effectively secreted IL-12 but not IL-10. These cells interacted with T cells and formed clusters. DCs pulsed with CA9 and AbOmpA elicited the secretion of interferon-γ and IL-2 in T cells. In conclusion, a combination of CA9 and AbOmpA enhanced the immunostimulatory activity of DCs, which may effectively induce anti-tumor immunity against human RCC.

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The Outer Membrane Proteins OmpA, CarO, and OprD of Acinetobacter baumannii Confer a Two-Pronged Defense in Facilitating Its Success as a Potent Human Pathogen
Siva R. Uppalapati, Abhiroop Sett, Ranjana Pathania
Frontiers in Microbiology.2020;[Epub] CrossRef
Host Innate Immune Responses to Acinetobacter baumannii Infection
Wangxue Chen
Frontiers in Cellular and Infection Microbiology.2020;[Epub] CrossRef
Generation of anti-tumour immune response using dendritic cells pulsed with carbonic anhydrase IX-Acinetobacter baumanniiouter membrane protein A fusion proteins against renal cell carcinoma
B-R Kim, E-K Yang, D-Y Kim, S-H Kim, D-C Moon, J-H Lee, H-J Kim, J-C Lee
Clinical and Experimental Immunology.2011; 167(1): 73. CrossRef

Periplasmic Domain of CusA in an Escherichia coli Cu+/Ag+ Transporter Has Metal Binding Sites: Bo-Young Yun , Yongbin Xu , Shunfu Piao , Nahee Kim , Jeong-Hyun Yoon , Hyun-Soo Cho , Kangseok Lee , Nam-Chul Ha; J. Microbiol. 2010;48(6):829-835. Published online January 9, 2011; DOI: https://doi.org/10.1007/s12275-010-0339-8

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Abstract PDF: The resistance nodulation division (RND)-type efflux systems are utilized in Gram-negative bacteria to export a variety of substrates. The CusCFBA system is the Cu+ and Ag+ efflux system in Escherichia coli, conferring resistance to lethal concentrations of Cu+ and Ag+. The periplasmic component, CusB, which is essential for the assembly of the protein complex, has Cu+ or Ag+ binding sites. The twelve-span membrane protein CusA is a homotrimeric transporter, and has a relatively large periplasmic domain. Here, we constructed the periplasmic domain of CusA by joining two DNA segments and then successfully expressed and purified the protein. Isothermal titration calorimetry experiments revealed Ag+ binding sites with Kds of 10-6-10-5 M. Our findings suggest that the metal binding in the periplasmic domain of CusA might play an important role in the function of the efflux pump.

NOTE] Analysis of Cytoplasmic Membrane Proteome of Streptococcus pneumoniae by Shotgun Proteomic Approach: Chi-Won Choi , Sung-Ho Yun , Sang-Oh Kwon , Sun-Hee Leem , Jong-Soon Choi , Chi-Young Yun , Seung Il Kim; J. Microbiol. 2010;48(6):872-876. Published online January 9, 2011; DOI: https://doi.org/10.1007/s12275-010-0220-9

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Abstract PDF

In this study, cytoplasmic membrane proteins of S. pneumoniae strain R6 (ATCC BBA-255) were effectively separated from cell wall or extracellular proteins by sodium carbonate precipitation (SCP) and ultracentrifugation. Forty seven proteins were analyzed as cytoplasmic membrane proteins from the 260 proteins identified by the shotgun proteomic method using SDS-PAGE/LC/MS-MS. ABC transporters for metabolites such as metals, oligopeptides, phosphate, sugar, and amino acids, and membrane proteins involved in phosphotransferse systems, were identified as the predominant and abundant, cytoplasmic membrane proteins that would be essential for nutrient uptake, antibiotic resistance and virulence mechanisms. Our result supports that gel-based shotgun proteomics combined with sodium carbonate precipitation and ultracentrifugation is an effective method for analysis of cytoplasmic membrane proteins of S. pneumoniae.

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Overexpression of Outer Membrane Protein OprT and Increase of Membrane Permeability in phoU Mutant of Toluene-Tolerant Bacterium Pseudomonas putida GM730: Kyunghee Lee , Juna Jung , Kwang Kim , Dongwon Bae , Dongbin Lim; J. Microbiol. 2009;47(5):557-562. Published online October 24, 2009; DOI: https://doi.org/10.1007/s12275-009-0105-y

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Eight toluene-sensitive mutants were previously isolated from the toluene-tolerant bacterium Pseudomonas putida GM730. One of these mutants was TOS6, in which Tn5 had been inserted into phoU. Susceptibility to multiple antibiotics, as well as toluene sensitivity, was increased in the phoU mutant of P. putida GM730. We compared the outer membrane proteins from the phoU mutant and wild-type via two-dimensional gel electrophoresis. A 45 kDa protein was dramatically overexpressed as the result of phoU inactivation, and this protein was identified by peptide mass fingerprinting and microsequencing as a conserved hypothetical protein consisting of 414 amino acids. The protein, designated as OprT, harbors a signal sequence and extended β-sheets, both of which are features common to the bacterial porins. The rate of ethidium bromide accumulation in TOS6 was higher than in GM730, which indicates that the TOS6 membranes may be more permeable to ethidium bromide than are the membranes of GM730. We propose that the toluene sensitivity and increased antibiotic susceptibility observed in the phoU mutant may be attributable to increased membrane permeability.

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Sublethal Paraquat Confers Multidrug Tolerance in Pseudomonas aeruginosa by Inducing Superoxide Dismutase Activity and Lowering Envelope Permeability
Dorival Martins, Geoffrey A. McKay, Ann M. English, Dao Nguyen
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Dorival Martins, Geoffrey McKay, Gowthami Sampathkumar, Malika Khakimova, Ann M. English, Dao Nguyen
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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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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
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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
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Ligand-Receptor Recognition for Activation of Quorum Sensing in Staphylococcus aureus: Li-Chun Chen , Li-Tse Tsou , Feng-Jui Chen; J. Microbiol. 2009;47(5):572-581. Published online October 24, 2009; DOI: https://doi.org/10.1007/s12275-009-0004-2

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The accessory gene regulator (agr) locus controls many of the virulence toxins involved in Staphylococcus aureus pathogenesis, and can be divided into four specificity groups. AgrC is the only group-specific receptor to mediate both intra-group activation and inter-group inhibition. We studied the ligand-receptor recognition of the agr system in depth by using a luciferase reporter system to identify the key residues responsible for AgrC activation in two closely related agr groups, AgrC-I, and AgrC-IV. Fusion PCR and site-directed mutagenesis were used to screen for functional residues of AgrC. Our data suggest that for AgrC-IV activation, residue 101 is critical for activating the receptor. In contrast, the key residues for the activation of AgrC-I are located at residues 49~59, 107, and 116. However, three residue changes, T101A, V107S, I116S, are sufficient to convert the AIP recognizing specificity from AgrC-IV to AgrC-I.

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Virulence attributes of successful methicillin-resistant Staphylococcus aureus lineages
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Proteoliposome‐based model for screening inhibitors targeting histidine kinase AgrC
Liying Zhang, Chunshan Quan, Xuning Zhang, Wen Xiong, Shengdi Fan
Chemical Biology & Drug Design.2019; 93(5): 712. CrossRef
Effect of a Point Mutation in mprF on Susceptibility to Daptomycin, Vancomycin, and Oxacillin in an MRSA Clinical Strain
Feng-Jui Chen, Tsai-Ling Lauderdale, Chen-Hsiang Lee, Yu-Chieh Hsu, I-Wen Huang, Pei-Chi Hsu, Chung-Shi Yang
Frontiers in Microbiology.2018;[Epub] CrossRef
Specificity and complexity in bacterial quorum-sensing systems
Lisa A. Hawver, Sarah A. Jung, Wai-Leung Ng, Aimee Shen
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Marisa D. Pinchas, Nathan C. LaCross, Suzanne Dawid, G. A. O'Toole
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Feng-Jui Chen, Chen-Her Wang, Ching-Yi Chen, Yu-Chieh Hsu, Kaun-Ting Wang
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Green Fluorescent Protein (GFP)-Based Overexpression Screening and Characterization of AgrC, a Receptor Protein of Quorum Sensing in Staphylococcus aureus
Lina Wang, Chunshan Quan, Baoquan Liu, Yongbin Xu, Pengchao Zhao, Wen Xiong, Shengdi Fan
International Journal of Molecular Sciences.2013; 14(9): 18470. CrossRef
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Lina Wang, Chunshan Quan, Baoquan Liu, Jianfeng Wang, Wen Xiong, Pengchao Zhao, Shengdi Fan, Gunnar F. Kaufmann
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Iso-Superoxide Dismutase in Deinococcus grandis, a UV Resistant Bacterium: Na-Rae Yun , Young Nam Lee; J. Microbiol. 2009;47(2):172-177. Published online May 2, 2009; DOI: https://doi.org/10.1007/s12275-008-0221-0

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Deinococcus grandis possesses two types of superoxide dismutase (SOD, E. C. 1.15.1.1.) that show distinct electrophoretic behavior, one that migrates slowly and the other that migrates rapidly (SOD-1 and SOD-2, respectively). In this study, SOD-1 was uniformly and abundantly detected, regardless of growth phase, whereas SOD-2 was not detected during early growth, but was detectable from the exponential growth phase. In addition, a substantial increase in SOD-2 was observed in cells that were treated with potassium superoxide or UV, which suggests that SOD-2 is an inducible protein produced in response to stressful environments. Insensitivity of SOD-1 to both H2O2 and cyanide treatment suggests that SOD-1 is MnSOD. However, SOD-2 would be FeSOD, since it lost activity in response to H2O2 treatment, but not to cyanide. Localization studies of D. grandis iso-SODs in sucrose-shocked cells suggest that SOD-1 is a membrane-associated enzyme, whereas SOD-2 is a cytosolic enzyme. In conclusion, SOD-1 seems to be an essential constitutive enzyme for viability and SOD-2 appears to be an inducible enzyme that is probably critical for survival upon UV irradiation and oxidative stress.

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Journal Article

Proteomic Analysis of Outer Membrane Proteins from Acinetobacter baumannii DU202 in Tetracycline Stress Condition: Sung-Ho Yun , Chi-Won Choi , Soon-Ho Park , Je Chul Lee , Sun-Hee Leem , Jong-Soon Choi , Soohyun Kim , Seung Il Kim; J. Microbiol. 2008;46(6):720-727. Published online December 24, 2008; DOI: https://doi.org/10.1007/s12275-008-0202-3

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Acinetobacter baumannii readily developed antimicrobial resistance to clinically available antibiotics. A. baumannii DU202 is a multi-drug resistant strain, and is highly resistant to tetracycline (MIC>1,024μg/ml). The surface proteome of A. baumannii DU202 in response to the sub-minimal inhibitory concentration (subMIC) of tetracycline was analyzed by 2-DE/MS-MS and 1-DE/LC/MS-MS to understand the pathways that form barriers for tetracycline. Membrane expression of major outer membrane proteins (Omps) was significantly decreased in response to the subMIC of tetracycline. These Omps with sizes of 38, 32, 28, and 21 kDa were identified as OmpA38, OmpA32, CarO, and OmpW, respectively. However, transcription level of these Omps was not significantly changed. 1-DE/LC/MS-MS analysis of secreted proteins showed that OmpA38, CarO, OmpW, and other Omps were increasingly secreted at tetracycline condition. This result suggests that A. baumannii actively regulates the membrane expression and the secretion of Omps to overcome antibiotic stress condition.

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Journal of Proteome Research.2011; 10(2): 459. CrossRef
Proteomics Analysis of Embryo and Endosperm from Mature Common Buckwheat Seeds
Abu Hena Mostafa Kamal, Ill-Dong Jang, Da-Eun Kim, Tatsuro Suzuki, Keun-Yook Chung, Jong-Soon Choi, Moon-Soon Lee, Cheol-Ho Park, Sang-Un Park, Seong Hee Lee, Heon Sang Jeong, Sun-Hee Woo
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Acinetobacter baumannii Secretes Cytotoxic Outer Membrane Protein A via Outer Membrane Vesicles
Jong Sook Jin, Sang-Oh Kwon, Dong Chan Moon, Mamata Gurung, Jung Hwa Lee, Seung Il Kim, Je Chul Lee, Stefan Bereswill
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Analysis of cytoplasmic membrane proteome of Streptococcus pneumoniae by shotgun proteomic approach
Chi-Won Choi, Sung-Ho Yun, Sang-Oh Kwon, Sun-Hee Leem, Jong-Soon Choi, Chi-Young Yun, Seung Il Kim
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Acinetobacter baumannii Increases Tolerance to Antibiotics in Response to Monovalent Cations
M. Indriati Hood, Anna C. Jacobs, Khalid Sayood, Paul M. Dunman, Eric P. Skaar
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Proteome analysis of outer membrane vesicles from a clinicalAcinetobacter baumanniiisolate
Sang-Oh Kwon, Yong Song Gho, Je Chul Lee, Seung Il Kim
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Research Support, Non-U.S. Gov't

Anti-Tumor Activity of Acinetobacter baumannii Outer Membrane Protein A on Dendritic Cell-Based Immunotherapy against Murine Melanoma: Jun Sik Lee , Jung Wook Kim , Chul Hee Choi , Won Kee Lee , Hae Young Chung , Je Chul Lee; J. Microbiol. 2008;46(2):221-227. Published online June 11, 2008; DOI: https://doi.org/10.1007/s12275-008-0052-z

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Abstract PDF

Acinetobacter baumannii outer membrane protein A (AbOmpA) is a major surface protein that is an important pathogen-associated molecular pattern. Based on our previous findings that AbOmpA induced the phenotypic maturation of dendritic cells (DCs) and drove the Th1 immune response in vitro, we investigated the therapeutic efficacy of AbOmpA-pulsed DC vaccines in a murine melanoma model. The surface expression of co-stimulatory molecules (CD80 and CD86) and major histocompatibility complex class I and II molecules was higher in DCs pulsed with AbOmpA alone or with a combination of B16F10 cell lysates than that of DCs pulsed with B16F10 cell lysates. AbOmpA stimulated the maturation of murine splenic DCs in vivo. In a therapeutic model of murine melanoma, AbOmpA-pulsed DCs significantly retarded tumor growth and improved the survival of tumor-bearing mice. AbOmpA-pulsed DCs significantly enhanced CD8+, interleukin-2+ T cells and CD4+, interferon-γ+ T cells in tumor-bearing mice. These results provide evidence that AbOmpA may be therapeutically useful in adjuvant DC immunotherapy against poorly immunogenic melanoma without tumor-specific antigens.

Citations

Citations to this article as recorded by

AbOmpA in Acinetobacter baumannii: exploring virulence mechanisms of outer membrane-integrated and outer membrane vesicle-associated AbOmpA and developing anti-infective agents targeting AbOmpA
Man Hwan Oh, Md Minarul Islam, Nayeong Kim, Chul Hee Choi, Minsang Shin, Woo Shik Shin, Je Chul Lee
Journal of Biomedical Science.2025;[Epub] CrossRef
Advances of bacteria-based delivery systems for modulating tumor microenvironment
Shuping Li, Hua Yue, Shuang Wang, Xin Li, Xiaojun Wang, Peilin Guo, Guanghui Ma, Wei Wei
Advanced Drug Delivery Reviews.2022; 188: 114444. CrossRef
Host Innate Immune Responses to Acinetobacter baumannii Infection
Wangxue Chen
Frontiers in Cellular and Infection Microbiology.2020;[Epub] CrossRef
The Outer Membrane Proteins OmpA, CarO, and OprD of Acinetobacter baumannii Confer a Two-Pronged Defense in Facilitating Its Success as a Potent Human Pathogen
Siva R. Uppalapati, Abhiroop Sett, Ranjana Pathania
Frontiers in Microbiology.2020;[Epub] CrossRef
Novel Treatment of Melanoma: Combined Parasite-Derived Peptide GK-1 and Anti-Programmed Death Ligand 1 Therapy
Jesus Vera-Aguilera, Armando Perez-Torres, Diego Beltran, Cynthia Villanueva-Ramos, Mitchell Wachtel, Eduardo Moreno-Aguilera, Carlos Vera-Aguilera, Gary Ventolini, Raul Martínez-Zaguilán, Souad R. Sennoune
Cancer Biotherapy and Radiopharmaceuticals.2017; 32(2): 49. CrossRef
Functional properties of the major outer membrane protein in Stenotrophomonas maltophilia
Yih-Yuan Chen, Han-Chiang Wu, Juey-Wen Lin, Shu-Fen Weng
Journal of Microbiology.2015; 53(8): 535. CrossRef
Current advances and challenges in the development ofAcinetobactervaccines
Wangxue Chen
Human Vaccines & Immunotherapeutics.2015; 11(10): 2495. CrossRef
The Synthetic Parasite-Derived Peptide GK1 Increases Survival in a Preclinical Mouse Melanoma Model
Armando Pérez-Torres, Jesús Vera-Aguilera, Juan Carlos Hernaiz-Leonardo, Eduardo Moreno-Aguilera, Diego Monteverde-Suarez, Carlos Vera-Aguilera, Daniel Estrada-Bárcenas
Cancer Biotherapy and Radiopharmaceuticals.2013; 28(9): 682. CrossRef
Inhibitory effect of live-attenuated Listeria Monocytogenes-based vaccines expressing MIA gene on malignant melanoma
Yue Qian, Na Zhang, Ping Jiang, Siyuan Chen, Shujuan Chu, Firas Hamze, Yan Wu, Qin Luo, Aiping Feng
Journal of Huazhong University of Science and Technology [Medical Sciences].2012; 32(4): 591. CrossRef
Deoxypodophyllotoxin Induces a Th1 Response and Enhances the Antitumor Efficacy of a Dendritic Cell-based Vaccine
Jun Sik Lee, Dae Hyun Kim, Chang-Min Lee, Tae Kwun Ha, Kyung Tae Noh, Jin Wook Park, Deok Rim Heo, Kwang Hee Son, In Duk Jung, Eun Kyung Lee, Yong Kyoo Shin, Soon-Cheol Ahn, Yeong-Min Park
Immune Network.2011; 11(1): 79. CrossRef
Immunostimulatory Activity of Dendritic cells pulsed with carbonic anhydrase IX and Acinetobacter baumannii outer membrane protein A
Bo Ra Kim, Eun Kyoung Yang, Sun Hee Kim, Dong Chan Moon, Hwa Jung Kim, Je Chul Lee, Duk Yoon Kim
The Journal of Microbiology.2011; 49(1): 115. CrossRef
Generation of anti-tumour immune response using dendritic cells pulsed with carbonic anhydrase IX-Acinetobacter baumanniiouter membrane protein A fusion proteins against renal cell carcinoma
B-R Kim, E-K Yang, D-Y Kim, S-H Kim, D-C Moon, J-H Lee, H-J Kim, J-C Lee
Clinical and Experimental Immunology.2011; 167(1): 73. CrossRef
The Acinetobacter baumannii 19606 OmpA Protein Plays a Role in Biofilm Formation on Abiotic Surfaces and in the Interaction of This Pathogen with Eukaryotic Cells
Jennifer A. Gaddy, Andrew P. Tomaras, Luis A. Actis
Infection and Immunity.2009; 77(8): 3150. CrossRef

Journal Articles

Outer Membrane Protein H for Protective Immunity Against Pasteurella multocida: Jeongmin Lee , Young Bong Kim , Moosik Kwon; J. Microbiol. 2007;45(2):179-184.; DOI: https://doi.org/2514 [pii]

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Abstract PDF: Pasteurella multocida, a Gram-negative facultative anaerobic bacterium, is a causative animal pathogen in porcine atrophic rhinitis and avian fowl cholera. For the development of recombinant subunit vaccine against P. multocida, we cloned and analyzed the gene for outer membrane protein H (ompH) from a native strain of Pasteurella multocida in Korea. The OmpH had significant similarity in both primary and secondary structure with those of other serotypes. The full-length, and three short fragments of ompH were expressed in E. coli and the recombinant OmpH proteins were purified, respectively. The recombinant OmpH proteins were antigenic and detectable with antisera produced by either immunization of commercial vaccine for respiratory disease or formalin-killed cell. Antibodies raised against the full-length OmpH provided strong protection against P. multocida, however, three short fragments of recombinant OmpHs, respectively, showed slightly lower protection in mice challenge. The recombinant OmpH might be a useful vaccine candidate antigen for P. multocida.

Nucleocapsid Amino Acids 211 to 254, in Particular, Tetrad Glutamines, are Essential for the Interaction Between the Nucleocapsid and Membrane Proteins of SARS-Associated Coronavirus: Xiaonan Fang , Lin-Bai Ye , Yijuan Zhang , Baozong Li , Shanshan Li , Lingbao Kong , Yuhua Wang , Hong Zheng , Wei Wang , Zhenghui Wu; J. Microbiol. 2006;44(5):577-580.; DOI: https://doi.org/2437 [pii]

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Abstract PDF: GST pull-down assays were used to characterize the SARS-CoV membrane (M) and nucleocapsid (N) interaction, and it was found that the amino acids 211-254 of N protein were essential for this interaction. When tetrad glutamines (Q) were replaced with glutamic acids (E) at positions of 240-243 of the N protein, the interaction was disrupted.

Immunization with Major Outer Membrane Protein of Vibrio vulnificus Elicits Protective Antibodies in a Murine Model: Cho-Rok Jung , Min-Jung Park , Moon-Soo Heo; J. Microbiol. 2005;43(5):437-442.; DOI: https://doi.org/2278 [pii]

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Abstract PDF: Sera from rabbits were infected with Vibrio vulnificus containing an antibody against major outer membrane protein (MOMP). MOMP of V. vulnificus ATCC 27562 were isolated and purified by Sarkosyl and TritonX-100 dual treatment. Molecular size of MOMP was identified as 36-kDa on 13% SDS-PAGE. The sequence of the first 26 amino acid residues from the N-terminal end of the protein is AELYNQDGTSLDMGGRAEARLSMKDG , which is a perfect match with OmpU of V. vulnificus CMCP6 and YJ016. MOMP specific IgM and IgG were investigated in groups of mice. The group of mice immunized with MOMP and Alum showed higher levels of IgG2b than the group immunized with only MOMP. Vaccination with MOMP resulted in protective antibodies in the mouse infection experiment.

Research Support, Non-U.S. Gov't

Isolation and Taxonomic Characterization of a Novel Type I Methanotrophic Bacterium: Hee Gon Kim , Gui Hwan Han , Chi-Yong Eom , Si Wouk Kim; J. Microbiol. 2008;46(1):45-50.; DOI: https://doi.org/10.1007/s12275-008-0017-2

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A methane-oxidizing bacterium was isolated from the effluent of manure and its molecular and biochemical properties were characterized. The isolate was aerobic, Gram-negative, and non-motile. The organism had a type I intracytoplasmic membrane structure and granular inclusion bodies. The outer cell wall surface (S-layers) was tightly packed with cup-shaped structures. Colonies were light yellow on nitrate mineral salt agar medium. In addition, the organism was catalase and oxidase positive. The isolate used the ribulose monophosphate (RuMP) pathway for carbon assimilation, and was able to utilize methane and methanol as a sole carbon and energy source, however, it could not utilize any other organic compounds that were tested. The cells grew well in a mixture of methane and air (methane:air=1:1, v/v) in a compulsory circulation diffusion system, and when grown under those conditions, the optimum pH was approximately 7.0 and the optimal temperature was 30°C. In addition, the specific growth rate and generation time were 0.13 per h and 5.43 h, respectively, when grown under the optimum conditions. The major ubiquinone was Q-8, and the G+C mol% of the DNA was 55.3. Phylogenetic analyses based on the 16S rRNA gene sequence comparisons showed that this bacterium belongs to a group of type I methanotrophs, and that it is most closely related to Methylomicrobium, with a sequence similarity of 99%. Therefore, the isolate was named Methylomicrobium sp. HG-1.

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Cultivation of Important Methanotrophs From Indian Rice Fields
Monali C. Rahalkar, Kumal Khatri, Pranitha Pandit, Rahul A. Bahulikar, Jyoti A. Mohite
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Bacterial community shift and antibiotics resistant genes analysis in response to biodegradation of oxytetracycline in dual graphene modified bioelectrode microbial fuel cell
Junfeng Chen, Yuewei Yang, Yanyan Liu, Meizhen Tang, Renjun Wang, Yuping Tian, Chuanxing Jia
Bioresource Technology.2019; 276: 236. CrossRef
Methane oxidation in industrial biogas plants—Insights in a novel methanotrophic environment evidenced by pmoA gene analyses and stable isotope labelling studies
Tobias May, Daniela Polag, Frank Keppler, Markus Greule, Liane Müller, Helmut König
Journal of Biotechnology.2018; 270: 77. CrossRef
Influence of nutrients on oxidation of low level methane by mixed methanotrophic consortia
Obulisamy Parthiba Karthikeyan, Karthigeyan Chidambarampadmavathy, Saravanan Nadarajan, Kirsten Heimann
Environmental Science and Pollution Research.2016; 23(5): 4346. CrossRef
Review of Sustainable Methane Mitigation and Biopolymer Production
O. P. Karthikeyan, K. Chidambarampadmavathy, Samuel Cirés, Kirsten Heimann
Critical Reviews in Environmental Science and Technology.2015; 45(15): 1579. CrossRef
Optimization of lab scale methanol production by Methylosinus trichosporium OB3b
Hee Gon Kim, Gui Hwan Han, Si Wouk Kim
Biotechnology and Bioprocess Engineering.2010; 15(3): 476. CrossRef
Comparative evaluation of antioxidant, nitrite scavenging, and antitumor effects of Antrodia camphorata extract
Wol-Suk Cha, Ji-Lu Ding, DuBok Choi
Biotechnology and Bioprocess Engineering.2009; 14(2): 232. CrossRef

Adsorption of Pb^2+ in the components of bacterial cell membrane: Kim , Mal Nam; J. Microbiol. 1995;33(4):278-282.

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Abstract PDF: S. epidermidis cell was fractionated into cell wall, cell membrane and cytoplasm. The cell membrane adsorbed the most abundant Pb^2+ per unit dry weight of the three fractions tested. Adsorption behavior of Pb^2+ in lipid and protein, which are the main components of the cell membrane, indicated that phosphatidylethanolamine and phosphatidylinositol having phosphoryl group and gangliosides containing carboxyl groups adsorbed much more Pb^2+ than triglycerides lacking any chargeable functional groups. Protein purified from cell membrane adsorbed larger amount of Pb^2+ than total native cell membrane or cell membrane lipid.

Analysis of fusogenic activity of autographa californica nuclear polyhedrosis virus (AcNPV) gp64 envelope glycoprotein: Kim, Hee Jin , Yang, Jai Myung; J. Microbiol. 1996;34(1):7-14.

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Abstract PDF: The baculovirus gp64 glycoprotein is a major component of the envelope of budded virus (BV) and has been shown that it plays an essential role in the infection process, especially virus-cell membrane fusion. We have cloned Autographa californica Nuclear Polyhedrosis Virus (AcNPV) gp64 protein were examined for membrane fusion activity by using a synchtium formation assay under various conditions. The optimal conditions required for inducing membrane fusion are 1) form pH 4.0 to 4.8 2) 15 min exposure of cells to acidic pH 3) at least 1㎍ of gp64 cloned plasmid DNA per 3 × 10^6 cells 4) and an exposure of cells to acidic pH at 72 h post-transfection. In order to investigate the role of hydrophobicity of the gp64 glycoprotein for the membrane fusion, the two leucine residues (amino acid position at 229 and 230) within hydrophobic region I were substituted to alanine by PCR-derived site-directed mutagenisis and the membrane fusion activity of the mutant was analysed. The gp64 glycoprotein carrying double alamine substitution mutation showed no significant difference in fusion activity. This result suggested that minor changes in hydrophobicity at the amino acid position 229 and 230 does not affect the acid-induced membrane fusion activity of the gp64 glycoprotein.

Isolation and characterization of a noval membrane-bound cytochrome C_553 from the strictly anaerobic phototroph, heliobacillus mobilis: Lee, Woo Yiel , Blankenship, Robert E. , Kim, Seung Ho; J. Microbiol. 1997;35(3):206-212.

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Abstract PDF: Heliobacillus mobilis is a strictly anaerobic Gram-positive bacterium which contains a primitive Photosystem I-type reaction center. The membrane-bound cytochrome c_553 from the heliobacterium suggested to be the immediate electron donor to the photooxidized pigment (P798+) has been isolated and characterized. The heme protein was visualized as a major component with an apparent molecular size of 17kDa in TMBZ-staining analysis of the membrane preparation and showed characteristic α (552.5 nm), β (522nm), and Soret absorption (416 nm) peaks of a typical reduced c-type cytochrome in the partially purified sample. The internal 43 amino acid sequence of the electron donor was obtained by chemical agent and protease treatments followed by N-terminal sequencing of the resulting fragments. The internal sequence carries lots of lysine residues and a Cys-X-X-Cys-His sequence motif which are the characteristics of typical c-type cytochromes. The analysis of the sequence by FAST or FASTA program, however, did not show any significant similarity to other known heme proteins.

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.

Energy Status of Neurospora crassa Mutant nap in Relation to Accumulation of Carotenoids: Tatyana A. Belozerskaya^ , Tatyana V. Potapova^† , Elena P. Isakova , Eugene I. Shurubor , Ludmila V. Savel'eva , Renata A. Zvyagilskaya; J. Microbiol. 2003;41(1):41-45.

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Abstract PDF: N. crassa mutant strain nap showed reduced growth rate, decreased electric membrane potential, and elevated intracellular ATP content in comparison to the wild type. Blue light induced a hyperpolarization of the membrane potential in both strains. The analysis of oxidative and phosphorylation activities of mitochondria isolated from the two strains has revealed that nap utilized more efficient oxidative pathways. The higher intracellular ATP content in the nap was presumably due to impaired transport systems of the plasma membrane, and to a lesser extent to the functioning of the fully competent respiratory chain. The excess ATP possibly accounts for carotenoid accumulation in the mutant.

High Prevalence of the China 1 Strain of Epstein-Barr Virus in Korea as Determined by Sequence Polymorphisms in the Carboxy-Terminal Tail of LMP1: Sung-Gyu Cho , Won-Keun Lee; J. Microbiol. 2003;41(2):129-136.

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Abstract PDF: The Epstein-Barr virus (EBV)-encoded latent membrane protein 1 (LMP1) exhibits considerable sequence heterogeneity among EBV isolates. Seven distinct EBV strains have been defined based on sequence polymorphisms in the LMP1 gene, which are designated China 1, China 2, China 3, Alaskan, Mediterranean, NC, and the B95-8 strains. In this study, we analyzed a 30-bp deletion and sequence variations in the carboxy-terminal region of the LMP1 gene in 12 EBV isolates from spontaneous lymphoblastoid cell lines derived from individuals with non-EBV associated cancers in Korea. Eleven of the 12 isolates showed a 30-bp deletion spanning LMP1 amino acids 342 to 353, suggesting a high prevalence of the LMP1 30-bp deletion variant among EBV isolates in Korea. In addition, all 12 isolates had a 15-bp common deletion in the 33-bp repeat region and multiple base-pair changes relative to the prototype B95-8 EBV strain along with variations in the number of the 33-bp repeats. The bp changes at positions 168746, 168694, 168687, 168395, 168357, 168355, 168631, 168320, 168308, 168295, and 168225 were highly conserved among the isolates. Comparative analysis of sequence change patterns in the LMP1 carboxy-terminal coding region identified nine 30-bp deletion variants as China 1, two deletion variants as a possible interstrain between the Alaskan and China 1 strains, and a single undeleted variant as a possible variant of the Alaskan strain. These results suggest the predominance of the China 1 EBV strain in the Korean population.

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