Journal of Microbiology

Journal Article

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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Abstract: 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.

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.

Citations

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Reduced Gut Bacterial Diversity in Early Life Predicts Feeding Intolerance in Preterm Neonates
Maria Di Chiara, Alessandro Lazzaro, Daniela Scribano, Maria Trancassini, Valeria Pietropaolo, Michele Sonnessa, Chiara De Luca, Rita Prota, Elisa Onestà, Gianluigi Laccetta, Gianluca Terrin
Tropical Medicine and Infectious Disease.2024; 9(8): 174. CrossRef
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
Frontiers in Endocrinology.2024;[Epub] CrossRef
Dynamics alteration of the gut microbiota and faecal metabolomes in very low or extremely low birth weight infants: a Chinese single-center, prospective cohort study
Ling Liu, Chaohong Chen, YeShan Li, Dang Ao, Jiayuan Wu, Nali Cai, Wen Li, Min Xiang
Frontiers in Microbiology.2024;[Epub] CrossRef
Metabolic and fecal microbial changes in adult fetal growth restricted mice
Stephanie P. Gilley, Miguel A. Zarate, Lijun Zheng, Purevsuren Jambal, Deaunabah N. Yazza, Sree V. Chintapalli, Paul S. MacLean, Clyde J. Wright, Paul J. Rozance, Kartik Shankar
Pediatric Research.2024; 95(3): 647. CrossRef
A digital twin of the infant microbiome to predict neurodevelopmental deficits
Nicholas Sizemore, Kaitlyn Oliphant, Ruolin Zheng, Camilia R. Martin, Erika C. Claud, Ishanu Chattopadhyay
Science Advances.2024;[Epub] CrossRef
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
Pediatric Research.2024; 95(1): 135. CrossRef
Novel scoring system for early diagnosis of necrotizing enterocolitis: integrating clinical and laboratory data with urinary caveolin-1 levels
Brigitta I.R.V. Corebima, Rinawati Rohsiswatmo, Dewi Santosaningsih, Wisnu Barlianto, Kusworini Handono
Archives of Medical Science.2023; 20(2): 444. CrossRef
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
Nutrients.2023; 15(22): 4849. CrossRef
Characteristics of Gut Microbiota in Small for Gestational Age Infants with Very Low Birth Weight
Hung-Yang Chang, Jen-Shiu Chiang Chiau, Jui-Hsing Chang, Chyong-Hsin Hsu, Chia-Ying Lin, Mary Hsin-Ju Ko, Hung-Chang Lee
Nutrients.2022; 14(23): 5158. CrossRef
Compositional Differences of Meconium Microbiomes of Preterm and Term Infants, and Infants That Developed Necrotizing Enterocolitis or Feeding Intolerance
Hyun Mi Kang, Sol Kim, Seok Hwang-Bo, In Hyuk Yoo, Yu-Mi Seo, Moon Yeon Oh, Soo-Ah Im, Young-Ah Youn
Pathogens.2022; 12(1): 55. CrossRef

Journal Articles

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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Abstract

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.

Citations

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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

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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Abstract

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.

Citations

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Siltation of check dams alters microbial communities and thus limits organic carbon mineralization
Xiaojun Liu, Yi Zhang, Peng Li, Lie Xiao
Soil and Tillage Research.2024; 236: 105949. CrossRef
Tree species mixing enhances rhizosphere soil organic carbon mineralization of conifers in subtropical plantations
Wen-Qing Li, Zi-Jun Wu, Ying-Ying Zong, G. Geoff Wang, Fu-Sheng Chen, Yuan-Qiu Liu, Jian-Jun Li, Xiang-Min Fang
Forest Ecology and Management.2022; 516: 120238. CrossRef
Response of soil structure and crop yield to soft rock in Mu Us sandy land, China
Jian Zhang, Zhen Guo
Scientific Reports.2022;[Epub] CrossRef

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

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.

Citations

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Antiviral Activities of Ethyl Pheophorbides a and b Isolated from Aster pseudoglehnii against Influenza Viruses
Subin Park, Ji-Young Kim, Hak Cheol Kwon, Dae Sik Jang, Yoon-Jae Song
Molecules.2022; 28(1): 41. CrossRef
Antiviral Activities of Quercetin and Isoquercitrin Against Human Herpesviruses
Chae Hyun Kim, Jung-Eun Kim, Yoon-Jae Song
Molecules.2020; 25(10): 2379. CrossRef
Human Cytomegalovirus IE2 86 kDa Protein Induces STING Degradation and Inhibits cGAMP-Mediated IFN-β Induction
Jung-Eun Kim, Young-Eui Kim, Mark F. Stinski, Jin-Hyun Ahn, Yoon-Jae Song
Frontiers in Microbiology.2017;[Epub] CrossRef
Primary lymphocyte infection models for KSHV and its putative tumorigenesis mechanisms in B cell lymphomas
Sangmin Kang, Jinjong Myoung
Journal of Microbiology.2017; 55(5): 319. CrossRef
Inhibition of human cytomegalovirus immediate-early gene expression and replication by the ethyl acetate (EtOAc) fraction of Elaeocarpus sylvestris in vitro
Sohee Bae, Se Chan Kang, Yoon-Jae Song
BMC Complementary and Alternative Medicine.2017;[Epub] CrossRef
Inhibition of varicella-zoster virus replication by an ethanol extract of Lysimachia mauritiana
Sohee Bae, Yoon-Jae Song
Molecular Medicine Reports.2017; 15(6): 3847. CrossRef

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.

Citations

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σ P -NagA-L1/L2 Regulatory Circuit Involved in ΔompA 299-356 -Mediated Increase in β-Lactam Susceptibility in Stenotrophomonas maltophilia
Li-Hua Li, Cheng-Mu Wu, Chia-Lun Chang, Hsin-Hui Huang, Chao-Jung Wu, Tsuey-Ching Yang, Silvia T. Cardona
Microbiology Spectrum.2022;[Epub] CrossRef
Advances in the Microbiology of Stenotrophomonas maltophilia
Joanna S. Brooke
Clinical Microbiology Reviews.2021;[Epub] CrossRef
Recombinant Ax21 protein is a promising subunit vaccine candidate against Stenotrophomonas maltophilia in a murine infection model
Amal Tarek Sarhan, Mohammed Bahey-El-Din, Taha Ibrahim Zaghloul
Vaccine.2021; 39(32): 4471. CrossRef
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
PLOS ONE.2019; 14(4): e0214596. CrossRef
The Major Outer Membrane Protein MopB Is Required for Twitching Movement and Affects Biofilm Formation and Virulence in Two Xylella fastidiosa strains
Hongyu Chen, Prem P. Kandel, Luisa F. Cruz, Paul A. Cobine, Leonardo De La Fuente
Molecular Plant-Microbe Interactions®.2017; 30(11): 896. CrossRef

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

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.

Citations

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Stenotrophomonas maltophilia virulence: a current view
Vladimir Mikhailovich, Rustam Heydarov, Danila Zimenkov, Igor Chebotar
Frontiers in Microbiology.2024;[Epub] CrossRef
Molecular-genetic portrait of virulence of Stenotrophomonas maltophilia
Vladimir M. Mikhailovich, Rustam N. Geydarov, Julia A. Bocharova, Igor V. Chebotar
Journal of microbiology, epidemiology and immunobiology.2023; 100(5): 380. CrossRef
p‐Aminobenzoic acid inhibits the growth of soybean pathogen Xanthomonas axonopodis pv. glycines by altering outer membrane integrity
Yong‐Hui Jiang, Ting Liu, Xin‐Chi Shi, Daniela D Herrera‐Balandrano, Mei‐Ting Xu, Su‐Yan Wang, Pedro Laborda
Pest Management Science.2023; 79(10): 4083. CrossRef
Expression and function of clpS and clpA in Xanthomonas campestris pv. campestris
Hsueh-Hsia Lo, Hsiao-Ching Chang, Chao-Tsai Liao, Yi-Min Hsiao
Antonie van Leeuwenhoek.2022; 115(5): 589. CrossRef
Outer Membrane Vesicles: Biogenesis, Functions, and Issues
Rokas Juodeikis, Simon R. Carding
Microbiology and Molecular Biology Reviews.2022;[Epub] CrossRef
Recombinant Ax21 protein is a promising subunit vaccine candidate against Stenotrophomonas maltophilia in a murine infection model
Amal Tarek Sarhan, Mohammed Bahey-El-Din, Taha Ibrahim Zaghloul
Vaccine.2021; 39(32): 4471. CrossRef
Deciphering the functions of the outer membrane porin OprBXo involved in virulence, motility, exopolysaccharide production, biofilm formation and stress tolerance in Xanthomonas oryzae pv. oryzae
Nahee Bae, Hye‐Jee Park, Hanbi Park, Minyoung Kim, Sang‐Wook Han
Molecular Plant Pathology.2018; 19(12): 2527. CrossRef
The Ax21 protein influences virulence and biofilm formation in Stenotrophomonas maltophilia
Shi-qi An, Ji-liang Tang
Archives of Microbiology.2018; 200(1): 183. CrossRef
Lsp family proteins regulate antibiotic biosynthesis in Lysobacter enzymogenes OH11
Ruping Wang, Huiyong Xu, Yangyang Zhao, Juan Zhang, Gary Y Yuen, Guoliang Qian, Fengquan Liu
AMB Express.2017;[Epub] CrossRef
Systems and synthetic biology perspective of the versatile plant-pathogenic and polysaccharide-producing bacterium Xanthomonas campestris
Sarah Schatschneider, Jessica Schneider, Jochen Blom, Fabien Létisse, Karsten Niehaus, Alexander Goesmann, Frank-Jörg Vorhölter
Microbiology.2017; 163(8): 1117. CrossRef
Functional and Proteomic Analyses Reveal That ScpBXv Is Involved in Bacterial Growth, Virulence, and Biofilm Formation in Xanthomonas campestris pv. vesicatoria
Hye-Jee Park, Sang-Wook Han
The Plant Pathology Journal.2017; 33(6): 602. CrossRef
Deciphering the Role of Tyrosine Sulfation in Xanthomonas oryzae pv. oryzae Using Shotgun Proteomic Analysis
Hye-Jee Park, Chang-Jin Park, Nahee Bae, Sang-Wook Han
The Plant Pathology Journal.2016; 32(3): 266. CrossRef
The effect of imipenem and diffusible signaling factors on the secretion of outer membrane vesicles and associated Ax21 proteins in Stenotrophomonas maltophilia
Simon Devos, Laurence Van Oudenhove, Stephan Stremersch, Wouter Van Putte, Riet De Rycke, Gonzalez Van Driessche, Jolien Vitse, Koen Raemdonck, Bart Devreese
Frontiers in Microbiology.2015;[Epub] CrossRef

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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Abstract

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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Gut Pathogens.2022;[Epub] CrossRef
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Suthathip Kittisenachai, Panadda Rojpibulstit, Ratha-Korn Vilaichone, Pornpen Gamnarai, Narumon Phaonakrop, Nuchanart Suealek, Denise Monack
Infection and Immunity.2021;[Epub] CrossRef
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Agnieszka Maszewska, Magdalena Moryl, Junli Wu, Bin Liu, Lu Feng, Antoni Rozalski
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Proteomic Applications in Antimicrobial Resistance and Clinical Microbiology Studies

Ehsaneh Khodadadi, Elham Zeinalzadeh, Sepehr Taghizadeh, Bahareh Mehramouz, Fadhil S Kamounah, Ehsan Khodadadi, Khudaverdi Ganbarov, Bahman Yousefi, Milad Bastami, Hossein Samadi Kafil
Infection and Drug Resistance.2020; Volume 13: 1785. CrossRef
Protective effects of Helicobacter pylori membrane vesicles against stress and antimicrobial agents
Benjamin Oliver Murray, Robin Andrew Dawson, Lolwah Mohammad Alsharaf, Jody Anne Winter
Microbiology .2020; 166(8): 751. CrossRef
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Bo Peng, Hui Li, Xuanxian Peng
Expert Review of Proteomics.2019; 16(10): 829. CrossRef
Helicobacter pylori eradication rates with concomitant and tailored therapy based on 23S rRNA point mutation: A multicenter randomized controlled trial
Sungmoon Ong, Sung Eun Kim, Ji Hyun Kim, Nam Hee Yi, Tae Young Kim, Kyoungwon Jung, Moo In Park, Hwoon‐Yong Jung
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Resistance mechanisms ofHelicobacter pyloriand its dual target precise therapy
Yuehua Gong, Yuan Yuan
Critical Reviews in Microbiology.2018; 44(3): 371. CrossRef
The Bifunctional Enzyme SpoT Is Involved in the Clarithromycin Tolerance of Helicobacter pylori by Upregulating the Transporters HP0939, HP1017, HP0497, and HP0471
Xiwen Geng, Wen Li, Zhenghong Chen, Sizhe Gao, Wei Hong, Xiaoran Ge, Guihua Hou, Zhekai Hu, Yabin Zhou, Beini Zeng, Wenjuan Li, Jihui Jia, Yundong Sun
Antimicrobial Agents and Chemotherapy.2017;[Epub] CrossRef
Application of proteomics to the study ofHelicobacter pyloriand implications for the clinic
Giulia Bernardini, Natale Figura, Antonio Ponzetto, Barbara Marzocchi, Annalisa Santucci
Expert Review of Proteomics.2017; 14(6): 477. CrossRef
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Primary Antibiotic Resistance of Helicobacter pylori in China
Yi Hu, Yin Zhu, Nong-hua Lu
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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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Abstract: 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.

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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Abstract: 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.

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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Abstract

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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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: 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.

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: 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.

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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Abstract: 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.

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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Abstract: 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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