Skip Navigation
Skip to contents

Journal of Microbiology : Journal of Microbiology

OPEN ACCESS
SEARCH
Search

Search

Page Path
HOME > Search
8 "Gram-negative"
Filter
Filter
Article category
Keywords
Publication year
Authors
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
  • 55 View
  • 0 Download
AbstractAbstract
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.
Journal Articles
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
  • 47 View
  • 0 Download
  • 4 Web of Science
  • 3 Crossref
AbstractAbstract
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

Citations to this article as recorded by  
  • 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
Rapid determination of carbapenem resistance by low-cost colorimetric methods: Propidium Iodide and alamar blue staining
Jiyoon Choi , Jiwon Baek , Daehyuk Kweon , Kwan Soo Ko , Hyunjin Yoon
J. Microbiol. 2020;58(5):415-421.   Published online March 28, 2020
DOI: https://doi.org/10.1007/s12275-020-9549-x
  • 53 View
  • 0 Download
  • 4 Web of Science
  • 4 Crossref
AbstractAbstract
Carbapenems are a class of β-lactam antibiotics with a broad antimicrobial activity spectrum. Owing to their sturdy structures resistant to most β-lactamases, they have been regarded as one of the last-resort antibiotics for combating multidrugresistant bacterial infections. However, the emergence of carbapenem resistance increases predominantly in nosocomial pathogens. To prevent spread of carbapenem resistance in early stages, it is imperative to develop rapid diagnostic tests that will substantially reduce the time and cost in determining carbapenem resistance. Thus, we devised a staining-based diagnostic method applicable to three different Gram-negative pathogens of Acinetobacter baumannii, Escherichia coli, and Klebsiella pneumoniae, all with the high potential to develop carbapenem resistance. Regardless of the resistance mechanisms presented by bacterial species and strains, double staining with propidium iodide (PI) and alamar blue (AB) identified resistant bacteria with an average sensitivity of 95.35%, 7 h after imipenem treatments in 343 clinical isolates. Among the three species tested, A. baumannii showed the highest diagnostic sensitivity of 98.46%. The PI and ABmediated staining method could be a promising diagnostic
method
with high-throughput efficacy and low cost.

Citations

Citations to this article as recorded by  
  • Cananga oil inhibits Salmonella infection by mediating the homeostasis of purine metabolism and the TCA cycle
    Xinyu Yao, Jinying Gao, Lanqiao Wang, Xiaoning Hou, Litao Ge, Xinxin Qin, Jiazhang Qiu, Xuming Deng, Wei Li, Jianfeng Wang
    Journal of Ethnopharmacology.2024; 325: 117864.     CrossRef
  • Gold nanoparticle-DNA aptamer-assisted delivery of antimicrobial peptide effectively inhibits Acinetobacter baumannii infection in mice
    Jaeyeong Park, Eunkyoung Shin, Ji-Hyun Yeom, Younkyung Choi, Minju Joo, Minho Lee, Je Hyeong Kim, Jeehyeon Bae, Kangseok Lee
    Journal of Microbiology.2022; 60(1): 128.     CrossRef
  • Rapid Determination of Antibiotic Resistance in Klebsiella pneumoniae by a Novel Antibiotic Susceptibility Testing Method Using SYBR Green I and Propidium Iodide Double Staining
    Yabin Zhang, Weihua Fan, Chunhong Shao, Jiajia Wang, Yan Jin, Jing Shao, Ying Zhang, Yong Wang
    Frontiers in Microbiology.2021;[Epub]     CrossRef
  • Optical-Switch-Enabled Microfluidics for Sensitive Multichannel Colorimetric Analysis
    Jiukai Tang, Xiaobao Cao, Guangyu Qiu, Andrew deMello, Jing Wang
    Analytical Chemistry.2021; 93(17): 6784.     CrossRef
PROTOCOL] Applications of different solvents and conditions for differential extraction of lipopolysaccharide in Gram-negative bacteria
Mai Phuong Nguyen , Le Viet Ha Tran , Hyun Namgoong , Yong-Hak Kim
J. Microbiol. 2019;57(8):644-654.   Published online May 23, 2019
DOI: https://doi.org/10.1007/s12275-019-9116-5
  • 50 View
  • 0 Download
  • 6 Web of Science
  • 6 Crossref
AbstractAbstract
Lipopolysaccharide (LPS) is one of the major components in the outer membrane of Gram-negative bacteria. However, its heterogeneity and variability in different bacteria and differentiation conditions make it difficult to extract all of the structural variants. We designed a solution to improve quality and biological activity of LPS extracted from various bacteria with different types of LPS, as compared to conventional
methods
. We introduced a quality index as a simple measure of LPS purity in terms of a degree of polysaccharide content detected by absorbance at 204 nm. Further experiments using gel electrophoresis, endotoxin test, and macrophage activation test were performed to evaluate the performance and reliability of a proposed ‘T-sol’ method and the biological effectiveness and character of the LPS products. We presented that the T-sol method had differential effects on extraction of a RAW 264.7 cell-activating LPS, which was effective in the macrophage activation with similar effects in stimulating the production of TNF-alpha. In conclusion, the T-sol method provides a simple way to improve quality and biological activity of LPS with high yield.

Citations

Citations to this article as recorded by  
  • Effective Modalities of Periodontitis Induction in Rat Model
    Fazle Khuda, Badiah Baharin, Nur Najmi Mohamad Anuar, Bellen Sharon Fred Satimin, Nurrul Shaqinah Nasruddin
    Journal of Veterinary Dentistry.2024; 41(1): 49.     CrossRef
  • LPS-Induced Mortality in Zebrafish: Preliminary Characterisation of Common Fish Pathogens
    Rafaela A. Santos, Cláudia Cardoso, Neide Pedrosa, Gabriela Gonçalves, Jorge Matinha-Cardoso, Filipe Coutinho, António P. Carvalho, Paula Tamagnini, Aires Oliva-Teles, Paulo Oliveira, Cláudia R. Serra
    Microorganisms.2023; 11(9): 2205.     CrossRef
  • Heterogeneity of Lipopolysaccharide as Source of Variability in Bioassays and LPS-Binding Proteins as Remedy
    Alexandra C. Fux, Cristiane Casonato Melo, Sara Michelini, Benjamin J. Swartzwelter, Andreas Neusch, Paola Italiani, Martin Himly
    International Journal of Molecular Sciences.2023; 24(9): 8395.     CrossRef
  • Identification workflow of endotoxins by pyrolysis–gas chromatography–mass spectrometry based on a database and chemometrics
    Jackie Jackie, Chun Kiang Chua, Norrapat Shih, Sam Fong Yau Li
    Journal of Analytical and Applied Pyrolysis.2022; 165: 105547.     CrossRef
  • Exploring the Lipidome: Current Lipid Extraction Techniques for Mass Spectrometry Analysis
    Julian Aldana, Adriana Romero-Otero, Mónica P. Cala
    Metabolites.2020; 10(6): 231.     CrossRef
  • The outer membrane glycolipids of bacteria from cold environments: isolation, characterization, and biological activity
    Angela Casillo, Ermenegilda Parrilli, Maria Luisa Tutino, Maria Michela Corsaro
    FEMS Microbiology Ecology.2019;[Epub]     CrossRef
Review
MINIREVIEW] Molecular architecture of the bacterial tripartite multidrug efflux pump focusing on the adaptor bridging model
Saemee Song , Jin-Sik Kim , Kangseok Lee , Nam-Chul Ha
J. Microbiol. 2015;53(6):355-364.   Published online May 30, 2015
DOI: https://doi.org/10.1007/s12275-015-5248-4
  • 47 View
  • 0 Download
  • 9 Crossref
AbstractAbstract
Gram-negative bacteria expel a wide range of toxic substances through tripartite drug efflux pumps consisting of an inner membrane transporter, an outer membrane channel protein, and a periplasmic adaptor protein. These pumps form tripartite assemblies which can span the entire cell envelope, including the inner and outer membranes. There have been controversial findings regarding the assembly of the individual components in tripartite drug efflux pumps. Recent structural and functional studies have advanced our understanding of the assembly and working mechanisms of the pumps. Here, we re-evaluate the assembly models based on recent structural and functional studies. In particular, this study focuses on the ‘adaptor bridging model’, highlighting the intermeshing cogwheel-like interactions between the tip regions of the outer membrane channel protein and the periplasmic adaptor protein in the hexameric assembly.

Citations

Citations to this article as recorded by  
  • Structural Features and Energetics of the Periplasmic Entrance Opening of the Outer Membrane Channel TolC Revealed by Molecular Dynamics Simulation and Markov State Model Analysis
    Jingwei Weng, Wenning Wang
    Journal of Chemical Information and Modeling.2019; 59(5): 2359.     CrossRef
  • Recent paradigm shift in the assembly of bacterial tripartite efflux pumps and the type I secretion system
    Inseong Jo, Jin-Sik Kim, Yongbin Xu, Jaekyung Hyun, Kangseok Lee, Nam-Chul Ha
    Journal of Microbiology.2019; 57(3): 185.     CrossRef
  • Antibiotic Hybrids: the Next Generation of Agents and Adjuvants against Gram-Negative Pathogens?
    Ronald Domalaon, Temilolu Idowu, George G. Zhanel, Frank Schweizer
    Clinical Microbiology Reviews.2018;[Epub]     CrossRef
  • Genetic identification of factors for extracellular cellulose accumulation in the thermophilic cyanobacterium Thermosynechococcus vulcanus: proposal of a novel tripartite secretion system
    Kaisei Maeda, Jyunya Tamura, Yukiko Okuda, Rei Narikawa, Takafumi Midorikawa, Masahiko Ikeuchi
    Molecular Microbiology.2018; 109(1): 121.     CrossRef
  • Switch Loop Flexibility Affects Substrate Transport of the AcrB Efflux Pump
    Reinke T. Müller, Timothy Travers, Hi-jea Cha, Joshua L. Phillips, S. Gnanakaran, Klaas M. Pos
    Journal of Molecular Biology.2017; 429(24): 3863.     CrossRef
  • Molecular Rationale behind the Differential Substrate Specificity of Bacterial RND Multi-Drug Transporters
    Venkata Krishnan Ramaswamy, Attilio V. Vargiu, Giuliano Malloci, Jürg Dreier, Paolo Ruggerone
    Scientific Reports.2017;[Epub]     CrossRef
  • Structure of the MacAB–TolC ABC-type tripartite multidrug efflux pump
    Anthony W. P. Fitzpatrick, Salomé Llabrés, Arthur Neuberger, James N. Blaza, Xiao-Chen Bai, Ui Okada, Satoshi Murakami, Hendrik W. van Veen, Ulrich Zachariae, Sjors H. W. Scheres, Ben F. Luisi, Dijun Du
    Nature Microbiology.2017;[Epub]     CrossRef
  • Structural Basis for the Serratia marcescens Lipase Secretion System: Crystal Structures of the Membrane Fusion Protein and Nucleotide-Binding Domain
    Daichi Murata, Hiroyuki Okano, Clement Angkawidjaja, Masato Akutsu, Shun-ichi Tanaka, Kenyu Kitahara, Takuya Yoshizawa, Hiroyoshi Matsumura, Yuji Kado, Eiichi Mizohata, Tsuyoshi Inoue, Satoshi Sano, Yuichi Koga, Shigenori Kanaya, Kazufumi Takano
    Biochemistry.2017; 56(47): 6281.     CrossRef
  • The Crystal Structure of the YknZ Extracellular Domain of ABC Transporter YknWXYZ from Bacillus amyloliquefaciens
    Yongbin Xu, Jianyun Guo, Lulu Wang, Rui Jiang, Xiaoling Jin, Jing Liu, Shengdi Fan, Chun-Shan Quan, Nam-Chul Ha, Bostjan Kobe
    PLOS ONE.2016; 11(5): e0155846.     CrossRef
Journal Articles
Lysobacter tyrosinelyticus sp. nov. isolated from Gyeryongsan national park soil
Juan Du , Hina Singh , Hien T.T. Ngo , KyungHwa Won , Ki-Young Kim , Tae-Hoo Yi
J. Microbiol. 2015;53(6):365-370.   Published online May 30, 2015
DOI: https://doi.org/10.1007/s12275-015-4729-9
  • 52 View
  • 0 Download
  • 7 Crossref
AbstractAbstract
A novel Gram-negative, rod-shaped (0.2-0.5 um x 1.5-2.5 um), aerobic, non-motile bacterium was isolated from Gyeryongsan national park soil, Republic of Korea. The novel isolate was designated as THG-DN8.2T. The strain grows optimally at 28oC, at pH 7 and in the absence of NaCl. Phylogenetic analysis based on 16S rRNA gene sequence showed that the novel isolate shared the highest sequence similarity with Lysobacter oryzae KCTC 22249T followed by Lysobacter yangpyeongensis KACC 11407T and Lysobacter niabensis KACC 11587T. The DNA G+C content of strain THG-DN8.2T is 66.0 mol% and ubiquinone Q-8 is the main isoprenoid quinone. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, and phosphatidyl-N-methylethanolamine. The major fatty acids of strain THG-DN8.2T were identified as iso-C15:0, iso-C16:0, and C16:1w7c alcohol. The phylogenetic distinctiveness and phenotypic characteristics differentiated strain THG-DN8.2T from closely related Lysobacter species. The results of polyphasic taxonomic analysis suggest that strain THG-DN8.2T represents a novel species of the genus Lysobacter, for which the name Lysobacter tyrosinelyticus sp. nov. is proposed. The type strain is THG-DN8.2T (=KCTC 42235T =JCM 30320T).

Citations

Citations to this article as recorded by  
  • Lysobacter ciconiae sp. nov., and Lysobacter avium sp. nov., isolated from the faeces of an Oriental stork
    So-Yeon Lee, Pil Soo Kim, Hojun Sung, Dong-Wook Hyun, Jin-Woo Bae
    Journal of Microbiology.2022; 60(5): 469.     CrossRef
  • Application of Bioorganic Fertilizer on Panax notoginseng Improves Plant Growth by Altering the Rhizosphere Microbiome Structure and Metabolism
    Rui Shi, Shu Wang, Bingjie Xiong, Haiyan Gu, Huiling Wang, Chao Ji, Weijia Jia, Abraham Rami Horowitz, Wenjie Zhen, Jiftah Ben Asher, Xiahong He
    Microorganisms.2022; 10(2): 275.     CrossRef
  • Lysobacter arenosi sp. nov. and Lysobacter solisilvae sp. nov. isolated from soil
    Kyeong Ryeol Kim, Kyung Hyun Kim, Shehzad Abid Khan, Hyung Min Kim, Dong Min Han, Che Ok Jeon
    Journal of Microbiology.2021; 59(8): 709.     CrossRef
  • Analysis of the Intestinal Flora in Male Versus Female Swamp Eels (Monopterus albus)
    Ying Wang, Jinhua Zhang, Qiubai Zhou, Zirui Wang, Miao Gao, Xin Yang, Yu Liu, Zhengzhou Zhang, Wenhao Jiang, Chonghua Hu, Wenping Zhang
    Frontiers in Microbiology.2020;[Epub]     CrossRef
  • Lysobacter terricola sp. nov., isolated from greenhouse soil
    Soo-Jin Kim, Jae-Hyung Ahn, Hang-Yeon Weon, Seung-Beom Hong, Soon-Ja Seok, Jeong-Seon Kim, Soon-Wo Kwon
    International Journal of Systematic and Evolutionary Microbiology.2016; 66(3): 1401.     CrossRef
  • Changes in the soil microbial community after reductive soil disinfestation and cucumber seedling cultivation
    Xinqi Huang, Liangliang Liu, Teng Wen, Jinbo Zhang, Fenghe Wang, Zucong Cai
    Applied Microbiology and Biotechnology.2016; 100(12): 5581.     CrossRef
  • Diversity and Activity of Lysobacter Species from Disease Suppressive Soils
    Ruth Gómez Expósito, Joeke Postma, Jos M. Raaijmakers, Irene De Bruijn
    Frontiers in Microbiology.2015;[Epub]     CrossRef
Epidemiological Features and Resistance Pattern in Uropathogens Isolated from Chronic Bacterial Prostatitis
Tommaso Cai , Sandra Mazzoli , Francesca Meacci , Vieri Boddi , Nicola Mondaini , Gianni Malossini , Riccardo Bartoletti
J. Microbiol. 2011;49(3):448-454.   Published online June 30, 2011
DOI: https://doi.org/10.1007/s12275-011-0391-z
  • 29 View
  • 0 Download
  • 44 Scopus
AbstractAbstract
Chronic bacterial prostatitis (CBP) is, usually, caused by uropathogens, especially gram-negative bacilli, although infection is sometimes due to Gram-positive and atypical microorganisms. A recent increasing in prevalence of Gram-positive strains has been reported. The aim of this study was to explore the epidemiological features and resistance rates in uropathogens isolated from CBP outpatients in last 10 years. All consecutive outpatients with demonstrated CBP attending a single Sexually Transmitted Disease centre from January 1997 and December 2008, were enrolled and underwent microbiological cultures in first void early morning urine, midstream urine, expressed prostatic secretion, and post prostate massage urine. Prevalence of different bacterial strains was stratified in four different periods: 1997-1999, 2000-2002, 2003-2005, 2006-2008. Any changes observed in epidemiological features and resistance rates in uropathogens over the whole study period have been analyzed. The present study has been planned, thus, as in vitro study. From 6,221 patients, 4,601 Gram-positive and 1,620 Gram-negative bacterial strains have been isolated. Enterococcus faecalis and Escherichia coli strains are the first and second frequent pathogens found, respectively. Significant differences between E. faecalis prevalence in the 1997-1999 and 2006-2008 periods were found. E. coli showed a significant difference between prevalence in 1997-1999 and 2006-2008 periods. Gram-positive organisms showed a decreasing of susceptibility to ciprofloxacin as well as Gram-negative strains, while a good susceptibility to the levofloxacin was evidenced. E. faecalis prevalence seemed to be raised in 2006-2008 periods. Moreover, a decreasing of activity of ciprofloxacin and a good activity profile of levofloxacin have been reported.
Research Support, Non-U.S. Gov't
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
  • 27 View
  • 0 Download
  • 6 Scopus
AbstractAbstract
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.

Journal of Microbiology : Journal of Microbiology
TOP