Journal of Microbiology

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: 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

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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.

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

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

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Abstract

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

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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

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Abstract

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
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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
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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

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

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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.

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