Review
- Structural Insights into the Lipopolysaccharide Transport (Lpt) System as a Novel Antibiotic Target
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Yurim Yoon, Saemee Song
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J. Microbiol. 2024;62(4):261-275. Published online May 31, 2024
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DOI: https://doi.org/10.1007/s12275-024-00137-w
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Abstract
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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
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Zhen Guo , Juan Li , Lei Ge , Chenxi Yang , Jichang Han
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J. Microbiol. 2020;58(9):750-760. Published online July 24, 2020
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DOI: https://doi.org/10.1007/s12275-020-0130-4
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47
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4
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3
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Abstract
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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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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
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Jiyoon Choi , Jiwon Baek , Daehyuk Kweon , Kwan Soo Ko , Hyunjin Yoon
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J. Microbiol. 2020;58(5):415-421. Published online March 28, 2020
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DOI: https://doi.org/10.1007/s12275-020-9549-x
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53
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4
Web of Science
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4
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Abstract
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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.
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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
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Mai Phuong Nguyen , Le Viet Ha Tran , Hyun Namgoong , Yong-Hak Kim
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J. Microbiol. 2019;57(8):644-654. Published online May 23, 2019
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DOI: https://doi.org/10.1007/s12275-019-9116-5
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50
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6
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6
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Abstract
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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.
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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
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Saemee Song , Jin-Sik Kim , Kangseok Lee , Nam-Chul Ha
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J. Microbiol. 2015;53(6):355-364. Published online May 30, 2015
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DOI: https://doi.org/10.1007/s12275-015-5248-4
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47
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9
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Abstract
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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.
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Citations
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- 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
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Juan Du , Hina Singh , Hien T.T. Ngo , KyungHwa Won , Ki-Young Kim , Tae-Hoo Yi
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J. Microbiol. 2015;53(6):365-370. Published online May 30, 2015
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DOI: https://doi.org/10.1007/s12275-015-4729-9
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52
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7
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Abstract
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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).
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- Lysobacter ciconiae sp. nov., and Lysobacter avium sp. nov., isolated from the faeces of an Oriental stork
So-Yeon Lee, Pil Soo Kim, Hojun Sung, Dong-Wook Hyun, Jin-Woo Bae
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
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Tommaso Cai , Sandra Mazzoli , Francesca Meacci , Vieri Boddi , Nicola Mondaini , Gianni Malossini , Riccardo Bartoletti
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J. Microbiol. 2011;49(3):448-454. Published online June 30, 2011
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DOI: https://doi.org/10.1007/s12275-011-0391-z
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Scopus
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Abstract
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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
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Bo-Young Yun , Yongbin Xu , Shunfu Piao , Nahee Kim , Jeong-Hyun Yoon , Hyun-Soo Cho , Kangseok Lee , Nam-Chul Ha
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J. Microbiol. 2010;48(6):829-835. Published online January 9, 2011
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DOI: https://doi.org/10.1007/s12275-010-0339-8
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6
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Abstract
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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.