Journal of Microbiology

Research Article

PneusPage: A WEB-BASED TOOL for the analysis of Whole-Genome Sequencing Data of Streptococcus pneumonia: Eunju Hong, Youngjin Shin, Hyunseong Kim, Woo Young Cho, Woo-Hyun Song, Seung-Hyun Jung, Minho Lee; J. Microbiol. 2025;63(1):e.2409020. Published online January 24, 2025; DOI: https://doi.org/10.71150/jm.2409020

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Abstract PDF Supplementary Material: With the advent of whole-genome sequencing, opportunities to investigate the population structure, transmission patterns, antimicrobial resistance profiles, and virulence determinants of Streptococcus pneumoniae at high resolution have been increasingly expanding. Consequently, a user-friendly bioinformatics tool is needed to automate the analysis of Streptococcus pneumoniae whole-genome sequencing data, summarize clinically relevant genomic features, and further guide treatment options. Here, we developed PneusPage, a web-based tool that integrates functions for species prediction, molecular typing, drug resistance determination, and data visualization of Streptococcus pneumoniae. To evaluate the performance of PneusPage, we analyzed 80 pneumococcal genomes with different serotypes from the Global Pneumococcal Sequencing Project and compared the results with those from another platform, PathogenWatch. We observed a high concordance between the two platforms in terms of serotypes (100% concordance rate), multilocus sequence typing (100% concordance rate), penicillin-binding protein typing (88.8% concordance rate), and the Global Pneumococcal Sequencing Clusters (98.8% concordance rate). In addition, PneusPage offers integrated analysis functions for the detection of virulence and mobile genetic elements that are not provided by previous platforms. By automating the analysis pipeline, PneusPage makes whole-genome sequencing data more accessible to non-specialist users, including microbiologists, epidemiologists, and clinicians, thereby enhancing the utility of whole-genome sequencing in both research and clinical settings. PneusPage is available at https://pneuspage.minholee.net/.

Journal Articles

Comparative Transcriptomic Analysis of Flagellar‑Associated Genes in Salmonella Typhimurium and Its rnc Mutant: Seungmok Han , Ji-Won Byun , Minho Lee; J. Microbiol. 2024;62(1):33-48. Published online January 5, 2024; DOI: https://doi.org/10.1007/s12275-023-00099-5

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Salmonella enterica serovar Typhimurium (S. Typhimurium) is a globally recognized foodborne pathogen that affects both animals and humans. Endoribonucleases mediate RNA processing and degradation in the adaptation of bacteria to environmental changes and have been linked to the pathogenicity of S. Typhimurium. Not much is known about the specific regulatory mechanisms of these enzymes in S. Typhimurium, particularly in the context of environmental adaptation. Thus, this study carried out a comparative transcriptomic analysis of wild-type S. Typhimurium SL1344 and its mutant (Δrnc), which lacks the rnc gene encoding RNase III, thereby elucidating the detailed regulatory characteristics that can be attributed to the rnc gene. Global gene expression analysis revealed that the Δrnc strain exhibited 410 upregulated and 301 downregulated genes (fold-change > 1.5 and p < 0.05), as compared to the wild-type strain. Subsequent bioinformatics analysis indicated that these differentially expressed genes are involved in various physiological functions, in both the wild-type and Δrnc strains. This study provides evidence for the critical role of RNase III as a general positive regulator of flagellar-associated genes and its involvement in the pathogenicity of S. Typhimurium.

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CspA regulates stress resistance, flagellar motility and biofilm formation in Salmonella Enteritidis
Xiang Li, Yan Cui, Xiaohui Sun, Chunlei Shi, Shoukui He, Xianming Shi
Food Bioscience.2025; 66: 106237. CrossRef
Influence of Flagella on Salmonella Enteritidis Sedimentation, Biofilm Formation, Disinfectant Resistance, and Interspecies Interactions
Huixue Hu, Jingguo Xu, Jingyu Chen, Chao Tang, Tianhao Zhou, Jun Wang, Zhuangli Kang
Foodborne Pathogens and Disease.2024;[Epub] CrossRef

Transcript-specific selective translation by specialized ribosomes bearing genome-encoded heterogeneous rRNAs in V. vulnificus CMCP6: Younkyung Choi , Minju Joo , Wooseok Song , Minho Lee , Hana Hyeon , Hyun-Lee Kim , Ji-Hyun Yeom , Kangseok Lee , Eunkyoung Shin; J. Microbiol. 2022;60(12):1162-1167. Published online November 24, 2022; DOI: https://doi.org/10.1007/s12275-022-2437-9

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Abstract

Ribosomes composed of genome-encoded heterogeneous rRNAs are implicated in the rapid adaptation of bacterial cells to environmental changes. A previous study showed that ribosomes bearing the most heterogeneous rRNAs expressed from the rrnI operon (I-ribosomes) are implicated in the preferential translation of a subset of mRNAs, including hspA and tpiA, in Vibrio vulnificus CMCP6. In this study, we show that HspA nascent peptides were predominantly bound to I-ribosomes. Specifically, I-ribosomes were enriched more than two-fold in ribosomes that were pulled down by immunoprecipitation of HspA peptides compared with the proportion of I-ribosomes in crude ribosomes and ribosomes pulled down by immunoprecipitation of RNA polymerase subunit ß peptides in the wild-type (WT) and rrnI-completed strains. Other methods that utilized the incorporation of an affinity tag in 23S rRNA or chimeric rRNA tethering 16S and 23S rRNAs, which generated specialized functional ribosomes in Escherichia coli, did not result in functional I-ribosomes in V. vulnificus CMCP6. This study provides direct evidence of the preferential translation of hspA mRNA by I-ribosomes.

Citations

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Functional conservation of specialized ribosomes bearing genome-encoded variant rRNAs in Vibrio species
Younkyung Choi, Eunkyoung Shin, Minho Lee, Ji-Hyun Yeom, Kangseok Lee, Bashir Sajo Mienda
PLOS ONE.2023; 18(12): e0289072. CrossRef
Relaxed Cleavage Specificity of Hyperactive Variants of Escherichia coli RNase E on RNA I
Dayeong Bae, Hana Hyeon, Eunkyoung Shin, Ji-Hyun Yeom, Kangseok Lee
Journal of Microbiology.2023; 61(2): 211. 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; J. Microbiol. 2022;60(1):128-136. Published online December 29, 2021; DOI: https://doi.org/10.1007/s12275-022-1620-3

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Abstract

Acinetobacter baumannii causes multidrug resistance, leading to fatal infections in humans. In this study, we showed that Lys AB2 P3-His–a hexahistidine-tagged form of an antimicrobial peptide (AMP) loaded onto DNA aptamer-functionalized gold nanoparticles (AuNP-Apt)–can effectively inhibit A. baumannii infection in mice. When A. baumannii-infected mice were intraperitoneally injected with AuNP-Apt loaded with Lys AB2 P3-His, a marked reduction in A. baumannii colonization was observed in the mouse organs, leading to prominently increased survival time and rate of the mice compared to those of the control mice treated with AuNP-Apt or Lys AB2 P3-His only. This study shows that AMPs loaded onto AuNP-Apt could be an effective therapeutic tool against infections caused by multidrug-resistant pathogenic bacteria in humans.

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Challenges and Emerging Molecular Approaches in Combating Antimicrobial Resistance
Gene Philip Levee Ynion, Christian Jay Rosal, Arvin Zulueta, Angelo Ordanel, Christopher Marlowe Caipang
Journal of Bacteriology and Virology.2024; 54(1): 12. CrossRef
Gold Nanoparticles and Antimicrobial Peptides: A Novel Combination
Şule Balcı, Bengü Ergüden
ChemistrySelect.2024;[Epub] CrossRef
Aptamers: A Cutting-Edge Approach for Gram-Negative Bacterial Pathogen Identification
María Guadalupe Córdova-Espinoza, Rosa González-Vázquez, Rolando Rafik Barron-Fattel, Raquel Gónzalez-Vázquez, Marco Antonio Vargas-Hernández, Exsal Manuel Albores-Méndez, Ana Laura Esquivel-Campos, Felipe Mendoza-Pérez, Lino Mayorga-Reyes, María Angélica
International Journal of Molecular Sciences.2024; 25(2): 1257. CrossRef
Antimicrobial Peptide Delivery Systems as Promising Tools Against Resistant Bacterial Infections
Kamila Botelho Sampaio de Oliveira, Michel Lopes Leite, Nadielle Tamires Moreira Melo, Letícia Ferreira Lima, Talita Cristina Queiroz Barbosa, Nathalia Lira Carmo, Douglas Afonso Bittencourt Melo, Hugo Costa Paes, Octávio Luiz Franco
Antibiotics.2024; 13(11): 1042. CrossRef
Optimizing Treatment for Carbapenem-Resistant Acinetobacter baumannii Complex Infections: A Review of Current Evidence
Seong Jin Choi, Eu Suk Kim
Infection & Chemotherapy.2024; 56(2): 171. CrossRef
Advances in skin gene therapy: utilizing innovative dressing scaffolds for wound healing, a comprehensive review
Fatemeh Karimzadeh, Elahe Soltani Fard, Akram Nadi, Rahim Malekzadeh, Fatemeh Elahian, Seyed Abbas Mirzaei
Journal of Materials Chemistry B.2024; 12(25): 6033. CrossRef
Colistin Resistance Mechanism and Management Strategies of Colistin-Resistant Acinetobacter baumannii Infections
Md Minarul Islam, Da Eun Jung, Woo Shik Shin, Man Hwan Oh
Pathogens.2024; 13(12): 1049. CrossRef
Progress in Programmable DNA-Aided Self-Assembly of the Master Frame of a Drug Delivery System
Gary Q. Yang, Weibin Cai, Zhiwen Zhang, Yujun Wang
ACS Applied Bio Materials.2023; 6(12): 5125. CrossRef
Neglected Zoonotic Diseases: Advances in the Development of Cell-Penetrating and Antimicrobial Peptides against Leishmaniosis and Chagas Disease
Sara M. Robledo, Silvia Pérez-Silanes, Celia Fernández-Rubio, Ana Poveda, Lianet Monzote, Víctor M. González, Paloma Alonso-Collado, Javier Carrión
Pathogens.2023; 12(7): 939. CrossRef
Applications and Challenges of Bacteriostatic Aptamers in the Treatment of Common Pathogenic Bacteria Infections
Diandian Li, Yuan Su, Jie Li, Rong Liu, Bing Fang, Jingjing He, Wentao Xu, Longjiao Zhu
Biomacromolecules.2023; 24(11): 4568. CrossRef
Promising Acinetobacter baumannii Vaccine Candidates and Drug Targets in Recent Years
Yong Chiang Tan, Chandrajit Lahiri
Frontiers in Immunology.2022;[Epub] CrossRef
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Preeti Garg, Prerna Attri, Rohit Sharma, Moondeep Chauhan, Ganga Ram Chaudhary
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Aptamer Decorated Emodin Nanoparticles-Assisted Delivery of Dermcidin-Derived Peptide DCD-1L: Photoactive Bio-Theragnostic Agent for Enterococcus Faecalis Biofilm Destruction
Maryam Pourhajibagher, Abbas Bahador
SSRN Electronic Journal .2022;[Epub] CrossRef
Development of DNA aptamers specific for small therapeutic peptides using a modified SELEX method
Jaemin Lee, Minkyung Ryu, Dayeong Bae, Hong-Man Kim, Seong-il Eyun, Jeehyeon Bae, Kangseok Lee
Journal of Microbiology.2022; 60(7): 659. CrossRef
Aptamer decorated emodin nanoparticles-assisted delivery of dermcidin-derived peptide DCD-1L: Photoactive bio-theragnostic agent for Enterococcus faecalis biofilm destruction
Maryam Pourhajibagher, Abbas Bahador
Photodiagnosis and Photodynamic Therapy.2022; 39: 103020. CrossRef

Regulator of ribonuclease activity modulates the pathogenicity of Vibrio vulnificus: Jaejin Lee , Eunkyoung Shin , Jaeyeong Park , Minho Lee , Kangseok Lee; J. Microbiol. 2021;59(12):1133-1141. Published online November 9, 2021; DOI: https://doi.org/10.1007/s12275-021-1518-5

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Abstract

RraA, a protein regulator of RNase E activity, plays a unique role in modulating the mRNA abundance in Escherichia coli. The marine pathogenic bacterium Vibrio vulnificus also possesses homologs of RNase E (VvRNase E) and RraA (VvRraA1 and VvRraA2). However, their physiological roles have not yet been investigated. In this study, we demonstrated that VvRraA1 expression levels affect the pathogenicity of V. vulnificus. Compared to the wild-type strain, the VvrraA1-deleted strain (ΔVvrraA1) showed decreased motility, invasiveness, biofilm formation ability as well as virulence in mice; these phenotypic changes of ΔVvrraA1 were restored by the exogenous expression of VvrraA1. Transcriptomic analysis indicated that VvRraA1 expression levels affect the abundance of a large number of mRNA species. Among them, the halflives of mRNA species encoding virulence factors (e.g., smcR and htpG) that have been previously shown to affect VvrraA1 expression-dependent phenotypes were positively correlated with VvrraA1 expression levels. These findings suggest that VvRraA1 modulates the pathogenicity of V. vulnificus by regulating the abundance of a subset of mRNA species.

Citations

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Identification of the global regulatory roles of RraA via the integrative transcriptome and proteome in Vibrio alginolyticus
Huizhen Chen, Qian Gao, Bing Liu, Ying Zhang, Jianxiang Fang, Songbiao Wang, Youqi Chen, Chang Chen, Nicolas E. Buchler
mSphere.2024;[Epub] CrossRef
Comparative Transcriptomic Analysis of Flagellar-Associated Genes in Salmonella Typhimurium and Its rnc Mutant
Seungmok Han, Ji-Won Byun, Minho Lee
Journal of Microbiology.2024; 62(1): 33. CrossRef
Eco-Evolutionary Drivers of Vibrio parahaemolyticus Sequence Type 3 Expansion: Retrospective Machine Learning Approach
Amy Marie Campbell, Chris Hauton, Ronny van Aerle, Jaime Martinez-Urtaza
JMIR Bioinformatics and Biotechnology.2024; 5: e62747. CrossRef
Relaxed Cleavage Specificity of Hyperactive Variants of Escherichia coli RNase E on RNA I
Dayeong Bae, Hana Hyeon, Eunkyoung Shin, Ji-Hyun Yeom, Kangseok Lee
Journal of Microbiology.2023; 61(2): 211. CrossRef
Regulator of RNase E activity modulates the pathogenicity of Salmonella Typhimurium
Jaejin Lee, Eunkyoung Shin, Ji-Hyun Yeom, Jaeyoung Park, Sunwoo Kim, Minho Lee, Kangseok Lee
Microbial Pathogenesis.2022; 165: 105460. CrossRef

Review

Trans-acting regulators of ribonuclease activity: Jaejin Lee , Minho Lee , Kangseok Lee; J. Microbiol. 2021;59(4):341-359. Published online March 29, 2021; DOI: https://doi.org/10.1007/s12275-021-0650-6

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Abstract

RNA metabolism needs to be tightly regulated in response to changes in cellular physiology. Ribonucleases (RNases) play an essential role in almost all aspects of RNA metabolism, including processing, degradation, and recycling of RNA molecules. Thus, living systems have evolved to regulate RNase activity at multiple levels, including transcription, post-transcription, post-translation, and cellular localization. In addition, various trans-acting regulators of RNase activity have been discovered in recent years. This review focuses on the physiological roles and underlying mechanisms of trans-acting regulators of RNase activity.

Citations

Citations to this article as recorded by

Comparative Transcriptomic Analysis of Flagellar-Associated Genes in Salmonella Typhimurium and Its rnc Mutant
Seungmok Han, Ji-Won Byun, Minho Lee
Journal of Microbiology.2024; 62(1): 33. CrossRef
Insights into the metabolism, signaling, and physiological effects of 2’,3’-cyclic nucleotide monophosphates in bacteria
Nick J. Marotta, Emily E. Weinert
Critical Reviews in Biochemistry and Molecular Biology.2023; 58(2-6): 118. CrossRef
Relaxed Cleavage Specificity of Hyperactive Variants of Escherichia coli RNase E on RNA I
Dayeong Bae, Hana Hyeon, Eunkyoung Shin, Ji-Hyun Yeom, Kangseok Lee
Journal of Microbiology.2023; 61(2): 211. CrossRef
Regulator of RNase E activity modulates the pathogenicity of Salmonella Typhimurium
Jaejin Lee, Eunkyoung Shin, Ji-Hyun Yeom, Jaeyoung Park, Sunwoo Kim, Minho Lee, Kangseok Lee
Microbial Pathogenesis.2022; 165: 105460. CrossRef

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

Functional analysis of Vibrio vulnificus RND efflux pumps homologous to Vibrio cholerae VexAB and VexCD, and to Escherichia coli AcrAB: Seunghwa Lee , Ji-Hyun Yeom , Sojin Seo , Minho Lee , Sarang Kim , Jeehyeon Bae , Kangseok Lee , Jihwan Hwang; J. Microbiol. 2015;53(4):256-261. Published online March 4, 2015; DOI: https://doi.org/10.1007/s12275-015-5037-0

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Abstract

Resistance-nodulation-division (RND) efflux pumps are associated with multidrug resistance in many gram-negative pathogens. The genome of Vibrio vulnificus encodes 11 putative RND pumps homologous to those of Vibrio cholerae and Escherichia coli. In this study, we analyzed three putative RND efflux pumps, showing homology to V. cholerae VexAB and VexCD and to E. coli AcrAB, for their functional roles in multidrug resistance of V. vulnificus. Deletion of the vexAB homolog resulted in increased susceptibility of V. vulnificus to bile acid, acriflavine, ethidium bromide, and erythromycin, whereas deletion of acrAB homologs rendered V. vulnificus more susceptible to acriflavine only. Deletion of vexCD had no effect on susceptibility of V. vulnificus to these chemicals. Upon exposure to these antibacterial chemicals, expression of tolCV1 and tolCV2, which are putative outer membrane factors of RND efflux pumps, was induced, whereas expression levels of vexAB, vexCD, and acrAB homologs were not significantly changed. Our results show that the V. vulnificus homologs of VexAB largely contributed to in vitro antimicrobial resistance with a broad substrate specificity that was partially redundant with the AcrAB pump homologs.

Citations

Citations to this article as recorded by

Dynamics of efflux pumps in antimicrobial resistance, persistence, and community living of Vibrionaceae
Sanath Kumar, Manjusha Lekshmi, Jerusha Stephen, Anely Ortiz-Alegria, Matthew Ayitah, Manuel F. Varela
Archives of Microbiology.2024;[Epub] CrossRef
Membrane Efflux Pumps of Pathogenic Vibrio Species: Role in Antimicrobial Resistance and Virulence
Jerusha Stephen, Manjusha Lekshmi, Parvathi Ammini, Sanath H. Kumar, Manuel F. Varela
Microorganisms.2022; 10(2): 382. CrossRef
TolCV1 Has Multifaceted Roles During Vibrio vulnificus Infection
Yue Gong, Rui Hong Guo, Joon Haeng Rhee, Young Ran Kim
Frontiers in Cellular and Infection Microbiology.2021;[Epub] CrossRef
The mechanisms that regulate Vibrio parahaemolyticus virulence gene expression differ between pathotypes
Nicholas Petronella, Jennifer Ronholm
Microbial Genomics .2018;[Epub] CrossRef
ATP-Binding Cassette Transporter VcaM from Vibrio cholerae is Dependent on the Outer Membrane Factor Family for Its Function
Wen-Jung Lu, Hsuan-Ju Lin, Thamarai Janganan, Cheng-Yi Li, Wei-Chiang Chin, Vassiliy Bavro, Hong-Ting Lin
International Journal of Molecular Sciences.2018; 19(4): 1000. CrossRef
Contribution of efflux systems to the detergent resistance, cytotoxicity, and biofilm formation of Vibrio vulnificus
Chung-Cheng Lo, Pei-Ting Lin, Chuan Chiang-Ni, Kuan-Hua Lin, Shin-Luen Lee, Tzu-Fang Kuo, Horng-Ren Lo
Gene Reports.2017; 9: 115. CrossRef
Survival of the Fittest: How Bacterial Pathogens Utilize Bile To Enhance Infection
Jeticia R. Sistrunk, Kourtney P. Nickerson, Rachael B. Chanin, David A. Rasko, Christina S. Faherty
Clinical Microbiology Reviews.2016; 29(4): 819. CrossRef
MdsABC-Mediated Pathway for Pathogenicity in Salmonella enterica Serovar Typhimurium
Saemee Song, Boeun Lee, Ji-Hyun Yeom, Soonhye Hwang, Ilnam Kang, Jang-Cheon Cho, Nam-Chul Ha, Jeehyeon Bae, Kangseok Lee, Yong-Hak Kim, S. M. Payne
Infection and Immunity.2015; 83(11): 4266. CrossRef
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
Journal of Microbiology.2015; 53(6): 355. CrossRef

Interaction between the α-Barrel Tip of Vibrio vulnificus TolC Homologs and AcrA Implies the Adapter Bridging Model: Seunghwa Lee , Saemee Song , Minho Lee , Soonhye Hwang , Ji-Sun Kim , Nam-Chul Ha , Kangseok Lee; J. Microbiol. 2014;52(2):148-153. Published online February 1, 2014; DOI: https://doi.org/10.1007/s12275-014-3578-2

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Abstract

The AcrAB-TolC multidrug efflux pump confers resistance to Escherichia coli against many antibiotics and toxic compounds. The TolC protein is an outer membrane factor that participates in the formation of type I secretion systems. The genome of Vibrio vulnificus encodes two proteins homologous to the E. coli TolC, designated TolCV1 and TolCV2. Here, we show that both TolCV1 and TolCV2 partially complement the E. coli TolC function and physically interact with the membrane fusion protein AcrA, a component of the E. coli AcrAB-TolC efflux pump. Using site-directed mutational analyses and an in vivo cross-linking assay, we demonstrated that the α-barrel tip region of TolC homologs plays a critical role in the formation of functional AcrAB-TolC efflux pumps. Our findings suggest the adapter bridging model as a general assembly mechanism for tripartite drug efflux pumps in Gram-negative bacteria.

Citations

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Progress of Antimicrobial Mechanisms of Stilbenoids
Xiancai Li, Yongqing Li, Binghong Xiong, Shengxiang Qiu
Pharmaceutics.2024; 16(5): 663. CrossRef
Membrane Efflux Pumps of Pathogenic Vibrio Species: Role in Antimicrobial Resistance and Virulence
Jerusha Stephen, Manjusha Lekshmi, Parvathi Ammini, Sanath H. Kumar, Manuel F. Varela
Microorganisms.2022; 10(2): 382. CrossRef
TolCV1 Has Multifaceted Roles During Vibrio vulnificus Infection
Yue Gong, Rui Hong Guo, Joon Haeng Rhee, Young Ran Kim
Frontiers in Cellular and Infection Microbiology.2021;[Epub] 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
NaCl promotes antibiotic resistance by reducing redox states in Vibrio alginolyticus
Jun Yang, Zao‐Hai Zeng, Man‐Jun Yang, Zhi‐Xue Cheng, Xuan‐Xian Peng, Hui Li
Environmental Microbiology.2018; 20(11): 4022. CrossRef
ATP-Binding Cassette Transporter VcaM from Vibrio cholerae is Dependent on the Outer Membrane Factor Family for Its Function
Wen-Jung Lu, Hsuan-Ju Lin, Thamarai Janganan, Cheng-Yi Li, Wei-Chiang Chin, Vassiliy Bavro, Hong-Ting Lin
International Journal of Molecular Sciences.2018; 19(4): 1000. CrossRef
Functional analysis of Vibrio vulnificus RND efflux pumps homologous to Vibrio cholerae VexAB and VexCD, and to Escherichia coli AcrAB
Seunghwa Lee, Ji-Hyun Yeom, Sojin Seo, Minho Lee, Sarang Kim, Jeehyeon Bae, Kangseok Lee, Jihwan Hwang
Journal of Microbiology.2015; 53(4): 256. CrossRef
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
Journal of Microbiology.2015; 53(6): 355. CrossRef
Interaction Mediated by the Putative Tip Regions of MdsA and MdsC in the Formation of a Salmonella-Specific Tripartite Efflux Pump
Saemee Song, Soonhye Hwang, Seunghwa Lee, Nam-Chul Ha, Kangseok Lee, Eric Cascales
PLoS ONE.2014; 9(6): e100881. CrossRef
Functional Analysis of TolC Homologs in Vibrio vulnificus
Seunghwa Lee, Saemee Song, Kangseok Lee
Current Microbiology.2014; 68(6): 729. CrossRef

The α-Barrel Tip Region of Escherichia coli TolC Homologs of Vibrio vulnificus Interacts with the MacA Protein to Form the Functional Macrolide-Specific Efflux Pump MacAB-TolC: Minho Lee , Hyun-Lee Kim , Saemee Song , Minju Joo , Seunghwa Lee , Daeyoung Kim , Yoonsoo Hahn , Nam-Chul Ha , Kangseok Lee; J. Microbiol. 2013;51(2):154-159. Published online April 27, 2013; DOI: https://doi.org/10.1007/s12275-013-2699-3

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Abstract: TolC and its homologous family of proteins are outer membrane factors that are essential for exporting small molecules and toxins across the outer membrane in Gram-negative bacteria. Two open reading frames in the Vibrio vulnificus genome that encode proteins homologous to Escherichia coli TolC, designated TolCV1 and TolCV2, have 51.3% and 29.6% amino acid identity to TolC, respectively. In this study, we show that TolCV1 and TolCV2 functionally and physically interacted with the membrane fusion protein, MacA, a component of the macrolide-specific MacAB-TolC pump of E. coli. We further show that the conserved residues located at the aperture tip region of the α-hairpin of TolCV1 and TolCV2 played an essential role in the formation of the functional MacAB-TolC pump using site-directed mutational analyses. Our findings suggest that these outer membrane factors have conserved tip-to-tip interaction with the MacA membrane fusion protein for action of the drug efflux pump in Gramnegative bacteria.

RNase G Participates in Processing of the 5′-end of 23S Ribosomal RNA: Woo-Seok Song , Minho Lee , Kangseok Lee; J. Microbiol. 2011;49(3):508-511. Published online June 30, 2011; DOI: https://doi.org/10.1007/s12275-011-1198-7

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Abstract: In Escherichia coli, primary rRNA transcripts must be processed by a complex process in which several ribonucleases are involved in order to generate mature 16S, 23S, and 5S rRNA molecules. While it is known that RNase G, a single-stranded RNA-specific endoribonuclease encoded by the rng gene, plays an active role in the maturation of the 5′-end of 16S rRNA, its involvement in the maturation of the 5′-end of 23S rRNA remains unclear. Here we show that E. coli cells deleted for the rng gene accumulate the 23S rRNA precursor containing an extra 77 nucleotides at its mature 5′-end. In vitro cleavage assays show that RNase G cleaves synthetic RNA containing a sequence encompassing the 5′-end to 77 nucleotides upstream of mature 23S rRNA at two sites present in single-stranded regions. Our results suggest the involvement of RNase G in the processing of the 5′-region of 23S rRNA precursors.

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