Journal of Microbiology

Dongbin Lim

4 Articles

Characterization of cell death in Escherichia coli mediated by XseA, a large subunit of exonuclease VII: Hyeim Jung , Junwei Liang , Yuna Jung , Dongbin Lim; J. Microbiol. 2015;53(12):820-828. Published online December 2, 2015; DOI: https://doi.org/10.1007/s12275-015-5304-0

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Exonuclease VII (ExoVII) of Escherichia coli is a single strandspecific DNA nuclease composed of two different subunits: the large subunit, XseA, and the small subunit, XseB. In this study, we found that multicopy single-stranded DNAs (msDNAs), Ec83 and Ec78, are the in vivo substrates of ExoVII; the enzyme cuts the phosphodiester bond between the fourth and fifth nucleotides from the 5′ end. We used this msDNA cleavage to assess ExoVII activity in vivo. Both subunits were required for enzyme activity. Expression of XseA without XseB caused cell death, even though no ExoVII activity was detected. The lethality caused by XseA was rescued by surplus XseB. In XseA-induced death, cells were elongated and multinucleated, and their chromosomes were fragmented and condensed; these are the morphological hallmarks of apoptotic cell death in bacteria. A putative caspase recognition sequence (FVAD) was found in XseA, and its hypothetical caspase product with 257 amino acids was as active as the intact protein in inducing cell death. We propose that under ordinary conditions, XseA protects chromosome as a component of the ExoVII enzyme, but in some conditions, the protein causes cell death; the destruction of cell is probably carried out by the amino terminal fragment derived from the cleavage of XseA by caspase-like enzyme.

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Structural insights into the assembly and function of Retron Ec78 PtuAB
Leyuan Duan, Lu Chen, Qian Hu, Xiao Li, Shanshan Li, Kaiming Zhang, Qingguo Gong
Communications Biology.2026;[Epub] CrossRef
The origin of the logic of adaptive mutations: standing by to grow again
Antoine Danchin, Agnieskza Sekowska
Comptes Rendus. Biologies.2026; 349(G1): 189. CrossRef
Phage nuclease-mediated defense activation of the bacterial Retron-Eco7 toxin–antitoxin system
Zhikang Dai, Chang Liu, Yanjing Wang, Xueting Chen, Xiaofang Fu, Kaiyue Yang, Rui Zhu, Xianyue Jia, Yanke Chen, Pan Tao, Zeyuan Guan, Tingting Zou
Nucleic Acids Research.2025;[Epub] CrossRef
Structural mechanism of the Retron-Eco7 anti-phage defense system
Junichiro Ishikawa, Kanta Yoneyama, Aa Haeruman Azam, Asuteka Nagao, Yoshihisa Mitsuda, Ren Nakazaki, Kotaro Chihara, Masahiro Hiraizumi, Keitaro Yamashita, Tsutomu Suzuki, Kotaro Kiga, Hiroshi Nishimasu
Nature Communications.2025;[Epub] CrossRef
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Wentao Zheng, Yuxuan Wang, Jie Cui, Guangyao Guo, Yufeng Li, Jin Hou, Qiang Tu, Yulong Yin, A. Francis Stewart, Youming Zhang, Xiaoying Bian, Xue Wang
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Juechun Tang, Allison M. Herzfeld, Gabrielle Leon, Mark P. Brynildsen, Nathalie Balaban
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Bacterial retrons encode phage-defending tripartite toxin–antitoxin systems
Jacob Bobonis, Karin Mitosch, André Mateus, Nicolai Karcher, George Kritikos, Joel Selkrig, Matylda Zietek, Vivian Monzon, Birgit Pfalz, Sarela Garcia-Santamarina, Marco Galardini, Anna Sueki, Callie Kobayashi, Frank Stein, Alex Bateman, Georg Zeller, Mik
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Yanjing Wang, Zeyuan Guan, Chen Wang, Yangfan Nie, Yibei Chen, Zhaoyang Qian, Yongqing Cui, Han Xu, Qiang Wang, Fen Zhao, Delin Zhang, Pan Tao, Ming Sun, Ping Yin, Shuangxia Jin, Shan Wu, Tingting Zou
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Christina Palka, Chloe B Fishman, Santi Bhattarai-Kline, Samuel A Myers, Seth L Shipman
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Transcriptional profile of gene clusters involved in the methylerythritol phosphate pathway in Bacillus subtilis 916
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Multi-copy single-stranded DNA in Escherichia coli
Xianxing Xie, Ruifu Yang
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Roberto C. Molina-Quiroz, David W. Lazinski, Andrew Camilli, Stuart B. Levy
Antimicrobial Agents and Chemotherapy.2016; 60(11): 6907. CrossRef

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 PDF

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.

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Sublethal Paraquat Confers Multidrug Tolerance in Pseudomonas aeruginosa by Inducing Superoxide Dismutase Activity and Lowering Envelope Permeability
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Superoxide dismutase activity confers (p)ppGpp-mediated antibiotic tolerance to stationary-phase Pseudomonas aeruginosa
Dorival Martins, Geoffrey McKay, Gowthami Sampathkumar, Malika Khakimova, Ann M. English, Dao Nguyen
Proceedings of the National Academy of Sciences.2018; 115(39): 9797. CrossRef
Screening of genes of secreting acetic acid from Aspergillus niger H1 to improve phosphate solubilization
Xue LIU, Chang-xiong ZHU, Delvigne Frank, Ming-bo GONG
Journal of Integrative Agriculture.2017; 16(9): 2110. CrossRef
Crystal structure of PhoU from Pseudomonas aeruginosa, a negative regulator of the Pho regulon
Sang Jae Lee, Ye Seol Park, Soon-Jong Kim, Bong-Jin Lee, Se Won Suh
Journal of Structural Biology.2014; 188(1): 22. CrossRef

Development of a Simple Cell Lysis Method for Recombinant DNA Using Bacteriophage Lambda Lysis Genes: Boyun Jang , Yuna Jung , Dongbin Lim; J. Microbiol. 2007;45(6):593-596.; DOI: https://doi.org/2602 [pii]

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Abstract PDF: In this study, we describe the development of a simple and efficient method for cell lysis via the insertion of a bacteriophage lambda lysis gene cluster into the pET22b expression vector in the following order; the T7 promoter, a gene for a target protein intended for production, Sam7 and R. This insertion of R and Sam7 into pET22b exerted no detrimental effects on cellular growth or the production of a target protein. The induction of the T7 promoter did not in itself result in the autolysis of cells in culture but the harvested cells were readily broken by freezing and thawing. We compared the efficiency of the cell lysis technique by freezing and thawing to that observed with sonication, and determined that both methods completely disintegrated the cells and released proteins into the solution. With our modification of pET22b, the lysis of cells became quite simple, efficient, and reliable. This strategy may prove useful for a broad variety of applications, particularly in experiments requiring extensive cell breakage, including library screening and culture condition exploration, in addition to protein purification.

A Proteomic Approach to Study msDNA Function in Escherichia coli: Mi-Ae Jeong , Dongbin Lim; J. Microbiol. 2004;42(3):200-204.; DOI: https://doi.org/2089 [pii]

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Abstract PDF: Retron is a prokaryotic genetic element that produces multicopy single-stranded DNA covalently linked to RNA (msDNA) by a reverse transcriptase. It was found that cells producing a large amount of msDNA, rather than those that did not, showed a higher rate of mutation. In order to understand the molecular mechanism connecting msDNA production to the high mutation rate the protein patterns were compared by two dimensional gel electrophoresis. Ten proteins were found to be differentially expressed at levels more than three fold greater in cells with than without msDNA, nine of which were identified by MALDI TOF MS. Eight of the nine identified proteins were repressed in msDNA-producing cells and, surprisingly, most were proteins functioning in the dissimilation of various carbon sources. One protein was induced four fold greater in the msDNA producing cells and was identified as a 30S ribosomal protein S2 involved in the regulation of translation. The molecular mechanism underlying the elevated mutation in msDNA-producing cell still remains elusive.

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