Journal of Microbiology

Kyoung Lee

7 Articles

Mutants defective in the production of encapsulin show a tan-phaselocked phenotype in Myxococcus xanthus: Dohee Kim , Juo Choi , Sunjin Lee , Hyesook Hyun , Kyoung Lee , Kyungyun Cho; J. Microbiol. 2019;57(9):795-802. Published online June 11, 2019; DOI: https://doi.org/10.1007/s12275-019-8683-9

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Myxococcus xanthus, a myxobacterium, displays phase variation between yellow phase and tan phase. We found that deletion of the encA gene encoding encapsulin and the encF gene encoding a metalloprotease causes formation of tan colonies that never transform into yellow colonies. The encA and encF mutants were defective in the production of DKxanthene and myxovirescin. They did not produce extracellular polysaccharides; hence, the cells did not aggregate in liquid and showed reduced swarming on agar plates. The mutants had defective sporulation, but were rescued extracellularly by wild type cells. All these traits indicate that the encA and encF mutants are likely to be tan-phase-locked, and encapsulin has a close relationship with phase variation in M. xanthus. The encA and encF genes are localized in the same gene cluster, encBAEFG (MXAN_3557~MXAN_3553). Unlike the encA and encF genes, deletion of other genes in the cluster did not show tan-phase-locked phenotype.

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Encapsulated Ferritin-like Proteins: A Structural Perspective
Elif Eren, Norman R. Watts, Felipe Montecinos, Paul T. Wingfield
Biomolecules.2024; 14(6): 624. CrossRef
A widespread bacterial protein compartment sequesters and stores elemental sulfur
Robert Benisch, Michael P. Andreas, Tobias W. Giessen
Science Advances.2024;[Epub] CrossRef
Structure and heterogeneity of a highly cargo-loaded encapsulin shell
Seokmu Kwon, Michael P. Andreas, Tobias W. Giessen
Journal of Structural Biology.2023; 215(4): 108022. CrossRef
Bacterial Nanocompartments: Structures, Functions, and Applications
Harry Benjamin McDowell, Egbert Hoiczyk, Michael Y. Galperin
Journal of Bacteriology.2022;[Epub] CrossRef
Condensation and Protection of DNA by the Myxococcus xanthus Encapsulin: A Novel Function
Ana V. Almeida, Ana J. Carvalho, Tomás Calmeiro, Nykola C. Jones, Søren V. Hoffmann, Elvira Fortunato, Alice S. Pereira, Pedro Tavares
International Journal of Molecular Sciences.2022; 23(14): 7829. CrossRef
Encapsulins
Tobias W. Giessen
Annual Review of Biochemistry.2022; 91(1): 353. CrossRef
Advances in encapsulin nanocompartment biology and engineering
Jesse A. Jones, Tobias W. Giessen
Biotechnology and Bioengineering.2021; 118(1): 491. CrossRef
Encapsulin nanocages: Protein encapsulation and iron sequestration
Ana V. Almeida, Ana J. Carvalho, Alice S. Pereira
Coordination Chemistry Reviews.2021; 448: 214188. CrossRef
Discovery and characterization of a novel family of prokaryotic nanocompartments involved in sulfur metabolism
Robert J Nichols, Benjamin LaFrance, Naiya R Phillips, Devon R Radford, Luke M Oltrogge, Luis E Valentin-Alvarado, Amanda J Bischoff, Eva Nogales, David F Savage
eLife.2021;[Epub] CrossRef
Nanotechnological Applications Based on Bacterial Encapsulins
Javier M. Rodríguez, Carolina Allende-Ballestero, Jeroen J. L. M. Cornelissen, José R. Castón
Nanomaterials.2021; 11(6): 1467. CrossRef

Circular pellicles formed by Pseudomonas alkylphenolica KL28 are a sophisticated architecture principally designed by matrix substance: Myeong Mi Song , Yaligara Veeranagouda , Munkhtsatsral Ganzorig , Kyoung Lee; J. Microbiol. 2018;56(11):790-797. Published online October 24, 2018; DOI: https://doi.org/10.1007/s12275-018-8252-7

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Abstract PDF

The colonization of liquid surfaces as floating biofilms or pellicles is a bacterial adaptation to optimally occupy the airliquid (A-L) niche. In aerobic heterotrophs, pellicle formation is beneficial for the utilization of O2 and nonpolar organic compounds. Pseudomonas alkylphenolica KL28, an alkylphenol degrader, forms flat circular pellicles that are 0.3– 0.5 mm in diameter. In this study, we first monitored the pellicle developmental patterns of multicellular organization from the initial settlement stage. The pellicles developed by clonal growth and mutants for flagella and pilus formation established normal pellicles. In contrast, the mutants of an epm gene cluster for biosynthesis of alginate-like polymer were incompetent in cell alignment for initial two-dimensional (2D) pellicle growth, suggesting the role of the Epm polymer as a structural scaffold for pellicle biofilms. Microscopic observation revealed that the initial 2D growth transited to multilayers by an accumulated self-produced extracellular polymeric substance that may exert a constraint force. Electron microscopy and confocal laser scanning microscopy revealed that the fully matured pellicle structures were densly packed with matrix-encased cells displaying distinct arrangements. The cells on the surface of the pellicle were relatively flat, and those inside were longitudinally cross-packed. The extracellular polysaccharide stained by Congo red was denser on the pellicle rim and a thin film was observed in the open spaces, indicative of its role in pellicle flotation. Our results demonstrate that P. alkylphenolica KL28 coordinately dictates the cell arrangements of pellicle biofilms by the controlled growth of constituent cells that accumulate extracellular polymeric substances.

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Beyond probiotics: Lacticaseibacillus rhamnosus as a multi-target antagonist of Pseudomonas aeruginosa infections
Weldson Ricardo Silva Gomes, Gessiane dos Santos Souza, João Inácio Diniz Ferreira, Rafaella Coelho Oliveira, Marliete Carvalho da Costa, Camila Guerra Martinez
Folia Microbiologica.2026;[Epub] CrossRef
Conserved residues in the CHASE3 domain of BmsA are involved in motility and biofilm formation in Pseudomonas alkylphenolica KL28
Gangsu Ha, Meriem Harrache, Kyoung Lee
Letters in Applied Microbiology.2026;[Epub] CrossRef
Characterization of the extracellular polymeric substances matrix of Pseudomonas biofilms formed at the air-liquid interface
Srinithi Muthuraman, Steve Flint, Jon Palmer
Food Bioscience.2025; 64: 105918. CrossRef

Effect of gacS and gacA Mutations on Colony Architecture, Surface Motility, Biofilm Formation and Chemical Toxicity in Pseudomonas sp. KL28: Kyung Soon Choi , Yaligara Veeraragouda , Kyoung Mi Cho , Soo O Lee , Geuk Rae Jo , Kyungyun Cho , Kyoung Lee; J. Microbiol. 2007;45(6):492-498.; DOI: https://doi.org/2646 [pii]

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Abstract PDF: GacS and GacA proteins form a two component signal transduction system in bacteria. Here, Tn5 transposon gacS and gacA (Gac) mutants of Pseudomonas sp. KL28, an alkylphenol degrader, were isolated by selecting for smooth colonies of strain KL28. The mutants exhibited reduced ability to migrate on a solid surface. This surface motility does not require the action of flagella unlike the well-studied swarming motility of other Pseudomonas sp. The Gac mutants also showed reduced levels of biofilm and pellicle formation in liquid culture. In addition, compared to the wild type KL28 strain, these mutants were more resistant to high concentrations of m-cresol but were more sensitive to H2O2, which are characteristics that they share with an rpoS mutant. These results indicate that the Gac regulatory cascade in strain KL28 positively controls wrinkling morphology, biofilm formation, surface translocation and H2O2 resistance, which are important traits for its capacity to survive in particular niches.

Identification and Expression of the cym, cmt, and tod Catabolic Genes from Pseudomonas putida KL47: Expression of the Regulatory todST Genes as a Factor for Catabolic Adaptation: Kyoung Lee , Eun Kyeong Ryu , Kyung Soon Choi , Min Chul Cho , Jae Jun Jeong , Eun Na Choi , Soo O Lee , Do-Young Yoon , Ingyu Hwang , Chi-Kyung Kim; J. Microbiol. 2006;44(2):192-199.; DOI: https://doi.org/2365 [pii]

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Abstract PDF: Pseudomonas putida KL47 is a natural isolate that assimilates benzene, 1-alkylbenzene (C1-C4), biphenyl, p-cumate, and p-cymene. The genetic background of strain KL47 underlying the broad range of growth substrates was examined. It was found that the cym and cmt operons are constitutively expressed due to a lack of the cymR gene, and the tod operon is still inducible by toluene and biphenyl. The entire array of gene clusters responsible for the catabolism of toluene and p-cymene/p-cumate has been cloned in a cosmid vector, pLAFR3, and were named pEK6 and pEK27, respectively. The two inserts overlap one another and the nucleotide sequence (42,505 bp) comprising the cym, cmt, and tod operons and its flanking genes in KL47 are almost identical (>99%) to those of P. putida F1. In the cloned DNA fragment, two genes with unknown functions, labeled cymZ and cmtR, were newly identified and show high sequence homology to dienelactone hydrolase and CymR proteins, respectively. The cmtR gene was identified in the place of the cmtI gene of previous annotation. Western blot analysis showed that, in strains F1 and KL47, the todT gene is not expressed during growth on Luria Bertani medium. In minimal basal salt medium, expression of the todT gene is inducible by toluene, but not by biphenyl in strain F1; however, it is constantly expressed in strain KL47, indicating that high levels of expression of the todST genes with one amino acid substitution in TodS might provide strain KL47 with a means of adaptation of the tod catabolic operon to various aromatic hydrocarbons.

Genetic Organization of the dhlA Gene Encoding 1,2-Dichloroethane Dechlorinase from Xanthobacter flavus UE15: Ji-Sook Song , Dong-Hun Lee , Kyoung Lee , Chi-Kyung Kim; J. Microbiol. 2004;42(3):188-193.; DOI: https://doi.org/2091 [pii]

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Abstract PDF: Xanthobacter flavus strain UE15 was isolated in wastewater obtained from the Ulsan industrial complex, Korea. This strain functions as a 1,2-dichloroethane (1,2-DCA) degrader, via a mechanism of hydrolytic dechlorination, under aerobic conditions. The UE15 strain was also capable of dechlorinating other chloroaliphatics, such as 2-chloroacetic acid and 2-chloropropionic acid. The dhlA gene encoding 1,2-DCA dechlorinase was cloned from the genomic DNA of the UE15 strain, and its nucleotide sequence was determined to consist of 933 base pairs. The deduced amino acid sequence of the DhlA dechlorinase exhibited 100% homology with the corresponding enzyme from X. autotrophicus GJ10, but only 27 to 29% homology with the corresponding enzymes from Rhodococcus rhodochrous, Pseudomonas pavonaceae, and Mycobacterium sp. strain GP1, which all dechlorinate haloalkane compounds. The UE15 strain has an ORF1 (1,356 bp) downstream from the dhlA gene. The OFR1 shows 99% amino acid sequence homology with the transposase reported from X. autotrophicus GJ10. The transposase gene was not found in the vicinity of the dhlA in the GJ10 strain, but rather beside the dhlB gene coding for haloacid dechlorinase. The dhlA and dhlB genes were confirmed to be located at separate chromosomal loci in the Xanthobacter flavus UE15 strain as well as in X. autotrophicus GJ10. The dhlA and transposase genes of the UE15 strain were found to be parenthesized by a pair of insertion sequences, IS1247, which were also found on both sides of the transposase gene in the GJ10 strain. This unique structure of the dhlA gene organization in X. flavus strain UE15 suggested that the dechlorinase gene, dhlA, is transferred with the help of the transposase gene.

Characteristics of Several Bacterial Isolates Capable of Degrading Chloroaliphatic Compounds via Hydrolytic Dechlorination: Ji-Sook Song , Dong-Hun Lee , Kyoung Lee , Chi-Kyung Kim; J. Microbiol. 2003;41(4):277-283.

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Abstract PDF: Haloaliphatic hydrocarbons have been widely used as solvents and ingredients of pesticides and herbicides. However, when these compounds contaminate the environment, they can be very hazardous to animals and humans because of their potential toxicity and carcinogenicity. Therefore, lots of studies have been made for microbial degradation of those pollutant chemicals. In this study, 11 bacterial strains capable of degrading 1,2-dichloroethane (1,2-DCA), 2-chloropropionic acid (2-CPA), 2,3-dichloropropionic acid (2,3-DCPA), and 2-monochloroacetic acid (2-MCA) by hydrolytic dechlorination under aerobic conditions were isolated from wastewaters and rice paddy soil samples. Their morphological and biochemical characteristics and their degradation capabilities of haloaliphatic hydrocarbons were examined. On the basis of the 16S rDNA sequences, 8 different kinds of microbial species, including Pseudomonas plecoglossicida, Xanthobacter flavus, Ralstonia eutropha, were identified. All of the isolated strains can degrade MCA. In particular, strains UE-2 and UE-15 degraded 1,2-DCA, and strain CA-11 degraded 2,3-DCPA, which are hardly degraded by other strains.

Structural Analysis of the fcbABC Gene Cluster Responsible for Hydrolytic Dechlorination of 4-Chlorobenzoate from pJS1 Plasmid of Comamonas sp. P08: Jeong-Soon Lee , Kyoung Lee , Jong-Ok Ka , Jong-Chan Chae , Chi-Kyung Kim; J. Microbiol. 2003;41(2):89-94.

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Abstract PDF: Bacterial strain No. P08 isolated from wastewater at the Cheongju industrial complex was found to be capable of degrading 4-chlorobenzoate under aerobic condition. P08 was identified as Comamonas sp. from its cellular fatty acid composition and 16S rDNA sequence. The fcb genes, responsible for the hydrolytic dechlorination of 4-chlorobenzoate, were cloned from the plasmid pJS1 of Comamonas sp. P08. The fcb gene cluster of comamonas sp. P08 was organized in the order fcbB-fcbA-fcbT1-fcbT2-fcbT3-fcbC. This organization of the fcb genes was very similar to that of the fcb genes carried on the chromosomal DNA of Pseudomonas sp. DJ-12. However, it differed from the fcbA-fcbB-fcbC ordering of Arthrobacter sp. SU. The nucleotide sequences of the fcbABC genes of strain P08 showed 98% and 53% identities to those of Pseudomonas sp. DJ-12 and Arthrobacter sp. SU, respectively. This suggests that the fcb genes might have been derived from Pseudomonas sp. DJ-12 to form plasmid pJS1 in Comamonas sp. P08, or that the fcb genes in strain DJ-12 were transposed from Comamonas sp. P08 plasmid.

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