Journal of Microbiology

Jin-Won Lee

6 Articles

Bacterial Regulatory Mechanisms for the Control of Cellular Processes: Simple Organisms’ Complex Regulation: Jin-Won Lee; J. Microbiol. 2023;61(3):273-276. Published online April 3, 2023; DOI: https://doi.org/10.1007/s12275-023-00036-6

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Bacteria employ a diverse array of cellular regulatory mechanisms to successfully adapt and thrive in ever-changing environments, including but not limited to temperature changes, fluctuations in nutrient availability, the presence or absence of electron acceptors such as oxygen, the availability of metal ions crucial for enzyme activity, and the existence of antibiotics. Bacteria can virtually modulate any step of gene expression from transcr!ptional initiation to posttranslational modification of a protein for the control of cellular processes. Furthermore, one gene regulator often controls another in a complex gene regulatory network. Thus, it is not easy to fully understand the intricacies of bacterial regulatory mechanisms in various environments. In this special issue, while acknowledging the challenge of covering all aspects of bacterial regulatory mechanisms across diverse environments, seven review articles are included to provide insight into the recent progress in understanding such mechanisms from different perspectives: positive regulatory mechanisms by secondary messenger (cAMP receptor protein), two-component signal transduction mechanisms (Rcs and Cpx), diverse regulatory mechanisms by a specific environmental factor in specific bacteria (oxygen availability in Mycobacterium and manganese ion availability in Salmonella), diverse regulatory mechanisms by a specific environmental factor (temperature and antibiotics), and regulatory mechanisms by antibiotics in cell wall synthesis. Bacteria, as ubiquitous organisms that can be found in almost every environment, carry out complex cellular processes that allow them to survive and thrive in a variety of different conditions despite their small size and relative simplicity. One of the key factors that allows bacteria to carry out these complex processes is their ability to regulate gene expression through various mechanisms. Gene expression is a fundamental biological process by which the genetic information encoded in a gene is transcribed into an RNA molecule and subsequently translated into a functional gene product, often a protein. Furthermore, the activity levels of proteins may further be altered by posttranslational modification. Regulation of gene expression refers to the control of the amount and timing of gene expression, and thus it can be divided into transcr!ptional, translational, and posttranslational levels.

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PhoPQ-mediated lipopolysaccharide modification governs intrinsic resistance to tetracycline and glycylcycline antibiotics in Escherichia coli
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Navigating the signaling landscape of Ralstonia solanacearum: a study of bacterial two-component systems
Mohit Yadav, Janhavi Sathe, Valentina Teronpi, Aditya Kumar
World Journal of Microbiology and Biotechnology.2024;[Epub] CrossRef

Gly184 of the Escherichia coli cAMP receptor protein provides optimal context for both DNA binding and RNA polymerase interaction: Matt N. Hicks , Sanjiva Gunasekara , Jose Serate , Jin Park , Pegah Mosharaf , Yue Zhou , Jin-Won Lee , Hwan Youn; J. Microbiol. 2017;55(10):816-822. Published online September 28, 2017; DOI: https://doi.org/10.1007/s12275-017-7266-x

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Abstract PDF

The Escherichia coli cAMP receptor protein (CRP) utilizes the helix-turn-helix motif for DNA binding. The CRP’s recognition helix, termed F-helix, includes a stretch of six amino acids (Arg180, Glu181, Thr182, Val183, Gly184, and Arg185) for direct DNA contacts. Arg180, Glu181 and Arg185 are known as important residues for DNA binding and specificity, but little has been studied for the other residues. Here we show that Gly184 is another F-helix residue critical for the transcriptional activation function of CRP. First, glycine was repeatedly selected at CRP position 184 for its unique ability to provide wild type-level transcriptional activation activity. To dissect the glycine requirement, wild type CRP and mutants G184A, G184F, G184S, and G184Y were purified and their in vitro DNA-binding activity was measured. G184A and G184F displayed reduced DNA binding, which may explain their low transcriptional activation activity. However, G184S and G184Y displayed apparently normal DNA affinity. Therefore, an additional factor is needed to account for the diminished transcriptional activation function in G184S and G184Y, and the best explanation is perturbations in their interaction with RNA polymerase. The fact that glycine is the smallest amino acid could not fully warrant its suitability, as shown in this study. We hypothesize that Gly184 fulfills the dual functions of DNA binding and RNA polymerase interaction by conferring conformational flexibility to the F-helix.

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cAMP-independent DNA binding of the CRP family protein DdrI from Deinococcus radiodurans
Yudong Wang, Jing Hu, Xufan Gao, Yuchen Cao, Shumai Ye, Cheng Chen, Liangyan Wang, Hong Xu, Miao Guo, Dong Zhang, Ruhong Zhou, Yuejin Hua, Ye Zhao, Paul Babitzke
mBio.2024;[Epub] CrossRef
Unexpected Requirement of Small Amino Acids at Position 183 for DNA Binding in the Escherichia coli cAMP Receptor Protein
Marcus Carranza, Amanda Rea, Daisy Pacheco, Christian Montiel, Jin Park, Hwan Youn
Journal of Microbiology.2024; 62(10): 871. CrossRef
cAMP Activation of the cAMP Receptor Protein, a Model Bacterial Transcription Factor
Hwan Youn, Marcus Carranza
Journal of Microbiology.2023; 61(3): 277. CrossRef

The inability of Bacillus licheniformis perR mutant to grow is mainly due to the lack of PerR-mediated fur repression: Jung-Hoon Kim , Yoon-Mo Yang , Chang-Jun Ji , Su-Hyun Ryu , Young-Bin Won , Shin-Yeong Ju , Yumi Kwon , Yeh-Eun Lee , Hwan Youn , Jin-Won Lee; J. Microbiol. 2017;55(6):457-463. Published online April 22, 2017; DOI: https://doi.org/10.1007/s12275-017-7051-x

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Abstract PDF

PerR, a member of Fur family protein, is a metal-dependent H2O2 sensing transcription factor that regulates genes in-volved in peroxide stress response. Industrially important bac-terium Bacillus licheniformis contains three PerR-like pro-teins (PerRBL, PerR2, and PerR3) compared to its close rela-tive Bacillus subtilis. Interestingly, unlike other bacteria in-cluding B. subtilis, no authentic perRBL null mutant could be established for B. licheniformis. Thus, we constructed a con-ditional perRBL mutant using a xylose-inducible promoter, and investigated the genes under the control of PerRBL. PerRBL regulon genes include katA, mrgA, ahpC, pfeT, hemA, fur, and perR as observed for PerRBS. However, there is some variation in the expression levels of fur and hemA genes be-tween B. subtilis and B. licheniformis in the derepressed state. Furthermore, katA, mrgA, and ahpC are strongly induced, whereas the others are only weakly or not induced by H2O2 treatment. In contrast to the B. subtilis perR null mutant which frequently gives rise to large colony phenotype mainly due to the loss of katA, the suppressors of B. licheniformis perR mutant, which can form colonies on LB agar, were all cata-lase-positive. Instead, many of the suppressors showed in-creased levels of siderophore production, suggesting that the suppressor mutation is linked to the fur gene. Consistent with this, perR fur double mutant could grow on LB agar without Fe supplementation, whereas perR katA double mutant could only grow on LB agar with Fe supplementation. Taken toge-ther, our data suggest that in B. licheniformis, despite the si-milarity in PerRBL and PerRBS regulon genes, perR is an essen-tial gene required for growth and that the inability of perR null mutant to grow is mainly due to elevated expression of Fur.

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Characterization of the dual regulation by a c-di-GMP riboswitch Bc1 with a long expression platform from Bacillus thuringiensis
Lu Liu, Dehua Luo, Yongji Zhang, Dingqi Liu, Kang Yin, Qing Tang, Shan-Ho Chou, Jin He, Beile Gao
Microbiology Spectrum.2024;[Epub] CrossRef
Meddling with Metal Sensors: Fur-Family Proteins as Signaling Hubs
Caroline H. Steingard, John D. Helmann, Tina M. Henkin
Journal of Bacteriology.2023;[Epub] CrossRef
Divergent Effects of Peptidoglycan Carboxypeptidase DacA on Intrinsic β-Lactam and Vancomycin Resistance
Si Hyoung Park, Umji Choi, Su-Hyun Ryu, Han Byeol Lee, Jin-Won Lee, Chang-Ro Lee, Krisztina M. Papp-Wallace
Microbiology Spectrum.2022;[Epub] CrossRef
Microbial Redox Regulator-Enabled Pulldown for Rapid Analysis of Plasma Low-Molecular-Weight Biothiols
Jin Oh Lee, Yoon-Mo Yang, Jae-Hoon Choi, Tae-Wuk Kim, Jin-Won Lee, Young-Pil Kim
Analytical Chemistry.2019; 91(15): 10064. CrossRef
Redox Sensing by Fe 2+ in Bacterial Fur Family Metalloregulators
Azul Pinochet-Barros, John D. Helmann
Antioxidants & Redox Signaling.2018; 29(18): 1858. CrossRef

Experimental Phasing Using Zinc and Sulfur Anomalous Signals Measured at the Zinc Absorption Peak: Sangmin Lee , Min-Kyu Kim , Chang-Jun Ji , Jin-Won Lee , Sun-Shin Cha; J. Microbiol. 2013;51(6):886-886.; DOI: https://doi.org/10.1007/s12275-013-0725-5

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Abstract PDF: In the article by Lee et al. published in the Journal of Microbiology 2013; 51, 639-643. Acknowledgement should appear as shown below. This work was supported by the National Research Foundation of Korea Grant NRF-2012R1A2A2A02005978, the CAP through Korea Research Council of Fundamental Science Technology (KRCF), Korea Institute of Science and Technology (KIST), & Korea Institute of Ocean Science and Technology (KIOST), the Marine and Extreme Genome Research Center program, and the Development of Biohydrogen Production Technology Using Hyperthermophilic Archaea program of MOF. Works performed at Hanyang University were supported by Basic Science Research Program through the National Research Foundation of Korea (NRF) funded by the Ministry of Education, Science and Technology (MEST) (KRF-2008-313-C00774).

Experimental Phasing Using Zinc and Sulfur Anomalous Signals Measured at the Zinc Absorption Peak: Sangmin Lee , Min-Kyu Kim , Chang-Jun Ji , Jin-Won Lee , Sun-Shin Cha; J. Microbiol. 2013;51(5):639-643. Published online October 31, 2013; DOI: https://doi.org/10.1007/s12275-013-3412-2

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Abstract PDF: Iron is an essential transition metal required for bacterial growth and survival. Excess free iron can lead to the generation of reactive oxygen species that can cause severe damage to cellular functions. Cells have developed iron-sensing regulators to maintain iron homeostasis at the transcription level. The ferric uptake regulator (Fur) is an iron-responsive regulator that controls the expression of genes involved in iron homeostasis, bacterial virulence, stress resistance, and redox metabolism. Here, we report the expression, purification, crystallization, and phasing of the apo-form of Bacillus subtilis Fur (BsFur) in the absence of regulatory metal ions. Crystals were obtained by microbatch crystallization method at 295 K and diffraction data at a resolution of 2.6 Å was collected at the zinc peak wavelength (λ=1.2823 Å). Experimental phasing identified the positions of one zinc atom and four sulfur atoms of cysteine residues coordinating the zinc atom, indicating that the data contained a meaningful anomalous scattering originating from the ordered zinc-coordinating sulfur atoms, in spite of the small anomalous signals of sulfur atoms at the examined wavelength.

Sequence Analysis and Functional Expression of the Structural and Regulatory Genes for Pyruvate Dehydrogenase Complex from Streptomyces seoulensis: Hwan Youn , Jangyul Kwak , Dong-Won Kim , Chang-Jin Lee , Yang-In Yim , Jin-Won Lee , In-Kwon Kim , Jeong-Il Yu , Hyung-Soon Yim , Sa-Ouk Kang; J. Microbiol. 2002;40(1):43-50.

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Abstract PDF: A cluster of genes encoding the pyruvate dehydrogenase complex (PDC) of Streptomyces seoulensis, a Gram-positive bacterium, was cloned and sequenced. The genes of S. seoulensis consist of four open reading frames. The first gene, lpd, which encodes a lipoamide dehydrogenase, is followed by pdhB encoding a dihydrolipoamide acetyltransferase (E2p), pdhR, a regulatory gene, and pdhA encoding a pyruvate dehydrogenase component (E1p). E1p had an unusual homodimeric subunit, which has been known only in Gram-negative bacteria. S. seoulensis E2p contains two lipoyl domains like those of humans and Streptococcus faecalis. The pdhR gene appears to be clustered with the structural genes of S. seoulensis PDC. The PdhR-overexpressed S. seoulensis showed growth retardation and the decrease of E1p, indicating that PdhR regulates the function of PDC by repressing the expression of E1p. A strain of Streptomyces lividans overexpressing S. seoulensis PdhR showed a significant decrease in the level of actinorhodin, implying a regulatory role for Streptomyces PDC in antibiotic biosynthesis.

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