• Genomics & Informatics
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• v.20 no.4
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• pp.47.1-47.13
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• 2022

Klebsiella pneumoniae is a gram-negative bacterium that is known for causing infection in nosocomial settings. As reported by the World Health Organization, carbapenem-resistant Enterobacteriaceae, a category that includes K. pneumoniae, are classified as an urgent threat, and the greatest concern is that these bacterial pathogens may acquire genetic traits that make them resistant towards antibiotics. The last class of antibiotics, carbapenems, are not able to combat these bacterial pathogens, allowing them to clonally expand antibiotic-resistant strains. Most antibiotics target essential pathways of bacterial cells; however, these targets are no longer susceptible to antibiotics. Hence, in our study, we focused on a hypothetical protein in K. pneumoniae that contains a DNA methylation protein domain, suggesting a new potential site as a drug target. DNA methylation regulates the attenuation of bacterial virulence. We integrated computational-aided drug design by using a bioinformatics approach to perform subtractive genomics, virtual screening, and fingerprint similarity search. We identified a new potential drug, koenimbine, which could be a novel antibiotic.

• Proceedings of the PSK Conference
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• 2001.04a
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• pp.78-79
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• 2001

• Biomolecules & Therapeutics
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• v.26 no.6
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• pp.533-538
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• 2018

Nitric oxide (NO) mediates various physiological and pathological processes, including cell proliferation, differentiation, and inflammation. Protein S-nitrosylation (SNO), a NO-mediated reversible protein modification, leads to changes in the activity and function of target proteins. Recent findings on protein-protein transnitrosylation reactions (transfer of an NO group from one protein to another) have unveiled the mechanism of NO modulation of specific signaling pathways. The intracellular level of S-nitrosoglutathione (GSNO), a major reactive NO species, is controlled by GSNO reductase (GSNOR), a major regulator of NO/SNO signaling. Increasing number of GSNOR-related studies have shown the important role that denitrosylation plays in cellular NO/SNO homeostasis and human pathophysiology. This review introduces recent evidence of GSNO-mediated NO/SNO signaling depending on GSNOR expression or activity. In addition, the applicability of GSNOR as a target for drug therapy will be discussed in this review.

• Molecules and Cells
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• v.44 no.7
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• pp.458-467
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• 2021

GPR43 (also known as FFAR2 or FFA2) is a G-protein-coupled receptor primarily expressed in immune cells, enteroendocrine cells and adipocytes that recognizes short-chain fatty acids, such as acetate, propionate, and butyrate, likely to be implicated in innate immunity and host energy homeostasis. Activated GPR43 suppresses the cAMP level and induces Ca²⁺ flux via coupling to Gα_i and Gα_q families, respectively. Additionally, GPR43 is reported to facilitate phosphorylation of ERK through G-protein-dependent pathways and interacts with β-arrestin 2 to inhibit NF-κB signaling. However, other G-protein-dependent and independent signaling pathways involving GPR43 remain to be established. Here, we have demonstrated that GPR43 augments Rho GTPase signaling. Acetate and a synthetic agonist effectively activated RhoA and stabilized YAP/TAZ transcriptional coactivators through interactions of GPR43 with Gα_q/11 and Gα_12/13. Acetate-induced nuclear accumulation of YAP was blocked by a GPR43-specific inverse agonist. The target genes induced by YAP/TAZ were further regulated by GPR43. Moreover, in THP-1-derived M1-like macrophage cells, the Rho-YAP/TAZ pathway was activated by acetate and a synthetic agonist. Our collective findings suggest that GPR43 acts as a mediator of the Rho-YAP/TAZ pathway.

• BMB Reports
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• v.41 no.12
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• pp.852-857
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• 2008

Little attention has been paid to the specificity between E2 and the target protein during ubiquitination, although RING-E3 induces a potential intra-molecular reaction by mediating the direct transfer of ubiquitin from E2 to the target protein. We have constructed artificial E2 fusion proteins in which a target protein (p27) is tethered to one of six E2s via a flexible linker. Interestingly, only three E2s (UbcH5b, hHR6b, and Cdc34) are able to ubiquitinate p27 via an intra-molecular reaction in this system. Although the first ubiquitination of p27 (p27-Ub) by Cdc34 is less efficient than that of UbcH5b and hHR6b, the additional ubiquitin attachment to p27-Ub by Cdc34 is highly efficient. The E2 core of Cdc34 provides specificity to p27, and the residues 184-196 are required for possessive ubiquitination by Cdc34. We demonstrate direct E2 specificity for p27 and also show that differential ubiquitin linkages can be dependent on E2 alone.

• Journal of Microbiology and Biotechnology
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• v.33 no.12
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• pp.1681-1691
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• 2023

Flavin mononucleotide-binding proteins or domains emit cyan-green fluorescence under aerobic and anaerobic conditions, but relatively low fluorescence and less thermostability limit their application as reporters. In this work, we incorporated the codon-optimized fluorescent protein from Chlamydomonas reinhardtii with two different linkers independently into the redox-responsive split intein construct, overexpressed the precursors in hyperoxic Escherichia coli SHuffle T7 strain, and cyclized the target proteins in vitro in the presence of the reducing agent. Compared with the purified linear protein, the cyclic protein with the short linker displayed enhanced fluorescence. In contrast, cyclized protein with incorporation of the long linker including the myc-tag and human rhinovirus 3C protease cleavable sequence emitted slightly increased fluorescence compared with the protein linearized with the protease cleavage. The cyclic protein with the short linker also exhibited increased thermal stability and exopeptidase resistance. Moreover, induction of the target proteins in an oxygen-deficient culture rendered fluorescent E. coli BL21 (DE3) cells brighter than those overexpressing the linear construct. Thus, the cyclic reporter can hopefully be used in certain thermophilic anaerobes.

• BMB Reports
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• v.43 no.6
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• pp.438-444
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• 2010

Dnd (dead end) gene encodes an RNA binding protein and is specifically expressed in primordial germ cells (PGCs) as a vertebrate-specific component of the germ plasma throughout embryogenesis. By utilizing a technique of specific nucleic acids associated with proteins (SNAAP), 13 potential target mRNAs of zebrafish Dnd (ZDnd) protein were identified from 8-cell embryo, and 8 target mRNAs have been confirmed using an RT-PCR analysis. Of the target mRNAs, the present study is focused on the regulation of geminin, which is an inhibitor of DNA replication. Using electrophoretic mobility shift assay (EMSA), we demonstrated that ZDND protein bound the 67-nucleotide region from 864 to 931 in the 3'UTR of geminin mRNA, a sequence containing 60.29% of uridine. Results from a dual-luciferase assay in HEK293 cells showed that ZDND increases the translation of geminin. Taken together, the identification of target mRNA for ZDnd will be helpful to further explore the biological function of Dnd in zebrafish germ-line development as well as in cancer cells.

• The Korean Journal of Zoology
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• v.32 no.4
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• pp.305-313
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• 1989

The present investigation aims at inquiring into a possible target for the heat inactivation of SCK tumor cells by comparing the kinetics of cell survival, rate of protein synthesis, and DNA polymerase activity in the presence of heat protector or heat sensitirer. A possible conclusion to be drawn from the present experiment is that there is no direct correlation between cell death and decrease in the rate of protein synthesis, but that the loss of DNA polvmerase $\beta$ activity correlates quite well with cell inactivation. Thus, protein degrada-tion and/or abnormal protein synthesis causes cell inactivation innireuv, possibly by altering the cellular environment which in turn affects the DNA polymerase $\beta$ activity. Accordingly, further studies, dealing with the correlation between changes in the cellular environment and DNA polymerase $\beta$ activity, are needed to set insight into a possible target for the heat inactivation of cells. 본 연구는 열보호제 또는 열증감제의 존재하에서 세포 생존곡선, 단백질 합성률, DNA 중합효소 $\beta$의 활성변화를 비교 검토함으로써 SCK 종양세포가 열에 의해서 불활성화될 때의 표적이 무엇인지를 밝혀보기 위해서 수행되었다. 본 실험의 결과로 추정하건대 열에 의한 세포치사는 단백질 합성률의 변화와는 직접적인 연관성이 없으나, DNA 중합효소 $\beta$의 활성도와는 밀접한 연관성이 있음을 알 수 있다. 즉, 단백질의 분해 또는 비정상적인 단백질의 합성이 세포의 환경을 변화시키고 이것이 DNA 중합효소 $\beta$의 활성에 영향을 미침으로써 간접적으로 세포의 치사를 초래할 것으로 짐작할 수 있다. 따라서, 세포의 열불화성화의 표적을 좀더 분명히 밝히기 위해서는 세포의 환경변화와 DNA 중합효소 $\beta$의 활성과의 관계를 추구하는 연구가 수행되어야 할 것으로 사료된다.

• Animal Bioscience
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• v.36 no.4
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• pp.601-608
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• 2023

Objective: This study was conducted to investigate the effects of energy and protein levels in the diet of Hanwoo heifers on growth response and animal behavior. Methods: Forty heifers were randomly allocated into three experimental groups according to the target daily weight gain in 8 pens (T-0.2, 2 replications; T-0.4 and -0.6, 3 replications) based on similar body weight (BW) and age in months. The target average daily gain (ADG) was set at 0.2 (T-0.2), 0.4 (T-0.4), and 0.6 kg/d (T-0.6), and feed was based on National Institute of Animal Science (NIAS, 2017). In order to minimize hunger stress of T-0.2 and -0.4, the feeding ratio of rice straw was set to 55%, 50%, and 45% for T-0.2, -0.4 and T-0.6, respectively, so that the dry matter (DM) intake for all treatment groups was uniform but the energy and protein levels in the diet were adjusted differently. A total of 6 items (lying, standing, eating, rumination, walking and drinking) of animal behavior were analyzed. Results: During the whole period of the experiment, the ADG of the T-0.2, -0.4 and -0.6 treatments were 0.48, 0.56, and 0.65 kg/d (p<0.05), respectively, showing higher gain than the predicted value, especially for the low target ADG group. Based on these results, regression equations for the total digestible nutrient (TDN) and crude protein (CP) requirements were derived. No behavioral differences were found according to the energy and protein levels in the diet because the DM intake was kept constant by adjusting the roughage and concentration ratio. However, eating time was longer (p<0.05) at T-0.2 than T-0.6 during the whole day. Conclusion: Through this study, it was possible to derive regression equations for predicting TDN and CP requirements according to the target ADG and BW.

• BMB Reports
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• v.31 no.4
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• pp.355-363
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• 1998

MHC unrestricted, antigen nonspecific killing by $CD4^+$ T-cells against virally-infected target cells was induced following cross-linking of CD4 molecules. The cytotoxicity of antibody-activated $CD4^+$ T-cells was abolished by genistein (4',5,7-trihydroxyisoflavone), a protein tyrosine kinase (PTK) inhibitor, but not by H-7, a protein kinase C (PKC) inhibitor. Genisteintreated human or bovine peripheral blood $CD4^+$ T-cells lacked PTK activity and failed to kill virally-infected target cells even after cross-linking of CD4 molecules. The cross-linking of CD4 molecules did not induce effector cell proliferation or the transcription of TNF ${\beta}$. TNF ${\beta}$ synthesis was up-regulated by incubating antibody activated effector cells with bovine herpesvirus type 1 (BHV-1) infected D17 target cells. Anti-TNF ${\beta}$ antibody partially abrogated direct effector cell-mediated antiviral cytotoxicity. On the other hand, this antibody effectively neutralized antiviral activity of effector and target cell culture supernatants against BHV-1 infected D17 cells. The inhibition level of the antiviral activity by the antibody was dependent on effector and target cell ratio. These findings have importance to define the mechanisms of how CD4 cytotoxic cells control viral infection.