• BMB Reports
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• v.41 no.8
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• pp.609-614
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• 2008

The concentrations and catalytic activities of enzymes control metabolic rates. Previous studies have focused on enzyme concentrations because there are no genome-wide techniques used for the measurement of enzyme activity. We propose a method for evaluating the significance of enzyme activity by integrating metabolic network topologies and genome-wide microarray gene expression profiles. We quantified the enzymatic activity of reactions and report the 388 significant reactions in five perturbation datasets. For the 388 enzymatic reactions, we identified 70 that were significantly regulated (P-value < 0.001). Thirty-one of these reactions were part of anaerobic metabolism, 23 were part of low-pH aerobic metabolism, 8 were part of high-pH anaerobic metabolism, 3 were part of low-pH aerobic reactions, and 5 were part of high-pH anaerobic metabolism.

• BMB Reports
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• v.51 no.3
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• pp.143-150
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• 2018

The Hippo signaling pathway plays an essential role in adult tissue homeostasis and organ size control. Abnormal regulation of Hippo signaling can be a cause for multiple types of human cancers. Since the awareness of the importance of the Hippo signaling in a wide range of biological fields has been continually grown, it is also understood that a thorough and well-rounded comprehension of the precise dynamics could provide fundamental insights for therapeutic applications. Several components in the Hippo signaling pathway are known to be targeted for proteasomal degradation via ubiquitination by E3 ligases. ${\beta}-TrCP$ is a well-known E3 ligase of YAP/TAZ, which leads to the reduction of YAP/TAZ levels. The Hippo signaling pathway can also be inhibited by the E3 ligases (such as ITCH) which target LATS1/2 for degradation. Regulation via ubiquitination involves not only complex network of E3 ligases but also deubiquitinating enzymes (DUBs), which remove ubiquitin from its targets. Interestingly, non-degradative ubiquitin modifications are also known to play important roles in the regulation of Hippo signaling. Although there has been much advanced progress in the investigation of ubiquitin modifications acting as regulators of the Hippo signaling pathway, research done to date still remains inadequate due to the sheer complexity and diversity of the subject. Herein, we review and discuss recent developments that implicate ubiquitin-mediated regulatory mechanisms at multiple steps of the Hippo signaling pathway.

• BMB Reports
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• v.51 no.1
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• pp.21-26
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• 2018

Delta-like ligand 4 (DLL4) expression in endothelial cells is intimately associated with angiogenic sprouting and vascular remodeling, but the precise mechanism of transcriptional regulation of DLL4 remains incompletely understood. Here, we showed that LIM-domain binding protein 2 (LDB2) plays an important role in regulating basal DLL4 and VEGF-induced DLL4 expression. Knockdown of LDB2 using siRNA enhanced endothelial sprouting and tubular network formation in vitro. Injection of ldb2-morpholino resulted in defective development of intersegmental vessels in zebrafish. Reduction or over-expression of LDB2 in endothelial cells decreased or increased DLL4 expression. LDB2 regulated DLL4 promoter activity by binding to its promoter region and the same promoter region was occupied and regulated by the LMO2/TAL1/GATA2 complex. Interestingly, LDB2 also mediated VEGF-induced DLL4 expression in endothelial cells. The regulation of DLL4 by the LDB2 complex provides a novel mechanism of DLL4 transcriptional control that may be exploited to develop therapeutics for aberrant vascular remodeling.

• Molecules and Cells
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• v.21 no.2
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• pp.213-217
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• 2006

Although AIMP1 (previously known as p43) is one of three auxiliary proteins bound to a macromolecular aminoacyl tRNA complex, it is also secreted as a cytokine controlling both angiogenesis and immune responses. Here we show that systemically administered purified recombinant human AIMP1 had anti-tumor activity in mouse xenograft models. In Meth A-bearing Balb/c mice, tumor volume increased about 28 fold in the vehicle treatment group, while an increase of about 16.7 fold was observed in the AIMP1-treated group. We also evaluated the anti-tumor activity of AIMP1 in combination with a sub-clinical dose of the cytotoxic anti-tumor drug, paclitaxel. The growth of NUGC-3 human stomach cancer cells was suppressed by 84% and 94% by the combinations of 5 mg/kg paclitaxel + 25 mg/kg AIMP1 (p = 0.03), and 5 mg/kg paclitaxel + 50 mg/kg AIMP1 (p = 0.02), respectively, while 5 mg/kg paclitaxel alone suppressed growth by only 54% (p = 0.02). A similar cooperative effect of AIMP1 and paclitaxel was observed in a lung cancer xenograft model. These results suggest that AIMP1 may be useful as a novel anti-tumor agent.

• Molecules and Cells
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• v.37 no.4
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• pp.286-294
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• 2014

Mammalian polo-like kinase 1 (Plk1) has been studied intensively as a key regulator of various cell cycle events that are critical for proper M-phase progression. The polobox domain (PBD) present in Plk1's C-terminal noncatalytic region has been shown to play a central role in targeting the N-terminal kinase domain of Plk1 to specific subcellular locations. Subsequent studies reveal that PBD binds to a phosphorylated motif generated by one of the two mechanisms - self-priming by Plk1 itself or non-self-priming by a Pro-directed kinase, such as Cdc2. Here, we comparatively review the differences in the biochemical steps of these mechanisms and discuss their physiological significance. Considering the diverse functions of Plk1 during the cell cycle, a better understanding of how the catalytic activity of Plk1 functions in concert with its cisacting PBD and how this coordinated process is intricately regulated to promote Plk1 functions will be important for providing new insights into different mechanisms underlying various Plk1-mediated biological events that occur at the multiple stages of the cell cycle.

• Molecules and Cells
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• v.41 no.5
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• pp.381-389
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• 2018

ARF is a tumor suppressor protein that has a pivotal role in the prevention of cancer development through regulating cell proliferation, senescence, and apoptosis. As a factor that induces senescence, the role of ARF as a tumor suppressor is closely linked to the p53-MDM2 axis, which is a key process that restrains tumor formation. Thus, many cancer cells either lack a functional ARF or p53, which enables them to evade cell oncogenic stress-mediated cycle arrest, senescence, or apoptosis. In particular, the ARF gene is a frequent target of genetic and epigenetic alterations including promoter hyper-methylation or gene deletion. However, as many cancer cells still express ARF, pathways that negatively modulate transcriptional or post-translational regulation of ARF could be potentially important means for cancer cells to induce cellular proliferation. These recent findings of regulators affecting ARF protein stability along with its low levels in numerous human cancers indicate the significance of an ARF post-translational mechanism in cancers. Novel findings of regulators stimulating or suppressing ARF function would provide new therapeutic targets to manage cancer- and senescence-related diseases. In this review, we present the current knowledge on the regulation and alterations of ARF expression in human cancers, and indicate the importance of regulators of ARF as a prognostic marker and in potential therapeutic strategies.

• Microbiology and Biotechnology Letters
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• v.48 no.2
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• pp.113-120
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• 2020

The objective of the study was to assess the survival of microencapsulated Lactobacillus plantarum ATCC8014 produced using the emulsion technique in alginate gel combined with pectin and maltodextrin components. The microcapsules were then added to cupcake dough that was further baked at 200℃ for 12 min. The viability of L. plantarum was assessed during baking and the 10 days of storage at 4℃ as well as in simulated gastrointestinal conditions. In addition, yeast-mold and water activity were investigated. After baking, the samples with microencapsulated L. plantarum contained more than 5 log CFU/g, which was higher compared to the bacterial concentration of the control samples. The concentration of L. plantarum was more than 6 logs CFU/g after the end of the storage; therefore, the probiotic functioned as a biopreservative in the cake. The prebiotic component strengthened the microcapsules network and helped protect the viability of L. plantarum in simulated gastric fluid (SGF) and simulated intestinal fluid (SIF) media. The results show that the addition of L. plantarum microencapsules did not affect the sensory scores of the cupcake while ensuring the viability of the probiotic during baking and storing.

• Journal of Plant Biology
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• v.30 no.3
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• pp.173-179
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• 1987

The effect of polyamine, Ca2+ and calmodulin on GS ($\beta$-glucan synthetase) activity was studied in Daucus carota root. The Ca2+ is shown to have no effect on the GS activity whereas the GS II activity is increased in response to increase in concentration of the Ca2+. When the protoplasts are cultured, for 4 days, the GS II activity increases as a tunction of time and reachs a maximum after 3 days at a time when the network of cellulose microfibrils is known to be synthesized. The effect of the Ca2+ and 1mM spermine on the GS II activity turns out to be synergistic, especially more synergistic at lower concentration of the Ca2+. The GS II activity seems to be enhanced by the Ca2+. The GS II activity in the protoplast treated by the calcium channel blocker, verapamil, turns out to be lower than that of the control. Cumulative results suggest that the Ca2+ stimulates the cell wall regeneration via enhancement of the GS II activity responsible for synthesizing the cell wall component throught synergistic effect with spermine.

• Molecules and Cells
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• v.44 no.10
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• pp.746-757
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• 2021

Plant somatic cells can be reprogrammed into a pluripotent cell mass, called callus, which can be subsequently used for de novo shoot regeneration through a two-step in vitro tissue culture method. MET1-dependent CG methylation has been implicated in plant regeneration in Arabidopsis, because the met1-3 mutant exhibits increased shoot regeneration compared with the wild-type. To understand the role of MET1 in de novo shoot regeneration, we compared the genome-wide DNA methylomes and transcriptomes of wildtype and met1-3 callus and leaf. The CG methylation patterns were largely unchanged during leaf-to-callus transition, suggesting that the altered regeneration phenotype of met1-3 was caused by the constitutively hypomethylated genes, independent of the tissue type. In particular, MET1-dependent CG methylation was observed at the blue light receptor genes, CRYPTOCHROME 1 (CRY1) and CRY2, which reduced their expression. Coexpression network analysis revealed that the CRY1 gene was closely linked to cytokinin signaling genes. Consistently, functional enrichment analysis of differentially expressed genes in met1-3 showed that gene ontology terms related to light and hormone signaling were overrepresented. Overall, our findings indicate that MET1-dependent repression of light and cytokinin signaling influences plant regeneration capacity and shoot identity establishment.

• Journal of Plant Biotechnology
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• v.48 no.3
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• pp.186-192
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• 2021

The roots of Korean ginseng (Panax ginseng) have a long history of usage as a medicinal drug. Ginsenosides, a group of triterpenioid saponins in ginseng, have been reported to show important pharmacological effects. Many studies have attempted to identify the ginsenoside synthesis pathways of P. ginseng and to increase crop productivity. Recent studies have shown that exogenous gibberellin (GA) treatments promote storage root secondary growth by integration of the modulating cambium stem cell homeostasis with a secondary cell wall-related gene network. However, the dynamic regulation of ginsenoside synthesis-related genes and their contents by external signaling cues has been rarely evaluated. In this study, we confirmed that GA treatment not only enhanced the secondary growth of P. ginseng storage roots, but also significantly enriched the terpenoid biosynthesis process in RNA-seq analysis. Consistently, we also found that the expression of most genes involved in the ginsenoside synthesis pathways, including those encoding methylerythritol-4-phosphate (MEP) and mevalonate (MVA), and the saponin content in both leaves and roots was increased by exogenous GA application. These results can be used in future development of biotechnology for ginseng breeding and enhancement of saponin content.