• Journal of Life Science
• /
• v.21 no.8
• /
• pp.1067-1075
• /
• 2011

Coiled-coil domain-containing protein 98 (CCDC98) plays a role in G2/M DNA damage checkpoint pathways by recruiting breast cancer 1 (BRCA1)-A complex to the DNA-damaged sites. However, the molecular mechanism of CCDC98 on the DNA damage-induced G2/M checkpoint pathways is unclear. In this study, we identifed Wilms tumor 1-associating protein (WTAP) as a novel CCDC98-binding protein, using tandem affinity purification. We confirmed the association between CCDC98 and WTAP using in vivo and in vitro binding assays. We demonstrated that CCDC98 regulates cyclin B1 expression by affecting WTAP protein stability. Based on these results, we suggest that CCDC98 may act as a novel cell cycle regulator by regulating the expression level of cyclin B1.

• Journal of Microbiology and Biotechnology
• /
• v.33 no.11
• /
• pp.1403-1411
• /
• 2023

Carbon dioxide (CO₂) is the most abundant component of greenhouse gases (GHGs) and directly creates environmental issues such as global warming and climate change. Carbon capture and storage have been proposed mainly to solve the problem of increasing CO₂ concentration in the atmosphere; however, more emphasis has recently been placed on its use. Among the many methods of using CO₂, one of the key environmentally friendly technologies involves biologically converting CO₂ into other organic substances such as biofuels, chemicals, and biomass via various metabolic pathways. Although an efficient biocatalyst for industrial applications has not yet been developed, biological CO₂ conversion is the needed direction. To this end, this review briefly summarizes seven known natural CO₂ fixation pathways according to carbon number and describes recent studies in which natural CO₂ assimilation systems have been applied to heterogeneous in vivo and in vitro systems. In addition, studies on the production of methanol through the reduction of CO₂ are introduced. The importance of redox cofactors, which are often overlooked in the CO₂ assimilation reaction by enzymes, is presented; methods for their recycling are proposed. Although more research is needed, biological CO₂ conversion will play an important role in reducing GHG emissions and producing useful substances in terms of resource cycling.

• The Journal of the Korea Contents Association
• /
• v.14 no.11
• /
• pp.467-475
• /
• 2014

With the development of genomics, wearable device and IT/NT, a vast amount of bio-medical data are generated recently. Also, healthcare industries based on big-data are booming and big-data technology based on bio-medical data is rising rapidly as a core technology for improving the national health and aged society. A pathway is the biological deep knowledge that represents the relations of dynamics and interaction among proteins, genes and cells by a network. A pathway is wildly being used as an important part of a bio-medical big-data analysis. However, a pathway analysis requires a lot of time and effort because a pathway is very diverse and high volume. Also, multidimensional analysis systems for various pathways are nonexistent even now. In this paper, we proposed a pathway analysis system that collects user interest pathways from KEGG pathway database that supports the most widely used pathways, constructs a network based on a hierarchy structure of pathways and analyzes the relations of dynamics and interaction among pathways by clustering and selecting core pathways from the network. Finally, to verify the superiority of our pathway analysis system, we evaluate the performance of our system in various experiments.

• Journal of Microbiology and Biotechnology
• /
• v.17 no.7
• /
• pp.1098-1105
• /
• 2007

Quantum mechanical and molecular dynamics simulation analysis has been performed on the model system for CALB (Candida antarctica lipase B) with esters to study the reaction mechanism and conformational preference of catalytic hydrolysis and the esterification reaction. Using quantum mechanical analysis, the ping-pong bi-bi mechanism was applied and energies and 3-dimensional binding configurations of the whole reaction pathways were calculated. Further molecular dynamics simulation analysis was performed on the basis of the transition state obtained from quantum mechanical study to observe the effect of structures of the substrates. Calculation results using substrates of different chain length and chiral configurations were compared for conformational preference. The calculated results showed very small influence on chain length, whereas chiral conformation showed big differences. Calculated results from molecular modeling studies have been compared qualitatively with the experimental data using racemic mixtures of (${\pm}$)-cis-4-acetamido-cyclopent-2-ene-1-ethyl acetate as substrates.

• Biotechnology and Bioprocess Engineering:BBE
• /
• v.7 no.6
• /
• pp.357-361
• /
• 2002

Continuous production of lactic acid from glucose by Lactobacillus rhamnosus with cell recycling using an acoustic cell settler was carried out. The performance of the system, such as the concentration of cell and product were compared with the control experiment without recycling. The acoustic settler showed cell separation efficiency of 67% during the continuous operation and the cell concentration in the fermentor with recycle exceeded that of the control by 29%. Com-pared with the control, tactic acid production was increased by 40%, while glucose consumption was only increased by 8%. The higher value of lactic acid production to substrate consumption (Yp/s, product yield coefficient) achieved by cell recycling is interpreted to indicate that the recycled cell mass consumes less substrate to produce the same amount of product than the control Within system environmental changes due to the longer mean cell residence time induced the cells maintaining the metabolic pathways to produce Less by-Product but more product, lactic acid.

• BMB Reports
• /
• v.37 no.5
• /
• pp.612-617
• /
• 2004

Autosomal dominant polycystic kidney disease (ADPKD) is a common genetic disorder characterized by the formation of fluid-filled cysts in the kidney and progressive renal failure. Other manifestations of ADPKD include the formation of cysts in other organs (liver, pancreas, and spleen), hypertension, cardiac defects, and cerebral aneurysms. The loss of function of the polycystin -1 and -2 results in the formation of epithelium-lined cysts, a process that depends on initial epithelial proliferation. cDNA microarrays powerfully monitor gene expression and have led to the discoveries of pathways regulating complex biological processes. We undertook to profile the gene expression patterns of epithelial cells derived from the cysts of ADPKD patients using the cDNA microarray technique. Candidate genes that were differently expressed in cyst tissues were identified. 19 genes were up-regulated, and 6 down-regulated. Semi-quantitative RT-PCR results were consistent with the microarray findings. To distinguish between normal and epithelial cells, we used the hierarchical method. The results obtained may provide a molecular basis for understanding the biological meaning of cytogenesis.

• BMB Reports
• /
• v.40 no.1
• /
• pp.82-87
• /
• 2007

Our heterologous expression system of the human ferritin H-chain gene (hfH) allowed us to characterize the cellular effects of ferritin in yeasts. The recombinant Saccharomyces cerevisiae (YGH2) evidenced impaired growth as compared to the control, which was correlated with ferritin expression and with the formation of core minerals. Growth was recovered via the administration of iron supplements. The modification of cellular iron metabolism, which involved the increased expression of high-affinity iron transport genes (FET3 and FTR1), was detected via Northern blot analysis. The findings may provide some evidence of cytosolic iron deficiency, as the genes were expressed transcriptionally under iron-deficient conditions. According to our results examining reactive oxygen species (ROS) generation via the fluorescence method, the ROS levels in YGH2 were decreased compared to the control. It suggests that the expression of active H-ferritins reduced the content of free iron in yeast. Therefore, present results may provide new insights into the regulatory network and pathways inherent to iron depletion conditions.

• Proceedings of the Botanical Society of Korea Conference
• /
• 1996.06a
• /
• pp.50-63
• /
• 1996

Nitrogen (N) is an important regulator of the expression of genes involved in carbon and N assimilation pathways in plants by selectively altering the levels of proteins and/or mRNAs. These in C4 plants include genes for such as phosphoenolpyruvate carboxylase, carbonic anhydrase, and pyruvate-Pi dikinase. The C4 genes are regulated in mesophyll cells by N availability both transcriptionally and posttranscriptionally through cytokinins and glutamine as signals. The level of both the signals is up-regulated by N availability: cytokinins in roots and glutamine in leaves. The level of glutamine is controlled by the differential expression by N of glutamine synthetase and ferrdoxin-dependent glutamate synthase genes which locate in the mesophyll cells of C4 plants. The results is discussed as molecular mechanism for the greater N use efficiency of the plants as well as N partitioning is the photosynthetic cells.

• Molecules and Cells
• /
• v.40 no.5
• /
• pp.315-321
• /
• 2017

The inositol polyphosphates are a group of multifunctional signaling metabolites whose synthesis is catalyzed by a family of inositol kinases that are evolutionarily conserved from yeast to humans. Inositol polyphosphate multikinase (IPMK) was first identified as a subunit of the arginine-responsive transcription complex in budding yeast. In addition to its role in the production of inositol tetrakis- and pentakisphosphates ($IP_4$ and $IP_5$), IPMK also exhibits phosphatidylinositol 3-kinase (PI3-kinase) activity. Through its PI3-kinase activity, IPMK activates Akt/PKB and its downstream signaling pathways. IPMK also regulates several protein targets non-catalytically via protein-protein interactions. These non-catalytic targets include cytosolic signaling factors and transcription factors in the nucleus. In this review, we highlight the many known functions of mammalian IPMK in controlling cellular signaling networks and discuss future challenges related to clarifying the unknown roles IPMK plays in physiology and disease.

• BMB Reports
• /
• v.56 no.7
• /
• pp.374-384
• /
• 2023

Fibrosis is a pathological condition that is characterized by an abnormal buildup of extracellular matrix (ECM) components, such as collagen, in tissues. This condition affects various organs of the body, including the liver and kidney. Early diagnosis and treatment of fibrosis are crucial, as it is a progressive and irreversible process in both organs. While there are certain similarities in the fibrosis process between the liver and kidney, there are also significant differences that must be identified to determine molecular diagnostic markers and potential therapeutic targets. Long non-coding RNAs (lncRNAs), a class of RNA molecules that do not code for proteins, are increasingly recognized as playing significant roles in gene expression regulation. Emerging evidence suggests that specific lncRNAs are involved in fibrosis development and progression by modulating signaling pathways, such as the TGF-β/Smad pathway and the β-catenin pathway. Thus, identifying the precise lncRNAs involved in fibrosis could lead to novel therapeutic approaches for fibrotic diseases. In this review, we summarize lncRNAs related to fibrosis in the liver and kidney, and propose their potential as therapeutic targets based on their functions.