• BMB Reports
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• v.49 no.7
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• pp.394-399
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• 2016

Glioma-Associated Oncogene Homolog1 (Gli1) is known to be activated in malignant glioma; however, its downstream pathway has not been fully explained. The aim of this study was to explore the role of Gli1-Aquaporin1 (AQP1) signal pathway in glioma cell survival. Our data suggests that both Gli1 and AQP1 are upregulated in glioma tissues, as in comparison to in normal tissues. These up-regulation phenomena were also observed in glioma U251 and U87 cells. It was demonstrated that Gli1 positively regulated the AQP1 expression. By luciferase reporter gene and ChIP assay, we observed that this modulation process was realized by combination of Gli1 with AQP1 promotor. In addition, knock down of Gli1 by siRNA interference reduced the viability of glioma cells as well as suppressed cell metastasis. Also, the inhibitory effects of cell survival by silenced Gli1 were abrogated by AQP1 overexpression. In summary, glioma cell survival is a regulatory process and can be mediated by Gli1-AQP1 pathway.

• Communications for Statistical Applications and Methods
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• v.29 no.5
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• pp.591-601
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• 2022

In gene set analysis with microarray expression data, a group of genes such as a gene regulatory pathway and a signaling pathway is often tested if there exists either differentially expressed (DE) or differentially co-expressed (DC) genes between two biological conditions. Recently, a statistical test based on covariance estimation have been proposed in order to identify DC genes. In particular, covariance regularization by hard thresholding indeed improved the power of the test when the proportion of DC genes within a biological pathway is relatively small. In this article, we compare covariance thresholding methods using four different regularization penalties such as lasso, hard, smoothly clipped absolute deviation (SCAD), and minimax concave plus (MCP) penalties. In our extensive simulation studies, we found that both SCAD and MCP thresholding methods can outperform the hard thresholding method when the proportion of DC genes is extremely small and the number of genes in a biological pathway is much greater than a sample size. We also applied four thresholding methods to 3 different microarray gene expression data sets related with mutant p53 transcriptional activity, and epithelium and stroma breast cancer to compare genetic pathways identified by each method.

• Journal of Microbiology and Biotechnology
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• v.14 no.3
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• pp.483-489
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• 2004

Pseudomonas sp. S-47 is a bacterium capable of degrading benzoate as well as 4-chlorobenzoate (4CBA). Benzoate and 4CBA are known to be degraded via a meta-cleavage pathway characterized by a series of enzymes encoded by xyl genes. The meta-cleavage pathway operon in Pseudomonas sp. S-47 encodes a set of enzymes which transform benzoate and 4CBA into TCA cycle intermediates via the meta-cleavage of (4-chloro )catechol to produce pyruvate and acetyl-CoA. In the current study, the meta-pathway gene cluster was cloned from the chromosomal DNA of S-47 strain to obtain pCS1, which included the degradation activities for 4CBA and catechol. The genetic organization of the operon was then examined by cloning the meta-pathway genes into a pBluescript SKII(+) vector. As such, the meta-pathway operon from Pseudomonas sp. S-47 was found to contain 13 genes in the order of xylXYZLTEGFlQKIH. The two regulatory genes, xylS and xylR, that control the expression of the meta-pathway operon, were located adjacently downstream of the meta-pathway operon. The xyl genes from strain S-47 exhibited a high nucleoside sequence homology to those from Pseudomonas putida mt-2, except for the xylJQK genes, which were more homologous to the corresponding three genes from P. stutzeri AN10. One open reading frame was found between the xylH and xylS genes, which may playa role of a transposase. Accordingly, the current results suggest that the xyl gene cluster in Pseudomonas sp. S-47 responsible for the complete degradation of benzoate was recombined with the corresponding genes from P. putida mt-2 and P. stutzeri AN10.

• BMB Reports
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• v.52 no.5
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• pp.336-341
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• 2019

The cGAS-STING pathway plays an important role in pathogen-induced activation of the innate immune response. The 29-kDa amino-terminal fibronectin fragment (29-kDa FN-f) found predominantly in the synovial fluid of osteoarthritis (OA) patients increases the expression of catabolic factors via the toll-like receptor-2 (TLR-2) signaling pathway. In this study, we investigated whether 29-kDa FN-f induces inflammatory responses via the cyclic GMP-AMP synthase (cGAS)/stimulator of interferon gene (STING) pathway in human primary chondrocytes. The levels of cGAS and STING were elevated in OA cartilage compared with normal cartilage. Long-term treatment of chondrocytes with 29-kDa FN-f activated the cGAS/STING pathway together with the increased level of gamma-H2AX, a marker of DNA breaks. In addition, the expression of pro-inflammatory cytokines, including granulocyte-macrophage colony-stimulating factor (GM-CSF/CSF-2), granulocyte colony-stimulating factor (G-CSF/CSF-3), and type I interferon ($IFN-{\alpha}$), was increased more than 100-fold in 29-kDa FN-f-treated chondrocytes. However, knockdown of cGAS and STING suppressed 29-kDa FN-f-induced expression of GM-CSF, G-CSF, and $IFN-{\alpha}$ together with the decreased activation of TANK-binding kinase 1 (TBK1), interferon regulatory factor 3 (IRF3), and inhibitor protein ${\kappa}B{\alpha}$ ($I{\kappa}B{\alpha}$). Furthermore, NOD2 or TLR-2 knockdown suppressed the expression of GM-CSF, G-CSF, and $IFN-{\alpha}$ as well as decreased the activation of the cGAS/STING pathway in 29-kDa FN-f-treated chondrocytes. These data demonstrate that the cGAS/STING/TBK1/IRF3 pathway plays a critical role in 29-kDa FN-f-induced expression of pro-inflammatory cytokines.

• The Microorganisms and Industry
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• v.25 no.1
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• pp.2-9
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• 1999

A study was made on enzymes of carbohydrate metabolism in T. concretivorus grown with and without glucose. The present results show that T. concretivorus possesses high activities of pentose shunt pathway and related enzymes, glucokinase, G-6-P dehydrogenase, 6-PG dehydrogenase, and phosphoglucoisomerase, but low activities of enzymes unique to EMP(fructose-1,6-diphosphate aldolase). Although the synthesis of the latter enzymes remains largely unaffected by the growth enviroment, that of the former is stimulated by glucose. And the failure to detect ED pathway enzymes in cells grown in thiosulate or thiosulfate-glucose medium eliminates the ED pathway as a significant route of glucose catabolism in T.concretivorus. These results suggest that pentose shunt pathway performs an energetic role in glucose metabolism by T.concretivorus with EMP as a subway. The absence of ED pathway and the presence of pentose shunt pathway which is the major route of catabolism in T.concretivorus are similar to those of other obligately chemolitho-trophic thiobacilli. The G-6-P and 6-PG dehydrogenase are both NAD and NADP specific, but MAD predominant. However, the 3-PGAL dehydrogenase is only NAD specific. Since the specific activity of 3-PGAL generated from glucose is converted mainly into pyruvate which is channeled into the TCA cycle. All enzymes of the TCA cycle tested and NADH oxidase are detected in the cells of T.concretivorus grown in thiosulfate. The specific activities of fumarase and isocitrate dehydrogenase are high and others are low. The presence of two isocitrate dehydrogenase (NAD-and NADP-linked) may have important regulatory function for this organism. The activity of NAD-oxidase, which is implicated in the energy generating metabolism, was very high in the crude cell-free extract of T.concretivorus, recording 55.11 m.mu. mole/min/mg protein. This well coincides with the fact that activities of NAD-linked G-6-P dehydrogenase, 6-PG dehydrogenase and 3-PGAL dehydrogenase were high.

• Korean Journal of Microbiology
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• v.11 no.1
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• pp.1-18
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• 1973

A study was made on enzymes of carbohydrate metabolism in T. concretivorus grown with and without glucose. The present results show that T. concretivorus possesses high activities of pentose shunt pathway and related enzymes, glucokinase, G-6-P dehydrogenase, 6-PG dehydrogenase, and phosphoglucoisomerase, but low activities of enzymes unique to EMP(fructose-1, 6-diphosphate aldolase). Although the synthesis of the latter enzymes remains largely unaffected by the growth enviroment, that of the former is stimulated by glucose. And the failure to detect ED pathway enzymes in cells grown in thiosulate or thiosulfate-glucose medium eliminates the ED pathway as a significant route of glucose catabolism in T.concretivorus. These results suggest that pentose shunt pathway performs an energetic role in glucose metabolism by T.concretivorus with EMP as a subway. The absence of ED pathway and the presence of pentose shunt pathway which is the major route of catabolism in T.concretivorus are similar to those of other obligately chemolitho-trophic thiobacilli. The G-6-P and 6-PG dehydrogenase are both NAD and NADP specific, but MAD predominant. However, the 3-PGAL dehydrogenase is only NAD specific. Since the specific activity of 3-PGAL generated from glucose is converted mainly into pyruvate which is channeled into the TCA cycle. All enzymes of the TCA cycle tested and NADH oxidase are detected in the cells of T.concretivorus grown in thiosulfate. The specific activities of fumarase and isocitrate dehydrogenase are high and others are low. The presence of two isocitrate dehydrogenase (NAD-and NADP-linked) may have important regulatory function for this organism. The activity of NAD-oxidase, which is implicated in the energy generating metabolism, was very high in the crude cell-free extract of T.concretivorus, recording 55.11 m$\mu$ mole/min/mg protein. This well coincides with the fact that activities of NAD-linked G-6-P dehydrogenase, 6-PG dehydrogenase and 3-PGAL dehydrogenase were high.

• BMB Reports
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• v.56 no.6
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• pp.321-325
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• 2023

RNAs are pivotal molecules acting as messengers of genetic information and regulatory molecules for cellular development and survival. From birth to death, RNAs face constant cellular decision for the precise control of cellular function and activity. Most eukaryotic cells employ conserved machineries for RNA decay including RNA silencing and RNA quality control (RQC). In plants, RQC monitors endogenous RNAs and degrades aberrant and dysfunctional species, whereas RNA silencing promotes RNA degradation to repress the expression of selected endogenous RNAs or exogenous RNA derived from transgenes and virus. Interestingly, emerging evidences have indicated that RQC and RNA silencing interact with each by sharing target RNAs and regulatory components. Such interaction should be tightly organized for proper cellular survival. However, it is still elusive that how each machinery specifically recognizes target RNAs. In this review, we summarize recent advances on RNA silencing and RQC pathway and discuss potential mechanisms underlying the interaction between the two machineries.

• Journal of Microbiology and Biotechnology
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• v.15 no.1
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• pp.66-71
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• 2005

Doxorubicin is a clinically important anticancer polyketide compound that is typically produced by Streptomyces peucetius var. caesius. To improve doxorubicin productivity by S. peucetius, a doxorubicin pathway-specific regulatory gene, dnrI, was cloned into a high-copy-number plasmid containing a catechol promoter system. The S. peucetius containing the recombinant plasmid exhibited approximately 9.5-fold higher doxorubicin productivity compared with the wild-type S. peucetius. The doxorubicin productivity by this recombinant S. peucetius strain was further improved through the optimization of culture media composition. Based on the Fractional Factorial Design (FFD), cornstarch, $K_2HPO_4$, and $MgSO_4$ were identified to be the key factors influencing doxorubicin productivity. The Response Surface Method (RSM) results based on 20 independent culture conditions with varying amounts of key factors predicted the highest theoretical doxorubicin productivity of 11.1 mg/l with corn starch of 46.33 g/l, $K_2HPO_4$ of 4.63 g/l, and $MgSO_4$ of 9.26 g/l. The doxorubicin productivity of the recombinant S. peucetius strain with the RSM-based optimized culture condition was experimentally verified to be 11.46 mg/l, which was approximately 30.8-fold higher productivity compared with the wild-type S. peucetius without culture media optimization.

• IMMUNE NETWORK
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• v.2 no.3
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• pp.125-132
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• 2002

In the past, bioinformatics was often regarded as a difficult and rather remote field, practiced only by computer scientists and not a practical tool available to biologists. However, the various on-going genome projects have had a serious impact on biological sciences in various ways and now there is little doubt that bioinformatics is an essential part of the research environment, with a wealth of biological information to analyze and predict. Fully sequenced genomes made us to have additional insights into the functional properties of the encoded proteins and made it possible to develop new tools and schemes for functional biology on a proteomic scale. Among those are the yeast two-hybrid system, mass spectrometry and microarray: the technology of choice to detect protein-protein interactions. These functional insights emerge as networks of interacting proteins, also known as "pathway informatics" or "interactomics". Without exception it is no longer possible to make advances in the signaling/regulatory pathway studies without integrating information technologies with experimental technologies. In this paper, we will introduce the databases of protein interaction worldwide and discuss several challenging issues regarding the actual implementation of databases.

• Journal of Microbiology and Biotechnology
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• v.24 no.10
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• pp.1377-1381
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• 2014

In order to discover and develop novel signaling inhibitors from plants, a screening system was established targeting the two-component system of Cryptococcus neoformans by using the wild type and a calcineurin mutant of C. neoformans, based on the counter-regulatory action of high-osmolarity glycerol (Hog1) mitogen-activated protein kinase and the calcineurin pathways in C. neoformans. Among 10,000 plant extracts, that from Harrisonia abyssinica Oliv. exhibited the most potent inhibitory activity against C. neoformans var. grubii H99 with fludioxonil. Bioassay-guided fractionation was used to isolate two bioactive compounds from H. abyssinica, and these compounds were identified as chebulagic acid and chebulanin using spectroscopic methods. These compounds specifically inhibited the calcineurin pathway in C. neoformans. Moreover, they exhibited potent antifungal activities against various human pathogenic fungi with minimum inhibitory concentrations ranging from 0.25 to over $64{\mu}g/ml$.