• Title/Summary/Keyword: transcription map

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KMS99220 Exerts Anti-Inflammatory Effects, Activates the Nrf2 Signaling and Interferes with IKK, JNK and p38 MAPK via HO-1

  • Lee, Ji Ae;Kim, Dong Jin;Hwang, Onyou
    • Molecules and Cells
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    • v.42 no.10
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    • pp.702-710
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    • 2019
  • Neuroinflammation is an important contributor to the pathogenesis of neurodegenerative disorders including Parkinson's disease (PD). We previously reported that our novel synthetic compound KMS99220 has a good pharmacokinetic profile, enters the brain, exerts neuroprotective effect, and inhibits $NF{\kappa}B$ activation. To further assess the utility of KMS99220 as a potential therapeutic agent for PD, we tested whether KMS99220 exerts an anti-inflammatory effect in vivo and examined the molecular mechanism mediating this phenomenon. In 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine-treated mice, oral administration of KMS99220 attenuated microglial activation and decreased the levels of inducible nitric oxide synthase and interleukin 1 beta ($IL-1{\beta}$) in the nigrostriatal system. In lipopolysaccharide (LPS)-challenged BV-2 microglial cells, KMS99220 suppressed the production and expression of $IL-1{\beta}$. In the activated microglia, KMS99220 reduced the phosphorylation of $I{\kappa}B$ kinase, c-Jun N-terminal kinase, and p38 MAP kinase; this effect was mediated by heme oxygenase-1 (HO-1), as both gene silencing and pharmacological inhibition of HO-1 abolished the effect of KMS99220. KMS99220 induced nuclear translocation of the transcription factor Nrf2 and expression of the Nrf2 target genes including HO-1. Together with our earlier findings, our current results show that KMS99220 may be a potential therapeutic agent for neuroinflammation-related neurodegenerative diseases such as PD.

Potential biomarkers and signaling pathways associated with the pathogenesis of primary salivary gland carcinoma: a bioinformatics study

  • Bayat, Zeynab;Ahmadi-Motamayel, Fatemeh;Salimi Parsa, Mohadeseh;Taherkhani, Amir
    • Genomics & Informatics
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    • v.19 no.4
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    • pp.42.1-42.17
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    • 2021
  • Salivary gland carcinoma (SGC) is rare cancer, constituting 6% of neoplasms in the head and neck area. The most responsible genes and pathways involved in the pathology of this disorder have not been fully understood. We aimed to identify differentially expressed genes (DEGs), the most critical hub genes, transcription factors, signaling pathways, and biological processes (BPs) associated with the pathogenesis of primary SGC. The mRNA dataset GSE153283 in the Gene Expression Omnibus database was re-analyzed for determining DEGs in cancer tissue of patients with primary SGC compared to the adjacent normal tissue (adjusted p-value < 0.001; |Log2 fold change| > 1). A protein interaction map (PIM) was built, and the main modules within the network were identified and focused on the different pathways and BP analyses. The hub genes of PIM were discovered, and their associated gene regulatory network was built to determine the master regulators involved in the pathogenesis of primary SGC. A total of 137 genes were found to be differentially expressed in primary SGC. The most significant pathways and BPs that were deregulated in the primary disease condition were associated with the cell cycle and fibroblast proliferation procedures. TP53, EGF, FN1, NOTCH1, EZH2, COL1A1, SPP1, CDKN2A, WNT5A, PDGFRB, CCNB1, and H2AFX were demonstrated to be the most critical genes linked with the primary SGC. SPIB, FOXM1, and POLR2A significantly regulate all the hub genes. This study illustrated several hub genes and their master regulators that might be appropriate targets for the therapeutic aims of primary SGC.

Polymorphism in the intron 20 of porcine O-linked N-acetylglucosamine transferase

  • Kim, Jong Gug;Nonneman, Dan;Kim, Doo-Wan;Shin, Sangsu;Rohrer, Gary A.
    • Asian-Australasian Journal of Animal Sciences
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    • v.30 no.8
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    • pp.1086-1092
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    • 2017
  • Objective: O-linked N-acetylglucosamine (O-GlcNAc) transferase (OGT) catalyzes the addition of O-GlcNAc and GlcNAcylation has extensive crosstalk with phosphorylation to regulate signaling and transcription. Pig OGT is located near the region of chromosome X that affects follicle stimulating hormone level and testes size. The objective of this study was to find the variations of OGT between European and Chinese pigs. Methods: Pigs were tested initially for polymorphism in OGT among European and Chinese pigs by polymerase chain reaction and sequencing at the U.S. Meat Animal Research Center (USMARC). The polymorphism was also determined in an independent population of pigs including European and Chinese Meishan (ME) breeds at the National Institute of Animal Science (NIAS, RDA, Korea). Results: The intron 20 of OGT from European and Chinese pigs was 514 and 233 bp, respectively, in the pigs tested initially. They included 1 White composite (WC) boar and 7 sows ($2Minzu{\times}WC$, $2Duroc\;[DU]{\times}WC$, $2ME{\times}WC$, $1Fengzing{\times}WC$) at USMARC. The 281-bp difference was due to an inserted 276-bp element and GACTT in European pigs. When additional WC and ME boars, the grandparents that were used to generate the $1/2ME{\times}1/2WC$ parents, and the 84 boars of 16 litters from mating of $1/2ME{\times}1/2WC$ parents were analyzed, the breeds of origin of X chromosome quantitative trait locus (QTL) were confirmed. The polymorphism was determined in an independent population of pigs including DU, Landrace, Yorkshire, and ME breeds at NIAS. OGT was placed at position 67 cM on the chromosome X of the USMARC swine linkage map. Conclusion: There was complete concordance with the insertion in European pigs at USMARC and NIAS. This polymorphism could be a useful marker to identify the breed of origin of X chromosome QTL in pigs produced by crossbreeding Chinese and European pigs.

Single Nucleotide Polymorphisms linked to the SlMYB12 Gene that Controls Fruit Peel Color in Domesticated Tomatoes (Solanum lycopersicum L.)

  • Kim, Bichsaem;Kim, Nahui;Kang, Jumsoon;Choi, Youngwhan;Sim, Sung-Chur;Min, Sung Ran;Park, Younghoon
    • Horticultural Science & Technology
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    • v.33 no.4
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    • pp.566-574
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    • 2015
  • Yellow or transparent fruit peel color is caused by the accumulation or lack of naringenin chalcone (NG, C) in fruit peel and determines the red or pink appearance of tomato fruit, respectively. NGC biosynthesis is regulated by the SlMYB12 gene of the Y locus on chromosome 1, and DNA markers derived from SlMYB12 would be useful for marker-assisted selection (MAS) of tomato fruit color. To develop a gene-based marker, 4.9 kb of the SlMYB12 gene including a potential promoter region was sequenced from the red-fruited (YY) line 'FCR' and pink-fruited (yy) line 'FCP'. Sequence alignment of these SlMYB12 alleles revealed no sequence variations between 'FCR' and 'FCP'. To identify SlMYB12-linked single nucleotide polymorphisms (SNPs), 'FCR' and 'FCP' were genotyped using a SolCAP Tomato SNP array and CAPS markers (CAPS-456, 531, 13762, and 38123) were developed from the four SNPs (solcap_snp_sl_456, 531, 13762, and 38123) most closely flanking the SlMYB12. These CAPS markers were mapped using $F_2$ plants derived from 'FCR' ${\times}$ 'FCP'. The map positions of the fruit peel color locus (Y) were CAPS-13762 (0 cM) - 456 (11.09 cM) - Y (15.71 cM) - 38123 (17.82 cM) - 531 (30.86 cM), and the DNA sequence of SlMYB12 was physically anchored in the middle of CAPS-456 and CAPS-38123, indicating that fruit peel color in domesticated tomato is controlled by SlMYB12. A total of 64 SolCAP tomato germplasms were evaluated for their fruit peel color and SNPs located between solcap_snp_sl_456 and 38123. Seven SNPs that were detected in this interval were highly conserved for pink-fruited accessions and specific to transparent fruit peel traits, as depicted by a phenetic tree of 64 accessions based on the seven SNPs.

Structural basis of novel TRP14, thioredoxin-related protein that regulates TNE-$\alpha$ signaling pathways

  • Woo, Joo-Rang;Jeong, Woo-Jin;Rhee, Sue-Goo;Ryu, Seong-Eon
    • Proceedings of the Korea Crystallographic Association Conference
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    • 2003.05a
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    • pp.18-18
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    • 2003
  • Thioredoxin (Trx) is a small redox protein that is ubiquitously distributed from achaes to human. In diverse organisms, the protein is involved in various physiological roles by acting as electron donor and regulators of transcription and apoptosis as well as antioxidants. Sequences of Trx within various species are 27~69% identical to that of E. coli and all Trx proteins have the same overall fold, which consists of central five β strands surrounded by four α helices. The N-terminal cysteine in WCGPC motif of Trx is redox sensitive and the motif is highly conserved. Compared with general cysteine, the N-terminal cysteine has low pKa value. The result leads to increased reduction activity of protein. Recently, novel thio.edoxin-related protein (TRP14) was found from rat brain. TRP14 acts as disulfide reductase like Trx1, and its redox potential and pKa are similar to those of Trx1. However, TRP14 takes up electrons from cytosolic thioredoxin reductase (TrxR1), not from the mitochondrial thioredoxin reductase (TrxR2). Biological roles of TES14 were reported to be involved in regulating TNF-α induced signaling pathways in different manner with Trx1. In depletion experiments, depletion of TRP14 increased TNF-α induced phosphorylation and degradation of IκBα more than the depletion Trx1 did. It also facilitated activation of JNK and p38 MAP kinase induced by TNF-α. Unlike Trx1, TRP14 shows neither interaction nor interference with ASK1. Here, we determined three-dimensional crystal structure of TRP14 by MAD method at 1.8Å. The structure reveals that the conserved cis-Pro (Pro90) and active site-W-C-X-X-C motif, which may be involved in substrate recognition similar to Trx1 , are located at the beginning position of strand β4 and helix α2, respectively. The TRP14 structure also shows that surface of TRP14 in the vicinity of the active site, which is surrounded by an extended flexible loop and an additional short a helix, is different from that of Trx1. In addition, the structure exhibits that TRP14 interact with a distinct target proteins compared with Trx1 and the binding may depend mainly on hydrophobic and charge interactions. Consequently, the structure supports biological data that the TRP14 is involved in regulating TNF-α induced signaling pathways in different manner with Trx1.

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Involvement of Early Growth Response Gene 1 (EGR-1) in Growth Suppression of the Human Colonic Tumor Cells By Apigenin and Its Derivative Isovitexin (Apigenin과 대사물 isovitexin에 의한 인체 대장암세포의 세포활성 억제효과에 있어서의 EGR-1의 역할 연구)

  • Moon, Yu-Seok;Cui, Lei-Guang;Yang, Hyun
    • Journal of Life Science
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    • v.17 no.1 s.81
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    • pp.110-115
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    • 2007
  • It has been previously described that transcription factor early growth response gene product 1 (EGR-1) functions as a tumor suppressor gene. This study was conducted to demonstrate that EGR-1 induction by phytochemical apigenin and its derivative isovitexin can mediate the growth suppression of the intestinal epithelial tumor cells. Apigenin and isovitexin induced EGR-1 gene expression both in the dose and time-dependent manners. Moreover the induction was relatively late around 9-12 hr after treatment of HCT-116 cells, while several anti-inflammatory agent such as NSAIDS and catechins elicit the ECR-1 gene expression at much earlier time about 1-3 hr after treatment. In terms of signal transduction, ERK1/2 was critical for apigenin-induced EGR-1 gene expression and its promoter activation. When EGR-1 gene expression was blocked with EGR-1 small interference RNA, the cytotoxicity of apigenin in the human epithelial cells was attenuated, suggesting the involvement of EGR-1 in the anti-tumoric activity of apigenin. To link the EGR-1 induction to EGR-1-regulated gene products in colon cancer, NSAID-Activated Gene 1 (NAG-1) was demonstrated to be elevated by apigenin and isovitexin at 24-48 hr after treatment. Taken together, apigenin-activated ERK1/2 mediated EGR-1 gene induction, which was associated with suppression of the cellular viability by apigenin compound.

Evaluation of Immune Enhancing Activity of Luthione, a Reduced Glutathione, in RAW 264.7 Macrophages (RAW 264.7 대식세포에서 환원형 glutathione인 luthione의 면역 증강 활성 평가)

  • Seon Yeong Ji;Da Hye Kwon;Hye Jin Hwang;Yung Hyun Choi
    • Journal of Life Science
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    • v.33 no.5
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    • pp.397-405
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    • 2023
  • Although glutathione (GSH) has been shown to play an important role in the prevention of oxidative damage as an antioxidant, studies on immune regulation by it have not been properly conducted. In this study, we investigated whether luthione®, a reduced GSH, has an immune enhancing effect in murine macrophage RAW 264.7 cells. The results of flow cytometry and immunofluorescence experiments indicated that luthione increased phagocytic activity, a representative function of macrophages, compared to the control cells. According to the results of the cytokine array, the expression of interleukin (IL)-5, IL-1β, and IL-27 was significantly increased in the luthione-treated cells. Luthione also enhanced the production of tumor necrosis factor-α and IL-1β through increased expression of their proteins, and increased release of the immune mediators such as nitric oxide (NO) and prostaglandin E2 was associated with increased expression of inducible NO synthase and cyclooxygenase-2. In addition, the expression of cluster of differentiation 86, an M1 macrophage marker, was dramatically enhanced in RAW 264.7 cells treated with luthione. Furthermore, as a result of heat map analysis, we found that cytokine signaling 1/3-mediated signal transducer and activator of transcription/Janus tyrosine kinase signaling pathway was involved in the immunomodulatory effect by luthione. In conclusion, our data suggested that luthione could act as a molecular regulator in M1 macrophage polarization and enhance immune capacity by promoting macrophage phagocytic function.

Loss of Specific Sequences in a Natural Variant of Potato Proteinase Inhibitor II Gene Results in a Loss of Wound-Inducible Gene Expression (감자의 단백질 분해효소 억제제 II 유전자의 특별한 염기서열의 자연적 제거로 인한 상처 유발성 발현의 소실)

  • Thornburg, Robert W.;Park, Sang-Gyu
    • Applied Biological Chemistry
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    • v.39 no.2
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    • pp.104-111
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    • 1996
  • We have isolated several proteinase inhibitor II genes pin2 from a Russet Burbank potato DNA library. One of these, pin2T was subcloned and a 1.8 kb Xbal/Nsil insert was sequenced. This fragment contained the complete Inhibitor II gene including 965 Up of flanking DNA upstream from the gene and 200 bp of flanking DNA downstream from the gene. The open reading frame encodes a protein that is similar to other reported proteinase Inhibitor II proteins. The DNA sequence of the 5' flanking region of pin2T from -714 to +1 is highly homologous (91% identity) with that of the previously isolated wound-inducible pin2K. There are, however, four small deletions in the pin2T promoter which are located at -221 to -200, -263 to -254, -523 to -426 and -759 to -708 relative to the transcription start site of the wound-inducible pin2K. Three of these deletions map to a portion of the promoter that controls the wound-inducibility of the proteinase inhibitor genes. Chimeric genes containing the promoter of the pin2T gene linked with the both CAT and GUS were constructed and transfered into tobacco plants. Analysis of these plants indicated that pin2T is not a wound-inducible gene but is expressed at low levels. Thus, wound-inducibility is lost with the concomitant natural deletion of three small regions of the promoter. Comparision of the sequences deleted in pin2T relative to the pin2K with Genebank sequences indicates that the deleted sequences contain a motif (consensus 5'-AGTAAA-3') that is found in many other wound-inducible genes but not easily found in the published promoter sequences of other plant genes. Nuclear proteins from unwounded and wounded potato leaves were bound to the proximal promoter region, downstream of the 5'-AGTAAA-3', of pin2T. The comparison of the pin2T gone with the pin2K gene indicates that the natural internal promoter deletions are likely responsible for loss of the wound-inducible phenotype in the pin2T gene.

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Amino Acid Biosynthesis and Gene Regulation in Seed (종자내 아미노산 합성 조절 유전자에 관한 연구)

  • ;;;;;Fumio Takaiwa
    • Proceedings of the Botanical Society of Korea Conference
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    • 1996.07a
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    • pp.61-74
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    • 1996
  • Human and monogastric animals can not synthesize 10 out of the 20 amino asids and therefor need to obtain these from their diet. The plant seed is a major source of dietary protein. It is particular important in their study to increase nutritional quality of the seed storage proteins. The low contents of lysine, asparagine and threonenein various cereal seeds and of cystein and methionine. In legume seeds is due to the low proportions of these amino acids in the major storage proteins, we have tried to apply the three strategies; (1) mutagenesis and selection of specific amino acid analogue resistance, (2) cloning and expression study of lysine biosynthesis related gene, (3) transfomation of lysine rich soybean glycinin gene. The 5-methyltryptophan (5MT) resistant cell lines, SAR1, SAR2 and SAR3 were selected from anther derived callus of rice (Oryza sativa L. "Sasanishiki"). Among these selected cell lines, two (SAR1 and SAR3) were able to grow stably at 200 mg/L of 5MT. Analysis of the freed amino acids in callus shows that 5MT resistant cells (SAR3) accumulated free tryptophan at least up to 50 times higher than those that of the higher than of SAS. These results indicated that the 5MT resistant cell lines are useful in studies of amino acid biosynthesis. Tr75, a rice (Oryza sativa L., var. Sasanishiki) mutant resistant to 5MT was segregated from the progenies of its initial mutant line, TR1. The 5MT resistant of TR75 was inherited in the M8 generations as a single dominant nuclear gene. The content of free amino acids in the TR75 homozygous seeds increased approximately 1.5 to 2.0 fold compared to wild-type seeds. Especially, the contents of tryptophan, phenylalanine and aspartic acid were 5.0, 5.3 and 2.7 times higher than those of wild-type seeds, respectively. The content of lysine is significantly low in rice. The lysine is synthesized by a complex pathway that is predominantly regulated by feedback inhibition of several enzymes including asparginase, aspatate kinase, dihydrodipicolinat synthase, etc. For understanding the regulation mechanism of lysine synthesis in rice, we try to clone the lysine biosynthetic metabolism related gene, DHPS and asparaginase, from rice. We have isolated a rice DHPS genomic clone which contains an ORF of 1044 nucleotides (347 amino acids, Mr. 38, 381 daltons), an intron of 587 nucleotides and 5'and 3'-flanking regions by screening of rice genomic DNA library. Deduced amino acid sequence of mature peptide domain of GDHPS clone is highly conserved in monocot and dicot plants whereas that of transit peptide domain is extremely different depending on plant specie. Southern blot analysis indicated that GDHPS is located two copy gene in rice genome. The transcripts of a rice GDHPS were expressed in leaves and roots but not detected in callus tissues. The transcription level of GDHPS is much higher in leaves indicating enormous chloroplast development than roots. Genomic DNA clones for asparaginase genes were screened from the rice genomic library by using plaque hybridization technique. Twelve different genomic clones were isolated from first and second screening, and 8 of 12 clones were analyzed by restriction patterns and identified by Southern Blotting, Restriction enzyme digestion patterns and Southern blot analysis of 8 clones show the different pattern for asparaginase gene. Genomic Southern blot analysis from rice were done. It is estimated that rice has at least 2-3 copy of asparaginase gene. One of 8 positive clones was subcloned into the pBluescript SK(+) vector, and was constructed the physical map. For transformation of lysine rich storage protein into tobacco, soybean glycinin genes are transformed into tobacco. To examine whether glycinin could be stably accumulated in endosperm tissue, the glycinin cDNA was transcriptionally fused to an endosperm-specific promotor of the rice storage protein glutelin gene and then introduced into tobacco genomic via Agrobacterium-mediated transformation. Consequently the glycinin gene was expressed in a seed-and developmentally-specific manner in transgenic tobacco seeds. Glycinin were targeted to vacuole-derived protein bodies in the endosperm tissue and highly accumulated in the matrix region of many transgenic plant (1-4% of total seed proteins). Synthesized glycinin was processed into mature form, and assembled into a hexamer in a similar manner as the glycinin in soybean seed. Modified glycinin, in which 4 contiguous methionine residues were inserted at the variable regions corresponding to the C - teminal regions of the acidic and basic polypeptides, were also found to be accumulated similarly as in the normal glycinin. There was no apparent difference in the expression level, processing and targeting to protein bodies, or accumulation level between normal and modified glycinin. glycinin.

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Mechanisms of Suppression of Matrix Metalloproteinases in UVB-Irradiated HaCaT Keratinocytes of Colored Rice Varieties (UVB에 조사된 HaCaT Keratinocytes에서의 유색미에 의한 Matrix Metalloproteinases 발현억제 메커니즘)

  • Choi, Eun-Young;Lee, Jae-Bong;Kim, Do-Hoon;Kwon, Yong-Sham;Cheon, Jung-Yoon;Lee, Jin-Tae
    • Journal of the Korean Society of Food Science and Nutrition
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    • v.46 no.5
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    • pp.562-571
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    • 2017
  • In this study, we investigated the anti-oxidant activities [electron-donating ability (EDA), 2,2'-azino-bis (3-ethylbenzothiazoline-6-sulfonic acid) (ABTS) radical scavenging ability, and reactive oxygen species (ROS) inhibitory activity], anti-wrinkle activities [collagenase inhibitory activity, suppression and/or phosphorylation of matrix metalloproteinases (MMPs), and mitogen-activated protein (MAP) kinase activity], and mRNA expression levels using reverse transcription-polymerase chain reaction (RT-PCR) assay in ultraviolet (UV) B ray ($50mJ/cm^2$)-irradiated human keratinocyte HaCaT cells. Josaengheugchal, Sinneungheugchal (SE), Shintoheug rice, Heugjinju rice, and Heugseol (HE) among colored rice varieties were reported to have excellent antioxidant properties. In the EDA and ABTS radical scavenging assays, extracts of the five colored rice varieties had scavenging activities of 72% at concentrations higher $50{\mu}g/mL$. In the collagenase inhibition assay, ethanol extracts of the five colored rice varieties showed high inhibitory effects of about 60% at concentrations higher $25{\mu}g/mL$. In the ROS inhibition assay, ethanol extracts of HE and SE showed very excellent inhibition efficacies at all concentrations. We determined molecular biological mechanisms of MMPs (MMP-1, -3, -8, and -13) and mitogen-activated protein kinase (MAPK) with HE, and the results show that HE suppressed expression of MMPs and phosphorylation of MAPK and increased expression of pro-collagen type I in UVB-irradiated cells. It was also confirmed by RT-PCR that HE reduced expression of MMPs mRNA. Therefore, these results suggest that HE has anti-wrinkle and collagen production effects and may be used as a material in the development of functional food and cosmetic industries.