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Mass Spectrometry Reviews 2013Transcription factors (TFs) are essential for the expression of all proteins, including those involved in human health and disease. However, TFs are resistant to... (Review)
Review
Transcription factors (TFs) are essential for the expression of all proteins, including those involved in human health and disease. However, TFs are resistant to proteomic characterization because they are frequently masked by more abundant proteins due to the limited dynamic range of capillary liquid chromatography-tandem mass spectrometry and protein database searching. Purification methods, particularly strategies that exploit the high affinity of TFs for DNA response elements (REs) on gene promoters, can enrich TFs prior to proteomic analysis to improve dynamic range and penetrance of the TF proteome. For example, trapping of TF complexes specific for particular REs has been achieved by recovering the element DNA-protein complex on solid supports. Additional methods for improving dynamic range include two- and three-dimensional gel electrophoresis incorporating electrophoretic mobility shift assays and Southwestern blotting for detection. Here we review methods for TF purification and characterization. We fully expect that future investigations will apply these and other methods to illuminate this important but challenging proteome.
Topics: Animals; Chromatography, Liquid; Databases, Protein; Electrophoresis; Humans; Proteomics; Response Elements; Tandem Mass Spectrometry; Transcription Factors; Transcriptional Activation
PubMed: 23832591
DOI: 10.1002/mas.21369 -
ChemMedChem Jul 2022Organic isothiocyanates (ITCs) are a class of anticancer agents which naturally result from the enzymatic degradation of glucosinolates produced by Brassica vegetables....
Organic isothiocyanates (ITCs) are a class of anticancer agents which naturally result from the enzymatic degradation of glucosinolates produced by Brassica vegetables. Previous studies have demonstrated that the structure of an ITC impacts its potency and mode(s) of anticancer properties, opening the way to preparation and evaluation of synthetic, non-natural ITC analogues. This study describes the preparation of a library of 79 non-natural ITC analogues intended to probe further structure-activity relationships for aryl ITCs and second-generation, functionalized biaryl ITC variants. ITC candidates were subjected to bifurcated evaluation of antiproliferative and antioxidant response element (ARE)-induction capacity against human MCF-7 cells. The results of this study led to the identification of (1) several key structure-activity relationships and (2) lead ITCs demonstrating potent antiproliferative properties.
Topics: Antineoplastic Agents; Antioxidant Response Elements; Humans; Isothiocyanates; MCF-7 Cells; Structure-Activity Relationship
PubMed: 35588002
DOI: 10.1002/cmdc.202200250 -
Oxidative Medicine and Cellular... 2017Oxidative stress is involved in pathophysiology and pathological conditions of numerous human diseases. Thus, understanding the mechanisms underlying the redox... (Review)
Review
Oxidative stress is involved in pathophysiology and pathological conditions of numerous human diseases. Thus, understanding the mechanisms underlying the redox homeostasis in cells and organs is valuable for discovery of therapeutic drugs for oxidative stress-related diseases. Recently, by applying chemical biology approach with an ARE activator, BTZO-1, we found macrophage migration inhibitory factor (MIF) as a new regulator of antioxidant response element- (ARE-) mediated gene transcription. BTZO-1 and its active derivatives bound to MIF and protected cells and organs from oxidative insults via ARE activation in animal models with oxidative stress such as ischemia/reperfusion injury, inflammatory bowel diseases, and septic shock. In this review, we briefly highlight key findings in understanding the MIF-ARE system.
Topics: Animals; Antioxidant Response Elements; Gene Expression Regulation; Humans; Macrophage Migration-Inhibitory Factors; Oxidative Stress
PubMed: 28191280
DOI: 10.1155/2017/8584930 -
Medicine Dec 2019Genetic variation and genotype of Hepatitis B virus (HBV) are related to the efficiency of interferon alpha (IFN-α)-based antiviral therapy. However, the correlation of... (Observational Study)
Observational Study
Genetic variation and genotype of Hepatitis B virus (HBV) are related to the efficiency of interferon alpha (IFN-α)-based antiviral therapy. However, the correlation of variation in interferon-stimulated response element (ISRE) and HBV genotype response to IFN-α therapy remains elusive.Differences of ISRE between genotype B and C HBV were explored using the HBV sequences retrieved from GenBank, and further investigated by ISRE region cloning and sequencing from 60 clinical samples post-IFN-α therapy. Additionally, ISRE mutants were constructed and their relation to responsiveness of IFN-α was evaluated by real-time PCR and Southern blot analysis.ISRE pattern between genotype B and C were found based on both clinical sample sequencing and full-length sequence alignment. The primary difference is the fourth base within the ISRE region, with T and C for genotype B and C, respectively. HBV with genotype C-type ISRE had a higher replicative capability as compared to HBV with genotype B-type ISRE after IFN-α treatment in huh7 cells. CONCLUSION:: Preference of ISRE between genotype B and C HBV are distinct. Single nucleotide difference (C to T) within the HBV ISRE region may link to the efficacy of IFN-α therapy to genotype B and C HBV. Therefore, this study provides a clue for the determination of IFN-α therapy response to HBV treatment.
Topics: Adult; Female; Genotype; Hepatitis B; Hepatitis B virus; Humans; Interferon-alpha; Male; Middle Aged; Mutation; Response Elements; Young Adult
PubMed: 31861015
DOI: 10.1097/MD.0000000000018442 -
BioMed Research International 2013The cyclic AMP response element-binding protein H (CREBH) plays important roles in hepatic lipogenesis, fatty acid oxidation, and lipolysis under metabolic stress. Here,...
The cyclic AMP response element-binding protein H (CREBH) plays important roles in hepatic lipogenesis, fatty acid oxidation, and lipolysis under metabolic stress. Here, we report CREBH as a novel regulator of human APOA5. Knockdown of endogenous CREBH expression via small interfering RNA resulted in the downregulation of human APOA5 mRNA expression in human hepatoma cells, HepG2. Sequence analysis suggested that putative CREBH response element (CREBHRE) is located in the human APOA5 promoter region and is highly conserved in both human and rodent. To clarify whether the human APOA5 promoter is regulated by CREBH, we analyzed the human APOA5 promoter region using a transient transfection assay and determined that transfection of CREBH induced human APOA5 promoter activity. Moreover, it was shown that CREBH directly regulated human APOA5 gene expression by binding to a unique CREBHRE located in the proximal human APOA5 promoter region, using 5'-deletion and mutagenesis of human APOA5 promoter analysis and chromatin immunoprecipitation assay. Taken together, our results demonstrated that human APOA5 is directly regulated by CREBH via CREBHRE and provided a new insight into the role of this liver-specific bZIP transcription factor in lipoprotein metabolism and triglyceride homeostasis.
Topics: Apolipoprotein A-V; Apolipoproteins A; Cyclic AMP Response Element-Binding Protein; Down-Regulation; Gene Expression Regulation; Gene Knockdown Techniques; Hep G2 Cells; Humans; Lipogenesis; Liver; Promoter Regions, Genetic; RNA, Messenger; Response Elements
PubMed: 23957007
DOI: 10.1155/2013/892491 -
PloS One 2014Thyroid hormone (TH) exerts its effects by binding to the thyroid hormone receptor (TR), which binds to TH response elements (TREs) to regulate target gene expression....
Thyroid hormone (TH) exerts its effects by binding to the thyroid hormone receptor (TR), which binds to TH response elements (TREs) to regulate target gene expression. We investigated the relative ability of liganded homodimers TR and retinoid X receptor (RXR), and the heterodimer TR/RXR, to regulate gene expression for the TRE half-site organizations: direct repeat 4 (DR4), inverted repeat 0 (IR0) and everted repeat 6 (ER6). Luciferase reporter assays using a DR4 TRE suggest that both the TR homodimer and TR/RXR heterodimer regulate luciferase expression in the presence of their respective ligands. However, in the presence of the IR0 TRE, transfection with TR/RXR and RXR alone increased luciferase activity and there was no effect of TR alone. The presence of 9-cis-retinoic acid was necessary for luciferase expression, whereas TH treatment alone was insufficient. For the ER6 TRE, transfection with TR/RXR, TR alone and RXR alone (in the presence of their respective ligands) all caused a significant increase in luciferase activity. When both ligands were present, transfection with both TR/RXR caused more activation. Finally, we investigated the efficacy of the TR-antagonist 1-850 in inhibiting transcription by TR or TR/RXR at DR4 and ER6 TREs. We found that 1-850 did not suppress luciferase activation in the presence of TR/RXR for the ER6 TRE, suggesting conformational changes of the ligand binding domain of the TR when bound to different TRE half-site organizations. Collectively, the findings indicate that there are fundamental differences between TRE configurations that affect nuclear receptor interactions with the response element and ability to bind ligands and antagonists.
Topics: Animals; COS Cells; Chlorocebus aethiops; Protein Binding; Protein Multimerization; Receptors, Thyroid Hormone; Response Elements; Retinoid X Receptors; Thyroid Hormones; Transcriptional Activation
PubMed: 24971931
DOI: 10.1371/journal.pone.0101155 -
Cancer Science Feb 2007Many studies on carcinogenesis carried out early in the last century are united on the consensus that cancer is a genetic disease. Cancer cells typically display gene... (Review)
Review
Many studies on carcinogenesis carried out early in the last century are united on the consensus that cancer is a genetic disease. Cancer cells typically display gene dysfunction and endogenous or exogenous insults resulting in gene dysfunction are often carcinogenic. Recent advances in stem cell biology added the new concept that cancer originates from a single cancer-initiating cell. To understand the molecular basis of carcinogenesis from the beginning to the full acquirement of malignancy, factors concerned with carcinogenesis were categorized into three groups: those guarding and stabilizing genomes, those regulating cell proliferation, and those conferring resistance to various micro-environmental stresses. One example of particular interest is the Keap1-Nrf2 system since, according to recent studies, it has turned out to be ambivalent. Nrf2 heterodimerizes with small Maf protein to strongly activate transcription through the Maf recognition element (MARE) and Keap1 is an inhibitory regulator of Nrf2. The genes regulated by Nrf2 are very important for cellular protection of the genome from xenobiotic and oxidative stresses and, consequently, for preventing carcinogenesis. This implies that enhancing Nrf2 activity is a promising method for thwarting cancer. On the contrary, the constitutive activation of Nrf2 due to mutations in the keap1 gene is characteristically observed in lung cancer cells, suggesting that induced expression of Nrf2 target genes favors the prevalence of cancer cells.
Topics: Animals; Cell Transformation, Neoplastic; Gene Expression Regulation, Neoplastic; Humans; Maf Transcription Factors; Oxidative Stress; Response Elements; Transcription, Genetic
PubMed: 17129360
DOI: 10.1111/j.1349-7006.2006.00358.x -
The Plant Cell Sep 2006Expression of alpha-amylase genes during cereal grain germination and seedling growth is regulated negatively by sugar in embryos and positively by gibberellin (GA) in...
Expression of alpha-amylase genes during cereal grain germination and seedling growth is regulated negatively by sugar in embryos and positively by gibberellin (GA) in endosperm through the sugar response complex (SRC) and the GA response complex (GARC), respectively. We analyzed two alpha-amylase promoters, alphaAmy3 containing only SRC and alphaAmy8 containing overlapped SRC and GARC. alphaAmy3 was sugar-sensitive but GA-nonresponsive in both rice (Oryza sativa) embryos and endosperms, whereas alphaAmy8 was sugar-sensitive in embryos and GA-responsive in endosperms. Mutation of the GA response element (GARE) in the alphaAmy8 promoter impaired its GA response but enhanced sugar sensitivity, and insertion of GARE in the alphaAmy3 promoter rendered it GA-responsive but sugar-insensitive in endosperms. Expression of the GARE-interacting transcription factor MYBGA was induced by GA in endosperms, correlating with the endosperm-specific alphaAmy8 GA response. alphaAmy8 became sugar-sensitive in MYBGA knockout mutant endosperms, suggesting that the MYBGA-GARE interaction overrides the sugar sensitivity of alphaAmy8. In embryos overexpressing MYBGA, alphaAmy8 became sugar-insensitive, indicating that MYBGA affects sugar repression. alpha-Amylase promoters active in endosperms contain GARE, whereas those active in embryos may or may not contain GARE, confirming that the GARE and GA-induced MYBGA interaction prevents sugar feedback repression of endosperm alpha-amylase genes. We demonstrate that the MYBGA-GARE interaction affects sugar feedback control in balanced energy production during seedling growth and provide insight into the control mechanisms of tissue-specific regulation of alpha-amylase expression by sugar and GA signaling interference.
Topics: Gene Expression Regulation, Plant; Germination; Gibberellins; Glucose; Molecular Sequence Data; Mutation; Oryza; Plant Proteins; Response Elements; Seeds; Transcription Factors; alpha-Amylases
PubMed: 16905658
DOI: 10.1105/tpc.105.038844 -
Free Radical Biology & Medicine Jan 2014We present arguments for an evolution in our understanding of how antioxidants in fruits and vegetables exert their health-protective effects. There is much... (Review)
Review
We present arguments for an evolution in our understanding of how antioxidants in fruits and vegetables exert their health-protective effects. There is much epidemiological evidence for disease prevention by dietary antioxidants and chemical evidence that such compounds react in one-electron reactions with free radicals in vitro. Nonetheless, kinetic constraints indicate that in vivo scavenging of radicals is ineffective in antioxidant defense. Instead, enzymatic removal of nonradical electrophiles, such as hydroperoxides, in two-electron redox reactions is the major antioxidant mechanism. Furthermore, we propose that a major mechanism of action for nutritional antioxidants is the paradoxical oxidative activation of the Nrf2 (NF-E2-related factor 2) signaling pathway, which maintains protective oxidoreductases and their nucleophilic substrates. This maintenance of "nucleophilic tone," by a mechanism that can be called "para-hormesis," provides a means for regulating physiological nontoxic concentrations of the nonradical oxidant electrophiles that boost antioxidant enzymes, and damage removal and repair systems (for proteins, lipids, and DNA), at the optimal levels consistent with good health.
Topics: Animals; Antioxidant Response Elements; Antioxidants; Diet; Gene Expression Regulation; Glutathione; Hormesis; Humans; Lipid Peroxidation; NF-E2-Related Factor 2; Oxidative Stress; Reactive Oxygen Species; Superoxide Dismutase; Vitamin E
PubMed: 23747930
DOI: 10.1016/j.freeradbiomed.2013.05.045 -
Scientific Reports Oct 2020After HSP70 binds to the J domain of the substrate and co-chaperone protein, ATP is hydrolyzed to ADP, and the nucleotide exchange factors (NEFs) promote the release of...
After HSP70 binds to the J domain of the substrate and co-chaperone protein, ATP is hydrolyzed to ADP, and the nucleotide exchange factors (NEFs) promote the release of ADP. Under physiological conditions, the nucleotide exchange step is the rate-limiting step, which is accelerated by NEFs. In this study, the promoter of nucleotide exchange factor ZjFes1 was cloned, and its expression in tissues and under heat stress was studied to understand the regulatory mechanism of ZjFes1 and provide the molecular basis to study heat tolerance mechanism of seagrass. It was found that the promoter has common cis-acting elements in promoter and enhancer regions CAAT-box, as well as light response elements AE-box, Box 4 and TCCC-motif, a cis-acting regulatory element essential for the anaerobic induction of ARE, hormone response elements CGTCA-motif and TGACG-motif (MeJA response element), GARE-motif (gibberellin response element), TGA-element (auxin response element), a cis-acting regulatory element related to meristem expression CAT-box, and a cis-acting element involved in defense and stress responsiveness of TC-rich repeats. Two-week-old seedlings exhibited weak GUS activities in their cotyledons. In addition, the AtFes1A promoter was constitutively active in the anthers. After exposure to 38 °C for 2 h, the root tips of two-week-old seedlings were stained a strong blue. Heat-inducible activities of GUS were also observed in the cotyledons, roots, leaves, anthers, sepals and siliques.
Topics: Base Sequence; Cloning, Molecular; Gene Expression Regulation, Plant; Plant Proteins; Promoter Regions, Genetic; Response Elements; Zosteraceae
PubMed: 33057160
DOI: 10.1038/s41598-020-74381-6