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protein DNA binding emsa

Francisco Javier Rendón-Gandarilla, Víctor Álvarez-Hernández, Elizabeth J Castañeda-Ortiz, Helios Cárdenas-Hernández, Rosa Elena Cárdenas-Guerra, Jesús Valdés, Abigail Betanzos, Bibiana Chávez-Munguía, Anel Lagunes-Guillen, Esther Orozco, Lilia López-Canovas, Elisa Azuara-Liceaga
Telomeric Repeat Binding Factors (TRFs) are architectural nuclear proteins with critical roles in telomere-length regulation, chromosome end protection and, fusion prevention, DNA damage detection, and senescence regulation. Entamoeba histolytica , the parasite responsible of human amoebiasis, harbors three homologs of human TRFs, based on sequence similarities to their Myb DNA binding domain. These proteins were dubbed EhTRF-like I, II and III. In this work, we revealed that EhTRF-like I and II share similarity with human TRF1, while EhTRF-like III shares similarity with human TRF2 by in silico approach...
2018: Frontiers in Cellular and Infection Microbiology
Jana Kleiner, Margrit Hollborn, Peter Wiedemann, Andreas Bringmann
Purpose: Systemic hypertension is a risk factor of neovascular age-related macular degeneration; consumption of dietary salt resulting in extracellular hyperosmolarity is a main cause of hypertension. Extracellular hyperosmolarity was shown to induce expression of angiogenic growth factors, such as vascular endothelial growth factor (VEGF) and placental growth factor (PlGF), in RPE cells. The aim of the present study was to determine whether the hyperosmotic expression of growth factor genes in RPE cells is mediated by activator protein-1 (AP-1), and whether c-Fos and c-Jun genes are regulated by extracellular osmolarity...
2018: Molecular Vision
Xueyu Li, Xiaolong Liu, Zhenkui Qin, Maokai Wei, Xitan Hou, Tingting Zhang, Zhifeng Zhang
Sulfide-quinone oxidoreductase (SQR) is a key enzyme of sulfide metabolism in metazoans, and responsible for oxidizing sulfide into thiosulfate and transmitting the generated electrons to the ubiquinone. It has been revealed that the sqr mRNA level increases significantly in echiuran worm Urechis unicinctus exposed to sulfide, and HSF1, NF1 and Sp1 have been verified to participate in its transcriptional regulation. In this study, we obtained 23 potential transcription factors interacting possibly with the proximal region (-391 to +50) of sqr promoter, and focused on the RWD domain-containing 1 (Rwdd1), a protein with the maximum number of clones in yeast one-hybrid (Y1H) screening, to investigate its transcriptional regulation to U...
September 20, 2018: Aquatic Toxicology
Prateek Jain, Koushik Shah, Vikas Rishi
Basic leucine zipper (bZIP) transcription factors (TFs) are eukaryote-specific proteins that bind to DNA as a homodimer or heterodimer and regulate gene expression. They are involved in several biological processes in plants; therefore inhibiting bZIP-DNA binding activity by targeting protein-protein interface is an attractive proposition with aspects of both basic and applied biology. Here, we describe the equilibrium and kinetic interactions studies of a designed peptide inhibitor A-ZIP53 and its four variants with the bZIP53 protein, a key regulator of seed maturation phase and stress response in Arabidopsis...
September 29, 2018: Biochimica et biophysica acta. Proteins and proteomics
Meera Kumari, Ravi Kant Pal, Alok K Mishra, Sarita Tripathi, Bichitra Kumar Biswal, Kishore K Srivastava, Ashish Arora
Rv3488 of Mycobacterium tuberculosis H37Rv has been assigned to the phenolic acid decarboxylase repressor (PadR) family of transcriptional regulators that play key roles in multi-drug resistance and virulence of prokaryotes. The binding of cadmium, zinc, and several other metals to Rv3488 was discovered and characterized by ITC to be an exothermic process. Crystal structures of apo-Rv3488 and Rv3488 in complex with cadmium or zinc ions were determined by X-ray crystallography. Structure of Rv3488 revealed a dimeric protein with N-terminal winged-helix-turn-helix DNA-binding domains composed of helices α1, α2, α3, strand β1 and β2, with the dimerization interface being formed of helices α4 and α1...
September 28, 2018: Biochemical Journal
Jie-Yun Hong, Chu-Gang Mei, Shi-Jun Li, Hong-Bao Wang, Chun-Ping Zhao, Lin-Sen Zan
Sirtuin6 (SIRT6) is an ADP-ribosyltransferase and NAD+ -dependent deacylase of acetyl groups and long-chain fatty acyl groups, and has been shown as a regulator of insulin secretion, glucose metabolism, lipid metabolism, and cancer. In this study, we determined that the bovine SIRT6 showed higher levels of mRNA expression in the testis, longissimus thoracis, and subcutaneous fat tissue. To elucidate the molecular regulation mechanism of bovine SIRT6 expression, we obtained a 2-kb fragment containing the 5'-regulatory region, and the functional proximal minimal promoter of bovine SIRT6 was identified in the -472/-73 bp region...
September 21, 2018: Archives of Biochemistry and Biophysics
Jiang-Nan Kong, Chao Zhang, Yan-Ce Zhu, Kai Zhong, Jiang Wang, Bei-Bei Chu, Guo-Yu Yang
EP0 is an important early gene that modulates the life cycle of pseudorabies virus (PRV). A guanine-rich sequence overlapping with three Sp1 binding sites is located upstream of the transcription start site (TSS) in the EP0 promoter. Using native polyacrylamide gel electrophoresis (PAGE) and circular dichroism (CD), we verified that the G-rich region in the EP0 promoter forms an intramolecular parallel G-quadruplex (G4) in the presence of K+ ions. Further dimethyl sulphate (DMS) footprinting and Taq polymerase stop assays indicates the potential polymorphic folding of G4...
September 19, 2018: Scientific Reports
Zhaokui Du, Junmin Li
Kandelia candel, a major species of mangrove in the tropical and subtropical area, is susceptible to low temperature in winter. K. candel was introduced into Zhejiang Province (the northern margin of South China) several decades ago, and suffered from low temperature causing growth retardation, in server cases, even death. To explore the molecular mechanisms of cold acclimation in K. candel, a novel C-repeat binding factor gene KcCBF3 (Genbank accession no. KF111715) of 729 bp open reading frame (ORF) encoding a protein of 242 amino acid residues was isolated, expressed, purified and characterized...
August 16, 2018: Protein Expression and Purification
Jennifer L Welch, Hussein Kaddour, Patrick M Schlievert, Jack T Stapleton, Chioma M Okeoma
Exosomes play various roles in host responses to cancer and infective agents, and semen exosomes (SE) inhibit HIV-1 infection and transmission, although the mechanism(s) by which this occurs is unclear. Here, we show that SE block HIV-1 proviral transcription at multiple transcriptional check points including transcription factor recruitment to the LTR, and transcription initiation and elongation. Biochemical and functional studies show that SE inhibit HIV-1 long terminal repeat (HIV-LTR)-driven viral gene expression and virus replication...
August 15, 2018: Journal of Virology
Haojie Cao, Julio Villatoro-Hernandez, Ruud Detert Oude Weme, Elrike Frenzel, Oscar P Kuipers
Bacillus subtilis is extensively applied as a microorganism for the high-level production of heterologous proteins. Traditional strategies for increasing the productivity of this microbial cell factory generally focused on the targeted modification of rate-limiting components or steps. However, the longstanding problems of limited productivity of the expression host, metabolic burden and non-optimal nutrient intake, have not yet been completely solved to achieve significant production-strain improvements. To tackle this problem, we systematically rewired the regulatory networks of the global nitrogen and carbon metabolism by random mutagenesis of the pleiotropic transcriptional regulators CodY and CcpA, to allow for optimal nutrient intake, translating into significantly higher heterologous protein production yields...
August 8, 2018: Metabolic Engineering
Meiying Wu, Yuting Jiang, Mingyuan Liu, Yu Shang, Jing An
The amino polycyclic aromatic hydrocarbons (amino-PAHs) were frequently detected in PM2.5 , and it was suggested that they contributed to the harmful health effects associated with PM2.5 . However, the process through which amino-PAHs induce oxidative stress responses as well as the pro-inflammatory processes along with the associated mechanisms is still not well-known. In this study, oxidative stress level, Nrf2/ARE anti-oxidative defense responses, oxidative damages and cytokine expressions were investigated in the A549 cell line after it was treated with typical airborne amino-PAHs including 1-aminopyrene (1-AP) and 3-aminofluoranthene (3-AF)...
May 8, 2018: Toxicology Research
Emanuela Blanco, Wilma Sabetta, Donatella Danzi, Donatella Negro, Valentina Passeri, Antonino De Lisi, Francesco Paolocci, Gabriella Sonnante
Flavonoids are a well-studied group of secondary metabolites, belonging to the phenylpropanoid pathway. Flavonoids are known to exhibit health promoting effects such as antioxidant capacities, anti-cancer and anti-inflammatory activity. Globe artichoke is an important source of bioactive phenolic compounds, including flavonoids. To study the regulation of their biosynthesis, a R2R3-MYB transcription factor, CcMYB12 , was isolated from artichoke leaves. Phylogenetic analysis showed that this protein belongs to the MYB subgroup 7 (flavonol-specific MYB), which includes Arabidopsis AtMYB12, grapevine VvMYBF1, and tomato SlMYB12...
2018: Frontiers in Plant Science
Gaëtan Le-Bel, Claude J Giasson, Alexandre Deschambeault, Patrick Carrier, Lucie Germain, Sylvain L Guérin
Based on the use of tissue-cultured human corneal endothelial cells (HCECs), cell therapy is a very promising avenue in the treatment of corneal endothelial pathologies such as Fuchs' dystrophy, and post-surgical corneal edema. However, once in culture, HCECs rapidly lose their phenotypic and physiological characteristics, and are therefore unsuitable for the reconstruction of a functional endothelial monolayer. Expression of NFI, a transcription factor that can either function as an activator or a repressor of gene transcription, has never been examined in endothelial cells...
July 9, 2018: Experimental Eye Research
Duan Liu, Sisi Qin, Bamiki Ray, Krishna R Kalari, Liewei Wang, Richard M Weinshilboum
CYP1A1 expression can be upregulated by the ligand-activated aryl hydrocarbon receptor (AHR). Based on prior observations with estrogen receptors and estrogen response elements, we tested the hypothesis that single-nucleotide polymorphisms (SNPs) mapping hundreds of base pairs (bp) from xenobiotic response elements (XREs) might influence AHR binding and subsequent gene expression. Specifically, we analyzed DNA sequences 5 kb upstream and downstream of the CYP1A1 gene for putative XREs. SNPs located ±500 bp of these putative XREs were studied using a genomic data-rich human lymphoblastoid cell line (LCL) model system...
September 2018: Drug Metabolism and Disposition: the Biological Fate of Chemicals
David I Bernstein, Zana L Lummus, Banu Kesavalu, Jianbo Yao, Leah Kottyan, Daniel Miller, André Cartier, Maria-Jesús Cruz, Catherine Lemiere, Xavier Muñoz, Santiago Quirce, Susan Tarlo, Joaquin Sastre, Louis Philippe Boulet, Matthew T Weirauch, Kenneth Kaufman
BACKGROUND: Isocyanates are major causes of occupational asthma, but susceptibility and mechanisms of diisocyanate-induced asthma (DA) remain uncertain. OBJECTIVE: The aim of this study was to identify DA-associated functional genetic variants through next-generation sequencing (NGS), bioinformatics, and functional assays. METHODS: NGS was performed in 91 workers with DA. Fourteen loci with known DA-associated single nucleotide polymorphisms (SNPs) were sequenced and compared with data from 238 unexposed subjects...
September 2018: Journal of Allergy and Clinical Immunology
Kenji Ohe, Shinsuke Miyajima, Tomoko Tanaka, Yuriko Hamaguchi, Yoshihiro Harada, Yuta Horita, Yuki Beppu, Fumiaki Ito, Takafumi Yamasaki, Hiroki Terai, Masayoshi Mori, Yusuke Murata, Makito Tanabe, Ichiro Abe, Kenji Ashida, Kunihisa Kobayashi, Munechika Enjoji, Takashi Nomiyama, Toshihiko Yanase, Nobuhiro Harada, Toshiaki Utsumi, Akila Mayeda
Objectives: The high-mobility group A protein 1a (HMGA1a) protein is known as a transcription factor that binds to DNA, but recent studies have shown it exerts novel functions through RNA-binding. We were prompted to decipher the mechanism of HMGA1a-induced alternative splicing of the estrogen receptor alpha (ERα) that we recently reported would alter tamoxifen sensitivity in MCF-7 TAMR1 cells. Methods: Endogenous expression of full length ERα66 and its isoform ERα46 were evaluated in MCF-7 breast cancer cells by transient expression of HMGA1a and an RNA decoy (2'-O-methylated RNA of the HMGA1a RNA-binding site) that binds to HMGA1a...
2018: Frontiers in Molecular Biosciences
Yezi Zou, Zhiquan Chen, Jie Li, Wenyan Gong, Lei Zhang, Futian Xu, Lihao Chen, Peiqing Liu, Heqing Huang
Background: Progestin and adipoQ receptor 3 (PAQR3), is a Golgi-anchored membrane protein containing seven transmembrane helices. It has been demonstrated that PAQR3 mediates insulin resistance, glucose and lipid metabolism, and inflammation. In addition, kidney inflammatory fibrosis is an important pathological feature of diabetic nephropathy (DN). Therefore, we aimed to investigate the role of PAQR3 in diabetic kidney fibrosis as well as inflammation in DN. Object: The effect of PAQR3 on NF-κB signaling pathway, expressions of fibronectin (FN) and intercellular adhesion molecule-1 (ICAM-1) in glomerular mesangial cells (GMCs) cultured by high glucose (HG) were examined...
2018: Frontiers in Endocrinology
Marina Piscopo, Marco Trifuoggi, Rosaria Notariale, Sofiane Labar, Jacopo Troisi, Antonella Giarra, Dea Rabbito, Raffaela Puoti, Domenico de Benedictis, Maria Violetta Brundo, Adriana Basile, Katrina V Good, Juan Ausió, Giulia Guerriero
Here we report the industrial pollution effects due to cadmium on the reproductive health of Mytilus galloprovincialis. Mussels were removed from the biofouling of a Conatex panel after one year exposition at a polluted site near a disposal metallurgical factory. A high cadmium bioaccumulation was observed in the testis of mussels housed at the polluted site, with respect to a control site, as determined by inductively coupled plasma-mass spectrometry, along with a 10 fold increase in metallothionein 20 kDa gene (mt20) expression levels determined by qPCR...
2018: Acta Biochimica Polonica
Akira Kitamura, Ai Shibasaki, Kayo Takeda, Ryoji Suno, Masataka Kinjo
Normal function and abnormal aggregation of transactivation response (TAR) DNA/RNA-binding protein 43 kDa (TDP-43) are directly associated with the lethal genetic diseases: cystic fibrosis, amyotrophic lateral sclerosis (ALS), and frontotemporal lobar degeneration (FTLD). The binding of TDP-43 to single-stranded DNA (ssDNA) or RNA is involved in transcriptional repression, regulation of RNA splicing, and RNA stabilization. Equilibrium dissociation constants ( K d ) of TDP-43 and ssDNA or RNA have been determined using various methods; however, methods that can measure K d with high sensitivity in a short time using a small amount of TDP-43 in solution would be advantageous...
July 2018: Biochemistry and Biophysics Reports
Farah Hanan Abu Hanifiah, Siti Nor Akmar Abdullah, Ashida Othman, Noor Azmi Shaharuddin, Halimi Mohd Saud, Hasnul Abdul Hakim Hasnulhadi, Umaiyal Munusamy
TAAAAT and a novel motif, GCTTCA found in the oil palm stearoyl-ACP desaturase (SAD1) promoter are involved in regulating mesocarp-specific expression. Two key fatty acid biosynthetic genes, stearoyl-ACP desaturase (SAD1), and acyl-carrier protein (ACP3) in Elaeis guineensis (oil palm) showed high level of expression during the period of oil synthesis in the mesocarp [12-19 weeks after anthesis (w.a.a.)] and kernel (12-15 w.a.a.). Both genes are expressed in spear leaves at much lower levels and the expression increased by 1...
August 2018: Plant Cell Reports
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