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protein DNA binding emsa

Kelly C M Barroso, Maristela Previato-Mello, Bianca B Batista, Juliana H Batista, José F da Silva Neto
Chromobacterium violaceum is an environmental Gram-negative bacterium that causes infections in humans. Treatment of C. violaceum infections is difficult and little is known about the mechanisms of antibiotic resistance in this bacterium. In this work, we identified mutations in the MarR family transcription factor EmrR and in the protein GyrA as key determinants of quinolone resistance in C. violaceum , and we defined EmrR as a repressor of the MFS-type efflux pump EmrCAB. Null deletion of emrR caused increased resistance to nalidixic acid, but not to other quinolones or antibiotics of different classes...
2018: Frontiers in Microbiology
Qi Xu, Zhengyuan Zhai, Haoran An, Yang Yang, Jia Yin, Guohong Wang, Fazheng Ren, Yanling Hao
In order to colonize the human gastrointestinal tract and exert their beneficial effects, bifidobacteria must effectively cope with the toxic bile salts in the intestine, but the molecular mechanism underlying bile tolerance is poorly understood. In this study, heterologous expression of a MarR family transcriptional regulator BmrR significantly reduced ox-bile resistance of Lactococcus lactis NZ9000, suggesting that it might play a role in bile stress response. In silico analysis combined with RT-PCR assay demonstrated that bmrR was co-transcribed with bmrA and bmrB , which encoded multidrug resistance (MDR) ABC transporters...
November 26, 2018: Applied and Environmental Microbiology
Buyun Kim, Ki Yong Lee, Byoungduck Park
BACKGROUND: Icariin is pharmacologically active prenylated flavonoid glycoside that has various biologic effects such as antioxidant, anticancer, and anti-inflammatory activities. In addition, icariin has been used in Chinese medicine for thousands of years to treat osteoporosis and it is still being used today. However, direct mechanism of icariin in the treatment of bone disease is not understood. PURPOSE: The purpose of this study is to investigate whether icariin influences RANKL-induced osteoclast formation in murine macrophages...
December 1, 2018: Phytomedicine: International Journal of Phytotherapy and Phytopharmacology
Qihao Hu, Zidan Zhu, Danhui Zhao, Baojuan Zeng, Sichun Zheng, Qisheng Song, Huimin Deng, Qili Feng
Stage-specific gene expression governs metamorphosis of the silkworm, Bombyx mori. B. mori wing cuticle protein gene 4 (BmWCP4) is an essential gene for wing disc development expressed specifically during pupation. BmWCP4 transcription is suppressed at the larval stage by unknown mechanisms, which we sought to elucidate here. Bioinformatics analysis predicted seven potential Forkhead box (Fox) cis-regulatory elements (CRE) in the BmWCP4 promoter region, and we found that Fox CRE6 contributes to suppression of BmWCP4 expression...
November 14, 2018: Journal of Biological Chemistry
Bhupinder Singh, Swapan K Nath
Single nucleotide polymorphisms (SNPs) are the most abundantly found common form of DNA variation in the human genome. Many genetic association studies have proved that some of these SNPs are involved in regulating several cellular/physiological processes ranging from gene regulation to disease development. Analysis of the protein complex that binds to these SNPs is a crucial step in studying the mechanisms by which gene expressions are regulated in cis- or trans-acting manner. Commonly used techniques to determine DNA-protein interaction, such as electrophoretic mobility shift assay (EMSA), have limited value for simultaneously analyzing a large number of proteins in the complex...
2019: Methods in Molecular Biology
Yan Li, Wanqiu Zhao, Haixu Wang, Chen Chen, Dongmei Zhou, Shengnan Li, Xiaohong Zhang, Haibo Zhao, Dangxia Zhou, Biliang Chen
BACKGROUND: Polycystic ovary syndrome (PCOS) is the most common endocrine disorder in women of reproductive age and has a prevalence of 1 in 15 women worldwide. This study aims to investigate the role of lncRNA SRA in the pathological processes of polycystic ovary syndrome (PCOS). METHODS: Twenty five-day old female C57BL/6 mice received subcutaneous injection of 60 mg/kg dehydroepiandrosterone for 20 days to induce PCOS. Lentivirus containing lncRNA SRA-specific shRNA was subcapsularly injected into the ovaries of PCOS mice...
November 1, 2018: Biochimie
Zhengchang Wu, Haiyue Feng, Yue Cao, Yanjie Huang, Chaohui Dai, Shenglong Wu, Wenbin Bao
Escherichia coli ( E. coli ) F18 is the main pathogen responsible for post-weaning diarrhea (PWD) in piglets. Resistance to E. coli F18 depends on the expression of the cognate receptors in the intestinal epithelial cells. However, the molecular mechanism of E. coli F18 resistance in weaned piglets remains unclear. Here, we performed a comparative transcriptome study of the duodenal tissue from Sutai E. coli F18 sensitive and resistant pigs by RNA-seq, and pig α(1,2) fucosyltransferase 2 ( FUT2 ) was identified as a host differentially expressed gene controlling the E...
October 24, 2018: International Journal of Molecular Sciences
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...
November 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...
December 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...
November 2018: Experimental Eye Research
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