THE PREGNANE X RECEPTOR BINDS TO RESPONSE ELEMENTS IN A GENOMIC CONTEXT-DEPENDENT MANNER, AND PXR ACTIVATOR RIFAMPICIN SELECTIVELY ALTERS THE BINDING AMONG TARGET GENES

2004 ◽  
Vol 32 (1) ◽  
pp. 35-42 ◽  
Author(s):  
Xiulong Song ◽  
Mingxing Xie ◽  
He Zhang ◽  
Yuxin Li ◽  
Karuna Sachdeva ◽  
...  
Keyword(s):  
Target Genes ◽  
Pregnane X Receptor ◽  
Dependent Manner ◽  
Genomic Context ◽  
Response Elements ◽  
Context Dependent

scholarly journals Gut Microbiome Critically Impacts PCB-induced Changes in Metabolic Fingerprints and the Hepatic Transcriptome in Mice

2020 ◽  
Vol 177 (1) ◽  
pp. 168-187 ◽  
Author(s):  
Joe Jongpyo Lim ◽  
Xueshu Li ◽  
Hans-Joachim Lehmler ◽  
Dongfang Wang ◽  
Haiwei Gu ◽  
...  
Keyword(s):  
Gut Microbiome ◽  
Target Genes ◽  
Metabolic Diseases ◽  
Corn Oil ◽  
Constitutive Androstane Receptor ◽  
Pregnane X Receptor ◽  
Dependent Manner ◽  
Integrated Network ◽  
Hepatic Transcriptome ◽  
Pcb Exposure

Abstract Polychlorinated biphenyls (PCBs) are ubiquitously detected and have been linked to metabolic diseases. Gut microbiome is recognized as a critical regulator of disease susceptibility; however, little is known how PCBs and gut microbiome interact to modulate hepatic xenobiotic and intermediary metabolism. We hypothesized the gut microbiome regulates PCB-mediated changes in the metabolic fingerprints and hepatic transcriptome. Ninety-day-old female conventional and germ-free mice were orally exposed to the Fox River Mixture (synthetic PCB mixture, 6 or 30 mg/kg) or corn oil (vehicle control, 10 ml/kg), once daily for 3 consecutive days. RNA-seq was conducted in liver, and endogenous metabolites were measured in liver and serum by LC-MS. Prototypical target genes of aryl hydrocarbon receptor, pregnane X receptor, and constitutive androstane receptor were more readily upregulated by PCBs in conventional conditions, indicating PCBs, to the hepatic transcriptome, act partly through the gut microbiome. In a gut microbiome-dependent manner, xenobiotic, and steroid metabolism pathways were upregulated, whereas response to misfolded proteins-related pathways was downregulated by PCBs. At the high PCB dose, NADP, and arginine appear to interact with drug-metabolizing enzymes (ie, Cyp1–3 family), which are highly correlated with Ruminiclostridium and Roseburia, providing a novel explanation of gut-liver interaction from PCB-exposure. Utilizing the Library of Integrated Network-based Cellular Signatures L1000 database, therapeutics targeting anti-inflammatory and endoplasmic reticulum stress pathways are predicted to be remedies that can mitigate PCB toxicity. Our findings demonstrate that habitation of the gut microbiota drives PCB-mediated hepatic responses. Our study adds knowledge of physiological response differences from PCB exposure and considerations for further investigations for gut microbiome-dependent therapeutics.

Pregnane X receptor activation ameliorates DSS-induced inflammatory bowel disease via inhibition of NF-κB target gene expression

2007 ◽  
Vol 292 (4) ◽  
pp. G1114-G1122 ◽  
Author(s):  
Yatrik M. Shah ◽  
Xiaochao Ma ◽  
Keiichirou Morimura ◽  
Insook Kim ◽  
Frank J. Gonzalez
Keyword(s):  
Inflammatory Bowel Disease ◽  
Bowel Disease ◽  
Target Genes ◽  
Clinical Symptoms ◽  
Pregnane X Receptor ◽  
Receptor Activation ◽  
Dependent Manner ◽  
Cytokine Analysis ◽  
Inflammatory Bowel

Pregnane X receptor (PXR) expression was shown to be protective in inflammatory bowel disease (IBD). However, the mechanism by which PXR provides protection remains unclear. Wild-type and Pxr-null mice were treated with the PXR agonist pregnenolone-16α-carbonitrile or vehicle and administered 2.5% dextran sulfate sodium (DSS) in drinking water to induce IBD. Typical clinical symptoms were evaluated on a daily basis. In vivo intestinal permeability assays and proinflammatory cytokine analysis were performed. PXR agonist-treated mice were protected from DSS-induced colitis compared with vehicle-treated mice, as defined by body weight loss, diarrhea, rectal bleeding, colon length, and histology. Pregnenolone-16α-carbonitrile did not decrease the severity of IBD in Pxr-null mice. PXR agonist treatment did not increase epithelial barrier function but did decrease mRNA expression of several NF-κB target genes in a PXR-dependent manner. The present study clearly demonstrates a protective role for PXR agonist in DSS-induced IBD. The data suggest that PXR-mediated repression of NF-κB target genes in the colon is a critical mechanism by which PXR activation decreases the susceptibility of mice to DSS-induced IBD.

ZFARED: A Database of the Antioxidant Response Elements in Zebrafish

2020 ◽  
Vol 15 (5) ◽  
pp. 415-419
Author(s):  
Azhwar Raghunath ◽  
Raju Nagarajan ◽  
Ekambaram Perumal
Keyword(s):  
Target Genes ◽  
Antioxidant Response ◽  
Zebrafish Genome ◽  
Promoter Regions ◽  
Protein Coding ◽  
Response Elements ◽  
Toxic Agents ◽  
Upstream Promoter ◽  
Its Gene ◽  
Antioxidant Response Elements

Background: Antioxidant Response Elements (ARE) play a key role in the expression of Nrf2 target genes by regulating the Keap1-Nrf2-ARE pathway, which offers protection against toxic agents and oxidative stress-induced diseases. Objective: To develop a database of putative AREs for all the genes in the zebrafish genome. This database will be helpful for researchers to investigate Nrf2 regulatory mechanisms in detail. Methods: To facilitate researchers functionally characterize zebrafish AREs, we have developed a database of AREs, Zebrafish Antioxidant Response Element Database (ZFARED), for all the protein-coding genes including antioxidant and mitochondrial genes in the zebrafish genome. The front end of the database was developed using HTML, JavaScript, and CSS and tested in different browsers. The back end of the database was developed using Perl scripts and Perl-CGI and Perl- DBI modules. Results: ZFARED is the first database on the AREs in zebrafish, which facilitates fast and efficient searching of AREs. AREs were identified using the in-house developed Perl algorithms and the database was developed using HTML, JavaScript, and Perl-CGI scripts. From this database, researchers can access the AREs based on chromosome number (1 to 25 and M for mitochondria), strand (positive or negative), ARE pattern and keywords. Users can also specify the size of the upstream/promoter regions (5 to 30 kb) from transcription start site to access the AREs located in those specific regions. Conclusion: ZFARED will be useful in the investigation of the Keap1-Nrf2-ARE pathway and its gene regulation. ZFARED is freely available at http://zfared.buc.edu.in/.

scholarly journals Disrupting the memory of places induced by drugs of abuse weakens motivational withdrawal in a context-dependent manner

2010 ◽  
Vol 107 (27) ◽  
pp. 12345-12350 ◽  
Author(s):  
S. M. Taubenfeld ◽  
E. V. Muravieva ◽  
A. Garcia-Osta ◽  
C. M. Alberini
Keyword(s):  
Drugs Of Abuse ◽  
Dependent Manner ◽  
Context Dependent

scholarly journals Alpha-Tocopherol Metabolites (The Vitamin E Metabolome) and Their Interindividual Variability during Supplementation

Antioxidants ◽  
2021 ◽  
Vol 10 (2) ◽  
pp. 173
Author(s):  
Desirée Bartolini ◽  
Rita Marinelli ◽  
Danilo Giusepponi ◽  
Roberta Galarini ◽  
Carolina Barola ◽  
...  
Keyword(s):  
Vitamin E ◽  
Target Genes ◽  
Interindividual Variability ◽  
Pregnane X Receptor ◽  
Alpha Tocopherol ◽  
Therapeutic Interventions ◽  
Intrinsic Variability ◽  
Blood Leukocytes ◽  
Definition Of ◽  
And Function

The metabolism of α-tocopherol (α-TOH, vitamin E) shows marked interindividual variability, which may influence the response to nutritional and therapeutic interventions with this vitamin. Recently, new metabolomics protocols have fostered the possibility to explore such variability for the different metabolites of α-TOH so far identified in human blood, i.e., the “vitamin E metabolome”, some of which have been reported to promote important biological functions. Such advances prompt the definition of reference values and degree of interindividual variability for these metabolites at different levels of α-TOH intake. To this end, a one-week oral administration protocol with 800 U RRR-α-TOH/day was performed in 17 healthy volunteers, and α-TOH metabolites were measured in plasma before and at the end of the intervention utilizing a recently validated LC-MS/MS procedure; the expression of two target genes of α-TOH with possible a role in the metabolism and function of this vitamin, namely pregnane X receptor (PXR) and the isoform 4F2 of cytochrome P450 (CYP4F2) was assessed by immunoblot in peripheral blood leukocytes. The levels of enzymatic metabolites showed marked interindividual variability that characteristically increased upon supplementation. With the exception of α-CEHC (carboxy-ethyl-hydroxychroman) and the long-chain metabolites M1 and α-13′OH, such variability was found to interfere with the possibility to utilize them as sensitive indicators of α-TOH intake. On the contrary, the free radical-derived metabolite α-tocopheryl quinone significantly correlated with the post-supplementation levels of α-TOH. The supplementation stimulated PXR, but not CYP4F2, expression of leucocytes, and significant correlations were observed between the baseline levels of α-TOH and both the baseline and post-supplementation levels of PXR. These findings provide original analytical and molecular information regarding the human metabolism of α-TOH and its intrinsic variability, which is worth considering in future nutrigenomics and interventions studies.

Identification of novel steroid target genes through the combination of bioinformatics and functional analysis of hormone response elements

2006 ◽  
Vol 339 (1) ◽  
pp. 99-106 ◽  
Author(s):  
Kuniko Horie-Inoue ◽  
Kenichi Takayama ◽  
Hidemasa U. Bono ◽  
Yasuyoshi Ouchi ◽  
Yasushi Okazaki ◽  
...  
Keyword(s):  
Functional Analysis ◽  
Target Genes ◽  
Hormone Response ◽  
Response Elements ◽  
Hormone Response Elements

fMLP induces Hsp27 expression, attenuates NF-κB activation, and confers intestinal epithelial cell protection

2007 ◽  
Vol 292 (4) ◽  
pp. G1070-G1078 ◽  
Author(s):  
Ryan M. Carlson ◽  
Stephan R. Vavricka ◽  
Jyrki J. Eloranta ◽  
Mark W. Musch ◽  
Donna L. Arvans ◽  
...  
Keyword(s):  
Epithelial Cell ◽  
Intestinal Epithelial Cell ◽  
Target Genes ◽  
Bacterial Flora ◽  
Epithelial Cell Line ◽  
Dependent Manner ◽  
Intestinal Epithelial ◽  
Cell Protection ◽  
Hsp27 Expression ◽  
Tnf Α

Sustained expression of cytoprotective intestinal epithelial heat shock proteins (Hsps), particularly Hsp27, depends on stimuli derived from bacterial flora. In this study, we examined the role of the bacterial chemotactic peptide fMLP in stimulating colonic epithelial Hsp expression at concentrations encountered in a physiological milieu. Treatment of the polarized human intestinal epithelial cell line Caco2bbe with physiological concentrations of fMLP (10–100 nM) induced expression of Hsp27, but not Hsp72, in a time- and concentration-dependent manner. Induction of Hsp27 by fMLP was specific since the fMLP analogs MRP and MLP were not effective. Hsp27 induction by fMLP was blocked by the fMLP-receptor antagonist BOC-FLFLF and was blocked when the dipeptide transporter PepT1, an entry pathway for fMLP, was silenced. fMLP activated both the p38 and ERK1/2 MAP kinase pathways in Caco2bbe cells, but not the SAPK/JNK pathway. The p38 inhibitor SB203580, but not the MEK-1 inhibitor PD98059, blocked Hsp27 induction by fMLP. fMLP treatment inhibited actin depolymerization and decreased transepithelial resistance caused by the oxidant monochloramine, and this inhibition was reversed by silencing Hsp27 expression. fMLP pretreatment also inhibited activation of proinflammatory transcription factor NF-κB by TNF-α in Caco2bbe cells, reducing induction of NF-κB target genes by TNF-α both in human intestinal biopsies and Caco2bbe cells. In conclusion, fMLP may contribute to the maintenance of intestinal homeostasis by mediating physiological expression of Hsp27, enhancing cellular protection, and negatively regulating the inflammatory response.

scholarly journals SirR, a Novel Iron-Dependent Repressor inStaphylococcus epidermidis

1998 ◽  
Vol 66 (9) ◽  
pp. 4123-4129 ◽  
Author(s):  
Philip J. Hill ◽  
Alan Cockayne ◽  
Patrick Landers ◽  
Julie A. Morrissey ◽  
Catriona M. Sims ◽  
...  
Keyword(s):  
Binding Site ◽  
Dna Sequences ◽  
Blot Analysis ◽  
Target Genes ◽  
Consensus Sequence ◽  
Dependent Manner ◽  
Chromosomal Dna ◽  
Iron Starvation ◽  
Mobility Shift ◽  
Western Blots

ABSTRACT In Staphylococcus epidermidis and Staphylococcus aureus, a number of cell wall- and cytoplasmic membrane-associated lipoproteins are induced in response to iron starvation. To gain insights into the molecular basis of iron-dependent gene regulation in the staphylococci, we sequenced the DNA upstream of the 3-kb S. epidermidis sitABC operon, which Northern blot analysis indicates is transcriptionally regulated by the growth medium iron content. We identified two DNA sequences which are homologous to elements of the Corynebacterium diphtheriae DtxR regulon, which controls, in response to iron stress, for example, production of diphtheria toxin, siderophore, and a heme oxygenase. Upstream of thesitABC operon and divergently transcribed lies a 645-bp open reading frame (ORF), which codes for a polypeptide of approximately 25 kDa with homology to the DtxR family of metal-dependent repressor proteins. This ORF has been designated SirR (staphylococcal iron regulator repressor). Within thesitABC promoter/operator region, we also located a region of dyad symmetry overlapping the transcriptional start ofsitABC which shows high homology to the DtxR operator consensus sequence, suggesting that this region, termed the Sir box, is the SirR-binding site. The SirR protein was overexpressed, purified, and used in DNA mobility shift assays; SirR retarded the migration of a synthetic oligonucleotide based on the Sir box in a metal (Fe2+ or Mn2+)-dependent manner, providing confirmatory evidence that this motif is the SirR-binding site. Furthermore, Southern blot analysis of staphylococcal chromosomal DNA with the synthetic Sir box as a probe confirmed that there are at least five Sir boxes in the S. epidermidis genome and at least three in the genome of S. aureus, suggesting that SirR controls the expression of multiple target genes. Using a monospecific polyclonal antibody raised against SirR to probe Western blots of whole-cell lysates of S. aureus, S. carnosus,S. epidermidis, S. hominis, S. cohnii, S. lugdunensis, and S. haemolyticus, we identified an approximately 25-kDa cross-reactive protein in each of the staphylococcal species examined. Taken together, these data suggest that SirR functions as a divalent metal cation-dependent transcriptional repressor which is widespread among the staphylococci.

scholarly journals Targeting the PI5P4K lipid kinase family in cancer using novel covalent inhibitors

2019 ◽  
Author(s):  
Sindhu Carmen Sivakumaren ◽  
Hyeseok Shim ◽  
Tinghu Zhang ◽  
Fleur M. Ferguson ◽  
Mark R. Lundquist ◽  
...  
Keyword(s):  
Cancer Metabolism ◽  
Target Genes ◽  
Therapeutic Potential ◽  
Dependent Manner ◽  
Cancer Cell Proliferation ◽  
Lipid Kinase ◽  
Covalent Inhibitors ◽  
Lipid Kinases ◽  
Disordered Loop

SummaryThe PI5P4Ks have been demonstrated to be important for cancer cell proliferation and other diseases. However, the therapeutic potential of targeting these kinases is understudied due to a lack of potent, specific small molecules available. Here we present the discovery and characterization of a novel pan-PI5P4K inhibitor, THZ-P1-2, that covalently targets cysteines on a disordered loop in PI5P4Kα/β/γ. THZ-P1-2 demonstrates cellular on-target engagement with limited off-targets across the kinome. AML/ALL cell lines were sensitive to THZ-P1-2, consistent with PI5P4K’s reported role in leukemogenesis. THZ-P1-2 causes autophagosome clearance defects and upregulation in TFEB nuclear localization and target genes, disrupting autophagy in a covalent-dependent manner and phenocopying the effects of PI5P4K genetic deletion. Our studies demonstrate that PI5P4Ks are tractable targets, with THZ-P1-2 as a useful tool to further interrogate the therapeutic potential of PI5P4K inhibition and inform drug discovery campaigns for these lipid kinases in cancer metabolism and other autophagy-dependent disorders.

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