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2.
Biochem Soc Trans ; 49(4): 1589-1599, 2021 08 27.
Article in English | MEDLINE | ID: mdl-34240738

ABSTRACT

Ribosome biogenesis requires prodigious transcriptional output in rapidly growing yeast cells and is highly regulated in response to both growth and stress signals. This minireview focuses on recent developments in our understanding of this regulatory process, with an emphasis on the 138 ribosomal protein genes (RPGs) themselves and a group of >200 ribosome biogenesis (RiBi) genes whose products contribute to assembly but are not part of the ribosome. Expression of most RPGs depends upon Rap1, a pioneer transcription factor (TF) required for the binding of a pair of RPG-specific TFs called Fhl1 and Ifh1. RPG expression is correlated with Ifh1 promoter binding, whereas Rap1 and Fhl1 remain promoter-associated upon stress-induced down regulation. A TF called Sfp1 has also been implicated in RPG regulation, though recent work reveals that its primary function is in activation of RiBi and other growth-related genes. Sfp1 plays an important regulatory role at a small number of RPGs where Rap1-Fhl1-Ifh1 action is subsidiary or non-existent. In addition, nearly half of all RPGs are bound by Hmo1, which either stabilizes or re-configures Fhl1-Ifh1 binding. Recent studies identified the proline rotamase Fpr1, known primarily for its role in rapamycin-mediated inhibition of the TORC1 kinase, as an additional TF at RPG promoters. Fpr1 also affects Fhl1-Ifh1 binding, either independently or in cooperation with Hmo1. Finally, a major recent development was the discovery of a protein homeostasis mechanism driven by unassembled ribosomal proteins, referred to as the Ribosome Assembly Stress Response (RASTR), that controls RPG transcription through the reversible condensation of Ifh1.


Subject(s)
Oxidative Stress , Ribosomes/metabolism , Saccharomyces cerevisiae/metabolism , Signal Transduction , Transcription, Genetic , Saccharomyces cerevisiae/genetics , Saccharomyces cerevisiae Proteins/metabolism
3.
Nucleic Acids Res ; 48(20): 11408-11420, 2020 11 18.
Article in English | MEDLINE | ID: mdl-33084907

ABSTRACT

While expression of ribosomal protein genes (RPGs) in the budding yeast has been extensively studied, a longstanding enigma persists regarding their co-regulation under fluctuating growth conditions. Most RPG promoters display one of two distinct arrangements of a core set of transcription factors (TFs) and are further differentiated by the presence or absence of the HMGB protein Hmo1. However, a third group of promoters appears not to be bound by any of these proteins, raising the question of how the whole suite of genes is co-regulated. We demonstrate here that all RPGs are regulated by two distinct, but complementary mechanisms driven by the TFs Ifh1 and Sfp1, both of which are required for maximal expression in optimal conditions and coordinated downregulation upon stress. At the majority of RPG promoters, Ifh1-dependent regulation predominates, whereas Sfp1 plays the major role at all other genes. We also uncovered an unexpected protein homeostasis-dependent binding property of Hmo1 at RPG promoters. Finally, we show that the Ifh1 paralog Crf1, previously described as a transcriptional repressor, can act as a constitutive RPG activator. Our study provides a more complete picture of RPG regulation and may serve as a paradigm for unravelling RPG regulation in multicellular eukaryotes.


Subject(s)
DNA-Binding Proteins/metabolism , Gene Expression Regulation, Fungal , High Mobility Group Proteins/metabolism , Ribosomal Proteins/genetics , Saccharomyces cerevisiae Proteins/metabolism , Saccharomyces cerevisiae/genetics , Stress, Physiological/genetics , Trans-Activators/metabolism , Transcription, Genetic , Chromatin Immunoprecipitation Sequencing , DNA-Binding Proteins/genetics , Gene Expression Regulation, Fungal/drug effects , High Mobility Group Proteins/genetics , Mechanistic Target of Rapamycin Complex 1/antagonists & inhibitors , Mechanistic Target of Rapamycin Complex 1/genetics , Mechanistic Target of Rapamycin Complex 1/metabolism , Promoter Regions, Genetic , Repressor Proteins/genetics , Repressor Proteins/metabolism , Ribosomal Proteins/biosynthesis , Saccharomyces cerevisiae/drug effects , Saccharomyces cerevisiae/metabolism , Saccharomyces cerevisiae Proteins/genetics , Sirolimus/pharmacology , Stress, Physiological/drug effects , Trans-Activators/genetics
4.
J Cancer Res Clin Oncol ; 146(7): 1671-1676, 2020 Jul.
Article in English | MEDLINE | ID: mdl-32333143

ABSTRACT

BACKGROUND: DNA topoisomerase and telomerase enzymes are popular targets of several anti-tumor drugs. Smooth proceeding of telomeric recombination requires Topoisomerase II (Top2), which is involved in telomere-telomere recombination through functioning in relaxation of positive supercoils among the cells adopting telomerase-independent Alternative lengthening of telomere (ALT) pathway. Most of the inhibitors reported so far have been designed to targetsolely telomerase-positive cells, which can potentially lead to therapeutic failure because tumor cells treated with telomerase inhibitors can activate the ALT pathway for telomere maintenance. Knowing that ALT cells are more sensitive against a Top2 inhibitor, ICRF-93 agent, compared to telomerase-positive cells, we analyzed two selected ellipticine derivatives that we recently reported as TopII-targeting compounds, to assess their effects on the formation of DNA breaks and suppression of ALT pathway. METHODS: Cell viability, Comet, C-Circle assays, dot blot, immunofluorescence staining, and telomere fluorescence in situ hybridization (FISH) staining were used for determining the effect of the compounds on ALT status of tumor cells. RESULTS AND CONCLUSIONS: Treatment of ALT cells with ellipticine derivatives resulted in the formation of DNA breaks and suppression of ALT-associated phenotypes in vitro. Our results will contribute to the development of therapeutic strategies combining telomerase and ALT pathway inhibitors.


Subject(s)
Antineoplastic Agents/pharmacology , Ellipticines/pharmacology , Telomerase/genetics , Telomere Homeostasis/drug effects , Topoisomerase II Inhibitors/pharmacology , Antineoplastic Agents/chemistry , Cell Line , Ellipticines/chemistry , Fluorescent Antibody Technique , Humans , In Situ Hybridization, Fluorescence
5.
Mol Cell ; 77(3): 488-500.e9, 2020 02 06.
Article in English | MEDLINE | ID: mdl-31761495

ABSTRACT

Pioneer transcription factors (pTFs) bind to target sites within compact chromatin, initiating chromatin remodeling and controlling the recruitment of downstream factors. The mechanisms by which pTFs overcome the chromatin barrier are not well understood. Here, we reveal, using single-molecule fluorescence, how the yeast transcription factor Rap1 invades and remodels chromatin. Using a reconstituted chromatin system replicating yeast promoter architecture, we demonstrate that Rap1 can bind nucleosomal DNA within a chromatin fiber but with shortened dwell times compared to naked DNA. Moreover, we show that Rap1 binding opens chromatin fiber structure by inhibiting inter-nucleosome contacts. Finally, we reveal that Rap1 collaborates with the chromatin remodeler RSC to displace promoter nucleosomes, paving the way for long-lived bound states on newly exposed DNA. Together, our results provide a mechanistic view of how Rap1 gains access and opens chromatin, thereby establishing an active promoter architecture and controlling gene expression.


Subject(s)
Chromatin/metabolism , Nucleosomes/genetics , Saccharomyces cerevisiae Proteins/metabolism , Telomere-Binding Proteins/metabolism , Transcription Factors/metabolism , Chromatin/genetics , Chromatin Assembly and Disassembly , DNA/metabolism , DNA-Binding Proteins/metabolism , Gene Expression Regulation/genetics , Nucleosomes/metabolism , Nucleosomes/physiology , Promoter Regions, Genetic/genetics , Saccharomyces cerevisiae/genetics , Saccharomyces cerevisiae Proteins/genetics , Shelterin Complex , Telomere-Binding Proteins/genetics , Transcription Factors/genetics
6.
PLoS One ; 12(12): e0189193, 2017.
Article in English | MEDLINE | ID: mdl-29232376

ABSTRACT

General Control Non-derepressible 5 (GCN5) and Alteration/Deficiency in Activation 2 and 3 proteins (ADA2 and ADA3, respectively) are subunits of the Histone AcetylTransferase (HAT) module of SAGA- and ATAC-type co-activators. We previously reported four new interacting partners of human ADA3 identified by screening a human fetal brain cDNA library using yeast two hybrid technology. One of these partners was Apoptosis-Antagonizing Transcription Factor (AATF), also known as Che-1, an RNA polymerase II-binding protein with a number of roles in different cellular processes including regulation of transcription, cell proliferation, cell cycle control, DNA damage responses and apoptosis. Che-1/AATF is a potential therapeutic target for cancer treatments. In this study, we aimed to identify whether besides ADA3, other components of the HAT modules of SAGA and ATAC complexes, human ADA2 and GCN5 also interact with Che-1/AATF. Co-immunoprecipitation and co-localization experiments were used to demonstrate association of AATF both with two ADA2 isoforms, ADA2A and ADA2B and with GCN5 proteins in human cells and yeast two-hybrid assays to delineate domains in the ADA2 and GCN5 proteins required for these interactions. These findings provide new insights into the pathways regulated by ADA-containing protein complexes.


Subject(s)
Histone Acetyltransferases/metabolism , Saccharomyces cerevisiae Proteins/metabolism , Saccharomyces cerevisiae/metabolism , Trans-Activators/metabolism , Acetyltransferases/metabolism , Adaptor Proteins, Signal Transducing/metabolism , DNA-Binding Proteins , Humans , Protein Binding , Transcription Factors/metabolism , Transcriptional Activation , p300-CBP Transcription Factors/metabolism
7.
Bioorg Med Chem Lett ; 26(7): 1809-12, 2016 Apr 01.
Article in English | MEDLINE | ID: mdl-26906637

ABSTRACT

Ellipticine (5,11-dimethyl-6H-pyrido[4,3-b]carbazole) is an antineoplastic agent that intercalates into DNA and alters topoisomerase II activity. Unfortunately, this compound displays a number of adverse properties. Therefore, to investigate new ellipticine-based compounds for their potential as topoisomerase II-targeted drugs, we synthesized two novel derivatives, N-methyl-5-demethyl ellipticine (ET-1) and 2-methyl-N-methyl-5-demethyl ellipticinium iodide (ET-2). As determined by DNA decatenation and cleavage assays, ET-1 and ET-2 act as catalytic inhibitors of human topoisomerase IIα and are both more potent than the parent compound. Neither compound impairs the ability of the type II enzyme to bind its DNA substrate. Finally, the potency of ET-1 and ET-2 as catalytic inhibitors of topoisomerase IIα appears to be related to their ability to intercalate into the double helix.


Subject(s)
DNA-Binding Proteins/antagonists & inhibitors , Ellipticines/chemistry , Ellipticines/pharmacology , Topoisomerase II Inhibitors/chemistry , Topoisomerase II Inhibitors/pharmacology , Antigens, Neoplasm/metabolism , DNA/metabolism , DNA Topoisomerases, Type II/metabolism , DNA-Binding Proteins/metabolism , Humans , Intercalating Agents/chemistry , Intercalating Agents/pharmacology , Methylation
8.
Chem Res Toxicol ; 29(3): 415-20, 2016 Mar 21.
Article in English | MEDLINE | ID: mdl-26894873

ABSTRACT

Two metabolites from the ascomycete fungus Septofusidium berolinense were recently identified as having antineoplastic activity [Ekiz et al. (2015) J. Antibiot. , DOI: 10.1038/ja.2015.84]. However, the basis for this activity is not known. One of the compounds [3,6-dihydroxy-2-propylbenzaldehyde (GE-1)] is a hydroquinone, and the other [2-hydroxymethyl-3-propylcyclohexa-2,5-diene-1,4-dione (GE-2)] is a quinone. Because some hydroquinones and quinones act as topoisomerase II poisons, the effects of GE-1 and GE-2 on DNA cleavage mediated by human topoisomerase IIα were assessed. GE-2 enhanced DNA cleavage ∼4-fold and induced scission with a site specificity similar to that of the anticancer drug etoposide. Similar to other quinone-based topoisomerase II poisons, GE-2 displayed several hallmark characteristics of covalent topoisomerase II poisons, including (1) the inability to poison a topoisomerase IIα construct that lacks the N-terminal domain, (2) the inhibition of DNA cleavage when the compound was incubated with the enzyme prior to the addition of plasmid, and (3) the loss of poisoning activity in the presence of a reducing agent. In contrast to GE-2, GE-1 did not enhance DNA cleavage mediated by topoisomerase IIα except at very high concentrations. However, the activity and potency of the metabolite were dramatically enhanced under oxidizing conditions. These results suggest that topoisomerase IIα may play a role in mediating the cytotoxic effects of these fungal metabolites.


Subject(s)
Antigens, Neoplasm/metabolism , Benzaldehydes/pharmacology , Cyclohexanones/pharmacology , DNA Cleavage , DNA Topoisomerases, Type II/metabolism , DNA-Binding Proteins/metabolism , Fungi/chemistry , Fungi/metabolism , Secondary Metabolism , Benzaldehydes/chemistry , Benzaldehydes/metabolism , Cyclohexanones/chemistry , Cyclohexanones/metabolism , Humans , Molecular Structure
9.
Mol Biol Cell ; 26(19): 3480-8, 2015 Oct 01.
Article in English | MEDLINE | ID: mdl-26246601

ABSTRACT

Two large phosphatidylinositol 3-kinase-related protein kinases (PIKKs), ATM and ATR, play a central role in the DNA damage response pathway. PIKKs contain a highly conserved extreme C-terminus called the FRAP-ATM-TRRAP-C-terminal (FATC) domain. In budding yeast, ATM and ATR correspond to Tel1 and Mec1, respectively. In this study, we characterized functions of the FATC domain of Tel1 by introducing substitution or truncation mutations. One substitution mutation, termed tel1-21, and a truncation mutation, called tel1-ΔC, did not significantly affect the expression level. The tel1-21 mutation impaired the cellular response to DNA damage and conferred moderate telomere maintenance defect. In contrast, the tel1-ΔC mutation behaved like a null mutation, conferring defects in both DNA damage response and telomere maintenance. Tel1-21 protein localized to DNA ends as effectively as wild-type Tel1 protein, whereas Tel1-ΔC protein failed. Introduction of a hyperactive TEL1-hy mutation suppressed the tel1-21 mutation but not the tel1-ΔC mutation. In vitro analyses revealed that both Tel1-21 and Tel1-ΔC proteins undergo efficient autophosphorylation but exhibit decreased kinase activities toward the exogenous substrate protein, Rad53. Our results show that the FATC domain of Tel1 mediates localization to DNA ends and contributes to phosphorylation of target proteins.


Subject(s)
DNA, Fungal/genetics , DNA, Fungal/metabolism , Intracellular Signaling Peptides and Proteins/genetics , Intracellular Signaling Peptides and Proteins/metabolism , Protein Serine-Threonine Kinases/genetics , Protein Serine-Threonine Kinases/metabolism , Saccharomyces cerevisiae Proteins/genetics , Saccharomyces cerevisiae Proteins/metabolism , Amino Acid Sequence , Ataxia Telangiectasia Mutated Proteins/genetics , Cell Cycle/genetics , Cell Cycle Proteins/metabolism , Checkpoint Kinase 2/genetics , Checkpoint Kinase 2/metabolism , DNA Damage , DNA-Binding Proteins/metabolism , Molecular Sequence Data , Mutation , Phosphatidylinositol 3-Kinases/metabolism , Phosphorylation/genetics , Protein Structure, Tertiary , Saccharomyces cerevisiae/genetics , Saccharomyces cerevisiae/metabolism , Telomere/metabolism
10.
PLoS Genet ; 11(8): e1005283, 2015 Aug.
Article in English | MEDLINE | ID: mdl-26263073

ABSTRACT

Telomeres, the ends of linear eukaryotic chromosomes, have a specialized chromatin structure that provides a stable chromosomal terminus. In budding yeast Rap1 protein binds to telomeric TG repeat and negatively regulates telomere length. Here we show that binding of multiple Rap1 proteins stimulates DNA double-stranded break (DSB) induction at both telomeric and non-telomeric regions. Consistent with the role of DSB induction, Rap1 stimulates nearby recombination events in a dosage-dependent manner. Rap1 recruits Rif1 and Rif2 to telomeres, but neither Rif1 nor Rif2 is required for DSB induction. Rap1-mediated DSB induction involves replication fork progression but inactivation of checkpoint kinase Mec1 does not affect DSB induction. Rap1 tethering shortens artificially elongated telomeres in parallel with telomerase inhibition, and this telomere shortening does not require homologous recombination. These results suggest that Rap1 contributes to telomere homeostasis by promoting chromosome breakage.


Subject(s)
Chromosomes, Fungal/genetics , Saccharomyces cerevisiae Proteins/metabolism , Saccharomyces cerevisiae/genetics , Telomere-Binding Proteins/metabolism , Transcription Factors/metabolism , DNA Breaks, Double-Stranded , DNA Replication , DNA, Fungal/genetics , DNA, Fungal/metabolism , Protein Binding , Saccharomyces cerevisiae/metabolism , Shelterin Complex , Telomere Homeostasis
11.
Genet Test Mol Biomarkers ; 19(7): 372-8, 2015 Jul.
Article in English | MEDLINE | ID: mdl-25978699

ABSTRACT

BACKGROUND: Myeloid differentiation primary response 88 (MYD88) is a common adaptor protein that is responsible for signaling from several receptors; mutations in this gene may play a role in the pathogenesis of lymphoma. AIM: We aimed to determine the MYD88 L265P mutation frequency, the level of MYD88 expression, and their associations with clinicopathological parameters in mature B-cell non-Hodgkin lymphomas (NHLs). METHODS: A total of 68 patients were included in the study. The presence of the MYD88 L265P mutation was analyzed by real-time polymerase chain reaction and direct sequencing. MYD88 protein expression was evaluated by immunohistochemistry (IHC) using two different scoring systems. RESULTS: MYD88 L265P mutation was present in eight (18.6%) diffuse large B-cell lymphoma (DLBCL) patients. We also observed a significant association between the loss of MYD88 expression and advanced stage in both mature B-cell NHL and DLBCL according to the first IHC scoring systems (p=0.015 and p=0.024, respectively). An association was also seen between MYD88 overexpression and low clinical risk in both mature B-cell NHL and DLBCL according to the second IHC scoring system (p=0.027 and p=0.024, respectively). CONCLUSIONS: The L265P mutation may be helpful for understanding the pathogenesis of immune-privileged site-associated DLBCLs. The presence of the mutation, together with its protein overexpression, could also be used as a prognostic marker in advanced stage DLBCLs.


Subject(s)
Lymphoma, Large B-Cell, Diffuse/genetics , Lymphoma, Large B-Cell, Diffuse/metabolism , Myeloid Differentiation Factor 88/biosynthesis , Myeloid Differentiation Factor 88/genetics , Adult , Female , Gene Expression , Genetic Association Studies , Humans , Lymphoma, Large B-Cell, Diffuse/pathology , Male , Mutation , Polymorphism, Single Nucleotide , Real-Time Polymerase Chain Reaction
12.
Biochem Biophys Res Commun ; 432(1): 10-5, 2013 Mar 01.
Article in English | MEDLINE | ID: mdl-23395680

ABSTRACT

Regulation of gene expression in cells is mediated by protein-protein, DNA-protein and receptor-ligand interactions. PDZ (PSD-95/Discs-large/ZO-1) domains are protein-protein interaction modules. PDZ-containing proteins function in the organization of multi-protein complexes controlling spatial and temporal fidelity of intracellular signaling pathways. In general, PDZ proteins possess multiple domains facilitating distinct interactions. The human glutaminase interacting protein (hGIP) is an unusual PDZ protein comprising entirely of a single PDZ domain and plays pivotal roles in many cellular processes through its interaction with the C-terminus of partner proteins. Here, we report the identification by yeast two-hybrid screening of two new hGIP-interacting partners, DTX1 and STAU1. Both proteins lack the typical C-terminal PDZ recognition motif but contain a novel internal hGIP recognition motif recently identified in a phage display library screen. Fluorescence resonance energy transfer and confocal microscopy analysis confirmed the in vivo association of hGIP with DTX1 and STAU1 in mammalian cells validating the previous discovery of S/T-X-V/L-D as a consensus internal motif for hGIP recognition. Similar to hGIP, DTX1 and STAU1 have been implicated in neuronal function. Identification of these new interacting partners furthers our understanding of GIP-regulated signaling cascades and these interactions may represent potential new drug targets in humans.


Subject(s)
Cytoskeletal Proteins/metabolism , Intracellular Signaling Peptides and Proteins/metabolism , RNA-Binding Proteins/metabolism , Ubiquitin-Protein Ligases/metabolism , Amino Acid Motifs , Brain , Cytoskeletal Proteins/genetics , Fetus , Fluorescence Resonance Energy Transfer , Gene Library , HeLa Cells , Humans , Intracellular Signaling Peptides and Proteins/chemistry , Intracellular Signaling Peptides and Proteins/genetics , Microscopy, Confocal , Molecular Sequence Data , PDZ Domains , Protein Interaction Mapping , RNA-Binding Proteins/genetics , Saccharomyces cerevisiae , Ubiquitin-Protein Ligases/genetics
13.
Cell Biochem Biophys ; 66(1): 199-204, 2013 May.
Article in English | MEDLINE | ID: mdl-23161103

ABSTRACT

A considerable number of agents with chemotherapeutic potentials reported over the past years were shown to interfere with the reactions of DNA topoisomerases, the essential enzymes that regulate conformational changes in DNA topology. Gossypol, a naturally occurring bioactive phytochemical is a chemopreventive agent against various types of cancer cell growth with a reported activity on mammalian topoisomerase II. The compounds targeting topoisomerases vary in their mode of action; class I compounds act by stabilizing covalent topoisomerase-DNA complexes resulting in DNA strand breaks while class II compounds interfere with the catalytic function of topoisomerases without generating strand breaks. In this study, we report Gossypol as the interfering agent with type I topoisomerases as well. We also carried out an extensive set of assays to analyze the type of interference manifested by Gossypol on DNA topoisomerases. Our results strongly suggest that Gossypol is a potential class II inhibitor as it blocked DNA topoisomerase reactions with no consequently formed strand breaks.


Subject(s)
DNA Breaks , DNA Topoisomerases, Type II/chemistry , DNA Topoisomerases, Type I/chemistry , Gossypol/chemistry , Animals , Enzyme Activation , Enzyme Assays , Enzyme Stability , Macromolecular Substances/chemistry , Plasmids/chemistry , Topoisomerase I Inhibitors/chemistry , Topoisomerase II Inhibitors/chemistry
14.
Biochem J ; 450(2): 311-20, 2013 Mar 01.
Article in English | MEDLINE | ID: mdl-23167988

ABSTRACT

ADA (alteration/deficiency in activation) 3 is a conserved component of several transcriptional adaptor and HAT (histone acetyltransferase) complexes that regulate RNA polymerase II-mediated gene expression. Within the HAT complexes ADA3 is associated with ADA2 and the HAT GCN5 (general control non-repressed 5). ADA3 plays roles in diverse cellular processes and also in malignancies by modulating GCN5 catalytic activity and/or by interactions with other regulators. To gain a better understanding of ADA3 function, we used a yeast two-hybrid approach to screen a human fetal cDNA library for proteins that interacted with hADA3 (human ADA3). We identified three novel hADA3-interacting partners, a transcriptional regulator, AATF (apoptosis-antagonizing transcription factor), and regulatory subunits of the PP1 (protein phosphatase 1) and PP2A (protein phosphatase 2A) [PPP1R7 (PP1 regulatory subunit 7) and PPP2R5D (PP2A 56 kDa regulatory subunit δ isoform) respectively]. Analysis of truncated versions of hADA3 indicated that the C-terminal ADA2-interacting domain was not required for these interactions. Fluorescent microscopy analysis and co-immunoprecipitation provided support for the co-localization and interaction of hADA3 with these proteins in human cells. Expression of the interacting proteins altered expression of an hADA3-regulated reporter gene, suggesting functional consequences for the interactions. The detected interactions of hADA3 might extend the spectrum of mechanisms by which ADA3 can contribute to the regulation of gene expression and shed light on processes mediated by these newly identified ADA3 partners.


Subject(s)
Apoptosis Regulatory Proteins/metabolism , Histone Acetyltransferases/metabolism , Protein Phosphatase 1/metabolism , Protein Phosphatase 2/metabolism , Repressor Proteins/metabolism , Transcription Factors/metabolism , Adaptor Proteins, Signal Transducing/genetics , Adaptor Proteins, Signal Transducing/metabolism , Apoptosis Regulatory Proteins/genetics , Cell Line, Tumor , DNA, Complementary/metabolism , DNA-Binding Proteins , Genes, Reporter , HeLa Cells , Histone Acetyltransferases/genetics , Humans , Microscopy, Fluorescence , Protein Phosphatase 1/genetics , Protein Phosphatase 2/genetics , Repressor Proteins/genetics , Transcription Factors/genetics , Transcriptional Activation
15.
DNA Cell Biol ; 31(11): 1580-4, 2012 Nov.
Article in English | MEDLINE | ID: mdl-22994211

ABSTRACT

Despite inherent limitations, the ease and rapidity of their use make transiently expressed reporter gene assays the most frequently used techniques for analyzing promoters and transcriptional regulators. The results of transient reporter gene assays are generally accepted to reflect transcriptional processes correctly, though these assays study regulatory sequences outside of the chromosomal environment and draw conclusions on transcription based on enzyme activity determination. For transient reporter gene assays, often more than one promoter is introduced into one cell. In addition to the one driving the primary reporter gene expression, a further one might serve to ensure the production of an internal control second reporter or/and a trans-acting factor. We demonstrate here by various examples that interference between physically unlinked promoters can profoundly affect reporter expression. Results of reporter gene assays performed by combinations of the cytomegalovirus promoter and various other promoter constructs (human immunodeficiency virus [HIV], Human T-cell Leukemia Virus Type I (HTLV-I), NF-κB-responsive, and p53-responsive) and trans-activator factors (HIV-Tat and p53) in different host cell lines (U2OS, HeLa, and L929) prove that interference between active transcription units can modify transcription responses dramatically. Since the interference depends on the promoters used, on the amount of transfected DNA, on the host cells, and on other factors, extra caution is required in interpreting results of transient reporter gene assays.


Subject(s)
Gene Expression Regulation , Genes, Reporter/genetics , Promoter Regions, Genetic/genetics , Transcriptional Activation , Animals , Cell Line, Tumor , Cytomegalovirus/genetics , Green Fluorescent Proteins/genetics , Green Fluorescent Proteins/metabolism , HeLa Cells , Human T-lymphotropic virus 1/genetics , Humans , Luciferases/genetics , Luciferases/metabolism , Luminescent Measurements/methods , Mice , NF-kappa B/metabolism , Plasmids/genetics , Protein Binding , Reproducibility of Results , Transfection , tat Gene Products, Human Immunodeficiency Virus
16.
Biochem Biophys Res Commun ; 411(4): 792-7, 2011 Aug 12.
Article in English | MEDLINE | ID: mdl-21787750

ABSTRACT

The vast majority of physiological processes in living cells are mediated by protein-protein interactions often specified by particular protein sequence motifs. PDZ domains, composed of 80-100 amino acid residues, are an important class of interaction motif. Among the PDZ-containing proteins, glutaminase interacting protein (GIP), also known as Tax Interacting Protein TIP-1, is unique in being composed almost exclusively of a single PDZ domain. GIP has important roles in cellular signaling, protein scaffolding and modulation of tumor growth and interacts with a number of physiological partner proteins, including Glutaminase L, ß-Catenin, FAS, HTLV-1 Tax, HPV16 E6, Rhotekin and Kir 2.3. To identify the network of proteins that interact with GIP, a human fetal brain cDNA library was screened using a yeast two-hybrid assay with GIP as bait. We identified brain-specific angiogenesis inhibitor 2 (BAI2), a member of the adhesion-G protein-coupled receptors (GPCRs), as a new partner of GIP. BAI2 is expressed primarily in neurons, further expanding GIP cellular functions. The interaction between GIP and the carboxy-terminus of BAI2 was characterized using fluorescence, circular dichroism (CD) and nuclear magnetic resonance (NMR) spectroscopy assays. These biophysical analyses support the interaction identified in the yeast two-hybrid assay. This is the first study reporting BAI2 as an interaction partner of GIP.


Subject(s)
Intracellular Signaling Peptides and Proteins/metabolism , Nerve Tissue Proteins/metabolism , Humans , Nerve Tissue Proteins/genetics , Peptides/genetics , Peptides/metabolism , Spectrometry, Fluorescence , Two-Hybrid System Techniques
17.
Cell Biochem Biophys ; 59(2): 71-7, 2011 Mar.
Article in English | MEDLINE | ID: mdl-20824388

ABSTRACT

We investigated the effect of extremely low-frequency electromagnetic field (ELF-EMF) with pulse trains exposure on lipid peroxidation, and, hence, oxidative stress in the rat liver tissue. The parameters that we measured were the levels of plasma alanine aminotransferase, aspartate aminotransferase, and alkaline phosphatase as well as plasma albumin, bilirubin, and total protein levels in 30 adult male Wistar rats exposed to ELF. We also determined the percentage of apoptotic and necrotic cells of the kidney extracts from the animals by flow cytometry method. Apoptotic cell death was further characterized by monitoring DNA degradation using gel electrophoresis. The results showed an increase in the levels of oxidative stress indicators, and the flow cytometric data suggested a possible relationship between the exposure to magnetic field and the cell death. We showed significantly lower necrotic cell percentages in experimental animals compared to either unexposed or sham control groups. However, DNA ladder analyses did not differentiate between the groups. Our results were discussed in relation to the response of biological systems to EMF.


Subject(s)
Apoptosis/radiation effects , Electromagnetic Fields , Oxidative Stress/radiation effects , Animals , Antioxidants/metabolism , DNA/metabolism , DNA/radiation effects , Flow Cytometry , Kidney/cytology , Kidney/metabolism , Lipid Peroxidation/radiation effects , Male , Rats , Rats, Wistar
18.
Hepatogastroenterology ; 57(98): 372-6, 2010.
Article in English | MEDLINE | ID: mdl-20583446

ABSTRACT

BACKGROUND/AIMS: Human Cytochrome P450 (CYP) comprises a multigene family of microsomal enzymes that metabolize a wide variety of xenobiotics, including drugs and carcinogens. Although the a number of CYP enzymes were also detected in epithelial cells along the gastrointestinal tract, little is known about the expression of CYP genes in gastric tissue. METHODOLOGY: In this study, the expression patterns of CYP isoforms was investigated in a total of 14 antral biopsy tissues obtained from the patients with either chronic gastritis (n = 6) or cancer (n = 8) by gene-specific real-time reverse transcriptase -PCR analyses. We employed primer sets specific for CYPs -1A1, -1A2, -2A6, -2B6, -2C, -2D6, -2E1, and -3A5. RESULTS: Among the isoforms CYP1A1, CYP2C and CYP2D6 gave rise to detectable mRNAs in all 14 gastric tissues while the mRNAs for the other CYPs were detected in some of the tissues. The expression patterns were compared to clinical parameters. There were no significant differences in the parameters between the two groups; however the mRNA expression of CYP2A6 was significantly higher in women than man (p < 0.05). CONCLUSIONS: Our data suggests that the CYP isoforms were independently expressed with respect to the pathological status in human gastric tissue.


Subject(s)
Cytochrome P-450 Enzyme System/metabolism , Gastritis/metabolism , Protein Isoforms/metabolism , RNA, Messenger/metabolism , Stomach Neoplasms/metabolism , Adult , Aged , Biopsy , Chi-Square Distribution , DNA Primers , Electrophoresis, Agar Gel , Female , Humans , Male , Middle Aged , Reverse Transcriptase Polymerase Chain Reaction
19.
J Enzyme Inhib Med Chem ; 24(3): 804-7, 2009 Jun.
Article in English | MEDLINE | ID: mdl-18830876

ABSTRACT

Chalcones (1,3-diaryl-2-propen-1-ones) are alpha, beta-unsaturated ketones with cytotoxic and anticancer properties. Several reports have shown that compounds with cytotoxic properties may also interfere with DNA topoisomerase functions. Five derivatives of 4'-hydroxychalcones were examined for cytotoxicity against transformed human T (Jurkat) cells as well as plasmid supercoil relaxation experiments using mammalian DNA topoisomerase I. The compounds were 3-phenyl-1-(4'-hydroxyphenyl)-2-propen-1-one (I), 3-(p-methylphenyl)-1-(4'-hydroxyphenyl)-2-propen-1-one (II), 3-(p-methoxyphenyl)-1-(4'-hydroxyphenyl)-2-propen-1-one (III), 3-(p-chlorophenyl)-1-(4'-hydroxyphenyl)-2-propen-1-one (IV), and 3-(2- thienyl)-1-(4'-hydroxyphenyl)-2-propen-1-one (V). The order of the cytotoxicity of the compounds was; IV > III > II > I > V. Compound IV, had the highest Hammett and log P values (0.23 and 4.21, respectively) and exerted both highest cytotoxicity and strongest DNA topoisomerase I inhibition. Compounds I and II gave moderate interference with the DNA topoisomerase I while III & V did not interfere with the enzyme.


Subject(s)
Antineoplastic Agents/chemical synthesis , Antineoplastic Agents/pharmacology , Chalcones/chemical synthesis , Chalcones/pharmacology , Topoisomerase I Inhibitors , Animals , Antineoplastic Agents/chemistry , Cattle , Cell Line , Chalcones/chemistry , DNA Topoisomerases, Type I/metabolism , Humans , Inhibitory Concentration 50 , Jurkat Cells , Plasmids/metabolism
20.
J Enzyme Inhib Med Chem ; 24(3): 844-9, 2009 Jun.
Article in English | MEDLINE | ID: mdl-18951286

ABSTRACT

Benzimidazoles of both natural and synthetic sources are the key components of many bio-active compounds. Several reports have shown antifungal, antiviral, H(2) receptor blocker and antitumor activities for benzimidazoles and their derivatives. In this study, we synthesized twelve bis-benzimidazole derivatives by selecting di(1H-benzo[d]imidazol-2-yl)methane as the main compound. The numbers of carbons at 2 positions of bis-benzimidazole derivatives were changed from 1 to 4, and derivatives were synthesized with methyl substitutions at 5- and/or 6- positions. The compounds were screened via in vitro plasmid superciol relaxation assays using mammalian DNA topoisomerase I and cytostatic assays were carried out against HeLa (cervix adenocarcinoma), MCF7 (breast adenocarcinoma) and A431 (skin epidermoid carcinoma) cells for selected derivatives. Our results suggest that the malonic acid derivatives of bis-benzimidazoles, namely, bis(5-methyl-1H-benzo[d]imidazol-2-yl)methane and bis(5,6-dimethyl-1H-benzo[d]imidazol-2-yl)methane, were remarkably active compounds in interfering with DNA topoisomerase I and the former compound was also found to be cytotoxic against MCF7 and A431 cells. The inhibitory effects obtained with these derivatives are significant as these compounds can be potential sources of anticancer agents.


Subject(s)
Antineoplastic Agents/chemical synthesis , Antineoplastic Agents/pharmacology , Benzimidazoles/chemical synthesis , Benzimidazoles/pharmacology , Topoisomerase I Inhibitors , Animals , Antineoplastic Agents/chemistry , Benzimidazoles/chemistry , Breast Neoplasms/pathology , Carcinoma, Squamous Cell/pathology , Cell Line, Tumor , DNA Topoisomerases, Type I/metabolism , Female , HeLa Cells , Humans , Spectrum Analysis , Structure-Activity Relationship , Uterine Cervical Neoplasms/pathology
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