Role of Polyamines in Regulation of Sequence-Specific DNA Binding Activity

2006 ◽  
pp. 91-122 ◽  
Author(s):  
Sripriya Venkiteswaran ◽  
Thresia Thomas ◽  
T. J. Thomas
Keyword(s):  
Dna Binding ◽  
Binding Activity ◽  
Dna Binding Activity

scholarly journals Overexpression of mitogen-activated protein kinase (ERK1) enhances T- cell cytokine gene expression: role of AP1, NF-AT, and NF-KB

Blood ◽  
1993 ◽  
Vol 82 (8) ◽  
pp. 2470-2477 ◽  
Author(s):  
JH Park ◽  
L Levitt
Keyword(s):  
Gene Expression ◽  
T Cell ◽  
Dna Binding ◽  
Map Kinase ◽  
Binding Activity ◽  
Cytokine Gene Expression ◽  
Cytokine Gene ◽  
Dna Binding Activity ◽  
Mitogen Activated Protein

Abstract Transfected Jurkat cells overexpressing extracellular signal-regulated kinase (ERK1), also referred to as mitogen-activated protein (MAP) kinase, were selected by Western blotting assay using anti-ERK1 and antiphosphotyrosine antibodies in combination with a functional MAP kinase assay. We then asked whether enhanced ERK1 expression had any effect on induction of T-cell cytokine genes. The results show that overexpression of ERK1 enhances expression of T-cell interleukin-2 (IL- 2), IL-3, and granulocyte-macrophage colony-stimulating factor mRNA; no change was seen in expression of the alpha-actin gene. DNA-binding activities of the transcription factors AP1, NF-AT, and NF-kB were specifically increased twofold to fourfold in ERK1-overexpressing clones relative to nontransformed or vector-transformed cells, whereas no enhancement of CK1-CK2 protein DNA binding activity was detected after ERK1 overexpression. Additionally, increased NF-AT DNA binding activity was associated with functional enhancement of NF-AT transactivating activity in ERK1-overexpressing cells. These results provide direct evidence for the role of MAP kinase in the regulation of cytokine gene expression and indicate that such regulation is likely mediated through the enhanced DNA binding activity of specific nuclear transcription factors.

scholarly journals Role of the p38 MAPK/C/EBPβ Pathway in the Regulation of Phenotype and IL-10 and IL-12 Production by Tolerogenic Bone Marrow-Derived Dendritic Cells

Cells ◽  
2018 ◽  
Vol 7 (12) ◽  
pp. 256 ◽  
Author(s):  
Chantal Guindi ◽  
Alexandre Cloutier ◽  
Simon Gaudreau ◽  
Echarki Zerif ◽  
Patrick P. McDonald ◽  
...  
Keyword(s):  
Bone Marrow ◽  
Dendritic Cells ◽  
Dna Binding ◽  
P38 Mapk ◽  
Costimulatory Molecules ◽  
Binding Activity ◽  
Gm Csf ◽  
Dna Binding Activity ◽  
Factor C

Dendritic cells (DCs) play a major role in innate and adaptive immunity and self-immune tolerance. Immunogenic versus tolerogenic DC functions are dictated by their levels of costimulatory molecules and their cytokine expression profile. The transcription factor C/EBPβ regulates the expression of several inflammatory genes in many cell types including macrophages. However, little is known regarding the role of C/EBPβ in tolerogenic versus immunogenic DCs functions. We have previously reported that bone marrow-derived DCs generated with GM-CSF (GM/DCs) acquire the signature of semi-mature tolerogenic IL-10-producing DCs as opposed to immunogenic DCs generated with GM-CSF and IL-4 (IL-4/DCs). Here, we show that tolerogenic GM/DCs exhibit higher levels of phosphorylation and enhanced DNA binding activity of C/EBPβ and CREB than immunogenic IL-4/DCs. We also show that the p38 MAPK/CREB axis and GSK3 play an important role in regulating C/EBPβ phosphorylation and DNA binding activity. Inhibition of p38 MAPK in GM/DCs resulted in a drastic decrease of C/EBPβ and CREB DNA binding activities, a reduction of their IL-10 production and an increase of their IL-12p70 production, a characteristic of immunogenic IL-4/DCs. We also present evidence that GSK3 inhibition in GM/DCs reduced C/EBPβ DNA binding activity and increased expression of costimulatory molecules in GM/DCs and their production of IL-10. Analysis of GM/DCs of C/EBPβ−/− mice showed that C/EBPβ was essential to maintain the semimature phenotype and the production of IL-10 as well as low CD4+ T cell proliferation. Our results highlight the importance of the p38MAPK-C/EBPβ pathway in regulating phenotype and function of tolerogenic GM/DCs.

scholarly journals Specific DNA Binding and Regulation of Its Own Expression by the AidB Protein in Escherichia coli

2010 ◽  
Vol 192 (23) ◽  
pp. 6136-6142 ◽  
Author(s):  
Valentina Rippa ◽  
Angela Amoresano ◽  
Carla Esposito ◽  
Paolo Landini ◽  
Michael Volkert ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Dna Binding ◽  
Alkylating Agents ◽  
Specific Interaction ◽  
Domain Architecture ◽  
Binding Activity ◽  
Dna Binding Activity ◽  
Preferential Binding

ABSTRACT Upon exposure to alkylating agents, Escherichia coli increases expression of aidB along with three genes (ada, alkA, and alkB) that encode DNA repair proteins. While the biological roles of the Ada, AlkA, and AlkB proteins have been defined, despite many efforts, the molecular functions of AidB remain largely unknown. In this study, we focused on the biological role of the AidB protein, and we demonstrated that AidB shows preferential binding to a DNA region that includes the upstream element of its own promoter, PaidB. The physiological significance of this specific interaction was investigated by in vivo gene expression assays, demonstrating that AidB can repress its own synthesis during normal cell growth. We also showed that the domain architecture of AidB is related to the different functions of the protein: the N-terminal region, comprising the first 439 amino acids (AidB “I-III”), possesses FAD-dependent dehydrogenase activity, while its C-terminal domain, corresponding to residues 440 to 541 (AidB “IV”), displays DNA binding activity and can negatively regulate the expression of its own gene in vivo. Our results define a novel role in gene regulation for the AidB protein and underline its multifunctional nature.

scholarly journals Multifunctional Role of the Pitx2 Homeodomain Protein C-Terminal Tail

1999 ◽  
Vol 19 (10) ◽  
pp. 7001-7010 ◽  
Author(s):  
Brad A. Amendt ◽  
Lillian B. Sutherland ◽  
Andrew F. Russo
Keyword(s):  
Amino Acid ◽  
Dna Binding ◽  
Inhibitory Effect ◽  
Binding Activity ◽  
Homeodomain Protein ◽  
Rieger Syndrome ◽  
Amino Acid Peptide ◽  
Dna Binding Activity ◽  
C Terminus

ABSTRACT Pitx2 is a newly described bicoid-like homeodomain transcription factor that is defective in Rieger syndrome and shows a striking leftward developmental asymmetry. We have previously shown that Pitx2 (also called Ptx2 and RIEG) transactivates a reporter gene containing abicoid enhancer and synergistically transactivates the prolactin promoter in the presence of the POU homeodomain protein Pit-1. In this report, we focused on the C-terminal region which is mutated in some Rieger patients and contains a highly conserved 14-amino-acid element. Deletion analysis of Pitx2 revealed that the C-terminal 39-amino-acid tail represses DNA binding activity and is required for Pitx2-Pit-1 interaction and Pit-1 synergism. Pit-1 interaction with the Pitx2 C terminus masks the inhibitory effect and promotes increased DNA binding activity. Interestingly, cotransfection of an expression vector encoding the C-terminal 39 amino acids of Pitx2 specifically inhibits Pitx2 transactivation activity. In contrast, the C-terminal 39-amino-acid peptide interacts with Pitx2 to increase its DNA binding activity. These data suggest that the C-terminal tail intrinsically inhibits the Pitx2 protein and that this inhibition can be overcome by interaction with other transcription factors to allow activation during development.

scholarly journals Evolution of Networks of Protein Domain Organization

2020 ◽  
Author(s):  
M. Fayez Aziz ◽  
Gustavo Caetano-Anollés
Keyword(s):  
Dna Binding ◽  
Protein Function ◽  
Preferential Attachment ◽  
Big Bang ◽  
Binding Activity ◽  
Protein Domain ◽  
Domain Organization ◽  
Evolving Networks ◽  
Dna Binding Activity

Abstract Domains are the structural, functional and evolutionary units of proteins. They combine to form multidomain proteins. The evolutionary history of this molecular combinatorics has been studied with phylogenomic methods. Here, we construct networks of domain organization and explore their evolution. These networks revealed two ancient waves of structural novelty arising from ancient ‘p-loop’ and ‘winged helix’ domains and a massive ‘big bang’ of domain organization. The evolutionary recruitment of domains was highly modular, hierarchical and ongoing. Domain rearrangements elicited non-random and scale-free network structure. Comparative analyses of preferential attachment, randomness and modularity of networks showed yin-and-yang complementary transition patterns along the evolutionary timeline. Remarkably, evolving networks highlighted a central evolutionary role of cofactor-supporting structures of non-ribosomal peptide synthesis (NRPS) pathways, likely crucial to the early development of the genetic code. Some highly modular domains featured dual response regulation in two-component signal transduction systems with DNA-binding activity linked to transcriptional regulation of responses to environmental change. Interestingly, hub domains across the evolving networks shared the historical role of DNA binding and editing, an ancient protein function in molecular evolution. Our investigation unfolds historical source-sink patterns of evolutionary recruitment that further our understanding of protein architectures and functions.

Molecular Mechanisms of Parthenolide-Mediated Pro-Apoptotic Activity in Acute Myeloid Leukemia Cells

Blood ◽  
2011 ◽  
Vol 118 (21) ◽  
pp. 2463-2463
Author(s):  
Mohammad Minhajuddin ◽  
Shanshan Pei ◽  
John M Ashton ◽  
Kevin Callahan ◽  
Eleni Lagadinou ◽  
...  
Keyword(s):  
Cell Death ◽  
Transcription Factor ◽  
Dna Binding ◽  
Myeloid Leukemia ◽  
Molecular Mechanisms ◽  
Lentiviral Vector ◽  
Binding Activity ◽  
Dna Binding Activity ◽  
Apoptotic Activity

Abstract Abstract 2463 Acute myeloid leukemia is malignant disease, characterized by an accumulation of immature myeloid cells. Recent studies have demonstrated that myeloid leukemia appears to arise from a population of leukemia stem cells (LSCs). LSCs typically reside in a quiescent state and therefore do not respond to standard chemotherapeutic agents, which generally target more actively dividing cells. However, LSCs do display certain unique molecular properties that can be exploited to target this relatively rare population of cells that drive disease pathogenesis. Specifically, NF-kB, a pro-survival transcription factor, is constitutively active in LSCs but not in normal hematopoietic stem cells (HSCs). Targeting this pathway by pharmaceutical approaches has been suggested as a potential strategy in the treatment of leukemia; however, inhibiting this pathway alone is not sufficient to strongly induce AML-specific cell death. Further investigation of pathways, that are unique to AML, is a key in designing more effective pharmacologic agents that specifically target the LSC. We have previously demonstrated that the naturally occurring compound parthenolide (PTL) induces apoptosis in primary AML cells, including the stem and progenitor cell. While the empirical anti-leukemic activity of PTL is clear, the underlying molecular mechanisms remain poorly understood. Here we investigate two properties associated with parthenolide-mediated cell death: i) activation of pro-apoptotic transcription factor p53, ii) inhibition of pro-survival transcription factor NF-kB. In order to evaluate the role of p53 signaling, AML cells were challenged with PTL resulting in the phosphorylation of p53 at serine-15, indicating activation p53 in response to PTL. To further investigate the role of p53 in PTL mediated responses, we generated a lentiviral vector expressing shRNAs specifically targeting p53. Leukemia cells were infected with the lentiviral vector encoding p53 shRNA or scramble control and evaluated by qPCR and western blot analysis. The data showed a significant knockdown of p53 mRNA and protein levels, as well as strong inhibition of p21 expression, indicating the specificity of p53 knockdown. Exposure of cells to PTL in which p53 has been specifically disrupted results in partial rescue from PTL mediated cell death, implicating the role of p53 in this response. Next, we performed a detailed analysis of the molecular mechanism by which PTL inhibits NF-kB pathway activity. Using a novel analog of PTL, we demonstrate that the compound directly binds to IKK-beta. Upon exposure to PTL, IKK-beta shows reduced kinase activity, indicating that binding of the drug directly impairs enzymatic function. Secondary to the inhibition of IKK-beta kinase activity, there is decreased phosphorylation of IkB-alpha at ser32/36, resulting in reduced proteosome mediated degradation. As expected, translocation of RelA/p65 to the nucleus was also impaired, resulting in decreased DNA binding activity as evidenced by electrophoretic mobility shift assay (EMSA). Interestingly, studies with a biotinylated analog also show that PTL appears to directly bind p65, we also observed a decreased phosphorylation of p65 at serine 536, an event mediating the transcriptional activity of DNA-bound p65. Inhibition of the NF-kB pathway by parthenolide also resulted in very significant inhibition of one of its well-known downstream target genes, ICAM-1 (CD54) at mRNA, protein and surface expression levels. Whether reduced ICAM-1 expression affects the biology of AML cells is as yet unknown. However, given the known role of ICAM-1 in integrin signaling, we propose that loss of ICAM-1 via NF-kB inhibition may impair the ability of AML cells to interact with their environment. Taken together, this study further elucidates the mechanisms by which PTL mediates pro-apoptotic activity in primary AML cells. PTL induces activation of p53 pathway and therefore knockdown of p53 by shRNA results in partial rescue from PTL mediated cell death. PTL also inhibits the NF-kB pathway, which includes binding of PTL to both IKK-beta and RelA/p65, which leads to decreased phosphorylation of IkB-alpha and reduced DNA binding of p65. In addition, we have discovered the ICAM-1 expression in AML cells is regulated by NF-kB, and that loss of NF-kB DNA binding activity results in loss of ICAM-1 expression. Disclosures: No relevant conflicts of interest to declare.

scholarly journals Molecular Mechanism Underlying the Action of Substituted Pro-Gly Dipeptide Noopept

Acta Naturae ◽  
2016 ◽  
Vol 8 (1) ◽  
pp. 82-89 ◽  
Author(s):  
Yu. V. Vakhitova ◽  
S. V. Sadovnikov ◽  
S. S. Borisevich ◽  
R. U. Ostrovskaya ◽  
T. A. Gudasheva ◽  
...  
Keyword(s):  
Dna Binding ◽  
Wide Spectrum ◽  
Binding Activity ◽  
Hek293 Cells ◽  
Luciferase Reporter ◽  
Additional Increase ◽  
Dna Binding Activity ◽  
Selective Increase ◽  
Positive Effect

This study was performed in order to reveal the effect of Noopept (ethyl ester of N-phenylacetyl-Lprolylglycine, GVS-111) on the DNA-binding activity of transcriptional factors (TF) in HEK293 cells transiently transfected with luciferase reporter constructs containing sequences for CREB, NFAT, NF-B, p53, STAT1, GAS, VDR, HSF1, and HIF-1. Noopept (10 M) was shown to increase the DNA-binding activity of HIF-1 only, while lacking the ability to affect that of CREB, NFAT, NF-B, p53, STAT1, GAS, VDR, and HSF1. Noopept provoked an additional increase in the DNA-binding activity of HIF-1 when applied in conditions of CoCl2-induced HIF- 1 stabilization. The degree of this HIF-positive effect of Noopept was shown to be concentration-dependent. Piracetam (1 mM) failed to affect significantly any of the TF under study. The results of molecular docking showed that Noopept (L-isomer), as well as its metabolite, L-isomer of N-phenyl-acetylprolyl, unlike its pharmacologically ineffective D-isomer, is able to bind to the active site of prolyl hydroxylase 2. Taking into account the important role of the genes activated by HIF-1 in the formation of an adaptive response to hypoxia, data on the ability of Noopept to provoke a selective increase in the DNA-binding activity of HIF-1 explain the wide spectrum of neurochemical and pharmacological effects of Noopept revealed before. The obtained data allow one to propose the HIF-positive effect as the primary mechanism of the activity of this Pro-Gly-containing dipeptide.

scholarly journals Role of ATP-binding motifs on DNA-binding activity and biological function of Rhp51, a Rad51 homologue in fission yeast

2002 ◽  
Vol 364 (3) ◽  
pp. 869-874 ◽  
Author(s):  
Woo J. KIM ◽  
Hyojin LEE ◽  
Eon J. PARK ◽  
Seung H. HONG ◽  
Sang D. PARK
Keyword(s):  
Dna Binding ◽  
Binding Activity ◽  
Single Amino Acid ◽  
Atp Binding ◽  
Single Mutation ◽  
Binding Ability ◽  
Binding Motifs ◽  
Dna Binding Activity

Rhp51, a RecA and Rad51 homologue of Schizosaccharomyces pombe, plays a pivotal role in homologous recombination and recombinational repair. It has a set of the well-conserved type A and type B ATP-binding motifs, which are highly conserved in all RecA homologues. In a previous study [Kim, Lee, Park, Park and Park (2001) Nucleic Acids Res. 29, 1724–1732], we reported that a single mutation of the conserved lysine in A motif [Lys155→Ala (K155A)] destroyed the DNA repair ability of Rhp51 and that overexpression of this mutant protein conferred dominant negativity. In the present paper, we investigated DNA-binding properties of recombinant Rhp51 and its mutant proteins. Purified Rhp51 protein showed ATP-dependent double- and single-strand DNA-binding activities. To characterize the role of ATP-binding motifs, we generated Rhp51 K155A and Rhp51 Asp244→Gln (D244Q), which have a single amino acid substitution in A and B motifs respectively. Interestingly, K155A and D244Q mutations impaired ATP-dependent DNA binding in a different manner. K155A lost the DNA binding itself, whereas D244Q maintained the binding ability but lost the ATP dependency. However, despite the difference in DNA-binding ability, both mutations failed to rescue the methylmethane sulphonate and UV sensitivity of the rhp51Δ mutant. Together, these results suggested that not only the DNA binding but also the ATP dependence in DNA binding is required for proper in vivo functioning of Rhp51.

scholarly journals Role of the Rad52 Amino-terminal DNA Binding Activity in DNA Strand Capture in Homologous Recombination

2009 ◽  
Vol 284 (48) ◽  
pp. 33275-33284 ◽  
Author(s):  
Idina Shi ◽  
Swee C. L. Hallwyl ◽  
Changhyun Seong ◽  
Uffe Mortensen ◽  
Rodney Rothstein ◽  
...  
Keyword(s):  
Dna Binding ◽  
Homologous Recombination ◽  
Binding Activity ◽  
Amino Terminal ◽  
Dna Binding Activity ◽  
Dna Strand
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