scholarly journals Constrained G4 structures unveil topology specificity of known and new G4 binding proteins

2021 ◽  
Author(s):  
Angelique Pipier ◽  
Alexandre Devaux ◽  
Thomas Lavergne ◽  
Annie Adrait ◽  
Yohann Couté ◽  
...  
Keyword(s):  
Binding Proteins ◽  
Cyclic Peptide ◽  
Essential Feature ◽  
Interacting Proteins ◽  
Rna Pol Ii ◽  
Cell Extracts ◽  
Different Types ◽  
Pol Ii Pausing ◽  
Clastogenic Effect

G-quadruplexes (G4) are non-canonical secondary structures consisting in stacked tetrads of hydrogen-bonded guanines bases. An essential feature of G4 is their intrinsic polymorphic nature, which is characterized by the equilibrium between several conformations (also called topologies) and the presence of different types of loops with variable lengths. In cells, G4 functions rely on protein or enzymatic factors that recognize and promote or resolve these structures. In order to characterize new G4-dependent mechanisms, extensive researches aimed at identifying new G4 binding proteins. Using G-rich single-stranded oligonucleotides that adopt non-controlled G4 conformations, a large number of G4-binding proteins have been identified in vitro, but their specificity towards G4 topology remained unknown. Constrained G4 structures are biomolecular objects based on the use of a rigid cyclic peptide scaffold as a template for directing the intramolecular assembly of the anchored oligonucleotides into a single and stabilized G4 topology. Here, using various constrained RNA or DNA G4 as baits in human cell extracts, we establish the topology preference of several well-known G4-interacting factors. Moreover, we identify new G4-interacting proteins such as the NELF complex involved in the RNA-Pol II pausing mechanism, and we show that it impacts the clastogenic effect of the G4-ligand pyridostatin.

scholarly journals Constrained G4 structures unveil topology specificity of known and new G4 binding proteins

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
A. Pipier ◽  
A. Devaux ◽  
T. Lavergne ◽  
A. Adrait ◽  
Y. Couté ◽  
...  
Keyword(s):  
Binding Proteins ◽  
Cyclic Peptide ◽  
Essential Feature ◽  
Interacting Proteins ◽  
Rna Pol Ii ◽  
Cell Extracts ◽  
Different Types ◽  
Pol Ii Pausing ◽  
Clastogenic Effect

AbstractG-quadruplexes (G4) are non-canonical secondary structures consisting in stacked tetrads of hydrogen-bonded guanines bases. An essential feature of G4 is their intrinsic polymorphic nature, which is characterized by the equilibrium between several conformations (also called topologies) and the presence of different types of loops with variable lengths. In cells, G4 functions rely on protein or enzymatic factors that recognize and promote or resolve these structures. In order to characterize new G4-dependent mechanisms, extensive researches aimed at identifying new G4 binding proteins. Using G-rich single-stranded oligonucleotides that adopt non-controlled G4 conformations, a large number of G4-binding proteins have been identified in vitro, but their specificity towards G4 topology remained unknown. Constrained G4 structures are biomolecular objects based on the use of a rigid cyclic peptide scaffold as a template for directing the intramolecular assembly of the anchored oligonucleotides into a single and stabilized G4 topology. Here, using various constrained RNA or DNA G4 as baits in human cell extracts, we establish the topology preference of several well-known G4-interacting factors. Moreover, we identify new G4-interacting proteins such as the NELF complex involved in the RNA-Pol II pausing mechanism, and we show that it impacts the clastogenic effect of the G4-ligand pyridostatin.

Effect of microenvironment and cell-line type on carbohydrate-binding proteins of macrophage-like cells

1988 ◽  
Vol 66 (11) ◽  
pp. 1169-1176 ◽  
Author(s):  
Hans-Joachim Gabius ◽  
Katalin Vehmeyer
Keyword(s):  
Binding Proteins ◽  
Cultured Cells ◽  
Sodium Dodecyl ◽  
Carbohydrate Binding ◽  
Intercellular Interaction ◽  
Cell Extracts ◽  
Carbohydrate Binding Proteins ◽  
Sugar Receptors

The pattern of sugar inhibition of rosette formation, a model for intercellular interaction between cultured cells and glutaraldehyde-fixed, trypsinated rabbit erythrocytes, served to infer the presence of carbohydrate-binding proteins. This profile from cell extracts for the two murine macrophage-like cell lines, P388D1 and J774A.1, was comparatively analyzed by affinity chromatography on supports with immobilized carbohydrates (lactose, L-fucose, N-acetyl-D-glucosamine, N-acetyl-D-galactosamine, and maltose) or with the immobilized mannose-rich yeast glycoprotein mannan or fetuin-derived glycopeptides containing sialic acid residues. After elution with specific sugar in the absence of Ca2+ ions, the proteins were separated by sodium dodecyl sulfate – polyacrylamide slab gel electrophoresis. The composition of carbohydrate-binding proteins of the two lines clearly exhibited quantitative and qualitative differences. Moreover, the pattern of P388D1 cells was also demonstrated to change significantly in response to alterations in the conditions of the physiological environment. These alterations were imposed by in vitro growth, by subsequent in vivo growth in nude mice, and by re-adaptation of cells to culture after in vivo passage. Collectively, our observations and other physiological and biochemical reports on macrophage lectins indicate that the presence of sugar receptors with different specificities may be an indicator of macrophage differentiation, being reversibly modulated to a considerable extent by external factors, e.g., microenvironment. Extensive but selective alterations in this respect could play an important role in the control of recognition and effector mechanisms within diverse functions of macrophage subpopulations.

scholarly journals Fission Yeast Homologs of Human CENP-B Have Redundant Functions Affecting Cell Growth and Chromosome Segregation

2000 ◽  
Vol 20 (8) ◽  
pp. 2852-2864 ◽  
Author(s):  
Mary Baum ◽  
Louise Clarke
Keyword(s):  
Dna Binding ◽  
Fission Yeast ◽  
Dna Sequence ◽  
Chromosome Segregation ◽  
Binding Proteins ◽  
Dna Binding Proteins ◽  
Central Core ◽  
Cell Extracts ◽  
Redundant Functions

ABSTRACT Two functionally important DNA sequence elements in centromeres of the fission yeast Schizosaccharomyces pombe are the centromeric central core and the K-type repeat. Both of these DNA elements show internal functional redundancy that is not correlated with a conserved DNA sequence. Specific, but degenerate, sequences in these elements are bound in vitro by the S. pombeDNA-binding proteins Abp1p (also called Cbp1p) and Cbhp, which are related to the mammalian centromere DNA-binding protein CENP-B. In this study, we determined that Abp1p binds to at least one of its target sequences within S. pombe centromere II central core (cc2) DNA with an affinity (Ks = 7 × 109 M−1) higher than those of other known centromere DNA-binding proteins for their cognate targets. In vivo, epitope-tagged Cbhp associated with centromeric K repeat chromatin, as well as with noncentromeric regions. Likeabp1+/cbp1 +, we found thatcbh + is not essential in fission yeast, but a strain carrying deletions of both genes (Δabp1 Δcbh) is extremely compromised in growth rate and morphology and missegregates chromosomes at very high frequency. The synergism between the two null mutations suggests that these proteins perform redundant functions in S. pombe chromosome segregation. In vitro assays with cell extracts with these proteins depleted allowed the specific assignments of several binding sites for them within cc2 and the K-type repeat. Redundancy observed at the centromere DNA level appears to be reflected at the protein level, as no single member of the CENP-B-related protein family is essential for proper chromosome segregation in fission yeast. The relevance of these findings to mammalian centromeres is discussed.

scholarly journals A Dictyostelium mutant lacking an F-actin cross-linking protein, the 120-kD gelation factor.

1990 ◽  
Vol 111 (4) ◽  
pp. 1477-1489 ◽  
Author(s):  
M Brink ◽  
G Gerisch ◽  
G Isenberg ◽  
A A Noegel ◽  
J E Segall ◽  
...  
Keyword(s):  
Binding Proteins ◽  
Mutant Cell ◽  
Actin Binding ◽  
In Vitro Assays ◽  
Cell Cortex ◽  
Cross Linking ◽  
Actin Binding Proteins ◽  
Cell Extracts ◽  
Nonmuscle Cells

Actin-binding proteins are known to regulate in vitro the assembly of actin into supramolecular structures, but evidence for their activities in living nonmuscle cells is scarce. Amebae of Dictyostelium discoideum are nonmuscle cells in which mutants defective in several actin-binding proteins have been described. Here we characterize a mutant deficient in the 120-kD gelation factor, one of the most abundant F-actin cross-linking proteins of D. discoideum cells. No F-actin cross-linking activity attributable to the 120-kD protein was detected in mutant cell extracts, and antibodies recognizing different epitopes on the polypeptide showed the entire protein was lacking. Under the conditions used, elimination of the gelation factor did not substantially alter growth, shape, motility, or chemotactic orientation of the cells towards a cAMP source. Aggregates of the mutant developed into fruiting bodies consisting of normally differentiated spores and stalk cells. In cytoskeleton preparations a dense network of actin filaments as typical of the cell cortex, and bundles as they extend along the axis of filopods, were recognized. A significant alteration found was an enhanced accumulation of actin in cytoskeletons of the mutant when cells were stimulated with cyclic AMP. Our results indicate that control of cell shape and motility does not require the fine-tuned interactions of all proteins that have been identified as actin-binding proteins by in vitro assays.

PMA induces stabilization of oncostatin M mRNA in human lymphoma U937 cells

2008 ◽  
Vol 410 (1) ◽  
pp. 177-186 ◽  
Author(s):  
Sumita Bandyopadhyay ◽  
Tapas K. Sengupta ◽  
Eleanor K. Spicer
Keyword(s):  
Binding Proteins ◽  
Protein Complexes ◽  
Oncostatin M ◽  
Dependent Manner ◽  
U937 Cells ◽  
Globin Mrna ◽  
Mrna Stabilization ◽  
Il Interleukin ◽  
Cell Extracts

OSM (oncostatin M) is a pleiotropic cytokine belonging to the IL (interleukin) 6 family that modulates the growth of some cancer cell lines. We have found that PMA treatment of human U937 lymphoma cells increased the steady-state levels of OSM mRNA. Furthermore, the half-life of OSM mRNA was increased from 2.3 to 6.2 h. Measurement of mRNA/hnRNA (heterogeneous nuclear RNA) ratios in PMA-treated cells suggests further that the increase in OSM mRNA is due to enhanced mRNA stability. Consistent with this, synthetic OSM mRNA transcripts decayed faster in extracts of untreated U937 cells than in extracts of PMA-treated cells. The 3′-untranslated region of OSM mRNA contains a putative ARE (AU-rich element) that may play a role in mRNA stabilization. Addition of the OSM ARE motif to the 3′-end of β-globin mRNA increased its decay rate in vitro. Decay assays with β-globin–AREOSM and β-globin transcripts indicate that PMA induces mRNA stabilization in an ARE-dependent manner. PMA also induces at least five OSM ARE-binding proteins. Supershift assays indicated that HuR is present in PMA-induced OSM mRNA–protein complexes. PMA treatment appears to induce translocation of HuR from the nucleus to the cytoplasm. RNA-decay assays indicated that HuR stabilizes OSM RNA in vitro. Additionally, immunodepletion of HuR from U937 cell extracts led to more rapid decay of OSM transcripts. Collectively, these findings suggest that the ARE plays a role in PMA-induced stabilization of OSM mRNA and that this process involves multiple ARE-binding proteins, including HuR.

scholarly journals Expression characteristics of triplet repeat-containing RNAs and triplet repeat-interacting proteins in human tissues.

2008 ◽  
Vol 55 (1) ◽  
pp. 1-8 ◽  
Author(s):  
Anna J Jasinska ◽  
Piotr Kozlowski ◽  
Wlodzimierz J Krzyzosiak
Keyword(s):  
Binding Sites ◽  
Binding Proteins ◽  
Tandem Repeats ◽  
Triplet Repeat ◽  
Interacting Proteins ◽  
Substantial Portion ◽  
Triplet Repeat Expansion ◽  
Different Types ◽  
Cug Repeats ◽  
Different Tissues

Numerous human transcripts contain tandem repeats of trinucleotide motifs, the function of which remains unknown. In this study we used the available gene expression EST data to characterize the abundance of a large group of these transcripts in different tissues and determine the mRNAs which had the highest contribution to the observed levels of transcripts containing different types of the CNG repeats. A more extensive characteristics was performed for transcripts containing the CUG repeats, and those encoding the repeat-binding proteins. The scarcity of double-stranded CUG repeats as well as various proportions of the single-stranded and double-stranded CUG repeat-binding proteins were revealed in the studied transcriptomes. The observed correlated levels of transcripts containing single-stranded CUG repeats and of proteins binding single-stranded CUG repeats may imply that in addition to transcripts which only provide binding sites for these proteins there may be a substantial portion of the transcripts whose metabolism is directly regulated by such proteins. Our results showing a highly variable composition of triplet repeat-containing transcripts and their interacting proteins in different tissues may contribute to a better understanding of the mechanism of RNA-mediated pathogenesis in triplet repeat expansion diseases.

scholarly journals Identification of Ebp1 as a component of cytoplasmic bcl-2 mRNP (messenger ribonucleoprotein particle) complexes

2006 ◽  
Vol 396 (1) ◽  
pp. 99-107 ◽  
Author(s):  
Sudeep K. Bose ◽  
Tapas K. Sengupta ◽  
Sumita Bandyopadhyay ◽  
Eleanor K. Spicer
Keyword(s):  
Binding Proteins ◽  
Rna Binding ◽  
Ribonucleoprotein Particle ◽  
Mobility Shift ◽  
Cell Extracts ◽  
Mrna Binding Proteins ◽  
Messenger Ribonucleoprotein ◽  
Co Precipitation ◽  
Mrna Binding

The 3′-UTR (untranslated region) of bcl-2 mRNA contains an ARE (AU-rich element) that potentially regulates the stability of bcl-2 mRNA in a cell specific fashion. Previous studies have demonstrated that multiple proteins interact with bcl-2 mRNA in HL-60 (human leukaemia-60) cells, potentially contributing to the overexpression of Bcl-2 protein. Treatment of HL-60 cells with taxol or okadaic acid has been shown to induce destabilization of bcl-2 mRNA, which was associated with decreased binding of trans-acting factors to bcl-2 mRNA. Nucleolin has been identified as one of the bcl-2 mRNA-binding proteins [Sengupta, Bandyopadhyay, Fernandes and Spicer (2004) J. Biol. Chem. 279, 10855–10863]. In an effort to identify additional bcl-2 mRNA-binding proteins, two polypeptides of approx. 45 kDa and 60 kDa were isolated from HL-60 cells by AREbcl-2 (transcripts that contain bcl-2 AREs) RNA affinity chromatography. These proteins were identified as the human proliferation associated protein, Ebp1, and human DRBP76 (double stranded RNA-binding protein 76) respectively, by MALDI (matrix-assisted laser-desorption ionization)-MS. RNA electrophoretic mobility shift assays indicated that recombinant Ebp1 binds to AREbcl-2 RNA but not to the group 1 ARE present in GM-CSF (granulocyte macrophage-colony stimulating factor) mRNA in vitro. Antibody supershift assays demonstrated that Ebp1 is present in protein–AREbcl-2 RNA complexes formed with cytosolic HL-60 extracts. The interaction of Ebp1 with bcl-2 mRNA in HL-60 cells was also demonstrated by RNA co-immunoprecipitation assays. This interaction was not detected in extracts of taxol-treated HL-60 cells. Immunoprecipitation assays further revealed that Ebp1 co-precipitates with nucleolin from HL-60 cytoplasmic extracts. The observation that co-precipitation was decreased when extracts were treated with RNase suggests that Ebp1 and nucleolin are present in the same bcl-2 mRNP (messenger ribonucleoprotein particle) complexes. RNA-decay assays further demonstrated that Ebp1 decreased the rate of decay of β-globin–AREbcl-2 transcripts in HL-60 cell extracts. Collectively, these results indicate a novel function for Ebp1 in contributing to the regulation of bcl-2 expression in HL-60 cells.

scholarly journals The Werner Syndrome Protein Is Involved in RNA Polymerase II Transcription

1999 ◽  
Vol 10 (8) ◽  
pp. 2655-2668 ◽  
Author(s):  
Adayabalam S. Balajee ◽  
Amrita Machwe ◽  
Alfred May ◽  
Matthew D. Gray ◽  
Junko Oshima ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Cell Lines ◽  
Werner Syndrome ◽  
Molecular Defect ◽  
Rna Pol Ii ◽  
Vitro Assay ◽  
Pol Ii ◽  
Cell Extracts

Werner syndrome (WS) is a human progeroid syndrome characterized by the early onset of a large number of clinical features associated with the normal aging process. The complex molecular and cellular phenotypes of WS involve characteristic features of genomic instability and accelerated replicative senescence. The gene involved (WRN) was recently cloned, and its gene product (WRNp) was biochemically characterized as a helicase. Helicases play important roles in a variety of DNA transactions, including DNA replication, transcription, repair, and recombination. We have assessed the role of the WRN gene in transcription by analyzing the efficiency of basal transcription in WS lymphoblastoid cell lines that carry homozygous WRN mutations. Transcription was measured in permeabilized cells by [3H]UTP incorporation and in vitro by using a plasmid template containing the RNA polymerase II (RNA pol II)–dependent adenovirus major late promoter. With both of these approaches, we find that the transcription efficiency in different WS cell lines is reduced to 40–60% of the transcription in cells from normal individuals. This defect can be complemented by the addition of normal cell extracts to the chromatin of WS cells. Addition of purified wild-type WRNp but not mutated WRNp to the in vitro transcription assay markedly stimulates RNA pol II–dependent transcription carried out by nuclear extracts. A nonhelicase domain (a direct repeat of 27 amino acids) also appears to have a role in transcription enhancement, as revealed by a yeast hybrid–protein reporter assay. This is further supported by the lack of stimulation of transcription when mutant WRNp lacking this domain was added to the in vitro assay. We have thus used several approaches to show a role for WRNp in RNA pol II transcription, possibly as a transcriptional activator. A deficit in either global or regional transcription in WS cells may be a primary molecular defect responsible for the WS clinical phenotype.

scholarly journals Actin-binding proteins from Drosophila embryos: a complex network of interacting proteins detected by F-actin affinity chromatography.

1989 ◽  
Vol 109 (6) ◽  
pp. 2963-2975 ◽  
Author(s):  
K G Miller ◽  
C M Field ◽  
B M Alberts
Keyword(s):  
Affinity Chromatography ◽  
Complex Network ◽  
Binding Proteins ◽  
Actin Binding ◽  
Small Subset ◽  
Interacting Proteins ◽  
Actin Binding Proteins ◽  
Cell Extracts ◽  
Drosophila Embryos

By using F-actin affinity chromatography columns to select proteins solely by their ability to bind to actin filaments, we have identified and partially purified greater than 40 proteins from early Drosophila embryos. These proteins represent approximately 0.5% of the total protein present in soluble cell extracts, and 2 mg are obtained by chromatography of an extract from 10 g of embryos. As judged by immunofluorescence of fixed embryos, 90% of the proteins that we have detected in F-actin column eluates are actin-associated in vivo (12 of 13 proteins tested). The distributions of antigens observed suggest that groups of these proteins cooperate in generating unique actin structures at different places in the cell. These structures change as cells progress through the cell cycle and as they undergo the specializations that accompany development. The variety of different spatial localizations that we have observed in a small subset of the total actin-binding proteins suggests that the actin cytoskeleton is a very complex network of interacting proteins.

Ultrastructural Investigations of the Contractile Filaments of Amoebae

1974 ◽  
Vol 32 ◽  
pp. 188-189
Author(s):  
P.L. Moore
Keyword(s):  
Cytoplasmic Streaming ◽  
Three Dimensional ◽  
Freeze Fracture ◽  
Amoeboid Movement ◽  
Different Types ◽  
Chemical Conditions ◽  
Complete Interpretation

Previous freeze fracture results on the intact giant, amoeba Chaos carolinensis indicated the presence of a fibrillar arrangement of filaments within the cytoplasm. A complete interpretation of the three dimensional ultrastructure of these structures, and their possible role in amoeboid movement was not possible, since comparable results could not be obtained with conventional fixation of intact amoebae. Progress in interpreting the freeze fracture images of amoebae required a more thorough understanding of the different types of filaments present in amoebae, and of the ways in which they could be organized while remaining functional.The recent development of a calcium sensitive, demembranated, amoeboid model of Chaos carolinensis has made it possible to achieve a better understanding of such functional arrangements of amoeboid filaments. In these models the motility of demembranated cytoplasm can be controlled in vitro, and the chemical conditions necessary for contractility, and cytoplasmic streaming can be investigated. It is clear from these studies that “fibrils” exist in amoeboid models, and that they are capable of contracting along their length under conditions similar to those which cause contraction in vertebrate muscles.

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