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PubMed1994

Purification of two isoforms of hnRNP-U and characterization of their nucleic acid binding activity.

The scaffold attachment factor A (SAF-A; Romig et al., 1992), a human nuclear protein which specifically binds vertebrate SAR (scaffold attached region) DNA, is identical with hnRNP-U (Kiledjian & Dreyfuss, 1992). In this paper, we report on the purification of two forms of this protein that can be chromatographically separated. We show that the purified proteins represent two isoforms, form 1 and form 2 hnRNP-U, which differ in their primary structure. Both isoforms bind to double- and single-stranded DNA and RNA. In addition, they form higher ordered nucleic acid/protein complexes and specifically bind and aggregate the human SAR element MII at physiological ionic strengths. Electron microscopic analysis shows that the isoforms differ from each other, as form 1 hnRNP-U aggregates into long unbranched filamentous protein/DNA complexes whereas form 2 hnRNP-U aggregates as spheres with an average diameter of 35 nm.

Amino Acid Sequence↗
PubMed1967

A possible mechanism of inhibition of protein synthesis by dimethylnitrosamine.

1. The incorporation of [(14)C]leucine into liver proteins of rats was measured in vivo at various times after treatment of the animals with dimethylnitrosamine and was correlated with the state of the liver ribosomal aggregates. Inhibition of incorporation ran parallel with breakdown of the aggregates. 2. Inhibition of leucine incorporation into protein and breakdown of ribosomal aggregates were not preceded by inhibition of incorporation of [(14)C]orotate into nuclear RNA of the liver. 3. Evidence was obtained of methylation of nuclear RNA in the livers of rats treated with [(14)C]dimethylnitrosamine. 4. Zonal centrifugation analysis of radioactive, nuclear, ribosomal and transfer RNA from livers of rats treated with [(14)C]dimethylnitrosamine revealed labelling of all centrifugal fractions to about the same extent. 5. It is suggested that methylation of messenger RNA might occur in the livers of dimethylnitrosamine-treated rats and the possible relation of this to inhibition of hepatic protein synthesis is discussed.

Animals↗
PubMed1961

The formation of fibrils from collagen solutions. IV. Effect of mucopolysaccharides and nucleic acids: an electron microscope study.

The kinetics of collagen reprecipitation from solutions of salt-extracted calf dermis in the presence of small amounts of mucopolysaccharide and nucleic acids (0.005 per cent in the final reaction mixture) has been reported by Wood (1960). The present paper is a parallel study using the same materials, and describes the electron microscopic (EM) morphology of the collagen precipitates replicated after 24 hours at room temperature. Satisfactory, uncontaminated EM preparations were obtained which showed that all the deposits were fibrous and bore the 640 A cross-banding characteristic of collagen except some narrow, background fibrils 200 to 1000 A wide precipitated in the presence of heparin. These exhibited fine striations about 220 A apart. Chondroitin sulfate greatly increased the rate of precipitation to give a deposit of low optical density consisting of narrow, rigid, discrete fibrils resembling fresh dermis. In contrast, heparin prevented macroscopic gelation, delayed precipitation, and only produced a scanty deposit of abnormal, short, wide, striated tactoids and compound fibers of varying length. The control preparations and the deposits formed in the presence of hyaluronic acid were intermediate between these two extremes. Delayed precipitation was associated with a coarser deposit and aggregation of the fibrils. A duplicate series of deposits precipitated in the presence of RNA and DNA, together with their controls, were examined after (1/2), 1, 1(1/2), 3, 9, and 24 hours. One set employed an acetic extract of whole calf dermis and the other salt-extracted dermis. The presence of 0.005 per cent DNA in the reaction mixture markedly delayed collagen precipitation with the slow formation of abnormal, short, wide tactoids and compound fibers. RNA also interfered with the quantity and quality of the deposits which contained far less collagen resembling unfixed, normal, adult human dermis, than the controls at the corresponding time intervals. Comparison of the experiments employing whole calf dermis with those employing the salt-extracted material demonstrated that at every time interval in all the experiments the deposits were retarded when salt-extracted dermis was used. This suggests that the salt-soluble components of the dermis play a part in fiber formation.

Animals↗
PubMed2003

Toll-like receptor expression in human keratinocytes: nuclear factor kappaB controlled gene activation by Staphylococcus aureus is toll-like receptor 2 but not toll-like receptor 4 or platelet activating factor receptor dependent.

Cultured primary human keratinocytes were screened for their expression of various members of the toll-like receptor (TLR) family. Keratinocytes were found to constitutively express TLR1, TLR2, TLR3, TLR5, and TLR9 but not TLR4, TLR6, TLR7, TLR8, or TLR10 as shown by polymerase chain reaction analysis. The expression of the crucial receptor for signaling of staphylococcal compounds TLR2 was also confirmed by immunohistochemistry, in contrast to TLR4, which showed a negative staining pattern. Next, we analyzed the activation of the proinflammatory nuclear transcription factor kappaB by Staphylococcus aureus strain 8325-4. Using nuclear extract gel shifts, RelA staining, and luciferase reporter transfection plasmids we found a clear induction of nuclear factor kappaB translocation by the bacteria. This translocation induced the transcription of nuclear factor kappaB controlled genes such as inducible nitric oxide synthetase, COX2, and interleukin-8. Transcription of these genes was followed by production of increased amounts of interleukin-8 protein and NO. Inhibition experiments using monoclonal antibodies and the specific platelet activating factor receptor inhibitor CV3988 showed that nuclear factor kappaB activation by S. aureus was TLR2 but not TLR4 or platelet activating factor receptor dependent. In line, the purified staphylococcal cell wall components lipoteichoic acid and peptidoglycan, known to signal through TLR2, also showed nuclear factor kappaB translocation in human keratinocytes, indicating a crucial role of the staphylococcal cell wall in the innate immune stimulation of human keratinocytes. These results help to explain the complex activation of human keratinocytes by S. aureus and its cell wall components in various inflammatory disorders of the skin.

Cells, Cultured↗
PubMed1991

A comprehensive study on the isolation and characterization of the HeLa S3 nuclear matrix.

Different agents have been employed to extract the histones and other soluble components from isolated HeLa S3 nuclei during nuclear matrix isolation. We report that 0.2M (NH4)2SO4 is a milder extracting agent than NaCl and LIS (lithium 3,5-diiodosalicylate), on the basis of the apparent preservation of the elaborate fibrogranular network and the residual nucleolus that resemble the in situ structures in whole cells and nuclei, minimal aggregation, and sufficient solubilization of DNA and histones. The importance of intermolecular disulfide bonds, RNA and 37 degrees C stabilization on the structural integrity of the nuclear matrix was examined in detail using sulfydryl alkylating, reducing and oxidizing agents, and RNase A. The data suggest that any disulfides formed during the isolation are not essential for maintaining the structural integrity of the in vitro matrix. However, structural integrity of the matrix is dependent upon RNA and to some degree on disulfides that presumably existed in situ. Sodium tetrathionate and 37 degrees C stabilization of isolated nuclei resulted in nuclear matrices containing an approximately twofold greater amount of protein, RNA and DNA than control preparations. The 37 degrees C incubation, unlike the sodium tetrathionate stabilization, does not appear to induce intermolecular disulfide bond formation. Neither stabilizations resulted in significant differences of the major matrix polypeptide pattern on two-dimensional (2-D) gels stained with Coomassie Blue as compared to that of unstabilized matrix. The major nuclear matrix proteins, other than the lamins, did not react to the Pruss murine monoclonal antibody (IFA) that recognizes all known intermediate filament proteins, suggesting that the internal matrix proteins are not related to the lamins in intermediate filament-like quality.

Blotting, Western↗
PubMed1986

Protein kinase C-activating tumor promoters enhance the differentiation of astrocytes in aggregating fetal brain cell cultures.

Serum-free aggregating cell cultures of fetal rat telencephalon treated with the potent tumor promoter phorbol 12-myristate 13-acetate (PMA) showed a marked, rapid, and sustained increase in the activity of the astrocyte-specific enzyme glutamine synthetase (GS). This effect was accompanied by a small increase in RNA synthesis and a progressive reduction in DNA synthesis. Only mitotically active cultures were responsive to PMA treatments. Since in aggregate cultures astrocytes are the preponderant cell type, both in number and mitotic activity, it can be concluded that PMA induces and/or enhances the terminal differentiation of astrocytes. The developmental expression of GS was also greatly stimulated by mezerein, a potent nonphorbol tumor promoter, but not by 4 alpha-phorbol 12,13-didecanoate, a nonpromoting phorbol ester. Since both tumor promoters, PMA and mezerein, are potent and specific activators of C-kinase, it is suggested that C-kinase plays a regulatory role in the growth and differentiation of normal astrocytes.

Animals↗
PubMed2005

The Lettuce infectious yellows virus (LIYV)-encoded P26 is associated with plasmalemma deposits within LIYV-infected cells.

Cytological, immunological, and mutagenesis approaches were used to identify the viral factors associated with the formation of plasmalemma deposits (PLDs) in whole plants and protoplasts infected by Lettuce infectious yellows virus (LIYV). Transmission electron microscopy and immunogold labeling using polyclonal antibodies to four of the five LIYV RNA 2-encoded large proteins, capsid protein (CP), minor capsid protein (CPm), HSP70 homolog (HSP70h), and P59, showed specific labeling of LIYV virions or virion aggregates around the vesiculated membranous inclusions, but not PLDs in LIYV-infected Nicotiana benthamiana, Nicotiana clevelandii, Lactuca sativa, and Chenopodium murale plants, and Nicotiana tabacum protoplasts. In contrast, antibodies to the RNA 2-encoded P26 showed specific labeling of PLDs but not virions in both LIYV-infected plants and protoplasts. Virion-like particles (VLPs) were seen in protoplasts infected by all LIYV RNA 2 mutants except for the CP (major capsid protein) mutant. PLDs were more difficult to find in protoplasts, but were seen in protoplasts infected by the CP and CPm mutants, but not in protoplasts infected by the P26, HSP70h, or P59 mutants. Interestingly, although the CPm mutant showed VLPs and PLDs, the PLDs did not show associated virions/virion-like particles as was always observed for PLDs seen in protoplasts infected by wild-type LIYV. Immunoblot analyses performed on purified LIYV virions showed that P26 was not detected with purified virions, but was detected in the cell wall, 1000 g and 30,000 g pellet fractions of LIYV-infected plants. These data suggest that P26 is associated with the LIYV-induced PLDs, and in contrast to the other RNA 2-encoded large proteins, P26 is not a virion protein.

Base Sequence↗
PubMed1994

Cell-specific regulation of agrin RNA splicing in the chick ciliary ganglion.

Alternative splicing results in production of four agrin proteins (agrin0, agrin8, agrin11, and agrin19) with different AChR aggregating activities. However, the cellular origin of mRNAs encoding each agrin isoform remains unknown. Using single-cell PCR, we demonstrate that in the chick ciliary ganglion, nonneuronal cells express only mRNA encoding agrin0, whereas neurons express one or any combination of agrin mRNAs. Moreover, significant differences were observed between the agrin mRNA profiles of ciliary and choroid neurons in the ganglion. The abundance of each agrin mRNA, the fraction of neurons expressing each transcript, and the combinations of transcripts expressed by neurons also change during development. Our results demonstrate that transcripts encoding agrin proteins with high AChR aggregating activity are expressed exclusively by neurons in the ciliary ganglion and that alternative splicing of agrin mRNA is regulated during development and in a cell-specific manner.

Agrin↗
PubMed1984

Changes in protein synthesis and in RNA poly A+ population after treatment of Dictyostelium amoebae by 5-bromo-2'-deoxyuridine.

Incorporation of 5-bromodeoxyuridine (5-BUdR) into nuclear DNA severely interrupts the life cycle of Dictyostelium discoideum after the first generation of growth. Loose cellular aggregates are then formed, but no spore or stalk cells are detectable and no other morphological transformations are observed. The perturbation of gene expression in the life cycle has been studied at the protein level by two-dimensional gel electrophoresis after pulse labelling with 35S-methionine and also by changes in the patterns of polysomal messenger RNA population. The latter was monitored by hybridisation studies using specific cDNA probes for "vegetative" and "18 hr" messenger RNAs. In the presence of 5-BUdR major anomalies in polypeptide synthesis were observed after the loose aggregation stage. Some vegetative polypeptides, including actin, which are normally abundant only during growth to the aggregation stage, are oversynthesised during the period 12-24 hr after starvation. In this same interval the normal decline in the abundance of vegetative mRNA species was not observed. In marked contrast virtually half the normal "18 hr-specific polypeptides" were poorly synthesised. Likewise, the normal increase in abundance of the corresponding "18 hr-specific" poly A + RNA species in the polysomes did not occur. No major alteration in the timing of the appearance of new macromolecules during the cell cycle was observed in spite of extensive modification of gene expression by the incorporation of 5-BUdR into genomic DNA.

Bromodeoxyuridine↗
PubMed1984

A method for isolation of undegraded free and membrane-bound ribosomes from rat lactating mammary gland.

Mammary gland polysomes are difficult to isolate from the lactating rat using methods developed for other species and tissues, most likely due to high calcium-stimulated ribonuclease activity in that tissue. A new method, utilizing ethyleneglycol-bis-(beta-aminoethylether)-N,N'-tetraacetic acid (EGTA) to bind calcium, yields highly aggregated polysomes from lactating rat mammary gland. Fresh mammary tissue is pulverized under liquid nitrogen. Free and membrane-bound polysomes are isolated by differential centrifugation in solutions containing 100 mM KCl, 100 mM MgCl2, 75 mM EGTA, 500 micrograms/ml heparin and 50 mM Tris buffer, pH 8.2 at 5 degrees C. Bound polysomes are released from the endoplasmic reticulum using Triton X-100 and deoxycholate. Polysome profiles are obtained on linear sucrose gradients and scanned at 254 nm. The method gives quantitative recovery of homogenate total RNA. To demonstrate that the method can be used to study nutritional effects on mammary gland polysome aggregation, lactating rats were fasted 22-66 h and then refed a stock diet for 71-95 h. Refeeding increased the percentage of polysomes (trimers or larger) in the bound fraction from 84 +/- 1 to 93 +/- 1% (P less than 0.001) and in the free fraction from 42 +/- 2 to 55 +/- 3% (P less than 0.001).

Animals↗
PubMed1979

Isolation of wheat ribosomes free of high molecular weight inhibitors of the natural messenger translation.

The cell-free extract from wheat germ contains an inhibitor interfering with translation of a natural template (BMV RNA). The inhibitor affects neither the translation of poly(U) nor the aminoacylation of tRNA. It exhibits the activity of protein kinase (ATP:protein phosphotransferase, EC 2.7.1.37). The inhibitor is found in lipoprotein aggregates which can be separated from ribosomes on Sepharose 2B column. Ribosomes purified on the Sepharose are several times more active in translation of BMV RNA than those isolated by conventional methods.

Chromatography, Gel↗
PubMed2002

Stress granules: sites of mRNA triage that regulate mRNA stability and translatability.

Mammalian stress granules (SGs) are cytoplasmic domains into which mRNAs are sorted dynamically in response to phosphorylation of eukaryotic initiation factor (eIF) 2alpha, a key regulatory step in translational initiation. The activation of one or more of the eIF2alpha kinases leads to SG assembly by decreasing the levels of eIF2-GTP-tRNA(Met), the ternary complex that is normally required for loading the initiator methionine onto the 48 S preinitiation complex to begin translation. This stress-induced scarcity of eIF2-GTP-tRNA(Met) allows the RNA-binding proteins TIA-1 (T-cell internal antigen-1) and TIAR (TIA-1-related protein) to bind the 48 S complex in lieu of the ternary complex, thereby promoting polysome disassembly and the concurrent routing of the mRNA into a SG. The actual formation of SGs occurs upon auto-aggregation of the prion-like C-termini of TIA-1 proteins; this aggregation is reversed in vivo by overexpression of the heat-shock protein (HSP) chaperone HSP70. Remarkably, HSP70 mRNA is excluded from SGs and is preferentially translated during stress, indicating that the RNA composition of the SG is selective. Moreover, the effects of HSP70 on TIA aggregation suggest a feedback loop whereby HSP70 synthesis is auto-regulated. Proteins that promote mRNA stability [e.g. HuR (Hu protein R)] and destabilize mRNA [i.e. tristetraprolin (TTP)] are also recruited to SGs, suggesting that SGs effect a process of mRNA triage, by promoting polysome disassembly and routing mRNAs to cytoplasmic domains enriched for HuR and TTP. This model reveals connections between the eIF2alpha kinase system, mRNA stability and cellular chaperone levels.

Animals↗
PubMed1994

The NTP-binding motif in cowpea mosaic virus B polyprotein is essential for viral replication.

We have assessed the functional importance of the NTP-binding motif (NTBM) in the cowpea mosaic virus (CPMV) B-RNA-encoded 58K domain by changing two conserved amino acids within the consensus A and B sites (GKSRTGK500S and MDD545, respectively). Both Lys-500 to Thr and Asp-545 to Pro substitutions are lethal as mutant B-RNAs were no longer replicated in cowpea protoplasts. Transiently produced mutant proteins were not able to support trans-replication of CPMV M-RNA in cowpea protoplasts in contrast to transiently produced wild-type B proteins. Therefore loss of viral RNA synthesis was a result of a protein defect rather than an RNA template defect. Mutant B polyproteins were correctly processed in vitro and in vivo and the regulatory function of the 32K protein on processing of B proteins was not affected by these mutations. Since regulation of processing by the 32K protein depends on interaction with the 58K domain, the mutations in the NTBM apparently do not interfere with this interaction. The Asp-545 to Pro substitution left intact the binding properties of the 84K precursor of the 58K protein, with respect to ATP-agarose, whereas the Lys-500 to Thr substitution decreased the binding capacity of the 84K protein, suggesting that the Lys-500 residue is directly involved in ATP binding. The Lys-500 to Thr substitution in the 58K domain resulted in an altered distribution of viral proteins, which failed to aggregate into large cytopathic structures as observed in protoplasts infected with wild-type B-RNA. However viral proteins containing the Asp-545 to Pro substitution showed a normal distribution in protoplasts.

Adenosine Triphosphate↗
PubMed2005

Metal-free catalysts for the hydrolysis of RNA derived from guanidines, 2-aminopyridines, and 2-aminobenzimidazoles.

2-aminopyridine and 2-aminobenzimidazole were chosen as structural analogues to substitute guanidinium groups in receptor molecules designed as phosphoryl transfer catalysts. Shifting the pKa of the guanidinium analogues toward 7 was expected to raise catalytic activities in aqueous buffer. Although the pKa's of both heterocycles are similar (6.2 and 7.0), only 2-aminobenzimidazole led to active RNA cleavers. All cleavage assays were run with fluorescently labeled substrates and a DNA sequencer. RNase contaminations would degrade RNA enantioselectively. In contrast, achiral catalysts such as 9b and 10b necessarily induce identical cleavage patterns in RNA and its mirror image. This principle allowed us to safely rule out contamination effects in this study. The most active catalysts, tris(2-aminobenzimidazoles) 9b and 10b, were shown by fluorescence correlation spectroscopy (FCS) to aggregate with oligonucleotides. However, at very low concentrations the compounds are still active in the nonaggregated state. Conjugates of 10b with antisense oligonucleotides or RNA binding peptides, therefore, will be promising candidates as site specific artificial ribonucleases.

Aminopyridines↗
PubMedDate not supplied

On-off switching of gene expression regulated with carbohydrate-lectin interaction.

A novel strategy for artificial regulation system of gene expression applying the specific molecular recognition between carbohydrate and lectin is proposed. Plasmid-lactose conjugates (pActin-lactose and pGFP-lactose) prepared via diazocoupling maintained the transcription activity with T7 RNA polymerase. Gel-shift assay showed that the pActin-lactose conjugates were specifically complexed with galactose-specific lectin RCA(120) with a strong binding affinity (K(a) = 7.6 x 10(5) M(-1) per Lac-unit). The complexes were observed to form aggregates of sub-several micrometer size by means of transmission electron microscopy (TEM) and atomic force microscopy (AFM). The activities of transcription and expression of the conjugates were evaluated, respectively, on the basis of the amount of transcript of pActin and the fluorescent intensity of the expressed GFP. These activities were repressed in the presence of an increasing concentration of RCA120, and then recovered by adding lactose, lactosylceramide-containing liposomes, and lactose-carrying polymers to the conjugate-RCA120 complex. Gel-shift assay and TEM observation revealed that the aggregation form of the complex was relaxed partially in the presence of the lactose derivatives, which increased the accessibility of T7 RNA polymerase to result in the recovery of transcription activity.

Actins↗
PubMed2004

Novel aspects of macromolecular repair and relationship to human disease.

Cellular and humoral defence mechanisms are essential for the survival of individuals and species. Thus, DNA repair prevents mutations and cytotoxicity from DNA damage, thereby reducing the risks of inappropriate cell death, developmental defects, premature ageing and cancer. Similarly, antigen-dependent acquired immune responses prevent infections and also have a role in cancer prevention. DNA repair is highly complex and functions in an intricate network that also involves transcription, replication, cell cycle regulation, and the immune system. DNA damage is repaired by at least four major mechanisms, each requiring many different proteins. In addition there are "subpathways", and back-up mechanisms both within and between pathways. Various defects in DNA repair result in different forms of cancer, e.g. the rare syndrome Xeroderma pigmentosum and the more common diseases early-onset breast cancer and hereditary non-polyposis colon cancer. Surprisingly, recent research has revealed molecular interactions between the ancient DNA repair mechanisms and the much younger acquired immune system. Thus, the classical base excision enzyme uracil-DNA glycosylase encoded by the UNG gene is also involved in somatic hypermutation and class switch recombination, e.g. from IgM antibodies to IgG, yielding secreted high affinity antibodies. Mutations in both alleles of UNG result in a hyper-IgM syndrome with life-threatening infections. Furthermore, it has recently become clear that not only DNA, but also RNA and proteins are repaired. Thus, certain aberrant methylations in RNA are repaired by oxidative demethylation in one step restoring the normal base, and at least in a bacterial model system this increases survival several-fold after exposure to methylating agents. Proteins are repaired both at the peptide amino acid level and at the structural level. RNA and protein repair are likely to be important to prevent the formation of cytotoxic protein aggregates of the types known to cause neurodegenerative diseases e.g. Alzheimer's, Parkinson's and Huntington's diseases, and other diseases as well. In conclusion, recent research has demonstrated an unexpected complexity of cellular defence mechanisms that function in intricate networks, rather than as independent mechanisms. The new knowledge opens for interventions that are based on a deeper understanding of the mechanisms of defence.

AlkB Homolog 1, Histone H2a Dioxygenase↗
PubMed2006

6,6'-Disubstituted benzothiazole trimethine cyanines--new fluorescent dyes for DNA detection.

The influence of methyl-, 2-hydroxyethyl-, dimethyl-, diethyl- and benzoyl-amino substituents in the 6,6'-positions of benzothiazole heterocycle of trimethine cyanines on their spectral-luminescent properties and behavior in presence of DNA, RNA and BSA was studied. It was shown that incorporation of 6,6'-substituents generally leads to the increase in dyes tendency to aggregation, resulting in the considerable decrease in the emission intensity of the disubstituted dyes as compared to the unsubstituted ones. Emission of the studied 6,6'-disubstited dyes in DNA presence is considerably more intensive than in presence of RNA, that points on the existing of DNA binding preference for the mentioned dyes. Insertion of benzoyl-amino groups into the 6,6'-positions permitted us to design the DNA-sensitive dyes on the basis of symmetric trimethine cyanines with unsubstituted polymethine chain, while typically such dyes slightly respond on the presence of biopolymers. 6,6'-Benzoyl-amino-disubstituted trimethine cyanines are proposed as efficient dyes for DNA detection.

Animals↗
PubMed1976

Hormone-induced dispersion or aggregation of carotenoid-containing smooth endoplasmic reticulum in cultured xanthophores from the goldfish, Carrassius auratus L.

A novel organelle movement is described in goldfish xanthophores. Smooth endoplasmic reticulum, containing carotenoids pigments, undergo MSH or c-AMP-induced dispersion. This dispersion is independent of RNA and protein synthesis, not modulated by c-GMP and inhibited by cytochalasin B but only at the relatively high concentration of 10 mug/ml. Epinephrine induces aggregation, a process that is inhibited by colchicine. These results suggest, but do not prove, the involvement of microfilaments in dispersion and microtubules in the aggregation of carotenoid-containing endoplasmic reticulum.

Adrenocorticotropic Hormone↗