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Results for “nucleoprotein complex”

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At least 541 records · Page 30Linked to original sources

PubMed1993

Contributions of promoter context and structure to regulated expression of the F plasmid traY promoter in Escherichia coli K-12.

Expression of the F plasmid traY promoter in vivo requires both host (E. coli) and plasmid encoded proteins. As judged by transcript size and primer extension analyses, the F plasmid traY promoter was utilized in vitro by purified E. coli sigma 70 RNA polymerase in the absence of other proteins. However, in vitro transcription required supercoiled templates. Endonuclease protection experiments showed that RNA polymerase is unable to form a stable complex at the traY promoter in linear or relaxed circular templates. In vitro transcription with linear templates could be elicited by altering the traY -10 and -35 hexamers to the consensus sequences. Alterations that reduced the effect of template supercoiling on apparent promoter strength in vitro also reduced the effect of the F plasmid TraJ protein on traY expression in vivo. Apparent traY promoter strength in vitro, estimated in template competition experiments, was unaltered by deletion of tra DNA normally upstream of the promoter, a change in promoter context that elicited high levels of promoter activity in TraJ- cells. These data suggest a model for regulated traY promoter activity in which a nucleoprotein complex involving tra DNA immediately upstream locally relaxes traY promoter DNA. TraJ and perhaps other activators could disrupt the complex, allowing promoter DNA to equilibrate at the prevailing negative superhelical density and thereby eliciting transcription initiation.

Bacterial Outer Membrane Proteins↗

PubMed1992

Transcription factors and the control of DNA replication.

Initiation of DNA replication is mediated by the assembly of nucleoprotein complexes at cis-acting DNA sequences known as origins of replication. Recent studies in several systems show that accessory transcription factors accentuate origin utilization by multiple mechanisms. The remarkable similarities in the activities of accessory transcription factors at promoters and origins of replication suggest that transcription factors play a pivotal role in the regulation of chromosomal DNA synthesis in eukaryotic organisms.

Animals↗

PubMed1997

Kinetic analysis of the endonuclease activity of phage lambda terminase: assembly of a catalytically competent nicking complex is rate-limiting.

The terminase enzyme from bacteriophage lambda is responsible for excision of a single genome from a concatameric DNA precursor and its insertion into an empty viral procapsid. The enzyme possesses a site-specific endonuclease activity which is responsible for excision of the viral genome and the formation of the 12 base-pair single-stranded "sticky" ends of mature lambda DNA. We have previously reported a kinetic analysis of the endonuclease activity of lambda terminase which showed an enzyme concentration-dependent change in the kinetic time course of the reaction [Tomka, M. A., & Catalano, C. E. (1993b) J. Biol. Chem. 268, 3056-3065]. We presented a model which suggested that the rate-limiting step in the nuclease reaction was the assembly of a catalytically competent prenicking complex. Here, we provide additional evidence for a slow assembly step in the nuclease reaction and demonstrate that the observed rate is affected by protein concentration, but not by the length of the DNA substrate. Consistent with our model, preincubation of terminase with DNA also yields an observable fast phase of the reaction, but only when large (> or = 3 kb) DNA substrates are used. Finally, we present data which demonstrate that phage lambda terminase can efficiently utilize DNA from the closely related phage phi21 as an endonuclease substrate and that the enzyme binds efficiently to the cosB region of both phage genomes. The implications of these results with respect to the assembly of a catalytically competent nucleoprotein complex required to initiate genome packaging are discussed.

Bacterial Proteins↗

PubMed1998

The mutagenesis protein MucB interacts with single strand DNA binding protein and induces a major conformational change in its complex with single-stranded DNA.

The MucA and MucB proteins are plasmid-encoded homologues of the Escherichia coli UmuD and UmuC proteins, respectively. These proteins are required for SOS mutagenesis, although their mechanism of action is unknown. By using the yeast two-hybrid system we have discovered that MucB interacts with SSB, the single strand DNA binding protein (SSB) of E. coli. To examine the interaction at the protein level, the MucA, MucA', and MucB proteins were overproduced, purified in denatured state, and refolded. Purified MucA and MucA' each formed homodimers, whereas MucB was a monomer under native conditions. RecA promoted the cleavage of MucA to MucA', and MucB was found to bind single-stranded DNA (ssDNA), similarly to the properties of the homologous UmuD and UmuC proteins. Purified MucB caused a shift in the migration of SSB in a sucrose density gradient, consistent with an interaction between these proteins. Addition of MucB to SSB-coated ssDNA caused increased electrophoretic mobility of the nucleoprotein complex and increased staining of the DNA by ethidium bromide. Analysis of radiolabeled SSB in the complexes revealed that only a marginal release of SSB occurred upon addition of MucB. These results suggest that MucB induces a major conformational change in the SSB.ssDNA complex but does not promote massive release of SSB from the DNA. The interaction with SSB might be related to the role of MucB in SOS-regulated mutagenesis.

Bacterial Proteins↗

PubMed1992

Surface Ig receptor-induced nuclear AP-1-dependent gene expression in B lymphocytes.

The relationship between signals generated via the sIgR complex of B lymphocytes and subsequent changes in gene expression is poorly understood at the molecular level. To illuminate mechanisms that may couple these events, we examined the expression and function of tetradecanoyl phorbol acetate-response element (TRE)-binding proteins (i.e., activator protein 1, (AP-1)) in the murine B lymphoma cell line BAL-17.7.1 (BAL-17), which models primary B lymphocyte responses in a number of respects. Cross-linking of sIgR led to substantial induction of nuclear AP-1, in BAL-17 B cells, that bound the TRE, as detected by electrophoretic mobility shift assay. The sIgR-induced TRE-binding activity consisted of both Jun and Fos proteins, on the basis of immunoreactivity of nucleoprotein complexes with specific antisera. In addition, immunoprecipitation with specific antisera showed that de novo synthesis of Jun-B and c-Jun proteins, accompanied by c-Fos, was stimulated after cross-linking of sIgR on BAL-17 B cells. Transient transfection of BAL-17 B cells with reporter gene constructs showed that B cell AP-1 failed to trans-activate the TRE-containing human collagenase gene promoter, for which activity is dependent upon functional expression of cellular c-Jun. In contrast, sIg-induced AP-1 trans-activated a HSV-tk promoter that contained three TRE; this pattern of gene expression is consistent with the presence of functional Jun-B-containing AP-1 in B lymphocytes. These results are the first to attribute a functional role to sIgR-mediated AP-1 in B lymphoid cells and suggest that AP-1 functions to couple the sIgR complex to changes in nuclear gene expression.

Animals↗

PubMed1990

Assembly of transcriptionally active chromatin in vitro: a possible role for topoisomerase II.

Some models of in vitro chromatin assembly suggest a biphasic molecular mechanism. The first phase, nucleosome formation, is comprised of the formation of histone-DNA complexes which mature into a canonical nucleosome structure. The second phase represents the process by which these nucleosomes become properly spaced with a regular periodicity on the DNA. In this report, we examine the role of DNA topoisomerases in the latter phase of chromatin assembly. To study this process, we use a Xenopus laevis cell-free extract, which assembles quantitative amounts of chromatin on circular DNA templates, and the type II topoisomerase-specific antitumor drugs VM-26 and endrofloxicin. Our results suggest that nucleosome formation is unaffected by the presence of VM-26 or endrofloxicin. However, periodic spacing of nucleosomes is inhibited significantly by these drugs. In the absence of proper chromatin assembly, circular DNA molecules are processed into nucleoprotein complexes which are transcribed poorly. Taken together, these results indicate that the antitumor drugs VM-26 and endrofloxicin influence gene expression indirectly by blocking the periodic spacing of nucleosomes.

Adenosine Triphosphate↗

PubMed1997

The in situ architecture of Escherichia coli ribosomal RNA derived by electron spectroscopic imaging and three-dimensional reconstruction.

The structures of the large and small ribosomal subunits of Escherichia coli were reconstructed using spectroscopic electron microscopy and quaternion-assisted angular reconstitution to resolutions of better than 4 nm. In addition, the distributions of phosphorus within these complexes were reconstructed. The three-dimensional reconstruction of the distribution of this atomic element is an extension of microanalysis (in two dimensions) for phosphorus identification and mapping, as a signature of the arrangement of the phosphate backbones of the constituent ribosomal RNAs. The results on both the phosphorus reconstructions and the total reconstructions (protein and ribosomal RNA) reveal several passageways through both subunits. The structures correspond favourably with other independent reconstructions of the whole E. coli ribosome from cryoelectron micrographs and their accompanying models of translation (Frank et al., Nature, 376, 441-444, 1995; Stark et al., Structure, 3, 815-821, 1995). The overall reconstructions in conjunction with the phosphorus (rRNA) distributions are the first to be achieved synchronously for this nucleoprotein complex.

Electron Probe Microanalysis↗

PubMed1982

Nucleic acid binding properties of major proteins from the heterogeneous nuclear ribonucleoproteins of wheat.

Glycine-rich core hnRNP proteins purified from wheat bind tightly to single-stranded but not to double-stranded nucleic acids with a preference for natural RNA over single-stranded DNA. Binding results in i) a progressive disruption of the residual secondary structure of the polynucleotide and the formation of an extended nucleoprotein filament until a protein to polynucleotide weight ratio of about 5:1 is attained. As more protein is added, this is followed by ii) the formation of globular structures along the polynucleotide chain with a concomitant reduction in the contour length of the nucleoprotein complex. These two features of the interaction--unwinding and condensation into beads--are analogous to the previously described behavior of the major glycine-rich core hnRNP protein from Artemia salina (Thomas et al. (1981) Proc. Natl. Acad. Sci. USA 78, 2888) and may represent the basic functional properties of this relatively well conserved group of nuclear proteins.

Circular Dichroism↗

PubMed1992

DNA binding, multimerization, and transcription stimulation by the Xenopus Y box proteins in vitro.

The Y box factors bind to a specific DNA sequence (the Y box, containing a reverse CCAAT element) and have been implicated in the regulation of transcription. We have used deletion mutagenesis to define the protein domains of two Xenopus Y box factors, FRG Y1 and FRG Y2, that are essential for DNA binding, multimerization, and transcription. A domain of the Y box factors homologous to an Escherichia coli cold shock protein is required for DNA binding. Both the E. coli protein and the Y box factors recognize DNA sequences with similar selectivity. The conserved region between these proteins does not contain any previously defined DNA-binding motifs. The hydrophilic C-terminal tail of the proteins contributes to the assembly of nucleoprotein complexes. This region contains an unusual pattern of basic and acidic amino acids and represents a new type of domain mediating protein-protein interactions in transcription factors. Both the DNA-binding and the multimerization domains are important for stimulating transcription from the Xenopus hsp70 promoter in vitro.

Amino Acid Sequence↗

PubMed2001

Structural organization of the hepatitis B virus minichromosome.

The replicative intermediate of hepatitis B virus (HBV), the covalently closed, circular DNA, is organized into minichromosomes in the nucleus of the infected cell by histone and non-histone proteins. In this study we investigated the architecture of the HBV minichromosome in more detail. In contrast to cellular chromatin the nucleosomal spacing of the HBV minichromosome has been shown to be unusually reduced by approximately 10 %. A potential candidate responsible for an alteration in the chromatin structure of the HBV minichromosome is the HBV core protein. The HBV core protein has been implicated in the nuclear targeting process of the viral genome. The association of the HBV core protein with nuclear HBV replicative intermediates could strengthen this role. Our findings, confirmed by in vivo and in vitro experiments indicate that HBV core protein is a component of the HBV minichromosome, binds preferentially to HBV double-stranded DNA, and its binding results in a reduction of the nucleosomal spacing of the HBV nucleoprotein complexes by 10 %. From this model of the HBV minichromosome we propose that the HBV core protein may have an impact on the nuclear targeting of the HBV genome and be involved in viral transcription by regulating the nucleosomal arrangement of the HBV regulatory elements, probably in a positive manner.

Chromatin↗

PubMed2025

Disassembly activates Retron-Septu for antiphage defense.

Retrons are antiphage defense systems that produce multicopy single-stranded DNA (msDNA) and hold promise for genome engineering. However, the mechanisms of defense remain unclear. The Retron-Septu system integrates retron and Septu antiphage defenses. Cryo-electron microscopy structures reveal asymmetric nucleoprotein complexes comprising a reverse transcriptase, msDNA (a hybrid of msdDNA and msrRNA), and two PtuAB copies. msdDNA and msrRNA are essential for assembling this complex, with msrRNA adopting a conserved lariat-like structure that regulates reverse transcription. Notably, the assembled Retron-Septu complex is inactive, with msdDNA occupying the PtuA DNA binding site. Activation occurs upon disassembly, releasing PtuAB, which degrades single-stranded DNA to restrict phage replication. This "arrest-and-release" mechanism underscores the dynamic regulatory roles of msDNA, advancing our understanding of antiphage defense strategies.

Cryoelectron Microscopy↗

PubMed2001

Murine recombinant prion protein induces ordered aggregation of linear nucleic acids to condensed globular structures.

Interaction between nucleic acid and recombinant murine prion protein, MoPrPC resulted in a time-dependent change in the nucleic acid morphology revealed by electron microscopy. After the addition of the protein to DNA, association of small number of nucleic acid molecules (nucleo-protein complex) was followed by aggregation of large number of them still retaining their initial linear morphology. With increase in the incubation time, ordered aggregation resulted in small condensed spherical globules. Subsequently, the formation of large condensed particles took place either by fusion of the already formed small globules or by accumulation of more nucleic acid molecules on them. The condensed nucleic acid structures observed here were different from other known morphologically altered nucleic acid structures induced by different cellular proteins. The condensed nucleic acid structures dissociated spontaneously. The formation of the prion protein-induced condensed nucleic acid structures resembled the human immunodeficiency virus 1 nucleocapsid protein NCp7-induced condensed ordered aggregates of nucleic acids. In the latter system, both the processes of condensation and dissociation of the nucleoprotein complex are believed to be responsible for the functional properties of the HIV-1 virus. Demonstration of functional activity of the prion protein-nucleic acid complex would be relevant for a role of nucleic acid in prion diseases.

Animals↗

PubMed1972

Birefringence of spermatozoa. I. Birefringence melting of squid, bull, and human sperm nucleoprotein.

In experiments designed to determine the thermal stability and bonding strength of a natural nucleoprotein structure, the loss of birefringence as a function of time and temperature was investigated for both mammalian and nonmammalian sperm nuclei. At a constant temperature, this reaction was found to be first order for both types over a range of temperatures. The methods of chemical kinetics applied to results of these reactions, called birefringence melting reactions, produced values for the enthalpy and entropy of activation in the reactions, which gave some indication of the strength of binding in the nucleoprotein structure; and these results, plus those on the influence of chemicals on the structure, were consistent with the molecular structures which have been proposed by others for the nucleoprotein complex of sperm nuclei. For both bull and human sperm in ethylene glycol, the rate-limiting step in the melting reactions appeared to be the breakage of disulfide bonds. For squid sperm in ethylene glycol, and bull or squid sperm in ethylene glycol plus beta-mercaptoethanol, the identity of this step was more ambiguous, but a possibility consistent with these and other results would be a cooperative breakage of ionic bonds.

Animals↗

PubMed2005

The transpososome: control of transposition at the level of catalysis.

Studies of several transposable genetic elements have pinpointed the importance of the transpososome, a nucleoprotein complex involving the transposon ends and a transposon-encoded enzyme--the transposase--as a key in regulating transposition. Transpososomes provide a precise architecture within which the chemical reactions involved in transposon displacement occur. Data are accumulating that suggest they are dynamic and undergo staged conformational changes to accommodate different steps in the transposition pathway. This has been underpinned by recent results obtained particularly with Tn5, Tn10 and bacteriophage Mu.

Bacteriophage mu↗

PubMed1994

Mass analysis of biological macromolecular complexes by STEM.

Scanning transmission electron microscopy (STEM) provides a superbly versatile method of measuring the masses of macromolecular complexes ranging in size from single protein subunits to large virus particles. The physical basis of the method is the elastic scattering of electrons by the component atoms of the specimen. Unstained molecules yield a dark-field signal that is proportional to their local mass density, thus allowing direct measurements of the total mass of an individual particle, as well as of the masses of its resolved domains by integrating over appropriate regions of the image. In this review, we present an introduction to the STEM method of mass analysis from a practical standpoint, stressing the essential points of specimen preparation, as well as the scope and current limitations of the method. Its potentialities are illustrated by applications to several classes of macromolecules: isolated oligomeric proteins (the envelope glycoprotein of HIV), nucleoprotein complexes (SV40 minichromosome, transcription factor TFIIIC), membranous specimens (clathrin-coated membranes, the VDAC channel), and viruses (vesicular stomatitis virus; herpes simplex virus). In the case of multicomponent complexes, STEM mass measurements of both the intact complex and of defined biochemical derivatives (for instance, after extraction of specific components), allow one to compile complete and precise molecular inventories. Finally, we briefly anticipate future advances that should allow even more precise and detailed mass mappings, the labelling of specific sites with heavy atom clusters, and elemental mapping based on weak inelastic signals acquired in parallel with the relatively intense dark-field signals that have been so successfully exploited to date.

Animals↗

PubMed1987

Nuclear proteins from lactating mammary glands bind to the promoter of a milk protein gene.

The gene for the whey acidic protein (WAP) is expressed specifically in the lactating mammary glands of rodents. We present evidence that nuclear proteins from mammary epithelial cells form a multiple nucleoprotein complex with the WAP gene promoter/upstream region. As monitored by mobility shifts, nuclear proteins from lactating mammary glands and from the mammary cell line MCF-7 form four high affinity complexes with a fragment spanning the region between nucleotides -175 and -88. Nuclear proteins from liver and HeLa cells generate only three high affinity complexes. DNAaseI and ExonucleaseIII protection confirmed the binding of mammary nuclear proteins to specific sequences in the WAP gene upstream region. This is the first report to describe the interaction of nuclear proteins from lactating mammary glands with cognate binding sites in the promoter/upstream region of a milk protein gene. The possibility of the binding sites being candidates for cis-acting regulatory elements governing the regulated expression of the WAP gene is discussed.

Animals↗

PubMed1993

Formation of a putative relaxation intermediate during T-DNA processing directed by the Agrobacterium tumefaciens VirD1,D2 endonuclease.

During the initial stages of crown gall tumorigenesis, the T-DNA region of the Agrobacterium tumefaciens Ti-plasmid is processed, resulting in the production of T-DNA molecules that are subsequently transferred to the plant cell. Processing of the T-DNA in the bacterium involves the nicking of T-DNA border sequences by an endonuclease encoded by the virD locus, and the subsequent tight (possibly covalent) association of the VirD2 protein with the 5' end of the processed single-stranded or double-stranded T-DNA molecule. To investigate the interaction of the VirD1,D2 endonuclease with a right T-DNA border, a set of plasmids containing both the border and virD sequences on the same high-copy-number replicon has been constructed and introduced into Escherichia coli. In this model system a tight nucleoprotein complex is formed between the relaxed double-stranded substrate plasmid and the VirD2 protein. This putative T-DNA processing complex may be analogous to the covalent relaxation complex formed between the pilot protein and plasmid DNA during bacterial conjugation. VirD2 attachment to the relaxed substrate plasmid was resistant to denaturing agents but sensitive to S1 nuclease digestion, indicating a single-stranded region near the site of protein attachment. We speculate that this structure may be an intermediate formed prior to T-strand unwinding from the substrate plasmid in a host bacterium.

Agrobacterium tumefaciens↗

PubMed1978

Folding of 140-base pair length DNA by a core of arginine-rich histones.

The nucleoprotein complex obtained by reconstitution of arginine-rich histones with 140-base pair length DNA has properties considerably closer to native core particles than the complex obtained with lysine-rich histones. A tetramer of arginine-rich histones folds 140-base pair length DNA into a particle (R body) with identical projections, on high resolution electron micrographs, as native core particles. The R body is more spherical in shape than the native nucleosome core particle. Both arginine- and lysine-rich histones contribute to the altered thermal stability and circular dichroism spectra of the core particle DNA.

Animals↗