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Induction of the transcription factors NF-kappa B, AP-1 and NF-AT during B cell stimulation through the CD40 receptor.

To address elements that might uniquely characterize CD40 mediated signaling, the nuclear expression of three transcription factors was evaluated following B cell stimulation by CD40L and by anti-Ig antibody. Cross-linked CD40L was found to induce nuclear expression of NF-kappa B, AP-1 and NF-AT with a time course and intensity similar to that produced by anti-Ig. Examination of NF-kappa B in more detail demonstrated that the CD40 mediated expression of DNA binding complexes correlated with induction of trans-activating activity which again attained similar levels following cross-linking of CD40 and slg. Despite the marked similarity in transcription factor induction triggered through CD40 and slg, differences in the intracellular signaling pathways utilized were apparent in that protein kinase C (PKC) depletion did not affect CD40 mediated induction of NF-kappa B even as induction by anti-Ig was abolished. These results suggest that a 'final common pathway' or convergence of transcription factor induction may exist for two distinct receptors, each of which is individually capable of triggering cell cycle progression, despite the use of separate intracellular signaling pathways that differ at the level of PKC. Although transcription factor induction was similar for CD40L and anti-Ig early on, subtle differences in expressed NF-kappa B and AP-1 nucleoprotein complexes were apparent at 24 h. Such differences may play a role in determining the variant effects on B cells of stimulation through these two receptors.

Animals↗

Simultaneous purification of DNA topoisomerase I and II from eukaryotic cells.

We have developed a procedure for the simultaneous purification of DNA topoisomerase I and II from calf thymus. Both enzymes were first extracted from isolated nucleoprotein complexes. After batchwise chromatography on hydroxylapatite the two enzyme activities were separated on a FPLC phenylsuperose column. The enzymes were further purified by a second chromatography on phenylsepharose (topo I) or FPLC Mono Q (topo II). The purification can be finished within three days, yielding 0.5-1.0 mg quantities of homogeneous, enzymatic active preparations of the two proteins from 200 g of starting material.

Animals↗

In situ nucleoprotein structure involving origin-proximal SV40 DNA control elements.

Nucleoprotein structures at the SV40 GC-box and adjacent AT-rich region have been probed by nucleases in permeabilized cells at nucleotide level resolution. The patterns of nuclease protection and hypersensitivity in these permeabilized cells that allow initiation of RNA and DNA synthesis are quite different from those observed in isolated nuclei that are inactive. Whereas simple DNA protection by factors is found in nuclei, the pattern in permeabilized cells includes very strong nuclease hypersensitive sites. Their arrangement suggests that the region exists as a higher order nucleoprotein complex in vivo, which is disturbed during the preparation of nuclei. The pattern is also found to be disturbed in permeabilized cells when T-antigen is inactivated by temperature-sensitive mutation. Since T-antigen origin binding sites and the GC-box region have been shown previously to interact functionally, the existence of a higher order structure involving both components provides a likely physical basis for the functional interaction of separate control elements.

Animals↗

Transcription of histone-covered T7 DNA by Escherichia coli RNA polymerase.

Purified core histones (H2A, H2B, H3, and H4) and bacteriophage T7 DNA have been reconstituted to form a nucleoprotein complex, and the properties of this complex as a template for transcription by Escherichia coli RNA polymerase have been studied. At low ionic strength, RNA chain elongation rates are slow, and the chains produced even after long incubation are short. At higher salt concentrations, chain-elongation rates approach those on naked DNA. Since the salt concentrations used are not in themselves sufficient to dissociate the histones from the DNA, some mechanism must exist that permits passage of the polymerase through histone-covered regions.

Chromatin↗

Organization, dynamics and transmission of mitochondrial DNA: focus on vertebrate nucleoids.

Eukaryotic cells contain numerous copies of the mitochondrial genome (from 50 to 100 copies in the budding yeast to some thousands in humans) that localize to numerous intramitochondrial nucleoprotein complexes called nucleoids. The transmission of mitochondrial DNA differs significantly from that of nuclear genomes and depends on the number, molecular composition and dynamic properties of nucleoids and on the organization and dynamics of the mitochondrial compartment. While the localization, dynamics and protein composition of mitochondrial DNA nucleoids begin to be described, we are far from knowing all mechanisms and molecules mediating and/or regulating these processes. Here, we review our current knowledge on vertebrate nucleoids and discuss similarities and differences to nucleoids of other eukaryots.

Animals↗

Physical interactions between bacteriophage and Escherichia coli proteins required for initiation of lambda DNA replication.

The process of initiation of lambda DNA replication requires the assembly of the proper nucleoprotein complex at the origin of replication, ori lambda. The complex is composed of both phage and host-coded proteins. The lambda O initiator protein binds specifically to ori lambda. The lambda P initiator protein binds to both lambda O and the host-coded dnaB helicase, giving rise to an ori lambda DNA.lambda O.lambda P.dnaB structure. The dnaK and dnaJ heat shock proteins have been shown capable of dissociating this complex. The thus freed dnaB helicase unwinds the duplex DNA template at the replication fork. In this report, through cross-linking, size chromatography, and protein affinity chromatography, we document some of the protein-protein interactions occurring at ori lambda. Our results show that the dnaK protein specifically interacts with both lambda O and lambda P, and that the dnaJ protein specifically interacts with the dnaB helicase.

Bacterial Proteins↗

Purification of ArcA and analysis of its specific interaction with the pfl promoter-regulatory region.

ArcA is one of several transcription factors required for optimal anaerobic induction of the pyruvate formatelyase (pfl) operon. To aid the study at the molecular level of the interaction of ArcA with the pfl promoter-regulatory region we developed a procedure for the isolation of ArcA. The purification of ArcA involved chromatography in heparin agarose, hydroxylapatite and Mono-Q matrices and delivered a protein that was > 95% pure. Gel retardation assays demonstrated that ArcA bound specifically to the pfl regulatory region. Three distinct ArcA-DNA complexes could be resolved depending on the ArcA concentration used. This finding suggested that either multiple ArcA-binding sites are present in the regulatory region or that ArcA can oligomerize at one or more sites. The DNA-binding activity of ArcA could be increased as estimated 10-fold by prior incubation of the protein with carbamoyl phosphate, suggesting that phosphorylation activates DNA binding or oligomerisation. DNase I footprint analyses identified four sites that were protected by ArcA from cleavage. Two of these sites spanned the transcription start site and -10 regions of promoters 6 and 7, while a third site partially overlapped the characterized binding site of integration host factor (IHF). ArcA exhibited the highest affinity for a stretch of DNA located between the IHF site and the transcription start site of promoter 7. These results are congruent with the hypothesis that a higher-order nucleoprotein complex comprising several proteins, including ArcA, is required to activate transcription from the multiple promoters of the pfl operon.

Acetyltransferases↗

Differential binding of wild-type and a mutant RepA protein to oriR sequence suggests a model for the initiation of plasmid R1 replication.

DNA replication of the enterobacterial plasmid R1 is initiated by RepA protein. We have developed a new procedure for the purification of RepA from inclusion bodies, which involves CHAPS-mediated solubilization. This method has been also used for the thermosensitive mutant protein RepA2623. The nucleoprotein complexes obtained with both proteins and oriR, the origin of replication, are studied in this paper. DNaseI and hydroxyl-radical footprinting suggest the presence in oriR of two sites with different affinity for RepA separated by eight helical turns. The pattern of hypersensitive sites in the footprints indicates that the oriR sequence, when complexed with RepA, is curved. The binding of RepA molecules to oriR is co-operative and this co-operativity is defective in the thermosensitive protein. Band-shift analysis of RepA-oriR complexes revealed the existence of a species with an anomalously high electrophoretic mobility that appears after formation of the first RepA-oriR complex and requires the sequential interaction of RepA with its two distal binding sites. These features lead us to propose that protein-protein interactions between RepA bound to both distal sites could be responsible for oriR looping. This model represents a novel mechanism that results in activation of an origin in a replicon that does not contain iterons.

Bacterial Proteins↗

Antirepression function in Escherichia coli for the cAMP-cAMP receptor protein transcriptional activator.

The cAMP receptor protein (CRP) complex (cAMP-CRP) is a global regulator of gene expression. It influences transcription from a number of promoters in Escherichia coli, including two divergently oriented promoters in the pap pili-adhesin gene system. To further define the role of cAMP-CRP in pap regulation we monitored protein-DNA interactions in vitro and levels of pap transcription in vivo in wild-type and mutant pap-containing clones. The results showed that activation was mediated by a single cAMP-CRP-binding site centered at nucleotide positions -215.5 and -115.5 relative to the transcriptional start points. A target for the pap-specific regulatory protein PapB was localized adjacent to the cAMP-CRP-binding site. The long-range effects exerted from the protein-binding sites were consistent with the idea that cAMP-CRP caused a change in the local DNA conformation and that a nucleoprotein complex (involving cAMP-CRP and PapB) was formed in the region between the pap promoters. Moreover, transcription became independent of activation of cAMP-CRP and the PapB protein in a mutant lacking the nucleoid-associated protein H-NS. Our findings suggest that the cAMP-CRP complex mediates its positive regulatory function by alleviating transcriptional silencing and, as such, plays a role as antirepressor.

Adhesins, Escherichia coli↗

cis-diamminedichloroplatinum (II) modified chromatin and nucleosomal core particle.

The influence of cis-diamminedichloroplatinum (II) (cis-DDP) binding to chromatin in chicken erythrocyte nuclei and the nucleosomal core particle is investigated. The cis-DDP modifications alter DNA-protein interactions associated with the higher order structure of chromatin to significantly inhibit the rate of micrococcal nuclease digestion and alter the digestion profile. However, cis-DDP modification of core particle has little effect on the digestion rate and the relative distribution of DNA fragments produced by microccocal nuclease digestion. Analysis of the monomer DNA fragments derived from the digestion of modified nuclei suggests that cis-DDP binding does not significantly disrupt the DNA structure within the core particle, with its major influence being on the internucleosomal DNA. Together these findings suggest that cis-DDP may preferentially bind to the internucleosomal region and/or that the formation of the intrastrand cross-link involving adjacent guanines exhibits a preference for the linker region. Sucrose gradient profiles of the modified nucleoprotein complexes further confirm that the digestion profile for micrococcal nuclease is altered by cis-DDP binding and that the greatest changes occur at the initial stages of digestion. The covalent cross-links within bulk chromatin fix a sub-population of subnucleosomal and nucleosomal products, which are released only after reversal by NaCN treatment. Coupled with our previous findings, it appears that this cis-DDP mediated cross-linking network is primarily associated with protein-protein crosslinks of the low mobility group (LMG) proteins.

Cell Nucleus↗

A method for differentiating proteins from nucleic acids in intermediate-resolution density maps: cryo-electron microscopy defines the quaternary structure of the Escherichia coli 70S ribosome.

BACKGROUND: This study addresses the general problem of dividing a density map of a nucleic-acid-protein complex obtained by cryo-electron microscopy (cryo-EM) or X-ray crystallography into its two components. When the resolution of the density map approaches approximately 3 A it is generally possible to interpret its shape (i. e., the envelope obtained for a standard choice of threshold) in terms of molecular structure, and assign protein and nucleic acid elements on the basis of their known sequences. The interpretation of low-resolution maps in terms of proteins and nucleic acid elements of known structure is of increasing importance in the study of large macromolecular complexes, but such analyses are difficult. RESULTS: Here we show that it is possible to separate proteins from nucleic acids in a cryo-EM density map, even at 11.5 A resolution. This is achieved by analysing the (continuous-valued) densities using the difference in scattering density between protein and nucleic acids, the contiguity constraints that the image of any nucleic acid molecule must obey, and the knowledge of the molecular volumes of all proteins. CONCLUSIONS: The new method, when applied to an 11.5 A cryo-EM map of the Escherichia coli 70S ribosome, reproduces boundary assignments between rRNA and proteins made from higher-resolution X-ray maps of the ribosomal subunits with a high degree of accuracy. Plausible predictions for the positions of as yet unassigned proteins and RNA components are also possible. One of the conclusions derived from this separation is that 23S rRNA is solely responsible for the catalysis of peptide bond formation. Application of the separation method to any nucleoprotein complex appears feasible.

Bacterial Proteins↗

Complete in vitro replication of SV40 DNA and chromatin in saponin-treated permeable cells.

A permeable cell system has been developed by treatment with saponin for studying in vitro replication of DNA and chromatin. DNA replication of simian virus 40 nucleoprotein complexes (SV40 chromatin) in saponin-treated permeable cells was found to be more efficient than that in digitonin-treated permeable cells. Autoradiography of the agarose-gel revealed that [alpha-32P]dCTP was incorporated into SV40 DNA I, II and replicating intermediates. The time course of the incorporation indicated complete replication of SV40 DNA and chromatin with a full number of nucleosomes. The saponin-treated permeable cell system will serve as a useful system for studying in vitro replication of DNA and chromatin in eukaryotic cells.

Animals↗

The stoichiometry of binding of the herpes simplex virus type 1 origin binding protein, UL9, to OriS.

A number of studies have demonstrated that the herpes simplex virus type 1 (HSV-1) UL9 protein, which is a homodimer in solution, binds to two high affinity binding sites in each origin of replication. Interaction between the proteins bound at the two sites leads to the formation of a complex nucleoprotein structure. The simplest models for this binding interaction predict two possible binding stoichiometries: 1) one UL9 dimer is bound at each site; or 2) one UL9 monomer is bound at each site so that one UL9 dimer occupies both sites. Two recent papers have addressed this issue by using indirect methods to measure the binding stoichiometry. Martin et al. (Martin, D. W., Muñoz, R. M., Oliver, D., Subler, M. A., and Deb, S. (1994) Virology 198, 71-80) reported that a monomer of UL9 binds to a single high affinity site, and Stabell and Olivo (Stabell, E. C., and Olivo, P.D. (1993) Nucleic Acids Res. 21, 5203-5211) concluded that a dimer of UL9 binds to a single high affinity site. We have directly measured the stoichiometry of binding of the carboxyl-terminal DNA binding domain of UL9 (t-UL9) to the origin of replication using a double-label gel shift assay. Using a short synthetic double-stranded oligonucleotide containing a single UL9 binding site, one protein-DNA complex was detected in the gel shift assay, and the molar ratio of UL9 DNA binding domains to DNA binding sites in this complex was determined to be 2.0 +/- 0.1 (n = 13). Using the minimal origin sequence excised from plasmid DNA, two protein-DNA complexes were detected. The binding stoichiometry of the faster migrating complex was 1.8 +/- 0.1 (n = 15), and the stoichiometry of the more slowly migrating band was 3.7 +/- 0.4 (n = 15). The simplest explanation for these data is that UL9 binds to the origin of replication as a homodimer with one dimer bound at both high affinity sites.

Animals↗

A comparison of the DNA bending activities of the DNA binding proteins CRP and TFIID.

Protein-induced DNA bending is of importance in the formation of complex nucleoprotein assemblies such as those involved in the initiation of DNA replication or transcription initiation. We have compared the DNA bending characteristics of the Escherichia coli cyclic AMP receptor protein (CRP or CAP), an archetypal DNA bending protein, to those of TFIID, the eukaryotic TATA-element binding transcription factor. By altering the helical phasing between a CRP binding site and the E. coli melR promoter we have mapped a DNA sequence-directed bend in the downstream region of the promoter. This intrinsic DNA bend may be important in the regulation of the melR promoter by CRP in vivo. Gel retardation assays and DNAse I footprinting show that human TFIID binds to the melR promoter - 10 region. Taking advantage of this fact, and using the CRP-induced DNA bend as a standard, we have employed phase sensitive detection to show that the DNA bend angle induced by TFIID is far less than that induced by CRP. Further evidence to support this conclusion comes from a comparison of the relative mobilities of CRP-DNA and TFIID-DNA complexes. These results place limits on the role of any DNA bending induced by TFIID alone in the initiation of transcription.

Bacterial Proteins↗

Time-resolved fluorescence of bacteriophage Pf1 DNA-binding protein. Determination of oligonucleotide and polynucleotide binding parameters.

The binding of oligonucleotides and polynucleotides to the Pf1 DNA-binding protein was followed by fluorescence spectral shift and lifetime measurements, which gave an anomalous value for the stoichiometry of binding. The anomaly was investigated in detail using fluorescence depolarisation to measure the aggregation during the titration and showed that all the fluorescence parameters are related to the specific aggregation of dimers on ligand binding. At saturation, complexes of the protein with the octanucleotide d(GCGTTGCG) and the hexadecanucleotide (dT)16 have rotational correlation times, phi, of 50 ns and 85 ns, corresponding to protein tetramers and octamers, respectively. In the presence of the tetranucleotide d(CGCA) the protein remains as the native dimer (phi = 19 ns). The titration curves could be analysed in terms of two non-equivalent binding sites, with binding constants K1 and K2. Comparison of K1 values for oligonucleotide binding leads to an estimated (single-site) intrinsic binding constant Kint approximately equal to 3 X 10(4) M-1 and a cooperativity parameter omega approximately equal to 100, in agreement with the apparent binding constant Kapp approximately equal to 3 X 10(6) M-1 for polynucleotides. Binding to the second site on the protein dimer is greatly reduced and cannot be determined accurately. The results suggest that the protein dimers bind cooperatively by lateral association along the DNA and that occupation of only one of the two DNA-binding sites of the protein dimers is sufficient to stabilize the nucleoprotein complexes.

Bacteriophages↗

PAM14, a novel MRG- and Rb-associated protein, is not required for development and T-cell function in mice.

PAM14 has been found to associate in complexes with the MORF4/MRG family of proteins as well as Rb, the tumor suppressor protein. This suggested that it might be involved in cell growth, immortalization, and/or senescence. To elucidate the in vivo function of PAM14, we characterized the expression pattern of mouse Pam14 and generated PAM14-deficient (Pam14(-/-)) mice. Pam14 was widely expressed in all mouse tissues and as early as 7 days during embryonic development. Despite this ubiquitous expression in wild-type mice, Pam14(-/-) mice were healthy and fertile. Response to mitogenic stimulation and production of interleukin-2 were the same in stimulated splenic T cells from Pam14(-/-) mice as in control littermates. Cell growth rates of mouse embryonic fibroblasts (MEFs) from all three genotypes were the same, and immortalized cells were obtained from all cell cultures during continuous culture. There was also no difference in expression of growth-related genes in response to serum stimulation in the null versus control MEFs. These data demonstrate that PAM14 is not essential for normal mouse development and cell cycle control. PAM14 likely acts as an adaptor protein in nucleoprotein complexes and is probably compensated for by another functionally redundant protein(s).

Animals↗

recA protein-promoted ATP hydrolysis occurs throughout recA nucleoprotein filaments.

When recA protein binds cooperatively to single-stranded DNA to form filamentous nucleoprotein complexes, it becomes competent to hydrolyze ATP. No correlation exists between the ends of such complexes and the rate of ATP hydrolysis. ATP hydrolysis is not, therefore, restricted to the terminal subunits on cooperatively bound recA oligomers, but occurs throughout the complex. Similarly, during recA protein-promoted branch migration (during DNA strand exchange), ATP hydrolysis is not restricted to recA protein monomers at the branch point. DNA cofactors of lengths varying from 16 bases to over 12,000 bases support ATP hydrolysis. The maximum value of kcat at infinite DNA concentration is about 29/min independent of the length of the DNA cofactor. The apparent dissociation constant, however, is a strong function of DNA length, providing evidence for a minimum site size of 30-50 bases for efficient binding of recA protein.

Adenosine Triphosphatases↗

High level expression of human immunodeficiency virus type-1 Vif inhibits viral infectivity by modulating proteolytic processing of the Gag precursor at the p2/nucleocapsid processing site.

The human immunodeficiency virus type-1 Vif protein has a crucial role in regulating viral infectivity. However, we found that newly synthesized Vif is rapidly degraded by cellular proteases. We tested the dose dependence of Vif in non-permissive H9 cells and found that Vif, when expressed at low levels, increased virus infectivity in a dose-dependent manner. Surprisingly, however, the range of Vif required for optimal virus infectivity was narrow, and further increases in Vif severely reduced viral infectivity. Inhibition of viral infectivity at higher levels of Vif was cell type-independent and was associated with an accumulation of Gag-processing intermediates. Vif did not act as a general protease inhibitor but selectively inhibited Gag processing at the capsid and nucleocapsid (NC) boundary. Identification of Vif variants that were efficiently packaged but were unable to modulate Gag processing suggests that Vif packaging was necessary but insufficient for the production of 33- and 34-kDa processing intermediates. Interestingly, these processing intermediates, like Vif, associated with viral nucleoprotein complexes more rigidly than mature capsid and NC. We conclude that virus-associated Vif inhibits processing of a subset of Gag precursor molecules at the p2/NC primary cleavage site. Modulation of processing of a small subset of Gag molecules by physiological levels of Vif may be important for virus maturation. However, the accumulation of such processing intermediates at high levels of Vif is inhibitory. Thus, rapid intracellular degradation of Vif may have evolved as a mechanism to prevent such inhibitory effects of Vif.

CD4-Positive T-Lymphocytes↗