Increased frequency of initiation of RNA synthesis due to a protein factor from chicken myeloblastosis nuclei.

The mechanism of the effect of an RNA polymerase II (RNA nucleotidyltransferase II) stimulation factor isolated from the nuclei of chicken myeloblastosis cells was studied. The stimulation requires the presence of all four nucleoside triphosphates and depends upon an exogenous DNA template. In the absence of the factor, RNA synthesis ceases after 20-30 min, but in the presence of the factor, synthesis continues up to 60-80 min. Addition of the factor at 35 min after incubation causes resumption of RNA synthesis. The factor greatly stimulates the activity of RNA polymerase II at low enzyme concentrations. The RNA polymerase activity is more sensitive to alpha-amanitin inhibition when the factor is present. Experiments of [gamma-32P]ATP incorporation reveal that the factor provides for an increased frequency of initiation of RNA chains, both of the primary initiation events and re-initiation after previous ones were completed. A slightly higher rate of RNA chain growth was also observed with this factor but the ultimate size of RNA synthesized was not affected, as determined by formaldehyde/sucrose gradient centrifugation. These data suggest that the factor functions at the initiation stages of the RNA polymerase reaction.     

The crystal structure of the second Z-DNA binding domain of human DAI (ZBP1) in complex with Z-DNA reveals an unusual binding mode to Z-DNA

Mammalian DAI (DNA-dependent activator of IFN-regulatory factors), an activator of the innate immune response, senses cytosolic DNA by using 2 N-terminal Z-DNA binding domains (ZBDs) and a third putative DNA binding domain located next to the second ZBD. Compared with other previously known ZBDs, the second ZBD of human DAI (hZβ_DAI) shows significant variation in the sequence of the residues that are essential for DNA binding. In this article, the crystal structure of the hZβ_DAI/Z-DNA complex reveals that hZβ_DAI has a similar fold to that of other ZBDs, but adopts an unusual binding mode for recognition of Z-DNA. A residue in the first β-strand rather than residues in the β-loop contributes to DNA binding, and part of the (α3) recognition helix adopts a 3₁₀ helix conformation. The role of each residue that makes contact with DNA was confirmed by mutational analysis. The 2 ZBDs of DAI can together bind to DNA and both are necessary for full B-to-Z conversion. It is possible that binding 2 DAIs to 1 dsDNA brings about dimerization of DAI that might facilitate DNA-mediated innate immune activation.     

Are many Z-DNA binding proteins actually phospholipid-binding proteins?

We used a Z-DNA affinity column to isolate a collection of Z-DNA binding proteins from a high salt extract of Escherichia coli. We identified one of the major Z-DNA binding proteins of this fraction, not as a protein involved in gene regulation or genetic recombination, but rather as an outer membrane porin protein. We then showed that several other known phospholipid-binding proteins (bovine lung annexins and human serum lipoproteins) also bind much more tightly to Z-DNA than to B-DNA. In all cases, this Z-DNA binding was strongly blocked by competition with acidic phospholipids, such as cardiolipin. Our results raise the question whether many of the Z-DNA binding proteins previously isolated are actually phospholipid-binding proteins.     

A role for Z-DNA binding in vaccinia virus pathogenesis

The N-terminal domain of the E3L protein of vaccinia virus has sequence similarity to a family of Z-DNA binding proteins of defined three-dimensional structure and it is necessary for pathogenicity in mice. When other Z-DNA-binding domains are substituted for the similar E3L domain, the virus retains its lethality after intracranial inoculation. Mutations decreasing Z-DNA binding in the chimera correlate with decreases in viral pathogenicity, as do analogous mutations in wild-type E3L. A chimeric virus incorporating a related protein that does not bind Z-DNA is not pathogenic, but a mutation that creates Z-DNA binding makes a lethal virus. The ability to bind the Z conformation is thus essential to E3L activity. This finding may allow the design of a class of antiviral agents, including agents against variola (smallpox), which has an almost identical E3L.     

Minimizing a binding domain from protein A.

We present a systematic approach to minimizing the Z-domain of protein A, a three-helix bundle (59 residues total) that binds tightly (Kd = 10 nM) to the Fc portion of an immunoglobin IgG1. Despite the fact that all the contacts seen in the x-ray structure of the complex with the IgG are derived from residues in the first two helices, when helix 3 is deleted, binding affinity is reduced > 10(5)-fold (Kd > 1 mM). By using structure-based design and phage display methods, we have iteratively improved the stability and binding affinity for a two-helix derivative, 33 residues in length, such that it binds IgG1, with a Kd of 43 nM. This was accomplished by stepwise selection of random mutations from three regions of the truncated Z-peptide: the 4 hydrophobic residues from helix 1 and helix 2 that contacted helix 3 (the exoface), followed by 5 residues between helix 1 and helix 2 (the intraface), and lastly by 19 residues at or near the interface that interacts with Fc (the interface). As selected mutations from each region were compiled (12 in total), they led to progressive increases in affinity for IgG, and concomitant increases in alpha-helical content reflecting increased stabilization of the two-helix scaffold. Thus, by sequential increases in the stability of the structure and improvements in the quality of the intermolecular contacts, one can reduce larger binding domains to smaller ones. Such mini-protein binding domains are more amenable to synthetic chemistry and thus may be useful starting points for the design of smaller organic mimics. Smaller binding motifs also provide simplified and more tractable models for understanding determinants of protein function and stability.     

A PKR-like eukaryotic initiation factor 2alpha kinase from zebrafish contains Z-DNA binding domains instead of dsRNA binding domains

The double-stranded RNA (dsRNA)-dependent protein kinase (PKR) is induced as part of the IFN response in mammals and acts to shut down protein synthesis by the phosphorylation of eukaryotic initiation factor 2alpha (eIF2alpha). In fish, a PKR-like kinase activity has been detected, but the enzyme responsible has eluded characterization. Here, we describe a PKR-like kinase from zebrafish. Phylogenetic analysis shows that the C-terminal kinase domain is more closely related to the kinase domain of PKR than to any of the other three known eIF2alpha kinases. Surprisingly, instead of the two dsRNA binding domains found at the N terminus of PKR, there are two Zalpha domains. Zalpha domains specifically bind dsDNA and RNA in the left-handed Z conformation, often with high affinity. They have been found previously in two other IFN-inducible proteins, the dsRNA editing enzyme, ADAR1, and Z-DNA binding protein 1 (ZBP1), as well as in the poxvirus virulence factor, E3L. This previously undescribed kinase, designated PKZ (protein kinase containing Z-DNA binding domains), is transcribed constitutively at low levels and is highly induced after injection of poly(inosinic)-poly(cytidylic) acid, which simulates viral infection. Binding of Z-DNA by the Zalpha domain of PKZ was demonstrated by circular dichroism. PKZ inhibits translation in transfected cells; site-directed mutagenesis indicates that this inhibition depends on its catalytic activity. Identification of a gene combining Zalpha domains with a PKR-like kinase domain strengthens the hypothesis that the ability to bind left-handed nucleic acid plays a role in the host response to viruses.     

Unoccupied binding sites for oestradiol in nuclei from human breast carcinomatous tissue.

The binding of oestradiol to a nuclear fraction extracted from human breast carcinomatous tissue was demonstrated. The material, which was extracted with KCl, sedimented at 3--4S and bound oestradiol with high affinity (dissociation constant approximately 2 X 10(-10) mol/l). Oestriol, diethylstilboestrol and 5 alpha-dihydrotestosterone (100-fold excesses) competed with [3H]oestradiol for the binding sites (binding inhibited by 89 +/- 8 (S.D.), 92 +/- 6 and 57 +/- 8% respectively), whereas progesterone and cortisol (100-fold excesses) did not (binding suppressed by 5 +/- 5 and 2 +/- 3% respectively). Similar competition patterns were found for cytoplasmic material which bound oestradiol. The binding occurred at 4 degrees C and was therefore considered to be a measure of the amount of binding material unoccupied by endogenous oestrogen, Unoccupied binding sites for oestradiol in the nucleus and cytoplasm were measured in 35 samples of breast carcinomatous tissue using sucrose gradient centrifugation. In 17 out of 35 tumorus, unoccupied nuclear and cytoplasmic 8S and 4S binding sites could be detected. Three out of 35 tumours contained unoccupied nuclear binding sites and 4S cytoplasmic binding sites. Nuclear binding sites only were found in two out of 35 tumours. Unoccupied nuclear binding sites were not detected in 13 out of 35 tumours and ten of these tumours also did not contain unoccupied cytoplasmic binding sites.     

Triiodothyronine binding to isolated liver cell nuclei.

Nuclei of euthyroid rat liver have been prepared from homogenates by sedimentation through 2.3M sucrose with or without a 0.25% Triton wash. Triiodothyronine is accumulated by these nuclei during incubation in vitro in solutions containing 0.32M sucrose, 1mM MgCl2 and 0.02M Tris-Cl buffer at pH 7.4 or 7.85. Specific T3 binding sites occupied at 10-1,000 pM T3 are saturated by excess unlabeled T3 (0.15 muM). Specific T3 binding at 20 C is maximal at 203 hr nad is proportional to amount of nuclei. Calcium ion enhances nuclear integrity by reduces T3 accumulation. EDTA and phosphate ion cause nuclear damage but increase T3 accumulation. Binding is unaffected by inhibition of energy dependent reactions or of RNA synthesis. It is markedly increased under certain conditions by addition of dithiothreitol (DDT). Binding does not require mediation of a cytosol protein. T3 binding is not prevented by RNAse or DNAse, but is obliterated by pronase. Te binds to a nuclear iodothyronine binding protein (NTBP) to form an NTBP-T3 complex similar to that form-d after in vivo administration of the hormone. The complex can be extracted from the nuclei by 0.4M KC-. T3 present in the NTBP-T3 complex resists accumulation by anion exchange resin at 0-2C, but is bound by resin after 20 min at 37C or after addition of 0.1 mM p-hydroxymercuribenzoate. At pH 7.85 and with 5 mM DTT, the apparent Ka for isolated nuclei is 0.2 times 10-10M-1 and the capacity is 508 pg T3/g wet tissue or 53 times 10-15 moles T3/100 mug DNA. The data may not represent total capacity, but rather the amount of T3 dissociated during the period of incubation so that NTBP-T3 can be exchanged with labeled T3. Among analogues tested, triiodothyroacetic acid appears to bind with four times the affinity of L-TX, D-T3 binds with equal affinity, and L-T4 with one-fourth the affinity of T3.     

Antibodies specific for left-handed Z-DNA.

We prepared a brominated poly(dG-dC).poly(dG-dC) which forms a stable Z-DNA helix under physiological salt conditions. Rabbits and mice were immunized with brominated and unbrominated poly(dG-dC).poly(dG-dC) complexed with methylated bovine serum albumin. Antibodies specific for Z-DNA were produced. These antibodies were found not only in the sera of animals immunized with the low-salt stabilized Z-DNA [Br-poly(dG-dC).poly(dG-dC)] but also in sera from animals immunized with the unbrominated B-DNA form of the polymer. From this it is inferred that the unbrominated poly(dG-dC).poly(dG-dC) was partially converted to Z-DNA by its combination with the basic protein methylated bovine serum albumin. In addition to specific anti-Z-DNA antibody populations, two other interesting types of antibody populations were found. One of these reacted with both the Z and B forms of poly(dG-dC).poly(dG-dC). This antibody may be converting the polymer from the B-DNA to the Z-DNA form. The other type of antibody was specific for a B form of poly(dG-dC).poly(dG-dC) and did not react at all with the Z form. The antibodies raised to Z-DNA were shown to be highly specific for Z-DNA and did not react with B-DNA, RNA, DNA.RNA hybrids, or a number of other polynucleotides. This specificity for Z-DNA will make possible their use as reagents for determining the presence of Z-DNA in biological systems. Sera of autoimmune lupus mice were also shown to have a considerable amount of naturally occurring anti-Z-DNA antibody activity.     

Glucose binding and transport proteins extracted from fast-growing chicken fibroblasts

Preconfluent or confluent fibroblasts grown in 5% serum medium yielded, without cell lysis, all the glucose-binding protein and most of the transport-stimulating activity in the cell wash fluid obtained with a 10 mM sodium octanoate-containing solution. For assay, octanoate was removed, and after the binding protein was labeled with [(14)C]glucose, the factors were chromatographed on Sephadex G-200 and the transport-stimulating and factor-bound [(14)C]glucose activities were measured. Three peaks were separated, which more or less overlapped for both functions; upon chromatography on DEAE-cellulose, these peaks yielded overlapping or separate peaks for the two functions, presumably indicating their separability. Serum, when similarly chromatographed, showed only peaks for transport which, with the exception of one major peak with both functions, more or less overlapped with those from the wash fluid. Glucose transport rates, when compared in fibroblasts grown in glucose and in fructose and in Rous sarcoma virus-transformed cells grown in glucose, were in the proportion of 1:3.7:6.3. Addition of extracted transport protein stimulated the transport of both the glucose-grown and fructose-grown normal cells but showed no effect on the transport of transformed cells. Addition of transport protein induced the formation of [(14)C]deoxyglucose 6-phosphate in amounts proportional to the increased transport of [(14)C]deoxyglucose into fibroblasts. On sodium dodecyl sulfate electrophoresis, using the tightly bound [(14)C]glucose for assay, purified binding protein yielded large fractions of 36,000 and 18,000 and small ones of 55,000 and 73,000 daltons; the 18,000-dalton fraction is supposedly the monomeric form of the binding protein.     

Purification of a calmodulin-binding protein from chicken gizzard that interacts with F-actin.

A calmodulin-binding protein called "caldesmon" was purified from chicken gizzard muscle as the major calmodulin-binding protein in this tissue. Its molecular weight estimated by sodium dodecyl sulfate/polyacrylamide gel electrophoresis was 150,000, and two of these polypeptides constituted the native molecule. Caldesmon is an actin-binding protein also, binding F-actin reversibly in the presence or absence of Ca2+. The interaction of caldesmon with F-actin was abolished by the binding of calmodulin with the caldesmon. Because the interaction between caldesmon and calmodulin was Ca2+-dependent but the interaction between caldesmon and F-actin was not, Ca2+ acts as a flip-flop switch between the formations of two complexes, caldesmon.calmodulin and caldesmon.F-actin: increasing the formation of the former complex at increased Ca2+ level and the formation of the latter complex at decreased Ca2+ level. The equilibrium of the formations of both complexes was achieved at a Ca2+ concentration near 1 microM.     

A prion-like protein from chicken brain copurifies with an acetylcholine receptor-inducing activity.

The mammalian prion protein (PrPC) is a cellular protein of unknown function, an altered isoform of which (PrPSc) is a component of the infectious particle (prion) thought to be responsible for spongiform encephalopathies in humans and animals. We report here the isolation of a cDNA that encodes a chicken protein that is homologous to PrPC. This chicken prion-like protein (ch-PrLP) is identical to the mouse PrP at 33% of its amino acid positions, including an uninterrupted stretch of 24 identical residues, and it displays the same structural domains. In addition, ch-PrLP, like its mammalian counterpart, is attached to the cell surface by a glycosyl-phosphatidylinositol anchor. We find that ch-PrLP is the major protein in preparations of an acetylcholine receptor-inducing activity that has been purified greater than 10(6)-fold from brain on the basis of its ability to stimulate synthesis of nicotinic receptors by cultured myotubes. The ch-PrLP gene is expressed in the spinal cord and brain as early as embryonic day 6; and in the spinal cord, the protein appears to be concentrated in motor neurons. Our results therefore raise the possibility that prion proteins serve normally to regulate the chemoreceptor number at the neuromuscular junction and perhaps in the central nervous system as well.     

Ecdysone binding proteins in nuclei and chromatin from Drosophila salivary glands

After treatment of salivary glands isolated from Drosophila hydei with tritiumlabeled eedysone, complexes of the radioactive hormone and protein(s) can be isolated. Fractions containing these complexes have been obtained from cytoplasmic and nuclear extracts by means of filtration, density gradient centrifugation, and agar electrophoresis.     

Enhanced binding of lupus sera to the polyamine-induced left-handed Z-DNA form of polynucleotides

The natural polyamines putrescine, spermidine, and spermine are small polyvalent cations present in all living cells. Spermidine and spermine are excellent promoters of left-handed Z-DNA, an immunogenic form of DNA that binds readily with anti-DNA antibodies in the sera of patients with systemic lupus erythematosus (SLE). We studied the binding of a panel of 16 SLE sera to poly(dA-dC).poly(dG-dT) and poly(dG-m5dC).poly(dG-m5dC) in the presence and absence of spermidine and spermine using an enzyme-linked immunosorbent assay. The majority of SLE sera showed a 50-150% mean increase in optical density values when incubated with the polynucleotides and either 0.25 mM spermidine or 0.025 mM spermine than when incubated with the polynucleotides alone. Under these conditions, the polynucleotides assumed the Z-DNA form. Since polyamines are ubiquitous cellular components and since potential Z-DNA-forming alternating purine-pyrimidine sequences are widely dispersed in native DNA, the increased binding of SLE sera to polyamine-induced Z-DNA suggests a pathogenic role for these compounds in SLE.