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E M Lafer

Publications and source records attributed to E M Lafer.

At least 37 records · Page 2Linked to original sources
PubMed1992

Characterization of a novel synapse-specific protein. II. cDNA cloning and sequence analysis of the F1-20 protein.

The F1-20 protein is a novel neuronal-specific, synapse-associated protein that is expressed nonuniformly in mouse brain. Expression of the F1-20 protein is developmentally regulated in a pattern coincident with active synaptogenesis and synaptic maturation. Here we report the cloning of the cDNA sequence for the F1-20 protein. We found two distinct isoforms of F1-20 cDNA that differed by the presence of 15 additional nucleotides, which does not interrupt the open reading frame. RNase protection analysis and PCR amplification of mouse brain RNA revealed that both isoforms are present in cellular RNA. It is likely that the two F1-20 mRNA isoforms are derived from RNA splicing events utilizing alternative 3' acceptor sites. Analysis of the deduced amino acid sequence for the complete open reading frame revealed that the predominant F1-20 mRNA encodes an 896 amino acid polypeptide with a molecular weight of 91,319 Da. The deduced amino acid sequence does not contain a signal sequence, or any extensive hydrophobic regions. The deduced amino acid sequence does contain a number of consensus sequences for protein kinases. Searches of the protein and nucleic acid sequence data bases revealed that the F1-20 protein has not been previously characterized at the primary structure level, although a weak similarity was found between rabbit calpastatin and the C-terminal portion of the F1-20 protein. We then determined biochemically that the F1-20 protein is a substrate for Ca(2+)-dependent proteolysis, which is specifically inhibited by calpain inhibitors in vitro. This indicates that the F1-20 protein is a substrate for neuronal calpain. We observed that treatment of a synaptosomal lysate with alkaline phosphatase led to an increase in the electrophoretic mobility of the F1-20 protein, as well as to an increase in the sharpness of the electrophoretic band. This indicates that the F1-20 protein is phosphorylated in vivo.

Amino Acid Sequence↗
PubMed1990

Single crystals of a chimeric T7/T3 RNA polymerase with T3 promoter specificity and a nonprocessive T7 RNAP mutant.

Two RNA polymerases homologous to bacteriophage T7 RNA polymerase, bacteriophage Sp6 and T3 RNA polymerases, were screened for crystallization under conditions identical or similar to those reported for the growth of large single crystals of T7 RNA polymerase (Sousa, R., Rose, J. P., Chung, Y. J., Lafer, E. M., and Wang, B.-C. (1989) Proteins 5, 266; Sousa, R., Lafer, E. M., and Wang, B.-C. (1990) J. Crystal Growth, in press; Sousa, R., and Lafer, E. M. (1990) Methods 1, in press). A number of mutant T7 RNAPs were also screened under these conditions as were three chimeric RNA polymerases consisting of T7 RNAP N-terminal and T3 RNAP C-terminal sequences. One chimeric polymerase and two mutant polymerases crystallized readily under T7 RNAP crystallization conditions. The chimeric polymerase crystallized in a space group different from T7 RNA polymerase: orthorombic with unit cell parameters a = 75 A, b = 98 A, c = 159 A; space group P2(1)2(1)2(1) and 4 molecules/unit cell. This chimeric enzyme exhibits T3 promoter specificity and will make it possible to investigate how structural differences between the T3 and T7 RNA polymerase promoter recognition domains determine their different promoter specificities. One of the mutant polymerases successfully crystallized was an enzyme which can carry out promoter recognition and abortive transcription but cannot carry out processive transcription. Its structure may provide information on the nature of the conformational changes undergone by T7 RNAP in the abortive-processive switch. Crystals of the second mutant T7 RNA polymerase were unsuitable for x-ray analysis.

Chimera↗
PubMed1990

Two new monoclonal antibodies provide immunohistochemical evidence for the unique biochemical similarity of the mouse globus pallidus, entopeduncular nucleus and substantia nigra pars reticulata.

Similarities in cellular morphology, afferentation, efferentation, and neurotransmitter content between the internal and external parts of the pallidum and the substantia nigra pars reticulata have long been noted. Here we present evidence that the globus pallidus, entopedunucular nucleus and substantia nigra pars reticulata are more closely related to each other antigenically than to any other anatomical subdivision in the murine central nervous system. In a monoclonal antibody library composed of 20 distinctive lines selected from 300 hybridomas screened immunohistochemically on mouse brain sagittal sections we found two antibodies whose staining patterns distinguish the pallidum and substantia nigra pars reticulata from all other brain gray matter regions but stain these two divisions similarly. One monoclonal antibody, F1-134, stains all brain gray matter regions moderately but gives intense staining of the globus pallidus, entopeduncular nucleus, and substantia nigra pars reticulata only. Another monoclonal antibody, F1-20, stains different brain gray matter regions to varying degrees but shows a complete and exclusive exclusion of staining from the globus pallidus, entopeduncular nucleus and substantia nigra pars reticulata. These results support the tripartite pallidum hypothesis. This study also provides an example of how the monoclonal antibody library strategy can be applied to general problems of brain organization.

Animals↗
PubMed1989

Single crystals of bacteriophage T7 RNA polymerase.

Single crystals of T7 RNA polymerase have been grown to a maximum size of 1.8 x 0.3 x 0.3 mm. The crystals are composed of fully intact T7 RNA polymerase which is enzymatically active upon dissolution. These crystals belong to the monoclinic space group P2(1) and have unit cell parameters a = 114.5 A, b = 139.6 A, c = 125.7 A, and beta = 98.1 degrees. Self-rotation function studies indicate that there are three molecules per asymmetric unit. The crystals diffract to at least 3.0 A resolution. These are the first crystals of a DNA-dependent RNA polymerase suitable for high-resolution X-ray structure determination.

Crystallization↗
PubMed1989

In situ hybridization mapping of glucocorticoid receptor messenger ribonucleic acid in rat brain.

We have mapped the distribution of glucocorticoid receptor (GR) mRNA in the male adult rat brain using T7 RNA polymerase transcripts of a 1155 base pair rat GR cDNA clone comprising the coding region for amino acids 140-525. Strong expression of GR mRNA was found in the neurons of the CA1 and CA2 fields of the hippocampus and in the paraventricular and periventricular hypothalamic nuclei. Moderate to strong hybridization was found in the dorsal thalamic nuclei, layers II and VI of the cerebral cortex, the anterior olfactory nucleus and primary olfactory cortex, the hypothalamic mammillary nuclei, the subthalamus, and the granule and mitral cells of the olfactory bulb. Weak to moderate hybridization was found in many other regions of the tel- and diencephalon. Mes- and rhomboencephalic neurons displayed very low levels of GR mRNA relative to the levels observed in the tel- and diencephalon. In the cerebellum, moderate to strong levels of mRNA were detected in the granule and Purkinje cell layers with very low levels elsewhere. Nonneuronal brain elements, such as glial cells, the pia mater, and the choroid plexus, were found to express low to moderate amounts of GR mRNA. These results confirm and extend mapping studies of steroid receptors in the brain using radiolabeled steroids or monoclonal antibodies against rat liver GR and demonstrate that the relative distribution of GR protein in different brain nuclei reflects differences in GR mRNA levels. The rat GR cDNA clone is also shown to provide suitable probes for mapping GR gene expression in the mouse brain.

Animals↗
PubMed1988

Z-DNA-binding proteins in Escherichia coli purification, generation of monoclonal antibodies and gene isolation.

Z-DNA affinity adsorption of an Escherichia coli lysate in the presence of excess B-DNA results in a 1000-fold enrichment for three proteins with apparent molecular weights, on SDS/polyacrylamide gel electrophoresis, of 50,000, 90,000 and 100,000. When retention of these proteins on resins constructed with Z-DNA (Br-poly(dG-dC).poly(dG-dC)) was compared with retention on resins constructed with B-DNA or Br-B-DNA, it was found that approximately 100-fold more of the 50,000 Mr protein, 1000-fold more of the 90,000 Mr protein, and greater than 1000-fold more of the 100,000 Mr protein was retained on the Z-DNA resin. No difference in retention on the B-DNA versus brominated B-DNA resin was found, indicating that the increased retention on the Z-DNA resin was not due to bromination of the Z-DNA. This demonstration of Z-DNA-specific binding in vitro makes these proteins candidates for binding to Z-DNA in vivo. In an effort to determine the function of these proteins we have prepared monoclonal antibodies against each protein and isolated its respective gene. Western blot analysis of lysogens carrying these genes confirms their identity and shows that the complete coding region and promoter for each gene has been cloned.

Antibodies, Monoclonal↗
PubMed1986

The effect of anti-Z-DNA antibodies on the B-DNA-Z-DNA equilibrium.

Four different preparations of rabbit and goat anti-Z-DNA antibodies were examined to determine the effects of antibody binding on the B-DNA-Z-DNA equilibrium. One of the four antibodies, a goat IgG, caused a marked lowering in the ionic strength required for the B-DNA to Z-DNA transition in poly(dG-dC) X poly(dG-dC), shifting the midpoint from 2.25 to 2.0 M NaCl. This IgG had a more prominent high affinity antibody population than did the other goat IgG, which caused little change in the midpoint of this transition. The presence of anti-Z-DNA antibodies also reduced the degree of negative supercoiling required for the formation of Z-DNA in (dG-dC)n sequences inserted into closed circular plasmid DNA. The goat IgG with the more marked effect on the salt-induced transition also had a greater effect in favoring Z-DNA formation in negatively supercoiled plasmids. A shift toward Z-DNA formation was observed in circular dichroism measurements upon antibody binding to poly(dG-dC) X poly(dG-dC) in very low ionic strength solution as well. We propose that the stabilization of Z-DNA by antibody binding in poly(dG-dC) X poly(dG-dC) occurs cooperatively, several antibody molecules binding to a single polymer molecule and stabilizing the entire molecule in Z-DNA through their combined binding energies. The stabilization of Z-DNA by antibody binding in a supercoiled plasmid can be significant, and failure to consider this effect and to choose appropriate conditions for measurement can lead to errors in estimating when Z-DNA will form in response to negative supercoiling.

Animals↗
PubMed1985

Anti-Z-DNA antibody binding can stabilize Z-DNA in relaxed and linear plasmids under physiological conditions.

It is shown that anti-Z-DNA antibody binding can stabilize sequences of d(CG/GC)n and d(CA/GT)n in the Z-DNA conformation in a plasmid in the complete absence of supercoiling. This effect is quantitated by using antibody preparations of different affinities and varying concentrations. The d(CG/GC)n sequence can be stabilized under physiological conditions. This is the first demonstration that a region of Z-DNA can be stabilized by protein binding in a completely relaxed plasmid under physiological conditions. The antibody-Z-DNA complex in the relaxed plasmid is shown to be an equilibrium state and not a long-lived kinetic intermediate since specific binding of the antibody to linearized plasmids containing Z-forming sequences is observed.

Antibodies↗
PubMed1985

Isolation and characterization of Z-DNA binding proteins from wheat germ.

The preparation of a heterogeneous non-histone protein extract from wheat germ utilizing Br-poly(dG-dC).poly(dG-dC) (Z-DNA) affinity chromatography is described. The binding characteristics of antibodies against Z-DNA are used as a model system to define important criteria that the DNA binding behavior of a Z-DNA binding protein should display. We show that the wheat germ extract contains DNA binding proteins specific for left-handed Z-DNA by these criteria. The affinity of the proteins measured by competition experiments was approximately 10(5) greater for Br-poly(dG-dC).poly(dG-dC) (Z-DNA) than for poly(dG-dC).poly(dG-dC) (B-DNA). The affinity of the proteins for plasmid DNA increases with increasing negative superhelicity which is known to stabilize Z-DNA. The proteins are shown to compete with Z-DNA antibodies for binding to supercoiled plasmids. Finally, the affinity for two plasmids at a given superhelical density is greater for the plasmid containing an insert known to form Z-DNA than for a plasmid without the insert. The proteins exhibit a 2-3-fold greater affinity for stretches of (dC-dA)n.(dT-dG)n over stretches of (dG-dC)n.(dG-dC)n when both sequences are induced to form Z-DNA by supercoiling.

Animals↗
PubMed1984

The specificity of antibodies elicited by poly(dG).poly(dC).

Antibodies have been raised to the synthetic DNA polymer poly(dG).poly(dC). These antibodies have the ability to distinguish this right-handed polymer from natural mixed sequence DNA, as well as from other right- and left-handed synthetic DNA polymers. They show reduced but measurable binding to synthetic polymers which contain various combinations of guanine and cytosine polynucleotides suggesting that both helical shape and sequence are recognized by this antiserum.

Antibody Specificity↗
PubMed1983

Antibodies against Z DNA react with the macronucleus but not the micronucleus of the hypotrichous ciliate stylonychia mytilus.

Using indirect immunofluorescence, we studied the reaction of antibodies specific for left-handed Z DNA with the nuclei of the hypotrichous ciliate Stylonychia mytilus. In the vegetative cell, the macronucleus reacts strongly with these antibodies, but no reaction can be detected with micronuclei. However, an antibody that binds to denatured and right-handed B DNA reacts with both types of nuclei. No reaction of the anti-Z DNA antibody is seen in the macronuclear replication band. Digestion of macronuclei with DNAase I leads to a decrease in the anti-Z DNA antibody reaction. Some stages of the developing macronucleus were also investigated. No reaction is seen at the polytene chromosome stage, but following DNA elimination the nucleus is seen to react with the antibody.

Animals↗
PubMed1983

Lack of Z-DNA conformation in mitomycin-modified polynucleotides having inverted circular dichroism.

Poly(dG-dC) . poly(dG-dC) and Micrococcus lysodeikticus DNA were modified by exposure to reductively activated mitomycin C, an antitumor antibiotic. The resulting covalent drug-polynucleotide complexes displayed varying degrees of CD inversions, which are strikingly similar to the inverted spectrum observed with Z-DNA. The following criteria have been used to establish, however, that the inverted CD pattern seen in mitomycin C-polynucleotide complexes does not reflect a Z-DNA conformation. (i) The ethanol-induced transition of poly(dG-dC) . poly(dG-dC) from B to Z conformation is not facilitated but rather is inhibited by mitomycin C modification. This may be due to the presence of crosslinks, (ii) Radioimmunoassay indicated no competition for Z-DNA-specific antibody by any of the mitomycin C-modified polynucleotides, (iii) 31P NMR of the complexes yielded a single relatively narrow resonance, which is inconsistent with the dinucleotide repeat characteristic of Z-DNA. Alternative explanations for the inverted CD pattern include a drug-induced left-handed but non-Z conformational change or the superposition of an induced CD onto the CD of B-DNA due to drug-base electronic interactions. These results illustrate the need for caution in interpreting CD changes alone as an indication of Z-DNA conformation.

Circular Dichroism↗
PubMed1983

Z-DNA and the polytene chromosome.

Indirect immunofluorescence shows that antibodies specific for the Z conformation of DNA bind to D. melanogaster polytene chromosomes in a specific and reproducible pattern. In our acetic-acid-fixed preparations, the binding is predominantly to interband regions, to puffs, and to some specific bands. As might be expected, the pattern of binding can be affected by cytological procedures. Bands and interbands show significant differences in their susceptibility to these procedures. Although further study is needed, our studies give no evidence that acetic acid treatment of intact cells is capable of causing conversion of B-form and Z-form DNAs. Instead, the experiments suggest that the Z conformation is preferentially available in interbands and a few other chromosome regions.

Animals↗
PubMed1983

Z-DNA-specific antibodies in human systemic lupus erythematosus.

Naturally occurring antibodies to left-handed Z-DNA have been shown to be present in the sera of human patients with systemic lupus erythematosus (SLE). These antibodies are of two types. One type reacts with both denatured DNA and Z-DNA. The other type is specific for Z-DNA and remained in the serum after removal of the cross-reactive antibody by extensive absorption on a denatured DNA affinity column. The antibodies appear to be specific for SLE and do not appear frequently in other rheumatic diseases. The presence of the antibody in SLE is correlated with the clinical manifestations of the disease, in parallel with antibodies to native and denatured DNA.

Antibody Specificity↗
PubMed1982

Monoclonal antibodies recognize different parts of Z-DNA.

Brominated poly(dG-dC) . poly(dG-dC), which forms a stable Z-DNA helix under physiological salt conditions, was used as an antigen to produce monoclonal antibodies from mice. The anti-Z-DNA antibodies were specific for the Z conformation as was shown by direct binding studies and a competitive solid phase assay. Competition could only be seen by brominated poly(dG-dC) . poly(dG-dC) under low and high salt conditions and unmodified poly(dG-dC) . poly(dG-dC) under high salt conditions. No binding could be seen to a number of other polynucleotides, including native and denatured DNA. Among the anti-Z-DNA monoclonal antibodies, examples differed in specificity: binding of one monoclonal antibody was blocked by methylation of cytosine; whereas the other antibody reacted equally well with the unmodified polymer or methyl cytosine-containing polymer in high ionic strength. The two antibodies are specific for different localized features of Z-DNA structure.

Animals↗
PubMed1982

Negatively supercoiled plasmids contain left-handed Z-DNA segments as detected by specific antibody binding.

Negative superhelical coiling of covalently closed DNA plasmids facilitates the formation of left-handed Z-DNA segments. This was demonstrated by binding of antibodies specific for Z-DNA. Plasmid pBR322 and two derivatives from it, pLP32 and pLP014, carrying inserts of alternating CG sequences of 32 bp and 14 bp, respectively, were used. Longer inserts required less negative superhelical density to induce the B-Z transitions. Antibody binding to supercoiled plasmids was also visualized by electron microscopy. Cross-linking of the antibody to the negatively supercoiled plasmid and restriction of the DNA with restriction endonucleases demonstrated that the antibodies combine with the CG insert in pLP32. For pBR322, however, evidence suggests that the antibody combines with a section of DNA containing 14 bases with alternating purine and pyrimidine residues with one residue out of alternation: CACGGGTGCGCATG. These cross-linking studies provide evidence for the binding specificity of the anti-Z-DNA antibodies. On the basis of experimental findings, we have calculated the changes in free energy associated with B-Z transitions in superhelical plasmids.

Antibodies↗