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Biomedical subjects

A Nordheim

Publications and source records attributed to A Nordheim.

At least 73 records · Page 4Linked to original sources
PubMed1991

Murine cyclophilin-S1: a variant peptidyl-prolyl isomerase with a putative signal sequence expressed in differentiating F9 cells.

Fractionation of differentiating murine teratocarcinoma F9 cells and extraction of the nuclear/microsomal pellets with ethidium bromide led to the purification and microsequencing of the protein mCyP-S1, a novel cyclosporin A-sensitive peptidyl-prolyl cis-trans isomerase (PPIase). mCyP-S1 is a new member of the cyclophilin class of proteins. Cloning and sequencing of the mCyP-S1 cDNA revealed extended coding capacity for a putative N-terminal signal sequence, suggesting processing of mCyP-S1 during intracellular translocation across the membrane of the endoplasmic reticulum. mCyP-S1 is abundantly expressed in a variety of mouse organ tissues and its mRNA levels increase during F9 cell differentiation. Specific subcellular localization of PPIases is postulated to contribute to functional specificities of this class of enzymes.

Amino Acid Isomerases↗
PubMed1991

Rapid and efficient purification of native histidine-tagged protein expressed by recombinant vaccinia virus.

Vaccinia virus has been used as a vector to express foreign genes for the production of functional and posttranslationally modified proteins. A procedure is described here that allows the rapid native purification of vaccinia-expressed proteins fused to an amino-terminal tag of six histidines. Extracts from cells infected with recombinant vaccinia virus are loaded onto Ni2+.nitrilotriacetic acid (Ni2+.NTA)-agarose and histidine-tagged proteins are selectively eluted with imidazole-containing buffers. In the case of the human serum response factor (SRF), a transcription factor involved in the regulation of the c-fos protooncogene, the vaccinia-expressed histidine-tagged SRF (SRF-6His) could be purified solely by this step to greater than 95% purity. SRF-6His was shown to resemble authentic SRF by functional criteria: it was transported to the nucleus, bound specifically the c-fos serum response element, interacted with the p62TCF protein to form a ternary complex, and stimulated in vitro transcription from the serum response element. Thus, the combination of vaccinia virus expression and affinity purification by Ni2+.NTA chromatography promises to be useful for the production of proteins in a functional and posttranslationally modified form.

Amino Acid Sequence↗
PubMed1991

Functional dissection in vitro of the human c-fos promoter.

Using internal and 5' deletions, the elements contributing to the in vitro activity of the human c-fos promoter have been identified. Wild type and mutant promoters were fused to the G-free cassette and tested, using HeLa nuclear and whole cell extracts, with the fos wild type promoter as the internal control. The proximal promoter domain, spanning from -124 to -58 in the fos promoter, is the primary determinant of activity. Two elements in this domain are important, the direct repeats and the -60 element, which contains overlapping MLTF/USF and CREB/ATF transcription factor binding sites. CREB/ATF appears to be dominant, since a canonical CRE functions well in place of the -60 element. Interestingly, the direct repeats appear to require the -60 element to exert their effect. Upstream elements do not Influence promoter activity in their normal position or adjacent to the TATA box, except the serum response element (SRE). Templates containing various lengths of the fos wild type SRE next to the TATA box are stimulated by adding purified serum response factor (SRF), while SRE mutants are not responsive. The stimulation is independent of small spacing differences between the SRE and TATA elements, and the CArG core of the fos SRE suffices to respond to added SRF in vitro.

Activating Transcription Factors↗
PubMed1991

In vitro transcriptional analysis of the human c-fos proto-oncogene.

The transcription of the human c-fos promoter was characterized in vitro using HeLa nuclear and whole cell extracts. The c-fos gene and c-fos promoter fusions to the SV40 early region and the G-free cassette were active as templates, yielding faithfully initiated transcripts that were sensitive to alpha-amanitin. c-fos-SV40 and -G-free cassette templates were less efficiently transcribed when linearized, suggesting that template topology affected fos activity in vitro. Transcription conditions were optimized for both extracts using a mixture of the fos wild type promoter, a deleted fos promoter retaining just the TATA box, and the adenovirus major late promoter, all driving differently sized G-free cassettes. The fos promoter was inactive at low protein and DNA concentrations, and then showed a sharp rise in efficiency with a subsequent 2-fold increase in the amount of either DNA or protein. In contrast, high protein or DNA concentrations were required for the deleted fos promoter to show only weak activity. Preincubation of templates with extracts shortened the lag time before transcription could be detected, but did not lead to increased activity. By comparing reactions in the presence and absence of Sarkosyl, we estimate that only a subset of fos-driven templates was active, and that these templates were used for several rounds of transcription.

Amanitins↗
PubMed1991

Transcription-induced conformational change in a topologically closed DNA domain.

We have tested in vitro the occurrence of a B-to-Z transition in a region of alternating purines and pyrimidines as a consequence of transcription-induced negative supercoiling. By using a monoclonal antibody as a specific Z-DNA stabilizing agent, we demonstrate that the formation of left-handed DNA can transiently occur when a topologically unconstrained template is transcribed. The B-to-Z transition, observed in a subpopulation of templates, appears to be induced by negative supercoiling generated in the wake of an elongating T7 RNA polymerase. Consistent with this, the presence of topoisomerases during the transcription period prevents the change in DNA conformation. These data agree with the 'twin-supercoiled-domain' model for transcription of Liu and Wang (1). Interestingly, our results suggest that the diffusion rate of transcription-induced superhelical twists must be relatively slow compared to their generation, and that under in vitro conditions localized transient supercoiling can reach unexpectedly high levels.

Antibodies↗
PubMed1991

A protein domain conserved between yeast MCM1 and human SRF directs ternary complex formation.

MCM1 and SRF bind to the same DNA sequence and form ternary complexes with STE12 and p62TCF, respectively. We show that in gel retardation assays, MCM1 recruits both ternary complex factors whereas SRF interacts only with p62TCF. A protein domain of 90 amino acids, shared by MCM1 and SRF, was found to be sufficient for ternary complex formation. The domain is also required for dimerization and DNA binding. Similar regions are found in other proteins, such as ARG80, Deficiens and Agamous. ARG80 and Agamous exhibit similar DNA binding specificities but do not interact with either STE12 or p62TCF. By exchanging three residues of ARG80 with those of corresponding positions in SRF (residues 198, 200 and 203), the ARG80 protein acquires the ability to recruit p62TCF into a ternary complex. Likewise, the substitution of four SRF amino acids by MCM1-derived residues (amino acids 73, 75, 77 and 78) confers on SRF the ability to interact with STE12. Thus, we have identified specific amino acids in MCM1 and SRF that are critical for ternary complex formation and which map to equivalent positions within the shared domains. Therefore, the structural basis for specific protein-protein interaction appears to be conserved in evolution between a class of transcription factors.

Amino Acid Sequence↗
PubMed1991

Multiple basal promoter elements determine the level of human c-fos transcription.

Three cis-acting domains that contribute to the basal promoter activity of the human c-fos gene were identified. One encompasses the serum response element and has been previously described. Another spans an NF1-like site situated at -170. Mutations and in vitro protein binding assays pinpoint this site as the sole basal element of the medial domain. The third, or promoter-proximal, domain can be divided into several distinct sites, one containing a directly repeated GC-rich element and the other consisting of partially overlapping recognition sites for transcription factors ATF/CREB and MLTF/USF. Each of these sites contributes to basal activity as assayed by transient transfections and by in vitro transcription. Consistent with this, several complexes could be visualized between this region and nuclear proteins in vitro and genomic footprinting demonstrated that both elements are constitutively bound in vivo. On the basis of these results, we conclude that all three domains are necessary for full c-fos promoter function.

Base Sequence↗
PubMed1990

Rapid induction of c-fos transcription reveals quantitative linkage of RNA polymerase II and DNA topoisomerase I enzyme activities.

The functional association between DNA topoisomerase I and gene activity has been analyzed using the tightly regulated c-fos proto-oncogene, which undergoes rapid transitions between active and inactive states of transcription. We show that the topoisomerase I inhibitor camptothecin can be used to measure topoisomerase I activity throughout the transcription cycle of the c-fos gene. Upon induction of c-fos transcription in the presence of camptothecin, topoisomerase I cleavages spread through the gene in the 5' to 3' direction and concomitantly transcriptional elongation is retarded. Parallel kinetic measurements of RNA polymerase II activity and topoisomerase I activity demonstrate a quantitative and temporal link between the two enzymes. Our results argue that topoisomerase I quantitatively relieves the torsional consequences of transcriptional elongation in intact cells.

Animals↗
PubMed1990

Synergism in ternary complex formation between the dimeric glycoprotein p67SRF, polypeptide p62TCF and the c-fos serum response element.

Transcriptional regulation of the c-fos proto-oncogene requires the serum response element (SRE) which is complexed by a multi-protein assembly observed both in vitro and in vivo. Two protein factors, p67SRF and p62TCF (previously called p62), are required to interact with the SRE for efficient induction of c-fos by serum. By quantitative band shift electrophoresis we measure at least a 50-fold increase in SRE affinity for p67SRF/p62TCF over p67SRF alone. Stoichiometrically we determine that the ternary complex with p62TCF involves p67SRF in dimeric form. We demonstrate that p67SRF is a glycosylated nuclear transcription factor carrying terminal N-acetylglucosamine (GlcNAc) as a post-translational modification. A proteolytic limit digestion product, approximately 13 kd in size, was generated from the p67SRF-SRE complex. This p67SRF-core domain binds SRE, can dimerize with p67SRF and is still able to form a ternary complex with p62TCF. Therefore, three functional activities can be ascribed to this small p67SRF-core domain: specific DNA binding, dimerization and interaction with p62TCF. We demonstrate that these functions map within the p67SRF core fragment containing the region between amino acids 93 and 222.

Base Sequence↗
PubMed1989

Occupation of the c-fos serum response element in vivo by a multi-protein complex is unaltered by growth factor induction.

Rapid, transient induction of the human c-fos proto-oncogene by extracellular signals requires the presence in cis of the serum response element (SRE). Two protein factors that bind to the SRE in vitro are the serum response factor (p67SRF) and polypeptide p62. These polypeptides must interact with one another and the SRE for efficient serum induction of the c-fos gene. Here we use dimethyl sulphate genomic footprinting to establish the in vivo protein contacts on the SRE and flanking sequences. In human A431 cells the patterns of protection and hyper-reactivity that we find are consistent with the presence of p67SRF, p62, and at least one other protein immediately 3' to p67SRF. The protein-DNA contacts we observe within the SRE are present before induction by epidermal growth factor and are unchanged during gene activation and subsequent repression. Our results indicate that a specific DNA-protein architecture may be maintained at the c-fos SRE, regardless of changes in the transcriptional state of the gene. Such established structures could be important generally in rapid transcriptional responses to extracellular signals.

Base Sequence↗
PubMed1989

The ability of a ternary complex to form over the serum response element correlates with serum inducibility of the human c-fos promoter.

Rapid induction of c-fos transcription by serum and phorbol esters requires the serum response element (SRE). The SRE contains a 20 bp element of interrupted dyad symmetry (DSE) that is bound by p67/SRF. We have identified a hitherto unrecognized protein with an apparent size of 62 kd. This novel component, p62, is shown to be an integral but physically separable part of a ternary complex formed with p67/SRF and the SRE. Alone, p62 fails to bind the SRE but requires DSE-bound p67/SRF and sequences both within and outside the DSE for its interaction with DNA. In vivo, the response of the c-fos promoter to serum is severely impaired by mutations that abolish ternary complex formation in vitro.

Base Sequence↗
PubMed1989

Repression of c-fos transcription is mediated through p67SRF bound to the SRE.

Human c-fos expression is subject to tight transcriptional control. The gene is expressed at a high, constitutive level in some cell types and at a very low, but rapidly inducible level in many others. Induction of transcription by serum growth factors is mediated by the serum response element (SRE) to which at least two transcription factors, p67SRF and p62, bind. In this paper it is demonstrated that the low basal level of transcription is mediated through p67SRF bound to the SRE and that high, constitutive expression is observed when binding is prohibited. In this situation, an AP-1 consensus binding site adjacent to the SRE permits transactivation of the gene. Thus three levels of c-fos expression, induced, repressed and constitutive, appear to be determined by occupation of the SRE by p67SRF and its interaction with other proteins.

Base Sequence↗
PubMed1988

Topoisomer gel retardation: detection of anti-Z-DNA antibodies bound to Z-DNA within supercoiled DNA minicircles.

Small DNA fragments of approximately 350 bp in length, either with or without d(CG)n tracts, are ligated into underwound DNA minicircles to generate topoisomeric rings with different topological linking numbers, Lk. These minicircles, differing by an Lk of one, can be separated by acrylamide gel electrophoresis. Furthermore, electrophoresis can be used to reveal DNA double helix conformational changes that are induced by supercoiling, such as left-handed Z-DNA. When anti-Z-DNA antibodies are added to such minicircles, their binding leads to a selective retardation of the electrophoretic migration of the Z-DNA containing circles. This effect is not seen with relaxed minicircles and those with insufficient torsional stress to induce a conformational transition. Thus the technique of 'topoisomer gel retardation' presents a very sensitive assay for the identification of proteins that selectively bind to DNA conformations stabilized by negative DNA supercoiling.

Antibodies, Monoclonal↗
PubMed1988

DNA supercoiling changes the spacing requirement of two lac operators for DNA loop formation with lac repressor.

We have used a gel retardation assay to investigate the influence of DNA supercoiling on loop formation between lac repressor and two lac operators. A series of 15 DNA minicircles of identical size (452 bp) was constructed carrying two lac operators at distances ranging from 153 to 168 bp. Low positive or negative supercoiling (sigma = +/- 0.023) changed the spacing between the two lac operators required for the formation of the most stable loops. This reveals the presence of altered double helical repeats (ranging from 10.3 to 10.7 bp) in supercoiled DNA minicircles. At elevated negative supercoiling (sigma = -0.046) extremely stable loops were formed at all operator distances tested, with a slight spacing periodicity remaining. After relaxation of minicircle-repressor complexes with topoisomerase I one superhelical turn was found to be constrained in those minicircles which carry operators at distances corresponding to a non-integral number of helical turns. This indicates that DNA loop formation can define local DNA domains with altered topological properties of the DNA helix.

Base Sequence↗
PubMed1987

Purification of intercalator-released p67, a polypeptide that interacts specifically with the c-fos serum response element.

Incubation of intact nuclei in buffers containing the DNA intercalating drug chloroquine leads to release of proteins that interact with DNA. We demonstrate here that a protein which binds to a motif within the human c-fos promoter, identified as the serum response element (SRE), is quantitatively released from HeLa nuclei, whereas nuclear factor 1 (NF 1) is not. Purification of the SRE binding protein by affinity chromatography to greater than 95% homogeneity allowed us to identify it as a polypeptide of approximately 67,000 daltons. The DNA contacts made by p67, as identified by methylation interference experiments, are indistinguishable from those of the serum response factor described previously.

Binding Sites↗
PubMed1987

Binding of anti-Z-DNA antibodies to negatively supercoiled SV40 DNA.

The binding of anti-Z-DNA antibody preparations to negatively supercoiled, protein-free SC40 DNA was analyzed. Covalent cross-linking with 0.1% glutaraldehyde followed by DNA restriction endonucleolytic fragmentation and nitrocellulose filtration allowed accurate mapping of antibody binding sites. The critical superhelical density necessary to allow antibody binding was -sigma = 0.056. The major region of antibody-DNA interaction was found within an SV40 segment spanning viral map positions 40 to 474. This region coincides with the nucleosome free region in SV40 minichromosomes and harbours the early and late promoter regions including the SV40 enhancer segment. Although it is unknown whether alternative, non-B-DNA conformations are generated in vivo within SV40 minichromosomes our results emphasize the high degree of DNA structural flexibility that can be realized under negative torsional stress.

Antibodies↗