[Protein factor from regenerating rat liver destabilizing secondary DNA structure]

In DNA preparations isolated from regenerating rat liver 22 hours after partial hepatectomy, i.e. at the period of the most intensive DNA synthesis a "Denaturating Protein Factor" (DPF) tightly bound to DNA was found. Isolated protein fraction with a molecular weight of 6500 dalton was found to be homogenous upon SDS-polyacrylamide electrophoresis. The degree of destabilisation of DNA was estimated by its reaction with water-soluble [14C]CME-carbodiimide which modifies selectively guanine and thymine residues only in the denatured DNA regions. Pronase treated DPF loses its DNA-denaturing capacity. Pronase treatment of DNA--DPF complex restores native DNA structure. DPF from rat liver was able to denature DNA from calf thymus and bacteriophage T7 DNA. A hypothesis is proposed that the DPF is responsible for the destabilization of DNA secondary structure in the process of replication.

[Influence of protein bound with single-stranded DNA on the synthesis of RNA and poly(A). III. Protein product of F1 gene 5]

Influence of the protein product of F1 phage gene 5 (protein 5) on the synthesis RNA and poly(A) in vitro was studied. It has been shown, that protein 5 has no effect on the transcription of the native DNA by E. coli RNA-polymerase, but completely prevents RNA and poly(A) synthesis on the denatured or single-stranded DNA at the protein/DNA ratio 10:1. Protein 5 inhibits poly(A) synthesis with oligo(dT)9 and oligo(dT)12 as a template, preventing binding of enzyme to the oligonucleotide. After the initiation of the poly(A) synthesis the inhibition becomes considerably wearer. The biological function of the inhibition of the transcription by "unwinding" proteins is discussed.

Intracellular DNA-protein complexes from bacteriophage T4-infected cells isolated by a rapid two-step procedure. Characterization and identification of the protein components

A simple technique has been developed for isolating intracellular DNA and its bound proteins from uninfected and phage-infected bacteria. This technique, which utilizes aqueous salt concentrations in the physiological range, is based upon the fact that DNA exists in normal cell lysates in a stiff random coil conformation, and has an unusually large excluded volume to mass ratio. Such stiff coils display a unique combination of low sedimentation coefficient and large Stokes radius, enabling them to be separated rapidly from all other cellular components by successive centrifugal and gel permeation steps. Analysis of this purified intracellular DNA fraction from bacteriophage T4-infected Escherichia coli reveals mainly DNA and protein, with a small amount of RNA also present. Among the major proteins obtained are the DNA-dependent RNA polymerase of the host and the products of T4 genes rIIA, rIIB, and 32 (DNA-"unwinding" protein). Small amounts of the proteins coded by T4 genes 43 (DNA polymerase) and 42 (dCMP hydroxymethylase) have also been identified, in addition to at least 13 other phage-coded proteins of unidentified genes. Much of the phage-coded protein in the complex, including the gene 32 protein, does not exchange readily with the same protein exogenously added in the lysate.

Association of a protein structure of probable membrane derivation with HeLa cell mitochondrial DNA near its origin of replication

Almost all (about 95%) of the mitochondrial DNA molecules released by Triton X-100 lysis of HeLa cell mitochondria in the presence of 0.15 M salt are associated with a single protein-containing structure varying in appearance between a 10-20 nm knob and a 100-500 nm membrane-like patch. Analysis by high resolution electron microscopy and by polyacrylamide gel electrophoresis after cleavage of mitochondrial DNA with the endonucleases EcoRI, HindIII, and Hpa II has shown that the protein structure is attached to the DNA in the region of the D-loop, and probably near the origin of mitochondrial DNA replication. The data strongly suggest that HeLa cell mitochondrial DNA is attached in vivo to the inner mitochondrial membrane at or near the origin of replication, and that a membrane fragment of variable size remains associated with the DNA during the isolation. After sodium dodecyl sulfate extraction of mitochondrial DNA, a small 5-10 nm protein is found at the same site on a fraction of the mitochondrial DNA molecules.

Photochemical attachment of cyclic AMP binding protein(s) to the nuclear genome

The nature of the cyclic AMP-receptor-nucleus interactions was examined by a novel combination of two photoreactions. A photosensitive derivative of cyclic AMP, N6-butyryl cyclic AMP, was covalently attached to its cytoplasmic receptod by photo-affinity labelling and this receptor complex was photo-crosslinked by the DNA in the rat liver nuclei. The photolytic reactions seemed to be specific since stable links were formed only when substantial noncovalent binding occured.

Gene control in eukaryotes and the c-value paradox "excess" DNA as an impediment to transcription of coding sequences

Ways in which control of gene activity may lead to the observed high DNA content per haploid eukaryote genome are examined. It is proposed that deoxyribonucleoprotein (DNP) acts as a barrier to transcription at two distinct structural levels. At the lower level, melting of the nucleosome supercoil (quaternary structure) and of the nucleosomes (tertiary structure) might be brought about by the process of transcription itself. After unwinding the barrier section, the polymerase would eventually reach the structural gene. The transcripts of noncoding sequences, at least as far as their "unique" sequence components are concerned, may thus have filled their main function through the very process of transcription. The possibility of an inverse relationship between the length of the DNP barrier and the rates of transcription of the coding sequences is to some extent supported by available data. Different modes of coordination between the transcription of mRNA and of hnRNA from a single functional unit of gene action (funga) are considered. An analysis of gene control at high structural levels of DNP is made on the basis of other data, in relation to the concepts of eurygenic and stenogenic control. The concept of a euryon is introduced, namely of a set of linked fugas under common eurygenic control. Structure of order higher than quaternary can be inferred to exist in larger chromomeres of polytene chromosomes and in corresponding sections of ordinary chromosomes. Only moderate amounts of highest order interphase euchromatic structure are likely to be able to be accomodated in average chromomeres and none in very thin chromomeres. Puffs are interpreted as the melting of highest order interphase structure, and the absence of puffs during transcription as the absence of this highest order structure in the resting state of the chromomeres. Genes that are constantly active in all tissues may dispense with highest order interphase structure and with the corresponding control mechanism, and the fugas involved thus may not puff. Puffs, large chromomeres and highest order interphase euchromatic DNP structure seem to be correlated with genes that need to be transcribed only under certain developmental conditions. It is proposed that the function of high order structure is to sequester genetic material, namely mainly controller sequences. Since such high order structure, in most cases, would be built up to house the controller dependencies of just one structural gene, the amount of DNA per structural gene needed for gene control would be considerable, and the concept, if correct, would go a long way towards explaining the c-value paradox ("excess" DNA in eukaryotes). In eurygenic determination, the high order structure is thought to be conditioned for melting or to actually melt to an intermediate level of structure. From there, stenogenic control, leading to transcription, is considered to carry the melting process further to yet lower structural levels...

Release of RNA--DNA-protein complex during differentiation of the water mould Allomyces arbuscula

A correlation between release of a nucleic acid protein complex into the external medium and sporangial differentiation was found. Conditions preventing differentiation also stopped the release. Lethal lysis is not involved in this release process. Extracellular nucleic acids are very heterogenous, consisting of nucleotides as well as acid-precipitable nucleic acids. RNA was found to be associated with proteins and a hetero-duplex RNA--DNA associated with this nucleoprotein. Some speculations are presented about possible correlation between the release of nucleoprotein complexes and the intracellular events of differentiation.

[Relationship between the structural state of chromatin and the biosynthesis of rapidly labeling nuclear RNA in the thymuses of rats subjected to total x-irradiation]

Accumulation of polydeoxyribonucleotides (PDN) was studied in thymus of rats, subjected to total body X-ray irradiation at doses 400 and 800 rad. The content of PDN correlated with the time of treatment; its low-polymer components prevailed after irradiation with 800 rad. Protein/DNA ratio was decreased in DNP within 30 min after the irradiation and it returned to the initial level within 4 hrs. Capacity of DNP to make a complex with actinomycin D was inhibited within 30 min; however it exceeded the control level within 4 hrs after irradiation. Biosynthesis of nuclear RNA, estimated by incorporation of 14C-uridine, was distinctly decreased within the whole experimental period.

Effects of estrogen on gene expression in chick oviduct. The role of chromatin proteins in regulating transcription of the ovalbumin gene

Histones, extractable non-histone proteins, and a tightly bound non-histone protein DNA complex were fractionated from chromatins which were isolated from estrogen-stimulated and hormone-withdrawn chick oviducts. Reconstitution of homologous constituents was performed and RNA was transcribed from these reconstituted chromatins using Escherichia coli RNA polymerase. DNA complementary to ovalbumin mRNA was then used as a hybridization probe to estimate the concentration of ovalbumin messenger RNA sequences in these in vitro transcripts. Our results demonstrated that 0.011% of the in vitro RNA transcripts produced from reconstituted estrogen-stimulated chromatin was ovalbumin mRNA sequences as compared to 0.0015% obtained for reconstituted hormone-withdrawn chromatin. Thus, the ratio of ovalbumin mRNA sequences in the in vitro transcripts of reconstituted stimulated and withdrawn chromatins was 8 to 1, identical with the value obtained from native estrogen-stimulated and hormone-withdrawn chromatins. Furthermore, the number of initiation sites for RNA synthesis on reconstituted and native chromatins are indistinguishable. Thus, the specificity of transcription of isolated chromatins appears to be conserved upon dissociation and fractionation of the chromatin proteins followed by reconstitution of these constituents to DNA. The effect of chromatin proteins on gene expression was further examined by reconstituting components from different development stages. Reconstitution of extractable non-histone proteins from estrogen-stimulated chromatins to tightly bound non-histone protein. DNA complexes from hormone-withdrawn chromatins resulted in the synthesis of a substantial amount of ovalbumin mRNA sequences. Conversely, when extractable non-histone proteins from withdrawn chromatins were reconstituted to tightly bound non-histone protein DNA complexes from estrogen-stimulated chromatins, very low levels of mRNAov sequences were detected. In contrast, interchange of the histones and tightly bound non-histone protein DNA complexes from hormone-withdrawn and estrogen-stimulated chromatins during reconstitution did not affect the level of mRNAOV sequences produced. Therefore, the extractable non-histone proteins of chromatin appear to be extremely important in regulating specific gene expression.

Isolation and characterization of the protein coded by gene A of bacteriophage phiX174 DNA

Replication of phiX174 circular replicative form (RFI) DNA by extracts of Escherichia coli infected with bacteriophage phiX174 (amber in gene A) requires the phiX174 gene A product. This requirement has been used as an assay for the isolation of this protein. The gene A product (purified 4000-fold) caused relaxation of superhelical phiX174 RFI and formation of discontinuities in the viral strand of phiX174 RFI uniquely situated in the A region of the genome, and yielded a complex after interacting with phiX174 RFI that is active in replication of phiX RFI.

Enhanced template activity in chromatin from adrenal medulla after phosphorylation of chromosomal proteins

Translocation of protein kinase to the nucleus had been implicated earlier in the transsynaptic control of gene expression mediated by cholinergic nerves in adrenal medulla. Phosphorylation of chromosomal proteins by adenosine 3',5'-monophosphate-dependent protein kinase and adenosine 3',5'-monophosphate enhances the template activity of chromatin from adrenal medulla. When homologous RNA polymerase II is used the relative activation is greater than that obtained with Escherichia coli RNA polymerase. The substrate for such phosphorylation does not seem to be RNA polymerase II. Phosphorylation of specific acidic protein probably mediates this enhancement of template activity.

Temporal relationships of chromatin protein synthesis, DNA synthesis, and assembly of deoxyribonucleoprotein

Chromatin assembly has been investigated in terms of the sites on DNA where newly synthesized chromatin proteins associate. Chromatin from cells labeled with [14C]-BrdUrd and [3H]lysine was fixed with formaldehyde and resolved in CsCl gradients. By varying the spacing of the labeling intervals of the two isotopes so as to encompass all possible periods in S-phase, the association of labeled, newly synthesized proteins on newly synthesized (BrdUrd-substituted) or preexisting chromatin DNA was determined. In all experiments it was found that newly synthesized chromatin proteins predominantly associated with nonreplicating DNA. Possible mechanisms by which cells recycle preexisting chromatin proteins to restore the protein content of newly synthesized DNA are discussed.

Control of RNA synthesis by chromatin proteins

The effect of chromatin proteins on template activity has been studied. Using both E. coli RNA polymerase and calf thymmus polymerase B we have measured the number of initiation sites on chromatin and various histone-DNA complexes. Chromatin can be reconstituted with histone proteins alone and this complex is still a restricted template for RNA synthesis. The removal of histone f1 causes a large increase in the template activity. Chromatin is then treated with Micrococcal nuclease and the DNA fragments protected from nuclease attack ("covered DNA") are isolated. Alternatively, the chromatin is titrated with poly-D-lysine, and by successive treatment with Pronase and nuclease, the DNA regions accessible to polylysine are isolated ("open DNA"). Both fractions were tested for template activity. It was found that RNA polymerase initiation sites are distributed equally in open and covered region DNA.

[Effect of the conditions of isolation and incubation of the nuclei on digestion of DNA chromatin by calcium- and magnesium-dependent endonuclease. Change in the spectrum of chromosomal proteins and possible role of DNA-protein interactions]

Digesting of chromosomal DNA of interphase rat liver nuclei by Ca, Mg-dependent endonuclease in situ in the presence of chelating agents results in the appearance of the soluble DNP--up to 30% of the total DNA. In addition, 50% of the chromatin is solubilised after mild ultrasonication. In the absence of the chelating agents the degree of fragmentation is considerably increased. The process is accompanied by a loss of some histone and nonhistone chromosomal proteins; the nonhistone proteins are lost selectively. The preliminary removal of the nuclear membrane and significant part of the proteins by tritone X-100 promotes the chromatin degradation and the appearance of low molecular weight fragments. The DNA-fragments of solubilised chromatin are similar to the DNA-fragments of residual chromatin, but in the presence of the chelating agents the latter does not contain monomeric fragments.

Isolation of a DNA-protein complex containing a single DNA fragment which is at or near the replication origin of the Bacillus subtilis chromosome

A chromosomal fragment containing purA, the nearest marker from the replication origin of the Bacillus subtilis chromosome, was highly purified as a complex containing at least proteins and being solubilized easily during cell lysis. The complex had a markedly higher sedimentation rate (70-120S) than the bulk of the solubilized DNA (40S). The electron microscopic observation showed the complex to be an aggregate of several DNA molecules with a local structure containing amorphous materials which stained black and bushes of RNA. This confirmed biochemical evidences suggesting that the complex is an intermolecular aggregate of the purA-DNA-protein-RNA complex.

[Incorporation of thymidine-H3 into the DNP of rat tissues following a single injection of DNA]

The injection of a homologous DNA to rats caused an increased incorporation of H3-thymidine into DNP of the bone marrow, the spleen, the thymus, and the intestinal mucosa 24 hours after the administration. This effect was not revealed on the 3d day.