Isolated HeLa Cell Nuclei Research Articles

RNA synthesis in isolated HeLa cell nuclei

RNA synthesis has been studied in isolated nuclei of HeLa cells. The incubation medium has been optimized for RNA synthesis and the requirements for the presence of specific components previously used by other investigators has been examined. Nuclei isolated by centrifugation through 2 M sucrose synthesize RNA linearly for at least 1 h only at low temperature (25°C). Low molecular weight RNA is found in the supernatant fraction after incubation; this RNA accounts for about 10% of the RNA synthesized. The RNA which remains within nuclei is of high molecular weight and processing of this RNA into molecules of the size of cytoplasmic mRNA does not seem to occur in isolated nuclei. We have studied the effect of an inhibitor of protein-nucleic acid interaction — aurintricarboxylic acid — on RNA synthesis by isolated nuclei. At concentrations below 0.1 mM, this drug does not inhibit RNA synthesis effectively, whereas at concentrations above 0.1 mM it inhibits RNA synthesis by about 80%. In view of the proposed mechanism of action of aurintricarboxylic acid, we suggest that completion of nucleotide chains initiated before nuclei isolation accounts for 20% of the RNA synthesized in our system by isolated nuclei, whereas nucleotide chains initiated during the in vitro incubation account for 80% of the RNA synthesized.

Synthesis of herpes simplex virus, vaccinia virus, and adenovirus DNA in isolated HeLa cell nuclei. I. Effect of viral-specific antisera and phosphonoacetic acid

Purified nuclei, isolated from appropriately infected HeLa cells, are shown to synthesize large amounts of either herpes simplex virus (HSV) or vaccinia virus DNA in vitro. The rate of synthesis of DNA by nuclei from infected cells is up to 30 times higher than the synthesis of host DNA in vitro by nuclei isolated from uninfected HeLa cells. Thus HSV nuclei obtained from HSV-infected cells make DNA in vitro at a rate comparable to that seen in the intact, infected cell. Molecular hybridization studies showed that 80% of the DNA sequences synthesized in vitro by nuclei from herpesvirus-infected cells are herpesvirus specific. Vaccinia virus nuclei from vaccinia virus-infected cells, also produce comparable percentages of vaccinia virus-specific DNA sequences. Adenovirus nuclei from adenovirus 2-infected HeLa cells, which also synthesize viral DNA in vitro, have been included in this study. Synthesis of DNA by HSV or vaccinia virus nuclei is markedly inhibited by the corresponding viral-specific antisera. These antisera inhibit in a similar fashion the purified herpesvirus-induced or vaccinia virus-induced DNA polymerase isolated from infected cells. Phosphonoacetic acid, reported to be a specific inhibitor of herpesvirus formation and the herpesvirus-induced DNA polymerase, is equally effective as an inhibitor of HSV DNA synthesis in isolated nuclei in vitro. However, we also find phosphonoacetic acid to be an effective inhibitor of vaccinia virus nuclear DNA synthesis and the purified vaccinia virus-induced DNA polymerase. In addition, this compound shows significant inhibition of DNA synthesis in isolated nuclei obtained from adenovirus-infected or uninfected cells and is a potent inhibitor of HeLa cell DNA polymerase alpha.

DNA synthesis in isolated HeLa cell nuclei. Evidence for in vitro initiation of synthesis of small pieces of DNA and their subsequent ligation

Optimum conditions for a DNA synthesizing system based on isolated nuclei have been described (Krokan, H., Bjorklid, E., and Prydz, H. (1975), Biochemistry, preceding paper in this issue) [3H]TTP-labeled nascent DNA produced during very short pulses was analyzed by centrifugation in alkaline sucrose gradients. More than 80% of the radioactivity appeared in 2-4S pieces (primary DNA pieces). It would therefore seem that the synthesis of DNA is discontinuous both in the 5' leads to 3' and in the 3' leads to 5' directions. The size of the primary DNA pieces increases from 2-4 S up to 14 S with increasing pulse length. Evidence is presented that this increase is not caused by ligation between 2-4S primary pieces. Pulse-chase experiments showed that in this nuclear system primary pieces were ligated to a product generally larger than 30 S. Evidence is also given for the initiation of primary DNA pieces in vitro.

DNA synthesis in isolated HeLa cell nuclei. Optimalization of the system and characterization of the product

DNA replication in isolated nuclei from synchronized HeLa cells has been studied in an effort to optimalize the system and characterize the product. The synthesis was highly dependent on the four deoxyribonucleoside triphosphates, ATP, and Mg2+. Optimum pH was about 7.8. The system was further stimulated by monovalent ions with NH4Cl and Tris-HCl (each 65 mM) being the most effective. The four ribonucleoside triphosphates and glycerol gave a slight but very reproducible and additive stimulation. Low concentrations of spermine and spermidine (0.2-1.5 X 10(-4) M) were also slightly stimulatory (10-15%) whereas higher concentrations were inhibitory. The reaction product was DNase sensitive, and banded at 1.699 g/ml in neutral CsCl together with bulk HeLa nuclear DNA. When studied by neutral CsCl and alkaline Cs2SO4 gradients, the incorporation of [3H]TTP was mainly (more than 85%) due to further elongation of strands initiated in vivo as evidenced by BrdUrd labeling.

Effect of DNA polymerase on nuclei from different phases of cell cycle.

DNA replication was investigated in isolated HeLa cell nuclei from different phases of the cell cycle. The addition of S‐phase cytoplasm to S‐phase nuclei restored the ability of these nuclei to synthesize DNA. The S‐phase cytoplasm requirement could be replaced by partially purified calf‐thymus DNA polymerases A and B. The activity of both the S‐phase cytoplasm and purified DNA polymerases in the nuclear system was ATP‐dependent. Using nuclei prelabelled with bromodeoxyuridine and CsCl equilibrium centrifugation, the DNA synthesis in vitro was shown to be of the replicative, not repair type when supported by either S‐phase cytoplasm or DNA polymerase A. DNA polymerase B, but not DNA polymerase A, was capable of using G1 nuclei to synthesize DNA; however, this synthesis was not ATP‐dependent. Gel‐filtration chromatography of HeLa cell‐free extracts have shown that DNA polymerases B and C are present in S‐phase and missing in G1‐phase cells.

Pre-4S RNA made in isolated HeLa cell nuclei terminates with U

Isolated HeLa cell nuclei are capable of synthesizing a precursor to 4S RNA. The 3′ terminus of the molecule made in vitro can be determined by four separate incubations with the four iritiated ribonucleoside triphosphates. The pre-4S was found to terminate specifically with uridine and be uniformly labeled. These facts are discussed in relation to specific termination of RNA molecules and possible reinitiation of RNA synthesis in isolated nuclei.

Synthesis and maturation of ribosomal ribonucleic acids in isolated HeLa cell nuclei. A tracer study on the topology of the 45S precursor of ribosomal ribonucleic acids.

The synthesis and processing of RNA by isolated HeLa cell nuclei was studied at low ionic strength in the presence of alpha-amanitin. The RNA polymerase reaction, with endogenous template and enzyme, rapidly reaches a plateau dependent on the amount of nuclei. Evidence is presented that incorporation of [(3)H]UMP proceeds only in growing RNA chains, whereas initiation of new RNA chains is arrested. The product formed contains all the main components of the 45S pre-rRNA (precursor of rRNA) maturation pathway (45S, 32S and 20S pre-rRNA; 28S and 18S rRNA). Most of the labelled material is in the mature rRNA components and their immediate precursors, even at very short times of incubation (2min). Small, but definite, 5S and 4S RNA peaks are also observed. At shorter incubation times a substantial amount of [(3)H]UMP is incorporated into RNA molecules in the 24S and 10-16S zones. This RNA material is considered to represent the non-conserved segments of 45S pre-rRNA in the process of nucleolytic degradation. A model for the tracer study of the topology of 45S pre-rRNA, on arrest of rRNA initiation, is discussed. The experimental evidence obtained supports the following structure of 45S pre-rRNA: 5'-end-28S rRNA unit-18S rRNA unit-nonconserved segment-3'-end.

Poly adenylic acid synthesis in vitro in isolated HeLa cell nuclei and whole cell homogenates

Homogenates of HeLa cells and purified HeLa cell nuclei were found to synthesize poly(A) in vitro. The poly(A) is the normal adenylate-rich species seen in growing cells and is contained in large RNA molecules, which themselves have been synthesized at least in part in vitro. Poly(A) synthesis in purified nuclei shows a dependence on ATP concentration that is about 75–200 times higher than the concentration for total RNA synthesis.

A polymerase activity forming 5S and pre-4S RNA in isolated HeLa cell nuclei

Isolated HeLa cell nuclei are capable of synthesizing 5S and pre-4S RNA. The labeling of these low molecular weight species has been compared with the labeling of nucleolar RNA and nuclear heterogeneous RNA. The 5S and pre-4S RNA molecules made in vitro were identified by their mobility on SDS acrylamide gels and by the sensitivity of pre-4S RNA to enzymes which cleave it in vitro to 4S RNA. Their mobilities and cleavage properties are similar to the RNA made in vivo. Unlike the nuclear heterogeneous RNA, the synthesis of the two small molecular weight RNAs is resistant to α-amanitin. A large proportion of 4S RNA labeled in vitro appears to be formed de novo. The ratio of the terminal uridine to the internal uridine 3′-monophosphate remains constant with time, even though there is linear incorporation into the pre-4S RNA in the isolated nuclei. Production of the nucleolar RNA and pre-4S RNA has been compared in the presence of various ions. The pre-4S RNA synthesis has a sharper maximum for (NH 4)SO 4 and MgCl 2 than does the synthesis of nucleolar RNA. The in vitro synthesis of pre-4S is more sensitive to ellipticine and pCMB than the production of nucleolar RNA. These differences between the production of pre-4S RNA and nucleolar RNA are discussed with respect to in vitro reinitiation and the possibility that different polymerases are involved in their synthesis.

DNA replication in isolated HeLa cell nuclei

DNA replication was investigated in HeLa cell nuclei isolated from different phases of the cell cycle. DNA synthesis occurred only in S-phase nuclei and was dependent on the presence of the four deoxynucleoside triphosphates, Mg ++, ATP and S-phase cytoplasm. G 1-phase cytoplasm was unable to support such DNA synthesis. A purified preparation of calf thymus DNA polymerase, however, was able to replace S-phase cytoplasm in supporting ATP dependent DNA synthesis, which suggests that the S-phase cytoplasmic factor is a DNA polymerase. G 1-phase nuclei could under no conditions be stimulated to initiate DNA replication prematurely.

The synthesis and assembly of DNA subunits in isolated HeLa cell nuclei

Nuclei from synchronized HeLa cells in S-phase continue to synthesize DNA in , vitro at or near the in , vivo replicating sites. Sedimentation of the product in an alkaline sucrose gradient reveals 10 and 24S segments in addition to the 40S non-replicating bulk DNA. Pulse chase experiments indicate that the 10S DNA is a precursor of the 24S product. ATP and the soluble protein fraction from the cytoplasm of S-phase cells support the accumulation of the 24S product.

Irreversible inhibition of nuclear exoribonuclease by thymidine-3'-fluorophosphate and p-haloacetamidophenyl nucleotides.

Exoribonuclease purified from Ehrlich ascites tumor cell nuclei and in intact HeLa cell nuclei is irreversibly inactivated by tow concentrations of p-bromo- and p-iodoacetamidophenyl nucleotides and by thymidine-3'-fluorophosphate. Iodoacetate, bromoacetate, and thymidine-5'-fluorophosphate do not affect the enzyme. Although p-haloacetamidophenyl nucleotides inactivate ribonucleic acid polymerase of isolated HeLa cell nuclei, thymidine-3'-fluorophosphate does not affect the activity of this enzyme in vitro.

Protein synthesis in nuclei isolated from HeLa cells.

Labeled amino acids were incorporated into isolated HeLa cell nuclei in vitro in the presence of a cytoplasmic pH 5 fraction and an energy generating system. Autoradiographically, the label appeared evenly distributed over the nuclei. Comparison of the nuclear and microsomal systems in vitro revealed differences in the ionic requirements for optimum function and in the polyacryl‐amide gel electrophoretic pattern of the proteins being synthesized. The inhibition of the protein synthesizing activity following inhibition of RNA synthesis in HeLa cells was more pronounced in the nuclear than in the microsomal system.

The loss of rapidly labelled ribonucleic acid from isolated HeLa cell nuclei.

1. The loss of nucleic acids and protein from isolated HeLa-cell nuclei was studied. During 4hr. incubation at 37 degrees DNA was conserved, but appreciable amounts of RNA and protein were lost. 2. Two classes of nuclear RNA were distinguished: at least 75% of the RNA was lost from the nuclei relatively slowly through degradation to acid-soluble fragments; the rest of the RNA was lost much more rapidly, not only through degradation to acid-soluble fragments but also through diffusion of RNA out of the nuclei into the incubation medium. 3. The RNA that was preferentially lost was the fraction of nuclear RNA that was rapidly labelled when intact HeLa cells were grown in a medium containing radioactive precursors of RNA. 4. The RNA appearing in the incubation medium was apparently partially degraded and had a sedimentation coefficient of about that of transfer RNA. 5. Both the degradation of RNA and the loss of RNA from the nuclei were sensitive to bivalent cations. Low concentrations of Mg(2+) and Mn(2+) greatly increased the rate of degradation of the rapidly labelled RNA to acid-soluble fragments, and produced a corresponding decrease in the amount of RNA diffusing into the medium. At higher concentrations they suppressed both degradation and diffusion of RNA. The cations Ca(2+), Cu(2+), Zn(2+) and Ni(2+) all progressively inhibited both forms of loss of RNA. 6. Salts of univalent cations produced appreciable effects only at ionic strengths of about 0.2, when degradation to acid-soluble fragments was preferentially inhibited. 7. Both ADP and ATP inhibited loss of RNA at about 30mm. 8. It was concluded that the diffusion of rapidly labelled RNA out of the isolated nuclei was not related to the movement of RNA from nucleus to cytoplasm in vivo, but reflected the ease with which the rapidly labelled RNA detached from the chromatin and the permeability of the membranes of isolated nuclei.

The fine structure of isolated HeLa cell nuclei

Nuclei were isolated from HeLa cells and were examined in the electron microscope. During the isolation procedure which was carried out in a hypotonic solution, swelling of the nuclei occurred and there was a reduction of approximately 30 per cent in their dry mass. This reduction in dry mass was due to a loss of soluble protein. Experiments with radioactive precursors demonstrated that no appreciable amount of nucleic acid was lost. The structures seen in thin sections of the swollen nuclei appeared to be a dispersed system of fine filaments. A statistical analysis of the structures seen in the thin sections was consistent with this interpretation. The swollen nuclei returned to normal size when they were placed in an isotonic solution, but their contents then became severely clumped. Swelling and contraction appeared not to be an osmotic phenomenon since the nuclear membrane of the isolated nuclei was not intact.