HeLa Nuclei Research Articles

Nuclear antigens in the HeLa cell cycle.

Antisera to 0.35 M NaCl extracts and residues of S phase HeLa nuclei were reacted with electrophoretically separated proteins from the nuclei or nuclear material of HeLa cells synchronized in G1, S, G2 or M phases of the cell cycle. Quantitative evaluation of the peroxidase-antiperoxidase stained nitrocellulose transfers (Western blots) revealed significant changes in the quantities of nuclear non-histone proteins during the cell cycle. Immunochemical staining of electrophoretically separated nuclear antigens permits their selective detection in minute quantities and in the presence of many additional proteins.

Characterization of a ribonuclease-sensitive nucleoside triphosphatase activity from HeLa nuclei

Approximately one-third of the total ATP-hydrolysis activity in isolated HeLa nuclei is sensitive to RNAase (ribonuclease). This activity is selectively extracted with pulse-labelled RNA. In the extracts it co-sediments with various particles with sedimentation coefficients from 10S to 50S, but especially with 24S and 40S particles. ATP hydrolysis by the isolated particles was inhibited extensively (greater than 80%) by RNAase A, heparin and 0.2 M-NaCl. The activity of RNAase-treated particles was recovered when poly(A) was added, but not when DNA was added. The isolated particles exhibited RNAase-sensitive hydrolysis activities for dATP, GTP, CTP and UTP as well as for ATP, and the UTPase activity in the extracts showed nearly the same sedimentation distribution as the ATPase activity. When samples of isolated particles were irradiated with u.v. light in the presence of [alpha-32P]ATP, a 39 kDa polypeptide with a broad distribution from 10S to 50S like that of the ATPase and a 55 kDa polypeptide with a sharp distribution at 24S were photolabelled. Taken together, the data suggest that ATP-hydrolysis activity found in nuclear ribonucleoprotein subfractions appears to be the result of one or two RNA-dependent NTPases that are normally associated with endogenous RNA in a wide variety of particles.

Further characterization and subcellular localization of Sm and Ul ribonucleoprotein antigens

Sera from patients with systemic autoimmune diseases often contain antibodies against small nuclear ribonucleoprotein (snRNP) particles. Anti-Sm antibodies react with the entire set of U1, U2, U4, U5 and U6 (U1-U6) RNP particles whereas anti-(U1)RNP sera specifically recognize particles containing U1 RNA. Here we performed semi-quantitative immunoblotting using 16 human anti-Sm, 15 human anti-(U1)RNP sera and two mouse monoclonal antibodies to establish which snRNA-associated proteins carry antigenic determinants. Almost every (15/16) human anti-Sm sera recognized epitopes present on a 28-kDa (B/B') protein doublet and on a 16-kDa (D) polypeptide. Nine anti-(U1)RNP sera also recognized the B/B' doublet, but in all cases a much stronger reaction was observed with one or more of the specifically U1 RNA-associated 70 kDa, A or C antigens. With affinity-purified antibody fractions eluted from individual antigen bands on nitrocellulose blots it is shown that the anti-Sm-reactive polypeptides B/B' and D contain common epitopes. We also report the finding of one human anti-Sm serum with exclusive specificity for the B/B' doublet and a mouse monoclonal anti-Sm antibody recognizing only the D protein, indicating that these antigens also carry unique epitopes. In immunoprecipitation assays, purified anti-B/B' and -D antibodies react with (U1-U6) RNP while purified anti-70 kDa, anti-A and anti-C antibodies precipitate exclusively U1 RNP particles. Finally, we established the subcellular localization of Sm and U1 RNP antigens using a biochemical cell fractionation procedure. Part of the 70 kDa and B/B' antigens were found in a nuclease and high salt-resistant nuclear substructure, usually referred to as nuclear matrix, while the A and D antigens could be extracted completely from HeLa nuclei by ribonuclease treatment and subsequent high salt extraction.

RBC-mediated microinjection of chromatin components into cultured mammalian cells.

Radiolabeled DNA fragments or nuclear proteins were encapsulated within human erythrocytes, and the erythrocytes were then fused with cultured mammalian cells using Sendai virus. Autoradiography revealed that 125I-labeled DNA fragments remained dispersed in the cytoplasm and disappeared with a half-life of 24 hours. In contrast, the nuclear proteins, HMG1, HMG2, HMG17 and histone H1, rapidly localized within HeLa nuclei and exhibited half lives greater than 80 hours. Several biochemical criteria indicate that the association of the injected nuclear proteins with chromatin faithfully mimics the behavior of their endogenous counterparts.

Protein-primed replication of plasmids containing the terminus of the adenovirus genome. I. Characterization of an in vitro DNA replication system dependent on adenoviral DNA sequences.

An in vitro system which replicates plasmid DNA containing the replication origin of adenovirus DNA has been established. Replication of plasmid pLA1 DNA, which contains the left-hand terminus (0-9.4 map units) of adenovirus serotype 5 DNA but which lacks the 55,000-dalton terminal protein, is initiated by a protein-primed mechanism in a manner similar to that found with adenovirus DNA. Initiation of DNA replication using plasmid pLA1 as a template requires (i) that the cloned adenovirus sequence be present at the terminus of a linearized (form III) DNA molecule ( Tamanoi , F., and Stillman , B. W. (1982) Proc. Natl. Acad. Sci. U. S. A., 79, 2221-2225; van Bergen, B. G. M., van der Ley , P. A., van Driel , W., van Mansfield , A. D. M., and van der Vliet , P. A. (1983) Nucleic Acid Res. 11, 1975-1979), and (ii) the presence of the 80,000-dalton precursor to the 55,000-dalton terminal protein and the adenovirus coded DNA-dependent DNA polymerase. In the presence of the four deoxy-nucleoside triphosphates, the preterminal protein, the adenovirus coded DNA binding protein, and an extract prepared from uninfected HeLa nuclei, the adenovirus DNA polymerase can elongate the preterminal-protein dCMP initiation complex formed on pLA1 DNA to full length (6.6 kilobase) DNA molecules. These results suggest that the 55,000-dalton terminal protein covalently linked to the 5' termini of adenovirus DNA is not essential for the replication of this DNA.

Protein-primed replication of plasmids containing the terminus of the adenovirus genome. II. Purification and characterization of a host protein required for the replication of DNA templates devoid of the terminal protein.

A host protein, which is required for the replication of a plasmid DNA (pLA1), has been purified from extracts of uninfected HeLa nuclei. This plasmid DNA contains the origin of adenovirus DNA replication but lacks the 55,000-dalton terminal proteins. The purified host protein has been designated factor pL. Factor pL is essential for the initiation of DNA replication of EcoRI-digested pLA1 DNA, which proceeds via the formation of a covalent complex between the 80,000-dalton adenovirus coded preterminal protein and 5' dCMP. Factor pL has been purified approximately 120-fold to greater than 75% homogeneity. It is a heat labile and N-ethylmaleimide-sensitive protein with a native Mr = 39,000 (+/- 2,000). Initiation of DNA replication using EcoRI-digested pLA1 DNA as the template requires the 80,000-dalton preterminal protein and the 140,000-dalton adenovirus DNA polymerase, in addition to factor pL, and is stimulated as much as 10-fold by nuclear factor I ( Nagata , K., Guggenheimer , R. A., Enomoto , T., Lichy , J. H., and Hurwitz , J. (1982) Proc. Natl. Acad. Sci. U. S. A. 79, 6438-6442). Factor pL has no effect on in vitro DNA replication when adenovirus DNA covalently linked to the 55,000-dalton terminal protein is used as the template, however the replication of adenovirus DNA treated with Pronase, becomes totally dependent upon the addition of factor pL.

Human anticentromere antibodies: Distribution, characterization of antigens, and effect on microtubule organization

Properties of human anticentromere autoantibodies were analyzed. In intact cells or isolated cell fractions, these sera stain the centromeres of mitotic chromosomes and discrete speckles (prekinetochores) in nuclei. Staining is also retained in matrix preparations from nuclei or chromosomes. Immunoprecipitation or immunoblotting demonstrates protein antigens of 14, 20, 23, and 34 kd in HeLa nuclei and chromosomes; immunoprecipitates of nuclei also contain a protein of 15.5 kd. Matrix preparations contain only the 20, 23, and 34 kd species. Absorption of the anticentromere serum with any one of the four nuclear antigens immobilized on nitrocellulose is sufficient to eliminate centromere staining. Using a lysed cell model for microtubule nucleation, anticentromere sera are shown to inhibit specifically the organization of microtubules at the kinetochore.

Crosslinking of chromosomal proteins to DNA in HeLa cells by UV, gamma radiation and some antitumor drugs

Immunochemical techniques were used to investigate the protein-DNA crosslinking by ultraviolet (UV) and gamma radiation as well as 1,3-bis-(2-chloroethyl)-1-nitrosourea (BCNU) or cis- and trans-diamminedichloroplatinum II (cis-DDP and trans-DDP). Antisera to 0.35 M NaCl extract and 0.35 M NaCl residue of HeLa nuclei were employed. Both gamma and UV irradiation, exposure to cis- or trans-DDP and, to a lesser extent, BCNU, resulted in crosslinking of various antigens to the DNA. Although several antigens were crosslinked by all the employed agents, other exhibited agent-specific crosslinking patterns.

Intracellular distribution and degradation of immunoglobulin G and immunoglobulin G fragments injected into HeLa cells.

Intact rabbit immunoglobulin G molecules (IgGs) and their papain or pepsin fragments were radio-iodinated and injected into HeLa cells. Whole IgGs, Fab2, and Fc fragments were degraded with half-lives of 60-90 h, whereas half-lives of Fab fragments were 110 h. These results indicate that proteolytic cleavage in the hinge region of the IgG molecule is not the rate-limiting step in its intracellular degradation. The hingeless human myeloma protein, Mcg, was degraded at the same rate as bulk human IgG, providing further evidence that the proteolytically susceptible hinge region is not important for intracellular degradation of IgG molecules. SDS acrylamide gel analysis of injected rabbit IgG molecules revealed that heavy and light chains were degraded at the same rate. Injected rabbit IgGs and rabbit IgG fragments were also examined on isoelectric focusing gels. Fab, Fab2, and Fc fragments were degraded without any correlation with respect to isoelectric point. Positively charged rabbit IgGs disappeared more rapidly than their negative counterparts, contrary to the trend reported for normal intracellular proteins. The isoelectric points of two mouse monoclonal antibodies were essentially unchanged after injection into HeLa cells, suggesting that the altered isoelectric profile observed for intact rabbit IgG resulted from degradation and not protein modification. The intracellular distributions of IgG fragments and intact rabbit IgG molecules were determined by autoradiography of thin sections through injected cells. Intact IgG molecules were excluded from HeLa nuclei whereas both Fab and Fc fragments readily entered them. Thus, for some proteins, entry into the nuclear compartment is determined primarily by size.

Acetylation and calcium-dependent phosphorylation of histone H3 in nuclei from butyrate-treated HeLa cells.

In HeLa nuclei, 1 microM Ca2+ stimulates 3-fold the phosphorylation of histone H3. Prior treatment of cells with Na butyrate increases the degree of H3 phosphorylation and reveals a correlation between the extents of H3 acetylation and phosphorylation. Acetylation of H3 increases its accessibility to the calcium-dependent kinase. Phosphorylation of H3 occurs at a serine residue located in the trypsin-sensitive region of the protein. Brief digestion of nuclei with DNase I preferentially releases the phosphorylated form of H3 from chromatin.

Association of eukaryotic DNA topoisomerase I with nucleosomes and chromosomal proteins.

A DNA topoisomerase activity is found to be associated with the nucleosomes released by the Staphylococcal nuclease digestion of HeLa nuclei. Such an association is found to be salt dependent. A number of criteria have established that this DNA topoisomerase activity is due to HeLa topo I (Liu, L. F. and Miller, K. G. (1980) Proc. Natl. Acad. Sci. USA 78, 3489-3491). A similar association has been demonstrated from the in vitro studies using purified mononucleosomes and eukaryotic DNA topoisomerase I. Nonhistone HMG proteins and histone H1 are found to stimulate topoisomerase activity in vitro and form tight complexes with eukaryotic DNA topoisomerase I. The intimate interactions of topoisomerase I with chromosomal proteins and nucleosomes may be an essential feature of the topoisomerase function in vivo.

Cross-linking of Nuclear Antigens to DNA in HeLa Cells

Publisher Summary This chapter reports an investigation of protein–DNA cross-linking by ultra-violet (UV) and irradiation, as well as by 1,3-bis(chloroethyl)-l-nitrosoure (BCNU) and cisplatin, to identify and characterize these specific protein–DNA complexes. Two antisera were employed in these experiments, one to a 0.35 M NaCl extract of HeLa nuclei and another to the residual, 0.35 M NaC1-washed nuclei. Control and treated nuclei were dissociated in 2% sodium dodecyl sulfate and then subjected to extensive ultracentrifugation. The DNA pellets, after sonication, were electrophoresed on polyacrylamide gels in NaDodSO 4 . Electrophoretically separated proteins were transferred to nitrocellulose sheets and the individual antigens were visualized by incubation with appropriate antisera, followed by peroxidaseantiperoxidase staining. UV irradiation and exposure to cisplatin and, to a lesser extent, BCNU resulted in the cross-linking of a selected group of antigens to the DNA. Although several antigens were cross-linked by all the agents employed, others exhibited agent-specific cross-linking patterns. Cisplatin was most potent because it cross-linked almost all the protein antigens detectable by the antisera in untreated, undissociated nuclei. Moreover, there were distinct differences among cross-linked proteins detectable by the two antisera. This indicated that not only the tightly DNA-bound, but also more easily extracted protein antigens could be cross-linked to DNA. Thus, radiation and chemical crosslinking of antigenic proteins to DNA followed by their immunochemical detection can be used to probe chromatin structure and functions.

Effects of the adenovirus H5t s125 and H5 ts107 DNA binding proteins on DNA replication in Vitro

Genetic and biochemical studies of adenovirus (Ad) DNA synthesis in vitro demonstrate that the Ad DNA binding protein (Ad DBP) is not necessary for the initiation of Ad DNA synthesis but is required for chain elongation. The DBP, which enhances early elongation to the 26th deoxynucleotide by approximately two- to fourfold, is absolutely required as chain elongation proceeds further. Ad DNA synthesis was assayed in a system requiring Ad DNA covalently linked at each 5′ terminus to a protein (Ad DNA-pro), various fractions of Ad-infected cytoplasm, and an extract of uninfected Hela nuclei. Initiation of Ad DNA replication was measured by the formation of a covalent complex between the 80,000 dalton preterminal protein (pTP) and 5′ dCMP. DNA binding proteins from two ts mutants, H5 ts125 and H5 ts107, have been purified and shown to be functional at 30° but inactive at 38° in an in vitro elongation system dependent on purified proteins. Chymotryptic cleavage of the 72K wild-type Ad2 DBP produces a 34K carboxyl terminal fragment which retains full activity in the in vitro elongation of Ad DNA.

Nuclear shearing and chromatin structure

Disruption of HeLa nuclei by sonication under mild conditions (up to 60 sec) does not alter the repeating subunit structure of the micrococcal nuclease digested chromatin DNA, but sonication greater than 60 sec does. Moreover, purified chromatin obtained from sonicated nuclei, or by the nuclease digestion procedure of Noll et al 1975, exhibits the same nuclease digestion pattern. In contrast, chromatin prepared by mechanical shearing, used conventionally for solubilizing chromatin, does not reveal the subunit structure. Furthermore, electron microscopy reveals that the beaded morphology of chromatin strands is maintained in mildly sonicated nuclei. Similarly, nucleosomes can be visualized in chromatin isolated from nuclear sonicates.

NMN adenylyltransferase: its association with chromatin and with poly(ADP-ribose) polymerase.

The nuclear location of NMN adenylytransferase, which catalyses the formation of NAD and pyrophosphate from ATP and NMN, has been examined to ascertain if the enzyme is bound to the domains of chromatin which undergo poly(ADP-ribos)ylation. This latter reaction utilizes much of the cellular NAD. A radioisotope assay using [alpha-32P]ATP was developed to enable precise measurement of picomole amounts of NAD. With this assay, it appeared that the reaction catalysed by NMN adenylyltransferase proceeded with a rapid, early 'burst' of NAD before steady-state velocities were established. From this it was calculated that there could be 10- active sites of NMN adenylyltransferase per HeLa nucleus in asynchronously growing cells: that is, approximately one per 10-20 nucleosomes. Very little enzyme activity was liberated by digesting HeLa nuclei with micrococcal nuclease in 80 mM NaCl, and the enzyme which was solubilized was not bound to oligonucleosomes separated by electrophoresis on polyacrylamide gels. In contrast, poly(ADP-ribose) polymerase activity was clearly demonstrated on these particles. The enzyme was readily liberated by DNase I digestion, especially when the digestion was carried out in low-ionic-strength buffer. The results demonstrated that the enzyme was neither bound to oligonucleosomes nor part of the nuclear envelope or matrix. Preliminary results suggested that there could be some direct channelling of NAD between the two enzymes in intact nuclei. It appears that NMN adenylyltransferase is bound within rather than to chromatin.

Small nuclear ribonucleoprotein complexes of Drosophila melanogaster.

We report here on the isolation and characterization of small nuclear ribonucleoproteins (snRNPs) and corresponding small nuclear RNA (snRNA) species from nuclei of Drosophila melanogaster. Velocity sedimentation in sucrose gradients was used to partially fractionate the RNPs; analysis of fractions so obtained suggests that, in general, one snRNP contains one snRNA. At least 11 species of snRNA are present in Drosophila nuclei; among them we identify a potential mammalian U1 homolog based on sequence homology. Autoimmune antiserum designated anti-Sm from patients with systemic lupus erythematosus recognizes nuclear antigens in Drosophila and precipitates seven species of snRNPs. The antigens in HeLa and Drosophila nuclei recognized by anti-Sm antibodies have been identified and compared. Anti-Sm antibodies at least bind to a 26,000-dalton polypeptide in HeLa extracts and to two polypeptides, one of 18,000 daltons and one of 26,000 daltons, in Drosophila extracts. This suggests that the 26,000-dalton polypeptide is an evolutionarily conserved antigenic component of Drosophila and HeLa snRNPs.

Conjugation of ubiquitin to denatured hemoglobin is proportional to the rate of hemoglobin degradation in HeLa cells.

Ubiquitin was radioiodinated and introduced into HeLa cells by the erythrocyte-mediated fusion procedure. Fractionation of injected HeLa cells and subsequent NaDodSO4/polyacrylamide gel electrophoresis showed that HeLa nuclei contained two major labeled proteins: ubiquitin and the histone H2A-ubiquitin conjugate, protein A24. HeLa cytosol contained ubiquitin and a series of ubiquitin-protein conjugates of diverse molecular weights. When injected HeLa cells were treated with phenylhydrazine to denature the cotransferred hemoglobin, a series of prominent ubiquitin-globin conjugates appeared. The identity of these conjugates was established by microinjection experiments in which both proteins were labeled. At low doses of phenylhydrazine, the intracellular concentration of globin-ubiquitin conjugates was proportional to the rate of hemoglobin degradation. This result, together with the observation that ubiquitin conjugation to globin is markedly enhanced by phenylhydrazine-induced denaturation of hemoglobin, provides support for the hypothesis that the covalent attachment of ubiquitin to proteins signals proteolysis.

Specific stimulation of alpha-amanitin-sensitive RNA synthesis in isolated HeLa nuclei by methyl mercury.

Methyl mercury has previously been shown to inhibit DNA and RNA synthesis in intact HeLa cells (Gruenwedel, D. W., and Cruikshank, M. K. (1979) Biochem. Pharmacol. 28, 651-655). Its effect on nucleic acid synthesis in vitro in isolated nuclei has now been investigated. DNA synthesis in nuclei was inhibited by methyl mercury; 50% inhibition was obtained with a concentration of 8 microM, compared to approximately 30 microM which is required in vivo. In contrast, RNA synthesis in HeLa nuclei was stimulated by methyl mercury. This stimulation is specific for alpha-amanitin-sensitive RNA synthesis (catalyzed by RNA polymerase II); in contrast, alpha-amanitin-resistant synthesis (catalyzed by polymerases I and III) was inhibited. Transcription of calf thymus DNA by solubilized RNA polymerases was inhibited by ethyl mercury. However, if the enzymes were preincubated with the DNA prior to addition of the methyl mercury, subsequent synthesis by RNA polymerase II was stimulated, whereas the inhibition of the other enzymes was unaffected. The most likely explanation for these results is that methyl mercury specifically stimulates chain elongation by RNA polymerase II whereas it inhibits elongation by polymerases I and III, and initiation by all three enzymes.

Influence of Heat on the Chromatin Structure in HeLa Nuclei

HeLa cells were heated at 450C for 30 min, their nuclei were removed, and their chromatin was digested with either micrococcal nuclease or DNase I. Comparison with results from unheated cells that were handled similarly indicated that no change in the basic chromatin structure occurred after heating. The types and quantities of the proteins released from the internucleosomal and core region of the chromatin from heated cells were identical to those released from unheated cells. Most of the additional protein bound in the nucleus during heating appeared to be located with a structure, the nucleoskeleton, comprising the nuclear matrix, nuclear envelope, and its associated DNA. Although the exact nature and location of the additional protein are still unknown, we suggest that even small quantities of any protein located near or at the DNA-nuclear matrix and/or DNA-nuclear envelope attachment sites could be very critical for maintaining the functional and reproductive integrity of a cell with or without subsequent damage from other cytotoxic agents.

Evidence for two levels of DNA folding in histone-depleted HeLa interphase nuclei

The long-range order of the DNA in interphase nuclei was investigated by sedimentation studies. From these studies, two discreet sedimentation forms have been characterized for histone-depleted HeLa nuclei. Type I structures, obtained by extraction of isolated nuclei with a buffer containing 2 m-NaCl, have an s value of 18,000 S. Histone-depletion with the polyanions dextran sulfate/heparin produces slightly slower type I structures of 15,000 S. When the thiols, β-mercaptoethanol or dithiothreitol, or the metal chelators, 1,10-phenanthroline or neocuproine, are included during histone extraction, the interphase DNA is further unfolded, generating type II structures of 8500 S. Both forms are destroyed by proteolytic agents, but are insensitive to RNAase A. Fluorescence studies of type I and type II structures show that both retain the spherical shape of nuclei, with type II structures having a more expanded DNA halo than that of type I. It is suggested that metalloprotein interactions are important in one level of the DNA folding of type I structures, since the chelators 1,10-phenanthroline and neocuproine bring about formation of type II structures. Metal-depleted nuclei, prepared in buffers containing β-mercaptoethanol, provide a means for identifying the metal involved. Such nuclei generate type II structures upon histone-depletion. Addition of as little as 1 × 10 −6 m-CuSO 4 or 1 × 10 −6 m-CaCl 2 to metal-depleted nuclei restores the capacity to generate type I structures. The restoration of the type I complex is reversible following exposure of nuclei to CuSO 4, but is irreversible after CaCl 2 treatment. These experiments suggest that one level of DNA compaction in histone-depleted nuclei is stabilized by either Cu or Ca.