Examination of newly synthesized DNA in Escherichia coli.

Summary The short (0-20S) Okazaki fragments seen upon pulse-labeling E. coli (thy ⁺, deo ⁺) with ³H-thymidine are actually composed of three types of DNA fragments: (1) true replication intermediates, (2) post-replication repair fragments (such as those which arise subsequent to the removal of misincorporated uracil), and (3) chromosomal fragments. Our experiments show that the number of pulse-labeled fragments decreases slightly with the introduction of the ung-1 mutation into E. coli K-12 (dut ⁺, thyl ⁺, polA ⁺), and that there are fewer fragments found in E. coli B/r than in E. coli K-12 ung-1. This suggests that while some fraction of pulse-labeled fragments may be due to repair, this fraction can vary among different strains; moreover, the majority of fragments appear to be replication intermediates. Selfhybridization (reannealing) of pulse-labeled fragments from E. coli B/r show that these fragments are asymmetric with respect to the strand origin and with respect to their size: the smaller (3-8S) fragments come from only one of the parental strands, whereas the larger (13-20S) fragments are synthesized equally from both parental strands. We interpret our results to mean that replication can be discontinuous on both strands but asymmetric with respect to both the size of the fragments and the size of the discontinuous region on the two strands.     

Conservation and progressive methylation of Epstein-Barr viral DNA sequences in transformed cells.

The structure of intracellular viral DNA from a number of cell lines arising by clonal transformation of human lymphocytes in vitro with Epstein-Barr virus was analyzed. Intracellular viral DNAs were partially purified and digested with several restriction endonucleases, and the products of digestion were separated by electrophoresis in agarose gels. The viral fragments were detected by transferring the DNA from the gel to nitrocellulose sheets, hybridizing radiolabeled recombinant vectors carrying fragments of viral DNA to those transfers, and visualizing the hybrids by autoradiography. These analyses indicated that: (i) regions of repetitious viral DNA do undergo expansion and contraction although one size predominates; (ii) novel sequence arrangements appear in the intracellular viral DNA of different clones but are not found in clones analyzed serially and propagated extensively; (iii) the viral DNA is increasingly methylated upon cell propagation. We have not identified a transformed cell phenotype or a viral phenotype that segregates with the observed progressive methylation. We have not detected in Epstein-Barr viral plasmids analogs of the gross rearrangements of viral DNAs observed after lytic infections with high multiplicities of papova-, adeno-, or herpes simplex viruses.     

Unintegrated viral DNA is synthesized in the cytoplasm of avian sarcoma virus-transformed duck cells by viral DNA polymerase.

We have examined the location, structure, and mechanism of synthesis of unintegrated viral DNA present in fully transformed cultures of avian sarcoma virus-infected duck cells. De novo synthesis of the unintegrated forms several weeks after the initial infection was documented by labeling unintegrated DNA in both strands with 5-bromodeoxyuridine. The unintegrated DNA is synthesized in, and probably confined to, the cytoplasm, and it consists of duplexes of short "plus" strands (ca. 0.5 X 10(6) to 1.0 X 10(6) daltons) and "minus" strands the length of a subunit of the viral genome (ca. 2.5 X 10(6) to 3.0 X 10(6) daltons). The structure of the duplex and the mode of incorporation of density label support the hypothesis that the unintegrated DNA is synthesized from an RNA templated by virus-coded DNA polymerase.     

Mechanisms of infection with Epstein-Barr virus. I. Viral DNA replication and formation of noninfectious virus particles in superinfected Raji cells.

Human lymphoblastoid Raji cells, which do not produce virus, supported replication of Epstein-Barr virus (EBV) upon superinfection. Early antigen, viral capsid antigen, and virions were produced in Raji cells superinfected with EBV. Viral DNA replicated under complete inhibition of host cell DNA synthesis to the extent that a few micrograms of EBV DNA were recovered from 107 superinfected Raji cells, corresponding to 5,000 viral genomes/cell. Homology of the synthesized viral DNA to parental EBV DNA was more than 90%. Virions produced by the Raji cells contained a 55S DNA but failed to induce early antigen, viral capsid antigen, and viral DNA synthesis after a second superinfection of Raji cells.     

Excretion of newly synthesized DNA by tonsil lymphocytes.

The main part of newly synthesized DNA is preferentially released in vitro both by non-stimulated or phytohemagglutinin-stimulated tonsil lymphocytes. Freshly isolated cells excrete DNA faster than phytohemagglutinin-stimulated ones. The acid-precipitable 3H-thymidine lost can be accounted for in the culture medium as labeled, double stranded DNA isolated on hydroxyapatite column.     

Defective viral DNA in Epstein-Barr virus-associated oral hairy leukoplakia.

Defective Epstein-Barr virus (EBV) has a deleted and rearranged genome (termed het DNA) that disrupts latency and induces standard EBV to replicate in vitro. We used the polymerase chain reaction to detect, in 2 of 10 patient samples, the junction of abnormally juxtaposed EBV DNA fragments BamHI W and Z, a genomic rearrangement responsible for the biologic activity of het DNA. By sequence analysis, the junction in wild-type defective DNA appears to be similar but not identical to the recombination in the DNA of laboratory strain P3HR-1. The presence of this marker for het DNA in the epithelial lesions of two patients suggests a role for defective EBV in a human pathologic process.     

Significance of dimers to the size of newly synthesized DNA in UV-irradiated Chinese hamster ovary cells.

DNA synthesized after UV irradiation is smaller than that in unirradiated cells even when pulse-labeling times are increased to compensate for the overall reduction in the rate of DNA replication. By isolating newly replicated DNA, incubating it with dimer-specific endonuclease from Micrococcus luteus, and analyzing it on alkaline sucrose gradients, we have been able to demonstrate that this DNA is synthesized in segments corresponding in size to the interdimer distance on the parental strand. In addition, the same DNA analyzed on neutral gradients shows no reduction in molecular weight as a result of UV irradiation and/or endonuclease digestion. Our data are thus inconsistent with the presence of "gaps" in newly synthesized DNA opposite the dimers on the parental strand. We suggest that if such gaps are produced as a result of delayed synthesis around dimers, they are filled before the growing point reaches the next dimer.     

Destiny of 5-methylcystosine of newly synthesized DNA fraction in bone marrow cells]

Methylation kinetics of newly formed DNA in bone marrow cell culture of animals and healthy humans was studied in order to investigate the role of DNA methylation in proliferation and differentiation of hematopoietic cells. Synthesis of a DNA fraction with extremely high cytosine methylation level was observed under the incubation of cells with 14C-orotic acid for 0.5-1 hour. Long-term incubation (3 and more hours) with 14C-orotic acid resulted in a rapid decrease of 5-methylcytosine radioactivity and in an increase of thymine radioactivity. Elimination of 14C-orotate from the medium and inhibition of DNA synthesis with hydroxyurea did not change kinetics of the radioactivity content in 5-methylcytosine and thymine in newly synthesized DNA. No synthesis of hypermethylated DNA fraction was observed under incubation of cells with preformed pyrimidine precursors.     

Integrated viral DNA sequences in Epstein-Barr virus-converted human lymphoma lines.

Most human lymphoid cell lines contain multiple copies of circular, nonintegrated Epstein-Barr virus (EBV) DNA molecules as well as viral DNA sequences with properties of integrated DNA. The physical state of the EBV DNA in a human lymphoma line that only contains one virus genome equivalent per cell has now been studied by three different methods, neutral CsCl density gradient centrifugation, actinomycin D-CsCl gradient centrifugation, and Hirt fractionation. This cell line, AW-Ramos, has been obtained by EBV infection in vitro of the apparently EBV-negative Ramos lymphoma line. The results indicate that the EBV DNA in AW-Ramos is present exclusively in a linearly integrated form. Similar data were obtained with two other EBV-converted sublines of Ramos cells.     

Epstein-Barr virus DNA. IX. Variation among viral DNAs from producer and nonproducer infected cells.

A comparative analysis of three Epstein-Barr virus DNAs from American patients with infectious mononucleosis (B95-8, Cherry, and Lamont) and four Epstein-Barr virus DNAs from African patients with Burkitt lymphoma (AG876, W91, Raji, and P3HR-1) indicated that the usual format of Epstein-Barr virus DNA includes a variable number of direct repeats of a 0.35 X 10(6)-dalton sequence (TR) at both ends of the DNA, a 9 X 10(6)-dalton sequence of largely unique DNA (Us), a variable number of repeats of a 2 X 10(6)-dalton sequence (IR), and a 89 X 10(6)-dalton sequence of largely unique DNA (UL). Within UL there was homology between DNA at 26 X 10(6) to 28 X 10(6) daltons and DNA at 93 X 10(6) to 95 X 10(6) daltons. The relative sequence order (TR, US, IR, UL, TR) did not vary among "standard" Epstein-Barr virus DNA molecules of each isolate. B95-8 DNA had an unusual deletion extending from 91 X 10(6) to 100 X 10(6) daltons, and P3HR-1 DNA had an unusual deletion extending from 23.5 X 10(6) to 26 X 10(6) daltons. There was sufficient variability among the EcoRI and BamHI fragments of the DNAs to identify each isolate specifically. However, we discerned no distinguishing features for the two geographic or pathogenic origins of the seven isolates. Three intracellular DNAs (Raji, Lamont, and Cherry) and one virion DNA (P3HR-1) were heterogenous in molecular organization and had subpopulations of rearranged or defective molecules. Some regions, particularly 59 X 10(6) to 63 X 10(6) daltons and sequences around TR, frequently participated in rearrangements. Restriction endonuclease maps of the standard and rearranged DNAs of the seven isolates are presented.     

Dissociation of newly synthesized Sendai viral proteins from the cytoplasmic surface of isolated plasma membranes of infected cells.

The interaction of Sendai viral proteins with the membranes of infected cells during budding of progeny virions was studied. BHK cells infected with Sendai virus were labeled with [35S]methionine, and the plasma membranes were purified on polycationic polyacrylamide beads. The isolated membranes were incubated with various agents which perturb protein structure to dissociate viral proteins from the membranes. Incubation of membranes with thiocyanate and guanidine removed both the M and nucleocapsid proteins. Urea (6 M) removed the nucleocapsid proteins but removed M protein only in the presence of 0.1 or 1.0 M KCl. In contrast, high salt concentrations alone eluted only the M protein, leaving the nucleocapsid proteins completely membrane bound. About 65% of the M protein was eluted in the presence of 4 M KCl. The remaining membrane-associated M protein was resistant to further extraction by 4 M KCl. Thus, M protein forms two types of interaction with the membrane, one of them being a more extensive association with the membrane than the other.     

Effect of the arginine analog canavanine on the synthesis of Epstein-Barr virus-induced proteins in superinfected Raji cells.

The addition of canavanine to cultures of superinfected Raji cells in the absence of arginine prevented the appearance of early antigens as defined by immunofluorescent staining. Addition of various amounts of arginine permitted the identification of at least three groups of proteins, each responding differently to the various concentrations of arginine-canavanine.