Purification and detection of reverse transcriptase in viruses and cells

High throughput detection of retrovirus-associated reverse transcriptase using an improved fluorescent product enhanced reverse transcriptase assay and its comparison to conventional detection methods

The development and application of a novel, sensitive TaqMan fluorescent probe-based product enhanced RT test (F-PERT) for the detection of retrovirus are described. The assay allows discrimination between the amplification signals generated by genuine positive signals that result from retroviral RT activity and the RT-like activity from DNA polymerases. The RT-like activity from DNA polymerases was suppressed by the addition of activated calf-thymus DNA with no reduction in the RT activity. A linear relationship between threshold cycle (C(T)) and the number of virus particles was demonstrated, allowing quantification of retroviruses in unknown samples. The F-PERT assay was able to detect a wide range of retroviral RT activities, including that from porcine endogenous retrovirus (PoERV), murine leukaemia virus (MLV), simian foamy virus (SFV), simian immunodeficiency virus (SIVmac) and squirrel monkey retrovirus (SMRV). The detection limit of SMRV, MLV and PoERV was approximately 100 virion particles and the test was able to detect at least 10(2) molecules of purified RT enzyme. RT activity was not detected in cellular lysates and supernatants from MRC-5, BT, VERO, or Raji cells, whereas RT activity was detected in C1271, Mus dunni, K-Balb, BHK-21, CHO-K1, SP2/0-Ag14 and NSO cell supernatants. RT activity was also detected in the Spodoptera cell line Sf9.

Detection of human immunodeficiency virus and other retroviruses in cell culture supernatants by a reverse transcriptase microassay

A micromethod for the detection of human immunodeficiency virus (HIV) and other retroviruses in cell culture supernatants is described which applies a DEAE ion exchanger for recovery of polynucleotides synthesized in vitro by the retroviral reverse transcriptase. Cell culture, sample preparation, and test performance including the washing step are adapted to microtitre plates. Compared to the standard method this technique produced less non-specific reactions, resulting in a more than 3-fold higher sensitivity, a higher reproducibility due to lower intrarun variations and allowed an increase in the daily sample accomplishment per person 3- to 4-fold at lower costs per sample.

Transformation-defective Rous sarcoma virus mutants with altered p19 of the gag gene and their inhibitory effect on host cell growth

Mutants (PH2010, PH2011, PH2012) of Rous sarcoma virus which have a growth-inhibitory effect on chicken embryo fibroblasts were isolated from a temperature-sensitive mutant of the Schmidt-Ruppin strain of Rous sarcoma virus (tsNY68). The growth rate of fibroblasts infected with these viruses was about 50 to 60% of that of uninfected fibroblasts. A morphological difference between mutant-infected and uninfected fibroblasts was observed at logarithmic phase but not at stationary phase. Neither the protein p60src nor its associated protein kinase activity was significantly detected by an immunoprecipitation assay in the cells infected with these mutants. Analysis of the unintegrated DNA of the mutant PH2010 showed that a sequence of about 1.4 kilobase pairs at the src gene region is deleted. Further examination of the viral structural proteins in infected cells as well as in virions by immunoprecipitation and peptide mapping revealed that the molecular size of the Pr76 gag protein of the mutant RSV is smaller than that of the mutant tsNY68 because of partial deletion at the p19 gag gene. The peptide maps suggest that the deleted region of the altered p19 of the mutant is near the carboxy terminal of p19. The amount of Prgp92env synthesized in the mutant-infected cells was about fivefold more than that in tsNY68-infected cells.

Enzyme inhibition VI: Inhibition of reverse transcriptase activity by protoberberine alkaloids and structure-activity relationships

Protoberberine alkaloids such as palmatine (I), 13-methylpalmatine iodide (II), 2,3-methylenedioxy-10,11-dimethoxy-13-methylprotoberberine iodide (III), 2,3-methylenedioxy-9,10-dimethoxy-13-methylprotoberberine chloride (IV), and berberine (V) showed inhibition of reverse transcriptase activity of RNA tumor viruses in the presence of polyriboadenylic acid-oligodeoxythymidylic acid (VI), polydeoxyadenylic acid-oligodeoxythymidylic acid (VII), activated calf thymus deoxyribonucleic acid (IX), and 70S ribonucleic acid (X), but not in the presence of polyribocytidylic acid-oligodeoxyguanylic acid (VIII). These results indicated that the alkaloids caused inhibition of the enzyme activity by interacting with the template primer, particularly of the adenine-thymine base pair. Furthermore, the alkaloids competed with the template primer-binding site of the enzyme. The time course inhibition indicated that the alkaloids stopped the DNA synthesis instantly when added after the initiation of polymerization processes. Inhibition of reverse transcriptase activity was correlated with the structure and antileukemic activity of the protoberberine alkaloids.

Inhibition of reverse transcriptases by seminalplasmin

Seminalplasmin, an antibacterial protein present in bovine seminal plasma, is shown to be a potent inhibitor of reverse transcriptases (RNA-dependent DNA nucleotidyltransferases). Seminalplasmin inhibits RNA-directed, hybrid-directed, and DNA-directed DNA-polymerizing activities of purified reverse transcriptase from avian myeloblastosis virus and from crude viral lysates of several retroviruses by binding to the enzyme, at least in the case of avian myeloblastosis virus. Seminalplasmin does not inhibit significantly DNA synthesis either by Escherichia coli DNA polymerase I, or a mammalian alpha-DNA polymerase. The presence of seminalplasmin in the seminal fluid could provide protection to the male and/or the female reproductive tract against retroviruses.

Insulin gene expression during development of the fetal bovine pancreas

Poly(A+) RNA was isolated from the bovine pancreas at three stages of fetal development. Approximately 1% of the total RNA from first, second, and third trimester fetuses was polyadenylated, and the mean chain length of each RNA population was 1350 nucleotides. In cell-free protein synthesis experiments the concentration of insulin-immunoreactive translation products was 10.2%, 11.3%, and 9.7% for first, second, and third trimesters, respectively. Insulin mRNA sequences were estimated by transcription of insulin mRNA to [3H]cDNA and hybridization of cDNA with plasmid pI19 DNA containing rat proinsulin I sequences. Hybridization experiments gave insulin mRNA concentrations of 7.6%, 12.9%, and 3.9% for first, second, and third trimesters, respectively. These results show that insulin mRNA levels vary during development and become proportionally lower in third trimester, when the exocrine tissue is rapidly increasing in mass.

Stimulation of growth rate of chondrocytes by Rous sarcoma virus is not coordinated with other expressions of the src gene phenotype

Infection and transformation of chondrocytes by Rous sarcoma viruses (RSVs) (Schmidt-Ruppin, Prague) stimulated the rate of cell growth. In contrast, several transformation-defective (td) mutants (tdPRA, tdNY105, tdNY106, tdNY107, and tdNY108) retaining various sizes of the src gene did not stimulate cell growth, indicating that the stimulation of growth of chondrocytes is due to the function of the src gene. With the use of various T (transformation)-class temperature-sensitive (ts) mutants of RSV, growth stimulation of chondrocytes by the src gene was examined. It was found that there are two types of T-class ts mutants with regard to the stimulatory effect on the growth of chondrocytes. One type (tsNY68) stimulates cell growth at both permissive (36 degrees C) and nonpermissive (41.5 degrees C) temperature, as does the wild type of RSV. Another type (ts GI201 [clone 9]) stimulates cell growth only at the permissive temperature. Chondrocytes infected with either of these two types of T-class ts mutants showed ts properties in other transformation markers, such as uptake of 2-deoxy-D-glucose, change of cell morphology, and focus formation. These data indicate that the effect of the src gene on cell growth does not occur coordinately with other transformation markers.

In vitro gene fusions that join an enzymatically active beta-galactosidase segment to amino-terminal fragments of exogenous proteins: Escherichia coli plasmid vectors for the detection and cloning of translational initiation signals

We report the construction and use of a series of plasmid vectors suitable for the detection and cloning of translational control signals and 5' coding sequences of exogenously derived genes. In these plasmids, the first eight codons of the amino-terminal end of the lactose operon beta-galactosidase gene, lacZ, were removed, and unique BamHI, EcoRI, and SmaI (XmaI) endonuclease cleavage sites were incorporated adjacent to the eighth codon of lacZ. Introduction of deoxyribonucleic acid fragments containing appropriate regulatory signals and 5' coding sequences into such lac fusion plasmids led to the production of hybrid proteins consisting of the carboxyl-terminal segment of a beta-galactosidase remnant plus a peptide fragment that contained the amino-terminal amino acids encoded by the exogenous deoxyribonucleic acid sequence. These hybrid peptides retained beta-galactosidase enzymatic activity and yielded a Lac+ phenotype. Such hybrid proteins are useful for purifying peptide sequences encoded by exogenous deoxyribonucleic acid fragments and for studies relating the structure and function of specific peptide segments.

RNA-dependent DNA polymerase of an endogenous type C virus of mice: purification and partial characterization

An RNA-dependent DNA polymerase was isolated from purified virions of endogenous oncornaviruses released by the MOPC-315 murine myeloma cell line. Upon sodium dodecyl sulfate-polyacrylamide gel electrophoresis, the purified enzyme was found to consist of two major polypeptides with molecular weights of about 28,000 and 26,500. The active enzyme had a molecular weight of approximately 56,000, as calculated from its sedimentation on glycerol density gradients, indicating that it is probably a dimer of the two subunit polypeptides. The isolated MOPC-315 virus polymerase exhibited all three activities known to be found in the DNA polymerase from oncornaviruses, namely, an RNA-dependent DNA polymerase, a DNA-dependent DNA polymerase, and an RNase H. The RNA-dependent polymerase activity showed a prounced preference for Mn2+ over Mg2+, whereas the DNA-dependent and RNase H reactions were catalyzed by these two cations to an almost equal extent. The purified polymerase was found to be immunologically related to the polymerase of Rauscher murine leukemia virus.

The effect of nitrofurantoin on deoxyribonucleic acid synthesis in plant mitochondria

Nitrofurantoin (1-([(5-nitrofuran-2-yl)methylene]amino)imidazolidine-2,4-dione), a widely used drug and also a well-known bacterial mutagen, inhibits DNA synthesis in mitochondria from 48 h etiolated seedlings of Vigna sinensis (Linn.) Savi (snake bean). The effect appears at the level of the uptake of radioactive deoxynucleoside triphosphates by the plant mitochondria. Nitrofurantoin does not inhibit DNA synthesis in vitro by homogeneous Escherichia coli DNA polymerase I and DNA polymerase from avian-myeloblastosis virus. No specific nitroreductase activity could be detected in mitochondria.

Sub-cellular distribution of the cytoplasmic myosin heavy chain mRNA during myogenesis

In the light of earlier work [1] which demonstrated the presence of a large number of myosin heavy chain (MHC) transcripts in chick myoblasts prior to cell fusion and the burst of MHC synthesis it was of great interest to determine the subcellular localization of the still inactive transcripts. It has been determined in differentiating muscle cells in culture. Two populations of cells were examined -- monucleated myoblasts just prior to cell fusion and myotubes where at least 80% of the cells were fused. Utilizing a myosin complementary DNA (cDNA) probe [2] it is observed that just prior to cell fusion, when the "burst" of myosin synthesis has not yet occurred, the vast majority of cytoplasmic myosin mRNA transcripts are found in a stored messenger RNA protein complex with a minimal amount found in the heavy polysome fraction. In differentiated myotube cultures, when myosin synthesis is progressing at a high rate, the reverse is found, i.e, the amount of stored myosin messenger RNA (mRNA) is minimal while the largest amount of myosin mRNA transcripts are localized in the polysome fraction. The number of total cytoplasmic myosin transcripts is found to decrease after cell fusion at a time when myosin synthesis is maximal suggesting that the efficiency of translation of myosin mRNA increases during terminal differentiation.

beta-Lapachone, an inhibitor of oncornavirus reverse transcriptase and eukaryotic DNA polymerase-alpha. Inhibitory effect, thiol dependence and specificity

beta-Lapachone is a naturally occuring compound that can be isolated from a number of tropical trees. It is shown to be a potent inhibitor of reverse transcriptase activity from both avian myeloblastosis virus and Rauscher murine leukaemia virus. In addition, it affects eukaryotic DNA-dependent DNA polymerase-alpha activity: 50% inhibition is reached in 60-min incubation time by about 8 micron beta-lapachone. Enzyme activity is inhibited irrespective of the purity of the enzyme used or of the amount or type of template/primer or substrate present. The inhibitory effect of the drug is only observed in the presence of dithiothreitol. The primary site of action of beta-lapachone appears to be the enzyme protein, as is also borne out by the specificity of its action. Eukaryotic DNA-dependent DNA polymerase-beta, prokaryotic DNA-dependent DNA polymerase I, several other nucleic acid polymerases and some completely unrelated enzymes are not affected. Reverse transcriptase and DNA-dependent DNA polymerase-alpha may be in someway related in possessing similarly exposed '--SH structures' in their active sites. beta-lapachone thus affords a novel means of studying such interrelationships and of further characterizing enzymes.

Quantification of myosin heavy-chain mRNA during myogenesis

Complementary DNA (cDNA) was synthesized from a 26-S poly(A)-containing RNA fraction consisting predominately of myosin mRNA, and used to quantitate the amounts of myosin mRNA during development. RNA . cDNAmyosin hybridizations were performed with RNA isolated from tertiary cultures of chick fibroblasts, and the proportion of myosin RNA determined. The levels of myosin RNA present in primary chick myoblast cultures undergoing development were also analyzed by RNA . cDNAmyosin hybridizations. Correlation of these values with the rate of myosin heavy chain synthesis indicates that myosin mRNA is subject to post-transcriptional or translational control.

Frequency distribution of messenger sequences within polysomal mRNA and nuclear RNA from rat liver

DNA complementary to polysomal poly(A)-containing mRNA (cDNA) of male rat liver was used to study the diversity of messenger sequences in the nucleus and in polysomes. 1. Hybridization of cDNA against an excess of its own polysomal mRNA template revealed that about 10,000 different mRNA species are expressed in the liver tissue. They are distributed in a wide frequency range derived from approximately 0.5% of the total genome. 2. Hybridization of the cDNA against total nuclear RNA shows that messenger sequences comprise less than 1% of the mass of total nuclear RNA. Messenger sequences have a different frequency distribution in nucleus and cytoplasm. 3. In hybridizations using cDNA, which had been fractionated into sequences representing abundant and scarce polysomal mRNA molecules, it was found that although abundant cytoplasmic messenger sequences are also abundant in the nucleus, they exist in a significantly lower frequency range in the nuclear compartment.

Infidelity of DNA synthesis as related to mutagenesis and carcinogenesis

An assay system has been developed for measuring the fidelity of DNA synthesis in vitro by using synthetic polynucleotide templates and purified DNA polymerases. Nearest-neighbor analysis of the synthesized product indicates that noncomplementary nucleotides are incorporated as single base substitutions. The accuracy of DNA synthesis can be decreased by (1) prior alkylation of the template, (2) increasing the relative concentration of incorrect nucleotides, and (3) addition of specific metal salts to the reaction mixture. As an initial evaluation of the utility of this system, the effects of 31 metal salts on the fidelity of DNA synthesis have been determined. The results indicate that potential metal mutagens and/or carcinogens may be detected by measuring alterations in the fidelity of DNA synthesis.

Chemical modification of DNA polymerase phosphoprotein from avian myeloblastosis virus

Fractionation of purified avian myeloblastosis virus DNA polymerase, after phosphorylation in vitro, revealed the presence of a small acidic proten, a phosphate acceptor polypeptide with high specific activity. Its presence in the phosphorylated form with the polymerase resulted in as much as a 10-fold increase in the rate of DNA synthesis. Its presence in the dephosphorylated form with the polymerase had no effect in the rate of DNA synthesis.

Organization of sequences of avian globin mRNA

Formamide polyacrylamide gel electrophoresis shows that chicken globin mRNA contains about 6.50 nucleotides, and since only 435 of these code for globin, a further 215 are not translated, and their function and position are not known. This work has produced the following conclusions. 1. 45-50 of these untranslated nucleotides are present as poly (A) at the 3' terminus. 2. The 3' untranslated region of chicken globin mRNA is at least 90 nucleotides in length. This minimal estimate is based on data derived from hybridization of defined lenghts of chicken globin cDNA to rabbit globin mRNA. The percentage of avian globin cDNA sequences which hybridize to rabbit globin mRNA is directly proportional to the length of the cDNA in each case. This relationship holds for lengths of cDNA from 115 up to 620 nucleotides. The low percentage homology for short cDNA molecules is not due to their being short per se. In homologous mRNA excess hybridizations (chicken cDNA/chicken mRNA), all cDNA preparations were completely protected from S1 nuclease digestion. 3. It is probable that there is greater evolutionary divergence in the 3' untranslated region of chicken and rabbit globin mRNA when compared with the coding regions of these molecules; The combined data is sued to formulate a regional map of chicken globin mRNA,

Infidelity of DNA synthesis in vitro: screening for potential metal mutagens or carcinogens

Thirty-one metal salts have been tested for their ability to affect the accuracy of DNA synthesis in vitro. All ten salts of metal carcinogens decreased the fidelity of DNA synthesis. Of the three metals which beforehand were considered to be possible mutagens or carcinogens, only one decreased fidelity. In contrast, 17 noncarcinogenic metal salts did not affect fidelity even when present at concentrations that were clearly inhibitory.

Poly rC-oligo dG specific template activity of mouse viral DNA polymerase detected by isoelectric focusing

An acid fraction from polyacrylamide gel isoelectric focusing contained only DNA polymerase template activity for (rC)n-(dG)12-18 with little or no activity with (rA)n-(dT)12-18. A factor which stimulated (rC)n-(dG) 12-18 activity was also detected in low molecular weight fractions from G-100 Sephadex chromatography of the purified enzyme. Since (rC)n-(dG)12-18 acitivty is thought to be descriptive of viral DNA polymerase, this stimulation is proposed to be significant for the regulation and specificity of viral DNA synthesis.

Presence of messenger specifying sequences in the DNA of chromatin subunits

Messenger-specifying sequences in subunits of human lymphocyte chromatin were detected by hybridization of DNA complementary to cytoplasmic polyadenylylated RNA with DNA isolated from the subunits. Comparison of the kinetics and extents of hybridization of complementary DNA with chromatin subunit DNA and with nuclear DNA showed that most of the repetitive sequences and single copy sequences in mRNA are present in chromatin subunits. This result indicates that inclusion of a DNA sequence into the subunit does not prevent its transcription in vivo.