DNA polymerase activity from two temperature-sensitive mutants of Rous sarcoma virus is thermolabile

Chemical Sensors using Single-Molecule Electrical Measurements

Driven by the digitization and informatization of contemporary society, electrical sensors are developing toward minimal structure, intelligent function, and high detection resolution. Single-molecule electrical measurement techniques have been proven to be capable of label-free molecular recognition and detection, which opens a new strategy for the design of efficient single-molecule detection sensors. In this review, we outline the main advances and potentials of single-molecule electronics for qualitative identification and recognition assays at the single-molecule level. Strategies for single-molecule electro-sensing and its main applications are reviewed, mainly in the detection of ions, small molecules, oligomers, genetic materials, and proteins. This review summarizes the remaining challenges in the current development of single-molecule electrical sensing and presents some potential perspectives for this field.

The alpha and beta chains of avian retrovirus reverse transcriptase independently expressed in Escherichia coli: characterization of enzymatic activities

Reverse transcriptase of the avian sarcoma and leukosis retroviruses is a heterodimer composed of a 63-kDa alpha and a 95-kDa beta polypeptide chain, both of which are encoded in the pol gene and are produced by proteolytic processing of a larger precursor. We previously constructed a bacterial expression clone of the entire pol coding region that produces a protein 4 kDa larger than the mature viral beta subunit. By use of this clone and synthetic oligonucleotides to introduce stop codons, two derivatives have been constructed: one that directs synthesis of a protein equivalent to the mature beta subunit and the other that directs synthesis of a protein equivalent to alpha subunit. Predicted amino acid sequences of these proteins differ from their viral counterparts only by an initiator methionine that was added to the N termini for expression in Escherichia coli. Both bacterially expressed proteins exhibit reverse transcriptase activity and appear to function as homodimers. The properties of these proteins resemble those of the viral reverse transcriptase heterodimer; however, the bacterially produced alpha dimer protein could be distinguished from the other proteins by its increased sensitivity to heat inactivation, which also has been reported for the corresponding viral product. These results show that correct folding and expression of enzymatic function does not require formation of a precursor. The alpha and beta clones provide a convenient source of individual pol gene products for further evaluation of their roles in the synthesis and integration of retroviral DNA.

Domain structure of the Moloney murine leukemia virus reverse transcriptase: mutational analysis and separate expression of the DNA polymerase and RNase H activities

The reverse transcriptase of Moloney murine leukemia virus, like that of all retroviruses, exhibits a DNA polymerase activity capable of synthesis on RNA or DNA templates and an RNase H activity with specificity for RNA in the form of an RNA.DNA hybrid. We have generated a library of linker insertion mutants of the Moloney murine leukemia virus enzyme expressed in bacteria and assayed these mutants for both enzymatic activities. Those mutations affecting the DNA polymerase activity were clustered in the 5'-proximal two-thirds of the gene, and those affecting RNase H were in the remaining 3' one-third. Based on these maps, plasmids were made that expressed each one of the domains separately; assays of the proteins encoded by these plasmids showed that each domain exhibited only the expected activity.

Neutral proteinases of the human intervertebral disc

Disc tissue consisting of pooled annuli fibrosus and nuclei pulposus from the cadaver of an adolescent aged 19 years was extracted with 4.0 M Gu-HCl. Proteins of low buoyant density (p less than or equal to 1.38 g/ml) containing the disc enzymes and inhibitors were separated from proteoglycans of high buoyant density (p greater than or equal to 1.50 g/ml) by density gradient ultracentrifugation. Sephadex G-75F gel chromatography followed by trypsin affinity chromatography was then used to resolve disc proteolytic and trypsin inhibitory activities. The results obtained were strongly suggestive of the presence of a high molecular weight zymogen which upon activation generated a population of smaller molecular weight proteinases. The disc proteinases obtained by this process showed similar properties in terms of: their pH optima (7.4-7.6); their inhibition patterns by class-specific proteinase inhibitors; their variation of activity as a function of NaCl and lysine concentrations; and the hydrodynamic size of their proteoglycan degradation products. The activated disc neutral proteinase demonstrated many characteristics in common with plasmin; however, unlike the latter, the disc proteinases also showed some calcium dependence.

Differential effects of captan on DNA polymerase and ribonuclease H activities of avian myeloblastosis virus reverse transcriptase

Captan was used as an inhibitor of avian myeloblastosis virus reverse transcriptase to study the polymerase and RNase H catalytic activities. With purified enzyme, RNase H activity was 10-fold more sensitive to captan than was either the DNA-dependent or RNA-dependent DNA polymerase activity. Inhibition of the RNA-dependent polymerase activity could be prevented by dTTP. Conversely, inhibition of this polymerase activity was enhanced by template/primer. The calculated KdTTP of the uninhibited reaction was 5.6 microM. Kinetic studies allow for the proposition of a model for the interaction of captan with the polymerase active center. RNase H activity showed a sigmoidal relationship between activity and substrate concentration. Nuclease activity decreased in Vmax with no change in the Hill coefficient in the presence of captan. Addition of dithiothreitol to the incubation cocktail prevented inhibition by captan of both RNA-dependent polymerase and RNase H activities, suggesting that the (trichloromethyl)thio moiety of captan is involved in the inhibitory action. Captan inhibition suggests the presence of essential amino residues in both polymerase and RNase H active centers.

Requirement of the avian retrovirus pp32 DNA binding protein domain for replication

The NH2-terminal amino acid sequence of the pp32 DNA binding protein has been determined, thus establishing its precise coding region in the polymerase gene of Rous sarcoma virus. Specific mutations were constructed in molecularly cloned Prague A DNA near the NH2- and COOH-termini of pp32 and the effects were assayed by transfection on chick embryo fibroblasts. Out-of-frame deletions at both sites and an in-frame deletion near the NH2 terminus rendered the DNA noninfectious and transformation negative. Single point mutations near the NH2 terminus reduced the transfection efficiency and the rate of virus replication. Biochemical studies indicated that the RNA-directed DNA polymerase and RNase H activities of the mutant viruses were not affected but the processing of the viral beta polypeptide was altered.

Rat liver DNA polymerase-beta: thermal inactivation of RNA- and DNA-dependent activities

Purified DNA polymerase-beta from rat liver was exposed to thermal inactivation and the remaining activities were then measured either with a hybrid template such as poly(A).(dT)12-18 (R-activity) or with a DNA template such as poly(dA).(dT)12-18 (D-activity). Time course of inhibition of R- and D-activities were identical. Neither activity was protected when the thermal treatment was performed in the presence of the template or dNTPs.

Antibody-mediated polysome precipitation as a method for the size determination of viral mRNA species: viral envelope glycoprotein mRNA of avian sarcoma viruses

A method was developed that allows the in situ isolation of viral mRNA, i.e. from polysomes of infected cells. This was achieved by precipitating intact polysomes via their nascent virus polypeptides using virus-specific antibodies. As a model, antibodies to the major envelope glycoprotein (gp85) of avian sarcoma viruses were employed to precipitate those polysomes from infected cells which synthesized the corresponding p70 virus glycoprotein precursor. Normal immunoglobulin and polysomes from uninfected chicken embryo fibroblasts served as controls. The radioactivity labelled mRNA from antibody-precipitated polysomes could subsequently be extracted and characterized for size. It was found that avian sarcoma virus gp85 envelope glycoprotein is predominantly synthesized by a 22--28 s viral mRNA. In addition, minor amounts of gp85-specific mRNAs of 16--21 s and 28--35 s could be demonstrated. The data indicate the presence in polysomes of viral mRNA species coding for i) gp85 only (16--21 s RNA), ii) gp85 and pp60src protein from the adjacent src-gene (22--28 s RNA), and iii) a large viral precursor protein (28--35 s RNA).

Discrimination of DNA polymerase and RNase H activities in reverse transcriptase of avian myeloblastosis virus

The active sites in reverse transcriptase of avian myeloblastosis virus have been selectively modified by various chemical reagents. The DNA polymerase activity is very sensitive to hydrophobic sulfhydryl reagents such as 5,5'-dithiobis(2-nitrobenzoic acid) and p-hydroxymercuribenzoate but resistant to sulfhydryl reagents with hydrophilic properties. The RNase H activity, on the other hand, is resistant to both hydrophobic and hydrophilic sulfhydryl reagents, indicating the absence of cysteinyl residues essential for RNase H activity. N-Ethylmaleimide (NEM), an amino and sulfhydryl group specific reagent, inactivates both DNA polymerase and RNase H, the later activity being fourfold more stable. Polynucleotides, but not nucleotide triphosphates, protect the two enzymatic activites of reverse transcriptase against NEM. Since pretreatment of the enzyme with 5,5' -dithiobis(2-nitrobenzoic acid) does not prevent N-ethylmaleimide from reacting with a residue necessary for DNA polymerase activity, two different reactive groups are probably involved with this enzymatic activity. The pH profile of reverse transcriptase inhibition by N-ethylmaleimide also suggests the involvement of two reactive groups essential for the DNA polymerase activity with apparent pKas of 5.5 and 6.5. Only one reactive group with a pKa of 7.5 is found associated with the RNase H activity.

Immunologic approaches toward detection of type C viral expression in man

Type C RNA viruses have been isolated from a large number of mammalian species. These agents may be horizontally transmitted as infectious cancer-inducing agents, or vertically transmitted from one generation to the next, often in an unexpressed form, within the host genome. To date, the translational products of three viral genes have been identified. With purified virus-coded proteins as probes, sensitive and highly specific radioimmunologic assays have been developed for the detection of antibodies and antigens related to the known type C viruses. These techniques have proved valuable in sero-epidemiologic studies of the horizontally transmitted oncogenic viruses of cats, cattle, and gibbons, and have been used to detect translational products of endogenous viruses in tissues of species from which complete virus has yet to be isolated. This review describes the application of radioimmunoassays in the search for immunologic evidence of type C virus expression in man.

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.

Specific binding of the type C viral core protein p12 with purified viral RNA

The major viral phosphoproteins (p12) of the Rauscher murine leukemia virus (R-MuLV) and the simian sarcoma-associated virus (SSAV) bind in vitro to their homologous 70S and 35S viral RNAs. Using purified 32P-labeled RNA and 125I-labeled p12 protein, complexes that are stabilized by formaldehyde-cross-linking can be readily detected after velocity gradient centrifugation. The in vitro reconstructed ribonucleoprotein complexes are seen only with p12 proteins incubated with viral RNAs isolated from the same type C viruses; no such complexes form with heterologous protein-RNA mixtures. Homologous but not heterologous p12 molecules compete with radiolabeled p12 protein for the specific viral RNA binding sites. The competition assay permits the detection of 10 ng of viral p12 protein. The major internal protein of type C viruses (p30) does not bind to viral RNA using identical assay conditions. From the specific activities of the radiolabeled components and also by equilibrium sedimentation analysis, we estimate that fewer than 15 molecules of p12 protein bind to each molecule of viral RNA. Both the specificity and stoichiometry of the p12-RNA interactions suggest that these RNA tumor virus proteins have a regulatory role in cells.

A quantitative comparison between in vivo-and in vitro-derived Friend leukemia virus

The biological activities of RNA viruses derived from Friend leukemia cells in culture (TCV) were compared with those of viruses derived from the plasma (PV) of mice infected with Friend leukemia virus (FLV). The comparison was quantitatively based on the actual number of viruses used in each experiment as determined by counting under the electron microscope. Electron microscopy also provided a qualitative assessment of the structural integrity of the concentrated virus particles used in various bioassays. The data shows that the leukemogenic and spleen-focus-forming (SFF) activities of TCV, although demonstrable, are respectively 10(5) and 10(4) lower than those of PV. Moreover, TCV has 10(4) less helper activity (S+L- test) than PV. The level of reverse transcriptase activity is ten times lower in TCV than in PV which indicates that there is little correlation between polymerase activity and the other biological activities measured. The decreased biological activity of the in vitro grown virus is thought to be intrinsic to this type of virus although all extrinsic factors have not been ruled out.

RNA processing and RNA tumor virus origin and evolution

The results of molecular hybridization experiments with high-molecular-weight RNA isolated from RNA tumor viruses and DNA from normal cells suggest that RNA tumor virus genomes originate from cell genes. Some RNA tumor viruses (here called class 1) appear to have been generated in recent times in that their RNA is closely related in nucleotide sequence to certain cell genes (class 1 genes). A second class of RNA tumor viruses (here called class 2) is more distantly related to genomic information of normal cells. Structural properties of the RNA of RNA tumor viruses lead us to propose that the tumor virus RNA is originated when RNA transcripts of class 1 genes are processed by a mechanism we call "paraprocessing." We postulate that RNA paraprocessing is normally used only at particular times during differentiation and is characterized by the cytoplasmic appearance of high-molecular-weight RNA chains containing terminal polyadenylic acid (200 residues). Paraprocessing of class 1 gene transcripts in committed or differentiated cells is considered to be aberrant in transcription that can lead to the generation of an RNA tumor virus genome. If the paraprocessed class 1 gene transcript codes for a reverse transcriptase, replication of the RNA becomes possible. Transfer of the replicating RNA to a new cell can result in genetic change such that the virus genome mutates, differing from the original progenitor genes. We propose that this genetic change causes class 1 viruses to become class 2. These ideas are applied to evidence concerning the biology of infection of RNA tumor viruses and concerning the involvement of RNA tumor viruses in human cancer. Genetic change can also occur during the origination of an RNA tumor virus genome by repeated reverse transcription and recombination (45) or by genetic alteration of particularly changeable cell genes ("hot spots") (43).