Effect of viral RNase H on the avian sarcoma viral genome during early transcription in vitro

Abortive reverse transcription by mutants of Moloney murine leukemia virus deficient in the reverse transcriptase-associated RNase H function

The reverse transcriptase enzymes of retroviruses are multifunctional proteins containing both DNA polymerase activity and a nuclease activity, termed RNase H, specific for RNA in RNA-DNA hybrid form. To determine the role of RNase H activity in retroviral replication, we constructed a series of mutant genomes of Moloney murine leukemia virus that encoded reverse transcriptase enzymes that were specifically altered to retain polymerase function but lack RNase H activity. The mutant genomes were all replication defective. Analysis of in vitro reverse transcription reactions carried out by mutant virions showed that minus-strand strong-stop DNA was formed but did not efficiently translocate to the 3' end of the genome; rather, the DNA was stably retained in RNA-DNA hybrid form. Plus-strand strong-stop DNA was not detected. These results suggest that RNase H normally promotes strong-stop translocation, perhaps by exposing single-stranded DNA sequences for base pairing. Four new DNA species were also detected among the reaction products. Analysis of these DNAs suggested that they were minus-strand DNAs formed from VL30 RNAs encoded by the mouse genome. We suggest that reverse transcriptase can initiate DNA synthesis at any one of four alternate tRNA primer-binding sites near the 5' ends of VL30 RNAs.

A single-stranded gap in human immunodeficiency virus unintegrated linear DNA defined by a central copy of the polypurine tract

The structure of unintegrated human immunodeficiency virus type 1 (HIV-1) DNA from acutely infected human lymphoid cells was analyzed by nuclease S1 cleavage. We observed a unique, discrete single-stranded gap in unintegrated linear DNA molecules, located near the center of the genome. Oligonucleotide primer extension experiments determined that the downstream limit of this gap coincides with the last nucleotide of a central copy of the polypurine tract found in all sequenced lentivirus genomes. Other retroviruses have only one copy of the polypurine tract at the 5' boundary of the 3' long terminal repeat, which has been shown to determine initiation of retroviral DNA plus-strand synthesis. We conclude from our observations that the central repeat of the polypurine tract can create an additional site for plus-strand synthesis initiation in lentiviruses. The central single-stranded gap was not found in circular DNA molecules, the vast majority of them carrying only one long terminal repeat. This finding suggests that the generation of such circular molecules is associated with early DNA ligation events.

Ribonucleases H of retroviral and cellular origin

Ribonucleases H (RNases H) are enzymes which catalyse the hydrolysis of the RNA-strand of an RNA-DNA hybrid. Retroviral reverse transcriptases possess RNase H activity in addition to their RNA- as well as DNA-dependent DNA-polymerizing activity. These enzymes transcribe the viral single stranded RNA-genome into double stranded DNA, which then can be handled by the host cell like one of its own genes. Various, sometimes highly repeated, sequences related to retroviruses and like these encompassing two separate domains, one of which potentially codes for a DNA polymerizing, the other for an RNase H activity, are found in genomes of uninfected cells. In addition proteins coded for by cellular genes (e.g. from E. coli and from yeast) are known, which exhibit RNase H activity, the biological function of which is not fully understood. In the light of these facts the question of whether retroviral RNases H could be promising targets for antiviral drugs is discussed.

Inhibition of human immunodeficiency virus type 1 RNase H by sulfated polyanions

The reverse transcriptase (RT) activity of human immunodeficiency virus type 1 and other retroviruses is closely associated with a hybrid-degrading RNase H activity which is essential for retroviral replication. We have analyzed the effect of sulfated polysaccharides on human immunodeficiency virus type 1 recombinant RT and RNase H activities in vitro. Heparin, dextran sulfates, and xylan polysulfate were found to be much more potent inhibitors of RNase H than of RT and exhibit 50% infective doses of 0.04 to 0.1 micrograms/ml (corresponding to 0.1 to 25 nM) which is up to 5,000-fold more efficient than that for RT. Inhibitors of RNase H activity are attractive as antiviral drugs.

The role of Moloney murine leukemia virus RNase H activity in the formation of plus-strand primers

On the basis of earlier studies with both detergent-disrupted virions (the endogenous reaction) and an in vitro reconstructed reaction, the RNase H activity associated with Moloney murine leukemia virus reverse transcriptase has been implicated in the generation of plus-strand RNA primers during reverse transcription. Here we used an oligonucleotide extension assay to show that the RNA primers remaining bound to the plus DNA strands initiated at the normal origin in the in vitro reaction are heterogeneous in length. This result indicates that, although a precise cleavage generates the 3' end of the priming RNA, RNase H exhibits less specificity at other break sites. During the endogenous reaction, a kinetic analysis of the synthesis of plus strands corresponding to different regions of the genome suggested that additional sites for the initiation of plus-strand DNA existed upstream of the normal origin. Direct analysis of fragments produced in the endogenous reaction, as well as in the in vitro reaction, confirmed the existence of upstream plus-strand initiation sites. Several of these sites were mapped to the nucleotide level by the oligonucleotide extension method. A comparison of the nucleotide sequences surrounding the upstream initiation sites with the sequence at the normal plus-strand origin revealed common features, which suggests a mechanism for plus-strand priming based on sequence recognition by the RNase H/reverse transcriptase protein. Although primer removal by RNase H is highly efficient for DNA fragments initiated at the normal origin, the RNA primers were inefficiently removed from the fragments initiated at the upstream sites. This result suggests that primer removal, like primer generation, involves sequence recognition by the enzyme.

RNase H-mediated release of the retrovirus RNA polyadenylate tail during reverse transcription

By examining enzymatic reactions in vitro, we found that an early event during reverse transcription of the avian myeloblastosis virus RNA genome is the release of the 3' polyadenylate tail from the viral RNA template. By using specially constructed molecules containing minus-strand, strong-stop DNA and the 3' end of the viral RNA genome, we found that the reverse transcriptase-associated RNase H is responsible for the endonucleolytic release of polyadenylate.

RNA-primed initiation of Moloney murine leukemia virus plus strands by reverse transcriptase in vitro

A 190-base-pair DNA-RNA hybrid containing the Moloney murine leukemia virus origin of plus-strand DNA synthesis was constructed and used as a source of template-primer for the reverse transcriptase in vitro. Synthesis was shown to initiate precisely at the known plus-strand origin. The observation that some of the origin fragments retained ribonucleotide residues on their 5' ends suggests that the primer for chain initiation is an RNA molecule left behind by RNase H during the degradation of the RNA moiety of the DNA-RNA hybrid. If the RNase H is responsible for creating the correct primer terminus, then it must possess a specific endonucleolytic activity capable of recognizing the sequence in the RNA where plus strands are initiated. The 16-base RNase A-resistant fragment which spans the plus-strand origin can also serve as a source of the specific plus-strand primer RNA. Evidence is presented that some of the plus-strand origin fragments synthesized in the endogenous reaction contain 5' ribonucleotides, suggesting that specific RNA primers for plus-strand initiation may be generated during reverse transcription in vivo as well.

Mechanism of RNA primer removal by the RNase H activity of avian myeloblastosis virus reverse transcriptase

The single-stranded DNA containing the Moloney murine leukemia virus origin for plus-strand synthesis was cloned in M13mp2 and used as a template for avian myeloblastosis virus reverse transcriptase in the presence of Moloney RNA which had been treated with pancreatic RNase A. The RNA pieces containing the polypurine stretch near the plus-strand origin were processed, presumably by RNase H, to generate primers for DNA synthesis which initiated both at the correct origin site and at one nucleotide downstream from the correct site. Approximately 50% of the labeled DNA fragments synthesized under these conditions retained the priming RNA on their 5' ends. When the isolated fragments were hybridized back to the template DNA and again treated with the reverse transcriptase, all of the RNA was removed from the labeled DNA. By using 5'-end-labeled pancreatic RNase A-resistant fragments, it was possible to show that the RNA primers were removed intact. It appears from these results that the RNase H activity associated with the enzyme shows a preference for cutting at the junction between the RNA and DNA moieties of such complexes and therefore is ideally suited for removing RNA primers.

Duplex DNA binding activity of the avian myeloblastosis virus DNA polymerase

Purified avian myeloblastosis virus DNA polymerase has a strong binding affinity for closed circular double-stranded DNA with no 3'-hydroxy termini. Because of this affinity the DNA polymerase can retain labeled native ColE1 DNA on nitrocellulose filters. When the reaction contains four enzyme molecules per ColE1 molecule about 50% of the DNA is retained. Higher enzyme: DNA ratios cause retention of nearly 100% of the DNA. The binding activity comigrates with DNA synthetic activity through ion-exchange chromatography and glycerol gradient centrifugation, in indication that it is an intrinsic activity of the DNA polymerase. Escherichia coli DNA polymerase I and bacteriophage T4 DNA polymerase do not show this binding activity, which suggests that it is not a common property of DNA polymerases. A novel application of enzyme kinetics using endonuclease-treated DNA reveals the relative quantities of enzyme molecules which are synthesizing at 3'-termini vs. molecules bound to double-stranded regions. Heat stability measurements indicate that the polymerizing activity of the enzyme can be almost completely eliminated while about half of the original binding activity is retained.

Viral DNA synthesized in vitro by avian retrovirus particles permeabilized with melittin. I. Kinetics of synthesis and size of minus- and plus-strand transcripts

We have examined the kinetics of synthesis of minus [(-)]- and plus [(+)]-strand viral DNA in melittin-permeabilized avian retrovirus particles. The reaction was biphasic. There was a very rapid initial rate, followed, after approximately 1 h, by a lower rate. Many discrete bands of subgenomic-length (-) strands were produced after 10 and 20 min of synthesis; genome-length (7.7-kilobase [kb]) (-) strands were detected within 30 min. Extension to an 8.0-kb (-)-strand species was evident by 60 min. This extension was inhibited by actinomycin D. Synthesis of (+) strands (which is also inhibited by actinomycin D) began early, before any (-) strands were completed, and continued for more than 4 h beyond the time when synthesis of full-length DNA had terminated. Two distinct species of (+)-strand DNA, 0.27 and 0.35 kb, could be observed at the earliest times. Their presence was quickly obscured by subsequent formation of (+)-strand molecules of molecular length between 0.2 and 2.0 kb.

Effect of actinomycin D on nucleic acid hybridization: the cause of erroneous DNA elongation during DNA synthesis of RNA tumor viruses in vitro

Actinomycin D, known for its suppression of cellular RNA synthesis and for the reduction of the rate of synthesis of double-stranded DNA by the RNA tumor virus RNA-dependent DNA polymerase, was found to interact with single-stranded DNA in such a way as to inhibit DNA . DNA and DNA . RNA hybridizations. This finding is discussed in the light of the observation that DNA elongation during DNA synthesis of RNA tumor viruses is blocked in vitro in the presence of actinomycin D. It thus supports the model that hybridization is a necessary step during RNA tumor virus DNA synthesis.

Two species of full-length cDNA are synthesized in high yield by melittin-treated avian retrovirus particles

A method of activating endogenous cDNA synthesis in avian retroviruses that results in the formation of two species of full-length cDNA in high yield is described. Tests of biological activity show infectivity of at least the same order of magnitude as for full-length cDNA made by other procedures. Melittin, the major component of bee venom, is used as an alternative to nonionic detergents to make the viral envelope permeable and thus activate the endogenous RNA-dependent DNA polymerase. This compound is a toxic peptide known to interact with phospholipid membranes. It appears to be less disruptive to the viral structure than detergents, resulting in a more efficient transcription of the viral genome. Preliminary tests indicate that this method will also prove useful for studying enzymatic activities associated with other enveloped viruses.

Structure of murine sarcoma virus DNA replicative intermediates synthesized in vitro

Moloney murine sarcoma virions synthesize discrete DNA products in vitro which closely resemble those found in vivo shortly after infection. These in vitro products have been isolated by electrophoresis and mapped with restriction endonucleases. In addition to the full-genome-length 6-kilobase pair linear DNA, a 5.4-kilobase pair circular DNA molecule, an incomplete linear DNA molecule, and a 600-base pair molecule were detected. The 6-kilobase pair DNA contained a 600-base pair direct terminal repeat which was missing from the circular form and was partially represented on the incomplete linear DNA molecule. The 600-base pair DNA contained sequences which were present in the 600-base pair direct repeat on the 6-kilobase pair DNA. The order of synthesis and the structure of these molecules detected in the in vitro reaction suggest that they are crucial intermediates in the formation of the final product of in vitro reverse transcription. A model which accounts for the synthesis of all of these molecules during the initial stages of viral replication is suggested.