Direct proof of the 5' to 3' transcriptional jump during reverse transcription of the avian retrovirus genome by DNA sequencing

Pausing by retroviral DNA polymerases promotes strand transfer from internal regions of RNA donor templates to homopolymeric acceptor templates

We have examined the ability of reverse transcriptases (RT) to catalyze strand transfer from internal regions of RNA templates, resulting in switching of a primer from one template to another. To study this phenomenon, we employed a system of donor and acceptor templates in which homologous strand transfer can occur from a homopolymeric sequence, positioned internally on the donor template. Our results indicate that reverse transcriptases from human immunodeficiency virus (HIV), avian myeloblastosis virus (AMV), and murine leukemia virus (MuLV) are all able to catalyze strand transfer from this sequence. Catalysis of this reaction is not dependent upon ribonuclease H (RNase H) activity, since an RNase H-deficient form of HIV-RT is able to catalyze the reaction efficiently. Additionally, N-ethylmaleimide, which inhibits RNase H but not polymerase activity, did not inhibit the template switching by either the native or RNase H-deficient forms of HIV-RT. Our data further indicate that template switching may be promoted by RT pausing at a specific site on the donor template. Conditions that increase RT pausing at this site also increase template switching. These results suggest that transient RT pausing at specific sites on the viral genome during reverse transcription may promote template switches that in turn lead to recombination.

Activation of the cellular src gene by transducing retrovirus

Newly isolated strains of avian sarcoma virus, S1 and S2, were shown to have the transduced cellular src gene as their viral transforming gene (Yamagishi et al., Virology 137:266-275, 1984). In this work, the S1 and S2 genomes were molecularly cloned, and the junction sequences between the viral genomes and the c-src genes and the complete nucleotide sequences of the v-src genes transduced in these viruses were determined. Data on the junction sequences suggested that 5' recombination had occurred between the 5'-noncoding region of c-src and the 5' region of the gag sequence encoding p19 in both viruses and that 3' recombination had occurred in the last coding exon of c-src with either the middle portion of the env sequence encoding gp85 for S1 or the 3' portion of pol coding for reverse transcriptase for S2. Comparison of the amino acid sequences of the S1 and S2 src products deduced from the nucleotide sequences (pp62S1-src and pp62S2-src with that of c-src protein (pp60c-src) indicated that in pp62S1-src the 8 carboxy-terminal amino acid residues of the total of 533 in pp60c-src are replaced by 43 residues translated from the env sequence at the wrong frame. In pp62S2-src, on the other hand, the 14 carboxy-terminal amino acids of pp60c-src are replaced by the 38 carboxy-terminal residues of reverse transcriptase. The mechanism of c-src transduction and the structural changes necessary for pp60c-src activation are discussed.

Activation of the cellular src gene by transducing retrovirus

Newly isolated strains of avian sarcoma virus, S1 and S2, were shown to have the transduced cellular src gene as their viral transforming gene (Yamagishi et al., Virology 137:266-275, 1984). In this work, the S1 and S2 genomes were molecularly cloned, and the junction sequences between the viral genomes and the c-src genes and the complete nucleotide sequences of the v-src genes transduced in these viruses were determined. Data on the junction sequences suggested that 5' recombination had occurred between the 5'-noncoding region of c-src and the 5' region of the gag sequence encoding p19 in both viruses and that 3' recombination had occurred in the last coding exon of c-src with either the middle portion of the env sequence encoding gp85 for S1 or the 3' portion of pol coding for reverse transcriptase for S2. Comparison of the amino acid sequences of the S1 and S2 src products deduced from the nucleotide sequences (pp62S1-src and pp62S2-src with that of c-src protein (pp60c-src) indicated that in pp62S1-src the 8 carboxy-terminal amino acid residues of the total of 533 in pp60c-src are replaced by 43 residues translated from the env sequence at the wrong frame. In pp62S2-src, on the other hand, the 14 carboxy-terminal amino acids of pp60c-src are replaced by the 38 carboxy-terminal residues of reverse transcriptase. The mechanism of c-src transduction and the structural changes necessary for pp60c-src activation are discussed.

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.

Involvement of retrovirus reverse transcriptase-associated RNase H in the initiation of strong-stop (+) DNA synthesis and the generation of the long terminal repeat

Reconstructed enzymatic reactions containing purified reverse transcriptase and defined analog substrates which mimic those purported to be natural substances for reverse transcription in vivo were employed to delineate the mechanism of strong-stop (+) DNA synthesis. Our analysis of this system has indicated that strong-stop (+) DNA synthesis is initiated after the introduction of a nick in the viral RNA genome between a polypurine sequence and an inverted repeat that represents the end of the long terminal repeat. Since inhibitors of the reverse transcriptase-associated RNase H activity prevent the introduction of the nick and the synthesis of strong-stop (+) DNA synthesis, it appears that this particular reverse transcriptase-associated enzymatic activity is responsible for the initiation of strong-stop (+) DNA. Our data also indicated that the RNase H activity creates a second nick in the viral RNA genome 11 nucleotides upstream from the strong-stop (+) DNA initiation site since the strong-stop (+) DNA synthesized in these reactions is covalently linked to an oligoribonucleotide 11 residues in length. Nucleotide sequence analysis of the oligoribonucleotide primer molecule indicated that a single homogenous oligomer was associated with strong-stop (+) DNA exhibiting the sequence rArGrGrGrArGrGrGrGrGrA. The oligoribonucleotide primer can be removed from strong-stop (+) DNA by the purified reverse transcriptase, which creates a nick at the junction between the primer and strong-stop (+) DNA. These data demonstrate that the initiation of strong-stop (+) DNA synthesis is mediated by RNase H and that the site of initiation is exactly at the end of the long terminal repeat, providing evidence for yet another function of this reverse transcriptase-associated enzymatic activity in the synthesis of retrovirus DNA.

Evidence for involvement of an RNA primer in initiation of strong-stop plus DNA synthesis during reverse transcription in vitro

Employing enzymatic reactions in vitro, we have identified the presence of oligoribonucleotides at the 5' end of strong-stop plus [(+)] DNA. Similar results were obtained whether the strong-stop (+) DNA was synthesized by preparations of detergent-disrupted avian sarcoma virus or reconstructed reactions containing purified reverse transcriptase and a template that mimics the purported natural template for strong-stop (+) DNA synthesis. The latter reactions provide a system to delineate more precisely the discrete requirements necessary for the initiation and synthesis of this species of (+) DNA.

Mechanism of release of the avian rotavirus tRNATrp primer molecule from viral DNA by ribonuclease H during reverse transcription

Employing enzymatic reactions containing reverse transcriptase and appropriately defined substrates, we have demonstrated that the tRNATrp primer molecule required for the initiation of DNA synthesis is cleaved from viral DNA by an enzymatic activity associated with the reverse transcriptase molecule. Since the alpha subunit of reverse transcriptase facilitates release of the tRNATrp primer from viral DNA and this activity is inhibited by a known inhibitor of reverse-transcriptase-associated RNAase H, it appears that the RNAase H activity, rather than the DNA endonuclease activity, is involved in this reaction. The cleavage site for RNAase H-mediated removal of the tRNATrp primer from viral DNA is located at or near the tRNATrp-viral DNA junction, and transcription of most, if not all, of the tRNATrp-binding site into (+) polarity DNA occurs before RNAase-H-mediated cleavage takes place. These studies indicate that an additional function can be ascribed to the reverse-transcriptase-associated RNAase H activity, which in this instance acts like an endonuclease, not requiring the unblocked termini of an RNA-DNA hybrid molecule for its activity.

Products of reverse transcription in avian retrovirus analyzed by electron microscopy

DNA products synthesized in avian retroviral particles permeabilized with melittin have been analyzed in an electron microscope. These studies have provided further insight and subsequent refinement in the melittin activation techniques. Our electron microscope analyses verify the existence of the plus-strand single-stranded DNA branches, presumed to originate by strand-displacement synthesis (L. R. Boone and A. M. Skalka, J. Virol. 37:117-126, 1981). The branches occur at many locations along the DNA molecules and are observed at very early times, even before the minus-strand copies of the RNA genome are completed. Circular forms of different derivations are observed at early and at late times, which are possible intermediates in viral replication. Novel forms termed H structures are also described. In addition to the identification of possible intermediates, these analyses have provided further information on the sequence of events in retroviral reverse transcription. These new data are combined with previous results to generate a model of reverse transcription which incorporates strand-displacement synthesis as an essential feature.

Structure of a replication intermediate in the synthesis of Rous sarcoma virus DNA in vivo

Intermediates in the synthesis of Rous sarcoma virus DNA in vivo contain a short second strand of DNA (plus strong-stop DNA) synthesized by using the region near the 5' end of the first (minus) strand of DNA as the template. In this report, we show that the 3' end of plus strong-stop DNA is extended about 15 to 20 nucleotides beyond the 5' end of the minus-strand DNA template, probably copying a portion of the tRNATrp molecule that serves as primer for synthesis of the minus strand of DNA. The extra sequences present in plus strong-stop DNA may play a central role in the generation of the long terminal repeat present in mature forms of viral DNA.