Mapping of alterations in noninfectious proviruses of spleen necrosis virus

Lethal mutagenesis of HIV

HIV-1 and other retroviruses exhibit mutation rates that are 1,000,000-fold greater than their host organisms. Error-prone viral replication may place retroviruses and other RNA viruses near the threshold of "error catastrophe" or extinction due to an intolerable load of deleterious mutations. Strategies designed to drive viruses to error catastrophe have been applied to HIV-1 and a number of RNA viruses. Here, we review the concept of extinguishing HIV infection by "lethal mutagenesis" and consider the utility of this new approach in combination with conventional antiretroviral strategies.

Sequence instability in the long terminal repeats of avian spleen necrosis virus and reticuloendotheliosis virus

Sequence divergence between the 3' long terminal repeats (LTR) of avian reticuloendotheliosis virus (REV), deletion variant proviral clone 2-20-4, and spleen necrosis virus (SNV)-proviral clones 14-44, 60, and 70-was found to involve two classes of base substitutions: low-frequency interspersed and high-frequency clustered substitutions. Clones 2-20-4 and 14-44 have diverged 4.4% owing to low-frequency substitutions. In contrast, two high-frequency substitution segments have diverged by 30% and 29%, respectively. Clustered substitutions appear to be located either within or next to tandem repeats, suggesting their introduction concomitant with sequence deletions and duplications commonly associated with such repeats. A new 19-bp tandem repeat is found in clone 2-20-4. Its sequence could have evolved from the 26-bp repeats found in the SNV clones.

Molecular cloning of the Mason-Pfizer monkey virus genome: biological characterization of genome length clones and molecular comparisons to other retroviruses

The molecular cloning of the DNA provirus of Mason-Pfizer monkey virus (M-PMV) is described. Fourteen independent clones of integrated M-PMV proviruses were isolated from a human embryo kidney cell line that had been previously derived from a single cell clone infected with M-PMV. Characterization of these clones for size of insert, restriction pattern of flanking DNA, and presence of repetitive DNA in the flanking sequences revealed that 10 of the isolates were identical while the four remaining clones were unique. Three independent clones of unintegrated M-PMV proviruses containing a single copy of the long terminal repeat (LTR) were cloned from acutely infected human embryo kidney cells, Transfection assays revealed that 13 of 14 integrated proviruses and 2 of 3 unintegrated proviruses were capable of producing infectious virus. One of the integrated provirus clones (clone 6A) produced consistently higher titers of virus than all of the other clones in all assays used and in two different cell lines, indicating that it contained a mutation that enhances virus replication. The virus recovered after transfection was shown to be capable of inducing cell fusion in nontransformed cell lines, confirming that this property is associated with M-PMV. One of the clones was hybridized under conditions of varying stringency, to molecular clones of type B, C, and D retroviruses. These studies revealed M-PMV to be most closely related to squirrel monkey retrovirus (D-type virus) and more distantly related to mouse mammary tumor virus (B-type virus). Hybridization was also detected with clones from the pol gene region of a family of human endogenous sequences. No homology was detected with Rous sarcoma virus or most mammalian C-type viruses tested. The exceptions were baboon endogenous virus and RD114 in which previously identified homology in the env gene was confirmed. These results suggest that the type D and type B viruses can be linked together in a group of viruses of similar ancestral origin analogous to that recently proposed for the human T-cell leukemia viruses and bovine leukemia virus.

Biologically active proviral clone of myeloblastosis-associated virus type 1: implications for the genesis of avian myeloblastosis virus

A biologically active myeloblastosis-associated virus (MAV) provirus was cloned from a bacteriophage recombinant library constructed from leukemic chicken myeloblast DNA. The restriction endonuclease map of this clone was consistent with that of a type 1 MAV (MAV-1). Interference assays of virus recovered from cultured chicken embryo fibroblasts after DNA transfection established that the provirus was infectious and confirmed that it belonged to avian retrovirus subgroup A (type 1). Antipeptide antibodies raised against the env-encoded carboxyl terminus of p48myb, the transforming protein of avian myeloblastosis virus, specifically immunoprecipitated the gp37env from quail cells transfected with MAV-1 proviral DNA but not from cells infected with MAV-2. This suggests that MAV-1 rather than MAV-2 is the progenitor helper virus from which avian myeloblastosis virus arose by the transduction of cellular proto-oncogene sequences.

Construction of chimaeric processed immunoglobulin genes containing mouse variable and human constant region sequences

The specificity of monoclonal antibodies provides a powerful diagnostic and therapeutic tool in investigating human neoplasia. Radiological scanning and immunotherapy with mouse tumour-specific monoclonal antibodies have been applied to patients with some success, but a major problem is the neutralization of the mouse antibody induced by repeated administration of heterologous antibodies. To avoid or reduce such immune reactions, chimaeric immunoglobulins consisting of mouse variable (V) and human constant (C) regions can be synthesized. We have constructed a recombinant retrovirus DNA carrying genomic heavy-chain (H) variable-diversity joining (VH-D-JH) and C gamma 1 genes from different species and show here that the chimaeric intervening sequences are spliced out precisely. This procedure provides a useful method to construct the chimaeric mouse-human immunoglobulin gene to be expressed in Escherichia coli, yeast and animal cells. Unexpectedly, a hidden splice donor site in the 5'-flanking region of a human VH gene is used in place of the donor site of the leader sequence exon, resulting in the formation of the V region without the leader sequence.

Treatment of mice with 5-azacytidine efficiently activates silent retroviral genomes in different tissues

The drug 5-azacytidine was injected into mice to activate silent retroviral genomes. The Mov-7 and Mov-10 substrains of mice were used, each of which carries a Moloney murine leukemia provirus with mutations in the coding regions at nonidentical positions. These proviral genomes are highly methylated and are not expressed in the animal. A single injection of the drug into postnatal mice induced transcription of the endogenous defective proviral genomes in thymus, spleen, and liver at 3 days after treatment. No viral transcription was detected in the brain of drug-exposed animals. When postnatal Mov-7/Mov-10 F1 mice were treated with the drug, infectious virus was generated efficiently and resulted in virus spread and viremia in all animals by 3 weeks of age. In contrast, infectious virus was not generated in F1 mice that had been treated during gestation with up to sublethal doses of the drug. Our results demonstrate that injection of 5-azacytidine can be used to efficiently and reproducibly activate silent genes in different cell populations of postnatal mice.

A rapid screening procedure for the isolation of nonconditional replication mutants of Mason-Pfizer monkey virus: identification of a mutant defective in pol

A rapid, sensitive, and reproducible method for the isolation of human cell clones containing nonconditional, replication-defective (rd) mutants of Mason-Pfizer monkey virus (M-PMV), the prototype of the D-type retroviruses is described. The two mutants, rd1 and rd2, thus far isolated have been analyzed for virus particle production (using radiolabeled precursors and by electron microscopy) and for the status of intracellular viral precursors. Thin sections of rd1 and rd2 infected cells showed typical M-PMV particles when observed under electron microscope. A more direct assay of virus production, by labeling the mutant cell clones with [3H]uridine, also showed a distinct virus peak at an approximate density of 1.16 g/ml when culture fluids from rd1 and rd2 were analyzed. Analyses of these two mutants showed no defect in either gag or env gene products, however, further analysis of rd1 showed that the Pr180gag-pol was altered in its migration on SDS-polyacrylamide gel electrophoresis and no reverse transcriptase activity could be detected in rd1 virions. Mutant rd2, on the other hand, assembles noninfectious virus particles that are otherwise indistinguishable from those produced by wild-type cell clones. The biochemical basis for the defect in this mutant remains to be established.

DNAs of two molecularly cloned endogenous ecotropic proviruses are poorly infectious in DNA transfection assays

Endogenous ecotropic murine leukemia virus expression varies with inbred mouse strain and age. The mechanism(s) regulating virus expression is unknown, but expression is thought to be controlled at the transcriptional level by linkage to cis-acting cellular DNA sequences or DNA methylation or both. To begin to differentiate between these different control mechanisms, we molecularly cloned two endogenous ecotropic proviruses, Emv-3 and Emv-13, complete with flanking cellular DNA sequences. Both proviruses are poorly expressed in vivo and in vitro, although they appear to be structurally nondefective by restriction enzyme analysis. Cloned DNAs of both proviruses were poorly infectious in DNA transfection experiments, suggesting that methylation may not regulate the expression of these genes in vivo. Removal of their flanking cellular sequences did not increase their infectivity. However, these DNAs were highly infectious when mixed together, indicating that both proviruses carry mutations, that inhibit their expression and belong to different complementation groups. Marker rescue experiments suggested that Emv-3 is defective in the gag region and Emv-13 is defective in p15E-U3. The infectivity of Emv-3, but not of Emv-13, DNA was increased by the addition of AKR xenotropic murine leukemia virus DNA, consistent with known regions of homology between ecotropic and xenotropic proviruses. Recombination between defective endogenous viruses also appears to occur in vivo, suggesting that this may be a common mechanism controlling endogenous murine leukemia virus expression.

Endogenous Moloney leukemia virus in nonviremic Mov substrains of mice carries defects in the proviral genome

Substrains of mice carrying Moloney murine leukemia virus as a Mendelian gene (Mov locus) have been derived previously. Some of these strains, i.e., Mov-3 and Mov-9, develop viremia, whereas others, i.e., Mov-2, Mov-7, and Mov-10, do not regularly activate virus. We previously have molecularly cloned the respective Mov loci and shown that proviral clones derived from the different viral loci were either infectious (Mov-3, Mov-9) or failed to induce infectious virus (Mov-2, Mov-7, Mov-10) in a transfection assay. To analyze the sites affecting infectivity of the latter clones, complementation assays, in vitro recombinations, and marker rescue experiments were performed. Our results show that the three endogenous Moloney murine leukemia virus clones derived from Mov-2, Mov-7, and Mov-10 carry different mutations in the gag-pol region of the proviral genome. No inhibitory effect of flanking mouse sequences on provirus infectivity was observed.

Genetic interactions in the spontaneous production of endogenous murine leukemia virus in low leukemic mouse strains

The spontaneous expression of ecotropic murine leukemia virus (MuLV) in spleen cells of BALB/c, C57BL/6 (B6), and derivative mice was examined as a function of age. The patterns of spontaneous virus induction in vivo correlate with the patterns of virus induction in vitro, which result from the action of two loci, Inc-l and Inb-l (7). Whereas mice carrying Inc-l or Inb-l have similar phenotypes in vitro, they have significantly different phenotypes in vivo. Mice of the Inb-l+/+ genotype, e.g., B6, rarely expressed MuLV, and the titer of MuLV recovered from rare MuLV-positive mice of this genotype was usually low. Mice of the Inc-l+/+ genotype, e.g., BALB/c, expressed low amounts of MuLV early in life, however, from 6-12 mo of age approximately one-half of the Inc-l+/+ mice expressed virus, frequently of high titer. Equal numbers of N-tropic and B-tropic MuLV were recovered from Inb-l+ mice, but predominantly N-tropic MuLV was recovered from Inc-l+ mice. Strains that carry dominant (+) alleles at both Inc-l and Inb-l show higher titers of MuLV earlier in life than strains that carry only Inc-l or Inb-l. The presence of dominant alleles at both loci results in the appearance of predominantly N-tropic virus early in life. These results demonstrate that the principal determinants of spontaneous virus expression in these low leukemic strains of mice are the In loci or genes linked to them. A further inference that can be drawn from these studies is that the appearance of B-tropic virus is by no means a random process but rather results from predictable patterns of MuLV expression and alteration.

Cloning of two genetically transmitted Moloney leukemia proviral genomes: correlation between biological activity of the cloned DNA and viral genome activation in the animal

The Mov-7 and Mov-9 substrains of mice, carrying Moloney murine leukemia virus (M-MuLV) in their germ line at the Mov-7 locus and Mov-9 locus, respectively, are different with respect to virus activation. Infectious virus appears in all mice carrying the Mov-9 locus but is not activated in animals carrying the Mov-7 locus. Consequently, only Mov-9 mice develop viremia and subsequent leukemia. The endogenous M-MuLV provirus with flanking mouse sequences corresponding to the Mov-7 and Mov-9 loci was molecularly cloned. Detailed restriction maps obtained from the cloned DNAs revealed no detectable differences in the proviral genomes. The flanking mouse sequences, however, were different, confirming that the Mov-7 and Mov-9 loci represent different integration sites of M-MuLV. Both clones induced XC plaques in a transfection assay. The specific infectivity of the clones, however, was different. A total of 10(-5) XC plaques per genome equivalent were induced by the Mov-9 clone, whereas only 10(-9) XC plaques per genome equivalent were induced by the Mov-7 clone. Moreover, NIH 3T3 cells transfected with the Mov-9 clone produced NB-tropic M-MuLV, whereas cells transfected with the Mov-7 clone did not produce infectious virus. The results suggest that M-MuLV integrated at the Mov-7 locus carries a mutation which prevents synthesis of infectious virus but permits XC plaque induction by partial genome expression or synthesis of noninfectious particles. Thus, the pattern of virus expression in Mov-7 and Mov-9 mice correlates with the biological properties of the respective clones. Genomic DNA from Mov-9 mice was not infectious in the transfection assay (specific infectivity < 10(-7) PFU per genome equivalent). As the only difference between the genomic and the cloned Mov-9 DNA appears to be the presence of 5-methylcytosine in CpG sequences, our results suggest that removal of methyl groups by molecular cloning in procaryotes permits genome expression in transfected eucaryotic cells. Our results support the hypothesis that DNA methylation is relevant not only in genome expression in the animal but also in expression of genes transfected into eucaryotic cells.

Infectivity and structure of molecular clones obtained from two genetically transmitted Moloney leukemia proviral genomes

The Mov-2 and Mov-10 substrains of mice, each carrying Moloney leukemia virus (= M-MuLV) in their germ line at the Mov-2 and Mov-10 locus, respectively, do occasionally at a later age (Mov-2) or not at all (Mov-10) activate infectious virus. The M-MuLV proviruses with flanking mouse sequences corresponding to the Mov-2 and Mov-10 locus, respectively, were molecularly cloned. Restriction enzyme analysis revealed no major deletions or insertions in the proviral genomes of the Mov-2 and Mov-10 locus. Both cloned DNAs induced XC plaques in a transfection assay. The specific infectivity, however, was very low and 3T3 cells transfected with the Mov-2 or Mov-10 clone did not produce infectious virus. Removing part of the 5' cellular sequences from the Mov-10 clone did not increase the infectivity. The results suggest that the M-MuLV integrated at the Mov-2 and Mov-10 locus carry a mutation which prevents synthesis of infectious virus but permits XC plaque induction by partial genome expression or synthesis of non-infectious particles.

Genome of reticuloendotheliosis virus: characterization by use of cloned proviral DNA

Reticuloendotheliosis virus is an avian type C retrovirus that is capable of transforming fibroblasts and hematopoietic cells both in vivo and in vitro. This virus is highly related to the three other members of the reticuloendotheliosis virus group, including spleen necrosis virus, but it is apparently unrelated to the avian leukosis-sarcoma virus family. Previous studies have shown that it consists of a replication-competent helper virus (designated REV-A) and a defective component (designated REV) that is responsible for transformation. In this study we used restriction endonuclease mapping and heteroduplex analysis to characterize the proviral DNAs of REV-A and REV. Both producer and nonproducer transformed chicken spleen cells were used as sources of REV proviral DNA; this genome was mapped in detail, and fragments of it were cloned in lambdagtWES.lambdaB. The infected canine thymus line Cf2Th(REV-A) was used as a source of REV-A proviral DNA. The restriction maps and heteroduplexes of the REV and REV-A genomes showed that (proceeding from 5' to 3') (i) REV contains a large fraction of the REV-A gag gene (assuming a gene order of gag-pol-env and gene sizes similar to those of other type C viruses), for the two genomes are very similar over a distance of 2.1 kilobases beginning at their 5' termini; (ii) most or all of REV-A pol is deleted in REV; (iii) REV contains a 1.1 kilobase segment derived from the 3' end of REV-A pol or the 5' end of env or both; (iv) this env region in REV is followed by a 1.9-kilobase segment which is unrelated to REV-A; and (v) the helper-unrelated segment of REV extends essentially all of the way to the beginning of the 3' long terminal repeat. Therefore, like avian myeloblastosis virus but unlike the other avian acute leukemia viruses and most mammalian and avian sarcoma viruses, REV appears to be an env gene recombinant. We also found that the REV-specific segment is derived from avian DNA, for a cloned REV fragment was able to hybridize with the DNA from an uninfected chicken. Therefore, like the other acute transforming viruses, REV appears to be the product of recombination between a replication-competent virus and host DNA. Two other defective genomes in virus-producing chicken cells were also cloned and characterized. One was very similar to REV in its presumptive gag and env segments, but instead of a host-derived insertion it contained additional env sequences. The second was similar (but not identical) to the first in its gag and env regions and appeared to contain an additional 1-kilobase inversion of REV-A sequences.

Spontaneous changes in nucleotide sequence in proviruses of spleen necrosis virus, an avian retrovirus

We determined the nucleotide sequence of about 1 kilobase of DNA 3' to the 5' long terminal repeat of three noninfectious ad one infectious proviral DNA clones of spleen necrosis virus, an avian retrovirus, to determine if the types of nucleic acid changes involved in retrovirus mutation shed light on special features of retrovirus replication. An open reading frame was found starting 411 base pairs from the end of the long terminal repeat. It contained sequences coding for the 36 amino acids at the amino terminus of the p30 of a related reticuloendotheliosis virus [Oroszlan, S., Barbacid, M., Copeland T., Aaronson, S. A. & Gilden, R. V. (1981) J. Virol. 39, 845-854]. Therefore, the open reading frame represents the 5' end of the gag gene. A mutation in one noninfectious provirus changed the initiation codon for the gag polypeptide; a mutation in another noninfectious provirus caused premature termination of gag polypeptide synthesis; and a nontandem duplication into gag resulting from a mistake in initial (+) strand DNA synthesis changed amino acids and the reading frame in a third noninfectious provirus. These mutations appear to be responsible for the lack of infectivity of these provirus clones and indicate a higher relative frequency of mutation in this region of the genome. In addition, all four clones have multiple other mutations. These mutations are mostly base pair substitutions and many are clustered for any one clone, reflecting certain special features of retrovirus replication.

Spontaneous variation and synthesis in the U3 region of the long terminal repeat of an avian retrovirus

Recombinant DNA clones of a viral clone of spleen necrosis virus, an avian retrovirus, were found to have long terminal repeats of different sizes. The variation was in the U3 region of the long terminal repeats, and any one clone had U3 of the same size in both long terminal repeats. The U3 regions in the 5' and 3' long terminal repeat were shown both to be derived from the 3' long terminal repeat of parental virus DNA.

Characterization of reticuloendotheliosis virus strain T DNA and isolation of a novel variant of reticuloendotheliosis virus strain T by molecular cloning

Reticuloendotheliosis virus strain T (REV-T) is a highly oncogenic avian retrovirus which causes a rapid neoplastic disease of the lymphoreticular system. Upon infection, this virus gives rise to two species of unintegrated linear viral DNA, which are 8.3 and 5.5 kilobase pairs long and represent the helper virus (REV-A) and the oncogenic component (REV-T), respectively. Restriction endonuclease cleavage maps of these two DNA components indicate that REV-T DNA has a large portion of the genome deleted with respect to REV-A DNA and a substitution about 0.8 to 1.5 kilobase pairs long that is unrelated to REV-A DNA. These additional sequences comprise the putative transforming region of REV-T (rel). A chicken spleen cell line transformed by REV-T produced virus which upon infection gives rise to three species of unintegrated linear viral DNA (8.3, 5.5, and 3,3 kilobase pairs). We isolated the proviruses of the 8.3- and 3.3-kilobase pair species from this cell line by cloning in the phage vector Charon 4A. Restriction enzyme mapping showed that the two proviral clones are proviruses of REV-A and a variant of REV-T, respectively. A subclone of the variant REV-T provirus specific for the rel sequences of REV-T was used as a hybridization probe to demonstrate that the rel sequences are different from the putative transforming sequences of Schmidt-Ruppin Rous sarcoma virus strain A, avain myelocytomatosis virus, avian myeloblastosis virus, avian erythroblastosis virus, Abelson murine leukemia virus, and Friend erythroleukemia virus. In addition, the rel-specific hybridization probe was used to identify a specific set of sequences which are present in uninfected avian DNAs digested with several restriction enzymes. The corresponding cell sequences are not arranged like rel in REV-T.

Formation of infectious progeny virus after insertion of herpes simplex thymidine kinase gene into DNA of an avian retrovirus

We have prepared several infectious stocks of an avian retrovirus, spleen necrosis virus, containing the herpes simplex virus type 1 thymidine kinase (tk) gene. The viruses were produced after cotransfection of chicken cells with DNA from recombinants between cloned spleen necrosis virus and tk DNAs and DNA of cloned reticuloendotheliosis virus strain A. removal of sequences in the tk gene for the end of tk mRNA increased a thousand fold the yield of infectious recombinant virus. Infection of chicken or rat tk- cells with the recombinant virus transformed them to a tk+ phenotype.