RNA of replication-defective strains of Rous sarcoma virus

Cancer Gene Discovery: Past to Present

Cancer is a complex disease that originates from genetic changes leading to multiple phenotypic manifestations that ultimately result in suffering and death from cancer. Attempts have been made to define the phenotypic and genetic "hallmarks" of cancer, but many of these "hallmarks" remain descriptive, while the underlying mechanisms responsible for these hallmarks remain elusive. For decades, cancer researchers have been methodically identifying the molecular mechanisms that result in tumor initiation, growth, metastases, and resistance to therapy. Great strides forward have been made and we are entering an era of "precision medicine" with the goal of treating each cancer based on its unique etiology. Increasingly, the decision to use targeted therapies and immunotherapies in the clinic is based on the genotype of the cancer being treated. For example, specific tyrosine kinase inhibitors are only prescribed to patients that express the tyrosine kinase protein on their cancer cells. Likewise, a genetically unstable cancer is predictive for successful immunotherapy. Knowledge of the specific genetic changes that result in overproduction of oncogenes and reduced production of tumor suppressors is crucial for advancing therapeutic options for cancer. The first chapter of this book presents a brief history of cancer gene discovery. In the remaining chapters of this book, we present protocols using in silico, in vitro, and in vivo techniques for identifying genetic drivers of cancer, in the hope that these protocols will be used to increase our knowledge of the molecular mechanisms driving cancer.

The early history of tumor virology: Rous, RIF, and RAV

One hundred years ago Peyton Rous recovered a virus, now known as the Rous sarcoma virus (RSV), from a chicken sarcoma, which reproduced all aspects of the tumor on injection into closely related chickens. There followed recovery of causal viruses of tumors of different morphology from 4 more of 60 chicken tumors. Subsequent studies in chickens of the biology of the first RSV isolated moved slowly for 45 y until an assay of ectodermal pocks of the chorioallantoic membrane of chicken embryos was introduced. The inadequacies of that assay were resolved with the production of transformed foci in cultures of chicken fibroblasts. There followed a productive period on the dynamics of RSV infection. An avian leukosis virus (ALV) was found in some chicken embryos and named resistance-inducing factor (RIF) because it interferes with RSV. Its epidemiology in chickens is described. Another ALV was found in stocks of RSV and called Rous-associated virus (RAV). Cells preinfected with RAV interfere with RSV infection, but RSV does not produce infectious virus unless RAV is added during or after RSV infection. Intracellular RAV provides the infectious coat for the otherwise defective RSV. The coat determines the antigenicity, host range, and maturation rate of RSV. RSV particles carry reverse transcriptase, an enzyme that converts their RNA into DNA and allows integration into the cell's DNA, where it functions as a cellular gene. This was the bridge that joined the biological era to the molecular era. Its relation to oncogenes and human cancer is discussed.

Polymerase-defective mutant of the Bryan high-titer strain of Rous sarcoma virus

A mutant of the Bryan high-titer strain of Rous sarcoma virus defective in reverse transcriptase is known as type alpha (BH-RSV alpha). BH-RSV alpha virion particles do not contain any polymerase-related proteins but they direct the synthesis of a normal sized Pr180 gag-pol polyprotein precursor in infected cells. Using a bioassay for polymerase gene function that is based on the requirement of viral replication for transformation of transfected chicken cells, we have localized the defect to the 2.5 kb EcoRI-KpnI DNA fragment containing more than 90% of the polymerase gene by comparison with the corresponding DNA fragment from the wild-type polymerase-positive BH-RSV, called type beta. In vitro recombination experiments with the polymerase gene of Schmidt-Ruppin RSV allowed us to map the defect to the 0.86 kb XbaI-BglII DNA fragment of the BH-RSV alpha polymerase. DNA sequence analysis of the entire polymerase gene of BH-RSV alpha and beta has revealed one point mutation that maps within that XbaI-BglII fragment and substitutes leucine in BH-RSV alpha for glutamine in the wild-type BH-RSV beta.

Partial nucleotide sequence of Rous sarcoma virus-29 provides evidence that the original Rous sarcoma virus was replication defective

Rous sarcoma virus-29 (RSV-29) is the strain of RSV that has the least number of passages beyond its isolation from chicken tumor no. 1 among all current strains of RSV. Biological characterization indicated that it was replication defective. RNA analysis of nonproducer clones of RSV-29-infected chicken embryonic fibroblasts showed the presence of a subgenomic message of 2.6 kilobases containing src and a genomic RNA of 7.7 kilobases that contains gag, pol, and src, but not env. The src-containing EcoRI fragment of RSV-29 proviral DNA was molecularly cloned. Sequence analysis of the regions flanking src revealed that the env gene was completely deleted in RSV-29 and that the sequence across the deletion was exactly the same as the Bryan high-titer strain of RSV. The sequence immediately 3' to src in RSV-29 was closely related to that of the Prague strain of RSV. The fact that the strain of RSV which has the minimal number of passages beyond its isolation is replication defective supports the hypothesis of Lerner and Hanafusa (J. Virol. 49:549-556, 1984) that the original RSV is a defective transforming virus. This defective transforming virus is postulated to be the precursor to other defective RSVs like the Bryan high-titer strain and to nondefective RSVs like the Prague strain. The particular clone of RSV-29 that we studied also had a short stretch of sequence duplication at the 3' end of the pol gene, which was presumably created by an error of reverse transcription.

DNA sequence of the Bryan high-titer strain of Rous sarcoma virus: extent of env deletion and possible genealogical relationship with other viral strains

The genetic structure of the Bryan high-titer strain of Rous sarcoma virus (BH-RSV) was analyzed by using a molecular clone obtained from proviral DNA. DNA sequencing of the pol-src junction of BH-RSV revealed that the env sequence was almost entirely absent; only six base pairs following the pol termination codon remained. Beginning at nucleotide 7 (relative to the end of pol), a 91-base pair sequence identical to the 91 base pairs immediately upstream from src in other strains of RSV was found. The helper virus-related sequence of about 100 base pairs, which is present as a direct repeat in the 5' and 3' regions flanking src in other RSVs, was present only on the 3' side of src in BH-RSV. The 3' end of BH-RSV, from the last 16 base pairs of src through the U3 region, was virtually identical to a region downstream of env through U3 in the nontransforming helper virus Rous-associated virus-2, suggesting that BH-RSV may have been derived by recombination between Rous-associated virus-2 and cellular src DNA. The possibility that the original RSV may have been a defective transforming virus and a precursor of the nondefective RSV strains is discussed.

Complete sequence of the Rous sarcoma virus env gene: identification of structural and functional regions of its product

The amino-terminal amino acid sequences of gp85 and gp37, the envelope glycoproteins of Rous sarcoma virus (RSV), were determined. Alignment of these sequences with the amino acid sequence predicted from the complete nucleotide sequence of the Prague strain of RSV, subgroup C (PR-C), has allowed us to delineate the env gene-coding region of this virus. The coding sequences for gp85 and gp37 have been placed in an open reading frame that extends from nucleotide 5045 to nucleotide 6862 and predict sizes of 341 amino acids (36,962 molecular weight) for gp85 and 198 amino acids (21,566 molecular weight) for gp37. Carbohydrate makes a significant contribution to the observed molecular weights of these polypeptides--the amino acid sequence contains 14 potential glycosylation sites (Asn-X-Ser/Thr) in gp85 and two in gp37. Experiments aimed at estimating the number of carbohydrate side chains yielded results consistent with most or all of these sites being occupied. Although an initiation codon is located early (codon 4) in the open reading frame, it is likely that splicing yields an mRNA on which translation initiates at the same AUG as that of the gag gene to produce a nascent polypeptide in which gp85 is preceded by a 62-amino-acid-long leader peptide. This leader contains the hydrophobic sequence (signal sequence) necessary for translocation across the endoplasmic reticulum and is completely removed from the env gene product during translation. The polyprotein precursor, Pr95env, is cleaved to gp85 and gp37 at the carboxyl side of the basic sequence:-Arg-Arg-Lys-Arg-. gp85 is attached through a disulphide linkage to gp37, and although the positions of the cysteines involved in this linkage are not known, the presence of a 27-amino-acid-long hydrophobic region at the carboxy-terminus of gp37 is consistent with its role as a membrane anchor for the viral glycoprotein complex. The location of host range variable regions with respect to the possible tertiary structure of the complex is discussed.

Particles of reduced infectivity and deficient in envelope glycoproteins are produced in cycloleucine-treated B77 avian sarcoma virus-infected chicken embryo fibroblasts

We have previously shown that the inhibition of methylation reactions by the treatment of B77 avian sarcoma virus-infected cells with medium containing cycloleucine results in an inhibition in the intracellular accumulation of the spliced subgenomic mRNA for the virion envelope protein precursor, whereas the genome-size RNA accumulates in larger than normal amounts (C. M. Stoltzfus and R. W. Dane, J. Virol. 42:918-931, 1982). To measure the production of virus particles, we have now determined the reverse transcriptase activity in the culture fluid from infected cells treated with various concentrations of cycloleucine. The activity was somewhat greater in the fluid from the cycloleucine-treated cells than it was in the fluid from the control cells, suggesting an enhancement of particle production in the presence of cycloleucine. In contrast, the production of infectious virions, as determined by the focus assay, decreased when the cycloleucine concentration of the medium increased. We determined the polypeptide compositions of purified particles produced from infected cells treated with or without cycloleucine and labeled with [(3)H]leucine. The relative amounts of radioactivity associated with p19 and p27 were approximately the same in all of the preparations. In contrast, significant decreases were observed in the relative amounts of [(3)H]leucine radioactivity associated with the virion glycoproteins gp85 and gp37. The extent of the decrease in the ratio of gp85 to p27 was a function of the cycloleucine concentration and correlated well with the decrease in the infectivity of the virus particles. Therefore, it is probable that the observed reduction of specific infectivity results from the reduced amounts of envelope glycoproteins in the particles budding from cycloleucine-treated cells.

Participation of subgenomic retroviral mRNAs in recombination

Envelope glycoprotein (env) mRNA from avian retroviruses was injected into cells transformed by env-deleted Bryan Rous sarcoma virus [RSV(-)]. The genetic deficiency of RSV(-) was complemented, and infectious transforming virus was released for many days after these injections. The long-term activity of the injected env mRNA is believed to be due to reverse transcription of the injected RNA after its incorporation into virus particles. The resulting subgenomic provirus, presumed to be integrated into host DNA, is able to direct the continuous synthesis of additional env mRNA. In some of these cultures, replication-competent viruses appeared many days after injection. The analysis by RNase T1 oligonucleotide fingerprinting showed that the RNA of these virus genomes contained oligonucleotides characteristic of both RSV(-) and the env mRNA injected. In all viruses analyzed the 5' two-thirds and the 3' terminus of the genome were derived from RSV(-) and the env gene from the injected mRNA. Our results thus strongly indicate that these viruses were generated via recombination between RSV(-) and env mRNA. The demonstration of involvement of an mRNA sequence in recombination may be of importance in the divergence of retroviruses and in the mechanism of interaction between retroviruses and host nucleotide sequences.

Rous sarcoma virus mutant LA3382 is defective in virion glycoprotein assembly

LA3382 is a temperature-sensitive replication-defective mutant of Rous sarcoma virus that contains four active mutations. In this study we performed experiments to determine the biochemical defect that blocks the synthesis of infections virus late in the replication cycle. At the nonpermissive temperature (41 degrees C) cells infected with LA3382 synthesized virus particles which were noninfectious and exhibited significant reductions in the amounts of gp85 and gp37 present in the virions. An analysis of the intracellular viral polypeptides indicated that the precursor of the viral glycoproteins (Pr95) were synthesized normally but underwent cleavage at a reduced rate at the restrictive temperature. Pr95 did not accumulate in infected cells ans was inserted into mutant virions at 41 degrees C; however, Pr95 was cleaved in such a way that gp85 was released from the viruses and could be detected in the supernatant medium by immunoprecipitation. The virus-free glycoprotein was indistinguishable from wild-type gp85 and may have been released due to an anomalous cleavage. Pulse-chase experiments also indicated that the Pr180 polyprotein precursor of the reverse transcriptase was cleaved to the active form of the enzyme more slowly at 41 degrees C in LA3382-infected cells. This accounted for the twofold lower level of polymerase activity found in mutant virions at 41 degrees C, defect which probably did not account for the observed 20- to 50-fold reduction in infectivity. Furthermore, the replication defect was not complemented by an env deletion mutant Rous sarcoma virus [RSV(-)[, which should complement a pol defect. Therefore, we conclude that the major lesion that impairs replication in LA3382 is within the env gene.

Integration of Rous sarcoma virus DNA into chicken embryo fibroblasts: no preferred proviral acceptor site in the DNA of clones of singly infected transformed chicken cells

We analyzed retroviral integration into a host genome by using avian sarcoma virus infection of natural target cells under conditions where secondary integration via virus spread was inhibited. This was accomplished by using the noninfectious pol- env- alpha variant of the Bryan high-titer strain of Rous sarcoma virus. A total of 12 independent Bryan high-titer Rous sarcoma virus-transformed chicken embryo fibroblast clones were obtained and mapped by using restriction endonucleases. Provirus-cell junction fragments were identified with appropriate hybridization probes. We found that expression of the viral genes could occur after proviral integration at many sites on the chicken genome and that there was no apparent preference for specific integration sites.

Evidence for a Gp85-related glycoprotein in cells transformed by the Bryan high titer strain of Rous sarcoma virus

The Bryan High Titer strain of Rous Sarcoma Virus (BH-RSV) is a deletion mutant in the env-gene coding for the viral envelope glycoproteins gp35 and gp85. In this report experimental evidence is described that cells, transformed by BH-RSV, express a glycoprotein immunologically related to gp85. Animals bearing BH-RSV induced tumors produce antibodies reacting with gp85 of nondefective RSV. Lysates of a BH-RSV transformed quail cell line, R(-):Q, inhibit the immunoprecipitation of gp85 by antibodies against the group-specific determinant of gp85. In R(-):Q cell lysates and in the culture supernatant a glycoprotein of an apparent molecular weight 40,000 (gp40) is found that reacts with monospecific antisera against gp85 of nondefective RSV. In newly synthesized BH-RSV a gp40 associated with the virion is detectable but is easily lost during purification of the virus. Further, a 95k glycoprotein and a 95k phosphoprotein are specifically precipitated from R(-):Q cells by an antiserum against gp85. From these results we conclude that the deletion of the env-gene is incomplete such that part of gp85, bearing group-specific antigenic determinants, is expressed in BH-RSV transformed cells. Analysis of BH-RSV particles freshly harvested from R(-):Q cells reveals that they contain almost exclusively the gag-precursor pr76 and little or no processed gag-proteins. Therefore the R(-):Q cell line seems to be suitable for the study of virus maturation occurring after the budding process.

src Genes of ten Rous sarcoma virus strains, including two reportedly transduced from the cell, are completely allelic; putative markers of transduction are not detected

The src genes of different Rous sarcoma virus (RSV) strains have been reported to be highly conserved by some investigators using RNA-cDNA hybridization, whereas others using oligonucleotide, peptide, and serological analyses have judged src genes to be variable in 30 to 50% of the respective markers. Moreover, distinctive src oligonucleotides and peptides of so-called recovered RSVs (rRSV's) whose src genes were reported to be experimentally transduced from the cell are thought to represent specific markers of host-derived src sequences. By contrast, we have pointed out previously that these markers may represent point mutations of parental equivalents. Here we have compared the src-specific sequences of eight RSV strains and of two rRSV's to each other and to a molecular clone of the src-related chicken locus. Our comparisons are based on RNase T(1)-resistant oligonucleotides of RNA hybridized to src-specific cDNA, which was prepared by hybridizing RSV cDNA with RNA of isogenic src deletion mutants, or to a cloned cellular src-related DNA. All of the approximately 20 src-oligonucleotides of a given RSV strain were recovered by src-specific cDNA's of all other RSV strains or by cellular src-related DNA. The number of oligonucleotides varied slightly with the length of the src deletion used to prepare src-specific cDNA, thus providing a measure for src deletion mutants. Our data indicate that the src genes of all RSV strains tested, including the two reportedly transduced from the cell, are about 98% conserved and completely allelic with only scattered single nucleotide differences in certain variable regions which are subject to point mutations. Hence, based on the src oligonucleotide markers analyzed by us and others, we cannot distinguish between a cellular and viral origin of rRSV's. However, the following are not compatible with a cellular origin of rRSV's. (i) The only putative oligonucleotide marker which is exclusively shared by the two rRSV's studied and which differs from a parental counterpart in a single base was not detectable in cellular src-related DNA. (ii) The number of different allelic src markers observed by us and others in rRSV's was too large to derive from one or two known cellular src-related loci. (iii) The known absence of linkage of the cellular src-related locus with other virion sequences was extended to all non-src oligonucleotides, including some mapping directly adjacent to src. This is difficult to reconcile with the claim that transformation-defective, partial src deletion mutants of RSV which contain both, one, or, as we show here, possibly no src termini nevertheless transduce at the same frequencies, even though homologous, single or double illegitimate recombinations would be involved. Given (i) our evidence that src genes are subject to point mutation under selective conditions similar to those prevailing when rRSV's were generated and (ii) the lack of absolute evidence for the clonal purity of the transformation-defective, partial src deletion mutants of RSV used to generate rRSV's, we submit that the src genes of rRSV's could have been generated by cross-reactivation of nonoverlapping src deletions or mutation of src variants possibly present in transformation-defective, partial src deletion mutants of RSV. To prove experimental transduction, unambiguous markers need to be identified, or it would be necessary to generate rRSV's with molecularly cloned transformation-defective, partial src deletion mutants of RSV. Although our evidence casts doubt on the idea that specific src sequences of rRSV's originated by transduction, the close relationship between viral src and cellular src-related sequences argues that src genes originated at one time in evolution from the cell by events that involved illegitimate recombination and deletion of non-src sequences that interrupt the cellular src locus.

Synthesis and processing of viral glycoproteins in two nonconditional mutants of Rous sarcoma virus

We have studied the pattern of glycoprotein synthesis in two nonconditional mutants of Rous sarcoma virus. One mutant, SE33, produces no viral particles but synthesizes Pr92env, which is cleaved intracellularly to mature glycoproteins. The second mutant, SE521, encodes a gPr92env which is not cleaved to gp85 or gp37 and therefore produces virions with the phenotype of Bryan RSV(-) or NY8. Neither of these mutants have detectable genomic deletions. The study of these mutants has led to the following conclusions. (i) In the absence of particle production or p15 synthesis, gPr92env can be cleaved to the mature glycoprotein which is found on the cell surface. (ii) Noncleaved gPr92env is not packaged into virions but is found on the cell surface. (iii) gPr92env alone can account for subgroup specific viral interference. (iv) gPr92env is probably transported to the cell surface before additional glycosylation or cleavage to mature virion glycoprotein. The nonprocessed precursor of SE521 appears to be glycosylated normally, and thus far we have been unable to determine the basis for the defect in this mutant.

Cellular sequences are present in the presumptive avian myeloblastosis virus genome

EcoRI restriction endonuclease fragments from a lambda proviral DNA hybrid containing the entire presumptive avian myeloblastosis virus (AMV) provirus, and from a lambda proviral hybrid containing a partial myeloblastosis-associated virus type 1 (MAV-1)-like provirus were compared by heteroduplex analysis. The cloned presumptive AMV provirus was also analyzed by electron microscopy, using R-loop formation with purified 35S RNA isolated from virions of the standard AMV complex. The results indicate that the putative AMV genome contains a segment absent in its MAV-1-like helper virus. This segment represents a substitution in the region of the genome that in MAV-1 virus is occupied by the envelope gene and is approximately 900 +/- 160 nucleotide pairs in length. Hybridization of specific probes from the presumptive AMV genome to Southern blots of EcoRI-digested cellular DNA has revealed that these substituted sequences are homologous to chicken and duck DNA that is not related to chicken endogenous proviral sequences.

Evidence for the common origin of viral and cellular sequences involved in sarcomagenic transformation

The src genes of six different strains of avian sarcoma virus (ASV) were compared with those of a series of newly isolated sarcoma viruses, termed "recovery avian sarcoma viruses" (rASV's). The rASV's were isolated recently from chicken and quail tumors induced by transformation-defective (td) deletion mutants of Schmidt-Ruppin Rous sarcoma virus. The RNase T1-resistant oligonucleotide maps were constructed for the RNA genomes of different strains of ASV and td mutants. The src-specific sequences, characterized by RNase T1-resistant oligonucleotides ranging from 9 to 19 nucleotides long, were defined as those mapping between approximately 600 and 2,800 nucleotides from the 3' polyadenylate end of individual sarcoma viral RNAs, and missing in the corresponding td viral RNAs. Our results revealed that 12 src-specific oligonucleotides were highly conserved among several strains of ASV, including the rASV's, whereas certain strains of ASV were found to contain one to three characteristic src-specific oligonucleotides. We previously presented evidence supporting the idea that most of the src-specific sequences present in rASV RNAs are derived from cellular genetic information. Our present data indicate that the src genes of rASV's are closely related to other known ASVs. We conclude that the src genes of different strains of ASV and the cellular sarc sequences are of common origin, although some divergence has occurred among different viral src genes and related cellular sequences.

Avian retroviruses that cause carcinoma and leukemia: identification of nucleotide sequences associated with pathogenicity

Avian myelocytomatosis virus (MC29V) is a retrovirus that transforms both fibroblasts and macrophages in culture and induces myelocytomatosis, carcinomas, and sarcomas in birds. Previous work identified a sequence of about 1,500 nucleotides (here denoted onc(MCV)) that apparently derived from a normal cellular sequence and that may encode the oncogenic capacity of MC29V. In an effort to further implicate onc(MCV) in tumorigenesis, we used molecular hybridization to examine the distribution of nucleotide sequences related to onc(MCV) among the genomes of various avian retroviruses. In addition, we characterized further the genetic composition of the remainder of the MC29V genome. Our work exploited the availability of radioactive DNAs (cDNA's) complementary to onc(MCV) (cDNA(MCV)) or to specific portions of the genome of avian sarcoma virus (ASV). We showed that genomic RNAs of avian erythroblastosis virus (AEV) and avian myeloblastosis virus (AMV) could not hybridize appreciably with cDNA(MCV). By contrast, cDNA(MCV) hybridized extensively (about 75%) and with essentially complete fidelity to the genome of Mill Hill 2 virus (MH2V), whose pathogenicity is very similar to that of MC29V, but different from that of AEV or AMV. Hybridization with the ASV cDNA's demonstrated that the MC29V genome includes about half of the ASV envelope protein gene and that the remainder of the MC29V genome is closely related to nucleotide sequences that are shared among the genomes of many avian leukosis and sarcoma viruses. We conclude that onc(MCV) probably specifies the unique set of pathogenicities displayed by MC29V and MH2V, whereas the oncogenic potentials of AEV and AMV are presumably encoded by a distinct nucleotide sequence unrelated to onc(MCV). The genomes of ASV, MC29V, and other avian oncoviruses thus share a set of common sequences, but apparently owe their various oncogenic potentials to unrelated transforming genes.

Deletion mutant of the Bratislava-77 strain of Rous sarcoma virus containing a fusion of the group-specific antigen and envelope genes

The genetic compositions of two independently derived preparations of the Bratislava-77 strain (B77) of Rous sarcoma virus were analyzed after each was passaged seven or more times in duck embryo fibroblasts. RNase, T1-resistant oligonucleotide fingerprint analysis of virion RNA from both preparations of duck-passaged B77 revealed the presence of two large noncontiguous deletions. Approximately 75% of the RNAs contained a deletion which spans oligonucleotides 304 to 4 on the viral genome (about 3,500 nucleotides) and encompasses all of the B77 polymerase gene. More than 90% of the RNAs also contained a deletion which spans src-specific oligonucleotides 6 and 5(about 2,200 nucleotides) and is identical to the deletion observed in transformation-defective B77. Virion RNA from duck-passaged B77 also contained two oligonucleotides (D1 and D2) not observed in the RNA of B77 virus grown on chicken embryo fibroblasts. Analysis of the virion RNA of duck-passaged B77 by denaturing agarose gel electrophoresis revealed four major subunits with molecular weights of 3.40 x 10(6), 2.65 x 10(6), 2.25 x 10(6), and 1.55 x 10(6). Whereas the 3.40- and 2.65-megadalton (Mdal) RNA species comigrated with the nondefective and transformation-defective RNAs of B77 propagated on chicken embryo fibroblasts, no counterparts to the 2.25- and 1.55-Mdal RNAs were observed in the RNA of B77 grown on chicken embryo fibroblasts. Oligonucleotide fingerprint analysis of these RNA species revealed that the 2.65-Mdal RNA contains the src-specific deletion and that 2.25-Mdal RNA contains the polymerase region deletion; both of these deletions were observed in the 1.55-Mdal RNA, which was the major RNA subunit species detected in duck-passaged B77. The new oligonucleotides (D1 and D2) observed in the duck-passaged virus were present in the 2.25- and 1.55-Mdal RNA species in vitro and in vivo and directs the synthesis of a 130,000-dalton protein (p130). p130 contains antigenic determinants specific for p27 (gag gene) and gp85 (env gene) but does not contain sequences which cross-react with antisera directed against the alpha beta form of RNA-dependent DNA polymerase (pol gene). This RNA, therefore, is generated by a fusion of the gag and env genes of Rous sarcoma virus B77.

Transformation-defective mutants of Rous sarcoma virus with src gene deletions of varying length

The RNAs of transformation-defective (td) deletion mutants of the Schmidt-Ruppin strain of Rous sarcoma virus were found to vary in size when compared by polyacrylamide gel electrophoresis. Three of seven td mutants appeared to recombine with a mutant of Rous sarcoma virus (Schmidt-Ruppin), which has a temperature-sensitive sarcoma (src) gene and is termed ts68, to give rise to recombinants with a reduced temperature sensitivity. The results suggested that different clones of td mutants exist: some in which the src gene appears to be deleted, and others in which the src gene is only partially deleted. A direct correlation between RNA size and the extent of src gene deletion measured by recombination was not obtained, possibly because the recombination assay could only detect src sequences homologous to the lesion(s) of ts68, whereas the electrophoretic analysis of the RNA measured src deletions as well as other possible alterations of the RNA.

Size and genetic content of viral RNAs in avian oncovirus-infected cells

Viral complementary DNA (cDNA) sequences corresponding to the gag, pol, env, src, and c regions of the Rous sarcoma virus genome were selected by hybridizing viral cDNA to RNA from viruses that lack the env or src gene or to polyadenylic acid [poly(A)]-containing RNA fragments of different lengths and isolating either hybridized or unhybridized DNA. The specificities, genetic complexities, and map locations of the selected cDNA's were shown to be in good agreement with the size and map locations of the corresponding viral genes. Analyses of virus-specific RNA, using the specific cDNA's as molecular probes, demonstrated that oncovirus-infected cells contained genome-length (30-40S) RNA plus either one or two species of subgenome-length viral RNA. The size and genetic content of these RNAs varied, depending on the genetic makeup of the infecting virus, but in each case the smaller RNAs contained only sequences located near the 3' end of the viral genome. Three RNA species were detected in Schmidt-Ruppin Rous sarcoma virus-infected cells: 39S (genome-length) RNA; 28S RNA, with an apparent sequence of env-src-c-poly(A); and 21S RNA, with an apparent sequence of src-c-poly(A). Cells infected with the Bryan high-titer strain of Rous sarcoma virus, which lacks the env gene, contained genome-length (35S) RNA and 21S src-specific RNA, but not the 28S RNA species. Leukosis virus-infected cells contained two detectable RNA species: 35S (genome-length) RNA and 21S RNA, with apparent sequence env-c-poly(A). Since gag and pol sequences were detected only in genome-length RNAs, it seems likely that the full-length transcripts function as mRNA for these two genes. The 28S and 21S RNAs could be the active messengers for the env and src genes. Analyses of sequence homologies among nucleic acids of different avian oncoviruses demonstrated substantial similarities within most of the genetic regions of these viruses. However, the "common" region of Rous-associated virus-0, an endogenous virus, was found to differ significantly from that of the other viruses tested.

Type C viral gag gene expression in chicken embryo fibroblasts and avian sarcoma virus-transformed mammalian cells

Sensitive radioimmunoassays were developed for avian type C viral gag gene-coded proteins. These assays were used to examine the restriction to virus production by avian embryo cells and mammalian cells transformed by avian sarcoma viruses. The results indicate that although a high-molecular-weight primary translational product of the gag gene is expressed, its cleavage and processing are incomplete. Furthermore, analysis of intermediate cleavage products provided information regarding the order of sequences coding for the individual viral proteins within the avian type C viral gag gene.

Complementation rescue of Rous sarcoma virus from transformed mammalian cells by polyethylene glycol-mediated cell fusion

Polyethylene glycol (PEG) is effective as a fusing agent for the rescue of virus from Rous sarcoma virus-transformed mammalian cells. The procedure of PEG-mediated rescue of virus from virogenic cell lines is described, and the technique is compared with that of Sendai virus-mediated rescue. Virus may be rescued quantitatively from virogenic cell lines by plating mitomycin C-killed transformed mammalian cells with chicken embryo cells, treating the monolayers with 50% PEG and overlaying the monolayers with focus agar. The number of foci that appeared reflected the number of heterokaryons in the fusion mixtures that released infectious virus. PEG gave reproducible results in virus rescue experiments with an efficiency equal to the best Sendai virus preparations. In addition to the description of the technique for PEG-mediated virus rescue from virogenic cell lines, a method for virus rescue from nonvirogenic lines is presented. Preinfection of the chicken embryo cells with helper avian leukosis virus (Rous-associated virus) prior to fusion with mammalian cells transformed by defective viruses complements the virus defect. We examined four nonvirogenic cell lines, and all released infectious virus in the complementation rescue assay.

Purification of DNA complementary to the env gene of avian sarcoma virus and analysis of relationships among the env genes of avian leukosis-sarcoma viruses

The env gene of avian leukosis-sarcoma viruses encodes a glycoprotein that determines the host range and surface antigenicitiy of virions. We have purified radioactive DNA (cDNAgp) complementary to at least a portion of the env gene for viral subgroups A and C; complementary DNA was synthesized with purified virions of wild-type avian sarcoma virus, and RNA from a mutant with a deletion in env was used to select DNA specific to env by molecular hybridization. The genetic complexity of cDNAgp for subgroup A (ca. 2,000 nucleotides) was sufficient to represent the entire deletion and most or all of the env cistron. The deletions in env in two independently isolated strains of virus (Bryan and rdNY8SR) overlap, and cDNAgp represents nucleotide sequences common to both deletions. By contrast, we could detect no overlap between deletions in env and deletions in the adjacent viral gene src. Laboratory stocks of viral subgroups A, B, C, D and E do not contain detectable amounts of env deletions when tested by molecular hybridization; hence, segregation of deletions in env is a less frequent event that the segregation of deletions in the viral transforming gene src (Vogt, 1971). We found extensive homology among the nucleotide sequences encoding the env genes of virus strains indigenous to chickens (subgroups A, B, C, D, and E) although subgorups B, D and E appear to differ slightly from subgroups A and C at the env locus. By contrast, viruses obtained from pheasant cells (subgroups F and G) have env genes with little or no relationship to env genes of chikcen viruses. According to available data, viruses of subgroup F arose by recombination between an avarian sarcoma virus and viral genes in the genome of ring-necked pheasants, whereas subgroup G viruses may be entirely endogenous to golden pheasants.

Cell-free translation of virion RNA from nondefective and transformation-defective Rous sarcoma viruses

Nondefective and transformation-defective virion subunit RNAs from two strains of Rous sarcoma virus (RSV) were translated in cell-free systems derived from Krebs IIA ascites cells, wheat germ, and L-cells. In each case the predominant viral-specific product was a polypeptide of molecular weight 76,000 that is related to the internal viral group-specific antigens, as judged by immunoprecipitation with monospecific antisera and tryptic peptide fingerprinting. No difference could be detected between the translation products of 35S RNA from nondefective and transformation-defective RSV virions, nor of 35S RNA from different strains of RSV. The 76,000-molecular-weight polypeptide synthesized in response to 35S RNA in vitro was labeled with formyl-methionine from initiator tRNA. Models for viral protein synthesis are discussed in the light of these results, and arguments positioning the group-specific antigen gene at the 5' end of the 35S RNA are presented.

Recombination between a temperature-sensitive mutant and a deletion mutant of Rous sarcoma virus

Cells doubly infected with two mutants of the Schmidt-Ruppin strain of Rous sarcoma virus (RSV), ts68, which is temperature sensitive for cell transformation (srcts), and a deletion mutant, N8, which is deficient in the envelope glycoprotein (env-), produced a recombinant which carried the defects of both parents. The frequency of formation of such a recombinant was exceptionally high and made up 45 to 55% of the progeny carrying the srcts marker. By contrast, the reciprocal recombinant, which is wild type in transformation (srcts) and contains the subgroup A envelope glycoprotein (envA), was almost undetectable. This remarkable difference in the frequency of the formation of the two possible recombinants suggests that a unique mechanism may be involved in the genetic interaction of the two virus genomes, one of which has a large deletion. When an RNA-dependent DNA polymerase-negative variant of the N8 (N8alpha) was crinants also became deficient in the polymerase. Cells infected by the srctsenv- recombinant were morphologically normal at the nonpermissive temperature (41 degrees C) and susceptible to all subgroups of RSV. The rate by which the wild-type RSV transformed the recombinant-preinfected cells was indistinguishable from that of transformation of uninfected chicken cells by the same wild-type virus. This indicates that no detectable interference exists at postpenetration stages between the preinfected and superinfecting virus genomes and confirms that the expression of the transformed state is dominant over the suppressed state.

Independent regulation of endogenous and exogenous avian RNA tumor virus genes

3H-Labeled complementary DNA specific for the envelope glycoprotein (env) gene of avian leukosis-sarcoma viruses was isolated by selective nucleic acid hybridization techniques, and used to analyze the expression of the endogenous provirus. The endogenous provirus in certain cell types termed chicken helper factor positive (chf+) can synthesize the envelope glycoprotein. Env DNA sequences were present in both chf+ and chf- cells, but env RNA was detectable only in positive cell types. When these cells were infected with the Bryan strain of Rous sarcoma virus (BH-RSV), a defective virus which is deleted in the env gene, the levels of endogenous env RNA remained unchanged, although exogenous BH-RSV specific RNA was synthesized in very high amounts. Thus, the infecting virus did not appear to influence the expression of the endogenous virus. Likewise, the endogenous virus did not influence the exogenous virus expression, since similar amounts of BH-RSV specific RNA were present in all infected cell types, regardless of the level of endogenous virus expression.

Viral glycoprotein synthesis studies in an established line of Japanese quail embryo cells infected with the Bryan high-titer strain of Rous sarcoma virus

Although a glycoprotein with an approximate molecular weight of 43,000 is associated with purified virions of the Bryan high-titer strain of Rous sarcoma virus propagated on R(-)Q cells, these virions lack gp85, the major glycoprotein of the avian tumor virus envelope. As measured by immune precipitation with a specific antiserum, gp85 does not accumulate to detectable levels in R(-)Q cells.

Location of envelope-specific and sarcoma-specific oligonucleotides on RNA of Schmidt-Ruppin Rous sarcoma virus

Envelope-specific and sarcoma-specific nucleotide sequences have been located within the 10,000 nucleotides of the RNA of nondefective Schmidt-Ruppin Rous sarcoma virus (nd SR). For this purpose, about 30 RNase-T1-resistant oligonucleotides were ordered relative to the 3'-poly(A) terminus of the RNA, to construct an oligonucleotide map of the nd SR RNA. A cluster of seven envelope-specific oligonucleotides, identified by their absence from an otherwise very similar oligonucleotide map of an envelop-defective deletion mutant (which lacks the major viral glycoprotein), mapped at a distance of 2800-5000 nucleotides from the poly(A) end of nd SR RNA. A cluster of two sarcoma-specific oligonucleotides, identified by their absence from an otherwise nearly identical oligonucleotide map of a transformation-defective deletion mutant, mapped at a distance of 1000-2000 nucleotides from the poly(A) end of nd SR RNA. The oligonucleotide maps of nd SR and of the two deletion mutants were the same from the poly(A) end up to 650 nucleotides and included one terminal oligonucleotid, termed C, which is found in all avian tumor viruses tested so far. A possible gene order consistent with our data suggests that sarcoma-specific nucleotide sequences map between envelope-specific nucleotide sequences and the poly(A) end of the RNA.

Sequences and functions of Rous sarcoma virus RNA

A procedure has been developed to map the genetic elements of avian tumor virus RNA, which has a molecular weight of about 3 X 10(6) daltons and a poly(A) sequence at the 3' end. For this purpose, about 30 RNase T1-resistant oligonucleotides were ordered relative to the 3'-poly(A) terminus of the RNA, to construct an oligonucleotide map of viral RNAs. A cluster of seven envelope gene (env)-specific oligonucleotides, identified by their absence from the otherwise very similar oligonucleotide map of an envelope-defective deletion mutant (which lacks the major viral glycoprotein), mapped at a distance of 0.9 to 1.6 X 10(6) daltons from the poly(A) end of sarcoma virus RNA. A cluster of three sarcoma gene (src)-specific oligonucleotides, identified by their absence from the otherwise nearly identical oligonucleotide map of a transformation-defective deletion mutant mapped at a distance of 0.2 to 0.6 X 10(6) daltons from the poly(A) end of sarcoma virus RNA. The oligonucleotide maps of sarcoma viruses and of related deletion mutants were the same from the poly(A) end up to 0.2 X 10(6) daltons and included one terminal oligonucleotide, termed C, which is found in all avian tumor viruses tested so far. Preliminary mapping experiments ordering the src-specific and env-specific oligonucleotides of recombinants, selected for sarcoma and envelope genes of different parents, agree with those obtained by comparing maps of wild type viruses and deletion mutants. A partial genetic map consistent with these results suggests that the src gene maps between the env gene and the 3'-poly(A) end of viral RNA. This map reads: poly(A)-src-env-(pol, gag).

Mapping of biological functions on RNA of avian tumor viruses: location of regions required for transformation and determination of host range

A map of the large T1 oligonucleotides of the RNA of Prague Rous sarcoma virus, strain B (Pr RSVb) has recently been established (Coffin and Billeter, submitted for publication). Since the RNA of Rous associated virus, type 1 (RAV-1) lacks many of the large 1 oligonucleotides of Pr RSV-B and contains others not present in the latter, the RNA of recombinants between RAV-1 and Pr RSV-B could be analyzed with regard to the origin of its sequences. Recombinants were selected for transforming capacity (characteristic for Pr RSV-B) and ability to grow on C/B chicken fibroblasts (characteristic for RAV-1). Four out of five recombinants examined had undergone at least two crossovers. The set of Pr RSV-B-specific oligonucleotides present in all recombinants defined an RNA region near the poly(A) segment; this must contain genetic information required for transformation required for transformation (the onc function). All recombinants lost a set of contiguous Pr RSV-B-specific oligonucleotides and concomitantly acquired a set of RAV-1-specific oligonucleotides. These define a region in the middle section of the oligonucleotide map, all or some of which must be required for determining growth capacity on C/B cells (the env function).

Mapping RNase T1-resistant oligonucleotides of avian tumor virus RNAs: sarcoma-specific oligonucleotides are near the poly(A) end and oligonucleotides common to sarcoma and transformation-defective viruses are at the poly(A) end

The large RNase T1-resistant oligonucleotides of the nondefective (nd) Rous sarcoma virus (RSV): Prague RSV of subgroup B (PR-B), PR-C and B77 of subgroup C; of their transformation-defective (td0 deletion mutants: td PR-B, td PR-C, and td B77; and of replication-defective (rd) RSV(-) were completely or partially mapped on the 30 to 40S viral RNAs. The location of a given oligonucleotide relative to the poly(A) terminus of the viral RNAs was directly deduced from the smallest size of the poly(A)-tagged RNA fragment from which it could be isolated. Identification of distinct oligonucleotides was based on their location in the electrophoretic/chromatographic fingerprint pattern and on analysis of their RNase A-resistant fragments. The following results were obtained. (i) The number of large oligonucleotides per poly(A)-tagged ffagment increased with increasing size of the fragment. This implies that the genetic map is linear and that a given RNase T1-resistant oligonucleotides has, relative to the poly(A) end, the same location on all 30 to 40S RNA subunits of a given 60 to 70S viral RNA complex, (ii) Three sarcoma-specific oligonucleotides were identified in the RNAs of Pr-B, PR-C and B77 by comparison with the RNAs of the corresponding td viruses...