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

Defining the borders of the chicken proto-fps gene, a precursor of Fujinami sarcoma virus

The transforming (onc) genes of retroviruses contain specific sequences, derived from as yet poorly defined, normal cellular genes, termed proto-onc genes. Proto-onc genes must be defined to explain their docility compared to the oncogenicity of the viral derivatives. Here we set out to determine the borders of the chicken proto-fps gene from which the onc genes of avian Fujinami (FSV) and PRC sarcoma viruses (PRCSV) are derived. These onc genes are hybrids of an element from the gag gene of retroviruses (delta gag) linked to a 2.8-kb domain from proto-fps. To identify the 5' border of proto-fps we have sequenced 1.5 kb beyond the 5' border of overlap with viral fps utilizing a proto-fps clone derived previously. A possible promoter was identified that maps 736 nucleotides from this border. The 736 nucleotides contain two possible exons with 121 codons, and short regions of homology with the delta gag termini of FSV and PRCII. A translation stop codon and an adjacent polyadenylation signal were identified just prior to the 3' border of overlap with viral fps within a 1.15-kb sequence of a newly isolated proto-fps clone. Comparing four exons within this 1.15 kb proto-fps sequence with known fps equivalents of FSV and PRCSV, we have detected strain-specific, but no common point mutations in each viral genome. A 3.3-kb polyadenylated proto-fps mRNA was detected in chicken liver RNA by gel electrophoresis and hybridization with proto-fps DNA. We conclude that the coding capacity of proto-fps is just over 3 kb, consistent with the size of the putative proto-fps protein of 98 kDa and hence slightly larger than that of viral fps. Thus proto-fps and the viral delta gag-fps genes each contain distinct 5' regulatory and coding sequences and share the 3' terminal fps domains. It is suggested that this difference, rather than scattered point mutations, is responsible for the oncogenic function of the viral genes and the unknown cellular function of proto-fps.

Induction of tumors and generation of recovered sarcoma viruses by, and mapping of deletions in, two molecularly cloned src deletion mutants

td108 , a transformation-defective (td) deletion mutant of the Schmidt-Ruppin strain of Rous sarcoma virus of subgroup A (SR-A), was molecularly cloned. Two isolates of td viruses, td108 -3b and td108 -4a, obtained by transfection of the molecularly cloned td108 DNAs into chicken embryo fibroblasts, were tested for their ability to induce tumors and generate recovered avian sarcoma viruses ( rASVs ) in chickens. Both td viruses were able to induce tumors with a latency and frequency similar to those observed previously with biologically purified td mutants of SR-A. rASVs were isolated from most of the tumors examined. The genomic RNAs of those newly obtained rASVs were analyzed by RNase T1 oligonucleotide fingerprinting. The results showed that they had regained the deleted src sequences and contained the same set of marker src oligonucleotides as those of rASVs analyzed previously. The src oligonucleotides of rASVs are distinguishable from those present in SR-A. We conclude that those rASVs must have been generated by recombination between the molecularly cloned td mutants and the c-src sequence. The deletions in the td mutants were mapped by restriction enzyme analysis and nucleotide sequencing. td108 -3b was found to contain an internal src deletion of 1,416 nucleotides and to retain 57 and 105 nucleotides of the 5' and 3' src coding sequences, respectively. td108 -4a contained a src deletion of 1,174 nucleotides and retained 180 and 225 nucleotides of the 5' and 3' src sequences, respectively. Comparison of sequences in the 5' src and its upstream region of td108 -3b with those of SR-A, rASV1441 (a td108 -derived rASV analyzed previously), and c-src suggested that the 5' recombination between td108 and c-src occurred from 7 to 20 nucleotides upstream from the beginning of the src coding sequence.

Complete env gene deletions of three replication-defective strains of Rous sarcoma virus and a model for the origin of their genetic structures

Replication-defective deletion mutants of Rous sarcoma virus (RSV) have been described which transform cells in culture and elaborate envelope (-) defective particles. The env deletions of two clonal variants of the Bryan strain of RSV, RSV(-)3, and RSV(-)16, and of a replication-defective variant of Schmidt-Ruppin RSV (SRN8) were analyzed by fingerprinting oligonucleotides hybridized by a molecularly cloned env DNA probe that spans from near the 3' end of pol to the 3' end of env. It was observed that all three replication-defective RSV strains are essentially complete env deletions but retain the 3' end of pol. Based on a common pol-src junction oligonucleotide that may reflect a homologous sequence repeated at both ends of env in nondefective RSV, the env deletions of RSV(-)3 and 16 appear to be isogenic. The original deletion may have involved recombination between these sequences. The absence of this oligonucleotide in SRN8 indicates that the env deletion of SRN8 has different borders and represents an independent env deletion of nondefective RSV. All three defective RSVs have the genetic structure gag-pol-src. This genetic structure is consistent with the need for a complete gag to make a particle and with the assumption that an independent src gene rather than a gag- or gag-pol-src hybrid gene functions in transformation. It is suggested that a complete pol is not necessary for, but may assist, virus particle formation.

The low tumorigenic potential of PRCII, among viruses of the Fujinami sarcoma virus subgroup, corresponds to an internal (fps) deletion of the transforming gene

The avian sarcoma viruses FSV, PRCII, PRCIIp, and PRCIV share a related class of hybrid onc genes (delta gag-fps) defined by a specific nucleotide sequence fps and by delta gag-fps proteins of different sizes. Among these viruses, PRCII appears to have a lower tumorigenic potential than the others. Here we have compared fibroblast-transforming function and onc gene structure of these viruses. The fibroblast transforming ability of PRCII was lower than those of FSV, PRCIIp, and PRCIV. By gel electrophoresis the genomic RNA of PRCII measured 3.5 kb and those of FSV, PRCIIp, and PRCIV 4.5 kb; the delta gag-fps protein of PRCII measured 105 kilodaltons (kd), that of FSV 140 kd, and those of PRCIIp and PRCIV about 150 kd. By fingerprinting viral RNAs hybridized with molecularly cloned viral DNA the delta gag regions of PRCII and PRCIIp were defined to be 1.45 kb and that of FSV to be 1.3 kb. Fingerprint analysis of viral RNA-proto fps DNA hybrids showed the fps regions (approximately 2.8 kb) of FSV and PRCIIp to be isogenic. Compared to FSV and PRCIIp, the fps sequence of PRCII lacked a 1-kb region which maps between 0.3 and 1.3 kb from the 5' end of fps in FSV and PRCIIp. Based on oligonucleotide analysis, the shared fps complements of PRCII and PRCIIp were indistinguishable while that of FSV differed from those of the PRC viruses in scattered point mutations amounting to 1-2% of the RNA. Since all other regions of PRCII are isogenic with those of the highly tumorigenic variants PRCIIp, PRCIV, and FSV, it is concluded that the low fibroblast-transforming and oncogenic potential of PRCII reflects the internal fps deletion. Since the fps deletion reduces but does not eliminate transforming function, we suggest that the complete onc genes of viruses in the FSV subgroup include either several functional, or a regulatory and a functional fibroblast transforming domain. It has been reported that the 3' domains of the onc genes of viruses in the Fujinami subgroup and the onc genes of certain feline sarcoma viruses are distantly related. Since full transforming potential of the avian viruses depends on the 5' fps region not shared with the feline sarcoma viruses, we suggest that despite their structural homology, the avian and feline onc genes must have functionally different domains.

Structural relationship between the chicken DNA locus, proto-fps, and the transforming gene of Fujinami sarcoma virus, delta gag-fps

The avian Fujinami sarcoma virus (FSV) contains a hybrid transforming gene (delta gag-fps) with a 5' 1.3-kb portion derived from the gag gene of avian retroviruses and a 3' 2.8-kb portion (fps) derived from a cellular prototype. A lambda recombinant DNA clone carrying fps sequences within a 16-kb insert of cellular DNA, termed lambda proto-fps clone 12, has been selected from a chicken DNA library for comparison with the viral onc gene. Mapping of endonuclease-resistant proto-fps DNA fragments and hybridization with cloned viral DNA located FSV-related sequences at the 3' end of the insert within a region of about 4.25 kb. Alignment of endonuclease-resistant proto-fps and viral DNA fragments relative to common RNase T1-resistant oligonucleotide sequences of viral RNA, identified by fingerprinting DNA-RNA hybrids, indicated: (i) that proto-fps is colinear with viral fps but is interrupted by 1.75 kb of scattered sequences unrelated to viral fps; (ii) that among the nine endonuclease sites compared, proto-fps and viral fps share one PvuII, one BamHI, and possibly a Kpn1 site at homologous locations, and that they each have unique endonuclease sites and common sites at unique locations; (iii) that within 12 kb upstream from the 5' boundary of overlap with viral fps, proto-fps lacks gag-related sequences; and (iv) that proto-fps clone 12, like several others isolated by us, lacks at the 3' end an equivalent of the 3' 10 to 20% of viral fps. The eight endonuclease site-map coordinates of proto-fps and viral DNA also divided 44 fps oligonucleotides of viral RNA into 9 map segments. We conclude that the onc gene of FSV differs from proto-fps in delta gag and in multiple point mutations, compatible with a transforming function for the viral gene and a normal function for the cellular sequence homolog. Since proto-fps is unrelated to essential virion genes, the onc gene of FSV must have originated from cellular proto-fps by rare, illegitimate recombination.

Retroviral transforming genes in normal cells?

The hallmark of retroviral transforming genes (onc genes) are specific sequences which are unrelated to essential virion genes but are closely related to sequences in normal cells. Viral onc genes probably originated from rare transductions of these cellular sequences by retroviruses without onc genes. Consequently, it has been suggested that retroviral transforming genes are present in normal cells in a latent form. However, recent structural analyses indicate that viral onc genes and cellular genes, which share specific sequences, are not isogenic. They differ from each other in scattered point mutations and in unique coding regions. The cellular genes containing onc-related sequences are expressed in normal cells compatible with a normal function. There is as yet no functional or consistent circumstantial evidence that these cellular genes cause cancer in animals that are not infected by viruses with onc genes. Therefore, it is still uncertain whether the onc-related cellular genes have oncogenic potential beyond their role as progenitors of retroviral onc genes.

DNA sequence of the viral and cellular src gene of chickens. II. Comparison of the src genes of two strains of avian sarcoma virus and of the cellular homolog

The nucleotide sequence of the src gene and flanking regions of the Schmidt-Ruppin strain of Rous sarcoma virus (SR-A) was determined. The src region of SR-A was very homologous to that of recovered avian sarcoma virus (rASV1441), with only 17 differences among 1,578 nucleotides. The size of the predicted protein was 526 amino acids in both viruses, of which 6 amino acids were different. The differences in nucleotides and amino acids between the two viruses localized within the 5' two-thirds of the src coding region. There were also viruses localized within the 5' two-thirds of the src coding region. There were also some differences in the region flanking the 5' end of src. Since rASVs are considered to be recombinatns between deletion mutants of SR-A and cellular-src (c-src) sequences, several segments of c-src DNA were also sequenced to understand the molecular basis for the recombination. At 14 of 17 bases where SR-A and rASV1441 differed, rASV1441 had the same sequence as c-src. Three of these sequences corresponded to sequences of oligonucleotides which were previously identified in RNAs of nearly all isolates of rASV but which were absent in SR-A RNA. In the 5'-flanking sequences of the src gene, c-src was more similar to rASV1441 than to SR-A. These results confirm the cellular origin of the src sequences of rASVs and provide information about the possible sites of the recombination.

DNA clone of avian Fujinami sarcoma virus with temperature-sensitive transforming function in mammalian cells

We have molecularly cloned an integrated proviral DNA of Fujinami sarcoma virus (FSV) into a lambda phage vector and further subcloned it into plasmid pBR322. The source of provirus was a quail nonproducer cell clone transformed by FSV. The FSV strain used is temperature sensitive in the maintenance of transformation of avian cells. The recombinant plasmid was shown to contain an entire FSV genome by fingerprinting the hybrids formed with 32P-labeled FSV RNA. This analysis also revealed a previously undetected env-related sequence in FSV which represents the 3' end of the gp85 env gene. A physical map of cloned FSV DNA identifying sites of several restriction enzymes is described. Upon transfection, FSV DNA cloned in pBR322 transformed mouse NIH-3T3 cells, which proved to be temperature sensitive in maintaining transformation. Phosphorylation but not synthesis of p140, the only known gene product of FSV, was also temperature sensitive in these cells. The correlation between transformation and phosphorylation of p140 suggests that phosphorylation of p140 is necessary for transformation of mouse cells, as was shown previously for avian cells. These results provide direct genetic evidence that the mechanisms for maintaining transformation of mammalian and avian cells involve the same FSV gene product, p140. Homology was detected by hybridization between transformation-specific sequences of FSV DNA and certain restriction endonuclease-resistant fragments of cellular DNA of two avian species, chicken and quail. Under the same conditions homology was also detected with DNA of non-avian species, although apparently to a lower degree than with avian cells.

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.