Nucleotide sequence of the 3' half of AKV

Detection of alternative DNA structures and its implications for human disease

Around 3% of the genome consists of simple DNA repeats that are prone to forming alternative (non-B) DNA structures, such as hairpins, cruciforms, triplexes (H-DNA), four-stranded guanine quadruplexes (G4-DNA), and others, as well as composite RNA:DNA structures (e.g., R-loops, G-loops, and H-loops). These DNA structures are dynamic and favored by the unwinding of duplex DNA. For many years, the association of alternative DNA structures with genome function was limited by the lack of methods to detect them in vivo. Here, we review the recent advancements in the field and present state-of-the-art technologies and methods to study alternative DNA structures. We discuss the limitations of these methods as well as how they are beginning to provide insights into causal relationships between alternative DNA structures, genome function and stability, and human disease.

Chemical reagents for investigating the major groove of DNA

Chemical modification provides an inexpensive and rapid method for characterizing the structure of DNA and its association with drugs and proteins. Numerous conformation-specific probes are available, but most investigations rely on only the most common and readily available of these. The major groove of DNA is typically characterized by reaction with dimethyl sulfate, diethyl pyrocarbonate, potassium permanganate, osmium tetroxide, and, quite recently, bromide with monoperoxysulfate. This commentary discusses the specificity of these reagents and their applications in protection, interference, and missing contact experiments.

The formation of parallel RNA-RNA duplexes in vitro

Over the years the structural properties of nucleic acids have been of interest, providing data that may be of importance for DNA and RNA organization and function in the cell. We have attempted to look for the formation of parallel RNA-RNA duplexes in vitro. RNA molecules comprising complementary in the same polarity alternating stretches of A and U of increasing length were enzymatically synthesized and annealed in physiological conditions. The fractionation in the denaturing polyacrylamide gels revealed the formation of two types of full-length parallel RNase A-stable duplexes established either by A-U or by A-A and U-U self pairs. These results suggest novel structural properties of versatile RNA molecules that potentially may be realized in vivo.

A structural analysis of the bent kinetoplast DNA from Crithidia fasciculata by high resolution chemical probing

The chemical probes potassium permanganate (KMnO4) and diethylpyrocarbonate (DEPC) have been used to study the conformation of bent kinetoplast DNA from Crithidia fasciculata at different temperatures. Chemical reactivity data shows that the numerous short A-tracts of this bent DNA adopt a similar structure at 43 degrees C. This conformation appears to be very similar to the conformation of A-tracts in DNA exhibiting normal gel mobility. The A-tract structure detected by chemical probing is characterized by a high degree of base stacking on the thymine strand, and by an abrupt conformational change at the 3' end of the adenine strand. In general, no major alteration of this A-tract specific structure was detected between 4-53 degrees C. However, probing with KMnO4 revealed two unusual features of the C. fasciculata sequence that may contribute to the highly aberrant gel mobility of this DNA: 1) the B DNA/A-tract junction 5' dC/A3-6 3'. 5' dT3-6/G 3' is disproportionately represented and is conformationally distinct from other 5' end junctions, and 2) low temperature favors a novel strand-specific conformational distortion over a 20 base pair region of the bent kinetoplast DNA. Presence of the minor groove binding drug distamycin had little detectable effect on the A-tract conformation. However, distamycin did inhibit formation of the novel KMnO4 sensitive low temperature structure and partially eliminated the anomalous gel mobility of the kinetoplast DNA. Finally, we describe a simple and reproducible procedure for the production of an adenine-specific chemical DNA sequence ladder.

Local supercoil-stabilized DNA structures

The DNA double helix exhibits local sequence-dependent polymorphism at the level of the single base pair and dinucleotide step. Curvature of the DNA molecule occurs in DNA regions with a specific type of nucleotide sequence periodicities. Negative supercoiling induces in vitro local nucleotide sequence-dependent DNA structures such as cruciforms, left-handed DNA, multistranded structures, etc. Techniques based on chemical probes have been proposed that make it possible to study DNA local structures in cells. Recent results suggest that the local DNA structures observed in vitro exist in the cell, but their occurrence and structural details are dependent on the DNA superhelical density in the cell and can be related to some cellular processes.

Localization of melted regions in supercoiled DNA

Diethyl pyrocarbonate (DEPC) was used as a probe of local denatured regions in ccDNA pAO3 plasmid. It was found that in native ccDNA molecules only adenosine residues in the loop of the cruciform structure react with DEPC. Denaturation of ccDNA is accompanied by the appearance of two short regions (20 bp long) at both borders of the cruciform structure. Further increase in the denaturation process is associated with considerable expansion of the region located to the left of the cruciform, while the cruciform structure itself and the denatured region located to the right of it disappear.

Tet repressor-tet operator contacts probed by operator DNA-modification interference studies

Contacts between tet operator DNA and Tet repressor protein are characterized by modification interference studies. The modified DNA fragments are separated into fractions with high, intermediate and low affinities for Tet repressor by polyacrylamide gel electrophoresis. Ethylation of the phosphates with N-ethylnitrosourea reveals 12 contacts of a repressor dimer to tet operator. Eight of these contacts appear to be important for Tet repressor binding, as judged by the strong interference at these positions, while four contacts are probably less important. All of the phosphate contacts are located on the same side of the B-DNA structure. The sequences of tet operators proposed to interact with the recognition alpha-helix of Tet repressor are TCTATC in three cases and CCTATC in one case. After methylation of N-7 with dimethylsulfate, strong interference is observed at the guanine residues at positions +/- 2. None of the N-7 functions of other guanine residues seems to be involved in tight contacts to Tet repressor. Tet repressor subunits form identical phosphate and guanine N-7 contacts with each half side of the two tet operators indicating twofold dyad symmetry of the complexes. Attempts to analyze the methylation interference at the adenine N-3 sites reveal different results for the operators. Modification of DNA fragments with diethylpyrocarbonate yields hypersensitive sites in the tet operators, indicating different local DNA structures. Carbethoxylation interference studies confirm the contacts at the purines found by methylation interference. All of the sequence-specific protein-DNA contacts detected in this study are centered at the inside four base-pairs in each tet operator half side. The contacts are discussed with respect to the structure of the repressor-operator complex.

Biological and molecular analysis of LCV, an endogenous retrovirus with defective env gene

Retrovirus infectivity is the result of a cooperative interaction of three structural genes, gag, pol, and env. Since the L-cell endogenous retrovirus (LCV) lacks the env gene translation product, our aim was to study the biological and molecular basis of its non-infectiousness. Fusion experiments between LCV and homologous or heterologous cells demonstrated that virus production could be obtained only after LCV artificial penetration in murine cells and that the new progeny was still noninfectious. Northern blot analysis and heteroduplex mapping of the genomic RNA revealed a 0.99 kb deletion including the 3' region of the pol reading frame, the whole xenotropic and part of the ecotropic domain of the env gene. The results suggest that the observed deletion is responsible for the absence of the gp 70 and the gp 15 E molecules in the virion and seems therefore to be the molecular basis for the non-infectiousness of this retrovirus.

Viral sequences are associated with many histocompatibility genes

A C57BL/6By 5.5 kb Pvu II polymorphic restriction fragment which hybridizes with a spleen focus-forming env probe and maps in the H-30 region has been cloned, and a 358 bp subfragment subcloned. Hybridization and sequencing studies show that the 358 bp fragment is encoded by the region of the pol gene of murine retrovirus which codes for an endonuclease critical for viral integration. Hybridizations of digested murine genomic DNAs with the 358 bp probe generate 31 restriction fragment length polymorphisms (RFLPs); 16 of these can be placed near the following 15 minor histocompatability (H) loci: H-3, H-4, H-7, H-13, H-15, H-16, H-17, H-19, H-22, H-24, H-27, H-30, H-34, H-36, and H-38. We suggest that the proximity of viral sequences to H loci is probably evolutionarily and functionally significant and that the closeness of viral sequences and minor H loci can probably be utilized to facilitate the cloning of minor H genes. During the course of these studies, it has become possible to tentatively assign H-17, H-34, and H-38 to chromosome 12. In addition, it was observed that several H-2 congenic strains retain portions of chromosome 12 from the parental donor strains used in their derivation.

Diethyl pyrocarbonate: a chemical probe for secondary structure in negatively supercoiled DNA

Purine residues located within regions of DNA that have the potential to form left-handed Z-helical structures are modified preferentially by diethyl pyrocarbonate; this hyperreactivity is dependent on the degree of negative superhelicity of the circular DNA molecules. As negative superhelical density increases, guanosines in a 32-base-pair alternating G-C sequence and adenosines (but not guanosines) in a 64-base-pair alternating A-C/G-T sequence become 5- to 10-fold more reactive to diethyl pyrocarbonate. The negative superhelical densities at which enhanced reactivity occurs are similar to those reported for the point at which left-handed helices form within plasmids carrying these DNA sequences. Probing of negatively supercoiled pBR322 with diethyl pyrocarbonate reveals a hyperreactive region 31 base pairs in length of which only 9 base pairs are a perfect alternating purine and pyrimidine sequence; the reactivity of purines within this sequence indicates that purines in the anti conformation, or guanosines in the syn conformation with neighboring 3' thymidines, are not hyperreactive in the Z-DNA form.

Functional analysis of reverse transcription by a frameshift pol mutant of murine leukemia virus

Endogenous reverse transcription by wild-type murine leukemia virus (MuLV) was compared to that catalyzed by clone 23, a pol mutant containing a reverse transcriptase protein which lacks the carboxyl-terminal third of the molecule (J. G. Levin, S. C. Hu, A. Rein, L. I. Messer, and B. I. Gerwin (1984), J. Virol. 51, 470-478). Competition immunoassays revealed that mutant virions contain normal amounts of polymerase protein, indicating that the lack of carboxyl-terminal sequences does not alter normal processing of enzyme precursors. Although the mutant enzyme was previously shown to have the ability to copy and degrade RNA:DNA hybrids, the present study demonstrates that it is defective in functions required to generate full-length copies of viral DNA. Analysis of products of endogenous reverse transcription showed that minus-strand strong-stop DNA is formed and that mutant virions synthesize a series of minus-strand DNA intermediates up to 2.2 kb in length. Comparison of mutant and wild-type MuLV reaction products indicated that the 2.2-kb termination site of the mutant corresponds to a normal pausing region for the wild-type enzyme. Computer analysis of sequences and structure within pausing regions suggested the involvement of C-rich consensus sequences plus multibranch loop structures in the general phenomenon of enzyme-pausing during reverse transcription.

Chemical probes of DNA conformation: detection of Z-DNA at nucleotide resolution

Chemical probes sensitive to alterations in DNA conformation, especially Z-DNA, have been identified. These permit cleavage of DNA at sites of unusual structure, the results of which can be displayed on a sequencing gel. Using supercoiled plasmids containing inserts of d(C-G)16 and d(C-A)31 X d(T-G)31, it was found that hydroxylamine and osmium tetraoxide react preferentially with cytosines and thymines, respectively, near B-DNA-Z-DNA junctions; diethylpyrocarbonate reacts more strongly with purines within Z-DNA regions; and dimethylsulfate and diethylsulfate react more strongly with guanines in Z-DNA that are out of phase with the usual pattern of purine-pyrimidine alternation. Our results show that B-Z boundaries are mobile and that with increasing torsional strain, the Z-DNA regions can expand to include nonalternating nucleotide sequences.

Complete nucleotide sequence of the Drosophila transposable element copia: homology between copia and retroviral proteins

We have determined the complete nucleotide sequence of the copia element present at the white-apricot allele of the white locus in Drosophila melanogaster. This transposable element is 5,146 nucleotides long and contains a single long open reading frame of 4,227 nucleotides. Analysis of the coding potential of the large open reading frame, which appears to encode a polyprotein, revealed weak homology to a number of retroviral proteins, including a protease, nucleic acid-binding protein, and reverse transcriptase. Better homology existed between another part of the copia open reading frame and a region of the retroviral pol gene recently shown to be distinct from reverse transcriptase and required for the integration of circular DNA forms of the retroviral genome to form proviruses. Comparison of the copia sequence with those of the Saccharomyces cerevisiae transposable element Ty, several vertebrate retroviruses, and the D. melanogaster copia-like element 17.6 showed that Ty was most similar to copia, sharing amino acid sequence homology and organizational features not found in the other genetic elements.

Complete nucleotide sequence of the Drosophila transposable element copia: homology between copia and retroviral proteins

We have determined the complete nucleotide sequence of the copia element present at the white-apricot allele of the white locus in Drosophila melanogaster. This transposable element is 5,146 nucleotides long and contains a single long open reading frame of 4,227 nucleotides. Analysis of the coding potential of the large open reading frame, which appears to encode a polyprotein, revealed weak homology to a number of retroviral proteins, including a protease, nucleic acid-binding protein, and reverse transcriptase. Better homology existed between another part of the copia open reading frame and a region of the retroviral pol gene recently shown to be distinct from reverse transcriptase and required for the integration of circular DNA forms of the retroviral genome to form proviruses. Comparison of the copia sequence with those of the Saccharomyces cerevisiae transposable element Ty, several vertebrate retroviruses, and the D. melanogaster copia-like element 17.6 showed that Ty was most similar to copia, sharing amino acid sequence homology and organizational features not found in the other genetic elements.

Nucleotide sequence analysis of the BALB/c murine sarcoma virus transforming gene

We determined the nucleotide sequence of the v-H-ras-related oncogene of BALB/c murine sarcoma virus. This oncogene contains an open reading frame of 189 amino acids that initiates and terminates entirely within the mouse cell-derived ras sequence. The protein encoded by this open reading frame matches the sequence predicted for the T24 human bladder carcinoma oncogene product, p21, in all but two positions. The presence of a lysine residue in position 12 of BALB/c murine sarcoma virus p21 likely accounts for its oncogenic properties.

Cell-type-specific contacts to immunoglobulin enhancers in nuclei

The introns separating the variable and constant regions of active immunoglobulin genes contain tissue-specific transcriptional enhancer elements, DNA segments which act in cis in an orientation- and distance-independent (up to a few kilobases (kb)) manner to enhance transcription initiation at adjacent promoters. The immunoglobulin heavy-chain enhancer is active only in lymphoid cells: in transfection assays it is capable of controlling in cis transcription from the simian virus 40 (SV40) T-antigen, rabbit beta-globin and immunoglobulin gene promoters up to at least 2 kb away. Genetic deletion analysis suggests that a region of as few as 140 base pairs (bp) is sufficient for the enhancement effect. These functional characteristics and DNA sequences are conserved between mouse and man. However, it is not known whether tissue-specific proteins bind to the enhancer. Proteins that interact with DNA at specific sequences can prevent or enhance the reactions of individual guanines or adenines with dimethyl sulphate (DMS), and this property has been used to display the DNA contacts of various regulatory proteins. Here we apply this DMS strategy in experiments involving single-copy genes within intact mammalian nuclei using genomic sequencing.

Construction of recombinants between molecular clones of murine retrovirus MCF 247 and Akv: determinant of an in vitro host range property that maps in the long terminal repeat

The leukemogenic mink cell focus-forming (MCF) retroviruses such as MCF 247 have biological properties distinct from those of their ecotropic progenitors. Nucleotide sequences encoding portions of gp70, Prp15E, and the long terminal repeat differ between the two types of viruses. To investigate the role of each of these genetic elements in determining the biological properties of MCF viruses, we prepared infectious molecular clones of MCF 247 and generated a set of recombinants between these clones and a molecular clone of Akv, the ecotropic parent of MCF 247. Each molecular clone of MCF 247 was distinct. All the recombinants between Akv and MCF 247 yielded infectious virus upon transfection. Most interestingly, recombinants which contain the long terminal repeat of MCF 247 were found to have an in vitro host range property that has been correlated with high oncogenic activity and thymotropism of certain MCF isolates; namely, they plated with higher efficiency on SC-1 cells than on NFS mouse embryo cells. Nononcogenic MCF isolates showed a slight preference for NFS cells, whereas Akv virus plated with approximately equal efficiency on the two cell types.

Generation of AKR mink cell focus-forming virus: nucleotide sequence of the 3' end of a somatically acquired AKR-MCF

The 3' end of an AKR-MCF provirus (MCFr35) was cloned and found to be biologically active. Comparison of the nucleotide sequence of MCFr35 with the sequence of other MuLVs revealed that the MCFr35 was most likely derived from the same xenotropic and ecotropic parents, which were involved in the generation of AKR-MCF247. Ecotropic sequences are present around the XbaI site at position 7.9 on the genomic map, and in the long terminal repeat. Most of the T1 oligonucleotide sequences, characteristic for the leukemogenic "class I" MCFs, are also present in MCFr35, with the exception of T1 oligonucleotides 108 and 18. The MCFr35 LTR contains a duplicated enhancer sequence from a xenotropic-like provirus, which is present only once per haploid genome equivalent. The 3' end of MCFr35 consist predominantly of nonecotropic sequences, thereby delimiting the positions of recombination in various MCF viruses.

Nucleotide sequence analysis establishes the role of endogenous murine leukemia virus DNA segments in formation of recombinant mink cell focus-forming murine leukemia viruses

The sequence of 363 nucleotides near the 3' end of the pol gene and 564 nucleotides from the 5' terminus of the env gene in an endogenous murine leukemia viral (MuLV) DNA segment, cloned from AKR/J mouse DNA and designated as A-12, was obtained. For comparison, the nucleotide sequence in an analogous portion of AKR mink cell focus-forming (MCF) 247 MuLV provirus was also determined. Sequence features unique to MCF247 MuLV DNA in the 3' pol and 5' env regions were identified by comparison with nucleotide sequences in analogous regions of NFS -Th-1 xenotropic and AKR ecotropic MuLV proviruses. These included (i) an insertion of 12 base pairs encoding four amino acids located 60 base pairs from the 3' terminus of the pol gene and immediately preceding the env gene, (ii) the deletion of 12 base pairs (encoding four amino acids) and the insertion of 3 base pairs (encoding one amino acid) in the 5' portion of the env gene, and (iii) single base substitutions resulting in 2 MCF247 -specific amino acids in the 3' pol and 23 in the 5' env regions. Nucleotide sequence comparison involving the 3' pol and 5' env regions of AKR MCF247 , NFS xenotropic, and AKR ecotropic MuLV proviruses with the cloned endogenous MuLV DNA indicated that MCF247 proviral DNA sequences were conserved in the cloned endogenous MuLV proviral segment. In fact, total nucleotide sequence identity existed between the endogenous MuLV DNA and the MCF247 MuLV provirus in the 3' portion of the pol gene. In the 5' env region, only 4 of 564 nucleotides were different, resulting in three amino acid changes between AKR MCF247 MuLV DNA and the endogenous MuLV DNA present in clone A-12. In addition, nucleotide sequence comparison indicated that Moloney-and Friend-MCF MuLVs were also highly related in the 3' pol and 5' env regions to the cloned endogenous MuLV DNA. These results establish the role of endogenous MuLV DNA segments in generation of recombinant MCF viruses.

Generation of AKR mink cell focus-forming viruses: a conserved single-copy xenotrope-like provirus provides recombinant long terminal repeat sequences

AKV and AKR mink cell focus-forming virus-specific probes from the envelope and long terminal repeat (LTR) regions were prepared for study of the structure of recombinant proviruses in tumor tissues of AKR mice. The results showed that (i) all somatically acquired proviruses possessed, besides a recombinant gp70 gene, an altered U3 LTR; (ii) in a substantial portion of the somatically acquired AKR mink cell focus-forming proviruses, the LTR comprised sequences derived from the same xenotropic-like provirus; (iii) this U3 LTR donating parental provirus (Xeno-dL) was present only once per genome equivalent in several mouse strains; (iv) in the strains containing the Xeno-dL provirus, the provirus was present in the same chromosomal site; (v) restriction analysis of the Xeno-dL revealed that the mink cell focus-forming gp70 sequences were derived from a parental provirus, different from Xeno-dL. Therefore, at least two non-ecotropic parents participate in the generation of leukemogenic AKR mink cell focus-forming viruses: a xenotropic-like virus, Xeno-dL, donating U3 LTR sequences, and another xenotropic-like virus or viruses providing gp70 sequences.

The nucleotide sequence of the Akv murine leukemia virus genome

The nucleotide sequence of an infectious molecular clone of the Akv murine leukemia virus has been determined by the dideoxy chain termination method after subcloning in bacteriophage M13 vectors. The sequence predicts an RNA genome of 8371 nucleotides containing three large open reading frames corresponding to the gag, pol, and env genes. Signal sequences for transcription, splicing, and translation have been identified. The positions of 95 major RNase T1 resistant oligonucleotides of the Akv RNA genome have been located.

Free and integrated recombinant murine leukemia virus DNAs appear in preleukemic thymuses of AKR/J mice

We studied the appearance and structure of murine leukemia viral genomes in preleukemic AKR/J mice by Southern hybridization. Up to an average of one to two copies per thymocyte of unintegrated murine leukemia virus DNA appears in the thymuses of preleukemic mice beginning at 4 to 5 months of age and disappears in leukemic thymuses. The free viral genomes are absent in the spleens, livers, and brains of preleukemic mice. Using a series of ecotropic and nonecotropic murine leukemia virus hybridization probes, we showed that the unintegrated viral genomes are structurally analogous to those of recombinant mink cell focus-forming viruses that appear as proviruses in leukemic AKR thymocytes, suggesting that these free viral DNAs are the direct precursors to the leukemia-specific proviruses. The mosaic of ecotropic and nonecotropic sequences within these unintegrated viral DNAs varies from one preleukemic thymus to another but often appears structurally homogeneous within individual thymuses, indicating that often each thymus was being infected by a unique mink cell focus-forming virus. Analysis of high-molecular-weight DNA shows that recombinant proviruses reside in the chromosomal DNA of thymocytes within the preleukemic thymus, with the number rising to an average of several copies per thymocyte, but we do not detect any preferred integration sites. These results suggest that, in general, before the development of thymic leukemias in AKR mice there is a massive infection by a unique mink cell focus-forming virus which then integrates into many different sites of individual thymocytes, one of which grows out to become a tumor.

Nucleotide sequences of the retroviral long terminal repeats and their adjacent regions

The nucleotide sequences of the LTRs and their adjacent regions from 19 type C and one type B retrovirus were compared. Salient features are: (a) The R regions in the genomes of most of the type C retroviruses begin with GC and end with CA. (b) The mammalian type C retroviruses have a polyadenylation signal "AATAAA" in the R region, and most have a "CAT" box and a "TATA" box in the U3 region. (c) The avian type C retroviruses have an AATAAA sequence, and some also have "CAT-like" and "TATA-like" boxes, in the U3 region. (d) As with many transposable elements, the IR regions of the proviruses begin with TG and end with CA, and the DR sequences in the host genomes flanking the proviruses are different from one another. Although SNV is an avian retrovirus, the nucleotide sequences in the R, U5, TBS, and PU region are more similar to the mammalian type C than to the avian type C retroviruses.

Nucleotide sequence of AKV murine leukemia virus

AKV is an endogenous, ecotropic murine leukemia virus that serves as one of the parents of the recombinant; oncogenic mink cell focus-forming viruses that arise in preleukemic AKR mice. I report the 8,374-nucleotide-long sequence of AKV, as determined from the infectious molecular clone AKR-623. The 5'-leader sequence of AKV extends to nucleotide 639, after which lies a long open reading frame encoding the gag and pol gene products. The reading frame is interrupted by a single amber codon separating the gag and pol genes. The pol gene overlaps the env gene within the 3' region of the AKV genome. The nucleotide sequence of the 5' region of AKV reveals the following features. (i) The 5'-leader sequence lacks any AUG codon to initiate translation of gPr80gag, suggesting that gPr80gag is not required for the replication of AKV. (ii) A short portion of the leader region diverges in sequence from the closely related Moloney murine leukemia virus and appears to be related to a sequence highly repeated in eucaryotic genomes. (iii) As in Moloney murine leukemia virus, there is a potential RNA secondary structure flanking the amber codon that separates the gag and pol genes. This structure might function as a regulatory protein binding site that controls the relative levels of synthesis of the gag and pol precursors. The nucleotide sequence of the 3' region of AKV is compared with sequences reported previously from both infectious and noninfectious molecular clones of AKV.

Nucleotide sequence of the gp70 gene of murine retrovirus MCF 247

We determined the nucleotide sequence and predicted the amino acid sequence of the gp70 gene of MCF 247, a recombinant murine retrovirus isolated from an AKR mouse. Information specifying the first 286 amino acids of the protein was probably derived from the presumptive nonecotropic parent of MCF 247, whereas the C-terminal 154 amino acids were probably derived from the ecotropic parent Akv. The nonecotropic sequences at the amino terminus of MCF 247 show only 38% homology, at the amino acid level, to those of Akv. In contrast, these sequences are strikingly similar (99% homologous) to those reported for another MCF virus. Moloney MCF, which was isolated from a BALB/c mouse. Moloney MCF also has ecotropic-derived sequences encoding the C-terminal portion of its gp70 protein; however, the recombination event that introduced these sequences occurs 213 nucleotides further towards the C terminus of gp70 than it does in MCF 247.

Comparison of structural domains of gp70s of ecotropic Akv and dualtropic MCF-247 MuLVs

Controlled proteolysis of MuLV gp70s results in the generation of several fragments which correspond to distinct structural domains of the molecules. The orientation of these regions in gp70 was determined by analysis of the immunoreactivities of proteolytic products generated from the MuLV PrENV polyprotein toward monoclonal alpha p15(E) and alpha gp70 antibodies, and by fragmentation analysis of gp70s specifically labeled with [35S]cysteine and [35S]methionine. These studies confirmed our previous assignment of a p15(E)-disulfide-linked 33K fragment to the carboxy terminus of Akv gp70 (Pinter, Honnen, Tung, O'Donnell, and Hammerling, Virology 116, 345-351, 1982). Using similar fragmentation procedures, the sizes and structural features of gp70 domains of Akv and MCF 247 MuLV gp70s were compared. Trypsinization of MCF-247 gp70 resulted in the production of a carboxy terminal fragment which resembled that of the ecotropic gp70 in that (1) it was disulfide linked to p15(E) but not to the amino terminal fragments, (2) reacted with monoclonal antibody 35/56, (3) contained cysteines but no methionines, and (4) carried only endo H-resistant oligosaccharide chains. Amino terminal MCF gp70 fragments were obtained with apparent molecular weights of 42K and 30K, considerably smaller than the corresponding Akv fragments of 49K and 35K. These MCF fragments were much more stable to degradation by trypsin than the Akv amino terminal components, indicating the loss or inaccessibility of several trypsin sites in the MCF amino terminal domain. These results demonstrated the Akv and MCF 247 gp70s contained highly conserved carboxy terminal domains but unique amino terminal sequences. Common features for both gp70s were the presence of an endo H-sensitive oligosaccharide chain near the amino terminus, and the presence of internal disulfide bonds in the amino terminal domains which resulted in an increased mobility for these fragments when analyzed under nonreducing conditions. Thus, while the amino terminal domains of the two gp70s are structurally different, certain aspects of glycosylation specificity and secondary conformation are conserved, suggesting that these structural features may be important for common biological properties of these molecules.

Localization of the leukemogenic determinants of SL3-3, an ecotropic, XC-positive murine leukemia virus of AKR mouse origin

SL3-3 is a potent leukemogenic retrovirus that closely resembles the non-leukemogenic virus Akv. Both viruses were isolated from AKR mice, have ecotropic host ranges, and form plaques in the XC assay. They differ at only 1 to 2% of the nucleotides in the viral genomes but differ markedly in virulence properties. SL3-3 induces leukemia in a high percentage of inoculated AKR, C3H, CBA, and NFS mice, whereas Akv does not induce disease in any of these strains. To determine which region of the genome accounts for the leukemogenic potential of SL3-3, we constructed recombinant genomes between molecular clones of SL3-3 and Akv. Recombinant, viral DNA genomes were cloned and then were transfected onto NIH 3T3 fibroblasts to generate infectious virus. The recombinant viruses were tested for leukemogenicity in AKR/J, CBA/J, and C3Hf/Bi mice. We localized the primary leukemogenic determinant to a 3.8-kilobase fragment of the SL3-3 genome containing the viral long terminal repeat, 5' untranslated sequences, gag gene, and 5', 30% of the pol gene. Reciprocal recombinants containing the equivalent region from Akv, linked to the env gene and the remainder of the pol gene from SL3-3, did not induce leukemia. We conclude that the primary virulence determinant of SL3-3 lies outside the region of the genome that encodes the envelope proteins gp70 and p15E.

Envelope gene of the Friend spleen focus-forming virus: deletion and insertions in 3' gp70/p15E-encoding region have resulted in unique features in the primary structure of its protein product

A nucleotide sequence was determined for the envelope (env) gene of the polycythemia-inducing strain of the acute leukemia-inducing Friend spleen focus-forming virus (SFFV) and from this the amino acid sequence of its gene product, gp52, was deduced. All major elements of the gene were found to be related to genes of other retroviruses that code for functional glycoproteins. Although the carboxyl terminus of gp52 is encoded by sequences highly related to sequences in its putative parent, ecotropic Friend murine leukemia virus, the majority of the protein (69%), including the amino terminus, is encoded by dualtropic virus-like sequences. Nucleotide sequence comparisons suggest that the nonecotropic region may be more closely related to the 5' substitution in dualtropic mink cell focus-inducing viruses that it is to the 5' end of xenotropic virus env genes. A large deletion and two unique insertions have been located in the env gene of polycythemia-inducing SFFV and may account for some of the unusual structural characteristics, aberrant processing, and pathogenic properties of gp52. As a consequence of the deletion, amino-terminal gp70 and carboxyl-terminal p15E-encoding sequences are juxtaposed and it appears that translation from the p15E region, 3' to the deletion, continues in the standard reading frame used by other retroviruses. Insertions of six base pairs and one base pair at the very 3' end of the gp52-encoding region results in a SFFV-unique amino acid sequence and a premature termination codon.

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.

Somatically acquired recombinant murine leukemia proviruses in thymic leukemias of AKR/J mice

We have probed the structure and arrangement of murine leukemia virus genomes in eight spontaneous AKR thymic leukemias by Southern hybridization with one ecotropic pol and four ecotropic env probes. These probes revealed many (in 2 cases over 15) somatically acquired proviruses that had undergone complex patterns of recombination. The large majority were not deleted and were structurally analogous to the oncogenic mink cell focus-inducing murine leukemia viruses isolated from AKR tumors in that the amino-terminal p15E-coding region derived from ecotropic AKR murine leukemia virus sequences, whereas certain gp70-coding sequences were nonecotropic. Nevertheless, we observed a few proviruses which did not appear to be gp70 recombinants; however, these proviruses were in general clearly recombinant within the p15E-coding sequences. Although the proviral recombination patterns were quite variable, in general the large majority of recombinant proviruses within each tumor appeared structurally identical, indicating that they originate from a common parent. Each tumor contained a unique pattern of provirus integrations; densitometer tracings of the Southern hybridizations indicated that many of the integrated proviruses were present at one copy per cell, suggesting that the tumors derive from a single cell which contained multiple integrated copies of a unique recombinant virus structurally similar to the mink cell focus-inducing viruses.

Isolation and mapping of cDNA hybridization probes specific for ecotropic and nonecotropic murine leukemia proviruses

To study the structure of murine leukemia proviruses in AKR mice by Southern hybridization, we have isolated and mapped ecotropic AKV and nonecotropic MCF-derived cDNA restriction fragments. The ecotropic-specific probes originate from four regions of the AKV genome which include the corresponding recombinant region of two MCF viruses (VI-36 and 247). We also isolated two nonecotropic probes from the recombinant region of MCF V1-36. The probes were characterized by (i) mapping of restriction fragments at the 3' end of AKV and MCF V1-36 by a two-dimensional gel strategy, (ii) hybridization of restriction fragments to the related viral RNA genomes followed by electrophoresis, (iii) two-dimensional fingerprinting of single-stranded restriction fragments, and (iv) DNA sequence analysis of the ecotropic probes. The ecotropic AKV and nonecotropic MCF probes discriminate between two populations of endogenous murine leukemia viruses and show that the MCF viruses are not present in the germ line of AKR mice.