bluuebunny/crossref_metadata_2025 huggingface dataset:
DNA Sequence Relationship of the Baboon Endogenous Virus Genome to the Genomes of Other Type C and Type D Retroviruses
Authors: Cohen Maurice , Rice Nancy , Stephens Robert , O'Connell Catherine
Published: January 2020

Baboon endogenous virus (BaEV) is a type C retrovirus present in multiple proviral copies in the DNA of baboons. Although interspecies antigenic determinants present on reverse transcriptase and
gag
proteins are shared among all mammalian type C viruses, no nucleic acid homology between BaEV and other type C viruses (except RD-114) has been found in conventional liquid hybridization experiments. In this study, we used restriction fragments of cloned BaEV DNA immobilized on nitrocellulose to test for relatedness with [
32
P]cDNA's of various type C and type D viruses. We detected the following distant relationships previously found only through immunological and protein sequencing techniques: (i) eight type C viral cDNA's (the endogenous virus of rhesus monkeys, feline leukemia virus, simian sarcoma virus, gibbon ape leukemia virus, Rauscher murine leukemia virus, BALB-2, NZB, and RD-114) and two type D viral cDNA's (Mason-Pfizer monkey virus and squirrel monkey retrovirus) were able to hybridize with cloned BaEV DNA; (ii) the eight type C probes hybridized to restriction fragments spanning most of the BaEV genome, but only RD-114 hybridized to fragments within the 1.9 kilobases at the 3′ end of the genome; (iii) the two type D probes hybridized primarily to fragments within the 1.9 kilobases at the 3′ terminus and weakly or not at all elsewhere; and (iv) [
32
P]cDNA's of several other oncornaviruses (mouse mammary tumor virus, equine infectious anemia virus, bovine leukemia virus, and reticuloendotheliosis virus) exhibited no homology with BaEV DNA. DNA sequence analysis has allowed us to orient the BaEV restriction map with the genetic map at both ends of the genome. Homologies between retroviral cDNA's and BaEV clone restriction fragments could thus be related to specific BaEV genes. Whereas type C cDNA's hybridized to fragments from
gag, pol
, and the
pol-env
junction, squirrel monkey retrovirus cDNA hybridized only to a fragment coding for the p15E portion of
env.
Mason-Pfizer monkey virus cDNA also hybridized within the p15E region, but exhibited homology to the 3′ half of gp70 as well. These results are discussed relative to previously reported antigenic relatedness of retroviral proteins. The data suggest that BaEV represents an important link in oncornavirus evolution.
Synthesis of Vesicular Stomatitis Virus Negative-Strand RNA In Vitro: Dependence on Viral Protein Synthesis
Authors: Davis Nancy L. , Wertz Gail W.
Published: January 2020

An in vitro system is described which supports the synthesis of vesicular stomatitis virus (VSV) negative-strand RNA. The major components of this system are (i) an mRNA-dependent rabbit reticulocyte lysate to carry out cell-free protein synthesis, (ii) the five VSV mRNAs to program VSV-specific protein synthesis, and (iii) nucleocapsids containing positive- and negative-strand genome-length RNA. The protein products synthesized in the system in response to addition of saturating amounts of the five VSV mRNA's included polypeptides which comigrated in acrylamide gels with the five VSV proteins. Approximately 200 pmol of protein per ml was synthesized during a 90-min reaction. The RNA products synthesized in the system included all five of the VSV mRNA's and, in addition, negative-strand, genome-sense RNA. All of the negative-strand RNA, which represented 2 to 5% of the total RNA product synthesized in vitro, banded in CsCl at the position of nucleocapsids. All of the mature mRNA's made in the system pelleted in CsCl. This technique allowed a clear separation of negative-strand product from the mRNA products and facilitated further analysis of the negative-strand product. The amount of negative-strand product produced in the system was shown to be a function of the amount of concurrent protein synthesis in the system. An increase in the level of protein synthesis led to an increase in the amount of negative-strand RNA synthesized, whereas inhibition of protein synthesis by cycloheximide resulted in a 70% inhibition of negative-strand synthesis. In contrast to the negative-strand RNA product, the amount of transcriptive product was decreased by 50% in the presence of maximum levels of viral protein synthesis. This inhibition was reversed by adding cycloheximide. Characterization of the negative-strand product by Northern blot analysis demonstrated that negative-strand product was being synthesized which hybridized to all five of the VSV mRNA's and, hence, that product representing all of the VSV cistrons was being made. This in vitro system offers an opportunity to study factors involved in the promotion of VSV genome replication as well as those responsible for the regulation of transcription.
Induction of a new ribonucleotide reductase after infection of mouse L cells with pseudorabies virus
Authors: Lankinen H , Gräslund A , Thelander L
Published: January 2020

The mammalian ribonucleotide reductase consists of two nonidentical subunits, protein M1 and M2. M1 binds nucleoside triphosphate allosteric effectors, whereas M2 contains a tyrosine free radical essential for activity. The activity of ribonucleotide reductase increased 10-fold in extracts of mouse L cells 6 h after infection with pseudorabies virus. The new activity was not influenced by antibodies against subunit M1 of calf thymus ribonucleotide reductase, whereas the reductase activity in uninfected cells was completely neutralized. Furthermore, packed infected cells (but not mock-infected cells) showed an electron paramagnetic resonance spectrum of the tyrosine free radical of subunit M2 of the cellular ribonucleotide reductase. These data given conclusive evidence that on infection, herpesvirus induces a new or modified ribonucleotide reductase. The virus-induced enzyme showed the same sensitivity to inhibition by hydroxyurea as the cellular reductase. The allosteric regulation of the virus enzyme was completely different from the regulation of the cellular reductase. Thus, CDP reduction catalyzed by the virus enzyme showed no requirement for ATP as a positive effector, and no feedback inhibition was observed by dTTP or dATP. The virus reductase did not even bind to a dATP-Sepharose column which bound the cellular enzyme with high affinity.
Identification and purification of a protein encoded by the human adenovirus type 2 transforming region
Authors: Green M , Brackmann K H , Cartas M A , Matsuo T
Published: January 2020

The human adenovirus type 2 (Ad2) transforming genes are located in early regions E1a (map position 1.3 to 4.5) and E1b (map position 4.6 to 11.2). We have identified and purified to near homogeneity a major 20,000-molecular-weight (20K) protein and have shown that it is coded by E1b. Using an Ad2-transformed cell antiserum which contained antibody to E1b-coded proteins, we immunoprecipitated 53K and 19K proteins from the nucleoplasm and 53K, 19K, and 20K proteins from the cytoplasmic S-100 fraction of Ad2 productively infected and Ad2-transformed cells. The 19K protein was present in both the nucleoplasm and the cytoplasm, whereas the 20K protein was found only in the cytoplasm. The 53K and 19K proteins are known Ad2 E1b-coded proteins. The 20K protein was purified to near homogeneity in 20 to 50% yields by sequential DEAE-Sephacel chromatography and reverse-phase high-performance liquid chromatography. Purified 20K protein shares most of its methionine-labeled tryptic peptides with E1b-53K, as shown by reverse-phase high-performance liquid chromatography, and therefore is closely related to the 53K protein. The 19K protein does not appear to share tryptic peptides with either 20K or 53K protein. To provide more direct evidence that 20K protein is virus-coded, we translated E1b-specific mRNA in vitro. Both immunoprecipitation analysis and high-performance liquid chromatography purification of the translated product identified a 20K protein that has the same tryptic peptides as the 20K protein isolated from infected and from transformed cells. These findings suggest that the Ad2 20K protein is a primary translation product of an Ad2 E1b mRNA.
Sequence homology between avian and human adenoviruses
Authors: Aleström P , Stenlund A , Li P , Bellett A , Pettersson U
Published: January 2020

Studies of hybridization between fowl adenovirus type 1 (chicken embryo lethal orphan virus) DNA and human adenovirus type 2 DNA revealed two short but distinct regions which cross-hybridized under stringent conditions. One of the homologous regions was located between map positions 18.1 and 19.3 and did not correspond to any gene recognized so far. The second region mapped in the hexon gene between position 57 and 58.
Structure of a replication intermediate in the synthesis of Rous sarcoma virus DNA in vivo
Authors: Swanstrom R , Bishop J M , Varmus H E
Published: January 2020

Intermediates in the synthesis of Rous sarcoma virus DNA in vivo contain a short second strand of DNA (plus strong-stop DNA) synthesized by using the region near the 5' end of the first (minus) strand of DNA as the template. In this report, we show that the 3' end of plus strong-stop DNA is extended about 15 to 20 nucleotides beyond the 5' end of the minus-strand DNA template, probably copying a portion of the tRNATrp molecule that serves as primer for synthesis of the minus strand of DNA. The extra sequences present in plus strong-stop DNA may play a central role in the generation of the long terminal repeat present in mature forms of viral DNA.
Analysis of proteins synthesized in respiratory syncytial virus-infected cells
Authors: Dubovi E J
Published: January 2020

The spectrum of respiratory syncytial virus-encoded proteins was examined in infected cell extracts by standard polyacrylamide gel electrophoresis and by two-dimensional gel analysis. Polyacrylamide gel electrophoresis analysis of a variety of respiratory syncytial virus-infected, actinomycin D-treated cell lines revealed the presence of as many as nine virus-encoded proteins. Seven of these nine proteins were immunoprecipitated by anti-respiratory syncytial serum. Only one major band of [3H]glucosamine was detected in infected cell extracts (Vp86), whereas the reported major virion glycoprotein (Vp48-53) was difficult to detect in infected cells when carbohydrate labels were employed. Two-dimensional gel analysis easily identified seven viral proteins, and one other was tentatively identified. The reported major virion glycoprotein again was not consistently detected. The results of this study confirm the existence of a virus-coded glycoprotein (Vp86) in infected cell extracts. The existence of this glycoprotein in the purified virion has been in dispute, but the apparent low methionine content of this protein may be the reason for this controversy.
Sequence Relationships Between the Genome and the Intracellular RNA Species 1, 3, 6, and 7 of Mouse Hepatitis Virus Strain A59
Authors: Spaan Willy J. M. , Rottier Peter J. M. , Horzinek Marian C. , van der Zeijst Bernard A. M.
Published: January 2020

We have shown by T
1
oligonucleotide fingerprinting that the genome of mouse hepatitis virus strain A59 and its intracellular RNA 1 have identical fingerprints and that RNA 1 and the subgenomic RNAs 3, 6, and 7 contain common sequences. To localize the homologous region between the RNAs, we compared fingerprints of the 3′ terminus of the genome with those of RNA 7. The genome was partially degraded with alkali, and polyadenylate-containing fragments were purified by oligodeoxythymidylate-cellulose chromatography. The fragments were size fractionated by agarose-urea gel electrophoresis, and two pools, x and z, containing 3′-derived fragments of the genome with apparent molecular weights of 0.1 × 10
6
to 0.14 × 10
6
and 0.6 × 10
6
to 0.8 × 10
6
, respectively, were further analyzed by RNase T
1
oligonucleotide fingerprinting. Comparison of the fingerprints of RNAs 6 and 7 with those of pools x and z showed that these subgenomic RNAs extend inwards from the 3′ terminus of the genome. The RNA fragments present in pool z were on average slightly larger than RNA 7 as confirmed by the presence in pool z of T
1
oligonucleotide spots specific for RNA 6 but not present in RNA 7. However, two large oligonucleotide spots derived from RNA 7, which were also present in RNAs 1, 3, and 6 and in the virion RNA, were not found in the T
1
oligonucleotide map of pool z. A possible explanation is that the two spots were derived from a leader sequence. The results of UV transcription mapping experiments (L. Jacobs, W. J. M. Spaan, M. C. Horzinek, and B. A. M. van der Zeijst, J. Virol. 39:401-406, 1981) excluded the possibility that such a leader sequence arises by splicing from a larger precursor molecule, but either a virus-specific RNA primer molecule for the synthesis of mRNAs or an RNA polymerase jumping mechanism could explain the presence of a leader sequence.
Virion functions of RNA+ temperature-sensitive mutants of Newcastle disease virus
Authors: Peeples M E , Bratt M A
Published: January 2020

Virions from Newcastle disease virus mutants in four temperature-sensitive RNA+ groups were grown in embryonated hen eggs at the permissive temperature, purified, and then analyzed for biological properties at both the permissive and nonpermissive temperatures. At the permissive temperature, virions of mutants in groups B, C, and BC (11 mutants) were all lower in specific (per milligram of protein) hemagglutination, neuraminidase, and hemolysis activities compared with the wild type. These deficiencies were related to decreased amounts of hemagglutinin-neuraminidase glycoprotein in the virions. Activities of these mutant virions at both the permissive and nonpermissive temperatures were similar, indicating that hemagglutinin-neuraminidase synthesized at the permissive temperature was not temperature sensitive in function. The three group D mutants displayed a different pattern. At the permissive temperature, they had wild-type hemagglutination and neuraminidase activities but were deficient compared with the wild type in hemolysis. Again, functions were similar at both temperatures. Most of the B, C, and BC mutants had specific infectivities similar to that of the wild type despite lower hemagglutination, neuraminidase, and hemolysis functions. However, the D mutants were all less infectious. This evidence is consistent with a shared hemagglutinin-neuraminidase defect in the B, C, and BC mutants and a defect in either the F glycoprotein or the M protein in the D mutants.
Restriction endonuclease map of the nontoxigenic corynephage gamma c and its relationship to the toxigenic corynephage beta c
Authors: Michel J L , Rappuoli R , Murphy J R , Pappenheimer A M
Published: January 2020

Clear-plaque-forming mutant gamma tox- corynephages were isolated independently from nontoxigenic lysogenic Corynebacterium diphtheriae strains C7s(gamma tox-) and C4(gamma tox-). A physical map was constructed by using restriction endonucleases BamHI, EcoRI, HindIII, and KpnI. A comparison of nontoxigenic gamma c with toxigenic corynephage beta c revealed large areas of homology, including common regions for cohesive ends (cos) and attachment sites (att). Localization of the att sites on the beta prophage and correlation of the physical and genetic maps defined the orientation of the diphtheria tox operon. Diphtheria tox sequence homologies were mapped on gamma c by hybridizing 32P-labeled diphtheria tox mRNA to restriction fragments of gamma c DNA. Two regions of heterogeneity between phages beta c and gamma c were localized and these regions accounted for the 3-kilobase larger molecular size of gamma c compared with beta c. One change occurs near the tox promoter and may explain the nontoxigenic phenotype of corynephage gamma tox-.
Nucleotide sequence at the junction between the nonstructural and the structural genes of the semliki forest virus genome
Authors: Riedel H , Lehrach H , Garoff H
Published: January 2020

The nucleotide sequence at the junction between the nonstructural and the structural genes of the Semliki Forest virus 42S RNA genome has been determined from cloned cDNA. With the aid of S1-mapping, we have located the 5' end of the viral 26S RNA on this sequence. The 26S RNA is homologous to the 3' end of the 42S RNA and is used as a messenger for the structural proteins of the virus. The nucleotide sequence in the noncoding 5' region of the 26S RNA (51 bases) was thus established, completing the primary structure of the 26S RNA molecule (for earlier sequence work, see Garoff et al., Proc. Natl. Acad. Sci. U.S.A. 77:6376-6380, 1980, and Garoff et al., Nature (London) 288:236-241, 1980). An examination of the nucleotide sequences upstream from the initiator codon for the structural proteins on the 42S RNA genome shows that all reading frames are effectively blocked by stop codons, which means that the nonstructural genes in the 5' end of the 42S RNA molecule do not overlap with the structural ones at the 3' end of the molecule.
Analysis of vaccinia virus transcriptional complexity in vitro and in vivo: characterization of RNase T1-resistant 5'-terminal oligonucleotides
Authors: Whitkop C , Lipinskas B R , Mercer S , Panicali D , Paoletti E
Published: January 2020

Vaccinia virus mRNAs synthesized in vitro and in vivo, polyadenylated leader sequences synthesized in vitro in the absence of added GTP, CTP, or UTP or in the presence of 20 micrograms of actinomycin D per ml, and high-molecular-weight RNA synthesized in vitro under limiting ATP concentrations were labeled specifically in the cap structure using [alpha-32P]GTP and vaccinia-soluble enzyme extracts. The complexity of RNase T1-resistant 5'-terminal oligonucleotides was analyzed by two-dimensional polyacrylamide gel electrophoresis. Approximately 190 unique T1-resistant 5'-terminal oligonucleotides were observed from vaccinia virus 8 to 12S RNA synthesized in vitro. A somewhat greater complexity was observed with polyadenylated leader sequences and actinomycin D RNAs where unique T1-resistant oligonucleotides ranged from approximately 210 to 280 5'-terminal fragments. On a composite fingerprint of the above RNAs, more than 300 identifiable unique T1-resistant 5'-terminal oligonucleotides were observed. Significantly, close to 300 T1-resistant fragments were derived from RNA sedimenting faster than 18S on denaturing sucrose gradients. Analysis of vaccinia RNAs synthesized in vivo in the absence of either de novo protein synthesis or DNA replication or in the presence of actinomycin D gave essentially similar profiles of 5'-terminal T1-resistant oligonucleotide fingerprints consisting of approximately 200 fragments. Analysis of the 5'-terminal T1-resistant oligonucleotides of vaccinia RNAs present after DNA replication showed essentially the same pattern of early T1-fragments albeit in reduced amounts but in addition revealed a complex pattern of T1-resistant oligonucleotides unique to this class of vaccinia RNA.
Intracellular ribonucleoprotein complexes of visna virus are infectious
Authors: Filippi P , Vigne R , Quérat G , Jouanny C , Sauze N
Published: January 2020

Sheep choroid plexus cells infected with visna virus produce intracytoplasmic viral ribonucleoprotein complexes with sedimentation values of 120S to 200S and buoyant densities of 1.29 to 1.32 g/cm3. These ribonucleoprotein complexes display an endogenous RNA-directed DNA polymerase activity and contain all of the species of RNA associated with polysomes. An analysis of the polypeptides present in the ribonucleoproteins allowed us to identify the mature internal virion core proteins and their precursor, Pr55gag, as well as the glycosylated envelope precursor gPr150env and small amounts of mature glycoprotein gp135. Ultracentrifugation-purified ribonucleoproteins could infect sheep choroid plexus cells and led to a normal lytic cycle with virus production. Our results suggest that visna virus can propagate by means of intracellular infectious particles.
Identification of some bacteriophage T4 prereplicative proteins on two-dimensional gel proteins
Authors: Cook K S , Seasholtz A F
Published: January 2020

Profiles of bacteriophage T4 early proteins resolved by a two-dimensional nonequilibrium pH gradient electrophoresis system (P. Z. O'Farrell, H. M. Goodman, and P. H. O'Farrell, Cell 12:1133--1142, 1977) are presented. Over 65 phage-induced proteins were resolved. Amber or deletion mutants were used to identify 17 proteins in the gel patterns as the products of specific genes.
Identification, synthesis, and modifications of simian rotavirus SA11 polypeptides in infected cells
Authors: Ericson B L , Graham D Y , Mason B B , Estes M K
Published: January 2020

The synthesis and processing of simian rotavirus SA11 polypeptides was investigated after infection of MA104 cells. [35S]methionine- or 3H-amino acid-labeled cell extracts were analyzed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Viral protein synthesis was maximal 3 to 5 h postinfection, and 12 major viral polypeptides were detected. Immunoprecipitation and peptide mapping experiments, demonstrated five viral structural proteins (125,000 daltons [125K], 94K, 88K, 41K, and 38K). Three proteins (53K, 35K, and 34K) were identified as nonstructural by comparison of their partial proteolysis maps with those from polypeptides of similar molecular weight synthesized in vitro from viral RNA transcripts. Assignment as to structural or nonstructural status of two other primary gene products (26K and 20K) remains tentative. Pulse-chase experiments and tunicamycin blockage of glycosylation revealed cotranslational or post-translational modifications (or both) and precursor-product relationships of several of the polypeptides. Tunicamycin inhibition of glycosylation identified a 35.5K polypeptide which was proven to be the precursor to the 38K structural glycoprotein by immunoprecipitation and peptide mapping analyses. Tunicamycin treatment of infected cells also resulted in the disappearance of other glycoprotein species (23K to 29K) and in the concomitant build-up of an unglycosylated 20K polypeptide, suggesting a precursor-product relationship between those polypeptides. Labeling with [3H]glucosamine or [3H]mannose suggested that the rotavirus glycoproteins contained high mannose oligosaccharides. The effects of amino acid analogs on rotavirus polypeptide synthesis and processing were also investigated.
Nucleotide sequence analysis of the long terminal repeat of avian myeloblastosis virus and adjacent host sequences
Authors: Rushlow K E , Lautenberger J A , Reddy E P , Souza L M , Baluda M A , Chirikjian J G , Papas T S
Published: January 2020

The nucleotide sequence of the integrated avian myeloblastosis virus long terminal repeat has been determined. The sequence is 385 base pairs long and is present at both ends of the viral DNA. The cell-virus junctions at each end consist of a 6-base-pair direct repeat of cell DNA next to the inverted repeat of viral DNA. The long terminal repeat also contains promoter-like sequences, an mRNA capping site, and polyadenylation signals. Several features of this long terminal repeat suggest a structural and functional similarity with sequences of transposable and other genetic elements. Comparison of these sequences with long terminal repeats of other avian retroviruses indicates that there is a great variation in the 3' unique sequence (U3), whereas the 5' specific sequences (U5) and the R region are highly conserved.
In vitro synthesis of triphosphate-initiated N-gene mRNA oligonucleotides is regulated by the matrix protein of vesicular stomatitis virus
Authors: Pinney D F , Emerson S U
Published: January 2020

Wild-type Indiana virus transcribed four 11- to 14-nucleotide-long, 5' N-gene mRNA sequences in vitro. The amount of oligonucleotides synthesized relative to leader by wild-type virions varied inversely with the salt concentration of the transcription reaction. Reduced oligonucleotide synthesis by nucleocapsids at all salt concentrations tested and a comparison of the proteins remaining bound to the template of nucleocapsids and virions transcribed in different NaCl concentrations suggested that the matrix (M) protein regulates oligonucleotide synthesis. Examination of the transcription products synthesized in no NaCl and 0.144 M NaCl by an M-protein mutant and an increase in oligonucleotide synthesis by nucleocapsids when purified M-protein was added to transcription reactions confirmed M-protein's role in oligonucleotide synthesis. Wild-type virion mRNA synthesis was inhibited, and oligonucleotide synthesis was greater than leader synthesis at high virus concentrations. As the virus was diluted, inhibition of mRNA synthesis was relieved and oligonucleotide synthesis was reduced. The M-protein mutant tsG33 exhibited neither transcription inhibition at high virus concentrations nor the reciprocal synthesis of mRNA and the oligonucleotides seen with wild-type virions. These results are entirely consistent with the stop-start model of transcription and suggest a model for the control of transcription by M-protein.
Purification of a native membrane-associated adenovirus tumor antigen
Authors: Persson H , Katze M G , Philipson L
Published: January 2020

A 15,000-dalton protein was purified from HeLa cells infected with adenovirus type 2. Proteins solubilized from a membrane fraction of lytically infected cells was used as the starting material for purification. Subsequent purification steps involved lentil-lectin, phosphocellulose, hydroxyapatite, DEAE-cellulose, and aminohexyl-Sepharose chromatographies. A monospecific antiserum, raised against the purified protein, immunoprecipitated a 15,000-dalton protein encoded in early-region E1B (E1B/15K protein) of the adenovirus type 2 DNA. Tryptic finger print analysis revealed that the purified protein was identical to the E1B/15K protein encoded in the transforming part of the viral genome. The antiserum immunoprecipitated the E1B/15K protein from a variety of viral transformed cell lines isolated from humans, rats, or hamsters. The E1B/15K protein was associated with the membrane fraction of both lytically and virus-transformed cell lines and could only be released by detergent treatment. Furthermore, a 11,000- to 12,000-dalton protein that could be precipitated with the anti-E1B/15K serum was recovered from membranes treated with trypsin or proteinase K, suggesting that a major part of the E1B/15K protein is protected in membrane vesicles. Translation of early viral mRNA in a cell-free system, supplemented with rough microsomes, showed that this protein was associated with the membrane fraction also in vitro.
Transcriptional regulation of bacteriophage SPO1 protein synthesis in vivo and in vitro
Authors: Heintz N , Shub D A
Published: January 2020

There are six classes of SPO1 transcripts which are, at least partially, regulated independently of each other. Analysis of proteins made in infections by phage mutants defective in DNA synthesis, or in genes which positively control transcription, permitted each protein to be assigned to one transcription class. Most of the late proteins belong to transcription class m2l. There seem to be few, if any, phage proteins in the l class whose mRNA synthesis depends absolutely on phage DNA synthesis, UV irradiation of host cells allowed the detection of many additional early proteins. The early proteins detected in vivo were compared with proteins synthesized in vitro, using bacterial or gp28 phage-modified RNA polymerase in an Escherichia coli cell-free system. Proteins characterized in vivo as belonging to the e transcription class could be made efficiently in vitro only when transcription was performed by bacterial RNA polymerase. em proteins could be elicited through the use of either bacterial or gp28 polymerase, indicating that their genes can be transcribed in either the early or the middle mode.
In Vitro Transcription of Vesicular Stomatitis Virus: Initiation with GTP at a Specific Site Within the N Cistron
Authors: Schubert Manfred , Harmison George G. , Sprague Judy , Condra Cindra S. , Lazzarini Robert A.
Published: January 2020

In vitro transcripts of vesicular stomatitis virus (VSV) were either 5′-terminally labeled by incorporation of [β-
32
P]GTP or were selected on Hg-agarose after incorporation of γ-thio-GTP. Capped RNAs ranged in size from 23 nucleotides, the shortest capped RNA detected, to full-length message size. The 5′-terminal sequences corresponded to those of N message and to a small amount of NS message. Approximately 14% of the capped
N
gene transcripts were terminated at positions 86 to 90 of the VSV genome, giving rise to specific, 36 to 40-nucleotide-long, capped RNA species. The GTP-initiated RNAs were short with a predominant 28-nucleotide-long RNA species. A minor portion was as large as mRNAs. Nucleotide sequence analyses of the short RNA revealed that it was specifically initiated at positon 91 of the VSV genome, 41 nucleotides within the N cistron. This corresponds exactly to the site where transcription of the 40-nucleotide-long, capped RNA terminated. Initiation with GTP at position 91 occurred at approximately the same frequency as termination of the capped RNA at position 90, suggesting that intracistronic initiation at position 91 may depend upon termination of transcription of the 5′-proximal region and therefore may be sequential. This unique RNA represents the first transcript of VSV which was initiated at an intracistronic site with GTP, and may also represent the first example of a transcript derived from a stop/start mechanism of VSV transcription in vitro. Although initiation occurred frequently at the beginning of the N cistron yielding 11 to 14-nucleotide-long, [β-
32
P]ATP-labeled transcripts (D. F. Pinney and S. U. Emerson, J. Virol.
42:
889-896, 1982), capping of these short RNAs was not detected. This suggests that transcripts may have to be 15 to 23 nucleotides long to be accepted as substrates by the guanyltransferase.
Organization, distribution, and stability of endogenous ecotropic murine leukemia virus DNA sequences in chromosomes of Mus musculus
Authors: Jenkins N A , Copeland N G , Taylor B A , Lee B K
Published: January 2020

The endogenous ecotropic murine leukemia virus DNA content and integration sites were characterized for 54 inbred strains and substrains of mice by restriction enzyme digestion, Southern blotting, and hybridization with an ecotropic murine leukemia virus DNA-specific probe. More than 75% of these strains carried endogenous ecotropic proviruses which were located in at least 29 distinct integration sites in chromosomes of Mus musculus. Fourteen of these proviruses have been assigned specific locus designations. Most, but not all, of the endogenous ecotropic proviruses were structurally indistinguishable by this analysis from the prototype AKR ecotropic virus, and the distribution of these proviruses followed known relationships among the inbred strains and substrains of mice. These results suggest that, in general, viral DNA integration preceded the establishment of inbred mouse strains and that these integrations are relatively stable.
Isolation and preliminary characterization of amber mutants of bacteriophage phi W-14 defective in DNA synthesis
Authors: Miller P B , Maltman K L , Warren R A
Published: January 2020

Of 42 amber mutants of bacteriophage phi W-14, 6 were defective in DNA synthesis. Three of the mutants synthesized DNA in the nonpermissive host, but were defective in post-replicational modification of the DNA. The DNA synthesized by two of these mutants, am36 and am42, contained more thymine and less alpha-putrescinylthymine than did wild-type DNA; that synthesized by the third mutant, am37, contained the normal amount of thymine, no alpha-putrescinylthymine, and hydroxymethyluracil. The properties of these mutants suggested that the presence of the normal amount of alpha-putrescinylthymine in phi W-14 DNA was essential for the production of viable progeny. Three of the mutants, am6, am35, and am45, failed to synthesize DNA in the nonpermissive host. These mutants were analogous to the DNA off mutants of T4. Nonpermissive cells infected with DNA off mutants accumulated dATP, dGTP, dCTP, and hydroxymethyl dUTP, but not dTTP or alpha-putrescinyldeoxythymidine triphosphate, confirming that both thymine and alpha-putrescinylthymidine in phi W-14 DNA are formed from hydroxymethyluracil at the polynucleotide level. The synthesis of phi W-14 DNA is unusual because (i) thymine is formed from hydroxymethyluracil at the polynucleotide level, (ii) the hypermodification forming alpha-putrescinylthymine is essential, and (iii) thymine and alpha-putrescinylthymine must be made in the correct proportions. Complementation tests showed that the mutants defined three genes involved in DNA polymerization and two genes involved in post-replicational modification.
Monoclonal antibody to spleen focus-forming virus-encoded gp52 provides a probe for the amino-terminal region of retroviral envelope proteins that confers dual tropism and xenotropism
Authors: Wolff L , Koller R , Ruscetti S
Published: January 2020

Monoclonal antibodies which recognize a region common to Friend spleen focus-forming virus encoded gp52 and Friend mink cell focus-inducing viral gp70 were isolated. One such antibody from hybridoma 7C10 was tested extensively in immune precipitation and was found to react with a determinant on envelope gp70s of all mink cell focus-inducing, xenotropic, and amphotropic mouse retroviruses tested, but not with envelope gp70s of ecotropic viruses, including Friend, Moloney, and AKR murine leukemia viruses. Monoclonal antibody from hybridoma 7C10 precipitated a 23,000-molecular-weight fragment, derived by V8 protease digestion of Friend mink cell focus-inducing gp70. This 23,000-molecular-weight peptide was determined to derive from the amino terminus of the molecule. These results correlate well with other genetic data which indicate that endogenously acquired sequences of mink cell focus-inducing viruses are found at the 5' end of the envelope gene.
Identification of proteins encoded by the Gazdar murine sarcoma virus genome by in vitro translation and comparison with Moloney murine sarcoma virus 124
Authors: Papkoff J , Hunter T
Published: January 2020

The gene products of Gazdar murine sarcoma virus (Gz-MuSV) were identified by in vitro translation of Gz-MuSV virion RNA. An overlapping set of proteins with approximate molecular weights of 37,000 (37K), 33K, 24K, and 18K were synthesized from the transforming gene of Gz-MuSV, v-mosGz. In addition, Gz-MuSV-specific RNA directed the in vitro synthesis of a 62K gag gene protein and a 37.5K env gene-related product. The Gz-MuSV-specific in vitro translation products were compared with the in vitro translation products of M-MuSV 124, an independent isolate with a similar v-mos gene. This analysis showed that the 62K Gz-MuSV gag gene protein and the 37K, 33K, 24K, and 18K v-mosGz proteins were almost identical to the M-MuSV 124 62K (gag) and 37K, 33K, 24K, and 18K (v-mosMo) proteins that we previously identified and characterized. The 37.5K env gene product from Gz-MuSV does not have a correlate in the M-MuSV 124 translation products. These results were analyzed in the context of expectations based on similarities and differences in genetic organization of these two viral genomes.
Evidence for two classes of chromatin-associated Epstein-Barr virus-determined nuclear antigen
Authors: Spelsberg T C , Sculley T B , Pikler G M , Gilbert J A , Pearson G R
Published: January 2020

A new class of Epstein-Barr virus nuclear antigen (EBNA) was identified by the complement fixation assay. This new species of EBNA is more tightly bound to chromatin and was termed class II EBNA, as opposed to the more weakly associated species, class I EBNA. Preparations of this new antigen(s) specifically reduced absorption with the titer of anti-EBNA antibodies as determined by the anticomplement immunofluorescence assay. Therefore, the complement fixation antigens (class II EBNA) appear to be related to the classical EBNA (class I EBNA). The class I EBNA was found to focus at the same pH (4.6) as the soluble antigen found in the cytosol. The class II EBNA differed from the class I EBNA with regard to its overall charge, molecular size, antigenicity, and affinity for chromatin. The class II EBNA appeared to be a basic protein, based on its apparent pI of 9.2 and its binding to cation-exchange resins. It differed from histones with regard to its molecular size (molecular weight between 60,000 and 70,000) and its elution from hydroxylapatite chromatography. Steps were taken to prevent proteolysis and artifacts in the immunological assays and in the overall charge estimation of the new antigen by nonspecific basic histone protein-acidic protein interactions. Both class I and class II EBNA were identified by radioimmunoelectrophoresis on two-dimensional polyacrylamide gels with pI values of 5.0 and 8.5, respectively, and a molecular weight range of 60,000 to 70,000 for both. A lower-molecular-weight antigen identified by molecular sieve chromatography appeared to be due to interference by histones in the immunoassays since it was not observed by the two-dimensional gel electrophoresis. Further characterization of this class II EBNA is in progress.
Resistance of Adenoviral DNA Replication to Aphidicolin Is Dependent on the 72-Kilodalton DNA-Binding Protein
Authors: Foster David A. , Hantzopoulos Petros , Zubay Geoffrey
Published: January 2020

Aphidicolin is a highly specific inhibitor of DNA polymerase α and has been most useful for assessing the role of this enzyme in various replication processes (J. A. Huberman, Cell
23
:647-648, 1981). Both nuclear DNA replication and simian virus 40 DNA replication are highly sensitive to this drug (Krokan et al., Biochemistry
18
:4431-4443, 1979), whereas mitochondrial DNA synthesis is completely insensitive (Zimmerman et al., J. Biol. Chem.
255
:11847-11852, 1980). Adenovirus DNA replication is sensitive to aphidicolin, but only at much higher concentrations. These patterns of sensitivity are seen both in vivo and in vitro (Krokan et al., Biochemistry
18
:4431-4443, 1979). A temperature-sensitive mutant of adenovirus type 5 known as H5
ts
125 is able to complete but not initiate new rounds of replication at nonpermissive temperatures (P. C. van der Vliet and J. S. Sussenbach, Virology
67
:415-426, 1975). When cells infected with H5
ts
125 were shifted from permissive (33°C) to nonpermissive (41°C) conditions, the residual DNA synthesis (elongation) showed a striking increase in sensitivity to aphidicolin. The temperature-sensitive mutation of H5
ts
125 is in the gene for the 72-kilodalton single-stranded DNA-binding protein. This demonstrated that the increased resistance to aphidicolin shown by adenovirus DNA replication was dependent on that protein. It also supports an elongation role for both DNA polymerase α and the 72-kilodalton single-stranded DNA-binding protein in adenovirus DNA replication. Further support for an elongation role of DNA polymerase α came from experiments with permissive temperature conditions and inhibiting levels of aphidicolin in which it was shown that newly initiated strands failed to elongate to completion.
DNA packaging in vitro by an isolated bacteriophage T7 procapsid
Authors: Masker W E , Serwer P
Published: January 2020

The results of previous in vivo studies indicate that a DNA-free procapsid (capsid I) packages bacteriophage T7 DNA during infection of Escherichia coli. It was shown here that capsid I, isolated by electrophoresis in metrizamide density gradients, packaged DNA and formed infectious phage particles when incubated in vitro with extracts deficient in capsid proteins.
Is progressive multifocal leukoencephalopathy a chronic disease because of defective interfering particles or temperature-sensitive mutants of JC virus?
Authors: Grinnell B W , Martin J D , Padgett B L , Walker D L
Published: January 2020

JC virus was examined for temperature sensitivity and for evidence of defective interfering particles as a means of explaining the slow chronic nature of progressive multifocal leukoencephalopathy (PML). JC virus direct from the brain tissue of seven persons with PML was not temperature sensitive as indicated by in vitro assay at 37 and 39 degrees C. In fact, more cells contained viral antigen at 39 than at 37 degrees C. The amount of infectious virus also was increased at 39 degrees C. Virions isolated directly from diseased brain tissue had a higher buoyant density than did virus from the same PML patient passaged in culture and containing genomic deletions. In contrast to DNA from culture-passed virus, DNA extracted from virions direct from brain tissue was homogeneous in length. In 13 separate cases examined, the viral DNA direct from the brain was homogeneous although variations in length were noted among DNAs from different cases. Restriction enzyme cleavage patterns identified all as JC virus DNA. It was concluded that neither temperature sensitivity nor DI particles can be used to explain the slow, progressive nature of PML.
Cell-free translation of murine coronavirus RNA
Authors: Leibowitz J L , Weiss S R , Paavola E , Bond C W
Published: January 2020

The coding assignments of the intracellular murine hepatitis virus-specific subgenomic RNA species and murine hepatitis virion RNA have been investigated by cell-free translation. The six murine hepatitis virus-specific subgenomic RNAs were partially purified by agarose gel electrophoresis and translated in an mRNA-dependent rabbit reticulocyte lysate, and the cell-free translation products were characterized by gel electrophoresis, immunoprecipitation, and tryptic peptide mapping. These studies have shown that RNA 7 codes for the nucleocapsid protein, RNA 6 codes for the E1 protein, RNA 3 codes for the E2 protein, and RNA 2 codes for a 35,000-dalton nonstructural protein. Genomic RNA directs the cell-free synthesis of three structurally related polypeptides of greater than 200,000 in molecular weight.
DNA sequence of the viral and cellular src gene of chickens. 1. Complete nucleotide sequence of an EcoRI fragment of recovered avian sarcoma virus which codes for gp37 and pp60src
Authors: Takeya T , Feldman R A , Hanafusa H
Published: January 2020

Recovered avian sarcoma virus is a class of virus obtained from chicken tumors induced by mutants of Rous sarcoma virus which have a deletion in the src gene. We have determined the entire nucleotide sequence of a 3.1-kilobase EcoRI DNA fragment of molecularly cloned recovered avian sarcoma virus DNA. This DNA fragment contains part of the env gene and the entire src gene. Amino acid sequences of both gene products were deduced from the DNA sequences; the predicted amino acid sequences were verified by protein studies. An env protein (gp37) was found to be composed of 205 amino acids with three glycosylation sites. gp37 had a long stretch of hydrophobic residues near the carboxyl terminus. The src gene product, pp60src, was composed of 526 amino acids and contained the possible sites for tyrosine and serine phosphorylation. The amino acid sequences predicted in this study differ significantly from the amino acid sequence predicted previously for the Schmidt-Ruppin strain of Rous sarcoma virus.
Recombination Occurs Mainly Between Parental Genomes and Precedes DNA Replication in Pseudorabies Virus-Infected Cells
Authors: Ben-Porat Tamar , Brown Linda , Veach Ruth Ann
Published: January 2020

The experiments described in this paper were part of an attempt to determine the mechanisms involved in the isomerization of the pseudorabies virus genome. To this end, [
14
C]thymidine-labeled parental virus DNA that was transferred to progeny virions produced by cells incubated in medium containing bromodeoxy-uridine was analyzed in neutral and alkaline CsCl density gradients. The buoyant density of the
14
C-labeled DNA indicated that the parental DNA strands had retained their integrity and had not undergone breakage and reunion with progeny DNA strands; neither massive intermolecular nor intramolecular recombination had occurred after replication of the DNA. Whereas breakage and reunion between parental and progeny virus DNA strands were not detectable, these processes were observed between differentially density-labeled parental DNAs. Furthermore, the frequency of recombination between progeny DNAs accumulating in the cells was low. These results indicate that in pseudorabies virus-infected rabbit kidney cells recombination occurs mainly between parental genomes and precedes DNA replication. An analysis of the kinetics of appearance of recombinants between pairwise combinations of temperature-sensitive mutants also indicated that recombination is an early event. The ratio between the number of recombinant virions and the number of temperature-sensitive mutant virions produced by the cells remained the same throughout infection. Since the relative amounts of viral DNAs synthesized early and late during the infective process that were integrated into virions were approximately the same, it appears that late viral DNA did not experience an increased number of recombinational events compared with early viral DNA. These results, which reinforce the conclusion reached from the results of the analysis of the behavior of the parental DNA molecules in density shift experiments, indicate that recombination is an early event.
Genetic specificity of DNA synthesized in the absence of T4 bacteriophage gene 44 protein
Authors: Kozinski A W , Ling S K
Published: January 2020

Upon infection of Escherichia coli B with T4 phage with DO amber mutation in gene 44, a minimal amount of phage DNA is synthesized. This progeny DNA is, for the most part, covalently attached to the parental DNA. Analysis of the genetic representation of this DNA was performed by hybridization to cloned genetic segments. It was shown that areas preferentially replicated differ from origins observed in "normal" replication: under normal conditions, there is a strong origin in the genetic area of genes 50-5 and lack of initiation within the group of genes 40-43 and 35-52. In contrast, in the absence of the gene 44 protein, the genetic area of 50-5 is underrepresented, genes 35-36, tRNA, and genes 40-41 are the most prominent among progeny DNA, and the area of gene 39 is least represented. Since the area of gene 35 is known from the genetic data or other to be a high-frequency recombination area, and since the area of gene 39 is known to display a low frequency of recombination, we postulate that the observed uptake of label occurs at the site-specific recombinational intersections.
Glycoproteins of herpes simplex virus type 2 as defined by monoclonal antibodies
Authors: Balachandran N , Harnish D , Rawls W E , Bacchetti S
Published: January 2020

We used monoclonal antibodies reacting with glycoproteins specified by herpes simplex virus type 2 (HSV-2) to characterize the individual antigens in terms of structure, processing, and kinetics of synthesis in BHK or Vero infected cells. Our results provided a direct demonstration of the structural identity of the gA and gB proteins of HSV-2 as well as confirmation of the existence of type-specific and type-common domains within the gD molecule. They also show that, with the exception of gC, processing of the viral glycoproteins differs to some extent in Vero and BHK infected cells, possibly as a result of different efficiency of glycosylation or different processing of underglycosylated and unglycosylated products in the two cell types. Finally, we showed that individual HSV-2 glycoproteins are synthesized at greatly different times during the infectious cycle, possibly in response to their different roles in virus replication and assembly.