Sequence homology between the structural proteins of Kilham rat virus.

The capsid proteins of the autonomous parvovirus Kilham rat virus were purified and analyzed for peptide composition. Partial proteolysis mapping and two-dimensional thin-layer chromatography of tryptic peptide digests revealed extensive amino acid sequence homology between the two major Kilham rat virus capsid proteins.

Transcription and translation in the autonomous parvovirus KRV.

We describe here the isolation and partial characterization of at least five viral specific RNAs synthesized in the rat nephroma (RN) cell after infection with the parvovirus KRV. The RNAs have the approximate lengths of 4.7, 3.4, 3.0, 1.25, and 0.95 kilobases (kb) and are probably the functional messages. The 4.7-kb RNA would represent a transcript of 95 to 100% of the viral genome. The most abundant message, about 3.0 kb, represents over 50% of the viral genome and probably codes in the reticulocyte transcribing system for the most abundant viral protein (MW 68,000) which is the main viral capsid protein. This abundant RNA, on the basis of R loop data, has an origin of transcription about 0.38 to 0.42 map units from the 3' end of the single-stranded KRV genome.

Synthesis of mRNA by the parvovirus KRV in isolated nuclei.

We have synthesized vial-specific transcripts in nuclei isolated from cells infected with the parvovirus Kilham rat virus. Radioactive vial-specific RNA synthesized in the nuclei was extracted, hybridized to viral DNA, incubated in glyoxal, and electrophoresed in an agarose gel. At least five viral-specific RNAs were detected containing 4.6 Kb (25-26S), 3.2 Kb (major species, 20-22S), 2.9 Kb, 1.3 Kb, and 1.0 Kb pairs. The 4.6 Kb RNA represents a transcript of 95-100% of the viral genome. The major 3.2 and 2.9 Kb RNAs represent a transcript of 50-60% of the viral genome. Over 65% of the viral-specific RNA in the isolated nuclei is polyadenylylated on the 3' terminus. The 5' terminus of the RNA is capped in vitro by the sequence m7G(5')ppp(5')A. Incorporation of [beta-32p]ATP into the 5' cap sequence suggests that initiation of viral RNA synthesis may occur in the infected isolated nuclei.

Nucleotide sequence of the self-priming 3' terminus of the single-stranded DNA extracted from the parvovirus Kilham rat virus.

The parvovirus genome is a linear, single-stranded DNA molecule with double-stranded hairpin termini. The 3' terminus can serve in vitro as a self-primer for the synthesis of a double-stranded viral DNA intermediate. We have sequenced the nucleotides in the 3' terminus and propose a model for the secondary structure of the terminus and the in vitro origin of replication for the complementary viral DNA strand.

In vitro synthesis of double-stranded DNA from the Kilham rat virus single-stranded DNA genome.

Double-stranded, full-length linear DNA was synthesized in vitro by using single-stranded linear DNA as a self-priming template from the parvovirus Kilham rat virus and Escherichia coli DNA polymerase "large fragment" as the polymerizing enzyme. To ascertain the order of the synthesis of the cleavage fragments and to assess the accuracy of the in vitro synthesis, restriction endonuclease cleavage sites with known recognition sequences were mapped on the DNA. Comparing the cleavage pattern of the synthesized DNA with that of double-stranded viral DNA isolated from infected cells confirms that the in vitro synthesis produces a faithful copy of the viral single-stranded genome. Electron micrographs of the in vitro product reveal it to be a double-stranded linear molecule.

Studies on the replication of KRV single-stranded linear DNA.

The autonomous parvovirus, Kilham rat virus (KRV), is composed of three structural proteins (Salzman & White, 1970) and a single molecule of DNA. The DNA molecule is linear and single-stranded (ss). It is believed to have both 3' and 5'-terminal palindromic sequences (Salzman, 1977). Replication of the ss DNA may involve double-stranded (ds) DNA intermediates of one unit length as found in the virion or multiple length concatamers (Salzman & White, 1973; Gunther & May, 1976; Lavelle & Li, 1977). We have attempted to determine when the synthesis of KRV ds DNA can be determined in synchronized infected cells and the structure of the ds DNA molecules.

Characterization of the deoxyribonucleic acid polymerase associated with Kilham rat virus.

Purified preparations of the parvovirus, Kilham rat virus, have associated with them a protein with DNA polymerase activity. The enzyme has been separated from the other two or three viral proteins and purified 63-fold. The viral associated enzyme was found in a single peak of DNA polymerase activity after chromatography on DEAE-cellulose, DNA-cellulose, and phosphocellulose columns. It shares some properties in common with the host cellular DNA polymerases, described in the preceding paper (Salzman, L.A., and McKerlie, L. (1975) J. Biol. Chem. 250, 5589-5595), but also has some important distinguishing characteristics. The Kilham rat virus-associated DNA polymerase has increased enzyme activity in the presence of 0.02 M KCl and has a strong preference for a synthetic DNA polymer containing deoxyadenylate and deoxythymidylate. The enzyme has a molecular weight of approximately 75,000 plus or minus 3,000 and appears to contain endonuclease activity.

Nuclear and cytoplasmic deoxyribonucleic acid polymerases from rat nephroma cells.

We have examined the DNA polymerases found in a rat nephroma cell line. Using DEAE- and DNA-cellulose chromatography, we have found two major cytoplasmic DNA polymerases and one major and three minor DNA polymerases from the nucleus. The enzymes were all purified, characterized, and distinguished from each other by several criteria. The enzyme require, for maximal activity, a natural or synthetic double-stranded DNA, four deoxynucleoside, triphosphates, and magnesium. They are inhibited to varying degrees by sodium pyrophosphate, ethidium bromide, and rho-chloromercuribenzoate.

Synthesis of viral-specific RNA in cells infected with the parvovirus, Kilham rat virus.

We have studied the viral-specific RNA synthesized after infection of a permissive cell line with Kilham rat virus (KRV). The RNA was shown to be virus specific by analysis of its nucleotide base ratios and by hybridization with KRV and cellular DNA. Viral RNA is synthesized as early as 2 h after infection. This viral RNA synthesis occurs before viral progeny DNA synthesis which is initiated at 7 to 8 h after infection. The predominant viral RNA synthesized before and after viral progeny DNA synthesis has a sedimentation coefficient of approximately 18S in dimethylsulfoxide-sucrose gradients and a calculated molecular weight of 6.5 x 10(5) to 7.5 x 10(5). KRV contains a molecule of single-stranded DNA with a molecular weight of approximately 1.6 x 10(6). If the viral-specific 18S RNA is a homogenous species, it would account for 40 to 50% of the viral genome. A small amount of 26S viral RNA with a molecular weight of 1.6 x 10(6) to 1.7 x 10(6) can also be detected. If this 26S RNA is a single viral-specific entity, it could represent a transcription of the entire KRV genome.

In vivo conversion of the single-stranded DNA of the kilham rat virus to a double-stranded form.

Kilham rat virus (KRV) contains linear, single-stranded DNA in the virion. The fate of radioactive viral DNA was followed after infection of monolayer cells. Within 60 min after infection of cells, 28 to 42% of the parental viral DNA is converted to a new form. This new DNA form is believed to be double stranded and linear on the basis of its sedimentation in neutral and alkaline sucrose gradients, elution from hydroxyapatite columns, its buoyant density in equilibrium CsCl density gradients, and appearance in the electron microscope. The double-stranded linear KRV DNA may be analogous to the replicative form of certain bacteriophages, including phiX174, which contain single-stranded circular genomes.

Growth characteristics of Kilham rat virus and its effect on cellular cellular macromolecular synthesis.

Kilham rat virus (KRV) is adsorbed into the rat nephroma cell within 1 hr after infection. There follows a latent period of about 12 hr during which less than 1% of the input infectious virus can be accounted for. New infectious virions can be detected at about 12 hr and the maximal yield of virus is attained by 23 hr after infection. The increase in final virus yield is about 200-fold over that found in the latent period. During this 23-hr period of virus growth, the rate of protein synthesis remains 75 to 100% of that in the uninfected cell. Ribonucleic acid (RNA) synthesis during this period is maintained at 100 to 150% of that found in the control cells. The addition of the inhibitor of deoxyribonucleic acid (DNA) synthesis, 5-fluoro-deoxyuridine (FUDR), up to 8 hr after infection completely suppresses virus production. After 8 hr, viral DNA production has started and FUDR inhibition progressively decreases until by 23 hr the addition of the inhibitor no longer causes a reduced virus yield. Viral DNA synthesis once initiated is required for the remainder of the 23-hr virus cycle. Viral DNA synthesis probably begins about 4 hr before the production of infectious virions. In the KRV-infected cells, DNA synthesis decreased sharply for 6 to 7 hr after infection in comparison to the uninfected cell. At 7 to 8 hr after infection, DNA synthesis in the infected cell increased and was maintained at a higher level than in the control cells for the rest of the virus growth period.

Linear, single-stranded deoxyribonucleic acid isolated from Kilham rat virus.

Kilham rat virus (KRV) was grown in a rat nephroma cell line and was purified by two isopycnic centrifugations in cesium chloride. The virus contains single-stranded deoxyribonucleic acid (DNA) with a molecular weight of approximately 1.6 x 10(6). The DNA was extracted from the virion by both phenol extraction and by 2% sodium dodecyl sulfate at 50 C. KRV DNA, extracted by both procedures, was observed in an electron microscope by using a cytochrome c or diethylaminoethyldextran monolayer. The DNA was also exposed to exonuclease I, an enzyme which hydrolyzes specifically linear, single-stranded DNA. Hydrolysis of 70 to 80% of the DNA was observed. Both the enzymatic and the electron microscope studies support the conclusion that extracted KRV DNA is a single-stranded, linear molecule. The length of the DNA was measured in the electron microscope and determined to be 1.505 +/- 0.206 mum.

Characterization of the Kilham rat virus.

Kilham rat virus (KRV) was found to grow in a rat nephroma cell line and to form plaques on secondary rat embryo monolayers. The virus was purified by enzymatic treatment and isopycnic cesium chloride sedimentation. KRV bands at a density of 1.41 g/cm(3) in cesium chloride. It contains about 26.5% deoxyribonucleic acid (DNA). The sedimentation coefficient S(20,w) in sucrose gradients was 122 corresponding to a molecular weight of 6.6 x 10(6) daltons. The reaction of formaldehyde with the KRV virion suggests that the DNA in situ is single-stranded. DNA extracted from KRV had a buoyant density of 1.715 g/cm(3) in cesium chloride. The S(20,w) was determined in sucrose gradients to be 16, and the molecular weight was calculated to be approximately 1.7 x 10(6) daltons. The base composition of the DNA is 26.7% adenine, 30.8% thymine, 20.0% guanine, and 22.5% cytosine. On the basis of its noncomplementary nucleotide ratio, melting curve, and the reaction with formaldehyde, the DNA of KRV is believed to be single-stranded.

Deoxyribonucleic acid replication in lambda bacteriophage mutants.

After ultraviolet light induction of Escherichia coli K-12 strain W3350(lambda), several structural intermediate forms of phage deoxyribonucleic acid (DNA) are synthesized. The early defective lysogens of lambda, sus O(8), sus P(3), and T(11), were found to synthesize none of the DNA structural intermediates. A lysogen believed to be defective in all known phage activities, lambdasus N(7), was found to be able to synthesize an early phage DNA intermediate. The lysogen lambdasus Q(21), defective in late phage functions, is able to synthesize the early phage DNA intermediate and a concatenated molecule of greater molecular weight than the mature lambda DNA.