Molecular structure of adeno-associated virus variant DNA

When lysates of human cells, infected jointly with the defective parvovirus, adeno-associated virus (AAV), and a helper adenovirus, are banded to equilibrium in CsCl buoyant density gradients, virus particles of various densities are obtained. Infectious AAV particles mainly band at a density of 1.41 g/cm3 with a minor component at 1.45 g/cm3. Noninfectious AAV particles band at densities between 1.41 and 1.32 g/cm3. We have analyzed, by mapping with site-specific endodeoxyribonucleases, the molecular structure of the variant AAV DNA molecules obtained from these light density particles. The size of variant DNA molecules ranged from 100 to 3% of genome length. In general, the variant DNAs are deleted for internal regions but retain the genome termini. Some of the variant DNAs appear to be cross-linked, spontaneously renaturing molecules having structures analogous to replicating forms of AAV DNA.     

Fractionation of somatic and sperm chromatin during spermatogenesis in fish

A new approach is suggested for studying changes in the interactions of protein with DNA in the cells. Measurements of the buoyant density of chromatin were performed in somatic cells and in cells undergoing meiosis in fish. During the process of spermatogenesis some of the somatic histones on the DNA are replaced by a new class of proteins; consequently, the mature sperm contains a unique type of protein having a low mol. wt and a high proportion of arginine.The chromatin obtained from mature sperm is composed of a single component with a density of 1.48–1.49 g/cm³ as measured by CsCl equilibrium sedimentation. On the other hand, somatic cells contain chromatin with lower densities. Chromatin obtained from erythrocytes contains a single component with a density of 1.41–1.42 g/cm³ while liver chromatin shows two components; a main component with a density of 1.45–1.46 and a more heterogeneous component with a lighter density (1.32–1.35). There is a correlation between the buoyant density of the chromatin, the type of its basic proteins and the level of biosynthetic activity in the cells.     

Fate of Sendai Virus Ribonucleoprotein in Virus-infected Cells

The cytoplasmic extracts of Ehrlich ascites tumor cells infected with (32)PO(4) and (3)H-leucine-labeled Sendai virus have been examined during the course of infection with respect to sedimentation behavior and buoyant densities of input virus radioactivity. It was found that (32)P and (3)H radioactivities were coincident, and, at 30 min after infection, the bulk of radioactivity was recovered in the polysome region of a sucrose gradient in the position of Sendai virus ribonucleoprotein (210S). The heterogeneity of radioactivity profiles appeared at 1 hr after infection and increased during 6 hr of incubation. The buoyant densities of input virus components were determined by banding in CsCl gradient. Here again the bulk of coincident (32)P and (3)H radioactivity at 30 min after infection banded at the same density as Sendai virus ribonucleoprotein (1.31 g/cm(3).) This component disappeared at 3 hr after infection, and (32)P and (3)H radioactivities were now found in components banded at densities 1.38, 1.41, 1.45, 1.49, and 1.55 g/cm(3). The results presented are consistent with the idea that virus ribonucleoprotein is retained in the cytoplasm of infected cells during at least 6 hr of incubation, being partly deproteinized in the course of infection. The nature of components which banded at rho = 1.41, 1.45, 1.49, and 1.55 as complexes of partly deproteinized ribonucleoprotein with ribosomes will be described in a separate paper.     

Characterization of ribonucleoprotein particles released from isolated nuclei of regenerating rat liver in two different in vitro systems.

The ribonucleoprotein particles released from isolated nuclei of regenerating rat liver in two in vitro systems were studied and the following results were obtained. 1. When the isolated nuclei of regenerating rat liver labeled in vivo with [14C] orotic acid were incubated in medium containing ATP and an energy-regenerating system (medium I) release of labeled 40-S particles was observed. Analysis of these 40-S particles showed that they contained heterogeneous RNA but no 18 S or 28 S ribosomal RNAs and their buoyant density in CsCl was 1.42-1.45 g/cm3, suggesting that they were nuclear informosome-like particles released during incubation. 2. When the same nuclei were incubated in the same medium fortified with dialyzed cytosol, spermidine and yeast RNA (medium II), release of labeled 60-S and 40-S particles was observed. Using CsCl buoyant density gradient centrifugation, two components were found in the labeled ribonucleoprotein particles released from nuclei in this medium. The labeled 60-S particles were found to contain 28-S RNA as the main component and their buoyant density in CsCl was 1.61 g/cm3, suggesting that they were labeled large ribosomal subunits. The labeled 40-S particles contained both 18 S RNA and heterogeneous RNA and they formed two discrete bands in CsCl, at 1.40 and 1.56 g/cm3, suggesting that they contained small ribosomal subunits and nuclear informosome-like particles. 3. These results clearly indicate that addition of dialyzed cytosol, spermidine and low molecular yeast RNA to medium I causes the release of ribosomal subunits or their precursors from isolated nuclei in the in vitro system.     

Identification and separation of components of calf thymus DNA using a CsCl-netropsin density gradient

Calf thymus DNA containing satellite components of various densities was used as a model to study the effect of netropsin on the density of DNA in a CsCl gradient. The binding of netropsin resulted in a decrease in density which depended upon the quantity of netropsin added and on the average composition of the DNA. Differences in density of DNA components were higher in CsCl - netropsin gradients than in simple CsCl gradients. By use of netropsin a main band and four satellite bands could be differentiated in calf thymus DNA. Satellite DNA's were isolated using preparative CsCl - netropsin gradient centrifugation and were characterised by density and homogeneity in native and in reassociated state. Two of the satellite components, with densities of 1.722 and 1.714 g/cm³, are probably of homogenous sequence, the other two components of densities 1.709 and 1.705 g/cm³ appear to be heterogeneous.     

Isolation and characterization of satellite DNA from mustard seedlings

The DNA from mustard (Sinapis alba L.) seedlings was examined by neutral CsCl and Ag⁺/Cs₂SO₄ density gradient centrifugation. Different satellite fractions were revealed by these two methods. The satellite fractions obtained from the Ag⁺/Cs₂SO₄ density gradient could not be generally correlated with satellite DNA fractions observed in CsCl. In CsCl density gradient centrifugation, a main band at density 1,695 g/cm³ and a heavy shoulder at density 1,703 g/cm³ are found. By preparative CsCl gradient centrifugation the heavy shoulder can be enriched but not completely separated from the main band DNA.—Gradient centrifugation by complexing the DNA with Ag⁺ rf. 0.25 to DNA phosphate reveals three distinct fractions which are further characterized: The heavy satelite DNA fraction revealed by Ag⁺/Cs₂SO₄ gradient centrifugation has the same density in a CsCl gradient and the same Tm value as the main band, but differs from main band DNA in the details of its melting profile and in its renaturation kinetics. The light Ag⁺/Cs₂SO₄ satellite DNA fraction had a higher melting temperature corresponding to a GC-rich base composition. Differences between these 3 fractions are observed in thermal denaturation and renaturation profiles, hybridization in situ with ribosomal RNA, and their response to restriction endonuclease digestion. The light satellite fraction from the Ag⁺/Cs₂SO₄ gradient, rich in ribosomal cistrons corresponds to the heavy shoulder DNA of neutral CsCl gradients which also is rich in ribosomal cistrons. The heavy satellite fraction from Ag⁺/Cs₂SO₄ gradient which contains highly repetitive short nucleotide sequences could not be revealed by the classical CsCl gradient centrifugation technique.     

S1 nuclease definition of highly repeated DNA sequences in the Guinea pig, Cavia porcellus.

Native DNA of the Guinea pig, Cavia porcellus, purified from liver or tissue culture cells, was heat denatured and reassociated to a Cot value of 0.01 (equivalent Cot value of 7.2 x 10(-2)). The reassociated DNA was isolated by digestion with the single-strand DNA specific enzyme S1 nuclease. Spectrophotometric and radioactivity assays demonstrated that 24% of the total DNA was resistant to S1 nuclease treatment. Zero-time reassociation indicated that approximately 3% of the DNA was inverted repeat sequences. Thus, highly repeated sequences comprised 21% of the total genome. CsCl buoyant density ultracentrifugation indicated that this fraction was composed of both main band and satellite sequences. Although actinomycin D - CsCl density gradients failed to give significant separation of the repetitive sequences, distamycin A - CsCl gradients were able to fractionate the DNA into several overlapping bands. The heterogeneity of the repetitive DNA was further demonstrated by the first derivative plots calculated from their thermal denaturation profiles. This analysis revealed six major thermalytes which indicate that there may be at least six discrete components in the repetitive DNA.     

Ribonucleoproteins containing mRNA in the cytoplasm of mouse plasmacytoma cells]

The rapidly labelled postribosomal ribonucleoprotein (RNP) found in the cytoplasm of mouse plasmacytoma cells were investigated. It has been shown that 45S and 80S particles contain relatively high molecular weight (approximately 12-17S) pulse-labelled RNA similar to the polyribosomal mRNA. No other postribosomal RNP was found which would contain an RNA with similar sedimentation characteristics. In CsC1 density gradients, the postribosomal RNP gives two peaks. One of them, the rapidly labelled component (rho 1.52 g/cm3) is found only in 45S RNP. The other rapidly labelled component (rho 1.36-1.41 g/cm3) is revealed in all investigated regions of sucrose gradients. The latter contains relatively low molecular weight RNA (approximately7-9S). These RNP are supposed to be informosome-like particles. The components with a buoyant density of 1.52 g/cm3 may represent an mRNP-45S subparticles complex. The rapidly labelled mRNA of 80S particles is released after EDTA treatment in the form of mRNP with a buoyant density of 1.45-1.47 g/cm3.     

Ribosomal DNA in spores of Physarum polycephalum

DNA was isolated from plasmodia, spores and newly hatched amoebae of the slime mould Physarum polycephalum. The DNA preparations were fractionated in CsCl gradients and each fraction hybridised to combined 19 S + 26 S rRNA. In all three DNA preparations hybridisation was found to be limited to satellite DNA (rho = 1.714 g/cm3) and at saturation was found to reach a level of 0.16--0.18 % of total DNA. The main band of nuclear DNA (rho = 1.702 g/cm3) did not hybridise appreciably. Further experiments using analytical CsCl gradients revealed that the ratio of satellite to main band DNA was similar in all three preparations. It is concluded that the genes for ribosomal RNA are equally reiterated in spores, hatching amoebae and in plasmodia. They appear to be similarly organised in all stages of the life cycle examined so far.     

An analysis of the bovine genome by Cs2SO4-Ag density gradient centrifugation

Calf DNA preparations having molecular weights of 5 to 7 × 10⁶ have been fractionated by preparative Cs₂SO₄—Ag⁺ density gradient centrifugation into a number of components. These may be divided into three groups: (1) the main DNA component (1.697 g/cm³; all densities quoted are those determined in CsCl density gradients), the 1.704 and 1.709 g/cm³ components form about 50, 25 and 10% of the genome, respectively; they are characterized by having symmetrical CsCl bands and melting curves, both of which have standard deviations close to those of bacterial DNAs of comparable molecular weight, and by their G + C contents being equal to 39, 48 and 54%, respectively; after heat-denaturation and reannealing, their buoyant densities in CsCl are greater than native DNA by 12, 10 and 3 mg/cm³, respectively. (2) The 1.705, 1.710, 1.714 and 1.723 g/cm³ components represent 4, 1.5, 7 and 1.5% of the DNA, respectively, and exhibit the properties of “satellite” DNAs; their CsCl bands and melting curves have standard deviations lower than those of bacterial DNAs; after heat-denaturation and reannealing, their buoyant densities are identical to native DNA, except for the 1.705 g/cm³ component, which remains heavier by 5 mg/cm³; in alkaline CsCl, only the 1.714 g/cm³ component shows a strand separation. (3) A number of minor components, forming 1% of the DNA, have been recognized, but they have not been investigated in detail; two of them (1.719 and 1.699 g/cm³) might correspond to ribosomal cistrons and mitochondrial DNA, respectively.     

DNA synthesis in circulating erythroblasts of anemic duck. Isolation and properties of nuclear and cytoplasmic-nonmitochondrial DNA.

In the circulating blood of anemic ducks, 5% of all erythroid cells synthesize DNA. Immature erythroblasts, at all stages of differentiation, synthesize DNA although to a varying degree, while reticulocytes and erythrocytes do not. In the erythroid cell population labeled in vitro 2 h with 32Pi, half of the labeled DNA sediments as small-molecular-weight molecules, suggesting that these molecules fail to integrate into the high-molecular-weight components. Labeled DNA is found in the cytoplasmic postmitochondrial fractions and it is in a form of deoxyribonucleoproteins which cosediment with ribosomes as well as subribosomal particles in sucrose gradients. However, fixation with HCHO and centrifugation to equilibrium in CsCl gradient of these particles shows that the deoxyribonucleoprotein bands at the density different than the ribosomes and, thus, not physically linked to them. In EDTA-dissociated ribosomes, the deoxyribonucleoprotein particles cosediment with ribosomes as well as subribosomal particles in sucorse gradients. However, fixation with HCHO and centrifugation to equilibrium in CsCl gradient of these particles shows that the deoxyribonucleoprotein bands at the density different than the ribosomes and, thus, not physically linked to them. In EDTA-dissociated ribosomes, the deoxyribonucleoprotein particles cosdeiment with ribosomal subunits in such a way that the larger the particle, the larger the molecular weight of the DNA cosedimenting with it. The specific radioactivity of the cytoplasmic ribosome-derived and postribosomal-particle-derived DNAs and the small molecular-weight nuclear DNA is similar and 10-20-fold higher than that of the bulk nuclear DNA. The former three DNA species sediment between 4-14 S. It is concluded that the cytoplasmic nonmitochondrial DNA species are of the nuclear origin. Less than 0.5% of the total cellular nonmitochondrial DNA can be purified from the nucleus and the cytoplasm as fast-labeled small-molecular-weight components. All of the cellular nonmitochondrial DNA species band at the same mean buoyand density in Cs2SO4/urea gradients. All behave as native structures in hydroxyapatite and contain less than 5% of their length as single-stranded regions.     

DNA fiber replication in chromosomes of a higher plant (Pisum sativum).

Ribosomal precursor particles were extracted from the yeast Saccharomyces carlsbergensis and analysed. After a brief labelling of yeast protoplasts with ³H-uridine, three basic ribonucleoprotein components were detected, sedimenting at approx. 90S, 66S and 43S in sucrose gradients containing magnesium. The 90S particles contained the 37S ribosomal precursor RNA as a major component and a small though variable amount of 29S ribosomal precursor RNA. The 66S and 43S particles contained 29S and 18S ribosomal precursor RNA, respectively. Kinetic data indicate a precursor-product relationship between the 90S particles and the two other ribonucleoprotein components, consistent with the conversion: 90S → 66S + 43S. The 90S and 66S preribosomes appeared to be present exclusively in the nucleus, whereas the 43S particles were mainly present in the cytoplasmic fraction. Apparently, the final maturation step in the formation of the 40S ribosomal subunits takes place in the cytoplasm. The 90S and 66S precursor particles have a relatively higher ratio of protein to RNA than the mature large ribosomal subunits, as judged from their buoyant densities in CsCl gradients. This finding suggests that also in a primitive eukaryotic organism, like yeast, ribosome maturation involves, in addition to a decrease in the size of the RNA components, an even stronger decrease in the amount of associated protein. In contrast, the 43S particles appeared to have the same buoyant density as the 40S ribosomal subunits.     

Generation of capsids from unstable polyoma virions.

Polyomavirus was purified from infected mouse cell lysates under mild physiological conditions. When analyzed in a sucrose gradient, a major virus peak (240S) was identified. This sucrose-isolated virus could be divided into two populations based on its stability to CsCl gradient centrifugation. Members of the unstable population were shown to eject their DNA cores when subjected to CsCl gradient centrifugation, forming empty capsids, whereas the stable population was unaffected by the same CsCl treatment. Formaldehyde fixation of the 240S virus particles stabilized the virions and prevented ejection of DNA and generation of empty capsids. When formaldehyde-fixed 240S virus was examined with the electron microscope, only full virions were observed. These results indicate that polyoma capsids are not preformed in vivo, but instead are generated when infected cell lysates are subjected to harsh CsCl purification procedures.     

Replication of non-repetitive DNA during early, middle and late S phase : The general class and the subset transcribed

Synchronized cultures of Chinese hamster ovary cells were pulse-labelled with 5-bromodeoxyuridine (BrdU) during early (0-2.0 h), middle (2.5-4.0 h) and late (4.5-6.0 h) S phase in two successive cell cycles. In each case, the DNA containing BrdU in both strands was duplicated at the same time in both cycles and was isolated for further characterization by centrifugation in CsCl gradients. These DNAs were then radiolabelled by nick-translation and used in either DNA-DNA or RNA-DNA hybridization experiments. In the DNA-DNA experiments, advantage was taken of the substantial rate increases attainable in high concentrations of dextran sulfate to obtain complete reassociation curves with relatively small amounts of material. Assuming that no unresolved low repetition frequency components exist, renaturation kinetics suggest that early replicating DNA contains a greater proportion of non-repetitive sequences than DNA synthesized at later times, the order being early greater than middle greater than late. However, in terms of complexity the non-repeated DNA duplicated early had only 74% of the diverse sequences present in log-phase cells, whereas that replicated in middle and late S phase had 82 and 79.5%, respectively. It therefore appears that while DNA synthesized at different times in S phase may contain varying proportions of non-repetitive sequences, when their diversity is taken into account very few of these sequences (25% or less) exhibit temporal control of replication. Finally, measurements with total cell RNA indicated that the transcribed fraction of non-repeated DNA showed a slight preference for replication in early S phase.     

Virus-like particles from killer, neutral, and sensitive strains of Saccharomyces cerevisiae.

Procedures were developed for purification of virus-like particles (VLPs) from killer, neutral, and sensitive strains of Saccharomyces cerevisiae. Morphologically similar spherical VLPs measuring 40 nm in diameter were extracted from all three phenotypes. The particles were partially purified by high-speed centrifugation through a layer of CsCl (1.26 g/cm3) and sucrose density gradient centrifugation. Gradient-purified preparations contained three centrifugal species that sedimented at approximately 43, 102, and 162S. The 43S component is considered to be an artifact. Preparations from killer strains contained three double-stranded RNA (ds-RNA) components with molecular weights of 1.19 x 10(6), 1.29 x 10(6) and 2.54 x 10(6). VLPs from neutral and sensitive strains contained only the largest ds-RNA species. VLP preparations were subsequently separated into two major density components by CsCl equilibrium gradient centrifugation. The light component banding at 1.28 to 1.30 g/cm3 was void of nucleic acid, and the heavy component banding at 1.40 g/cm3 contained only the largest ds-RNA species.     

Properties of a host range and coat protein variant of broad bean true mosaic comovirus from Vicia faba

Unlike other described isolates of broad bean true mosaic comovirus (BBTMV), a variant, code name SB, infected some non-leguminous plant species and, in N. benthamiana, induced systemic mottling and puckering of the leaves. However, like other described BBTMV isolates, purified SB particle preparations contained isometric particles c. 28 nm in diameter that sedimented as two nucleoprotein components with S_{20, w} values of 90S and 109S; some preparations occasionally contained a component of c. 50S. Virus particles contained two ssRNA species which, when denatured in glyoxal, had estimated M_T values of 2.1 × 10⁶ and 1.3 × 10⁶ and co-electrophoresed with cowpea mosaic virus RNA-1 and RNA-2 respectively. Isolate SB was serologically indistinguishable from British and German isolates of BBTMV. However, SB virus particles contained a major polypeptide (L) of M_r between c. 31 000 and up to three minor ones (S) or M_r between c. 20 000 and 24 000. This contrasts with protein preparations from other BBTMV isolates that typically contain only two polypeptides of M_r c. 37 000 (L) and 21 000 (S). Following isopycnic centrifugation in CsCl, SB particles purified from pea separated into two major components with densities of 1.39 and 1.44 g cm^-3 and a minor component of estimated density 1.43 g cm^-3. In Cs₂SO₄, virus preparations separated into three major components with densities of 1.30, 1.32 and 1.36 g cm^-3 and a minor one of density 1.27 g cm^-3. In CsCl isopycnic gradients, SB particles purified from TV. benthamiana separated into two components with densities of 1.38 and 1.43 g cm^-3. During immuno-electrophoresis in agarose gels, freshly prepared virus and preparations stored for up to 4 days at 4°C contained a single component that migrated rapidly to the anode, whereas similar preparations of an English isolate of BBTMV migrated as a single component that moved only slowly toward the anode but which, within 48 h, contained an additional component with a migration rate similar to that of isolate SB. Isolate SB is therefore a host range variant of BBTMV which, in comparison with previously described isolates of BBTMV, has an increased negative charge of its particles prior to any appreciable degradation of its S protein, and S protein that is degraded less rapidly. These features probably account for the anomalies observed in isopycnic centrifugation.     

Role of lysine in the replication of reovirus: I. Synthesis of complete and empty virions

Lysine is essential for the replication of infectious reovirus. Omission of lysine from the extracellular medium not only permitted the continued synthesis of structural viral proteins and viral double-stranded ribonucleic acid (RNA), but also caused an enhanced formation of viral structures which were separable by isopycnic sedimentation of CsCl into a top band consisting of empty particles with a buoyant density of 1.29 g/cm³ and essentially free of viral RNA, and two lower bands which were difficult to resolve and had an average buoyant density of 1.37 g/cm³. The lower bands contained most of the viral nucleic acid. The above effects were reversed when lysine was restored early after infection. In contrast, a single band with a buoyant density of 1.38 g/cm³ was obtained from lysine-plus infected cells.     

Characterization and classification of virus particles associated with hepatitis A. I. Size, density, and sedimentation.

Virus-like particles were purified from stools of patients in an epidemic of hepatitis A in Germany. When reference MS-1 chimpanzee pre-inoculation and convalescent sera were used, the close serological relationship of the purified particles to well-known isolates of hepatitis A could be established. On the other hand, the physicochemical characteristics of the particles were determined in parallel to the characteristics of a marker parvovirus (LuIII) and a marker picornavirus (poliovirus type 2). It could be shown that the majority of the hepatitis A-associated particles band at 1.34 g/ml in CsCl and, like poliovirus, sediment at about 160S. In addition, a distinct hepatitis A antigen was observed, which banded at 1.305 g/ml and sedimented between 50 and 90S. A further component accumulated in the density range of between 1.38 and 1.44 g/ml. However, it seemed to be rather labile. Upon reisolation from CsCl and sedimentation in sucrose, it resolved into a 160S, a 90 to 100S, and a 50S form. The size of the 160S particles (27 to 29 nm) could be readily distinguished from that of the parvovirus (22 to 24 nm). It is concluded, therefore, that hepatitis A-associated virus particles are more likely to be classified with the picornaviruses than with the parvoviruses.     

Composition and synthesis of DNA in synchronously growing cells of Chlorella pyrenoidosa

Summary The composition and synthesis of DNA in synchronous cultures of Chlorella pyrenoidosa strain 211/8b has been investigated. Analytical CsCl density gradient centrifugation gave a homogenous major DNA component with a (G+C) content of 51% and a minor component containing 28% (G+C). The (G+C) contents derived from melting profiles were 2–3% lower. A second minor component with approximately 41% (G+C) content was inferred from banding patterns of labelled DNA in preparative CsCl density gradients. ¹⁴C-uracil was readily incorporated into the pyrimidine moieties of the major (nuclear) DNA between the 10th and 18th hour after beginning of the light period, but not at any other time. ¹⁴C-uracil incorporation into the minor (satellite) component was low but continuous throughout the whole cell cycle. The incorporation is correlated with an increase in the proportion of satellite DNA from 6% up to 20% during the time when no nuclear DNA replication takes place. The results suggest that different regulatory mechanisms exist for the nuclear and for satellite DNA synthesis.     

Isolation and characterisation of subribosomal ribonucleoprotein particles from radish seeds and seedlings

Ribonucleoprotein (RNP) particles were isolated from the postribosomal supernatant of radish seeds and seedlings. Most of them sediment at about 20 S and have a buoyant density in CsCl of 1.38 g · cm⁻³. A minor fraction appears as a shoulder on the heavy side of the 20 S peak; it bands at 1.41 – 1.43 g · cm⁻³. Two types of RNA families have been identified in the particulate fraction : heterogenous RNA (18-4 S) and RNA comigrating with 4 S tRNA. Poly(A) has been found in this RNA but it accounts for less than 10% of total stored poly(A). The polypeptide moiety of the particles was analysed and compared with ribosomal and soluble proteins. It was shown that the 20 S RNP gradually disappears during germination. These results indicate that the post-ribosomal supernatant of seeds contains some mRNA (or nuclear precursor) associated with proteins and a large amount of another type of RNP in which tRNA is associated with proteins.