Structures and roles of the polymorphic forms of tobacco mosaic virus protein. 8. Initial stages of assembly of nucleoprotein rods from virus RNA and the protein disks

The initial stages of the assembly of tobacco mosaic virus have been investigated by reassembling the RNA with a radioactively labelled protein disk preparation and then completing the reaction by the addition of a large excess of an unlabelled disk preparation. This gives measurements of the numbers of subunits incorporated at early times and the growth curves have been plotted.These curves have been analysed in terms of a bimolecular nucleation reaction, which is first order in the disk concentration, with a rate constant of 1.3 × 10³ mol^?1 s^?1, and then an elongation which saturates at high protein concentrations to a maximum rate of 7.6 subunits s^?1, with a K_m of 0.84 mg/ml for the disk preparation.These kinetic parameters, and the predicted overall assembly curves, have been compared with data previously determined by other methods and agree closely, showing that the different experimental techniques give consistent results. The measurements are fully compatible with our earlier hypotheses Butler &; Klug 1971 that the nucleation with virus RNA and protein disks is rapid compared with the subsequent rod elongation and that this elongation can occur most rapidly directly from the protein disks. They are not compatible with the contention of some other workers that elongation cannot occur directly from disks, but only from the smaller A-protein.     

Rottboellia yellow mottle virus,a new sobemovirus affecting Rottboellia cochinchinensis (Itch grass) in Nigeria1

A hitherto undescribed virus, termed rottboellia yellow mottle virus (RoYMV), affecting Rottboellia cochinchinensis (syn. R. exaltata, itch grass) at Ibadan, Nigeria, was investigated. RoYMV virions are isometric, c. 29 nm in diameter, and sediment homogeneously at 114s. In isopycnic CsCl gradients, RoYMV virions band sharply at a buoyant density of 1.379 g cm^-3, but in Cs₂SO₄ gradients, virions band at two zones, at the densities of 1.300 g cm^-3 and 1.325 g cm^-3. Treatment with EDTA at pH 8.0 reduced the sedimentation value of RoYMV to c. 87s and rendered it susceptible to proteinase-K, SDS and NaCl. The apparent molecular weight of RoYMV coat protein was c. 27 000. Virions encapsidate a single-stranded RNA of mol. wt 1.4 × 10⁶ Da. Besides R. cochinchinensis, RoYMV was mechanically transmissible only to maize (Zea mays). No reaction occurred when RoYMV was tested against antisera to 44 isometric plant viruses (belonging to 12 groups), including several that affect Gramineae. RoYMV exhibits striking similarities with other viruses belonging to the sobemovirus group, and it is tentatively designated as a new member of the sobemovirus group.     

An improved method for obtaining thermal titration curves using micromolar quantities of protein

Two simple modifications of a commerclally available microcalorimeter allow rapid and accurate equilibration of sample with titrant and result in increased sensitivity. The modifications permit the rapid equilibration of the reaction vessel vapor space with solvent vapor and unambiguous determination of the temperature difference between the thermostat and the contents of the reaction vessel. A procedure is described for performing a thermal titration under conditions in which the system is undergoing a continuous thermal drift. The procedure is used to determine the standard enthalpy and free energy changes for the binding of ADP to bovine liver glutamate dehydrogenase. Only 0.3 μmol of protein sample was required. The observed values (ΔH^ot = −13.0 ± 0.7 kcal mol⁻¹, ΔG^ot = −7.4 kcal mol⁻¹) agree within 5% of the values determined by S. Subramanian, D. C. Stickel, and H. F. Fisher (1975, J. Biol. Chem. 250, 5885–5889).     

Some Properties of Cucumber Fruit Streak Virus

An isometric virus c. 30 nm in diameter with a single RNA species (mol.wt 1.45 × 10⁶) isolated from cucumber plants from the island of Crete (Greece) is described under the name of cucumber fruit streak virus (CFSV). The most evident symptom on naturally infected plants consisted of longitudinal chlorotic streak of the fruits. In glasshouse, the virus was soil-transmitted to C. sativus, and, mechanically, to a wide range of herbaceous hosts, most of which were infected only locally. Purified virus preparations sedimented as a single component with sedimentation coefficient of 132S. At equilibrium these preparations were homogeneous in CsCl gradients but formed two bands in Cs₂SO₄ gradients. Virus particles were stabilized by forces involving divalent cations, pH-dependent bonds and salt links between protein and RNA. Although some of the properties of CFSV are similar to those of other small spherical viruses with single RNA species there are differences which do not allow for the assignment of the virus to any of established taxonomic group of plant viruses.     

A study of the intermolecular association in living systems. IV. Studies on a model molecular fragment (pentane)

The low-lying energy states for the association of two molecules of n-pentane are determined by keeping one molecule fixed and rotating the second molecule simultaneously about its own x-, y-, and z- axes and also around the first molecule, all rotations being carried out from 0° to 360° in steps of 20° The interaction energy is calculated at each step, the form of the interaction energy used is the one given by Claverie &; Rein (1969). Results show that only a very limited number of orientations lead to energy states that are within 5 kcal mol^?1 of the minimum energy state.     

Structure of DNA in Spores of Bacillus cereus

The structure of DNA extracted from dormant and germinating spores of B. cereus T was investigated using circular dichroism and other methods. No significant differences between DNAs extracted from vegetative cells and from spores of various stages could be found by analyses of CD spectra, CsCl density gradient centrifugation, melting profiles and template activity. All the DNA preparations were in B conformation and had the same density (1.695), Tm (83°C) and template activity in the reaction of DNA-dependent RNA polymerase. An abnormal DNA fraction of high density which was formerly found in B. cereus spores or a stable DNA complex with protein and/or RNA was not detected in the present extracts of spores. Preliminary X-ray analyses of intact spores indicate that the structure of DNA in spores is not so different from B form.     

Thermodynamics of the slow–fast transition in bacteriophage T2L

We have measured the thermodynamic parameters of the slow-fast tail-fiber reorientation transition on T2L bateriophage. Proportions of the virus in each form were determined from peak-height measurements in sedimention-velocity runs and from average diffusion coefficients obtained by quasielastic laser light scattering. Computer simulation of sedimentation confirmed that there were no undetected intermediates in the transition, which was analyzed as a two-state process. Van't Hoff-type plots of the apparent equilibrium constant and of the pH midpoint of the transition as function of reciprocal temperature led to the following estimates of the thermodynamic parameters for the transition at pH 6.0 and 20°C: ΔH° = ?139 ± 18Kcal mol^?1, ΔS° = ?247 ± 46 cal K^?1 mol^?1, and ΔG° = ?66 ± 22 kcal mol^?1. Per mole of protons taken up in the transition, the analogous quantities were ?15.9 ± 1.7 kcal mol^?1, ?26.3 ± 2.2 cal K^?1 mol^?1, and ?8.22 ± 1.8 kcal mol^?1. The net number of protons taken up was about 8.5 ± 1.5. The large values of the thermodynamic functions are consistent with a highly cooperative reaction and with multiple interactions between the fibres and the remainder of the phage. The negative entropy of the transition is probably due to immobilization of the fibres.     

Synthesis of fragments by classical solution methods for use in cytochrome c semisynthesis

We report details of the chemical synthesis of two fragments reproducing the C-terminal sequences 71-108 and 70-108 of Saccharomices cerevisiae cytochrome c. Preparation of the fragments employed classical solution methods and a fragment-condensation strategy; they have been used, together with a third fragment (sequence 67-108) [L. Moroder, B. Filippi, G. Borin & F. Marchiori (1975) Biopolymers 14 , 2061–2074], in the semisynthesis of chimeric cytochromes [C. J. A. Wallace, G. Corradin, F. Marchiori & G. Borin (1986) Biopolymers 25 , 2121–2132].     

Circular dichroism of flow-oriented nucleic acids. II. Comparison between observed and calculated spectra.

The ultraviolet circular dichroism (CD) of oriented DNA and RNA molecules is calculated by an extension of Johnson and Tinoco's theory [(1969) Biopolymers 7 , 727–749] for unoriented molecules. The calculations are carried out for molecular models of A-DNA, B-DNA, planar B-DNA, C-DNA, and RNA-11-α. The calculated curves are compared to measured spectra [(1975) J. Mol. Biol. 92 , 449–466] Chung and Holzwarth, for oriented solutions of DNA in buffer, DNA in 6 M LiCl or in ethylene glycol, and double-stranded viral RNA. The calculation, which considers only base–base interactions, predicts that the CD of B-DNA, measured with light propagating parallel to the helix axis, should be large and semiconservative, whereas the CD for light propagating perpendicular to the helix axis should be nonconservative. These predictions agree qualitatively with the experimental observations for DNA in buffer; agreement improves if one assumes the bases to be exactly perpendicular to the helix axis. For the other geometries, agreement is less satisfactory, but qualitative agreement with experiment is obtained and the signs of the specific CD spectra are in accord with observations.     

Kinetic and thermodynamics study of the pyrolytic process of the freshwater macroalga,Chara vulgaris

This is the first study where the pyrolysis of the freshwater macroalga Chara vulgaris was explored to reveal its bioenergy potential. The suitability of C. vulgaris to bioenergy conversion via pyrolysis was accessed in terms of kinetic triplet and thermodynamic parameters. For this purpose, pyrolysis experiments under a thermogravimetric scale were conducted at multiple heating rates (5, 10, and 20 °C min^?1) in an inert atmosphere. The mass-loss profiles of C. vulgaris pyrolysis showed that there are two dominant decomposition stages that are related to distinct chemical components inside its structure and that directly affect the calculated kinetic triplet and thermodynamics parameters. The average activation energy obtained using isoconversional methods of Flynn-Wall-Ozawa, Kissinger-Akahira-Sunose, Starink, and Friedman was in the range of 52.87–72.91 kJ mol^?1 for the first decomposition stage and 156.14–174.65 kJ mol^?1 for the second decomposition stage. The pyrolytic conversion of C. vulgaris initially follows a second-order reaction model (first decomposition stage), while in second decomposition stage is controlled by a second-order Avrami-Erofeev reaction model. The kinetic results derived from the non-isothermal decomposition of C. vulgaris proved its suitable characteristics for pyrolysis. Additionally, multi-stage kinetic interpretation was successfully attained based on two kinetic triplets, where reconstructed pyrolysis behavior correlated well with experimental pyrolysis behavior. The changes in enthalpy, Gibbs free energy, and entropy for first decomposition stage were 67.58±0.25 kJ mol^?1, 180.77±5.30 kJ mol^?1, and ?176.65±0.41 J mol^?1 K^?1, and for the second decomposition stage the values were 166.70±0.09 kJ mol^?1, 285.51±1.29 kJ mol^?1, and ?124.29±0.09 J mol^?1 K^?1, respectively. Based on thermodynamic aspects, C. vulgaris is particularly interesting for use as a raw material to produce biofuels and bioenergy.

     

The maize mitochondrial plasmid RNA b is associated with protein during synthesis but is not encapsidated

RNA b is the most abundant member of a family of autonomously replicating single- and double-stranded RNA plasmids found in maize mitochondria. The extent to which this molecule is associated with proteins was investigated by rate zonal and CsCl equilibrium density gradient centrifugation of clarified lysates of S cytoplasm maize mitochondria. A soluble complex of RNA b, responsible for synthesis of the more abundant (+) RNA b strand in mitochondrial lysates, was identified. The complex had a buoyant density of 1.49 g/cm³, indicating a substantial non-nucleic acids content. The sedimentation coefficient of the complex, however, was only slightly larger than that of deproteinized RNA b. Synthesis of RNA b as well as the larger RNA plasmid, RNA a, was resistant to heparin, suggesting that, for both RNAs, preformed complexes between an RNA template and an RNA-dependent RNA polymerase capable of elongating in vivo preinitiated RNA plasmid strands, were present in the lysate. Only a small fraction of RNA b molecules were bound in the complex; the bulk of RNA b sedimented at the same rate as the deproteinized RNA. Thus, after replication, maize mitochondrial plasmids are not associated with nucleoprotein capsids although their synthesis takes place through ribonucleoprotein replication complexes.     

Extraction, separation and labeling with 14C-glucose of HeLa cell polyglucose, RNA and DNA and comparison of the molecular weights and buoyant densities of polyglucose from poliovirus-infected and noninfected cultures

The aqueous phase of phenol extracts of HeLa cells contains polyglucose (CHO)_n, RNA, and DNA. These macromolecules were precipitated together and removed from 50% (v/v) ethanol solutions with a stirring rod. The viscous precipitate had the classical white appearance of DNA, but contained an average of 439, 670, and 220 μg (from 3 × 10⁷ cells) of (CHO)_n, RNA, and DNA, respectively. The (CHO)_n was separated from the RNA, either by CsCl density gradient centrifugation or by precipitating the RNA with trichloroacetic acid (TCA). Both methods of separation resulted in preparations of (CHO)_n with similar specific activities (radioactive counts/μg min). However, electron micrographs showed that the (CHO)_n separated by using TCA had a greater variation in particle size when compared with (CHO)_n separated by CsCl centrifugation. With the CsCl methods, the number-average molecular weights, as determined by electron microscope particle-counting, and the buoyant densities of (CHO)_n whose synthesis was stimulated by poliovirus infection and (CHO)_n from noninfected cultures, were found to be similar. When the (CHO)_n was extracted from HeLa cells with TCA, rather than phenol, the yield was 1.68-fold greater and its specific activity was an average of twice that of the (CHO)_n extracted with phenol. The time at which cells were pulse-labeled with ¹⁴C-glucose, after reducing the glucose in the culture medium to 0.01 of normal, was found to be important, in that the specific activity of the (CHO)_n increased 23.4-fold over a 4-hr period and the amount extracted decreased 8.2-fold. The increase in the specific activities of RNA and DNA was not as large as that of the (CHO)_n and the amounts extracted were not significantly changed. The sedimentation coefficients of RNA and (CHO)_n which were separated from each other with TCA were 6.4 and 116 S, respectively, whereas, without separation, two peaks were seen, with values of 25.4 and 31.4 S. Chloride ions reduce the sensitivity of the Burton test for DNA. However, the Burton reagent will detect (CHO)_n even in the presence of DNA if the assay mixture is heated. Chloride ions increase the sensitivity of the Burton reagent to detect melizitose and, at concentrations above l.5M, synthetic- polyglucose by increasing the absorption of the colored (CHO)_n reaction product(s).     

Sedimentation studies of giant DNA molecules present in unsheared whole-cell lysates of D. melanogaster cells.

We have used band sedimentation in shallow density gradients of CsCl in the preparative centrifuge to analyze the distribution of sedimentation coefficients present in tritium labelled DNA from D. melanogaster cells. The cells were lysed according to the method of Kavenoff and Zimm to preserve very high molecular weight DNA. Sedimentation measurements have been carried out as a function of speed of centrifugation. The resulting distribution functions have been interpreted with the aid of the Zimm-Schumaker equation for the speed dependence of the sedimentation coefficient of very high molecular weight DNA. Low-speed centrifugation (3000 rpm) indicates that DNA molecules from the lysate are evenly distributed over values of S_20,w from 0 to 514S. This distribution is very sensitive to changes in speed of centrifugation and is transformed into a bimodal distribution at 12,080 rpm. Analysis of this transformation allows us to postulate that perhaps 55% of the DNA in the lysate may have molecular weights in excess of 40 × 10⁹ g/mol. Some of these molecules may also possess a variety of configurations including partially replicated branched structures.     

Identification of viral ribonucleoproteins in the cytoplasm of murine cells chronically infected by a retrovirus.

Ribonucleoproteins were isolated from the cytoplasm of Friend-Eveline cells which produce the Friend virus complex, after a short labelling with [³H] uridine. These particles moved with a sedimentation coefficient of 53S in sucrose gradient and had a buoyant density of 1.46 g/cm³ in CsCl gradient. Analysis of their RNA content showed that they possessed a 35S major species having the size of the viral genome subunit. Moreover, a positive hybridization was observed when RNA of the 53S particles was annealed with viral complementary DNA. No such particles were found in cultures of uninfected murine cells suggesting that 53S RNPs have a viral origin.     

Purification and some properties of Tephrosia symptomless virus

Tephrosia symptomless virus (TSV), isolated from Tephrosia villosa, is widely distributed in coastal districts of Kenya. The virus was readily transmitted by inoculation of sap, but not by Aphis craccivora or Apion sp. (Curculionidae) or through soil. Host range was very restricted and it infected only 10 of 70 species tested in one of nine plant families; susceptible species were confined to five genera within the Papilionaceae. The virus was cultured, propagated and assayed in soybean. TSV remained infective after 10 min at 85°C, 3 wk at 20°C and 26 wk at -12°C; crude infective sap of Glycine max retained infectivity when diluted 10^-6 but not 10^-7. Virus was purified from systemically infected soybean by clarifying sap extracted in 0.06 m phosphate buffer containing 0.001 m EDTA and 0.1% thioglycollic acid (pH 7.5) with equal volumes of 1:1 n-butanol/chloroform followed by two cycles of differential and one of sucrose density gradient centrifugation. Purified preparations contained c. 33 nm isometric particles. TSV contained RNA and one protein of molecular weight 1.53. 10⁶ and c. 42 000, respectively. Analytical centrifugation indicated a single component with a sedimentation coefficient (s.20, w) of 127 S; in Cs₂SO₄ and CsCl isopycnic gradients a single virus band formed; buoyant density in CsCl was 1.361. TSV was not related serologically to any of 44 viruses in nine plant virus groups but it resembled the tombusviruses and other ungrouped viruses such as carnation mottle in some of its properties.     

Biological activity of invitro synthesised protein: Binding of Semliki Forest virus capsid protein to the large ribosomal subunit

Cell-free translation of the Semliki Forest virus-specific 26S RNA yielded primarily capsid protein. After treatment of the protein synthesising reaction with 25 mM EDTA, the capsid protein cosedimented with the large ribosomal subunit in sucrose gradients, and banded with the subunit at a density of 1.54 gm/cm³ in CsCl. Exposure to 0.5 M KCl released the protein from the subunit. Similar binding of the virus capsid protein to the large ribosomal subunit has been observed in infected HeLa cells, although its function is not clear. The nonstructural proteins, which are the major products translated from the virion 42S RNA, did not associate with sedimenting structures.     

Preferential solvent binding and change in conformation of bovine serum albumin in 2-chloroethanol-water mixed solvents.

Solvent binding to bovine serum albumin in 2-chloroethanol-water mixed solvents of different composition, measured previously by Inoue and Timasheff (Biopolymers (1972) 11 , 737–43) is applied to a hydrodynamic study of the solvated protein. From sedimentation and diffusion data, the apparent molecular weight of the solvated protein particle can be calculated, provided an average partial specific volume, computed from the composition of the particle, is introduced in Svedberg's equation. The unsolvated molecular weight of the protein can than be calculated by subtraction of the bound solvent. Further data on the hydrodynamic particle (f/f_min and axial ratio of the equivalent ellipsoid) are readily calculated from these experiments, and reinforce the supposition that 2-chloroethanol is a strong helix-inducing solvent.     

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.     

Hepatitis E virus capsid protein assembles in 4M urea in the presence of salts

The hepatitis E virus (HEV) capsid protein has been demonstrated to be able to assemble into particles in vitro. However, this process and the mechanism of protein–protein interactions during particle assembly remain unclear. In this study, we investigated the assembly mechanism of HEV structural protein subunits, the capsid protein p239 (aa368–606), using analytical ultracentrifugation. It was the first to observe that the p239 can form particles in 4M urea as a result of supplementation with salt, including ammonium sulfate [(NH₄)₂SO₄], sodium sulfate (Na₂SO₄), sodium chloride (NaCl), and ammonium chloride (NH₄Cl). Interestingly, it is the ionic strength that determines the efficiency of promoting particle assembly. The assembly rate was affected by temperature and salt concentration. When (NH₄)₂SO₄ was used, assembling intermediates of p239 with sedimentation coefficient values of approximately 5 S, which were mostly dodecamers, were identified for the first time. A highly conserved 28‐aa region (aa368–395) of p239 was found to be critical for particle assembly, and the hydrophobic residues Leu³⁷², Leu³⁷⁵, and Leu³⁹⁵of p239 was found to be critical for particle assembly, which was revealed by site‐directed mutagenesis. This study provides new insights into the assembly mechanism of native HEV, and contributes a valuable basis for further investigations of protein assembly by hydrophobic interactions under denaturing conditions.     

Replication of Sindbis virus. I. Relative size and genetic content of 26 s and 49 s RNA

The genome of Sindbis virus, 49 s RNA, is a single, intact polynucleotide chain having a molecular weight of 4.3±0.3 × 10⁶ daltons. This has been determined using a variety of methods including polyacrylamide gel electrophoresis, sedimentation after reaction with formaldehyde, determination of the molecular weights of the double-stranded forms of Sindbis-specific RNA and hybridization competition. The second major species of single-stranded RNA made after infection with Sindbis, 26 s RNA, has been found to have a molecular weight of 1.6 × 10⁶ daltons as determined by sedimentation in dimethylsulfoxide. Hybridizationcompetition experiments carried out between these two species of RNA, using double-stranded forms of Sindbis RNA isolated from infected cells, showed that 26 s RNA contains only one-third of the base sequences in 49 s RNA and thus represents a unique fraction of the viral genome.