Kinetic study of the self-assembly of brome mosaic virus capsid

The protein of brome mosaic virus can self assemble in-vitro to form empty capsids. In the absence of RNA at pH=7 and 0.5 M KCl there is a dynamic equilibrium between monomers and oligomers. At pH=5 the protein assembles into empty capsids. The kinetics of this assembly, triggered by pH jump from neutral to acidic pH, was investigated by X-ray and light scattering.Cryoelectron microscopy observations suggested that reconstitution is achieved by progressive incorporation of small building units in a spherical shell. This hypothesis has been tested by the analysis of the scattering data in terms of four classes of incomplete capsids represented as spherical shells with holes of different sizes. The time dependence of the population of each class was determined by a least squares analysis of the experimental data. Although the basic polymerizing unit has not been uniquely characterized, the results are compatible with a dimer for this species. The characteristic times for capsid assembly are found to vary as the inverse of the square of the concentration.     

Evolutionary relationship of alfalfa mosaic virus with cucumber mosaic virus and brome mosaic virus

The amino acid sequences of the non-structural protein (molecular weight 35,000; 3a protein) from three plant viruses — cucumber mosaic, brome mosaic and alfalfa mosaic have been systematically compared using the partial genomic sequences for these three viruses already available. The 3a protein of cucumber mosaic virus has an amino acid sequence homology of 33.7% with the corresponding protein of brome mosaic virus. A similar protein from alfalfa mosaic virus has a homology of 18.2% and 14.2% with the protein from brome mosaic virus and cucumber mosaic virus, respectively. These results suggest that the three plant viruses are evolutionarily related, although, the evolutionary distance between alfalfa mosaic virus and cucumber mosaic virus or brome mosaic virus is much larger than the corresponding distance between the latter two viruses.     

Pressure-induced dissociation of brome mosaic virus

Brome mosaic virus reversibly dissociates into subunits in the pressure range of 600 x 10(5) to 1600 x 10(5) Pa, as demonstrated by studies of the spectral shift of intrinsic fluorescence, of filtration chromatography and of electron microscopy of samples fixed under pressure. Smaller shell particles (T = 1) were detected as intermediates in the dissociation pathway. Dissociation was facilitated by decreasing the concentration, as expected for a multimolecular reaction. The estimated change in volume upon dissociation into 90 dimer particles was -2960 ml/mol. Large increases in the intrinsic fluorescence intensity and in the binding of bis(8-anilinonaphthalene-1-sulfonate) occurred at pressures higher than 1400 x 10(5) Pa. The pressure-dependence profile of the different spectral properties shifted to lower pressures when 5 mM-MgCl2 was included in the buffer or when the pH was raised from 5.5 to 5.9. When the pressure was progressively increased above 1400 x 10(5) Pa, a value that led to 75% dissociation, the capsid subunits lost the ability to reassociate into regular shells and only amorphous aggregates were formed after decompression, as evidenced by both electron microscopy and gel filtration chromatography. The formation of these random aggregates of brome mosaic virus can be explained by a conformational drift of the separated subunits, similar in nature to that found in simpler oligomeric proteins.     

Serological differentiation of brome mosaic virus morphomers

Abstract The effects of solution conditions and of formalinisation on the antigenicity of "native" and "pseudo-top" virions of brome mosaic virus (BMV) were studied by double-antibody "sandwich" enzyme-linked immunosorbent assay (DAS-ELISA). Physically characterised BMV morphomers differed serologically from one another and from free coat protein, proving that capsid swelling or lack of RNA cause conformational changes affecting antibody binding. Formaldehyde treatment reduced the antigenicity of virions relative to "native" forms. The results indicate that ELISA detection of viruses is affected both by their physical environment and by chemical treatment.     

The crystallographic structure of brome mosaic virus

The structure of brome mosaic virus (BMV), the type member of the bromoviridae family, has been determined from a single rhombohedral crystal by X-ray diffraction, and refined to an R value of 0.237 for data in the range 3.4-40.0 A. The structure, which represents the native, compact form at pH 5.2 in the presence of 0.1 M Mg(2+), was solved by molecular replacement using the model of cowpea chlorotic mottle virus (CCMV), which BMV closely resembles. The BMV model contains amino acid residues 41-189 for the pentameric capsid A subunits, and residues 25-189 and 1-189 for the B and C subunits, respectively, which compose the hexameric capsomeres. In the model there are two Mg ions and one molecule of polyethylene glycol (PEG). The first 25 amino acid residues of the C subunit are modeled as polyalanine. The coat protein has the canonical "jellyroll" beta-barrel topology with extended amino-terminal polypeptides as seen in other icosahedral plant viruses. Mass spectrometry shows that in native BMV virions, a significant fraction of the amino-terminal peptides are apparently cleaved. No recognizable nucleic acid residue is visible in the electron density maps except at low resolution where it appears to exhibit a layered arrangement in the virion interior. It is juxtaposed closely with the interior surface of the capsid but does not interpenetrate. The protein subunits forming hexameric capsomeres, and particularly dimers, appear to interact extensively, but the subunits otherwise contact one another sparsely about the 5-fold and quasi 3-fold axes. Thus, the virion appears to be an assembly of loosely associated hexameric capsomeres, which may be the basis for the swelling and dissociation that occurs at neutral pH and elevated salt concentration. A Mg ion is observed to lie exactly on the quasi-3-fold axis and is closely coordinated by side-chains of three quasi-symmetry-related residues glutamates 84, with possible participation of side-chains from threonines 145, and asparagines 148. A presumptive Mg(2+) is also present on the 5-fold axis where there is a concentration of negatively charged side-chains, but the precise coordination is unclear. In both cases these cations appear to be essential for maintenance of virion stability. Density that is contiguous with the viral interior is present on the 3-fold axis at the center of the hexameric capsomere, where there is a pore of about 6 A diameter. The density cannot be attributed to cations and it was modeled as a PEG molecule.     

Comparison of the nucleotide sequences of cucumber mosaic virus and brome mosaic virus

Cucumber mosaic virus (CMV) and brome mosaic virus (BMV) are isometric plant viruses. Although biologically distinct, they share many common chemical properties. An analysis of the partial genomic RNA sequence available for these two viruses reveals that they are evolutionarily related. Different segments of the genome exhibit different evolutionary rates. The coat proteins, which serve as carriers of genetic material, possess little or no homology. In contrast, the 3a proteins show over 35% homology. The non-coding regions of the genome also exhibit extensive but variable homology suggesting the functional importance of the nucleic acid.     

Chemical reactivity of brome mosaic virus capsid protein

Viral particles are biological machines that have evolved to package, protect, and deliver the viral genome into the host via regulated conformational changes of virions. We have developed a procedure to modify lysine residues with S-methylthioacetimidate across the pH range from 5.5 to 8.5. Lysine residues that are not completely modified are involved in tertiary or quaternary structural interactions, and their extent of modification can be quantified as a function of pH. This procedure was applied to the pH-dependent structural transitions of brome mosaic virus (BMV). As the reaction pH increases from 5.5 to 8.5, the average number of modified lysine residues in the BMV capsid protein increases from 6 to 12, correlating well with the known pH-dependent swelling behavior of BMV virions. The extent of reaction of each of the capsid protein's lysine residues has been quantified at eight pH values using coupled liquid chromatography-tandem mass spectrometry. Each lysine can be assigned to one of three structural classes identified by inspection of the BMV virion crystal structure. Several lysine residues display reactivity that indicates their involvement in dynamic interactions that are not obvious in the crystal structure. The influence of several capsid protein mutants on the pH-dependent structural transition of BMV has also been investigated. Mutant H75Q exhibits an altered swelling transition accompanying solution pH increases. The H75Q capsids show increased reactivity at lysine residues 64 and 130, residues distal from the dimer interface occupied by H75, across the entire pH range.     

Nucleotide sequence of the brome mosaic virus genome and its implications for viral replication

The nucleotide sequences of brome mosaic virus (BMV) RNAs 1 (3234 bases) and 2 (2865 bases) have been determined, completing the primary structure of the 8200 base tripartite BMV genome. cDNA clones covering 99% of BMV RNA1 and a full-length cDNA clone of BMV RNA2 were isolated in the course of this work. Extensive sequence homology and known interaction with several proteins suggest that the 3' ends of the BMV RNAs are the major regulatory regions of the genome. Smaller regions at the 5' ends of RNAs 1 and 2 show strong homology to each other and lesser homology to RNA3. These and other features of the sequences are discussed in relation to replication, regulation and evolution of the BMV genome.     

Translation of the RNAs of brome mosaic virus: The monocistronic nature of RNA1 and RNA2

Each of the two largest brome mosaic virus RNAs, RNA1 and RNA2, directs the synthesis of a large protein in cell-free extracts derived from wheat embryo. The size of each protein represents the translation of almost the entire length of the corresponding RNA. It was shown previously that brome mosaic virus RNA4 directs the synthesis of the coat protein and that brome mosaic virus RNA3, although it also contains the coat protein cistron, is translated mostly into a single product unrelated to the coat protein (Shih & Kaesberg, 1973). Thus, the brome mosaic virus genome encodes a total of four proteins.     

Reassembly of living cells from dissociated components in Bryopsis

Protoplasm from Bryopsis maxima, a coenocytic green alga, wasdissociated into two fractions: chloroplasts, and protoplasmicfraction without chloroplasts (PF). The protoplasmic fraction(PF) included nuclei, mitochondria, dictyosomes, endoplasmicreticuli, etc. These two fractions were reassembled and formedprotoplasts, which developed into mature plants. (Received June 9, 1977; )     

Birth and growth kinetics of brome mosaic virus microcrystals

The early steps of crystal nucleation and growth in Brome Mosa?c virus and polyethylene glycol mixtures were analyzed using time-resolved x-ray scattering (at the European Synchrotron Radiation Facility, Grenoble, France). The system was chosen as a crystallization model since the phase diagram of the macromolecule/polymer mixture was known to present, at high polymer concentration, a solid, precipitated phase made of the synchronized formation of a large number of microcrystals. The precipitation and crystallization of the samples was induced by the controlled mixing of virus and polymer using a stopped-flow device. Appearance and growth of Bragg diffraction peaks were used to follow the crystal nucleation and growth as a function of time, virus and polymer concentration, and polymer size. In all samples, the crystallization starts after a few seconds and proceeds for approximately 1-20 min until there is almost no virus left in the solution. The crystalline system was found to be face-centered cubic, with a unit cell size of 391 angstroms. The data analysis allowed us to show the presence of viruses in only two states, in solution or in crystals, revealing that the formation of periodic order proceeds without any detectable intermediate amorphous state.     

Localization of the replicase recognition site within brome mosaic virus RNA by hybrid-arrested RNA synthesis

Summary 3 terminal fragments of BMV RNA as short as 153 bases in length serve as efficient templates in vitro for BMV-specific RNA polymerase. Template activity of such fragments or of native BMV RNA is abolished when cDNA fragments as short as 39 bases are hybridized to their 3 termini. Hybridization of cDNa fragments to regions of BMV RNA 200 or more bases distal to the 3 end has no discernible effect on initiation and little effect on elongation. We conclude that BMV RNA polymerase initiates binding with an RNA template through a mechanism mediated by the tRNA-like 3 end of BMV RNA, requiring at least some of the last 39, but no more than the last 153 bases.     

Two types of non-homologous RNA recombination in brome mosaic virus

Non-homologous RNA recombination is a process enabling the exchange of genetic material between various (related or unrelated) RNA-based viruses. Despite extensive investigations its molecular mechanism remains unclear. Studies on genetic recombination in brome mosaic virus (BMV) have shown that local hybridization between genomic RNAs induces frequent non-homologous crossovers. A detailed analysis of recombinant structures suggested that local complementary regions might be involved in two types of non-homologous recombination in BMV: site-specific and heteroduplex-mediated. To verify the above hypothesis and better recognize the mechanism of the phenomenon studied we have tested how the putative types of recombination are affected by a specific mutation in the BMV polymerase gene or by changes in RNA structure. The experiments undertaken revealed substantial differences between site-specific and heteroduplex-mediated recombination, indicating that they occur according to different mechanisms. The former can be classified as homology-assisted, and the latter as homology-independent. In addition to local RNA/RNA hybridization, short regions of homology are required for site-specific crossovers to occur. They are most efficiently mediated if one homologous sequence is located at the beginning of and the second just before a double-stranded region. At present it is difficult to state what is the mechanism of heteroduplex-mediated recombination. Earlier it was postulated that strong RNA/RNA interaction enforces template switching by the viral replicase. There are, however, several observations questioning this model and indicating that some other factors, which are still unknown, may influence heteroduplex-mediated crossovers.     

Distinction of strains of bean common mosaic virus and blackeye cowpea mosaic virus using antibodies to N- and C- or N-terminal peptide domains of coat proteins

Earlier attempts to discriminate serologically strains NL1, NL3 and NY15 of bean common mosaic virus (BCMV) and strain W of blackeye cowpea mosaic virus (B1CMV) had been unsuccessful. Antibodies directed towards N- and C-, or N-terminal peptide regions of the coat proteins of the above strains enabled the distinction between B1CMV-W, BCMV-NY15 and BCMV-NL3 in electroblot immunoassay and in ELISA. The distinction was better with antibodies directed towards N-termini than with those to N- and C-termini. Strain NL1 of BCMV cross-reacted with both B1CMV-W and BCMV-NY15, but not with BCMV-NL3. Taxonomic implications of these findings are discussed.     

The 3′-untranslated region of brome mosaic virus RNA does not enhancetranslation of capped mRNAs in vitro

The translation enhancing ability of cis-acting 3′-terminal untranslated region (3′-UTR) of brome mosaic virus (BMV) was examined. Two chimeric mRNA constructs translated in rabbit reticulocyte lysates contained the BMV coat protein (CP) gene and NPTI gene, respectively. It was shown that the 3′-UTR of BMV RNA enhanced the translational efficiency of uncapped but not capped messages.     

Interactions between brome mosaic virus RNAs and cytoplasmic processing bodies

Cytoplasmic processing bodies are sites where nontranslating mRNAs accumulate for different fates, including decapping and degradation, storage, or returning to translation. Previous work has also shown that the Lsm1-7p complex, Dhh1p, and Pat1p, which are all components of P bodies, are required for translation and subsequent recruitment to replication of the plant virus brome mosaic virus (BMV) genomic RNAs when replication is reproduced in yeast cells. To better understand the role of P bodies in BMV replication, we examined the subcellular locations of BMV RNAs in yeast cells. We observed that BMV genomic RNA2 and RNA3 accumulated in P bodies in a manner dependent on cis-acting RNA replication signals, which also directed nonviral RNAs to P bodies. Furthermore, the viral RNA-dependent RNA polymerase coimmunoprecipitates and shows partial colocalization with the P-body component Lsm1p. These observations suggest that the accumulation of BMV RNAs in P bodies may be an important step in RNA replication complex assembly for BMV, and possibly for other positive-strand RNA viruses.     

Differences of reconstitution process between tobacco mosaic virus and cucumber green mottle mosaic virus by synchrotron small angle X-ray scattering using low-temperature quenching

The differences of the reconstitution process of tobacco mosaic virus (TMV) and its mutant, cucumber green mottle mosaic virus (CGMMV) were investigated by the solution X-ray scattering measurements with the synchrotron radiation source using low-temperature quenching. The reconstitution in an aqueous solution is completely stopped below 5°C. The TMV and CGMMV assembly was traced by the small-angle X-ray scattering (SAXS) measurements at 5°C on a series of solutions prepared by low-temperature quenching after incubation at 20°C for an appropriate interval between 0 and 60 min. The SAXS results were analyzed by the Guinier plot, the Kratky plot and the distance distribution function. The incubation of RNA and protein of CGMMV did not reconstitute at the initial reaction stages below 5 min and then began to reconstitute gradually. After 60 min, the radius of gyration for CGMMV reconstitution process reached almost the value for the initial stage of TMV reconstitution process. This is due to the fact the formation of double-layered disk in CGMMV protein is much slower than in TMV protein.     

High genetic stability in natural populations of the plant RNA virus tobacco mild green mosaic virus

Summary Quantitative studies on the genetic variation of plant viruses are very scarce, in spite of their theoretical and applied importance. We report here on the genetic variability of field isolates of the plant RNA virus tobacco mild green mosaic virus (TMGMV) naturally infecting the wild plantNicotiana glauca Grah. The populations studied were composed of a high number of haplotypes. Two main features are found regarding TMGMV variation: First, there is no correlation between genetic proximity of isolates and geographic proximity of the sites from which they were obtained; and second, the estimated divergence among haplotypes is low, and values are maintained regardless of the scale of the distance between the sites from which the isolates come. No comparable studies have been done with a plant RNA virus, and these two features seem to be unique for this system as compared with other RNA viruses.