Limited proteolysis of southern bean mosaic virus by trypsin

Intermediates of the in vitro assembly and disassembly of southern bean mosaic virus

Southern bean mosaic virus (SBMV) was swollen by treatment with EDTA at pH 7.5 and dissociated into RNA and protein in 1 M NaCl. Aliquots of this preparation were diluted with appropriate buffers to obtain samples in varying concentrations of NaCl, and components of these samples were sedimented through sucrose solutions and dissolved in 0.01 M Tris-HCI buffer, pH 7.5. The protein content and sedimentation properties of components in these preparations were determined. When the NaCl molarity in the treatment exceeded 0.6 M the preparations contained RNA with approximately six protein subunits per SBMV RNA molecule. The protein content of the preparations increased from 30 protein subunits per RNA molecule to 145 protein subunits per RNA molecule as the NaCl molarity used in the treatment was decreased from 0.5 to 0.1 M. The positions of sedimentation of components in these preparations in density gradient centrifugation were intermediate between those of RNA and EDTA-swollen virus. The sedimentation rate of these assembled components increased as the NaCl molarity used in the treatment was decreased. Similar components were assembled when preparations of RNA and protein dissociated from SBMV by dialysis in neutral buffers containing EDTA and 1 M NaCl were diluted to lower NaCl molarities. When SBMV was swollen by treatment with EDTA and dissociated in various concentrations of NaCl, the components formed were similar to those obtained by assembly in the same NaCl molarities. Preparations in the pH 7.5 buffer contained single components which sedimented at 56 S, 55 S, 54 S, 51 S, 46 S, 38 S, 33 S, and 24 S. With the exception of the 24 S component, components formed by disassembly in the same NaCl molarities and dissolved in pH 5.0 buffer sedimented faster.

Structure-function relationships of icosahedral plant viruses

X-ray diffraction studies on single crystals of a few viruses have led to the elucidation of their three dimensional structure at near atomic resolution. Both the tertiary structure of the coat protein subunit and the quaternary organization of the icosahedral capsid in these viruses are remarkably similar. These studies have led to a critical re-examination of the structural principles in the architecture of isometric viruses and suggestions of alternative mechanisms of assembly. Apart from their role in the assembly of the virus particle, the coat proteins of certian viruses have been shown to inhibit the replication of the cognate RNA leading to cross-protection. The coat protein amino acid sequence and the genomic sequence of several spherical plant RNA viruses have been determined in the last decade. Experimental data on the mechanisms of uncoating, gene expression and replication of several classes of viruses have also become available. The function of the non-structural proteins of some viruses have been determined. This rapid progress has provided a wealth of information on several key steps in the life cycle of RNA viruses. The function of the viral coat protein, capsid architecture, assembly and disassembly and replication of isometric RNA plant viruses are discussed in the light of this accumulated knowledge.

The structure of a T = 1 icosahedral empty particle from southern bean mosaic virus

The structure of a T = 1 icosahedral particle (where T is the triangulation number), assembled from southern bean mosaic virus coat protein fragments that lacked the amino-terminal arm, was solved by means of model building procedures with the use of 6-angstrom resolution x-ray diffraction data. The icosahedral five-, three-, and twofold contacts were found to be similar, at this resolution, to the analogous contacts (icosahedral five-, quasi-three-, and quasi-twofolds) found in the parent T = 3 southern bean mosaic virus. However, the icosahedral fivefold contacts of the T = 3 structure are the most conserved in the T = 1 capsid. These results are consistent with a mechanism in which pentameric caps of dimers are the building blocks for the assembly of T = 1 and T = 3 icosahedral viruses.

Constraints on the assembly of spherical virus particles

Examination of protein structure shows that it is not possible to deform protein domains to the extent required by the Caspar-Klug quasi-symmetry surface lattices for the description of viral capsids (D. L. D. Caspar and A. Klug (1962). Cold Spring Harbor Symp. Quant. Biol. 27, 1-24). However, flexibility in proteins can be achieved by a number of ligand-induced events. One type of alteration is that of quaternary structural changes in oligomers. This strategy has been used by southern bean mosaic virus and tomato bushy stunt virus where dimers attain two different states in the assembled capsid. Alterations of subunit interactions can be induced by association with RNA, cations, or other oligomeric units and, hence, successful assembly results from a stepwise aggregation. The nature of the oligomers (dimers, trimers, or pentamers) must be the underlying reason for the occurrence of the Caspar-Klug lattices and the organization into icosahedra. An analysis of the surface lattices shows which types of oligomers will be necessary for assembly.

RNA-protein interactions in some small plant viruses

The structure of the three quasi-equivalent protein subunits A, B and C of the spherical, T = 3 southern bean mosaic virus (SBMV) have been carefully built in accordance with a refined electron density map of the complete virus. The lower electron density in the RNA portion of the map could not be explicitly interpreted in terms of a preferred RNA structure on which some icosahedral symmetry might have been imposed. However, the extremely basic nature of the interior surface of the coat protein must be associated with the binding and organization of the RNA. Comparison with the small spherical, T = 1 satellite tobacco necrosis virus (STNV; Liljas et al., J. Mol. Biol. 159, 93-108, 1982) and the T = 1 aggregate of alfalfa mosaic virus (AMV) protein (Fukuyama et al., J. Mol. Biol. 150, 33-41, 1981) showed similar results. The pattern of basic residues on the SBMV coat protein surface facing the RNA is able to dock a 9 base pair double-helical A-RNA structure with surprising accuracy. The basic residues are each associated with a different phosphate and the protein can make interactions with five bases in the minor groove. This may be one of a small number of ways in which the RNA interacts with SBMV coat protein. The self-assembly of SBMV has been studied in relation to the presence of the 63 basic amino-terminal coat protein sequence, pH, Ca2+ and Mg2+ ions and RNA. These results have led to a two-state model where the "relaxed" dimers initially self-assemble into 10-mer caps which nucleate the assembly of T = 1 or T = 3 capsids depending on the charge state of the carboxyl group clusters in the subunit contact region. The two-state condition of dimers in a viral coat protein extends the range of structures originally envisaged by Caspar and Klug (Cold Spring Harbor Symp. Quant. Biol. 27, 1-24, 1962).

Structure of a T = 1 aggregate of alfalfa mosaic virus coat protein seen at 4.5 A resolution

A T = 1 empty aggregate of alfalfa mosaic virus coat protein had been crystallized in a hexagonal unit cell and its orientation was determined with the rotation function. A single heavy-atom derivative has now been prepared and the position of the two Hg atoms per protein subunit were determined using a systematic Patterson search procedure, given the particle orientation. Phases, initially determined by single isomorphous replacement, were refined by six cycles of electron density averaging and solvent leveling to produce a 4.5 A resolution electron density map. The protein coat is confined between 95 and 58 A radius. The subunit boundary could be delineated easily. It has a central cavity reminiscent of the beta-barrel in other spherical plant viruses, but its topology could not be determined unambiguously. The spherical particle has large holes at the 5-fold axes, consistent with previous observations. The subunits have substantial interactions at the 2 and 3-fold axes. The structure of the elongated particles is discussed in relation to these results.