Structure and assembly of simple RNA bacteriophages

Ribonucleoprotein complexes of R17 coat protein and a translational operator analog

The coat protein of the simple spherical (triangulation no. T = 3) RNA coliphage R17 protects the genomic RNA in the virus particle and acts as a translational repressor of the phage-encoded replicase gene. It has been suggested that these two functions are related and that the translational repression complex serves as a nucleation complex for subsequent assembly of the bacteriophage. We have used a translational operation fragment to examine the relationship between formation of the translational repression complex and the assembly of the protein into T = 3 capsids. In vitro analysis of the aggregation properties of R17 coat protein reveals that binding of the translational operator fragment to the protein dimer triggers polymerization of the protein into T = 3 capsids of well-defined composition. The data further implicate the translational operator in nucleation of assembly and suggest a possible physical-chemical basis of the nucleation step.

Structure and assembly of turnip crinkle virus. II. Mechanism of reassembly in vitro

Dissociation of turnip crinkle virus (TCV) at elevated pH and ionic strength produces free dimers of the coat protein and a ribonucleoprotein complex that contains the viral RNA, six coat-protein subunits, and the minor protein species, p80 (a covalently linked coat-protein dimer). This "rp-complex" is stable for several days in high salt at pH 8.5. Reassembly of TCV can be accomplished under physiological conditions, using isolated coat protein and either rp-complex or protein-free RNA. If rp-complex is used in reassembly, the same subunits remain bound to RNA on subsequent dissociation; if free RNA is used, rp-complex is regenerated. In both cases, the assembly is selective for viral RNA in competition experiments with heterologous RNA. Electron microscopy shows that assembly proceeds by continuous growth of a shell from an initiating structure, rather than by formation of distinct intermediates. We suggest that rp-complex is the initiating structure, suggest a model based on the organization of the TCV particle, and propose a mechanism for TCV assembly.

Chemical evidence for the capsomeric structure of phage q beta

Novel capsomeric complexes, pentamers and hexamers were detected as chemical entities in phage Q beta. Both were composed of identical protein subunits and stabilized by intermolecular disulphide bonds. Their numbers per particle were about 12 for pentamers and about 20 for hexamers--consistent with theoretical expectation from the quasi-equivalent packing of 180 identical subunits in a coat protein shell.

Electron microscopy of human hepatitis B virus cores by negative staining-carbon film technique

The ultrastructure of the nucleocapsid component of human hepatitis B virus (core particle) was studied by negative staining-carbon film technique. Using this method an improved image of core particles was obtained in respect of resolution and contrast. Two-dimensional crystalline arrays of core particles were formed in vitro. Under these arrays the distance between the particle centers was 28.3 nm, corresponding to the capsid diameter, when analyzed through optical diffraction patterns. Positively stained images of these arrays revealed that core particles contain an electron-dense center of nucleoid-like area about 21 nm in diameter. The capsid surface rarely exhibited small capsomeres, ie, small spheres or ring-like structures measuring 4.0-4.2 nm. From the dimension of these structures and the analysis by Markham's rotational technique, it was suggested that each of these capsomeres is an individual subunit (monomer) and 180 of these subunits build up the core particle capsid according to the icosahedral symmetry (T = 3), but not clustering into distinct morphological features.

Movement and self-control in protein assemblies. Quasi-equivalence revisited

Purposeful switching among different conformational states exerts self-control in the construction and action of protein assemblies. Quasi-equivalence, conceived to explain icosahedral virus structure, arises by differentiation of identical protein subunits into different conformations that conserve essential bonding specificity. Mechanical models designed to represent the energy distribution in the structure, rather than just the arrangement of matter, are used to explore flexibility and self-controlled movements in virus particles. Information about the assembly of bacterial flagella, actin, tobacco mosaic virus and the T4 bacteriophage tail structure show that assembly can be controlled by switching the subunits from an inactive, unsociable form to an active, associable form. Energy to drive this change is provided by the intersubunit bonding in the growing structure; this self-control of assembly by conformational switching is called "autostery", by homology with allostery. A mechanical model of the contractile T4 tail sheath has been constructed to demonstrate how self-controlled activation of a latent bonding potential can drive a purposeful movement. The gradient of quasi-equivalent conformations modelled in the contracting tail sheath has suggested a workable mechanism for self-determination of tail tube length. Concerted action by assemblies of identical proteins may often depend on individually differentiated movements.

Fibrous projections from the core of a bacteriophage T7 procapsid

A cylindrical core previously demonstrated in a bacteriophage T7 procapsid (capsid I) has been further examined by electron microscopy. Fibrous extensions of the core have been observed; these fibers appear to connect the core to the capsid I envelope. After infection of a nonpermissive host with bacteriophage T7 amber mutant in any gene coding for a core protein, the resulting lysates contained more noncapsid assemblies of capsid envelope protein than did wild-type lysates; these assemblies had a mass two to at least 500 times greater than the mass of capsid I. This suggests that the internal core and fibers assist the assembly of subunits in the envelope of capsid I.

Comparative neutron small-angle scattering study of small spherical RNA viruses

Small-angle neutron scattering from solutions of small RNA viruses has been used to study protein-nucleic acid organisation. In the five viruses investigated the RNA is confined to a sphere of about 100 A radius, with a central hole (with one possible exception). The interpenetration of RNA and protein varies with viruses and seems to be related to the natrue of the forces stabilising the virus.

Selective decrease in the rate of cleavage of an intracellular precursor to Rauscher leukemia virus p30 by treatment of infected cells with actinomycin D

The cleavage of an intracellular 67,000- to 70,000-dalton precursor, termed Pr4 to Rauscher leukemia virus (RLV) p30 protein proceeded at a slower rate when virus-producing cells were treated with actinomycin D (AMD). Treatment with AMD also caused a slight accumulation of Pr4 in purified early virus particles produced by a cell line which usually produces virions that contain little Pr4. The cleavage of other intracellular viral precursor polypeptides was not affected by treatment with AMD. Treatment of infected cells with cycloheximide, on the other hand, allowed the cleavage of Pr4 to proceed at the usual rate for a short period of time before further cleavage was drastically slowed or prevented. The cleavage of several other viral precursor polypeptides was also inhibited by treatment with cycloheximide. Different lines of evidence suggest that the mechanism of action of AMD is not due to a possible indirect effect on protein synthesis. Thus, the rate of cleavage of Pr4 was not affected by the length of pretreatment with AMD between 1 to 8 h. In addition, the combined effect of AMD and cycloheximide, at their maximal inhibitory concentrations, was greater than the effect of either drug alone, indicating the involvement of two at least partially different mechanisms in the action of AMD and cycloheximide. Furthermore, AMD did not affect the pulse labeling of viral precursor polypeptides. These results suggest that the interaction with viral RNA, whose production is inhibited by AMD, accelerates the cleavage of Pr4 to p30 during virus assembly. A hypothetical model is presented to illustrate th possible advantages of having a step in virus assembly in which genomic RNA interacts with a precursor to capsid proteins before the cleavage of that precursor.

Head length control in T4 bacteriophage morphogenesis: effect of canavanine on assembly

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Intermediates of bacteriophage MS2 assembly in vivo

The in vivo process of virion assembly was studied in rifampin-treated, MS2-infected Escherichia coli during late times of infection-after 18 min postinfection. Differential sucrose gradient sedimentation of infected-cell lysates taken at various times after radioactive labeling indicated a definite temporal order of appearance of phage-specific protein in assembly-related structures. Labeled MS2 protein appears first as a low-molecular-weight peak at the tops of gradients, then as a peak at 40S and as a large number of almost unseparable structures between 40 and 80S, and finally as 80S mature phage particles. During the chase of a short labeling period, radioactive phage protein was found to disappear from gradients in the same temporal order as it appeared; the soluble peak disappears first, followed by the 40 to 70S region. The chased label appears quantitatively in the 80S phage peak. Labeled phage RNA was found to appear first in the 40S peak, then in the structures between 40 and 70S, and finally in 80S phage particles. The order of disappearance of labeled phage RNA during a chase is the same as its appearance. Resedimentation of the 40 to 70S region indicated the presence of distinct structures at 60 and 70S and many indistinct ones between 40 and 60S. The smaller intermediates exhibit separable maturation protein-rich and coat protein-rich segments, indicating nonrandom binding of the two proteins during the initial steps of assembly. Larger, discrete intermediates appear at 60 and 70S. Treatment of the various structures with pancreatic RNase results in destruction of those from 40 through 60S; treatment of the 70S structure results in the conversion of some of it to a 45S peak, presumably the complete capsid. A small fraction of the 80S phage peak is also sensitive to RNase, resulting in a similar 45S peak. Pulse-chase experiments indicate that structures from 40 through 60S as well as the RNase-sensitive 70S structure are assembly intermediates, but that the RNase-insensitive 70S and the RNase-sensitive 80S structures are not.

Localization of coliphage MS2 A-protein

The purification of coliphage MS2 dinitrophenol (DNP) conjugates provided a system for localization of the single molecule of A-protein in the capsid of the MS2 phage particle. Three A-protein preparations isolated from unconjugated MS2, overconjugated DNP-MS2, and purified 78S DNP-MS2 were tested for the presence of covalently bound DNP. The binding characteristics to Dowex 1-X8 and rabbit anti-DNP bovine serum albumin (DNP-BSA) immunoglobulin G of the 78S DNP-MS2 and overconjugated DNP-MS2 A-protein preparations indicate that the A-protein is located on the surface of the phage particle where it can be covalently conjugated with hapten. Extensive enzymatic iodination of the A-protein of intact unconjugated MS2 substantiates this conclusion.

Characteristics of PRD1, a plasmid-dependent broad host range DNA bacteriophage

Several distinctive properties of PRD1, an icosahedral plasmid-dependent phage, are described. The drug-resistance plasmid-dependent host range of PRD1 extends beyond the P incompatibility group and includes gram-negative bacteria containing plasmids of incompatibility groups N and W. PRD1 phage will infect pseudomonads and Enterobacteriaceae containing either a P or W incompatibility group plasmid. PRD1 adsorbs to the cell wall of R(+) bacteria and thus its infectivity indicates cell wall alterations by these drug-resistance plasmid groups. PRD1 nucleic acid is duplex DNA with an estimated molecular weight of 24 x 10(6). The appearance of PRD1 in electron micrographs is suggestive of lipid content in addition to its buoyant density of 1.348 in CsCl and its sensitivity to chloroform. The latent period of PRD1 varies with the R(+) host bacterial strain used for growth of the phage.

Activity of empty, headlike particles for packaging of DNA of bacteriophage lambda in vitro

A precursor head of phage lambda is synthesized after induction of cells lysogenic for lambdaD(-)F(-) and lambdaA(-) (head-defective) mutants. This precursor head can be assayed by complementation in vitro and can be purified by CsCl gradient centrifugation and sucrose gradient sedimentation. The precursor head contains no DNA and has the same dimensions as the petit lambda particle. It can be packed with lambda DNA in an extract from induced Escherichia coli lysogenic for a lambdaE(-) mutant.

Structure and infectivity of picornaviral RNA encapsidated by cowpea chlorotic mottle virus protein

Poliovirus and Mengo virus RNA were shown to associate efficiently with cowpea chlorotic mottle virus protein to form pseudovirions. The sedimentation coefficient for the pseudovirions was similar to that of poliovirus, and electron microscope observations showed the Mengo pseudovirions to be similar in size to Mengo virus. Such pseudovirions were infectious and were more resistant to ribonuclease than viral RNA; however, under our assay conditions, their infectivity was about equal to that of viral RNA.

Characteristics and purification of PRR1, an RNA phage specific for the broad host range Pseudomonas R1822 drug resistance plasmid

A new drug resistance plasmid-dependent RNA containing phage resembling coliphage f2 in its particle size and density is described. The phage, PRR1, will only productively infect some R(+) hosts containing the Pseudomonas drug resistance plasmid R1822. The membrane filter-salt elution patterns, RNase sensitivity, inactivation in low ionic strength solutions, and host range serve to distinguish PRR1 from coliphage f2 and two other Pseudomonas RNA phages, 7s and PP7.

Mechanism of adsorption and eclipse of bacteriophage phi X174. II. Attachment and eclipse with isolated Escherichia coli cell wall lipopolysaccharide

A mixture of aqueous phenol, choloroform, and ether extracts the lipopolysaccharides (LPS) from the phiX174-sensitive strain, Escherichia coli C/1, and resistant strains, C/phiX and K12. Interaction of the C/1 LPS with phiX in a starvation buffer containing 10(-3) M CaCl(2) at 37 C, but not at 15 C, results in a first-order inactivation that is specific for C/1 LPS. After interaction for 60 min at 15 C, followed by centrifugation, 37 and 20% of a (14)C-phiX preparation are bound to the C/1 and C/phiX LPS pellets, respectively. The results for intact cells are 75 and 10%. Supporting the conclusion that this represents specific attachment of phiX to its receptor site in the LPS is the fact that EDTA-borate buffer is required to elute 85% of the (14)C-phiX from the C/1 LPS, whereas starvation buffer elutes the same amount from C/phiX LPS. Moreover, 95% of the PFU are found in the C/1 LPS pellets as compared with 50% in the resistant strain LPS pellets. When the products of interaction between phiX and LPS at 37 C are examined by sucrose density gradients in EDTA-borate, a single 60 to 90S peak is observed in the C/1 sample, and the single peak cosediments with the 120S marker phiX in the C/phiX sample. This change in S(20, w) is very similar to that reported for the eclipse of phiX in vivo. If the inactivation at 37 C is carried out on phiX-LPS complexes first formed at 15 C, the first-order kinetics are biphasic and nearly identical to that observed for the eclipse kinetics of phiX attached to intact cells. Thus, the phiX-LPS system is suitable for in vitro studies on the early events in phiX infection.