Electron microscopy of bacteriophage phi 6 nucleocapsid: three-dimensional image analysis

Discovery and Classification of the φ6 Bacteriophage: An Historical Review

The year 2023 marks the fiftieth anniversary of the discovery of the bacteriophage φ6. The review provides a look back on the initial discovery and classification of the lipid-containing and segmented double-stranded RNA (dsRNA) genome-containing bacteriophage-the first identified cystovirus. The historical discussion describes, for the most part, the first 10 years of the research employing contemporary mutation techniques, biochemical, and structural analysis to describe the basic outline of the virus replication mechanisms and structure. The physical nature of φ6 was initially controversial as it was the first bacteriophage found that contained segmented dsRNA, resulting in a series of early publications that defined the unusual genomic quality. The technology and methods utilized in the initial research (crude by current standards) meant that the first studies were quite time-consuming, hence the lengthy period covered by this review. Yet when the data were accepted, the relationship to the reoviruses was apparent, launching great interest in cystoviruses, research that continues to this day.

Intermediates in the assembly pathway of the double-stranded RNA virus phi6

The double-stranded RNA bacteriophage phi6 contains a nucleocapsid enclosed by a lipid envelope. The nucleocapsid has an outer layer of protein P8 and a core consisting of the four proteins P1, P2, P4 and P7. These four proteins form the polyhedral structure which acts as the RNA packaging and polymerase complex. Simultaneous expression of these four proteins in Escherichia coli gives rise to procapsids that can carry out the entire RNA replication cycle. Icosahedral image reconstruction from cryo-electron micrographs was used to determine the three-dimensional structures of the virion-isolated nucleocapsid and core, and of several procapsid-related particles expressed and assembled in E. coli. The nucleocapsid has a T = 13 surface lattice, composed primarily of P8. The core is a rounded structure with turrets projecting from the 5-fold vertices, while the procapsid is smaller than the core and more dodecahedral. The differences between the core and the procapsid suggest that maturation involves extensive structural rearrangements producing expansion. These rearrangements are co-ordinated with the packaging and RNA polymerization reactions that result in virus assembly. This structural characterization of the phi6 assembly intermediates reveals the ordered progression of obligate stages leading to virion assembly along with striking similarities to the corresponding Reoviridae structures.

Bacteriophage structure

The purpose of this review is to provide information of the role played by electron microscopy in respect of bacteriophage structure. This 40 years' "love story" between phages and microscopy was a valuable contribution to the progress of scientific knowledge in molecular biology. In spite of the rather drastic treatment required for electron microscopical analysis, it was possible to reveal the molecular organization and morphogenic pathway of many of the bacteriophages cited in this paper.

Generation of infectious nucleocapsids by in vitro assembly of the shell protein on to the polymerase complex of the dsRNA bacteriophage phi 6

A method for the in vitro uncoating of the phi 6 nucleocapsid (NC) was developed. The resulting particle, designated as the NC core, containing the genomic double-stranded (ds) RNA segments and the proteins P1, P2, P4 and P7, was not infectious but had a highly enhanced in vitro transcriptase activity compared to that of the intact NC. The NC shell protein P8 was purified by immunoaffinity chromatography, and it was shown to self-assemble to shell-like structures upon addition of calcium ions. The conditions for the self-assembly of the shell were optimized. Shell reassembly on to the NC cores restored the infectivity but resulted in a decrease of transcriptase activity. No reassembly of the shell on to RNA-less cores (procapsids) produced from a cDNA construction in Escherichia coli was observed. Our results suggest that the intracellular uncoating of the NC is the event activating the phi 6 dsRNA transcriptase and that the NC shell is necessary for infectivity, probably for the passage of the NC through the host cytoplasmic membrane. Packaging of the dsRNA segments into the procapsid appears to be a prerequisite for NC shell assembly.

Purified phi 6 nucleocapsids are capable of productive infection of host cells with partially disrupted outer membranes

Purified nucleocapsids of bacteriophage phi 6, lacking the phage lipid envelope, are unable to infect intact Pseudomonas syringae host cells. A method for studying the process by which a naked virus particle, the phi 6 nucleocapsid, penetrates the host cytoplasmic membrane was developed. Host cells were rendered competent for nucleocapsid infection by treatment with repeated washings with salt and sucrose and the subsequent addition of lysozyme. This treatment disrupts the outer membrane, permitting the nucleocapsid to reach the cytoplasmic membrane and to infect the cell. The nucleocapsid infection is blocked by monoclonal antibodies raised against the nucleocapsid shell protein P8.

Quantitation of the adsorption and penetration stages of bacteriophage phi 6 infection

The enveloped dsRNA bacteriophage phi 6 uses the pilus of Pseudomonas syringae as its receptor. It enters the host cell by fusion of the virus envelope with the host outer membrane, followed by penetration of the cytoplasmic membrane by the phage nucleocapsid. In this investigation we quantitated the adsorption and penetration of phi 6wt and a host range mutant, phi 6h 1s, to five bacterial strains. Adsorption rate constants were measured for the different phage-host combinations, the constant for phi 6wt with the standard host was 3.3 X 10(10) ml/min. Infections with 14C-labeled phage at different phage/cell ratios were used to measure the numbers of adsorbing and entering virions/sensitive cell. At high phage/cell ratios (200-250) the standard host adsorbed on the average 35-40 wild-type virions/cell, the saturation level being somewhat higher. It was shown that at phage/host cell ratios of 0.1-1 practically every virion produces an infectious center. The average number of entering phage particles per infectious center reached saturation around the phage/cell ratio of 50 and did not exceed 3 for the standard host. The phi 6 preparations used in this study had a specific infectivity of 0.7-0.9.

In vitro assembly of the outer shell of bacteriophage phi 6 nucleocapsid

Following dissociation of bacteriophage phi 6 nucleocapsid (NC) by EDTA, a particle composed of protein P8 and corresponding to the outer shell of the NC was assembled in vitro in the presence of Ca2+ and Mg2+. Assembly was obtained from soluble protein constituents above 100 micrograms/ml and was optimal within a temperature range of 22-30 degrees. Assembly did not require the presence of genomic RNA. Crosslinking results of intact NCs and in vitro-assembled outer shells suggested that protein P8 dimers are the structural subunits of the shell. Analysis of the assembly kinetics by electron microscopy suggested that ring-like particles of uniform size, packed in flat hexagonal arrays, are intermediates in outer shell assembly.

Chemical crosslinking of bacteriophage phi 6 nucleocapsid proteins

phi 6 is a lipid-containing dsRNA bacteriophage of Pseudomonas syringae. Its nucleocapsid (NC) has common features with Reoviridae core particles. We report here the crosslinking of phi 6 NC proteins with cleavable 12-A span chemical crosslinker, dithiobis(succinimidyl propionate). The crosslinked complexes were analyzed in two-dimensional polyacrylamide gels or by using monoclonal antibodies to uncleaved protein complexes in one-dimensional protein gels. The NC surface protein (P8) forms a series of multimeric homopolymers. The phi 6 lytic enzyme, protein P5, is associated with P8 on the NC surface. The interior NC proteins P1 and P4, associated with the virus polymerase activity, are also in contact with the P8 shell. A P1 + P4 complex is also formed. Only one of the NC proteins (P7) did not easily form complexes with the other NC proteins. These results indicate a very closely packed P8 surface lattice with specific contacts to the internal NC proteins.

Nucleotide sequence of the large double-stranded RNA segment of bacteriophage phi 6: genes specifying the viral replicase and transcriptase

The genome of the lipid-containing bacteriophage phi 6 contains three segments of double-stranded RNA. We determined the nucleotide sequence of cDNA derived from the largest RNA segment (L). This segment specifies the procapsid proteins necessary for transcription and replication of the phi 6 genome. The coding sequences of the four proteins on this segment were identified on the basis of size and the correlation of predicted N-terminal amino acid sequences with those found through analysis of isolated proteins. This report completes the sequence analysis of phi 6. This constitutes the first complete sequence of a double-stranded RNA genome virus.

Production of a polyhedral particle in Escherichia coli from a cDNA copy of the large genomic segment of bacteriophage phi 6

A polyhedral particle that resembles in composition and structure the procapsid of bacteriophage phi 6 was produced in Escherichia coli containing cDNA copies of the entire large genomic segment inserted into expression vector plasmids under the control of lac or tac promoters. The particles were composed of proteins P1, P2, P4, and P7 in the same stoichiometry as in the intact virion. In electron micrographs of negatively stained samples, the particles appeared as hexagons, stars, or rings of 10 knobs, which are characteristic of the five-, three-, and twofold axes of symmetry characteristic of phi 6 procapsids. Stable particles were also produced from cDNA deletions that produce only P1 and P4. Other cDNA deletions producing P1 and P7 and P1 alone resulted in unstable particles which could only be visualized in electron micrographs of thin sections of E. coli transformed by the recombinant plasmids. Our results indicate that the assembly of the phi procapsid is independent of other phage proteins and of normal phage RNA.

The nucleocapsid of the lipid-containing double-stranded RNA bacteriophage phi 6 contains a protein skeleton consisting of a single polypeptide species

The nucleocapsid of the enveloped double-stranded RNA bacteriophage phi 6 was isolated by extraction with the nonionic detergent Triton X-114 and subjected to disruption analysis with chelating and protein-denaturing agents. The subnucleocapsid particles were separated in rate-zonal sucrose gradients, and their ultrastructure and protein composition were analyzed. The role of divalent cations in the nucleocapsid structure was studied by using a precipitation assay of the isolated nucleocapsid proteins. The phi 6 nucleocapsid had a cagelike skeleton consisting of a single polypeptide species (P1). Two other proteins (P2 and P4) were associated with the P1 cage. These three early proteins were previously known to be involved in the RNA synthesis machinery of the virus. The stability of the nucleocapsid surface lattice consisting of protein P8 was dependent on Ca2+ ions.

The dodecahedral framework of the bacteriophage phi 6 nucleocapsid is composed of protein P1

The outer layer of the bacteriophage phi 6 nucleocapsid (NC) was removed by EDTA and reassociated with the core in the presence of Ca2+ or Mg2+. The core was relatively inaccessible to trypsin digestion, was composed of protein P1, and was in the dodecahedral framework reported previously. (H.T. Steely, Jr., and D. Lang, J. Virol. 51:479-483, 1984; Y. Yang and D. Lang, J. Virol. 51:484-488, 1984). The double-stranded RNA genome became RNase sensitive after EDTA treatment of the nucleocapsid.

Electron microscopy of bacteriophage phi 6 nucleocapsid: two-dimensional image analysis

Electron micrographs of negatively stained nucleocapsids isolated from intact, wild-type phi 6 bacteriophage revealed three distinct morphological forms. Two-dimensional analysis of electron micrographs of two of these forms and image averaging of all forms are consistent with a dodecahedral structure embodied in the phi 6 nucleocapsid.