Morphogenetic pathway of bacteriophage phi 6. A flow analysis of subviral and viral particles in infected cells

Tracking in atomic detail the functional specializations in viral RecA helicases that occur during evolution

Many complex viruses package their genomes into empty protein shells and bacteriophages of the Cystoviridae family provide some of the simplest models for this. The cystoviral hexameric NTPase, P4, uses chemical energy to translocate single-stranded RNA genomic precursors into the procapsid. We previously dissected the mechanism of RNA translocation for one such phage, ɸ12, and have now investigated three further highly divergent, cystoviral P4 NTPases (from ɸ6, ɸ8 and ɸ13). High-resolution crystal structures of the set of P4s allow a structure-based phylogenetic analysis, which reveals that these proteins form a distinct subfamily of the RecA-type ATPases. Although the proteins share a common catalytic core, they have different specificities and control mechanisms, which we map onto divergent N- and C-terminal domains. Thus, the RNA loading and tight coupling of NTPase activity with RNA translocation in ɸ8 P4 is due to a remarkable C-terminal structure, which wraps right around the outside of the molecule to insert into the central hole where RNA binds to coupled L1 and L2 loops, whereas in ɸ12 P4, a C-terminal residue, serine 282, forms a specific hydrogen bond to the N7 of purines ring to confer purine specificity for the ɸ12 enzyme.

Precise packaging of the three genomic segments of the double-stranded-RNA bacteriophage phi6

Bacteriophage phi6 has a genome of three segments of double-stranded RNA. Each virus particle contains one each of the three segments. Packaging is effected by the acquisition, in a serially dependent manner, of the plus strands of the genomic segments into empty procapsids. The empty procapsids are compressed in shape and expand during packaging. The packaging program involves discrete steps that are determined by the amount of RNA inside the procapsid. The steps involve the exposure and concealment of binding sites on the outer surface of the procapsid for the plus strands of the three genomic segments. The plus strand of segment S can be packaged alone, while packaging of the plus strand of segment M depends upon prior packaging of S. Packaging of the plus strand of L depends upon the prior packaging of M. Minus-strand synthesis begins when the particle has a full complement of plus strands. Plus-strand synthesis commences upon the completion of minus-strand synthesis. All of the reactions of packaging, minus-strand synthesis, and plus-strand synthesis can be accomplished in vitro with isolated procapsids. Live-virus constructions that are in accord with the model have been prepared. Mutant virus with changes in the packaging program have been isolated and analyzed.

Structure and NTPase activity of the RNA-translocating protein (P4) of bacteriophage phi 6

The RNA polymerase complex of bacteriophage phi 6 comprises four proteins, P1, P2, P4 and P7, and forms the core of the virion. Protein P4 is a non-specific NTPase that provides the energy required for RNA translocation (packaging). Characterization of purified recombinant P4 shows that the protein assembles into stable hexamers in the presence of ADP and divalent cations. Image averaging of electron micrographs reveals this hexamer as a slightly skewed ring with outer and inner diameters of 12 and 2 nm, respectively. NTPase activity of P4 is associated only with the hexameric form. Ca2+ and Zn2+ and non-specific single-stranded RNA stimulate the NTPase activity, while Mg2+ acts as a non-competitive inhibitor, presumably via a separate Mg2+ binding site. Binding affinities of different nucleotide mono-, di- and triphosphates and non-hydrolyzable analogs indicate that the beta-phosphate moiety is required for substrate binding. A slight preference for binding of purine nucleotides is also observed. Analysis of P4 by CD and Raman spectroscopy indicates an alpha/beta subunit fold that is altered only slightly by hexamer assembly. Raman markers of P4 secondary and tertiary structures are also largely invariant to nucleotide exchange and hydrolysis, suggesting that the mechanisms of RNA translocation involves movement of subunits relative to one another rather than large scale changes in the alpha/beta subunit fold. The stoichiometry of P4 in the mature phi 6 virion is estimated as 120 copies. Because the recombinant P4 hexamers exhibit hydrodynamic and enzymatic properties that are identical to those of P4 oligomers released from native phi 6, we propose that P4 occurs as hexamers in the native viral core particle.

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.

In vitro packaging of the bacteriophage phi 6 ssRNA genomic precursors

Bacteriophage phi 6 contains three segments of double-stranded RNA within a nucleocapsid. Plasmids containing cDNA copies of the large genomic segment direct the synthesis of viral proteins that assemble into procapsids in Escherichia coli or Pseudomonas phaseolicola. These structures are dodecahedral assemblages of proteins P1, P2, P4, and P7. We report in this paper that these particles are capable of packaging viral single-stranded plus-sense RNA in vitro. The packaging reaction requires the presence of ATP or dATP. Synthesis of minus strands takes place within this filled procapsid in the presence of all four nucleoside triphosphates. Packaged ssRNA is found to be protected from added ribonuclease.

In vitro assembly of infectious nucleocapsids of bacteriophage phi 6: formation of a recombinant double-stranded RNA virus

A system is described for assembling infectious bacteriophage phi 6 nucleocapsids in vitro. Procapsids encoded by cDNA copies of genomic segment L in Escherichia coli were used to package and replicate viral RNA segments. The resulting filled particles were shown to be capable of infecting host cell spheroplasts after incubation with purified nucleocapsid shell protein P8. The infected spheroplasts yielded infectious virions. A modified cDNA-derived RNA segment was inserted into virions by this method. The resulting infectious virions contained the same 4-base-pair deletion as the modified cDNA. These findings support the contention that the preformed procapsids are the "machine" that replicates the phi 6 genome, by showing that the cDNA-derived procapsids are competent to package and replicate RNA properly.

RNA-protein complexes responsible for replication and transcription of the double-stranded RNA bacteriophage phi 6

RNA-protein complexes active for transcription and replication of the double-stranded RNA bacteriophage phi 6 have been partially purified from lysates of infected Pseudomonas phaseolicola. Transcribing particles (filled procapsids) contain the three viral dsRNAs and all four procapsid proteins P1, P2, P4, and P7. Particles with replicase activity contain the same four proteins as well as single plus RNA strands duplexed with various extents of minus strands initiated in vivo. The in vitro replication reaction is insensitive to RNaseA. Sarkosyl destroys transcription complexes but does not reduce the activity of replication complexes, although the latter lose 80% of their P4 and the single-strand RNA template becomes sensitive to RNase. The detection of complexes that replicate small only, or both small and medium, RNA suggests that the RNAs are packaged sequentially in the order small, medium, large.

Minus-strand RNA synthesis by the segmented double-stranded RNA bacteriophage phi 6 requires continuous protein synthesis

Bacteriophage phi 6 contains three dsRNA chromosomes. Strand-separating agarose gels were used to study plus- and minus-strand synthesis in vivo and the effect of protein synthesis inhibitors. Analysis of phi 6 RNA synthesis shows low levels of all three dsRNAs and ssRNAs at 10 min, increasing label uptake into all RNAs except the large message from 20 to 60 min, and a greater abundance of medium and small messages than large mRNAs at late times. Isoconformers of the small message are synthesized throughout infection. Northern analysis suggests that large messages made early may persist to direct continuing translation of L-segment-encoded transcription and replication proteins. The time course of phi 6 minus-strand RNA synthesis in vivo, in the absence of background label in host RNAs, is reported for the first time. Label in minus strands is detected only after heat denaturation of RNA samples and appears sequentially in the small, medium, and large strands beginning at 20 min. At both early and late times, chloramphenicol arrests minus-strand synthesis rapidly and all three mRNAs accumulate. The results are consistent with the reovirus asynchronous model for dsRNA viral replication: plus ssRNAs made first are used as templates for minus-strand synthesis. They also indicate that replication protein(s) acts stoichiometrically.

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.

In vitro replication and transcription of the segmented double-stranded RNA bacteriophage phi 6

In vitro conditions that support viral-specific replication and transcription have been developed from Pseudomonas phaseolicola cells infected with the segmented double-stranded RNA bacteriophage phi 6. Transcription activity, previously shown to occur by semiconservative strand displacement, labeled (+) strands of all three genome segments and produced all three corresponding genome length messenger RNAs. Replication activity for each of the three double-stranded RNA segments is observed. Our criteria for replication were formation of genomic length double-stranded RNA products and at least (-) strand synthesis activity. Mn2+ and Sarkosyl together selectively inhibited transcription. Analysis of replication alone suggested that replication templates are the viral (+) messenger RNAs.

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.

Generation of cDNA clones of the bacteriophage phi 6 segmented dsRNA genome: characterization and expression of L segment clones

Bacteriophage phi 6 has three dsRNA genome segments of about 3.0, 4.0, and 6.4 kbp. More than 90% of the segmented phi 6 dsRNA genome has been cloned as subchromosomal cDNA fragments, generated by reverse transcription of denatured polyadenylated dsRNA, RNA removal, annealing, filling, size fractionation, tailing, and insertion at the PstI site of pBR322. All of the large (L) segment is represented by five overlapping fragments, 98% of the small (S) segment is present in three fragments, and 67% of the medium (M) segment is contained in two fragments. Fragments have been aligned in linear arrays by Southern blot hybridization and restriction enzyme analysis. The orientation of the ordered fragments with respect to genomic RNA and phi 6 transcriptional direction was determined by comparison of terminal DNA sequences with RNA sequences at the genomic ends of phi 6 RNA. Expression of L segment clones using both Escherichia coli minicells and T7 polymerase/promoter vectors indicate that the order of known phi 6 genes on the large chromosome is: 5'--gene 7, gene 2, gene 4, gene 1--3'. cDNA complementation of a ts mutant, ts411, has located this mutation in gene 4.

Terminal sequences of the bacteriophage phi 6 segmented dsRNA genome and its messenger RNAs

The ends of the three dsRNA genome segments (L, M, and S) of bacteriophage phi 6 (strand separated and/or intact) and the 5' ends of the middle and small single-strand messenger RNAs have been sequenced by base-specific partial enzymatic digestion. Terminal sequences for the large and middle dsRNA strands extend about 60 bases. The three dsRNA segments have 18 homologous bases at the left end except for position 2, which differs in the L segment. A 17-base homology defines the right ends of L and M dsRNAs and probably S dsRNA as well. The 5' ends of middle and small messenger RNAs are identical to the corresponding viral (+) strands.

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.

Characterization of phi 6 mutants that are temperature sensitive in the morphogenetic protein P12

P12 is a morphogenetic protein necessary for the envelopment of the bacteriophage phi 6 nucleocapsid with the viral membrane. Gene 12 is located along with three other genes on the smallest chromosome of the virion. ts mutants in P12 were obtained by first characterizing the isoelectric focusing behavior of phi 6 proteins and then screening ts mutants of phi 6 that had previously been assigned to chromosome C for changes in the behavior of P12. In this manner, three independently isolated mutants were identified and were found to have morphogenetic consequences at restrictive temperatures similar to gene 12 nonsense mutants in nonsuppressor cells in that only unenveloped nucleocapsids were formed. When infected cells were labeled at restrictive temperature, 27 degrees, and then shifted to 21 degrees, normal phage particles were formed; however, the hydrophobic membrane proteins in the particles were not labeled, indicating that functional P12 must be present at the time of synthesis of the membrane proteins for them to assemble into virions or that the defective P12 leads the membrane proteins into a nonfunctional pathway.

Virion-associated RNA polymerase of bacteriophage phi 6 synthesizes three complete transcripts of double-stranded RNA genome in vitro

Three single-stranded RNA transcripts synthesized in vitro by a virion-associated RNA polymerase of bacteriophage phi 6 were sequenced at their 5'- and 3'-termini. The sequences agreed with those of the + strands of the 3 double-stranded RNA segments [FEBS Lett. (1982) 141,111-115]. The results show that the transcription by phi 6 RNA polymerase initiates exactly at the 3'-ends of the template RNAs (-strands of the genomic RNA) and terminates exactly at the 5'-ends.