Regulation of coat protein polymerization by the scaffolding protein of bacteriophage P22.

In the morphogenesis of double stranded DNA phages, a precursor protein shell empty of DNA is first assembled and then filled with DNA. The assembly of the correctly dimensioned precursor shell (procapsid) of Salmonella bacteriophage P22 requires the interaction of some 420 coat protein subunits with approximately 200 scaffolding protein subunits to form a double shelled particle with the scaffolding protein on the inside. In the course of DNA packaging, all of the scaffolding protein subunits exit from the procapsid and participate in further rounds of procapsid assembly (King and Casjens. 1974. Nature (Lond.). 251:112-119). To study the mechanism of shell assembly we have purified the coat and scaffolding protein subunits by selective dissociation of isolated procapsids. Both proteins can be obtained as soluble subunits in Tris buffer at near neutral pH. The coat protein sedimented in sucrose gradients as a roughly spherical monomer, while the scaffolding protein sedimented as if it were an elongated monomer. When the two proteins were mixed together in 1.5 M guanidine hydrochloride and dialyzed back to buffer at room temperature, procapsids formed which were very similar in morphology, sedimentation behavior, and protein composition to procapsids formed in vivo. Incubation of either protein alone under the same conditions did not yield any large structures. We interpret these results to mean that the assembly of the shell involves a switching of both proteins from their nonaggregating to their aggregating forms through their mutual interaction. The results are discussed in terms of the general problem of self-regulated assembly and the control of protein polymerization in morphogenesis.     

Conformational changes in bacteriophage P22 scaffolding protein induced by interaction with coat protein

Many prokaryotic and eukaryotic double-stranded DNA viruses use a scaffolding protein to assemble their capsid. Assembly of the double-stranded DNA bacteriophage P22 procapsids requires the interaction of 415 molecules of coat protein and 60-300 molecules of scaffolding protein. Although the 303-amino-acid scaffolding protein is essential for proper assembly of procapsids, little is known about its structure beyond an NMR structure of the extreme C-terminus, which is known to interact with coat protein. Deletion mutagenesis indicates that other regions of scaffolding protein are involved in interactions with coat protein and other capsid proteins. Single-cysteine and double-cysteine variants of scaffolding protein were generated for use in fluorescence resonance energy transfer and cross-linking experiments designed to probe the conformation of scaffolding protein in solution and within procapsids. We showed that the N-terminus and the C-terminus are proximate in solution, and that the middle of the protein is near the N-terminus but not accessible to the C-terminus. In procapsids, the N-terminus was no longer accessible to the C-terminus, indicating that there is a conformational change in scaffolding protein upon assembly. In addition, our data are consistent with a model where scaffolding protein dimers are positioned parallel with one another with the associated C-termini.     

Molecular genetics of bacteriophage P22 scaffolding protein's functional domains

The assembly intermediates of the Salmonella bacteriophage P22 are well defined but the molecular interactions between the subunits that participate in its assembly are not. The first stable intermediate in the assembly of the P22 virion is the procapsid, a preformed protein shell into which the viral genome is packaged. The procapsid consists of an icosahedrally symmetric shell of 415 molecules of coat protein, a dodecameric ring of portal protein at one of the icosahedral vertices through which the DNA enters, and approximately 250 molecules of scaffolding protein in the interior. Scaffolding protein is required for assembly of the procapsid but is not present in the mature virion. In order to define regions of scaffolding protein that contribute to the different aspects of its function, truncation mutants of the scaffolding protein were expressed during infection with scaffolding deficient phage P22, and the products of assembly were analyzed. Scaffolding protein amino acids 1-20 are not essential, since a mutant missing them is able to fully complement scaffolding deficient phage. Mutants lacking 57 N-terminal amino acids support the assembly of DNA containing virion-like particles; however, these particles have at least three differences from wild-type virions: (i) a less than normal complement of the gene 16 protein, which is required for DNA injection from the virion, (ii) a fraction of the truncated scaffolding protein was retained within the virions, and (iii) the encapsidated DNA molecule is shorter than the wild-type genome. Procapsids assembled in the presence of a scaffolding protein mutant consisting of only the C-terminal 75 amino acids contained the portal protein, but procapsids assembled with the C-terminal 66 did not, suggesting portal recruitment function for the region about 75 amino acids from the C terminus. Finally, scaffolding protein amino acids 280 through 294 constitute its minimal coat protein binding site.     

Bacteriophage P22 tail protein gene expression.

We have found that mutations which block bacteriophage P22 head assembly at or before the DNA packaging stage (1-, 2-, 3-, 5-, and 8-) cause up to a 20-fold increase in the amount of tail (gene 9) protein made during infection. This correlation seems strong enough to warrant consideration of a control mechanism in which the failure to package DNA per se causes a large increase in the synthesis of tail protein. Our results indicate that one of the repressors required for maintenance of lysogeny, the mnt gene product, may be partially responsible for this phenomenon.     

A proposed structure of bacteriophage T4 gene product 22--a major prohead scaffolding core protein

Gene 22 of bacteriophage T4 encodes a major prohead scaffolding core protein of 269 amino acid residues. From its nucleotide sequence the gene product (gp) 22 has a predicted Mr of 29.9 and a pI of 4.3. The protein is rich in charged residues (glutamic acid and lysine) and contains low amounts of proline and glycine and no cysteine residues. We suggest that gp22 undergoes limited proteolytic processing which eliminates the short C-terminal piece from the molecule during the early steps of prohead assembly. Most amino acid residues of the gp22 polypeptide chain (80%) have an alpha-helical conformation and form seven peculiar alpha-helices. A model suggesting the spatial organization of gp22 is presented. Three long alpha-helices numbered 1 (1A and 1B), 3, and 5 (5A and 5B) are packed in an antiparallel fashion along the major axis of the road-shaped molecule. Two rather short alpha-helices (2 and 4) are located at the distal and proximal ends of the protein molecule, respectively. Helix number 2, which is a proteolytic fragment of gp22 found in mature T4 heads, is packed with helices 1A and 3, similar to a novel element of supersecondary structure, the alpha alpha-corner. Helix number 4 probably interacts with the gp20 connector of the prohead. The implications of the structure of the gp22 molecule for the assembly of the prohead core are discussed.     

Kinetic and calorimetric evidence for two distinct scaffolding protein binding populations within the bacteriophage P22 procapsid

A wide variety of viruses require the transient presence of scaffolding proteins to direct capsid assembly. In the case of bacteriophage P22, a model in which the scaffolding protein selectively stabilizes on-pathway growing intermediates has been proposed. The stoichiometry and thermodynamics of binding of the bacteriophage P22 scaffolding protein within the procapsid were analyzed by light scattering and isothermal titration calorimetry. Calorimetric experiments carried out between 10 and 37 degrees C were consistent with the presence of at least two distinct populations of binding sites, in agreement with kinetic evidence obtained by a light scattering assay. Binding to the high-affinity sites occurred at 20 degrees C with a stoichiometry of approximately 60 scaffolding molecules per procapsid and an apparent K(d) of approximately 100-300 nM and was almost completely enthalpy-driven. For the second binding population, precise fitting of the data was impossible due to small heats of binding, but the thermodynamics of binding were clearly distinct from the high-affinity phase. The heat capacity change (DeltaC(p)()) of binding was large for the high-affinity sites and negative for both sets of sites. Addition of sodium chloride (1 M) greatly reduced the magnitude of the apparent DeltaH, in agreement with previous evidence that electrostatic interactions play a major role in binding. A mutant scaffolding protein that forms covalent dimers (R74C/L177I) bound only to the high-affinity sites. These data comprise the first quantitative measurements of the energetics of the coat protein/scaffolding protein interaction.     

Assembly in vitro of bacteriophage P22 procapsids from purified coat and scaffolding subunits

The coat and scaffolding proteins of bacteriophage P22 procapsids have been purified in soluble form. By incubating both purified proteins with a mutant-infected cell extract lacking procapsids, but competent for DNA packaging in vitro (Poteete et al., 1979), we were able to obtain assembly of biologically active procapsids in vitro. The active species for complementation in vitro in both protein preparations copurified with the soluble subunits, indicating that these subunits represent precursors in procapsid polymerization.When the purified coat and scaffolding subunits were mixed directly, they polymerized into double-shelled procapsid-like structures during dialysis from 1.5 m-guanidine hydrochloride to buffer. When dialyzed separately under the same conditions, the scaffolding subunits did not polymerize but remained as soluble subunits, as did most of the coat subunits. No evidence was found for self-assembly of the scaffolding protein in the absence of the coat protein.The unassembled coat subunits sedimented at 3.9 S and the unassembled scaffolding subunits sedimented at 2.4 S in sucrose gradients. The Stokes' radius, determined by gel filtration, was 25 Å for the coat subunits and 34 Å for the scaffolding subunits. These results indicate that the scaffolding subunits are relatively slender elongated molecules, whereas the coat subunits are more globular.The experiments suggest that the procapsid is built by copolymerization of the two protein species. Their interaction on the growing surface of the shell structure, and not in solution, appears to regulate successive binding interactions.     

Purification and characterization of bacteriophage P22 Xis protein

The temperate bacteriophages λ and P22 share similarities in their site-specific recombination reactions. Both require phage-encoded integrase (Int) proteins for integrative recombination and excisionase (Xis) proteins for excision. These proteins bind to core-type, arm-type, and Xis binding sites to facilitate the reaction. λ and P22 Xis proteins are both small proteins (λ Xis, 72 amino acids; P22 Xis, 116 amino acids) and have basic isoelectric points (for P22 Xis, 9.42; for λ Xis, 11.16). However, the P22 Xis and λ Xis primary sequences lack significant similarity at the amino acid level, and the linear organizations of the P22 phage attachment site DNA-binding sites have differences that could be important in quaternary intasome structure. We purified P22 Xis and studied the protein in vitro by means of electrophoretic mobility shift assays and footprinting, cross-linking, gel filtration stoichiometry, and DNA bending assays. We identified one protected site that is bent approximately 137 degrees when bound by P22 Xis. The protein binds cooperatively and at high protein concentrations protects secondary sites that may be important for function. Finally, we aligned the attP arms containing the major Xis binding sites from bacteriophages λ, P22, L5, HP1, and P2 and the conjugative transposon Tn916. The similarity in alignments among the sites suggests that Xis-containing bacteriophage arms may form similar structures.     

UV sensitivity of a nonrepressor regulatory protein of bacteriophage P22.

The product of phage P22 gene c1 has two functions: it promotes synthesis of P22 repressor and it retards expression of some lytic genes. We present evidence that this product is inactivated in UV-irradiated hosts. The conditions for inactivation of c1 product include a functional DNA recombination system involving the host recA gene.     

Structure of phage P22 coat protein aggregates formed in the absence of the scaffolding protein.

Previous studies have shown that the assembly of the precursor shell (prohead) of bacteriophage P22 requires the copolymerization of the gene 5 coat protein with the gene 8 scaffolding protein. Removal of the scaffolding protein by mutation prevents efficient coat protein assembly, but some aberrant particles do form. We have now isolated these structures and characterized them with respect to morphology, protein composition, and small-angle X-ray scattering properties.The aberrant particles fall into three morphological classes, i.e. complex spirals and closed shells of two sizes. Small-angle X-ray scattering studies confirm that the larger particles are hollow shells with the radius of proheads ($\text{r = 260}\text{A}\text{?}$), and not of the mature virus ($\text{r = 285}\text{A}\text{?}$). These structures lack the inner shell of scaffolding protein found in proheads. The small particles have a radius of 195 Å, smaller than proheads, and appear to contain material, not scaffolding protein, within the outer shell.The aberrant particles contain two minor protein species, the gene 9 tail-spike protein, and an unidentified 67,000 molecular weight polypeptide, probably from the host. Neither is found in normal proheads. Removal of gene.9 product by mutation did not affect the formation of the aggregates. Fractionation of the morphological classes of particles revealed that the 67,000 molecular weight band was associated with the closed shells. It may be serving as a pseudo-initiator.Earlier studies had shown that treatment of proheads with sodium dodecyl sulfate in vitro resulted in loss of the scaffolding protein, and expansion of the shell to the mature radius of 285 Å. When the 8^? prohead-sized shells were treated similarly, they also expanded to the mature-sized shell. These results support the idea that there are at least two stable states of the coat protein, one of which, the prohead form, is an obligatory precursor of the mature form.     

Cloning, purification, and preliminary characterization by circular dichroism and NMR of a carboxyl-terminal domain of the bacteriophage P22 scaffolding protein.

Assembly of double-stranded DNA viruses and bacteriophages involves the polymerization of several hundred molecules of coat protein, directed by an internal scaffolding protein. A 163-amino acid carboxyl-terminal fragment of the 303-amino acid bacteriophage P22 scaffolding protein was cloned, overexpressed, and purified. This fragment is active in procapsid assembly reactions in vitro. The circular dichroism spectrum of the fragment, as well as the 1D-NMR and 15N-1H HSQC spectra of the uniformly-labeled protein, indicate that stable secondary structure elements are present. Determination of the three dimensional packing of these elements into the folded scaffolding protein fragment is underway. Structure-based drug design targeted at structural proteins required for viral assembly may have potential as a therapeutic strategy.     

Preliminary crystallographic analysis of the bacteriophage P22 portal protein

Portal proteins are components of large oligomeric dsDNA pumps connecting the icosahedral capsid of tailed bacteriophages to the tail. Prior to the tail attachment, dsDNA is actively pumped through a central cavity formed by the subunits. We have studied the portal protein of bacteriophage P22, which is the largest connector characterized among the tailed bacteriophages. The molecular weight of the monomer is 82.7 kDa, and it spontaneously assembles into an oligomeric structure of approximately 1.0 MDa. Here we present a preliminary biochemical and crystallographic characterization of this large macromolecular complex. The main difficulties related to the crystallization of P22 portal protein lay in the intrinsic dynamic nature of the portal oligomer. Recombinant connectors assembled from portal monomers expressed in Escherichia coli form rings of different stoichiometry in solution, which cannot be separated on the basis of their size. To overcome this intrinsic heterogeneity we devised a biochemical purification that separates different ring populations on the basis of their charge. Small ordered crystals were grown from drops containing a high concentration of the kosmotropic agent tert-butanol and used for data collection. A preliminary crystallographic analysis to 7.0-A resolution revealed that the P22 portal protein crystallized in space group I4 with unit cell dimensions a=b=409.4A, c=260.4A. This unit cell contains a total of eight connectors. Analysis of the noncrystallographic symmetry by the self-rotation function unambiguously confirmed that bacteriophage P22 portal protein is a dodecamer with a periodicity of 30 degrees. The cryo-EM reconstruction of the dodecahedral bacteriophage T3 portal protein will be used as a model to initiate phase extension and structure determination.     

Identification and characterization of the domain structure of bacteriophage P22 coat protein.

The bacteriophage P22 serves as a model for assembly of icosahedral dsDNA viruses. The P22 procapsid, which constitutes the precursor for DNA packaging, is built from 420 copies of a single coat protein with the aid of stoichiometric amounts of scaffolding protein. Upon DNA entry, the procapsid shell expands and matures into a stable virion. It was proposed that expansion is mediated by hinge bending and domain movement. We have used limited proteolysis to map the dynamic stability of the coat protein domain structures. The coat protein monomer is susceptible to proteolytic digestion, but limited proteolysis by small quantities of elastase or chymotrypsin yielded two metastable fragments (domains). The N-terminal domain (residues 1-180) is linked to the C-terminal domain (residues 205-429) by a protease-susceptible loop (residues 180-205). The two domains remain associated after the loop cleavage. Although only a small change of secondary structure results from the loop cleavage, both tertiary interdomain contacts and subunit thermostability are diminished. The intact loop is also required for assembly of the monomeric coat protein into procapsids. Upon assembly, coat protein becomes largely protease-resistant, baring cleavage within the loop region of about half of the subunits. Loop cleavage decreases the stability of the procapsids and facilitates heat-induced shell expansion. Upon expansion, the loop becomes protease-resistant. Our data suggest the loop region becomes more ordered during assembly and maturation and thereby plays an important role in both of these stages.