Bacteriophage PRD1 proteins: cross-linking and scanning transmission electron microscopy analysis

Probing protein interactions in the membrane-containing virus PRD1

PRD1 is a Gram-negative bacteria infecting complex tailless icosahedral virus with an inner membrane. This type virus of the family Tectiviridae contains at least 18 structural protein species, of which several are membrane associated. Vertices of the PRD1 virion consist of complexes recognizing the host cell, except for one special vertex through which the genome is packaged. Despite extensive knowledge of the overall structure of the PRD1 virion and several individual proteins at the atomic level, the locations and interactions of various integral membrane proteins and membrane-associated proteins still remain a mystery. Here, we demonstrated that blue native PAGE can be used to probe protein-protein interactions in complex membrane-containing viruses. Using this technique and PRD1 as a model, we identified the known PRD1 multiprotein vertex structure composed of penton protein P31, spike protein P5, receptor-binding protein P2 and stabilizing protein P16 linking the vertex to the internal membrane. Our results also indicated that two transmembrane proteins, P7 and P14, involved in viral nucleic acid delivery, make a complex. In addition, we performed a zymogram analysis using mutant particles devoid of the special vertex that indicated that the lytic enzyme P15 of PRD1 was not part of the packaging vertex, thus contradicting previously published results.

Bacteriophage PRD1 DNA entry uses a viral membrane-associated transglycosylase activity

Amino acid sequence analyses have indicated that the amino-terminal part of bacteriophage PRD1 structural protein P7 carries a conserved transglycosylase domain. We analysed wild-type PRD1 and different mutant particles in zymograms and found a glycolytic activity that was associated with protein P7. This is the first time a putative bacteriophage or plasmid lytic transglycosylase has been shown to have an enzymatic activity. In the absence of protein P7, the phage DNA replication and host cell lysis were delayed. Gene VII of PRD1 is known to encode proteins P7 and P14. In this investigation, the open reading frame coding for P14 was mapped to the 3' end of gene VII. Proteins P7 and P14 probably form a heteromultimeric complex, which is located at the particle vertices and is involved in the early steps of the PRD1 life cycle

Viral evolution revealed by bacteriophage PRD1 and human adenovirus coat protein structures

The unusual bacteriophage PRD1 features a membrane beneath its icosahedral protein coat. The crystal structure of the major coat protein, P3, at 1.85 A resolution reveals a molecule with three interlocking subunits, each with two eight-stranded viral jelly rolls normal to the viral capsid, and putative membrane-interacting regions. Surprisingly, the P3 molecule closely resembles hexon, the equivalent protein in human adenovirus. Both viruses also have similar overall architecture, with identical capsid lattices and attachment proteins at their vertices. Although these two dsDNA viruses infect hosts from very different kingdoms, their striking similarities, from major coat protein through capsid architecture, strongly suggest their evolutionary relationship.

Bacteriophage PRD1 contains a labile receptor-binding structure at each vertex

Bacteriophage PRD1 is a membrane-containing virus with an unexpected similarity to adenovirus. We mutagenized unassigned PRD1 genes to identify minor capsid proteins that could be structural or functional analogs to adenovirus proteins. We report here the identification of an amber mutant, sus525, in an essential PRD1 gene XXXI. The gene was cloned and the gene product was overexpressed and purified to near homogeneity. Analytical ultracentrifugation and gel filtration showed that P31 is a homopentamer of about 70 kDa. The protein was shown to be accessible on the virion surface and its absence in the sus525 particles led to the deficiency of two other viral coat proteins, protein P5 and the adsorption protein P2. Cryo-electron microscopy and image reconstruction of the sus525 particles indicate that these proteins are located on the capsid vertices, because in these particles the entire vertex structure was missing along with the peripentonal major capsid protein P3 trimers. Sus525 particles package DNA effectively but loose it upon purification. All of the PRD1 vertex structures are labile and potentially capable of mediating DNA delivery; this is in contrast to other dsDNA phages which employ a single vertex for packaging and delivery. We propose that this arises from a symmetry mismatch between protein P2 and the pentameric P31 in analogy to that between the adenovirus penton base and the receptor-binding spike.

Purification and characterization of the assembly factor P17 of the lipid-containing bacteriophage PRD1

Assembly factors, proteins assisting the formation of viral structures, have been found in many viral systems. The gene encoding the assembly factor P17 of bacteriophage PRD1 has been cloned and expressed in Escherichia coli. P17 acts late in phage assembly, after capsid protein folding and multimerization, and sorting of membrane proteins has occurred. P17 has been purified to near homogeneity. It is a tetrameric protein displaying a rather high heat stability. The protein is largely in an alpha-helical conformation and possesses a putative leucine zipper which is not essential for protein function, as judged by in vitro mutagenesis and complementation analysis. Although heating does not cause structural changes in the conformation of the protein, the dissociation of the tetramer into smaller units is evident as diminished self-quenching of the fluorescently labeled P17. Similarly, dissociation of the tetramer is also obtained by dialysis of the protein against 6-M guanidine hydrochloride (GdnHCl) or 1% SDS. The reassembly of these smaller units upon cooling is evident from resonance energy transfer.

Mass Measurement in the Scanning Transmission Electron Microscope: A Powerful Tool for Studying Membrane Proteins

The technique of mass measurement in the scanning transmission electron microscope is briefly presented. Results obtained for membrane proteins, with particular emphasis on the channel forming proteins, are discussed. The data illustrate the versatility of the technique which is applicable to particulate, filamentous, and sheet-like structures. When combined with composition analysis, the absolute mass values measured with the STEM allow protein stoichiometries to be unambiguously defined. Copyright 1998 Academic Press.

Functional organization of the bacteriophage PRD1 genome

PRD1 is a broad-host-range virus that infects Escherichia coli cells. It has a linear double-stranded DNA genome that replicates by a protein-primed mechanism. The virus particle is composed of a protein coat enclosing a lipid membrane. On the basis of this structure, PRD1 is being used as a membrane biosynthesis and structure model. In this investigation, we constructed the transcription map of the 15-kb-long phage genome. This was achieved by a computer search of putative promoters, which were then tested for activity by primer extension and for the capability to promote the synthesis of chloramphenicol acetyltransferase.