PRD1 is a tailless icosahedrally symmetric virus containing an internal lipid membrane beneath the protein capsid. Its linear dsDNA genome and covalently attached terminal proteins are delivered into the cell where replication occurs via a protein-primed mechanism. Extensive studies have been carried out to decipher the roles of the 37 viral proteins in PRD1 assembly, their association in virus particles and lately, especially the functioning of the unique packaging machinery that translocates the genome into the procapsid. These issues will be addressed in this chapter especially in the context of the structure of PRD1. We will also discuss the major challenges still to be addressed in PRD1 assembly.

The assembly of bacteriophage PRD1 proceeds via formation of empty procapsids containing an internal lipid membrane, into which the linear double-stranded DNA genome is subsequently packaged. The packaging ATPase P9 and other putative packaging proteins have been shown to be located at a unique vertex of the PRD1 capsid. Here, we describe the isolation and characterization of a suppressor-sensitive PRD1 mutant deficient in the unique vertex protein P6. Protein P6 was found to be an essential part of the PRD1 packaging machinery; its absence leads to greatly reduced packaging efficiency. Lack of P6 was not found to affect particle assembly, because in the P6-deficient mutant infection, wild-type (wt) amounts of particles were produced, although most were empty. P6 was determined not to be a specificity factor, as the few filled particles seen in the P6-deficient infection contained only PRD1-specific DNA. The presence of P6 was not necessary for retention of DNA in the capsid once packaging had occurred, and P6-deficient DNA-containing particles were found to be stable and infectious, albeit not as infectious as wt PRD1 virions. A packaging model for bacteriophage PRD1, based on previous results and those obtained in this study, is presented.The encapsidation of viral double-stranded DNA (dsDNA) genomes in a protective spherical protein capsid presents a unique set of challenges. First, the genomes of icosahedral dsDNA viruses are enormous in length compared to the inner diameter and volume of the capsids they are to occupy. Packaging DNA to such a high density is energetically extremely unfavorable. Second, the DNA needs to be topologically organized so that when a suitable host cell is encountered, the genome can efficiently be translocated into the cell and a new round of infection can be initiated. Specificity is an additional challenge, because energy and material should not be wasted for nonproductive packaging of host DNA into the viral capsids.Icosahedral dsDNA viruses have developed ingenious machinery to perform such a complicated task. Encapsidation of the dsDNA genomes proceeds via formation of empty procapsids, devoid of DNA, that subsequently are packaged with DNA by a specific enzyme, called the terminase or packaging ATPase (for recent reviews, see references 24 and 46). This process requires a large amount of energy, usually provided in the form of ATP. It has been estimated that, for example, in the case of bacteriophage phi29, an average of 1 molecule of ATP per each 2 bp of DNA packaged is needed (38). Packaging occurs through a specific vertex of the capsid, which contains a ring-like portal structure, through which the DNA is threaded into the particle. However, packaging machineries are not quite as simple as this; many additional proteins, and in some cases even RNAs, are involved, with the details varying from one virus to another.The problem with studying these intricate apparatuses is their asymmetric location in the virion, which makes conventional structure determination methods that ...