Popping the cork: mechanisms of phage genome ejection

• Published in: Nature reviews. Microbiology Vol. 11; no. 3; pp. 194 - 204
• Main Authors: Molineux, Ian J., Panja, Debabrata
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 01.03.2013; Nature Publishing Group
• Subjects: 41; 631/326/1321; 631/326/596/2557; Bacterial genetics; Bacteriophages; Bacteriophages - physiology; Biomedical and Life Sciences; Brownian motion; Deoxyribonucleic acid; DNA; DNA, Viral - metabolism; Electron microscopy; Genetic aspects; Genome, Viral; Genomes; Genomics; Infections; Infectious Diseases; Life Sciences; Medical Microbiology; Microbiology; Models, Biological; Nucleic acids; Osmotic pressure; Packaging; Parasitology; Physiological aspects; Proteins; review-article; RNA polymerase; Virology; Virus Uncoating; United States; Netherlands
• ISSN: 1740-1526; 1740-1534; 1740-1534
• DOI: 10.1038/nrmicro2988

Key Points The double-stranded DNA genomes of most tailed phages are contained within the capsid at a concentration of ∼500 mg per ml. The DNA inside the capsid is in the B form, arranged on a closely packed but imperfect hexagonal lattice. Packaging is thought to occur from the outside of the spool inwards. The energy for packaging DNA into the capsid is derived from the hydrolysis of ATP by terminase, a packaging nanomotor. Terminase can generate a force of up to 100 pN. At this concentration, DNA is highly condensed, and much of the water that normally hydrates the DNA and its counterions must be removed in order to package a complete genome. Water removal during the packaging process occurs by reverse osmosis, the energy for which is derived from the activity of terminase. Only about 10% of the energy stored in the packaged phage DNA is due to bending DNA more tightly than its persistence length. Most of the energy internal to the capsid is due to the dehydrated state of the DNA, which is reflected by internal osmotic pressures that reach tens of atmospheres. The continuum mechanics model posits that the energy stored in the packaged DNA is used to drive ejection of the phage genome. This model is supported by the experimental suppression of DNA ejection through the application of an increased external osmotic pressure. The hydrodynamic model of phage genome ejection proposes that following opening of the exit channel, water diffuses through the capsid shell to neutralize the osmotic imbalance, and DNA is pushed out by the hydrostatic pressure gradient across the tail. The data used to support the continuum mechanics model for in vitro ejection is also fully consistent with the hydrodynamic model. According to the continuum mechanics model, during infection of a bacterial cell, the osmotic pressure of the cytoplasm opposes phage DNA ejection driven by forces internal to the phage capsid; only about half the genome, at most, can enter the cell by this process. Various ad hoc secondary mechanisms have been proposed to complete the infection process. The hydrodynamic model has no such problem, as continued water flow up the osmotic gradient (from the growth medium, through the capsid and into the cytoplasm) provides the necessary force for complete genome transport into the cell. A general mechanism of phage genome ejection in vivo can be proposed, in which the width of the exit channel determines whether hydrodynamic flow can facilitate genome ejection. When the channel is wide enough for water and ions to pass through at the same time as the double-stranded DNA genome, then hydrodynamic flow is sufficient; this is likely to be the pathway used by most phage types. However, if the exit channel is only wide enough for double-stranded DNA alone, then energy-requiring motors are necessary to translocate the infecting phage genome into the cell. Despite 60 years of investigation, our understanding of the mechanisms by which phages eject their genomes into target bacterial cells remains incomplete. Here, Molineux and Panja describe the structure of DNA inside the phage head and discuss the current models for DNA ejection both in vitro and in vivo . Sixty years after Hershey and Chase showed that nucleic acid is the major component of phage particles that is ejected into cells, we still do not fully understand how the process occurs. Advances in electron microscopy have revealed the structure of the condensed DNA confined in a phage capsid, and the mechanisms and energetics of packaging a phage genome are beginning to be better understood. Condensing DNA subjects it to high osmotic pressure, which has been suggested to provide the driving force for its ejection during infection. However, forces internal to a phage capsid cannot, alone, cause complete genome ejection into cells. Here, we describe the structure of the DNA inside mature phages and summarize the current models of genome ejection, both in vitro and in vivo .