Basic phage biology

Abstract

As discussed throughout this book, bacteriophages are viruses that only infect bacteria. They are like complex space ships (Fig. 1), each carrying its genome from one susceptible bacterial cell to another in which it can direct the production of more phages. Each phage particle (virion) contains its nucleic acid genome (DNA or RNA) enclosed in a protein or lipoprotein coat or capsid; the combined nucleic acid and capsid form the nucleocapsid. The target host for each phage is a specific group of bacteria. This group is often some subset of one species,1 but sometimes several related species can be infected by the same phage. Phages, like all viruses, are absolute parasites. While they carry all the information to direct their own reproduction in an appropriate host, they have no machinery for generating energy and no ribosomes for making proteins. They are the most abundant living entities on earth, found in very large numbers wherever their hosts live—in sewage and feces, in the soil, in deep thermal vents, and in natural bodies of water, as discussed in chapter 5. Their high level of specificity, long-term survivability, and ability to reproduce rapidly in appropriate hosts contribute to their maintaining a dynamic balance among the wide variety of bacterial species in any natural ecosystem. When no appropriate hosts are present, many phages can maintain their ability to infect for decades, unless damaged by external agents. Some phages have only a few thousand bases in their genome, while phage G, the largest sequenced to date, has 480,000 base pairs—as much as an average bacterium, though still lacking the genes for such essential bacterial machinery as ribosomes. Over 95% of the phages described in the literature to date belong to the Caudovirales (tailed phages; see chapter 4). Their virions are approximately half doublestranded DNA and half protein by mass, with icosahedral heads assembled from many copies of a specific protein or two; generally the corners are made up of pentamers of a protein, and the rest of each side is made up of hexamers of the same or a similar protein. The three main families are defined by their very distinct tail morphologies: 60% of the characterized phages are Siphoviridae, with long, flexible tails; 25% are Myoviridae, with double-layered, contractile tails; and 15% are Podoviridae, with short, stubby, tails. The latter may have some key infection proteins enclosed inside the head that can form a sort of extensible tail upon contact with the host, as shown most clearly for coliphage T7 (Molineux 2001). Archaea have their own set of infecting viruses, often called “archaephages.” Many of these have unusual, often pleiomorphic shapes that are unique to the Archaea, as discussed in chapter 4. However, many viruses identified to date for the Crenarchaeota kingdom of Archaea look like typical tailed bacteriophages (Prangishvili 2003); some of these are discussed in section 8.