Basic Phage Biology

BURTON GUTTMAN, RAUL RAYA, AND ELIZABETH KUTTER

Bacteriophages. Biology and Applications.

CRC Press

Lugar: Boca Raton, Florida, USA; Año: 2005; p. 29 - 66

1. Introduction  1.1.  The nature of bacteriophages.   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 double-stranded 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.   The ten families of tailless phages described to date have very few members each.  They are differentiated by shape (rods, spherical, lemon-shaped or pleiomorphic); by whether or not they are enveloped in a lipid coat; by having double- or single-stranded DNA or RNA genomes, segmented or not; and by being released by lysis of their host cell or continually extruded from the cell surface.  Their general structures, sizes, nucleic acids, adsorption sites and modes of release are all described in detail in chapter 4.  The basic infection processes of the Inoviridae, Leviviridae, Microviridae and Tectiviridae are further described in section 7 below. Relatively little is known about most of the others, which have generally been isolated under extremes of pH, temperature or salinity and have only been observed in Archaea.   Phages can also be divided into two classes based on lifestyle: virulent or temperate. Virulent phages can only multiply by means of a lytic cycle; the phage virion adsorbs to the surface of a host cell and injects its genome, which takes over much of host metabolism and sets up molecular machinery for making more phages.  The host cell then lyses minutes or hours later, liberating many new phage.  Temperate phages, in contrast, have a choice of reproductive modes when they infect a new host cell.  Sometimes the infecting phage initiates a lytic cycle, resulting in lysis of the cell and release of new phage, as above.  Alternatively, the infecting phage may initiate a lysogenic cycle; instead of replicating, the phage genome assumes a quiescent state called a prophage, often integrated into the host genome but sometimes maintained as a plasmid.  It remains in this condition indefinitely, being replicated as its host cell reproduces to make a clone of cells all containing prophages; these cells are said to be lysogenized or lysogenic (that is, capable of producing lysis) because occasionally one of these prophages comes out of its quiescent condition and enters the lytic cycle. The factors affecting the choice to lysogenize or to reenter into a lytic cycle are described below.  As discussed by (Levin 1985), the lysogenic state is highly evolved, requiring coevolution of virus and host that presumably reflects various advantages to both. Temperate phages can help protect their hosts from infection by other phages and can lead to significant changes in the properties of their hosts, including restriction systems and resistance to antibiotics and other environmental insults. As discussed in chapter 9, they may even convert the host to a pathogenic phenotype, as in diphtheria or enterohemorrhagic E. coli (EHEC) strains.  Bacteriophages lambda (l), P1, Mu and various dairy phages are among the best-studied temperate phages.  (Note that mutation of certain genes can create virulent derivatives of temperate phages; these are still considered members of their temperate phage families.)   The larger virulent phages generally encode many host-lethal proteins. Some of them disrupt host replication, transcription, or translation; they may also degrade the host genome, destroy or redirect certain host enzymes, or alter the bacterial membrane.  The temperate phages, in contrast, generally do much less restructuring of the host, and they carry few if any host-lethal proteins that would need to be kept under tight control during long-term lysogeny.  They always encode a repressor protein, which acts at a few operator sites to block transcription of other phage genes.  This repressor may be the only phage-encoded protein produced during the lysogenic state, but often a few other genes that may be beneficial to host survival are also expressed from the prophages.  The repressor also blocks lytic infection by other phages of the same immunity group—that is, other phages whose genes can be regulated by the same repressor.  In this way, a temperate phage generally protects its host bacterium from infection by several kinds of phages. [1] It is well to keep in mind that the concept of “species” for asexual organisms such as bacteria is quite different from the concept of a sexual species, which can generally be defined as the group of individuals that share a common gene pool.  Asexual “species” must simply be collections of organisms with similar features, probably maintained by continuous selection for adaptation to a particular niche.