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Chapter 2 : Introduction to Bacteriophage Biology and Diversity

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Abstract:

Bacteriophages are a driver of global geochemical cycles, and are a reservoir of the greatest genetic diversity on earth. The study of phages played a central role in some of the most significant discoveries in the biological sciences, from the identification of DNA as the genetic material to the deciphering of the genetic code to the development of molecular recombinant technology. This chapter focuses on basic aspects of phage biology and phage classification, and on the abundance and diversity of these organisms. The International Committee on the Taxonomy of Viruses (ICTV) classification method is currently being reevaluated, since it ignores the vast amount of available genome sequence data which occasionally causes contradictory issues. In essence, phages carry their genomes from one susceptible bacterial cell to another, in which they direct the production of progeny phages. The target host for each phage is a specific group of bacteria: this group is often a subset of one species, but several related species can sometimes be infected by the same phage. The bacteriophage infection cycle follows a number of tightly programmed steps, of which the efficiency and timing depend strongly on the metabolic state of the host. In an analysis of marine viromes across four oceanic regions, no fewer than 129,000 genotypes were predicted in the viral metagenome of British Columbian coastal waters.

Citation: Pieter-Jan C, Rob L. 2010. Introduction to Bacteriophage Biology and Diversity, p 11-29. In Sabour P, Griffiths M (ed), Bacteriophages in the Control of Food-and Waterborne Pathogens. ASM Press, Washington, DC. doi: 10.1128/9781555816629.ch2

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Image of FIGURE 1
FIGURE 1

Transmission electron microscopic recordings of negatively stained phage particles. Phages A and B are short-tailed phage C has a flexible tail and belongs to the The myovirus on the right is displayed with noncontracted (D) and contracted (E) tail. The scale bar represents 100 nm; the different parts of the myovirus particle are indicated on the right.

Citation: Pieter-Jan C, Rob L. 2010. Introduction to Bacteriophage Biology and Diversity, p 11-29. In Sabour P, Griffiths M (ed), Bacteriophages in the Control of Food-and Waterborne Pathogens. ASM Press, Washington, DC. doi: 10.1128/9781555816629.ch2
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Image of FIGURE 2
FIGURE 2

Schematic overview of the infection cycle of virulent bacteriophages. The bacteriophage adsorbs to the host cell. Immediately after internalization of the genome, the first phage proteins involved in transition from host directed to phage-directed metabolism are produced. Next, replication of the bacteriophage genome takes place. Afterwards the new phage particles are assembled and the genome is packed inside. Finally, the new virions are released. The phage shown in this scheme has the characteristics of a member of the phages with an icosahedral head and a contractile tail.

Citation: Pieter-Jan C, Rob L. 2010. Introduction to Bacteriophage Biology and Diversity, p 11-29. In Sabour P, Griffiths M (ed), Bacteriophages in the Control of Food-and Waterborne Pathogens. ASM Press, Washington, DC. doi: 10.1128/9781555816629.ch2
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Image of FIGURE 3
FIGURE 3

After circularization of phage DNA upon infection, temperate phages make a choice between a lytic or a lysogenic cycle. In the lytic cycle, new phage particles are produced and released upon lysis of the host cell. If the phage enters a lysogenic stage, the phage DNA in most cases enters the bacterial chromosome and replicates along with the host DNA, and a stable relationship is established. Occasionally, the prophage may excise from the host genome by another recombination event and a lytic cycle is initiated.

Citation: Pieter-Jan C, Rob L. 2010. Introduction to Bacteriophage Biology and Diversity, p 11-29. In Sabour P, Griffiths M (ed), Bacteriophages in the Control of Food-and Waterborne Pathogens. ASM Press, Washington, DC. doi: 10.1128/9781555816629.ch2
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Image of FIGURE 4
FIGURE 4

Map of the critical regulatory region of phage λ, controlling the switch between lytic and lysogenic life cycles. The proteins CII and CIII bind to promoting transcription of the I gene. The DNA-binding CI protein represses various operator sites and prevents formation of the N protein, which is required for expression of late genes of the lytic cycle. CI also promotes its own transcription by binding to These processes are in competition with transcription of genes and (not depicted) from which are required for lytic growth. Cro and CI compete for binding sites in the complex promoter/operator site that includes both and and determine in this way the decision between lytic and lysogenic growth.

Citation: Pieter-Jan C, Rob L. 2010. Introduction to Bacteriophage Biology and Diversity, p 11-29. In Sabour P, Griffiths M (ed), Bacteriophages in the Control of Food-and Waterborne Pathogens. ASM Press, Washington, DC. doi: 10.1128/9781555816629.ch2
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Image of FIGURE 5
FIGURE 5

(A) Classical single-step growth curve. After synchronized infection of host cells, the cells are diluted (to avoid infection by newly released phage) and samples are plated at various times to determine An infective center is either a single phage particle or an infected cell that lyses on the plate to produce a plaque. Initially, the number of plaques remains constant for a time (the latent period), rises sharply at a certain moment, and levels off as each host cell has liberated its progeny phage. The ratio between the numbers of infected centers before and after lysis is the burst size. (B) Differences in plaque morphologies between lytic and temperate phages. Shown in this picture are lytic phage ε15 (top) and temperate phage LKR3 (bottom).

Citation: Pieter-Jan C, Rob L. 2010. Introduction to Bacteriophage Biology and Diversity, p 11-29. In Sabour P, Griffiths M (ed), Bacteriophages in the Control of Food-and Waterborne Pathogens. ASM Press, Washington, DC. doi: 10.1128/9781555816629.ch2
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Image of FIGURE 6
FIGURE 6

Schematic overview of the genome build-up of the (48,502 bp), T7 (39,937 bp), and T4 (168,904 bp), all infecting The genomes are divided into functional blocks, arranged head to tail for reasons of simplicity. For lambda and T7, the timing of gene expression is indicated with arrows. In contrast to these two phages, the early and late transcription units of T4 (and related phages) are not clearly separated but are interdigitated (e.g., late genes and and the middle gene . The direction of T4 transcription does not unambiguously distinguish between early and late transcription, and in many cases early and late genes are cotranscribed ( ).

Citation: Pieter-Jan C, Rob L. 2010. Introduction to Bacteriophage Biology and Diversity, p 11-29. In Sabour P, Griffiths M (ed), Bacteriophages in the Control of Food-and Waterborne Pathogens. ASM Press, Washington, DC. doi: 10.1128/9781555816629.ch2
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