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Chapter 10 : Phages

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Abstract:

species are small, aerobic, gram-negative betaproteobacteria which are capable of infecting a broad range of host species. The first reported isolation of a phage dates back to 1935, when a phage was isolated from river water in the Ukraine by researchers at the USSR Academy of Sciences. Until recently, nearly all of the published work on phages has been performed by Russian investigators. Much of this work was motivated by the potential use of phages for antimicrobial therapy, particularly for diseases such as whooping cough, in which the microbe is exposed on the respiratory epithelial surface. Tropism switching by phage BPP-1 is mediated by a variability-generating cassette (VGC) carried in the phage genome. Downstream from , there is a second copy of the 134-bp repeat, called the template repeat (TR), which is approximately 90% identical to variable repeat (VR). The properties of the homing reaction can be elucidated genetically by the classical technique of haplotype mapping. The observation that the transmission of sequence information is characterized by such flexible mosaicism has important mechanistic consequences. The role of diversity-generating retroelements (DGRs) in phages is to introduce diversity into the phage tail fiber protein that binds to bacterial receptors. It is tempting to speculate that the adaptation of mobility to generate protein variability has allowed DGRs to evolve an alternative strategy as stable and beneficial components of host genomes.

Citation: Hodes A, Doulatov S, Miller J. 2005. Phages, p 206-222. In Waldor M, Friedman D, Adhya S (ed), Phages. ASM Press, Washington, DC. doi: 10.1128/9781555816506.ch10

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Type III Secretion System
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Figures

Image of FIGURE 1
FIGURE 1

BPP-1 virion morphology. The images show negative-stain transmission electron micrographs of an intact phage particle (A), an isolated tail (side view) with partially dissociated tail fibers (B), and isolated tails with tail fibers (top view) (C and D).

Citation: Hodes A, Doulatov S, Miller J. 2005. Phages, p 206-222. In Waldor M, Friedman D, Adhya S (ed), Phages. ASM Press, Washington, DC. doi: 10.1128/9781555816506.ch10
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Image of FIGURE 2
FIGURE 2

Predicted phage coding sequences. Arrows represent predicted coding sequences (49 total) encoding proteins of >7 kDa. Most predicted coding sequences are named with the prefix bbp (for phage). The genome is organized in a major leftward unit of transcription, which includes to , and a rightward unit of transcription, containing I through . Functional assignments for several gene clusters are indicated. For detailed information, see reference .

Citation: Hodes A, Doulatov S, Miller J. 2005. Phages, p 206-222. In Waldor M, Friedman D, Adhya S (ed), Phages. ASM Press, Washington, DC. doi: 10.1128/9781555816506.ch10
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Image of FIGURE 3
FIGURE 3

Tropism switching by bacteriophage. Specificities and tropism switching frequencies are depicted above the BvgAS-mediated phase transition. Bvg-regulated gene products, including adhesins and toxins in the Bvg phase and lipopolysaccharide and flagellum in the Bvg phase, are depicted schematically.

Citation: Hodes A, Doulatov S, Miller J. 2005. Phages, p 206-222. In Waldor M, Friedman D, Adhya S (ed), Phages. ASM Press, Washington, DC. doi: 10.1128/9781555816506.ch10
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Image of FIGURE 4
FIGURE 4

Cross-neutralization of ϕ3865 and ϕ214 with antisera against ϕ3865 (A) and ϕ214 (B), measured as PFU remaining as a function of incubation time. Reprinted from reference (in Russian) with permission of the publisher.

Citation: Hodes A, Doulatov S, Miller J. 2005. Phages, p 206-222. In Waldor M, Friedman D, Adhya S (ed), Phages. ASM Press, Washington, DC. doi: 10.1128/9781555816506.ch10
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Image of FIGURE 5
FIGURE 5

Components of the VGC. The 3′ portion of is expanded and the 134-bp VR sequence is underlined.Variable bases (in bold; 23 total) occur in the first two positions of a codon and correspond to adenine residues in TR ( ).

Citation: Hodes A, Doulatov S, Miller J. 2005. Phages, p 206-222. In Waldor M, Friedman D, Adhya S (ed), Phages. ASM Press, Washington, DC. doi: 10.1128/9781555816506.ch10
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Image of FIGURE 6
FIGURE 6

Nucleotide sequence alignment of VRs from various BPP, BMP, and BIP phages. All sequences are aligned with the VR of BPP-1 (top) and with TR (middle). Nucleotides in highly variable positions are shown in bold. For an expanded data set and the pedigree of strains, see reference .

Citation: Hodes A, Doulatov S, Miller J. 2005. Phages, p 206-222. In Waldor M, Friedman D, Adhya S (ed), Phages. ASM Press, Washington, DC. doi: 10.1128/9781555816506.ch10
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Image of FIGURE 7
FIGURE 7

In wild-type (wt) BPP-1, information is transferred unidirectionally from TR to VR and is accompanied by adenine-specific mutagenesis (white lines). Replacement of the 9-bp sequence at the 3′ end of VR (IMH) with the corresponding TR sequence (asterisk) abolishes the variation in VR (BPP-3′TR), whereas the introduction of an IMH site into TR generates de novo variability in TR (BPP-3′VR).

Citation: Hodes A, Doulatov S, Miller J. 2005. Phages, p 206-222. In Waldor M, Friedman D, Adhya S (ed), Phages. ASM Press, Washington, DC. doi: 10.1128/9781555816506.ch10
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Image of FIGURE 8
FIGURE 8

Schematic of the proposed diversity-generating mechanism. Asterisks represent heteroduplexes formed during complementary base pairing between a mutagenized cDNA and genomic DNA. See the text for details.

Citation: Hodes A, Doulatov S, Miller J. 2005. Phages, p 206-222. In Waldor M, Friedman D, Adhya S (ed), Phages. ASM Press, Washington, DC. doi: 10.1128/9781555816506.ch10
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Image of FIGURE 9
FIGURE 9

Phylogenetic tree of DGRs and other classes of retroelements. GenBank accession numbers are shown. G2, group II introns; Rpls, mitochondrial retroplasmids; Rtn, retrons;NLTR,non-LTR elements;LTR,LTR retroelements;Telo, telomerases; PLE, -like elements. RT domains were analyzed by the neighbor-joining algorithm of PHYLIP 3.6b with 1,000 bootstrap samplings, which are expressed as percentages. DGRs form a well-defined clade with 92% bootstrap support.

Citation: Hodes A, Doulatov S, Miller J. 2005. Phages, p 206-222. In Waldor M, Friedman D, Adhya S (ed), Phages. ASM Press, Washington, DC. doi: 10.1128/9781555816506.ch10
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Image of FIGURE 10
FIGURE 10

Nine putative DGRs are shown for comparison to the phage DGR. All DGRs include an ORF that contains a 103- to 190-bp VR (gray arrows) which is always located at the C terminus, a spacer region which in some cases contains an ortholog, and a TR (black arrows) of equal length to the VR in close proximity to an RT domain.

Citation: Hodes A, Doulatov S, Miller J. 2005. Phages, p 206-222. In Waldor M, Friedman D, Adhya S (ed), Phages. ASM Press, Washington, DC. doi: 10.1128/9781555816506.ch10
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