Chapter 29 : A Plethora of Putative Phages and Prophages

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Several facts enticed the author to look beyond for undocumented prophages in other bacterial genome sequences. At the beginning the author was very uncertain about whether there would be any interest in prophages or, on the other hand, whether the prophage abundance he was finding was considered to already be known and thus boring. In addition to fully intact prophages, many bacterial genomes harbor "defective" prophages that have suffered deletions of genes essential for full phage functionality. The prophages, whose genomic locations are shown in this chapter, are in fact very instructive cases. A curious observation regarding the prophages is that the genome-wide screen of Lawley and others for genes that are required for long-term systemic infection of the mouse was answered by mutations in (among many others) genes that encode virion assembly proteins in five of the above prophages. The remaining possibly phage-related genes in the LT2 chromosome consist of a few other fragmentary integrase-like sequences and phage lysis-like genes. These could be the remains of otherwise essentially completely deleted prophages, but the former could also be from other types of mobile elements. Another interesting feature that emerged from early prophage surveys was the fact that different isolates of the same bacterial species often have quite different prophage contents, indicating that prophages are coming and going rather quickly on the overall evolutionary scale.

Citation: Casjens S. 2011. A Plethora of Putative Phages and Prophages, p 291-306. In Maloy S, Hughes K, Casadesús J (ed), The Lure of Bacterial Genetics. ASM Press, Washington, DC. doi: 10.1128/9781555816810.ch29
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Image of FIGURE 1

Prophages in the serovar Typhimurium LT2 chromosome. The LT2 chromosome is represented by the circle and the prophages are shown as expanded regions on the outside; Def1–4 are the four defective prophages. Gene locus tag names are given on the outside for the genes at each end of the prophage elements. A scale in mbp is shown by ticks that cross the circle. Ticks inside the circle denote the prophage end adjacent to the integrase gene (if this gene is present), and the native gene into which the prophage integrated is given inside the circle.

Citation: Casjens S. 2011. A Plethora of Putative Phages and Prophages, p 291-306. In Maloy S, Hughes K, Casadesús J (ed), The Lure of Bacterial Genetics. ASM Press, Washington, DC. doi: 10.1128/9781555816810.ch29
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Image of FIGURE 2

Gifsy-1 prophage excision. The Gifsy-1 prophage is shown as an open rounded rectangle with the identical sequences at the two ends of the prophage aligned vertically at the bottom (only one strand, 5’ to 3’ left to right, is shown). Translation (of the strand not shown) is right to left of the gene below and the putative orphan N-terminal fragment above (the translated regions are shown in bold). Two regions of identity between the two prophage ends (14 bp on the left and 13 bp on the right) are indicated by thin horizontal lines between the two sequences. Excisive and integrative recombination has been reported to occur between the left 14-bp regions which is the site ( ); such a recombination event during integration or excision regenerates an intact gene that encodes a protein with unchanged amino acid sequence.

Citation: Casjens S. 2011. A Plethora of Putative Phages and Prophages, p 291-306. In Maloy S, Hughes K, Casadesús J (ed), The Lure of Bacterial Genetics. ASM Press, Washington, DC. doi: 10.1128/9781555816810.ch29
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Image of FIGURE 3

Comparison of serovar Typhimurium LT2 and serovar Choleraesuis SC-67 Gifsy-2 prophages. The matrix comparison was performed with DNA Strider ( ) using a scanning window of 17 identities per 23 bp. Above, the phage lambda-like transcription pattern of Gifsy-2 is shown along with the locations of some of the gene clusters.

Citation: Casjens S. 2011. A Plethora of Putative Phages and Prophages, p 291-306. In Maloy S, Hughes K, Casadesús J (ed), The Lure of Bacterial Genetics. ASM Press, Washington, DC. doi: 10.1128/9781555816810.ch29
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