Chapter 4 : Bacteriophage Evolution and the Role of Phages in Host Evolution

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Comparative analyses of phage genome sequences imply that a major component of phage evolution is large numbers of intrinsically very improbable events. In addition, there are comparable numbers of prophage sequences that are found in the genomic sequences of bacteria and, sometimes, archaea. There are stretches of sequence that match well, with abrupt transitions to regions with no detectable similarity or sometimes a different level of similarity. These transition points are considered the products of nonhomologous recombination events in the ancestry of one of the phages being compared; in this sense, they are fossils of past events in the history of the genome. It is believed that there are at least two factors that can restrict the horizontal flow of genes across the expanses of phage sequence space. Many of the beneficial genes carried by prophages appear to be morons, i.e., the genes that have entered the genome recently and are typically flanked by a transcription promoter and a terminator. The understanding of how phages evolve began in the late 1960s with the hetero duplex mapping of the chromosomes of phage lambda and some close relatives, showing that these molecules are mosaic with respect to each other. Genome sequences for such phages are just now becoming available, and the largest genome to date is 10 times as big as that of phage lambda, with a corresponding increase in gene number.

Citation: Hendrix R. 2005. Bacteriophage Evolution and the Role of Phages in Host Evolution, p 55-65. In Waldor M, Friedman D, Adhya S (ed), Phages. ASM Press, Washington, DC. doi: 10.1128/9781555816506.ch4
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Image of FIGURE 1

Hypothesis on the origin of the sequence around the end of the HK97 gene. (A) The DNA sequence crossing the ends of the HK97 gene is shown, with three frames of translation represented below. The N protein amino acid sequence is shown in the top translation frame and ends in the middle of the line. The corresponding part of the P22 gene region is shown at the top, with amino acid identities indicated in bold and underlined. The end of the 21 gene is shown at the bottom, with the termination codon near the right end of the line and identities indicated as described above. (B) The out-of-register nonhomologous recombination event that is hypothesized to have given rise to the HK97 sequence in this region is shown in the first reaction. The second reaction shows a hypothetical future deletion that would give this region of HK97 the appearance of having arisen through a single in-register nonhomologous recombination event.

Citation: Hendrix R. 2005. Bacteriophage Evolution and the Role of Phages in Host Evolution, p 55-65. In Waldor M, Friedman D, Adhya S (ed), Phages. ASM Press, Washington, DC. doi: 10.1128/9781555816506.ch4
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