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The cryptic prophage puzzle by Prof. Lindi Wahl.
Gene sequencing in bacteria has revealed an unexpected abundance of prophages, that is, DNA sequences from temperate viruses, integrated in the bacterial genome. Many of these prophages are cryptic and unable to induce lysis in their hosts. The frequency of cryptic prophages, however, is much higher than predicted if they were simply decaying by mutational degradation. What factors maintain prophage sequences at such high frequencies in bacterial genomes? Which genes are preferentially carried by cryptic prophages? We have used bioinformatics, mathematical modelling and computation to suggest some answers (and further questions!).