prophage

Edge evidence

• prophage enables lysogeny RO:0002327

  Prophage carriage is the genomic state realized during lysogeny.

  • DOI:10.1128/MMBR.67.2.238-276.2003 Canchaya et al. document widespread prophage maintenance in sequenced bacterial genomes.
• prophage contributes to host phenotype RO:0002326

  Prophage-encoded genes can alter host virulence or fitness (lysogenic conversion).

  • DOI:10.1038/ismej.2017.16 Howard-Varona et al. review host-phenotype effects of lysogeny in nature.
• prophage integrates into bacterial chromosome

  Temperate prophages canonically integrate into the host chromosome (though some persist extrachromosomally).

  • DOI:10.1038/s41586-023-06376-y Temperate phages remain dormant as prophages integrated into the host genome and passed to host progeny.
• CI master repressor represses lytic gene expression

  Lysogeny is maintained by a phage-encoded CI repressor that binds the lysis promoter PR to block lytic gene expression.

  • DOI:10.1038/s41586-023-06376-y cI repressor binds the lysis promoter (PR) to block lytic gene expression.
• DNA damage / replication stress activates RecA-LexA SOS response RO:0002213

  DNA damage / replication stress generates ssDNA that triggers the RecA-LexA SOS response.

  • DOI:10.1073/pnas.2407832121 Replication inhibition creates ssDNA gaps that trigger the classical SOS response.
• RecA* nucleoprotein filament promotes autocleavage of LexA repressor

  Activated RecA* promotes LexA autoproteolysis, de-repressing the SOS regulon.

  • DOI:10.1128/aem.01716-22 RecA* activation induces LexA autoproteolysis; SOS response is mediated by RecA and LexA.
• RecA* nucleoprotein filament promotes autocleavage of CI master repressor

  RecA* stimulates self-cleavage/inactivation of the phage CI repressor, de-repressing lysis and triggering induction.

  • DOI:10.1038/s41586-023-06376-y Host RecA activation leads to autoproteolysis and inactivation of cI, de-repressing lysis.
• CI master repressor prevents prophage induction RO:0002212

  While intact, the CI repressor maintains lysogeny and prevents prophage induction; its inactivation triggers induction.

  • DOI:10.1038/s41586-023-06376-y CI repression must be relieved (cI inactivation) to de-repress lysis and drive prophage induction.
• phage-plasmid enables extrachromosomal prophage maintenance RO:0002327

  Phage-plasmids are temperate phages maintained extrachromosomally, so prophages need not be integrated.

  • DOI:10.1038/s41467-024-45757-3 Phage-plasmids are temperate phages maintained extrachromosomally as low-copy-number episomal forms.