Integration-dependent bacteriophage immunity provides insights into the evolution of genetic switches

Mol Cell. 2013 Jan 24;49(2):237-48. doi: 10.1016/j.molcel.2012.11.012. Epub 2012 Dec 13.


Genetic switches are critical components of developmental circuits. Because temperate bacteriophages are vastly abundant and greatly diverse, they are rich resources for understanding the mechanisms and evolution of switches and the molecular control of genetic circuitry. Here, we describe a new class of small, compact, and simple switches that use site-specific recombination as the key decision point. The phage attachment site attP is located within the phage repressor gene such that chromosomal integration results in removal of a C-terminal tag that destabilizes the virally encoded form of the repressor. Integration thus not only confers prophage stability but also is a requirement for lysogenic establishment. The variety of these self-contained integration-dependent immunity systems in different genomic contexts suggests that these represent ancestral states in switch evolution from which more-complex switches have evolved. They also provide a powerful toolkit for building synthetic biological circuits.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Amino Acid Sequence
  • Amino Acid Substitution
  • Base Sequence
  • Binding Sites
  • Conserved Sequence
  • Evolution, Molecular
  • Gene Expression Regulation, Viral*
  • Integrases / genetics
  • Integrases / metabolism
  • Integrases / physiology
  • Lysogeny
  • Microbial Viability
  • Models, Genetic
  • Molecular Sequence Data
  • Mycobacteriophages / genetics*
  • Mycobacteriophages / physiology
  • Mycobacterium smegmatis / growth & development
  • Mycobacterium smegmatis / virology*
  • Promoter Regions, Genetic
  • Prophages / genetics*
  • Prophages / physiology
  • Repressor Proteins / genetics
  • Repressor Proteins / metabolism
  • Repressor Proteins / physiology
  • Sequence Analysis, DNA
  • Viral Proteins / genetics
  • Viral Proteins / metabolism
  • Viral Proteins / physiology


  • Repressor Proteins
  • Viral Proteins
  • Integrases