Physical model of the immune response of bacteria against bacteriophage through the adaptive CRISPR-Cas immune system

Phys Biol. 2013 Apr;10(2):025004. doi: 10.1088/1478-3975/10/2/025004. Epub 2013 Mar 15.


Bacteria and archaea have evolved an adaptive, heritable immune system that recognizes and protects against viruses or plasmids. This system, known as the CRISPR-Cas system, allows the host to recognize and incorporate short foreign DNA or RNA sequences, called 'spacers' into its CRISPR system. Spacers in the CRISPR system provide a record of the history of bacteria and phage coevolution. We use a physical model to study the dynamics of this coevolution as it evolves stochastically over time. We focus on the impact of mutation and recombination on bacteria and phage evolution and evasion. We discuss the effect of different spacer deletion mechanisms on the coevolutionary dynamics. We make predictions about bacteria and phage population growth, spacer diversity within the CRISPR locus, and spacer protection against the phage population.

Publication types

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

MeSH terms

  • Bacteriophages / genetics
  • Bacteriophages / growth & development
  • Bacteriophages / immunology*
  • Base Sequence
  • Biological Evolution
  • Models, Biological
  • Monte Carlo Method
  • Mutation
  • RNA, Bacterial / genetics
  • Recombination, Genetic
  • Streptococcus thermophilus / genetics
  • Streptococcus thermophilus / immunology*
  • Streptococcus thermophilus / virology*


  • RNA, Bacterial