Understanding key features of bacterial restriction-modification systems through quantitative modeling

BMC Syst Biol. 2017 Feb 24;11(Suppl 1):377. doi: 10.1186/s12918-016-0377-x.


Background: Restriction-modification (R-M) systems are rudimentary bacterial immune systems. The main components include restriction enzyme (R), which cuts specific unmethylated DNA sequences, and the methyltransferase (M), which protects the same DNA sequences. The expression of R-M system components is considered to be tightly regulated, to ensure successful establishment in a naïve bacterial host. R-M systems are organized in different architectures (convergent or divergent) and are characterized by different features, i.e. binding cooperativities, dissociation constants of dimerization, translation rates, which ensure this tight regulation. It has been proposed that R-M systems should exhibit certain dynamical properties during the system establishment, such as: i) a delayed expression of R with respect to M, ii) fast transition of R from "OFF" to "ON" state, iii) increased stability of the toxic molecule (R) steady-state levels. It is however unclear how different R-M system features and architectures ensure these dynamical properties, particularly since it is hard to address this question experimentally.

Results: To understand design of different R-M systems, we computationally analyze two R-M systems, representative of the subset controlled by small regulators called 'C proteins', and differing in having convergent or divergent promoter architecture. We show that, in the convergent system, abolishing any of the characteristic system features adversely affects the dynamical properties outlined above. Moreover, an extreme binding cooperativity, accompanied by a very high dissociation constant of dimerization, observed in the convergent system, but absent from other R-M systems, can be explained in terms of the same properties. Furthermore, we develop the first theoretical model for dynamics of a divergent R-M system, which does not share any of the convergent system features, but has overlapping promoters. We show that i) the system dynamics exhibits the same three dynamical properties, ii) introducing any of the convergent system features to the divergent system actually diminishes these properties.

Conclusions: Our results suggest that different R-M architectures and features may be understood in terms of constraints imposed by few simple dynamical properties of the system, providing a unifying framework for understanding these seemingly diverse systems. We also provided predictions for the perturbed R-M systems dynamics, which may in future be tested through increasingly available experimental techniques, such as re-engineering R-M systems and single-cell experiments.

Keywords: Bacterial immune systems; Biophysical modeling; Gene expression dynamics; Restriction-modification; Transcription regulation.

MeSH terms

  • DNA Restriction-Modification Enzymes / biosynthesis
  • DNA Restriction-Modification Enzymes / chemistry
  • DNA Restriction-Modification Enzymes / metabolism*
  • Deoxyribonucleases, Type II Site-Specific / metabolism
  • Escherichia coli / enzymology*
  • Escherichia coli / genetics
  • Escherichia coli / immunology
  • Escherichia coli / metabolism
  • Models, Biological*
  • Protein Multimerization
  • Protein Structure, Quaternary


  • DNA Restriction-Modification Enzymes
  • Deoxyribonucleases, Type II Site-Specific
  • GATATC-specific type II deoxyribonucleases