Marko Djordjevic1*, Lidija Zivkovic2, and Magdalena Djordjevic2
1Faculty of Biology, University of Belgrade, Serbia
2Institute of Physics Belgrade, National Institute of the Republic of Serbia, Serbia
dmarko [at] bio.bg.ac.rs
Abstract
Restriction-modification (R-M) systems consist of genes encoding restriction enzyme and methyltransferase, often co-expressed with a specialized regulator (C protein). These systems tightly regulate their function through complex cooperative positive and negative feedback loops. R-M systems defend bacterial cells against invasion by foreign DNA, such as plasmids and bacteriophages, consequently modulating horizontal gene transfer, including transmitting pathogenic genes like antibiotic resistance determinants or virulence factors. Recent experiments have directly confirmed that the R-to-M ratio significantly impacts bacteriophage infection efficiency, rendering a subset of cells more susceptible to horizontal gene transfer.
To understand the regulatory mechanisms of R-M systems, we develop a mathematical model tightly constrained by biophysical measurements of system interaction parameters. Despite the technical complexity arising from C protein forming dimer and tetramer complexes, we analytically derive a system stability diagram that can be easily modified for various R-M system architectures. A single free parameter determines the bistability of the system, which we infer from experimental measurements across three different architectures. Surprisingly, while one class exhibits monostability, the other two demonstrate bistability.
Our model successfully explains the experimental data and reveals that modulation of the barrier to horizontal gene transfer can occur through distinct mechanisms. Bistability leads to long-lasting states susceptible to acquiring pathogenic genes, whereas stochastic fluctuations only transiently lower the transfer barrier. The precise implications of these differences for bacterial pathogenicity and evolution require further investigation. However, we propose that R-M systems capable of bistable gene expression may give rise to genetically distinct bacterial populations with potentially diverse phenotypes concerning pathogenicity and antibiotic resistance.
Keywords: restriction-modification systems; nonlinear dynamics modeling; biophysical modeling; bistability; antibiotic resistance;
Acknowledgments: This work is supported by The Science Fund of the Republic of Serbia (Grant no. 7750294, q-bioBDS).
