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Updated: Mar 28, 2026

In Vitro Directed Evolution of a Restriction Endonuclease with More Stringent Specificity
Published on: March 25, 2020
Temporal dynamics of methyltransferase and restriction endonuclease accumulation in individual cells after
Natalia Morozova1, Anton Sabantsev1, Ekaterina Bogdanova2
1Peter the Great St. Petersburg Polytechnic University, St. Petersburg, 195251, Russia.
Abstract:
Type II restriction-modification (R-M) systems encode a restriction endonuclease that cleaves DNA at specific sites, and a methyltransferase that modifies same sites protecting them from restriction endonuclease cleavage. Type II R-M systems benefit bacteria by protecting them from bacteriophages. Many type II R-M systems are plasmid-based and thus capable of horizontal transfer. Upon the entry of such plasmids into a naïve host with unmodified genomic recognition sites, methyltransferase should be synthesized first and given sufficient time to methylate recognition sites in the bacterial genome before the toxic restriction endonuclease activity appears. Here, we directly demonstrate a delay in restriction endonuclease synthesis after transformation of Escherichia coli cells with a plasmid carrying the Esp1396I type II R-M system, using single-cell microscopy. We further demonstrate that before the appearance of the Esp1396I restriction endonuclease the intracellular concentration of Esp1396I methyltransferase undergoes a sharp peak, which should allow rapid methylation of host genome recognition sites. A mathematical model that satisfactorily describes the observed dynamics of both Esp1396I enzymes is presented. The results reported here were obtained using a functional Esp1396I type II R-M system encoding both enzymes fused to fluorescent proteins. Similar approaches should be applicable to the studies of other R-M systems at single-cell level.
Insights
Bacteria use restriction-modification systems to defend against phages. This study shows that the methyltransferase is produced before the toxic restriction enzyme, protecting the bacterial genome during plasmid transfer.
Area of Science:
- Molecular Biology
- Genetics
- Microbiology
Background:
- Type II restriction-modification (R-M) systems protect bacteria from bacteriophages.
- These systems involve a restriction endonuclease and a methyltransferase.
- Plasmid-based R-M systems can transfer horizontally between bacteria.
Purpose of the Study:
- To investigate the temporal expression of enzymes in the Esp1396I Type II R-M system.
- To confirm the hypothesis that methyltransferase synthesis precedes endonuclease activity during plasmid transformation.
- To understand the protective mechanism of R-M systems during horizontal gene transfer.
Main Methods:
- Single-cell microscopy was used to observe enzyme dynamics in real-time.
- Escherichia coli cells were transformed with a plasmid encoding the Esp1396I R-M system.
- Fluorescent proteins were fused to both the methyltransferase and endonuclease for visualization.
- A mathematical model was developed to describe enzyme kinetics.
Main Results:
- A delay in restriction endonuclease synthesis was directly observed after plasmid transformation.
- A transient peak in intracellular methyltransferase concentration preceded endonuclease appearance.
- The observed dynamics support a mechanism for rapid host genome methylation.
- The mathematical model accurately described the experimental data.
Conclusions:
- The Esp1396I R-M system exhibits a temporal separation of enzyme synthesis, prioritizing host protection.
- This sequential expression ensures bacterial genome methylation before the onset of potentially lethal restriction.
- Single-cell approaches are valuable for studying R-M system dynamics.
- The findings have implications for understanding bacterial defense mechanisms and R-M system evolution.
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