RM

Description

Restriction modification systems are the most abundant antiphage systems. They already have their own Wikipedia page

Molecular Mechanisms

Several reviews detail the molecular mechanisms of restriction-modification systems. For example in (N/A) :

"Bacterial restriction-modification (R-M) systems function as prokaryotic immune systems that attack foreign DNA entering the cell (N/A) . Typically, R-M systems have enzymes responsible for two opposing activities: a restriction endonuclease (REase) that recognizes a specific DNA sequence for cleavage and a cognate methyltransferase (MTase) that confers protection from cleavage by methylation of adenine or cytosine bases within the same recognition sequence. REases recognize ‘non-self’ DNA (Figure 1), such as that of phage and plasmids, by its lack of characteristic modification within specific recognition sites (N/A) . Foreign DNA is then inactivated by endonucleolytic cleavage. Generally, methylation of a specific cytosine or adenine within the recognition sequence confers protection from restriction. Host DNA is normally methylated by the MTase following replication, whereas invading non-self DNA is not."

Figure 1. The function of R-M systems, as illustrated by Type I R-M enzymes. From (N/A) .

Example of genomic structure

A total of 5 subsystems have been described for the RM system.

Here is some examples found in the RefSeq database:

The RM_Type_I system in Tessaracoccus flavescens (GCF_001998865.1, NZ_CP019607) is composed of 3 proteins Type_I_MTases (WP_237268350.1) Type_I_S (WP_077346826.1) Type_I_REases (WP_237268249.1)

The RM_Type_II system in Aeromonas caviae (GCF_000783775.2, NZ_CP026055) is composed of 2 proteins Type_II_MTases (WP_042865101.1) Type_II_REases (WP_042865102.1)

The RM_Type_IIG system in Microbacterium wangchenii (GCF_004564355.1, NZ_CP038266) is composed of 1 protein: Type_IIG (WP_135067980.1)

The RM_Type_III system in Sphingobacterium spiritivorum (GCF_016725325.1, NZ_CP068083) is composed of 2 proteins Type_III_REases (WP_139420208.1) Type_III_MTases (WP_139420206.1)

The RM_Type_IV system in Halobaculum rubrum (GCF_019880225.1, NZ_CP082284) is composed of 1 protein: Type_IV_REases (WP_222915961.1)

Distribution of the system among prokaryotes

Structure

Experimental validation

Many RM systems defend against many phages, as such we cannot map this correctly.