Conflicts targeting epigenetic systems and their resolution by cell death: novel concepts for methyl-specific and other restriction systems

Abstract

Epigenetic modification of genomic DNA by methylation is important for defining the epigenome and the transcriptome in eukaryotes as well as in prokaryotes. In prokaryotes, the DNA methyltransferase genes often vary, are mobile, and are paired with the gene for a restriction enzyme. Decrease in a certain epigenetic methylation may lead to chromosome cleavage by the partner restriction enzyme, leading to eventual cell death. Thus, the pairing of a DNA methyltransferase and a restriction enzyme forces an epigenetic state to be maintained within the genome. Although restriction enzymes were originally discovered for their ability to attack invading DNAs, it may be understood because such DNAs show deviation from this epigenetic status. DNAs with epigenetic methylation, by a methyltransferase linked or unlinked with a restriction enzyme, can also be the target of DNases, such as McrBC of Escherichia coli, which was discovered because of its methyl-specific restriction. McrBC responds to specific genome methylation systems by killing the host bacterial cell through chromosome cleavage. Evolutionary and genomic analysis of McrBC homologues revealed their mobility and wide distribution in prokaryotes similar to restriction-modification systems. These findings support the hypothesis that this family of methyl-specific DNases evolved as mobile elements competing with specific genome methylation systems through host killing. These restriction systems clearly demonstrate the presence of conflicts between epigenetic systems.

Figure 1.

Action of a Type II restriction–modification system. (A) Restriction enzyme and modification enzyme. The modification enzyme protects the restriction enzyme targets through DNA methylation. (B) Attack on incoming DNA lacking proper methylation. (C) Enforcement of an epigenetic state. After loss of the restriction–modification gene complex or imbalance between restriction and modification, DNA methylation decreases. The restriction enzyme will attack exposed sites, killing the cell. Chromosome breakage may be repaired or may generate a variety of mutated and rearranged genomes, some of which might survive. Ds, double strand; rm, restriction–modification gene complex; RM, restriction modification.

Figure 2.

Models for Type I restriction enzyme activity. (A) Cleavage upon enzyme collision. After binding to an unmethylated recognition site, a Type I restriction enzyme complex begins pulling dsDNA. DNA is cleaved where two complexes collide. (B) Cleavage at an arrested DNA replication fork. DNA damage leads to aberrant DNA replication initiation, which exposes the unmethylated recognition sites. A Type I restriction enzyme complex begins pulling DNA. DNA is cleaved where the complex reaches an arrested replication fork. Ellipse, Type I restriction enzyme; open square, unmethylated recognition site; filled circle with a bar, methyl group.

Figure 3.

Host attack by Type II restriction–modification systems and by methyl-specific DNases (McrBC) in competition. (A) Type II systems. When a resident restriction–modification gene complex is replaced by a competitor genetic element, the modification enzyme level decrease exposes newly replicated chromosomal restriction sites to lethal cleavage by the remaining restriction enzymes. Intact genome copies survive in uninfected and unaltered neighbouring clonal cells. (B) McrBC. When a DNA methylation system enters a cell and begins methylating chromosomal recognition sites, McrBC senses the change and triggers cell death by chromosomal cleavage. The intact genome copies survive in uninfected and unaltered neighbouring clonal cells. From Fukuda et al.

Figure 4.

Action of McrBC, a methyl-specific DNase. (A) Reaction in vitro. McrBC recognizes R^mC (R = A or G) and cleaves the DNA, usually near a recognition site. Cleavage requires two recognition sites about 40–2000 bp (adapted from Raleigh). (B) Restriction in vivo. McrBC strongly restricts T-even phages whose DNA carries hydroxymethyl C in place of C. However, it only weakly restricts plasmids and phages whose DNA has been methylated by a modification enzyme.

Figure 5.

Cooperation in epigenome maintenance between McrBC and a DNA methyltransferase. A methyltransferase gene with DNA methylation specificity not subject to McrBC (filled circle) establishes itself in mcrBC⁺ cells and confers an epigenome state. A methyltransferase gene with specificity subject to McrBC (open circle) cannot establish itself because of host killing through chromosome cleavage by McrBC. Cells with the intact epigenome survive and increase their frequency. Filled circle with a bar, DNA methylation by DNA methyltransferase A; open circle with a bar, DNA methylation by B.

Figure 6.

Defence against viral infection through cell death. (A) Virus infection followed by secondary infection. The virus produces progeny that infect sibling cells. (B) Virus infection to cells that have a gene programming cell death upon the infection. The virus cannot produce progeny. Sibling cells are not infected and survive, together with the death gene.