The other face of restriction: modification-dependent enzymes

Abstract

The 1952 observation of host-induced non-hereditary variation in bacteriophages by Salvador Luria and Mary Human led to the discovery in the 1960s of modifying enzymes that glucosylate hydroxymethylcytosine in T-even phages and of genes encoding corresponding host activities that restrict non-glucosylated phage DNA: rglA and rglB (restricts glucoseless phage). In the 1980’s, appreciation of the biological scope of these activities was dramatically expanded with the demonstration that plant and animal DNA was also sensitive to restriction in cloning experiments. The rgl genes were renamed mcrA and mcrBC (modified cytosine restriction). The new class of modification-dependent restriction enzymes was named Type IV, as distinct from the familiar modification-blocked Types I–III. A third Escherichia coli enzyme, mrr (modified DNA rejection and restriction) recognizes both methylcytosine and methyladenine. In recent years, the universe of modification-dependent enzymes has expanded greatly. Technical advances allow use of Type IV enzymes to study epigenetic mechanisms in mammals and plants. Type IV enzymes recognize modified DNA with low sequence selectivity and have emerged many times independently during evolution. Here, we review biochemical and structural data on these proteins, the resurgent interest in Type IV enzymes as tools for epigenetic research and the evolutionary pressures on these systems.

Identification of the minimal bacterial 2′‐deoxy‐7‐amido‐7‐deazaguanine synthesis machinery

“…Here again, biochemical studies will be required to provide a definitive confirmation and to elucidate the specific role(s) of each protein. Though the classification scheme for R‐M systems was initially designed specifically for methylations, the dpd system would be most similar to a type I RM system (Loenen and Raleigh, ). Indeed, we identified a ‘modification complex’ (DpdABC), composed of a potential DNA sequence specificity protein and two modification proteins, and a ‘restriction complex’ (potentially DpdEFGHIJKD) that contains SNF2 helicase homologs (see Thiaville et al ., for description).…”

Evolutionary Genomics of Defense Systems in Archaea and Bacteria

“…Type III RM systems resemble type II systems in that they consist of only R and M subunits, but they are similar to type I systems in that the R subunit also contains the helicase domain and the reaction is ATP dependent (19, 136). Type IV RM systems are distinct two-subunit complexes that consist of a AAA + family GTPase and an endonuclease (15, 100). Their mode of action is fundamentally different from the other three types in that they nonspecifically cleave modified phage DNA containing 5-hydroxymethylcytosine or 5-hydroxymethyluracil.…”

“…In fact, type IV systems are best denoted R, because modification enzymes in this case are not parts of the defense machinery. These modifications protect phage DNA from cleavage by the conventional REases of types I, II, and III, and apparently type IV R systems have evolved on multiple occasions during the bacterial-phage arms race, as a counter-counterdefense mechanism that overcomes such protection (15, 100). …”

High pressure activation of the Mrr restriction endonuclease in Escherichia coli involves tetramer dissociation

“…Contrary to Type I-III REases, Type IV enzymes are not found in conjunction with their cognate methyltransferases (MTases) (3). Typically, MTases modify the bacterial chromosome at specific sequences to protect it from cleavage by the cognate REase.…”