A FAMILY OF PHASE-VARIABLE RESTRICTION ENZYMES WITH DIFFERING SPECIFICITIES GENERATED BY HIGH-FREQUENCY GENE REARRANGEMENTS

The hsd genes of Mycoplasma pulmonis encode restriction and modificati on enzymes exhibiting a high degree of sequence similarity to the type I enzymes of enteric bacteria. The S subunits of type I systems dicta te the DNA sequence specificity of the holoenzyme and are required for both the restriction and the modification reactions. The M. pulmonis chromosome has two hsd loci, both of which contain two hsdS genes each and are complex, site-specific DNA inversion systems. Embedded within the coding region of each hsdS gene are a minimum of three sites at w hich DNA inversions occur to generate extensive amino acid sequence va riations in the predicted S subunits. We show that the polymorphic hsd S genes produced by gene rearrangement encode a family of functional S subunits with differing DNA sequence specificities. In addition to tr eating polymorphisms in hsdS sequences, DNA inversions regulate the ph ase-variable production of restriction activity because the other gene s required for restriction activity (hsdR and hsdM) are expressed only from loci that are oriented appropriately in the chromosome relative to the hsd promoter. These data cast doubt on the prevailing paradigms that restriction systems are either selfish or function to confer pro tection from invasion by foreign DNA.