EVIDENCE FOR AN EVOLUTIONARY RELATIONSHIP AMONG TYPE-II RESTRICTION ENDONUCLEASES

Type-II restriction-modification (R-M) systems comprise two enzymes, a DNA methyltransferase (MTase) and a restriction endonuclease (ENase), each of which specifically interact with the same 4-8-bp sequence. Al l type-II MTases share several amino acid (aa) sequence motifs, which makes an evolutionary relatedness among these enzymes probable. The ty pe-II ENases, in contrast, except for some homologous isoschizomers, d o not share significant aa sequence similarity. Therefore, ENases in g eneral have been considered unrelated. Here we show that in addition t o the analysis of the genotype (aa sequence), a comparison of the phen otype (recognition sequence) of these enzymes can provide independent information regarding evolutionary relationships, and thereby, help to analyze the significance of weak aa sequence similarities. Multistep Monte-Carlo analyses were employed to demonstrate that the recognition sequences of those ENases, which were found to be related by a progre ssive multiple aa sequence alignment, are more similar to each other t han would be expected by chance. This analysis supports the notion tha t not only type-II MTases, but also type-II ENases did not arise indep endently in evolution, but rather evolved from one or a few primordial DNA-modifying and DNA-cleaving enzymes, respectively.