A Nomenclature for Restriction Enzymes, DNA Methyltransferases, Homing Endonucleases, and Their Genes

Abstract

There are three main groups of restriction endonucleases (REases) called Types I, II, and III (1,2). Since 1973, REases and DNA methyltransferases (MTases) have been named based on an original suggestion by Smith and Nathans (3). They proposed that the enzyme names should begin with a three-letter acronym in which the first letter was the first letter of the genus from which the enzyme was isolated and the next two letters were the first two letters of the species name. Extra letters or numbers could be added to indicate individual strains or serotypes. Thus, the enzyme Hindll was one of four enzymes isolated from H aemophilus in fluenzae serotype d.The first three letters of the name were italicized. Later, a formal proposition for naming the genes encoding REases and MTases was adopted (4). When there were only a handful of enzymes known, these schemes were very useful, but as more enzymes have been found, often from different genera and species with names whose three-letter acronyms would be identical, considerable laxity in naming conventions has appeared. In addition, we now know that each major type of enzyme can contain subtypes. This especially applies to the Type II enzymes, of which more than 3500 have been characterized (5). In this paper we revisit the naming conventions and outline an updated scheme that incorporates current knowledge about the complexities of these enzymes. We describe a set of naming conventions for REases and their associated MTases.

Originally published in Nucleic Acids Research, Vol. 31 No.7, 1805-1812 by Oxford University Press 2003. Reprinted with permission of Oxford University Press.