Restriction-Modification Systems
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A systematic method of nomenclature has been developed for all restriction enzymes based upon the name of the organism from which they were isolated: e.g. EcoRI - from Escherichia coli hence Eco. The R indicates the restriction system was originally isolated on a R-factor (a plasmid carrying an antibiotic resistance) and the roman numeral I indicates this was the first system isolated from the strain in question. However, in many early papers Type I restriction enzymes are named without the roman numeral (probably reflecting the fact they were the first system isolated and their naming preceded the systematic system of nomenclature). More recently the systematic system has also been applied to Type I enzymes and this led to some re-naming of certain enzymes (Roberts et al 2003). Therefore, EcoK is now named EcoKI and EcoR124/3 was renamed EcoR124II. Roberts et al (2003) made a number of simple changes to this basic nomenclature system of which perhaps the most obvious is to drop the use of italics for the abbreviation of the host name. Therefore EcoRI can now be written EcoRI. Type I restriction enzymes are multifunctional, multisubunit enzymes and as a consequence the use of various terms can often be confusing. A Type I Restriction-Modification (R-M) system refers to the hsd genes in the natural host. The R-M enzyme refers the enzyme consisting of all Hsd subunits prior to the conformational changes that switch the system to restriction activity. The restriction enzyme (e.g. R.EcoKI), endonuclease or ENase (or REase) also contains all Hsd subunits, but has bound to unmethylated DNA, recognised the substrate DNA as unmethylated and undergone an ATP-induced conformational change that results in restriction activity. The modification methyltransferase (e.g. M.EcoKI) can either consist of only the HsdM and HsdS subunits only (with a M2S1 stoichiometry) capable of only methylation activity. Proposed nomenclature for the subunits:Roberts et al. described a systematic nomenclature for the R-M genes (i.e. ecoKIhsdr), which in turn suggests a simple mechanism for naming the individual subunits (which is only required for Type I R-M Systems) i.e. HsdR(EcoKI) etc. In addition, it is permissible to abbreviate the subunit names to the appropriate letter, therefore, HsdS can become the S subunit. However, it is not possible to add the name of the R-M system to this abbreviation WITHOUT the brackets as the modification subunit (M) would be mistaken for the MTase. Therefore one can use M(EcoKI) for HsdM(EcoKI), but NOT M.EcoKI, which is the MTase. |
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