Families of restriction enzymes: an analysis prompted by molecular and genetic data for type ID restriction and modification systems

Abstract

Current genetic and molecular evidence places all the known type I restriction and modification systems of Escherichia coli and Salmonella enterica into one of four discrete families: type IA, IB, IC or ID. StySBLI is the founder member of the ID family. Similarities of coding sequences have identified restriction systems in E.coli and Klebsiella pneumoniae as probable members of the type ID family. We present complementation tests that confirm the allocation of EcoR9I and KpnAI to the ID family. An alignment of the amino acid sequences of the HsdS subunits of StySBLI and EcoR9I identify two variable regions, each predicted to be a target recognition domain (TRD). Consistent with two TRDs, StySBLI was shown to recognise a bipartite target sequence, but one in which the adenine residues that are the substrates for methylation are separated by only 6 bp. Implications of family relationships are discussed and evidence is presented that extends the family affiliations identified in enteric bacteria to a wide range of other genera.

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

“…When referring to phenotypes the preferred convention is r KI + m KI + etc. Four sub-categories of Type I enzymes (A, B, C and D) are in common use (12). These are based on genetic complementation and their use will be continued.…”

Diversity within the Campylobacter jejuni type I restriction–modification loci

“…HsdM) have been used to assign R-M systems into one of four discrete families (Titheradge et al, 2001). The amino acid sequences of several HsdM proteins from eubacteria and archaea are available in the GenBank database.…”

“…3), several GBS isolates were classified as either 'IF' (strains RM3264, RM3266) or 'unknown' (strains RM3148, RM3149, RM3193, RM3196, RM3197, RM3198, RM3211 and RM3265) ( Table 1). Titheradge et al (2001) used an HsdM identity value of 45 % to place novel HsdM polypeptides into the four existing families of type I enzymes; HsdM proteins with >45 % identity were placed into the same family. Based on this sole criterion, many of the newly characterized type I R-M systems can be assigned to one of four families identified in the Enterobacteriaceae (Fuller-Pace et al, 1985;Price et al, 1987;Suri & Bickle, 1985;Titheradge et al, 1996Titheradge et al, , 2001.…”

“…Cje30, Cje1516) can clearly be assigned as a member of a monophyletic group of an existing family (type IC). The placement of this group in the type IC family is based not only on sequence similarity to and immediate phylogenetic affiliation with other type IC enzymes, but also on the presence of IC-specific motifs, (Titheradge et al, 2001). HsdM polypeptides labeled with a star indicate that the associated HsdS subunits are predicted to contain spacer repeats.…”

“…A fourth family, type ID, was first identified in Salmonella enterica serovar Blegdam (Titheradge et al, 1996). HsdM and HsdR proteins within the same family are highly conserved, with any pairwise amino acid sequences having >90 % identity; however, sequence identity between HsdM proteins from different families is usually very low (<35 %) (Sharp et al, 1992;Titheradge et al, 2001). …”