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The Type ID FamilyType ID restriction endonucleasesAcknowledgement: Much of the material below is taken directly from the abstracts of published papers and as a consequence I have cited the relevant paper in each section. My thanks to all those workers who have contributed either knowingly or unknowingly to this page (KF). Salmonella enterica serovar blegdam has a restriction and modification system encoded by genes linked to serB. Titheradge et al. (1996) have cloned these genes, putative alleles of the hsd locus of Escherichia coli K-12, and confirmed by the sequence similarities of flanking DNA that the hsd genes of S. enterica serovar blegdam have the same chromosomal location as those of E. coli K-12 and Salmonella enterica serovar typhimurium LT2. There is, however, no obvious similarity in their nucleotide sequences, and while the gene order in S. enterica serovar blegdam is serB hsdM, S and R, that in E. coli K-12 and S. enterica serovar typhimurium LT2 is serB hsdR, M and S. Therefore, the hsd genes of S. enterica serovar blegdam identify a third family of serB-linked hsd genes (Type I ID. The Polypeptide sequence predicted from the three hsd genes show some similarities (18-50% identity) with the polypeptides of known and putative Type I restriction and modification systems; the highest levels of identity are with sequences of Haemophilus influenzae Rd. The HsdM polypeptide has the motifs characteristic of adenine methyltransferases. Comparisons of the HsdR sequence with those for three other families of Type I systems and three putative HsdR polypeptides identify two highly conserved regions in addition to the seven proposed DEAD-box motifs. In enteric bacteria three discrete families of Type I I restriction and modification system (IA, IB and ID) are encoded by alleles of the serB-linked hsd locus. Probes specific for each of the three families were used by Barcus et al. (1995) to monitor the distribution of related systems in 37 of the 72 wild-type Escherichia coli strains comprising the ECOR collection. All 25 members of group A in this collection were screened; 12 were probe-positive, nine have hsd genes in the IA family, two in the IB and one in the ID. Twelve strains, representing all groups other than A, were screened; five were probe-positive, one has hsd genes in the IA family, one in the IB and three in the ID. The Type I ID genes are the first representatives of this family in E. coli, the probe-negative strains could have alternative families of hsd genes. The Type I IA and IB systems added at least five new specificities to the five already identified in natural isolates of E. coli. The distribution of alleles is consistent with the dissimilar coding sequences of allelic hsd genes both imply lateral transfer of hsd genes. Lee et al. (1997) first identified the KpnAI restriction-modification (R-M) system in Klebsiella pneumoniae strain M5a1. The restriction gene of KpnAI was first cloned into pBR322 using an r-m+ M5a1 derivative and phage SBS for screening. Subsequently, an adjacent DNA fragment showing modification activity was cloned into pUC19. A total of 7.2 kb DNA sequencing data revealed three open reading frames, corresponding to hsdR, hsdM and hsdS genes of Type I I R-M systems. The predicted hsdR, hsdM and hsdS-coded peptides shared 95% , 98% and 44% identity, respectively, with the corresponding peptides of the recently identified StySBLI system, a prototype of the Type I ID family. This high homology suggests that KpnAI is also a member of the Type I ID family. The KpnAI system seems to be the first Type I I system identified in Klebsiella species. Titherage et al (2001) have shown using complementation assays that EcoR9I and KpnAI also belong to the Type ID family. |
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