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Nucleic Acids Research, 2001, Vol. 29, No. 20 4195-4205
© 2001 Oxford University Press

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

Annette J. B. Titheradge, Jonathan King1, Junichi Ryu1 and Noreen E. Murray*

Institute of Cell and Molecular Biology, University of Edinburgh, King’s Buildings, Edinburgh EH9 3JR, UK and 1Department of Microbiology and Molecular Genetics, Loma Linda University, Loma Linda, CA 92350, USA

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.

* To whom correspondence should be addressed. Tel: +44 131 650 5374; Fax: +44 131 650 8650; Email: noreen.murray{at}ed.ac.ukPresent address: Annette J. B. Titheradge, John Hughes Bennett Laboratories, Department of Oncology, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, UK


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