title: Non-contact positions impose site selectivity on Cre recombinase.
abstract: A first step in Cre-mediated site-specific DNA recombination is binding to the two 13 bp repeats of the 34 bp site loxP. Several nucleotides within loxP do not directly contact the bound enzyme, yet mutation at two of these base pairs, at positions 11 and 12 in each repeat, results in a 100 000-fold reduction in recombination. To understand better how Cre selects DNA sequences for recombination, we combined DNA shuffling mutagenesis and a forward selection strategy to obtain Cre mutants that recombine at 100% efficiency a mutant loxK2 site carrying these dinucleotide changes. The role of the several mutations found in these Cre isolates was analyzed both in vivo and biochemically with purified enzymes. A single mutation at E262 accounts for most but not all of the enhanced activity at loxK2. Secondary mutations act in one or more of three ways: enhancement of loxK2 binding, accelerated synthesis of Cre in vivo or faster DNA recombination at the alternative spacer region present in loxK2. Systematic analysis of all 20 natural amino acids at position E262 shows that the naturally occurring glutamate residue at this position provides the optimal balance of efficiency of recombination at loxP and maximal discrimination against loxK2.
authors.affiliation: Stowers Institute for Medical Research, 1000 East 50th Street, Kansas City, MO 64110, USA.
authors.forename: Andreas W
authors.initials: AW
authors.lastname: Rüfer
authors.forename: Brian
authors.initials: B
authors.lastname: Sauer
mesh_terms: D000595:Amino Acid Sequence; D001483:Base Sequence; D001665:Binding Sites / Q000187:drug effects; D004269:DNA, Bacterial / Q000235:genetics / Q000378:metabolism; D024202:Electrophoretic Mobility Shift Assay; D004926:Escherichia coli / Q000235:genetics; D019426:Integrases / Q000235:genetics* / Q000378:metabolism; D009154:Mutation; D011485:Protein Binding; D011995:Recombination, Genetic / Q000235:genetics*; D017386:Sequence Homology, Amino Acid; D014764:Viral Proteins / Q000235:genetics* / Q000378:metabolism
chemical_list: D004269:DNA, Bacterial; D014764:Viral Proteins; C045073:Cre recombinase; D019426:Integrases