title: Context dependence between subdomains in the DNA binding interface of the I-CreI homing endonuclease.
abstract: Homing endonucleases (HE) have emerged as precise tools for achieving gene targeting events. Redesigned HEs with tailored specificities can be used to cleave new sequences, thereby considerably expanding the number of targetable genes and loci. With HEs, as well as with other protein scaffolds, context dependence of DNA/protein interaction patterns remains one of the major limitations for rational engineering of new DNA binders. Previous studies have shown strong crosstalk between different residues and regions of the DNA binding interface. To investigate this phenomenon, we systematically combined mutations from three groups of amino acids in the DNA binding regions of the I-CreI HE. Our results confirm that important crosstalk occurs throughout this interface in I-CreI. Detailed analysis of success rates identified a nearest-neighbour effect, with a more pronounced level of dependence between adjacent regions. Taken together, these data suggest that combinatorial engineering does not necessarily require the identification of separable functional or structural regions, and that groups of amino acids provide acceptable building blocks that can be assembled, overcoming the context dependency of the DNA binding interface. Furthermore, the present work describes a sequential method to engineer tailored HEs, wherein three contiguous regions are individually mutated and assembled to create HEs with engineered specificity.
authors.affiliation: CELLECTIS SA, 102 Avenue Gaston Roussel, 93235 Romainville, France.
authors.forename: Sylvestre
authors.initials: S
authors.lastname: Grizot
authors.forename: Aymeric
authors.initials: A
authors.lastname: Duclert
authors.forename: Séverine
authors.initials: S
authors.lastname: Thomas
authors.forename: Philippe
authors.initials: P
authors.lastname: Duchateau
authors.forename: Frédéric
authors.initials: F
authors.lastname: Pâques
mesh_terms: D001665:Binding Sites; D004262:DNA Restriction Enzymes / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D004268:DNA-Binding Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D008958:Models, Molecular; D009154:Mutation; D015202:Protein Engineering / Q000379:methods; D017434:Protein Structure, Tertiary; D013379:Substrate Specificity
chemical_list: D004268:DNA-Binding Proteins; D004262:DNA Restriction Enzymes; C048901:endodeoxyribonuclease CreI