STATISTICAL MODELING AND ANALYSIS OF THE LAGLIDADG FAMILY OF SITE-SPECIFIC ENDONUCLEASES AND IDENTIFICATION OF AN INTEIN THAT ENCODES A SITE-SPECIFIC ENDONUCLEASE OF THE HNH FAMILY

The LAGLIDADG and HNH families of site-specific DNA endonucleases enco ded by viruses, bacteriophages as well as archaeal, eucaryotic nuclear and organellar genomes are characterized by the sequence motifs 'LAGL IDADG' and 'HNH', respectively, These endonucleases have been shown to occur in different environments: LAGILIDADG endonucleases are found i n inteins, archaeal and group I introns and as free standing open read ing frames (ORFs); HNH endonucleases occur in group I and group II int rons and as ORFs, Here, statistical models (hidden Markov models, HMMs ) that encompass both the conserved motifs and more variable regions o f these families have been created and employed to characterize known and potential new family members, A number of new, putative LAGLIDADG and HNH endonucleases have been identified including an intein-encoded HNH sequence. Analysis of an HMM-generated multiple alignment of 130 LAGLIDADG family members and the th ree-dimensional structure of the I -CreI endonuclease has enabled definition of the core elements of the repeated domain (similar to 90 residues) that is present in this famil y of proteins, A conserved negatively charged residue is proposed to b e involved in catalysis, Phylogenetic analysis of the two families ind icates a lack of exchange of endonucleases between different mobile el ements (environments) and between hosts from different phylogenetic ki ngdoms, However, there does appear to have been considerable exchange of endonuclease domains amongst elements of the same type, Such events are suggested to be important for the formation of elements of new sp ecficity.