Homing endonucleases are a large class of proteins (several hundreds of members) found in bacteria, archae, fungi and algae. They are encoded by mobile genetic elements such as group I introns and inteins, which promote their proper dissemination through their endonuclease activity (see Figure).
They recognize sites that usually correspond to intron-free or intein-free genes, where they produce a DSB. Eventually, DSB repair by homologous recombination with an intron- or intein-containing gene results in the insertion of the intron or intein where the DSB has occurred.
Homing endonucleases spreading
When an intron or intein containing gene meets an intron or intein-free copy of the same gene.
Intron or intein (grey box) encodes an homing endonuclease.
Intron or intein-free gene.
Homing endonuclease cuts the intron or intein-free gene
Homologous recombination with intron or intein-containing gene occurs. This process is referred to as a "gene conversion" event.
Outcome : the intron or intein is now found in both genes.
Homing endonucleases have been classified in four major families. The largest one and also the best characterized is the LAGLIDADG family, named after a more or less conserved peptidic motif. A few structures are available, including I-SceI, I-CreI, I-DmoI, PI-SceI, PI-PfuI and I-MsoI. Although LAGLIDADG proteins display almost no similarity in terms of primary sequence, they share a very conserved tridimensional structure (see Figure).
This structure is very compact, with the catalytic domain embedded in the DNA-binding domain. The I-CreI protein, shown in the figure with its DNA target is functional as an homodimer, and binds a nearly palindromic sequence. Actually, most LAGLIDADG proteins are monomers, but keep an internal two-fold symmetry, with two half-DNA binding sites each interacting with one half of the DNA target site. We and others could show the modularity of these domains by building a functional hybrid protein with an I-CreI peptide and an I-DmoI moiety.
Other homing endonucleases families are the GIY-YIG family, whose most extensively characterized member is the T4 phage I-TevI protein, the His-Cys box family, including I-PpoI, and the HNH family.
