Figure 1. Sequence of events during unidirectional and nonreciprocal transfer of an intron from the intron-plus (donor) to the intron-minus (recipient) strain. Subsequent to target cleavage by the endonuclease (1), the break in the recipient allele is enlarged by exonucleolytic degradation, leaving single-stranded 3¢ ends (2). The 3¢ extensions of the recipient allele invade the homologous region of the intron-plus donor duplex and displace the strands of the donor duplex (3). After D-loop formation the 3¢ ends function as primers in the repair process that uses the complementary intron-containing DNA strands as template (4). Co-conversion of flanking exon sequences observed with intron homing is due to exonucleolytic degradation of the cleaved recipient DNA and possibly to branch migration during recombination. The homing process is completed by cleavage and ligation of the two Holliday junctions that results in resolution of the two intron-containing alleles (5). Thus, the intron is said to ‘home’ to an intron-minus allele, and intron-encoded proteins that mediate this process are commonly referred to as homing endonucleases.

Figure 2. The retrohoming pathway of a group II intron can be divided into three stages. (a) Splicing of the intron-plus allele pre-mRNA promoted by the maturase function to yield mRNA and intron lariat. (b) Cleavage of intron-minus allele by an RNP complex consisting of the intron lariat and endonuclease function of the intron-encoded protein. (c) Completion of intron homing by either complete- or partial-reverse splicing reactions and mediated by the reverse transcriptase function. Red rectangles indicate exons of the intron-plus allele, and blue rectangles indicate exons of the intron-minus allele. Black rectangles represent the group II intron. The group II intron-encoded protein is represented as a green oval and the biochemical activities of the protein are indicated by circles and letters within it. M, maturase; E, endonuclease; RT, reverse transcriptase. Shaded and bold letters within the circles indicate that a particular biochemical activity is required in the homing pathway (for example, maturase function is required for splicing of pre-mRNA, but not the endonuclease or reverse transcriptase functions). Triangles indicate cleavage sites on the intron-minus allele and homing products, and the solid line between the two strands of the intron-minus allele indicates the intron insertion site.