Figure 5.

Comparison of the ORFs encoded by group II introns and non-LTR retrotransposable elements. The group II intron shown is the ltrB intron of Lactococcus lactis (37). The protein domains shared by other group II introns are shaded and are similar to those identified previously (41), except that the domains referred to as Z and X in that study are shown here as part of the RT domain (see ref. 8). The putative endonuclease domain of the group II introns is identified as HNH (38, 39). In the case of the non-LTR retrotransposons, schematic diagrams of the R2, L1, and Jockey elements are shown as representatives of the major non-LTR structures found to date. Other major lineages of non-LTR elements with these basic structures are listed within the parentheses (8). The CCHH, c-myb, CCHC, and PD..D domains of the R2 elements are described in Fig. 1. The AP-like endonuclease domain identified at the amino-terminal end of L1 and Jockey elements is labeled APE. Elements with structures similar to L1 contain a CCHC domain downstream of their RT domain; thus, this region is likely to be involved in DNA binding. Arrows represent the likely path of non-LTR evolution in eukaryotes based on the phylogeny of their RT domains (8).