Ty3/Gypsy retrotransposon fossils in mammalian genomes: Did they evolve into new cellular functions?

摘要

Long-terminal-repeat (LTR) retrotransposons from the Ty3/Gypsy superfamily have been detected in various eukaryotic taxa, including some vertebrate lineages (lampreys, bony fishes, amphibians, and reptiles; Miller et al. 1999 and references therein). Nevertheless, molecular and database screenings failed to detect such elements in the genome of mammals. Considering the huge amount of sequence information, available on mammalian genomes and transcriptomes, this suggested that Ty3/Gypsy retrotransposons either have been lost or are present at an extremely low copy number in mammals. By examination of public sequence databases, we identified Ty3/Gypsy-like sequences in mammals. The human protein KIAA1051, obtained from a brain cDNA library (Kikuno et al. 1999), shows significant similarities to the Gag structural core protein of some Ty3/Gypsy retrotransposons from the Ty3 family, including Sushi from the pufferfish Fugu rubripes (Poulter and Butler 1998) (42.5 percent similarities, expected value E = 10~(-24)) and Skippy (Anaya and Roncero 1995), Maggy (Farman et al. 1996), and Cftl (Curtis and Oliver 1996) from different fungi (fig. 1). In particular, the C-terminal putative nucleic acid-binding site CX_2CX_4HX_4C is conserved. No significant similarity to other families of Ty3/Gypsy retrotransposons and retroviruses was found. Two additional human proteins, the brain protein KIAA1318 (accession number BAA92556; Nagase et al. 2000) and the putative nuclear protein LDOC1 (Nagasaki et al. 1999), also showed significant similarities to the KIAA1051 and Sushi Gag(-like) proteins, but outside of the nucleic acid-binding domain.