RESULTS: A new diverse eukaryotic superfamily of
DNA transposons, named Ginger (for 'Gypsy
INteGrasE Related')
DNA transposons is defined and analyzed. Analogously to the IS3 and IS481 bacterial transposons, the Ginger termini resemble those of the Gypsy LTR
retrotransposons. Currently, Ginger transposons can be divided into two distinct groups named Ginger1 and Ginger2/
Tdd. Elements from the Ginger1 group are characterized by approximately 40 to 270 base pair (bp) terminal inverted repeats (TIRs), and are flanked by CCGG-specific or CCGT-specific target site duplication (TSD) sequences. The Ginger1-encoded
transposases contain an approximate 400
amino acid N-terminal portion sharing high
amino acid identity to the entire Gypsy-encoded
integrases, including the YPYY motif, zinc finger,
DDE domain, and, importantly, the GPY/F motif, a hallmark of Gypsy and endogenous retrovirus (ERV)
integrases. Ginger1
transposases also contain additional C-terminal domains: ovarian
tumor (OTU)-like
protease domain or
Ulp1 protease domain. In vertebrate genomes, at least two host genes, which were previously thought to be derived from the Gypsy
integrases, apparently have evolved from the Ginger1
transposase genes. We also introduce a second Ginger group, designated Ginger2/
Tdd, which includes the previously reported
DNA transposon TDD-4.
CONCLUSIONS: