Repbase Reports

2003, Volume 3, Issue 5
May 31, 2003
Copyright © 2001-2016 - Genetic Information Research Institute
ISSN# 1534-830X
Page 93


DNA transposon Merlin1_CI - a consensus.

Key Words:
DNA transposon, Merlin/IS1016 superfamily; 9-bp TSD; Merlin1m_CI; Merlin1_CI
Ciona intestinalis
Eukaryota; Metazoa; Chordata; Urochordata; Ascidiacea; Enterogona; Phlebobranchia; Cionidae; Ciona
[1] Authors:
Feschotte,C. and Wessler,S.R.
Merlin1_CI, a family of Merlin/IS1016-like DNA transposons from the sea squirt Ciona intestinalis
Repbase Reports 3:(5) p. 93 (2003)
The Merlin1_CI family is one of the founding members of a new superfamily of eukaryotic DNA transposons related to the IS1016 group of bacterial insertion sequences. There are at least 3 copies of Merlin1_CI containing large ORFs in the C. intestinalis draft genome sequence (WGS assembly 1.0, 116.7 Mb). The sequence below is a consensus constructed from these 3 copies. Merlin1_CI has been recently active because the three copies are ~94-98% similar to the consensus. Merlin1_CI are related and have probably provided the transposase to a large family of nonautonomous elements (Merlin1m_CI, see description in RR). The Merlin1_CI consensus sequence is 1791-bp long with 155-bp TIRs (8 mismatches). It contains one predicted gene (positions 518-1435), which can encode a 273-aa protein, Merlin1_CIp. The C-terminal half of this protein has strong similarity with the putative transposases of IS1016 from Haemophilus influenzae (and related IS) and with ORFs from a wide range of eukaryotes, including other ascidians (annotated transposase, GenBank AAM76104), nematodes, flat worms, mosquito (described previosly in the AF293351 GenBank locus as an IS1016-like insertion), zebrafish, Xenopus and humans. Many of these ORFs are clearly parts of transposable elements. Multiple alignments reveal that the most conserved domain of these proteins contains a putative DDE motif (D(60)D(36)E in Merlin1_CIp). A HTH DNA-binding domain is predicted in the N-terminal region of Merlin1_CIp. Thus, this protein is likely to represent the Merlin1_CI transposase. Merlin1_CI elements create a 9-bp TSD upon insertion, unlike most other members of the Merlin/IS1016, which create an 8-bp TSD. There may be other lineages of Merlin transposases in Ciona intestinalis. Putative Merlin1_CIp transposase: MQKDFEGENSESLPCIRCKSCGTYVSPRKNSFFAFMDNRNRANVKISYKQVMAILINWVQRVPVGTTQQ NYGFGAHTVTDWYNFCREMCMLGFSKREPMGGPNTIVEIDESLLRGKRKYNRAGIEGPWIFGMCHVTVD SEGARSTQEVRFFHVLRRDKQTLLPIIQNEVLPSTTIHSDQWAAYTGLDQLGYSHQSVNHSENFIDPQT GAHTQTIESTWHHMKTTLLRNMRGVEPELLDSYLAELWARKLYRDHAALLEKLFDWIVEAYPIRNI
[1] (Consensus)
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