Repbase Reports

2003, Volume 3, Issue 5
May 31, 2003
Copyright © 2001-2016 - Genetic Information Research Institute
ISSN# 1534-830X
Page 92


DNA transposon Merlin1_CB - a consensus.

Key Words:
DNA transposon, Merlin/IS1016 superfamily; 8-bp TSD; Merlin1_CB
Caenorhabditis briggsae
Eukaryotae; mitochondrial eukaryotes; Metazoa/Eumycota group; Metazoa; Eumetazoa; Bilateria; Pseudocoelomata; Nematoda; Secernentea; Rhabditia; Rhabditida; Rhabditina; Rhabditoidea; Rhabditidae; Caenorhabditis
[1] Authors:
Feschotte,C. and Wessler,S.R.
Merlin1_CB, a family of Merlin/IS1016-like DNA transposons from the nematode C. briggsae
Repbase Reports 3:(5) p. 92 (2003)
The Merlin1_CB 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 6 copies of Merlin1_CB with partial or complete coding capacity in the C. briggsae draft genome sequence (Jim Mullikin's WGS assembly 6/24/02). The sequence below is a consensus constructed from these 6 copies. Merlin1_CB has been recently active because the 6 copies are 96-99% similar to the consensus. There are also a few short nonautonomous elements more distantly related to Merlin1_CB and more ancient. The Merlin1_CB consensus sequence is 1915-bp long with 141-bp TIRs (3 mismatches). It contains one predicted gene (positions 340-1402), interrupted by one intron (593-639), which can encode a 338-aa protein, Merlin1_CBp. 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 nematodes, flat worms, mosquito (described previously in the AF293351 GenBank locus as an IS1016-like insertion), ascidians (annotated transposase, GenBank AAM76104), zebrafish, Xenopus and humans. Many of these ORFs are clearly part 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_CBp). A HTH DNA-binding domain is predicted in the N-terminal region of Merlin1_CBp. Thus, this protein is likely to represent the Merlin1_CB transposase. Finally, there are striking sequence similarities in the TIRs of Merlin/IS1016 elements; most of them (including Merlin1_CB) create an 8-bp TSD upon insertion. The putative Merlin1_CBp transposase: MLAVISCFCCYSLLLASILIFAMTAVAAILDLKSFNLIKTWPELANKTDDEFDEYLAERGLLWRENPCP SCHESRKISKQKNASGAFCKQKFECYKRACRNSRFNCKTGYLKGTFFEGLRGSRKKIFLCSFLYLNGKM VMKELAETLETEEKTVIQWCQWFRDIMAESLYQPAIMIGGVGETVQIDETNIVKRKYNVGRIVRNGWLI GGIQNNTRAVFIEIVDKRDQATCERIIQQYVAPGTTVITDCWRGYNGLAALGYDHKTVNHSQNFVDPAT GLHTQRVESLWSHLKRRIKPKCGLKGDLWDDHWFEALWHFKHHEEAKLYELWAEIARRYPLT
[1] (Consensus)
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