A candidate autonomous version of the wheat MITE Hikkoshi is present in the rice genome

Mol Genet Genomics. 2005 Jun;273(5):404-14. doi: 10.1007/s00438-005-1144-7. Epub 2005 May 10.

Abstract

A miniature inverted-repeat transposable element (MITE), designated as Hikkoshi, was previously identified in the null Wx-A1 allele of Turkish bread wheat lines. This MITE is 165 bp in size and has 12-bp terminal inverted repeats (TIRs) flanked by 8-bp target site duplications (TSDs). Southern and PCR analyses demonstrated the presence of multiple copies of Hikkoshi in the wheat genome. Database searches indicated that Hikkoshi MITEs are also present in barley, rice and maize. A 3.4-kb element that has Hikkoshi-like TIRs flanked by 8-bp TSDs has now been identified in the rice genome. This element shows high similarity to the 5' subterminal region of the wheat Hikkoshi MITE and contains a transposase (TPase) coding region. The TPase has two conserved domains, ZnF_TTF and hATC, and its amino acid sequence shows a high degree of homology to TPases encoded by Tip100 transposable elements belonging to the hAT superfamily. We designated the 3.4-kb element as OsHikkoshi. Several wheat clones deposited in EST databases showed sequence similarity to the TPase ORF of OsHikkoshi. The sequence information from the TPase of OsHikkoshi will thus be useful in isolating the autonomous element of the Hikkoshi system from wheat.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Alleles
  • Base Sequence
  • Blotting, Southern
  • Cloning, Molecular
  • Computational Biology
  • Conserved Sequence
  • DNA Transposable Elements
  • Exons
  • Expressed Sequence Tags
  • Genome, Plant*
  • Models, Genetic
  • Molecular Sequence Data
  • Open Reading Frames
  • Oryza / genetics*
  • Phylogeny
  • Polymerase Chain Reaction
  • Protein Structure, Tertiary
  • Sequence Homology, Nucleic Acid
  • Transposases / metabolism
  • Triticum / genetics*

Substances

  • DNA Transposable Elements
  • Transposases