Molecular and General Genetics MGG

, Volume 260, Issue 5, pp 401–409

Molecular characterization of a retrotransposon in Drosophila melanogaster, nomad, and its relationship to other retrovirus-like mobile elements

  • J. H. Whalen
  • T. A. Grigliatti
ORIGINAL PAPER

DOI: 10.1007/s004380050910

Cite this article as:
Whalen, J. & Grigliatti, T. Mol Gen Genet (1998) 260: 401. doi:10.1007/s004380050910

Abstract

The nomad element was identified as a retrovirus-like transposon in Drosophila melanogaster. DNA sequence analysis showed that the nomad element contains three long ORFs that are similar to the gag, pol and env genes of retrovirus- and the copia-like elements of D.melanogaster. The nomad element terminates with 519-bp terminal repeats, each of which contains eukaryotic consensus transcription initiation and termination signals. nomad elements are located at approximately 10–15 sites within the euchromatic arms of the genome and at the chromocenter, as shown by in situ hybridization. The host DNA sequence TANA was found to be duplicated on each side of the nomad element and appears to be a preferential target site for insertion of nomad elements. Analysis of the zinc finger motif in the pol gene product of retrotransposons known to have target site preference suggests involvement of the integrase subunit in target site selection for those retrotransposons that display insert site specificity. A comparison of the predicted amino acid sequence of the pol-like genes of several known retrotransposons was made and the phylogenetic relationship between nomad and other retrovirus-like mobile elements was determined. It was clear from this conceptual protein analysis and from analysis of their structural characteristics that retrotransposons of the gypsy class can be generally classified as members of one of two distinct groups. The phylogenetic relationships of these groups are also discussed.

Key wordsNomad element Transposable element D. melanogaster Gypsy-like elements Phylogenetics 

Copyright information

© Springer-Verlag Berlin Heidelberg 1998

Authors and Affiliations

  • J. H. Whalen
    • 1
  • T. A. Grigliatti
    • 1
  1. 1.Department of Zoology, University of British Columbia 6270 University Boulevard, Vancouver, BC Canada, V6T 1Z4 e-mail: jhwhalen@unixg.ubc.ca, Fax: +604‐822‐2416CA

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