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RNA (2003), 9:1422-1430. Published by Cold Spring Harbor Laboratory Press. Copyright © 2003 RNA Society

BIOINFORMATICS

Translational recoding signals between gag and pol in diverse LTR retrotransposons

XIANG GAO1, ERICKA R. HAVECKER1, PAVEL V. BARANOV2, JOHN F. ATKINS2 and DANIEL F. VOYTAS1

1 Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa 50011, USA
2 Department of Human Genetics, University of Utah, Salt Lake City, Utah 84112-5330, USA

Reprint requests to: Daniel F. Voytas, Department of Genetics, Development and Cell Biology, 2208 Molecular Biology Building, Iowa State University, Ames, IA 50011, USA; e-mail: voytas{at}iastate.edu; fax: (515) 294-7155.

Because of their compact genomes, retroelements (including retrotransposons and retroviruses) employ a variety of translational recoding mechanisms to express Gag and Pol. To assess the diversity of recoding strategies, we surveyed gag/pol gene organization among retroelements from diverse host species, including elements exhaustively recovered from the genome sequences of Caenorhabditis elegans, Drosophila melanogaster, Schizosaccharomyces pombe, Candida albicans, and Arabidopsis thaliana. In contrast to the retroviruses, which typically encode pol in the -1 frame relative to gag, nearly half of the retroelements surveyed encode a single gag-pol open reading frame. This was particularly true for the Ty1/copia group retroelements. Most animal Ty3/gypsy retroelements, on the other hand, encode gag and pol in separate reading frames, and likely express Pol through +1 or -1 frameshifting. Conserved sequences conforming to slippery sites that specify viral ribosomal frameshifting were identified among retroelements with pol in the -1 frame. None of the plant retroelements encoded pol in the -1 frame relative to gag; however, two closely related plant Ty3/gypsy elements encode pol in the +1 frame. Interestingly, a group of plant Ty1/copia retroelements encode pol either in a +1 frame relative to gag or in two nonoverlapping reading frames. These retroelements have a conserved stem–loop at the end of gag, and likely express pol either by a novel means of internal ribosomal entry or by a bypass mechanism.

Keywords: Translational regulation; recoding; retrotransposon; frameshifting


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