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Nucleic Acids Research 2005 33(7):2227-2238; doi:10.1093/nar/gki507
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Published online 20 April 2005

© The Author 2005. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions{at}oupjournals.org

Article

Nematode selenoproteome: the use of the selenocysteine insertion system to decode one codon in an animal genome?

Kalin Taskov, Charles Chapple1, Gregory V. Kryukov, Sergi Castellano1, Alexey V. Lobanov, Konstantin V. Korotkov, Roderic Guigó1 and Vadim N. Gladyshev*

Department of Biochemistry, University of Nebraska Lincoln, NE 68588, USA 1Grup de Recerca en Informàtica Biomèdica, Institut Municipal d'Investigació Mèdica, Universitat Pompeu Fabra, Centre de Regulació genòmica Dr Aiguader 80, 08003 Barcelona, Catalonia, Spain

*To whom correspondence should be addressed. Tel: +1 402 472 4948; Fax: +1 402 472 7842; Email: vgladyshev1{at}unl.edu

Received February 21, 2005. Revised March 24, 2005. Accepted March 24, 2005.

Selenocysteine (Sec) is co-translationally inserted into selenoproteins in response to codon UGA with the help of the selenocysteine insertion sequence (SECIS) element. The number of selenoproteins in animals varies, with humans having 25 and mice having 24 selenoproteins. To date, however, only one selenoprotein, thioredoxin reductase, has been detected in Caenorhabditis elegans, and this enzyme contains only one Sec. Here, we characterize the selenoproteomes of C.elegans and Caenorhabditis briggsae with three independent algorithms, one searching for pairs of homologous nematode SECIS elements, another searching for Cys- or Sec-containing homologs of potential nematode selenoprotein genes and the third identifying Sec-containing homologs of annotated nematode proteins. These methods suggest that thioredoxin reductase is the only Sec-containing protein in the C.elegans and C.briggsae genomes. In contrast, we identified additional selenoproteins in other nematodes. Assuming that Sec insertion mechanisms are conserved between nematodes and other eukaryotes, the data suggest that nematode selenoproteomes were reduced during evolution, and that in an extreme reduction case Sec insertion systems probably decode only a single UGA codon in C.elegans and C.briggsae genomes. In addition, all detected genes had a rare form of SECIS element containing a guanosine in place of a conserved adenosine present in most other SECIS structures, suggesting that in organisms with small selenoproteomes SECIS elements may change rapidly.


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