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MBE Advance Access published online on March 31, 2006
Molecular Biology and Evolution, doi:10.1093/molbev/msk015
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© The Author 2006. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oxfordjournals.org
Accepted March 27, 2006

Research Article

Transposon-Mediated Expansion and Diversification of a Family of ULP-like Genes

Douglas R. Hoen 1 *, Kyong-Cheul Park 1 *, Nabil Elrouby 2, Zhihui Yu 1, Nadia Mohabir 1, Rebecca K. Cowan 1, and Thomas E. Bureau 1 *

1 McGill University, Department of Biology, 1205 Dr. Penfield, Montreal, Québec, Canada, H3A 1B1
2 McGill University, Department of Biology, 1205 Dr. Penfield, Montreal, Québec, Canada, H3A 1B1; Current address: Max Planck Institute for Plant Breeding Research, Köln, Germany

* To whom correspondence should be addressed.
Thomas E. Bureau, E-mail: thomas.bureau{at}mcgill.ca


  Abstract

Transposons comprise a major component of eukaryotic genomes, yet it remains controversial whether they are merely genetic parasites, or instead significant contributors to organismal function and evolution. In plants, thousands of DNA transposons were recently shown to contain duplicated cellular gene fragments, a process termed transduplication. Although transduplication is a potentially rich source of novel coding sequences, virtually all appear to be pseudogenes in rice. Here we report the results of a genome-wide survey of transduplication in Mutator-like elements (MULEs) in Arabidopsis thaliana, which shows that the phenomenon is generally similar to rice transduplication, with one important exception: KAONASHI (KI). A family of more than 97 potentially functional genes and apparent pseudogenes, evidently derived at least 15 MYA from a cellular small ubiquitin-like modifier (SUMO)-specific protease gene (ULP), KI is predominantly located in potentially autonomous non-TIR (terminal inverted repeat) MULEs and has evolved under purifying selection to maintain a conserved peptidase domain. Similar to the associated transposase gene but unlike cellular genes, KI is targeted by small RNAs and silenced in most tissues, but has elevated expression in pollen. In an Arabidopsis double mutant deficient in histone and DNA methylation with elevated KI expression compared to wild type, at least one KI-MULE is mobile. The existence of KI demonstrates that transduplicated genes can retain protein-coding capacity and evolve novel functions. However, in this case our evidence suggests that the function of KI may be selfish rather than cellular.

Keywords: genome evolution; gene duplication; transposable element; Mutator; Arabidopsis thaliana; SUMO.

*The first two authors contributed equally to this work.


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