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DNA Research Advance Access originally published online on June 15, 2007
DNA Research 2007 14(3):103-116; doi:10.1093/dnares/dsm013
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© The Author 2007. Kazusa DNA Research Institute
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@oxfordjournals.org

Genome-Wide Analysis of LIM Gene Family in Populus trichocarpa, Arabidopsis thaliana, and Oryza sativa

Dominique Arnaud, Annabelle Déjardin, Jean-Charles Leplé, Marie-Claude Lesage-Descauses and Gilles Pilate*

Equipe ‘Xylème’ Unité Amélioration, Génétique et Physiologie Forestières, INRA-Orléans, Avenue de la Pomme de Pin, BP 20619 Ardon, F-45166 Olivet Cedex, France

Received 11 January 2007 ; accepted 12 May 2007.

In Eukaryotes, LIM proteins act as developmental regulators in basic cellular processes such as regulating the transcription or organizing the cytoskeleton. The LIM domain protein family in plants has mainly been studied in sunflower and tobacco plants, where several of its members exhibit a specific pattern of expression in pollen. In this paper, we finely characterized in poplar six transcripts encoding these proteins. In Populus trichocarpa genome, the 12 LIM gene models identified all appear to be duplicated genes. In addition, we describe several new LIM domain proteins deduced from Arabidopsis and rice genomes, raising the number of LIM gene models to six for both species. Plant LIM genes have a core structure of four introns with highly conserved coding regions. We also identified new LIM domain proteins in several other species, and a phylogenetic analysis of plant LIM proteins reveals that they have undergone one or several duplication events during the evolution. We gathered several LIM protein members within new monophyletic groups. We propose to classify the plant LIM proteins into four groups: {alpha}LIM1, ßLIM1, {gamma}LIM2, and {delta}LIM2, subdivided according to their specificity to a taxonomic class and/or to their tissue-specific expression. Our investigation of the structure of the LIM domain proteins revealed that they contain many conserved motifs potentially involved in their function.

Key words: poplar; Arabidopsis; rice; LIM domain protein; tension wood

* To whom correspondence should be addressed. Tel. +33 2-38417875. Fax: +33 2-38417879. E-mail: pilate{at}orleans.inra.fr

Edited by Kazuo Shinozaki


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