Journal Article

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

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

in DNA Research

Published on behalf of Kazusa DNA Research Institute

Volume 14, issue 3, pages 103-116
Published in print January 2007 | ISSN: 1340-2838
Published online June 2007 | e-ISSN: 1756-1663 | DOI: http://dx.doi.org/10.1093/dnares/dsm013

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Abstract

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: αLIM1, βLIM1, γLIM2, and δLIM2, 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.

Keywords: poplar; Arabidopsis; rice; LIM domain protein; tension wood

Journal Article.  8010 words.  Illustrated.

Subjects: Genetics and Genomics

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