Genome-wide analysis of LIM gene family in Populus trichocarpa, Arabidopsis thaliana, and Oryza sativa.
Genome-wide analysis of LIM gene family in Populus trichocarpa, Arabidopsis thaliana, and Oryza sativa.
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DOI：
10.1093/dnares/dsm013
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发表时间：
2007-06-30
期刊：
影响因子：
--
通讯作者：
Pilate G
中科院分区：
文献类型：
--
作者：
Arnaud D;Déjardin A;Leplé JC;Lesage-Descauses MC;Pilate G
在真核生物中，LIM蛋白在基本的细胞过程中作为发育调节因子，例如调节转录或组织细胞骨架。植物中的LIM结构域蛋白家族主要在向日葵和烟草植物中进行了研究，其中其几个成员在花粉中表现出特定的表达模式。在本文中，我们很好的特点，在白杨六个转录编码这些蛋白。在大叶杨基因组中，鉴定的12个LIM基因模型均为重复基因。此外，我们描述了几个新的LIM结构域蛋白推导出拟南芥和水稻基因组，提高LIM基因模型的数量为6个物种。植物LIM基因具有四个内含子的核心结构，具有高度保守的编码区。我们还确定了新的LIM结构域蛋白在其他几个物种，和植物LIM蛋白的系统发育分析表明，他们经历了一个或几个重复的事件在进化过程中。我们在新的单系群中收集了几个LIM蛋白成员。我们建议将植物LIM蛋白分为四组：α LIM 1，β LIM 1，γ LIM 2和δ LIM 2，根据它们对分类类别的特异性和/或它们的组织特异性表达进行细分。我们对LIM结构域蛋白结构的研究表明，它们含有许多可能参与其功能的保守基序。
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.
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DOI：
10.1093/bioinformatics/8.3.275
发表时间：
1992-06-01
期刊：
COMPUTER APPLICATIONS IN THE BIOSCIENCES
影响因子：
--
作者：
JONES, DT;TAYLOR, WR;THORNTON, JM
通讯作者：
THORNTON, JM
影响因子：
--
作者：
Baltz, R;Schmit, AC;Steinmetz, A
通讯作者：
Steinmetz, A
影响因子：
7.2
作者：
Rider, SD;Henderson, JT;Ogas, J
通讯作者：
Ogas, J
影响因子：
7
作者：
Laitinen, RAE;Immanen, J;Elomaa, P
通讯作者：
Elomaa, P
影响因子：
14.9
作者：
Chenna, R;Sugawara, H;Thompson, JD
通讯作者：
Thompson, JD