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

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.

Actin bundling in plants

“…As LILIM1 is preferentially expressed in pollen and pollen tubes, it is likely contributing to actin bundle formation and/or maintenance in the elongating pollen tube. Supporting a significant role of LIM proteins in pollen tube growth, three out of the six Arabidopsis LIM genes are abundantly and almost exclusively expressed in pollen [Eliasson et al, 2000;Arnaud et al, 2007]. In contrast to LILIM1, NtWLIM1, which is a non-pollen LIM protein, does not display any obvious regulation by pH and calcium, indicating a different mode of regulation for pollen and non-pollen LIM proteins (our unpublished results).…”

“…Whereas animals possess numerous LIM proteins of diverse structures and functions, plants only contain a limited number of LIM proteins [Arnaud et al, 2007]. One family of these proteins is related to the vertebrate cysteine-rich proteins (CRPs), which function as actin-binding and possibly -bundling proteins [Grubinger and Gimona, 2004;Tran et al, 2005].…”

The plant LIM proteins: unlocking the hidden attractions

“…The known LIM domain in the plant always has either H (in 2LIMs) or C (in DA1/DAR) as last amino acid residue and not D (aspartate) which is reported in some animal CRPs (Schmeichel and Beckerle 1997). Moreover, the plant LIM proteins also have comparatively longer C-terminal and are short of glycine-rich region (GRR) following each LIM domain (Arnaud et al 2007). Few plant 2LIMs have also been shown to demonstrate acidic residue at their C-terminal Kawaoka et al 2000), responsible for transcription activation.…”

“…Two such domains separated by inter-LIM spacer constitute 2LIM proteins. The independent first and second LIM domains in such protein are represented by (CX 2 CX 17 HX 2 C)X 2 (CX 2 CX 17 CX 2 H) and (CX 2 CX 17 HX 2 C)X 2 (CX 4 CX 15 CX 2 H), respectively (Arnaud et al 2007;Park et al 2014;Srivastava and Verma 2015). The unusual domain structure of second LIM domain is comprised of additional glycine residues in the second Zn finger.…”

“…Currently, the 2LIM sub-family of LIM proteins has been studied in representative genus of diverse plant families which includes Brassicaceae, Solanaceae, Poaceae, Malvaceae, and Fabaceae (Kawaoka et al 2000, Arnaud et al 2007Han et al 2013;Park et al 2014;Srivastava and Verma 2015;Khatun et al 2016). In an early episode of LIM protein characterization, the search was focussed primarily around 2LIMs, offering function related to development.…”