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Identified of a novel cis -element regulating the alternative splicing of LcDREB2

View Article: PubMed Central - PubMed

ABSTRACT

Alternative splicing (AS) is an important gene regulation mechanism in plants. Despite the widespread use of AS in plant gene expression regulation, the identification of the cis-elements involved in the AS mechanism is rarely reported in plants. To explore the regulation mechanism of the AS of LcDREB2, a DREB2 ortholog from Sheepgrass (Leymus chinensis), the genomic sequences of LcDREB2 and its homologs in Poaceae were aligned, and six mutations were introduced in the conserved sequence of LcDREB2. By analyzing the distinct transcript patterns of the LcDREB2 mutants in transgenic Oryza sativa, a novel cis-element that affected the AS of LcDREB2 was identified as Exonic Splicing Enhancer 1 (ESE1). In addition, five serine-arginine rich (SR) proteins were confirmed to interact with ESE1 by electrophoretic mobility shift assay (EMSA). To further explore the expression regulation mechanism of the DREB subfamily, phylogenetic analysis of DREB2 paralogous genes was performed. The results strongly supported the hypothesis that AS is conserved in Poaceae plants and that it is an evolutionary strategy for the regulation of the functional expression of genes. The findings and methods of our study will promote a substantial step forward in understanding of the plant AS regulation mechanism.

No MeSH data available.


Phylogenetic tree of the A-2 group of the DREB subfamily.(a) The phylogenetic tree of the A-2 group of the DREB subfamily proteins of 53 species. The phylogenetic tree is divided into three subgroups. The green, blue and red points denote genes of A. thaliana, rice and Amborella trichopoda, respectively. The gray branch in subgroup 2 is the AS branch, and the blue branch in subgroup 2 is the one-intron member branch. (b) The phylogenetic tree of the A-2 group of the DREB subfamily proteins in Poaceae and Brassicaceae. The A-2 group of Poaceae and Brassicaceae is divided into three subgroups. In subgroup 2, the red branch is the AS branch, and the blue branch is the one-intron branch. The red point represents LcDREB2, and the blue point represents PjDREB2, which are both located in the AS branch of subgroup 2.
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f6: Phylogenetic tree of the A-2 group of the DREB subfamily.(a) The phylogenetic tree of the A-2 group of the DREB subfamily proteins of 53 species. The phylogenetic tree is divided into three subgroups. The green, blue and red points denote genes of A. thaliana, rice and Amborella trichopoda, respectively. The gray branch in subgroup 2 is the AS branch, and the blue branch in subgroup 2 is the one-intron member branch. (b) The phylogenetic tree of the A-2 group of the DREB subfamily proteins in Poaceae and Brassicaceae. The A-2 group of Poaceae and Brassicaceae is divided into three subgroups. In subgroup 2, the red branch is the AS branch, and the blue branch is the one-intron branch. The red point represents LcDREB2, and the blue point represents PjDREB2, which are both located in the AS branch of subgroup 2.

Mentions: To phylogenetically analyze the expression regulation of the DREB subfamily, all A-2 group DREB proteins from 53 selected species (see Supplementary Table S1) were aligned for phylogenetic analysis. The sequence alignment and phylogenetic analysis results suggested that this group can be further separated into three subgroups, subgroups 1 to 3 (Fig. 6a). In A. trichopoda, a basal angiosperm in phylogenetics, we found one member in each subgroup of the A-2 group DREBs. This classification was also supported by the conserved hallmark site of AP2 domains (Fig. 7). The DREB genes with AS were only clustered in subgroup 2, and LcDREB2 belongs to this subgroup.


Identified of a novel cis -element regulating the alternative splicing of LcDREB2
Phylogenetic tree of the A-2 group of the DREB subfamily.(a) The phylogenetic tree of the A-2 group of the DREB subfamily proteins of 53 species. The phylogenetic tree is divided into three subgroups. The green, blue and red points denote genes of A. thaliana, rice and Amborella trichopoda, respectively. The gray branch in subgroup 2 is the AS branch, and the blue branch in subgroup 2 is the one-intron member branch. (b) The phylogenetic tree of the A-2 group of the DREB subfamily proteins in Poaceae and Brassicaceae. The A-2 group of Poaceae and Brassicaceae is divided into three subgroups. In subgroup 2, the red branch is the AS branch, and the blue branch is the one-intron branch. The red point represents LcDREB2, and the blue point represents PjDREB2, which are both located in the AS branch of subgroup 2.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC5382683&req=5

f6: Phylogenetic tree of the A-2 group of the DREB subfamily.(a) The phylogenetic tree of the A-2 group of the DREB subfamily proteins of 53 species. The phylogenetic tree is divided into three subgroups. The green, blue and red points denote genes of A. thaliana, rice and Amborella trichopoda, respectively. The gray branch in subgroup 2 is the AS branch, and the blue branch in subgroup 2 is the one-intron member branch. (b) The phylogenetic tree of the A-2 group of the DREB subfamily proteins in Poaceae and Brassicaceae. The A-2 group of Poaceae and Brassicaceae is divided into three subgroups. In subgroup 2, the red branch is the AS branch, and the blue branch is the one-intron branch. The red point represents LcDREB2, and the blue point represents PjDREB2, which are both located in the AS branch of subgroup 2.
Mentions: To phylogenetically analyze the expression regulation of the DREB subfamily, all A-2 group DREB proteins from 53 selected species (see Supplementary Table S1) were aligned for phylogenetic analysis. The sequence alignment and phylogenetic analysis results suggested that this group can be further separated into three subgroups, subgroups 1 to 3 (Fig. 6a). In A. trichopoda, a basal angiosperm in phylogenetics, we found one member in each subgroup of the A-2 group DREBs. This classification was also supported by the conserved hallmark site of AP2 domains (Fig. 7). The DREB genes with AS were only clustered in subgroup 2, and LcDREB2 belongs to this subgroup.

View Article: PubMed Central - PubMed

ABSTRACT

Alternative splicing (AS) is an important gene regulation mechanism in plants. Despite the widespread use of AS in plant gene expression regulation, the identification of the cis-elements involved in the AS mechanism is rarely reported in plants. To explore the regulation mechanism of the AS of LcDREB2, a DREB2 ortholog from Sheepgrass (Leymus chinensis), the genomic sequences of LcDREB2 and its homologs in Poaceae were aligned, and six mutations were introduced in the conserved sequence of LcDREB2. By analyzing the distinct transcript patterns of the LcDREB2 mutants in transgenic Oryza sativa, a novel cis-element that affected the AS of LcDREB2 was identified as Exonic Splicing Enhancer 1 (ESE1). In addition, five serine-arginine rich (SR) proteins were confirmed to interact with ESE1 by electrophoretic mobility shift assay (EMSA). To further explore the expression regulation mechanism of the DREB subfamily, phylogenetic analysis of DREB2 paralogous genes was performed. The results strongly supported the hypothesis that AS is conserved in Poaceae plants and that it is an evolutionary strategy for the regulation of the functional expression of genes. The findings and methods of our study will promote a substantial step forward in understanding of the plant AS regulation mechanism.

No MeSH data available.