Genome-wide identification of heterotrimeric G protein genes in castor (Ricinus communis L.) and expression patterns under salt stress

Abstract

Background: Heterotrimeric G proteins are crucial signaling molecules involved in cell signaling, plant development, and stress response. However, the genome-wide identification and analysis of G proteins in castor (Ricinus communis L.) have not been researched.

Results: In this study, RcG-protein genes were identified using a sequence alignment method and analyzed by bioinformatics and expression analysis in response to salt stress. The results showed that a total of 9 G-protein family members were identified in the castor genome, which were classified into three subgroups, with the majority of RcG-proteins showing homology to soybean G-protein members. The promoter regions of all RcG-protein genes contained antioxidant response elements and ABA-responsive elements. Go enrichment analysis displayed that RcG-protein genes were involved in the G protein-coupled receptor signaling pathway, regulation of root development, and response to the bacterium. Real-time PCR showed varying responses of all RcG-protein genes to salt stress. RcGB1 was notably expressed in both roots and leaves under salt treatment, suggesting that it may be an essential gene associated with salt tolerance in the castor.

Conclusions: This study offers a theoretical framework for exploring G-protein function and presents potential genetic assets for improving crop resilience through genetic enhancement.

Keywords: Ricinus communis; Bioinformatics; Gene expression analysis; Heterotrimeric G protein; Salt stress.

Fig. 1

Chromosomal distribution of RcG-protein genes in castor. Chromosome numbers were displayed in black font on the side. The RcG-protein gene was shown in the black italicized font on the side. The scale of the chromosome was in millions of bases (Mb)

Fig. 2

The phylogenetic analysis was conducted to explore the relationships among G proteins in Ricinus communis (Rc), Arabidopsis thaliana (At), Zea mays(Zm), Oryza sativa(Os), Solanum lycopersicum(Sl), and Glycine max(Gm). The Neighbor Joining (NJ) method used 1000 bootstrap replicates and was applied to draw the phylogenetic trees. A: Phylogenetic tree of RcG-proteins. B: Phylogenetic tree of Gα proteins of 6 plant species. C: Phylogenetic tree of Gβ proteins of 6 plant species. D: Phylogenetic tree of Gγ proteins of 6 plant species. Distinct groups were indicated by branches colored differently. Red stars indicated castor G proteins

Fig. 3

Cis-acting elements analysis of the promoter region of RcG-protein genes. The PlantCARE software was used to analyze the 2000 bp DNA sequence upstream of RcG-protein genes. The heat map represented the number of elements. The color scale changes represented an increase in the number of cis-acting elements

Fig. 4

Protein-protein interaction network of heterotrimeric G-protein family members in castor. Interaction networks were constructed by using the STRING database. The yellow nodes represented castor G proteins. The double-arrowed dotted line represented the existence of an interaction between two proteins

Fig. 5

GO enrichment analysis of RcG-protein genes. The enrichment results were classified into three categories: Biological Process, Cellular Component, and Molecular Function. The color scale represented the size of the p-value. The size of the circle represented the amount of enrichment

Fig. 6

Heatmap of expression levels for the RcG-protein genes in various tissues of castor (germinating seeds, male flowers, endosperm development II/III, endosperm development V/VI). The normalization of transcript levels for each specific RcG-protein across diverse tissues was performed using fragments per kilobase of exon per million fragments mapped (FPKM) values as a standard reference. The color scale changes indicated the difference in expression levels for each gene

Fig. 7

qRT-PCR analysis of RcG-protein genes in roots, stems, and leaves of castor. All data were expressed as the mean ± standard error (SE) of three independent replicates. The X-axis showed different tissues, and the Y-axis represented relative expression level. T-test (^*P < 0.05, ^**P < 0.01, ^***P < 0.001) was used to determine the significance of the differences with roots. Different colors represented different tissues of the castor

Fig. 8

qRT-PCR analysis of RcG-protein genes in leaves under salt stress. All data were expressed as the mean ± standard error (SE) of three independent replicates. The X-axis showed different treatment times, and the Y-axis represented relative expression level. T-test (^*P < 0.05, ^**P < 0.01, ^***P < 0.001) was used to determine the significance of the differences with the 0 h leaves. Different colors represented different varieties of castor

Fig. 9

qRT-PCR analysis of RcG-protein genes in roots under salt stress. All data were expressed as the mean ± standard error (SE) of three independent replicates. The X-axis showed different treatment times, and the Y-axis represented the relative expression level. T-test (^*P < 0.05, ^**P < 0.01, ^***P < 0.001) was used to determine the significance of the differences with the 0 h roots. Different colors represented different varieties of castor