Evolutionary History of the Glycoside Hydrolase 3 (GH3) Family Based on the Sequenced Genomes of 48 Plants and Identification of Jasmonic Acid-Related GH3 Proteins in Solanum tuberosum

Abstract

Glycoside Hydrolase 3 (GH3) is a phytohormone-responsive family of proteins found in many plant species. These proteins contribute to the biological activity of indolacetic acid (IAA), jasmonic acid (JA), and salicylic acid (SA). They also affect plant growth and developmental processes as well as some types of stress. In this study, GH3 genes were identified in 48 plant species, including algae, mosses, ferns, gymnosperms, and angiosperms. No GH3 representative protein was found in algae, but we identified 4 genes in mosses, 19 in ferns, 7 in gymnosperms, and several in angiosperms. The results showed that GH3 proteins are mainly present in seed plants. Phylogenetic analysis of all GH3 proteins showed three separate clades. Group I was related to JA adenylation, group II was related to IAA adenylation, and group III was separated from group II, but its function was not clear. The structure of the GH3 proteins indicated highly conserved sequences in the plant kingdom. The analysis of JA adenylation in relation to gene expression of GH3 in potato (Solanum tuberosum) showed that StGH3.12 greatly responded to methyl jasmonate (MeJA) treatment. The expression levels of StGH3.1, StGH3.11, and StGH3.12 were higher in the potato flowers, and StGH3.11 expression was also higher in the stolon. Our research revealed the evolution of the GH3 family, which is useful for studying the precise function of GH3 proteins related to JA adenylation in S. tuberosum when the plants are developing and under biotic stress.

Keywords: GH3 family; biotic; jasmonic acids; potato; sequencing plants; tissues.

Figure 1

Unrooted Neighbor-Joining tree constructs from GH3 proteins of 48 plant species. The protein names and lines having different colors in the phylogenetic tree represent the proteins belonging to different lineages. Information for each color is displayed in the lower right corner of the figure. Subfamilies are distinguished by three curves with different colors. Blue, green, and purple indicate group I, II, and III, respectively.

Figure 2

Gene motifs of seven plant species. The species belong to different lineages, including M.a polymorpha L., P. patens, S. moellendorffii, P. abies, S. tuberosum, A. thaliana and O. sativa. On the left, the protein name and phylogenetic tree are shown. The different color boxes indicate 20 motifs, which were found by using the MEME program.

Figure 3

Predictions of protein structure by analyzing 10 GH3 proteins. The selected proteins belonged to groups I and II. AtGH3.11 plays a key role in the JA pathway, and its mutant is named JAR1 [13]. YDK1-D is an AtGH3.2 mutant and responds to auxin [25]. The grey numbers (124, 137, 176, and so on) stand for the location of amino acids. The black annotates symbolize the secondary structure of the protein.

Figure 4

Information from gene ontology annotations and the KEGG pathway. (A) GO annotation for StGH3 proteins. BP, MF, and CC indicate Biological Process, Molecular Function, and Cellular Component, respectively. The numbers on the abscissa indicate the number of predicted proteins; and (B) the GH3 proteins are related to the KEGG pathway. StGH3.1, StGH3.5, and StGH3.12 are predicted to be part of the JA pathway. The red box is a functional site for of these three proteins according to prediction. COI1 is a receptor [41] which can combine with ASK (Arabidopsis Skp-like protein) and AtRbx (Arabidopsis ring-box protein) to form the complex SCF^COI1 [42]. Jasmonate ZIM (JAZ) is a JA pathway suppressor. In the absence of JA, these proteins interact with MYC proteins to block their activity. The bHLH transcription factor MYC is a master regulator of the response to the JA pathway [43]. ORCA3 regulates basic and secondary metabolism of plants by JA induction [44].

Figure 5

The heatmap based on the RNA-seq database under 10 treatments, which include biotics, abiotics, and hormones. The RNA-seq database was processed by log2 and stress, and hormonal data were compared with the control data. In the heat map, upregulated expression is in red and downregulated expression is in blue.

Figure 6

StGH3 gene expression in different tissues and expression changes upon MeJA treatment for different time periods. (A) Expression changes upon MeJA treatment for different time periods; and (B) Expression in different tissues.