Putative DHHC-cysteine-rich domain S-acyltransferase in plants

Abstract

Protein S-acyltransferases (PATs) containing Asp-His-His-Cys within a Cys-rich domain (DHHC-CRD) are polytopic transmembrane proteins that are found in eukaryotic cells and mediate the S-acylation of target proteins. S-acylation is an important secondary and reversible modification that regulates the membrane association, trafficking and function of target proteins. However, little is known about the characteristics of PATs in plants. Here, we identified 804 PATs from 31 species with complete genomes. The analysis of the phylogenetic relationships suggested that all of the PATs fell into 8 groups. In addition, we analysed the phylogeny, genomic organization, chromosome localisation and expression pattern of PATs in Arabidopsis, Oryza sative, Zea mays and Glycine max. The microarray data revealed that PATs genes were expressed in different tissues and during different life stages. The preferential expression of the ZmPATs in specific tissues and the response of Zea mays to treatments with phytohormones and abiotic stress demonstrated that the PATs play roles in plant growth and development as well as in stress responses. Our data provide a useful reference for the identification and functional analysis of the members of this protein family.

Figure 1. The phylogenetic relationships among the plants with completely sequenced genomes.

The number in the table corresponds to the number of PAT genes in 8 subgroups and the total number of PATs in each species.

Figure 2. Phylogenetic relationships between the PATs in plants.

The amino acid sequences of the plant PATs were aligned using MUSCLE, and the phylogenetic tree was constructed using the neighbour-joining method in the MEGA 5 software.

Figure 3. Evolutionary relationship and gene structure analysis of the AtPATs in Arabidopsis.

The amino acid sequences of the AtPATs were aligned with Clustal X, and the phylogenetic tree was constructed using the neighbour-joining method in the MEGA 5.0 software program. Each node is represented by a number that indicates the bootstrap value. The scale bar represents 0.1 substitutions per sequence position (left). The right side illustrates the exon-intron organisation of the corresponding AtPAT gene. The exons and introns are represented by the green boxes and black lines, respectively. The scale bar represents 1 kb (right).

Figure 4. Evolutionary relationship and gene structure analysis of the OsPATs in Oryza sative.

The amino acid sequences of the OsPATs were aligned with Clustal X, and the phylogenetic tree was constructed using the neighbour-joining method in the MEGA 5.0 software program. Each node is represented by a number that indicates the bootstrap value. The scale bar represents 0.1 substitutions per sequence position (left). The right side illustrates the exon-intron organisation of the corresponding OsPATs genes. The exons and introns are represented by the green boxes and black lines, respectively. The scale bar represents 1 kb (right).

Figure 5. Evolutionary relationship and gene structure analysis of the ZmPATs in Zea mays.

The amino acid sequences of ZmPATs were aligned with Clustal X, and the phylogenetic tree was constructed using the neighbour-joining method in the MEGA 5.0 software program. Each node is represented by a number that indicates the bootstrap value. The scale bar represents 0.1 substitutions per sequence position (left). The right side illustrates the exon-intron organisation of the corresponding ZmPATs genes. The exons and introns are represented by the green boxes and black lines, respectively. The scale bar represents 1 kb (right).

Figure 6. Evolutionary relationship and gene structure analysis of the GmPATs in Glycine max.

The amino acid sequences of GmPATs were aligned with Clustal X, and the phylogenetic tree was constructed using the neighbour-joining method in the MEGA 5.0 software program. Each node is represented by a number that indicates the bootstrap value. The scale bar represents 0.1 substitutions per sequence position (left). The right side illustrates the exon-intron organisation of the corresponding GmPATs genes. The exons and introns are represented by the green boxes and black lines, respectively. The scale bar represents 1 kb (right).

Figure 7. Chromosomal locations of PATs genes in Arabidopsis, Oryza sative, Zea mays and Glycine max.

(A)Chromosomal locations of AtPATs genes in Arabidopsis. (B)Chromosomal locations of OsPATs genes in Oryza sative. (C)Chromosomal locations of ZmPATs genes in Zea mays. (D)Chromosomal locations of GmPATs genes in Glycine max.

Figure 8. Expression analysis of AtPATs genes in Arabidopsis.

The heatmap was prepared using the Genevestigator tool, and the microarray expression data were from the results of many chips available on the web (https://www.genevestigator.com/gv/). The dark and light colour shadings represent relatively high or low expression levels, respectively. (A)Expression analysis of AtPATs genes in different tissues. (B)Expression analysis of AtPATs genes in different life stages

Figure 9. Expression analysis of OsPATs genes in Oryza sative.

The heatmap was prepared using the Genevestigator tool, and the microarray expression data were from the results of many chips available on the web (https://www.genevestigator.com/gv/). The dark and light colour shadings represent relatively high or low expression levels, respectively. (A)Expression analysis of OsPATs genes in different tissues. (B)Expression analysis of OsPATs genes in different life stages

Figure 10. Expression analysis of ZmPATs genes in Zea mays.

The heatmap was prepared using the Genevestigator tool, and the microarray expression data were from the results of many chips available on the web (https://www.genevestigator.com/gv/). The dark and light colour shadings represent relatively high or low expression levels, respectively. (A)Expression analysis of ZmPATs genes in different tissues. (B)Expression analysis of ZmPATs genes in different life stages

Figure 11. Expression analysis of GmPATs genes in Glycine max.

The heatmap was prepared using the Genevestigator tool, and the microarray expression data were from the results of many chips available on the web (https://www.genevestigator.com/gv/). The dark and light colour shadings represent relatively high or low expression levels, respectively. (A)Expression analysis of GmPATs genes in different tissues (B)Expression analysis of GmPATs genes in different life stages

Figure 12. Quantitative RT-PCR to measure the expression patterns of 30 ZmPATs genes in Zea mays.

Error bars indicate standard deviations (n = 3). 1, primary root; 2, pericarp; 3, internode; 4, adult leaf; 5, silk; 6, culm; 7, seedling; 8, endosperm; 9, embryo; 10, tassel.

Figure 13. The expression profiles of some ZmPATs genes response to phytohormones and mimic abiotic stress.

(A)The expression profiles of some ZmPATs genes are responsive to phytohormones. (B)The expression profiles of some ZmPATs genes mimic the response to abiotic stress. 5-day-old (Zea mays) wild type seedlings were transferred to liquid MS media supplemented with 5 µM 6-BA, 5 µM IAA, 100 µM SA, 100 µM ABA, 100 mM NaCl, 300 mM mannitol or 15% PEG 6000 (or solvent control) for 6 h with gentle shaking. Representative experiments are shown, and the experiments were performed three times. Each bar represents a mean±SEM (n = 3).