Investigation and Computational Analysis of the Sulfotransferase (SOT) Gene Family in Potato (Solanum tuberosum): Insights into Sulfur Adjustment for Proper Development and Stimuli Responses

Abstract

Various kinds of primary metabolisms in plants are modulated through sulfate metabolism, and sulfotransferases (SOTs), which are engaged in sulfur metabolism, catalyze sulfonation reactions. In this study, a genome-wide approach was utilized for the recognition and characterization of SOT family genes in the significant nutritional crop potato (Solanum tuberosum L.). Twenty-nine putative StSOT genes were identified in the potato genome and were mapped onto the nine S. tuberosum chromosomes. The protein motifs structure revealed two highly conserved 5'-phosphosulfate-binding (5' PSB) regions and a 3'-phosphate-binding (3' PB) motif that are essential for sulfotransferase activities. The protein-protein interaction networks also revealed an interesting interaction between SOTs and other proteins, such as PRTase, APS-kinase, protein phosphatase, and APRs, involved in sulfur compound biosynthesis and the regulation of flavonoid and brassinosteroid metabolic processes. This suggests the importance of sulfotransferases for proper potato growth and development and stress responses. Notably, homology modeling of StSOT proteins and docking analysis of their ligand-binding sites revealed the presence of proline, glycine, serine, and lysine in their active sites. An expression essay of StSOT genes via potato RNA-Seq data suggested engagement of these gene family members in plants' growth and extension and responses to various hormones and biotic or abiotic stimuli. Our predictions may be informative for the functional characterization of the SOT genes in potato and other nutritional crops.

Keywords: bioinformatics; potato; protein structure; stimuli coping; sulfotransferase; sulfur.

Figure 1

Phosphorylation prediction with scores ≥ 0.95 in StSOT proteins based on serine, threonine, and tyrosine, using NetPhos 3.1 server.

Figure 2

Phylogenetic relationships of SOT proteins from potato, tomato, Arabidopsis, and sorghum. The four main clusters were detected based on the ML method in the phylogenetic tree. Abbreviations: St, potato; Solyc, tomato; Sobic, sorghum; At, Arabidopsis.

Figure 3

Conserved motifs predicted in the StSOT protein sequences (a). Exon–intron structure predicted in the StSOT family genes (b). Two important functional 5′ PSB and 3′ PB regions were detected in the motif 1 and motif 6, respectively.

Figure 4

Chromosomal map of StSOT family genes in the potato genome. Five series of duplicated/triplicated StSOTs are indicated in different colors. The scale is in mega bases.

Figure 5

Synteny relationships of StSOT genes with orthologs from (a) tomato and (b) Arabidopsis.

Figure 6

Interaction network between micro-RNAs and StSOT genes.

Figure 7

Protein–protein interaction network of SOT proteins, using Arabidopsis interactome data through STRING server v11, and improved by using Cytoscape.

Figure 8

Three-dimensional docking analysis of StSOT protein ligand-binding sites. The binding residues, metallic heterogeneous and non-metallic heterogeneous are shown in blue spacefill, green spacefill, and colorful wireframe, respectively.

Figure 9

Tissue-specific (a) and stimuli-induced gene expression analysis (b) of StSOT genes in the potato genome based on RNA-Seq data reported by the potato genome sequencing consortium.