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.
1. Introduction
The chemical element sulfur (S) is a necessary factor for life found in the amino acid cysteine (Cys) and methionine (Met), certain vitamins (e.g., thiamin and biotin), co-enzymes (e.g., S-adenosyl methionine), iron–sulfur complexes, prosthetic substances, glutathione (GSH) antioxidants, and others natural secondary metabolites
[1]. The adequate S in the soil helps plant growth and development, and it is helpful to get a high plant yield of high quality
[2]. Moreover, the deficiency of S makes plants susceptible to various biotic and abiotic stresses
[3]. An S content ≤ 0.25% in any plant tissue may be considered severe S deficiency; plants with such deficiency have overall chlorosis and yellowish color due to lack of chlorophyll in the early stage of development
[4].
Sulfotransferases (SOTs) (EC 2.8.2.-) are sulfate-regulating proteins in various organisms. In plants, the conjugate reaction of sulfate play a vital role in plant growth and development and in response to various stresses
[5]. Sulfate is activated by two subsequent steps for the formation of adenosine-5′-phosphosulfate (APS) and 3′-phosphoadenosine-5′-phosphosulfate (PAPS) before being involved in further biochemical reactions
[6]. Sulfotransferases (
SOTs) (EC 2.8.2.-) catalyze the transfer of a sulfate group from PAPS to a hydroxyl group of different substrates
[7]. Sulfated substances in plants function as secondary metabolites, hormones in coping with stimulus situations, and use as important S storage substances during the life cycle
[8]. Plant SOTs are directly engaged in the sulfation process of desulpho-glucosinolate compounds (ds-Gl), which are important secondary metabolites that provide resistance against multiple biotic/abiotic stimuli in brassicales plants
[9]. All SOT proteins can be identified by a histidine residue in their PAPS-binding region and by a specific SOT domain (Pfam: PF00685)
[10]. SOT family members are specified by four conserved regions (I to IV) in their protein sequences
[11], in which the I and IV regions are highly conserved sections
[8]. Three
AtSOT16,
AtSOT17, and
AtSOT18 genes in the
Arabidopsis thaliana (At) genome are responsible for transferring a sulfuryl group to various ds-Gl compounds
[8][12][8,12]. Various substances, such as brassinosteroids, gibberellic acids, glucosinolates, flavonoids, coumarins, and phenolic acids, can be sulfated by SOT proteins in various plant species
[13][14][13,14].
Multiple studies indicate that
SOT genes can regulate plant stimuli responses, stress sensing and signaling mechanisms, and developmental processes. For example, in rice,
Oryza sativa, expression of some
SOT gene was observed in root, stigma, and ovary tissues in response to indole acetic acid and Benzyl aminopurine
[15];
BrSOT16 in
Brassica rapa indicated strong expression in all tissues except for stamen
[16];
ds-Gl AtSOTs, such as
AtSOT15, is responsible for circadian control
[13]; and expression levels of 11
OsSOTs exhibited some up- and downregulation in response to dehydration, high or low temperatures, and hormone stresses in various tissues
[15]. Northern blotting of
AtSOT12 revealed that the deduced protein employs flavonoids, brassinosteroids, and salicylic acid compounds as substrates; may be expressed in leaves, flowers, and roots; and responds to abiotic stimuli (such as salt, sorbitol, and cold), hormones, and interactions with biotic pathogens
[17][18][17,18]. Studies on homologous genes from
B. napus revealed increased
BNST3 and
BNST4 transcripts during exposure to hormones, low oxygen, xenobiotics, and herbicides
[14][19][14,19]. This provides evidence for the role of these genes in stress responses and detoxification. Some experimental evidence suggests that SOT may also act as a tyrosyl protein and may involve in phytosulphokines biosynthesis
[8]. The glucosinolate and their degradation products provide a defense to plant against insects and fungi. Some evidence shows the role of sulphotransferases in the biosynthesis of glucosinolate. Hence, further exploration of SOT can provide important information for the control of pests
[8].
The importance of S during the plant life cycle and associated biological and chemical processes is helpful to overcome S shortage for crop production and improvement. Potato is considered an important food crop after wheat, maize, and rice. Adequate S content in potato plants facilitates the uptake of multiple nutrients, carbohydrate formation, vitamin synthesis, chlorophyll production, seed development and stress, and pest resistance
[3][20][3,20]. Defective S contents lead to upward curving of potato leaves, along with light-green-to-yellow color. Hence, this leads to poor plant growth, prolate form, and postponed maturity
[21]. Previous studies have shown that sufficient S elevated the yield of potato tubers and quality and increased tolerance against various pathogens through the sulfur-induced resistance (SIR) mechanism
[3], whereas insufficient S lead to a reduction of several important compounds.
[22]. These important aspects necessitate the understanding of plant S biology and adjustment of S nutrition in agricultural programs. Therefore, the identification of important sulfotransferases in the S metabolism may elucidate the S-mediated proper growth and resistance mechanisms in potato.
SOTs have been identified in
Arabidopsis (22 members)
[8], rice (35 members)
[15], and
B. rapa (56 members)
[16]. However, the identification and characterization of SOT proteins in the potato (
Solanum tuberosum) genome are currently limited. In the current study, various bioinformatics approaches have been utilized to distinguish important cluster
SOTs and their expression patterns in multiple tissues and during different biotic or abiotic stimuli. Our predictions may assist functional evaluation of the SOT gene family members in potato and related crop species.
2. Identification of StSOT Genes
The deduced amino acid sequence of sulfotransferase domain (PF00685) was searched against the Hidden Markov Model (HMM) program and Phytozome database. This led to the identification of 29 putative StSOT proteins; all contained the Sulfotransfer_1 domain and were named according to their chromosomal order (
Table 1).
Table 1. Identified StSOT gene family members and their characteristics in the potato genome.
Gene ID |
Gene Symbol |
Protein Length (aa) |
MW (KDa) |
Isoelectric Point |
Subcellular Localization |
). A remarkable proportion of residues in each protein model was included in the lowest energy regions, indicating decreasing energies in various parts of these putative StSOT proteins.
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.
Table 4. Properties of secondary and tertiary structures of StSOT proteins, validation, and channel numbers.
Protein Name |
α-Helixes (%) |
β-Sheets (%) |
Coils (%) |
Turns (%) |
Channel Number |
Ramachandran Plot (%) |
z-Values |
PGSC0003DMG400000144 |
StSOT01 |
296 |
34.38 |
6.54 |
Nuclear, Cyt., Extra. |
PGSC0003DMG400027779 |
StSOT02 |
345 |
40.01 |
7.12 |
Cyt. |
PGSC0003DMG400003287 |
StSOT03 |
337 |
38.80 |
5.73 |
Cyt. |
PGSC0003DMG400031776 |
StSOT04 |
344 |
40.10 |
5.4 |
Cyt. |
PGSC0003DMG400024622 |
StSOT05 |
350 |
40.15 |
6.54 |
Cyt. |
PGSC0003DMG400018798 |
StSOT06 |
326 |
37.56 |
5.62 |
Cyt. |
PGSC0003DMG400026753 |
StSOT07 |
101 |
11.83 |
5.74 |
Nuclear, Cyt. |
PGSC0003DMG400026752 |
StSOT08 |
101 |
11.98 |
7.68 |
Nuclear, Cyt. |
12.10 |
8.99 |
Cyt., Mitochondrial, Nuclear |