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.

Genome-wide analysis of the C2H2 zinc finger protein gene family and its response to salt stress in ginseng, Panax ginseng Meyer

“…The PgZFP gene family was categorized into 17 subcategories at Level 2 and revealed to have 53 types of cis-regulatory elements responsive to multiple biological processes, suggesting that during the evolutionary process, changes have substantially occurred in the structure and upstream regions of PgZFP genes and these changes have affected their functional diversity 36 – 38 . The functional diversity of the gene family is larger than those of PgbHLH 49 , PgNAC 50 , and PgGRAS 51 gene families in ginseng that were categorized into 11, 8, and 15 subcategories, respectively.…”

“…The transcripts with complete CDS were used for Ka/Ks calculation using the KaKs_Calculator 35 . The time of the gene duplication and divergence was estimated by T = Ks/2λ × 10 −6 , where Ks is synonymous nucleotide substitution rate and λ is the number of substitutions per synonymous site per generation, for which λ = 6.5 × 10 −9 was used 36 – 38 .…”

FAR1/FHY3 Transcription Factors Positively Regulate the Salt and Temperature Stress Responses in Eucalyptus grandis

“…This suggested that the FAR1/FHY3 genes might have been involved in the responses to heat shock rather than the cold stress, despite of their lagged response under high-temperature stress. In conclusion, FAR1/FHY3 genes in E. grandis showed a diverse expression in response to abiotic stresses, indicating that they are involved in different cellular processes and cell signaling (Faraji et al, 2021 ; Heidari et al, 2021 ).…”

Genome-Wide Identification and Functional Characterization of the Chloride Channel TaCLC Gene Family in Wheat (Triticum aestivum L.)

“…It seems that evolutionary pressures can extend the members of the gene family ( Abdullah et al, 2021 ; Musavizadeh et al, 2021 ). Moreover, mutations in coding sites and promoter regions can affect the function of members of the gene family ( Faraji et al, 2021 ).…”