Sulfur (S) is an essential nutrient present in nearly all proteins as well as numerous secondary metabolites and critical biochemical intermediates. Research across many crop species has demonstrated that post-stress S fertilization can improve plant recovery from various abiotic and biotic stresses. Furthermore, reported findings from these studies suggest that, in the absence of stress, enhanced S fertilization improves the expression of enzymes and metabolites with known stress-defense functions. As part of a new project seeking to test the impact of pre-stress tomato S status on heat stress resilience, we conducted a genome-wide mining and characterization study of the tomato sulfate transporter (SULTR) gene family. Following the typical steps in similar genome mining studies, we identified 14 putative SlSULTR genes through a BLASTp search of known A. thaliana SULTR proteins in the Phytozome database. Then, phylogenetic relationships between the putative SlSULTR genes were characterized using a neighbor-joining tree method after aligning the sequences with the MUSCLE algorithm in MEGA v12. The putative genes were also characterized for their exon-intron structure and intron cycle, which were retrieved from Phytozome and the GSDS server, respectively. Characterization of the putative SlSULTR proteins included transmembrane topology prediction using the SCAMPI2 server and motif analysis using MEME Suite v5.5.7. De novo motif discovery using the MEME algorithm produced 10 amino acid motifs with E-values under 1E-164. These de novo motifs were scanned against Ensembl’s A. thaliana protein database using the MAST algorithm which returned 27 A. thaliana transcripts, each from an AtSULTR gene and with highly significant motif similarities. To characterize the regulation of the putative SlSULTR genes, we searched for SlSULTR-targeted miRNAs in the psRNATarget database as well as identified cis-regulatory motifs in the 1000 bp upstream region of each genomic sequence through the PlantCARE server. Predicted miRNA were from various miRNA families known for their responses to biotic and abiotic stresses and their regulation of nutrient uptake and distribution, plant development, disease resistance, and signal transduction. Lastly, the identified cis-regulatory motifs were largely associated with plant light response but also included motifs associated with general stress and hormone signal response. This work represents the first genomic mining study of tomato SULTR genes. Our phylogenetic and amino acid motif results provide strong evidence that the selected sequences operate as SULTR genes in tomatoes, and the identified miRNA targets and cis-regulatory sequences reflect established research demonstrating the role of S in plant stress response.
