Identification of microRNA-Controlled Regulatory Networks in the Sulfate Deficiency Response of Solanum lycopersicum

Sulfur is an essential element for biological molecules, with sulfate as the primary sulfur source for plants. Under sulfate-deficiency, plants undergo physiological, metabolic, transcriptional, and post-transcriptional changes. Although Solanum lycopersicum (tomato) exhibits extensive transcriptome reprogramming during sulfate deficiency, the role of microRNAs (miRNAs) in this response remains poorly explored. In this study, we analyzed miRNAs expression in tomato roots and leaves at 3- and 4-weeks post-sowing under sulfate-sufficient and sulfate-deficient conditions, leveraging a de novo annotation of miRNA genes in the SL4.0 genome. We identified several miRNAs showing tissue- and time-specific expression changes in response to sulfate deficiency, with a potential role in processes such as lignin, chlorophyll, and polysaccharides metabolism. Consistent with other plants, miR395 emerged as a key sulfur metabolism and transport regulator. Notably, we identified a novel miR395 target, SlERF2a, an Ethylene-Responsive Factor predicted to regulate numerous sulfate deficiency-responsive genes, including genes involved in plastid organization, detoxification, sulfur assimilation and starvation response. These results suggest a broader role for miR395 in sulfate-deficiency responses in tomato compared to other plants. This work provides new insights into the post-transcriptional regulation of sulfate-deficiency in tomato, providing an updated miRNA annotation for future studies on miRNA-mediated regulation in this relevant crop.