Sulfate Deficiency-Responsive MicroRNAs in Tomato Uncover an Expanded and Functionally Integrated Regulatory Network
Year: 2025
Type: article
Abstract: Sulfate availability critically influences plant growth, yet the role of small RNAs, particularly microRNAs (miRNAs), in regulating responses to sulfate deficiency remains poorly understood. Here, we conducted a temporal analysis of sulfate deficiency-responsive miRNAs in the roots and leaves of Solanum lycopersicum (tomato), using an updated miRNA annotation in the SL4.0 genome. We found 40 differentially expressed miRNAs, including 2 novel, tomato-specific miRNAs. Tomato miRNAs showed an important time- and organ-specific regulation, similar to the described response of the mRNA transcriptome. Integration with transcriptomic data and Degradome-seq analysis highlighted both canonical and non-canonical targets for sulfate-responsive miRNAs. miR395, the most extensively studied miRNA, was found to control not only its conserved targets involved in sulfate transport and assimilation, but also genes involved in redox homeostasis, photosynthesis and chloride transport. Notably, most targets were repressed in leaves, suggesting miRNA-mediated downregulation of energy-intensive processes, while root targets were predominantly upregulated, including genes related to protein remodeling and antioxidant defense. Comparative analysis with Arabidopsis thaliana revealed a broader functional repertoire in tomato, suggesting species-specific adaptations to sulfate deficiency. Overall, our results underscore the critical role of miRNAs in fine-tuning organ-specific metabolic reprogramming during nutrient stress, expanding the current understanding of the regulatory landscape underlying sulfate deficiency in plants.
DOI: 10.3390/ijms26178392
Institutions: Universidad Mayor, Millennium Institute for Integrative Biology, Agencia Nacional de Investigación y Desarrollo, Consejo Superior de Investigaciones Científicas, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Centre for Plant Biotechnology and Genomics, Universidad Politécnica de Madrid, Austral University of Chile
Language: English
Subfield: Plant Science
Domain: Life Sciences
SDG: Zero hunger
Open Access status: gold
Estimated APC paid: $3,499
Awards: G1009090993, G1098294640, G1527626597, G1560399041, G1773654064, G1788871225, G2878874739, MILLENIUM NUCLEUS IN DATA SCIENCE FOR PLANT RESILIENCE, G3247760402, G3342884345, G3524548417, G4705533723, G5035199027, G5099039979, G5284675477, RESILOMICSNET ESTABLECIMIENTO DE UNA ALIANZA INTERNACIONAL PARA POTENCIAR LA RESILIENCIA CLIMATICA DE ESPECIES DE INTERES PRODUCTIVO, G5423120872, G5603956265, G5917503556, G5974437094, MODELING OF EPIGENETIC GENE REGULATORY NETWORKS IN SWEET CHERRY FLORAL BUDS IN RESPONSE TO DIFFERENTIAL SEASONAL CLIMATE CONDITIONS, G6359253120, G6545815140, G6610973221, G6775998215, G6799989317, UNRAVELING THE TANLP5 REGULATORY NETWORK UNDER SULFUR DEFICIENCY FOR IMPROVING NUTRIENT USE EFFICIENCY AND GRAIN YIELD IN WHEAT, G6888330965, G713401243, G7226781968, G7282653627, G7308176281, ROLE OF THE SLEIL3 TRANSCRIPTION FACTOR IN THE SULFATE DEFICIENCY RESPONSE OF SOLANUM LYCOPERSICUM., A GRN STRATEGY TO UNVEIL HUBS REGULATING TRICHODERMA ATROVIRIDE MYCOPARASITISM PROGRESSION AND MODULATION BY NITROGEN AVAILABILITY, IDENTIFICACION Y CARACTERIZACION DE LA FUNCION DE ARN PEQUENOS DE SOLANUM LYCOPERSICUM TRANSFERIDOS A BOTRYTIS CINEREA DURANTE EL PROCESO DE INFECCION, G7559899507, G7605437855, G7696279958, G7726111094, G8083817010, EPIGENETIC CONTROL OF SULFATE-STARVATION RESPONSIVE GENES IN SOLANUM LYCOPERSICUM, G8099540477, G832909193, G8531795418, G8567281349, G8741276362, G8843694625
OpenAlex ID: W4413824646