Tissue-Specific Metabolic Reprogramming during Wound-Induced Organ Formation in Tomato Hypocotyl Explants

Abstract

Plants have remarkable regenerative capacity, which allows them to survive tissue damage after exposure to biotic and abiotic stresses. Some of the key transcription factors and hormone crosstalk mechanisms involved in wound-induced organ regeneration have been extensively studied in the model plant Arabidopsis thaliana. However, little is known about the role of metabolism in wound-induced organ formation. Here, we performed detailed transcriptome analysis and used a targeted metabolomics approach to study de novo organ formation in tomato hypocotyl explants and found tissue-specific metabolic differences and divergent developmental pathways. Our results indicate that successful regeneration in the apical region of the hypocotyl depends on a specific metabolic switch involving the upregulation of photorespiratory pathway components and the differential regulation of photosynthesis-related gene expression and gluconeogenesis pathway activation. These findings provide a useful resource for further investigation of the molecular mechanisms involved in wound-induced organ formation in crop species such as tomato.

Dynamic Hormone Gradients Regulate Wound-Induced de novo Organ Formation in Tomato Hypocotyl Explants

“…To investigate the hormonal regulation of wound-induced de novo organ formation in tomato hypocotyl explants, we performed targeted profiling of several phytohormonerelated metabolites on different regions of the hypocotyl and at different times after excision and found that endogenous levels of several hormones changed shortly after root and shoot excision. Cross-validation with previous RNA-seq data [9] allowed us to confirm that genes related to auxin and cytokinin (CK) crosstalk were dynamically regulated during de novo organ formation both in the apical and the basal region of the explants within a short developmental window, which contributed to the observed region-specific regenerative responses.…”

“…To enhance our understanding of de novo organ formation in plants, we established a new experimental system using 'Micro-Tom' hypocotyl explants after shoot and root excision, as these explants can regenerate the missing structures without the exogenous application of plant hormones [8,9]. We found that endogenous hormone levels were layered along the apical-basal axis of the hypocotyl before wounding (this work).…”

“…Our results using hypocotyl explants of different lengths favored the hypothesis that an endogenous pre-established auxin response gradient within the hypocotyl is established before wounding. As a result, the highest auxin responses were observed on the most basal region of the hypocotyl which determine subsequent AR formation in this region, and de novo shoot formation was later observed in the apical region of the explants [8,9]. Besides, we performed detailed transcriptome and targeted metabolomics analyses and found metabolic differences and divergent developmental pathways that contributed to the observed tissue-specific organ formation responses of 'Micro-Tom' hypocotyl explants [9].…”

“…As a result, the highest auxin responses were observed on the most basal region of the hypocotyl which determine subsequent AR formation in this region, and de novo shoot formation was later observed in the apical region of the explants [8,9]. Besides, we performed detailed transcriptome and targeted metabolomics analyses and found metabolic differences and divergent developmental pathways that contributed to the observed tissue-specific organ formation responses of 'Micro-Tom' hypocotyl explants [9]. Our results indicate that callus growth in the apical region of the hypocotyl, which precedes de novo shoot formation, depends on a specific metabolic switch involving the upregulation of the photorespiratory pathway and the differential regulation of genes involved in photosynthesis and glycolysis [9].…”

“…We gathered data from a previous RNA-seq experiment [9] and found 129 expressed genes related to the auxin pathway, 95 of which were deregulated (Table S2). Enrichment of upregulated differentially expressed genes (DEGs) related to auxin homeostasis and auxin transport was observed in both regions of the hypocotyl explants during the time course (Figure S2b).…”