Integration of Transcriptomics and Proteomics Data for Understanding the Mechanisms of Positive Effects of Carbon-Based Nanomaterials on Plant Tolerance to Salt Stress

Carbon-based nanomaterials (CBNs) can regulate seed germination, plant growth, and response to environmental stresses. Understanding of the biological mechanisms underlying these positive effects is limited. Integrating transcriptomics, proteomics, and metabolomics data—known as multi-omics data integration—is a powerful strategy for uncovering the molecular mechanisms underlying the effects of CBNs on a plant's molecular level, providing detailed insights into their biological impacts. Here, we combined transcriptomic (RNA-Seq) and proteomics (Tandem MS) data to understand mechanisms of improvement of tolerance to salt stress in tomato plants exposed to CBNs (carbon nanotubes (CNTs) and graphene). At the proteome level,exposure to CNTs resulted in complete restoration of the expression of 358 proteins and partial restoration of the expression of 697 proteins in tomato seedlingsexposed to salt stress.Similarly, exposure to graphene resulted in the complete restoration of 587 proteins and the partial restoration of 644 proteins affected by salt stress. In the integrative analysis of transcriptomics and proteomics data86 upregulated and 58 downregulated features showed the same expression trend (restoration expression towards normal level) at both “omics” levels in NaCl-stressed seedlings exposed to CBNs. Our data indicated that elevated salt tolerance of CBN-treated tomato plants can be associated with the activation of MAPK and inositol signaling pathways, enhancing the ROS clearance, stimulation of hormonal and sugar metabolisms, regulation of water uptake through work of aquaporins, regulation of the production of heat-shock proteins, and promotion of the production of secondary metabolites with defense functions.